From 57d8339d20ad1780d1c603e23297db86fbb29152 Mon Sep 17 00:00:00 2001 From: Aditya Wibawa Sakti Date: Tue, 26 Jul 2022 10:25:27 +0700 Subject: [PATCH] addition to xTB functions --- bin/cmmde.py | 2 +- cmmde_gui/gui.py | 20 +- cmmde_gui/test/ala/cmmd.engrad | 34 + cmmde_gui/test/ala/cmmd.gbw | Bin 0 -> 652112 bytes cmmde_gui/test/ala/cmmd.in | 11 + cmmde_gui/test/ala/cmmd.opt | 164 + cmmde_gui/test/ala/cmmd.out | 1136 +++++++ cmmde_gui/test/ala/cmmd.xtbrestart | Bin 0 -> 488 bytes cmmde_gui/test/ala/cmmd.xyz | 7 + cmmde_gui/test/ala/cmmd_property.txt | 6 + cmmde_gui/test/ala/cmmd_trj.xyz | 21 + cmmde_gui/test/ala/freq/cmmd.engrad | 34 + cmmde_gui/test/ala/freq/cmmd.gbw | Bin 0 -> 652112 bytes cmmde_gui/test/ala/freq/cmmd.hess | 192 ++ cmmde_gui/test/ala/freq/cmmd.in | 13 + cmmde_gui/test/ala/freq/cmmd.out | 711 +++++ cmmde_gui/test/ala/freq/cmmd.xtbrestart | Bin 0 -> 488 bytes cmmde_gui/test/ala/freq/cmmd_property.txt | 48 + cmmde_gui/test/ala/freq/run.sh | 10 + cmmde_gui/test/ala/freq/slurm-2915.out | 0 cmmde_gui/test/ala/geom.smi | 1 + cmmde_gui/test/ala/geom.xyz | 7 + cmmde_gui/test/ala/run.sh | 10 + cmmde_gui/test/ala/run_babel.sh | 8 + cmmde_gui/test/ala/slurm-2913.out | 1 + cmmde_gui/test/ala/slurm-2914.out | 0 cmmde_gui/test/alala/alala/cmmd.engrad | 74 + cmmde_gui/test/alala/alala/cmmd.gbw | Bin 0 -> 652792 bytes cmmde_gui/test/alala/alala/cmmd.in | 11 + cmmde_gui/test/alala/alala/cmmd.opt | 1566 ++++++++++ cmmde_gui/test/alala/alala/cmmd.out | 2742 +++++++++++++++++ cmmde_gui/test/alala/alala/cmmd.xtbrestart | Bin 0 -> 1320 bytes cmmde_gui/test/alala/alala/cmmd.xyz | 17 + cmmde_gui/test/alala/alala/cmmd_property.txt | 6 + cmmde_gui/test/alala/alala/cmmd_trj.xyz | 102 + cmmde_gui/test/alala/alala/freq/cmmd.engrad | 74 + cmmde_gui/test/alala/alala/freq/cmmd.gbw | Bin 0 -> 652792 bytes cmmde_gui/test/alala/alala/freq/cmmd.hess | 1024 ++++++ cmmde_gui/test/alala/alala/freq/cmmd.in | 13 + cmmde_gui/test/alala/alala/freq/cmmd.out | 1193 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cmmde_gui/test/alala/freq/cmmd.hess | 1024 ++++++ cmmde_gui/test/alala/freq/cmmd.in | 13 + cmmde_gui/test/alala/freq/cmmd.out | 1193 +++++++ cmmde_gui/test/alala/freq/cmmd.xtbrestart | Bin 0 -> 1320 bytes cmmde_gui/test/alala/freq/cmmd_property.txt | 78 + cmmde_gui/test/alala/freq/run.sh | 10 + cmmde_gui/test/alala/freq/slurm-2889.out | 0 cmmde_gui/test/alala/geom.smi | 1 + cmmde_gui/test/alala/geom.xyz | 17 + cmmde_gui/test/alala/run.sh | 10 + cmmde_gui/test/alala/run_babel.sh | 8 + cmmde_gui/test/alala/slurm-2885.out | 1 + cmmde_gui/test/alala/slurm-2886.out | 0 cmmde_gui/test/metana3/cmmd.engrad | 34 + cmmde_gui/test/metana3/cmmd.gbw | Bin 0 -> 652112 bytes cmmde_gui/test/metana3/cmmd.in | 11 + cmmde_gui/test/metana3/cmmd.opt | 164 + cmmde_gui/test/metana3/cmmd.out | 1136 +++++++ cmmde_gui/test/metana3/cmmd.xtbrestart | Bin 0 -> 488 bytes cmmde_gui/test/metana3/cmmd.xyz | 7 + cmmde_gui/test/metana3/cmmd_property.txt | 6 + cmmde_gui/test/metana3/cmmd_trj.xyz | 21 + 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cmmde_gui/test/metana4/cmmd.in | 11 + cmmde_gui/test/metana4/cmmd.opt | 164 + cmmde_gui/test/metana4/cmmd.out | 1136 +++++++ cmmde_gui/test/metana4/cmmd.xtbrestart | Bin 0 -> 488 bytes cmmde_gui/test/metana4/cmmd.xyz | 7 + cmmde_gui/test/metana4/cmmd_property.txt | 6 + cmmde_gui/test/metana4/cmmd_trj.xyz | 21 + cmmde_gui/test/metana4/freq/cmmd.engrad | 34 + cmmde_gui/test/metana4/freq/cmmd.gbw | Bin 0 -> 652112 bytes cmmde_gui/test/metana4/freq/cmmd.hess | 192 ++ cmmde_gui/test/metana4/freq/cmmd.in | 13 + cmmde_gui/test/metana4/freq/cmmd.out | 711 +++++ cmmde_gui/test/metana4/freq/cmmd.xtbrestart | Bin 0 -> 488 bytes cmmde_gui/test/metana4/freq/cmmd_property.txt | 48 + cmmde_gui/test/metana4/freq/run.sh | 10 + cmmde_gui/test/metana4/freq/slurm-2912.out | 0 cmmde_gui/test/metana4/geom.smi | 1 + cmmde_gui/test/metana4/geom.xyz | 7 + cmmde_gui/test/metana4/run.sh | 10 + cmmde_gui/test/metana4/run_babel.sh | 8 + cmmde_gui/test/metana4/slurm-2910.out | 1 + cmmde_gui/test/metana4/slurm-2911.out | 0 cmmde_gui/test/metana5/cmmd.engrad | 34 + cmmde_gui/test/metana5/cmmd.gbw | Bin 0 -> 652112 bytes cmmde_gui/test/metana5/cmmd.in | 11 + cmmde_gui/test/metana5/cmmd.opt | 164 + cmmde_gui/test/metana5/cmmd.out | 1136 +++++++ cmmde_gui/test/metana5/cmmd.xtbrestart | Bin 0 -> 488 bytes cmmde_gui/test/metana5/cmmd.xyz | 7 + cmmde_gui/test/metana5/cmmd_property.txt | 6 + cmmde_gui/test/metana5/cmmd_trj.xyz | 21 + cmmde_gui/test/metana5/freq/cmmd.engrad | 34 + cmmde_gui/test/metana5/freq/cmmd.gbw | Bin 0 -> 652112 bytes cmmde_gui/test/metana5/freq/cmmd.hess | 192 ++ cmmde_gui/test/metana5/freq/cmmd.in | 13 + cmmde_gui/test/metana5/freq/cmmd.out | 711 +++++ cmmde_gui/test/metana5/freq/cmmd.xtbrestart | Bin 0 -> 488 bytes cmmde_gui/test/metana5/freq/cmmd_property.txt | 48 + cmmde_gui/test/metana5/freq/freq/cmmd.in | 13 + cmmde_gui/test/metana5/freq/freq/cmmd.out | 142 + cmmde_gui/test/metana5/freq/freq/run.sh | 10 + 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create mode 100644 cmmde_gui/test/test/test/cmmd.in create mode 100644 cmmde_gui/test/test/test/cmmd.opt create mode 100644 cmmde_gui/test/test/test/cmmd.out create mode 100644 cmmde_gui/test/test/test/cmmd.xtbrestart create mode 100644 cmmde_gui/test/test/test/cmmd.xyz create mode 100644 cmmde_gui/test/test/test/cmmd_property.txt create mode 100644 cmmde_gui/test/test/test/cmmd_trj.xyz create mode 100644 cmmde_gui/test/test/test/geom.smi create mode 100644 cmmde_gui/test/test/test/geom.xyz create mode 100644 cmmde_gui/test/test/test/run.sh create mode 100644 cmmde_gui/test/test/test/run_babel.sh create mode 100644 cmmde_gui/test/test/test/slurm-2893.out create mode 100644 cmmde_gui/test/test/test/slurm-2894.out diff --git a/bin/cmmde.py b/bin/cmmde.py index ffca855..8663249 100755 --- a/bin/cmmde.py +++ b/bin/cmmde.py @@ -400,4 +400,4 @@ if opt.job == 'ligprep' and opt.software == 'gmx': # Program XTB Standalone if opt.software == 'xtb': - xtb(opt.job,geom,opt.nproc,opt.produk,opt.temp,opt.nrun,opt.npoint,opt.anopt,opt.kpush,opt.kpull,opt.ppull,opt.alp,opt.distance,opt.angle,opt.dihedral,opt.scanmode,opt.iter,opt.scan,opt.solvent) \ No newline at end of file + xtb(opt.job,geom,opt.nproc,opt.produk,opt.temp,opt.nrun,opt.npoint,opt.anopt,opt.kpush,opt.kpull,opt.ppull,opt.alp,opt.distance,opt.angle,opt.dihedral,opt.scanmode,opt.iter,opt.scan,opt.solvent,opt.charge,opt.mult,opt.method) \ No newline at end of file diff --git a/cmmde_gui/gui.py b/cmmde_gui/gui.py index f49d90c..a56560e 100755 --- a/cmmde_gui/gui.py +++ b/cmmde_gui/gui.py @@ -59,14 +59,20 @@ def cmmde_gui(): Run_btn.on_click(run) # Post calculations post_btn = pn.widgets.MultiChoice(name="Post calculation",value=['Frequency calculation'], options=['Frequency calculation','Radial distribution function', 'Mean Square Displacement','Time-dependent calculation','Thermochemistry calculation']) - post_calc = {'Frequency calculation':'freq', 'Radial distribution function':'rdf','Mean Square Displacement':'msd','Time-dependent calculation':'td','Thermochemistry':'thermo'} + post_calc = {'Frequency calculation':'freq', 'Radial distribution function':'rdf','Mean Square Displacement':'msd','Time-dependent calculation':'td','Thermochemistry calculation':'thermo'} +# Post Calculation CMMDE software options + post_software_btn = pn.widgets.MultiSelect(name="Software selections for post calculations",value=['Orca'],options=['Orca','GROMACS','Dcdftbmd','Quantum Espresso']) + post_software = {'Orca':'orca','GROMACS':'gromacs','Dcdftbmd':'dcdftb','Quantum Espresso':'qe'} + # Post CMMDE method options + post_method_btn = pn.widgets.MultiChoice(name="Method selections for post calculations",value=['GFN2-xTB'],options=['GFN2-xTB','GFN1-xTB','DFTB2','DFTB2-gammah','DFTB3','DFTB3-diag']) + post_method = {'GFN2-xTB':'XTB2', 'GFN1-xTB':'XTB1','DFTB2':'DFTB2','DFTB2-gammah':'DFTB2_gammah','DFTB3':'DFTB3','DFTB3-diag':'DFTB3-diag'} def post_calculation(event): - os.makedirs(post_calc[post_btn.value[0]]) - os.chdir(post_calc[post_btn.value[0]]) - if post_calc[post_btn.value[0]] == 'thermo' and software[software_btn.value[0]] == 'orca': - terminal.subprocess.run("cmmdepost.py","-j{}".format(post_calc[post_btn.value[0]]),"-s{}".format(software[software_btn.value[0]])) + if post_calc[post_btn.value[0]] == 'thermo' and post_software[post_software_btn.value[0]] == 'orca': + terminal.subprocess.run("cmmdepost.py","-j{}".format(post_calc[post_btn.value[0]]),"-s{}".format(post_software[post_software_btn.value[0]])) else: - terminal.subprocess.run("cmmde.py","-i{}".format("../cmmd.xyz"),"-s{}".format(software[software_btn.value[0]]), "-j{}".format(post_calc[post_btn.value[0]]), "-m{}".format(method[method_btn.value[0]])) + os.makedirs(post_calc[post_btn.value[0]]) + os.chdir(post_calc[post_btn.value[0]]) + terminal.subprocess.run("cmmde.py","-i{}".format("../cmmd.xyz"),"-s{}".format(post_software[post_software_btn.value[0]]), "-j{}".format(post_calc[post_btn.value[0]]), "-m{}".format(post_method[post_method_btn.value[0]])) runpost_btn = pn.widgets.Button(name="Run post calculation!",button_type='primary') runpost_btn.on_click(post_calculation) # Check the progress @@ -116,7 +122,7 @@ def cmmde_gui(): site="CMMDE-GUI", title="CMMDE Editor", main=[editor, terminal, terminal.subprocess.param.running,visual_btn,pn.Tabs(xyzviewer)], - sidebar=[pn.Row(software_btn,height=200),Name_input,pn.Column(job_btn, height=400),pn.Column(method_btn,height=400),pn.Row(Run_btn,Progress_btn),pn.Column(post_btn,height=400),pn.Row(runpost_btn,Progress_btn)], + sidebar=[pn.Row(software_btn,height=200),Name_input,pn.Column(job_btn, height=400),pn.Column(method_btn,height=400),pn.Row(Run_btn,Progress_btn),pn.Column(post_btn,height=400),pn.Row(post_software_btn,height=200),pn.Row(post_method_btn,height=400),pn.Row(runpost_btn,Progress_btn)], header_background=accent, accent_base_color=accent ) diff --git a/cmmde_gui/test/ala/cmmd.engrad b/cmmde_gui/test/ala/cmmd.engrad new file mode 100644 index 0000000..5341504 --- /dev/null +++ b/cmmde_gui/test/ala/cmmd.engrad @@ -0,0 +1,34 @@ +# +# Number of atoms +# + 5 +# +# The current total energy in Eh +# + -4.175218519970 +# +# The current gradient in Eh/bohr +# + 0.000000009773 + 0.000000207326 + 0.000000451564 + 0.000099433721 + -0.000000459326 + 0.000000273611 + -0.000032618166 + -0.000065629718 + 0.000066668309 + -0.000033396983 + -0.000024690189 + -0.000090646633 + -0.000033428344 + 0.000090571907 + 0.000023253149 +# +# The atomic numbers and current coordinates in Bohr +# + 6 2.0184922 0.1320357 0.0411923 + 1 4.0634786 0.1320373 0.0411913 + 1 1.3368371 -1.2210494 1.4146831 + 1 1.3368281 -0.3808997 -1.8173559 + 1 1.3368243 1.9980519 0.5262503 diff --git a/cmmde_gui/test/ala/cmmd.gbw b/cmmde_gui/test/ala/cmmd.gbw new file mode 100644 index 0000000000000000000000000000000000000000..e1c5ac0a9b492adcaf21bcaaed8c66907f4c1aa8 GIT binary patch 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+================================================================================ +NAME = cmmd.in +| 1> #CMMDE generated Orca input file +| 2> !XTB2 opt +| 3> %pal +| 4> nprocs 1 +| 5> end +| 6> %geom +| 7> maxiter 9999 +| 8> end +| 9> +| 10> *xyzfile 0 1 geom.xyz +| 11> +| 12> +| 13> ****END OF INPUT**** +================================================================================ + + ***************************** + * Geometry Optimization Run * + ***************************** + +Geometry optimization settings: +Update method Update .... BFGS +Choice of coordinates CoordSys .... Z-matrix Internals +Initial Hessian InHess .... Almoef's Model + +Convergence Tolerances: +Energy Change TolE .... 5.0000e-06 Eh +Max. Gradient TolMAXG .... 3.0000e-04 Eh/bohr +RMS Gradient TolRMSG .... 1.0000e-04 Eh/bohr +Max. Displacement TolMAXD .... 4.0000e-03 bohr +RMS Displacement TolRMSD .... 2.0000e-03 bohr +Strict Convergence .... False +------------------------------------------------------------------------------ + ORCA OPTIMIZATION COORDINATE SETUP +------------------------------------------------------------------------------ + +The optimization will be done in new redundant internal coordinates +Making redundant internal coordinates ... (new redundants) done +Evaluating the initial hessian ... (Almloef) done +Evaluating the coordinates ... done +Calculating the B-matrix .... done +Calculating the G-matrix .... done +Diagonalizing the G-matrix .... done +The first mode is .... 1 +The number of degrees of freedom .... 9 + + ----------------------------------------------------------------- + Redundant Internal Coordinates + + + ----------------------------------------------------------------- + Definition Initial Value Approx d2E/dq + ----------------------------------------------------------------- + 1. B(H 1,C 0) 1.0922 0.357201 + 2. B(H 2,C 0) 1.0922 0.357209 + 3. B(H 3,C 0) 1.0922 0.357196 + 4. B(H 4,C 0) 1.0922 0.357208 + 5. A(H 1,C 0,H 3) 109.4713 0.290102 + 6. A(H 2,C 0,H 3) 109.4715 0.290103 + 7. A(H 1,C 0,H 4) 109.4715 0.290103 + 8. A(H 2,C 0,H 4) 109.4713 0.290104 + 9. A(H 3,C 0,H 4) 109.4708 0.290102 + 10. A(H 1,C 0,H 2) 109.4710 0.290103 + ----------------------------------------------------------------- + +Number of atoms .... 5 +Number of degrees of freedom .... 10 + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 1 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.068140 0.069870 0.021800 + H 2.160340 0.069870 0.021800 + H 0.704080 -0.652790 0.755360 + H 0.704070 -0.204080 -0.970830 + H 0.704070 1.066480 0.280860 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.018492 0.132035 0.041196 + 1 H 1.0000 0 1.008 4.082451 0.132035 0.041196 + 2 H 1.0000 0 1.008 1.330518 -1.233594 1.427424 + 3 H 1.0000 0 1.008 1.330499 -0.385655 -1.834603 + 4 H 1.0000 0 1.008 1.330499 2.015355 0.530748 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 20:31:26.370 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 5 + number of electrons : 8 + charge : 0 + spin : 0.0 + first test random number : 0.29814689341337 + + ID Z sym. atoms + 1 6 C 1 + 2 1 H 2-5 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 8 : + : # atomic orbitals 8 : + : # shells 6 : + : # electrons 8 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -4.2288352 -0.422884E+01 0.246E+00 17.25 0.0 T + 2 -4.2416604 -0.128252E-01 0.917E-01 17.07 1.0 T + 3 -4.2418083 -0.147906E-03 0.503E-01 16.97 1.0 T + 4 -4.2418548 -0.465207E-04 0.968E-02 16.85 1.0 T + 5 -4.2418547 0.611467E-07 0.615E-03 16.85 7.3 T + 6 -4.2418548 -0.109446E-06 0.181E-04 16.85 247.0 T + 7 -4.2418548 -0.991482E-10 0.316E-06 16.85 14169.3 T + + *** convergence criteria satisfied after 7 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.5801036 -15.7854 + 2 2.0000 -0.4667177 -12.7000 + 3 2.0000 -0.4667170 -12.7000 + 4 2.0000 -0.4667166 -12.7000 (HOMO) + 5 0.1525565 4.1513 (LUMO) + 6 0.2134380 5.8079 + 7 0.2134454 5.8081 + 8 0.2134515 5.8083 + ------------------------------------------------------------- + HL-Gap 0.6192731 Eh 16.8513 eV + Fermi-level -0.1570801 Eh -4.2744 eV + + SCC (total) 0 d, 0 h, 0 min, 0.021 sec + SCC setup ... 0 min, 0.000 sec ( 0.345%) + Dispersion ... 0 min, 0.000 sec ( 0.055%) + classical contributions ... 0 min, 0.000 sec ( 0.038%) + integral evaluation ... 0 min, 0.000 sec ( 0.561%) + iterations ... 0 min, 0.021 sec ( 96.546%) + molecular gradient ... 0 min, 0.000 sec ( 1.703%) + printout ... 0 min, 0.000 sec ( 0.707%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -4.174962272512 Eh :: + :: gradient norm 0.013368988744 Eh/a0 :: + :: HOMO-LUMO gap 16.851277556927 eV :: + ::.................................................:: + :: SCC energy -4.241854831492 Eh :: + :: -> isotropic ES 0.001954141270 Eh :: + :: -> anisotropic ES 0.002520380309 Eh :: + :: -> anisotropic XC 0.003827620759 Eh :: + :: -> dispersion -0.000662667304 Eh :: + :: repulsion energy 0.066892553015 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -4.174962272512 Eh | + | GRADIENT NORM 0.013368988744 Eh/α | + | HOMO-LUMO GAP 16.851277556927 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 20:31:26.399 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.029 sec + * cpu-time: 0 d, 0 h, 0 min, 0.011 sec + * ratio c/w: 0.373 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.021 sec + * cpu-time: 0 d, 0 h, 0 min, 0.003 sec + * ratio c/w: 0.154 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -4.174962272510 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 5 +Number of internal coordinates .... 10 +Current Energy .... -4.174962273 Eh +Current gradient norm .... 0.013368989 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Evaluating the initial hessian .... (Almloef) done +Projecting the Hessian .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999302304 +Lowest eigenvalues of augmented Hessian: + -0.000499659 0.290101854 0.290102538 0.290102901 0.290103263 +Length of the computed step .... 0.037374519 +The final length of the internal step .... 0.037374519 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0118188607 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0096500592 RMS(Int)= 0.0118188607 + Iter 1: RMS(Cart)= 0.0000000109 RMS(Int)= 0.0000000124 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + RMS gradient 0.0042276451 0.0001000000 NO + MAX gradient 0.0066879145 0.0003000000 NO + RMS step 0.0118188607 0.0020000000 NO + MAX step 0.0186972216 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0099 Max(Angles) 0.00 + Max(Dihed) 0.00 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(H 1,C 0) 1.0922 0.006686 -0.0099 1.0823 + 2. B(H 2,C 0) 1.0922 0.006682 -0.0099 1.0823 + 3. B(H 3,C 0) 1.0922 0.006688 -0.0099 1.0823 + 4. B(H 4,C 0) 1.0922 0.006683 -0.0099 1.0823 + 5. A(H 1,C 0,H 3) 109.47 0.000000 -0.00 109.47 + 6. A(H 2,C 0,H 3) 109.47 0.000001 -0.00 109.47 + 7. A(H 1,C 0,H 4) 109.47 0.000000 -0.00 109.47 + 8. A(H 2,C 0,H 4) 109.47 -0.000000 0.00 109.47 + 9. A(H 3,C 0,H 4) 109.47 -0.000001 0.00 109.47 + 10. A(H 1,C 0,H 2) 109.47 0.000000 -0.00 109.47 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 2 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.068140 0.069870 0.021798 + H 2.150450 0.069870 0.021798 + H 0.707375 -0.646250 0.748718 + H 0.707369 -0.201600 -0.961839 + H 0.707366 1.057460 0.278514 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.018492 0.132036 0.041193 + 1 H 1.0000 0 1.008 4.063761 0.132035 0.041193 + 2 H 1.0000 0 1.008 1.336745 -1.221236 1.414873 + 3 H 1.0000 0 1.008 1.336733 -0.380969 -1.817613 + 4 H 1.0000 0 1.008 1.336729 1.998309 0.526316 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 20:31:26.436 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 5 + number of electrons : 8 + charge : 0 + spin : 0.0 + first test random number : 0.68469617721121 + + ID Z sym. atoms + 1 6 C 1 + 2 1 H 2-5 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 8 : + : # atomic orbitals 8 : + : # shells 6 : + : # electrons 8 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -4.2473771 -0.424738E+01 0.106E-01 17.33 0.0 T + 2 -4.2473844 -0.729542E-05 0.561E-02 17.34 1.0 T + 3 -4.2473846 -0.259698E-06 0.204E-02 17.34 2.2 T + 4 -4.2473847 -0.370492E-07 0.422E-03 17.35 10.6 T + 5 -4.2473847 -0.969891E-11 0.246E-05 17.35 1817.7 T + 6 -4.2473847 -0.112621E-11 0.118E-07 17.35 100000.0 T + + *** convergence criteria satisfied after 6 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.5818102 -15.8319 + 2 2.0000 -0.4674475 -12.7199 + 3 2.0000 -0.4674469 -12.7199 + 4 2.0000 -0.4674468 -12.7199 (HOMO) + 5 0.1699963 4.6258 (LUMO) + 6 0.2290165 6.2319 + 7 0.2290174 6.2319 + 8 0.2290203 6.2320 + ------------------------------------------------------------- + HL-Gap 0.6374431 Eh 17.3457 eV + Fermi-level -0.1487252 Eh -4.0470 eV + + SCC (total) 0 d, 0 h, 0 min, 0.002 sec + SCC setup ... 0 min, 0.000 sec ( 2.613%) + Dispersion ... 0 min, 0.000 sec ( 0.410%) + classical contributions ... 0 min, 0.000 sec ( 0.322%) + integral evaluation ... 0 min, 0.000 sec ( 4.036%) + iterations ... 0 min, 0.002 sec ( 82.743%) + molecular gradient ... 0 min, 0.000 sec ( 6.984%) + printout ... 0 min, 0.000 sec ( 2.708%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -4.175218465764 Eh :: + :: gradient norm 0.000198762862 Eh/a0 :: + :: HOMO-LUMO gap 17.345708956675 eV :: + ::.................................................:: + :: SCC energy -4.247384679937 Eh :: + :: -> isotropic ES 0.002034388482 Eh :: + :: -> anisotropic ES 0.002324462897 Eh :: + :: -> anisotropic XC 0.003588680038 Eh :: + :: -> dispersion -0.000661035657 Eh :: + :: repulsion energy 0.072166208576 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -4.175218465764 Eh | + | GRADIENT NORM 0.000198762862 Eh/α | + | HOMO-LUMO GAP 17.345708956675 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 20:31:26.446 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.011 sec + * cpu-time: 0 d, 0 h, 0 min, 0.010 sec + * ratio c/w: 0.954 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.003 sec + * cpu-time: 0 d, 0 h, 0 min, 0.002 sec + * ratio c/w: 0.808 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -4.175218465760 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 5 +Number of internal coordinates .... 10 +Current Energy .... -4.175218466 Eh +Current gradient norm .... 0.000198763 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999999841 +Lowest eigenvalues of augmented Hessian: + -0.000000112 0.290101853 0.290102533 0.290102901 0.290103257 +Length of the computed step .... 0.000564055 +The final length of the internal step .... 0.000564055 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0001783699 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0001456396 RMS(Int)= 0.0001783699 + Iter 1: RMS(Cart)= 0.0000000002 RMS(Int)= 0.0000000002 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0002561933 0.0000050000 NO + RMS gradient 0.0000628544 0.0001000000 YES + MAX gradient 0.0000997078 0.0003000000 YES + RMS step 0.0001783699 0.0020000000 YES + MAX step 0.0002829584 0.0040000000 YES + ........................................................ + Max(Bonds) 0.0001 Max(Angles) 0.00 + Max(Dihed) 0.00 Max(Improp) 0.00 + --------------------------------------------------------------------- + + Everything but the energy has converged. However, the energy + appears to be close enough to convergence to make sure that the + final evaluation at the new geometry represents the equilibrium energy. + Convergence will therefore be signaled now + + + ***********************HURRAY******************** + *** THE OPTIMIZATION HAS CONVERGED *** + ************************************************* + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + + --- Optimized Parameters --- + (Angstroem and degrees) + + Definition OldVal dE/dq Step FinalVal + ---------------------------------------------------------------------------- + 1. B(H 1,C 0) 1.0823 0.000099 -0.0001 1.0822 + 2. B(H 2,C 0) 1.0823 0.000099 -0.0001 1.0822 + 3. B(H 3,C 0) 1.0823 0.000100 -0.0001 1.0822 + 4. B(H 4,C 0) 1.0823 0.000099 -0.0001 1.0822 + 5. A(H 1,C 0,H 3) 109.47 0.000000 -0.00 109.47 + 6. A(H 2,C 0,H 3) 109.47 0.000000 -0.00 109.47 + 7. A(H 1,C 0,H 4) 109.47 0.000001 -0.00 109.47 + 8. A(H 2,C 0,H 4) 109.47 0.000000 -0.00 109.47 + 9. A(H 3,C 0,H 4) 109.47 -0.000000 0.00 109.47 + 10. A(H 1,C 0,H 2) 109.47 -0.000001 0.00 109.47 + ---------------------------------------------------------------------------- + ******************************************************* + *** FINAL ENERGY EVALUATION AT THE STATIONARY POINT *** + *** (AFTER 2 CYCLES) *** + ******************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.068140 0.069870 0.021798 + H 2.150300 0.069871 0.021797 + H 0.707424 -0.646152 0.748618 + H 0.707419 -0.201563 -0.961703 + H 0.707417 1.057324 0.278480 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.018492 0.132036 0.041192 + 1 H 1.0000 0 1.008 4.063479 0.132037 0.041191 + 2 H 1.0000 0 1.008 1.336837 -1.221049 1.414683 + 3 H 1.0000 0 1.008 1.336828 -0.380900 -1.817356 + 4 H 1.0000 0 1.008 1.336824 1.998052 0.526250 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 20:31:26.466 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 5 + number of electrons : 8 + charge : 0 + spin : 0.0 + first test random number : 0.31192593964749 + + ID Z sym. atoms + 1 6 C 1 + 2 1 H 2-5 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 8 : + : # atomic orbitals 8 : + : # shells 6 : + : # electrons 8 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -4.2474673 -0.424747E+01 0.161E-03 17.35 0.0 T + 2 -4.2474673 -0.163784E-08 0.849E-04 17.35 52.7 T + 3 -4.2474673 -0.599902E-10 0.305E-04 17.35 146.8 T + + *** convergence criteria satisfied after 3 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.5818333 -15.8325 + 2 2.0000 -0.4674558 -12.7201 + 3 2.0000 -0.4674555 -12.7201 + 4 2.0000 -0.4674554 -12.7201 (HOMO) + 5 0.1702655 4.6332 (LUMO) + 6 0.2292577 6.2384 + 7 0.2292581 6.2384 + 8 0.2292598 6.2385 + ------------------------------------------------------------- + HL-Gap 0.6377209 Eh 17.3533 eV + Fermi-level -0.1485950 Eh -4.0435 eV + + SCC (total) 0 d, 0 h, 0 min, 0.003 sec + SCC setup ... 0 min, 0.000 sec ( 1.774%) + Dispersion ... 0 min, 0.000 sec ( 0.412%) + classical contributions ... 0 min, 0.000 sec ( 0.233%) + integral evaluation ... 0 min, 0.000 sec ( 3.297%) + iterations ... 0 min, 0.003 sec ( 87.961%) + molecular gradient ... 0 min, 0.000 sec ( 4.531%) + printout ... 0 min, 0.000 sec ( 1.664%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -4.175218519967 Eh :: + :: gradient norm 0.000005339437 Eh/a0 :: + :: HOMO-LUMO gap 17.353269079928 eV :: + ::.................................................:: + :: SCC energy -4.247467308180 Eh :: + :: -> isotropic ES 0.002035507823 Eh :: + :: -> anisotropic ES 0.002321507900 Eh :: + :: -> anisotropic XC 0.003585039043 Eh :: + :: -> dispersion -0.000661012503 Eh :: + :: repulsion energy 0.072248782622 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -4.175218519967 Eh | + | GRADIENT NORM 0.000005339437 Eh/α | + | HOMO-LUMO GAP 17.353269079928 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 20:31:26.477 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.011 sec + * cpu-time: 0 d, 0 h, 0 min, 0.009 sec + * ratio c/w: 0.830 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.003 sec + * cpu-time: 0 d, 0 h, 0 min, 0.002 sec + * ratio c/w: 0.476 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -4.175218519970 +------------------------- -------------------- + + *** OPTIMIZATION RUN DONE *** + +Timings for individual modules: + +Sum of individual times ... 0.107 sec (= 0.002 min) +Geometry relaxation ... 0.022 sec (= 0.000 min) 20.4 % +XTB module ... 0.085 sec (= 0.001 min) 79.6 % + ****ORCA TERMINATED NORMALLY**** +TOTAL RUN TIME: 0 days 0 hours 0 minutes 0 seconds 151 msec diff --git a/cmmde_gui/test/ala/cmmd.xtbrestart b/cmmde_gui/test/ala/cmmd.xtbrestart new file mode 100644 index 0000000000000000000000000000000000000000..e1b1439fd025e1c6c2c7b2bcc9ab14cbc1906445 GIT binary patch literal 488 zcmXqDU|?VZVi17QtPm~(8q8M(6NWdnQ4i z-tRzhtH`9cQjQDun>73FTvfDpzhKC(wQRGN?sq$^nfGSK6=Nu_NZB@?!hy^NVtm*KM(nyC`f`2vpyi w66ZXtbLD<9#<#N{e%)ffG%ihNZEx59H6^>Z%jzt$KVop~Z=mz?{UARB04kr-8UO$Q literal 0 HcmV?d00001 diff --git a/cmmde_gui/test/ala/cmmd.xyz b/cmmde_gui/test/ala/cmmd.xyz new file mode 100644 index 0000000..0f9192b --- /dev/null +++ b/cmmde_gui/test/ala/cmmd.xyz @@ -0,0 +1,7 @@ +5 +Coordinates from ORCA-job cmmd + C 1.06814007280221 0.06987026850103 0.02179803932415 + H 2.15030026068978 0.06987112958641 0.02179749602221 + H 0.70742370687918 -0.64615150469397 0.74861807400167 + H 0.70741898627439 -0.20156341603182 -0.96170330012855 + H 0.70741697335444 1.05732352263836 0.27847969078052 diff --git a/cmmde_gui/test/ala/cmmd_property.txt b/cmmde_gui/test/ala/cmmd_property.txt new file mode 100644 index 0000000..8f1a67f --- /dev/null +++ b/cmmde_gui/test/ala/cmmd_property.txt @@ -0,0 +1,6 @@ +------------------------------------------------------------- +----------------------- !PROPERTIES! ------------------------ +------------------------------------------------------------- +# ------------------------------------------------------------- +----------------------- !GEOMETRIES! ------------------------ +# ------------------------------------------------------------- diff --git a/cmmde_gui/test/ala/cmmd_trj.xyz b/cmmde_gui/test/ala/cmmd_trj.xyz new file mode 100644 index 0000000..b31ee46 --- /dev/null +++ b/cmmde_gui/test/ala/cmmd_trj.xyz @@ -0,0 +1,21 @@ +5 +Coordinates from ORCA-job cmmd E -4.174962272510 + C 1.068140 0.069870 0.021800 + H 2.160340 0.069870 0.021800 + H 0.704080 -0.652790 0.755360 + H 0.704070 -0.204080 -0.970830 + H 0.704070 1.066480 0.280860 +5 +Coordinates from ORCA-job cmmd E -4.175218465760 + C 1.068140 0.069870 0.021798 + H 2.150450 0.069870 0.021798 + H 0.707375 -0.646250 0.748718 + H 0.707369 -0.201600 -0.961839 + H 0.707366 1.057460 0.278514 +5 +Coordinates from ORCA-job cmmd E -4.175218519970 + C 1.068140 0.069870 0.021798 + H 2.150300 0.069871 0.021797 + H 0.707424 -0.646152 0.748618 + H 0.707419 -0.201563 -0.961703 + H 0.707417 1.057324 0.278480 diff --git a/cmmde_gui/test/ala/freq/cmmd.engrad b/cmmde_gui/test/ala/freq/cmmd.engrad new file mode 100644 index 0000000..07d0f8e --- /dev/null +++ b/cmmde_gui/test/ala/freq/cmmd.engrad @@ -0,0 +1,34 @@ +# +# Number of atoms +# + 5 +# +# The current total energy in Eh +# + -4.175218519980 +# +# The current gradient in Eh/bohr +# + 0.000000045326 + 0.000000167733 + 0.000000029765 + -0.000003309957 + -0.000000249790 + 0.000000129141 + 0.000001317460 + 0.000002127091 + -0.000002151036 + 0.000001016219 + 0.000001006359 + 0.000002966352 + 0.000000930952 + -0.000003051392 + -0.000000974223 +# +# The atomic numbers and current coordinates in Bohr +# + 6 2.0184922 0.1320357 0.0411923 + 1 4.0634786 0.1320373 0.0411913 + 1 1.3368371 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0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 5 6 7 8 9 + 0 0.0000000000E+00 1.1460429268E-01 -3.4379236967E-02 -4.7849264525E-02 -6.2196180136E-08 + 1 0.0000000000E+00 5.8576857374E-02 7.7750867247E-02 8.4434109433E-02 5.7988235870E-06 + 2 0.0000000000E+00 -6.3442646325E-03 9.6842579071E-02 -8.4775157264E-02 5.6540900942E-06 + 3 0.0000000000E+00 5.3322377490E-02 -1.5995533024E-02 -2.2262979463E-02 2.3670438248E-07 + 4 0.0000000000E+00 -2.7535711067E-01 -3.6548194224E-01 -3.9692559975E-01 -3.6560167528E-01 + 5 0.0000000000E+00 2.9827653543E-02 -4.5522985733E-01 3.9852923127E-01 -3.4113931628E-01 + 6 0.0000000000E+00 -3.9889455056E-01 1.1846683962E-01 3.9173216657E-01 1.2781240094E-02 + 7 0.0000000000E+00 2.2582223879E-03 -4.5119127032E-01 -6.5843512581E-02 3.5285840880E-01 + 8 0.0000000000E+00 -2.5200659617E-01 -3.6833527333E-01 6.2452757104E-02 3.5395910859E-01 + 9 0.0000000000E+00 -4.5760273347E-01 3.2700273115E-01 1.0126357845E-01 4.0172057861E-01 + 10 0.0000000000E+00 -2.1431150072E-01 -2.4104848320E-01 -4.8999373348E-01 2.1441650987E-01 + 11 0.0000000000E+00 2.5110611645E-01 -4.2335079059E-03 6.1322674707E-02 -2.0650819767E-01 + 12 0.0000000000E+00 -5.6241255314E-01 -1.9822236936E-02 9.9423500526E-02 -4.1450131430E-01 + 13 0.0000000000E+00 -2.1057238274E-01 1.3126766153E-01 -5.3326527601E-02 -2.0174234028E-01 + 14 0.0000000000E+00 4.6669019129E-02 -3.2614602137E-01 4.8784852530E-01 1.9362103306E-01 + 10 11 12 13 14 + 0 -1.1685424666E-06 1.0305848845E-04 -1.6400025343E-02 -3.1979547838E-03 8.5675284564E-02 + 1 -5.0070919903E-07 5.4593202416E-05 -5.8809524764E-02 -6.3052970933E-02 -1.3611266360E-02 + 2 7.9760804626E-07 -4.9746676876E-05 6.2385950041E-02 -6.0279016142E-02 9.6922378022E-03 + 3 -1.3626230096E-06 4.9897892641E-01 1.6230624130E-01 3.1593465320E-02 -8.4545192635E-01 + 4 3.4111349028E-01 2.6482553553E-05 -2.7197780136E-02 -2.9159539116E-02 -6.2950067490E-03 + 5 -3.6557650895E-01 -2.3880077608E-05 2.8851914775E-02 -2.7876771652E-02 4.4822877101E-03 + 6 -4.7122878139E-01 -1.6697405729E-01 2.8914304946E-01 6.4174313555E-03 -5.0797945399E-03 + 7 1.2657588124E-01 -3.3151699796E-01 5.6180656381E-01 -1.3489457042E-02 -9.5034841166E-02 + 8 -1.0916974631E-01 3.3651927657E-01 -5.6903524917E-01 -4.3792105404E-02 9.4560503801E-02 + 9 2.4669155397E-01 -1.6662718301E-01 -1.3331926298E-01 2.4512947958E-01 -7.7040068406E-02 + 10 -4.3392019027E-01 -1.2539328656E-01 -1.2181111507E-01 1.5640546240E-01 -9.4081351994E-02 + 11 2.9276305623E-02 -4.5446595783E-01 -3.1396261364E-01 6.4450414089E-01 -3.1360477361E-01 + 12 2.2455251402E-01 -1.6660569754E-01 -1.2271266231E-01 -2.4503458766E-01 -9.3307023098E-02 + 13 -3.3763214961E-02 4.5623328713E-01 2.8795749205E-01 6.3756221815E-01 3.5759862079E-01 + 14 4.4546044560E-01 1.1856332655E-01 1.1077526755E-01 1.4542987792E-01 9.9072430276E-02 + +# +# The atoms: label mass x y z (in bohrs) +# +$atoms +5 + C 12.01100 2.018492210263 0.132035672370 0.041192324579 + H 1.00800 4.063478598403 0.132037299586 0.041191297887 + H 1.00800 1.336837066645 -1.221049384893 1.414683138767 + H 1.00800 1.336828145995 -0.380899654918 -1.817355859331 + H 1.00800 1.336824342127 1.998051892739 0.526250349434 + +$actual_temperature + 0.000000 + +$frequency_scale_factor + 1.000000 + +$dipole_derivatives +15 + -0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 + -2.0000000000E-01 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 + -0.0000000000E+00 -0.0000000000E+00 2.0000000000E-01 + 0.0000000000E+00 2.0000000000E-01 -0.0000000000E+00 + 0.0000000000E+00 -0.0000000000E+00 -0.0000000000E+00 + -0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 + -0.0000000000E+00 -0.0000000000E+00 -2.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 -2.0000000000E-01 -0.0000000000E+00 + 0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 + +# +# The IR spectrum +# wavenumber eps Int TX TY TZ +# +$ir_spectrum +15 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 1385.80 0.00043085 2.17736113 -0.002037 -0.001583 -0.009506 + 1385.80 0.00291380 14.72516324 0.000611 -0.019085 -0.017074 + 1385.82 0.00019488 0.98483488 0.000850 0.004423 -0.004858 + 1557.27 0.00475914 24.05072327 -0.000000 0.021765 0.021908 + 1557.28 0.00011600 0.58621836 0.000000 -0.002953 0.003811 + 3090.01 0.00213139 10.77118066 -0.013874 -0.003329 0.003419 + 3103.91 0.01079707 54.56396020 -0.004326 -0.022844 0.023344 + 3103.94 0.00634783 32.07932697 -0.000842 -0.018162 -0.017539 + 3103.96 0.00587823 29.70617211 0.022536 -0.007011 0.005826 + + +$end + diff --git a/cmmde_gui/test/ala/freq/cmmd.in b/cmmde_gui/test/ala/freq/cmmd.in new file mode 100644 index 0000000..247d130 --- /dev/null +++ b/cmmde_gui/test/ala/freq/cmmd.in @@ -0,0 +1,13 @@ +#CMMDE generated Orca input file +!XTB2 Numfreq +%pal + nprocs 1 +end + +*xyzfile 0 1 ../cmmd.xyz + +%freq + scalfreq 1 + Temp 298.15 + Pressure 1.0 +end diff --git a/cmmde_gui/test/ala/freq/cmmd.out b/cmmde_gui/test/ala/freq/cmmd.out new file mode 100644 index 0000000..36f7fe7 --- /dev/null +++ b/cmmde_gui/test/ala/freq/cmmd.out @@ -0,0 +1,711 @@ + + ***************** + * O R C A * + ***************** + + #, + ### + #### + ##### + ###### + ########, + ,,################,,,,, + ,,#################################,, + ,,##########################################,, + ,#########################################, ''#####, + ,#############################################,, '####, + ,##################################################,,,,####, + ,###########'''' ''''############################### + ,#####'' ,,,,##########,,,, '''####''' '#### + ,##' ,,,,###########################,,, '## + ' ,,###'''' '''############,,, + ,,##'' '''############,,,, ,,,,,,###'' + ,#'' '''#######################''' + ' ''''####'''' + ,#######, #######, ,#######, ## + ,#' '#, ## ## ,#' '#, #''# ###### ,####, + ## ## ## ,#' ## #' '# # #' '# + ## ## ####### ## ,######, #####, # # + '#, ,#' ## ## '#, ,#' ,# #, ## #, ,# + '#######' ## ## '#######' #' '# #####' # '####' + + + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship and core code : Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 5.0.2 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Marcus Kettner : VPT2 + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : Initial AUTO-CI + Lucas Lang : DCDCAS + Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, + C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT + MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, + LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, + nearIR, NL-DFT gradient (VV10), updates on ESD, + ML-optimized integration grids + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + Liviu Ungur et al : ANISO software + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 5.1.0 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + Shared memory : Shared parallel matrices + BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED + Core in use : SkylakeX + Copyright (c) 2011-2014, The OpenBLAS Project + + + + +*************************************** +The coordinates will be read from file: ../cmmd.xyz +*************************************** + + +Your calculation utilizes the semiempirical GFN2-xTB method +Please cite in your paper: +C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. + + +================================================================================ + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + +WARNING: Gradients needed for Numerical Frequencies + ===> : Setting RunTyp to EnGrad + +WARNING: Found dipole moment calculation with XTB calculation + ===> : Switching off dipole moment calculation + + +WARNING: TRAH-SCF for XTB is not implemented! + ===> : Turning TRAH off! + +================================================================================ + INPUT FILE +================================================================================ +NAME = cmmd.in +| 1> #CMMDE generated Orca input file +| 2> !XTB2 Numfreq +| 3> %pal +| 4> nprocs 1 +| 5> end +| 6> +| 7> *xyzfile 0 1 ../cmmd.xyz +| 8> +| 9> %freq +| 10> scalfreq 1 +| 11> Temp 298.15 +| 12> Pressure 1.0 +| 13> end +| 14> +| 15> ****END OF INPUT**** +================================================================================ + + ******************************* + * Energy+Gradient Calculation * + ******************************* + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 20:31:34.411 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 5 + number of electrons : 8 + charge : 0 + spin : 0.0 + first test random number : 0.60690392607394 + + ID Z sym. atoms + 1 6 C 1 + 2 1 H 2-5 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 8 : + : # atomic orbitals 8 : + : # shells 6 : + : # electrons 8 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -4.2352961 -0.423530E+01 0.243E+00 17.75 0.0 T + 2 -4.2472613 -0.119651E-01 0.928E-01 17.57 1.0 T + 3 -4.2474252 -0.163901E-03 0.500E-01 17.46 1.0 T + 4 -4.2474673 -0.421128E-04 0.924E-02 17.36 1.0 T + 5 -4.2474672 0.111480E-06 0.698E-03 17.35 6.4 T + 6 -4.2474673 -0.145702E-06 0.191E-04 17.35 233.9 T + 7 -4.2474673 -0.109869E-09 0.432E-06 17.35 10350.2 T + + *** convergence criteria satisfied after 7 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.5818361 -15.8326 + 2 2.0000 -0.4674583 -12.7202 + 3 2.0000 -0.4674579 -12.7202 + 4 2.0000 -0.4674579 -12.7202 (HOMO) + 5 0.1702647 4.6331 (LUMO) + 6 0.2292565 6.2384 + 7 0.2292569 6.2384 + 8 0.2292585 6.2384 + ------------------------------------------------------------- + HL-Gap 0.6377226 Eh 17.3533 eV + Fermi-level -0.1485966 Eh -4.0435 eV + + SCC (total) 0 d, 0 h, 0 min, 0.023 sec + SCC setup ... 0 min, 0.000 sec ( 0.165%) + Dispersion ... 0 min, 0.000 sec ( 0.028%) + classical contributions ... 0 min, 0.000 sec ( 0.021%) + integral evaluation ... 0 min, 0.000 sec ( 0.275%) + iterations ... 0 min, 0.023 sec ( 97.223%) + molecular gradient ... 0 min, 0.000 sec ( 1.597%) + printout ... 0 min, 0.000 sec ( 0.655%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -4.175218519975 Eh :: + :: gradient norm 0.000006627564 Eh/a0 :: + :: HOMO-LUMO gap 17.353313970090 eV :: + ::.................................................:: + :: SCC energy -4.247467308188 Eh :: + :: -> isotropic ES 0.002035567944 Eh :: + :: -> anisotropic ES 0.002321540929 Eh :: + :: -> anisotropic XC 0.003585096736 Eh :: + :: -> dispersion -0.000661011606 Eh :: + :: repulsion energy 0.072248782622 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -4.175218519975 Eh | + | GRADIENT NORM 0.000006627564 Eh/α | + | HOMO-LUMO GAP 17.353313970090 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 20:31:34.439 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.028 sec + * cpu-time: 0 d, 0 h, 0 min, 0.007 sec + * ratio c/w: 0.264 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.023 sec + * cpu-time: 0 d, 0 h, 0 min, 0.003 sec + * ratio c/w: 0.126 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -4.175218519980 +------------------------- -------------------- + + +---------------------------------------------------------------------------- + ORCA NUMERICAL FREQUENCIES +---------------------------------------------------------------------------- + +Number of atoms ... 5 +Central differences ... used +Number of displacements ... 30 +Numerical increment ... 5.000e-03 bohr +IR-spectrum generation ... on +Raman-spectrum generation ... off +Surface Crossing Hessian ... off + +The output will be reduced. Please look at the following files: +SCF program output ... >cmmd.lastscf +Integral program output ... >cmmd.lastint +Gradient program output ... >cmmd.lastgrad +Dipole moment program output ... >cmmd.lastmom +AutoCI program output ... >cmmd.lastautoci + + << Calculating on displaced geometry 1 (of 30) >> + << Calculating on displaced geometry 2 (of 30) >> + << Calculating on displaced geometry 3 (of 30) >> + << Calculating on displaced geometry 4 (of 30) >> + << Calculating on displaced geometry 5 (of 30) >> + << Calculating on displaced geometry 6 (of 30) >> + << Calculating on displaced geometry 7 (of 30) >> + << Calculating on displaced geometry 8 (of 30) >> + << Calculating on displaced geometry 9 (of 30) >> + << Calculating on displaced geometry 10 (of 30) >> + << Calculating on displaced geometry 11 (of 30) >> + << Calculating on displaced geometry 12 (of 30) >> + << Calculating on displaced geometry 13 (of 30) >> + << Calculating on displaced geometry 14 (of 30) >> + << Calculating on displaced geometry 15 (of 30) >> + << Calculating on displaced geometry 16 (of 30) >> + << Calculating on displaced geometry 17 (of 30) >> + << Calculating on displaced geometry 18 (of 30) >> + << Calculating on displaced geometry 19 (of 30) >> + << Calculating on displaced geometry 20 (of 30) >> + << Calculating on displaced geometry 21 (of 30) >> + << Calculating on displaced geometry 22 (of 30) >> + << Calculating on displaced geometry 23 (of 30) >> + << Calculating on displaced geometry 24 (of 30) >> + << Calculating on displaced geometry 25 (of 30) >> + << Calculating on displaced geometry 26 (of 30) >> + << Calculating on displaced geometry 27 (of 30) >> + << Calculating on displaced geometry 28 (of 30) >> + << Calculating on displaced geometry 29 (of 30) >> + << Calculating on displaced geometry 30 (of 30) >> + +----------------------- +VIBRATIONAL FREQUENCIES +----------------------- + +Scaling factor for frequencies = 1.000000000 (already applied!) + + 0: 0.00 cm**-1 + 1: 0.00 cm**-1 + 2: 0.00 cm**-1 + 3: 0.00 cm**-1 + 4: 0.00 cm**-1 + 5: 0.00 cm**-1 + 6: 1385.80 cm**-1 + 7: 1385.80 cm**-1 + 8: 1385.82 cm**-1 + 9: 1557.27 cm**-1 + 10: 1557.28 cm**-1 + 11: 3090.01 cm**-1 + 12: 3103.91 cm**-1 + 13: 3103.94 cm**-1 + 14: 3103.96 cm**-1 + + +------------ +NORMAL MODES +------------ + +These modes are the cartesian displacements weighted by the diagonal matrix +M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom +Thus, these vectors are normalized but *not* orthogonal + + 0 1 2 3 4 5 + 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 1 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 2 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 7 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 8 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 9 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 10 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 11 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 12 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 13 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 14 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 6 7 8 9 10 11 + 0 0.114604 -0.034379 -0.047849 -0.000000 -0.000001 0.000103 + 1 0.058577 0.077751 0.084434 0.000006 -0.000001 0.000055 + 2 -0.006344 0.096843 -0.084775 0.000006 0.000001 -0.000050 + 3 0.053322 -0.015996 -0.022263 0.000000 -0.000001 0.498979 + 4 -0.275357 -0.365482 -0.396926 -0.365602 0.341113 0.000026 + 5 0.029828 -0.455230 0.398529 -0.341139 -0.365577 -0.000024 + 6 -0.398895 0.118467 0.391732 0.012781 -0.471229 -0.166974 + 7 0.002258 -0.451191 -0.065844 0.352858 0.126576 -0.331517 + 8 -0.252007 -0.368335 0.062453 0.353959 -0.109170 0.336519 + 9 -0.457603 0.327003 0.101264 0.401721 0.246692 -0.166627 + 10 -0.214312 -0.241048 -0.489994 0.214417 -0.433920 -0.125393 + 11 0.251106 -0.004234 0.061323 -0.206508 0.029276 -0.454466 + 12 -0.562413 -0.019822 0.099424 -0.414501 0.224553 -0.166606 + 13 -0.210572 0.131268 -0.053327 -0.201742 -0.033763 0.456233 + 14 0.046669 -0.326146 0.487849 0.193621 0.445460 0.118563 + 12 13 14 + 0 -0.016400 -0.003198 0.085675 + 1 -0.058810 -0.063053 -0.013611 + 2 0.062386 -0.060279 0.009692 + 3 0.162306 0.031593 -0.845452 + 4 -0.027198 -0.029160 -0.006295 + 5 0.028852 -0.027877 0.004482 + 6 0.289143 0.006417 -0.005080 + 7 0.561807 -0.013489 -0.095035 + 8 -0.569035 -0.043792 0.094561 + 9 -0.133319 0.245129 -0.077040 + 10 -0.121811 0.156405 -0.094081 + 11 -0.313963 0.644504 -0.313605 + 12 -0.122713 -0.245035 -0.093307 + 13 0.287957 0.637562 0.357599 + 14 0.110775 0.145430 0.099072 + + +----------- +IR SPECTRUM +----------- + + Mode freq eps Int T**2 TX TY TZ + cm**-1 L/(mol*cm) km/mol a.u. +---------------------------------------------------------------------------- + 6: 1385.80 0.000431 2.18 0.000097 (-0.002037 -0.001583 -0.009506) + 7: 1385.80 0.002914 14.73 0.000656 ( 0.000611 -0.019085 -0.017074) + 8: 1385.82 0.000195 0.98 0.000044 ( 0.000850 0.004423 -0.004858) + 9: 1557.27 0.004759 24.05 0.000954 (-0.000000 0.021765 0.021908) + 10: 1557.28 0.000116 0.59 0.000023 ( 0.000000 -0.002953 0.003811) + 11: 3090.01 0.002131 10.77 0.000215 (-0.013874 -0.003329 0.003419) + 12: 3103.91 0.010797 54.56 0.001086 (-0.004326 -0.022844 0.023344) + 13: 3103.94 0.006348 32.08 0.000638 (-0.000842 -0.018162 -0.017539) + 14: 3103.96 0.005878 29.71 0.000591 ( 0.022536 -0.007011 0.005826) + +* The epsilon (eps) is given for a Dirac delta lineshape. +** The dipole moment derivative (T) already includes vibrational overlap. + +The first frequency considered to be a vibration is 6 +The total number of vibrations considered is 9 + + +-------------------------- +THERMOCHEMISTRY AT 298.15K +-------------------------- + +Temperature ... 298.15 K +Pressure ... 1.00 atm +Total Mass ... 16.04 AMU + +Throughout the following assumptions are being made: + (1) The electronic state is orbitally nondegenerate + (2) There are no thermally accessible electronically excited states + (3) Hindered rotations indicated by low frequency modes are not + treated as such but are treated as vibrations and this may + cause some error + (4) All equations used are the standard statistical mechanics + equations for an ideal gas + (5) All vibrations are strictly harmonic + +freq. 1385.80 E(vib) ... 0.00 +freq. 1385.80 E(vib) ... 0.00 +freq. 1385.82 E(vib) ... 0.00 +freq. 1557.27 E(vib) ... 0.00 +freq. 1557.28 E(vib) ... 0.00 +freq. 3090.01 E(vib) ... 0.00 +freq. 3103.91 E(vib) ... 0.00 +freq. 3103.94 E(vib) ... 0.00 +freq. 3103.96 E(vib) ... 0.00 + +------------ +INNER ENERGY +------------ + +The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans) + E(el) - is the total energy from the electronic structure calculation + = E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc) + E(ZPE) - the the zero temperature vibrational energy from the frequency calculation + E(vib) - the the finite temperature correction to E(ZPE) due to population + of excited vibrational states + E(rot) - is the rotational thermal energy + E(trans)- is the translational thermal energy + +Summary of contributions to the inner energy U: +Electronic energy ... -4.17521852 Eh +Zero point energy ... 0.04482019 Eh 28.13 kcal/mol +Thermal vibrational correction ... 0.00003140 Eh 0.02 kcal/mol +Thermal rotational correction ... 0.00141627 Eh 0.89 kcal/mol +Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol +----------------------------------------------------------------------- +Total thermal energy -4.12753439 Eh + + +Summary of corrections to the electronic energy: +(perhaps to be used in another calculation) +Total thermal correction 0.00286394 Eh 1.80 kcal/mol +Non-thermal (ZPE) correction 0.04482019 Eh 28.13 kcal/mol +----------------------------------------------------------------------- +Total correction 0.04768413 Eh 29.92 kcal/mol + + +-------- +ENTHALPY +-------- + +The enthalpy is H = U + kB*T + kB is Boltzmann's constant +Total free energy ... -4.12753439 Eh +Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol +----------------------------------------------------------------------- +Total Enthalpy ... -4.12659018 Eh + + +Note: Rotational entropy computed according to Herzberg +Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945 +Point Group: Td, Symmetry Number: 12 +Rotational constants in cm-1: 5.355318 5.355306 5.355302 + +Vibrational entropy computed according to the QRRHO of S. Grimme +Chem.Eur.J. 2012 18 9955 + + +------- +ENTROPY +------- + +The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans)) + S(el) - electronic entropy + S(vib) - vibrational entropy + S(rot) - rotational entropy + S(trans)- translational entropy +The entropies will be listed as multiplied by the temperature to get +units of energy + +Electronic entropy ... 0.00000000 Eh 0.00 kcal/mol +Vibrational entropy ... 0.00003597 Eh 0.02 kcal/mol +Rotational entropy ... 0.00478798 Eh 3.00 kcal/mol +Translational entropy ... 0.01627961 Eh 10.22 kcal/mol +----------------------------------------------------------------------- +Final entropy term ... 0.02110356 Eh 13.24 kcal/mol + +In case the symmetry of your molecule has not been determined correctly +or in case you have a reason to use a different symmetry number we print +out the resulting rotational entropy values for sn=1,12 : + -------------------------------------------------------- +| sn= 1 | S(rot)= 0.00713418 Eh 4.48 kcal/mol| +| sn= 2 | S(rot)= 0.00647973 Eh 4.07 kcal/mol| +| sn= 3 | S(rot)= 0.00609689 Eh 3.83 kcal/mol| +| sn= 4 | S(rot)= 0.00582527 Eh 3.66 kcal/mol| +| sn= 5 | S(rot)= 0.00561458 Eh 3.52 kcal/mol| +| sn= 6 | S(rot)= 0.00544244 Eh 3.42 kcal/mol| +| sn= 7 | S(rot)= 0.00529689 Eh 3.32 kcal/mol| +| sn= 8 | S(rot)= 0.00517081 Eh 3.24 kcal/mol| +| sn= 9 | S(rot)= 0.00505960 Eh 3.17 kcal/mol| +| sn=10 | S(rot)= 0.00496012 Eh 3.11 kcal/mol| +| sn=11 | S(rot)= 0.00487013 Eh 3.06 kcal/mol| +| sn=12 | S(rot)= 0.00478798 Eh 3.00 kcal/mol| + -------------------------------------------------------- + + +------------------- +GIBBS FREE ENERGY +------------------- + +The Gibbs free energy is G = H - T*S + +Total enthalpy ... -4.12659018 Eh +Total entropy correction ... -0.02110356 Eh -13.24 kcal/mol +----------------------------------------------------------------------- +Final Gibbs free energy ... -4.14769375 Eh + +For completeness - the Gibbs free energy minus the electronic energy +G-E(el) ... 0.02752477 Eh 17.27 kcal/mol + + + +Timings for individual modules: + +Sum of individual times ... 63.185 sec (= 1.053 min) +Numerical frequency calculation ... 63.123 sec (= 1.052 min) 99.9 % +XTB module ... 0.061 sec (= 0.001 min) 0.1 % + ****ORCA TERMINATED NORMALLY**** +TOTAL RUN TIME: 0 days 0 hours 1 minutes 3 seconds 196 msec diff --git a/cmmde_gui/test/ala/freq/cmmd.xtbrestart b/cmmde_gui/test/ala/freq/cmmd.xtbrestart new file mode 100644 index 0000000000000000000000000000000000000000..016661799492f0a9fbaeea4caeb2864ae7065811 GIT binary patch literal 488 zcmXqDU|?VZVi17QtPm~(82@^T~m0YRQKTimj9~KNpBY0 zS8|_hNC474JKGL}=+pcDt0V(yke&)4K3y5Of1ypbU4wk=$-B=x>}ok})B~o(+9eC8 zx;7Xeu-|ZUp||Gwnft6h-?ehzVTn1~HcMCA&3zxGESDW=7r#_u zU-O^c_5$*Pe@tsO*sah08s73}_5QBc-8 cmmd.out --oversubscribe diff --git a/cmmde_gui/test/ala/freq/slurm-2915.out b/cmmde_gui/test/ala/freq/slurm-2915.out new file mode 100644 index 0000000..e69de29 diff --git a/cmmde_gui/test/ala/geom.smi b/cmmde_gui/test/ala/geom.smi new file mode 100644 index 0000000..3cc58df --- /dev/null +++ b/cmmde_gui/test/ala/geom.smi @@ -0,0 +1 @@ +C diff --git a/cmmde_gui/test/ala/geom.xyz b/cmmde_gui/test/ala/geom.xyz new file mode 100644 index 0000000..4a7bea1 --- /dev/null +++ b/cmmde_gui/test/ala/geom.xyz @@ -0,0 +1,7 @@ +5 + +C 1.06814 0.06987 0.02180 +H 2.16034 0.06987 0.02180 +H 0.70408 -0.65279 0.75536 +H 0.70407 -0.20408 -0.97083 +H 0.70407 1.06648 0.28086 diff --git a/cmmde_gui/test/ala/run.sh b/cmmde_gui/test/ala/run.sh new file mode 100644 index 0000000..f72e163 --- /dev/null +++ b/cmmde_gui/test/ala/run.sh @@ -0,0 +1,10 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH +export PATH=/home/adit/opt/openmpi411/bin:$PATH +export OMP_NUM_THREADS=1 +cd $PWD +$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe diff --git a/cmmde_gui/test/ala/run_babel.sh b/cmmde_gui/test/ala/run_babel.sh new file mode 100644 index 0000000..0d5d00e --- /dev/null +++ b/cmmde_gui/test/ala/run_babel.sh @@ -0,0 +1,8 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export OMP_NUM_THREADS=1 +cd $PWD +obabel geom.smi -O geom.xyz --gen3d diff --git a/cmmde_gui/test/ala/slurm-2913.out b/cmmde_gui/test/ala/slurm-2913.out new file mode 100644 index 0000000..b7d75ac --- /dev/null +++ b/cmmde_gui/test/ala/slurm-2913.out @@ -0,0 +1 @@ +1 molecule converted diff --git a/cmmde_gui/test/ala/slurm-2914.out b/cmmde_gui/test/ala/slurm-2914.out new file mode 100644 index 0000000..e69de29 diff --git a/cmmde_gui/test/alala/alala/cmmd.engrad b/cmmde_gui/test/alala/alala/cmmd.engrad new file mode 100644 index 0000000..5454e34 --- /dev/null +++ b/cmmde_gui/test/alala/alala/cmmd.engrad @@ -0,0 +1,74 @@ +# +# Number of atoms +# + 15 +# +# The current total energy in Eh +# + -15.814313366050 +# +# The current gradient in Eh/bohr +# + 0.000227495798 + -0.000049478208 + 0.000259008811 + 0.000082454763 + -0.000273081820 + -0.000428388240 + -0.000389851164 + -0.000263790724 + 0.000131258810 + -0.000267765264 + 0.000279977188 + 0.000405328706 + 0.000065519654 + 0.000232417966 + -0.000346430104 + -0.000091428520 + -0.000003594258 + -0.000047833688 + 0.000020375247 + 0.000036476347 + -0.000092535766 + -0.000051248393 + 0.000118951949 + 0.000073438073 + 0.000077590295 + 0.000013581623 + 0.000136037554 + 0.000084963869 + -0.000004747271 + -0.000102722280 + 0.000081476300 + 0.000093731217 + 0.000038224552 + 0.000050966115 + 0.000038809074 + -0.000147860440 + 0.000094397666 + -0.000112630042 + -0.000050618890 + -0.000060968602 + -0.000087995984 + 0.000064681824 + 0.000076022236 + -0.000018627056 + 0.000108411078 +# +# The atomic numbers and current coordinates in Bohr +# + 6 2.3703954 -0.1651194 0.4670557 + 6 0.6244121 -2.3149509 -0.3431616 + 6 -2.0569278 -1.2859578 0.0884502 + 6 -1.7932022 1.6093409 0.2505151 + 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-2.18273939 2.25303203 2.16645091 + -3.10841648 2.57250982 -1.01091545 1.64006194 3.90818160 0.44503195 + 1.16001267 2.37008393 -2.47970073 + 2.37116000 -0.16536281 0.46554758 0.62419926 -2.31577839 -0.34252757 + -2.05772611 -1.28632367 0.08850319 -1.79406931 1.60964952 0.25033390 + 0.95721384 2.17677820 -0.44120424 4.25359723 -0.32802208 -0.35075708 + 2.54788993 -0.12617923 2.51952128 0.96944193 -4.04675545 0.71586606 + 0.91678080 -2.72067721 -2.34244489 -2.84850098 -2.03426920 1.83651504 + -3.31193703 -1.84060013 -1.44683341 -2.17340042 2.25096767 2.17129773 + -3.10986628 2.57303630 -1.00521341 1.64092011 3.91068258 0.43186542 + 1.15657452 2.35564736 -2.48561420 + +# redundant internal coordinates +# nbonds nangles ndihedrals nimpropers ncartesians +# bond definitions A B +# angle definitions A B C +# dihedral definitions A B C D +# improper torsion definitions A B C D +# cartesian definitions A x/y/z +$redundant_internals + 15 30 45 0 0 + 1 0 0 + 2 1 0 + 3 2 0 + 4 3 0 + 4 0 0 + 5 0 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,,#################################,, + ,,##########################################,, + ,#########################################, ''#####, + ,#############################################,, '####, + ,##################################################,,,,####, + ,###########'''' ''''############################### + ,#####'' ,,,,##########,,,, '''####''' '#### + ,##' ,,,,###########################,,, '## + ' ,,###'''' '''############,,, + ,,##'' '''############,,,, ,,,,,,###'' + ,#'' '''#######################''' + ' ''''####'''' + ,#######, #######, ,#######, ## + ,#' '#, ## ## ,#' '#, #''# ###### ,####, + ## ## ## ,#' ## #' '# # #' '# + ## ## ####### ## ,######, #####, # # + '#, ,#' ## ## '#, ,#' ,# #, ## #, ,# + '#######' ## ## '#######' #' '# #####' # '####' + + + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship and core code : Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 5.0.2 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Marcus Kettner : VPT2 + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : Initial AUTO-CI + Lucas Lang : DCDCAS + Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, + C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT + MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, + LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, + nearIR, NL-DFT gradient (VV10), updates on ESD, + ML-optimized integration grids + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + Liviu Ungur et al : ANISO software + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 5.1.0 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + Shared memory : Shared parallel matrices + BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED + Core in use : SkylakeX + Copyright (c) 2011-2014, The OpenBLAS Project + + + + +*************************************** +The coordinates will be read from file: geom.xyz +*************************************** + + +Your calculation utilizes the semiempirical GFN2-xTB method +Please cite in your paper: +C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. + + +================================================================================ + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + + +WARNING: Geometry Optimization + ===> : Switching off AutoStart + For restart on a previous wavefunction, please use MOREAD + +WARNING: Found dipole moment calculation with XTB calculation + ===> : Switching off dipole moment calculation + + +WARNING: TRAH-SCF for XTB is not implemented! + ===> : Turning TRAH off! + +================================================================================ + INPUT FILE +================================================================================ +NAME = cmmd.in +| 1> #CMMDE generated Orca input file +| 2> !XTB2 opt +| 3> %pal +| 4> nprocs 1 +| 5> end +| 6> %geom +| 7> maxiter 9999 +| 8> end +| 9> +| 10> *xyzfile 0 1 geom.xyz +| 11> +| 12> +| 13> ****END OF INPUT**** +================================================================================ + + ***************************** + * Geometry Optimization Run * + ***************************** + +Geometry optimization settings: +Update method Update .... BFGS +Choice of coordinates CoordSys .... Z-matrix Internals +Initial Hessian InHess .... Almoef's Model + +Convergence Tolerances: +Energy Change TolE .... 5.0000e-06 Eh +Max. Gradient TolMAXG .... 3.0000e-04 Eh/bohr +RMS Gradient TolRMSG .... 1.0000e-04 Eh/bohr +Max. Displacement TolMAXD .... 4.0000e-03 bohr +RMS Displacement TolRMSD .... 2.0000e-03 bohr +Strict Convergence .... False +------------------------------------------------------------------------------ + ORCA OPTIMIZATION COORDINATE SETUP +------------------------------------------------------------------------------ + +The optimization will be done in new redundant internal coordinates +Making redundant internal coordinates ... (new redundants) done +Evaluating the initial hessian ... (Almloef) done +Evaluating the coordinates ... done +Calculating the B-matrix .... done +Calculating the G-matrix .... done +Diagonalizing the G-matrix .... done +The first mode is .... 51 +The number of degrees of freedom .... 39 + + ----------------------------------------------------------------- + Redundant Internal Coordinates + + + ----------------------------------------------------------------- + Definition Initial Value Approx d2E/dq + ----------------------------------------------------------------- + 1. B(C 1,C 0) 1.5200 0.387533 + 2. B(C 2,C 1) 1.5261 0.378985 + 3. B(C 3,C 2) 1.5283 0.375898 + 4. B(C 4,C 3) 1.5220 0.384658 + 5. B(C 4,C 0) 1.5184 0.389816 + 6. B(H 5,C 0) 1.0936 0.355363 + 7. B(H 6,C 0) 1.0965 0.351602 + 8. B(H 7,C 1) 1.0940 0.354874 + 9. B(H 8,C 1) 1.0969 0.351103 + 10. B(H 9,C 2) 1.0956 0.352775 + 11. B(H 10,C 2) 1.0952 0.353314 + 12. B(H 11,C 3) 1.0967 0.351366 + 13. B(H 12,C 3) 1.0945 0.354152 + 14. B(H 13,C 4) 1.0937 0.355216 + 15. B(H 14,C 4) 1.0966 0.351497 + 16. A(C 4,C 0,H 5) 112.3841 0.325885 + 17. A(C 1,C 0,C 4) 103.1297 0.368316 + 18. A(C 1,C 0,H 5) 112.2933 0.325571 + 19. A(H 5,C 0,H 6) 108.3256 0.289151 + 20. A(C 1,C 0,H 6) 110.2991 0.325002 + 21. A(C 4,C 0,H 6) 110.3632 0.325316 + 22. A(C 2,C 1,H 8) 109.6622 0.323738 + 23. A(C 2,C 1,H 7) 112.2441 0.324306 + 24. A(H 7,C 1,H 8) 107.7743 0.289024 + 25. A(C 0,C 1,H 7) 112.2767 0.325497 + 26. A(C 0,C 1,C 2) 104.9844 0.366541 + 27. A(C 0,C 1,H 8) 109.8821 0.324926 + 28. A(H 9,C 2,H 10) 107.3415 0.289040 + 29. A(C 1,C 2,C 3) 106.3541 0.364632 + 30. A(C 1,C 2,H 10) 110.7808 0.324071 + 31. A(C 3,C 2,H 9) 110.0769 0.323556 + 32. A(C 1,C 2,H 9) 110.8158 0.323990 + 33. A(C 3,C 2,H 10) 111.5139 0.323637 + 34. A(H 11,C 3,H 12) 107.5009 0.288966 + 35. A(C 4,C 3,H 12) 111.7898 0.324990 + 36. A(C 2,C 3,H 12) 112.0750 0.323763 + 37. A(C 4,C 3,H 11) 110.0374 0.324568 + 38. A(C 2,C 3,H 11) 109.6080 0.323343 + 39. A(C 2,C 3,C 4) 105.8354 0.365561 + 40. A(H 13,C 4,H 14) 108.1093 0.289118 + 41. A(C 3,C 4,H 14) 110.0318 0.324588 + 42. A(C 0,C 4,H 14) 110.1672 0.325300 + 43. A(C 3,C 4,H 13) 112.2832 0.325150 + 44. A(C 0,C 4,H 13) 112.4281 0.325863 + 45. A(C 0,C 4,C 3) 103.7901 0.367846 + 46. D(H 7,C 1,C 0,H 5) 80.9311 0.011947 + 47. D(H 7,C 1,C 0,H 6) -39.9976 0.011947 + 48. D(C 2,C 1,C 0,H 5) -156.8515 0.011947 + 49. D(H 7,C 1,C 0,C 4) -157.8535 0.011947 + 50. D(H 8,C 1,C 0,H 6) -159.9281 0.011947 + 51. D(C 2,C 1,C 0,C 4) -35.6361 0.011947 + 52. D(C 2,C 1,C 0,H 6) 82.2198 0.011947 + 53. D(H 8,C 1,C 0,H 5) -38.9994 0.011947 + 54. D(H 8,C 1,C 0,C 4) 82.2160 0.011947 + 55. D(H 9,C 2,C 1,H 7) 20.3280 0.011450 + 56. D(C 3,C 2,C 1,H 8) -100.2882 0.011450 + 57. D(C 3,C 2,C 1,C 0) 17.7131 0.011450 + 58. D(H 10,C 2,C 1,H 8) 21.0534 0.011450 + 59. D(H 9,C 2,C 1,H 8) 140.0881 0.011450 + 60. D(H 10,C 2,C 1,H 7) -98.7067 0.011450 + 61. D(H 10,C 2,C 1,C 0) 139.0547 0.011450 + 62. D(C 3,C 2,C 1,H 7) 139.9516 0.011450 + 63. D(H 9,C 2,C 1,C 0) -101.9106 0.011450 + 64. D(H 12,C 3,C 2,H 9) -110.8121 0.011275 + 65. D(H 12,C 3,C 2,C 1) 129.0845 0.011275 + 66. D(H 11,C 3,C 2,H 10) 127.4851 0.011275 + 67. D(H 11,C 3,C 2,H 9) 8.4601 0.011275 + 68. D(C 4,C 3,C 2,H 9) 127.0880 0.011275 + 69. D(C 4,C 3,C 2,C 1) 6.9845 0.011275 + 70. D(H 11,C 3,C 2,C 1) -111.6433 0.011275 + 71. D(H 12,C 3,C 2,H 10) 8.2128 0.011275 + 72. D(C 4,C 3,C 2,H 10) -113.8871 0.011275 + 73. D(H 13,C 4,C 0,C 1) 161.5189 0.012081 + 74. D(C 3,C 4,C 0,H 6) -77.8722 0.012081 + 75. D(C 3,C 4,C 0,H 5) 161.0924 0.012081 + 76. D(C 3,C 4,C 0,C 1) 39.9387 0.012081 + 77. D(H 14,C 4,C 3,H 12) -33.4345 0.011778 + 78. D(H 14,C 4,C 3,H 11) -152.8096 0.011778 + 79. D(H 13,C 4,C 3,H 12) 87.0267 0.011778 + 80. D(H 13,C 4,C 3,H 11) -32.3484 0.011778 + 81. D(H 13,C 4,C 3,C 2) -150.6910 0.011778 + 82. D(C 0,C 4,C 3,H 12) -151.2963 0.011778 + 83. D(C 0,C 4,C 3,H 11) 89.3286 0.011778 + 84. D(C 0,C 4,C 3,C 2) -29.0139 0.011778 + 85. D(H 14,C 4,C 0,H 6) 164.3599 0.012081 + 86. D(H 14,C 4,C 0,H 5) 43.3246 0.012081 + 87. D(H 14,C 4,C 3,C 2) 88.8478 0.011778 + 88. D(H 14,C 4,C 0,C 1) -77.8292 0.012081 + 89. D(H 13,C 4,C 0,H 6) 43.7080 0.012081 + 90. D(H 13,C 4,C 0,H 5) -77.3273 0.012081 + ----------------------------------------------------------------- + +Number of atoms .... 15 +Number of degrees of freedom .... 90 + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 1 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.253970 -0.087850 0.236110 + C 0.326710 -1.222030 -0.169190 + C -1.082040 -0.675110 0.043510 + C -0.946150 0.845120 0.122080 + C 0.504630 1.150760 -0.222060 + H 2.240750 -0.172920 -0.227570 + H 1.384620 -0.073870 1.324710 + H 0.508830 -2.133100 0.408370 + H 0.473010 -1.462750 -1.229290 + H -1.513940 -1.062630 0.972820 + H -1.743910 -0.977410 -0.775000 + H -1.169630 1.182400 1.141400 + H -1.640100 1.355580 -0.553100 + H 0.864040 2.060640 0.266980 + H 0.614500 1.279940 -1.305450 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.369660 -0.166012 0.446183 + 1 C 6.0000 0 12.011 0.617392 -2.309302 -0.319723 + 2 C 6.0000 0 12.011 -2.044759 -1.275773 0.082222 + 3 C 6.0000 0 12.011 -1.787964 1.597045 0.230698 + 4 C 6.0000 0 12.011 0.953612 2.174621 -0.419633 + 5 H 1.0000 0 1.008 4.234404 -0.326771 -0.430045 + 6 H 1.0000 0 1.008 2.616553 -0.139594 2.503339 + 7 H 1.0000 0 1.008 0.961549 -4.030975 0.771707 + 8 H 1.0000 0 1.008 0.893859 -2.764197 -2.323021 + 9 H 1.0000 0 1.008 -2.860932 -2.008080 1.838363 + 10 H 1.0000 0 1.008 -3.295512 -1.847037 -1.464538 + 11 H 1.0000 0 1.008 -2.210280 2.234412 2.156933 + 12 H 1.0000 0 1.008 -3.099340 2.561675 -1.045208 + 13 H 1.0000 0 1.008 1.632799 3.894045 0.504519 + 14 H 1.0000 0 1.008 1.161237 2.418736 -2.466943 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:59:33.411 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.48288039371525 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0004270 -0.160004E+02 0.266E+00 13.67 0.0 T + 2 -16.0453832 -0.449562E-01 0.158E+00 13.37 1.0 T + 3 -16.0456958 -0.312551E-03 0.831E-01 13.37 1.0 T + 4 -16.0458078 -0.112067E-03 0.803E-02 13.35 1.0 T + 5 -16.0458081 -0.244111E-06 0.462E-03 13.36 5.6 T + 6 -16.0458081 -0.449080E-07 0.200E-03 13.36 12.9 T + 7 -16.0458081 -0.395713E-08 0.530E-04 13.36 48.7 T + 8 -16.0458081 -0.689152E-09 0.104E-04 13.36 249.2 T + + *** convergence criteria satisfied after 8 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6335396 -17.2395 + ... ... ... ... + 9 2.0000 -0.4827275 -13.1357 + 10 2.0000 -0.4415401 -12.0149 + 11 2.0000 -0.4388939 -11.9429 + 12 2.0000 -0.4365247 -11.8784 + 13 2.0000 -0.4363620 -11.8740 + 14 2.0000 -0.4202600 -11.4359 + 15 2.0000 -0.4131029 -11.2411 (HOMO) + 16 0.0776863 2.1140 (LUMO) + 17 0.0785880 2.1385 + 18 0.0830294 2.2593 + 19 0.1250432 3.4026 + 20 0.1388223 3.7775 + ... ... ... + 30 0.3462224 9.4212 + ------------------------------------------------------------- + HL-Gap 0.4907892 Eh 13.3551 eV + Fermi-level -0.1677083 Eh -4.5636 eV + + SCC (total) 0 d, 0 h, 0 min, 0.033 sec + SCC setup ... 0 min, 0.000 sec ( 0.462%) + Dispersion ... 0 min, 0.000 sec ( 0.321%) + classical contributions ... 0 min, 0.000 sec ( 0.119%) + integral evaluation ... 0 min, 0.002 sec ( 5.244%) + iterations ... 0 min, 0.026 sec ( 78.861%) + molecular gradient ... 0 min, 0.005 sec ( 14.404%) + printout ... 0 min, 0.000 sec ( 0.554%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.813823527310 Eh :: + :: gradient norm 0.022707407200 Eh/a0 :: + :: HOMO-LUMO gap 13.355054326678 eV :: + ::.................................................:: + :: SCC energy -16.045808110944 Eh :: + :: -> isotropic ES 0.002215602953 Eh :: + :: -> anisotropic ES 0.004256460236 Eh :: + :: -> anisotropic XC 0.009822111034 Eh :: + :: -> dispersion -0.008145854109 Eh :: + :: repulsion energy 0.231974178511 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.813823527310 Eh | + | GRADIENT NORM 0.022707407200 Eh/α | + | HOMO-LUMO GAP 13.355054326678 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:59:33.456 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.045 sec + * cpu-time: 0 d, 0 h, 0 min, 0.025 sec + * ratio c/w: 0.547 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.033 sec + * cpu-time: 0 d, 0 h, 0 min, 0.012 sec + * ratio c/w: 0.376 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.813823527310 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 15 +Number of internal coordinates .... 90 +Current Energy .... -15.813823527 Eh +Current gradient norm .... 0.022707407 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Evaluating the initial hessian .... (Almloef) done +Projecting the Hessian .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.997969285 +Lowest eigenvalues of augmented Hessian: + -0.000703095 0.011851271 0.014610511 0.045627515 0.045959147 +Length of the computed step .... 0.063826607 +The final length of the internal step .... 0.063826607 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0067279151 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0094581950 RMS(Int)= 0.0067336744 + Iter 1: RMS(Cart)= 0.0000326158 RMS(Int)= 0.0000283370 + Iter 2: RMS(Cart)= 0.0000001703 RMS(Int)= 0.0000001533 + Iter 3: RMS(Cart)= 0.0000000016 RMS(Int)= 0.0000000013 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + RMS gradient 0.0016312823 0.0001000000 NO + MAX gradient 0.0070910449 0.0003000000 NO + RMS step 0.0067279151 0.0020000000 NO + MAX step 0.0192770234 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0102 Max(Angles) 0.32 + Max(Dihed) 0.79 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.5200 -0.004296 0.0057 1.5257 + 2. B(C 2,C 1) 1.5261 -0.006170 0.0087 1.5348 + 3. B(C 3,C 2) 1.5283 -0.007091 0.0102 1.5385 + 4. B(C 4,C 3) 1.5220 -0.005057 0.0069 1.5290 + 5. B(C 4,C 0) 1.5184 -0.004058 0.0053 1.5237 + 6. B(H 5,C 0) 1.0936 0.002177 -0.0032 1.0904 + 7. B(H 6,C 0) 1.0965 0.003068 -0.0046 1.0919 + 8. B(H 7,C 1) 1.0940 0.002576 -0.0038 1.0901 + 9. B(H 8,C 1) 1.0969 0.003094 -0.0047 1.0922 + 10. B(H 9,C 2) 1.0956 0.002937 -0.0044 1.0912 + 11. B(H 10,C 2) 1.0952 0.002998 -0.0045 1.0907 + 12. B(H 11,C 3) 1.0967 0.003132 -0.0047 1.0920 + 13. B(H 12,C 3) 1.0945 0.002871 -0.0043 1.0903 + 14. B(H 13,C 4) 1.0937 0.002299 -0.0034 1.0903 + 15. B(H 14,C 4) 1.0966 0.002975 -0.0045 1.0921 + 16. A(C 4,C 0,H 5) 112.38 -0.000181 0.16 112.55 + 17. A(C 1,C 0,C 4) 103.13 -0.000495 -0.01 103.12 + 18. A(C 1,C 0,H 5) 112.29 0.000177 0.10 112.40 + 19. A(H 5,C 0,H 6) 108.33 0.000036 -0.07 108.26 + 20. A(C 1,C 0,H 6) 110.30 -0.000080 -0.01 110.29 + 21. A(C 4,C 0,H 6) 110.36 0.000540 -0.18 110.18 + 22. A(C 2,C 1,H 8) 109.66 -0.000870 0.28 109.94 + 23. A(C 2,C 1,H 7) 112.24 0.000292 0.01 112.25 + 24. A(H 7,C 1,H 8) 107.77 0.000145 -0.07 107.70 + 25. A(C 0,C 1,H 7) 112.28 -0.000281 0.05 112.33 + 26. A(C 0,C 1,C 2) 104.98 -0.000100 -0.06 104.92 + 27. A(C 0,C 1,H 8) 109.88 0.000804 -0.20 109.68 + 28. A(H 9,C 2,H 10) 107.34 0.000437 -0.15 107.20 + 29. A(C 1,C 2,C 3) 106.35 0.000677 -0.14 106.22 + 30. A(C 1,C 2,H 10) 110.78 -0.000392 0.07 110.85 + 31. A(C 3,C 2,H 9) 110.08 -0.000687 0.21 110.29 + 32. A(C 1,C 2,H 9) 110.82 0.000071 -0.02 110.79 + 33. A(C 3,C 2,H 10) 111.51 -0.000128 0.03 111.54 + 34. A(H 11,C 3,H 12) 107.50 0.000287 -0.10 107.40 + 35. A(C 4,C 3,H 12) 111.79 -0.000205 -0.01 111.78 + 36. A(C 2,C 3,H 12) 112.07 0.000005 0.03 112.10 + 37. A(C 4,C 3,H 11) 110.04 0.000490 -0.12 109.92 + 38. A(C 2,C 3,H 11) 109.61 -0.000934 0.32 109.93 + 39. A(C 2,C 3,C 4) 105.84 0.000338 -0.11 105.72 + 40. A(H 13,C 4,H 14) 108.11 0.000048 -0.06 108.05 + 41. A(C 3,C 4,H 14) 110.03 -0.000554 0.14 110.18 + 42. A(C 0,C 4,H 14) 110.17 0.000850 -0.24 109.92 + 43. A(C 3,C 4,H 13) 112.28 0.000385 0.04 112.32 + 44. A(C 0,C 4,H 13) 112.43 -0.000364 0.15 112.58 + 45. A(C 0,C 4,C 3) 103.79 -0.000368 -0.03 103.76 + 46. D(H 7,C 1,C 0,H 5) 80.93 0.000464 -0.64 80.29 + 47. D(H 7,C 1,C 0,H 6) -40.00 0.000354 -0.62 -40.62 + 48. D(C 2,C 1,C 0,H 5) -156.85 0.000595 -0.64 -157.49 + 49. D(H 7,C 1,C 0,C 4) -157.85 0.000032 -0.40 -158.25 + 50. D(H 8,C 1,C 0,H 6) -159.93 -0.000193 -0.42 -160.35 + 51. D(C 2,C 1,C 0,C 4) -35.64 0.000163 -0.40 -36.03 + 52. D(C 2,C 1,C 0,H 6) 82.22 0.000485 -0.62 81.60 + 53. D(H 8,C 1,C 0,H 5) -39.00 -0.000083 -0.45 -39.44 + 54. D(H 8,C 1,C 0,C 4) 82.22 -0.000515 -0.20 82.01 + 55. D(H 9,C 2,C 1,H 7) 20.33 0.000224 0.03 20.36 + 56. D(C 3,C 2,C 1,H 8) -100.29 -0.000372 0.29 -99.99 + 57. D(C 3,C 2,C 1,C 0) 17.71 0.000085 0.16 17.88 + 58. D(H 10,C 2,C 1,H 8) 21.05 -0.000331 0.29 21.34 + 59. D(H 9,C 2,C 1,H 8) 140.09 0.000008 0.13 140.22 + 60. D(H 10,C 2,C 1,H 7) -98.71 -0.000115 0.18 -98.53 + 61. D(H 10,C 2,C 1,C 0) 139.05 0.000126 0.15 139.21 + 62. D(C 3,C 2,C 1,H 7) 139.95 -0.000156 0.19 140.14 + 63. D(H 9,C 2,C 1,C 0) -101.91 0.000465 0.00 -101.91 + 64. D(H 12,C 3,C 2,H 9) -110.81 0.000109 0.01 -110.80 + 65. D(H 12,C 3,C 2,C 1) 129.08 0.000002 0.00 129.09 + 66. D(H 11,C 3,C 2,H 10) 127.49 -0.000133 0.09 127.58 + 67. D(H 11,C 3,C 2,H 9) 8.46 -0.000148 0.12 8.58 + 68. D(C 4,C 3,C 2,H 9) 127.09 0.000137 0.08 127.17 + 69. D(C 4,C 3,C 2,C 1) 6.98 0.000029 0.07 7.06 + 70. D(H 11,C 3,C 2,C 1) -111.64 -0.000256 0.11 -111.53 + 71. D(H 12,C 3,C 2,H 10) 8.21 0.000124 -0.01 8.20 + 72. D(C 4,C 3,C 2,H 10) -113.89 0.000152 0.06 -113.83 + 73. D(H 13,C 4,C 0,C 1) 161.52 -0.000300 0.58 162.10 + 74. D(C 3,C 4,C 0,H 6) -77.87 -0.000222 0.58 -77.29 + 75. D(C 3,C 4,C 0,H 5) 161.09 -0.000525 0.68 161.78 + 76. D(C 3,C 4,C 0,C 1) 39.94 -0.000335 0.48 40.42 + 77. D(H 14,C 4,C 3,H 12) -33.43 0.000420 -0.49 -33.93 + 78. D(H 14,C 4,C 3,H 11) -152.81 -0.000135 -0.28 -153.09 + 79. D(H 13,C 4,C 3,H 12) 87.03 0.000355 -0.44 86.59 + 80. D(H 13,C 4,C 3,H 11) -32.35 -0.000200 -0.23 -32.58 + 81. D(H 13,C 4,C 3,C 2) -150.69 0.000461 -0.49 -151.18 + 82. D(C 0,C 4,C 3,H 12) -151.30 -0.000109 -0.26 -151.55 + 83. D(C 0,C 4,C 3,H 11) 89.33 -0.000664 -0.05 89.28 + 84. D(C 0,C 4,C 3,C 2) -29.01 -0.000003 -0.31 -29.32 + 85. D(H 14,C 4,C 0,H 6) 164.36 0.000223 0.55 164.91 + 86. D(H 14,C 4,C 0,H 5) 43.32 -0.000080 0.65 43.97 + 87. D(H 14,C 4,C 3,C 2) 88.85 0.000526 -0.54 88.31 + 88. D(H 14,C 4,C 0,C 1) -77.83 0.000110 0.45 -77.38 + 89. D(H 13,C 4,C 0,H 6) 43.71 -0.000186 0.69 44.40 + 90. D(H 13,C 4,C 0,H 5) -77.33 -0.000489 0.79 -76.54 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 2 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.257123 -0.088091 0.238226 + C 0.328826 -1.226976 -0.172935 + C -1.088491 -0.679714 0.044787 + C -0.950523 0.850465 0.125720 + C 0.506368 1.154273 -0.224938 + H 2.245041 -0.172991 -0.215333 + H 1.379029 -0.071943 1.323172 + H 0.512114 -2.137358 0.398053 + H 0.479548 -1.461348 -1.229026 + H -1.516833 -1.070415 0.969225 + H -1.749798 -0.979717 -0.769026 + H -1.167689 1.190610 1.140388 + H -1.642768 1.360747 -0.544398 + H 0.866704 2.064442 0.255169 + H 0.616638 1.274786 -1.304765 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.375619 -0.166468 0.450183 + 1 C 6.0000 0 12.011 0.621391 -2.318648 -0.326800 + 2 C 6.0000 0 12.011 -2.056950 -1.284472 0.084635 + 3 C 6.0000 0 12.011 -1.796228 1.607146 0.237576 + 4 C 6.0000 0 12.011 0.956896 2.181259 -0.425072 + 5 H 1.0000 0 1.008 4.242513 -0.326906 -0.406921 + 6 H 1.0000 0 1.008 2.605988 -0.135952 2.500433 + 7 H 1.0000 0 1.008 0.967755 -4.039021 0.752212 + 8 H 1.0000 0 1.008 0.906214 -2.761547 -2.322522 + 9 H 1.0000 0 1.008 -2.866399 -2.022792 1.831570 + 10 H 1.0000 0 1.008 -3.306639 -1.851397 -1.453248 + 11 H 1.0000 0 1.008 -2.206613 2.249927 2.155022 + 12 H 1.0000 0 1.008 -3.104381 2.571440 -1.028762 + 13 H 1.0000 0 1.008 1.637834 3.901230 0.482199 + 14 H 1.0000 0 1.008 1.165278 2.408997 -2.465649 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:59:33.533 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.55779783813730 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0481639 -0.160482E+02 0.731E-02 13.22 0.0 T + 2 -16.0481684 -0.452038E-05 0.459E-02 13.23 1.0 T + 3 -16.0481684 -0.549547E-07 0.558E-03 13.23 4.6 T + 4 -16.0481684 -0.241912E-08 0.823E-04 13.23 31.4 T + 5 -16.0481684 -0.304503E-10 0.236E-04 13.23 109.6 T + + *** convergence criteria satisfied after 5 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6320181 -17.1981 + ... ... ... ... + 9 2.0000 -0.4822072 -13.1215 + 10 2.0000 -0.4411536 -12.0044 + 11 2.0000 -0.4387072 -11.9378 + 12 2.0000 -0.4364153 -11.8755 + 13 2.0000 -0.4362258 -11.8703 + 14 2.0000 -0.4204451 -11.4409 + 15 2.0000 -0.4139272 -11.2635 (HOMO) + 16 0.0721558 1.9635 (LUMO) + 17 0.0724999 1.9728 + 18 0.0886728 2.4129 + 19 0.1319823 3.5914 + 20 0.1333845 3.6296 + ... ... ... + 30 0.3496123 9.5134 + ------------------------------------------------------------- + HL-Gap 0.4860831 Eh 13.2270 eV + Fermi-level -0.1708857 Eh -4.6500 eV + + SCC (total) 0 d, 0 h, 0 min, 0.032 sec + SCC setup ... 0 min, 0.000 sec ( 0.468%) + Dispersion ... 0 min, 0.000 sec ( 0.314%) + classical contributions ... 0 min, 0.000 sec ( 0.120%) + integral evaluation ... 0 min, 0.002 sec ( 6.135%) + iterations ... 0 min, 0.025 sec ( 78.111%) + molecular gradient ... 0 min, 0.005 sec ( 14.256%) + printout ... 0 min, 0.000 sec ( 0.559%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814241222376 Eh :: + :: gradient norm 0.005064544877 Eh/a0 :: + :: HOMO-LUMO gap 13.226993409773 eV :: + ::.................................................:: + :: SCC energy -16.048168432480 Eh :: + :: -> isotropic ES 0.002305024320 Eh :: + :: -> anisotropic ES 0.004275171918 Eh :: + :: -> anisotropic XC 0.009706949492 Eh :: + :: -> dispersion -0.008130395581 Eh :: + :: repulsion energy 0.233916722051 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814241222376 Eh | + | GRADIENT NORM 0.005064544877 Eh/α | + | HOMO-LUMO GAP 13.226993409773 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:59:33.579 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.046 sec + * cpu-time: 0 d, 0 h, 0 min, 0.024 sec + * ratio c/w: 0.534 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.033 sec + * cpu-time: 0 d, 0 h, 0 min, 0.012 sec + * ratio c/w: 0.356 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814241222380 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 15 +Number of internal coordinates .... 90 +Current Energy .... -15.814241222 Eh +Current gradient norm .... 0.005064545 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.998743425 +Lowest eigenvalues of augmented Hessian: + -0.000064929 0.011851251 0.013592534 0.045406129 0.045899005 +Length of the computed step .... 0.050178623 +The final length of the internal step .... 0.050178623 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0052892913 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0072406891 RMS(Int)= 0.0052881724 + Iter 1: RMS(Cart)= 0.0000247280 RMS(Int)= 0.0000172505 + Iter 2: RMS(Cart)= 0.0000001558 RMS(Int)= 0.0000001513 + Iter 3: RMS(Cart)= 0.0000000013 RMS(Int)= 0.0000000010 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0004176951 0.0000050000 NO + RMS gradient 0.0002952155 0.0001000000 NO + MAX gradient 0.0009148389 0.0003000000 NO + RMS step 0.0052892913 0.0020000000 NO + MAX step 0.0127713249 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0023 Max(Angles) 0.15 + Max(Dihed) 0.73 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.5257 -0.000661 0.0013 1.5270 + 2. B(C 2,C 1) 1.5348 -0.000869 0.0020 1.5368 + 3. B(C 3,C 2) 1.5385 -0.000915 0.0023 1.5408 + 4. B(C 4,C 3) 1.5290 -0.000781 0.0016 1.5306 + 5. B(C 4,C 0) 1.5237 -0.000679 0.0012 1.5249 + 6. B(H 5,C 0) 1.0904 0.000422 -0.0009 1.0894 + 7. B(H 6,C 0) 1.0919 0.000370 -0.0009 1.0910 + 8. B(H 7,C 1) 1.0901 0.000447 -0.0010 1.0891 + 9. B(H 8,C 1) 1.0922 0.000542 -0.0012 1.0910 + 10. B(H 9,C 2) 1.0912 0.000591 -0.0013 1.0899 + 11. B(H 10,C 2) 1.0907 0.000564 -0.0012 1.0894 + 12. B(H 11,C 3) 1.0920 0.000619 -0.0014 1.0906 + 13. B(H 12,C 3) 1.0903 0.000493 -0.0011 1.0891 + 14. B(H 13,C 4) 1.0903 0.000438 -0.0010 1.0893 + 15. B(H 14,C 4) 1.0921 0.000429 -0.0010 1.0911 + 16. A(C 4,C 0,H 5) 112.55 -0.000129 0.10 112.65 + 17. A(C 1,C 0,C 4) 103.12 0.000010 -0.12 103.00 + 18. A(C 1,C 0,H 5) 112.40 0.000043 0.05 112.45 + 19. A(H 5,C 0,H 6) 108.26 -0.000122 0.09 108.35 + 20. A(C 1,C 0,H 6) 110.29 -0.000023 -0.02 110.27 + 21. A(C 4,C 0,H 6) 110.18 0.000236 -0.12 110.06 + 22. A(C 2,C 1,H 8) 109.94 -0.000325 0.14 110.08 + 23. A(C 2,C 1,H 7) 112.25 0.000257 -0.07 112.19 + 24. A(H 7,C 1,H 8) 107.70 -0.000163 0.12 107.82 + 25. A(C 0,C 1,H 7) 112.33 -0.000106 0.01 112.34 + 26. A(C 0,C 1,C 2) 104.92 -0.000011 -0.08 104.84 + 27. A(C 0,C 1,H 8) 109.68 0.000353 -0.12 109.56 + 28. A(H 9,C 2,H 10) 107.19 -0.000136 0.10 107.30 + 29. A(C 1,C 2,C 3) 106.22 0.000072 -0.06 106.16 + 30. A(C 1,C 2,H 10) 110.85 -0.000104 0.01 110.87 + 31. A(C 3,C 2,H 9) 110.29 -0.000203 0.08 110.37 + 32. A(C 1,C 2,H 9) 110.79 0.000196 -0.07 110.73 + 33. A(C 3,C 2,H 10) 111.54 0.000178 -0.07 111.48 + 34. A(H 11,C 3,H 12) 107.40 -0.000160 0.12 107.52 + 35. A(C 4,C 3,H 12) 111.78 -0.000051 -0.03 111.75 + 36. A(C 2,C 3,H 12) 112.10 0.000212 -0.07 112.03 + 37. A(C 4,C 3,H 11) 109.92 0.000274 -0.08 109.84 + 38. A(C 2,C 3,H 11) 109.93 -0.000325 0.14 110.07 + 39. A(C 2,C 3,C 4) 105.72 0.000053 -0.08 105.65 + 40. A(H 13,C 4,H 14) 108.05 -0.000151 0.11 108.16 + 41. A(C 3,C 4,H 14) 110.18 -0.000209 0.07 110.24 + 42. A(C 0,C 4,H 14) 109.92 0.000360 -0.15 109.77 + 43. A(C 3,C 4,H 13) 112.32 0.000203 -0.02 112.30 + 44. A(C 0,C 4,H 13) 112.58 -0.000177 0.09 112.67 + 45. A(C 0,C 4,C 3) 103.75 -0.000014 -0.10 103.65 + 46. D(H 7,C 1,C 0,H 5) 80.29 0.000001 -0.42 79.87 + 47. D(H 7,C 1,C 0,H 6) -40.62 0.000144 -0.56 -41.18 + 48. D(C 2,C 1,C 0,H 5) -157.49 0.000249 -0.55 -158.04 + 49. D(H 7,C 1,C 0,C 4) -158.25 -0.000125 -0.34 -158.59 + 50. D(H 8,C 1,C 0,H 6) -160.35 0.000179 -0.63 -160.98 + 51. D(C 2,C 1,C 0,C 4) -36.03 0.000123 -0.47 -36.50 + 52. D(C 2,C 1,C 0,H 6) 81.60 0.000392 -0.69 80.91 + 53. D(H 8,C 1,C 0,H 5) -39.44 0.000036 -0.49 -39.94 + 54. D(H 8,C 1,C 0,C 4) 82.01 -0.000090 -0.42 81.60 + 55. D(H 9,C 2,C 1,H 7) 20.36 0.000054 0.13 20.48 + 56. D(C 3,C 2,C 1,H 8) -99.99 -0.000296 0.34 -99.65 + 57. D(C 3,C 2,C 1,C 0) 17.88 -0.000049 0.22 18.10 + 58. D(H 10,C 2,C 1,H 8) 21.34 -0.000094 0.23 21.57 + 59. D(H 9,C 2,C 1,H 8) 140.22 -0.000204 0.32 140.55 + 60. D(H 10,C 2,C 1,H 7) -98.53 0.000164 0.03 -98.49 + 61. D(H 10,C 2,C 1,C 0) 139.21 0.000153 0.11 139.32 + 62. D(C 3,C 2,C 1,H 7) 140.14 -0.000038 0.15 140.29 + 63. D(H 9,C 2,C 1,C 0) -101.91 0.000043 0.20 -101.70 + 64. D(H 12,C 3,C 2,H 9) -110.80 0.000239 -0.11 -110.91 + 65. D(H 12,C 3,C 2,C 1) 129.09 0.000073 -0.04 129.05 + 66. D(H 11,C 3,C 2,H 10) 127.58 -0.000232 0.23 127.80 + 67. D(H 11,C 3,C 2,H 9) 8.58 -0.000043 0.09 8.67 + 68. D(C 4,C 3,C 2,H 9) 127.17 0.000143 0.02 127.19 + 69. D(C 4,C 3,C 2,C 1) 7.06 -0.000024 0.10 7.16 + 70. D(H 11,C 3,C 2,C 1) -111.53 -0.000210 0.17 -111.37 + 71. D(H 12,C 3,C 2,H 10) 8.20 0.000051 0.02 8.22 + 72. D(C 4,C 3,C 2,H 10) -113.83 -0.000046 0.16 -113.67 + 73. D(H 13,C 4,C 0,C 1) 162.10 -0.000011 0.50 162.60 + 74. D(C 3,C 4,C 0,H 6) -77.29 -0.000239 0.68 -76.61 + 75. D(C 3,C 4,C 0,H 5) 161.78 -0.000161 0.58 162.35 + 76. D(C 3,C 4,C 0,C 1) 40.42 -0.000152 0.54 40.96 + 77. D(H 14,C 4,C 3,H 12) -33.93 0.000145 -0.43 -34.36 + 78. D(H 14,C 4,C 3,H 11) -153.09 0.000197 -0.51 -153.60 + 79. D(H 13,C 4,C 3,H 12) 86.59 -0.000056 -0.26 86.33 + 80. D(H 13,C 4,C 3,H 11) -32.58 -0.000005 -0.33 -32.91 + 81. D(H 13,C 4,C 3,C 2) -151.18 0.000208 -0.42 -151.59 + 82. D(C 0,C 4,C 3,H 12) -151.55 -0.000169 -0.23 -151.78 + 83. D(C 0,C 4,C 3,H 11) 89.28 -0.000117 -0.30 88.98 + 84. D(C 0,C 4,C 3,C 2) -29.32 0.000095 -0.39 -29.71 + 85. D(H 14,C 4,C 0,H 6) 164.91 -0.000157 0.73 165.64 + 86. D(H 14,C 4,C 0,H 5) 43.97 -0.000079 0.63 44.60 + 87. D(H 14,C 4,C 3,C 2) 88.31 0.000409 -0.59 87.72 + 88. D(H 14,C 4,C 0,C 1) -77.38 -0.000070 0.59 -76.80 + 89. D(H 13,C 4,C 0,H 6) 44.40 -0.000097 0.64 45.04 + 90. D(H 13,C 4,C 0,H 5) -76.54 -0.000020 0.54 -76.00 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 3 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.256840 -0.087971 0.240929 + C 0.329515 -1.227180 -0.176191 + C -1.089636 -0.680681 0.045702 + C -0.950883 0.851597 0.128554 + C 0.506606 1.153997 -0.227959 + H 2.247193 -0.173216 -0.204973 + H 1.369029 -0.069993 1.325991 + H 0.512598 -2.138785 0.390994 + H 0.482449 -1.454647 -1.232210 + H -1.514223 -1.073592 0.969408 + H -1.751405 -0.977871 -0.767095 + H -1.162122 1.192254 1.142832 + H -1.643824 1.361220 -0.539544 + H 0.867356 2.066207 0.245741 + H 0.615797 1.265430 -1.307858 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.375084 -0.166241 0.455289 + 1 C 6.0000 0 12.011 0.622693 -2.319034 -0.332953 + 2 C 6.0000 0 12.011 -2.059113 -1.286301 0.086365 + 3 C 6.0000 0 12.011 -1.796908 1.609286 0.242933 + 4 C 6.0000 0 12.011 0.957346 2.180739 -0.430780 + 5 H 1.0000 0 1.008 4.246579 -0.327331 -0.387344 + 6 H 1.0000 0 1.008 2.587090 -0.132267 2.505760 + 7 H 1.0000 0 1.008 0.968671 -4.041718 0.738872 + 8 H 1.0000 0 1.008 0.911696 -2.748884 -2.328540 + 9 H 1.0000 0 1.008 -2.861466 -2.028795 1.831915 + 10 H 1.0000 0 1.008 -3.309676 -1.847909 -1.449600 + 11 H 1.0000 0 1.008 -2.196092 2.253033 2.159640 + 12 H 1.0000 0 1.008 -3.106377 2.572333 -1.019591 + 13 H 1.0000 0 1.008 1.639064 3.904566 0.464382 + 14 H 1.0000 0 1.008 1.163688 2.391316 -2.471493 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:59:33.657 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.77942745104358 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0488829 -0.160489E+02 0.223E-02 13.19 0.0 T + 2 -16.0488832 -0.334759E-06 0.136E-02 13.19 1.9 T + 3 -16.0488832 -0.530733E-08 0.165E-03 13.19 15.6 T + 4 -16.0488832 -0.105686E-09 0.251E-04 13.19 102.9 T + 5 -16.0488832 -0.115072E-10 0.542E-05 13.19 476.2 T + + *** convergence criteria satisfied after 5 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6317594 -17.1910 + ... ... ... ... + 9 2.0000 -0.4821118 -13.1189 + 10 2.0000 -0.4409588 -11.9991 + 11 2.0000 -0.4384705 -11.9314 + 12 2.0000 -0.4362883 -11.8720 + 13 2.0000 -0.4361380 -11.8679 + 14 2.0000 -0.4207098 -11.4481 + 15 2.0000 -0.4142571 -11.2725 (HOMO) + 16 0.0706137 1.9215 (LUMO) + 17 0.0711297 1.9355 + 18 0.0905748 2.4647 + 19 0.1317725 3.5857 + 20 0.1343975 3.6571 + ... ... ... + 30 0.3513169 9.5598 + ------------------------------------------------------------- + HL-Gap 0.4848708 Eh 13.1940 eV + Fermi-level -0.1718217 Eh -4.6755 eV + + SCC (total) 0 d, 0 h, 0 min, 0.012 sec + SCC setup ... 0 min, 0.000 sec ( 1.323%) + Dispersion ... 0 min, 0.000 sec ( 0.832%) + classical contributions ... 0 min, 0.000 sec ( 0.334%) + integral evaluation ... 0 min, 0.002 sec ( 14.471%) + iterations ... 0 min, 0.005 sec ( 43.644%) + molecular gradient ... 0 min, 0.005 sec ( 38.023%) + printout ... 0 min, 0.000 sec ( 1.289%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814284974998 Eh :: + :: gradient norm 0.001341145210 Eh/a0 :: + :: HOMO-LUMO gap 13.194005848187 eV :: + ::.................................................:: + :: SCC energy -16.048883232525 Eh :: + :: -> isotropic ES 0.002333401920 Eh :: + :: -> anisotropic ES 0.004266749554 Eh :: + :: -> anisotropic XC 0.009690521656 Eh :: + :: -> dispersion -0.008129206700 Eh :: + :: repulsion energy 0.234587788549 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814284974998 Eh | + | GRADIENT NORM 0.001341145210 Eh/α | + | HOMO-LUMO GAP 13.194005848187 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:59:33.681 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.024 sec + * cpu-time: 0 d, 0 h, 0 min, 0.024 sec + * ratio c/w: 0.977 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.012 sec + * cpu-time: 0 d, 0 h, 0 min, 0.011 sec + * ratio c/w: 0.954 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814284975000 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 15 +Number of internal coordinates .... 90 +Current Energy .... -15.814284975 Eh +Current gradient norm .... 0.001341145 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.998367055 +Lowest eigenvalues of augmented Hessian: + -0.000029892 0.007767788 0.011851329 0.045071205 0.045882488 +Length of the computed step .... 0.057218068 +The final length of the internal step .... 0.057218068 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0060313139 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0083484502 RMS(Int)= 0.0060274104 + Iter 1: RMS(Cart)= 0.0000328622 RMS(Int)= 0.0000212088 + Iter 2: RMS(Cart)= 0.0000002431 RMS(Int)= 0.0000002261 + Iter 3: RMS(Cart)= 0.0000000023 RMS(Int)= 0.0000000017 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0000437526 0.0000050000 NO + RMS gradient 0.0001059703 0.0001000000 NO + MAX gradient 0.0002571587 0.0003000000 YES + RMS step 0.0060313139 0.0020000000 NO + MAX step 0.0154142059 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0007 Max(Angles) 0.16 + Max(Dihed) 0.88 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.5270 0.000064 0.0004 1.5274 + 2. B(C 2,C 1) 1.5368 0.000207 0.0006 1.5375 + 3. B(C 3,C 2) 1.5408 0.000257 0.0007 1.5415 + 4. B(C 4,C 3) 1.5306 0.000125 0.0005 1.5311 + 5. B(C 4,C 0) 1.5249 -0.000013 0.0004 1.5253 + 6. B(H 5,C 0) 1.0894 -0.000041 -0.0003 1.0891 + 7. B(H 6,C 0) 1.0910 -0.000159 -0.0001 1.0909 + 8. B(H 7,C 1) 1.0891 -0.000108 -0.0002 1.0889 + 9. B(H 8,C 1) 1.0910 -0.000090 -0.0003 1.0907 + 10. B(H 9,C 2) 1.0899 -0.000082 -0.0004 1.0895 + 11. B(H 10,C 2) 1.0894 -0.000109 -0.0003 1.0891 + 12. B(H 11,C 3) 1.0906 -0.000071 -0.0004 1.0902 + 13. B(H 12,C 3) 1.0891 -0.000125 -0.0002 1.0889 + 14. B(H 13,C 4) 1.0893 -0.000065 -0.0003 1.0891 + 15. B(H 14,C 4) 1.0911 -0.000123 -0.0002 1.0909 + 16. A(C 4,C 0,H 5) 112.65 -0.000081 0.11 112.76 + 17. A(C 1,C 0,C 4) 102.99 0.000058 -0.15 102.84 + 18. A(C 1,C 0,H 5) 112.45 -0.000004 0.06 112.51 + 19. A(H 5,C 0,H 6) 108.35 -0.000097 0.13 108.48 + 20. A(C 1,C 0,H 6) 110.27 0.000026 -0.04 110.23 + 21. A(C 4,C 0,H 6) 110.06 0.000111 -0.12 109.94 + 22. A(C 2,C 1,H 8) 110.08 -0.000089 0.08 110.16 + 23. A(C 2,C 1,H 7) 112.19 0.000125 -0.06 112.13 + 24. A(H 7,C 1,H 8) 107.82 -0.000135 0.15 107.97 + 25. A(C 0,C 1,H 7) 112.34 -0.000057 0.03 112.36 + 26. A(C 0,C 1,C 2) 104.84 0.000017 -0.10 104.74 + 27. A(C 0,C 1,H 8) 109.56 0.000145 -0.11 109.45 + 28. A(H 9,C 2,H 10) 107.30 -0.000163 0.15 107.45 + 29. A(C 1,C 2,C 3) 106.16 -0.000055 -0.05 106.11 + 30. A(C 1,C 2,H 10) 110.87 -0.000025 0.01 110.87 + 31. A(C 3,C 2,H 9) 110.37 -0.000048 0.04 110.41 + 32. A(C 1,C 2,H 9) 110.73 0.000150 -0.08 110.64 + 33. A(C 3,C 2,H 10) 111.48 0.000149 -0.08 111.40 + 34. A(H 11,C 3,H 12) 107.52 -0.000158 0.16 107.69 + 35. A(C 4,C 3,H 12) 111.75 -0.000017 -0.02 111.73 + 36. A(C 2,C 3,H 12) 112.03 0.000136 -0.07 111.96 + 37. A(C 4,C 3,H 11) 109.84 0.000148 -0.09 109.75 + 38. A(C 2,C 3,H 11) 110.07 -0.000087 0.09 110.16 + 39. A(C 2,C 3,C 4) 105.65 -0.000017 -0.07 105.57 + 40. A(H 13,C 4,H 14) 108.16 -0.000114 0.14 108.30 + 41. A(C 3,C 4,H 14) 110.24 -0.000042 0.02 110.27 + 42. A(C 0,C 4,H 14) 109.77 0.000142 -0.13 109.64 + 43. A(C 3,C 4,H 13) 112.30 0.000077 -0.01 112.29 + 44. A(C 0,C 4,H 13) 112.67 -0.000100 0.10 112.77 + 45. A(C 0,C 4,C 3) 103.65 0.000048 -0.13 103.51 + 46. D(H 7,C 1,C 0,H 5) 79.87 -0.000028 -0.47 79.41 + 47. D(H 7,C 1,C 0,H 6) -41.18 0.000080 -0.64 -41.81 + 48. D(C 2,C 1,C 0,H 5) -158.04 0.000104 -0.59 -158.63 + 49. D(H 7,C 1,C 0,C 4) -158.59 -0.000091 -0.40 -158.99 + 50. D(H 8,C 1,C 0,H 6) -160.98 0.000188 -0.77 -161.76 + 51. D(C 2,C 1,C 0,C 4) -36.50 0.000041 -0.52 -37.03 + 52. D(C 2,C 1,C 0,H 6) 80.91 0.000212 -0.76 80.15 + 53. D(H 8,C 1,C 0,H 5) -39.93 0.000080 -0.60 -40.54 + 54. D(H 8,C 1,C 0,C 4) 81.60 0.000017 -0.54 81.06 + 55. D(H 9,C 2,C 1,H 7) 20.48 -0.000015 0.21 20.69 + 56. D(C 3,C 2,C 1,H 8) -99.65 -0.000172 0.40 -99.25 + 57. D(C 3,C 2,C 1,C 0) 18.10 -0.000036 0.25 18.35 + 58. D(H 10,C 2,C 1,H 8) 21.57 -0.000040 0.28 21.85 + 59. D(H 9,C 2,C 1,H 8) 140.55 -0.000163 0.42 140.96 + 60. D(H 10,C 2,C 1,H 7) -98.49 0.000109 0.07 -98.42 + 61. D(H 10,C 2,C 1,C 0) 139.32 0.000096 0.14 139.45 + 62. D(C 3,C 2,C 1,H 7) 140.29 -0.000023 0.19 140.47 + 63. D(H 9,C 2,C 1,C 0) -101.70 -0.000028 0.28 -101.43 + 64. D(H 12,C 3,C 2,H 9) -110.91 0.000149 -0.11 -111.02 + 65. D(H 12,C 3,C 2,C 1) 129.05 0.000029 -0.00 129.05 + 66. D(H 11,C 3,C 2,H 10) 127.80 -0.000159 0.28 128.08 + 67. D(H 11,C 3,C 2,H 9) 8.67 -0.000019 0.11 8.78 + 68. D(C 4,C 3,C 2,H 9) 127.19 0.000102 0.01 127.20 + 69. D(C 4,C 3,C 2,C 1) 7.16 -0.000019 0.11 7.27 + 70. D(H 11,C 3,C 2,C 1) -111.37 -0.000139 0.21 -111.15 + 71. D(H 12,C 3,C 2,H 10) 8.22 0.000009 0.06 8.28 + 72. D(C 4,C 3,C 2,H 10) -113.67 -0.000039 0.18 -113.50 + 73. D(H 13,C 4,C 0,C 1) 162.60 0.000032 0.55 163.15 + 74. D(C 3,C 4,C 0,H 6) -76.61 -0.000149 0.78 -75.83 + 75. D(C 3,C 4,C 0,H 5) 162.35 -0.000048 0.63 162.98 + 76. D(C 3,C 4,C 0,C 1) 40.96 -0.000038 0.59 41.55 + 77. D(H 14,C 4,C 3,H 12) -34.36 0.000071 -0.50 -34.86 + 78. D(H 14,C 4,C 3,H 11) -153.60 0.000182 -0.64 -154.24 + 79. D(H 13,C 4,C 3,H 12) 86.33 -0.000052 -0.31 86.02 + 80. D(H 13,C 4,C 3,H 11) -32.91 0.000059 -0.45 -33.36 + 81. D(H 13,C 4,C 3,C 2) -151.59 0.000094 -0.46 -152.05 + 82. D(C 0,C 4,C 3,H 12) -151.78 -0.000100 -0.29 -152.07 + 83. D(C 0,C 4,C 3,H 11) 88.98 0.000010 -0.42 88.56 + 84. D(C 0,C 4,C 3,C 2) -29.70 0.000046 -0.43 -30.14 + 85. D(H 14,C 4,C 0,H 6) 165.64 -0.000191 0.88 166.52 + 86. D(H 14,C 4,C 0,H 5) 44.60 -0.000091 0.73 45.33 + 87. D(H 14,C 4,C 3,C 2) 87.72 0.000217 -0.65 87.07 + 88. D(H 14,C 4,C 0,C 1) -76.80 -0.000081 0.70 -76.10 + 89. D(H 13,C 4,C 0,H 6) 45.03 -0.000079 0.73 45.77 + 90. D(H 13,C 4,C 0,H 5) -76.00 0.000022 0.58 -75.42 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 4 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.255759 -0.087735 0.244138 + C 0.330030 -1.226385 -0.179456 + C -1.089550 -0.680907 0.046501 + C -0.950251 0.851938 0.131194 + C 0.506593 1.152913 -0.231316 + H 2.249411 -0.173472 -0.193485 + H 1.356785 -0.067973 1.330167 + H 0.512793 -2.140292 0.383710 + H 0.484505 -1.445960 -1.236559 + H -1.510226 -1.075841 0.970688 + H -1.752335 -0.975396 -0.766044 + H -1.155056 1.192253 1.146436 + H -1.644903 1.361314 -0.534953 + H 0.867883 2.068121 0.235501 + H 0.613852 1.254194 -1.312201 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.373041 -0.165795 0.461354 + 1 C 6.0000 0 12.011 0.623666 -2.317532 -0.339122 + 2 C 6.0000 0 12.011 -2.058951 -1.286729 0.087873 + 3 C 6.0000 0 12.011 -1.795713 1.609929 0.247921 + 4 C 6.0000 0 12.011 0.957321 2.178690 -0.437123 + 5 H 1.0000 0 1.008 4.250770 -0.327815 -0.365634 + 6 H 1.0000 0 1.008 2.563951 -0.128451 2.513651 + 7 H 1.0000 0 1.008 0.969038 -4.044566 0.725107 + 8 H 1.0000 0 1.008 0.915581 -2.732469 -2.336759 + 9 H 1.0000 0 1.008 -2.853913 -2.033046 1.834334 + 10 H 1.0000 0 1.008 -3.311434 -1.843231 -1.447613 + 11 H 1.0000 0 1.008 -2.182739 2.253032 2.166451 + 12 H 1.0000 0 1.008 -3.108416 2.572510 -1.010915 + 13 H 1.0000 0 1.008 1.640062 3.908182 0.445032 + 14 H 1.0000 0 1.008 1.160013 2.370084 -2.479701 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:59:33.750 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.25553019749379 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0490204 -0.160490E+02 0.205E-02 13.18 0.0 T + 2 -16.0490204 -0.500114E-07 0.122E-02 13.18 2.1 T + 3 -16.0490204 -0.715285E-08 0.591E-04 13.18 43.7 T + 4 -16.0490204 -0.246786E-09 0.274E-04 13.18 94.3 T + + *** convergence criteria satisfied after 4 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6317548 -17.1909 + ... ... ... ... + 9 2.0000 -0.4820936 -13.1184 + 10 2.0000 -0.4408037 -11.9949 + 11 2.0000 -0.4382078 -11.9242 + 12 2.0000 -0.4362017 -11.8697 + 13 2.0000 -0.4360766 -11.8662 + 14 2.0000 -0.4210091 -11.4562 + 15 2.0000 -0.4144723 -11.2784 (HOMO) + 16 0.0700262 1.9055 (LUMO) + 17 0.0707046 1.9240 + 18 0.0914037 2.4872 + 19 0.1318050 3.5866 + 20 0.1346092 3.6629 + ... ... ... + 30 0.3521963 9.5837 + ------------------------------------------------------------- + HL-Gap 0.4844985 Eh 13.1839 eV + Fermi-level -0.1722231 Eh -4.6864 eV + + SCC (total) 0 d, 0 h, 0 min, 0.032 sec + SCC setup ... 0 min, 0.000 sec ( 0.555%) + Dispersion ... 0 min, 0.000 sec ( 0.313%) + classical contributions ... 0 min, 0.000 sec ( 0.124%) + integral evaluation ... 0 min, 0.002 sec ( 5.407%) + iterations ... 0 min, 0.025 sec ( 77.890%) + molecular gradient ... 0 min, 0.005 sec ( 14.947%) + printout ... 0 min, 0.000 sec ( 0.718%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814304882812 Eh :: + :: gradient norm 0.001602921921 Eh/a0 :: + :: HOMO-LUMO gap 13.183876432817 eV :: + ::.................................................:: + :: SCC energy -16.049020413886 Eh :: + :: -> isotropic ES 0.002345852688 Eh :: + :: -> anisotropic ES 0.004257241237 Eh :: + :: -> anisotropic XC 0.009701964224 Eh :: + :: -> dispersion -0.008131094784 Eh :: + :: repulsion energy 0.234705100573 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814304882812 Eh | + | GRADIENT NORM 0.001602921921 Eh/α | + | HOMO-LUMO GAP 13.183876432817 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:59:33.796 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.045 sec + * cpu-time: 0 d, 0 h, 0 min, 0.024 sec + * ratio c/w: 0.543 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.032 sec + * cpu-time: 0 d, 0 h, 0 min, 0.011 sec + * ratio c/w: 0.353 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814304882810 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 15 +Number of internal coordinates .... 90 +Current Energy .... -15.814304883 Eh +Current gradient norm .... 0.001602922 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999205442 +Lowest eigenvalues of augmented Hessian: + -0.000010844 0.004886037 0.011851371 0.045590400 0.045966844 +Length of the computed step .... 0.039887491 +The final length of the internal step .... 0.039887491 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0042045107 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0057429193 RMS(Int)= 0.0042020683 + Iter 1: RMS(Cart)= 0.0000153504 RMS(Int)= 0.0000096794 + Iter 2: RMS(Cart)= 0.0000000770 RMS(Int)= 0.0000000700 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0000199078 0.0000050000 NO + RMS gradient 0.0001182037 0.0001000000 NO + MAX gradient 0.0004967062 0.0003000000 NO + RMS step 0.0042045107 0.0020000000 NO + MAX step 0.0107828207 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0003 Max(Angles) 0.10 + Max(Dihed) 0.62 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.5274 0.000259 -0.0002 1.5272 + 2. B(C 2,C 1) 1.5375 0.000444 -0.0003 1.5372 + 3. B(C 3,C 2) 1.5415 0.000497 -0.0003 1.5412 + 4. B(C 4,C 3) 1.5311 0.000352 -0.0002 1.5309 + 5. B(C 4,C 0) 1.5253 0.000204 -0.0001 1.5252 + 6. B(H 5,C 0) 1.0891 -0.000141 0.0000 1.0892 + 7. B(H 6,C 0) 1.0909 -0.000215 0.0002 1.0911 + 8. B(H 7,C 1) 1.0889 -0.000189 0.0001 1.0891 + 9. B(H 8,C 1) 1.0907 -0.000229 0.0002 1.0908 + 10. B(H 9,C 2) 1.0895 -0.000231 0.0002 1.0897 + 11. B(H 10,C 2) 1.0891 -0.000234 0.0002 1.0893 + 12. B(H 11,C 3) 1.0902 -0.000240 0.0001 1.0903 + 13. B(H 12,C 3) 1.0889 -0.000216 0.0002 1.0891 + 14. B(H 13,C 4) 1.0891 -0.000160 0.0001 1.0891 + 15. B(H 14,C 4) 1.0909 -0.000213 0.0002 1.0911 + 16. A(C 4,C 0,H 5) 112.76 -0.000032 0.08 112.84 + 17. A(C 1,C 0,C 4) 102.84 0.000032 -0.10 102.74 + 18. A(C 1,C 0,H 5) 112.51 -0.000031 0.05 112.56 + 19. A(H 5,C 0,H 6) 108.48 -0.000032 0.07 108.55 + 20. A(C 1,C 0,H 6) 110.23 0.000051 -0.05 110.18 + 21. A(C 4,C 0,H 6) 109.94 0.000018 -0.07 109.88 + 22. A(C 2,C 1,H 8) 110.16 0.000060 -0.00 110.16 + 23. A(C 2,C 1,H 7) 112.13 -0.000006 -0.01 112.12 + 24. A(H 7,C 1,H 8) 107.97 -0.000041 0.08 108.05 + 25. A(C 0,C 1,H 7) 112.37 -0.000022 0.04 112.40 + 26. A(C 0,C 1,C 2) 104.74 0.000016 -0.06 104.67 + 27. A(C 0,C 1,H 8) 109.45 -0.000002 -0.06 109.40 + 28. A(H 9,C 2,H 10) 107.45 -0.000073 0.09 107.54 + 29. A(C 1,C 2,C 3) 106.11 -0.000070 -0.02 106.08 + 30. A(C 1,C 2,H 10) 110.87 0.000011 0.01 110.88 + 31. A(C 3,C 2,H 9) 110.41 0.000036 0.00 110.41 + 32. A(C 1,C 2,H 9) 110.64 0.000052 -0.05 110.60 + 33. A(C 3,C 2,H 10) 111.40 0.000048 -0.03 111.37 + 34. A(H 11,C 3,H 12) 107.69 -0.000060 0.09 107.78 + 35. A(C 4,C 3,H 12) 111.73 -0.000007 0.01 111.74 + 36. A(C 2,C 3,H 12) 111.96 0.000018 -0.01 111.94 + 37. A(C 4,C 3,H 11) 109.75 0.000030 -0.06 109.69 + 38. A(C 2,C 3,H 11) 110.16 0.000059 0.00 110.16 + 39. A(C 2,C 3,C 4) 105.57 -0.000036 -0.04 105.53 + 40. A(H 13,C 4,H 14) 108.30 -0.000032 0.08 108.38 + 41. A(C 3,C 4,H 14) 110.27 0.000062 -0.02 110.24 + 42. A(C 0,C 4,H 14) 109.64 -0.000008 -0.07 109.57 + 43. A(C 3,C 4,H 13) 112.29 -0.000025 0.02 112.31 + 44. A(C 0,C 4,H 13) 112.77 -0.000032 0.07 112.84 + 45. A(C 0,C 4,C 3) 103.51 0.000041 -0.09 103.42 + 46. D(H 7,C 1,C 0,H 5) 79.41 0.000015 -0.36 79.05 + 47. D(H 7,C 1,C 0,H 6) -41.81 0.000042 -0.45 -42.27 + 48. D(C 2,C 1,C 0,H 5) -158.63 0.000005 -0.38 -159.01 + 49. D(H 7,C 1,C 0,C 4) -158.99 -0.000019 -0.30 -159.30 + 50. D(H 8,C 1,C 0,H 6) -161.76 0.000110 -0.55 -162.30 + 51. D(C 2,C 1,C 0,C 4) -37.03 -0.000029 -0.33 -37.35 + 52. D(C 2,C 1,C 0,H 6) 80.15 0.000032 -0.48 79.67 + 53. D(H 8,C 1,C 0,H 5) -40.54 0.000083 -0.45 -40.99 + 54. D(H 8,C 1,C 0,C 4) 81.06 0.000049 -0.40 80.67 + 55. D(H 9,C 2,C 1,H 7) 20.69 -0.000052 0.20 20.90 + 56. D(C 3,C 2,C 1,H 8) -99.25 -0.000037 0.27 -98.99 + 57. D(C 3,C 2,C 1,C 0) 18.35 -0.000002 0.16 18.52 + 58. D(H 10,C 2,C 1,H 8) 21.85 -0.000017 0.22 22.07 + 59. D(H 9,C 2,C 1,H 8) 140.96 -0.000067 0.30 141.27 + 60. D(H 10,C 2,C 1,H 7) -98.42 -0.000002 0.12 -98.31 + 61. D(H 10,C 2,C 1,C 0) 139.45 0.000019 0.11 139.57 + 62. D(C 3,C 2,C 1,H 7) 140.47 -0.000022 0.17 140.64 + 63. D(H 9,C 2,C 1,C 0) -101.43 -0.000031 0.20 -101.23 + 64. D(H 12,C 3,C 2,H 9) -111.02 0.000016 -0.02 -111.04 + 65. D(H 12,C 3,C 2,C 1) 129.05 -0.000024 0.05 129.10 + 66. D(H 11,C 3,C 2,H 10) 128.08 -0.000045 0.18 128.27 + 67. D(H 11,C 3,C 2,H 9) 8.78 -0.000008 0.09 8.87 + 68. D(C 4,C 3,C 2,H 9) 127.20 0.000037 0.00 127.20 + 69. D(C 4,C 3,C 2,C 1) 7.27 -0.000003 0.07 7.34 + 70. D(H 11,C 3,C 2,C 1) -111.15 -0.000048 0.16 -110.99 + 71. D(H 12,C 3,C 2,H 10) 8.28 -0.000020 0.08 8.36 + 72. D(C 4,C 3,C 2,H 10) -113.50 0.000001 0.09 -113.40 + 73. D(H 13,C 4,C 0,C 1) 163.15 0.000023 0.37 163.52 + 74. D(C 3,C 4,C 0,H 6) -75.83 -0.000039 0.51 -75.32 + 75. D(C 3,C 4,C 0,H 5) 162.98 0.000011 0.41 163.39 + 76. D(C 3,C 4,C 0,C 1) 41.55 0.000045 0.37 41.92 + 77. D(H 14,C 4,C 3,H 12) -34.86 0.000032 -0.38 -35.24 + 78. D(H 14,C 4,C 3,H 11) -154.24 0.000092 -0.46 -154.70 + 79. D(H 13,C 4,C 3,H 12) 86.02 0.000017 -0.28 85.74 + 80. D(H 13,C 4,C 3,H 11) -33.36 0.000077 -0.36 -33.72 + 81. D(H 13,C 4,C 3,C 2) -152.05 0.000012 -0.31 -152.37 + 82. D(C 0,C 4,C 3,H 12) -152.07 -0.000009 -0.24 -152.30 + 83. D(C 0,C 4,C 3,H 11) 88.56 0.000051 -0.32 88.23 + 84. D(C 0,C 4,C 3,C 2) -30.14 -0.000014 -0.27 -30.41 + 85. D(H 14,C 4,C 0,H 6) 166.52 -0.000129 0.62 167.14 + 86. D(H 14,C 4,C 0,H 5) 45.33 -0.000079 0.52 45.85 + 87. D(H 14,C 4,C 3,C 2) 87.07 0.000027 -0.41 86.66 + 88. D(H 14,C 4,C 0,C 1) -76.10 -0.000045 0.48 -75.62 + 89. D(H 13,C 4,C 0,H 6) 45.77 -0.000061 0.51 46.28 + 90. D(H 13,C 4,C 0,H 5) -75.42 -0.000011 0.41 -75.01 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 5 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.254764 -0.087506 0.246357 + C 0.330312 -1.225457 -0.181258 + C -1.088902 -0.680693 0.046834 + C -0.949381 0.851790 0.132471 + C 0.506536 1.151901 -0.233475 + H 2.250907 -0.173582 -0.185613 + H 1.348285 -0.066771 1.333273 + H 0.513007 -2.141451 0.378820 + H 0.485140 -1.439720 -1.239568 + H -1.507362 -1.076489 0.971842 + H -1.752602 -0.974004 -0.765631 + H -1.150114 1.191161 1.149001 + H -1.645670 1.361592 -0.531936 + H 0.868338 2.069444 0.228533 + H 0.612033 1.246555 -1.315330 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.371160 -0.165363 0.465548 + 1 C 6.0000 0 12.011 0.624199 -2.315778 -0.342528 + 2 C 6.0000 0 12.011 -2.057726 -1.286324 0.088503 + 3 C 6.0000 0 12.011 -1.794069 1.609650 0.250334 + 4 C 6.0000 0 12.011 0.957214 2.176778 -0.441204 + 5 H 1.0000 0 1.008 4.253597 -0.328022 -0.350757 + 6 H 1.0000 0 1.008 2.547890 -0.126179 2.519521 + 7 H 1.0000 0 1.008 0.969442 -4.046755 0.715866 + 8 H 1.0000 0 1.008 0.916781 -2.720677 -2.342445 + 9 H 1.0000 0 1.008 -2.848501 -2.034269 1.836515 + 10 H 1.0000 0 1.008 -3.311937 -1.840600 -1.446833 + 11 H 1.0000 0 1.008 -2.173400 2.250968 2.171298 + 12 H 1.0000 0 1.008 -3.109866 2.573036 -1.005213 + 13 H 1.0000 0 1.008 1.640920 3.910683 0.431865 + 14 H 1.0000 0 1.008 1.156575 2.355647 -2.485614 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:59:33.881 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.05355975097572 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0489182 -0.160489E+02 0.136E-02 13.19 0.0 T + 2 -16.0489182 -0.127713E-07 0.804E-03 13.19 3.2 T + 3 -16.0489182 -0.358794E-08 0.399E-04 13.19 64.7 T + 4 -16.0489182 -0.197563E-09 0.195E-04 13.19 132.3 T + + *** convergence criteria satisfied after 4 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6318700 -17.1941 + ... ... ... ... + 9 2.0000 -0.4821051 -13.1187 + 10 2.0000 -0.4407362 -11.9930 + 11 2.0000 -0.4380500 -11.9199 + 12 2.0000 -0.4362018 -11.8697 + 13 2.0000 -0.4360772 -11.8663 + 14 2.0000 -0.4211887 -11.4611 + 15 2.0000 -0.4145210 -11.2797 (HOMO) + 16 0.0701668 1.9093 (LUMO) + 17 0.0709287 1.9301 + 18 0.0914226 2.4877 + 19 0.1321255 3.5953 + 20 0.1343143 3.6549 + ... ... ... + 30 0.3523020 9.5866 + ------------------------------------------------------------- + HL-Gap 0.4846878 Eh 13.1890 eV + Fermi-level -0.1721771 Eh -4.6852 eV + + SCC (total) 0 d, 0 h, 0 min, 0.011 sec + SCC setup ... 0 min, 0.000 sec ( 1.779%) + Dispersion ... 0 min, 0.000 sec ( 0.951%) + classical contributions ... 0 min, 0.000 sec ( 0.410%) + integral evaluation ... 0 min, 0.002 sec ( 17.281%) + iterations ... 0 min, 0.004 sec ( 39.263%) + molecular gradient ... 0 min, 0.004 sec ( 38.808%) + printout ... 0 min, 0.000 sec ( 1.410%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814311679880 Eh :: + :: gradient norm 0.001141863631 Eh/a0 :: + :: HOMO-LUMO gap 13.189027371246 eV :: + ::.................................................:: + :: SCC energy -16.048918175778 Eh :: + :: -> isotropic ES 0.002346087271 Eh :: + :: -> anisotropic ES 0.004248869227 Eh :: + :: -> anisotropic XC 0.009715009573 Eh :: + :: -> dispersion -0.008133598494 Eh :: + :: repulsion energy 0.234596097647 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814311679880 Eh | + | GRADIENT NORM 0.001141863631 Eh/α | + | HOMO-LUMO GAP 13.189027371246 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:59:33.906 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.025 sec + * cpu-time: 0 d, 0 h, 0 min, 0.025 sec + * ratio c/w: 0.981 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.011 sec + * cpu-time: 0 d, 0 h, 0 min, 0.011 sec + * ratio c/w: 0.958 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814311679880 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 15 +Number of internal coordinates .... 90 +Current Energy .... -15.814311680 Eh +Current gradient norm .... 0.001141864 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999880028 +Lowest eigenvalues of augmented Hessian: + -0.000002546 0.004105100 0.011851528 0.045612633 0.045945469 +Length of the computed step .... 0.015491507 +The final length of the internal step .... 0.015491507 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0016329482 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0020702309 RMS(Int)= 0.0016326180 + Iter 1: RMS(Cart)= 0.0000019856 RMS(Int)= 0.0000012638 + Iter 2: RMS(Cart)= 0.0000000036 RMS(Int)= 0.0000000032 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0000067971 0.0000050000 NO + RMS gradient 0.0000635176 0.0001000000 YES + MAX gradient 0.0002263290 0.0003000000 YES + RMS step 0.0016329482 0.0020000000 YES + MAX step 0.0038269066 0.0040000000 YES + ........................................................ + Max(Bonds) 0.0003 Max(Angles) 0.04 + Max(Dihed) 0.22 Max(Improp) 0.00 + --------------------------------------------------------------------- + + Everything but the energy has converged. However, the energy + appears to be close enough to convergence to make sure that the + final evaluation at the new geometry represents the equilibrium energy. + Convergence will therefore be signaled now + + + ***********************HURRAY******************** + *** THE OPTIMIZATION HAS CONVERGED *** + ************************************************* + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + + --- Optimized Parameters --- + (Angstroem and degrees) + + Definition OldVal dE/dq Step FinalVal + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.5272 0.000144 -0.0002 1.5270 + 2. B(C 2,C 1) 1.5372 0.000213 -0.0003 1.5369 + 3. B(C 3,C 2) 1.5412 0.000226 -0.0003 1.5409 + 4. B(C 4,C 3) 1.5309 0.000183 -0.0003 1.5306 + 5. B(C 4,C 0) 1.5252 0.000137 -0.0002 1.5250 + 6. B(H 5,C 0) 1.0892 -0.000064 0.0001 1.0893 + 7. B(H 6,C 0) 1.0911 -0.000090 0.0002 1.0913 + 8. B(H 7,C 1) 1.0891 -0.000071 0.0001 1.0892 + 9. B(H 8,C 1) 1.0908 -0.000124 0.0002 1.0910 + 10. B(H 9,C 2) 1.0897 -0.000118 0.0002 1.0899 + 11. B(H 10,C 2) 1.0893 -0.000103 0.0002 1.0895 + 12. B(H 11,C 3) 1.0903 -0.000135 0.0002 1.0905 + 13. B(H 12,C 3) 1.0891 -0.000082 0.0001 1.0892 + 14. B(H 13,C 4) 1.0891 -0.000067 0.0001 1.0892 + 15. B(H 14,C 4) 1.0911 -0.000102 0.0002 1.0913 + 16. A(C 4,C 0,H 5) 112.84 -0.000002 0.03 112.87 + 17. A(C 1,C 0,C 4) 102.74 -0.000006 -0.03 102.70 + 18. A(C 1,C 0,H 5) 112.56 -0.000029 0.03 112.59 + 19. A(H 5,C 0,H 6) 108.55 0.000013 0.01 108.56 + 20. A(C 1,C 0,H 6) 110.18 0.000040 -0.03 110.15 + 21. A(C 4,C 0,H 6) 109.88 -0.000017 -0.01 109.86 + 22. A(C 2,C 1,H 8) 110.16 0.000084 -0.04 110.12 + 23. A(C 2,C 1,H 7) 112.13 -0.000058 0.03 112.15 + 24. A(H 7,C 1,H 8) 108.05 0.000025 0.00 108.06 + 25. A(C 0,C 1,H 7) 112.41 -0.000005 0.03 112.44 + 26. A(C 0,C 1,C 2) 104.67 0.000002 -0.02 104.65 + 27. A(C 0,C 1,H 8) 109.40 -0.000048 -0.01 109.38 + 28. A(H 9,C 2,H 10) 107.54 0.000017 0.01 107.54 + 29. A(C 1,C 2,C 3) 106.08 -0.000026 -0.01 106.08 + 30. A(C 1,C 2,H 10) 110.88 0.000015 0.01 110.89 + 31. A(C 3,C 2,H 9) 110.41 0.000046 -0.02 110.40 + 32. A(C 1,C 2,H 9) 110.60 -0.000021 -0.00 110.59 + 33. A(C 3,C 2,H 10) 111.37 -0.000031 0.01 111.38 + 34. A(H 11,C 3,H 12) 107.78 0.000021 0.00 107.78 + 35. A(C 4,C 3,H 12) 111.74 -0.000005 0.03 111.77 + 36. A(C 2,C 3,H 12) 111.94 -0.000048 0.03 111.97 + 37. A(C 4,C 3,H 11) 109.69 -0.000027 -0.02 109.67 + 38. A(C 2,C 3,H 11) 110.16 0.000081 -0.04 110.12 + 39. A(C 2,C 3,C 4) 105.53 -0.000020 -0.01 105.52 + 40. A(H 13,C 4,H 14) 108.38 0.000022 0.01 108.39 + 41. A(C 3,C 4,H 14) 110.24 0.000071 -0.03 110.21 + 42. A(C 0,C 4,H 14) 109.57 -0.000049 -0.01 109.57 + 43. A(C 3,C 4,H 13) 112.31 -0.000053 0.03 112.34 + 44. A(C 0,C 4,H 13) 112.84 0.000003 0.03 112.87 + 45. A(C 0,C 4,C 3) 103.42 0.000007 -0.03 103.39 + 46. D(H 7,C 1,C 0,H 5) 79.05 0.000048 -0.17 78.88 + 47. D(H 7,C 1,C 0,H 6) -42.27 0.000023 -0.18 -42.45 + 48. D(C 2,C 1,C 0,H 5) -159.01 -0.000024 -0.13 -159.14 + 49. D(H 7,C 1,C 0,C 4) -159.30 0.000027 -0.14 -159.43 + 50. D(H 8,C 1,C 0,H 6) -162.30 0.000026 -0.20 -162.50 + 51. D(C 2,C 1,C 0,C 4) -37.35 -0.000045 -0.09 -37.45 + 52. D(C 2,C 1,C 0,H 6) 79.67 -0.000050 -0.14 79.53 + 53. D(H 8,C 1,C 0,H 5) -40.99 0.000052 -0.19 -41.17 + 54. D(H 8,C 1,C 0,C 4) 80.67 0.000031 -0.15 80.51 + 55. D(H 9,C 2,C 1,H 7) 20.90 -0.000047 0.12 21.01 + 56. D(C 3,C 2,C 1,H 8) -98.99 0.000032 0.09 -98.90 + 57. D(C 3,C 2,C 1,C 0) 18.52 0.000018 0.05 18.56 + 58. D(H 10,C 2,C 1,H 8) 22.07 -0.000013 0.11 22.17 + 59. D(H 9,C 2,C 1,H 8) 141.27 0.000004 0.11 141.38 + 60. D(H 10,C 2,C 1,H 7) -98.31 -0.000063 0.11 -98.20 + 61. D(H 10,C 2,C 1,C 0) 139.57 -0.000026 0.06 139.63 + 62. D(C 3,C 2,C 1,H 7) 140.64 -0.000019 0.09 140.73 + 63. D(H 9,C 2,C 1,C 0) -101.23 -0.000010 0.07 -101.16 + 64. D(H 12,C 3,C 2,H 9) -111.04 -0.000056 0.05 -110.99 + 65. D(H 12,C 3,C 2,C 1) 129.10 -0.000040 0.07 129.17 + 66. D(H 11,C 3,C 2,H 10) 128.27 0.000025 0.05 128.32 + 67. D(H 11,C 3,C 2,H 9) 8.87 -0.000006 0.05 8.92 + 68. D(C 4,C 3,C 2,H 9) 127.20 -0.000009 0.00 127.21 + 69. D(C 4,C 3,C 2,C 1) 7.34 0.000007 0.02 7.36 + 70. D(H 11,C 3,C 2,C 1) -110.99 0.000010 0.06 -110.93 + 71. D(H 12,C 3,C 2,H 10) 8.36 -0.000025 0.06 8.42 + 72. D(C 4,C 3,C 2,H 10) -113.40 0.000022 0.01 -113.39 + 73. D(H 13,C 4,C 0,C 1) 163.52 -0.000002 0.14 163.66 + 74. D(C 3,C 4,C 0,H 6) -75.32 0.000020 0.16 -75.16 + 75. D(C 3,C 4,C 0,H 5) 163.39 0.000017 0.14 163.53 + 76. D(C 3,C 4,C 0,C 1) 41.92 0.000056 0.11 42.03 + 77. D(H 14,C 4,C 3,H 12) -35.24 0.000018 -0.17 -35.40 + 78. D(H 14,C 4,C 3,H 11) -154.70 0.000013 -0.18 -154.88 + 79. D(H 13,C 4,C 3,H 12) 85.74 0.000060 -0.16 85.58 + 80. D(H 13,C 4,C 3,H 11) -33.72 0.000055 -0.17 -33.90 + 81. D(H 13,C 4,C 3,C 2) -152.37 -0.000015 -0.12 -152.48 + 82. D(C 0,C 4,C 3,H 12) -152.30 0.000039 -0.13 -152.43 + 83. D(C 0,C 4,C 3,H 11) 88.23 0.000034 -0.14 88.10 + 84. D(C 0,C 4,C 3,C 2) -30.41 -0.000035 -0.08 -30.49 + 85. D(H 14,C 4,C 0,H 6) 167.14 -0.000042 0.22 167.36 + 86. D(H 14,C 4,C 0,H 5) 45.85 -0.000046 0.20 46.05 + 87. D(H 14,C 4,C 3,C 2) 86.66 -0.000057 -0.12 86.54 + 88. D(H 14,C 4,C 0,C 1) -75.62 -0.000007 0.17 -75.45 + 89. D(H 13,C 4,C 0,H 6) 46.28 -0.000038 0.20 46.47 + 90. D(H 13,C 4,C 0,H 5) -75.01 -0.000041 0.17 -74.84 + ---------------------------------------------------------------------------- + ******************************************************* + *** FINAL ENERGY EVALUATION AT THE STATIONARY POINT *** + *** (AFTER 5 CYCLES) *** + ******************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.254359 -0.087377 0.247155 + C 0.330425 -1.225019 -0.181593 + C -1.088479 -0.680500 0.046806 + C -0.948922 0.851627 0.132567 + C 0.506553 1.151472 -0.234149 + H 2.251512 -0.173549 -0.182679 + H 1.345388 -0.066448 1.334450 + H 0.513299 -2.142065 0.376923 + H 0.484946 -1.437484 -1.240528 + H -1.506574 -1.076197 0.972249 + H -1.752594 -0.973990 -0.765485 + H -1.148462 1.190193 1.149840 + H -1.646034 1.362100 -0.530685 + H 0.868686 2.069982 0.225902 + H 0.611188 1.244027 -1.316453 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.370395 -0.165119 0.467056 + 1 C 6.0000 0 12.011 0.624412 -2.314951 -0.343162 + 2 C 6.0000 0 12.011 -2.056928 -1.285958 0.088450 + 3 C 6.0000 0 12.011 -1.793202 1.609341 0.250515 + 4 C 6.0000 0 12.011 0.957247 2.175966 -0.442477 + 5 H 1.0000 0 1.008 4.254741 -0.327960 -0.345213 + 6 H 1.0000 0 1.008 2.542415 -0.125568 2.521746 + 7 H 1.0000 0 1.008 0.969995 -4.047917 0.712281 + 8 H 1.0000 0 1.008 0.916414 -2.716451 -2.344258 + 9 H 1.0000 0 1.008 -2.847013 -2.033718 1.837284 + 10 H 1.0000 0 1.008 -3.311923 -1.840575 -1.446556 + 11 H 1.0000 0 1.008 -2.170279 2.249138 2.172882 + 12 H 1.0000 0 1.008 -3.110554 2.573997 -1.002848 + 13 H 1.0000 0 1.008 1.641579 3.911699 0.426893 + 14 H 1.0000 0 1.008 1.154978 2.350870 -2.487736 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:59:33.979 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.58148283834824 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0488369 -0.160488E+02 0.500E-03 13.20 0.0 T + 2 -16.0488369 -0.731859E-08 0.298E-03 13.20 8.7 T + 3 -16.0488369 -0.448981E-09 0.228E-04 13.20 113.0 T + 4 -16.0488369 -0.946798E-11 0.689E-05 13.20 374.8 T + + *** convergence criteria satisfied after 4 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6319477 -17.1962 + ... ... ... ... + 9 2.0000 -0.4821074 -13.1188 + 10 2.0000 -0.4407302 -11.9929 + 11 2.0000 -0.4380154 -11.9190 + 12 2.0000 -0.4362468 -11.8709 + 13 2.0000 -0.4361111 -11.8672 + 14 2.0000 -0.4212283 -11.4622 + 15 2.0000 -0.4144836 -11.2787 (HOMO) + 16 0.0704309 1.9165 (LUMO) + 17 0.0711941 1.9373 + 18 0.0912106 2.4820 + 19 0.1322569 3.5989 + 20 0.1341636 3.6508 + ... ... ... + 30 0.3520732 9.5804 + ------------------------------------------------------------- + HL-Gap 0.4849145 Eh 13.1952 eV + Fermi-level -0.1720264 Eh -4.6811 eV + + SCC (total) 0 d, 0 h, 0 min, 0.011 sec + SCC setup ... 0 min, 0.000 sec ( 1.371%) + Dispersion ... 0 min, 0.000 sec ( 0.926%) + classical contributions ... 0 min, 0.000 sec ( 0.359%) + integral evaluation ... 0 min, 0.002 sec ( 16.009%) + iterations ... 0 min, 0.005 sec ( 40.507%) + molecular gradient ... 0 min, 0.005 sec ( 39.329%) + printout ... 0 min, 0.000 sec ( 1.411%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814313366053 Eh :: + :: gradient norm 0.000497848720 Eh/a0 :: + :: HOMO-LUMO gap 13.195196441405 eV :: + ::.................................................:: + :: SCC energy -16.048836878888 Eh :: + :: -> isotropic ES 0.002342725001 Eh :: + :: -> anisotropic ES 0.004244905299 Eh :: + :: -> anisotropic XC 0.009717418625 Eh :: + :: -> dispersion -0.008134806430 Eh :: + :: repulsion energy 0.234513126374 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814313366053 Eh | + | GRADIENT NORM 0.000497848720 Eh/α | + | HOMO-LUMO GAP 13.195196441405 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:59:34.004 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.025 sec + * cpu-time: 0 d, 0 h, 0 min, 0.024 sec + * ratio c/w: 0.978 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.012 sec + * cpu-time: 0 d, 0 h, 0 min, 0.011 sec + * ratio c/w: 0.955 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814313366050 +------------------------- -------------------- + + *** OPTIMIZATION RUN DONE *** + +Timings for individual modules: + +Sum of individual times ... 0.498 sec (= 0.008 min) +Geometry relaxation ... 0.193 sec (= 0.003 min) 38.7 % +XTB module ... 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803.10 0.00257585 13.01731160 -0.006638 0.004376 -0.030622 + 840.54 0.00038498 1.94553063 0.003428 0.006004 0.009753 + 876.38 0.00073464 3.71257432 -0.002562 -0.004049 -0.015448 + 954.58 0.00011539 0.58313879 -0.003609 -0.001996 0.004551 + 965.59 0.00012990 0.65645639 0.004167 0.004871 -0.000943 + 980.31 0.00072888 3.68344180 0.009998 0.009993 -0.005676 + 1000.25 0.00103158 5.21320763 0.004459 0.015939 0.006922 + 1030.24 0.00010245 0.51772262 0.004598 0.002103 0.002338 + 1101.22 0.00013448 0.67959773 0.000215 -0.005072 -0.003513 + 1125.95 0.00113831 5.75255973 0.002735 -0.006389 -0.016346 + 1163.25 0.00015958 0.80646270 -0.001528 0.006282 -0.001007 + 1191.48 0.00006704 0.33878187 -0.001822 -0.003210 -0.001983 + 1205.00 0.00128027 6.46996497 0.005350 -0.004225 -0.016884 + 1219.58 0.00017162 0.86731602 0.001333 0.003743 -0.005303 + 1239.15 0.00073705 3.72474819 -0.004600 -0.006588 0.011002 + 1296.43 0.00095855 4.84412946 -0.007658 -0.012866 -0.002561 + 1307.22 0.00056148 2.83748162 -0.002810 0.001789 -0.011088 + 1323.33 0.00007904 0.39941107 -0.001509 0.001715 -0.003663 + 1324.02 0.00010272 0.51912552 -0.002056 0.003289 0.003027 + 1324.99 0.00032752 1.65516605 0.005816 -0.004043 -0.005192 + 1483.49 0.00022702 1.14729045 0.006418 0.001978 0.001630 + 1487.62 0.00099922 5.04966622 -0.003783 -0.004743 0.013146 + 1497.58 0.00079885 4.03704674 -0.000907 0.010301 0.007716 + 1498.38 0.00094050 4.75288767 0.000107 -0.000655 -0.013980 + 1516.09 0.00023885 1.20705417 -0.004273 -0.005461 -0.001041 + 2971.92 0.00169187 8.55003705 -0.004728 0.011549 0.004682 + 2972.55 0.00030160 1.52418460 -0.005163 -0.001834 -0.001281 + 2984.88 0.00082539 4.17115936 0.007991 0.003960 0.002599 + 2986.62 0.00307726 15.55122166 0.005703 -0.001857 -0.016899 + 2999.16 0.00475957 24.05289995 0.005780 0.000320 0.021488 + 3000.31 0.00240908 12.17451857 -0.004745 -0.015100 -0.000224 + 3005.88 0.03470973 175.40875634 -0.008980 0.004079 0.059213 + 3008.88 0.01427541 72.14208921 -0.029057 -0.025187 0.001377 + 3009.44 0.02549954 128.86420457 0.029874 -0.023499 0.034634 + 3012.88 0.00217129 10.97281054 -0.014390 -0.000813 -0.004143 + + +$end + diff --git a/cmmde_gui/test/alala/alala/freq/cmmd.in b/cmmde_gui/test/alala/alala/freq/cmmd.in new file mode 100644 index 0000000..247d130 --- /dev/null +++ b/cmmde_gui/test/alala/alala/freq/cmmd.in @@ -0,0 +1,13 @@ +#CMMDE generated Orca input file +!XTB2 Numfreq +%pal + nprocs 1 +end + +*xyzfile 0 1 ../cmmd.xyz + +%freq + scalfreq 1 + Temp 298.15 + Pressure 1.0 +end diff --git a/cmmde_gui/test/alala/alala/freq/cmmd.out b/cmmde_gui/test/alala/alala/freq/cmmd.out new file mode 100644 index 0000000..1695aaa --- /dev/null +++ b/cmmde_gui/test/alala/alala/freq/cmmd.out @@ -0,0 +1,1193 @@ + + ***************** + * O R C A * + ***************** + + #, + ### + #### + ##### + ###### + ########, + ,,################,,,,, + ,,#################################,, + ,,##########################################,, + ,#########################################, ''#####, + ,#############################################,, '####, + ,##################################################,,,,####, + ,###########'''' ''''############################### + ,#####'' ,,,,##########,,,, '''####''' '#### + ,##' ,,,,###########################,,, '## + ' ,,###'''' '''############,,, + ,,##'' '''############,,,, ,,,,,,###'' + ,#'' '''#######################''' + ' ''''####'''' + ,#######, #######, ,#######, ## + ,#' '#, ## ## ,#' '#, #''# ###### ,####, + ## ## ## ,#' ## #' '# # #' '# + ## ## ####### ## ,######, #####, # # + '#, ,#' ## ## '#, ,#' ,# #, ## #, ,# + '#######' ## ## '#######' #' '# #####' # '####' + + + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship and core code : Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 5.0.2 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Marcus Kettner : VPT2 + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : Initial AUTO-CI + Lucas Lang : DCDCAS + Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, + C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT + MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, + LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, + nearIR, NL-DFT gradient (VV10), updates on ESD, + ML-optimized integration grids + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + Liviu Ungur et al : ANISO software + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 5.1.0 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + Shared memory : Shared parallel matrices + BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED + Core in use : SkylakeX + Copyright (c) 2011-2014, The OpenBLAS Project + + + + +*************************************** +The coordinates will be read from file: ../cmmd.xyz +*************************************** + + +Your calculation utilizes the semiempirical GFN2-xTB method +Please cite in your paper: +C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. + + +================================================================================ + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + +WARNING: Gradients needed for Numerical Frequencies + ===> : Setting RunTyp to EnGrad + +WARNING: Found dipole moment calculation with XTB calculation + ===> : Switching off dipole moment calculation + + +WARNING: TRAH-SCF for XTB is not implemented! + ===> : Turning TRAH off! + +================================================================================ + INPUT FILE +================================================================================ +NAME = cmmd.in +| 1> #CMMDE generated Orca input file +| 2> !XTB2 Numfreq +| 3> %pal +| 4> nprocs 1 +| 5> end +| 6> +| 7> *xyzfile 0 1 ../cmmd.xyz +| 8> +| 9> %freq +| 10> scalfreq 1 +| 11> Temp 298.15 +| 12> Pressure 1.0 +| 13> end +| 14> +| 15> ****END OF INPUT**** +================================================================================ + + ******************************* + * Energy+Gradient Calculation * + ******************************* + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 19:10:29.375 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.94791337893003 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0054351 -0.160054E+02 0.262E+00 13.70 0.0 T + 2 -16.0484055 -0.429703E-01 0.153E+00 13.20 1.0 T + 3 -16.0487278 -0.322317E-03 0.804E-01 13.20 1.0 T + 4 -16.0488365 -0.108768E-03 0.796E-02 13.19 1.0 T + 5 -16.0488367 -0.199985E-06 0.579E-03 13.20 4.5 T + 6 -16.0488369 -0.123847E-06 0.221E-03 13.20 11.7 T + 7 -16.0488369 -0.538951E-08 0.667E-04 13.20 38.7 T + 8 -16.0488369 -0.692037E-09 0.113E-04 13.20 229.0 T + + *** convergence criteria satisfied after 8 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6319470 -17.1962 + ... ... ... ... + 9 2.0000 -0.4821072 -13.1188 + 10 2.0000 -0.4407301 -11.9929 + 11 2.0000 -0.4380151 -11.9190 + 12 2.0000 -0.4362468 -11.8709 + 13 2.0000 -0.4361108 -11.8672 + 14 2.0000 -0.4212279 -11.4622 + 15 2.0000 -0.4144832 -11.2787 (HOMO) + 16 0.0704311 1.9165 (LUMO) + 17 0.0711944 1.9373 + 18 0.0912106 2.4820 + 19 0.1322572 3.5989 + 20 0.1341634 3.6508 + ... ... ... + 30 0.3520733 9.5804 + ------------------------------------------------------------- + HL-Gap 0.4849143 Eh 13.1952 eV + Fermi-level -0.1720261 Eh -4.6811 eV + + SCC (total) 0 d, 0 h, 0 min, 0.033 sec + SCC setup ... 0 min, 0.000 sec ( 0.578%) + Dispersion ... 0 min, 0.000 sec ( 0.366%) + classical contributions ... 0 min, 0.000 sec ( 0.156%) + integral evaluation ... 0 min, 0.002 sec ( 5.403%) + iterations ... 0 min, 0.026 sec ( 78.579%) + molecular gradient ... 0 min, 0.005 sec ( 14.309%) + printout ... 0 min, 0.000 sec ( 0.569%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814313366037 Eh :: + :: gradient norm 0.000497859982 Eh/a0 :: + :: HOMO-LUMO gap 13.195188817416 eV :: + ::.................................................:: + :: SCC energy -16.048836878872 Eh :: + :: -> isotropic ES 0.002342731977 Eh :: + :: -> anisotropic ES 0.004244875878 Eh :: + :: -> anisotropic XC 0.009717391897 Eh :: + :: -> dispersion -0.008134804860 Eh :: + :: repulsion energy 0.234513126374 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814313366037 Eh | + | GRADIENT NORM 0.000497859982 Eh/α | + | HOMO-LUMO GAP 13.195188817416 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 19:10:29.420 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.045 sec + * cpu-time: 0 d, 0 h, 0 min, 0.025 sec + * ratio c/w: 0.546 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.033 sec + * cpu-time: 0 d, 0 h, 0 min, 0.012 sec + * ratio c/w: 0.377 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814313366040 +------------------------- -------------------- + + +---------------------------------------------------------------------------- + ORCA NUMERICAL FREQUENCIES +---------------------------------------------------------------------------- + +Number of atoms ... 15 +Central differences ... used +Number of displacements ... 90 +Numerical increment ... 5.000e-03 bohr +IR-spectrum generation ... on +Raman-spectrum generation ... off +Surface Crossing Hessian ... off + +The output will be reduced. Please look at the following files: +SCF program output ... >cmmd.lastscf +Integral program output ... >cmmd.lastint +Gradient program output ... >cmmd.lastgrad +Dipole moment program output ... >cmmd.lastmom +AutoCI program output ... >cmmd.lastautoci + + << Calculating on displaced geometry 1 (of 90) >> + << Calculating on displaced geometry 2 (of 90) >> + << Calculating on displaced geometry 3 (of 90) >> + << Calculating on displaced geometry 4 (of 90) >> + << Calculating on displaced geometry 5 (of 90) >> + << Calculating on displaced geometry 6 (of 90) >> + << Calculating on displaced geometry 7 (of 90) >> + << Calculating on displaced geometry 8 (of 90) >> + << Calculating on displaced geometry 9 (of 90) >> + << Calculating on displaced geometry 10 (of 90) >> + << Calculating on displaced geometry 11 (of 90) >> + << Calculating on displaced geometry 12 (of 90) >> + << Calculating on displaced geometry 13 (of 90) >> + << Calculating on displaced geometry 14 (of 90) >> + << Calculating on displaced geometry 15 (of 90) >> + << Calculating on displaced geometry 16 (of 90) >> + << Calculating on displaced geometry 17 (of 90) >> + << Calculating on displaced geometry 18 (of 90) >> + << Calculating on displaced geometry 19 (of 90) >> + << Calculating on displaced geometry 20 (of 90) >> + << Calculating on displaced geometry 21 (of 90) >> + << Calculating on displaced geometry 22 (of 90) >> + << Calculating on displaced geometry 23 (of 90) >> + << Calculating on displaced geometry 24 (of 90) >> + << Calculating on displaced geometry 25 (of 90) >> + << Calculating on displaced geometry 26 (of 90) >> + << Calculating on displaced geometry 27 (of 90) >> + << Calculating on displaced geometry 28 (of 90) >> + << Calculating on displaced geometry 29 (of 90) >> + << Calculating on displaced geometry 30 (of 90) >> + << Calculating on displaced geometry 31 (of 90) >> + << Calculating on displaced geometry 32 (of 90) >> + << Calculating on displaced geometry 33 (of 90) >> + << Calculating on displaced geometry 34 (of 90) >> + << Calculating on displaced geometry 35 (of 90) >> + << Calculating on displaced geometry 36 (of 90) >> + << Calculating on displaced geometry 37 (of 90) >> + << Calculating on displaced geometry 38 (of 90) >> + << Calculating on displaced geometry 39 (of 90) >> + << Calculating on displaced geometry 40 (of 90) >> + << Calculating on displaced geometry 41 (of 90) >> + << Calculating on displaced geometry 42 (of 90) >> + << Calculating on displaced geometry 43 (of 90) >> + << Calculating on displaced geometry 44 (of 90) >> + << Calculating on displaced geometry 45 (of 90) >> + << Calculating on displaced geometry 46 (of 90) >> + << Calculating on displaced geometry 47 (of 90) >> + << Calculating on displaced geometry 48 (of 90) >> + << Calculating on displaced geometry 49 (of 90) >> + << Calculating on displaced geometry 50 (of 90) >> + << Calculating on displaced geometry 51 (of 90) >> + << Calculating on displaced geometry 52 (of 90) >> + << Calculating on displaced geometry 53 (of 90) >> + << Calculating on displaced geometry 54 (of 90) >> + << Calculating on displaced geometry 55 (of 90) >> + << Calculating on displaced geometry 56 (of 90) >> + << Calculating on displaced geometry 57 (of 90) >> + << Calculating on displaced geometry 58 (of 90) >> + << Calculating on displaced geometry 59 (of 90) >> + << Calculating on displaced geometry 60 (of 90) >> + << Calculating on displaced geometry 61 (of 90) >> + << Calculating on displaced geometry 62 (of 90) >> + << Calculating on displaced geometry 63 (of 90) >> + << Calculating on displaced geometry 64 (of 90) >> + << Calculating on displaced geometry 65 (of 90) >> + << Calculating on displaced geometry 66 (of 90) >> + << Calculating on displaced geometry 67 (of 90) >> + << Calculating on displaced geometry 68 (of 90) >> + << Calculating on displaced geometry 69 (of 90) >> + << Calculating on displaced geometry 70 (of 90) >> + << Calculating on displaced geometry 71 (of 90) >> + << Calculating on displaced geometry 72 (of 90) >> + << Calculating on displaced geometry 73 (of 90) >> + << Calculating on displaced geometry 74 (of 90) >> + << Calculating on displaced geometry 75 (of 90) >> + << Calculating on displaced geometry 76 (of 90) >> + << Calculating on displaced geometry 77 (of 90) >> + << Calculating on displaced geometry 78 (of 90) >> + << Calculating on displaced geometry 79 (of 90) >> + << Calculating on displaced geometry 80 (of 90) >> + << Calculating on displaced geometry 81 (of 90) >> + << Calculating on displaced geometry 82 (of 90) >> + << Calculating on displaced geometry 83 (of 90) >> + << Calculating on displaced geometry 84 (of 90) >> + << Calculating on displaced geometry 85 (of 90) >> + << Calculating on displaced geometry 86 (of 90) >> + << Calculating on displaced geometry 87 (of 90) >> + << Calculating on displaced geometry 88 (of 90) >> + << Calculating on displaced geometry 89 (of 90) >> + << Calculating on displaced geometry 90 (of 90) >> + +----------------------- +VIBRATIONAL FREQUENCIES +----------------------- + +Scaling factor for frequencies = 1.000000000 (already applied!) + + 0: 0.00 cm**-1 + 1: 0.00 cm**-1 + 2: 0.00 cm**-1 + 3: 0.00 cm**-1 + 4: 0.00 cm**-1 + 5: 0.00 cm**-1 + 6: -13.35 cm**-1 ***imaginary mode*** + 7: 252.24 cm**-1 + 8: 557.18 cm**-1 + 9: 613.24 cm**-1 + 10: 803.10 cm**-1 + 11: 840.54 cm**-1 + 12: 876.38 cm**-1 + 13: 954.58 cm**-1 + 14: 965.59 cm**-1 + 15: 980.31 cm**-1 + 16: 1000.25 cm**-1 + 17: 1030.24 cm**-1 + 18: 1101.22 cm**-1 + 19: 1125.95 cm**-1 + 20: 1163.25 cm**-1 + 21: 1191.48 cm**-1 + 22: 1205.00 cm**-1 + 23: 1219.58 cm**-1 + 24: 1239.15 cm**-1 + 25: 1296.43 cm**-1 + 26: 1307.22 cm**-1 + 27: 1323.33 cm**-1 + 28: 1324.02 cm**-1 + 29: 1324.99 cm**-1 + 30: 1483.49 cm**-1 + 31: 1487.62 cm**-1 + 32: 1497.58 cm**-1 + 33: 1498.38 cm**-1 + 34: 1516.09 cm**-1 + 35: 2971.92 cm**-1 + 36: 2972.55 cm**-1 + 37: 2984.88 cm**-1 + 38: 2986.62 cm**-1 + 39: 2999.16 cm**-1 + 40: 3000.31 cm**-1 + 41: 3005.88 cm**-1 + 42: 3008.88 cm**-1 + 43: 3009.44 cm**-1 + 44: 3012.88 cm**-1 + + +------------ +NORMAL MODES +------------ + +These modes are the cartesian displacements weighted by the diagonal matrix +M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom +Thus, these vectors are normalized but *not* orthogonal + + 0 1 2 3 4 5 + 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 1 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 2 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 7 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 8 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 9 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 10 0.000000 0.000000 0.000000 0.000000 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0.368951 + 33 -0.012697 -0.007446 0.027638 + 34 0.024378 0.028115 -0.061088 + 35 0.084756 0.132597 -0.233769 + 36 -0.064687 -0.347009 0.302826 + 37 0.044034 0.248947 -0.216428 + 38 -0.066458 -0.349307 0.311583 + 39 0.214416 -0.007581 -0.092336 + 40 0.549350 -0.024387 -0.235296 + 41 0.297417 -0.008768 -0.128759 + 42 0.010692 0.007649 -0.006218 + 43 -0.005572 0.007430 0.000773 + 44 -0.220092 -0.081964 0.113637 + + +----------- +IR SPECTRUM +----------- + + Mode freq eps Int T**2 TX TY TZ + cm**-1 L/(mol*cm) km/mol a.u. +---------------------------------------------------------------------------- + 7: 252.24 0.000158 0.80 0.000196 ( 0.006793 -0.012199 0.000883) + 8: 557.18 0.003325 16.80 0.001862 (-0.006401 -0.003125 -0.042564) + 9: 613.24 0.000202 1.02 0.000103 (-0.003489 -0.005541 0.007726) + 10: 803.10 0.002576 13.02 0.001001 (-0.006638 0.004376 -0.030622) + 11: 840.54 0.000385 1.95 0.000143 ( 0.003428 0.006004 0.009753) + 12: 876.38 0.000735 3.71 0.000262 (-0.002562 -0.004049 -0.015448) + 13: 954.58 0.000115 0.58 0.000038 (-0.003609 -0.001996 0.004551) + 14: 965.59 0.000130 0.66 0.000042 ( 0.004167 0.004871 -0.000943) + 15: 980.31 0.000729 3.68 0.000232 ( 0.009998 0.009993 -0.005676) + 16: 1000.25 0.001032 5.21 0.000322 ( 0.004459 0.015939 0.006922) + 17: 1030.24 0.000102 0.52 0.000031 ( 0.004598 0.002103 0.002338) + 18: 1101.22 0.000134 0.68 0.000038 ( 0.000215 -0.005072 -0.003513) + 19: 1125.95 0.001138 5.75 0.000315 ( 0.002735 -0.006389 -0.016346) + 20: 1163.25 0.000160 0.81 0.000043 (-0.001528 0.006282 -0.001007) + 21: 1191.48 0.000067 0.34 0.000018 (-0.001822 -0.003210 -0.001983) + 22: 1205.00 0.001280 6.47 0.000332 ( 0.005350 -0.004225 -0.016884) + 23: 1219.58 0.000172 0.87 0.000044 ( 0.001333 0.003743 -0.005303) + 24: 1239.15 0.000737 3.72 0.000186 (-0.004600 -0.006588 0.011002) + 25: 1296.43 0.000959 4.84 0.000231 (-0.007658 -0.012866 -0.002561) + 26: 1307.22 0.000561 2.84 0.000134 (-0.002810 0.001789 -0.011088) + 27: 1323.33 0.000079 0.40 0.000019 (-0.001509 0.001715 -0.003663) + 28: 1324.02 0.000103 0.52 0.000024 (-0.002056 0.003289 0.003027) + 29: 1324.99 0.000328 1.66 0.000077 ( 0.005816 -0.004043 -0.005192) + 30: 1483.49 0.000227 1.15 0.000048 ( 0.006418 0.001978 0.001630) + 31: 1487.62 0.000999 5.05 0.000210 (-0.003783 -0.004743 0.013146) + 32: 1497.58 0.000799 4.04 0.000166 (-0.000907 0.010301 0.007716) + 33: 1498.38 0.000940 4.75 0.000196 ( 0.000107 -0.000655 -0.013980) + 34: 1516.09 0.000239 1.21 0.000049 (-0.004273 -0.005461 -0.001041) + 35: 2971.92 0.001692 8.55 0.000178 (-0.004728 0.011549 0.004682) + 36: 2972.55 0.000302 1.52 0.000032 (-0.005163 -0.001834 -0.001281) + 37: 2984.88 0.000825 4.17 0.000086 ( 0.007991 0.003960 0.002599) + 38: 2986.62 0.003077 15.55 0.000322 ( 0.005703 -0.001857 -0.016899) + 39: 2999.16 0.004760 24.05 0.000495 ( 0.005780 0.000320 0.021488) + 40: 3000.31 0.002409 12.17 0.000251 (-0.004745 -0.015100 -0.000224) + 41: 3005.88 0.034710 175.41 0.003603 (-0.008980 0.004079 0.059213) + 42: 3008.88 0.014275 72.14 0.001481 (-0.029057 -0.025187 0.001377) + 43: 3009.44 0.025500 128.86 0.002644 ( 0.029874 -0.023499 0.034634) + 44: 3012.88 0.002171 10.97 0.000225 (-0.014390 -0.000813 -0.004143) + +* The epsilon (eps) is given for a Dirac delta lineshape. +** The dipole moment derivative (T) already includes vibrational overlap. + +The first frequency considered to be a vibration is 7 +The total number of vibrations considered is 38 + + +-------------------------- +THERMOCHEMISTRY AT 298.15K +-------------------------- + +Temperature ... 298.15 K +Pressure ... 1.00 atm +Total Mass ... 70.13 AMU + +Throughout the following assumptions are being made: + (1) The electronic state is orbitally nondegenerate + (2) There are no thermally accessible electronically excited states + (3) Hindered rotations indicated by low frequency modes are not + treated as such but are treated as vibrations and this may + cause some error + (4) All equations used are the standard statistical mechanics + equations for an ideal gas + (5) All vibrations are strictly harmonic + +freq. 252.24 E(vib) ... 0.30 +freq. 557.18 E(vib) ... 0.12 +freq. 613.24 E(vib) ... 0.10 +freq. 803.10 E(vib) ... 0.05 +freq. 840.54 E(vib) ... 0.04 +freq. 876.38 E(vib) ... 0.04 +freq. 954.58 E(vib) ... 0.03 +freq. 965.59 E(vib) ... 0.03 +freq. 980.31 E(vib) ... 0.02 +freq. 1000.25 E(vib) ... 0.02 +freq. 1030.24 E(vib) ... 0.02 +freq. 1101.22 E(vib) ... 0.02 +freq. 1125.95 E(vib) ... 0.01 +freq. 1163.25 E(vib) ... 0.01 +freq. 1191.48 E(vib) ... 0.01 +freq. 1205.00 E(vib) ... 0.01 +freq. 1219.58 E(vib) ... 0.01 +freq. 1239.15 E(vib) ... 0.01 +freq. 1296.43 E(vib) ... 0.01 +freq. 1307.22 E(vib) ... 0.01 +freq. 1323.33 E(vib) ... 0.01 +freq. 1324.02 E(vib) ... 0.01 +freq. 1324.99 E(vib) ... 0.01 +freq. 1483.49 E(vib) ... 0.00 +freq. 1487.62 E(vib) ... 0.00 +freq. 1497.58 E(vib) ... 0.00 +freq. 1498.38 E(vib) ... 0.00 +freq. 1516.09 E(vib) ... 0.00 +freq. 2971.92 E(vib) ... 0.00 +freq. 2972.55 E(vib) ... 0.00 +freq. 2984.88 E(vib) ... 0.00 +freq. 2986.62 E(vib) ... 0.00 +freq. 2999.16 E(vib) ... 0.00 +freq. 3000.31 E(vib) ... 0.00 +freq. 3005.88 E(vib) ... 0.00 +freq. 3008.88 E(vib) ... 0.00 +freq. 3009.44 E(vib) ... 0.00 +freq. 3012.88 E(vib) ... 0.00 + +------------ +INNER ENERGY +------------ + +The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans) + E(el) - is the total energy from the electronic structure calculation + = E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc) + E(ZPE) - the the zero temperature vibrational energy from the frequency calculation + E(vib) - the the finite temperature correction to E(ZPE) due to population + of excited vibrational states + E(rot) - is the rotational thermal energy + E(trans)- is the translational thermal energy + +Summary of contributions to the inner energy U: +Electronic energy ... -15.81431337 Eh +Zero point energy ... 0.13926653 Eh 87.39 kcal/mol +Thermal vibrational correction ... 0.00142864 Eh 0.90 kcal/mol +Thermal rotational correction ... 0.00141627 Eh 0.89 kcal/mol +Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol +----------------------------------------------------------------------- +Total thermal energy -15.67078566 Eh + + +Summary of corrections to the electronic energy: +(perhaps to be used in another calculation) +Total thermal correction 0.00426118 Eh 2.67 kcal/mol +Non-thermal (ZPE) correction 0.13926653 Eh 87.39 kcal/mol +----------------------------------------------------------------------- +Total correction 0.14352771 Eh 90.06 kcal/mol + + +-------- +ENTHALPY +-------- + +The enthalpy is H = U + kB*T + kB is Boltzmann's constant +Total free energy ... -15.67078566 Eh +Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol +----------------------------------------------------------------------- +Total Enthalpy ... -15.66984145 Eh + + +Note: Only C1 symmetry has been detected, increase convergence thresholds + if your molecule has a higher symmetry. Symmetry factor of 1.0 is + used for the rotational entropy correction. + + +Note: Rotational entropy computed according to Herzberg +Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945 +Point Group: C1, Symmetry Number: 1 +Rotational constants in cm-1: 0.219384 0.219301 0.127017 + +Vibrational entropy computed according to the QRRHO of S. Grimme +Chem.Eur.J. 2012 18 9955 + + +------- +ENTROPY +------- + +The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans)) + S(el) - electronic entropy + S(vib) - vibrational entropy + S(rot) - rotational entropy + S(trans)- translational entropy +The entropies will be listed as multiplied by the temperature to get +units of energy + +Electronic entropy ... 0.00000000 Eh 0.00 kcal/mol +Vibrational entropy ... 0.00200620 Eh 1.26 kcal/mol +Rotational entropy ... 0.01191737 Eh 7.48 kcal/mol +Translational entropy ... 0.01836882 Eh 11.53 kcal/mol +----------------------------------------------------------------------- +Final entropy term ... 0.03229240 Eh 20.26 kcal/mol + +In case the symmetry of your molecule has not been determined correctly +or in case you have a reason to use a different symmetry number we print +out the resulting rotational entropy values for sn=1,12 : + -------------------------------------------------------- +| sn= 1 | S(rot)= 0.01191737 Eh 7.48 kcal/mol| +| sn= 2 | S(rot)= 0.01126292 Eh 7.07 kcal/mol| +| sn= 3 | S(rot)= 0.01088009 Eh 6.83 kcal/mol| +| sn= 4 | S(rot)= 0.01060846 Eh 6.66 kcal/mol| +| sn= 5 | S(rot)= 0.01039777 Eh 6.52 kcal/mol| +| sn= 6 | S(rot)= 0.01022563 Eh 6.42 kcal/mol| +| sn= 7 | S(rot)= 0.01008008 Eh 6.33 kcal/mol| +| sn= 8 | S(rot)= 0.00995401 Eh 6.25 kcal/mol| +| sn= 9 | S(rot)= 0.00984280 Eh 6.18 kcal/mol| +| sn=10 | S(rot)= 0.00974332 Eh 6.11 kcal/mol| +| sn=11 | S(rot)= 0.00965333 Eh 6.06 kcal/mol| +| sn=12 | S(rot)= 0.00957117 Eh 6.01 kcal/mol| + -------------------------------------------------------- + + +------------------- +GIBBS FREE ENERGY +------------------- + +The Gibbs free energy is G = H - T*S + +Total enthalpy ... -15.66984145 Eh +Total entropy correction ... -0.03229240 Eh -20.26 kcal/mol +----------------------------------------------------------------------- +Final Gibbs free energy ... -15.70213385 Eh + +For completeness - the Gibbs free energy minus the electronic energy +G-E(el) ... 0.11217952 Eh 70.39 kcal/mol + + + +Timings for individual modules: + +Sum of individual times ... 154.450 sec (= 2.574 min) +Numerical frequency calculation ... 154.328 sec (= 2.572 min) 99.9 % +XTB module ... 0.122 sec (= 0.002 min) 0.1 % + ****ORCA TERMINATED NORMALLY**** +TOTAL RUN TIME: 0 days 0 hours 2 minutes 34 seconds 448 msec diff --git a/cmmde_gui/test/alala/alala/freq/cmmd.xtbrestart b/cmmde_gui/test/alala/alala/freq/cmmd.xtbrestart new file mode 100644 index 0000000000000000000000000000000000000000..5189ccd61205c0d69770471b5d8d4b584f0ad1b3 GIT binary patch literal 1320 zcmXw%do&aX6o-dQD{GsT$7+w*+7N9I6>Y?=wdI-Tk+NELY9?e0Gu~xA3Zt?}$V>*~ zF*Byo7?UyL&T7{p+nSxzOFKv&Nu`HJ6fI}#p7T53z5m^N&$pRCAgC{7u|AUY|47jL zK;sYmh|LR4=|cKS$JE9z@NmN1=HYl;G`=zw-@N9+Q zgpiJ`mFxsP79StT>{aP38dAvNlDZxqs;#^6@SP1E9U}bhyN4G;gK-WwZk`Q_^H~nC zfeGjGm5z~?B`}}qqwCIQfr}QU*~f|niORH@OF@^xFwac`1x(1H9WwXe6vL{C_n#Sf zuwik>5H$j!|8i0WF|`5Rxi&M>BXmfilgGHuLY$rT^)J4~Ms;J)YlH?V@E!=~{ytF! 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0000000..e69de29 diff --git a/cmmde_gui/test/alala/alala/geom.smi b/cmmde_gui/test/alala/alala/geom.smi new file mode 100644 index 0000000..40f2cf3 --- /dev/null +++ b/cmmde_gui/test/alala/alala/geom.smi @@ -0,0 +1 @@ +C1CCCC1 diff --git a/cmmde_gui/test/alala/alala/geom.xyz b/cmmde_gui/test/alala/alala/geom.xyz new file mode 100644 index 0000000..852a0a3 --- /dev/null +++ b/cmmde_gui/test/alala/alala/geom.xyz @@ -0,0 +1,17 @@ +15 + +C 1.25397 -0.08785 0.23611 +C 0.32671 -1.22203 -0.16919 +C -1.08204 -0.67511 0.04351 +C -0.94615 0.84512 0.12208 +C 0.50463 1.15076 -0.22206 +H 2.24075 -0.17292 -0.22757 +H 1.38462 -0.07387 1.32471 +H 0.50883 -2.13310 0.40837 +H 0.47301 -1.46275 -1.22929 +H -1.51394 -1.06263 0.97282 +H -1.74391 -0.97741 -0.77500 +H -1.16963 1.18240 1.14140 +H -1.64010 1.35558 -0.55310 +H 0.86404 2.06064 0.26698 +H 0.61450 1.27994 -1.30545 diff --git a/cmmde_gui/test/alala/alala/run.sh b/cmmde_gui/test/alala/alala/run.sh new file mode 100644 index 0000000..f72e163 --- /dev/null +++ b/cmmde_gui/test/alala/alala/run.sh @@ -0,0 +1,10 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH +export PATH=/home/adit/opt/openmpi411/bin:$PATH +export OMP_NUM_THREADS=1 +cd $PWD +$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe diff --git a/cmmde_gui/test/alala/alala/run_babel.sh b/cmmde_gui/test/alala/alala/run_babel.sh new file mode 100644 index 0000000..0d5d00e --- /dev/null +++ b/cmmde_gui/test/alala/alala/run_babel.sh @@ -0,0 +1,8 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export OMP_NUM_THREADS=1 +cd $PWD +obabel geom.smi -O geom.xyz --gen3d diff --git a/cmmde_gui/test/alala/alala/slurm-2887.out b/cmmde_gui/test/alala/alala/slurm-2887.out new file mode 100644 index 0000000..b7d75ac --- /dev/null +++ b/cmmde_gui/test/alala/alala/slurm-2887.out @@ -0,0 +1 @@ +1 molecule converted diff --git a/cmmde_gui/test/alala/alala/slurm-2888.out b/cmmde_gui/test/alala/alala/slurm-2888.out new file mode 100644 index 0000000..e69de29 diff --git a/cmmde_gui/test/alala/cmmd.engrad b/cmmde_gui/test/alala/cmmd.engrad new file mode 100644 index 0000000..5454e34 --- /dev/null +++ b/cmmde_gui/test/alala/cmmd.engrad @@ -0,0 +1,74 @@ +# +# Number of atoms +# + 15 +# +# The current total energy in Eh +# + -15.814313366050 +# +# The current gradient in Eh/bohr +# + 0.000227495798 + -0.000049478208 + 0.000259008811 + 0.000082454763 + -0.000273081820 + -0.000428388240 + -0.000389851164 + -0.000263790724 + 0.000131258810 + -0.000267765264 + 0.000279977188 + 0.000405328706 + 0.000065519654 + 0.000232417966 + -0.000346430104 + -0.000091428520 + -0.000003594258 + -0.000047833688 + 0.000020375247 + 0.000036476347 + -0.000092535766 + -0.000051248393 + 0.000118951949 + 0.000073438073 + 0.000077590295 + 0.000013581623 + 0.000136037554 + 0.000084963869 + -0.000004747271 + 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b/cmmde_gui/test/alala/cmmd.in @@ -0,0 +1,11 @@ +#CMMDE generated Orca input file +!XTB2 opt +%pal + nprocs 1 +end +%geom + maxiter 9999 +end + +*xyzfile 0 1 geom.xyz + diff --git a/cmmde_gui/test/alala/cmmd.opt b/cmmde_gui/test/alala/cmmd.opt new file mode 100644 index 0000000..3fb272c --- /dev/null +++ b/cmmde_gui/test/alala/cmmd.opt @@ -0,0 +1,1566 @@ + +$orca_opt_file + +$trust + 0.300000000000 + +$epredict + 0.000000000000 + +$ediffsc + 1000.000000000000 + +$ctyp + 3 + +$coordinates + 5 45 + 2.36965988 -0.16601244 0.44618324 0.61739243 -2.30930203 -0.31972276 + -2.04475927 -1.27577301 0.08222198 -1.78796438 1.59704535 0.23069777 + 0.95361250 2.17462125 -0.41963259 4.23440383 -0.32677144 -0.43004498 + 2.61655260 -0.13959407 2.50333911 0.96154935 -4.03097482 0.77170746 + 0.89385936 -2.76419690 -2.32302144 -2.86093198 -2.00807968 1.83836338 + -3.29551230 -1.84703722 -1.46453775 -2.21028038 2.23441218 2.15693341 + -3.09933983 2.56167495 -1.04520752 1.63279897 3.89404526 0.50451908 + 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-0.425267 -0.282352 -0.066173 + 85 -0.425267 -0.282352 -0.066173 + 86 -0.095664 0.506779 0.035010 + 87 -0.425267 -0.282352 -0.066173 + 88 0.000000 0.000000 0.000000 + 89 0.000000 0.000000 0.000000 + diff --git a/cmmde_gui/test/alala/cmmd.out b/cmmde_gui/test/alala/cmmd.out new file mode 100644 index 0000000..afc7efb --- /dev/null +++ b/cmmde_gui/test/alala/cmmd.out @@ -0,0 +1,2742 @@ + + ***************** + * O R C A * + ***************** + + #, + ### + #### + ##### + ###### + ########, + ,,################,,,,, + ,,#################################,, + ,,##########################################,, + ,#########################################, ''#####, + ,#############################################,, '####, + ,##################################################,,,,####, + ,###########'''' ''''############################### + ,#####'' ,,,,##########,,,, '''####''' '#### + ,##' ,,,,###########################,,, '## + ' ,,###'''' '''############,,, + ,,##'' '''############,,,, ,,,,,,###'' + ,#'' '''#######################''' + ' ''''####'''' + ,#######, #######, ,#######, ## + ,#' '#, ## ## ,#' '#, #''# ###### ,####, + ## ## ## ,#' ## #' '# # #' '# + ## ## ####### ## ,######, #####, # # + '#, ,#' ## ## '#, ,#' ,# #, ## #, ,# + '#######' ## ## '#######' #' '# #####' # '####' + + + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship and core code : Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 5.0.2 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Marcus Kettner : VPT2 + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : Initial AUTO-CI + Lucas Lang : DCDCAS + Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, + C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT + MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, + LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, + nearIR, NL-DFT gradient (VV10), updates on ESD, + ML-optimized integration grids + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + Liviu Ungur et al : ANISO software + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 5.1.0 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + Shared memory : Shared parallel matrices + BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED + Core in use : SkylakeX + Copyright (c) 2011-2014, The OpenBLAS Project + + + + +*************************************** +The coordinates will be read from file: geom.xyz +*************************************** + + +Your calculation utilizes the semiempirical GFN2-xTB method +Please cite in your paper: +C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. + + +================================================================================ + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + + +WARNING: Geometry Optimization + ===> : Switching off AutoStart + For restart on a previous wavefunction, please use MOREAD + +WARNING: Found dipole moment calculation with XTB calculation + ===> : Switching off dipole moment calculation + + +WARNING: TRAH-SCF for XTB is not implemented! + ===> : Turning TRAH off! + +================================================================================ + INPUT FILE +================================================================================ +NAME = cmmd.in +| 1> #CMMDE generated Orca input file +| 2> !XTB2 opt +| 3> %pal +| 4> nprocs 1 +| 5> end +| 6> %geom +| 7> maxiter 9999 +| 8> end +| 9> +| 10> *xyzfile 0 1 geom.xyz +| 11> +| 12> +| 13> ****END OF INPUT**** +================================================================================ + + ***************************** + * Geometry Optimization Run * + ***************************** + +Geometry optimization settings: +Update method Update .... BFGS +Choice of coordinates CoordSys .... Z-matrix Internals +Initial Hessian InHess .... Almoef's Model + +Convergence Tolerances: +Energy Change TolE .... 5.0000e-06 Eh +Max. Gradient TolMAXG .... 3.0000e-04 Eh/bohr +RMS Gradient TolRMSG .... 1.0000e-04 Eh/bohr +Max. Displacement TolMAXD .... 4.0000e-03 bohr +RMS Displacement TolRMSD .... 2.0000e-03 bohr +Strict Convergence .... False +------------------------------------------------------------------------------ + ORCA OPTIMIZATION COORDINATE SETUP +------------------------------------------------------------------------------ + +The optimization will be done in new redundant internal coordinates +Making redundant internal coordinates ... (new redundants) done +Evaluating the initial hessian ... (Almloef) done +Evaluating the coordinates ... done +Calculating the B-matrix .... done +Calculating the G-matrix .... done +Diagonalizing the G-matrix .... done +The first mode is .... 51 +The number of degrees of freedom .... 39 + + ----------------------------------------------------------------- + Redundant Internal Coordinates + + + ----------------------------------------------------------------- + Definition Initial Value Approx d2E/dq + ----------------------------------------------------------------- + 1. B(C 1,C 0) 1.5200 0.387533 + 2. B(C 2,C 1) 1.5261 0.378985 + 3. B(C 3,C 2) 1.5283 0.375898 + 4. B(C 4,C 3) 1.5220 0.384658 + 5. B(C 4,C 0) 1.5184 0.389816 + 6. B(H 5,C 0) 1.0936 0.355363 + 7. B(H 6,C 0) 1.0965 0.351602 + 8. B(H 7,C 1) 1.0940 0.354874 + 9. B(H 8,C 1) 1.0969 0.351103 + 10. B(H 9,C 2) 1.0956 0.352775 + 11. B(H 10,C 2) 1.0952 0.353314 + 12. B(H 11,C 3) 1.0967 0.351366 + 13. B(H 12,C 3) 1.0945 0.354152 + 14. B(H 13,C 4) 1.0937 0.355216 + 15. B(H 14,C 4) 1.0966 0.351497 + 16. A(C 4,C 0,H 5) 112.3841 0.325885 + 17. A(C 1,C 0,C 4) 103.1297 0.368316 + 18. A(C 1,C 0,H 5) 112.2933 0.325571 + 19. A(H 5,C 0,H 6) 108.3256 0.289151 + 20. A(C 1,C 0,H 6) 110.2991 0.325002 + 21. A(C 4,C 0,H 6) 110.3632 0.325316 + 22. A(C 2,C 1,H 8) 109.6622 0.323738 + 23. A(C 2,C 1,H 7) 112.2441 0.324306 + 24. A(H 7,C 1,H 8) 107.7743 0.289024 + 25. A(C 0,C 1,H 7) 112.2767 0.325497 + 26. A(C 0,C 1,C 2) 104.9844 0.366541 + 27. A(C 0,C 1,H 8) 109.8821 0.324926 + 28. A(H 9,C 2,H 10) 107.3415 0.289040 + 29. A(C 1,C 2,C 3) 106.3541 0.364632 + 30. A(C 1,C 2,H 10) 110.7808 0.324071 + 31. A(C 3,C 2,H 9) 110.0769 0.323556 + 32. A(C 1,C 2,H 9) 110.8158 0.323990 + 33. A(C 3,C 2,H 10) 111.5139 0.323637 + 34. A(H 11,C 3,H 12) 107.5009 0.288966 + 35. A(C 4,C 3,H 12) 111.7898 0.324990 + 36. A(C 2,C 3,H 12) 112.0750 0.323763 + 37. A(C 4,C 3,H 11) 110.0374 0.324568 + 38. A(C 2,C 3,H 11) 109.6080 0.323343 + 39. A(C 2,C 3,C 4) 105.8354 0.365561 + 40. A(H 13,C 4,H 14) 108.1093 0.289118 + 41. A(C 3,C 4,H 14) 110.0318 0.324588 + 42. A(C 0,C 4,H 14) 110.1672 0.325300 + 43. A(C 3,C 4,H 13) 112.2832 0.325150 + 44. A(C 0,C 4,H 13) 112.4281 0.325863 + 45. A(C 0,C 4,C 3) 103.7901 0.367846 + 46. D(H 7,C 1,C 0,H 5) 80.9311 0.011947 + 47. D(H 7,C 1,C 0,H 6) -39.9976 0.011947 + 48. D(C 2,C 1,C 0,H 5) -156.8515 0.011947 + 49. D(H 7,C 1,C 0,C 4) -157.8535 0.011947 + 50. D(H 8,C 1,C 0,H 6) -159.9281 0.011947 + 51. D(C 2,C 1,C 0,C 4) -35.6361 0.011947 + 52. D(C 2,C 1,C 0,H 6) 82.2198 0.011947 + 53. D(H 8,C 1,C 0,H 5) -38.9994 0.011947 + 54. D(H 8,C 1,C 0,C 4) 82.2160 0.011947 + 55. D(H 9,C 2,C 1,H 7) 20.3280 0.011450 + 56. D(C 3,C 2,C 1,H 8) -100.2882 0.011450 + 57. D(C 3,C 2,C 1,C 0) 17.7131 0.011450 + 58. D(H 10,C 2,C 1,H 8) 21.0534 0.011450 + 59. D(H 9,C 2,C 1,H 8) 140.0881 0.011450 + 60. D(H 10,C 2,C 1,H 7) -98.7067 0.011450 + 61. D(H 10,C 2,C 1,C 0) 139.0547 0.011450 + 62. D(C 3,C 2,C 1,H 7) 139.9516 0.011450 + 63. D(H 9,C 2,C 1,C 0) -101.9106 0.011450 + 64. D(H 12,C 3,C 2,H 9) -110.8121 0.011275 + 65. D(H 12,C 3,C 2,C 1) 129.0845 0.011275 + 66. D(H 11,C 3,C 2,H 10) 127.4851 0.011275 + 67. D(H 11,C 3,C 2,H 9) 8.4601 0.011275 + 68. D(C 4,C 3,C 2,H 9) 127.0880 0.011275 + 69. D(C 4,C 3,C 2,C 1) 6.9845 0.011275 + 70. D(H 11,C 3,C 2,C 1) -111.6433 0.011275 + 71. D(H 12,C 3,C 2,H 10) 8.2128 0.011275 + 72. D(C 4,C 3,C 2,H 10) -113.8871 0.011275 + 73. D(H 13,C 4,C 0,C 1) 161.5189 0.012081 + 74. D(C 3,C 4,C 0,H 6) -77.8722 0.012081 + 75. D(C 3,C 4,C 0,H 5) 161.0924 0.012081 + 76. D(C 3,C 4,C 0,C 1) 39.9387 0.012081 + 77. D(H 14,C 4,C 3,H 12) -33.4345 0.011778 + 78. D(H 14,C 4,C 3,H 11) -152.8096 0.011778 + 79. D(H 13,C 4,C 3,H 12) 87.0267 0.011778 + 80. D(H 13,C 4,C 3,H 11) -32.3484 0.011778 + 81. D(H 13,C 4,C 3,C 2) -150.6910 0.011778 + 82. D(C 0,C 4,C 3,H 12) -151.2963 0.011778 + 83. D(C 0,C 4,C 3,H 11) 89.3286 0.011778 + 84. D(C 0,C 4,C 3,C 2) -29.0139 0.011778 + 85. D(H 14,C 4,C 0,H 6) 164.3599 0.012081 + 86. D(H 14,C 4,C 0,H 5) 43.3246 0.012081 + 87. D(H 14,C 4,C 3,C 2) 88.8478 0.011778 + 88. D(H 14,C 4,C 0,C 1) -77.8292 0.012081 + 89. D(H 13,C 4,C 0,H 6) 43.7080 0.012081 + 90. D(H 13,C 4,C 0,H 5) -77.3273 0.012081 + ----------------------------------------------------------------- + +Number of atoms .... 15 +Number of degrees of freedom .... 90 + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 1 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.253970 -0.087850 0.236110 + C 0.326710 -1.222030 -0.169190 + C -1.082040 -0.675110 0.043510 + C -0.946150 0.845120 0.122080 + C 0.504630 1.150760 -0.222060 + H 2.240750 -0.172920 -0.227570 + H 1.384620 -0.073870 1.324710 + H 0.508830 -2.133100 0.408370 + H 0.473010 -1.462750 -1.229290 + H -1.513940 -1.062630 0.972820 + H -1.743910 -0.977410 -0.775000 + H -1.169630 1.182400 1.141400 + H -1.640100 1.355580 -0.553100 + H 0.864040 2.060640 0.266980 + H 0.614500 1.279940 -1.305450 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.369660 -0.166012 0.446183 + 1 C 6.0000 0 12.011 0.617392 -2.309302 -0.319723 + 2 C 6.0000 0 12.011 -2.044759 -1.275773 0.082222 + 3 C 6.0000 0 12.011 -1.787964 1.597045 0.230698 + 4 C 6.0000 0 12.011 0.953612 2.174621 -0.419633 + 5 H 1.0000 0 1.008 4.234404 -0.326771 -0.430045 + 6 H 1.0000 0 1.008 2.616553 -0.139594 2.503339 + 7 H 1.0000 0 1.008 0.961549 -4.030975 0.771707 + 8 H 1.0000 0 1.008 0.893859 -2.764197 -2.323021 + 9 H 1.0000 0 1.008 -2.860932 -2.008080 1.838363 + 10 H 1.0000 0 1.008 -3.295512 -1.847037 -1.464538 + 11 H 1.0000 0 1.008 -2.210280 2.234412 2.156933 + 12 H 1.0000 0 1.008 -3.099340 2.561675 -1.045208 + 13 H 1.0000 0 1.008 1.632799 3.894045 0.504519 + 14 H 1.0000 0 1.008 1.161237 2.418736 -2.466943 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:59:18.376 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.04531904930793 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0004270 -0.160004E+02 0.266E+00 13.67 0.0 T + 2 -16.0453832 -0.449562E-01 0.158E+00 13.37 1.0 T + 3 -16.0456958 -0.312551E-03 0.831E-01 13.37 1.0 T + 4 -16.0458078 -0.112067E-03 0.803E-02 13.35 1.0 T + 5 -16.0458081 -0.244111E-06 0.462E-03 13.36 5.6 T + 6 -16.0458081 -0.449080E-07 0.200E-03 13.36 12.9 T + 7 -16.0458081 -0.395713E-08 0.530E-04 13.36 48.7 T + 8 -16.0458081 -0.689152E-09 0.104E-04 13.36 249.2 T + + *** convergence criteria satisfied after 8 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6335396 -17.2395 + ... ... ... ... + 9 2.0000 -0.4827275 -13.1357 + 10 2.0000 -0.4415401 -12.0149 + 11 2.0000 -0.4388939 -11.9429 + 12 2.0000 -0.4365247 -11.8784 + 13 2.0000 -0.4363620 -11.8740 + 14 2.0000 -0.4202600 -11.4359 + 15 2.0000 -0.4131029 -11.2411 (HOMO) + 16 0.0776863 2.1140 (LUMO) + 17 0.0785880 2.1385 + 18 0.0830294 2.2593 + 19 0.1250432 3.4026 + 20 0.1388223 3.7775 + ... ... ... + 30 0.3462224 9.4212 + ------------------------------------------------------------- + HL-Gap 0.4907892 Eh 13.3551 eV + Fermi-level -0.1677083 Eh -4.5636 eV + + SCC (total) 0 d, 0 h, 0 min, 0.031 sec + SCC setup ... 0 min, 0.000 sec ( 0.489%) + Dispersion ... 0 min, 0.000 sec ( 0.335%) + classical contributions ... 0 min, 0.000 sec ( 0.126%) + integral evaluation ... 0 min, 0.002 sec ( 5.618%) + iterations ... 0 min, 0.024 sec ( 76.935%) + molecular gradient ... 0 min, 0.005 sec ( 15.823%) + printout ... 0 min, 0.000 sec ( 0.629%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.813823527310 Eh :: + :: gradient norm 0.022707407200 Eh/a0 :: + :: HOMO-LUMO gap 13.355054326678 eV :: + ::.................................................:: + :: SCC energy -16.045808110944 Eh :: + :: -> isotropic ES 0.002215602953 Eh :: + :: -> anisotropic ES 0.004256460236 Eh :: + :: -> anisotropic XC 0.009822111034 Eh :: + :: -> dispersion -0.008145854109 Eh :: + :: repulsion energy 0.231974178511 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.813823527310 Eh | + | GRADIENT NORM 0.022707407200 Eh/α | + | HOMO-LUMO GAP 13.355054326678 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:59:18.420 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.044 sec + * cpu-time: 0 d, 0 h, 0 min, 0.025 sec + * ratio c/w: 0.568 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.031 sec + * cpu-time: 0 d, 0 h, 0 min, 0.013 sec + * ratio c/w: 0.410 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.813823527310 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 15 +Number of internal coordinates .... 90 +Current Energy .... -15.813823527 Eh +Current gradient norm .... 0.022707407 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Evaluating the initial hessian .... (Almloef) done +Projecting the Hessian .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.997969285 +Lowest eigenvalues of augmented Hessian: + -0.000703095 0.011851271 0.014610511 0.045627515 0.045959147 +Length of the computed step .... 0.063826607 +The final length of the internal step .... 0.063826607 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0067279151 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0094581950 RMS(Int)= 0.0067336744 + Iter 1: RMS(Cart)= 0.0000326158 RMS(Int)= 0.0000283370 + Iter 2: RMS(Cart)= 0.0000001703 RMS(Int)= 0.0000001533 + Iter 3: RMS(Cart)= 0.0000000016 RMS(Int)= 0.0000000013 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + RMS gradient 0.0016312823 0.0001000000 NO + MAX gradient 0.0070910449 0.0003000000 NO + RMS step 0.0067279151 0.0020000000 NO + MAX step 0.0192770234 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0102 Max(Angles) 0.32 + Max(Dihed) 0.79 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.5200 -0.004296 0.0057 1.5257 + 2. B(C 2,C 1) 1.5261 -0.006170 0.0087 1.5348 + 3. B(C 3,C 2) 1.5283 -0.007091 0.0102 1.5385 + 4. B(C 4,C 3) 1.5220 -0.005057 0.0069 1.5290 + 5. B(C 4,C 0) 1.5184 -0.004058 0.0053 1.5237 + 6. B(H 5,C 0) 1.0936 0.002177 -0.0032 1.0904 + 7. B(H 6,C 0) 1.0965 0.003068 -0.0046 1.0919 + 8. B(H 7,C 1) 1.0940 0.002576 -0.0038 1.0901 + 9. B(H 8,C 1) 1.0969 0.003094 -0.0047 1.0922 + 10. B(H 9,C 2) 1.0956 0.002937 -0.0044 1.0912 + 11. B(H 10,C 2) 1.0952 0.002998 -0.0045 1.0907 + 12. B(H 11,C 3) 1.0967 0.003132 -0.0047 1.0920 + 13. B(H 12,C 3) 1.0945 0.002871 -0.0043 1.0903 + 14. B(H 13,C 4) 1.0937 0.002299 -0.0034 1.0903 + 15. B(H 14,C 4) 1.0966 0.002975 -0.0045 1.0921 + 16. A(C 4,C 0,H 5) 112.38 -0.000181 0.16 112.55 + 17. A(C 1,C 0,C 4) 103.13 -0.000495 -0.01 103.12 + 18. A(C 1,C 0,H 5) 112.29 0.000177 0.10 112.40 + 19. A(H 5,C 0,H 6) 108.33 0.000036 -0.07 108.26 + 20. A(C 1,C 0,H 6) 110.30 -0.000080 -0.01 110.29 + 21. A(C 4,C 0,H 6) 110.36 0.000540 -0.18 110.18 + 22. A(C 2,C 1,H 8) 109.66 -0.000870 0.28 109.94 + 23. A(C 2,C 1,H 7) 112.24 0.000292 0.01 112.25 + 24. A(H 7,C 1,H 8) 107.77 0.000145 -0.07 107.70 + 25. A(C 0,C 1,H 7) 112.28 -0.000281 0.05 112.33 + 26. A(C 0,C 1,C 2) 104.98 -0.000100 -0.06 104.92 + 27. A(C 0,C 1,H 8) 109.88 0.000804 -0.20 109.68 + 28. A(H 9,C 2,H 10) 107.34 0.000437 -0.15 107.20 + 29. A(C 1,C 2,C 3) 106.35 0.000677 -0.14 106.22 + 30. A(C 1,C 2,H 10) 110.78 -0.000392 0.07 110.85 + 31. A(C 3,C 2,H 9) 110.08 -0.000687 0.21 110.29 + 32. A(C 1,C 2,H 9) 110.82 0.000071 -0.02 110.79 + 33. A(C 3,C 2,H 10) 111.51 -0.000128 0.03 111.54 + 34. A(H 11,C 3,H 12) 107.50 0.000287 -0.10 107.40 + 35. A(C 4,C 3,H 12) 111.79 -0.000205 -0.01 111.78 + 36. A(C 2,C 3,H 12) 112.07 0.000005 0.03 112.10 + 37. A(C 4,C 3,H 11) 110.04 0.000490 -0.12 109.92 + 38. A(C 2,C 3,H 11) 109.61 -0.000934 0.32 109.93 + 39. A(C 2,C 3,C 4) 105.84 0.000338 -0.11 105.72 + 40. A(H 13,C 4,H 14) 108.11 0.000048 -0.06 108.05 + 41. A(C 3,C 4,H 14) 110.03 -0.000554 0.14 110.18 + 42. A(C 0,C 4,H 14) 110.17 0.000850 -0.24 109.92 + 43. A(C 3,C 4,H 13) 112.28 0.000385 0.04 112.32 + 44. A(C 0,C 4,H 13) 112.43 -0.000364 0.15 112.58 + 45. A(C 0,C 4,C 3) 103.79 -0.000368 -0.03 103.76 + 46. D(H 7,C 1,C 0,H 5) 80.93 0.000464 -0.64 80.29 + 47. D(H 7,C 1,C 0,H 6) -40.00 0.000354 -0.62 -40.62 + 48. D(C 2,C 1,C 0,H 5) -156.85 0.000595 -0.64 -157.49 + 49. D(H 7,C 1,C 0,C 4) -157.85 0.000032 -0.40 -158.25 + 50. D(H 8,C 1,C 0,H 6) -159.93 -0.000193 -0.42 -160.35 + 51. D(C 2,C 1,C 0,C 4) -35.64 0.000163 -0.40 -36.03 + 52. D(C 2,C 1,C 0,H 6) 82.22 0.000485 -0.62 81.60 + 53. D(H 8,C 1,C 0,H 5) -39.00 -0.000083 -0.45 -39.44 + 54. D(H 8,C 1,C 0,C 4) 82.22 -0.000515 -0.20 82.01 + 55. D(H 9,C 2,C 1,H 7) 20.33 0.000224 0.03 20.36 + 56. D(C 3,C 2,C 1,H 8) -100.29 -0.000372 0.29 -99.99 + 57. D(C 3,C 2,C 1,C 0) 17.71 0.000085 0.16 17.88 + 58. D(H 10,C 2,C 1,H 8) 21.05 -0.000331 0.29 21.34 + 59. D(H 9,C 2,C 1,H 8) 140.09 0.000008 0.13 140.22 + 60. D(H 10,C 2,C 1,H 7) -98.71 -0.000115 0.18 -98.53 + 61. D(H 10,C 2,C 1,C 0) 139.05 0.000126 0.15 139.21 + 62. D(C 3,C 2,C 1,H 7) 139.95 -0.000156 0.19 140.14 + 63. D(H 9,C 2,C 1,C 0) -101.91 0.000465 0.00 -101.91 + 64. D(H 12,C 3,C 2,H 9) -110.81 0.000109 0.01 -110.80 + 65. D(H 12,C 3,C 2,C 1) 129.08 0.000002 0.00 129.09 + 66. D(H 11,C 3,C 2,H 10) 127.49 -0.000133 0.09 127.58 + 67. D(H 11,C 3,C 2,H 9) 8.46 -0.000148 0.12 8.58 + 68. D(C 4,C 3,C 2,H 9) 127.09 0.000137 0.08 127.17 + 69. D(C 4,C 3,C 2,C 1) 6.98 0.000029 0.07 7.06 + 70. D(H 11,C 3,C 2,C 1) -111.64 -0.000256 0.11 -111.53 + 71. D(H 12,C 3,C 2,H 10) 8.21 0.000124 -0.01 8.20 + 72. D(C 4,C 3,C 2,H 10) -113.89 0.000152 0.06 -113.83 + 73. D(H 13,C 4,C 0,C 1) 161.52 -0.000300 0.58 162.10 + 74. D(C 3,C 4,C 0,H 6) -77.87 -0.000222 0.58 -77.29 + 75. D(C 3,C 4,C 0,H 5) 161.09 -0.000525 0.68 161.78 + 76. D(C 3,C 4,C 0,C 1) 39.94 -0.000335 0.48 40.42 + 77. D(H 14,C 4,C 3,H 12) -33.43 0.000420 -0.49 -33.93 + 78. D(H 14,C 4,C 3,H 11) -152.81 -0.000135 -0.28 -153.09 + 79. D(H 13,C 4,C 3,H 12) 87.03 0.000355 -0.44 86.59 + 80. D(H 13,C 4,C 3,H 11) -32.35 -0.000200 -0.23 -32.58 + 81. D(H 13,C 4,C 3,C 2) -150.69 0.000461 -0.49 -151.18 + 82. D(C 0,C 4,C 3,H 12) -151.30 -0.000109 -0.26 -151.55 + 83. D(C 0,C 4,C 3,H 11) 89.33 -0.000664 -0.05 89.28 + 84. D(C 0,C 4,C 3,C 2) -29.01 -0.000003 -0.31 -29.32 + 85. D(H 14,C 4,C 0,H 6) 164.36 0.000223 0.55 164.91 + 86. D(H 14,C 4,C 0,H 5) 43.32 -0.000080 0.65 43.97 + 87. D(H 14,C 4,C 3,C 2) 88.85 0.000526 -0.54 88.31 + 88. D(H 14,C 4,C 0,C 1) -77.83 0.000110 0.45 -77.38 + 89. D(H 13,C 4,C 0,H 6) 43.71 -0.000186 0.69 44.40 + 90. D(H 13,C 4,C 0,H 5) -77.33 -0.000489 0.79 -76.54 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 2 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.257123 -0.088091 0.238226 + C 0.328826 -1.226976 -0.172935 + C -1.088491 -0.679714 0.044787 + C -0.950523 0.850465 0.125720 + C 0.506368 1.154273 -0.224938 + H 2.245041 -0.172991 -0.215333 + H 1.379029 -0.071943 1.323172 + H 0.512114 -2.137358 0.398053 + H 0.479548 -1.461348 -1.229026 + H -1.516833 -1.070415 0.969225 + H -1.749798 -0.979717 -0.769026 + H -1.167689 1.190610 1.140388 + H -1.642768 1.360747 -0.544398 + H 0.866704 2.064442 0.255169 + H 0.616638 1.274786 -1.304765 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.375619 -0.166468 0.450183 + 1 C 6.0000 0 12.011 0.621391 -2.318648 -0.326800 + 2 C 6.0000 0 12.011 -2.056950 -1.284472 0.084635 + 3 C 6.0000 0 12.011 -1.796228 1.607146 0.237576 + 4 C 6.0000 0 12.011 0.956896 2.181259 -0.425072 + 5 H 1.0000 0 1.008 4.242513 -0.326906 -0.406921 + 6 H 1.0000 0 1.008 2.605988 -0.135952 2.500433 + 7 H 1.0000 0 1.008 0.967755 -4.039021 0.752212 + 8 H 1.0000 0 1.008 0.906214 -2.761547 -2.322522 + 9 H 1.0000 0 1.008 -2.866399 -2.022792 1.831570 + 10 H 1.0000 0 1.008 -3.306639 -1.851397 -1.453248 + 11 H 1.0000 0 1.008 -2.206613 2.249927 2.155022 + 12 H 1.0000 0 1.008 -3.104381 2.571440 -1.028762 + 13 H 1.0000 0 1.008 1.637834 3.901230 0.482199 + 14 H 1.0000 0 1.008 1.165278 2.408997 -2.465649 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:59:18.502 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.86344531130104 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0481639 -0.160482E+02 0.731E-02 13.22 0.0 T + 2 -16.0481684 -0.452038E-05 0.459E-02 13.23 1.0 T + 3 -16.0481684 -0.549547E-07 0.558E-03 13.23 4.6 T + 4 -16.0481684 -0.241912E-08 0.823E-04 13.23 31.4 T + 5 -16.0481684 -0.304503E-10 0.236E-04 13.23 109.6 T + + *** convergence criteria satisfied after 5 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6320181 -17.1981 + ... ... ... ... + 9 2.0000 -0.4822072 -13.1215 + 10 2.0000 -0.4411536 -12.0044 + 11 2.0000 -0.4387072 -11.9378 + 12 2.0000 -0.4364153 -11.8755 + 13 2.0000 -0.4362258 -11.8703 + 14 2.0000 -0.4204451 -11.4409 + 15 2.0000 -0.4139272 -11.2635 (HOMO) + 16 0.0721558 1.9635 (LUMO) + 17 0.0724999 1.9728 + 18 0.0886728 2.4129 + 19 0.1319823 3.5914 + 20 0.1333845 3.6296 + ... ... ... + 30 0.3496123 9.5134 + ------------------------------------------------------------- + HL-Gap 0.4860831 Eh 13.2270 eV + Fermi-level -0.1708857 Eh -4.6500 eV + + SCC (total) 0 d, 0 h, 0 min, 0.012 sec + SCC setup ... 0 min, 0.000 sec ( 1.285%) + Dispersion ... 0 min, 0.000 sec ( 0.899%) + classical contributions ... 0 min, 0.000 sec ( 0.341%) + integral evaluation ... 0 min, 0.002 sec ( 15.511%) + iterations ... 0 min, 0.005 sec ( 40.874%) + molecular gradient ... 0 min, 0.005 sec ( 39.569%) + printout ... 0 min, 0.000 sec ( 1.424%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814241222376 Eh :: + :: gradient norm 0.005064544877 Eh/a0 :: + :: HOMO-LUMO gap 13.226993409773 eV :: + ::.................................................:: + :: SCC energy -16.048168432480 Eh :: + :: -> isotropic ES 0.002305024320 Eh :: + :: -> anisotropic ES 0.004275171918 Eh :: + :: -> anisotropic XC 0.009706949492 Eh :: + :: -> dispersion -0.008130395581 Eh :: + :: repulsion energy 0.233916722051 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814241222376 Eh | + | GRADIENT NORM 0.005064544877 Eh/α | + | HOMO-LUMO GAP 13.226993409773 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:59:18.526 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.024 sec + * cpu-time: 0 d, 0 h, 0 min, 0.023 sec + * ratio c/w: 0.979 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.012 sec + * cpu-time: 0 d, 0 h, 0 min, 0.011 sec + * ratio c/w: 0.956 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814241222380 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 15 +Number of internal coordinates .... 90 +Current Energy .... -15.814241222 Eh +Current gradient norm .... 0.005064545 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.998743425 +Lowest eigenvalues of augmented Hessian: + -0.000064929 0.011851251 0.013592534 0.045406129 0.045899005 +Length of the computed step .... 0.050178623 +The final length of the internal step .... 0.050178623 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0052892913 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0072406891 RMS(Int)= 0.0052881724 + Iter 1: RMS(Cart)= 0.0000247280 RMS(Int)= 0.0000172505 + Iter 2: RMS(Cart)= 0.0000001558 RMS(Int)= 0.0000001513 + Iter 3: RMS(Cart)= 0.0000000013 RMS(Int)= 0.0000000010 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0004176951 0.0000050000 NO + RMS gradient 0.0002952155 0.0001000000 NO + MAX gradient 0.0009148389 0.0003000000 NO + RMS step 0.0052892913 0.0020000000 NO + MAX step 0.0127713249 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0023 Max(Angles) 0.15 + Max(Dihed) 0.73 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.5257 -0.000661 0.0013 1.5270 + 2. B(C 2,C 1) 1.5348 -0.000869 0.0020 1.5368 + 3. B(C 3,C 2) 1.5385 -0.000915 0.0023 1.5408 + 4. B(C 4,C 3) 1.5290 -0.000781 0.0016 1.5306 + 5. B(C 4,C 0) 1.5237 -0.000679 0.0012 1.5249 + 6. B(H 5,C 0) 1.0904 0.000422 -0.0009 1.0894 + 7. B(H 6,C 0) 1.0919 0.000370 -0.0009 1.0910 + 8. B(H 7,C 1) 1.0901 0.000447 -0.0010 1.0891 + 9. B(H 8,C 1) 1.0922 0.000542 -0.0012 1.0910 + 10. B(H 9,C 2) 1.0912 0.000591 -0.0013 1.0899 + 11. B(H 10,C 2) 1.0907 0.000564 -0.0012 1.0894 + 12. B(H 11,C 3) 1.0920 0.000619 -0.0014 1.0906 + 13. B(H 12,C 3) 1.0903 0.000493 -0.0011 1.0891 + 14. B(H 13,C 4) 1.0903 0.000438 -0.0010 1.0893 + 15. B(H 14,C 4) 1.0921 0.000429 -0.0010 1.0911 + 16. A(C 4,C 0,H 5) 112.55 -0.000129 0.10 112.65 + 17. A(C 1,C 0,C 4) 103.12 0.000010 -0.12 103.00 + 18. A(C 1,C 0,H 5) 112.40 0.000043 0.05 112.45 + 19. A(H 5,C 0,H 6) 108.26 -0.000122 0.09 108.35 + 20. A(C 1,C 0,H 6) 110.29 -0.000023 -0.02 110.27 + 21. A(C 4,C 0,H 6) 110.18 0.000236 -0.12 110.06 + 22. A(C 2,C 1,H 8) 109.94 -0.000325 0.14 110.08 + 23. A(C 2,C 1,H 7) 112.25 0.000257 -0.07 112.19 + 24. A(H 7,C 1,H 8) 107.70 -0.000163 0.12 107.82 + 25. A(C 0,C 1,H 7) 112.33 -0.000106 0.01 112.34 + 26. A(C 0,C 1,C 2) 104.92 -0.000011 -0.08 104.84 + 27. A(C 0,C 1,H 8) 109.68 0.000353 -0.12 109.56 + 28. A(H 9,C 2,H 10) 107.19 -0.000136 0.10 107.30 + 29. A(C 1,C 2,C 3) 106.22 0.000072 -0.06 106.16 + 30. A(C 1,C 2,H 10) 110.85 -0.000104 0.01 110.87 + 31. A(C 3,C 2,H 9) 110.29 -0.000203 0.08 110.37 + 32. A(C 1,C 2,H 9) 110.79 0.000196 -0.07 110.73 + 33. A(C 3,C 2,H 10) 111.54 0.000178 -0.07 111.48 + 34. A(H 11,C 3,H 12) 107.40 -0.000160 0.12 107.52 + 35. A(C 4,C 3,H 12) 111.78 -0.000051 -0.03 111.75 + 36. A(C 2,C 3,H 12) 112.10 0.000212 -0.07 112.03 + 37. A(C 4,C 3,H 11) 109.92 0.000274 -0.08 109.84 + 38. A(C 2,C 3,H 11) 109.93 -0.000325 0.14 110.07 + 39. A(C 2,C 3,C 4) 105.72 0.000053 -0.08 105.65 + 40. A(H 13,C 4,H 14) 108.05 -0.000151 0.11 108.16 + 41. A(C 3,C 4,H 14) 110.18 -0.000209 0.07 110.24 + 42. A(C 0,C 4,H 14) 109.92 0.000360 -0.15 109.77 + 43. A(C 3,C 4,H 13) 112.32 0.000203 -0.02 112.30 + 44. A(C 0,C 4,H 13) 112.58 -0.000177 0.09 112.67 + 45. A(C 0,C 4,C 3) 103.75 -0.000014 -0.10 103.65 + 46. D(H 7,C 1,C 0,H 5) 80.29 0.000001 -0.42 79.87 + 47. D(H 7,C 1,C 0,H 6) -40.62 0.000144 -0.56 -41.18 + 48. D(C 2,C 1,C 0,H 5) -157.49 0.000249 -0.55 -158.04 + 49. D(H 7,C 1,C 0,C 4) -158.25 -0.000125 -0.34 -158.59 + 50. D(H 8,C 1,C 0,H 6) -160.35 0.000179 -0.63 -160.98 + 51. D(C 2,C 1,C 0,C 4) -36.03 0.000123 -0.47 -36.50 + 52. D(C 2,C 1,C 0,H 6) 81.60 0.000392 -0.69 80.91 + 53. D(H 8,C 1,C 0,H 5) -39.44 0.000036 -0.49 -39.94 + 54. D(H 8,C 1,C 0,C 4) 82.01 -0.000090 -0.42 81.60 + 55. D(H 9,C 2,C 1,H 7) 20.36 0.000054 0.13 20.48 + 56. D(C 3,C 2,C 1,H 8) -99.99 -0.000296 0.34 -99.65 + 57. D(C 3,C 2,C 1,C 0) 17.88 -0.000049 0.22 18.10 + 58. D(H 10,C 2,C 1,H 8) 21.34 -0.000094 0.23 21.57 + 59. D(H 9,C 2,C 1,H 8) 140.22 -0.000204 0.32 140.55 + 60. D(H 10,C 2,C 1,H 7) -98.53 0.000164 0.03 -98.49 + 61. D(H 10,C 2,C 1,C 0) 139.21 0.000153 0.11 139.32 + 62. D(C 3,C 2,C 1,H 7) 140.14 -0.000038 0.15 140.29 + 63. D(H 9,C 2,C 1,C 0) -101.91 0.000043 0.20 -101.70 + 64. D(H 12,C 3,C 2,H 9) -110.80 0.000239 -0.11 -110.91 + 65. D(H 12,C 3,C 2,C 1) 129.09 0.000073 -0.04 129.05 + 66. D(H 11,C 3,C 2,H 10) 127.58 -0.000232 0.23 127.80 + 67. D(H 11,C 3,C 2,H 9) 8.58 -0.000043 0.09 8.67 + 68. D(C 4,C 3,C 2,H 9) 127.17 0.000143 0.02 127.19 + 69. D(C 4,C 3,C 2,C 1) 7.06 -0.000024 0.10 7.16 + 70. D(H 11,C 3,C 2,C 1) -111.53 -0.000210 0.17 -111.37 + 71. D(H 12,C 3,C 2,H 10) 8.20 0.000051 0.02 8.22 + 72. D(C 4,C 3,C 2,H 10) -113.83 -0.000046 0.16 -113.67 + 73. D(H 13,C 4,C 0,C 1) 162.10 -0.000011 0.50 162.60 + 74. D(C 3,C 4,C 0,H 6) -77.29 -0.000239 0.68 -76.61 + 75. D(C 3,C 4,C 0,H 5) 161.78 -0.000161 0.58 162.35 + 76. D(C 3,C 4,C 0,C 1) 40.42 -0.000152 0.54 40.96 + 77. D(H 14,C 4,C 3,H 12) -33.93 0.000145 -0.43 -34.36 + 78. D(H 14,C 4,C 3,H 11) -153.09 0.000197 -0.51 -153.60 + 79. D(H 13,C 4,C 3,H 12) 86.59 -0.000056 -0.26 86.33 + 80. D(H 13,C 4,C 3,H 11) -32.58 -0.000005 -0.33 -32.91 + 81. D(H 13,C 4,C 3,C 2) -151.18 0.000208 -0.42 -151.59 + 82. D(C 0,C 4,C 3,H 12) -151.55 -0.000169 -0.23 -151.78 + 83. D(C 0,C 4,C 3,H 11) 89.28 -0.000117 -0.30 88.98 + 84. D(C 0,C 4,C 3,C 2) -29.32 0.000095 -0.39 -29.71 + 85. D(H 14,C 4,C 0,H 6) 164.91 -0.000157 0.73 165.64 + 86. D(H 14,C 4,C 0,H 5) 43.97 -0.000079 0.63 44.60 + 87. D(H 14,C 4,C 3,C 2) 88.31 0.000409 -0.59 87.72 + 88. D(H 14,C 4,C 0,C 1) -77.38 -0.000070 0.59 -76.80 + 89. D(H 13,C 4,C 0,H 6) 44.40 -0.000097 0.64 45.04 + 90. D(H 13,C 4,C 0,H 5) -76.54 -0.000020 0.54 -76.00 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 3 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.256840 -0.087971 0.240929 + C 0.329515 -1.227180 -0.176191 + C -1.089636 -0.680681 0.045702 + C -0.950883 0.851597 0.128554 + C 0.506606 1.153997 -0.227959 + H 2.247193 -0.173216 -0.204973 + H 1.369029 -0.069993 1.325991 + H 0.512598 -2.138785 0.390994 + H 0.482449 -1.454647 -1.232210 + H -1.514223 -1.073592 0.969408 + H -1.751405 -0.977871 -0.767095 + H -1.162122 1.192254 1.142832 + H -1.643824 1.361220 -0.539544 + H 0.867356 2.066207 0.245741 + H 0.615797 1.265430 -1.307858 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.375084 -0.166241 0.455289 + 1 C 6.0000 0 12.011 0.622693 -2.319034 -0.332953 + 2 C 6.0000 0 12.011 -2.059113 -1.286301 0.086365 + 3 C 6.0000 0 12.011 -1.796908 1.609286 0.242933 + 4 C 6.0000 0 12.011 0.957346 2.180739 -0.430780 + 5 H 1.0000 0 1.008 4.246579 -0.327331 -0.387344 + 6 H 1.0000 0 1.008 2.587090 -0.132267 2.505760 + 7 H 1.0000 0 1.008 0.968671 -4.041718 0.738872 + 8 H 1.0000 0 1.008 0.911696 -2.748884 -2.328540 + 9 H 1.0000 0 1.008 -2.861466 -2.028795 1.831915 + 10 H 1.0000 0 1.008 -3.309676 -1.847909 -1.449600 + 11 H 1.0000 0 1.008 -2.196092 2.253033 2.159640 + 12 H 1.0000 0 1.008 -3.106377 2.572333 -1.019591 + 13 H 1.0000 0 1.008 1.639064 3.904566 0.464382 + 14 H 1.0000 0 1.008 1.163688 2.391316 -2.471493 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:59:18.602 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.51840533364865 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0488829 -0.160489E+02 0.223E-02 13.19 0.0 T + 2 -16.0488832 -0.334759E-06 0.136E-02 13.19 1.9 T + 3 -16.0488832 -0.530733E-08 0.165E-03 13.19 15.6 T + 4 -16.0488832 -0.105686E-09 0.251E-04 13.19 102.9 T + 5 -16.0488832 -0.115072E-10 0.542E-05 13.19 476.2 T + + *** convergence criteria satisfied after 5 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6317594 -17.1910 + ... ... ... ... + 9 2.0000 -0.4821118 -13.1189 + 10 2.0000 -0.4409588 -11.9991 + 11 2.0000 -0.4384705 -11.9314 + 12 2.0000 -0.4362883 -11.8720 + 13 2.0000 -0.4361380 -11.8679 + 14 2.0000 -0.4207098 -11.4481 + 15 2.0000 -0.4142571 -11.2725 (HOMO) + 16 0.0706137 1.9215 (LUMO) + 17 0.0711297 1.9355 + 18 0.0905748 2.4647 + 19 0.1317725 3.5857 + 20 0.1343975 3.6571 + ... ... ... + 30 0.3513169 9.5598 + ------------------------------------------------------------- + HL-Gap 0.4848708 Eh 13.1940 eV + Fermi-level -0.1718217 Eh -4.6755 eV + + SCC (total) 0 d, 0 h, 0 min, 0.012 sec + SCC setup ... 0 min, 0.000 sec ( 1.328%) + Dispersion ... 0 min, 0.000 sec ( 0.885%) + classical contributions ... 0 min, 0.000 sec ( 0.330%) + integral evaluation ... 0 min, 0.002 sec ( 14.748%) + iterations ... 0 min, 0.005 sec ( 41.718%) + molecular gradient ... 0 min, 0.005 sec ( 39.558%) + printout ... 0 min, 0.000 sec ( 1.343%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814284974998 Eh :: + :: gradient norm 0.001341145210 Eh/a0 :: + :: HOMO-LUMO gap 13.194005848187 eV :: + ::.................................................:: + :: SCC energy -16.048883232525 Eh :: + :: -> isotropic ES 0.002333401920 Eh :: + :: -> anisotropic ES 0.004266749554 Eh :: + :: -> anisotropic XC 0.009690521656 Eh :: + :: -> dispersion -0.008129206700 Eh :: + :: repulsion energy 0.234587788549 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814284974998 Eh | + | GRADIENT NORM 0.001341145210 Eh/α | + | HOMO-LUMO GAP 13.194005848187 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:59:18.626 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.024 sec + * cpu-time: 0 d, 0 h, 0 min, 0.023 sec + * ratio c/w: 0.974 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.012 sec + * cpu-time: 0 d, 0 h, 0 min, 0.011 sec + * ratio c/w: 0.955 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814284975000 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 15 +Number of internal coordinates .... 90 +Current Energy .... -15.814284975 Eh +Current gradient norm .... 0.001341145 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.998367055 +Lowest eigenvalues of augmented Hessian: + -0.000029892 0.007767788 0.011851329 0.045071205 0.045882488 +Length of the computed step .... 0.057218068 +The final length of the internal step .... 0.057218068 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0060313139 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0083484502 RMS(Int)= 0.0060274104 + Iter 1: RMS(Cart)= 0.0000328622 RMS(Int)= 0.0000212088 + Iter 2: RMS(Cart)= 0.0000002431 RMS(Int)= 0.0000002261 + Iter 3: RMS(Cart)= 0.0000000023 RMS(Int)= 0.0000000017 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0000437526 0.0000050000 NO + RMS gradient 0.0001059703 0.0001000000 NO + MAX gradient 0.0002571587 0.0003000000 YES + RMS step 0.0060313139 0.0020000000 NO + MAX step 0.0154142059 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0007 Max(Angles) 0.16 + Max(Dihed) 0.88 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.5270 0.000064 0.0004 1.5274 + 2. B(C 2,C 1) 1.5368 0.000207 0.0006 1.5375 + 3. B(C 3,C 2) 1.5408 0.000257 0.0007 1.5415 + 4. B(C 4,C 3) 1.5306 0.000125 0.0005 1.5311 + 5. B(C 4,C 0) 1.5249 -0.000013 0.0004 1.5253 + 6. B(H 5,C 0) 1.0894 -0.000041 -0.0003 1.0891 + 7. B(H 6,C 0) 1.0910 -0.000159 -0.0001 1.0909 + 8. B(H 7,C 1) 1.0891 -0.000108 -0.0002 1.0889 + 9. B(H 8,C 1) 1.0910 -0.000090 -0.0003 1.0907 + 10. B(H 9,C 2) 1.0899 -0.000082 -0.0004 1.0895 + 11. B(H 10,C 2) 1.0894 -0.000109 -0.0003 1.0891 + 12. B(H 11,C 3) 1.0906 -0.000071 -0.0004 1.0902 + 13. B(H 12,C 3) 1.0891 -0.000125 -0.0002 1.0889 + 14. B(H 13,C 4) 1.0893 -0.000065 -0.0003 1.0891 + 15. B(H 14,C 4) 1.0911 -0.000123 -0.0002 1.0909 + 16. A(C 4,C 0,H 5) 112.65 -0.000081 0.11 112.76 + 17. A(C 1,C 0,C 4) 102.99 0.000058 -0.15 102.84 + 18. A(C 1,C 0,H 5) 112.45 -0.000004 0.06 112.51 + 19. A(H 5,C 0,H 6) 108.35 -0.000097 0.13 108.48 + 20. A(C 1,C 0,H 6) 110.27 0.000026 -0.04 110.23 + 21. A(C 4,C 0,H 6) 110.06 0.000111 -0.12 109.94 + 22. A(C 2,C 1,H 8) 110.08 -0.000089 0.08 110.16 + 23. A(C 2,C 1,H 7) 112.19 0.000125 -0.06 112.13 + 24. A(H 7,C 1,H 8) 107.82 -0.000135 0.15 107.97 + 25. A(C 0,C 1,H 7) 112.34 -0.000057 0.03 112.36 + 26. A(C 0,C 1,C 2) 104.84 0.000017 -0.10 104.74 + 27. A(C 0,C 1,H 8) 109.56 0.000145 -0.11 109.45 + 28. A(H 9,C 2,H 10) 107.30 -0.000163 0.15 107.45 + 29. A(C 1,C 2,C 3) 106.16 -0.000055 -0.05 106.11 + 30. A(C 1,C 2,H 10) 110.87 -0.000025 0.01 110.87 + 31. A(C 3,C 2,H 9) 110.37 -0.000048 0.04 110.41 + 32. A(C 1,C 2,H 9) 110.73 0.000150 -0.08 110.64 + 33. A(C 3,C 2,H 10) 111.48 0.000149 -0.08 111.40 + 34. A(H 11,C 3,H 12) 107.52 -0.000158 0.16 107.69 + 35. A(C 4,C 3,H 12) 111.75 -0.000017 -0.02 111.73 + 36. A(C 2,C 3,H 12) 112.03 0.000136 -0.07 111.96 + 37. A(C 4,C 3,H 11) 109.84 0.000148 -0.09 109.75 + 38. A(C 2,C 3,H 11) 110.07 -0.000087 0.09 110.16 + 39. A(C 2,C 3,C 4) 105.65 -0.000017 -0.07 105.57 + 40. A(H 13,C 4,H 14) 108.16 -0.000114 0.14 108.30 + 41. A(C 3,C 4,H 14) 110.24 -0.000042 0.02 110.27 + 42. A(C 0,C 4,H 14) 109.77 0.000142 -0.13 109.64 + 43. A(C 3,C 4,H 13) 112.30 0.000077 -0.01 112.29 + 44. A(C 0,C 4,H 13) 112.67 -0.000100 0.10 112.77 + 45. A(C 0,C 4,C 3) 103.65 0.000048 -0.13 103.51 + 46. D(H 7,C 1,C 0,H 5) 79.87 -0.000028 -0.47 79.41 + 47. D(H 7,C 1,C 0,H 6) -41.18 0.000080 -0.64 -41.81 + 48. D(C 2,C 1,C 0,H 5) -158.04 0.000104 -0.59 -158.63 + 49. D(H 7,C 1,C 0,C 4) -158.59 -0.000091 -0.40 -158.99 + 50. D(H 8,C 1,C 0,H 6) -160.98 0.000188 -0.77 -161.76 + 51. D(C 2,C 1,C 0,C 4) -36.50 0.000041 -0.52 -37.03 + 52. D(C 2,C 1,C 0,H 6) 80.91 0.000212 -0.76 80.15 + 53. D(H 8,C 1,C 0,H 5) -39.93 0.000080 -0.60 -40.54 + 54. D(H 8,C 1,C 0,C 4) 81.60 0.000017 -0.54 81.06 + 55. D(H 9,C 2,C 1,H 7) 20.48 -0.000015 0.21 20.69 + 56. D(C 3,C 2,C 1,H 8) -99.65 -0.000172 0.40 -99.25 + 57. D(C 3,C 2,C 1,C 0) 18.10 -0.000036 0.25 18.35 + 58. D(H 10,C 2,C 1,H 8) 21.57 -0.000040 0.28 21.85 + 59. D(H 9,C 2,C 1,H 8) 140.55 -0.000163 0.42 140.96 + 60. D(H 10,C 2,C 1,H 7) -98.49 0.000109 0.07 -98.42 + 61. D(H 10,C 2,C 1,C 0) 139.32 0.000096 0.14 139.45 + 62. D(C 3,C 2,C 1,H 7) 140.29 -0.000023 0.19 140.47 + 63. D(H 9,C 2,C 1,C 0) -101.70 -0.000028 0.28 -101.43 + 64. D(H 12,C 3,C 2,H 9) -110.91 0.000149 -0.11 -111.02 + 65. D(H 12,C 3,C 2,C 1) 129.05 0.000029 -0.00 129.05 + 66. D(H 11,C 3,C 2,H 10) 127.80 -0.000159 0.28 128.08 + 67. D(H 11,C 3,C 2,H 9) 8.67 -0.000019 0.11 8.78 + 68. D(C 4,C 3,C 2,H 9) 127.19 0.000102 0.01 127.20 + 69. D(C 4,C 3,C 2,C 1) 7.16 -0.000019 0.11 7.27 + 70. D(H 11,C 3,C 2,C 1) -111.37 -0.000139 0.21 -111.15 + 71. D(H 12,C 3,C 2,H 10) 8.22 0.000009 0.06 8.28 + 72. D(C 4,C 3,C 2,H 10) -113.67 -0.000039 0.18 -113.50 + 73. D(H 13,C 4,C 0,C 1) 162.60 0.000032 0.55 163.15 + 74. D(C 3,C 4,C 0,H 6) -76.61 -0.000149 0.78 -75.83 + 75. D(C 3,C 4,C 0,H 5) 162.35 -0.000048 0.63 162.98 + 76. D(C 3,C 4,C 0,C 1) 40.96 -0.000038 0.59 41.55 + 77. D(H 14,C 4,C 3,H 12) -34.36 0.000071 -0.50 -34.86 + 78. D(H 14,C 4,C 3,H 11) -153.60 0.000182 -0.64 -154.24 + 79. D(H 13,C 4,C 3,H 12) 86.33 -0.000052 -0.31 86.02 + 80. D(H 13,C 4,C 3,H 11) -32.91 0.000059 -0.45 -33.36 + 81. D(H 13,C 4,C 3,C 2) -151.59 0.000094 -0.46 -152.05 + 82. D(C 0,C 4,C 3,H 12) -151.78 -0.000100 -0.29 -152.07 + 83. D(C 0,C 4,C 3,H 11) 88.98 0.000010 -0.42 88.56 + 84. D(C 0,C 4,C 3,C 2) -29.70 0.000046 -0.43 -30.14 + 85. D(H 14,C 4,C 0,H 6) 165.64 -0.000191 0.88 166.52 + 86. D(H 14,C 4,C 0,H 5) 44.60 -0.000091 0.73 45.33 + 87. D(H 14,C 4,C 3,C 2) 87.72 0.000217 -0.65 87.07 + 88. D(H 14,C 4,C 0,C 1) -76.80 -0.000081 0.70 -76.10 + 89. D(H 13,C 4,C 0,H 6) 45.03 -0.000079 0.73 45.77 + 90. D(H 13,C 4,C 0,H 5) -76.00 0.000022 0.58 -75.42 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 4 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.255759 -0.087735 0.244138 + C 0.330030 -1.226385 -0.179456 + C -1.089550 -0.680907 0.046501 + C -0.950251 0.851938 0.131194 + C 0.506593 1.152913 -0.231316 + H 2.249411 -0.173472 -0.193485 + H 1.356785 -0.067973 1.330167 + H 0.512793 -2.140292 0.383710 + H 0.484505 -1.445960 -1.236559 + H -1.510226 -1.075841 0.970688 + H -1.752335 -0.975396 -0.766044 + H -1.155056 1.192253 1.146436 + H -1.644903 1.361314 -0.534953 + H 0.867883 2.068121 0.235501 + H 0.613852 1.254194 -1.312201 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.373041 -0.165795 0.461354 + 1 C 6.0000 0 12.011 0.623666 -2.317532 -0.339122 + 2 C 6.0000 0 12.011 -2.058951 -1.286729 0.087873 + 3 C 6.0000 0 12.011 -1.795713 1.609929 0.247921 + 4 C 6.0000 0 12.011 0.957321 2.178690 -0.437123 + 5 H 1.0000 0 1.008 4.250770 -0.327815 -0.365634 + 6 H 1.0000 0 1.008 2.563951 -0.128451 2.513651 + 7 H 1.0000 0 1.008 0.969038 -4.044566 0.725107 + 8 H 1.0000 0 1.008 0.915581 -2.732469 -2.336759 + 9 H 1.0000 0 1.008 -2.853913 -2.033046 1.834334 + 10 H 1.0000 0 1.008 -3.311434 -1.843231 -1.447613 + 11 H 1.0000 0 1.008 -2.182739 2.253032 2.166451 + 12 H 1.0000 0 1.008 -3.108416 2.572510 -1.010915 + 13 H 1.0000 0 1.008 1.640062 3.908182 0.445032 + 14 H 1.0000 0 1.008 1.160013 2.370084 -2.479701 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:59:18.704 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.61289789058676 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0490204 -0.160490E+02 0.205E-02 13.18 0.0 T + 2 -16.0490204 -0.500114E-07 0.122E-02 13.18 2.1 T + 3 -16.0490204 -0.715285E-08 0.591E-04 13.18 43.7 T + 4 -16.0490204 -0.246786E-09 0.274E-04 13.18 94.3 T + + *** convergence criteria satisfied after 4 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6317548 -17.1909 + ... ... ... ... + 9 2.0000 -0.4820936 -13.1184 + 10 2.0000 -0.4408037 -11.9949 + 11 2.0000 -0.4382078 -11.9242 + 12 2.0000 -0.4362017 -11.8697 + 13 2.0000 -0.4360766 -11.8662 + 14 2.0000 -0.4210091 -11.4562 + 15 2.0000 -0.4144723 -11.2784 (HOMO) + 16 0.0700262 1.9055 (LUMO) + 17 0.0707046 1.9240 + 18 0.0914037 2.4872 + 19 0.1318050 3.5866 + 20 0.1346092 3.6629 + ... ... ... + 30 0.3521963 9.5837 + ------------------------------------------------------------- + HL-Gap 0.4844985 Eh 13.1839 eV + Fermi-level -0.1722231 Eh -4.6864 eV + + SCC (total) 0 d, 0 h, 0 min, 0.029 sec + SCC setup ... 0 min, 0.000 sec ( 0.647%) + Dispersion ... 0 min, 0.000 sec ( 0.394%) + classical contributions ... 0 min, 0.000 sec ( 0.150%) + integral evaluation ... 0 min, 0.002 sec ( 6.765%) + iterations ... 0 min, 0.021 sec ( 74.203%) + molecular gradient ... 0 min, 0.005 sec ( 17.142%) + printout ... 0 min, 0.000 sec ( 0.638%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814304882812 Eh :: + :: gradient norm 0.001602921921 Eh/a0 :: + :: HOMO-LUMO gap 13.183876432817 eV :: + ::.................................................:: + :: SCC energy -16.049020413886 Eh :: + :: -> isotropic ES 0.002345852688 Eh :: + :: -> anisotropic ES 0.004257241237 Eh :: + :: -> anisotropic XC 0.009701964224 Eh :: + :: -> dispersion -0.008131094784 Eh :: + :: repulsion energy 0.234705100573 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814304882812 Eh | + | GRADIENT NORM 0.001602921921 Eh/α | + | HOMO-LUMO GAP 13.183876432817 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:59:18.747 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.043 sec + * cpu-time: 0 d, 0 h, 0 min, 0.026 sec + * ratio c/w: 0.612 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.029 sec + * cpu-time: 0 d, 0 h, 0 min, 0.012 sec + * ratio c/w: 0.414 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814304882810 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 15 +Number of internal coordinates .... 90 +Current Energy .... -15.814304883 Eh +Current gradient norm .... 0.001602922 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999205442 +Lowest eigenvalues of augmented Hessian: + -0.000010844 0.004886037 0.011851371 0.045590400 0.045966844 +Length of the computed step .... 0.039887491 +The final length of the internal step .... 0.039887491 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0042045107 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0057429193 RMS(Int)= 0.0042020683 + Iter 1: RMS(Cart)= 0.0000153504 RMS(Int)= 0.0000096794 + Iter 2: RMS(Cart)= 0.0000000770 RMS(Int)= 0.0000000700 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0000199078 0.0000050000 NO + RMS gradient 0.0001182037 0.0001000000 NO + MAX gradient 0.0004967062 0.0003000000 NO + RMS step 0.0042045107 0.0020000000 NO + MAX step 0.0107828207 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0003 Max(Angles) 0.10 + Max(Dihed) 0.62 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.5274 0.000259 -0.0002 1.5272 + 2. B(C 2,C 1) 1.5375 0.000444 -0.0003 1.5372 + 3. B(C 3,C 2) 1.5415 0.000497 -0.0003 1.5412 + 4. B(C 4,C 3) 1.5311 0.000352 -0.0002 1.5309 + 5. B(C 4,C 0) 1.5253 0.000204 -0.0001 1.5252 + 6. B(H 5,C 0) 1.0891 -0.000141 0.0000 1.0892 + 7. B(H 6,C 0) 1.0909 -0.000215 0.0002 1.0911 + 8. B(H 7,C 1) 1.0889 -0.000189 0.0001 1.0891 + 9. B(H 8,C 1) 1.0907 -0.000229 0.0002 1.0908 + 10. B(H 9,C 2) 1.0895 -0.000231 0.0002 1.0897 + 11. B(H 10,C 2) 1.0891 -0.000234 0.0002 1.0893 + 12. B(H 11,C 3) 1.0902 -0.000240 0.0001 1.0903 + 13. B(H 12,C 3) 1.0889 -0.000216 0.0002 1.0891 + 14. B(H 13,C 4) 1.0891 -0.000160 0.0001 1.0891 + 15. B(H 14,C 4) 1.0909 -0.000213 0.0002 1.0911 + 16. A(C 4,C 0,H 5) 112.76 -0.000032 0.08 112.84 + 17. A(C 1,C 0,C 4) 102.84 0.000032 -0.10 102.74 + 18. A(C 1,C 0,H 5) 112.51 -0.000031 0.05 112.56 + 19. A(H 5,C 0,H 6) 108.48 -0.000032 0.07 108.55 + 20. A(C 1,C 0,H 6) 110.23 0.000051 -0.05 110.18 + 21. A(C 4,C 0,H 6) 109.94 0.000018 -0.07 109.88 + 22. A(C 2,C 1,H 8) 110.16 0.000060 -0.00 110.16 + 23. A(C 2,C 1,H 7) 112.13 -0.000006 -0.01 112.12 + 24. A(H 7,C 1,H 8) 107.97 -0.000041 0.08 108.05 + 25. A(C 0,C 1,H 7) 112.37 -0.000022 0.04 112.40 + 26. A(C 0,C 1,C 2) 104.74 0.000016 -0.06 104.67 + 27. A(C 0,C 1,H 8) 109.45 -0.000002 -0.06 109.40 + 28. A(H 9,C 2,H 10) 107.45 -0.000073 0.09 107.54 + 29. A(C 1,C 2,C 3) 106.11 -0.000070 -0.02 106.08 + 30. A(C 1,C 2,H 10) 110.87 0.000011 0.01 110.88 + 31. A(C 3,C 2,H 9) 110.41 0.000036 0.00 110.41 + 32. A(C 1,C 2,H 9) 110.64 0.000052 -0.05 110.60 + 33. A(C 3,C 2,H 10) 111.40 0.000048 -0.03 111.37 + 34. A(H 11,C 3,H 12) 107.69 -0.000060 0.09 107.78 + 35. A(C 4,C 3,H 12) 111.73 -0.000007 0.01 111.74 + 36. A(C 2,C 3,H 12) 111.96 0.000018 -0.01 111.94 + 37. A(C 4,C 3,H 11) 109.75 0.000030 -0.06 109.69 + 38. A(C 2,C 3,H 11) 110.16 0.000059 0.00 110.16 + 39. A(C 2,C 3,C 4) 105.57 -0.000036 -0.04 105.53 + 40. A(H 13,C 4,H 14) 108.30 -0.000032 0.08 108.38 + 41. A(C 3,C 4,H 14) 110.27 0.000062 -0.02 110.24 + 42. A(C 0,C 4,H 14) 109.64 -0.000008 -0.07 109.57 + 43. A(C 3,C 4,H 13) 112.29 -0.000025 0.02 112.31 + 44. A(C 0,C 4,H 13) 112.77 -0.000032 0.07 112.84 + 45. A(C 0,C 4,C 3) 103.51 0.000041 -0.09 103.42 + 46. D(H 7,C 1,C 0,H 5) 79.41 0.000015 -0.36 79.05 + 47. D(H 7,C 1,C 0,H 6) -41.81 0.000042 -0.45 -42.27 + 48. D(C 2,C 1,C 0,H 5) -158.63 0.000005 -0.38 -159.01 + 49. D(H 7,C 1,C 0,C 4) -158.99 -0.000019 -0.30 -159.30 + 50. D(H 8,C 1,C 0,H 6) -161.76 0.000110 -0.55 -162.30 + 51. D(C 2,C 1,C 0,C 4) -37.03 -0.000029 -0.33 -37.35 + 52. D(C 2,C 1,C 0,H 6) 80.15 0.000032 -0.48 79.67 + 53. D(H 8,C 1,C 0,H 5) -40.54 0.000083 -0.45 -40.99 + 54. D(H 8,C 1,C 0,C 4) 81.06 0.000049 -0.40 80.67 + 55. D(H 9,C 2,C 1,H 7) 20.69 -0.000052 0.20 20.90 + 56. D(C 3,C 2,C 1,H 8) -99.25 -0.000037 0.27 -98.99 + 57. D(C 3,C 2,C 1,C 0) 18.35 -0.000002 0.16 18.52 + 58. D(H 10,C 2,C 1,H 8) 21.85 -0.000017 0.22 22.07 + 59. D(H 9,C 2,C 1,H 8) 140.96 -0.000067 0.30 141.27 + 60. D(H 10,C 2,C 1,H 7) -98.42 -0.000002 0.12 -98.31 + 61. D(H 10,C 2,C 1,C 0) 139.45 0.000019 0.11 139.57 + 62. D(C 3,C 2,C 1,H 7) 140.47 -0.000022 0.17 140.64 + 63. D(H 9,C 2,C 1,C 0) -101.43 -0.000031 0.20 -101.23 + 64. D(H 12,C 3,C 2,H 9) -111.02 0.000016 -0.02 -111.04 + 65. D(H 12,C 3,C 2,C 1) 129.05 -0.000024 0.05 129.10 + 66. D(H 11,C 3,C 2,H 10) 128.08 -0.000045 0.18 128.27 + 67. D(H 11,C 3,C 2,H 9) 8.78 -0.000008 0.09 8.87 + 68. D(C 4,C 3,C 2,H 9) 127.20 0.000037 0.00 127.20 + 69. D(C 4,C 3,C 2,C 1) 7.27 -0.000003 0.07 7.34 + 70. D(H 11,C 3,C 2,C 1) -111.15 -0.000048 0.16 -110.99 + 71. D(H 12,C 3,C 2,H 10) 8.28 -0.000020 0.08 8.36 + 72. D(C 4,C 3,C 2,H 10) -113.50 0.000001 0.09 -113.40 + 73. D(H 13,C 4,C 0,C 1) 163.15 0.000023 0.37 163.52 + 74. D(C 3,C 4,C 0,H 6) -75.83 -0.000039 0.51 -75.32 + 75. D(C 3,C 4,C 0,H 5) 162.98 0.000011 0.41 163.39 + 76. D(C 3,C 4,C 0,C 1) 41.55 0.000045 0.37 41.92 + 77. D(H 14,C 4,C 3,H 12) -34.86 0.000032 -0.38 -35.24 + 78. D(H 14,C 4,C 3,H 11) -154.24 0.000092 -0.46 -154.70 + 79. D(H 13,C 4,C 3,H 12) 86.02 0.000017 -0.28 85.74 + 80. D(H 13,C 4,C 3,H 11) -33.36 0.000077 -0.36 -33.72 + 81. D(H 13,C 4,C 3,C 2) -152.05 0.000012 -0.31 -152.37 + 82. D(C 0,C 4,C 3,H 12) -152.07 -0.000009 -0.24 -152.30 + 83. D(C 0,C 4,C 3,H 11) 88.56 0.000051 -0.32 88.23 + 84. D(C 0,C 4,C 3,C 2) -30.14 -0.000014 -0.27 -30.41 + 85. D(H 14,C 4,C 0,H 6) 166.52 -0.000129 0.62 167.14 + 86. D(H 14,C 4,C 0,H 5) 45.33 -0.000079 0.52 45.85 + 87. D(H 14,C 4,C 3,C 2) 87.07 0.000027 -0.41 86.66 + 88. D(H 14,C 4,C 0,C 1) -76.10 -0.000045 0.48 -75.62 + 89. D(H 13,C 4,C 0,H 6) 45.77 -0.000061 0.51 46.28 + 90. D(H 13,C 4,C 0,H 5) -75.42 -0.000011 0.41 -75.01 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 5 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.254764 -0.087506 0.246357 + C 0.330312 -1.225457 -0.181258 + C -1.088902 -0.680693 0.046834 + C -0.949381 0.851790 0.132471 + C 0.506536 1.151901 -0.233475 + H 2.250907 -0.173582 -0.185613 + H 1.348285 -0.066771 1.333273 + H 0.513007 -2.141451 0.378820 + H 0.485140 -1.439720 -1.239568 + H -1.507362 -1.076489 0.971842 + H -1.752602 -0.974004 -0.765631 + H -1.150114 1.191161 1.149001 + H -1.645670 1.361592 -0.531936 + H 0.868338 2.069444 0.228533 + H 0.612033 1.246555 -1.315330 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.371160 -0.165363 0.465548 + 1 C 6.0000 0 12.011 0.624199 -2.315778 -0.342528 + 2 C 6.0000 0 12.011 -2.057726 -1.286324 0.088503 + 3 C 6.0000 0 12.011 -1.794069 1.609650 0.250334 + 4 C 6.0000 0 12.011 0.957214 2.176778 -0.441204 + 5 H 1.0000 0 1.008 4.253597 -0.328022 -0.350757 + 6 H 1.0000 0 1.008 2.547890 -0.126179 2.519521 + 7 H 1.0000 0 1.008 0.969442 -4.046755 0.715866 + 8 H 1.0000 0 1.008 0.916781 -2.720677 -2.342445 + 9 H 1.0000 0 1.008 -2.848501 -2.034269 1.836515 + 10 H 1.0000 0 1.008 -3.311937 -1.840600 -1.446833 + 11 H 1.0000 0 1.008 -2.173400 2.250968 2.171298 + 12 H 1.0000 0 1.008 -3.109866 2.573036 -1.005213 + 13 H 1.0000 0 1.008 1.640920 3.910683 0.431865 + 14 H 1.0000 0 1.008 1.156575 2.355647 -2.485614 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:59:18.824 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.10135873966339 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0489182 -0.160489E+02 0.136E-02 13.19 0.0 T + 2 -16.0489182 -0.127713E-07 0.804E-03 13.19 3.2 T + 3 -16.0489182 -0.358794E-08 0.399E-04 13.19 64.7 T + 4 -16.0489182 -0.197563E-09 0.195E-04 13.19 132.3 T + + *** convergence criteria satisfied after 4 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6318700 -17.1941 + ... ... ... ... + 9 2.0000 -0.4821051 -13.1187 + 10 2.0000 -0.4407362 -11.9930 + 11 2.0000 -0.4380500 -11.9199 + 12 2.0000 -0.4362018 -11.8697 + 13 2.0000 -0.4360772 -11.8663 + 14 2.0000 -0.4211887 -11.4611 + 15 2.0000 -0.4145210 -11.2797 (HOMO) + 16 0.0701668 1.9093 (LUMO) + 17 0.0709287 1.9301 + 18 0.0914226 2.4877 + 19 0.1321255 3.5953 + 20 0.1343143 3.6549 + ... ... ... + 30 0.3523020 9.5866 + ------------------------------------------------------------- + HL-Gap 0.4846878 Eh 13.1890 eV + Fermi-level -0.1721771 Eh -4.6852 eV + + SCC (total) 0 d, 0 h, 0 min, 0.012 sec + SCC setup ... 0 min, 0.000 sec ( 1.286%) + Dispersion ... 0 min, 0.000 sec ( 0.836%) + classical contributions ... 0 min, 0.000 sec ( 0.336%) + integral evaluation ... 0 min, 0.002 sec ( 15.387%) + iterations ... 0 min, 0.005 sec ( 40.668%) + molecular gradient ... 0 min, 0.005 sec ( 40.086%) + printout ... 0 min, 0.000 sec ( 1.310%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814311679880 Eh :: + :: gradient norm 0.001141863631 Eh/a0 :: + :: HOMO-LUMO gap 13.189027371246 eV :: + ::.................................................:: + :: SCC energy -16.048918175778 Eh :: + :: -> isotropic ES 0.002346087271 Eh :: + :: -> anisotropic ES 0.004248869227 Eh :: + :: -> anisotropic XC 0.009715009573 Eh :: + :: -> dispersion -0.008133598494 Eh :: + :: repulsion energy 0.234596097647 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814311679880 Eh | + | GRADIENT NORM 0.001141863631 Eh/α | + | HOMO-LUMO GAP 13.189027371246 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:59:18.849 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.024 sec + * cpu-time: 0 d, 0 h, 0 min, 0.024 sec + * ratio c/w: 0.978 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.012 sec + * cpu-time: 0 d, 0 h, 0 min, 0.011 sec + * ratio c/w: 0.955 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814311679880 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 15 +Number of internal coordinates .... 90 +Current Energy .... -15.814311680 Eh +Current gradient norm .... 0.001141864 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999880028 +Lowest eigenvalues of augmented Hessian: + -0.000002546 0.004105100 0.011851528 0.045612633 0.045945469 +Length of the computed step .... 0.015491507 +The final length of the internal step .... 0.015491507 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0016329482 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0020702309 RMS(Int)= 0.0016326180 + Iter 1: RMS(Cart)= 0.0000019856 RMS(Int)= 0.0000012638 + Iter 2: RMS(Cart)= 0.0000000036 RMS(Int)= 0.0000000032 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0000067971 0.0000050000 NO + RMS gradient 0.0000635176 0.0001000000 YES + MAX gradient 0.0002263290 0.0003000000 YES + RMS step 0.0016329482 0.0020000000 YES + MAX step 0.0038269066 0.0040000000 YES + ........................................................ + Max(Bonds) 0.0003 Max(Angles) 0.04 + Max(Dihed) 0.22 Max(Improp) 0.00 + --------------------------------------------------------------------- + + Everything but the energy has converged. However, the energy + appears to be close enough to convergence to make sure that the + final evaluation at the new geometry represents the equilibrium energy. + Convergence will therefore be signaled now + + + ***********************HURRAY******************** + *** THE OPTIMIZATION HAS CONVERGED *** + ************************************************* + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + + --- Optimized Parameters --- + (Angstroem and degrees) + + Definition OldVal dE/dq Step FinalVal + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.5272 0.000144 -0.0002 1.5270 + 2. B(C 2,C 1) 1.5372 0.000213 -0.0003 1.5369 + 3. B(C 3,C 2) 1.5412 0.000226 -0.0003 1.5409 + 4. B(C 4,C 3) 1.5309 0.000183 -0.0003 1.5306 + 5. B(C 4,C 0) 1.5252 0.000137 -0.0002 1.5250 + 6. B(H 5,C 0) 1.0892 -0.000064 0.0001 1.0893 + 7. B(H 6,C 0) 1.0911 -0.000090 0.0002 1.0913 + 8. B(H 7,C 1) 1.0891 -0.000071 0.0001 1.0892 + 9. B(H 8,C 1) 1.0908 -0.000124 0.0002 1.0910 + 10. B(H 9,C 2) 1.0897 -0.000118 0.0002 1.0899 + 11. B(H 10,C 2) 1.0893 -0.000103 0.0002 1.0895 + 12. B(H 11,C 3) 1.0903 -0.000135 0.0002 1.0905 + 13. B(H 12,C 3) 1.0891 -0.000082 0.0001 1.0892 + 14. B(H 13,C 4) 1.0891 -0.000067 0.0001 1.0892 + 15. B(H 14,C 4) 1.0911 -0.000102 0.0002 1.0913 + 16. A(C 4,C 0,H 5) 112.84 -0.000002 0.03 112.87 + 17. A(C 1,C 0,C 4) 102.74 -0.000006 -0.03 102.70 + 18. A(C 1,C 0,H 5) 112.56 -0.000029 0.03 112.59 + 19. A(H 5,C 0,H 6) 108.55 0.000013 0.01 108.56 + 20. A(C 1,C 0,H 6) 110.18 0.000040 -0.03 110.15 + 21. A(C 4,C 0,H 6) 109.88 -0.000017 -0.01 109.86 + 22. A(C 2,C 1,H 8) 110.16 0.000084 -0.04 110.12 + 23. A(C 2,C 1,H 7) 112.13 -0.000058 0.03 112.15 + 24. A(H 7,C 1,H 8) 108.05 0.000025 0.00 108.06 + 25. A(C 0,C 1,H 7) 112.41 -0.000005 0.03 112.44 + 26. A(C 0,C 1,C 2) 104.67 0.000002 -0.02 104.65 + 27. A(C 0,C 1,H 8) 109.40 -0.000048 -0.01 109.38 + 28. A(H 9,C 2,H 10) 107.54 0.000017 0.01 107.54 + 29. A(C 1,C 2,C 3) 106.08 -0.000026 -0.01 106.08 + 30. A(C 1,C 2,H 10) 110.88 0.000015 0.01 110.89 + 31. A(C 3,C 2,H 9) 110.41 0.000046 -0.02 110.40 + 32. A(C 1,C 2,H 9) 110.60 -0.000021 -0.00 110.59 + 33. A(C 3,C 2,H 10) 111.37 -0.000031 0.01 111.38 + 34. A(H 11,C 3,H 12) 107.78 0.000021 0.00 107.78 + 35. A(C 4,C 3,H 12) 111.74 -0.000005 0.03 111.77 + 36. A(C 2,C 3,H 12) 111.94 -0.000048 0.03 111.97 + 37. A(C 4,C 3,H 11) 109.69 -0.000027 -0.02 109.67 + 38. A(C 2,C 3,H 11) 110.16 0.000081 -0.04 110.12 + 39. A(C 2,C 3,C 4) 105.53 -0.000020 -0.01 105.52 + 40. A(H 13,C 4,H 14) 108.38 0.000022 0.01 108.39 + 41. A(C 3,C 4,H 14) 110.24 0.000071 -0.03 110.21 + 42. A(C 0,C 4,H 14) 109.57 -0.000049 -0.01 109.57 + 43. A(C 3,C 4,H 13) 112.31 -0.000053 0.03 112.34 + 44. A(C 0,C 4,H 13) 112.84 0.000003 0.03 112.87 + 45. A(C 0,C 4,C 3) 103.42 0.000007 -0.03 103.39 + 46. D(H 7,C 1,C 0,H 5) 79.05 0.000048 -0.17 78.88 + 47. D(H 7,C 1,C 0,H 6) -42.27 0.000023 -0.18 -42.45 + 48. D(C 2,C 1,C 0,H 5) -159.01 -0.000024 -0.13 -159.14 + 49. D(H 7,C 1,C 0,C 4) -159.30 0.000027 -0.14 -159.43 + 50. D(H 8,C 1,C 0,H 6) -162.30 0.000026 -0.20 -162.50 + 51. D(C 2,C 1,C 0,C 4) -37.35 -0.000045 -0.09 -37.45 + 52. D(C 2,C 1,C 0,H 6) 79.67 -0.000050 -0.14 79.53 + 53. D(H 8,C 1,C 0,H 5) -40.99 0.000052 -0.19 -41.17 + 54. D(H 8,C 1,C 0,C 4) 80.67 0.000031 -0.15 80.51 + 55. D(H 9,C 2,C 1,H 7) 20.90 -0.000047 0.12 21.01 + 56. D(C 3,C 2,C 1,H 8) -98.99 0.000032 0.09 -98.90 + 57. D(C 3,C 2,C 1,C 0) 18.52 0.000018 0.05 18.56 + 58. D(H 10,C 2,C 1,H 8) 22.07 -0.000013 0.11 22.17 + 59. D(H 9,C 2,C 1,H 8) 141.27 0.000004 0.11 141.38 + 60. D(H 10,C 2,C 1,H 7) -98.31 -0.000063 0.11 -98.20 + 61. D(H 10,C 2,C 1,C 0) 139.57 -0.000026 0.06 139.63 + 62. D(C 3,C 2,C 1,H 7) 140.64 -0.000019 0.09 140.73 + 63. D(H 9,C 2,C 1,C 0) -101.23 -0.000010 0.07 -101.16 + 64. D(H 12,C 3,C 2,H 9) -111.04 -0.000056 0.05 -110.99 + 65. D(H 12,C 3,C 2,C 1) 129.10 -0.000040 0.07 129.17 + 66. D(H 11,C 3,C 2,H 10) 128.27 0.000025 0.05 128.32 + 67. D(H 11,C 3,C 2,H 9) 8.87 -0.000006 0.05 8.92 + 68. D(C 4,C 3,C 2,H 9) 127.20 -0.000009 0.00 127.21 + 69. D(C 4,C 3,C 2,C 1) 7.34 0.000007 0.02 7.36 + 70. D(H 11,C 3,C 2,C 1) -110.99 0.000010 0.06 -110.93 + 71. D(H 12,C 3,C 2,H 10) 8.36 -0.000025 0.06 8.42 + 72. D(C 4,C 3,C 2,H 10) -113.40 0.000022 0.01 -113.39 + 73. D(H 13,C 4,C 0,C 1) 163.52 -0.000002 0.14 163.66 + 74. D(C 3,C 4,C 0,H 6) -75.32 0.000020 0.16 -75.16 + 75. D(C 3,C 4,C 0,H 5) 163.39 0.000017 0.14 163.53 + 76. D(C 3,C 4,C 0,C 1) 41.92 0.000056 0.11 42.03 + 77. D(H 14,C 4,C 3,H 12) -35.24 0.000018 -0.17 -35.40 + 78. D(H 14,C 4,C 3,H 11) -154.70 0.000013 -0.18 -154.88 + 79. D(H 13,C 4,C 3,H 12) 85.74 0.000060 -0.16 85.58 + 80. D(H 13,C 4,C 3,H 11) -33.72 0.000055 -0.17 -33.90 + 81. D(H 13,C 4,C 3,C 2) -152.37 -0.000015 -0.12 -152.48 + 82. D(C 0,C 4,C 3,H 12) -152.30 0.000039 -0.13 -152.43 + 83. D(C 0,C 4,C 3,H 11) 88.23 0.000034 -0.14 88.10 + 84. D(C 0,C 4,C 3,C 2) -30.41 -0.000035 -0.08 -30.49 + 85. D(H 14,C 4,C 0,H 6) 167.14 -0.000042 0.22 167.36 + 86. D(H 14,C 4,C 0,H 5) 45.85 -0.000046 0.20 46.05 + 87. D(H 14,C 4,C 3,C 2) 86.66 -0.000057 -0.12 86.54 + 88. D(H 14,C 4,C 0,C 1) -75.62 -0.000007 0.17 -75.45 + 89. D(H 13,C 4,C 0,H 6) 46.28 -0.000038 0.20 46.47 + 90. D(H 13,C 4,C 0,H 5) -75.01 -0.000041 0.17 -74.84 + ---------------------------------------------------------------------------- + ******************************************************* + *** FINAL ENERGY EVALUATION AT THE STATIONARY POINT *** + *** (AFTER 5 CYCLES) *** + ******************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.254359 -0.087377 0.247155 + C 0.330425 -1.225019 -0.181593 + C -1.088479 -0.680500 0.046806 + C -0.948922 0.851627 0.132567 + C 0.506553 1.151472 -0.234149 + H 2.251512 -0.173549 -0.182679 + H 1.345388 -0.066448 1.334450 + H 0.513299 -2.142065 0.376923 + H 0.484946 -1.437484 -1.240528 + H -1.506574 -1.076197 0.972249 + H -1.752594 -0.973990 -0.765485 + H -1.148462 1.190193 1.149840 + H -1.646034 1.362100 -0.530685 + H 0.868686 2.069982 0.225902 + H 0.611188 1.244027 -1.316453 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.370395 -0.165119 0.467056 + 1 C 6.0000 0 12.011 0.624412 -2.314951 -0.343162 + 2 C 6.0000 0 12.011 -2.056928 -1.285958 0.088450 + 3 C 6.0000 0 12.011 -1.793202 1.609341 0.250515 + 4 C 6.0000 0 12.011 0.957247 2.175966 -0.442477 + 5 H 1.0000 0 1.008 4.254741 -0.327960 -0.345213 + 6 H 1.0000 0 1.008 2.542415 -0.125568 2.521746 + 7 H 1.0000 0 1.008 0.969995 -4.047917 0.712281 + 8 H 1.0000 0 1.008 0.916414 -2.716451 -2.344258 + 9 H 1.0000 0 1.008 -2.847013 -2.033718 1.837284 + 10 H 1.0000 0 1.008 -3.311923 -1.840575 -1.446556 + 11 H 1.0000 0 1.008 -2.170279 2.249138 2.172882 + 12 H 1.0000 0 1.008 -3.110554 2.573997 -1.002848 + 13 H 1.0000 0 1.008 1.641579 3.911699 0.426893 + 14 H 1.0000 0 1.008 1.154978 2.350870 -2.487736 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:59:18.913 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.48141552839993 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0488369 -0.160488E+02 0.500E-03 13.20 0.0 T + 2 -16.0488369 -0.731859E-08 0.298E-03 13.20 8.7 T + 3 -16.0488369 -0.448981E-09 0.228E-04 13.20 113.0 T + 4 -16.0488369 -0.946798E-11 0.689E-05 13.20 374.8 T + + *** convergence criteria satisfied after 4 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6319477 -17.1962 + ... ... ... ... + 9 2.0000 -0.4821074 -13.1188 + 10 2.0000 -0.4407302 -11.9929 + 11 2.0000 -0.4380154 -11.9190 + 12 2.0000 -0.4362468 -11.8709 + 13 2.0000 -0.4361111 -11.8672 + 14 2.0000 -0.4212283 -11.4622 + 15 2.0000 -0.4144836 -11.2787 (HOMO) + 16 0.0704309 1.9165 (LUMO) + 17 0.0711941 1.9373 + 18 0.0912106 2.4820 + 19 0.1322569 3.5989 + 20 0.1341636 3.6508 + ... ... ... + 30 0.3520732 9.5804 + ------------------------------------------------------------- + HL-Gap 0.4849145 Eh 13.1952 eV + Fermi-level -0.1720264 Eh -4.6811 eV + + SCC (total) 0 d, 0 h, 0 min, 0.012 sec + SCC setup ... 0 min, 0.000 sec ( 1.323%) + Dispersion ... 0 min, 0.000 sec ( 0.868%) + classical contributions ... 0 min, 0.000 sec ( 0.336%) + integral evaluation ... 0 min, 0.002 sec ( 14.873%) + iterations ... 0 min, 0.005 sec ( 39.456%) + molecular gradient ... 0 min, 0.005 sec ( 40.841%) + printout ... 0 min, 0.000 sec ( 2.201%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814313366053 Eh :: + :: gradient norm 0.000497848720 Eh/a0 :: + :: HOMO-LUMO gap 13.195196441405 eV :: + ::.................................................:: + :: SCC energy -16.048836878888 Eh :: + :: -> isotropic ES 0.002342725001 Eh :: + :: -> anisotropic ES 0.004244905299 Eh :: + :: -> anisotropic XC 0.009717418625 Eh :: + :: -> dispersion -0.008134806430 Eh :: + :: repulsion energy 0.234513126374 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814313366053 Eh | + | GRADIENT NORM 0.000497848720 Eh/α | + | HOMO-LUMO GAP 13.195196441405 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:59:18.937 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.024 sec + * cpu-time: 0 d, 0 h, 0 min, 0.023 sec + * ratio c/w: 0.969 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.012 sec + * cpu-time: 0 d, 0 h, 0 min, 0.011 sec + * ratio c/w: 0.937 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814313366050 +------------------------- -------------------- + + *** OPTIMIZATION RUN DONE *** + +Timings for individual modules: + +Sum of individual times ... 0.468 sec (= 0.008 min) +Geometry relaxation ... 0.192 sec (= 0.003 min) 41.0 % +XTB module ... 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4.4033946328E-04 -5.8365610110E-02 6.4928914427E-03 2.1388095472E-03 1.7026726770E-02 + 26 9.1428633366E-02 -2.8199384954E-01 8.8188876567E-02 1.3311093695E-01 1.6795908699E-01 + 27 -1.2500148795E-01 1.3204861199E-01 1.0475430168E-01 3.6842711241E-02 1.2154767710E-01 + 28 -1.2561756230E-01 1.2410758177E-01 1.0513688101E-01 3.1889572953E-02 1.2410167822E-01 + 29 3.3567764047E-01 -2.8712160179E-01 -2.7482914367E-01 -6.5140652417E-02 -3.2863199872E-01 + 30 -2.9280798575E-01 -1.6390580970E-01 1.9860439030E-01 -1.3539590739E-01 2.7305546487E-01 + 31 -1.2438066317E-01 -7.2335087166E-02 8.2872691226E-02 -5.9817161141E-02 1.1416162487E-01 + 32 -3.9327157699E-01 -1.8983883056E-01 2.6983632086E-01 -1.6824557946E-01 3.6895051168E-01 + 33 1.7889072685E-02 6.6607235522E-02 -1.2697494391E-02 -7.4457242288E-03 2.7638270880E-02 + 34 -4.3976201932E-02 -1.1066848005E-01 2.4377985206E-02 2.8114508382E-02 -6.1087743630E-02 + 35 -1.8384028283E-01 -3.4015961400E-01 8.4756307202E-02 1.3259675017E-01 -2.3376928352E-01 + 36 3.2943173907E-01 -9.1392150032E-02 -6.4686505935E-02 -3.4700948288E-01 3.0282600136E-01 + 37 -2.3654853356E-01 6.7284038842E-02 4.4033851881E-02 2.4894744027E-01 -2.1642792926E-01 + 38 3.3287773617E-01 -7.3572428857E-02 -6.6457545147E-02 -3.4930712258E-01 3.1158332871E-01 + 39 8.5670422817E-02 -1.3913908702E-01 2.1441552418E-01 -7.5811596295E-03 -9.2335582065E-02 + 40 2.2050477319E-01 -3.5284557999E-01 5.4935042958E-01 -2.4386932612E-02 -2.3529565495E-01 + 41 1.1680191037E-01 -1.7946671375E-01 2.9741703411E-01 -8.7676375973E-03 -1.2875900264E-01 + 42 -1.1394110478E-04 1.9957011198E-02 1.0691801674E-02 7.6491833756E-03 -6.2179211559E-03 + 43 -6.0623685095E-03 2.6611457136E-02 -5.5722505947E-03 7.4304667838E-03 7.7304076151E-04 + 44 -4.2031229883E-02 -1.6281251086E-01 -2.2009153219E-01 -8.1963566647E-02 1.1363680073E-01 + +# +# The atoms: label mass x y z (in bohrs) +# +$atoms +15 + C 12.01100 2.370395352817 -0.165119353961 0.467055728119 + C 12.01100 0.624412131949 -2.314950932304 -0.343161574722 + C 12.01100 -2.056927759615 -1.285957826935 0.088450162102 + C 12.01100 -1.793202202238 1.609340899461 0.250515117168 + C 12.01100 0.957246671361 2.175966165264 -0.442477210832 + H 1.00800 4.254740993136 -0.327959685002 -0.345213491899 + H 1.00800 2.542414779212 -0.125568188166 2.521745543173 + H 1.00800 0.969994772545 -4.047916766116 0.712280980995 + H 1.00800 0.916414418106 -2.716451472732 -2.344257789036 + H 1.00800 -2.847012969354 -2.033718431842 1.837284122808 + H 1.00800 -3.311922552795 -1.840574580092 -1.446556301222 + H 1.00800 -2.170278796780 2.249138108127 2.172881776807 + H 1.00800 -3.110553923969 2.573996549726 -1.002848448212 + H 1.00800 1.641578571847 3.911698868900 0.426893181903 + H 1.00800 1.154977994402 2.350870091600 -2.487736396235 + +$actual_temperature + 0.000000 + +$frequency_scale_factor + 1.000000 + +$dipole_derivatives +45 + 1.0000000000E-01 0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 2.0000000000E-01 + 1.0000000000E-01 -0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 1.0000000000E-01 -1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 2.0000000000E-01 + 1.0000000000E-01 0.0000000000E+00 1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 -0.0000000000E+00 2.0000000000E-01 + 1.0000000000E-01 -0.0000000000E+00 1.0000000000E-01 + 0.0000000000E+00 1.0000000000E-01 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 2.0000000000E-01 + 1.0000000000E-01 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 1.0000000000E-01 1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 2.0000000000E-01 + -2.0000000000E-01 0.0000000000E+00 1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 1.0000000000E-01 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + -0.0000000000E+00 0.0000000000E+00 -2.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 -2.0000000000E-01 1.0000000000E-01 + 0.0000000000E+00 1.0000000000E-01 -1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 -0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 -0.0000000000E+00 1.0000000000E-01 + -0.0000000000E+00 -0.0000000000E+00 1.0000000000E-01 + 1.0000000000E-01 0.0000000000E+00 -1.0000000000E-01 + -1.0000000000E-01 -0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 -1.0000000000E-01 + -1.0000000000E-01 -0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 1.0000000000E-01 + 0.0000000000E+00 -0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 -0.0000000000E+00 -1.0000000000E-01 + -1.0000000000E-01 1.0000000000E-01 -1.0000000000E-01 + 1.0000000000E-01 -0.0000000000E+00 1.0000000000E-01 + -1.0000000000E-01 0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 -0.0000000000E+00 -1.0000000000E-01 + -1.0000000000E-01 -2.0000000000E-01 -1.0000000000E-01 + 0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 -2.0000000000E-01 + +# +# The IR spectrum +# wavenumber eps Int TX TY TZ +# +$ir_spectrum +45 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + -13.35 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 252.24 0.00015822 0.79956500 0.006793 -0.012199 0.000883 + 557.18 0.00332525 16.80444475 -0.006401 -0.003125 -0.042564 + 613.24 0.00020155 1.01857442 -0.003489 -0.005541 0.007726 + 803.10 0.00257585 13.01731160 -0.006638 0.004376 -0.030622 + 840.54 0.00038498 1.94553063 0.003428 0.006004 0.009753 + 876.38 0.00073464 3.71257432 -0.002562 -0.004049 -0.015448 + 954.58 0.00011539 0.58313879 -0.003609 -0.001996 0.004551 + 965.59 0.00012990 0.65645639 0.004167 0.004871 -0.000943 + 980.31 0.00072888 3.68344180 0.009998 0.009993 -0.005676 + 1000.25 0.00103158 5.21320763 0.004459 0.015939 0.006922 + 1030.24 0.00010245 0.51772262 0.004598 0.002103 0.002338 + 1101.22 0.00013448 0.67959773 0.000215 -0.005072 -0.003513 + 1125.95 0.00113831 5.75255973 0.002735 -0.006389 -0.016346 + 1163.25 0.00015958 0.80646270 -0.001528 0.006282 -0.001007 + 1191.48 0.00006704 0.33878187 -0.001822 -0.003210 -0.001983 + 1205.00 0.00128027 6.46996497 0.005350 -0.004225 -0.016884 + 1219.58 0.00017162 0.86731602 0.001333 0.003743 -0.005303 + 1239.15 0.00073705 3.72474819 -0.004600 -0.006588 0.011002 + 1296.43 0.00095855 4.84412946 -0.007658 -0.012866 -0.002561 + 1307.22 0.00056148 2.83748162 -0.002810 0.001789 -0.011088 + 1323.33 0.00007904 0.39941107 -0.001509 0.001715 -0.003663 + 1324.02 0.00010272 0.51912552 -0.002056 0.003289 0.003027 + 1324.99 0.00032752 1.65516605 0.005816 -0.004043 -0.005192 + 1483.49 0.00022702 1.14729045 0.006418 0.001978 0.001630 + 1487.62 0.00099922 5.04966622 -0.003783 -0.004743 0.013146 + 1497.58 0.00079885 4.03704674 -0.000907 0.010301 0.007716 + 1498.38 0.00094050 4.75288767 0.000107 -0.000655 -0.013980 + 1516.09 0.00023885 1.20705417 -0.004273 -0.005461 -0.001041 + 2971.92 0.00169187 8.55003705 -0.004728 0.011549 0.004682 + 2972.55 0.00030160 1.52418460 -0.005163 -0.001834 -0.001281 + 2984.88 0.00082539 4.17115936 0.007991 0.003960 0.002599 + 2986.62 0.00307726 15.55122166 0.005703 -0.001857 -0.016899 + 2999.16 0.00475957 24.05289995 0.005780 0.000320 0.021488 + 3000.31 0.00240908 12.17451857 -0.004745 -0.015100 -0.000224 + 3005.88 0.03470973 175.40875634 -0.008980 0.004079 0.059213 + 3008.88 0.01427541 72.14208921 -0.029057 -0.025187 0.001377 + 3009.44 0.02549954 128.86420457 0.029874 -0.023499 0.034634 + 3012.88 0.00217129 10.97281054 -0.014390 -0.000813 -0.004143 + + +$end + diff --git a/cmmde_gui/test/alala/freq/cmmd.in b/cmmde_gui/test/alala/freq/cmmd.in new file mode 100644 index 0000000..247d130 --- /dev/null +++ b/cmmde_gui/test/alala/freq/cmmd.in @@ -0,0 +1,13 @@ +#CMMDE generated Orca input file +!XTB2 Numfreq +%pal + nprocs 1 +end + +*xyzfile 0 1 ../cmmd.xyz + +%freq + scalfreq 1 + Temp 298.15 + Pressure 1.0 +end diff --git a/cmmde_gui/test/alala/freq/cmmd.out b/cmmde_gui/test/alala/freq/cmmd.out new file mode 100644 index 0000000..7e68957 --- /dev/null +++ b/cmmde_gui/test/alala/freq/cmmd.out @@ -0,0 +1,1193 @@ + + ***************** + * O R C A * + ***************** + + #, + ### + #### + ##### + ###### + ########, + ,,################,,,,, + ,,#################################,, + ,,##########################################,, + ,#########################################, ''#####, + ,#############################################,, '####, + ,##################################################,,,,####, + ,###########'''' ''''############################### + ,#####'' ,,,,##########,,,, '''####''' '#### + ,##' ,,,,###########################,,, '## + ' ,,###'''' '''############,,, + ,,##'' '''############,,,, ,,,,,,###'' + ,#'' '''#######################''' + ' ''''####'''' + ,#######, #######, ,#######, ## + ,#' '#, ## ## ,#' '#, #''# ###### ,####, + ## ## ## ,#' ## #' '# # #' '# + ## ## ####### ## ,######, #####, # # + '#, ,#' ## ## '#, ,#' ,# #, ## #, ,# + '#######' ## ## '#######' #' '# #####' # '####' + + + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship and core code : Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 5.0.2 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Marcus Kettner : VPT2 + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : Initial AUTO-CI + Lucas Lang : DCDCAS + Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, + C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT + MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, + LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, + nearIR, NL-DFT gradient (VV10), updates on ESD, + ML-optimized integration grids + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + Liviu Ungur et al : ANISO software + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 5.1.0 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + Shared memory : Shared parallel matrices + BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED + Core in use : SkylakeX + Copyright (c) 2011-2014, The OpenBLAS Project + + + + +*************************************** +The coordinates will be read from file: ../cmmd.xyz +*************************************** + + +Your calculation utilizes the semiempirical GFN2-xTB method +Please cite in your paper: +C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. + + +================================================================================ + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + +WARNING: Gradients needed for Numerical Frequencies + ===> : Setting RunTyp to EnGrad + +WARNING: Found dipole moment calculation with XTB calculation + ===> : Switching off dipole moment calculation + + +WARNING: TRAH-SCF for XTB is not implemented! + ===> : Turning TRAH off! + +================================================================================ + INPUT FILE +================================================================================ +NAME = cmmd.in +| 1> #CMMDE generated Orca input file +| 2> !XTB2 Numfreq +| 3> %pal +| 4> nprocs 1 +| 5> end +| 6> +| 7> *xyzfile 0 1 ../cmmd.xyz +| 8> +| 9> %freq +| 10> scalfreq 1 +| 11> Temp 298.15 +| 12> Pressure 1.0 +| 13> end +| 14> +| 15> ****END OF INPUT**** +================================================================================ + + ******************************* + * Energy+Gradient Calculation * + ******************************* + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:59:41.414 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.54618873828428 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0054351 -0.160054E+02 0.262E+00 13.70 0.0 T + 2 -16.0484055 -0.429703E-01 0.153E+00 13.20 1.0 T + 3 -16.0487278 -0.322317E-03 0.804E-01 13.20 1.0 T + 4 -16.0488365 -0.108768E-03 0.796E-02 13.19 1.0 T + 5 -16.0488367 -0.199985E-06 0.579E-03 13.20 4.5 T + 6 -16.0488369 -0.123847E-06 0.221E-03 13.20 11.7 T + 7 -16.0488369 -0.538951E-08 0.667E-04 13.20 38.7 T + 8 -16.0488369 -0.692037E-09 0.113E-04 13.20 229.0 T + + *** convergence criteria satisfied after 8 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6319470 -17.1962 + ... ... ... ... + 9 2.0000 -0.4821072 -13.1188 + 10 2.0000 -0.4407301 -11.9929 + 11 2.0000 -0.4380151 -11.9190 + 12 2.0000 -0.4362468 -11.8709 + 13 2.0000 -0.4361108 -11.8672 + 14 2.0000 -0.4212279 -11.4622 + 15 2.0000 -0.4144832 -11.2787 (HOMO) + 16 0.0704311 1.9165 (LUMO) + 17 0.0711944 1.9373 + 18 0.0912106 2.4820 + 19 0.1322572 3.5989 + 20 0.1341634 3.6508 + ... ... ... + 30 0.3520733 9.5804 + ------------------------------------------------------------- + HL-Gap 0.4849143 Eh 13.1952 eV + Fermi-level -0.1720261 Eh -4.6811 eV + + SCC (total) 0 d, 0 h, 0 min, 0.012 sec + SCC setup ... 0 min, 0.000 sec ( 1.161%) + Dispersion ... 0 min, 0.000 sec ( 0.794%) + classical contributions ... 0 min, 0.000 sec ( 0.308%) + integral evaluation ... 0 min, 0.002 sec ( 13.863%) + iterations ... 0 min, 0.006 sec ( 46.361%) + molecular gradient ... 0 min, 0.004 sec ( 35.935%) + printout ... 0 min, 0.000 sec ( 1.490%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814313366037 Eh :: + :: gradient norm 0.000497859982 Eh/a0 :: + :: HOMO-LUMO gap 13.195188817416 eV :: + ::.................................................:: + :: SCC energy -16.048836878872 Eh :: + :: -> isotropic ES 0.002342731977 Eh :: + :: -> anisotropic ES 0.004244875878 Eh :: + :: -> anisotropic XC 0.009717391897 Eh :: + :: -> dispersion -0.008134804860 Eh :: + :: repulsion energy 0.234513126374 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814313366037 Eh | + | GRADIENT NORM 0.000497859982 Eh/α | + | HOMO-LUMO GAP 13.195188817416 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:59:41.439 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.025 sec + * cpu-time: 0 d, 0 h, 0 min, 0.024 sec + * ratio c/w: 0.966 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.013 sec + * cpu-time: 0 d, 0 h, 0 min, 0.012 sec + * ratio c/w: 0.952 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814313366040 +------------------------- -------------------- + + +---------------------------------------------------------------------------- + ORCA NUMERICAL FREQUENCIES +---------------------------------------------------------------------------- + +Number of atoms ... 15 +Central differences ... used +Number of displacements ... 90 +Numerical increment ... 5.000e-03 bohr +IR-spectrum generation ... on +Raman-spectrum generation ... off +Surface Crossing Hessian ... off + +The output will be reduced. Please look at the following files: +SCF program output ... >cmmd.lastscf +Integral program output ... >cmmd.lastint +Gradient program output ... >cmmd.lastgrad +Dipole moment program output ... >cmmd.lastmom +AutoCI program output ... >cmmd.lastautoci + + << Calculating on displaced geometry 1 (of 90) >> + << Calculating on displaced geometry 2 (of 90) >> + << Calculating on displaced geometry 3 (of 90) >> + << Calculating on displaced geometry 4 (of 90) >> + << Calculating on displaced geometry 5 (of 90) >> + << Calculating on displaced geometry 6 (of 90) >> + << Calculating on displaced geometry 7 (of 90) >> + << Calculating on displaced geometry 8 (of 90) >> + << Calculating on displaced geometry 9 (of 90) >> + << Calculating on displaced geometry 10 (of 90) >> + << Calculating on displaced geometry 11 (of 90) >> + << Calculating on displaced geometry 12 (of 90) >> + << Calculating on displaced geometry 13 (of 90) >> + << Calculating on displaced geometry 14 (of 90) >> + << Calculating on displaced geometry 15 (of 90) >> + << Calculating on displaced geometry 16 (of 90) >> + << Calculating on displaced geometry 17 (of 90) >> + << Calculating on displaced geometry 18 (of 90) >> + << Calculating on displaced geometry 19 (of 90) >> + << Calculating on displaced geometry 20 (of 90) >> + << Calculating on displaced geometry 21 (of 90) >> + << Calculating on displaced geometry 22 (of 90) >> + << Calculating on displaced geometry 23 (of 90) >> + << Calculating on displaced geometry 24 (of 90) >> + << Calculating on displaced geometry 25 (of 90) >> + << Calculating on displaced geometry 26 (of 90) >> + << Calculating on displaced geometry 27 (of 90) >> + << Calculating on displaced geometry 28 (of 90) >> + << Calculating on displaced geometry 29 (of 90) >> + << Calculating on displaced geometry 30 (of 90) >> + << Calculating on displaced geometry 31 (of 90) >> + << Calculating on displaced geometry 32 (of 90) >> + << Calculating on displaced geometry 33 (of 90) >> + << Calculating on displaced geometry 34 (of 90) >> + << Calculating on displaced geometry 35 (of 90) >> + << Calculating on displaced geometry 36 (of 90) >> + << Calculating on displaced geometry 37 (of 90) >> + << Calculating on displaced geometry 38 (of 90) >> + << Calculating on displaced geometry 39 (of 90) >> + << Calculating on displaced geometry 40 (of 90) >> + << Calculating on displaced geometry 41 (of 90) >> + << Calculating on displaced geometry 42 (of 90) >> + << Calculating on displaced geometry 43 (of 90) >> + << Calculating on displaced geometry 44 (of 90) >> + << Calculating on displaced geometry 45 (of 90) >> + << Calculating on displaced geometry 46 (of 90) >> + << Calculating on displaced geometry 47 (of 90) >> + << Calculating on displaced geometry 48 (of 90) >> + << Calculating on displaced geometry 49 (of 90) >> + << Calculating on displaced geometry 50 (of 90) >> + << Calculating on displaced geometry 51 (of 90) >> + << Calculating on displaced geometry 52 (of 90) >> + << Calculating on displaced geometry 53 (of 90) >> + << Calculating on displaced geometry 54 (of 90) >> + << Calculating on displaced geometry 55 (of 90) >> + << Calculating on displaced geometry 56 (of 90) >> + << Calculating on displaced geometry 57 (of 90) >> + << Calculating on displaced geometry 58 (of 90) >> + << Calculating on displaced geometry 59 (of 90) >> + << Calculating on displaced geometry 60 (of 90) >> + << Calculating on displaced geometry 61 (of 90) >> + << Calculating on displaced geometry 62 (of 90) >> + << Calculating on displaced geometry 63 (of 90) >> + << Calculating on displaced geometry 64 (of 90) >> + << Calculating on displaced geometry 65 (of 90) >> + << Calculating on displaced geometry 66 (of 90) >> + << Calculating on displaced geometry 67 (of 90) >> + << Calculating on displaced geometry 68 (of 90) >> + << Calculating on displaced geometry 69 (of 90) >> + << Calculating on displaced geometry 70 (of 90) >> + << Calculating on displaced geometry 71 (of 90) >> + << Calculating on displaced geometry 72 (of 90) >> + << Calculating on displaced geometry 73 (of 90) >> + << Calculating on displaced geometry 74 (of 90) >> + << Calculating on displaced geometry 75 (of 90) >> + << Calculating on displaced geometry 76 (of 90) >> + << Calculating on displaced geometry 77 (of 90) >> + << Calculating on displaced geometry 78 (of 90) >> + << Calculating on displaced geometry 79 (of 90) >> + << Calculating on displaced geometry 80 (of 90) >> + << Calculating on displaced geometry 81 (of 90) >> + << Calculating on displaced geometry 82 (of 90) >> + << Calculating on displaced geometry 83 (of 90) >> + << Calculating on displaced geometry 84 (of 90) >> + << Calculating on displaced geometry 85 (of 90) >> + << Calculating on displaced geometry 86 (of 90) >> + << Calculating on displaced geometry 87 (of 90) >> + << Calculating on displaced geometry 88 (of 90) >> + << Calculating on displaced geometry 89 (of 90) >> + << Calculating on displaced geometry 90 (of 90) >> + +----------------------- +VIBRATIONAL FREQUENCIES +----------------------- + +Scaling factor for frequencies = 1.000000000 (already applied!) + + 0: 0.00 cm**-1 + 1: 0.00 cm**-1 + 2: 0.00 cm**-1 + 3: 0.00 cm**-1 + 4: 0.00 cm**-1 + 5: 0.00 cm**-1 + 6: -13.35 cm**-1 ***imaginary mode*** + 7: 252.24 cm**-1 + 8: 557.18 cm**-1 + 9: 613.24 cm**-1 + 10: 803.10 cm**-1 + 11: 840.54 cm**-1 + 12: 876.38 cm**-1 + 13: 954.58 cm**-1 + 14: 965.59 cm**-1 + 15: 980.31 cm**-1 + 16: 1000.25 cm**-1 + 17: 1030.24 cm**-1 + 18: 1101.22 cm**-1 + 19: 1125.95 cm**-1 + 20: 1163.25 cm**-1 + 21: 1191.48 cm**-1 + 22: 1205.00 cm**-1 + 23: 1219.58 cm**-1 + 24: 1239.15 cm**-1 + 25: 1296.43 cm**-1 + 26: 1307.22 cm**-1 + 27: 1323.33 cm**-1 + 28: 1324.02 cm**-1 + 29: 1324.99 cm**-1 + 30: 1483.49 cm**-1 + 31: 1487.62 cm**-1 + 32: 1497.58 cm**-1 + 33: 1498.38 cm**-1 + 34: 1516.09 cm**-1 + 35: 2971.92 cm**-1 + 36: 2972.55 cm**-1 + 37: 2984.88 cm**-1 + 38: 2986.62 cm**-1 + 39: 2999.16 cm**-1 + 40: 3000.31 cm**-1 + 41: 3005.88 cm**-1 + 42: 3008.88 cm**-1 + 43: 3009.44 cm**-1 + 44: 3012.88 cm**-1 + + +------------ +NORMAL MODES +------------ + +These modes are the cartesian displacements weighted by the diagonal matrix +M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom +Thus, these vectors are normalized but *not* orthogonal + + 0 1 2 3 4 5 + 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 1 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 2 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 7 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 8 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 9 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 10 0.000000 0.000000 0.000000 0.000000 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-0.001500 + 3 0.003379 0.009777 0.006349 + 4 -0.018795 -0.041518 -0.027511 + 5 0.005176 0.016541 0.003390 + 6 -0.024457 0.008525 -0.032456 + 7 -0.015714 0.001203 -0.019579 + 8 0.000413 0.019508 -0.003326 + 9 0.005643 0.028741 -0.027148 + 10 -0.006768 -0.022427 0.022632 + 11 -0.001655 0.018171 -0.006366 + 12 -0.018662 0.001152 0.007792 + 13 -0.044016 0.000912 0.019442 + 14 -0.006382 0.007605 0.000992 + 15 0.377639 -0.360812 -0.221865 + 16 -0.034692 0.030435 0.019298 + 17 -0.176182 0.172082 0.103937 + 18 -0.005276 -0.001966 0.002609 + 19 0.003757 -0.005265 -0.002247 + 20 0.133598 -0.220433 -0.082719 + 21 -0.045092 -0.097607 -0.061496 + 22 0.225313 0.511068 0.318029 + 23 -0.148304 -0.331112 -0.211030 + 24 -0.009914 -0.013444 -0.019639 + 25 0.006493 0.002139 0.017027 + 26 0.088189 0.133111 0.167959 + 27 0.104754 0.036843 0.121548 + 28 0.105137 0.031890 0.124102 + 29 -0.274829 -0.065141 -0.328632 + 30 0.198604 -0.135396 0.273055 + 31 0.082873 -0.059817 0.114162 + 32 0.269836 -0.168246 0.368951 + 33 -0.012697 -0.007446 0.027638 + 34 0.024378 0.028115 -0.061088 + 35 0.084756 0.132597 -0.233769 + 36 -0.064687 -0.347009 0.302826 + 37 0.044034 0.248947 -0.216428 + 38 -0.066458 -0.349307 0.311583 + 39 0.214416 -0.007581 -0.092336 + 40 0.549350 -0.024387 -0.235296 + 41 0.297417 -0.008768 -0.128759 + 42 0.010692 0.007649 -0.006218 + 43 -0.005572 0.007430 0.000773 + 44 -0.220092 -0.081964 0.113637 + + +----------- +IR SPECTRUM +----------- + + Mode freq eps Int T**2 TX TY TZ + cm**-1 L/(mol*cm) km/mol a.u. +---------------------------------------------------------------------------- + 7: 252.24 0.000158 0.80 0.000196 ( 0.006793 -0.012199 0.000883) + 8: 557.18 0.003325 16.80 0.001862 (-0.006401 -0.003125 -0.042564) + 9: 613.24 0.000202 1.02 0.000103 (-0.003489 -0.005541 0.007726) + 10: 803.10 0.002576 13.02 0.001001 (-0.006638 0.004376 -0.030622) + 11: 840.54 0.000385 1.95 0.000143 ( 0.003428 0.006004 0.009753) + 12: 876.38 0.000735 3.71 0.000262 (-0.002562 -0.004049 -0.015448) + 13: 954.58 0.000115 0.58 0.000038 (-0.003609 -0.001996 0.004551) + 14: 965.59 0.000130 0.66 0.000042 ( 0.004167 0.004871 -0.000943) + 15: 980.31 0.000729 3.68 0.000232 ( 0.009998 0.009993 -0.005676) + 16: 1000.25 0.001032 5.21 0.000322 ( 0.004459 0.015939 0.006922) + 17: 1030.24 0.000102 0.52 0.000031 ( 0.004598 0.002103 0.002338) + 18: 1101.22 0.000134 0.68 0.000038 ( 0.000215 -0.005072 -0.003513) + 19: 1125.95 0.001138 5.75 0.000315 ( 0.002735 -0.006389 -0.016346) + 20: 1163.25 0.000160 0.81 0.000043 (-0.001528 0.006282 -0.001007) + 21: 1191.48 0.000067 0.34 0.000018 (-0.001822 -0.003210 -0.001983) + 22: 1205.00 0.001280 6.47 0.000332 ( 0.005350 -0.004225 -0.016884) + 23: 1219.58 0.000172 0.87 0.000044 ( 0.001333 0.003743 -0.005303) + 24: 1239.15 0.000737 3.72 0.000186 (-0.004600 -0.006588 0.011002) + 25: 1296.43 0.000959 4.84 0.000231 (-0.007658 -0.012866 -0.002561) + 26: 1307.22 0.000561 2.84 0.000134 (-0.002810 0.001789 -0.011088) + 27: 1323.33 0.000079 0.40 0.000019 (-0.001509 0.001715 -0.003663) + 28: 1324.02 0.000103 0.52 0.000024 (-0.002056 0.003289 0.003027) + 29: 1324.99 0.000328 1.66 0.000077 ( 0.005816 -0.004043 -0.005192) + 30: 1483.49 0.000227 1.15 0.000048 ( 0.006418 0.001978 0.001630) + 31: 1487.62 0.000999 5.05 0.000210 (-0.003783 -0.004743 0.013146) + 32: 1497.58 0.000799 4.04 0.000166 (-0.000907 0.010301 0.007716) + 33: 1498.38 0.000940 4.75 0.000196 ( 0.000107 -0.000655 -0.013980) + 34: 1516.09 0.000239 1.21 0.000049 (-0.004273 -0.005461 -0.001041) + 35: 2971.92 0.001692 8.55 0.000178 (-0.004728 0.011549 0.004682) + 36: 2972.55 0.000302 1.52 0.000032 (-0.005163 -0.001834 -0.001281) + 37: 2984.88 0.000825 4.17 0.000086 ( 0.007991 0.003960 0.002599) + 38: 2986.62 0.003077 15.55 0.000322 ( 0.005703 -0.001857 -0.016899) + 39: 2999.16 0.004760 24.05 0.000495 ( 0.005780 0.000320 0.021488) + 40: 3000.31 0.002409 12.17 0.000251 (-0.004745 -0.015100 -0.000224) + 41: 3005.88 0.034710 175.41 0.003603 (-0.008980 0.004079 0.059213) + 42: 3008.88 0.014275 72.14 0.001481 (-0.029057 -0.025187 0.001377) + 43: 3009.44 0.025500 128.86 0.002644 ( 0.029874 -0.023499 0.034634) + 44: 3012.88 0.002171 10.97 0.000225 (-0.014390 -0.000813 -0.004143) + +* The epsilon (eps) is given for a Dirac delta lineshape. +** The dipole moment derivative (T) already includes vibrational overlap. + +The first frequency considered to be a vibration is 7 +The total number of vibrations considered is 38 + + +-------------------------- +THERMOCHEMISTRY AT 298.15K +-------------------------- + +Temperature ... 298.15 K +Pressure ... 1.00 atm +Total Mass ... 70.13 AMU + +Throughout the following assumptions are being made: + (1) The electronic state is orbitally nondegenerate + (2) There are no thermally accessible electronically excited states + (3) Hindered rotations indicated by low frequency modes are not + treated as such but are treated as vibrations and this may + cause some error + (4) All equations used are the standard statistical mechanics + equations for an ideal gas + (5) All vibrations are strictly harmonic + +freq. 252.24 E(vib) ... 0.30 +freq. 557.18 E(vib) ... 0.12 +freq. 613.24 E(vib) ... 0.10 +freq. 803.10 E(vib) ... 0.05 +freq. 840.54 E(vib) ... 0.04 +freq. 876.38 E(vib) ... 0.04 +freq. 954.58 E(vib) ... 0.03 +freq. 965.59 E(vib) ... 0.03 +freq. 980.31 E(vib) ... 0.02 +freq. 1000.25 E(vib) ... 0.02 +freq. 1030.24 E(vib) ... 0.02 +freq. 1101.22 E(vib) ... 0.02 +freq. 1125.95 E(vib) ... 0.01 +freq. 1163.25 E(vib) ... 0.01 +freq. 1191.48 E(vib) ... 0.01 +freq. 1205.00 E(vib) ... 0.01 +freq. 1219.58 E(vib) ... 0.01 +freq. 1239.15 E(vib) ... 0.01 +freq. 1296.43 E(vib) ... 0.01 +freq. 1307.22 E(vib) ... 0.01 +freq. 1323.33 E(vib) ... 0.01 +freq. 1324.02 E(vib) ... 0.01 +freq. 1324.99 E(vib) ... 0.01 +freq. 1483.49 E(vib) ... 0.00 +freq. 1487.62 E(vib) ... 0.00 +freq. 1497.58 E(vib) ... 0.00 +freq. 1498.38 E(vib) ... 0.00 +freq. 1516.09 E(vib) ... 0.00 +freq. 2971.92 E(vib) ... 0.00 +freq. 2972.55 E(vib) ... 0.00 +freq. 2984.88 E(vib) ... 0.00 +freq. 2986.62 E(vib) ... 0.00 +freq. 2999.16 E(vib) ... 0.00 +freq. 3000.31 E(vib) ... 0.00 +freq. 3005.88 E(vib) ... 0.00 +freq. 3008.88 E(vib) ... 0.00 +freq. 3009.44 E(vib) ... 0.00 +freq. 3012.88 E(vib) ... 0.00 + +------------ +INNER ENERGY +------------ + +The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans) + E(el) - is the total energy from the electronic structure calculation + = E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc) + E(ZPE) - the the zero temperature vibrational energy from the frequency calculation + E(vib) - the the finite temperature correction to E(ZPE) due to population + of excited vibrational states + E(rot) - is the rotational thermal energy + E(trans)- is the translational thermal energy + +Summary of contributions to the inner energy U: +Electronic energy ... -15.81431337 Eh +Zero point energy ... 0.13926653 Eh 87.39 kcal/mol +Thermal vibrational correction ... 0.00142864 Eh 0.90 kcal/mol +Thermal rotational correction ... 0.00141627 Eh 0.89 kcal/mol +Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol +----------------------------------------------------------------------- +Total thermal energy -15.67078566 Eh + + +Summary of corrections to the electronic energy: +(perhaps to be used in another calculation) +Total thermal correction 0.00426118 Eh 2.67 kcal/mol +Non-thermal (ZPE) correction 0.13926653 Eh 87.39 kcal/mol +----------------------------------------------------------------------- +Total correction 0.14352771 Eh 90.06 kcal/mol + + +-------- +ENTHALPY +-------- + +The enthalpy is H = U + kB*T + kB is Boltzmann's constant +Total free energy ... -15.67078566 Eh +Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol +----------------------------------------------------------------------- +Total Enthalpy ... -15.66984145 Eh + + +Note: Only C1 symmetry has been detected, increase convergence thresholds + if your molecule has a higher symmetry. Symmetry factor of 1.0 is + used for the rotational entropy correction. + + +Note: Rotational entropy computed according to Herzberg +Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945 +Point Group: C1, Symmetry Number: 1 +Rotational constants in cm-1: 0.219384 0.219301 0.127017 + +Vibrational entropy computed according to the QRRHO of S. Grimme +Chem.Eur.J. 2012 18 9955 + + +------- +ENTROPY +------- + +The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans)) + S(el) - electronic entropy + S(vib) - vibrational entropy + S(rot) - rotational entropy + S(trans)- translational entropy +The entropies will be listed as multiplied by the temperature to get +units of energy + +Electronic entropy ... 0.00000000 Eh 0.00 kcal/mol +Vibrational entropy ... 0.00200620 Eh 1.26 kcal/mol +Rotational entropy ... 0.01191737 Eh 7.48 kcal/mol +Translational entropy ... 0.01836882 Eh 11.53 kcal/mol +----------------------------------------------------------------------- +Final entropy term ... 0.03229240 Eh 20.26 kcal/mol + +In case the symmetry of your molecule has not been determined correctly +or in case you have a reason to use a different symmetry number we print +out the resulting rotational entropy values for sn=1,12 : + -------------------------------------------------------- +| sn= 1 | S(rot)= 0.01191737 Eh 7.48 kcal/mol| +| sn= 2 | S(rot)= 0.01126292 Eh 7.07 kcal/mol| +| sn= 3 | S(rot)= 0.01088009 Eh 6.83 kcal/mol| +| sn= 4 | S(rot)= 0.01060846 Eh 6.66 kcal/mol| +| sn= 5 | S(rot)= 0.01039777 Eh 6.52 kcal/mol| +| sn= 6 | S(rot)= 0.01022563 Eh 6.42 kcal/mol| +| sn= 7 | S(rot)= 0.01008008 Eh 6.33 kcal/mol| +| sn= 8 | S(rot)= 0.00995401 Eh 6.25 kcal/mol| +| sn= 9 | S(rot)= 0.00984280 Eh 6.18 kcal/mol| +| sn=10 | S(rot)= 0.00974332 Eh 6.11 kcal/mol| +| sn=11 | S(rot)= 0.00965333 Eh 6.06 kcal/mol| +| sn=12 | S(rot)= 0.00957117 Eh 6.01 kcal/mol| + -------------------------------------------------------- + + +------------------- +GIBBS FREE ENERGY +------------------- + +The Gibbs free energy is G = H - T*S + +Total enthalpy ... -15.66984145 Eh +Total entropy correction ... -0.03229240 Eh -20.26 kcal/mol +----------------------------------------------------------------------- +Final Gibbs free energy ... -15.70213385 Eh + +For completeness - the Gibbs free energy minus the electronic energy +G-E(el) ... 0.11217952 Eh 70.39 kcal/mol + + + +Timings for individual modules: + +Sum of individual times ... 152.038 sec (= 2.534 min) +Numerical frequency calculation ... 151.959 sec (= 2.533 min) 99.9 % +XTB module ... 0.079 sec (= 0.001 min) 0.1 % + ****ORCA TERMINATED NORMALLY**** +TOTAL RUN TIME: 0 days 0 hours 2 minutes 32 seconds 57 msec diff --git a/cmmde_gui/test/alala/freq/cmmd.xtbrestart b/cmmde_gui/test/alala/freq/cmmd.xtbrestart new file mode 100644 index 0000000000000000000000000000000000000000..5189ccd61205c0d69770471b5d8d4b584f0ad1b3 GIT binary patch literal 1320 zcmXw%do&aX6o-dQD{GsT$7+w*+7N9I6>Y?=wdI-Tk+NELY9?e0Gu~xA3Zt?}$V>*~ zF*Byo7?UyL&T7{p+nSxzOFKv&Nu`HJ6fI}#p7T53z5m^N&$pRCAgC{7u|AUY|47jL zK;sYmh|LR4=|cKS$JE9z@NmN1=HYl;G`=zw-@N9+Q zgpiJ`mFxsP79StT>{aP38dAvNlDZxqs;#^6@SP1E9U}bhyN4G;gK-WwZk`Q_^H~nC zfeGjGm5z~?B`}}qqwCIQfr}QU*~f|niORH@OF@^xFwac`1x(1H9WwXe6vL{C_n#Sf zuwik>5H$j!|8i0WF|`5Rxi&M>BXmfilgGHuLY$rT^)J4~Ms;J)YlH?V@E!=~{ytF! ztrJq!QDZ6C-7+g2wx|W=ersmQ>onA(n!CvI#n8Az{K9^>7#XQHExbTBiY5bBIzFjD z>(PLdwMq%PEu-8U4-$Z<#QO*8^=3G@zN~VM!5K^uIna{>`S>YME0pP*29#dKHd5jd z@ZZ$nZ&Z)a(rmhM&gddEn%W9tJezRC7d1n6S|U)snS0?|l?&NU9l65ih1kgZC;j`r z7Ch^*Rp<4*b23@9Y+P15X1gH69@x)!G*F8;cEK_U`^cH8K?INUwi`)+R6 zS?Hxj-<}tBK&nL;cs;ldXO?=*g%9Uo=iQFy&&JzP%F-=8@J%~31#hc*UCo2!(#o-# z))MHyf6&80GY{%y@ew1?0DWGWtArX|$WmT+>hib-gQEstdDV;X=-a|*e(4Q(b_Vk9 zEaPLhL~%suT@5ajm`k6x-@>yhp7`;VCWxAEysUmf0$Z2A(k411bX8EF_N|xT;hZ7~ znHYtmll%Io68^${=GkAyCH?^h{j!t|`N5`T+?@N*p=XxuOCC#sV$WFO;E;rq4S1i5MskTOzksQ1F$& zKF)|#h1!+VW&txn;AgqD+sh{lUvLKOL#Knmgv|3BJ?;#QSXaSSjsS*c&BB=RC0M9a z>$UM|21Ybb>AdYIfB(;MrD1Vaqfoyl4%GIV z{K!qO#_ocIM~|GtP-mL_$uTPiSi!O_t6%b9FvPpSVQCrGO>{lMZIS5Epe8TSi^4X0 z8y0Un3&m98G0W|_*w6Mpu5ji++JII|r)DIczu1^08x6!>rCqM%eF5I{3-74jTn_5v zAvzYFxsZ9TW!K}~Oo+c5JE{9`8OC~t?J()h1FB_-Zd* cmmd.out --oversubscribe diff --git a/cmmde_gui/test/alala/freq/slurm-2889.out b/cmmde_gui/test/alala/freq/slurm-2889.out new file mode 100644 index 0000000..e69de29 diff --git a/cmmde_gui/test/alala/geom.smi b/cmmde_gui/test/alala/geom.smi new file mode 100644 index 0000000..40f2cf3 --- /dev/null +++ b/cmmde_gui/test/alala/geom.smi @@ -0,0 +1 @@ +C1CCCC1 diff --git a/cmmde_gui/test/alala/geom.xyz b/cmmde_gui/test/alala/geom.xyz new file mode 100644 index 0000000..852a0a3 --- /dev/null +++ b/cmmde_gui/test/alala/geom.xyz @@ -0,0 +1,17 @@ +15 + +C 1.25397 -0.08785 0.23611 +C 0.32671 -1.22203 -0.16919 +C -1.08204 -0.67511 0.04351 +C -0.94615 0.84512 0.12208 +C 0.50463 1.15076 -0.22206 +H 2.24075 -0.17292 -0.22757 +H 1.38462 -0.07387 1.32471 +H 0.50883 -2.13310 0.40837 +H 0.47301 -1.46275 -1.22929 +H -1.51394 -1.06263 0.97282 +H -1.74391 -0.97741 -0.77500 +H -1.16963 1.18240 1.14140 +H -1.64010 1.35558 -0.55310 +H 0.86404 2.06064 0.26698 +H 0.61450 1.27994 -1.30545 diff --git a/cmmde_gui/test/alala/run.sh b/cmmde_gui/test/alala/run.sh new file mode 100644 index 0000000..f72e163 --- /dev/null +++ b/cmmde_gui/test/alala/run.sh @@ -0,0 +1,10 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH +export PATH=/home/adit/opt/openmpi411/bin:$PATH +export OMP_NUM_THREADS=1 +cd $PWD +$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe diff --git a/cmmde_gui/test/alala/run_babel.sh b/cmmde_gui/test/alala/run_babel.sh new file mode 100644 index 0000000..0d5d00e --- /dev/null +++ b/cmmde_gui/test/alala/run_babel.sh @@ -0,0 +1,8 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export OMP_NUM_THREADS=1 +cd $PWD +obabel geom.smi -O geom.xyz --gen3d diff --git a/cmmde_gui/test/alala/slurm-2885.out b/cmmde_gui/test/alala/slurm-2885.out new file mode 100644 index 0000000..b7d75ac --- /dev/null +++ b/cmmde_gui/test/alala/slurm-2885.out @@ -0,0 +1 @@ +1 molecule converted diff --git a/cmmde_gui/test/alala/slurm-2886.out b/cmmde_gui/test/alala/slurm-2886.out new file mode 100644 index 0000000..e69de29 diff --git a/cmmde_gui/test/metana3/cmmd.engrad b/cmmde_gui/test/metana3/cmmd.engrad new file mode 100644 index 0000000..45979cd --- /dev/null +++ b/cmmde_gui/test/metana3/cmmd.engrad @@ -0,0 +1,34 @@ +# +# Number of atoms +# + 5 +# +# The current total energy in Eh +# + -4.175218519970 +# +# The current gradient in Eh/bohr +# + -0.000000733096 + -0.000000718518 + 0.000000020579 + 0.000099514185 + 0.000000241014 + -0.000000088710 + -0.000033024105 + -0.000054585621 + 0.000075974379 + -0.000032878360 + -0.000038400839 + -0.000085447395 + -0.000032878624 + 0.000093463963 + 0.000009541147 +# +# The atomic numbers and current coordinates in Bohr +# + 6 1.9735191 0.1551682 0.0678978 + 1 4.0185060 0.1551840 0.0678980 + 1 1.2918650 -0.9719763 1.6321424 + 1 1.2918649 -0.6359402 -1.6903579 + 1 1.2918469 2.0734103 0.2619089 diff --git a/cmmde_gui/test/metana3/cmmd.gbw b/cmmde_gui/test/metana3/cmmd.gbw new file mode 100644 index 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-0.460970 -0.162152 -0.016400 + 7 0.230484 0.123684 -0.413080 + 8 0.230484 0.038468 0.429480 + 9 0.000000 0.000000 0.000000 + diff --git a/cmmde_gui/test/metana3/cmmd.out b/cmmde_gui/test/metana3/cmmd.out new file mode 100644 index 0000000..2083d90 --- /dev/null +++ b/cmmde_gui/test/metana3/cmmd.out @@ -0,0 +1,1136 @@ + + ***************** + * O R C A * + ***************** + + #, + ### + #### + ##### + ###### + ########, + ,,################,,,,, + ,,#################################,, + ,,##########################################,, + ,#########################################, ''#####, + ,#############################################,, '####, + ,##################################################,,,,####, + ,###########'''' ''''############################### + ,#####'' ,,,,##########,,,, '''####''' '#### + ,##' ,,,,###########################,,, '## + ' ,,###'''' '''############,,, + ,,##'' '''############,,,, ,,,,,,###'' + ,#'' '''#######################''' + ' ''''####'''' + ,#######, #######, ,#######, ## + ,#' '#, ## ## ,#' '#, #''# ###### ,####, + ## ## ## ,#' ## #' '# # #' '# + ## ## ####### ## ,######, #####, # # + '#, ,#' ## ## '#, ,#' ,# #, ## #, ,# + '#######' ## ## '#######' #' '# #####' # '####' + + + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship and core code : Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 5.0.2 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Marcus Kettner : VPT2 + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : Initial AUTO-CI + Lucas Lang : DCDCAS + Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, + C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT + MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, + LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, + nearIR, NL-DFT gradient (VV10), updates on ESD, + ML-optimized integration grids + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + Liviu Ungur et al : ANISO software + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 5.1.0 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + Shared memory : Shared parallel matrices + BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED + Core in use : SkylakeX + Copyright (c) 2011-2014, The OpenBLAS Project + + + + +*************************************** +The coordinates will be read from file: geom.xyz +*************************************** + + +Your calculation utilizes the semiempirical GFN2-xTB method +Please cite in your paper: +C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. + + +================================================================================ + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + + +WARNING: Geometry Optimization + ===> : Switching off AutoStart + For restart on a previous wavefunction, please use MOREAD + +WARNING: Found dipole moment calculation with XTB calculation + ===> : Switching off dipole moment calculation + + +WARNING: TRAH-SCF for XTB is not implemented! + ===> : Turning TRAH off! + +================================================================================ + INPUT FILE +================================================================================ +NAME = cmmd.in +| 1> #CMMDE generated Orca input file +| 2> !XTB2 opt +| 3> %pal +| 4> nprocs 1 +| 5> end +| 6> %geom +| 7> maxiter 9999 +| 8> end +| 9> +| 10> *xyzfile 0 1 geom.xyz +| 11> +| 12> +| 13> ****END OF INPUT**** +================================================================================ + + ***************************** + * Geometry Optimization Run * + ***************************** + +Geometry optimization settings: +Update method Update .... BFGS +Choice of coordinates CoordSys .... Z-matrix Internals +Initial Hessian InHess .... Almoef's Model + +Convergence Tolerances: +Energy Change TolE .... 5.0000e-06 Eh +Max. Gradient TolMAXG .... 3.0000e-04 Eh/bohr +RMS Gradient TolRMSG .... 1.0000e-04 Eh/bohr +Max. Displacement TolMAXD .... 4.0000e-03 bohr +RMS Displacement TolRMSD .... 2.0000e-03 bohr +Strict Convergence .... False +------------------------------------------------------------------------------ + ORCA OPTIMIZATION COORDINATE SETUP +------------------------------------------------------------------------------ + +The optimization will be done in new redundant internal coordinates +Making redundant internal coordinates ... (new redundants) done +Evaluating the initial hessian ... (Almloef) done +Evaluating the coordinates ... done +Calculating the B-matrix .... done +Calculating the G-matrix .... done +Diagonalizing the G-matrix .... done +The first mode is .... 1 +The number of degrees of freedom .... 9 + + ----------------------------------------------------------------- + Redundant Internal Coordinates + + + ----------------------------------------------------------------- + Definition Initial Value Approx d2E/dq + ----------------------------------------------------------------- + 1. B(H 1,C 0) 1.0922 0.357201 + 2. B(H 2,C 0) 1.0922 0.357207 + 3. B(H 3,C 0) 1.0922 0.357204 + 4. B(H 4,C 0) 1.0922 0.357199 + 5. A(H 1,C 0,H 3) 109.4711 0.290103 + 6. A(H 2,C 0,H 3) 109.4714 0.290103 + 7. A(H 1,C 0,H 4) 109.4709 0.290102 + 8. A(H 2,C 0,H 4) 109.4712 0.290103 + 9. A(H 3,C 0,H 4) 109.4714 0.290102 + 10. A(H 1,C 0,H 2) 109.4712 0.290103 + ----------------------------------------------------------------- + +Number of atoms .... 5 +Number of degrees of freedom .... 10 + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 1 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.044340 0.082110 0.035930 + H 2.136540 0.082120 0.035930 + H 0.680280 -0.519880 0.871370 + H 0.680280 -0.340410 -0.903130 + H 0.680270 1.106620 0.139550 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 1.973517 0.155165 0.067898 + 1 H 1.0000 0 1.008 4.037475 0.155184 0.067898 + 2 H 1.0000 0 1.008 1.285543 -0.982431 1.646651 + 3 H 1.0000 0 1.008 1.285543 -0.643282 -1.706668 + 4 H 1.0000 0 1.008 1.285524 2.091209 0.263711 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 20:01:40.799 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 5 + number of electrons : 8 + charge : 0 + spin : 0.0 + first test random number : 0.77593226296461 + + ID Z sym. atoms + 1 6 C 1 + 2 1 H 2-5 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 8 : + : # atomic orbitals 8 : + : # shells 6 : + : # electrons 8 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -4.2288348 -0.422883E+01 0.246E+00 17.25 0.0 T + 2 -4.2416600 -0.128252E-01 0.917E-01 17.07 1.0 T + 3 -4.2418079 -0.147905E-03 0.503E-01 16.97 1.0 T + 4 -4.2418545 -0.465210E-04 0.968E-02 16.85 1.0 T + 5 -4.2418544 0.611435E-07 0.615E-03 16.85 7.3 T + 6 -4.2418545 -0.109444E-06 0.181E-04 16.85 247.0 T + 7 -4.2418545 -0.991456E-10 0.316E-06 16.85 14145.1 T + + *** convergence criteria satisfied after 7 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.5801035 -15.7854 + 2 2.0000 -0.4667173 -12.7000 + 3 2.0000 -0.4667172 -12.7000 + 4 2.0000 -0.4667166 -12.7000 (HOMO) + 5 0.1525555 4.1512 (LUMO) + 6 0.2134394 5.8080 + 7 0.2134443 5.8081 + 8 0.2134484 5.8082 + ------------------------------------------------------------- + HL-Gap 0.6192721 Eh 16.8513 eV + Fermi-level -0.1570806 Eh -4.2744 eV + + SCC (total) 0 d, 0 h, 0 min, 0.004 sec + SCC setup ... 0 min, 0.000 sec ( 2.473%) + Dispersion ... 0 min, 0.000 sec ( 0.399%) + classical contributions ... 0 min, 0.000 sec ( 0.314%) + integral evaluation ... 0 min, 0.000 sec ( 4.526%) + iterations ... 0 min, 0.003 sec ( 75.052%) + molecular gradient ... 0 min, 0.000 sec ( 9.044%) + printout ... 0 min, 0.000 sec ( 7.938%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -4.174962243010 Eh :: + :: gradient norm 0.013369740823 Eh/a0 :: + :: HOMO-LUMO gap 16.851251491626 eV :: + ::.................................................:: + :: SCC energy -4.241854501533 Eh :: + :: -> isotropic ES 0.001954136445 Eh :: + :: -> anisotropic ES 0.002520392001 Eh :: + :: -> anisotropic XC 0.003827634963 Eh :: + :: -> dispersion -0.000662667402 Eh :: + :: repulsion energy 0.066892252559 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -4.174962243010 Eh | + | GRADIENT NORM 0.013369740823 Eh/α | + | HOMO-LUMO GAP 16.851251491626 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 20:01:40.813 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.014 sec + * cpu-time: 0 d, 0 h, 0 min, 0.014 sec + * ratio c/w: 0.956 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.004 sec + * cpu-time: 0 d, 0 h, 0 min, 0.004 sec + * ratio c/w: 0.847 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -4.174962243010 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 5 +Number of internal coordinates .... 10 +Current Energy .... -4.174962243 Eh +Current gradient norm .... 0.013369741 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Evaluating the initial hessian .... (Almloef) done +Projecting the Hessian .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999302222 +Lowest eigenvalues of augmented Hessian: + -0.000499717 0.290102138 0.290102473 0.290102705 0.290102937 +Length of the computed step .... 0.037376698 +The final length of the internal step .... 0.037376698 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0118195497 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0096506218 RMS(Int)= 0.0118195497 + Iter 1: RMS(Cart)= 0.0000000082 RMS(Int)= 0.0000000097 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + RMS gradient 0.0042278831 0.0001000000 NO + MAX gradient 0.0066865430 0.0003000000 NO + RMS step 0.0118195497 0.0020000000 NO + MAX step 0.0186932250 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0099 Max(Angles) 0.00 + Max(Dihed) 0.00 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(H 1,C 0) 1.0922 0.006685 -0.0099 1.0823 + 2. B(H 2,C 0) 1.0922 0.006683 -0.0099 1.0823 + 3. B(H 3,C 0) 1.0922 0.006684 -0.0099 1.0823 + 4. B(H 4,C 0) 1.0922 0.006687 -0.0099 1.0823 + 5. A(H 1,C 0,H 3) 109.47 -0.000000 0.00 109.47 + 6. A(H 2,C 0,H 3) 109.47 0.000000 -0.00 109.47 + 7. A(H 1,C 0,H 4) 109.47 -0.000001 0.00 109.47 + 8. A(H 2,C 0,H 4) 109.47 0.000000 -0.00 109.47 + 9. A(H 3,C 0,H 4) 109.47 0.000001 -0.00 109.47 + 10. A(H 1,C 0,H 2) 109.47 -0.000000 0.00 109.47 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 2 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.044341 0.082111 0.035930 + H 2.126651 0.082120 0.035930 + H 0.683576 -0.514430 0.863807 + H 0.683576 -0.336583 -0.894627 + H 0.683567 1.097342 0.138611 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 1.973518 0.155167 0.067898 + 1 H 1.0000 0 1.008 4.018787 0.155185 0.067898 + 2 H 1.0000 0 1.008 1.291771 -0.972132 1.632359 + 3 H 1.0000 0 1.008 1.291771 -0.636050 -1.690601 + 4 H 1.0000 0 1.008 1.291754 2.073675 0.261936 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 20:01:40.852 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 5 + number of electrons : 8 + charge : 0 + spin : 0.0 + first test random number : 0.94557732742326 + + ID Z sym. atoms + 1 6 C 1 + 2 1 H 2-5 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 8 : + : # atomic orbitals 8 : + : # shells 6 : + : # electrons 8 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -4.2473771 -0.424738E+01 0.106E-01 17.33 0.0 T + 2 -4.2473844 -0.729627E-05 0.561E-02 17.34 1.0 T + 3 -4.2473846 -0.259728E-06 0.204E-02 17.34 2.2 T + 4 -4.2473847 -0.370536E-07 0.422E-03 17.35 10.6 T + 5 -4.2473847 -0.969802E-11 0.246E-05 17.35 1817.5 T + 6 -4.2473847 -0.113154E-11 0.892E-08 17.35 100000.0 T + + *** convergence criteria satisfied after 6 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.5818102 -15.8319 + 2 2.0000 -0.4674472 -12.7199 + 3 2.0000 -0.4674471 -12.7199 + 4 2.0000 -0.4674468 -12.7199 (HOMO) + 5 0.1699963 4.6258 (LUMO) + 6 0.2290163 6.2319 + 7 0.2290184 6.2319 + 8 0.2290194 6.2319 + ------------------------------------------------------------- + HL-Gap 0.6374431 Eh 17.3457 eV + Fermi-level -0.1487253 Eh -4.0470 eV + + SCC (total) 0 d, 0 h, 0 min, 0.004 sec + SCC setup ... 0 min, 0.000 sec ( 3.080%) + Dispersion ... 0 min, 0.000 sec ( 0.502%) + classical contributions ... 0 min, 0.000 sec ( 0.384%) + integral evaluation ... 0 min, 0.000 sec ( 5.138%) + iterations ... 0 min, 0.003 sec ( 76.753%) + molecular gradient ... 0 min, 0.000 sec ( 9.969%) + printout ... 0 min, 0.000 sec ( 3.907%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -4.175218465761 Eh :: + :: gradient norm 0.000198773486 Eh/a0 :: + :: HOMO-LUMO gap 17.345710383199 eV :: + ::.................................................:: + :: SCC energy -4.247384675788 Eh :: + :: -> isotropic ES 0.002034388422 Eh :: + :: -> anisotropic ES 0.002324463044 Eh :: + :: -> anisotropic XC 0.003588680218 Eh :: + :: -> dispersion -0.000661035659 Eh :: + :: repulsion energy 0.072166204431 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -4.175218465761 Eh | + | GRADIENT NORM 0.000198773486 Eh/α | + | HOMO-LUMO GAP 17.345710383199 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 20:01:40.866 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.015 sec + * cpu-time: 0 d, 0 h, 0 min, 0.014 sec + * ratio c/w: 0.965 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.004 sec + * cpu-time: 0 d, 0 h, 0 min, 0.003 sec + * ratio c/w: 0.863 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -4.175218465760 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 5 +Number of internal coordinates .... 10 +Current Energy .... -4.175218466 Eh +Current gradient norm .... 0.000198773 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999999841 +Lowest eigenvalues of augmented Hessian: + -0.000000112 0.290102133 0.290102473 0.290102705 0.290102937 +Length of the computed step .... 0.000564077 +The final length of the internal step .... 0.000564077 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0001783768 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0001456437 RMS(Int)= 0.0001783768 + Iter 1: RMS(Cart)= 0.0000000001 RMS(Int)= 0.0000000001 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0002562228 0.0000050000 NO + RMS gradient 0.0000628570 0.0001000000 YES + MAX gradient 0.0000995361 0.0003000000 YES + RMS step 0.0001783768 0.0020000000 YES + MAX step 0.0002824680 0.0040000000 YES + ........................................................ + Max(Bonds) 0.0001 Max(Angles) 0.00 + Max(Dihed) 0.00 Max(Improp) 0.00 + --------------------------------------------------------------------- + + Everything but the energy has converged. However, the energy + appears to be close enough to convergence to make sure that the + final evaluation at the new geometry represents the equilibrium energy. + Convergence will therefore be signaled now + + + ***********************HURRAY******************** + *** THE OPTIMIZATION HAS CONVERGED *** + ************************************************* + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + + --- Optimized Parameters --- + (Angstroem and degrees) + + Definition OldVal dE/dq Step FinalVal + ---------------------------------------------------------------------------- + 1. B(H 1,C 0) 1.0823 0.000100 -0.0001 1.0822 + 2. B(H 2,C 0) 1.0823 0.000099 -0.0001 1.0822 + 3. B(H 3,C 0) 1.0823 0.000099 -0.0001 1.0822 + 4. B(H 4,C 0) 1.0823 0.000100 -0.0001 1.0822 + 5. A(H 1,C 0,H 3) 109.47 -0.000000 0.00 109.47 + 6. A(H 2,C 0,H 3) 109.47 0.000000 -0.00 109.47 + 7. A(H 1,C 0,H 4) 109.47 -0.000001 0.00 109.47 + 8. A(H 2,C 0,H 4) 109.47 0.000000 -0.00 109.47 + 9. A(H 3,C 0,H 4) 109.47 0.000000 -0.00 109.47 + 10. A(H 1,C 0,H 2) 109.47 0.000000 -0.00 109.47 + ---------------------------------------------------------------------------- + ******************************************************* + *** FINAL ENERGY EVALUATION AT THE STATIONARY POINT *** + *** (AFTER 2 CYCLES) *** + ******************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.044341 0.082111 0.035930 + H 2.126502 0.082120 0.035930 + H 0.683625 -0.514348 0.863693 + H 0.683625 -0.336525 -0.894499 + H 0.683616 1.097201 0.138596 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 1.973519 0.155168 0.067898 + 1 H 1.0000 0 1.008 4.018506 0.155184 0.067898 + 2 H 1.0000 0 1.008 1.291865 -0.971976 1.632142 + 3 H 1.0000 0 1.008 1.291865 -0.635940 -1.690358 + 4 H 1.0000 0 1.008 1.291847 2.073410 0.261909 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 20:01:40.902 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 5 + number of electrons : 8 + charge : 0 + spin : 0.0 + first test random number : 0.65390006167704 + + ID Z sym. atoms + 1 6 C 1 + 2 1 H 2-5 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 8 : + : # atomic orbitals 8 : + : # shells 6 : + : # electrons 8 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -4.2474673 -0.424747E+01 0.161E-03 17.35 0.0 T + 2 -4.2474673 -0.163799E-08 0.849E-04 17.35 52.7 T + 3 -4.2474673 -0.599947E-10 0.305E-04 17.35 146.7 T + + *** convergence criteria satisfied after 3 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.5818333 -15.8325 + 2 2.0000 -0.4674557 -12.7201 + 3 2.0000 -0.4674556 -12.7201 + 4 2.0000 -0.4674555 -12.7201 (HOMO) + 5 0.1702655 4.6332 (LUMO) + 6 0.2292576 6.2384 + 7 0.2292588 6.2384 + 8 0.2292592 6.2385 + ------------------------------------------------------------- + HL-Gap 0.6377209 Eh 17.3533 eV + Fermi-level -0.1485950 Eh -4.0435 eV + + SCC (total) 0 d, 0 h, 0 min, 0.004 sec + SCC setup ... 0 min, 0.000 sec ( 6.098%) + Dispersion ... 0 min, 0.000 sec ( 1.200%) + classical contributions ... 0 min, 0.000 sec ( 0.808%) + integral evaluation ... 0 min, 0.000 sec ( 6.077%) + iterations ... 0 min, 0.003 sec ( 69.334%) + molecular gradient ... 0 min, 0.000 sec ( 11.268%) + printout ... 0 min, 0.000 sec ( 4.884%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -4.175218519968 Eh :: + :: gradient norm 0.000005349369 Eh/a0 :: + :: HOMO-LUMO gap 17.353270065095 eV :: + ::.................................................:: + :: SCC energy -4.247467308443 Eh :: + :: -> isotropic ES 0.002035507827 Eh :: + :: -> anisotropic ES 0.002321507885 Eh :: + :: -> anisotropic XC 0.003585039027 Eh :: + :: -> dispersion -0.000661012503 Eh :: + :: repulsion energy 0.072248782884 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -4.175218519968 Eh | + | GRADIENT NORM 0.000005349369 Eh/α | + | HOMO-LUMO GAP 17.353270065095 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 20:01:40.922 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.020 sec + * cpu-time: 0 d, 0 h, 0 min, 0.019 sec + * ratio c/w: 0.970 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.005 sec + * cpu-time: 0 d, 0 h, 0 min, 0.004 sec + * ratio c/w: 0.868 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -4.175218519970 +------------------------- -------------------- + + *** OPTIMIZATION RUN DONE *** + +Timings for individual modules: + +Sum of individual times ... 0.141 sec (= 0.002 min) +Geometry relaxation ... 0.041 sec (= 0.001 min) 29.1 % +XTB module ... 0.100 sec (= 0.002 min) 70.9 % + ****ORCA TERMINATED NORMALLY**** +TOTAL RUN TIME: 0 days 0 hours 0 minutes 0 seconds 221 msec diff --git a/cmmde_gui/test/metana3/cmmd.xtbrestart b/cmmde_gui/test/metana3/cmmd.xtbrestart new file mode 100644 index 0000000000000000000000000000000000000000..161cd8a8a8f5c4233331d2e7840f102e1454b44c GIT binary patch literal 488 zcmXqDU|?VZVi17QtPm~(8beK_hX?-XjD54% z-k|JMekzdeVbyq>0;GAH@_7?L;y^tWKwRnC(03|j?mp&yN-npy&Df{(@bjdK$?E%B z&N9Ds)rYcuXEr50xHEI<{)*+7@4dUdasRK~EiYf6*kLbt z)Bp7~p!jEdr?hi|EBEjJwMX{;?cMuBq}RRs1{B}Lb6Wpw%0Bx=y5~ifP4BP=+5G{C zSE}2F@+@CzcQnZCt7iA2eG?^4iG5g^wa?u=#W+HJvRzh?*ye@z>h{&~EeOv2vwYvv zs8`>X{@HE+$UZx>d(R5Hz~}v<%l@q1@6DLSU9Qw_cS!D+ci^{3yJ_cKZY%|g7qIP{ zR=#43ZPJtEnzCZTK%f4N0ztwE%b3?9;_A5&CEGB@VR?Dm6@LiY*{WwehhCCfwm_U;I zyEEVZzkAR9&OPUM&OP6~cklOob6RnF`2MG*XIl>4%aiz%R!4U_54Q%|X%60qO`J37J?e-rY=^1P+L8B{P@BhmO zmNy!q!IiJuzk6`l6~Jb8g4F)qUBkLS6MI12{(S@8O{}{*r{n+b-eDHa6sY(ALA!r5 zTfe>k4-Pp2Y-AUx_y2Qy7d5i-Djl!?4Gy^a)6l+9@Bc$ReGRRCo>I%)a~!;Z&RB;9{(@z9vbwqzee_fdjDU(*!{naZ2ffo zuWQA~fF97u9uVLEm-X}wE^TD}n_lUGk%57}xAkUn1~1)5#! zy8WwLf0p$Oy9c0wU7>FOq3Y;Q>o>6V^Z)<*db;{oI0R^552*M56(ha=0ocICuc}

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Temp 298.15 +| 12> Pressure 1.0 +| 13> end +| 14> +| 15> ****END OF INPUT**** +================================================================================ + + ******************************* + * Energy+Gradient Calculation * + ******************************* + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 20:01:44.804 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 5 + number of electrons : 8 + charge : 0 + spin : 0.0 + first test random number : 0.28638523637135 + + ID Z sym. atoms + 1 6 C 1 + 2 1 H 2-5 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 8 : + : # atomic orbitals 8 : + : # shells 6 : + : # electrons 8 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -4.2352961 -0.423530E+01 0.243E+00 17.75 0.0 T + 2 -4.2472613 -0.119651E-01 0.928E-01 17.57 1.0 T + 3 -4.2474252 -0.163901E-03 0.500E-01 17.46 1.0 T + 4 -4.2474673 -0.421128E-04 0.924E-02 17.36 1.0 T + 5 -4.2474672 0.111480E-06 0.698E-03 17.35 6.4 T + 6 -4.2474673 -0.145702E-06 0.191E-04 17.35 233.9 T + 7 -4.2474673 -0.109869E-09 0.432E-06 17.35 10344.8 T + + *** convergence criteria satisfied after 7 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.5818361 -15.8326 + 2 2.0000 -0.4674581 -12.7202 + 3 2.0000 -0.4674581 -12.7202 + 4 2.0000 -0.4674579 -12.7202 (HOMO) + 5 0.1702647 4.6331 (LUMO) + 6 0.2292564 6.2384 + 7 0.2292575 6.2384 + 8 0.2292580 6.2384 + ------------------------------------------------------------- + HL-Gap 0.6377226 Eh 17.3533 eV + Fermi-level -0.1485966 Eh -4.0435 eV + + SCC (total) 0 d, 0 h, 0 min, 0.021 sec + SCC setup ... 0 min, 0.000 sec ( 0.604%) + Dispersion ... 0 min, 0.000 sec ( 0.142%) + classical contributions ... 0 min, 0.000 sec ( 0.098%) + integral evaluation ... 0 min, 0.000 sec ( 0.910%) + iterations ... 0 min, 0.020 sec ( 95.478%) + molecular gradient ... 0 min, 0.000 sec ( 1.911%) + printout ... 0 min, 0.000 sec ( 0.795%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -4.175218519976 Eh :: + :: gradient norm 0.000006636122 Eh/a0 :: + :: HOMO-LUMO gap 17.353314919929 eV :: + ::.................................................:: + :: SCC energy -4.247467308451 Eh :: + :: -> isotropic ES 0.002035567940 Eh :: + :: -> anisotropic ES 0.002321540923 Eh :: + :: -> anisotropic XC 0.003585096725 Eh :: + :: -> dispersion -0.000661011606 Eh :: + :: repulsion energy 0.072248782884 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -4.175218519976 Eh | + | GRADIENT NORM 0.000006636122 Eh/α | + | HOMO-LUMO GAP 17.353314919929 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 20:01:44.835 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.032 sec + * cpu-time: 0 d, 0 h, 0 min, 0.014 sec + * ratio c/w: 0.452 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.021 sec + * cpu-time: 0 d, 0 h, 0 min, 0.004 sec + * ratio c/w: 0.185 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -4.175218519980 +------------------------- -------------------- + + +---------------------------------------------------------------------------- + ORCA NUMERICAL FREQUENCIES +---------------------------------------------------------------------------- + +Number of atoms ... 5 +Central differences ... used +Number of displacements ... 30 +Numerical increment ... 5.000e-03 bohr +IR-spectrum generation ... on +Raman-spectrum generation ... off +Surface Crossing Hessian ... off + +The output will be reduced. Please look at the following files: +SCF program output ... >cmmd.lastscf +Integral program output ... >cmmd.lastint +Gradient program output ... >cmmd.lastgrad +Dipole moment program output ... >cmmd.lastmom +AutoCI program output ... >cmmd.lastautoci + + << Calculating on displaced geometry 1 (of 30) >> + << Calculating on displaced geometry 2 (of 30) >> + << Calculating on displaced geometry 3 (of 30) >> + << Calculating on displaced geometry 4 (of 30) >> + << Calculating on displaced geometry 5 (of 30) >> + << Calculating on displaced geometry 6 (of 30) >> + << Calculating on displaced geometry 7 (of 30) >> + << Calculating on displaced geometry 8 (of 30) >> + << Calculating on displaced geometry 9 (of 30) >> + << Calculating on displaced geometry 10 (of 30) >> + << Calculating on displaced geometry 11 (of 30) >> + << Calculating on displaced geometry 12 (of 30) >> + << Calculating on displaced geometry 13 (of 30) >> + << Calculating on displaced geometry 14 (of 30) >> + << Calculating on displaced geometry 15 (of 30) >> + << Calculating on displaced geometry 16 (of 30) >> + << Calculating on displaced geometry 17 (of 30) >> + << Calculating on displaced geometry 18 (of 30) >> + << Calculating on displaced geometry 19 (of 30) >> + << Calculating on displaced geometry 20 (of 30) >> + << Calculating on displaced geometry 21 (of 30) >> + << Calculating on displaced geometry 22 (of 30) >> + << Calculating on displaced geometry 23 (of 30) >> + << Calculating on displaced geometry 24 (of 30) >> + << Calculating on displaced geometry 25 (of 30) >> + << Calculating on displaced geometry 26 (of 30) >> + << Calculating on displaced geometry 27 (of 30) >> + << Calculating on displaced geometry 28 (of 30) >> + << Calculating on displaced geometry 29 (of 30) >> + << Calculating on displaced geometry 30 (of 30) >> + +----------------------- +VIBRATIONAL FREQUENCIES +----------------------- + +Scaling factor for frequencies = 1.000000000 (already applied!) + + 0: 0.00 cm**-1 + 1: 0.00 cm**-1 + 2: 0.00 cm**-1 + 3: 0.00 cm**-1 + 4: 0.00 cm**-1 + 5: 0.00 cm**-1 + 6: 1385.80 cm**-1 + 7: 1385.81 cm**-1 + 8: 1385.82 cm**-1 + 9: 1557.27 cm**-1 + 10: 1557.28 cm**-1 + 11: 3090.01 cm**-1 + 12: 3103.92 cm**-1 + 13: 3103.94 cm**-1 + 14: 3103.96 cm**-1 + + +------------ +NORMAL MODES +------------ + +These modes are the cartesian displacements weighted by the diagonal matrix +M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom +Thus, these vectors are normalized but *not* orthogonal + + 0 1 2 3 4 5 + 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 1 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 2 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 7 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 8 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 9 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 10 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 11 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 12 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 13 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 14 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 6 7 8 9 10 11 + 0 0.096798 0.082365 -0.021256 0.000001 -0.000001 0.000098 + 1 0.084411 -0.089026 0.039430 0.000008 -0.000000 0.000065 + 2 0.010518 -0.043542 -0.120826 0.000003 0.000001 -0.000022 + 3 0.045040 0.038319 -0.009889 0.000004 -0.000001 0.499033 + 4 -0.396782 0.418488 -0.185363 -0.479370 0.142288 0.000034 + 5 -0.049440 0.204683 0.568001 -0.142299 -0.479333 -0.000010 + 6 -0.333231 -0.367059 0.284304 0.155352 -0.445070 -0.166911 + 7 -0.195392 0.451828 0.119524 0.350856 0.225673 -0.276043 + 8 -0.329034 0.158506 0.144889 0.320509 -0.031334 0.383124 + 9 -0.327694 -0.463680 -0.064905 0.307768 0.357083 -0.166753 + 10 -0.249018 0.329744 -0.376666 0.300713 -0.349484 -0.193551 + 11 0.279107 0.007359 0.142840 -0.254612 0.018810 -0.430254 + 12 -0.537524 -0.189019 0.043767 -0.463140 0.087997 -0.166531 + 13 -0.164623 -0.139255 -0.027336 -0.172300 -0.018473 0.468783 + 14 -0.025964 0.148290 0.583993 0.076373 0.491844 0.047399 + 12 13 14 + 0 -0.009344 0.020992 -0.084211 + 1 -0.030512 0.078496 0.022954 + 2 0.081248 0.031893 -0.001065 + 3 0.092484 -0.207489 0.830944 + 4 -0.014110 0.036300 0.010621 + 5 0.037575 0.014749 -0.000492 + 6 0.278034 -0.079154 0.011151 + 7 0.452776 -0.110634 0.093456 + 8 -0.610369 0.218675 -0.115458 + 9 -0.193492 -0.213085 0.030085 + 10 -0.233658 -0.222264 0.090733 + 11 -0.450372 -0.559929 0.177571 + 12 -0.065684 0.249590 0.131247 + 13 0.158564 -0.638735 -0.468319 + 14 0.055040 -0.053523 -0.048931 + + +----------- +IR SPECTRUM +----------- + + Mode freq eps Int T**2 TX TY TZ + cm**-1 L/(mol*cm) km/mol a.u. +---------------------------------------------------------------------------- + 6: 1385.80 0.000189 0.95 0.000043 (-0.001721 0.006289 0.000000) + 7: 1385.81 0.000135 0.68 0.000030 (-0.001464 0.005320 0.000000) + 8: 1385.82 0.000005 0.03 0.000001 ( 0.000378 0.001044 0.000000) + 9: 1557.27 0.000227 1.15 0.000046 (-0.000000 0.006748 0.000000) + 10: 1557.28 0.000003 0.01 0.000001 ( 0.000000 0.000724 0.000000) + 11: 3090.01 0.003589 18.14 0.000362 (-0.013875 -0.013034 0.000000) + 12: 3103.92 0.000238 1.20 0.000024 (-0.002465 -0.004227 0.000000) + 13: 3103.94 0.003188 16.11 0.000320 ( 0.005531 0.017026 0.000000) + 14: 3103.96 0.006430 32.49 0.000646 (-0.022149 0.012483 0.000000) + +* The epsilon (eps) is given for a Dirac delta lineshape. +** The dipole moment derivative (T) already includes vibrational overlap. + +The first frequency considered to be a vibration is 6 +The total number of vibrations considered is 9 + + +-------------------------- +THERMOCHEMISTRY AT 298.15K +-------------------------- + +Temperature ... 298.15 K +Pressure ... 1.00 atm +Total Mass ... 16.04 AMU + +Throughout the following assumptions are being made: + (1) The electronic state is orbitally nondegenerate + (2) There are no thermally accessible electronically excited states + (3) Hindered rotations indicated by low frequency modes are not + treated as such but are treated as vibrations and this may + cause some error + (4) All equations used are the standard statistical mechanics + equations for an ideal gas + (5) All vibrations are strictly harmonic + +freq. 1385.80 E(vib) ... 0.00 +freq. 1385.81 E(vib) ... 0.00 +freq. 1385.82 E(vib) ... 0.00 +freq. 1557.27 E(vib) ... 0.00 +freq. 1557.28 E(vib) ... 0.00 +freq. 3090.01 E(vib) ... 0.00 +freq. 3103.92 E(vib) ... 0.00 +freq. 3103.94 E(vib) ... 0.00 +freq. 3103.96 E(vib) ... 0.00 + +------------ +INNER ENERGY +------------ + +The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans) + E(el) - is the total energy from the electronic structure calculation + = E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc) + E(ZPE) - the the zero temperature vibrational energy from the frequency calculation + E(vib) - the the finite temperature correction to E(ZPE) due to population + of excited vibrational states + E(rot) - is the rotational thermal energy + E(trans)- is the translational thermal energy + +Summary of contributions to the inner energy U: +Electronic energy ... -4.17521852 Eh +Zero point energy ... 0.04482019 Eh 28.13 kcal/mol +Thermal vibrational correction ... 0.00003140 Eh 0.02 kcal/mol +Thermal rotational correction ... 0.00141627 Eh 0.89 kcal/mol +Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol +----------------------------------------------------------------------- +Total thermal energy -4.12753439 Eh + + +Summary of corrections to the electronic energy: +(perhaps to be used in another calculation) +Total thermal correction 0.00286394 Eh 1.80 kcal/mol +Non-thermal (ZPE) correction 0.04482019 Eh 28.13 kcal/mol +----------------------------------------------------------------------- +Total correction 0.04768413 Eh 29.92 kcal/mol + + +-------- +ENTHALPY +-------- + +The enthalpy is H = U + kB*T + kB is Boltzmann's constant +Total free energy ... -4.12753439 Eh +Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol +----------------------------------------------------------------------- +Total Enthalpy ... -4.12659018 Eh + + +Note: Rotational entropy computed according to Herzberg +Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945 +Point Group: Td, Symmetry Number: 12 +Rotational constants in cm-1: 5.355312 5.355310 5.355304 + +Vibrational entropy computed according to the QRRHO of S. Grimme +Chem.Eur.J. 2012 18 9955 + + +------- +ENTROPY +------- + +The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans)) + S(el) - electronic entropy + S(vib) - vibrational entropy + S(rot) - rotational entropy + S(trans)- translational entropy +The entropies will be listed as multiplied by the temperature to get +units of energy + +Electronic entropy ... 0.00000000 Eh 0.00 kcal/mol +Vibrational entropy ... 0.00003597 Eh 0.02 kcal/mol +Rotational entropy ... 0.00478798 Eh 3.00 kcal/mol +Translational entropy ... 0.01627961 Eh 10.22 kcal/mol +----------------------------------------------------------------------- +Final entropy term ... 0.02110356 Eh 13.24 kcal/mol + +In case the symmetry of your molecule has not been determined correctly +or in case you have a reason to use a different symmetry number we print +out the resulting rotational entropy values for sn=1,12 : + -------------------------------------------------------- +| sn= 1 | S(rot)= 0.00713418 Eh 4.48 kcal/mol| +| sn= 2 | S(rot)= 0.00647973 Eh 4.07 kcal/mol| +| sn= 3 | S(rot)= 0.00609689 Eh 3.83 kcal/mol| +| sn= 4 | S(rot)= 0.00582527 Eh 3.66 kcal/mol| +| sn= 5 | S(rot)= 0.00561458 Eh 3.52 kcal/mol| +| sn= 6 | S(rot)= 0.00544244 Eh 3.42 kcal/mol| +| sn= 7 | S(rot)= 0.00529689 Eh 3.32 kcal/mol| +| sn= 8 | S(rot)= 0.00517081 Eh 3.24 kcal/mol| +| sn= 9 | S(rot)= 0.00505960 Eh 3.17 kcal/mol| +| sn=10 | S(rot)= 0.00496012 Eh 3.11 kcal/mol| +| sn=11 | S(rot)= 0.00487013 Eh 3.06 kcal/mol| +| sn=12 | S(rot)= 0.00478798 Eh 3.00 kcal/mol| + -------------------------------------------------------- + + +------------------- +GIBBS FREE ENERGY +------------------- + +The Gibbs free energy is G = H - T*S + +Total enthalpy ... -4.12659018 Eh +Total entropy correction ... -0.02110356 Eh -13.24 kcal/mol +----------------------------------------------------------------------- +Final Gibbs free energy ... -4.14769375 Eh + +For completeness - the Gibbs free energy minus the electronic energy +G-E(el) ... 0.02752477 Eh 17.27 kcal/mol + + + +Timings for individual modules: + +Sum of individual times ... 51.025 sec (= 0.850 min) +Numerical frequency calculation ... 50.947 sec (= 0.849 min) 99.8 % +XTB module ... 0.078 sec (= 0.001 min) 0.2 % + ****ORCA TERMINATED NORMALLY**** +TOTAL RUN TIME: 0 days 0 hours 0 minutes 51 seconds 56 msec diff --git a/cmmde_gui/test/metana3/freq/cmmd.xtbrestart b/cmmde_gui/test/metana3/freq/cmmd.xtbrestart new file mode 100644 index 0000000000000000000000000000000000000000..d6bb96ac1f2c6a759cf283778926e859b122d206 GIT binary patch literal 488 zcmXqDU|?VZVi17QtPm~(8LoBB&Zbl(TlZSg=Fq^AO;&%ySc<-fW6p4IoU#{ZqMPjcJ#E&SQ~`-J_D zSk@aKus{84{v-3~t#-^YOhSzk<@+4N9|ydfxpaT*{lBh%Z*SaxCY=5G{}Vgxox56t zUI4`tuU=g8NO0x;Eq3bDzTV!wzhkFkFvqN=`!^|1+4MAJpS|VFVy0cwJM2Mre*ogG zR{w;HmaepGI@i z>%O)>yY0iDs+(jfPZCsR>+Pj&^lt%&8 z&*rMKvRFRVUe7jk*0JmJ_OCnr@9jJO74|{N`fvZfS#2Misr*QeYooob+f4%tp!(Y% vFK%AyuxkG-$I3TLK5nz$7NH<=%C>a>x@~OHk015gKe3TqA!xmNKgiDj2Ugkx literal 0 HcmV?d00001 diff --git a/cmmde_gui/test/metana3/freq/cmmd_property.txt b/cmmde_gui/test/metana3/freq/cmmd_property.txt new file mode 100644 index 0000000..3fe5d91 --- /dev/null +++ b/cmmde_gui/test/metana3/freq/cmmd_property.txt @@ -0,0 +1,48 @@ +------------------------------------------------------------- +----------------------- !PROPERTIES! ------------------------ +------------------------------------------------------------- +# ----------------------------------------------------------- +$ THERMOCHEMISTRY_Energies + description: The Thermochemistry energies + geom. index: 0 + prop. index: 1 + Temperature (Kelvin) : 298.1500000000 + Pressure (atm) : 1.0000000000 + Total Mass (AMU) : 16.0430000000 + Spin Degeneracy : 1.0000000000 + Electronic Energy (Hartree) : -4.1752185200 + Translational Energy (Hartree) : 0.0014162714 + Rotational Energy (Hartree) : 0.0014162714 + Vibrational Energy (Hartree) : 0.0000314005 + Number of frequencies : 15 + Scaling Factor for frequencies : 1.0000000000 + Vibrational frequencies : + 0 + 0 0.000000 + 1 0.000000 + 2 0.000000 + 3 0.000000 + 4 0.000000 + 5 0.000000 + 6 1385.801243 + 7 1385.807833 + 8 1385.817738 + 9 1557.267071 + 10 1557.277517 + 11 3090.006354 + 12 3103.916950 + 13 3103.935349 + 14 3103.957551 + Zero Point Energy (Hartree) : 0.0448201861 + Inner Energy (Hartree) : -4.1275343905 + Enthalpy (Hartree) : -4.1265901815 + Electronic entropy : 0.0000000000 + Rotational entropy : 0.0047879801 + Vibrational entropy : 0.0000359731 + Translational entropy : 0.0047879801 + Entropy : 0.0211035637 + Gibbs Energy (Hartree) : -4.1476937451 + Is Linear : false +# ------------------------------------------------------------- +----------------------- !GEOMETRIES! ------------------------ +# ------------------------------------------------------------- diff --git a/cmmde_gui/test/metana3/freq/freq/cmmd.in b/cmmde_gui/test/metana3/freq/freq/cmmd.in new file mode 100644 index 0000000..247d130 --- /dev/null +++ b/cmmde_gui/test/metana3/freq/freq/cmmd.in @@ -0,0 +1,13 @@ +#CMMDE generated Orca input file +!XTB2 Numfreq +%pal + nprocs 1 +end + +*xyzfile 0 1 ../cmmd.xyz + +%freq + scalfreq 1 + Temp 298.15 + Pressure 1.0 +end diff --git a/cmmde_gui/test/metana3/freq/freq/cmmd.out b/cmmde_gui/test/metana3/freq/freq/cmmd.out new file mode 100644 index 0000000..378084e --- /dev/null +++ b/cmmde_gui/test/metana3/freq/freq/cmmd.out @@ -0,0 +1,142 @@ + + ***************** + * O R C A * + ***************** + + #, + ### + #### + ##### + ###### + ########, + ,,################,,,,, + ,,#################################,, + ,,##########################################,, + ,#########################################, ''#####, + ,#############################################,, '####, + ,##################################################,,,,####, + ,###########'''' ''''############################### + ,#####'' ,,,,##########,,,, '''####''' '#### + ,##' ,,,,###########################,,, '## + ' ,,###'''' '''############,,, + ,,##'' '''############,,,, ,,,,,,###'' + ,#'' '''#######################''' + ' ''''####'''' + ,#######, #######, ,#######, ## + ,#' '#, ## ## ,#' '#, #''# ###### ,####, + ## ## ## ,#' ## #' '# # #' '# + ## ## ####### ## ,######, #####, # # + '#, ,#' ## ## '#, ,#' ,# #, ## #, ,# + '#######' ## ## '#######' #' '# #####' # '####' + + + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship and core code : Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 5.0.2 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Marcus Kettner : VPT2 + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : Initial AUTO-CI + Lucas Lang : DCDCAS + Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, + C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT + MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, + LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, + nearIR, NL-DFT gradient (VV10), updates on ESD, + ML-optimized integration grids + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + Liviu Ungur et al : ANISO software + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 5.1.0 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + Shared memory : Shared parallel matrices + BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED + Core in use : SkylakeX + Copyright (c) 2011-2014, The OpenBLAS Project + + + + +*************************************** +The coordinates will be read from file: ../cmmd.xyz +*************************************** + + diff --git a/cmmde_gui/test/metana3/freq/freq/run.sh b/cmmde_gui/test/metana3/freq/freq/run.sh new file mode 100644 index 0000000..f72e163 --- /dev/null +++ b/cmmde_gui/test/metana3/freq/freq/run.sh @@ -0,0 +1,10 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH +export PATH=/home/adit/opt/openmpi411/bin:$PATH +export OMP_NUM_THREADS=1 +cd $PWD +$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe diff --git a/cmmde_gui/test/metana3/freq/freq/slurm-2909.out b/cmmde_gui/test/metana3/freq/freq/slurm-2909.out new file mode 100644 index 0000000..7315e3d --- /dev/null +++ b/cmmde_gui/test/metana3/freq/freq/slurm-2909.out @@ -0,0 +1,7 @@ + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!! FATAL ERROR ENCOUNTERED !!! +!!! ----------------------- !!! +!!! CANNOT OPEN FILE !!! +!!! Filename: ../cmmd.xyz !!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! diff --git a/cmmde_gui/test/metana3/freq/run.sh b/cmmde_gui/test/metana3/freq/run.sh new file mode 100644 index 0000000..f72e163 --- /dev/null +++ b/cmmde_gui/test/metana3/freq/run.sh @@ -0,0 +1,10 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH +export PATH=/home/adit/opt/openmpi411/bin:$PATH +export OMP_NUM_THREADS=1 +cd $PWD +$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe diff --git a/cmmde_gui/test/metana3/freq/slurm-2908.out b/cmmde_gui/test/metana3/freq/slurm-2908.out new file mode 100644 index 0000000..e69de29 diff --git a/cmmde_gui/test/metana3/geom.smi b/cmmde_gui/test/metana3/geom.smi new file mode 100644 index 0000000..3cc58df --- /dev/null +++ b/cmmde_gui/test/metana3/geom.smi @@ -0,0 +1 @@ +C diff --git a/cmmde_gui/test/metana3/geom.xyz b/cmmde_gui/test/metana3/geom.xyz new file mode 100644 index 0000000..6c84cd7 --- /dev/null +++ b/cmmde_gui/test/metana3/geom.xyz @@ -0,0 +1,7 @@ +5 + +C 1.04434 0.08211 0.03593 +H 2.13654 0.08212 0.03593 +H 0.68028 -0.51988 0.87137 +H 0.68028 -0.34041 -0.90313 +H 0.68027 1.10662 0.13955 diff --git a/cmmde_gui/test/metana3/run.sh b/cmmde_gui/test/metana3/run.sh new file mode 100644 index 0000000..f72e163 --- /dev/null +++ b/cmmde_gui/test/metana3/run.sh @@ -0,0 +1,10 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH +export PATH=/home/adit/opt/openmpi411/bin:$PATH +export OMP_NUM_THREADS=1 +cd $PWD +$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe diff --git a/cmmde_gui/test/metana3/run_babel.sh b/cmmde_gui/test/metana3/run_babel.sh new file mode 100644 index 0000000..0d5d00e --- /dev/null +++ b/cmmde_gui/test/metana3/run_babel.sh @@ -0,0 +1,8 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export OMP_NUM_THREADS=1 +cd $PWD +obabel geom.smi -O geom.xyz --gen3d diff --git a/cmmde_gui/test/metana3/slurm-2906.out b/cmmde_gui/test/metana3/slurm-2906.out new file mode 100644 index 0000000..b7d75ac --- /dev/null +++ b/cmmde_gui/test/metana3/slurm-2906.out @@ -0,0 +1 @@ +1 molecule converted diff --git a/cmmde_gui/test/metana3/slurm-2907.out b/cmmde_gui/test/metana3/slurm-2907.out new file mode 100644 index 0000000..e69de29 diff --git a/cmmde_gui/test/metana4/cmmd.engrad b/cmmde_gui/test/metana4/cmmd.engrad new file mode 100644 index 0000000..8cf5880 --- /dev/null +++ b/cmmde_gui/test/metana4/cmmd.engrad @@ -0,0 +1,34 @@ +# +# Number of atoms +# + 5 +# +# The current total energy in Eh +# + -4.175218519970 +# +# The current gradient in Eh/bohr +# + 0.000000006993 + -0.000000060266 + -0.000001064609 + 0.000099422562 + 0.000000016927 + 0.000000569180 + -0.000032858532 + 0.000011350835 + 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previous wavefunction, please use MOREAD + +WARNING: Found dipole moment calculation with XTB calculation + ===> : Switching off dipole moment calculation + + +WARNING: TRAH-SCF for XTB is not implemented! + ===> : Turning TRAH off! + +================================================================================ + INPUT FILE +================================================================================ +NAME = cmmd.in +| 1> #CMMDE generated Orca input file +| 2> !XTB2 opt +| 3> %pal +| 4> nprocs 1 +| 5> end +| 6> %geom +| 7> maxiter 9999 +| 8> end +| 9> +| 10> *xyzfile 0 1 geom.xyz +| 11> +| 12> +| 13> ****END OF INPUT**** +================================================================================ + + ***************************** + * Geometry Optimization Run * + ***************************** + +Geometry optimization settings: +Update method Update .... BFGS +Choice of coordinates CoordSys .... Z-matrix Internals +Initial Hessian InHess .... Almoef's Model + +Convergence Tolerances: +Energy Change TolE .... 5.0000e-06 Eh +Max. Gradient TolMAXG .... 3.0000e-04 Eh/bohr +RMS Gradient TolRMSG .... 1.0000e-04 Eh/bohr +Max. Displacement TolMAXD .... 4.0000e-03 bohr +RMS Displacement TolRMSD .... 2.0000e-03 bohr +Strict Convergence .... False +------------------------------------------------------------------------------ + ORCA OPTIMIZATION COORDINATE SETUP +------------------------------------------------------------------------------ + +The optimization will be done in new redundant internal coordinates +Making redundant internal coordinates ... (new redundants) done +Evaluating the initial hessian ... (Almloef) done +Evaluating the coordinates ... done +Calculating the B-matrix .... done +Calculating the G-matrix .... done +Diagonalizing the G-matrix .... done +The first mode is .... 1 +The number of degrees of freedom .... 9 + + ----------------------------------------------------------------- + Redundant Internal Coordinates + + + ----------------------------------------------------------------- + Definition Initial Value Approx d2E/dq + ----------------------------------------------------------------- + 1. B(H 1,C 0) 1.0922 0.357201 + 2. B(H 2,C 0) 1.0922 0.357206 + 3. B(H 3,C 0) 1.0922 0.357200 + 4. B(H 4,C 0) 1.0922 0.357205 + 5. A(H 1,C 0,H 3) 109.4714 0.290102 + 6. A(H 2,C 0,H 3) 109.4711 0.290103 + 7. A(H 1,C 0,H 4) 109.4715 0.290103 + 8. A(H 2,C 0,H 4) 109.4709 0.290103 + 9. A(H 3,C 0,H 4) 109.4715 0.290103 + 10. A(H 1,C 0,H 2) 109.4709 0.290103 + ----------------------------------------------------------------- + +Number of atoms .... 5 +Number of degrees of freedom .... 10 + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 1 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.083670 -0.046790 0.028460 + H 2.175870 -0.046790 0.028460 + H 0.719610 0.077060 1.050720 + H 0.719600 -0.994020 -0.375410 + H 0.719600 0.776590 -0.589920 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.047840 -0.088420 0.053782 + 1 H 1.0000 0 1.008 4.111798 -0.088420 0.053782 + 2 H 1.0000 0 1.008 1.359866 0.145622 1.985573 + 3 H 1.0000 0 1.008 1.359847 -1.878426 -0.709422 + 4 H 1.0000 0 1.008 1.359847 1.467542 -1.114787 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 20:29:34.231 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 5 + number of electrons : 8 + charge : 0 + spin : 0.0 + first test random number : 0.44068138003632 + + ID Z sym. atoms + 1 6 C 1 + 2 1 H 2-5 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 8 : + : # atomic orbitals 8 : + : # shells 6 : + : # electrons 8 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -4.2288349 -0.422883E+01 0.246E+00 17.25 0.0 T + 2 -4.2416601 -0.128252E-01 0.917E-01 17.07 1.0 T + 3 -4.2418080 -0.147906E-03 0.503E-01 16.97 1.0 T + 4 -4.2418545 -0.465209E-04 0.968E-02 16.85 1.0 T + 5 -4.2418545 0.611446E-07 0.615E-03 16.85 7.3 T + 6 -4.2418546 -0.109445E-06 0.181E-04 16.85 247.0 T + 7 -4.2418546 -0.991474E-10 0.316E-06 16.85 14162.4 T + + *** convergence criteria satisfied after 7 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.5801035 -15.7854 + 2 2.0000 -0.4667173 -12.7000 + 3 2.0000 -0.4667171 -12.7000 + 4 2.0000 -0.4667168 -12.7000 (HOMO) + 5 0.1525556 4.1513 (LUMO) + 6 0.2134423 5.8081 + 7 0.2134441 5.8081 + 8 0.2134461 5.8082 + ------------------------------------------------------------- + HL-Gap 0.6192724 Eh 16.8513 eV + Fermi-level -0.1570806 Eh -4.2744 eV + + SCC (total) 0 d, 0 h, 0 min, 0.003 sec + SCC setup ... 0 min, 0.001 sec ( 15.588%) + Dispersion ... 0 min, 0.000 sec ( 0.286%) + classical contributions ... 0 min, 0.000 sec ( 0.184%) + integral evaluation ... 0 min, 0.000 sec ( 2.787%) + iterations ... 0 min, 0.002 sec ( 70.868%) + molecular gradient ... 0 min, 0.000 sec ( 4.268%) + printout ... 0 min, 0.000 sec ( 5.863%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -4.174962248344 Eh :: + :: gradient norm 0.013369604418 Eh/a0 :: + :: HOMO-LUMO gap 16.851260314652 eV :: + ::.................................................:: + :: SCC energy -4.241854561123 Eh :: + :: -> isotropic ES 0.001954137326 Eh :: + :: -> anisotropic ES 0.002520389886 Eh :: + :: -> anisotropic XC 0.003827632398 Eh :: + :: -> dispersion -0.000662667385 Eh :: + :: repulsion energy 0.066892306814 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -4.174962248344 Eh | + | GRADIENT NORM 0.013369604418 Eh/α | + | HOMO-LUMO GAP 16.851260314652 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 20:29:34.244 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.013 sec + * cpu-time: 0 d, 0 h, 0 min, 0.007 sec + * ratio c/w: 0.522 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.003 sec + * cpu-time: 0 d, 0 h, 0 min, 0.002 sec + * ratio c/w: 0.514 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -4.174962248340 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 5 +Number of internal coordinates .... 10 +Current Energy .... -4.174962248 Eh +Current gradient norm .... 0.013369604 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Evaluating the initial hessian .... (Almloef) done +Projecting the Hessian .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999302237 +Lowest eigenvalues of augmented Hessian: + -0.000499706 0.290102299 0.290102655 0.290102741 0.290102826 +Length of the computed step .... 0.037376304 +The final length of the internal step .... 0.037376304 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0118194251 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0096505202 RMS(Int)= 0.0118194251 + Iter 1: RMS(Cart)= 0.0000000075 RMS(Int)= 0.0000000084 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + RMS gradient 0.0042278401 0.0001000000 NO + MAX gradient 0.0066861607 0.0003000000 NO + RMS step 0.0118194251 0.0020000000 NO + MAX step 0.0186920877 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0099 Max(Angles) 0.00 + Max(Dihed) 0.00 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(H 1,C 0) 1.0922 0.006686 -0.0099 1.0823 + 2. B(H 2,C 0) 1.0922 0.006683 -0.0099 1.0823 + 3. B(H 3,C 0) 1.0922 0.006686 -0.0099 1.0823 + 4. B(H 4,C 0) 1.0922 0.006684 -0.0099 1.0823 + 5. A(H 1,C 0,H 3) 109.47 0.000000 -0.00 109.47 + 6. A(H 2,C 0,H 3) 109.47 -0.000000 0.00 109.47 + 7. A(H 1,C 0,H 4) 109.47 0.000000 -0.00 109.47 + 8. A(H 2,C 0,H 4) 109.47 -0.000001 0.00 109.47 + 9. A(H 3,C 0,H 4) 109.47 0.000000 -0.00 109.47 + 10. A(H 1,C 0,H 2) 109.47 0.000000 -0.00 109.47 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 2 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.083670 -0.046790 0.028460 + H 2.165980 -0.046790 0.028460 + H 0.722906 0.075938 1.041466 + H 0.722897 -0.985442 -0.371753 + H 0.722897 0.769134 -0.584323 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.047840 -0.088421 0.053781 + 1 H 1.0000 0 1.008 4.093108 -0.088421 0.053781 + 2 H 1.0000 0 1.008 1.366095 0.143502 1.968086 + 3 H 1.0000 0 1.008 1.366078 -1.862215 -0.702512 + 4 H 1.0000 0 1.008 1.366077 1.453453 -1.104210 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 20:29:34.260 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 5 + number of electrons : 8 + charge : 0 + spin : 0.0 + first test random number : 0.99308267625035 + + ID Z sym. atoms + 1 6 C 1 + 2 1 H 2-5 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 8 : + : # atomic orbitals 8 : + : # shells 6 : + : # electrons 8 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -4.2473771 -0.424738E+01 0.106E-01 17.33 0.0 T + 2 -4.2473844 -0.729612E-05 0.561E-02 17.34 1.0 T + 3 -4.2473846 -0.259723E-06 0.204E-02 17.34 2.2 T + 4 -4.2473847 -0.370531E-07 0.422E-03 17.35 10.6 T + 5 -4.2473847 -0.969536E-11 0.246E-05 17.35 1817.6 T + 6 -4.2473847 -0.113420E-11 0.946E-08 17.35 100000.0 T + + *** convergence criteria satisfied after 6 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.5818102 -15.8319 + 2 2.0000 -0.4674473 -12.7199 + 3 2.0000 -0.4674472 -12.7199 + 4 2.0000 -0.4674467 -12.7199 (HOMO) + 5 0.1699963 4.6258 (LUMO) + 6 0.2290160 6.2318 + 7 0.2290189 6.2319 + 8 0.2290192 6.2319 + ------------------------------------------------------------- + HL-Gap 0.6374430 Eh 17.3457 eV + Fermi-level -0.1487252 Eh -4.0470 eV + + SCC (total) 0 d, 0 h, 0 min, 0.002 sec + SCC setup ... 0 min, 0.000 sec ( 2.277%) + Dispersion ... 0 min, 0.000 sec ( 0.368%) + classical contributions ... 0 min, 0.000 sec ( 0.276%) + integral evaluation ... 0 min, 0.000 sec ( 3.607%) + iterations ... 0 min, 0.001 sec ( 82.827%) + molecular gradient ... 0 min, 0.000 sec ( 7.165%) + printout ... 0 min, 0.000 sec ( 3.287%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -4.175218465760 Eh :: + :: gradient norm 0.000198772521 Eh/a0 :: + :: HOMO-LUMO gap 17.345707963371 eV :: + ::.................................................:: + :: SCC energy -4.247384676533 Eh :: + :: -> isotropic ES 0.002034388433 Eh :: + :: -> anisotropic ES 0.002324463018 Eh :: + :: -> anisotropic XC 0.003588680186 Eh :: + :: -> dispersion -0.000661035658 Eh :: + :: repulsion energy 0.072166205177 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -4.175218465760 Eh | + | GRADIENT NORM 0.000198772521 Eh/α | + | HOMO-LUMO GAP 17.345707963371 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 20:29:34.266 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.006 sec + * cpu-time: 0 d, 0 h, 0 min, 0.006 sec + * ratio c/w: 0.910 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.002 sec + * cpu-time: 0 d, 0 h, 0 min, 0.001 sec + * ratio c/w: 0.696 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -4.175218465760 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 5 +Number of internal coordinates .... 10 +Current Energy .... -4.175218466 Eh +Current gradient norm .... 0.000198773 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999999841 +Lowest eigenvalues of augmented Hessian: + -0.000000112 0.290102298 0.290102652 0.290102739 0.290102819 +Length of the computed step .... 0.000564079 +The final length of the internal step .... 0.000564079 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0001783773 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0001456448 RMS(Int)= 0.0001783773 + Iter 1: RMS(Cart)= 0.0000000001 RMS(Int)= 0.0000000002 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0002562174 0.0000050000 NO + RMS gradient 0.0000628569 0.0001000000 YES + MAX gradient 0.0000994650 0.0003000000 YES + RMS step 0.0001783773 0.0020000000 YES + MAX step 0.0002822650 0.0040000000 YES + ........................................................ + Max(Bonds) 0.0001 Max(Angles) 0.00 + Max(Dihed) 0.00 Max(Improp) 0.00 + --------------------------------------------------------------------- + + Everything but the energy has converged. However, the energy + appears to be close enough to convergence to make sure that the + final evaluation at the new geometry represents the equilibrium energy. + Convergence will therefore be signaled now + + + ***********************HURRAY******************** + *** THE OPTIMIZATION HAS CONVERGED *** + ************************************************* + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + + --- Optimized Parameters --- + (Angstroem and degrees) + + Definition OldVal dE/dq Step FinalVal + ---------------------------------------------------------------------------- + 1. B(H 1,C 0) 1.0823 0.000099 -0.0001 1.0822 + 2. B(H 2,C 0) 1.0823 0.000099 -0.0001 1.0822 + 3. B(H 3,C 0) 1.0823 0.000099 -0.0001 1.0822 + 4. B(H 4,C 0) 1.0823 0.000099 -0.0001 1.0822 + 5. A(H 1,C 0,H 3) 109.47 0.000000 -0.00 109.47 + 6. A(H 2,C 0,H 3) 109.47 -0.000000 0.00 109.47 + 7. A(H 1,C 0,H 4) 109.47 0.000000 -0.00 109.47 + 8. A(H 2,C 0,H 4) 109.47 -0.000000 0.00 109.47 + 9. A(H 3,C 0,H 4) 109.47 0.000000 -0.00 109.47 + 10. A(H 1,C 0,H 2) 109.47 -0.000001 0.00 109.47 + ---------------------------------------------------------------------------- + ******************************************************* + *** FINAL ENERGY EVALUATION AT THE STATIONARY POINT *** + *** (AFTER 2 CYCLES) *** + ******************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.083670 -0.046790 0.028461 + H 2.165830 -0.046790 0.028459 + H 0.722955 0.075921 1.041327 + H 0.722947 -0.985312 -0.371698 + H 0.722947 0.769021 -0.584239 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.047840 -0.088421 0.053783 + 1 H 1.0000 0 1.008 4.092826 -0.088421 0.053779 + 2 H 1.0000 0 1.008 1.366188 0.143469 1.967823 + 3 H 1.0000 0 1.008 1.366173 -1.861969 -0.702407 + 4 H 1.0000 0 1.008 1.366172 1.453240 -1.104051 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 20:29:34.279 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 5 + number of electrons : 8 + charge : 0 + spin : 0.0 + first test random number : 0.98349576822260 + + ID Z sym. atoms + 1 6 C 1 + 2 1 H 2-5 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 8 : + : # atomic orbitals 8 : + : # shells 6 : + : # electrons 8 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -4.2474673 -0.424747E+01 0.161E-03 17.35 0.0 T + 2 -4.2474673 -0.163796E-08 0.849E-04 17.35 52.7 T + 3 -4.2474673 -0.599991E-10 0.305E-04 17.35 146.7 T + + *** convergence criteria satisfied after 3 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.5818333 -15.8325 + 2 2.0000 -0.4674557 -12.7201 + 3 2.0000 -0.4674557 -12.7201 + 4 2.0000 -0.4674554 -12.7201 (HOMO) + 5 0.1702655 4.6332 (LUMO) + 6 0.2292572 6.2384 + 7 0.2292592 6.2385 + 8 0.2292593 6.2385 + ------------------------------------------------------------- + HL-Gap 0.6377209 Eh 17.3533 eV + Fermi-level -0.1485950 Eh -4.0435 eV + + SCC (total) 0 d, 0 h, 0 min, 0.002 sec + SCC setup ... 0 min, 0.000 sec ( 2.043%) + Dispersion ... 0 min, 0.000 sec ( 0.336%) + classical contributions ... 0 min, 0.000 sec ( 0.347%) + integral evaluation ... 0 min, 0.000 sec ( 3.119%) + iterations ... 0 min, 0.002 sec ( 82.033%) + molecular gradient ... 0 min, 0.000 sec ( 6.761%) + printout ... 0 min, 0.000 sec ( 5.027%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -4.175218519967 Eh :: + :: gradient norm 0.000005386320 Eh/a0 :: + :: HOMO-LUMO gap 17.353268526972 eV :: + ::.................................................:: + :: SCC energy -4.247467308411 Eh :: + :: -> isotropic ES 0.002035507833 Eh :: + :: -> anisotropic ES 0.002321507881 Eh :: + :: -> anisotropic XC 0.003585039024 Eh :: + :: -> dispersion -0.000661012503 Eh :: + :: repulsion energy 0.072248782853 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -4.175218519967 Eh | + | GRADIENT NORM 0.000005386320 Eh/α | + | HOMO-LUMO GAP 17.353268526972 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 20:29:34.285 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.006 sec + * cpu-time: 0 d, 0 h, 0 min, 0.006 sec + * ratio c/w: 0.915 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.002 sec + * cpu-time: 0 d, 0 h, 0 min, 0.002 sec + * ratio c/w: 0.755 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -4.175218519970 +------------------------- -------------------- + + *** OPTIMIZATION RUN DONE *** + +Timings for individual modules: + +Sum of individual times ... 0.074 sec (= 0.001 min) +Geometry relaxation ... 0.024 sec (= 0.000 min) 32.6 % +XTB module ... 0.050 sec (= 0.001 min) 67.4 % + ****ORCA TERMINATED NORMALLY**** +TOTAL RUN TIME: 0 days 0 hours 0 minutes 0 seconds 153 msec diff --git a/cmmde_gui/test/metana4/cmmd.xtbrestart b/cmmde_gui/test/metana4/cmmd.xtbrestart new 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0.07592075234087 1.04132725136236 + H 0.72294748574004 -0.98531158697568 -0.37169802557748 + H 0.72294692009187 0.76902145625821 -0.58423860447090 diff --git a/cmmde_gui/test/metana4/cmmd_property.txt b/cmmde_gui/test/metana4/cmmd_property.txt new file mode 100644 index 0000000..8f1a67f --- /dev/null +++ b/cmmde_gui/test/metana4/cmmd_property.txt @@ -0,0 +1,6 @@ +------------------------------------------------------------- +----------------------- !PROPERTIES! ------------------------ +------------------------------------------------------------- +# ------------------------------------------------------------- +----------------------- !GEOMETRIES! ------------------------ +# ------------------------------------------------------------- diff --git a/cmmde_gui/test/metana4/cmmd_trj.xyz b/cmmde_gui/test/metana4/cmmd_trj.xyz new file mode 100644 index 0000000..84d2f8d --- /dev/null +++ b/cmmde_gui/test/metana4/cmmd_trj.xyz @@ -0,0 +1,21 @@ +5 +Coordinates from ORCA-job cmmd E 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-5.8817293981E-02 1.3006525326E-01 -2.4760547280E-01 + 11 0.0000000000E+00 3.0552155499E-01 -2.7554011002E-01 -3.8476591359E-01 2.8623114672E-01 + 12 0.0000000000E+00 2.7122942133E-01 4.0292981312E-01 3.0114284016E-01 1.3094750542E-01 + 13 0.0000000000E+00 3.5213481603E-01 -1.2089868609E-01 1.4785499777E-01 3.2543782368E-01 + 14 0.0000000000E+00 2.5201120601E-01 -4.1920091674E-01 1.0619854293E-01 3.5623338751E-01 + 10 11 12 13 14 + 0 1.0014311110E-06 1.0290061187E-04 -1.0176487343E-02 1.2672520211E-02 8.5762969210E-02 + 1 -2.9203658457E-07 -2.6969005241E-05 7.7938004982E-02 3.9156529066E-02 3.4622386334E-03 + 2 3.8359155697E-07 5.8809942981E-05 -3.7969175584E-02 7.6978116084E-02 -1.5879895054E-02 + 3 1.1597211473E-08 4.9898051195E-01 1.0074002977E-01 -1.2531004362E-01 -8.4633174647E-01 + 4 4.6747654061E-01 -1.2809380563E-05 3.6043802392E-02 1.8108442747E-02 1.6010828377E-03 + 5 -1.7739199026E-01 2.6255546419E-05 -1.7560046302E-02 3.5600350344E-02 -7.3409102184E-03 + 6 -1.1302714223E-01 -1.6655344110E-01 -8.5045638859E-02 2.5466279270E-01 -1.0832525338E-01 + 7 -4.8669795438E-01 5.6662584925E-02 6.3375190611E-02 -6.6530273844E-02 5.1945122224E-02 + 8 1.8711023358E-02 4.6783776123E-01 2.0802888988E-01 -6.6302768601E-01 4.0820833562E-01 + 9 -3.3983245918E-01 -1.6673120206E-01 -1.7745758668E-01 -2.2338906827E-01 -4.8657481235E-02 + 10 -2.5386764497E-02 -4.3394122843E-01 -4.1341709300E-01 -5.7835529070E-01 -2.2819686209E-01 + 11 3.6588378054E-01 -1.8498522421E-01 -2.0919837005E-01 -2.1871053739E-01 -1.0532210206E-01 + 12 4.5284765708E-01 -1.6692199901E-01 2.8302290755E-01 -5.6965308051E-02 -1.8609153023E-02 + 13 4.4611658080E-02 3.7761280678E-01 -6.1468580659E-01 1.6020066286E-01 1.3339574807E-01 + 14 -2.0720738439E-01 -2.8357955271E-01 4.7115786768E-01 -7.1108309765E-02 -1.0632566115E-01 + +# +# The atoms: label mass x y z (in bohrs) +# +$atoms +5 + C 12.01100 2.047839617847 -0.088420596684 0.053783088045 + H 1.00800 4.092826018168 -0.088421149627 0.053778949384 + H 1.00800 1.366187516126 0.143469429806 1.967823320864 + H 1.00800 1.366172757256 -1.861969055963 -0.702407472861 + H 1.00800 1.366171688335 1.453239943437 -1.104050959314 + +$actual_temperature + 0.000000 + +$frequency_scale_factor + 1.000000 + +$dipole_derivatives +15 + -0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 + -2.0000000000E-01 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 + 0.0000000000E+00 -0.0000000000E+00 -2.0000000000E-01 + 0.0000000000E+00 -0.0000000000E+00 -0.0000000000E+00 + -0.0000000000E+00 -0.0000000000E+00 -0.0000000000E+00 + -0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 + 0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 + -0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + +# +# The IR spectrum +# wavenumber eps Int TX TY TZ +# +$ir_spectrum +15 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 1385.80 0.00013958 0.70539308 0.001478 0.000000 -0.005408 + 1385.81 0.00019152 0.96784245 0.001690 0.000000 -0.006346 + 1385.82 0.00000740 0.03739717 0.000452 0.000000 0.001209 + 1557.27 0.00023456 1.18537657 0.000000 0.000000 0.006856 + 1557.28 0.00000268 0.01354396 -0.000000 0.000000 -0.000733 + 3090.01 0.00358146 18.09925570 -0.013874 0.000000 -0.013008 + 3103.92 0.00037757 1.90806915 -0.002685 0.000000 -0.005545 + 3103.93 0.00321780 16.26144196 0.003340 0.000000 0.017674 + 3103.96 0.00623980 31.53339117 0.022560 0.000000 -0.010881 + + +$end + diff --git a/cmmde_gui/test/metana4/freq/cmmd.in b/cmmde_gui/test/metana4/freq/cmmd.in new file mode 100644 index 0000000..247d130 --- /dev/null +++ b/cmmde_gui/test/metana4/freq/cmmd.in @@ -0,0 +1,13 @@ +#CMMDE generated Orca input file +!XTB2 Numfreq +%pal + nprocs 1 +end + +*xyzfile 0 1 ../cmmd.xyz + +%freq + scalfreq 1 + Temp 298.15 + Pressure 1.0 +end diff --git a/cmmde_gui/test/metana4/freq/cmmd.out b/cmmde_gui/test/metana4/freq/cmmd.out new file mode 100644 index 0000000..a67dfe5 --- /dev/null +++ b/cmmde_gui/test/metana4/freq/cmmd.out @@ -0,0 +1,711 @@ + + ***************** + * O R C A * + ***************** + + #, + ### + #### + ##### + ###### + ########, + ,,################,,,,, + ,,#################################,, + ,,##########################################,, + ,#########################################, ''#####, + ,#############################################,, '####, + ,##################################################,,,,####, + ,###########'''' ''''############################### + ,#####'' ,,,,##########,,,, '''####''' '#### + ,##' ,,,,###########################,,, '## + ' ,,###'''' '''############,,, + ,,##'' '''############,,,, ,,,,,,###'' + ,#'' '''#######################''' + ' ''''####'''' + ,#######, #######, ,#######, ## + ,#' '#, ## ## ,#' '#, #''# ###### ,####, + ## ## ## ,#' ## #' '# # #' '# + ## ## ####### ## ,######, #####, # # + '#, ,#' ## ## '#, ,#' ,# #, ## #, ,# + '#######' ## ## '#######' #' '# #####' # '####' + + + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship and core code : Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 5.0.2 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Marcus Kettner : VPT2 + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : Initial AUTO-CI + Lucas Lang : DCDCAS + Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, + C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT + MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, + LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, + nearIR, NL-DFT gradient (VV10), updates on ESD, + ML-optimized integration grids + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + Liviu Ungur et al : ANISO software + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 5.1.0 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + Shared memory : Shared parallel matrices + BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED + Core in use : SkylakeX + Copyright (c) 2011-2014, The OpenBLAS Project + + + + +*************************************** +The coordinates will be read from file: ../cmmd.xyz +*************************************** + + +Your calculation utilizes the semiempirical GFN2-xTB method +Please cite in your paper: +C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. + + +================================================================================ + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + +WARNING: Gradients needed for Numerical Frequencies + ===> : Setting RunTyp to EnGrad + +WARNING: Found dipole moment calculation with XTB calculation + ===> : Switching off dipole moment calculation + + +WARNING: TRAH-SCF for XTB is not implemented! + ===> : Turning TRAH off! + +================================================================================ + INPUT FILE +================================================================================ +NAME = cmmd.in +| 1> #CMMDE generated Orca input file +| 2> !XTB2 Numfreq +| 3> %pal +| 4> nprocs 1 +| 5> end +| 6> +| 7> *xyzfile 0 1 ../cmmd.xyz +| 8> +| 9> %freq +| 10> scalfreq 1 +| 11> Temp 298.15 +| 12> Pressure 1.0 +| 13> end +| 14> +| 15> ****END OF INPUT**** +================================================================================ + + ******************************* + * Energy+Gradient Calculation * + ******************************* + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 20:29:38.199 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 5 + number of electrons : 8 + charge : 0 + spin : 0.0 + first test random number : 0.25075805179724 + + ID Z sym. atoms + 1 6 C 1 + 2 1 H 2-5 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 8 : + : # atomic orbitals 8 : + : # shells 6 : + : # electrons 8 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -4.2352961 -0.423530E+01 0.243E+00 17.75 0.0 T + 2 -4.2472613 -0.119651E-01 0.928E-01 17.57 1.0 T + 3 -4.2474252 -0.163901E-03 0.500E-01 17.46 1.0 T + 4 -4.2474673 -0.421128E-04 0.924E-02 17.36 1.0 T + 5 -4.2474672 0.111480E-06 0.698E-03 17.35 6.4 T + 6 -4.2474673 -0.145702E-06 0.191E-04 17.35 233.9 T + 7 -4.2474673 -0.109871E-09 0.432E-06 17.35 10345.9 T + + *** convergence criteria satisfied after 7 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.5818361 -15.8326 + 2 2.0000 -0.4674581 -12.7202 + 3 2.0000 -0.4674581 -12.7202 + 4 2.0000 -0.4674578 -12.7202 (HOMO) + 5 0.1702647 4.6331 (LUMO) + 6 0.2292559 6.2384 + 7 0.2292579 6.2384 + 8 0.2292581 6.2384 + ------------------------------------------------------------- + HL-Gap 0.6377225 Eh 17.3533 eV + Fermi-level -0.1485966 Eh -4.0435 eV + + SCC (total) 0 d, 0 h, 0 min, 0.024 sec + SCC setup ... 0 min, 0.000 sec ( 0.144%) + Dispersion ... 0 min, 0.000 sec ( 0.025%) + classical contributions ... 0 min, 0.000 sec ( 0.021%) + integral evaluation ... 0 min, 0.000 sec ( 0.242%) + iterations ... 0 min, 0.023 sec ( 97.633%) + molecular gradient ... 0 min, 0.000 sec ( 1.343%) + printout ... 0 min, 0.000 sec ( 0.558%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -4.175218519975 Eh :: + :: gradient norm 0.000006666600 Eh/a0 :: + :: HOMO-LUMO gap 17.353313369013 eV :: + ::.................................................:: + :: SCC energy -4.247467308419 Eh :: + :: -> isotropic ES 0.002035567941 Eh :: + :: -> anisotropic ES 0.002321540923 Eh :: + :: -> anisotropic XC 0.003585096726 Eh :: + :: -> dispersion -0.000661011606 Eh :: + :: repulsion energy 0.072248782853 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -4.175218519975 Eh | + | GRADIENT NORM 0.000006666600 Eh/α | + | HOMO-LUMO GAP 17.353313369013 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 20:29:38.227 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.028 sec + * cpu-time: 0 d, 0 h, 0 min, 0.007 sec + * ratio c/w: 0.245 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.024 sec + * cpu-time: 0 d, 0 h, 0 min, 0.003 sec + * ratio c/w: 0.117 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -4.175218519980 +------------------------- -------------------- + + +---------------------------------------------------------------------------- + ORCA NUMERICAL FREQUENCIES +---------------------------------------------------------------------------- + +Number of atoms ... 5 +Central differences ... used +Number of displacements ... 30 +Numerical increment ... 5.000e-03 bohr +IR-spectrum generation ... on +Raman-spectrum generation ... off +Surface Crossing Hessian ... off + +The output will be reduced. Please look at the following files: +SCF program output ... >cmmd.lastscf +Integral program output ... >cmmd.lastint +Gradient program output ... >cmmd.lastgrad +Dipole moment program output ... >cmmd.lastmom +AutoCI program output ... >cmmd.lastautoci + + << Calculating on displaced geometry 1 (of 30) >> + << Calculating on displaced geometry 2 (of 30) >> + << Calculating on displaced geometry 3 (of 30) >> + << Calculating on displaced geometry 4 (of 30) >> + << Calculating on displaced geometry 5 (of 30) >> + << Calculating on displaced geometry 6 (of 30) >> + << Calculating on displaced geometry 7 (of 30) >> + << Calculating on displaced geometry 8 (of 30) >> + << Calculating on displaced geometry 9 (of 30) >> + << Calculating on displaced geometry 10 (of 30) >> + << Calculating on displaced geometry 11 (of 30) >> + << Calculating on displaced geometry 12 (of 30) >> + << Calculating on displaced geometry 13 (of 30) >> + << Calculating on displaced geometry 14 (of 30) >> + << Calculating on displaced geometry 15 (of 30) >> + << Calculating on displaced geometry 16 (of 30) >> + << Calculating on displaced geometry 17 (of 30) >> + << Calculating on displaced geometry 18 (of 30) >> + << Calculating on displaced geometry 19 (of 30) >> + << Calculating on displaced geometry 20 (of 30) >> + << Calculating on displaced geometry 21 (of 30) >> + << Calculating on displaced geometry 22 (of 30) >> + << Calculating on displaced geometry 23 (of 30) >> + << Calculating on displaced geometry 24 (of 30) >> + << Calculating on displaced geometry 25 (of 30) >> + << Calculating on displaced geometry 26 (of 30) >> + << Calculating on displaced geometry 27 (of 30) >> + << Calculating on displaced geometry 28 (of 30) >> + << Calculating on displaced geometry 29 (of 30) >> + << Calculating on displaced geometry 30 (of 30) >> + +----------------------- +VIBRATIONAL FREQUENCIES +----------------------- + +Scaling factor for frequencies = 1.000000000 (already applied!) + + 0: 0.00 cm**-1 + 1: 0.00 cm**-1 + 2: 0.00 cm**-1 + 3: 0.00 cm**-1 + 4: 0.00 cm**-1 + 5: 0.00 cm**-1 + 6: 1385.80 cm**-1 + 7: 1385.81 cm**-1 + 8: 1385.82 cm**-1 + 9: 1557.27 cm**-1 + 10: 1557.28 cm**-1 + 11: 3090.01 cm**-1 + 12: 3103.92 cm**-1 + 13: 3103.93 cm**-1 + 14: 3103.96 cm**-1 + + +------------ +NORMAL MODES +------------ + +These modes are the cartesian displacements weighted by the diagonal matrix +M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom +Thus, these vectors are normalized but *not* orthogonal + + 0 1 2 3 4 5 + 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 1 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 2 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 7 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 8 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 9 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 10 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 11 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 12 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 13 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 14 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 6 7 8 9 10 11 + 0 -0.083181 -0.095074 -0.025444 0.000002 0.000001 0.000103 + 1 -0.017257 0.046888 -0.118782 0.000003 -0.000000 -0.000027 + 2 -0.096895 0.073267 0.042998 0.000008 0.000000 0.000059 + 3 -0.038700 -0.044237 -0.011840 -0.000001 0.000000 0.498981 + 4 0.081116 -0.220410 0.558397 -0.177404 0.467477 -0.000013 + 5 0.455472 -0.344408 -0.202135 -0.467516 -0.177392 0.000026 + 6 0.502800 0.265142 0.058899 -0.457679 -0.113027 -0.166553 + 7 0.043095 -0.158575 0.579054 0.099538 -0.486698 0.056663 + 8 0.141567 0.166120 -0.031650 -0.175046 0.018711 0.467838 + 9 0.255833 0.509037 -0.045014 0.326713 -0.339832 -0.166731 + 10 -0.270718 -0.058817 0.130065 -0.247605 -0.025387 -0.433941 + 11 0.305522 -0.275540 -0.384766 0.286231 0.365884 -0.184985 + 12 0.271229 0.402930 0.301143 0.130948 0.452848 -0.166922 + 13 0.352135 -0.120899 0.147855 0.325438 0.044612 0.377613 + 14 0.252011 -0.419201 0.106199 0.356233 -0.207207 -0.283580 + 12 13 14 + 0 -0.010176 0.012673 0.085763 + 1 0.077938 0.039157 0.003462 + 2 -0.037969 0.076978 -0.015880 + 3 0.100740 -0.125310 -0.846332 + 4 0.036044 0.018108 0.001601 + 5 -0.017560 0.035600 -0.007341 + 6 -0.085046 0.254663 -0.108325 + 7 0.063375 -0.066530 0.051945 + 8 0.208029 -0.663028 0.408208 + 9 -0.177458 -0.223389 -0.048657 + 10 -0.413417 -0.578355 -0.228197 + 11 -0.209198 -0.218711 -0.105322 + 12 0.283023 -0.056965 -0.018609 + 13 -0.614686 0.160201 0.133396 + 14 0.471158 -0.071108 -0.106326 + + +----------- +IR SPECTRUM +----------- + + Mode freq eps Int T**2 TX TY TZ + cm**-1 L/(mol*cm) km/mol a.u. +---------------------------------------------------------------------------- + 6: 1385.80 0.000140 0.71 0.000031 ( 0.001478 0.000000 -0.005408) + 7: 1385.81 0.000192 0.97 0.000043 ( 0.001690 0.000000 -0.006346) + 8: 1385.82 0.000007 0.04 0.000002 ( 0.000452 0.000000 0.001209) + 9: 1557.27 0.000235 1.19 0.000047 ( 0.000000 0.000000 0.006856) + 10: 1557.28 0.000003 0.01 0.000001 (-0.000000 0.000000 -0.000733) + 11: 3090.01 0.003581 18.10 0.000362 (-0.013874 0.000000 -0.013008) + 12: 3103.92 0.000378 1.91 0.000038 (-0.002685 0.000000 -0.005545) + 13: 3103.93 0.003218 16.26 0.000324 ( 0.003340 0.000000 0.017674) + 14: 3103.96 0.006240 31.53 0.000627 ( 0.022560 0.000000 -0.010881) + +* The epsilon (eps) is given for a Dirac delta lineshape. +** The dipole moment derivative (T) already includes vibrational overlap. + +The first frequency considered to be a vibration is 6 +The total number of vibrations considered is 9 + + +-------------------------- +THERMOCHEMISTRY AT 298.15K +-------------------------- + +Temperature ... 298.15 K +Pressure ... 1.00 atm +Total Mass ... 16.04 AMU + +Throughout the following assumptions are being made: + (1) The electronic state is orbitally nondegenerate + (2) There are no thermally accessible electronically excited states + (3) Hindered rotations indicated by low frequency modes are not + treated as such but are treated as vibrations and this may + cause some error + (4) All equations used are the standard statistical mechanics + equations for an ideal gas + (5) All vibrations are strictly harmonic + +freq. 1385.80 E(vib) ... 0.00 +freq. 1385.81 E(vib) ... 0.00 +freq. 1385.82 E(vib) ... 0.00 +freq. 1557.27 E(vib) ... 0.00 +freq. 1557.28 E(vib) ... 0.00 +freq. 3090.01 E(vib) ... 0.00 +freq. 3103.92 E(vib) ... 0.00 +freq. 3103.93 E(vib) ... 0.00 +freq. 3103.96 E(vib) ... 0.00 + +------------ +INNER ENERGY +------------ + +The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans) + E(el) - is the total energy from the electronic structure calculation + = E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc) + E(ZPE) - the the zero temperature vibrational energy from the frequency calculation + E(vib) - the the finite temperature correction to E(ZPE) due to population + of excited vibrational states + E(rot) - is the rotational thermal energy + E(trans)- is the translational thermal energy + +Summary of contributions to the inner energy U: +Electronic energy ... -4.17521852 Eh +Zero point energy ... 0.04482019 Eh 28.13 kcal/mol +Thermal vibrational correction ... 0.00003140 Eh 0.02 kcal/mol +Thermal rotational correction ... 0.00141627 Eh 0.89 kcal/mol +Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol +----------------------------------------------------------------------- +Total thermal energy -4.12753439 Eh + + +Summary of corrections to the electronic energy: +(perhaps to be used in another calculation) +Total thermal correction 0.00286394 Eh 1.80 kcal/mol +Non-thermal (ZPE) correction 0.04482019 Eh 28.13 kcal/mol +----------------------------------------------------------------------- +Total correction 0.04768413 Eh 29.92 kcal/mol + + +-------- +ENTHALPY +-------- + +The enthalpy is H = U + kB*T + kB is Boltzmann's constant +Total free energy ... -4.12753439 Eh +Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol +----------------------------------------------------------------------- +Total Enthalpy ... -4.12659018 Eh + + +Note: Rotational entropy computed according to Herzberg +Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945 +Point Group: Td, Symmetry Number: 12 +Rotational constants in cm-1: 5.355313 5.355311 5.355302 + +Vibrational entropy computed according to the QRRHO of S. Grimme +Chem.Eur.J. 2012 18 9955 + + +------- +ENTROPY +------- + +The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans)) + S(el) - electronic entropy + S(vib) - vibrational entropy + S(rot) - rotational entropy + S(trans)- translational entropy +The entropies will be listed as multiplied by the temperature to get +units of energy + +Electronic entropy ... 0.00000000 Eh 0.00 kcal/mol +Vibrational entropy ... 0.00003597 Eh 0.02 kcal/mol +Rotational entropy ... 0.00478798 Eh 3.00 kcal/mol +Translational entropy ... 0.01627961 Eh 10.22 kcal/mol +----------------------------------------------------------------------- +Final entropy term ... 0.02110356 Eh 13.24 kcal/mol + +In case the symmetry of your molecule has not been determined correctly +or in case you have a reason to use a different symmetry number we print +out the resulting rotational entropy values for sn=1,12 : + -------------------------------------------------------- +| sn= 1 | S(rot)= 0.00713418 Eh 4.48 kcal/mol| +| sn= 2 | S(rot)= 0.00647973 Eh 4.07 kcal/mol| +| sn= 3 | S(rot)= 0.00609689 Eh 3.83 kcal/mol| +| sn= 4 | S(rot)= 0.00582527 Eh 3.66 kcal/mol| +| sn= 5 | S(rot)= 0.00561458 Eh 3.52 kcal/mol| +| sn= 6 | S(rot)= 0.00544244 Eh 3.42 kcal/mol| +| sn= 7 | S(rot)= 0.00529689 Eh 3.32 kcal/mol| +| sn= 8 | S(rot)= 0.00517081 Eh 3.24 kcal/mol| +| sn= 9 | S(rot)= 0.00505960 Eh 3.17 kcal/mol| +| sn=10 | S(rot)= 0.00496012 Eh 3.11 kcal/mol| +| sn=11 | S(rot)= 0.00487013 Eh 3.06 kcal/mol| +| sn=12 | S(rot)= 0.00478798 Eh 3.00 kcal/mol| + -------------------------------------------------------- + + +------------------- +GIBBS FREE ENERGY +------------------- + +The Gibbs free energy is G = H - T*S + +Total enthalpy ... -4.12659018 Eh +Total entropy correction ... -0.02110356 Eh -13.24 kcal/mol +----------------------------------------------------------------------- +Final Gibbs free energy ... -4.14769375 Eh + +For completeness - the Gibbs free energy minus the electronic energy +G-E(el) ... 0.02752477 Eh 17.27 kcal/mol + + + +Timings for individual modules: + +Sum of individual times ... 37.777 sec (= 0.630 min) +Numerical frequency calculation ... 37.715 sec (= 0.629 min) 99.8 % +XTB module ... 0.063 sec (= 0.001 min) 0.2 % + ****ORCA TERMINATED NORMALLY**** +TOTAL RUN TIME: 0 days 0 hours 0 minutes 37 seconds 784 msec diff --git a/cmmde_gui/test/metana4/freq/cmmd.xtbrestart b/cmmde_gui/test/metana4/freq/cmmd.xtbrestart new file mode 100644 index 0000000000000000000000000000000000000000..974288da439a28d93e6bdb9fd71a362587d37b04 GIT binary patch literal 488 zcmXqDU|?VZVi17QtPm~(8A#dz;Q1Y3XLF-nvh>+XJDyDY zYt4Ul+edc-50^JVsG=G)%(3z|6aNKb;mxN?+X~}8G`LLoV@l9BpziDXOy&J z(f;$l*L-zOuH3(Q=Lcz>7pwO3S3X^~-Eh_ZpLv(>gkG9x|FuM2-TlNid&R4tM1z3p zEo7G7>v3ISKePD&!`mqv?U}NsKU}bBihY3VDyjExR@uKd?0enbxM07a@3N3kpn7q+ vosZ=um+nta?ApG6*J69s>kkT_Z cmmd.out --oversubscribe diff --git a/cmmde_gui/test/metana4/freq/slurm-2912.out b/cmmde_gui/test/metana4/freq/slurm-2912.out new file mode 100644 index 0000000..e69de29 diff --git a/cmmde_gui/test/metana4/geom.smi b/cmmde_gui/test/metana4/geom.smi new file mode 100644 index 0000000..3cc58df --- /dev/null +++ b/cmmde_gui/test/metana4/geom.smi @@ -0,0 +1 @@ +C diff --git a/cmmde_gui/test/metana4/geom.xyz b/cmmde_gui/test/metana4/geom.xyz new file mode 100644 index 0000000..017e7f8 --- /dev/null +++ b/cmmde_gui/test/metana4/geom.xyz @@ -0,0 +1,7 @@ +5 + +C 1.08367 -0.04679 0.02846 +H 2.17587 -0.04679 0.02846 +H 0.71961 0.07706 1.05072 +H 0.71960 -0.99402 -0.37541 +H 0.71960 0.77659 -0.58992 diff --git a/cmmde_gui/test/metana4/run.sh b/cmmde_gui/test/metana4/run.sh new file mode 100644 index 0000000..f72e163 --- /dev/null +++ b/cmmde_gui/test/metana4/run.sh @@ -0,0 +1,10 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH +export PATH=/home/adit/opt/openmpi411/bin:$PATH +export OMP_NUM_THREADS=1 +cd $PWD +$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe diff --git a/cmmde_gui/test/metana4/run_babel.sh b/cmmde_gui/test/metana4/run_babel.sh new file mode 100644 index 0000000..0d5d00e --- /dev/null +++ b/cmmde_gui/test/metana4/run_babel.sh @@ -0,0 +1,8 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export OMP_NUM_THREADS=1 +cd $PWD +obabel geom.smi -O geom.xyz --gen3d diff --git a/cmmde_gui/test/metana4/slurm-2910.out b/cmmde_gui/test/metana4/slurm-2910.out new file mode 100644 index 0000000..b7d75ac --- /dev/null +++ b/cmmde_gui/test/metana4/slurm-2910.out @@ -0,0 +1 @@ +1 molecule converted diff --git a/cmmde_gui/test/metana4/slurm-2911.out b/cmmde_gui/test/metana4/slurm-2911.out new file mode 100644 index 0000000..e69de29 diff --git a/cmmde_gui/test/metana5/cmmd.engrad b/cmmde_gui/test/metana5/cmmd.engrad new file mode 100644 index 0000000..ac8d095 --- /dev/null +++ b/cmmde_gui/test/metana5/cmmd.engrad @@ -0,0 +1,34 @@ +# +# 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z=G)KdC~rCC*bg25j?Kl(H@yC$PxQ}-=f#(_()s4i#W&9WkAFV+@XbZ+uOBPE{=BP) zR(^DI@rnKeE*SgPKIL~GKJD%+Kh-K<^$)9l{OFpFbe?=xyC2W}X3T%9ERH$z`jhvc zk^1-j%1aKM_2xfXnD@_Srv0?-k6--sFF$w7DZg!(tIAB3#ZAS3e(UmAU;AK3SUI#%RFUjjMoXT zOZVUH+g|Q}zqIb%tFD zYjY+~%Xjij7bkvdYiUpXd|r0qaueroYkL0NbTOwj-EvdsPh9WRd5<^#MAx^iG@ocb zc2#=YTF>4#Jv-;Px8;A@{8snjg|g+}?}~9v`}a8(zVf;E{@`T?x5uYV&jL?Pf%<;U z_&Y5ZpSfYf!*6Mo$6fQ|pMJUbqGI^Ijh8&|qZ`)7f*)A@rqh+z-*fWUj}O1Na``^< z%YC;Z^6@|T-m@+`eNK7z>NAHwU8QmD&n`H=bx%%Xyt=RLgtuM1X2bDstbZV7>hBT7 z1po2aB}ae%n-3LhFFW9l@r94BU3u*VA9~KMzfAeqzBIl+c+y|rS*0=j)hpk7)=M`P xcfI$=R~@_JfgMWYSy#XHIUB1q{{7djgATmy`r : Switching off AutoStart + For restart on a previous wavefunction, please use MOREAD + +WARNING: Found dipole moment calculation with XTB calculation + ===> : Switching off dipole moment calculation + + +WARNING: TRAH-SCF for XTB is not implemented! + ===> : Turning TRAH off! + +================================================================================ + INPUT FILE +================================================================================ +NAME = cmmd.in +| 1> #CMMDE generated Orca input file +| 2> !XTB2 opt +| 3> %pal +| 4> nprocs 1 +| 5> end +| 6> %geom +| 7> maxiter 9999 +| 8> end +| 9> +| 10> *xyzfile 0 1 geom.xyz +| 11> +| 12> +| 13> ****END OF INPUT**** +================================================================================ + + ***************************** + * Geometry Optimization Run * + ***************************** + +Geometry optimization settings: +Update method Update .... BFGS +Choice of coordinates CoordSys .... Z-matrix Internals +Initial Hessian InHess .... Almoef's Model + +Convergence Tolerances: +Energy Change TolE .... 5.0000e-06 Eh +Max. Gradient TolMAXG .... 3.0000e-04 Eh/bohr +RMS Gradient TolRMSG .... 1.0000e-04 Eh/bohr +Max. Displacement TolMAXD .... 4.0000e-03 bohr +RMS Displacement TolRMSD .... 2.0000e-03 bohr +Strict Convergence .... False +------------------------------------------------------------------------------ + ORCA OPTIMIZATION COORDINATE SETUP +------------------------------------------------------------------------------ + +The optimization will be done in new redundant internal coordinates +Making redundant internal coordinates ... (new redundants) done +Evaluating the initial hessian ... (Almloef) done +Evaluating the coordinates ... done +Calculating the B-matrix .... done +Calculating the G-matrix .... done +Diagonalizing the G-matrix .... done +The first mode is .... 1 +The number of degrees of freedom .... 9 + + ----------------------------------------------------------------- + Redundant Internal Coordinates + + + ----------------------------------------------------------------- + Definition Initial Value Approx d2E/dq + ----------------------------------------------------------------- + 1. B(H 1,C 0) 1.0922 0.357201 + 2. B(H 2,C 0) 1.0922 0.357206 + 3. B(H 3,C 0) 1.0922 0.357210 + 4. B(H 4,C 0) 1.0922 0.357197 + 5. A(H 1,C 0,H 3) 109.4710 0.290103 + 6. A(H 2,C 0,H 3) 109.4715 0.290104 + 7. A(H 1,C 0,H 4) 109.4708 0.290102 + 8. A(H 2,C 0,H 4) 109.4717 0.290102 + 9. A(H 3,C 0,H 4) 109.4714 0.290103 + 10. A(H 1,C 0,H 2) 109.4709 0.290103 + ----------------------------------------------------------------- + +Number of atoms .... 5 +Number of degrees of freedom .... 10 + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 1 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.081340 0.007600 -0.057670 + H 2.173540 0.007600 -0.057670 + H 0.717280 -0.907330 -0.530170 + H 0.717280 0.874260 -0.613770 + H 0.717280 0.055870 0.970940 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.043436 0.014362 -0.108981 + 1 H 1.0000 0 1.008 4.107395 0.014362 -0.108981 + 2 H 1.0000 0 1.008 1.355463 -1.714605 -1.001876 + 3 H 1.0000 0 1.008 1.355463 1.652112 -1.159857 + 4 H 1.0000 0 1.008 1.355463 0.105579 1.834811 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/23 at 18:46:45.983 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 5 + number of electrons : 8 + charge : 0 + spin : 0.0 + first test random number : 0.74772564092488 + + ID Z sym. atoms + 1 6 C 1 + 2 1 H 2-5 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 8 : + : # atomic orbitals 8 : + : # shells 6 : + : # electrons 8 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -4.2288352 -0.422884E+01 0.246E+00 17.25 0.0 T + 2 -4.2416604 -0.128252E-01 0.917E-01 17.07 1.0 T + 3 -4.2418083 -0.147906E-03 0.503E-01 16.97 1.0 T + 4 -4.2418548 -0.465207E-04 0.968E-02 16.85 1.0 T + 5 -4.2418547 0.611469E-07 0.615E-03 16.85 7.3 T + 6 -4.2418549 -0.109447E-06 0.181E-04 16.85 247.0 T + 7 -4.2418549 -0.991518E-10 0.317E-06 16.85 14126.0 T + + *** convergence criteria satisfied after 7 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.5801036 -15.7854 + 2 2.0000 -0.4667175 -12.7000 + 3 2.0000 -0.4667173 -12.7000 + 4 2.0000 -0.4667165 -12.7000 (HOMO) + 5 0.1525565 4.1513 (LUMO) + 6 0.2134380 5.8079 + 7 0.2134451 5.8081 + 8 0.2134519 5.8083 + ------------------------------------------------------------- + HL-Gap 0.6192730 Eh 16.8513 eV + Fermi-level -0.1570800 Eh -4.2744 eV + + SCC (total) 0 d, 0 h, 0 min, 0.036 sec + SCC setup ... 0 min, 0.000 sec ( 0.170%) + Dispersion ... 0 min, 0.000 sec ( 0.042%) + classical contributions ... 0 min, 0.000 sec ( 0.782%) + integral evaluation ... 0 min, 0.000 sec ( 0.279%) + iterations ... 0 min, 0.034 sec ( 95.709%) + molecular gradient ... 0 min, 0.000 sec ( 0.514%) + printout ... 0 min, 0.001 sec ( 2.487%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -4.174962274603 Eh :: + :: gradient norm 0.013368935124 Eh/a0 :: + :: HOMO-LUMO gap 16.851277165007 eV :: + ::.................................................:: + :: SCC energy -4.241854854840 Eh :: + :: -> isotropic ES 0.001954141581 Eh :: + :: -> anisotropic ES 0.002520379492 Eh :: + :: -> anisotropic XC 0.003827619754 Eh :: + :: -> dispersion -0.000662667298 Eh :: + :: repulsion energy 0.066892574272 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -4.174962274603 Eh | + | GRADIENT NORM 0.013368935124 Eh/α | + | HOMO-LUMO GAP 16.851277165007 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/23 at 18:46:46.046 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.063 sec + * cpu-time: 0 d, 0 h, 0 min, 0.015 sec + * ratio c/w: 0.239 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.036 sec + * cpu-time: 0 d, 0 h, 0 min, 0.005 sec + * ratio c/w: 0.127 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -4.174962274600 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 5 +Number of internal coordinates .... 10 +Current Energy .... -4.174962275 Eh +Current gradient norm .... 0.013368935 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Evaluating the initial hessian .... (Almloef) done +Projecting the Hessian .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999302309 +Lowest eigenvalues of augmented Hessian: + -0.000499655 0.290101956 0.290102552 0.290102915 0.290103277 +Length of the computed step .... 0.037374365 +The final length of the internal step .... 0.037374365 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0118188118 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0096500193 RMS(Int)= 0.0118188118 + Iter 1: RMS(Cart)= 0.0000000144 RMS(Int)= 0.0000000176 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + RMS gradient 0.0042276282 0.0001000000 NO + MAX gradient 0.0066875949 0.0003000000 NO + RMS step 0.0118188118 0.0020000000 NO + MAX step 0.0186962756 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0099 Max(Angles) 0.00 + Max(Dihed) 0.00 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(H 1,C 0) 1.0922 0.006685 -0.0099 1.0823 + 2. B(H 2,C 0) 1.0922 0.006684 -0.0099 1.0823 + 3. B(H 3,C 0) 1.0922 0.006682 -0.0099 1.0823 + 4. B(H 4,C 0) 1.0922 0.006688 -0.0099 1.0823 + 5. A(H 1,C 0,H 3) 109.47 -0.000001 0.00 109.47 + 6. A(H 2,C 0,H 3) 109.47 0.000000 -0.00 109.47 + 7. A(H 1,C 0,H 4) 109.47 -0.000001 0.00 109.47 + 8. A(H 2,C 0,H 4) 109.47 0.000001 -0.00 109.47 + 9. A(H 3,C 0,H 4) 109.47 0.000000 -0.00 109.47 + 10. A(H 1,C 0,H 2) 109.47 -0.000001 0.00 109.47 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 2 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.081342 0.007600 -0.057669 + H 2.163652 0.007600 -0.057669 + H 0.720575 -0.899047 -0.525890 + H 0.720574 0.866416 -0.608735 + H 0.720577 0.055432 0.961623 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.043440 0.014362 -0.108978 + 1 H 1.0000 0 1.008 4.088710 0.014361 -0.108978 + 2 H 1.0000 0 1.008 1.361689 -1.698953 -0.993788 + 3 H 1.0000 0 1.008 1.361688 1.637289 -1.150343 + 4 H 1.0000 0 1.008 1.361693 0.104751 1.817204 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/23 at 18:46:46.068 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 5 + number of electrons : 8 + charge : 0 + spin : 0.0 + first test random number : 0.35247950262600 + + ID Z sym. atoms + 1 6 C 1 + 2 1 H 2-5 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 8 : + : # atomic orbitals 8 : + : # shells 6 : + : # electrons 8 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -4.2473771 -0.424738E+01 0.106E-01 17.33 0.0 T + 2 -4.2473844 -0.729535E-05 0.561E-02 17.34 1.0 T + 3 -4.2473846 -0.259696E-06 0.204E-02 17.34 2.2 T + 4 -4.2473847 -0.370487E-07 0.422E-03 17.35 10.6 T + 5 -4.2473847 -0.969713E-11 0.246E-05 17.35 1817.7 T + 6 -4.2473847 -0.112799E-11 0.116E-07 17.35 100000.0 T + + *** convergence criteria satisfied after 6 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.5818102 -15.8319 + 2 2.0000 -0.4674473 -12.7199 + 3 2.0000 -0.4674472 -12.7199 + 4 2.0000 -0.4674467 -12.7199 (HOMO) + 5 0.1699963 4.6258 (LUMO) + 6 0.2290154 6.2318 + 7 0.2290188 6.2319 + 8 0.2290200 6.2320 + ------------------------------------------------------------- + HL-Gap 0.6374430 Eh 17.3457 eV + Fermi-level -0.1487252 Eh -4.0470 eV + + SCC (total) 0 d, 0 h, 0 min, 0.005 sec + SCC setup ... 0 min, 0.000 sec ( 1.480%) + Dispersion ... 0 min, 0.000 sec ( 0.377%) + classical contributions ... 0 min, 0.000 sec ( 0.125%) + integral evaluation ... 0 min, 0.000 sec ( 2.680%) + iterations ... 0 min, 0.004 sec ( 86.764%) + molecular gradient ... 0 min, 0.000 sec ( 5.987%) + printout ... 0 min, 0.000 sec ( 2.449%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -4.175218465764 Eh :: + :: gradient norm 0.000198767447 Eh/a0 :: + :: HOMO-LUMO gap 17.345708045043 eV :: + ::.................................................:: + :: SCC energy -4.247384680229 Eh :: + :: -> isotropic ES 0.002034388487 Eh :: + :: -> anisotropic ES 0.002324462887 Eh :: + :: -> anisotropic XC 0.003588680025 Eh :: + :: -> dispersion -0.000661035657 Eh :: + :: repulsion energy 0.072166208869 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -4.175218465764 Eh | + | GRADIENT NORM 0.000198767447 Eh/α | + | HOMO-LUMO GAP 17.345708045043 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/23 at 18:46:46.079 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.011 sec + * cpu-time: 0 d, 0 h, 0 min, 0.011 sec + * ratio c/w: 0.942 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.005 sec + * cpu-time: 0 d, 0 h, 0 min, 0.005 sec + * ratio c/w: 0.882 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -4.175218465760 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 5 +Number of internal coordinates .... 10 +Current Energy .... -4.175218466 Eh +Current gradient norm .... 0.000198767 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999999841 +Lowest eigenvalues of augmented Hessian: + -0.000000112 0.290101948 0.290102550 0.290102911 0.290103277 +Length of the computed step .... 0.000564053 +The final length of the internal step .... 0.000564053 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0001783691 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0001456367 RMS(Int)= 0.0001783691 + Iter 1: RMS(Cart)= 0.0000000001 RMS(Int)= 0.0000000002 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0002561912 0.0000050000 NO + RMS gradient 0.0000628542 0.0001000000 YES + MAX gradient 0.0000996228 0.0003000000 YES + RMS step 0.0001783691 0.0020000000 YES + MAX step 0.0002827128 0.0040000000 YES + ........................................................ + Max(Bonds) 0.0001 Max(Angles) 0.00 + Max(Dihed) 0.00 Max(Improp) 0.00 + --------------------------------------------------------------------- + + Everything but the energy has converged. However, the energy + appears to be close enough to convergence to make sure that the + final evaluation at the new geometry represents the equilibrium energy. + Convergence will therefore be signaled now + + + ***********************HURRAY******************** + *** THE OPTIMIZATION HAS CONVERGED *** + ************************************************* + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + + --- Optimized Parameters --- + (Angstroem and degrees) + + Definition OldVal dE/dq Step FinalVal + ---------------------------------------------------------------------------- + 1. B(H 1,C 0) 1.0823 0.000100 -0.0001 1.0822 + 2. B(H 2,C 0) 1.0823 0.000099 -0.0001 1.0822 + 3. B(H 3,C 0) 1.0823 0.000099 -0.0001 1.0822 + 4. B(H 4,C 0) 1.0823 0.000100 -0.0001 1.0822 + 5. A(H 1,C 0,H 3) 109.47 -0.000000 0.00 109.47 + 6. A(H 2,C 0,H 3) 109.47 0.000001 -0.00 109.47 + 7. A(H 1,C 0,H 4) 109.47 -0.000001 0.00 109.47 + 8. A(H 2,C 0,H 4) 109.47 0.000000 -0.00 109.47 + 9. A(H 3,C 0,H 4) 109.47 0.000000 -0.00 109.47 + 10. A(H 1,C 0,H 2) 109.47 -0.000000 0.00 109.47 + ---------------------------------------------------------------------------- + ******************************************************* + *** FINAL ENERGY EVALUATION AT THE STATIONARY POINT *** + *** (AFTER 2 CYCLES) *** + ******************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.081343 0.007600 -0.057668 + H 2.163503 0.007600 -0.057669 + H 0.720624 -0.898922 -0.525825 + H 0.720624 0.866297 -0.608659 + H 0.720626 0.055425 0.961482 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.043442 0.014362 -0.108977 + 1 H 1.0000 0 1.008 4.088429 0.014362 -0.108978 + 2 H 1.0000 0 1.008 1.361782 -1.698716 -0.993665 + 3 H 1.0000 0 1.008 1.361781 1.637064 -1.150200 + 4 H 1.0000 0 1.008 1.361786 0.104738 1.816937 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/23 at 18:46:46.101 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 5 + number of electrons : 8 + charge : 0 + spin : 0.0 + first test random number : 0.00923344480437 + + ID Z sym. atoms + 1 6 C 1 + 2 1 H 2-5 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 8 : + : # atomic orbitals 8 : + : # shells 6 : + : # electrons 8 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -4.2474673 -0.424747E+01 0.161E-03 17.35 0.0 T + 2 -4.2474673 -0.163783E-08 0.849E-04 17.35 52.7 T + 3 -4.2474673 -0.599965E-10 0.305E-04 17.35 146.8 T + + *** convergence criteria satisfied after 3 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.5818333 -15.8325 + 2 2.0000 -0.4674557 -12.7201 + 3 2.0000 -0.4674557 -12.7201 + 4 2.0000 -0.4674554 -12.7201 (HOMO) + 5 0.1702655 4.6332 (LUMO) + 6 0.2292571 6.2384 + 7 0.2292590 6.2385 + 8 0.2292595 6.2385 + ------------------------------------------------------------- + HL-Gap 0.6377209 Eh 17.3533 eV + Fermi-level -0.1485950 Eh -4.0435 eV + + SCC (total) 0 d, 0 h, 0 min, 0.003 sec + SCC setup ... 0 min, 0.000 sec ( 4.599%) + Dispersion ... 0 min, 0.000 sec ( 0.724%) + classical contributions ... 0 min, 0.000 sec ( 0.473%) + integral evaluation ... 0 min, 0.000 sec ( 3.824%) + iterations ... 0 min, 0.002 sec ( 81.147%) + molecular gradient ... 0 min, 0.000 sec ( 6.480%) + printout ... 0 min, 0.000 sec ( 2.568%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -4.175218519967 Eh :: + :: gradient norm 0.000005402957 Eh/a0 :: + :: HOMO-LUMO gap 17.353268451038 eV :: + ::.................................................:: + :: SCC energy -4.247467308156 Eh :: + :: -> isotropic ES 0.002035507816 Eh :: + :: -> anisotropic ES 0.002321507907 Eh :: + :: -> anisotropic XC 0.003585039049 Eh :: + :: -> dispersion -0.000661012503 Eh :: + :: repulsion energy 0.072248782598 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -4.175218519967 Eh | + | GRADIENT NORM 0.000005402957 Eh/α | + | HOMO-LUMO GAP 17.353268451038 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/23 at 18:46:46.110 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.009 sec + * cpu-time: 0 d, 0 h, 0 min, 0.009 sec + * ratio c/w: 0.896 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.003 sec + * cpu-time: 0 d, 0 h, 0 min, 0.002 sec + * ratio c/w: 0.680 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -4.175218519970 +------------------------- -------------------- + + *** OPTIMIZATION RUN DONE *** + +Timings for individual modules: + +Sum of individual times ... 0.159 sec (= 0.003 min) +Geometry relaxation ... 0.040 sec (= 0.001 min) 25.0 % +XTB module ... 0.119 sec (= 0.002 min) 75.0 % + ****ORCA TERMINATED NORMALLY**** +TOTAL RUN TIME: 0 days 0 hours 0 minutes 0 seconds 267 msec diff --git a/cmmde_gui/test/metana5/cmmd.xtbrestart b/cmmde_gui/test/metana5/cmmd.xtbrestart new 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+$normal_modes +15 15 + 0 1 2 3 4 + 0 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 1 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 2 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 3 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 4 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 5 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 6 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 7 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 8 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 9 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 10 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 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-1.2995464812E-01 -2.6788493062E-01 + 7 0.0000000000E+00 2.9099460503E-01 5.2286366308E-02 1.5676980114E-01 2.7291280052E-01 + 8 0.0000000000E+00 -2.1306253368E-01 -3.9442808543E-01 -3.1309282747E-01 -3.2206546012E-01 + 9 0.0000000000E+00 -3.5505152961E-01 3.8437266310E-01 2.2977400381E-01 -2.0198790287E-01 + 10 0.0000000000E+00 -3.0913561181E-01 -1.3091832357E-01 1.5964008458E-01 -3.0405607972E-01 + 11 0.0000000000E+00 -1.8411528768E-01 -4.4772038599E-01 1.9608827343E-01 -3.4163278167E-01 + 12 0.0000000000E+00 -5.4811022662E-01 1.6043325688E-01 2.0337255488E-02 4.6989044207E-01 + 13 0.0000000000E+00 -7.2137433220E-03 -6.7527469103E-02 6.0138423114E-01 -3.2516835117E-02 + 14 0.0000000000E+00 -1.7351984003E-01 1.1990870272E-01 -1.3767832842E-02 1.6783071716E-01 + 10 11 12 13 14 + 0 3.1994872509E-07 -9.2432081897E-05 -5.4343359797E-03 -2.8446098991E-02 -8.2345029786E-02 + 1 -1.5108210556E-06 1.0770600240E-05 8.5682011078E-02 -1.6677843455E-02 1.0678227446E-04 + 2 1.4964506359E-07 -6.8753951946E-05 -1.5767957277E-02 -8.0821547902E-02 2.8960646009E-02 + 3 7.9423020652E-08 -4.9908240777E-01 5.3770757743E-02 2.8109924355E-01 8.1247173594E-01 + 4 4.9593792877E-01 5.0587520831E-06 3.9625362479E-02 -7.7129039652E-03 4.9442937052E-05 + 5 -6.3669189237E-02 -3.2026734230E-05 -7.2923242998E-03 -3.7377773813E-02 1.3391944848E-02 + 6 -3.8789758809E-01 1.6679977207E-01 -2.1987020400E-01 1.8768978701E-01 1.2818429973E-02 + 7 -8.5213488594E-03 4.1930269185E-01 -5.0661386304E-01 4.9703773487E-01 1.2797468300E-01 + 8 3.1537773018E-01 2.1650437726E-01 -2.8938826281E-01 2.2328633840E-01 7.9457830564E-02 + 9 4.2593938445E-01 1.6687857714E-01 2.6526509960E-01 1.1535825898E-01 5.7892675694E-03 + 10 1.1045794906E-02 -3.9735996097E-01 -5.9782550379E-01 -3.1364808990E-01 -1.0439388788E-01 + 11 -2.6163413879E-01 2.5493902886E-01 4.0173391290E-01 1.5892227387E-01 8.0410742753E-02 + 12 -3.8045688189E-02 1.6650544917E-01 -3.4411874126E-02 -2.4519283024E-01 1.5011714664E-01 + 13 -4.9844437237E-01 -2.2076128599E-02 4.3855041007E-02 2.3051014690E-02 -2.4902620899E-02 + 14 9.9238147318E-03 -4.7059212967E-01 8.2832522273E-02 6.1821242727E-01 -5.1834615230E-01 + +# +# The atoms: label mass x y z (in bohrs) +# +$atoms +5 + C 12.01100 2.043441533093 0.014361775768 -0.108977471450 + H 1.00800 4.088428822464 0.014361600955 -0.108978286738 + H 1.00800 1.361782268872 -1.698716011169 -0.993665474494 + H 1.00800 1.361781467806 1.637064463077 -1.150199588032 + H 1.00800 1.361785990560 0.104737764458 1.816937187259 + +$actual_temperature + 0.000000 + +$frequency_scale_factor + 1.000000 + +$dipole_derivatives +15 + -0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 + -2.0000000000E-01 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 -0.0000000000E+00 -0.0000000000E+00 + -0.0000000000E+00 -0.0000000000E+00 -0.0000000000E+00 + -0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 + 0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 + -0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 + 0.0000000000E+00 -0.0000000000E+00 -2.0000000000E-01 + +# +# The IR spectrum +# wavenumber eps Int TX TY TZ +# +$ir_spectrum +15 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 1385.80 0.00020962 1.05933867 -0.001807 0.000000 0.006629 + 1385.81 0.00010184 0.51465292 0.001397 0.000000 -0.004581 + 1385.82 0.00000136 0.00687560 0.000173 0.000000 0.000526 + 1557.27 0.00021562 1.08966649 0.000000 0.000000 -0.006573 + 1557.28 0.00000075 0.00380985 -0.000000 0.000000 -0.000389 + 3090.01 0.00360203 18.20318438 0.013877 0.000000 0.013085 + 3103.92 0.00006892 0.34831316 -0.001433 0.000000 -0.002208 + 3103.94 0.00325946 16.47198631 -0.007493 0.000000 -0.016479 + 3103.96 0.00656406 33.17206637 -0.021657 0.000000 0.013817 + + +$end + diff --git a/cmmde_gui/test/metana5/freq/cmmd.in b/cmmde_gui/test/metana5/freq/cmmd.in new file mode 100644 index 0000000..247d130 --- /dev/null +++ b/cmmde_gui/test/metana5/freq/cmmd.in @@ -0,0 +1,13 @@ +#CMMDE generated Orca input file +!XTB2 Numfreq +%pal + nprocs 1 +end + +*xyzfile 0 1 ../cmmd.xyz + +%freq + scalfreq 1 + Temp 298.15 + Pressure 1.0 +end diff --git a/cmmde_gui/test/metana5/freq/cmmd.out b/cmmde_gui/test/metana5/freq/cmmd.out new file mode 100644 index 0000000..1290569 --- /dev/null +++ b/cmmde_gui/test/metana5/freq/cmmd.out @@ -0,0 +1,711 @@ + + ***************** + * O R C A * + ***************** + + #, + ### + #### + ##### + ###### + ########, + ,,################,,,,, + ,,#################################,, + ,,##########################################,, + ,#########################################, ''#####, + ,#############################################,, '####, + ,##################################################,,,,####, + ,###########'''' ''''############################### + ,#####'' ,,,,##########,,,, '''####''' '#### + ,##' ,,,,###########################,,, '## + ' ,,###'''' '''############,,, + ,,##'' '''############,,,, ,,,,,,###'' + ,#'' '''#######################''' + ' ''''####'''' + ,#######, #######, ,#######, ## + ,#' '#, ## ## ,#' '#, #''# ###### ,####, + ## ## ## ,#' ## #' '# # #' '# + ## ## ####### ## ,######, #####, # # + '#, ,#' ## ## '#, ,#' ,# #, ## #, ,# + '#######' ## ## '#######' #' '# #####' # '####' + + + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship and core code : Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 5.0.2 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Marcus Kettner : VPT2 + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : Initial AUTO-CI + Lucas Lang : DCDCAS + Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, + C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT + MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, + LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, + nearIR, NL-DFT gradient (VV10), updates on ESD, + ML-optimized integration grids + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + Liviu Ungur et al : ANISO software + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 5.1.0 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + Shared memory : Shared parallel matrices + BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED + Core in use : SkylakeX + Copyright (c) 2011-2014, The OpenBLAS Project + + + + +*************************************** +The coordinates will be read from file: ../cmmd.xyz +*************************************** + + +Your calculation utilizes the semiempirical GFN2-xTB method +Please cite in your paper: +C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. + + +================================================================================ + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + +WARNING: Gradients needed for Numerical Frequencies + ===> : Setting RunTyp to EnGrad + +WARNING: Found dipole moment calculation with XTB calculation + ===> : Switching off dipole moment calculation + + +WARNING: TRAH-SCF for XTB is not implemented! + ===> : Turning TRAH off! + +================================================================================ + INPUT FILE +================================================================================ +NAME = cmmd.in +| 1> #CMMDE generated Orca input file +| 2> !XTB2 Numfreq +| 3> %pal +| 4> nprocs 1 +| 5> end +| 6> +| 7> *xyzfile 0 1 ../cmmd.xyz +| 8> +| 9> %freq +| 10> scalfreq 1 +| 11> Temp 298.15 +| 12> Pressure 1.0 +| 13> end +| 14> +| 15> ****END OF INPUT**** +================================================================================ + + ******************************* + * Energy+Gradient Calculation * + ******************************* + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/23 at 18:47:11.612 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 5 + number of electrons : 8 + charge : 0 + spin : 0.0 + first test random number : 0.94188544177967 + + ID Z sym. atoms + 1 6 C 1 + 2 1 H 2-5 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 8 : + : # atomic orbitals 8 : + : # shells 6 : + : # electrons 8 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -4.2352961 -0.423530E+01 0.243E+00 17.75 0.0 T + 2 -4.2472613 -0.119651E-01 0.928E-01 17.57 1.0 T + 3 -4.2474252 -0.163901E-03 0.500E-01 17.46 1.0 T + 4 -4.2474673 -0.421128E-04 0.924E-02 17.36 1.0 T + 5 -4.2474672 0.111480E-06 0.698E-03 17.35 6.4 T + 6 -4.2474673 -0.145702E-06 0.191E-04 17.35 233.9 T + 7 -4.2474673 -0.109876E-09 0.432E-06 17.35 10342.4 T + + *** convergence criteria satisfied after 7 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.5818361 -15.8326 + 2 2.0000 -0.4674581 -12.7202 + 3 2.0000 -0.4674581 -12.7202 + 4 2.0000 -0.4674578 -12.7202 (HOMO) + 5 0.1702647 4.6331 (LUMO) + 6 0.2292559 6.2384 + 7 0.2292578 6.2384 + 8 0.2292583 6.2384 + ------------------------------------------------------------- + HL-Gap 0.6377225 Eh 17.3533 eV + Fermi-level -0.1485966 Eh -4.0435 eV + + SCC (total) 0 d, 0 h, 0 min, 0.027 sec + SCC setup ... 0 min, 0.000 sec ( 0.362%) + Dispersion ... 0 min, 0.000 sec ( 0.066%) + classical contributions ... 0 min, 0.000 sec ( 0.044%) + integral evaluation ... 0 min, 0.000 sec ( 0.653%) + iterations ... 0 min, 0.026 sec ( 96.955%) + molecular gradient ... 0 min, 0.000 sec ( 1.344%) + printout ... 0 min, 0.000 sec ( 0.535%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -4.175218519975 Eh :: + :: gradient norm 0.000006679583 Eh/a0 :: + :: HOMO-LUMO gap 17.353313284543 eV :: + ::.................................................:: + :: SCC energy -4.247467308164 Eh :: + :: -> isotropic ES 0.002035567932 Eh :: + :: -> anisotropic ES 0.002321540934 Eh :: + :: -> anisotropic XC 0.003585096737 Eh :: + :: -> dispersion -0.000661011606 Eh :: + :: repulsion energy 0.072248782598 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -4.175218519975 Eh | + | GRADIENT NORM 0.000006679583 Eh/α | + | HOMO-LUMO GAP 17.353313284543 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/23 at 18:47:11.650 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.038 sec + * cpu-time: 0 d, 0 h, 0 min, 0.014 sec + * ratio c/w: 0.375 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.027 sec + * cpu-time: 0 d, 0 h, 0 min, 0.004 sec + * ratio c/w: 0.132 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -4.175218519970 +------------------------- -------------------- + + +---------------------------------------------------------------------------- + ORCA NUMERICAL FREQUENCIES +---------------------------------------------------------------------------- + +Number of atoms ... 5 +Central differences ... used +Number of displacements ... 30 +Numerical increment ... 5.000e-03 bohr +IR-spectrum generation ... on +Raman-spectrum generation ... off +Surface Crossing Hessian ... off + +The output will be reduced. Please look at the following files: +SCF program output ... >cmmd.lastscf +Integral program output ... >cmmd.lastint +Gradient program output ... >cmmd.lastgrad +Dipole moment program output ... >cmmd.lastmom +AutoCI program output ... >cmmd.lastautoci + + << Calculating on displaced geometry 1 (of 30) >> + << Calculating on displaced geometry 2 (of 30) >> + << Calculating on displaced geometry 3 (of 30) >> + << Calculating on displaced geometry 4 (of 30) >> + << Calculating on displaced geometry 5 (of 30) >> + << Calculating on displaced geometry 6 (of 30) >> + << Calculating on displaced geometry 7 (of 30) >> + << Calculating on displaced geometry 8 (of 30) >> + << Calculating on displaced geometry 9 (of 30) >> + << Calculating on displaced geometry 10 (of 30) >> + << Calculating on displaced geometry 11 (of 30) >> + << Calculating on displaced geometry 12 (of 30) >> + << Calculating on displaced geometry 13 (of 30) >> + << Calculating on displaced geometry 14 (of 30) >> + << Calculating on displaced geometry 15 (of 30) >> + << Calculating on displaced geometry 16 (of 30) >> + << Calculating on displaced geometry 17 (of 30) >> + << Calculating on displaced geometry 18 (of 30) >> + << Calculating on displaced geometry 19 (of 30) >> + << Calculating on displaced geometry 20 (of 30) >> + << Calculating on displaced geometry 21 (of 30) >> + << Calculating on displaced geometry 22 (of 30) >> + << Calculating on displaced geometry 23 (of 30) >> + << Calculating on displaced geometry 24 (of 30) >> + << Calculating on displaced geometry 25 (of 30) >> + << Calculating on displaced geometry 26 (of 30) >> + << Calculating on displaced geometry 27 (of 30) >> + << Calculating on displaced geometry 28 (of 30) >> + << Calculating on displaced geometry 29 (of 30) >> + << Calculating on displaced geometry 30 (of 30) >> + +----------------------- +VIBRATIONAL FREQUENCIES +----------------------- + +Scaling factor for frequencies = 1.000000000 (already applied!) + + 0: 0.00 cm**-1 + 1: 0.00 cm**-1 + 2: 0.00 cm**-1 + 3: 0.00 cm**-1 + 4: 0.00 cm**-1 + 5: 0.00 cm**-1 + 6: 1385.80 cm**-1 + 7: 1385.81 cm**-1 + 8: 1385.82 cm**-1 + 9: 1557.27 cm**-1 + 10: 1557.28 cm**-1 + 11: 3090.01 cm**-1 + 12: 3103.92 cm**-1 + 13: 3103.94 cm**-1 + 14: 3103.96 cm**-1 + + +------------ +NORMAL MODES +------------ + +These modes are the cartesian displacements weighted by the diagonal matrix +M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom +Thus, these vectors are normalized but *not* orthogonal + + 0 1 2 3 4 5 + 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 1 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 2 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 7 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 8 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 9 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 10 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 11 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 12 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 13 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 14 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 6 7 8 9 10 11 + 0 0.101670 -0.078579 -0.009705 -0.000001 0.000000 -0.000092 + 1 0.003514 0.020258 -0.127211 -0.000001 -0.000002 0.000011 + 2 0.079098 0.100103 0.018126 -0.000009 0.000000 -0.000069 + 3 0.047303 -0.036561 -0.004516 -0.000000 0.000000 -0.499082 + 4 -0.016516 -0.095227 0.598016 0.063675 0.495938 0.000005 + 5 -0.371808 -0.470552 -0.085209 0.495976 -0.063669 -0.000032 + 6 -0.355610 0.428077 -0.129955 -0.267885 -0.387898 0.166800 + 7 0.290995 0.052286 0.156770 0.272913 -0.008521 0.419303 + 8 -0.213063 -0.394428 -0.313093 -0.322065 0.315378 0.216504 + 9 -0.355052 0.384373 0.229774 -0.201988 0.425939 0.166879 + 10 -0.309136 -0.130918 0.159640 -0.304056 0.011046 -0.397360 + 11 -0.184115 -0.447720 0.196088 -0.341633 -0.261634 0.254939 + 12 -0.548110 0.160433 0.020337 0.469890 -0.038046 0.166505 + 13 -0.007214 -0.067527 0.601384 -0.032517 -0.498444 -0.022076 + 14 -0.173520 0.119909 -0.013768 0.167831 0.009924 -0.470592 + 12 13 14 + 0 -0.005434 -0.028446 -0.082345 + 1 0.085682 -0.016678 0.000107 + 2 -0.015768 -0.080822 0.028961 + 3 0.053771 0.281099 0.812472 + 4 0.039625 -0.007713 0.000049 + 5 -0.007292 -0.037378 0.013392 + 6 -0.219870 0.187690 0.012818 + 7 -0.506614 0.497038 0.127975 + 8 -0.289388 0.223286 0.079458 + 9 0.265265 0.115358 0.005789 + 10 -0.597826 -0.313648 -0.104394 + 11 0.401734 0.158922 0.080411 + 12 -0.034412 -0.245193 0.150117 + 13 0.043855 0.023051 -0.024903 + 14 0.082833 0.618212 -0.518346 + + +----------- +IR SPECTRUM +----------- + + Mode freq eps Int T**2 TX TY TZ + cm**-1 L/(mol*cm) km/mol a.u. +---------------------------------------------------------------------------- + 6: 1385.80 0.000210 1.06 0.000047 (-0.001807 0.000000 0.006629) + 7: 1385.81 0.000102 0.51 0.000023 ( 0.001397 0.000000 -0.004581) + 8: 1385.82 0.000001 0.01 0.000000 ( 0.000173 0.000000 0.000526) + 9: 1557.27 0.000216 1.09 0.000043 ( 0.000000 0.000000 -0.006573) + 10: 1557.28 0.000001 0.00 0.000000 (-0.000000 0.000000 -0.000389) + 11: 3090.01 0.003602 18.20 0.000364 ( 0.013877 0.000000 0.013085) + 12: 3103.92 0.000069 0.35 0.000007 (-0.001433 0.000000 -0.002208) + 13: 3103.94 0.003259 16.47 0.000328 (-0.007493 0.000000 -0.016479) + 14: 3103.96 0.006564 33.17 0.000660 (-0.021657 0.000000 0.013817) + +* The epsilon (eps) is given for a Dirac delta lineshape. +** The dipole moment derivative (T) already includes vibrational overlap. + +The first frequency considered to be a vibration is 6 +The total number of vibrations considered is 9 + + +-------------------------- +THERMOCHEMISTRY AT 298.15K +-------------------------- + +Temperature ... 298.15 K +Pressure ... 1.00 atm +Total Mass ... 16.04 AMU + +Throughout the following assumptions are being made: + (1) The electronic state is orbitally nondegenerate + (2) There are no thermally accessible electronically excited states + (3) Hindered rotations indicated by low frequency modes are not + treated as such but are treated as vibrations and this may + cause some error + (4) All equations used are the standard statistical mechanics + equations for an ideal gas + (5) All vibrations are strictly harmonic + +freq. 1385.80 E(vib) ... 0.00 +freq. 1385.81 E(vib) ... 0.00 +freq. 1385.82 E(vib) ... 0.00 +freq. 1557.27 E(vib) ... 0.00 +freq. 1557.28 E(vib) ... 0.00 +freq. 3090.01 E(vib) ... 0.00 +freq. 3103.92 E(vib) ... 0.00 +freq. 3103.94 E(vib) ... 0.00 +freq. 3103.96 E(vib) ... 0.00 + +------------ +INNER ENERGY +------------ + +The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans) + E(el) - is the total energy from the electronic structure calculation + = E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc) + E(ZPE) - the the zero temperature vibrational energy from the frequency calculation + E(vib) - the the finite temperature correction to E(ZPE) due to population + of excited vibrational states + E(rot) - is the rotational thermal energy + E(trans)- is the translational thermal energy + +Summary of contributions to the inner energy U: +Electronic energy ... -4.17521852 Eh +Zero point energy ... 0.04482019 Eh 28.13 kcal/mol +Thermal vibrational correction ... 0.00003140 Eh 0.02 kcal/mol +Thermal rotational correction ... 0.00141627 Eh 0.89 kcal/mol +Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol +----------------------------------------------------------------------- +Total thermal energy -4.12753439 Eh + + +Summary of corrections to the electronic energy: +(perhaps to be used in another calculation) +Total thermal correction 0.00286394 Eh 1.80 kcal/mol +Non-thermal (ZPE) correction 0.04482019 Eh 28.13 kcal/mol +----------------------------------------------------------------------- +Total correction 0.04768413 Eh 29.92 kcal/mol + + +-------- +ENTHALPY +-------- + +The enthalpy is H = U + kB*T + kB is Boltzmann's constant +Total free energy ... -4.12753439 Eh +Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol +----------------------------------------------------------------------- +Total Enthalpy ... -4.12659018 Eh + + +Note: Rotational entropy computed according to Herzberg +Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945 +Point Group: Td, Symmetry Number: 12 +Rotational constants in cm-1: 5.355313 5.355311 5.355302 + +Vibrational entropy computed according to the QRRHO of S. Grimme +Chem.Eur.J. 2012 18 9955 + + +------- +ENTROPY +------- + +The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans)) + S(el) - electronic entropy + S(vib) - vibrational entropy + S(rot) - rotational entropy + S(trans)- translational entropy +The entropies will be listed as multiplied by the temperature to get +units of energy + +Electronic entropy ... 0.00000000 Eh 0.00 kcal/mol +Vibrational entropy ... 0.00003597 Eh 0.02 kcal/mol +Rotational entropy ... 0.00478798 Eh 3.00 kcal/mol +Translational entropy ... 0.01627961 Eh 10.22 kcal/mol +----------------------------------------------------------------------- +Final entropy term ... 0.02110356 Eh 13.24 kcal/mol + +In case the symmetry of your molecule has not been determined correctly +or in case you have a reason to use a different symmetry number we print +out the resulting rotational entropy values for sn=1,12 : + -------------------------------------------------------- +| sn= 1 | S(rot)= 0.00713418 Eh 4.48 kcal/mol| +| sn= 2 | S(rot)= 0.00647973 Eh 4.07 kcal/mol| +| sn= 3 | S(rot)= 0.00609689 Eh 3.83 kcal/mol| +| sn= 4 | S(rot)= 0.00582527 Eh 3.66 kcal/mol| +| sn= 5 | S(rot)= 0.00561458 Eh 3.52 kcal/mol| +| sn= 6 | S(rot)= 0.00544244 Eh 3.42 kcal/mol| +| sn= 7 | S(rot)= 0.00529689 Eh 3.32 kcal/mol| +| sn= 8 | S(rot)= 0.00517081 Eh 3.24 kcal/mol| +| sn= 9 | S(rot)= 0.00505960 Eh 3.17 kcal/mol| +| sn=10 | S(rot)= 0.00496012 Eh 3.11 kcal/mol| +| sn=11 | S(rot)= 0.00487013 Eh 3.06 kcal/mol| +| sn=12 | S(rot)= 0.00478798 Eh 3.00 kcal/mol| + -------------------------------------------------------- + + +------------------- +GIBBS FREE ENERGY +------------------- + +The Gibbs free energy is G = H - T*S + +Total enthalpy ... -4.12659018 Eh +Total entropy correction ... -0.02110356 Eh -13.24 kcal/mol +----------------------------------------------------------------------- +Final Gibbs free energy ... -4.14769375 Eh + +For completeness - the Gibbs free energy minus the electronic energy +G-E(el) ... 0.02752477 Eh 17.27 kcal/mol + + + +Timings for individual modules: + +Sum of individual times ... 51.916 sec (= 0.865 min) +Numerical frequency calculation ... 51.828 sec (= 0.864 min) 99.8 % +XTB module ... 0.088 sec (= 0.001 min) 0.2 % + ****ORCA TERMINATED NORMALLY**** +TOTAL RUN TIME: 0 days 0 hours 0 minutes 51 seconds 950 msec diff --git a/cmmde_gui/test/metana5/freq/cmmd.xtbrestart b/cmmde_gui/test/metana5/freq/cmmd.xtbrestart new file mode 100644 index 0000000000000000000000000000000000000000..de1c2009f1741375f4df6ca3204f8b9c02bccc55 GIT binary patch literal 488 zcmXqDU|?VZVi17QtPm~(82?(n~`**RQKTiQ<@&%BHk>v z4?1rzkOrh}!qiGrfwaQE#T-dM8lzPaUUq0UAyG>>He&Or(a1*k8TV;Ou>%xcQ6L%8r+1_ByK``Leg{vj^Gz0f>7e zYx_+1>ot(5KDw{)TMIg^xy`^q+~ zZtDEA+y2k9tmu8m^X%r-ZOZNZvwHu9|DRt=^3L5Cy5_`RJEt(az(-4_gTy8N1?hOK zShW9URwK*a!sYfRre>22-mSB*blmmzpV5q+b-45v1gTOnEUAKhW!iP?@hn_uw(zS{aKrRf$H=B v%nJE`GI_t-l&iZtF0J10xx|P)Eqc{{J~QLhsb8w?MYR@~XWMSK2l*KQSP cmmd.out --oversubscribe diff --git a/cmmde_gui/test/metana5/freq/freq/slurm-2919.out b/cmmde_gui/test/metana5/freq/freq/slurm-2919.out new file mode 100644 index 0000000..7315e3d --- /dev/null +++ b/cmmde_gui/test/metana5/freq/freq/slurm-2919.out @@ -0,0 +1,7 @@ + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!! FATAL ERROR ENCOUNTERED !!! +!!! ----------------------- !!! +!!! CANNOT OPEN FILE !!! +!!! Filename: ../cmmd.xyz !!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! diff --git a/cmmde_gui/test/metana5/freq/run.sh b/cmmde_gui/test/metana5/freq/run.sh new file mode 100644 index 0000000..f72e163 --- /dev/null +++ b/cmmde_gui/test/metana5/freq/run.sh @@ -0,0 +1,10 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH +export PATH=/home/adit/opt/openmpi411/bin:$PATH +export OMP_NUM_THREADS=1 +cd $PWD +$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe diff --git a/cmmde_gui/test/metana5/freq/slurm-2918.out b/cmmde_gui/test/metana5/freq/slurm-2918.out new file mode 100644 index 0000000..e69de29 diff --git a/cmmde_gui/test/metana5/geom.smi b/cmmde_gui/test/metana5/geom.smi new file mode 100644 index 0000000..3cc58df --- /dev/null +++ b/cmmde_gui/test/metana5/geom.smi @@ -0,0 +1 @@ +C diff --git a/cmmde_gui/test/metana5/geom.xyz b/cmmde_gui/test/metana5/geom.xyz new file mode 100644 index 0000000..00b429b --- /dev/null +++ b/cmmde_gui/test/metana5/geom.xyz @@ -0,0 +1,7 @@ +5 + +C 1.08134 0.00760 -0.05767 +H 2.17354 0.00760 -0.05767 +H 0.71728 -0.90733 -0.53017 +H 0.71728 0.87426 -0.61377 +H 0.71728 0.05587 0.97094 diff --git a/cmmde_gui/test/metana5/run.sh b/cmmde_gui/test/metana5/run.sh new file mode 100644 index 0000000..f72e163 --- /dev/null +++ b/cmmde_gui/test/metana5/run.sh @@ -0,0 +1,10 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH +export PATH=/home/adit/opt/openmpi411/bin:$PATH +export OMP_NUM_THREADS=1 +cd $PWD +$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe diff --git a/cmmde_gui/test/metana5/run_babel.sh b/cmmde_gui/test/metana5/run_babel.sh new file mode 100644 index 0000000..0d5d00e --- /dev/null +++ b/cmmde_gui/test/metana5/run_babel.sh @@ -0,0 +1,8 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export OMP_NUM_THREADS=1 +cd $PWD +obabel geom.smi -O geom.xyz --gen3d diff --git a/cmmde_gui/test/metana5/slurm-2916.out b/cmmde_gui/test/metana5/slurm-2916.out new file mode 100644 index 0000000..b7d75ac --- /dev/null +++ b/cmmde_gui/test/metana5/slurm-2916.out @@ -0,0 +1 @@ +1 molecule converted diff --git a/cmmde_gui/test/metana5/slurm-2917.out b/cmmde_gui/test/metana5/slurm-2917.out new file mode 100644 index 0000000..e69de29 diff --git a/cmmde_gui/test/siklopentana/cmmd.engrad b/cmmde_gui/test/siklopentana/cmmd.engrad new file mode 100644 index 0000000..5454e34 --- /dev/null +++ b/cmmde_gui/test/siklopentana/cmmd.engrad @@ -0,0 +1,74 @@ +# +# Number of atoms +# + 15 +# +# The current total energy in Eh +# + -15.814313366050 +# +# The current gradient in Eh/bohr +# + 0.000227495798 + -0.000049478208 + 0.000259008811 + 0.000082454763 + -0.000273081820 + -0.000428388240 + -0.000389851164 + 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,,#################################,, + ,,##########################################,, + ,#########################################, ''#####, + ,#############################################,, '####, + ,##################################################,,,,####, + ,###########'''' ''''############################### + ,#####'' ,,,,##########,,,, '''####''' '#### + ,##' ,,,,###########################,,, '## + ' ,,###'''' '''############,,, + ,,##'' '''############,,,, ,,,,,,###'' + ,#'' '''#######################''' + ' ''''####'''' + ,#######, #######, ,#######, ## + ,#' '#, ## ## ,#' '#, #''# ###### ,####, + ## ## ## ,#' ## #' '# # #' '# + ## ## ####### ## ,######, #####, # # + '#, ,#' ## ## '#, ,#' ,# #, ## #, ,# + '#######' ## ## '#######' #' '# #####' # '####' + + + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship and core code : Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 5.0.2 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Marcus Kettner : VPT2 + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : Initial AUTO-CI + Lucas Lang : DCDCAS + Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, + C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT + MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, + LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, + nearIR, NL-DFT gradient (VV10), updates on ESD, + ML-optimized integration grids + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + Liviu Ungur et al : ANISO software + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 5.1.0 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + Shared memory : Shared parallel matrices + BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED + Core in use : SkylakeX + Copyright (c) 2011-2014, The OpenBLAS Project + + + + +*************************************** +The coordinates will be read from file: geom.xyz +*************************************** + + +Your calculation utilizes the semiempirical GFN2-xTB method +Please cite in your paper: +C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. + + +================================================================================ + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + + +WARNING: Geometry Optimization + ===> : Switching off AutoStart + For restart on a previous wavefunction, please use MOREAD + +WARNING: Found dipole moment calculation with XTB calculation + ===> : Switching off dipole moment calculation + + +WARNING: TRAH-SCF for XTB is not implemented! + ===> : Turning TRAH off! + +================================================================================ + INPUT FILE +================================================================================ +NAME = cmmd.in +| 1> #CMMDE generated Orca input file +| 2> !XTB2 opt +| 3> %pal +| 4> nprocs 1 +| 5> end +| 6> %geom +| 7> maxiter 9999 +| 8> end +| 9> +| 10> *xyzfile 0 1 geom.xyz +| 11> +| 12> +| 13> ****END OF INPUT**** +================================================================================ + + ***************************** + * Geometry Optimization Run * + ***************************** + +Geometry optimization settings: +Update method Update .... BFGS +Choice of coordinates CoordSys .... Z-matrix Internals +Initial Hessian InHess .... Almoef's Model + +Convergence Tolerances: +Energy Change TolE .... 5.0000e-06 Eh +Max. Gradient TolMAXG .... 3.0000e-04 Eh/bohr +RMS Gradient TolRMSG .... 1.0000e-04 Eh/bohr +Max. Displacement TolMAXD .... 4.0000e-03 bohr +RMS Displacement TolRMSD .... 2.0000e-03 bohr +Strict Convergence .... False +------------------------------------------------------------------------------ + ORCA OPTIMIZATION COORDINATE SETUP +------------------------------------------------------------------------------ + +The optimization will be done in new redundant internal coordinates +Making redundant internal coordinates ... (new redundants) done +Evaluating the initial hessian ... (Almloef) done +Evaluating the coordinates ... done +Calculating the B-matrix .... done +Calculating the G-matrix .... done +Diagonalizing the G-matrix .... done +The first mode is .... 51 +The number of degrees of freedom .... 39 + + ----------------------------------------------------------------- + Redundant Internal Coordinates + + + ----------------------------------------------------------------- + Definition Initial Value Approx d2E/dq + ----------------------------------------------------------------- + 1. B(C 1,C 0) 1.5200 0.387533 + 2. B(C 2,C 1) 1.5261 0.378985 + 3. B(C 3,C 2) 1.5283 0.375898 + 4. B(C 4,C 3) 1.5220 0.384658 + 5. B(C 4,C 0) 1.5184 0.389816 + 6. B(H 5,C 0) 1.0936 0.355363 + 7. B(H 6,C 0) 1.0965 0.351602 + 8. B(H 7,C 1) 1.0940 0.354874 + 9. B(H 8,C 1) 1.0969 0.351103 + 10. B(H 9,C 2) 1.0956 0.352775 + 11. B(H 10,C 2) 1.0952 0.353314 + 12. B(H 11,C 3) 1.0967 0.351366 + 13. B(H 12,C 3) 1.0945 0.354152 + 14. B(H 13,C 4) 1.0937 0.355216 + 15. B(H 14,C 4) 1.0966 0.351497 + 16. A(C 4,C 0,H 5) 112.3841 0.325885 + 17. A(C 1,C 0,C 4) 103.1297 0.368316 + 18. A(C 1,C 0,H 5) 112.2933 0.325571 + 19. A(H 5,C 0,H 6) 108.3256 0.289151 + 20. A(C 1,C 0,H 6) 110.2991 0.325002 + 21. A(C 4,C 0,H 6) 110.3632 0.325316 + 22. A(C 2,C 1,H 8) 109.6622 0.323738 + 23. A(C 2,C 1,H 7) 112.2441 0.324306 + 24. A(H 7,C 1,H 8) 107.7743 0.289024 + 25. A(C 0,C 1,H 7) 112.2767 0.325497 + 26. A(C 0,C 1,C 2) 104.9844 0.366541 + 27. A(C 0,C 1,H 8) 109.8821 0.324926 + 28. A(H 9,C 2,H 10) 107.3415 0.289040 + 29. A(C 1,C 2,C 3) 106.3541 0.364632 + 30. A(C 1,C 2,H 10) 110.7808 0.324071 + 31. A(C 3,C 2,H 9) 110.0769 0.323556 + 32. A(C 1,C 2,H 9) 110.8158 0.323990 + 33. A(C 3,C 2,H 10) 111.5139 0.323637 + 34. A(H 11,C 3,H 12) 107.5009 0.288966 + 35. A(C 4,C 3,H 12) 111.7898 0.324990 + 36. A(C 2,C 3,H 12) 112.0750 0.323763 + 37. A(C 4,C 3,H 11) 110.0374 0.324568 + 38. A(C 2,C 3,H 11) 109.6080 0.323343 + 39. A(C 2,C 3,C 4) 105.8354 0.365561 + 40. A(H 13,C 4,H 14) 108.1093 0.289118 + 41. A(C 3,C 4,H 14) 110.0318 0.324588 + 42. A(C 0,C 4,H 14) 110.1672 0.325300 + 43. A(C 3,C 4,H 13) 112.2832 0.325150 + 44. A(C 0,C 4,H 13) 112.4281 0.325863 + 45. A(C 0,C 4,C 3) 103.7901 0.367846 + 46. D(H 7,C 1,C 0,H 5) 80.9311 0.011947 + 47. D(H 7,C 1,C 0,H 6) -39.9976 0.011947 + 48. D(C 2,C 1,C 0,H 5) -156.8515 0.011947 + 49. D(H 7,C 1,C 0,C 4) -157.8535 0.011947 + 50. D(H 8,C 1,C 0,H 6) -159.9281 0.011947 + 51. D(C 2,C 1,C 0,C 4) -35.6361 0.011947 + 52. D(C 2,C 1,C 0,H 6) 82.2198 0.011947 + 53. D(H 8,C 1,C 0,H 5) -38.9994 0.011947 + 54. D(H 8,C 1,C 0,C 4) 82.2160 0.011947 + 55. D(H 9,C 2,C 1,H 7) 20.3280 0.011450 + 56. D(C 3,C 2,C 1,H 8) -100.2882 0.011450 + 57. D(C 3,C 2,C 1,C 0) 17.7131 0.011450 + 58. D(H 10,C 2,C 1,H 8) 21.0534 0.011450 + 59. D(H 9,C 2,C 1,H 8) 140.0881 0.011450 + 60. D(H 10,C 2,C 1,H 7) -98.7067 0.011450 + 61. D(H 10,C 2,C 1,C 0) 139.0547 0.011450 + 62. D(C 3,C 2,C 1,H 7) 139.9516 0.011450 + 63. D(H 9,C 2,C 1,C 0) -101.9106 0.011450 + 64. D(H 12,C 3,C 2,H 9) -110.8121 0.011275 + 65. D(H 12,C 3,C 2,C 1) 129.0845 0.011275 + 66. D(H 11,C 3,C 2,H 10) 127.4851 0.011275 + 67. D(H 11,C 3,C 2,H 9) 8.4601 0.011275 + 68. D(C 4,C 3,C 2,H 9) 127.0880 0.011275 + 69. D(C 4,C 3,C 2,C 1) 6.9845 0.011275 + 70. D(H 11,C 3,C 2,C 1) -111.6433 0.011275 + 71. D(H 12,C 3,C 2,H 10) 8.2128 0.011275 + 72. D(C 4,C 3,C 2,H 10) -113.8871 0.011275 + 73. D(H 13,C 4,C 0,C 1) 161.5189 0.012081 + 74. D(C 3,C 4,C 0,H 6) -77.8722 0.012081 + 75. D(C 3,C 4,C 0,H 5) 161.0924 0.012081 + 76. D(C 3,C 4,C 0,C 1) 39.9387 0.012081 + 77. D(H 14,C 4,C 3,H 12) -33.4345 0.011778 + 78. D(H 14,C 4,C 3,H 11) -152.8096 0.011778 + 79. D(H 13,C 4,C 3,H 12) 87.0267 0.011778 + 80. D(H 13,C 4,C 3,H 11) -32.3484 0.011778 + 81. D(H 13,C 4,C 3,C 2) -150.6910 0.011778 + 82. D(C 0,C 4,C 3,H 12) -151.2963 0.011778 + 83. D(C 0,C 4,C 3,H 11) 89.3286 0.011778 + 84. D(C 0,C 4,C 3,C 2) -29.0139 0.011778 + 85. D(H 14,C 4,C 0,H 6) 164.3599 0.012081 + 86. D(H 14,C 4,C 0,H 5) 43.3246 0.012081 + 87. D(H 14,C 4,C 3,C 2) 88.8478 0.011778 + 88. D(H 14,C 4,C 0,C 1) -77.8292 0.012081 + 89. D(H 13,C 4,C 0,H 6) 43.7080 0.012081 + 90. D(H 13,C 4,C 0,H 5) -77.3273 0.012081 + ----------------------------------------------------------------- + +Number of atoms .... 15 +Number of degrees of freedom .... 90 + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 1 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.253970 -0.087850 0.236110 + C 0.326710 -1.222030 -0.169190 + C -1.082040 -0.675110 0.043510 + C -0.946150 0.845120 0.122080 + C 0.504630 1.150760 -0.222060 + H 2.240750 -0.172920 -0.227570 + H 1.384620 -0.073870 1.324710 + H 0.508830 -2.133100 0.408370 + H 0.473010 -1.462750 -1.229290 + H -1.513940 -1.062630 0.972820 + H -1.743910 -0.977410 -0.775000 + H -1.169630 1.182400 1.141400 + H -1.640100 1.355580 -0.553100 + H 0.864040 2.060640 0.266980 + H 0.614500 1.279940 -1.305450 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.369660 -0.166012 0.446183 + 1 C 6.0000 0 12.011 0.617392 -2.309302 -0.319723 + 2 C 6.0000 0 12.011 -2.044759 -1.275773 0.082222 + 3 C 6.0000 0 12.011 -1.787964 1.597045 0.230698 + 4 C 6.0000 0 12.011 0.953612 2.174621 -0.419633 + 5 H 1.0000 0 1.008 4.234404 -0.326771 -0.430045 + 6 H 1.0000 0 1.008 2.616553 -0.139594 2.503339 + 7 H 1.0000 0 1.008 0.961549 -4.030975 0.771707 + 8 H 1.0000 0 1.008 0.893859 -2.764197 -2.323021 + 9 H 1.0000 0 1.008 -2.860932 -2.008080 1.838363 + 10 H 1.0000 0 1.008 -3.295512 -1.847037 -1.464538 + 11 H 1.0000 0 1.008 -2.210280 2.234412 2.156933 + 12 H 1.0000 0 1.008 -3.099340 2.561675 -1.045208 + 13 H 1.0000 0 1.008 1.632799 3.894045 0.504519 + 14 H 1.0000 0 1.008 1.161237 2.418736 -2.466943 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:47:44.624 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.07527712256406 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0004270 -0.160004E+02 0.266E+00 13.67 0.0 T + 2 -16.0453832 -0.449562E-01 0.158E+00 13.37 1.0 T + 3 -16.0456958 -0.312551E-03 0.831E-01 13.37 1.0 T + 4 -16.0458078 -0.112067E-03 0.803E-02 13.35 1.0 T + 5 -16.0458081 -0.244111E-06 0.462E-03 13.36 5.6 T + 6 -16.0458081 -0.449080E-07 0.200E-03 13.36 12.9 T + 7 -16.0458081 -0.395713E-08 0.530E-04 13.36 48.7 T + 8 -16.0458081 -0.689152E-09 0.104E-04 13.36 249.2 T + + *** convergence criteria satisfied after 8 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6335396 -17.2395 + ... ... ... ... + 9 2.0000 -0.4827275 -13.1357 + 10 2.0000 -0.4415401 -12.0149 + 11 2.0000 -0.4388939 -11.9429 + 12 2.0000 -0.4365247 -11.8784 + 13 2.0000 -0.4363620 -11.8740 + 14 2.0000 -0.4202600 -11.4359 + 15 2.0000 -0.4131029 -11.2411 (HOMO) + 16 0.0776863 2.1140 (LUMO) + 17 0.0785880 2.1385 + 18 0.0830294 2.2593 + 19 0.1250432 3.4026 + 20 0.1388223 3.7775 + ... ... ... + 30 0.3462224 9.4212 + ------------------------------------------------------------- + HL-Gap 0.4907892 Eh 13.3551 eV + Fermi-level -0.1677083 Eh -4.5636 eV + + SCC (total) 0 d, 0 h, 0 min, 0.042 sec + SCC setup ... 0 min, 0.000 sec ( 0.816%) + Dispersion ... 0 min, 0.000 sec ( 0.232%) + classical contributions ... 0 min, 0.000 sec ( 1.008%) + integral evaluation ... 0 min, 0.002 sec ( 3.616%) + iterations ... 0 min, 0.036 sec ( 86.101%) + molecular gradient ... 0 min, 0.003 sec ( 7.364%) + printout ... 0 min, 0.000 sec ( 0.826%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.813823527310 Eh :: + :: gradient norm 0.022707407200 Eh/a0 :: + :: HOMO-LUMO gap 13.355054326678 eV :: + ::.................................................:: + :: SCC energy -16.045808110944 Eh :: + :: -> isotropic ES 0.002215602953 Eh :: + :: -> anisotropic ES 0.004256460236 Eh :: + :: -> anisotropic XC 0.009822111034 Eh :: + :: -> dispersion -0.008145854109 Eh :: + :: repulsion energy 0.231974178511 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.813823527310 Eh | + | GRADIENT NORM 0.022707407200 Eh/α | + | HOMO-LUMO GAP 13.355054326678 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:47:44.705 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.080 sec + * cpu-time: 0 d, 0 h, 0 min, 0.025 sec + * ratio c/w: 0.305 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.042 sec + * cpu-time: 0 d, 0 h, 0 min, 0.011 sec + * ratio c/w: 0.260 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.813823527310 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 15 +Number of internal coordinates .... 90 +Current Energy .... -15.813823527 Eh +Current gradient norm .... 0.022707407 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Evaluating the initial hessian .... (Almloef) done +Projecting the Hessian .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.997969285 +Lowest eigenvalues of augmented Hessian: + -0.000703095 0.011851271 0.014610511 0.045627515 0.045959147 +Length of the computed step .... 0.063826607 +The final length of the internal step .... 0.063826607 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0067279151 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0094581950 RMS(Int)= 0.0067336744 + Iter 1: RMS(Cart)= 0.0000326158 RMS(Int)= 0.0000283370 + Iter 2: RMS(Cart)= 0.0000001703 RMS(Int)= 0.0000001533 + Iter 3: RMS(Cart)= 0.0000000016 RMS(Int)= 0.0000000013 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + RMS gradient 0.0016312823 0.0001000000 NO + MAX gradient 0.0070910449 0.0003000000 NO + RMS step 0.0067279151 0.0020000000 NO + MAX step 0.0192770234 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0102 Max(Angles) 0.32 + Max(Dihed) 0.79 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.5200 -0.004296 0.0057 1.5257 + 2. B(C 2,C 1) 1.5261 -0.006170 0.0087 1.5348 + 3. B(C 3,C 2) 1.5283 -0.007091 0.0102 1.5385 + 4. B(C 4,C 3) 1.5220 -0.005057 0.0069 1.5290 + 5. B(C 4,C 0) 1.5184 -0.004058 0.0053 1.5237 + 6. B(H 5,C 0) 1.0936 0.002177 -0.0032 1.0904 + 7. B(H 6,C 0) 1.0965 0.003068 -0.0046 1.0919 + 8. B(H 7,C 1) 1.0940 0.002576 -0.0038 1.0901 + 9. B(H 8,C 1) 1.0969 0.003094 -0.0047 1.0922 + 10. B(H 9,C 2) 1.0956 0.002937 -0.0044 1.0912 + 11. B(H 10,C 2) 1.0952 0.002998 -0.0045 1.0907 + 12. B(H 11,C 3) 1.0967 0.003132 -0.0047 1.0920 + 13. B(H 12,C 3) 1.0945 0.002871 -0.0043 1.0903 + 14. B(H 13,C 4) 1.0937 0.002299 -0.0034 1.0903 + 15. B(H 14,C 4) 1.0966 0.002975 -0.0045 1.0921 + 16. A(C 4,C 0,H 5) 112.38 -0.000181 0.16 112.55 + 17. A(C 1,C 0,C 4) 103.13 -0.000495 -0.01 103.12 + 18. A(C 1,C 0,H 5) 112.29 0.000177 0.10 112.40 + 19. A(H 5,C 0,H 6) 108.33 0.000036 -0.07 108.26 + 20. A(C 1,C 0,H 6) 110.30 -0.000080 -0.01 110.29 + 21. A(C 4,C 0,H 6) 110.36 0.000540 -0.18 110.18 + 22. A(C 2,C 1,H 8) 109.66 -0.000870 0.28 109.94 + 23. A(C 2,C 1,H 7) 112.24 0.000292 0.01 112.25 + 24. A(H 7,C 1,H 8) 107.77 0.000145 -0.07 107.70 + 25. A(C 0,C 1,H 7) 112.28 -0.000281 0.05 112.33 + 26. A(C 0,C 1,C 2) 104.98 -0.000100 -0.06 104.92 + 27. A(C 0,C 1,H 8) 109.88 0.000804 -0.20 109.68 + 28. A(H 9,C 2,H 10) 107.34 0.000437 -0.15 107.20 + 29. A(C 1,C 2,C 3) 106.35 0.000677 -0.14 106.22 + 30. A(C 1,C 2,H 10) 110.78 -0.000392 0.07 110.85 + 31. A(C 3,C 2,H 9) 110.08 -0.000687 0.21 110.29 + 32. A(C 1,C 2,H 9) 110.82 0.000071 -0.02 110.79 + 33. A(C 3,C 2,H 10) 111.51 -0.000128 0.03 111.54 + 34. A(H 11,C 3,H 12) 107.50 0.000287 -0.10 107.40 + 35. A(C 4,C 3,H 12) 111.79 -0.000205 -0.01 111.78 + 36. A(C 2,C 3,H 12) 112.07 0.000005 0.03 112.10 + 37. A(C 4,C 3,H 11) 110.04 0.000490 -0.12 109.92 + 38. A(C 2,C 3,H 11) 109.61 -0.000934 0.32 109.93 + 39. A(C 2,C 3,C 4) 105.84 0.000338 -0.11 105.72 + 40. A(H 13,C 4,H 14) 108.11 0.000048 -0.06 108.05 + 41. A(C 3,C 4,H 14) 110.03 -0.000554 0.14 110.18 + 42. A(C 0,C 4,H 14) 110.17 0.000850 -0.24 109.92 + 43. A(C 3,C 4,H 13) 112.28 0.000385 0.04 112.32 + 44. A(C 0,C 4,H 13) 112.43 -0.000364 0.15 112.58 + 45. A(C 0,C 4,C 3) 103.79 -0.000368 -0.03 103.76 + 46. D(H 7,C 1,C 0,H 5) 80.93 0.000464 -0.64 80.29 + 47. D(H 7,C 1,C 0,H 6) -40.00 0.000354 -0.62 -40.62 + 48. D(C 2,C 1,C 0,H 5) -156.85 0.000595 -0.64 -157.49 + 49. D(H 7,C 1,C 0,C 4) -157.85 0.000032 -0.40 -158.25 + 50. D(H 8,C 1,C 0,H 6) -159.93 -0.000193 -0.42 -160.35 + 51. D(C 2,C 1,C 0,C 4) -35.64 0.000163 -0.40 -36.03 + 52. D(C 2,C 1,C 0,H 6) 82.22 0.000485 -0.62 81.60 + 53. D(H 8,C 1,C 0,H 5) -39.00 -0.000083 -0.45 -39.44 + 54. D(H 8,C 1,C 0,C 4) 82.22 -0.000515 -0.20 82.01 + 55. D(H 9,C 2,C 1,H 7) 20.33 0.000224 0.03 20.36 + 56. D(C 3,C 2,C 1,H 8) -100.29 -0.000372 0.29 -99.99 + 57. D(C 3,C 2,C 1,C 0) 17.71 0.000085 0.16 17.88 + 58. D(H 10,C 2,C 1,H 8) 21.05 -0.000331 0.29 21.34 + 59. D(H 9,C 2,C 1,H 8) 140.09 0.000008 0.13 140.22 + 60. D(H 10,C 2,C 1,H 7) -98.71 -0.000115 0.18 -98.53 + 61. D(H 10,C 2,C 1,C 0) 139.05 0.000126 0.15 139.21 + 62. D(C 3,C 2,C 1,H 7) 139.95 -0.000156 0.19 140.14 + 63. D(H 9,C 2,C 1,C 0) -101.91 0.000465 0.00 -101.91 + 64. D(H 12,C 3,C 2,H 9) -110.81 0.000109 0.01 -110.80 + 65. D(H 12,C 3,C 2,C 1) 129.08 0.000002 0.00 129.09 + 66. D(H 11,C 3,C 2,H 10) 127.49 -0.000133 0.09 127.58 + 67. D(H 11,C 3,C 2,H 9) 8.46 -0.000148 0.12 8.58 + 68. D(C 4,C 3,C 2,H 9) 127.09 0.000137 0.08 127.17 + 69. D(C 4,C 3,C 2,C 1) 6.98 0.000029 0.07 7.06 + 70. D(H 11,C 3,C 2,C 1) -111.64 -0.000256 0.11 -111.53 + 71. D(H 12,C 3,C 2,H 10) 8.21 0.000124 -0.01 8.20 + 72. D(C 4,C 3,C 2,H 10) -113.89 0.000152 0.06 -113.83 + 73. D(H 13,C 4,C 0,C 1) 161.52 -0.000300 0.58 162.10 + 74. D(C 3,C 4,C 0,H 6) -77.87 -0.000222 0.58 -77.29 + 75. D(C 3,C 4,C 0,H 5) 161.09 -0.000525 0.68 161.78 + 76. D(C 3,C 4,C 0,C 1) 39.94 -0.000335 0.48 40.42 + 77. D(H 14,C 4,C 3,H 12) -33.43 0.000420 -0.49 -33.93 + 78. D(H 14,C 4,C 3,H 11) -152.81 -0.000135 -0.28 -153.09 + 79. D(H 13,C 4,C 3,H 12) 87.03 0.000355 -0.44 86.59 + 80. D(H 13,C 4,C 3,H 11) -32.35 -0.000200 -0.23 -32.58 + 81. D(H 13,C 4,C 3,C 2) -150.69 0.000461 -0.49 -151.18 + 82. D(C 0,C 4,C 3,H 12) -151.30 -0.000109 -0.26 -151.55 + 83. D(C 0,C 4,C 3,H 11) 89.33 -0.000664 -0.05 89.28 + 84. D(C 0,C 4,C 3,C 2) -29.01 -0.000003 -0.31 -29.32 + 85. D(H 14,C 4,C 0,H 6) 164.36 0.000223 0.55 164.91 + 86. D(H 14,C 4,C 0,H 5) 43.32 -0.000080 0.65 43.97 + 87. D(H 14,C 4,C 3,C 2) 88.85 0.000526 -0.54 88.31 + 88. D(H 14,C 4,C 0,C 1) -77.83 0.000110 0.45 -77.38 + 89. D(H 13,C 4,C 0,H 6) 43.71 -0.000186 0.69 44.40 + 90. D(H 13,C 4,C 0,H 5) -77.33 -0.000489 0.79 -76.54 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 2 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.257123 -0.088091 0.238226 + C 0.328826 -1.226976 -0.172935 + C -1.088491 -0.679714 0.044787 + C -0.950523 0.850465 0.125720 + C 0.506368 1.154273 -0.224938 + H 2.245041 -0.172991 -0.215333 + H 1.379029 -0.071943 1.323172 + H 0.512114 -2.137358 0.398053 + H 0.479548 -1.461348 -1.229026 + H -1.516833 -1.070415 0.969225 + H -1.749798 -0.979717 -0.769026 + H -1.167689 1.190610 1.140388 + H -1.642768 1.360747 -0.544398 + H 0.866704 2.064442 0.255169 + H 0.616638 1.274786 -1.304765 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.375619 -0.166468 0.450183 + 1 C 6.0000 0 12.011 0.621391 -2.318648 -0.326800 + 2 C 6.0000 0 12.011 -2.056950 -1.284472 0.084635 + 3 C 6.0000 0 12.011 -1.796228 1.607146 0.237576 + 4 C 6.0000 0 12.011 0.956896 2.181259 -0.425072 + 5 H 1.0000 0 1.008 4.242513 -0.326906 -0.406921 + 6 H 1.0000 0 1.008 2.605988 -0.135952 2.500433 + 7 H 1.0000 0 1.008 0.967755 -4.039021 0.752212 + 8 H 1.0000 0 1.008 0.906214 -2.761547 -2.322522 + 9 H 1.0000 0 1.008 -2.866399 -2.022792 1.831570 + 10 H 1.0000 0 1.008 -3.306639 -1.851397 -1.453248 + 11 H 1.0000 0 1.008 -2.206613 2.249927 2.155022 + 12 H 1.0000 0 1.008 -3.104381 2.571440 -1.028762 + 13 H 1.0000 0 1.008 1.637834 3.901230 0.482199 + 14 H 1.0000 0 1.008 1.165278 2.408997 -2.465649 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:47:44.776 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.68743187006654 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0481639 -0.160482E+02 0.731E-02 13.22 0.0 T + 2 -16.0481684 -0.452038E-05 0.459E-02 13.23 1.0 T + 3 -16.0481684 -0.549547E-07 0.558E-03 13.23 4.6 T + 4 -16.0481684 -0.241912E-08 0.823E-04 13.23 31.4 T + 5 -16.0481684 -0.304503E-10 0.236E-04 13.23 109.6 T + + *** convergence criteria satisfied after 5 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6320181 -17.1981 + ... ... ... ... + 9 2.0000 -0.4822072 -13.1215 + 10 2.0000 -0.4411536 -12.0044 + 11 2.0000 -0.4387072 -11.9378 + 12 2.0000 -0.4364153 -11.8755 + 13 2.0000 -0.4362258 -11.8703 + 14 2.0000 -0.4204451 -11.4409 + 15 2.0000 -0.4139272 -11.2635 (HOMO) + 16 0.0721558 1.9635 (LUMO) + 17 0.0724999 1.9728 + 18 0.0886728 2.4129 + 19 0.1319823 3.5914 + 20 0.1333845 3.6296 + ... ... ... + 30 0.3496123 9.5134 + ------------------------------------------------------------- + HL-Gap 0.4860831 Eh 13.2270 eV + Fermi-level -0.1708857 Eh -4.6500 eV + + SCC (total) 0 d, 0 h, 0 min, 0.032 sec + SCC setup ... 0 min, 0.000 sec ( 1.142%) + Dispersion ... 0 min, 0.000 sec ( 0.534%) + classical contributions ... 0 min, 0.000 sec ( 0.196%) + integral evaluation ... 0 min, 0.002 sec ( 7.303%) + iterations ... 0 min, 0.027 sec ( 83.699%) + molecular gradient ... 0 min, 0.002 sec ( 6.739%) + printout ... 0 min, 0.000 sec ( 0.349%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814241222376 Eh :: + :: gradient norm 0.005064544877 Eh/a0 :: + :: HOMO-LUMO gap 13.226993409773 eV :: + ::.................................................:: + :: SCC energy -16.048168432480 Eh :: + :: -> isotropic ES 0.002305024320 Eh :: + :: -> anisotropic ES 0.004275171918 Eh :: + :: -> anisotropic XC 0.009706949492 Eh :: + :: -> dispersion -0.008130395581 Eh :: + :: repulsion energy 0.233916722051 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814241222376 Eh | + | GRADIENT NORM 0.005064544877 Eh/α | + | HOMO-LUMO GAP 13.226993409773 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:47:44.824 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.048 sec + * cpu-time: 0 d, 0 h, 0 min, 0.025 sec + * ratio c/w: 0.521 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.032 sec + * cpu-time: 0 d, 0 h, 0 min, 0.010 sec + * ratio c/w: 0.313 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814241222380 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 15 +Number of internal coordinates .... 90 +Current Energy .... -15.814241222 Eh +Current gradient norm .... 0.005064545 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.998743425 +Lowest eigenvalues of augmented Hessian: + -0.000064929 0.011851251 0.013592534 0.045406129 0.045899005 +Length of the computed step .... 0.050178623 +The final length of the internal step .... 0.050178623 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0052892913 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0072406891 RMS(Int)= 0.0052881724 + Iter 1: RMS(Cart)= 0.0000247280 RMS(Int)= 0.0000172505 + Iter 2: RMS(Cart)= 0.0000001558 RMS(Int)= 0.0000001513 + Iter 3: RMS(Cart)= 0.0000000013 RMS(Int)= 0.0000000010 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0004176951 0.0000050000 NO + RMS gradient 0.0002952155 0.0001000000 NO + MAX gradient 0.0009148389 0.0003000000 NO + RMS step 0.0052892913 0.0020000000 NO + MAX step 0.0127713249 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0023 Max(Angles) 0.15 + Max(Dihed) 0.73 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.5257 -0.000661 0.0013 1.5270 + 2. B(C 2,C 1) 1.5348 -0.000869 0.0020 1.5368 + 3. B(C 3,C 2) 1.5385 -0.000915 0.0023 1.5408 + 4. B(C 4,C 3) 1.5290 -0.000781 0.0016 1.5306 + 5. B(C 4,C 0) 1.5237 -0.000679 0.0012 1.5249 + 6. B(H 5,C 0) 1.0904 0.000422 -0.0009 1.0894 + 7. B(H 6,C 0) 1.0919 0.000370 -0.0009 1.0910 + 8. B(H 7,C 1) 1.0901 0.000447 -0.0010 1.0891 + 9. B(H 8,C 1) 1.0922 0.000542 -0.0012 1.0910 + 10. B(H 9,C 2) 1.0912 0.000591 -0.0013 1.0899 + 11. B(H 10,C 2) 1.0907 0.000564 -0.0012 1.0894 + 12. B(H 11,C 3) 1.0920 0.000619 -0.0014 1.0906 + 13. B(H 12,C 3) 1.0903 0.000493 -0.0011 1.0891 + 14. B(H 13,C 4) 1.0903 0.000438 -0.0010 1.0893 + 15. B(H 14,C 4) 1.0921 0.000429 -0.0010 1.0911 + 16. A(C 4,C 0,H 5) 112.55 -0.000129 0.10 112.65 + 17. A(C 1,C 0,C 4) 103.12 0.000010 -0.12 103.00 + 18. A(C 1,C 0,H 5) 112.40 0.000043 0.05 112.45 + 19. A(H 5,C 0,H 6) 108.26 -0.000122 0.09 108.35 + 20. A(C 1,C 0,H 6) 110.29 -0.000023 -0.02 110.27 + 21. A(C 4,C 0,H 6) 110.18 0.000236 -0.12 110.06 + 22. A(C 2,C 1,H 8) 109.94 -0.000325 0.14 110.08 + 23. A(C 2,C 1,H 7) 112.25 0.000257 -0.07 112.19 + 24. A(H 7,C 1,H 8) 107.70 -0.000163 0.12 107.82 + 25. A(C 0,C 1,H 7) 112.33 -0.000106 0.01 112.34 + 26. A(C 0,C 1,C 2) 104.92 -0.000011 -0.08 104.84 + 27. A(C 0,C 1,H 8) 109.68 0.000353 -0.12 109.56 + 28. A(H 9,C 2,H 10) 107.19 -0.000136 0.10 107.30 + 29. A(C 1,C 2,C 3) 106.22 0.000072 -0.06 106.16 + 30. A(C 1,C 2,H 10) 110.85 -0.000104 0.01 110.87 + 31. A(C 3,C 2,H 9) 110.29 -0.000203 0.08 110.37 + 32. A(C 1,C 2,H 9) 110.79 0.000196 -0.07 110.73 + 33. A(C 3,C 2,H 10) 111.54 0.000178 -0.07 111.48 + 34. A(H 11,C 3,H 12) 107.40 -0.000160 0.12 107.52 + 35. A(C 4,C 3,H 12) 111.78 -0.000051 -0.03 111.75 + 36. A(C 2,C 3,H 12) 112.10 0.000212 -0.07 112.03 + 37. A(C 4,C 3,H 11) 109.92 0.000274 -0.08 109.84 + 38. A(C 2,C 3,H 11) 109.93 -0.000325 0.14 110.07 + 39. A(C 2,C 3,C 4) 105.72 0.000053 -0.08 105.65 + 40. A(H 13,C 4,H 14) 108.05 -0.000151 0.11 108.16 + 41. A(C 3,C 4,H 14) 110.18 -0.000209 0.07 110.24 + 42. A(C 0,C 4,H 14) 109.92 0.000360 -0.15 109.77 + 43. A(C 3,C 4,H 13) 112.32 0.000203 -0.02 112.30 + 44. A(C 0,C 4,H 13) 112.58 -0.000177 0.09 112.67 + 45. A(C 0,C 4,C 3) 103.75 -0.000014 -0.10 103.65 + 46. D(H 7,C 1,C 0,H 5) 80.29 0.000001 -0.42 79.87 + 47. D(H 7,C 1,C 0,H 6) -40.62 0.000144 -0.56 -41.18 + 48. D(C 2,C 1,C 0,H 5) -157.49 0.000249 -0.55 -158.04 + 49. D(H 7,C 1,C 0,C 4) -158.25 -0.000125 -0.34 -158.59 + 50. D(H 8,C 1,C 0,H 6) -160.35 0.000179 -0.63 -160.98 + 51. D(C 2,C 1,C 0,C 4) -36.03 0.000123 -0.47 -36.50 + 52. D(C 2,C 1,C 0,H 6) 81.60 0.000392 -0.69 80.91 + 53. D(H 8,C 1,C 0,H 5) -39.44 0.000036 -0.49 -39.94 + 54. D(H 8,C 1,C 0,C 4) 82.01 -0.000090 -0.42 81.60 + 55. D(H 9,C 2,C 1,H 7) 20.36 0.000054 0.13 20.48 + 56. D(C 3,C 2,C 1,H 8) -99.99 -0.000296 0.34 -99.65 + 57. D(C 3,C 2,C 1,C 0) 17.88 -0.000049 0.22 18.10 + 58. D(H 10,C 2,C 1,H 8) 21.34 -0.000094 0.23 21.57 + 59. D(H 9,C 2,C 1,H 8) 140.22 -0.000204 0.32 140.55 + 60. D(H 10,C 2,C 1,H 7) -98.53 0.000164 0.03 -98.49 + 61. D(H 10,C 2,C 1,C 0) 139.21 0.000153 0.11 139.32 + 62. D(C 3,C 2,C 1,H 7) 140.14 -0.000038 0.15 140.29 + 63. D(H 9,C 2,C 1,C 0) -101.91 0.000043 0.20 -101.70 + 64. D(H 12,C 3,C 2,H 9) -110.80 0.000239 -0.11 -110.91 + 65. D(H 12,C 3,C 2,C 1) 129.09 0.000073 -0.04 129.05 + 66. D(H 11,C 3,C 2,H 10) 127.58 -0.000232 0.23 127.80 + 67. D(H 11,C 3,C 2,H 9) 8.58 -0.000043 0.09 8.67 + 68. D(C 4,C 3,C 2,H 9) 127.17 0.000143 0.02 127.19 + 69. D(C 4,C 3,C 2,C 1) 7.06 -0.000024 0.10 7.16 + 70. D(H 11,C 3,C 2,C 1) -111.53 -0.000210 0.17 -111.37 + 71. D(H 12,C 3,C 2,H 10) 8.20 0.000051 0.02 8.22 + 72. D(C 4,C 3,C 2,H 10) -113.83 -0.000046 0.16 -113.67 + 73. D(H 13,C 4,C 0,C 1) 162.10 -0.000011 0.50 162.60 + 74. D(C 3,C 4,C 0,H 6) -77.29 -0.000239 0.68 -76.61 + 75. D(C 3,C 4,C 0,H 5) 161.78 -0.000161 0.58 162.35 + 76. D(C 3,C 4,C 0,C 1) 40.42 -0.000152 0.54 40.96 + 77. D(H 14,C 4,C 3,H 12) -33.93 0.000145 -0.43 -34.36 + 78. D(H 14,C 4,C 3,H 11) -153.09 0.000197 -0.51 -153.60 + 79. D(H 13,C 4,C 3,H 12) 86.59 -0.000056 -0.26 86.33 + 80. D(H 13,C 4,C 3,H 11) -32.58 -0.000005 -0.33 -32.91 + 81. D(H 13,C 4,C 3,C 2) -151.18 0.000208 -0.42 -151.59 + 82. D(C 0,C 4,C 3,H 12) -151.55 -0.000169 -0.23 -151.78 + 83. D(C 0,C 4,C 3,H 11) 89.28 -0.000117 -0.30 88.98 + 84. D(C 0,C 4,C 3,C 2) -29.32 0.000095 -0.39 -29.71 + 85. D(H 14,C 4,C 0,H 6) 164.91 -0.000157 0.73 165.64 + 86. D(H 14,C 4,C 0,H 5) 43.97 -0.000079 0.63 44.60 + 87. D(H 14,C 4,C 3,C 2) 88.31 0.000409 -0.59 87.72 + 88. D(H 14,C 4,C 0,C 1) -77.38 -0.000070 0.59 -76.80 + 89. D(H 13,C 4,C 0,H 6) 44.40 -0.000097 0.64 45.04 + 90. D(H 13,C 4,C 0,H 5) -76.54 -0.000020 0.54 -76.00 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 3 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.256840 -0.087971 0.240929 + C 0.329515 -1.227180 -0.176191 + C -1.089636 -0.680681 0.045702 + C -0.950883 0.851597 0.128554 + C 0.506606 1.153997 -0.227959 + H 2.247193 -0.173216 -0.204973 + H 1.369029 -0.069993 1.325991 + H 0.512598 -2.138785 0.390994 + H 0.482449 -1.454647 -1.232210 + H -1.514223 -1.073592 0.969408 + H -1.751405 -0.977871 -0.767095 + H -1.162122 1.192254 1.142832 + H -1.643824 1.361220 -0.539544 + H 0.867356 2.066207 0.245741 + H 0.615797 1.265430 -1.307858 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.375084 -0.166241 0.455289 + 1 C 6.0000 0 12.011 0.622693 -2.319034 -0.332953 + 2 C 6.0000 0 12.011 -2.059113 -1.286301 0.086365 + 3 C 6.0000 0 12.011 -1.796908 1.609286 0.242933 + 4 C 6.0000 0 12.011 0.957346 2.180739 -0.430780 + 5 H 1.0000 0 1.008 4.246579 -0.327331 -0.387344 + 6 H 1.0000 0 1.008 2.587090 -0.132267 2.505760 + 7 H 1.0000 0 1.008 0.968671 -4.041718 0.738872 + 8 H 1.0000 0 1.008 0.911696 -2.748884 -2.328540 + 9 H 1.0000 0 1.008 -2.861466 -2.028795 1.831915 + 10 H 1.0000 0 1.008 -3.309676 -1.847909 -1.449600 + 11 H 1.0000 0 1.008 -2.196092 2.253033 2.159640 + 12 H 1.0000 0 1.008 -3.106377 2.572333 -1.019591 + 13 H 1.0000 0 1.008 1.639064 3.904566 0.464382 + 14 H 1.0000 0 1.008 1.163688 2.391316 -2.471493 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:47:44.871 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.25237798133713 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0488829 -0.160489E+02 0.223E-02 13.19 0.0 T + 2 -16.0488832 -0.334759E-06 0.136E-02 13.19 1.9 T + 3 -16.0488832 -0.530733E-08 0.165E-03 13.19 15.6 T + 4 -16.0488832 -0.105686E-09 0.251E-04 13.19 102.9 T + 5 -16.0488832 -0.115072E-10 0.542E-05 13.19 476.2 T + + *** convergence criteria satisfied after 5 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6317594 -17.1910 + ... ... ... ... + 9 2.0000 -0.4821118 -13.1189 + 10 2.0000 -0.4409588 -11.9991 + 11 2.0000 -0.4384705 -11.9314 + 12 2.0000 -0.4362883 -11.8720 + 13 2.0000 -0.4361380 -11.8679 + 14 2.0000 -0.4207098 -11.4481 + 15 2.0000 -0.4142571 -11.2725 (HOMO) + 16 0.0706137 1.9215 (LUMO) + 17 0.0711297 1.9355 + 18 0.0905748 2.4647 + 19 0.1317725 3.5857 + 20 0.1343975 3.6571 + ... ... ... + 30 0.3513169 9.5598 + ------------------------------------------------------------- + HL-Gap 0.4848708 Eh 13.1940 eV + Fermi-level -0.1718217 Eh -4.6755 eV + + SCC (total) 0 d, 0 h, 0 min, 0.032 sec + SCC setup ... 0 min, 0.000 sec ( 1.009%) + Dispersion ... 0 min, 0.000 sec ( 0.336%) + classical contributions ... 0 min, 0.000 sec ( 0.176%) + integral evaluation ... 0 min, 0.003 sec ( 8.613%) + iterations ... 0 min, 0.023 sec ( 71.684%) + molecular gradient ... 0 min, 0.006 sec ( 17.467%) + printout ... 0 min, 0.000 sec ( 0.641%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814284974998 Eh :: + :: gradient norm 0.001341145210 Eh/a0 :: + :: HOMO-LUMO gap 13.194005848187 eV :: + ::.................................................:: + :: SCC energy -16.048883232525 Eh :: + :: -> isotropic ES 0.002333401920 Eh :: + :: -> anisotropic ES 0.004266749554 Eh :: + :: -> anisotropic XC 0.009690521656 Eh :: + :: -> dispersion -0.008129206700 Eh :: + :: repulsion energy 0.234587788549 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814284974998 Eh | + | GRADIENT NORM 0.001341145210 Eh/α | + | HOMO-LUMO GAP 13.194005848187 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:47:44.919 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.048 sec + * cpu-time: 0 d, 0 h, 0 min, 0.030 sec + * ratio c/w: 0.630 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.032 sec + * cpu-time: 0 d, 0 h, 0 min, 0.015 sec + * ratio c/w: 0.465 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814284975000 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 15 +Number of internal coordinates .... 90 +Current Energy .... -15.814284975 Eh +Current gradient norm .... 0.001341145 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.998367055 +Lowest eigenvalues of augmented Hessian: + -0.000029892 0.007767788 0.011851329 0.045071205 0.045882488 +Length of the computed step .... 0.057218068 +The final length of the internal step .... 0.057218068 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0060313139 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0083484502 RMS(Int)= 0.0060274104 + Iter 1: RMS(Cart)= 0.0000328622 RMS(Int)= 0.0000212088 + Iter 2: RMS(Cart)= 0.0000002431 RMS(Int)= 0.0000002261 + Iter 3: RMS(Cart)= 0.0000000023 RMS(Int)= 0.0000000017 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0000437526 0.0000050000 NO + RMS gradient 0.0001059703 0.0001000000 NO + MAX gradient 0.0002571587 0.0003000000 YES + RMS step 0.0060313139 0.0020000000 NO + MAX step 0.0154142059 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0007 Max(Angles) 0.16 + Max(Dihed) 0.88 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.5270 0.000064 0.0004 1.5274 + 2. B(C 2,C 1) 1.5368 0.000207 0.0006 1.5375 + 3. B(C 3,C 2) 1.5408 0.000257 0.0007 1.5415 + 4. B(C 4,C 3) 1.5306 0.000125 0.0005 1.5311 + 5. B(C 4,C 0) 1.5249 -0.000013 0.0004 1.5253 + 6. B(H 5,C 0) 1.0894 -0.000041 -0.0003 1.0891 + 7. B(H 6,C 0) 1.0910 -0.000159 -0.0001 1.0909 + 8. B(H 7,C 1) 1.0891 -0.000108 -0.0002 1.0889 + 9. B(H 8,C 1) 1.0910 -0.000090 -0.0003 1.0907 + 10. B(H 9,C 2) 1.0899 -0.000082 -0.0004 1.0895 + 11. B(H 10,C 2) 1.0894 -0.000109 -0.0003 1.0891 + 12. B(H 11,C 3) 1.0906 -0.000071 -0.0004 1.0902 + 13. B(H 12,C 3) 1.0891 -0.000125 -0.0002 1.0889 + 14. B(H 13,C 4) 1.0893 -0.000065 -0.0003 1.0891 + 15. B(H 14,C 4) 1.0911 -0.000123 -0.0002 1.0909 + 16. A(C 4,C 0,H 5) 112.65 -0.000081 0.11 112.76 + 17. A(C 1,C 0,C 4) 102.99 0.000058 -0.15 102.84 + 18. A(C 1,C 0,H 5) 112.45 -0.000004 0.06 112.51 + 19. A(H 5,C 0,H 6) 108.35 -0.000097 0.13 108.48 + 20. A(C 1,C 0,H 6) 110.27 0.000026 -0.04 110.23 + 21. A(C 4,C 0,H 6) 110.06 0.000111 -0.12 109.94 + 22. A(C 2,C 1,H 8) 110.08 -0.000089 0.08 110.16 + 23. A(C 2,C 1,H 7) 112.19 0.000125 -0.06 112.13 + 24. A(H 7,C 1,H 8) 107.82 -0.000135 0.15 107.97 + 25. A(C 0,C 1,H 7) 112.34 -0.000057 0.03 112.36 + 26. A(C 0,C 1,C 2) 104.84 0.000017 -0.10 104.74 + 27. A(C 0,C 1,H 8) 109.56 0.000145 -0.11 109.45 + 28. A(H 9,C 2,H 10) 107.30 -0.000163 0.15 107.45 + 29. A(C 1,C 2,C 3) 106.16 -0.000055 -0.05 106.11 + 30. A(C 1,C 2,H 10) 110.87 -0.000025 0.01 110.87 + 31. A(C 3,C 2,H 9) 110.37 -0.000048 0.04 110.41 + 32. A(C 1,C 2,H 9) 110.73 0.000150 -0.08 110.64 + 33. A(C 3,C 2,H 10) 111.48 0.000149 -0.08 111.40 + 34. A(H 11,C 3,H 12) 107.52 -0.000158 0.16 107.69 + 35. A(C 4,C 3,H 12) 111.75 -0.000017 -0.02 111.73 + 36. A(C 2,C 3,H 12) 112.03 0.000136 -0.07 111.96 + 37. A(C 4,C 3,H 11) 109.84 0.000148 -0.09 109.75 + 38. A(C 2,C 3,H 11) 110.07 -0.000087 0.09 110.16 + 39. A(C 2,C 3,C 4) 105.65 -0.000017 -0.07 105.57 + 40. A(H 13,C 4,H 14) 108.16 -0.000114 0.14 108.30 + 41. A(C 3,C 4,H 14) 110.24 -0.000042 0.02 110.27 + 42. A(C 0,C 4,H 14) 109.77 0.000142 -0.13 109.64 + 43. A(C 3,C 4,H 13) 112.30 0.000077 -0.01 112.29 + 44. A(C 0,C 4,H 13) 112.67 -0.000100 0.10 112.77 + 45. A(C 0,C 4,C 3) 103.65 0.000048 -0.13 103.51 + 46. D(H 7,C 1,C 0,H 5) 79.87 -0.000028 -0.47 79.41 + 47. D(H 7,C 1,C 0,H 6) -41.18 0.000080 -0.64 -41.81 + 48. D(C 2,C 1,C 0,H 5) -158.04 0.000104 -0.59 -158.63 + 49. D(H 7,C 1,C 0,C 4) -158.59 -0.000091 -0.40 -158.99 + 50. D(H 8,C 1,C 0,H 6) -160.98 0.000188 -0.77 -161.76 + 51. D(C 2,C 1,C 0,C 4) -36.50 0.000041 -0.52 -37.03 + 52. D(C 2,C 1,C 0,H 6) 80.91 0.000212 -0.76 80.15 + 53. D(H 8,C 1,C 0,H 5) -39.93 0.000080 -0.60 -40.54 + 54. D(H 8,C 1,C 0,C 4) 81.60 0.000017 -0.54 81.06 + 55. D(H 9,C 2,C 1,H 7) 20.48 -0.000015 0.21 20.69 + 56. D(C 3,C 2,C 1,H 8) -99.65 -0.000172 0.40 -99.25 + 57. D(C 3,C 2,C 1,C 0) 18.10 -0.000036 0.25 18.35 + 58. D(H 10,C 2,C 1,H 8) 21.57 -0.000040 0.28 21.85 + 59. D(H 9,C 2,C 1,H 8) 140.55 -0.000163 0.42 140.96 + 60. D(H 10,C 2,C 1,H 7) -98.49 0.000109 0.07 -98.42 + 61. D(H 10,C 2,C 1,C 0) 139.32 0.000096 0.14 139.45 + 62. D(C 3,C 2,C 1,H 7) 140.29 -0.000023 0.19 140.47 + 63. D(H 9,C 2,C 1,C 0) -101.70 -0.000028 0.28 -101.43 + 64. D(H 12,C 3,C 2,H 9) -110.91 0.000149 -0.11 -111.02 + 65. D(H 12,C 3,C 2,C 1) 129.05 0.000029 -0.00 129.05 + 66. D(H 11,C 3,C 2,H 10) 127.80 -0.000159 0.28 128.08 + 67. D(H 11,C 3,C 2,H 9) 8.67 -0.000019 0.11 8.78 + 68. D(C 4,C 3,C 2,H 9) 127.19 0.000102 0.01 127.20 + 69. D(C 4,C 3,C 2,C 1) 7.16 -0.000019 0.11 7.27 + 70. D(H 11,C 3,C 2,C 1) -111.37 -0.000139 0.21 -111.15 + 71. D(H 12,C 3,C 2,H 10) 8.22 0.000009 0.06 8.28 + 72. D(C 4,C 3,C 2,H 10) -113.67 -0.000039 0.18 -113.50 + 73. D(H 13,C 4,C 0,C 1) 162.60 0.000032 0.55 163.15 + 74. D(C 3,C 4,C 0,H 6) -76.61 -0.000149 0.78 -75.83 + 75. D(C 3,C 4,C 0,H 5) 162.35 -0.000048 0.63 162.98 + 76. D(C 3,C 4,C 0,C 1) 40.96 -0.000038 0.59 41.55 + 77. D(H 14,C 4,C 3,H 12) -34.36 0.000071 -0.50 -34.86 + 78. D(H 14,C 4,C 3,H 11) -153.60 0.000182 -0.64 -154.24 + 79. D(H 13,C 4,C 3,H 12) 86.33 -0.000052 -0.31 86.02 + 80. D(H 13,C 4,C 3,H 11) -32.91 0.000059 -0.45 -33.36 + 81. D(H 13,C 4,C 3,C 2) -151.59 0.000094 -0.46 -152.05 + 82. D(C 0,C 4,C 3,H 12) -151.78 -0.000100 -0.29 -152.07 + 83. D(C 0,C 4,C 3,H 11) 88.98 0.000010 -0.42 88.56 + 84. D(C 0,C 4,C 3,C 2) -29.70 0.000046 -0.43 -30.14 + 85. D(H 14,C 4,C 0,H 6) 165.64 -0.000191 0.88 166.52 + 86. D(H 14,C 4,C 0,H 5) 44.60 -0.000091 0.73 45.33 + 87. D(H 14,C 4,C 3,C 2) 87.72 0.000217 -0.65 87.07 + 88. D(H 14,C 4,C 0,C 1) -76.80 -0.000081 0.70 -76.10 + 89. D(H 13,C 4,C 0,H 6) 45.03 -0.000079 0.73 45.77 + 90. D(H 13,C 4,C 0,H 5) -76.00 0.000022 0.58 -75.42 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 4 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.255759 -0.087735 0.244138 + C 0.330030 -1.226385 -0.179456 + C -1.089550 -0.680907 0.046501 + C -0.950251 0.851938 0.131194 + C 0.506593 1.152913 -0.231316 + H 2.249411 -0.173472 -0.193485 + H 1.356785 -0.067973 1.330167 + H 0.512793 -2.140292 0.383710 + H 0.484505 -1.445960 -1.236559 + H -1.510226 -1.075841 0.970688 + H -1.752335 -0.975396 -0.766044 + H -1.155056 1.192253 1.146436 + H -1.644903 1.361314 -0.534953 + H 0.867883 2.068121 0.235501 + H 0.613852 1.254194 -1.312201 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.373041 -0.165795 0.461354 + 1 C 6.0000 0 12.011 0.623666 -2.317532 -0.339122 + 2 C 6.0000 0 12.011 -2.058951 -1.286729 0.087873 + 3 C 6.0000 0 12.011 -1.795713 1.609929 0.247921 + 4 C 6.0000 0 12.011 0.957321 2.178690 -0.437123 + 5 H 1.0000 0 1.008 4.250770 -0.327815 -0.365634 + 6 H 1.0000 0 1.008 2.563951 -0.128451 2.513651 + 7 H 1.0000 0 1.008 0.969038 -4.044566 0.725107 + 8 H 1.0000 0 1.008 0.915581 -2.732469 -2.336759 + 9 H 1.0000 0 1.008 -2.853913 -2.033046 1.834334 + 10 H 1.0000 0 1.008 -3.311434 -1.843231 -1.447613 + 11 H 1.0000 0 1.008 -2.182739 2.253032 2.166451 + 12 H 1.0000 0 1.008 -3.108416 2.572510 -1.010915 + 13 H 1.0000 0 1.008 1.640062 3.908182 0.445032 + 14 H 1.0000 0 1.008 1.160013 2.370084 -2.479701 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:47:45.002 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.01608723041583 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0490204 -0.160490E+02 0.205E-02 13.18 0.0 T + 2 -16.0490204 -0.500114E-07 0.122E-02 13.18 2.1 T + 3 -16.0490204 -0.715285E-08 0.591E-04 13.18 43.7 T + 4 -16.0490204 -0.246786E-09 0.274E-04 13.18 94.3 T + + *** convergence criteria satisfied after 4 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6317548 -17.1909 + ... ... ... ... + 9 2.0000 -0.4820936 -13.1184 + 10 2.0000 -0.4408037 -11.9949 + 11 2.0000 -0.4382078 -11.9242 + 12 2.0000 -0.4362017 -11.8697 + 13 2.0000 -0.4360766 -11.8662 + 14 2.0000 -0.4210091 -11.4562 + 15 2.0000 -0.4144723 -11.2784 (HOMO) + 16 0.0700262 1.9055 (LUMO) + 17 0.0707046 1.9240 + 18 0.0914037 2.4872 + 19 0.1318050 3.5866 + 20 0.1346092 3.6629 + ... ... ... + 30 0.3521963 9.5837 + ------------------------------------------------------------- + HL-Gap 0.4844985 Eh 13.1839 eV + Fermi-level -0.1722231 Eh -4.6864 eV + + SCC (total) 0 d, 0 h, 0 min, 0.009 sec + SCC setup ... 0 min, 0.000 sec ( 1.837%) + Dispersion ... 0 min, 0.000 sec ( 1.201%) + classical contributions ... 0 min, 0.000 sec ( 0.476%) + integral evaluation ... 0 min, 0.002 sec ( 21.513%) + iterations ... 0 min, 0.004 sec ( 44.606%) + molecular gradient ... 0 min, 0.002 sec ( 27.667%) + printout ... 0 min, 0.000 sec ( 2.510%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814304882812 Eh :: + :: gradient norm 0.001602921921 Eh/a0 :: + :: HOMO-LUMO gap 13.183876432817 eV :: + ::.................................................:: + :: SCC energy -16.049020413886 Eh :: + :: -> isotropic ES 0.002345852688 Eh :: + :: -> anisotropic ES 0.004257241237 Eh :: + :: -> anisotropic XC 0.009701964224 Eh :: + :: -> dispersion -0.008131094784 Eh :: + :: repulsion energy 0.234705100573 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814304882812 Eh | + | GRADIENT NORM 0.001602921921 Eh/α | + | HOMO-LUMO GAP 13.183876432817 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:47:45.024 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.022 sec + * cpu-time: 0 d, 0 h, 0 min, 0.021 sec + * ratio c/w: 0.963 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.009 sec + * cpu-time: 0 d, 0 h, 0 min, 0.008 sec + * ratio c/w: 0.907 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814304882810 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 15 +Number of internal coordinates .... 90 +Current Energy .... -15.814304883 Eh +Current gradient norm .... 0.001602922 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999205442 +Lowest eigenvalues of augmented Hessian: + -0.000010844 0.004886037 0.011851371 0.045590400 0.045966844 +Length of the computed step .... 0.039887491 +The final length of the internal step .... 0.039887491 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0042045107 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0057429193 RMS(Int)= 0.0042020683 + Iter 1: RMS(Cart)= 0.0000153504 RMS(Int)= 0.0000096794 + Iter 2: RMS(Cart)= 0.0000000770 RMS(Int)= 0.0000000700 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0000199078 0.0000050000 NO + RMS gradient 0.0001182037 0.0001000000 NO + MAX gradient 0.0004967062 0.0003000000 NO + RMS step 0.0042045107 0.0020000000 NO + MAX step 0.0107828207 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0003 Max(Angles) 0.10 + Max(Dihed) 0.62 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.5274 0.000259 -0.0002 1.5272 + 2. B(C 2,C 1) 1.5375 0.000444 -0.0003 1.5372 + 3. B(C 3,C 2) 1.5415 0.000497 -0.0003 1.5412 + 4. B(C 4,C 3) 1.5311 0.000352 -0.0002 1.5309 + 5. B(C 4,C 0) 1.5253 0.000204 -0.0001 1.5252 + 6. B(H 5,C 0) 1.0891 -0.000141 0.0000 1.0892 + 7. B(H 6,C 0) 1.0909 -0.000215 0.0002 1.0911 + 8. B(H 7,C 1) 1.0889 -0.000189 0.0001 1.0891 + 9. B(H 8,C 1) 1.0907 -0.000229 0.0002 1.0908 + 10. B(H 9,C 2) 1.0895 -0.000231 0.0002 1.0897 + 11. B(H 10,C 2) 1.0891 -0.000234 0.0002 1.0893 + 12. B(H 11,C 3) 1.0902 -0.000240 0.0001 1.0903 + 13. B(H 12,C 3) 1.0889 -0.000216 0.0002 1.0891 + 14. B(H 13,C 4) 1.0891 -0.000160 0.0001 1.0891 + 15. B(H 14,C 4) 1.0909 -0.000213 0.0002 1.0911 + 16. A(C 4,C 0,H 5) 112.76 -0.000032 0.08 112.84 + 17. A(C 1,C 0,C 4) 102.84 0.000032 -0.10 102.74 + 18. A(C 1,C 0,H 5) 112.51 -0.000031 0.05 112.56 + 19. A(H 5,C 0,H 6) 108.48 -0.000032 0.07 108.55 + 20. A(C 1,C 0,H 6) 110.23 0.000051 -0.05 110.18 + 21. A(C 4,C 0,H 6) 109.94 0.000018 -0.07 109.88 + 22. A(C 2,C 1,H 8) 110.16 0.000060 -0.00 110.16 + 23. A(C 2,C 1,H 7) 112.13 -0.000006 -0.01 112.12 + 24. A(H 7,C 1,H 8) 107.97 -0.000041 0.08 108.05 + 25. A(C 0,C 1,H 7) 112.37 -0.000022 0.04 112.40 + 26. A(C 0,C 1,C 2) 104.74 0.000016 -0.06 104.67 + 27. A(C 0,C 1,H 8) 109.45 -0.000002 -0.06 109.40 + 28. A(H 9,C 2,H 10) 107.45 -0.000073 0.09 107.54 + 29. A(C 1,C 2,C 3) 106.11 -0.000070 -0.02 106.08 + 30. A(C 1,C 2,H 10) 110.87 0.000011 0.01 110.88 + 31. A(C 3,C 2,H 9) 110.41 0.000036 0.00 110.41 + 32. A(C 1,C 2,H 9) 110.64 0.000052 -0.05 110.60 + 33. A(C 3,C 2,H 10) 111.40 0.000048 -0.03 111.37 + 34. A(H 11,C 3,H 12) 107.69 -0.000060 0.09 107.78 + 35. A(C 4,C 3,H 12) 111.73 -0.000007 0.01 111.74 + 36. A(C 2,C 3,H 12) 111.96 0.000018 -0.01 111.94 + 37. A(C 4,C 3,H 11) 109.75 0.000030 -0.06 109.69 + 38. A(C 2,C 3,H 11) 110.16 0.000059 0.00 110.16 + 39. A(C 2,C 3,C 4) 105.57 -0.000036 -0.04 105.53 + 40. A(H 13,C 4,H 14) 108.30 -0.000032 0.08 108.38 + 41. A(C 3,C 4,H 14) 110.27 0.000062 -0.02 110.24 + 42. A(C 0,C 4,H 14) 109.64 -0.000008 -0.07 109.57 + 43. A(C 3,C 4,H 13) 112.29 -0.000025 0.02 112.31 + 44. A(C 0,C 4,H 13) 112.77 -0.000032 0.07 112.84 + 45. A(C 0,C 4,C 3) 103.51 0.000041 -0.09 103.42 + 46. D(H 7,C 1,C 0,H 5) 79.41 0.000015 -0.36 79.05 + 47. D(H 7,C 1,C 0,H 6) -41.81 0.000042 -0.45 -42.27 + 48. D(C 2,C 1,C 0,H 5) -158.63 0.000005 -0.38 -159.01 + 49. D(H 7,C 1,C 0,C 4) -158.99 -0.000019 -0.30 -159.30 + 50. D(H 8,C 1,C 0,H 6) -161.76 0.000110 -0.55 -162.30 + 51. D(C 2,C 1,C 0,C 4) -37.03 -0.000029 -0.33 -37.35 + 52. D(C 2,C 1,C 0,H 6) 80.15 0.000032 -0.48 79.67 + 53. D(H 8,C 1,C 0,H 5) -40.54 0.000083 -0.45 -40.99 + 54. D(H 8,C 1,C 0,C 4) 81.06 0.000049 -0.40 80.67 + 55. D(H 9,C 2,C 1,H 7) 20.69 -0.000052 0.20 20.90 + 56. D(C 3,C 2,C 1,H 8) -99.25 -0.000037 0.27 -98.99 + 57. D(C 3,C 2,C 1,C 0) 18.35 -0.000002 0.16 18.52 + 58. D(H 10,C 2,C 1,H 8) 21.85 -0.000017 0.22 22.07 + 59. D(H 9,C 2,C 1,H 8) 140.96 -0.000067 0.30 141.27 + 60. D(H 10,C 2,C 1,H 7) -98.42 -0.000002 0.12 -98.31 + 61. D(H 10,C 2,C 1,C 0) 139.45 0.000019 0.11 139.57 + 62. D(C 3,C 2,C 1,H 7) 140.47 -0.000022 0.17 140.64 + 63. D(H 9,C 2,C 1,C 0) -101.43 -0.000031 0.20 -101.23 + 64. D(H 12,C 3,C 2,H 9) -111.02 0.000016 -0.02 -111.04 + 65. D(H 12,C 3,C 2,C 1) 129.05 -0.000024 0.05 129.10 + 66. D(H 11,C 3,C 2,H 10) 128.08 -0.000045 0.18 128.27 + 67. D(H 11,C 3,C 2,H 9) 8.78 -0.000008 0.09 8.87 + 68. D(C 4,C 3,C 2,H 9) 127.20 0.000037 0.00 127.20 + 69. D(C 4,C 3,C 2,C 1) 7.27 -0.000003 0.07 7.34 + 70. D(H 11,C 3,C 2,C 1) -111.15 -0.000048 0.16 -110.99 + 71. D(H 12,C 3,C 2,H 10) 8.28 -0.000020 0.08 8.36 + 72. D(C 4,C 3,C 2,H 10) -113.50 0.000001 0.09 -113.40 + 73. D(H 13,C 4,C 0,C 1) 163.15 0.000023 0.37 163.52 + 74. D(C 3,C 4,C 0,H 6) -75.83 -0.000039 0.51 -75.32 + 75. D(C 3,C 4,C 0,H 5) 162.98 0.000011 0.41 163.39 + 76. D(C 3,C 4,C 0,C 1) 41.55 0.000045 0.37 41.92 + 77. D(H 14,C 4,C 3,H 12) -34.86 0.000032 -0.38 -35.24 + 78. D(H 14,C 4,C 3,H 11) -154.24 0.000092 -0.46 -154.70 + 79. D(H 13,C 4,C 3,H 12) 86.02 0.000017 -0.28 85.74 + 80. D(H 13,C 4,C 3,H 11) -33.36 0.000077 -0.36 -33.72 + 81. D(H 13,C 4,C 3,C 2) -152.05 0.000012 -0.31 -152.37 + 82. D(C 0,C 4,C 3,H 12) -152.07 -0.000009 -0.24 -152.30 + 83. D(C 0,C 4,C 3,H 11) 88.56 0.000051 -0.32 88.23 + 84. D(C 0,C 4,C 3,C 2) -30.14 -0.000014 -0.27 -30.41 + 85. D(H 14,C 4,C 0,H 6) 166.52 -0.000129 0.62 167.14 + 86. D(H 14,C 4,C 0,H 5) 45.33 -0.000079 0.52 45.85 + 87. D(H 14,C 4,C 3,C 2) 87.07 0.000027 -0.41 86.66 + 88. D(H 14,C 4,C 0,C 1) -76.10 -0.000045 0.48 -75.62 + 89. D(H 13,C 4,C 0,H 6) 45.77 -0.000061 0.51 46.28 + 90. D(H 13,C 4,C 0,H 5) -75.42 -0.000011 0.41 -75.01 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 5 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.254764 -0.087506 0.246357 + C 0.330312 -1.225457 -0.181258 + C -1.088902 -0.680693 0.046834 + C -0.949381 0.851790 0.132471 + C 0.506536 1.151901 -0.233475 + H 2.250907 -0.173582 -0.185613 + H 1.348285 -0.066771 1.333273 + H 0.513007 -2.141451 0.378820 + H 0.485140 -1.439720 -1.239568 + H -1.507362 -1.076489 0.971842 + H -1.752602 -0.974004 -0.765631 + H -1.150114 1.191161 1.149001 + H -1.645670 1.361592 -0.531936 + H 0.868338 2.069444 0.228533 + H 0.612033 1.246555 -1.315330 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.371160 -0.165363 0.465548 + 1 C 6.0000 0 12.011 0.624199 -2.315778 -0.342528 + 2 C 6.0000 0 12.011 -2.057726 -1.286324 0.088503 + 3 C 6.0000 0 12.011 -1.794069 1.609650 0.250334 + 4 C 6.0000 0 12.011 0.957214 2.176778 -0.441204 + 5 H 1.0000 0 1.008 4.253597 -0.328022 -0.350757 + 6 H 1.0000 0 1.008 2.547890 -0.126179 2.519521 + 7 H 1.0000 0 1.008 0.969442 -4.046755 0.715866 + 8 H 1.0000 0 1.008 0.916781 -2.720677 -2.342445 + 9 H 1.0000 0 1.008 -2.848501 -2.034269 1.836515 + 10 H 1.0000 0 1.008 -3.311937 -1.840600 -1.446833 + 11 H 1.0000 0 1.008 -2.173400 2.250968 2.171298 + 12 H 1.0000 0 1.008 -3.109866 2.573036 -1.005213 + 13 H 1.0000 0 1.008 1.640920 3.910683 0.431865 + 14 H 1.0000 0 1.008 1.156575 2.355647 -2.485614 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:47:45.073 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.94212220679923 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0489182 -0.160489E+02 0.136E-02 13.19 0.0 T + 2 -16.0489182 -0.127713E-07 0.804E-03 13.19 3.2 T + 3 -16.0489182 -0.358794E-08 0.399E-04 13.19 64.7 T + 4 -16.0489182 -0.197563E-09 0.195E-04 13.19 132.3 T + + *** convergence criteria satisfied after 4 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6318700 -17.1941 + ... ... ... ... + 9 2.0000 -0.4821051 -13.1187 + 10 2.0000 -0.4407362 -11.9930 + 11 2.0000 -0.4380500 -11.9199 + 12 2.0000 -0.4362018 -11.8697 + 13 2.0000 -0.4360772 -11.8663 + 14 2.0000 -0.4211887 -11.4611 + 15 2.0000 -0.4145210 -11.2797 (HOMO) + 16 0.0701668 1.9093 (LUMO) + 17 0.0709287 1.9301 + 18 0.0914226 2.4877 + 19 0.1321255 3.5953 + 20 0.1343143 3.6549 + ... ... ... + 30 0.3523020 9.5866 + ------------------------------------------------------------- + HL-Gap 0.4846878 Eh 13.1890 eV + Fermi-level -0.1721771 Eh -4.6852 eV + + SCC (total) 0 d, 0 h, 0 min, 0.007 sec + SCC setup ... 0 min, 0.000 sec ( 1.641%) + Dispersion ... 0 min, 0.000 sec ( 1.040%) + classical contributions ... 0 min, 0.000 sec ( 0.343%) + integral evaluation ... 0 min, 0.001 sec ( 14.755%) + iterations ... 0 min, 0.003 sec ( 37.245%) + molecular gradient ... 0 min, 0.003 sec ( 36.193%) + printout ... 0 min, 0.000 sec ( 5.602%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814311679880 Eh :: + :: gradient norm 0.001141863631 Eh/a0 :: + :: HOMO-LUMO gap 13.189027371246 eV :: + ::.................................................:: + :: SCC energy -16.048918175778 Eh :: + :: -> isotropic ES 0.002346087271 Eh :: + :: -> anisotropic ES 0.004248869227 Eh :: + :: -> anisotropic XC 0.009715009573 Eh :: + :: -> dispersion -0.008133598494 Eh :: + :: repulsion energy 0.234596097647 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814311679880 Eh | + | GRADIENT NORM 0.001141863631 Eh/α | + | HOMO-LUMO GAP 13.189027371246 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:47:45.088 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.015 sec + * cpu-time: 0 d, 0 h, 0 min, 0.014 sec + * ratio c/w: 0.944 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.007 sec + * cpu-time: 0 d, 0 h, 0 min, 0.007 sec + * ratio c/w: 0.894 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814311679880 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 15 +Number of internal coordinates .... 90 +Current Energy .... -15.814311680 Eh +Current gradient norm .... 0.001141864 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999880028 +Lowest eigenvalues of augmented Hessian: + -0.000002546 0.004105100 0.011851528 0.045612633 0.045945469 +Length of the computed step .... 0.015491507 +The final length of the internal step .... 0.015491507 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0016329482 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0020702309 RMS(Int)= 0.0016326180 + Iter 1: RMS(Cart)= 0.0000019856 RMS(Int)= 0.0000012638 + Iter 2: RMS(Cart)= 0.0000000036 RMS(Int)= 0.0000000032 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0000067971 0.0000050000 NO + RMS gradient 0.0000635176 0.0001000000 YES + MAX gradient 0.0002263290 0.0003000000 YES + RMS step 0.0016329482 0.0020000000 YES + MAX step 0.0038269066 0.0040000000 YES + ........................................................ + Max(Bonds) 0.0003 Max(Angles) 0.04 + Max(Dihed) 0.22 Max(Improp) 0.00 + --------------------------------------------------------------------- + + Everything but the energy has converged. However, the energy + appears to be close enough to convergence to make sure that the + final evaluation at the new geometry represents the equilibrium energy. + Convergence will therefore be signaled now + + + ***********************HURRAY******************** + *** THE OPTIMIZATION HAS CONVERGED *** + ************************************************* + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + + --- Optimized Parameters --- + (Angstroem and degrees) + + Definition OldVal dE/dq Step FinalVal + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.5272 0.000144 -0.0002 1.5270 + 2. B(C 2,C 1) 1.5372 0.000213 -0.0003 1.5369 + 3. B(C 3,C 2) 1.5412 0.000226 -0.0003 1.5409 + 4. B(C 4,C 3) 1.5309 0.000183 -0.0003 1.5306 + 5. B(C 4,C 0) 1.5252 0.000137 -0.0002 1.5250 + 6. B(H 5,C 0) 1.0892 -0.000064 0.0001 1.0893 + 7. B(H 6,C 0) 1.0911 -0.000090 0.0002 1.0913 + 8. B(H 7,C 1) 1.0891 -0.000071 0.0001 1.0892 + 9. B(H 8,C 1) 1.0908 -0.000124 0.0002 1.0910 + 10. B(H 9,C 2) 1.0897 -0.000118 0.0002 1.0899 + 11. B(H 10,C 2) 1.0893 -0.000103 0.0002 1.0895 + 12. B(H 11,C 3) 1.0903 -0.000135 0.0002 1.0905 + 13. B(H 12,C 3) 1.0891 -0.000082 0.0001 1.0892 + 14. B(H 13,C 4) 1.0891 -0.000067 0.0001 1.0892 + 15. B(H 14,C 4) 1.0911 -0.000102 0.0002 1.0913 + 16. A(C 4,C 0,H 5) 112.84 -0.000002 0.03 112.87 + 17. A(C 1,C 0,C 4) 102.74 -0.000006 -0.03 102.70 + 18. A(C 1,C 0,H 5) 112.56 -0.000029 0.03 112.59 + 19. A(H 5,C 0,H 6) 108.55 0.000013 0.01 108.56 + 20. A(C 1,C 0,H 6) 110.18 0.000040 -0.03 110.15 + 21. A(C 4,C 0,H 6) 109.88 -0.000017 -0.01 109.86 + 22. A(C 2,C 1,H 8) 110.16 0.000084 -0.04 110.12 + 23. A(C 2,C 1,H 7) 112.13 -0.000058 0.03 112.15 + 24. A(H 7,C 1,H 8) 108.05 0.000025 0.00 108.06 + 25. A(C 0,C 1,H 7) 112.41 -0.000005 0.03 112.44 + 26. A(C 0,C 1,C 2) 104.67 0.000002 -0.02 104.65 + 27. A(C 0,C 1,H 8) 109.40 -0.000048 -0.01 109.38 + 28. A(H 9,C 2,H 10) 107.54 0.000017 0.01 107.54 + 29. A(C 1,C 2,C 3) 106.08 -0.000026 -0.01 106.08 + 30. A(C 1,C 2,H 10) 110.88 0.000015 0.01 110.89 + 31. A(C 3,C 2,H 9) 110.41 0.000046 -0.02 110.40 + 32. A(C 1,C 2,H 9) 110.60 -0.000021 -0.00 110.59 + 33. A(C 3,C 2,H 10) 111.37 -0.000031 0.01 111.38 + 34. A(H 11,C 3,H 12) 107.78 0.000021 0.00 107.78 + 35. A(C 4,C 3,H 12) 111.74 -0.000005 0.03 111.77 + 36. A(C 2,C 3,H 12) 111.94 -0.000048 0.03 111.97 + 37. A(C 4,C 3,H 11) 109.69 -0.000027 -0.02 109.67 + 38. A(C 2,C 3,H 11) 110.16 0.000081 -0.04 110.12 + 39. A(C 2,C 3,C 4) 105.53 -0.000020 -0.01 105.52 + 40. A(H 13,C 4,H 14) 108.38 0.000022 0.01 108.39 + 41. A(C 3,C 4,H 14) 110.24 0.000071 -0.03 110.21 + 42. A(C 0,C 4,H 14) 109.57 -0.000049 -0.01 109.57 + 43. A(C 3,C 4,H 13) 112.31 -0.000053 0.03 112.34 + 44. A(C 0,C 4,H 13) 112.84 0.000003 0.03 112.87 + 45. A(C 0,C 4,C 3) 103.42 0.000007 -0.03 103.39 + 46. D(H 7,C 1,C 0,H 5) 79.05 0.000048 -0.17 78.88 + 47. D(H 7,C 1,C 0,H 6) -42.27 0.000023 -0.18 -42.45 + 48. D(C 2,C 1,C 0,H 5) -159.01 -0.000024 -0.13 -159.14 + 49. D(H 7,C 1,C 0,C 4) -159.30 0.000027 -0.14 -159.43 + 50. D(H 8,C 1,C 0,H 6) -162.30 0.000026 -0.20 -162.50 + 51. D(C 2,C 1,C 0,C 4) -37.35 -0.000045 -0.09 -37.45 + 52. D(C 2,C 1,C 0,H 6) 79.67 -0.000050 -0.14 79.53 + 53. D(H 8,C 1,C 0,H 5) -40.99 0.000052 -0.19 -41.17 + 54. D(H 8,C 1,C 0,C 4) 80.67 0.000031 -0.15 80.51 + 55. D(H 9,C 2,C 1,H 7) 20.90 -0.000047 0.12 21.01 + 56. D(C 3,C 2,C 1,H 8) -98.99 0.000032 0.09 -98.90 + 57. D(C 3,C 2,C 1,C 0) 18.52 0.000018 0.05 18.56 + 58. D(H 10,C 2,C 1,H 8) 22.07 -0.000013 0.11 22.17 + 59. D(H 9,C 2,C 1,H 8) 141.27 0.000004 0.11 141.38 + 60. D(H 10,C 2,C 1,H 7) -98.31 -0.000063 0.11 -98.20 + 61. D(H 10,C 2,C 1,C 0) 139.57 -0.000026 0.06 139.63 + 62. D(C 3,C 2,C 1,H 7) 140.64 -0.000019 0.09 140.73 + 63. D(H 9,C 2,C 1,C 0) -101.23 -0.000010 0.07 -101.16 + 64. D(H 12,C 3,C 2,H 9) -111.04 -0.000056 0.05 -110.99 + 65. D(H 12,C 3,C 2,C 1) 129.10 -0.000040 0.07 129.17 + 66. D(H 11,C 3,C 2,H 10) 128.27 0.000025 0.05 128.32 + 67. D(H 11,C 3,C 2,H 9) 8.87 -0.000006 0.05 8.92 + 68. D(C 4,C 3,C 2,H 9) 127.20 -0.000009 0.00 127.21 + 69. D(C 4,C 3,C 2,C 1) 7.34 0.000007 0.02 7.36 + 70. D(H 11,C 3,C 2,C 1) -110.99 0.000010 0.06 -110.93 + 71. D(H 12,C 3,C 2,H 10) 8.36 -0.000025 0.06 8.42 + 72. D(C 4,C 3,C 2,H 10) -113.40 0.000022 0.01 -113.39 + 73. D(H 13,C 4,C 0,C 1) 163.52 -0.000002 0.14 163.66 + 74. D(C 3,C 4,C 0,H 6) -75.32 0.000020 0.16 -75.16 + 75. D(C 3,C 4,C 0,H 5) 163.39 0.000017 0.14 163.53 + 76. D(C 3,C 4,C 0,C 1) 41.92 0.000056 0.11 42.03 + 77. D(H 14,C 4,C 3,H 12) -35.24 0.000018 -0.17 -35.40 + 78. D(H 14,C 4,C 3,H 11) -154.70 0.000013 -0.18 -154.88 + 79. D(H 13,C 4,C 3,H 12) 85.74 0.000060 -0.16 85.58 + 80. D(H 13,C 4,C 3,H 11) -33.72 0.000055 -0.17 -33.90 + 81. D(H 13,C 4,C 3,C 2) -152.37 -0.000015 -0.12 -152.48 + 82. D(C 0,C 4,C 3,H 12) -152.30 0.000039 -0.13 -152.43 + 83. D(C 0,C 4,C 3,H 11) 88.23 0.000034 -0.14 88.10 + 84. D(C 0,C 4,C 3,C 2) -30.41 -0.000035 -0.08 -30.49 + 85. D(H 14,C 4,C 0,H 6) 167.14 -0.000042 0.22 167.36 + 86. D(H 14,C 4,C 0,H 5) 45.85 -0.000046 0.20 46.05 + 87. D(H 14,C 4,C 3,C 2) 86.66 -0.000057 -0.12 86.54 + 88. D(H 14,C 4,C 0,C 1) -75.62 -0.000007 0.17 -75.45 + 89. D(H 13,C 4,C 0,H 6) 46.28 -0.000038 0.20 46.47 + 90. D(H 13,C 4,C 0,H 5) -75.01 -0.000041 0.17 -74.84 + ---------------------------------------------------------------------------- + ******************************************************* + *** FINAL ENERGY EVALUATION AT THE STATIONARY POINT *** + *** (AFTER 5 CYCLES) *** + ******************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.254359 -0.087377 0.247155 + C 0.330425 -1.225019 -0.181593 + C -1.088479 -0.680500 0.046806 + C -0.948922 0.851627 0.132567 + C 0.506553 1.151472 -0.234149 + H 2.251512 -0.173549 -0.182679 + H 1.345388 -0.066448 1.334450 + H 0.513299 -2.142065 0.376923 + H 0.484946 -1.437484 -1.240528 + H -1.506574 -1.076197 0.972249 + H -1.752594 -0.973990 -0.765485 + H -1.148462 1.190193 1.149840 + H -1.646034 1.362100 -0.530685 + H 0.868686 2.069982 0.225902 + H 0.611188 1.244027 -1.316453 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.370395 -0.165119 0.467056 + 1 C 6.0000 0 12.011 0.624412 -2.314951 -0.343162 + 2 C 6.0000 0 12.011 -2.056928 -1.285958 0.088450 + 3 C 6.0000 0 12.011 -1.793202 1.609341 0.250515 + 4 C 6.0000 0 12.011 0.957247 2.175966 -0.442477 + 5 H 1.0000 0 1.008 4.254741 -0.327960 -0.345213 + 6 H 1.0000 0 1.008 2.542415 -0.125568 2.521746 + 7 H 1.0000 0 1.008 0.969995 -4.047917 0.712281 + 8 H 1.0000 0 1.008 0.916414 -2.716451 -2.344258 + 9 H 1.0000 0 1.008 -2.847013 -2.033718 1.837284 + 10 H 1.0000 0 1.008 -3.311923 -1.840575 -1.446556 + 11 H 1.0000 0 1.008 -2.170279 2.249138 2.172882 + 12 H 1.0000 0 1.008 -3.110554 2.573997 -1.002848 + 13 H 1.0000 0 1.008 1.641579 3.911699 0.426893 + 14 H 1.0000 0 1.008 1.154978 2.350870 -2.487736 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:47:45.143 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.44644092075084 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0488369 -0.160488E+02 0.500E-03 13.20 0.0 T + 2 -16.0488369 -0.731859E-08 0.298E-03 13.20 8.7 T + 3 -16.0488369 -0.448981E-09 0.228E-04 13.20 113.0 T + 4 -16.0488369 -0.946798E-11 0.689E-05 13.20 374.8 T + + *** convergence criteria satisfied after 4 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6319477 -17.1962 + ... ... ... ... + 9 2.0000 -0.4821074 -13.1188 + 10 2.0000 -0.4407302 -11.9929 + 11 2.0000 -0.4380154 -11.9190 + 12 2.0000 -0.4362468 -11.8709 + 13 2.0000 -0.4361111 -11.8672 + 14 2.0000 -0.4212283 -11.4622 + 15 2.0000 -0.4144836 -11.2787 (HOMO) + 16 0.0704309 1.9165 (LUMO) + 17 0.0711941 1.9373 + 18 0.0912106 2.4820 + 19 0.1322569 3.5989 + 20 0.1341636 3.6508 + ... ... ... + 30 0.3520732 9.5804 + ------------------------------------------------------------- + HL-Gap 0.4849145 Eh 13.1952 eV + Fermi-level -0.1720264 Eh -4.6811 eV + + SCC (total) 0 d, 0 h, 0 min, 0.009 sec + SCC setup ... 0 min, 0.000 sec ( 1.176%) + Dispersion ... 0 min, 0.000 sec ( 0.759%) + classical contributions ... 0 min, 0.000 sec ( 0.301%) + integral evaluation ... 0 min, 0.001 sec ( 13.271%) + iterations ... 0 min, 0.004 sec ( 42.488%) + molecular gradient ... 0 min, 0.003 sec ( 40.125%) + printout ... 0 min, 0.000 sec ( 1.776%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814313366053 Eh :: + :: gradient norm 0.000497848720 Eh/a0 :: + :: HOMO-LUMO gap 13.195196441405 eV :: + ::.................................................:: + :: SCC energy -16.048836878888 Eh :: + :: -> isotropic ES 0.002342725001 Eh :: + :: -> anisotropic ES 0.004244905299 Eh :: + :: -> anisotropic XC 0.009717418625 Eh :: + :: -> dispersion -0.008134806430 Eh :: + :: repulsion energy 0.234513126374 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814313366053 Eh | + | GRADIENT NORM 0.000497848720 Eh/α | + | HOMO-LUMO GAP 13.195196441405 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:47:45.164 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.021 sec + * cpu-time: 0 d, 0 h, 0 min, 0.020 sec + * ratio c/w: 0.963 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.009 sec + * cpu-time: 0 d, 0 h, 0 min, 0.008 sec + * ratio c/w: 0.919 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814313366050 +------------------------- -------------------- + + *** OPTIMIZATION RUN DONE *** + +Timings for individual modules: + +Sum of individual times ... 0.482 sec (= 0.008 min) +Geometry relaxation ... 0.168 sec (= 0.003 min) 34.8 % +XTB module ... 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4.4033946328E-04 -5.8365610110E-02 6.4928914427E-03 2.1388095472E-03 1.7026726770E-02 + 26 9.1428633366E-02 -2.8199384954E-01 8.8188876567E-02 1.3311093695E-01 1.6795908699E-01 + 27 -1.2500148795E-01 1.3204861199E-01 1.0475430168E-01 3.6842711241E-02 1.2154767710E-01 + 28 -1.2561756230E-01 1.2410758177E-01 1.0513688101E-01 3.1889572953E-02 1.2410167822E-01 + 29 3.3567764047E-01 -2.8712160179E-01 -2.7482914367E-01 -6.5140652417E-02 -3.2863199872E-01 + 30 -2.9280798575E-01 -1.6390580970E-01 1.9860439030E-01 -1.3539590739E-01 2.7305546487E-01 + 31 -1.2438066317E-01 -7.2335087166E-02 8.2872691226E-02 -5.9817161141E-02 1.1416162487E-01 + 32 -3.9327157699E-01 -1.8983883056E-01 2.6983632086E-01 -1.6824557946E-01 3.6895051168E-01 + 33 1.7889072685E-02 6.6607235522E-02 -1.2697494391E-02 -7.4457242288E-03 2.7638270880E-02 + 34 -4.3976201932E-02 -1.1066848005E-01 2.4377985206E-02 2.8114508382E-02 -6.1087743630E-02 + 35 -1.8384028283E-01 -3.4015961400E-01 8.4756307202E-02 1.3259675017E-01 -2.3376928352E-01 + 36 3.2943173907E-01 -9.1392150032E-02 -6.4686505935E-02 -3.4700948288E-01 3.0282600136E-01 + 37 -2.3654853356E-01 6.7284038842E-02 4.4033851881E-02 2.4894744027E-01 -2.1642792926E-01 + 38 3.3287773617E-01 -7.3572428857E-02 -6.6457545147E-02 -3.4930712258E-01 3.1158332871E-01 + 39 8.5670422817E-02 -1.3913908702E-01 2.1441552418E-01 -7.5811596295E-03 -9.2335582065E-02 + 40 2.2050477319E-01 -3.5284557999E-01 5.4935042958E-01 -2.4386932612E-02 -2.3529565495E-01 + 41 1.1680191037E-01 -1.7946671375E-01 2.9741703411E-01 -8.7676375973E-03 -1.2875900264E-01 + 42 -1.1394110478E-04 1.9957011198E-02 1.0691801674E-02 7.6491833756E-03 -6.2179211559E-03 + 43 -6.0623685095E-03 2.6611457136E-02 -5.5722505947E-03 7.4304667838E-03 7.7304076151E-04 + 44 -4.2031229883E-02 -1.6281251086E-01 -2.2009153219E-01 -8.1963566647E-02 1.1363680073E-01 + +# +# The atoms: label mass x y z (in bohrs) +# +$atoms +15 + C 12.01100 2.370395352817 -0.165119353961 0.467055728119 + C 12.01100 0.624412131949 -2.314950932304 -0.343161574722 + C 12.01100 -2.056927759615 -1.285957826935 0.088450162102 + C 12.01100 -1.793202202238 1.609340899461 0.250515117168 + C 12.01100 0.957246671361 2.175966165264 -0.442477210832 + H 1.00800 4.254740993136 -0.327959685002 -0.345213491899 + H 1.00800 2.542414779212 -0.125568188166 2.521745543173 + H 1.00800 0.969994772545 -4.047916766116 0.712280980995 + H 1.00800 0.916414418106 -2.716451472732 -2.344257789036 + H 1.00800 -2.847012969354 -2.033718431842 1.837284122808 + H 1.00800 -3.311922552795 -1.840574580092 -1.446556301222 + H 1.00800 -2.170278796780 2.249138108127 2.172881776807 + H 1.00800 -3.110553923969 2.573996549726 -1.002848448212 + H 1.00800 1.641578571847 3.911698868900 0.426893181903 + H 1.00800 1.154977994402 2.350870091600 -2.487736396235 + +$actual_temperature + 0.000000 + +$frequency_scale_factor + 1.000000 + +$dipole_derivatives +45 + 1.0000000000E-01 0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 2.0000000000E-01 + 1.0000000000E-01 -0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 1.0000000000E-01 -1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 2.0000000000E-01 + 1.0000000000E-01 0.0000000000E+00 1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 -0.0000000000E+00 2.0000000000E-01 + 1.0000000000E-01 -0.0000000000E+00 1.0000000000E-01 + 0.0000000000E+00 1.0000000000E-01 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 2.0000000000E-01 + 1.0000000000E-01 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 1.0000000000E-01 1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 2.0000000000E-01 + -2.0000000000E-01 0.0000000000E+00 1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 1.0000000000E-01 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + -0.0000000000E+00 0.0000000000E+00 -2.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 -2.0000000000E-01 1.0000000000E-01 + 0.0000000000E+00 1.0000000000E-01 -1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 -0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 -0.0000000000E+00 1.0000000000E-01 + -0.0000000000E+00 -0.0000000000E+00 1.0000000000E-01 + 1.0000000000E-01 0.0000000000E+00 -1.0000000000E-01 + -1.0000000000E-01 -0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 -1.0000000000E-01 + -1.0000000000E-01 -0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 1.0000000000E-01 + 0.0000000000E+00 -0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 -0.0000000000E+00 -1.0000000000E-01 + -1.0000000000E-01 1.0000000000E-01 -1.0000000000E-01 + 1.0000000000E-01 -0.0000000000E+00 1.0000000000E-01 + -1.0000000000E-01 0.0000000000E+00 -1.0000000000E-01 + 0.0000000000E+00 -0.0000000000E+00 -1.0000000000E-01 + -1.0000000000E-01 -2.0000000000E-01 -1.0000000000E-01 + 0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 1.0000000000E-01 + 0.0000000000E+00 0.0000000000E+00 -2.0000000000E-01 + +# +# The IR spectrum +# wavenumber eps Int TX TY TZ +# +$ir_spectrum +45 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + -13.35 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 252.24 0.00015822 0.79956500 0.006793 -0.012199 0.000883 + 557.18 0.00332525 16.80444475 -0.006401 -0.003125 -0.042564 + 613.24 0.00020155 1.01857442 -0.003489 -0.005541 0.007726 + 803.10 0.00257585 13.01731160 -0.006638 0.004376 -0.030622 + 840.54 0.00038498 1.94553063 0.003428 0.006004 0.009753 + 876.38 0.00073464 3.71257432 -0.002562 -0.004049 -0.015448 + 954.58 0.00011539 0.58313879 -0.003609 -0.001996 0.004551 + 965.59 0.00012990 0.65645639 0.004167 0.004871 -0.000943 + 980.31 0.00072888 3.68344180 0.009998 0.009993 -0.005676 + 1000.25 0.00103158 5.21320763 0.004459 0.015939 0.006922 + 1030.24 0.00010245 0.51772262 0.004598 0.002103 0.002338 + 1101.22 0.00013448 0.67959773 0.000215 -0.005072 -0.003513 + 1125.95 0.00113831 5.75255973 0.002735 -0.006389 -0.016346 + 1163.25 0.00015958 0.80646270 -0.001528 0.006282 -0.001007 + 1191.48 0.00006704 0.33878187 -0.001822 -0.003210 -0.001983 + 1205.00 0.00128027 6.46996497 0.005350 -0.004225 -0.016884 + 1219.58 0.00017162 0.86731602 0.001333 0.003743 -0.005303 + 1239.15 0.00073705 3.72474819 -0.004600 -0.006588 0.011002 + 1296.43 0.00095855 4.84412946 -0.007658 -0.012866 -0.002561 + 1307.22 0.00056148 2.83748162 -0.002810 0.001789 -0.011088 + 1323.33 0.00007904 0.39941107 -0.001509 0.001715 -0.003663 + 1324.02 0.00010272 0.51912552 -0.002056 0.003289 0.003027 + 1324.99 0.00032752 1.65516605 0.005816 -0.004043 -0.005192 + 1483.49 0.00022702 1.14729045 0.006418 0.001978 0.001630 + 1487.62 0.00099922 5.04966622 -0.003783 -0.004743 0.013146 + 1497.58 0.00079885 4.03704674 -0.000907 0.010301 0.007716 + 1498.38 0.00094050 4.75288767 0.000107 -0.000655 -0.013980 + 1516.09 0.00023885 1.20705417 -0.004273 -0.005461 -0.001041 + 2971.92 0.00169187 8.55003705 -0.004728 0.011549 0.004682 + 2972.55 0.00030160 1.52418460 -0.005163 -0.001834 -0.001281 + 2984.88 0.00082539 4.17115936 0.007991 0.003960 0.002599 + 2986.62 0.00307726 15.55122166 0.005703 -0.001857 -0.016899 + 2999.16 0.00475957 24.05289995 0.005780 0.000320 0.021488 + 3000.31 0.00240908 12.17451857 -0.004745 -0.015100 -0.000224 + 3005.88 0.03470973 175.40875634 -0.008980 0.004079 0.059213 + 3008.88 0.01427541 72.14208921 -0.029057 -0.025187 0.001377 + 3009.44 0.02549954 128.86420457 0.029874 -0.023499 0.034634 + 3012.88 0.00217129 10.97281054 -0.014390 -0.000813 -0.004143 + + +$end + diff --git a/cmmde_gui/test/siklopentana/freq/cmmd.in b/cmmde_gui/test/siklopentana/freq/cmmd.in new file mode 100644 index 0000000..247d130 --- /dev/null +++ b/cmmde_gui/test/siklopentana/freq/cmmd.in @@ -0,0 +1,13 @@ +#CMMDE generated Orca input file +!XTB2 Numfreq +%pal + nprocs 1 +end + +*xyzfile 0 1 ../cmmd.xyz + +%freq + scalfreq 1 + Temp 298.15 + Pressure 1.0 +end diff --git a/cmmde_gui/test/siklopentana/freq/cmmd.out b/cmmde_gui/test/siklopentana/freq/cmmd.out new file mode 100644 index 0000000..a109d75 --- /dev/null +++ b/cmmde_gui/test/siklopentana/freq/cmmd.out @@ -0,0 +1,1193 @@ + + ***************** + * O R C A * + ***************** + + #, + ### + #### + ##### + ###### + ########, + ,,################,,,,, + ,,#################################,, + ,,##########################################,, + ,#########################################, ''#####, + ,#############################################,, '####, + ,##################################################,,,,####, + ,###########'''' ''''############################### + ,#####'' ,,,,##########,,,, '''####''' '#### + ,##' ,,,,###########################,,, '## + ' ,,###'''' '''############,,, + ,,##'' '''############,,,, ,,,,,,###'' + ,#'' '''#######################''' + ' ''''####'''' + ,#######, #######, ,#######, ## + ,#' '#, ## ## ,#' '#, #''# ###### ,####, + ## ## ## ,#' ## #' '# # #' '# + ## ## ####### ## ,######, #####, # # + '#, ,#' ## ## '#, ,#' ,# #, ## #, ,# + '#######' ## ## '#######' #' '# #####' # '####' + + + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship and core code : Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 5.0.2 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Marcus Kettner : VPT2 + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : Initial AUTO-CI + Lucas Lang : DCDCAS + Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, + C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT + MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, + LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, + nearIR, NL-DFT gradient (VV10), updates on ESD, + ML-optimized integration grids + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + Liviu Ungur et al : ANISO software + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 5.1.0 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + Shared memory : Shared parallel matrices + BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED + Core in use : SkylakeX + Copyright (c) 2011-2014, The OpenBLAS Project + + + + +*************************************** +The coordinates will be read from file: ../cmmd.xyz +*************************************** + + +Your calculation utilizes the semiempirical GFN2-xTB method +Please cite in your paper: +C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. + + +================================================================================ + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + +WARNING: Gradients needed for Numerical Frequencies + ===> : Setting RunTyp to EnGrad + +WARNING: Found dipole moment calculation with XTB calculation + ===> : Switching off dipole moment calculation + + +WARNING: TRAH-SCF for XTB is not implemented! + ===> : Turning TRAH off! + +================================================================================ + INPUT FILE +================================================================================ +NAME = cmmd.in +| 1> #CMMDE generated Orca input file +| 2> !XTB2 Numfreq +| 3> %pal +| 4> nprocs 1 +| 5> end +| 6> +| 7> *xyzfile 0 1 ../cmmd.xyz +| 8> +| 9> %freq +| 10> scalfreq 1 +| 11> Temp 298.15 +| 12> Pressure 1.0 +| 13> end +| 14> +| 15> ****END OF INPUT**** +================================================================================ + + ******************************* + * Energy+Gradient Calculation * + ******************************* + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 18:50:12.704 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 15 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.50985592449299 + + ID Z sym. atoms + 1 6 C 1-5 + 2 1 H 6-15 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 20 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.0054351 -0.160054E+02 0.262E+00 13.70 0.0 T + 2 -16.0484055 -0.429703E-01 0.153E+00 13.20 1.0 T + 3 -16.0487278 -0.322317E-03 0.804E-01 13.20 1.0 T + 4 -16.0488365 -0.108768E-03 0.796E-02 13.19 1.0 T + 5 -16.0488367 -0.199985E-06 0.579E-03 13.20 4.5 T + 6 -16.0488369 -0.123847E-06 0.221E-03 13.20 11.7 T + 7 -16.0488369 -0.538951E-08 0.667E-04 13.20 38.7 T + 8 -16.0488369 -0.692037E-09 0.113E-04 13.20 229.0 T + + *** convergence criteria satisfied after 8 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6319470 -17.1962 + ... ... ... ... + 9 2.0000 -0.4821072 -13.1188 + 10 2.0000 -0.4407301 -11.9929 + 11 2.0000 -0.4380151 -11.9190 + 12 2.0000 -0.4362468 -11.8709 + 13 2.0000 -0.4361108 -11.8672 + 14 2.0000 -0.4212279 -11.4622 + 15 2.0000 -0.4144832 -11.2787 (HOMO) + 16 0.0704311 1.9165 (LUMO) + 17 0.0711944 1.9373 + 18 0.0912106 2.4820 + 19 0.1322572 3.5989 + 20 0.1341634 3.6508 + ... ... ... + 30 0.3520733 9.5804 + ------------------------------------------------------------- + HL-Gap 0.4849143 Eh 13.1952 eV + Fermi-level -0.1720261 Eh -4.6811 eV + + SCC (total) 0 d, 0 h, 0 min, 0.015 sec + SCC setup ... 0 min, 0.000 sec ( 1.045%) + Dispersion ... 0 min, 0.000 sec ( 1.476%) + classical contributions ... 0 min, 0.000 sec ( 0.266%) + integral evaluation ... 0 min, 0.002 sec ( 12.707%) + iterations ... 0 min, 0.008 sec ( 52.183%) + molecular gradient ... 0 min, 0.005 sec ( 31.014%) + printout ... 0 min, 0.000 sec ( 1.214%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.814313366037 Eh :: + :: gradient norm 0.000497859982 Eh/a0 :: + :: HOMO-LUMO gap 13.195188817416 eV :: + ::.................................................:: + :: SCC energy -16.048836878872 Eh :: + :: -> isotropic ES 0.002342731977 Eh :: + :: -> anisotropic ES 0.004244875878 Eh :: + :: -> anisotropic XC 0.009717391897 Eh :: + :: -> dispersion -0.008134804860 Eh :: + :: repulsion energy 0.234513126374 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.814313366037 Eh | + | GRADIENT NORM 0.000497859982 Eh/α | + | HOMO-LUMO GAP 13.195188817416 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 18:50:12.735 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.031 sec + * cpu-time: 0 d, 0 h, 0 min, 0.030 sec + * ratio c/w: 0.980 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.016 sec + * cpu-time: 0 d, 0 h, 0 min, 0.015 sec + * ratio c/w: 0.962 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.814313366040 +------------------------- -------------------- + + +---------------------------------------------------------------------------- + ORCA NUMERICAL FREQUENCIES +---------------------------------------------------------------------------- + +Number of atoms ... 15 +Central differences ... used +Number of displacements ... 90 +Numerical increment ... 5.000e-03 bohr +IR-spectrum generation ... on +Raman-spectrum generation ... off +Surface Crossing Hessian ... off + +The output will be reduced. Please look at the following files: +SCF program output ... >cmmd.lastscf +Integral program output ... >cmmd.lastint +Gradient program output ... >cmmd.lastgrad +Dipole moment program output ... >cmmd.lastmom +AutoCI program output ... >cmmd.lastautoci + + << Calculating on displaced geometry 1 (of 90) >> + << Calculating on displaced geometry 2 (of 90) >> + << Calculating on displaced geometry 3 (of 90) >> + << Calculating on displaced geometry 4 (of 90) >> + << Calculating on displaced geometry 5 (of 90) >> + << Calculating on displaced geometry 6 (of 90) >> + << Calculating on displaced geometry 7 (of 90) >> + << Calculating on displaced geometry 8 (of 90) >> + << Calculating on displaced geometry 9 (of 90) >> + << Calculating on displaced geometry 10 (of 90) >> + << Calculating on displaced geometry 11 (of 90) >> + << Calculating on displaced geometry 12 (of 90) >> + << Calculating on displaced geometry 13 (of 90) >> + << Calculating on displaced geometry 14 (of 90) >> + << Calculating on displaced geometry 15 (of 90) >> + << Calculating on displaced geometry 16 (of 90) >> + << Calculating on displaced geometry 17 (of 90) >> + << Calculating on displaced geometry 18 (of 90) >> + << Calculating on displaced geometry 19 (of 90) >> + << Calculating on displaced geometry 20 (of 90) >> + << Calculating on displaced geometry 21 (of 90) >> + << Calculating on displaced geometry 22 (of 90) >> + << Calculating on displaced geometry 23 (of 90) >> + << Calculating on displaced geometry 24 (of 90) >> + << Calculating on displaced geometry 25 (of 90) >> + << Calculating on displaced geometry 26 (of 90) >> + << Calculating on displaced geometry 27 (of 90) >> + << Calculating on displaced geometry 28 (of 90) >> + << Calculating on displaced geometry 29 (of 90) >> + << Calculating on displaced geometry 30 (of 90) >> + << Calculating on displaced geometry 31 (of 90) >> + << Calculating on displaced geometry 32 (of 90) >> + << Calculating on displaced geometry 33 (of 90) >> + << Calculating on displaced geometry 34 (of 90) >> + << Calculating on displaced geometry 35 (of 90) >> + << Calculating on displaced geometry 36 (of 90) >> + << Calculating on displaced geometry 37 (of 90) >> + << Calculating on displaced geometry 38 (of 90) >> + << Calculating on displaced geometry 39 (of 90) >> + << Calculating on displaced geometry 40 (of 90) >> + << Calculating on displaced geometry 41 (of 90) >> + << Calculating on displaced geometry 42 (of 90) >> + << Calculating on displaced geometry 43 (of 90) >> + << Calculating on displaced geometry 44 (of 90) >> + << Calculating on displaced geometry 45 (of 90) >> + << Calculating on displaced geometry 46 (of 90) >> + << Calculating on displaced geometry 47 (of 90) >> + << Calculating on displaced geometry 48 (of 90) >> + << Calculating on displaced geometry 49 (of 90) >> + << Calculating on displaced geometry 50 (of 90) >> + << Calculating on displaced geometry 51 (of 90) >> + << Calculating on displaced geometry 52 (of 90) >> + << Calculating on displaced geometry 53 (of 90) >> + << Calculating on displaced geometry 54 (of 90) >> + << Calculating on displaced geometry 55 (of 90) >> + << Calculating on displaced geometry 56 (of 90) >> + << Calculating on displaced geometry 57 (of 90) >> + << Calculating on displaced geometry 58 (of 90) >> + << Calculating on displaced geometry 59 (of 90) >> + << Calculating on displaced geometry 60 (of 90) >> + << Calculating on displaced geometry 61 (of 90) >> + << Calculating on displaced geometry 62 (of 90) >> + << Calculating on displaced geometry 63 (of 90) >> + << Calculating on displaced geometry 64 (of 90) >> + << Calculating on displaced geometry 65 (of 90) >> + << Calculating on displaced geometry 66 (of 90) >> + << Calculating on displaced geometry 67 (of 90) >> + << Calculating on displaced geometry 68 (of 90) >> + << Calculating on displaced geometry 69 (of 90) >> + << Calculating on displaced geometry 70 (of 90) >> + << Calculating on displaced geometry 71 (of 90) >> + << Calculating on displaced geometry 72 (of 90) >> + << Calculating on displaced geometry 73 (of 90) >> + << Calculating on displaced geometry 74 (of 90) >> + << Calculating on displaced geometry 75 (of 90) >> + << Calculating on displaced geometry 76 (of 90) >> + << Calculating on displaced geometry 77 (of 90) >> + << Calculating on displaced geometry 78 (of 90) >> + << Calculating on displaced geometry 79 (of 90) >> + << Calculating on displaced geometry 80 (of 90) >> + << Calculating on displaced geometry 81 (of 90) >> + << Calculating on displaced geometry 82 (of 90) >> + << Calculating on displaced geometry 83 (of 90) >> + << Calculating on displaced geometry 84 (of 90) >> + << Calculating on displaced geometry 85 (of 90) >> + << Calculating on displaced geometry 86 (of 90) >> + << Calculating on displaced geometry 87 (of 90) >> + << Calculating on displaced geometry 88 (of 90) >> + << Calculating on displaced geometry 89 (of 90) >> + << Calculating on displaced geometry 90 (of 90) >> + +----------------------- +VIBRATIONAL FREQUENCIES +----------------------- + +Scaling factor for frequencies = 1.000000000 (already applied!) + + 0: 0.00 cm**-1 + 1: 0.00 cm**-1 + 2: 0.00 cm**-1 + 3: 0.00 cm**-1 + 4: 0.00 cm**-1 + 5: 0.00 cm**-1 + 6: -13.35 cm**-1 ***imaginary mode*** + 7: 252.24 cm**-1 + 8: 557.18 cm**-1 + 9: 613.24 cm**-1 + 10: 803.10 cm**-1 + 11: 840.54 cm**-1 + 12: 876.38 cm**-1 + 13: 954.58 cm**-1 + 14: 965.59 cm**-1 + 15: 980.31 cm**-1 + 16: 1000.25 cm**-1 + 17: 1030.24 cm**-1 + 18: 1101.22 cm**-1 + 19: 1125.95 cm**-1 + 20: 1163.25 cm**-1 + 21: 1191.48 cm**-1 + 22: 1205.00 cm**-1 + 23: 1219.58 cm**-1 + 24: 1239.15 cm**-1 + 25: 1296.43 cm**-1 + 26: 1307.22 cm**-1 + 27: 1323.33 cm**-1 + 28: 1324.02 cm**-1 + 29: 1324.99 cm**-1 + 30: 1483.49 cm**-1 + 31: 1487.62 cm**-1 + 32: 1497.58 cm**-1 + 33: 1498.38 cm**-1 + 34: 1516.09 cm**-1 + 35: 2971.92 cm**-1 + 36: 2972.55 cm**-1 + 37: 2984.88 cm**-1 + 38: 2986.62 cm**-1 + 39: 2999.16 cm**-1 + 40: 3000.31 cm**-1 + 41: 3005.88 cm**-1 + 42: 3008.88 cm**-1 + 43: 3009.44 cm**-1 + 44: 3012.88 cm**-1 + + +------------ +NORMAL MODES +------------ + +These modes are the cartesian displacements weighted by the diagonal matrix +M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom +Thus, these vectors are normalized but *not* orthogonal + + 0 1 2 3 4 5 + 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 1 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 2 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 4 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 7 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 8 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 9 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 10 0.000000 0.000000 0.000000 0.000000 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-0.001500 + 3 0.003379 0.009777 0.006349 + 4 -0.018795 -0.041518 -0.027511 + 5 0.005176 0.016541 0.003390 + 6 -0.024457 0.008525 -0.032456 + 7 -0.015714 0.001203 -0.019579 + 8 0.000413 0.019508 -0.003326 + 9 0.005643 0.028741 -0.027148 + 10 -0.006768 -0.022427 0.022632 + 11 -0.001655 0.018171 -0.006366 + 12 -0.018662 0.001152 0.007792 + 13 -0.044016 0.000912 0.019442 + 14 -0.006382 0.007605 0.000992 + 15 0.377639 -0.360812 -0.221865 + 16 -0.034692 0.030435 0.019298 + 17 -0.176182 0.172082 0.103937 + 18 -0.005276 -0.001966 0.002609 + 19 0.003757 -0.005265 -0.002247 + 20 0.133598 -0.220433 -0.082719 + 21 -0.045092 -0.097607 -0.061496 + 22 0.225313 0.511068 0.318029 + 23 -0.148304 -0.331112 -0.211030 + 24 -0.009914 -0.013444 -0.019639 + 25 0.006493 0.002139 0.017027 + 26 0.088189 0.133111 0.167959 + 27 0.104754 0.036843 0.121548 + 28 0.105137 0.031890 0.124102 + 29 -0.274829 -0.065141 -0.328632 + 30 0.198604 -0.135396 0.273055 + 31 0.082873 -0.059817 0.114162 + 32 0.269836 -0.168246 0.368951 + 33 -0.012697 -0.007446 0.027638 + 34 0.024378 0.028115 -0.061088 + 35 0.084756 0.132597 -0.233769 + 36 -0.064687 -0.347009 0.302826 + 37 0.044034 0.248947 -0.216428 + 38 -0.066458 -0.349307 0.311583 + 39 0.214416 -0.007581 -0.092336 + 40 0.549350 -0.024387 -0.235296 + 41 0.297417 -0.008768 -0.128759 + 42 0.010692 0.007649 -0.006218 + 43 -0.005572 0.007430 0.000773 + 44 -0.220092 -0.081964 0.113637 + + +----------- +IR SPECTRUM +----------- + + Mode freq eps Int T**2 TX TY TZ + cm**-1 L/(mol*cm) km/mol a.u. +---------------------------------------------------------------------------- + 7: 252.24 0.000158 0.80 0.000196 ( 0.006793 -0.012199 0.000883) + 8: 557.18 0.003325 16.80 0.001862 (-0.006401 -0.003125 -0.042564) + 9: 613.24 0.000202 1.02 0.000103 (-0.003489 -0.005541 0.007726) + 10: 803.10 0.002576 13.02 0.001001 (-0.006638 0.004376 -0.030622) + 11: 840.54 0.000385 1.95 0.000143 ( 0.003428 0.006004 0.009753) + 12: 876.38 0.000735 3.71 0.000262 (-0.002562 -0.004049 -0.015448) + 13: 954.58 0.000115 0.58 0.000038 (-0.003609 -0.001996 0.004551) + 14: 965.59 0.000130 0.66 0.000042 ( 0.004167 0.004871 -0.000943) + 15: 980.31 0.000729 3.68 0.000232 ( 0.009998 0.009993 -0.005676) + 16: 1000.25 0.001032 5.21 0.000322 ( 0.004459 0.015939 0.006922) + 17: 1030.24 0.000102 0.52 0.000031 ( 0.004598 0.002103 0.002338) + 18: 1101.22 0.000134 0.68 0.000038 ( 0.000215 -0.005072 -0.003513) + 19: 1125.95 0.001138 5.75 0.000315 ( 0.002735 -0.006389 -0.016346) + 20: 1163.25 0.000160 0.81 0.000043 (-0.001528 0.006282 -0.001007) + 21: 1191.48 0.000067 0.34 0.000018 (-0.001822 -0.003210 -0.001983) + 22: 1205.00 0.001280 6.47 0.000332 ( 0.005350 -0.004225 -0.016884) + 23: 1219.58 0.000172 0.87 0.000044 ( 0.001333 0.003743 -0.005303) + 24: 1239.15 0.000737 3.72 0.000186 (-0.004600 -0.006588 0.011002) + 25: 1296.43 0.000959 4.84 0.000231 (-0.007658 -0.012866 -0.002561) + 26: 1307.22 0.000561 2.84 0.000134 (-0.002810 0.001789 -0.011088) + 27: 1323.33 0.000079 0.40 0.000019 (-0.001509 0.001715 -0.003663) + 28: 1324.02 0.000103 0.52 0.000024 (-0.002056 0.003289 0.003027) + 29: 1324.99 0.000328 1.66 0.000077 ( 0.005816 -0.004043 -0.005192) + 30: 1483.49 0.000227 1.15 0.000048 ( 0.006418 0.001978 0.001630) + 31: 1487.62 0.000999 5.05 0.000210 (-0.003783 -0.004743 0.013146) + 32: 1497.58 0.000799 4.04 0.000166 (-0.000907 0.010301 0.007716) + 33: 1498.38 0.000940 4.75 0.000196 ( 0.000107 -0.000655 -0.013980) + 34: 1516.09 0.000239 1.21 0.000049 (-0.004273 -0.005461 -0.001041) + 35: 2971.92 0.001692 8.55 0.000178 (-0.004728 0.011549 0.004682) + 36: 2972.55 0.000302 1.52 0.000032 (-0.005163 -0.001834 -0.001281) + 37: 2984.88 0.000825 4.17 0.000086 ( 0.007991 0.003960 0.002599) + 38: 2986.62 0.003077 15.55 0.000322 ( 0.005703 -0.001857 -0.016899) + 39: 2999.16 0.004760 24.05 0.000495 ( 0.005780 0.000320 0.021488) + 40: 3000.31 0.002409 12.17 0.000251 (-0.004745 -0.015100 -0.000224) + 41: 3005.88 0.034710 175.41 0.003603 (-0.008980 0.004079 0.059213) + 42: 3008.88 0.014275 72.14 0.001481 (-0.029057 -0.025187 0.001377) + 43: 3009.44 0.025500 128.86 0.002644 ( 0.029874 -0.023499 0.034634) + 44: 3012.88 0.002171 10.97 0.000225 (-0.014390 -0.000813 -0.004143) + +* The epsilon (eps) is given for a Dirac delta lineshape. +** The dipole moment derivative (T) already includes vibrational overlap. + +The first frequency considered to be a vibration is 7 +The total number of vibrations considered is 38 + + +-------------------------- +THERMOCHEMISTRY AT 298.15K +-------------------------- + +Temperature ... 298.15 K +Pressure ... 1.00 atm +Total Mass ... 70.13 AMU + +Throughout the following assumptions are being made: + (1) The electronic state is orbitally nondegenerate + (2) There are no thermally accessible electronically excited states + (3) Hindered rotations indicated by low frequency modes are not + treated as such but are treated as vibrations and this may + cause some error + (4) All equations used are the standard statistical mechanics + equations for an ideal gas + (5) All vibrations are strictly harmonic + +freq. 252.24 E(vib) ... 0.30 +freq. 557.18 E(vib) ... 0.12 +freq. 613.24 E(vib) ... 0.10 +freq. 803.10 E(vib) ... 0.05 +freq. 840.54 E(vib) ... 0.04 +freq. 876.38 E(vib) ... 0.04 +freq. 954.58 E(vib) ... 0.03 +freq. 965.59 E(vib) ... 0.03 +freq. 980.31 E(vib) ... 0.02 +freq. 1000.25 E(vib) ... 0.02 +freq. 1030.24 E(vib) ... 0.02 +freq. 1101.22 E(vib) ... 0.02 +freq. 1125.95 E(vib) ... 0.01 +freq. 1163.25 E(vib) ... 0.01 +freq. 1191.48 E(vib) ... 0.01 +freq. 1205.00 E(vib) ... 0.01 +freq. 1219.58 E(vib) ... 0.01 +freq. 1239.15 E(vib) ... 0.01 +freq. 1296.43 E(vib) ... 0.01 +freq. 1307.22 E(vib) ... 0.01 +freq. 1323.33 E(vib) ... 0.01 +freq. 1324.02 E(vib) ... 0.01 +freq. 1324.99 E(vib) ... 0.01 +freq. 1483.49 E(vib) ... 0.00 +freq. 1487.62 E(vib) ... 0.00 +freq. 1497.58 E(vib) ... 0.00 +freq. 1498.38 E(vib) ... 0.00 +freq. 1516.09 E(vib) ... 0.00 +freq. 2971.92 E(vib) ... 0.00 +freq. 2972.55 E(vib) ... 0.00 +freq. 2984.88 E(vib) ... 0.00 +freq. 2986.62 E(vib) ... 0.00 +freq. 2999.16 E(vib) ... 0.00 +freq. 3000.31 E(vib) ... 0.00 +freq. 3005.88 E(vib) ... 0.00 +freq. 3008.88 E(vib) ... 0.00 +freq. 3009.44 E(vib) ... 0.00 +freq. 3012.88 E(vib) ... 0.00 + +------------ +INNER ENERGY +------------ + +The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans) + E(el) - is the total energy from the electronic structure calculation + = E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc) + E(ZPE) - the the zero temperature vibrational energy from the frequency calculation + E(vib) - the the finite temperature correction to E(ZPE) due to population + of excited vibrational states + E(rot) - is the rotational thermal energy + E(trans)- is the translational thermal energy + +Summary of contributions to the inner energy U: +Electronic energy ... -15.81431337 Eh +Zero point energy ... 0.13926653 Eh 87.39 kcal/mol +Thermal vibrational correction ... 0.00142864 Eh 0.90 kcal/mol +Thermal rotational correction ... 0.00141627 Eh 0.89 kcal/mol +Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol +----------------------------------------------------------------------- +Total thermal energy -15.67078566 Eh + + +Summary of corrections to the electronic energy: +(perhaps to be used in another calculation) +Total thermal correction 0.00426118 Eh 2.67 kcal/mol +Non-thermal (ZPE) correction 0.13926653 Eh 87.39 kcal/mol +----------------------------------------------------------------------- +Total correction 0.14352771 Eh 90.06 kcal/mol + + +-------- +ENTHALPY +-------- + +The enthalpy is H = U + kB*T + kB is Boltzmann's constant +Total free energy ... -15.67078566 Eh +Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol +----------------------------------------------------------------------- +Total Enthalpy ... -15.66984145 Eh + + +Note: Only C1 symmetry has been detected, increase convergence thresholds + if your molecule has a higher symmetry. Symmetry factor of 1.0 is + used for the rotational entropy correction. + + +Note: Rotational entropy computed according to Herzberg +Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945 +Point Group: C1, Symmetry Number: 1 +Rotational constants in cm-1: 0.219384 0.219301 0.127017 + +Vibrational entropy computed according to the QRRHO of S. Grimme +Chem.Eur.J. 2012 18 9955 + + +------- +ENTROPY +------- + +The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans)) + S(el) - electronic entropy + S(vib) - vibrational entropy + S(rot) - rotational entropy + S(trans)- translational entropy +The entropies will be listed as multiplied by the temperature to get +units of energy + +Electronic entropy ... 0.00000000 Eh 0.00 kcal/mol +Vibrational entropy ... 0.00200620 Eh 1.26 kcal/mol +Rotational entropy ... 0.01191737 Eh 7.48 kcal/mol +Translational entropy ... 0.01836882 Eh 11.53 kcal/mol +----------------------------------------------------------------------- +Final entropy term ... 0.03229240 Eh 20.26 kcal/mol + +In case the symmetry of your molecule has not been determined correctly +or in case you have a reason to use a different symmetry number we print +out the resulting rotational entropy values for sn=1,12 : + -------------------------------------------------------- +| sn= 1 | S(rot)= 0.01191737 Eh 7.48 kcal/mol| +| sn= 2 | S(rot)= 0.01126292 Eh 7.07 kcal/mol| +| sn= 3 | S(rot)= 0.01088009 Eh 6.83 kcal/mol| +| sn= 4 | S(rot)= 0.01060846 Eh 6.66 kcal/mol| +| sn= 5 | S(rot)= 0.01039777 Eh 6.52 kcal/mol| +| sn= 6 | S(rot)= 0.01022563 Eh 6.42 kcal/mol| +| sn= 7 | S(rot)= 0.01008008 Eh 6.33 kcal/mol| +| sn= 8 | S(rot)= 0.00995401 Eh 6.25 kcal/mol| +| sn= 9 | S(rot)= 0.00984280 Eh 6.18 kcal/mol| +| sn=10 | S(rot)= 0.00974332 Eh 6.11 kcal/mol| +| sn=11 | S(rot)= 0.00965333 Eh 6.06 kcal/mol| +| sn=12 | S(rot)= 0.00957117 Eh 6.01 kcal/mol| + -------------------------------------------------------- + + +------------------- +GIBBS FREE ENERGY +------------------- + +The Gibbs free energy is G = H - T*S + +Total enthalpy ... -15.66984145 Eh +Total entropy correction ... -0.03229240 Eh -20.26 kcal/mol +----------------------------------------------------------------------- +Final Gibbs free energy ... -15.70213385 Eh + +For completeness - the Gibbs free energy minus the electronic energy +G-E(el) ... 0.11217952 Eh 70.39 kcal/mol + + + +Timings for individual modules: + +Sum of individual times ... 162.968 sec (= 2.716 min) +Numerical frequency calculation ... 162.871 sec (= 2.715 min) 99.9 % +XTB module ... 0.097 sec (= 0.002 min) 0.1 % + ****ORCA TERMINATED NORMALLY**** +TOTAL RUN TIME: 0 days 0 hours 2 minutes 42 seconds 998 msec diff --git a/cmmde_gui/test/siklopentana/freq/cmmd.xtbrestart b/cmmde_gui/test/siklopentana/freq/cmmd.xtbrestart new file mode 100644 index 0000000000000000000000000000000000000000..5189ccd61205c0d69770471b5d8d4b584f0ad1b3 GIT binary patch literal 1320 zcmXw%do&aX6o-dQD{GsT$7+w*+7N9I6>Y?=wdI-Tk+NELY9?e0Gu~xA3Zt?}$V>*~ zF*Byo7?UyL&T7{p+nSxzOFKv&Nu`HJ6fI}#p7T53z5m^N&$pRCAgC{7u|AUY|47jL zK;sYmh|LR4=|cKS$JE9z@NmN1=HYl;G`=zw-@N9+Q zgpiJ`mFxsP79StT>{aP38dAvNlDZxqs;#^6@SP1E9U}bhyN4G;gK-WwZk`Q_^H~nC zfeGjGm5z~?B`}}qqwCIQfr}QU*~f|niORH@OF@^xFwac`1x(1H9WwXe6vL{C_n#Sf zuwik>5H$j!|8i0WF|`5Rxi&M>BXmfilgGHuLY$rT^)J4~Ms;J)YlH?V@E!=~{ytF! ztrJq!QDZ6C-7+g2wx|W=ersmQ>onA(n!CvI#n8Az{K9^>7#XQHExbTBiY5bBIzFjD z>(PLdwMq%PEu-8U4-$Z<#QO*8^=3G@zN~VM!5K^uIna{>`S>YME0pP*29#dKHd5jd z@ZZ$nZ&Z)a(rmhM&gddEn%W9tJezRC7d1n6S|U)snS0?|l?&NU9l65ih1kgZC;j`r z7Ch^*Rp<4*b23@9Y+P15X1gH69@x)!G*F8;cEK_U`^cH8K?INUwi`)+R6 zS?Hxj-<}tBK&nL;cs;ldXO?=*g%9Uo=iQFy&&JzP%F-=8@J%~31#hc*UCo2!(#o-# z))MHyf6&80GY{%y@ew1?0DWGWtArX|$WmT+>hib-gQEstdDV;X=-a|*e(4Q(b_Vk9 zEaPLhL~%suT@5ajm`k6x-@>yhp7`;VCWxAEysUmf0$Z2A(k411bX8EF_N|xT;hZ7~ znHYtmll%Io68^${=GkAyCH?^h{j!t|`N5`T+?@N*p=XxuOCC#sV$WFO;E;rq4S1i5MskTOzksQ1F$& zKF)|#h1!+VW&txn;AgqD+sh{lUvLKOL#Knmgv|3BJ?;#QSXaSSjsS*c&BB=RC0M9a z>$UM|21Ybb>AdYIfB(;MrD1Vaqfoyl4%GIV z{K!qO#_ocIM~|GtP-mL_$uTPiSi!O_t6%b9FvPpSVQCrGO>{lMZIS5Epe8TSi^4X0 z8y0Un3&m98G0W|_*w6Mpu5ji++JII|r)DIczu1^08x6!>rCqM%eF5I{3-74jTn_5v zAvzYFxsZ9TW!K}~Oo+c5JE{9`8OC~t?J()h1FB_-Zd* cmmd.out --oversubscribe diff --git a/cmmde_gui/test/siklopentana/freq/slurm-2884.out b/cmmde_gui/test/siklopentana/freq/slurm-2884.out new file mode 100644 index 0000000..e69de29 diff --git a/cmmde_gui/test/siklopentana/geom.smi b/cmmde_gui/test/siklopentana/geom.smi new file mode 100644 index 0000000..40f2cf3 --- /dev/null +++ b/cmmde_gui/test/siklopentana/geom.smi @@ -0,0 +1 @@ +C1CCCC1 diff --git a/cmmde_gui/test/siklopentana/geom.xyz b/cmmde_gui/test/siklopentana/geom.xyz new file mode 100644 index 0000000..852a0a3 --- /dev/null +++ b/cmmde_gui/test/siklopentana/geom.xyz @@ -0,0 +1,17 @@ +15 + +C 1.25397 -0.08785 0.23611 +C 0.32671 -1.22203 -0.16919 +C -1.08204 -0.67511 0.04351 +C -0.94615 0.84512 0.12208 +C 0.50463 1.15076 -0.22206 +H 2.24075 -0.17292 -0.22757 +H 1.38462 -0.07387 1.32471 +H 0.50883 -2.13310 0.40837 +H 0.47301 -1.46275 -1.22929 +H -1.51394 -1.06263 0.97282 +H -1.74391 -0.97741 -0.77500 +H -1.16963 1.18240 1.14140 +H -1.64010 1.35558 -0.55310 +H 0.86404 2.06064 0.26698 +H 0.61450 1.27994 -1.30545 diff --git a/cmmde_gui/test/siklopentana/run.sh b/cmmde_gui/test/siklopentana/run.sh new file mode 100644 index 0000000..f72e163 --- /dev/null +++ b/cmmde_gui/test/siklopentana/run.sh @@ -0,0 +1,10 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH +export PATH=/home/adit/opt/openmpi411/bin:$PATH +export OMP_NUM_THREADS=1 +cd $PWD +$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe diff --git a/cmmde_gui/test/siklopentana/run_babel.sh b/cmmde_gui/test/siklopentana/run_babel.sh new file mode 100644 index 0000000..0d5d00e --- /dev/null +++ b/cmmde_gui/test/siklopentana/run_babel.sh @@ -0,0 +1,8 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export OMP_NUM_THREADS=1 +cd $PWD +obabel geom.smi -O geom.xyz --gen3d diff --git a/cmmde_gui/test/siklopentana/slurm-2882.out b/cmmde_gui/test/siklopentana/slurm-2882.out new file mode 100644 index 0000000..b7d75ac --- /dev/null +++ b/cmmde_gui/test/siklopentana/slurm-2882.out @@ -0,0 +1 @@ +1 molecule converted diff --git a/cmmde_gui/test/siklopentana/slurm-2883.out b/cmmde_gui/test/siklopentana/slurm-2883.out new file mode 100644 index 0000000..e69de29 diff --git a/cmmde_gui/test/test/cmmd.engrad b/cmmde_gui/test/test/cmmd.engrad new file mode 100644 index 0000000..169b237 --- /dev/null +++ b/cmmde_gui/test/test/cmmd.engrad @@ -0,0 +1,62 @@ +# +# Number of atoms +# + 12 +# +# The current total energy in Eh +# + -15.879640652450 +# +# The current gradient in Eh/bohr +# + 0.000083151256 + 0.000032627904 + -0.000000801280 + -0.000011773444 + -0.000092719019 + -0.000008798638 + 0.000004092498 + -0.000045349095 + 0.000008265502 + -0.000095719643 + 0.000023986034 + -0.000000346361 + -0.000010542094 + 0.000056660251 + -0.000008827102 + 0.000027808309 + 0.000031909554 + 0.000010537622 + -0.000055844305 + -0.000000629739 + 0.000001035977 + -0.000012931289 + 0.000055053936 + 0.000010215618 + 0.000028823167 + 0.000043789233 + -0.000010112181 + 0.000056885559 + -0.000009417128 + 0.000000682946 + 0.000014817015 + -0.000052034477 + 0.000010200866 + -0.000028767027 + -0.000043877452 + -0.000012052970 +# +# The atomic numbers and current coordinates in Bohr +# + 6 2.5938463 -0.4162363 0.0103377 + 6 0.9500210 -2.4517633 -0.0164952 + 6 -1.6347236 -2.0458335 -0.0259782 + 6 -2.5758034 0.3955182 -0.0084365 + 6 -0.9319776 2.4309707 0.0184779 + 6 1.6528189 2.0250743 0.0277733 + 1 4.6108664 -0.7330783 0.0176863 + 1 1.6844131 -4.3568328 -0.0299365 + 1 -2.9175367 -3.6341720 -0.0471728 + 1 -4.5928432 0.7121836 -0.0157500 + 1 -1.6662937 4.3360760 0.0323392 + 1 2.9355884 3.6134472 0.0485120 diff --git a/cmmde_gui/test/test/cmmd.gbw b/cmmde_gui/test/test/cmmd.gbw new file mode 100644 index 0000000000000000000000000000000000000000..23effab815d83334dfa45d02bd6ff71be2ea7fc8 GIT binary patch literal 652588 zcmeI*3z!{MeE{&gNx+Dx0iquw#aN<5V*r6bE6vXM;uRx76f96B*=)#S_QCE32~u4Z z5L*iR-)GLej{beRdm69a zwmDTOwlYS6qQc)hr>nc8tDi{)1jjsW&O8x^z>-}m23)S{r4>FcJyD#>W{~N 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nprocs 1 +end +%geom + maxiter 9999 +end + +*xyzfile 0 1 geom.xyz + diff --git a/cmmde_gui/test/test/cmmd.opt b/cmmde_gui/test/test/cmmd.opt new file mode 100644 index 0000000..9c9c252 --- /dev/null +++ b/cmmde_gui/test/test/cmmd.opt @@ -0,0 +1,789 @@ + +$orca_opt_file + +$trust + 0.300000000000 + +$epredict + 0.000000000000 + +$ediffsc + 1000.000000000000 + +$ctyp + 3 + +$coordinates + 3 36 + 2.61288653 -0.41908456 0.01052577 0.95684393 -2.46996654 -0.01536347 + -1.64670735 -2.06091642 -0.02753331 -2.59502862 0.39856214 -0.00842818 + -0.93887264 2.44900948 0.01999330 1.66482983 2.04001605 0.02668293 + 4.64154533 -0.73782467 0.01814137 1.69553788 -4.38584649 -0.02672073 + -2.93691787 -3.65837751 -0.05119268 -4.62334727 0.71699989 -0.01574142 + -1.67749099 4.36532406 0.03615046 2.95509704 3.63745825 0.04484320 + + 2.59550649 -0.41643815 0.01036785 0.95059732 -2.45337629 -0.01616171 + -1.63568287 -2.04709654 -0.02637120 -2.57753162 0.39582279 -0.00841789 + -0.93258418 2.43251905 0.01884428 1.65382183 2.02632143 0.02742870 + 4.61219663 -0.73330531 0.01783196 1.68493943 -4.35810299 -0.02863830 + -2.91832796 -3.63515895 -0.04859871 -4.59420509 0.71241063 -0.01568095 + -1.66681407 4.33733453 0.03371620 2.93645989 3.61442347 0.04703701 + + 2.59388908 -0.41622532 0.01034226 0.95003032 -2.45180768 -0.01642596 + -1.63471042 -2.04583567 -0.02605385 -2.57586432 0.39554159 -0.00842982 + -0.93199846 2.43099668 0.01854548 1.65282602 2.02508075 0.02770048 + 4.61075286 -0.73308274 0.01772377 1.68439784 -4.35672268 -0.02958857 + -2.91745011 -3.63404503 -0.04754841 -4.59274904 0.71216783 -0.01572644 + -1.66627328 4.33595684 0.03269999 2.93552530 3.61332910 0.04811831 + + +# redundant internal coordinates +# nbonds nangles ndihedrals nimpropers ncartesians +# bond definitions A B +# angle definitions A B C +# dihedral definitions A B C D +# improper torsion definitions A B C D +# cartesian definitions A x/y/z +$redundant_internals + 12 18 24 0 0 + 1 0 0 + 2 1 0 + 3 2 0 + 4 3 0 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-0.565556 0.000000 0.000000 0.000000 + 48 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 49 0.000000 0.000000 0.000000 0.002723 0.005071 -0.565528 + 50 0.000000 0.000000 0.000000 0.002723 0.005071 -0.565528 + 51 0.000000 0.000000 0.000000 -0.002791 -0.005017 0.565552 + 52 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 53 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + diff --git a/cmmde_gui/test/test/cmmd.out b/cmmde_gui/test/test/cmmd.out new file mode 100644 index 0000000..c35f3b9 --- /dev/null +++ b/cmmde_gui/test/test/cmmd.out @@ -0,0 +1,1712 @@ + + ***************** + * O R C A * + ***************** + + #, + ### + #### + ##### + ###### + ########, + ,,################,,,,, + ,,#################################,, + ,,##########################################,, + ,#########################################, ''#####, + ,#############################################,, '####, + ,##################################################,,,,####, + ,###########'''' ''''############################### + ,#####'' ,,,,##########,,,, '''####''' '#### + ,##' ,,,,###########################,,, '## + ' ,,###'''' '''############,,, + ,,##'' '''############,,,, ,,,,,,###'' + ,#'' '''#######################''' + ' ''''####'''' + ,#######, #######, ,#######, ## + ,#' '#, ## ## ,#' '#, #''# ###### ,####, + ## ## ## ,#' ## #' '# # #' '# + ## ## ####### ## ,######, #####, # # + '#, ,#' ## ## '#, ,#' ,# #, ## #, ,# + '#######' ## ## '#######' #' '# #####' # '####' + + + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship and core code : Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 5.0.2 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Marcus Kettner : VPT2 + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : Initial AUTO-CI + Lucas Lang : DCDCAS + Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, + C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT + MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, + LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, + nearIR, NL-DFT gradient (VV10), updates on ESD, + ML-optimized integration grids + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + Liviu Ungur et al : ANISO software + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 5.1.0 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + Shared memory : Shared parallel matrices + BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED + Core in use : SkylakeX + Copyright (c) 2011-2014, The OpenBLAS Project + + + + +*************************************** +The coordinates will be read from file: geom.xyz +*************************************** + + +Your calculation utilizes the semiempirical GFN2-xTB method +Please cite in your paper: +C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. + + +================================================================================ + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + + +WARNING: Geometry Optimization + ===> : Switching off AutoStart + For restart on a previous wavefunction, please use MOREAD + +WARNING: Found dipole moment calculation with XTB calculation + ===> : Switching off dipole moment calculation + + +WARNING: TRAH-SCF for XTB is not implemented! + ===> : Turning TRAH off! + +================================================================================ + INPUT FILE +================================================================================ +NAME = cmmd.in +| 1> #CMMDE generated Orca input file +| 2> !XTB2 opt +| 3> %pal +| 4> nprocs 1 +| 5> end +| 6> %geom +| 7> maxiter 9999 +| 8> end +| 9> +| 10> *xyzfile 0 1 geom.xyz +| 11> +| 12> +| 13> ****END OF INPUT**** +================================================================================ + + ***************************** + * Geometry Optimization Run * + ***************************** + +Geometry optimization settings: +Update method Update .... BFGS +Choice of coordinates CoordSys .... Z-matrix Internals +Initial Hessian InHess .... Almoef's Model + +Convergence Tolerances: +Energy Change TolE .... 5.0000e-06 Eh +Max. Gradient TolMAXG .... 3.0000e-04 Eh/bohr +RMS Gradient TolRMSG .... 1.0000e-04 Eh/bohr +Max. Displacement TolMAXD .... 4.0000e-03 bohr +RMS Displacement TolRMSD .... 2.0000e-03 bohr +Strict Convergence .... False +------------------------------------------------------------------------------ + ORCA OPTIMIZATION COORDINATE SETUP +------------------------------------------------------------------------------ + +The optimization will be done in new redundant internal coordinates +Making redundant internal coordinates ... (new redundants) done +Evaluating the initial hessian ... (Almloef) done +Evaluating the coordinates ... done +Calculating the B-matrix .... done +Calculating the G-matrix .... done +Diagonalizing the G-matrix .... done +The first mode is .... 24 +The number of degrees of freedom .... 30 + + ----------------------------------------------------------------- + Redundant Internal Coordinates + + + ----------------------------------------------------------------- + Definition Initial Value Approx d2E/dq + ----------------------------------------------------------------- + 1. B(C 1,C 0) 1.3950 0.613451 + 2. B(C 2,C 1) 1.3947 0.614202 + 3. B(C 3,C 2) 1.3949 0.613576 + 4. B(C 4,C 3) 1.3949 0.613739 + 5. B(C 5,C 4) 1.3947 0.614057 + 6. B(C 5,C 0) 1.3947 0.614134 + 7. B(H 6,C 0) 1.0867 0.364496 + 8. B(H 7,C 1) 1.0866 0.364619 + 9. B(H 8,C 2) 1.0867 0.364500 + 10. B(H 9,C 3) 1.0865 0.364768 + 11. B(H 10,C 4) 1.0868 0.364328 + 12. B(H 11,C 5) 1.0867 0.364525 + 13. A(C 1,C 0,C 5) 119.9985 0.432498 + 14. A(C 1,C 0,H 6) 119.9915 0.352999 + 15. A(C 5,C 0,H 6) 120.0100 0.353066 + 16. A(C 2,C 1,H 7) 120.0112 0.353093 + 17. A(C 0,C 1,C 2) 119.9923 0.432506 + 18. A(C 0,C 1,H 7) 119.9965 0.353020 + 19. A(C 3,C 2,H 8) 119.9904 0.353012 + 20. A(C 1,C 2,H 8) 119.9986 0.353073 + 21. A(C 1,C 2,C 3) 120.0110 0.432522 + 22. A(C 4,C 3,H 9) 120.0060 0.353072 + 23. A(C 2,C 3,H 9) 120.0051 0.353056 + 24. A(C 2,C 3,C 4) 119.9889 0.432464 + 25. A(C 3,C 4,H 10) 119.9962 0.353000 + 26. A(C 3,C 4,C 5) 120.0006 0.432525 + 27. A(C 5,C 4,H 10) 120.0032 0.353031 + 28. A(C 0,C 5,C 4) 120.0085 0.432575 + 29. A(C 4,C 5,H 11) 120.0010 0.353063 + 30. A(C 0,C 5,H 11) 119.9904 0.353071 + 31. D(H 7,C 1,C 0,C 5) -179.9604 0.026008 + 32. D(H 7,C 1,C 0,H 6) 0.0383 0.026008 + 33. D(C 2,C 1,C 0,H 6) -179.9399 0.026008 + 34. D(C 2,C 1,C 0,C 5) 0.0614 0.026008 + 35. D(H 8,C 2,C 1,C 0) 179.8875 0.026075 + 36. D(C 3,C 2,C 1,C 0) -0.1354 0.026075 + 37. D(C 3,C 2,C 1,H 7) 179.8864 0.026075 + 38. D(H 8,C 2,C 1,H 7) -0.0907 0.026075 + 39. D(H 9,C 3,C 2,H 8) 0.0470 0.026019 + 40. D(H 9,C 3,C 2,C 1) -179.9301 0.026019 + 41. D(C 4,C 3,C 2,H 8) -179.9511 0.026019 + 42. D(C 4,C 3,C 2,C 1) 0.0718 0.026019 + 43. D(H 10,C 4,C 3,C 2) -179.9591 0.026033 + 44. D(C 5,C 4,C 3,H 9) -179.9323 0.026033 + 45. D(C 5,C 4,C 3,C 2) 0.0658 0.026033 + 46. D(H 10,C 4,C 3,H 9) 0.0427 0.026033 + 47. D(H 11,C 5,C 4,H 10) -0.1033 0.026062 + 48. D(C 0,C 5,C 4,H 10) 179.8851 0.026062 + 49. D(C 0,C 5,C 4,C 3) -0.1398 0.026062 + 50. D(H 11,C 5,C 0,H 6) 0.0659 0.026069 + 51. D(H 11,C 5,C 0,C 1) -179.9354 0.026069 + 52. D(H 11,C 5,C 4,C 3) 179.8717 0.026062 + 53. D(C 4,C 5,C 0,H 6) -179.9225 0.026069 + 54. D(C 4,C 5,C 0,C 1) 0.0762 0.026069 + ----------------------------------------------------------------- + +Number of atoms .... 12 +Number of degrees of freedom .... 54 + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 1 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.382680 -0.221770 0.005570 + C 0.506340 -1.307050 -0.008130 + C -0.871400 -1.090590 -0.014570 + C -1.373230 0.210910 -0.004460 + C -0.496830 1.295960 0.010580 + C 0.880990 1.079530 0.014120 + H 2.456200 -0.390440 0.009600 + H 0.897240 -2.320890 -0.014140 + H -1.554150 -1.935930 -0.027090 + H -2.446570 0.379420 -0.008330 + H -0.887690 2.310030 0.019130 + H 1.563770 1.924860 0.023730 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.612887 -0.419085 0.010526 + 1 C 6.0000 0 12.011 0.956844 -2.469967 -0.015363 + 2 C 6.0000 0 12.011 -1.646707 -2.060916 -0.027533 + 3 C 6.0000 0 12.011 -2.595029 0.398562 -0.008428 + 4 C 6.0000 0 12.011 -0.938873 2.449009 0.019993 + 5 C 6.0000 0 12.011 1.664830 2.040016 0.026683 + 6 H 1.0000 0 1.008 4.641545 -0.737825 0.018141 + 7 H 1.0000 0 1.008 1.695538 -4.385846 -0.026721 + 8 H 1.0000 0 1.008 -2.936918 -3.658378 -0.051193 + 9 H 1.0000 0 1.008 -4.623347 0.717000 -0.015741 + 10 H 1.0000 0 1.008 -1.677491 4.365324 0.036150 + 11 H 1.0000 0 1.008 2.955097 3.637458 0.044843 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 19:28:18.875 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 12 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.85673906472794 + + ID Z sym. atoms + 1 6 C 1-6 + 2 1 H 7-12 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 18 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.1615201 -0.161615E+02 0.494E+00 4.84 0.0 T + 2 -16.1767145 -0.151944E-01 0.296E+00 4.83 1.0 T + 3 -16.1770942 -0.379688E-03 0.492E-01 4.83 1.0 T + 4 -16.1774041 -0.309971E-03 0.515E-02 4.82 1.0 T + 5 -16.1774041 0.174099E-07 0.659E-03 4.82 4.4 T + 6 -16.1774041 -0.309461E-07 0.180E-03 4.82 16.0 T + 7 -16.1774042 -0.311983E-07 0.588E-04 4.82 49.1 T + 8 -16.1774042 0.808171E-10 0.178E-04 4.82 162.4 T + + *** convergence criteria satisfied after 8 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6387825 -17.3822 + ... ... ... ... + 9 2.0000 -0.4756453 -12.9430 + 10 2.0000 -0.4756384 -12.9428 + 11 2.0000 -0.4718343 -12.8393 + 12 2.0000 -0.4219300 -11.4813 + 13 2.0000 -0.4218886 -11.4802 + 14 2.0000 -0.4009568 -10.9106 + 15 2.0000 -0.4009234 -10.9097 (HOMO) + 16 -0.2236200 -6.0850 (LUMO) + 17 -0.2235509 -6.0831 + 18 -0.0961178 -2.6155 + 19 0.1107873 3.0147 + 20 0.1226310 3.3370 + ... ... ... + 30 0.6433999 17.5078 + ------------------------------------------------------------- + HL-Gap 0.1773034 Eh 4.8247 eV + Fermi-level -0.3122717 Eh -8.4973 eV + + SCC (total) 0 d, 0 h, 0 min, 0.012 sec + SCC setup ... 0 min, 0.000 sec ( 1.152%) + Dispersion ... 0 min, 0.000 sec ( 0.676%) + classical contributions ... 0 min, 0.000 sec ( 0.225%) + integral evaluation ... 0 min, 0.002 sec ( 14.106%) + iterations ... 0 min, 0.005 sec ( 46.843%) + molecular gradient ... 0 min, 0.004 sec ( 35.442%) + printout ... 0 min, 0.000 sec ( 1.463%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.878848475482 Eh :: + :: gradient norm 0.019149425975 Eh/a0 :: + :: HOMO-LUMO gap 4.824670438233 eV :: + ::.................................................:: + :: SCC energy -16.177404175194 Eh :: + :: -> isotropic ES 0.000752368509 Eh :: + :: -> anisotropic ES 0.002689473865 Eh :: + :: -> anisotropic XC 0.013008868445 Eh :: + :: -> dispersion -0.007987832843 Eh :: + :: repulsion energy 0.298548672022 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.878848475482 Eh | + | GRADIENT NORM 0.019149425975 Eh/α | + | HOMO-LUMO GAP 4.824670438233 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 19:28:18.899 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.023 sec + * cpu-time: 0 d, 0 h, 0 min, 0.023 sec + * ratio c/w: 0.975 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.012 sec + * cpu-time: 0 d, 0 h, 0 min, 0.011 sec + * ratio c/w: 0.955 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.878848475480 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 12 +Number of internal coordinates .... 54 +Current Energy .... -15.878848475 Eh +Current gradient norm .... 0.019149426 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Evaluating the initial hessian .... (Almloef) done +Projecting the Hessian .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.998622698 +Lowest eigenvalues of augmented Hessian: + -0.001470266 0.026024439 0.026025966 0.026033561 0.026041952 +Length of the computed step .... 0.052538613 +The final length of the internal step .... 0.052538613 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0071495997 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0141313345 RMS(Int)= 0.0071497568 + Iter 1: RMS(Cart)= 0.0000052351 RMS(Int)= 0.0000037874 + Iter 2: RMS(Cart)= 0.0000000333 RMS(Int)= 0.0000000244 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + RMS gradient 0.0039083086 0.0001000000 NO + MAX gradient 0.0109681387 0.0003000000 NO + RMS step 0.0071495997 0.0020000000 NO + MAX step 0.0178357525 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0094 Max(Angles) 0.00 + Max(Dihed) 0.10 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.3950 0.010968 -0.0094 1.3855 + 2. B(C 2,C 1) 1.3947 0.010773 -0.0093 1.3854 + 3. B(C 3,C 2) 1.3949 0.010938 -0.0094 1.3855 + 4. B(C 4,C 3) 1.3949 0.010920 -0.0094 1.3855 + 5. B(C 5,C 4) 1.3947 0.010783 -0.0093 1.3855 + 6. B(C 5,C 0) 1.3947 0.010796 -0.0093 1.3854 + 7. B(H 6,C 0) 1.0867 0.004434 -0.0064 1.0803 + 8. B(H 7,C 1) 1.0866 0.004380 -0.0063 1.0803 + 9. B(H 8,C 2) 1.0867 0.004421 -0.0064 1.0803 + 10. B(H 9,C 3) 1.0865 0.004318 -0.0062 1.0803 + 11. B(H 10,C 4) 1.0868 0.004506 -0.0065 1.0803 + 12. B(H 11,C 5) 1.0867 0.004409 -0.0064 1.0803 + 13. A(C 1,C 0,C 5) 120.00 0.000006 -0.00 120.00 + 14. A(C 1,C 0,H 6) 119.99 -0.000013 0.00 119.99 + 15. A(C 5,C 0,H 6) 120.01 0.000007 -0.00 120.01 + 16. A(C 2,C 1,H 7) 120.01 0.000017 -0.00 120.01 + 17. A(C 0,C 1,C 2) 119.99 -0.000022 0.00 120.00 + 18. A(C 0,C 1,H 7) 120.00 0.000005 -0.00 120.00 + 19. A(C 3,C 2,H 8) 119.99 -0.000005 0.00 119.99 + 20. A(C 1,C 2,H 8) 120.00 -0.000008 0.00 120.00 + 21. A(C 1,C 2,C 3) 120.01 0.000013 -0.00 120.01 + 22. A(C 4,C 3,H 9) 120.01 0.000010 -0.00 120.00 + 23. A(C 2,C 3,H 9) 120.01 0.000016 -0.00 120.00 + 24. A(C 2,C 3,C 4) 119.99 -0.000026 0.00 119.99 + 25. A(C 3,C 4,H 10) 120.00 -0.000002 0.00 120.00 + 26. A(C 3,C 4,C 5) 120.00 -0.000002 0.00 120.00 + 27. A(C 5,C 4,H 10) 120.00 0.000004 -0.00 120.00 + 28. A(C 0,C 5,C 4) 120.01 0.000030 -0.00 120.00 + 29. A(C 4,C 5,H 11) 120.00 -0.000005 0.00 120.00 + 30. A(C 0,C 5,H 11) 119.99 -0.000026 0.00 119.99 + 31. D(H 7,C 1,C 0,C 5) -179.96 0.000006 -0.01 -179.97 + 32. D(H 7,C 1,C 0,H 6) 0.04 0.000007 -0.01 0.02 + 33. D(C 2,C 1,C 0,H 6) -179.94 0.000021 -0.04 -179.98 + 34. D(C 2,C 1,C 0,C 5) 0.06 0.000020 -0.04 0.02 + 35. D(H 8,C 2,C 1,C 0) 179.89 -0.000030 0.06 179.95 + 36. D(C 3,C 2,C 1,C 0) -0.14 -0.000045 0.09 -0.04 + 37. D(C 3,C 2,C 1,H 7) 179.89 -0.000031 0.06 179.95 + 38. D(H 8,C 2,C 1,H 7) -0.09 -0.000016 0.03 -0.06 + 39. D(H 9,C 3,C 2,H 8) 0.05 0.000008 -0.02 0.03 + 40. D(H 9,C 3,C 2,C 1) -179.93 0.000023 -0.05 -179.98 + 41. D(C 4,C 3,C 2,H 8) -179.95 0.000008 -0.02 -179.97 + 42. D(C 4,C 3,C 2,C 1) 0.07 0.000024 -0.05 0.02 + 43. D(H 10,C 4,C 3,C 2) -179.96 0.000006 -0.01 -179.97 + 44. D(C 5,C 4,C 3,H 9) -179.93 0.000024 -0.05 -179.98 + 45. D(C 5,C 4,C 3,C 2) 0.07 0.000023 -0.05 0.02 + 46. D(H 10,C 4,C 3,H 9) 0.04 0.000007 -0.01 0.03 + 47. D(H 11,C 5,C 4,H 10) -0.10 -0.000019 0.04 -0.06 + 48. D(C 0,C 5,C 4,H 10) 179.89 -0.000031 0.06 179.95 + 49. D(C 0,C 5,C 4,C 3) -0.14 -0.000048 0.10 -0.04 + 50. D(H 11,C 5,C 0,H 6) 0.07 0.000014 -0.03 0.04 + 51. D(H 11,C 5,C 0,C 1) -179.94 0.000014 -0.03 -179.97 + 52. D(H 11,C 5,C 4,C 3) 179.87 -0.000036 0.07 179.95 + 53. D(C 4,C 5,C 0,H 6) -179.92 0.000025 -0.05 -179.97 + 54. D(C 4,C 5,C 0,C 1) 0.08 0.000026 -0.05 0.02 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 2 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.373483 -0.220370 0.005486 + C 0.503034 -1.298271 -0.008552 + C -0.865566 -1.083277 -0.013955 + C -1.363971 0.209460 -0.004455 + C -0.493502 1.287234 0.009972 + C 0.875165 1.072283 0.014515 + H 2.440669 -0.388048 0.009436 + H 0.891632 -2.306209 -0.015155 + H -1.544313 -1.923643 -0.025717 + H -2.431149 0.376991 -0.008298 + H -0.882040 2.295219 0.017842 + H 1.553908 1.912671 0.024891 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.595506 -0.416438 0.010368 + 1 C 6.0000 0 12.011 0.950597 -2.453376 -0.016162 + 2 C 6.0000 0 12.011 -1.635683 -2.047097 -0.026371 + 3 C 6.0000 0 12.011 -2.577532 0.395823 -0.008418 + 4 C 6.0000 0 12.011 -0.932584 2.432519 0.018844 + 5 C 6.0000 0 12.011 1.653822 2.026321 0.027429 + 6 H 1.0000 0 1.008 4.612197 -0.733305 0.017832 + 7 H 1.0000 0 1.008 1.684939 -4.358103 -0.028638 + 8 H 1.0000 0 1.008 -2.918328 -3.635159 -0.048599 + 9 H 1.0000 0 1.008 -4.594205 0.712411 -0.015681 + 10 H 1.0000 0 1.008 -1.666814 4.337335 0.033716 + 11 H 1.0000 0 1.008 2.936460 3.614423 0.047037 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 19:28:18.953 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 12 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.19063662090805 + + ID Z sym. atoms + 1 6 C 1-6 + 2 1 H 7-12 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 18 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.1955129 -0.161955E+02 0.125E-01 4.92 0.0 T + 2 -16.1955133 -0.403352E-06 0.742E-02 4.92 1.0 T + 3 -16.1955134 -0.164805E-06 0.315E-03 4.92 9.2 T + 4 -16.1955134 -0.155953E-08 0.132E-03 4.92 21.9 T + 5 -16.1955134 -0.140488E-08 0.609E-04 4.92 47.4 T + 6 -16.1955134 -0.245915E-08 0.596E-05 4.92 484.2 T + + *** convergence criteria satisfied after 6 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6413965 -17.4533 + ... ... ... ... + 9 2.0000 -0.4762976 -12.9607 + 10 2.0000 -0.4762924 -12.9606 + 11 2.0000 -0.4744819 -12.9113 + 12 2.0000 -0.4214505 -11.4683 + 13 2.0000 -0.4214244 -11.4675 + 14 2.0000 -0.4023732 -10.9491 + 15 2.0000 -0.4023625 -10.9488 (HOMO) + 16 -0.2213940 -6.0244 (LUMO) + 17 -0.2213674 -6.0237 + 18 -0.0904365 -2.4609 + 19 0.1184369 3.2228 + 20 0.1371976 3.7333 + ... ... ... + 30 0.6721149 18.2892 + ------------------------------------------------------------- + HL-Gap 0.1809685 Eh 4.9244 eV + Fermi-level -0.3118783 Eh -8.4866 eV + + SCC (total) 0 d, 0 h, 0 min, 0.012 sec + SCC setup ... 0 min, 0.000 sec ( 1.213%) + Dispersion ... 0 min, 0.000 sec ( 0.686%) + classical contributions ... 0 min, 0.000 sec ( 0.232%) + integral evaluation ... 0 min, 0.002 sec ( 15.681%) + iterations ... 0 min, 0.005 sec ( 42.910%) + molecular gradient ... 0 min, 0.004 sec ( 37.435%) + printout ... 0 min, 0.000 sec ( 1.743%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.879635904823 Eh :: + :: gradient norm 0.002431966060 Eh/a0 :: + :: HOMO-LUMO gap 4.924403565589 eV :: + ::.................................................:: + :: SCC energy -16.195513428874 Eh :: + :: -> isotropic ES 0.000795412668 Eh :: + :: -> anisotropic ES 0.002526209138 Eh :: + :: -> anisotropic XC 0.012416937729 Eh :: + :: -> dispersion -0.008017088770 Eh :: + :: repulsion energy 0.315870723599 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.879635904823 Eh | + | GRADIENT NORM 0.002431966060 Eh/α | + | HOMO-LUMO GAP 4.924403565589 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 19:28:18.978 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.025 sec + * cpu-time: 0 d, 0 h, 0 min, 0.024 sec + * ratio c/w: 0.969 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.012 sec + * cpu-time: 0 d, 0 h, 0 min, 0.011 sec + * ratio c/w: 0.952 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.879635904820 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 12 +Number of internal coordinates .... 54 +Current Energy .... -15.879635905 Eh +Current gradient norm .... 0.002431966 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999990087 +Lowest eigenvalues of augmented Hessian: + -0.000009204 0.026024381 0.026025797 0.026033356 0.026041404 +Length of the computed step .... 0.004452581 +The final length of the internal step .... 0.004452581 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0006059195 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0009627615 RMS(Int)= 0.0006059190 + Iter 1: RMS(Cart)= 0.0000000996 RMS(Int)= 0.0000001111 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0007874293 0.0000050000 NO + RMS gradient 0.0003080612 0.0001000000 NO + MAX gradient 0.0009650443 0.0003000000 NO + RMS step 0.0006059195 0.0020000000 YES + MAX step 0.0017122026 0.0040000000 YES + ........................................................ + Max(Bonds) 0.0009 Max(Angles) 0.00 + Max(Dihed) 0.03 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.3855 0.000965 -0.0009 1.3846 + 2. B(C 2,C 1) 1.3854 0.000884 -0.0008 1.3846 + 3. B(C 3,C 2) 1.3855 0.000952 -0.0009 1.3846 + 4. B(C 4,C 3) 1.3855 0.000928 -0.0009 1.3846 + 5. B(C 5,C 4) 1.3855 0.000905 -0.0008 1.3846 + 6. B(C 5,C 0) 1.3854 0.000890 -0.0008 1.3846 + 7. B(H 6,C 0) 1.0803 -0.000065 0.0001 1.0804 + 8. B(H 7,C 1) 1.0803 -0.000072 0.0001 1.0804 + 9. B(H 8,C 2) 1.0803 -0.000064 0.0001 1.0804 + 10. B(H 9,C 3) 1.0803 -0.000080 0.0001 1.0804 + 11. B(H 10,C 4) 1.0803 -0.000057 0.0001 1.0804 + 12. B(H 11,C 5) 1.0803 -0.000062 0.0001 1.0804 + 13. A(C 1,C 0,C 5) 120.00 -0.000003 0.00 120.00 + 14. A(C 1,C 0,H 6) 119.99 -0.000010 0.00 120.00 + 15. A(C 5,C 0,H 6) 120.01 0.000013 -0.00 120.01 + 16. A(C 2,C 1,H 7) 120.01 0.000017 -0.00 120.01 + 17. A(C 0,C 1,C 2) 120.00 -0.000014 0.00 120.00 + 18. A(C 0,C 1,H 7) 120.00 -0.000003 0.00 120.00 + 19. A(C 3,C 2,H 8) 119.99 -0.000015 0.00 119.99 + 20. A(C 1,C 2,H 8) 120.00 -0.000005 0.00 120.00 + 21. A(C 1,C 2,C 3) 120.01 0.000020 -0.00 120.01 + 22. A(C 4,C 3,H 9) 120.00 0.000010 -0.00 120.00 + 23. A(C 2,C 3,H 9) 120.00 0.000013 -0.00 120.00 + 24. A(C 2,C 3,C 4) 119.99 -0.000023 0.00 120.00 + 25. A(C 3,C 4,H 10) 120.00 -0.000009 0.00 120.00 + 26. A(C 3,C 4,C 5) 120.00 0.000004 -0.00 120.00 + 27. A(C 5,C 4,H 10) 120.00 0.000005 -0.00 120.00 + 28. A(C 0,C 5,C 4) 120.00 0.000016 -0.00 120.00 + 29. A(C 4,C 5,H 11) 120.00 0.000001 -0.00 120.00 + 30. A(C 0,C 5,H 11) 119.99 -0.000017 0.00 120.00 + 31. D(H 7,C 1,C 0,C 5) -179.97 0.000006 -0.01 -179.99 + 32. D(H 7,C 1,C 0,H 6) 0.02 0.000006 -0.01 0.01 + 33. D(C 2,C 1,C 0,H 6) -179.98 0.000005 -0.01 -180.00 + 34. D(C 2,C 1,C 0,C 5) 0.02 0.000006 -0.01 0.01 + 35. D(H 8,C 2,C 1,C 0) 179.95 -0.000013 0.03 179.98 + 36. D(C 3,C 2,C 1,C 0) -0.04 -0.000012 0.03 -0.01 + 37. D(C 3,C 2,C 1,H 7) 179.95 -0.000013 0.03 179.98 + 38. D(H 8,C 2,C 1,H 7) -0.06 -0.000013 0.03 -0.03 + 39. D(H 9,C 3,C 2,H 8) 0.03 0.000007 -0.02 0.01 + 40. D(H 9,C 3,C 2,C 1) -179.98 0.000007 -0.02 -179.99 + 41. D(C 4,C 3,C 2,H 8) -179.97 0.000007 -0.02 -179.99 + 42. D(C 4,C 3,C 2,C 1) 0.02 0.000007 -0.02 0.01 + 43. D(H 10,C 4,C 3,C 2) -179.97 0.000006 -0.02 -179.99 + 44. D(C 5,C 4,C 3,H 9) -179.98 0.000006 -0.01 -180.00 + 45. D(C 5,C 4,C 3,C 2) 0.02 0.000006 -0.01 0.00 + 46. D(H 10,C 4,C 3,H 9) 0.03 0.000007 -0.02 0.01 + 47. D(H 11,C 5,C 4,H 10) -0.06 -0.000015 0.03 -0.03 + 48. D(C 0,C 5,C 4,H 10) 179.95 -0.000013 0.03 179.98 + 49. D(C 0,C 5,C 4,C 3) -0.04 -0.000012 0.03 -0.01 + 50. D(H 11,C 5,C 0,H 6) 0.04 0.000009 -0.02 0.02 + 51. D(H 11,C 5,C 0,C 1) -179.97 0.000008 -0.02 -179.98 + 52. D(H 11,C 5,C 4,C 3) 179.95 -0.000014 0.03 179.98 + 53. D(C 4,C 5,C 0,H 6) -179.97 0.000007 -0.02 -179.99 + 54. D(C 4,C 5,C 0,C 1) 0.02 0.000007 -0.02 0.01 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 3 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.372627 -0.220257 0.005473 + C 0.502734 -1.297441 -0.008692 + C -0.865051 -1.082610 -0.013787 + C -1.363089 0.209312 -0.004461 + C -0.493192 1.286428 0.009814 + C 0.874638 1.071627 0.014658 + H 2.439905 -0.387931 0.009379 + H 0.891345 -2.305478 -0.015658 + H -1.543848 -1.923054 -0.025162 + H -2.430378 0.376863 -0.008322 + H -0.881754 2.294490 0.017304 + H 1.553413 1.912091 0.025463 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.593889 -0.416225 0.010342 + 1 C 6.0000 0 12.011 0.950030 -2.451808 -0.016426 + 2 C 6.0000 0 12.011 -1.634710 -2.045836 -0.026054 + 3 C 6.0000 0 12.011 -2.575864 0.395542 -0.008430 + 4 C 6.0000 0 12.011 -0.931998 2.430997 0.018545 + 5 C 6.0000 0 12.011 1.652826 2.025081 0.027700 + 6 H 1.0000 0 1.008 4.610753 -0.733083 0.017724 + 7 H 1.0000 0 1.008 1.684398 -4.356723 -0.029589 + 8 H 1.0000 0 1.008 -2.917450 -3.634045 -0.047548 + 9 H 1.0000 0 1.008 -4.592749 0.712168 -0.015726 + 10 H 1.0000 0 1.008 -1.666273 4.335957 0.032700 + 11 H 1.0000 0 1.008 2.935525 3.613329 0.048118 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 19:28:19.030 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 12 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.43222975619697 + + ID Z sym. atoms + 1 6 C 1-6 + 2 1 H 7-12 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 18 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.1966048 -0.161966E+02 0.940E-03 4.93 0.0 T + 2 -16.1966048 -0.207695E-07 0.559E-03 4.93 5.2 T + 3 -16.1966048 -0.612392E-09 0.508E-04 4.93 56.8 T + 4 -16.1966048 -0.514106E-09 0.150E-04 4.93 192.2 T + + *** convergence criteria satisfied after 4 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6416541 -17.4603 + ... ... ... ... + 9 2.0000 -0.4763535 -12.9622 + 10 2.0000 -0.4763484 -12.9621 + 11 2.0000 -0.4747520 -12.9187 + 12 2.0000 -0.4214048 -11.4670 + 13 2.0000 -0.4213893 -11.4666 + 14 2.0000 -0.4025242 -10.9532 + 15 2.0000 -0.4025215 -10.9532 (HOMO) + 16 -0.2212009 -6.0192 (LUMO) + 17 -0.2211879 -6.0188 + 18 -0.0899223 -2.4469 + 19 0.1181313 3.2145 + 20 0.1377925 3.7495 + ... ... ... + 30 0.6741822 18.3454 + ------------------------------------------------------------- + HL-Gap 0.1813206 Eh 4.9340 eV + Fermi-level -0.3118612 Eh -8.4862 eV + + SCC (total) 0 d, 0 h, 0 min, 0.034 sec + SCC setup ... 0 min, 0.000 sec ( 0.419%) + Dispersion ... 0 min, 0.000 sec ( 0.232%) + classical contributions ... 0 min, 0.000 sec ( 0.082%) + integral evaluation ... 0 min, 0.002 sec ( 6.257%) + iterations ... 0 min, 0.027 sec ( 78.741%) + molecular gradient ... 0 min, 0.005 sec ( 13.706%) + printout ... 0 min, 0.000 sec ( 0.521%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.879640611397 Eh :: + :: gradient norm 0.000229130871 Eh/a0 :: + :: HOMO-LUMO gap 4.933984539935 eV :: + ::.................................................:: + :: SCC energy -16.196604837071 Eh :: + :: -> isotropic ES 0.000792285296 Eh :: + :: -> anisotropic ES 0.002517056106 Eh :: + :: -> anisotropic XC 0.012386338819 Eh :: + :: -> dispersion -0.008019545150 Eh :: + :: repulsion energy 0.316957441898 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.879640611397 Eh | + | GRADIENT NORM 0.000229130871 Eh/α | + | HOMO-LUMO GAP 4.933984539935 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 19:28:19.079 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.048 sec + * cpu-time: 0 d, 0 h, 0 min, 0.026 sec + * ratio c/w: 0.547 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.034 sec + * cpu-time: 0 d, 0 h, 0 min, 0.012 sec + * ratio c/w: 0.352 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.879640611400 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 12 +Number of internal coordinates .... 54 +Current Energy .... -15.879640611 Eh +Current gradient norm .... 0.000229131 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999999659 +Lowest eigenvalues of augmented Hessian: + -0.000000069 0.025858500 0.026024548 0.026026832 0.026034093 +Length of the computed step .... 0.000825581 +The final length of the internal step .... 0.000825581 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0001123473 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0001364097 RMS(Int)= 0.0001123433 + Iter 1: RMS(Cart)= 0.0000000115 RMS(Int)= 0.0000000096 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0000047066 0.0000050000 YES + RMS gradient 0.0000197543 0.0001000000 YES + MAX gradient 0.0000576598 0.0003000000 YES + RMS step 0.0001123473 0.0020000000 YES + MAX step 0.0002850650 0.0040000000 YES + ........................................................ + Max(Bonds) 0.0001 Max(Angles) 0.00 + Max(Dihed) 0.02 Max(Improp) 0.00 + --------------------------------------------------------------------- + + ***********************HURRAY******************** + *** THE OPTIMIZATION HAS CONVERGED *** + ************************************************* + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + + --- Optimized Parameters --- + (Angstroem and degrees) + + Definition OldVal dE/dq Step FinalVal + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.3846 0.000030 -0.0000 1.3846 + 2. B(C 2,C 1) 1.3846 -0.000006 -0.0000 1.3846 + 3. B(C 3,C 2) 1.3846 0.000022 -0.0000 1.3846 + 4. B(C 4,C 3) 1.3846 0.000009 -0.0000 1.3846 + 5. B(C 5,C 4) 1.3846 0.000010 -0.0000 1.3846 + 6. B(C 5,C 0) 1.3846 -0.000003 -0.0000 1.3846 + 7. B(H 6,C 0) 1.0804 -0.000055 0.0001 1.0805 + 8. B(H 7,C 1) 1.0804 -0.000056 0.0001 1.0805 + 9. B(H 8,C 2) 1.0804 -0.000052 0.0001 1.0805 + 10. B(H 9,C 3) 1.0804 -0.000058 0.0001 1.0805 + 11. B(H 10,C 4) 1.0804 -0.000054 0.0001 1.0805 + 12. B(H 11,C 5) 1.0804 -0.000052 0.0001 1.0805 + 13. A(C 1,C 0,C 5) 120.00 -0.000004 0.00 120.00 + 14. A(C 1,C 0,H 6) 120.00 -0.000008 0.00 120.00 + 15. A(C 5,C 0,H 6) 120.01 0.000011 -0.00 120.00 + 16. A(C 2,C 1,H 7) 120.01 0.000012 -0.00 120.00 + 17. A(C 0,C 1,C 2) 120.00 -0.000008 0.00 120.00 + 18. A(C 0,C 1,H 7) 120.00 -0.000004 0.00 120.00 + 19. A(C 3,C 2,H 8) 119.99 -0.000013 0.00 120.00 + 20. A(C 1,C 2,H 8) 120.00 -0.000002 0.00 120.00 + 21. A(C 1,C 2,C 3) 120.01 0.000015 -0.00 120.00 + 22. A(C 4,C 3,H 9) 120.00 0.000007 -0.00 120.00 + 23. A(C 2,C 3,H 9) 120.00 0.000006 -0.00 120.00 + 24. A(C 2,C 3,C 4) 120.00 -0.000013 0.00 120.00 + 25. A(C 3,C 4,H 10) 120.00 -0.000006 0.00 120.00 + 26. A(C 3,C 4,C 5) 120.00 0.000002 -0.00 120.00 + 27. A(C 5,C 4,H 10) 120.00 0.000004 -0.00 120.00 + 28. A(C 0,C 5,C 4) 120.00 0.000008 -0.00 120.00 + 29. A(C 4,C 5,H 11) 120.00 0.000001 -0.00 120.00 + 30. A(C 0,C 5,H 11) 120.00 -0.000009 0.00 120.00 + 31. D(H 7,C 1,C 0,C 5) -179.99 0.000003 -0.01 -179.99 + 32. D(H 7,C 1,C 0,H 6) 0.01 0.000003 -0.01 0.00 + 33. D(C 2,C 1,C 0,H 6) -180.00 0.000001 -0.00 -180.00 + 34. D(C 2,C 1,C 0,C 5) 0.01 0.000001 -0.00 0.00 + 35. D(H 8,C 2,C 1,C 0) 179.98 -0.000005 0.01 179.99 + 36. D(C 3,C 2,C 1,C 0) -0.01 -0.000003 0.01 -0.00 + 37. D(C 3,C 2,C 1,H 7) 179.98 -0.000005 0.01 179.99 + 38. D(H 8,C 2,C 1,H 7) -0.03 -0.000007 0.02 -0.01 + 39. D(H 9,C 3,C 2,H 8) 0.01 0.000004 -0.01 0.01 + 40. D(H 9,C 3,C 2,C 1) -179.99 0.000002 -0.00 -180.00 + 41. D(C 4,C 3,C 2,H 8) -179.99 0.000004 -0.01 -179.99 + 42. D(C 4,C 3,C 2,C 1) 0.01 0.000002 -0.00 0.00 + 43. D(H 10,C 4,C 3,C 2) -179.99 0.000003 -0.01 -179.99 + 44. D(C 5,C 4,C 3,H 9) -180.00 0.000001 -0.00 -180.00 + 45. D(C 5,C 4,C 3,C 2) 0.00 0.000001 -0.00 0.00 + 46. D(H 10,C 4,C 3,H 9) 0.01 0.000003 -0.01 0.01 + 47. D(H 11,C 5,C 4,H 10) -0.03 -0.000007 0.02 -0.01 + 48. D(C 0,C 5,C 4,H 10) 179.98 -0.000005 0.01 179.99 + 49. D(C 0,C 5,C 4,C 3) -0.01 -0.000003 0.01 -0.00 + 50. D(H 11,C 5,C 0,H 6) 0.02 0.000004 -0.01 0.01 + 51. D(H 11,C 5,C 0,C 1) -179.98 0.000004 -0.01 -179.99 + 52. D(H 11,C 5,C 4,C 3) 179.98 -0.000005 0.01 179.99 + 53. D(C 4,C 5,C 0,H 6) -179.99 0.000002 -0.00 -180.00 + 54. D(C 4,C 5,C 0,C 1) 0.01 0.000002 -0.00 0.00 + ---------------------------------------------------------------------------- + ******************************************************* + *** FINAL ENERGY EVALUATION AT THE STATIONARY POINT *** + *** (AFTER 3 CYCLES) *** + ******************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.372604 -0.220263 0.005470 + C 0.502729 -1.297417 -0.008729 + C -0.865058 -1.082608 -0.013747 + C -1.363056 0.209299 -0.004464 + C -0.493181 1.286414 0.009778 + C 0.874634 1.071623 0.014697 + H 2.439965 -0.387928 0.009359 + H 0.891353 -2.305537 -0.015842 + H -1.543894 -1.923121 -0.024963 + H -2.430428 0.376871 -0.008335 + H -0.881765 2.294553 0.017113 + H 1.553446 1.912154 0.025671 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.593846 -0.416236 0.010338 + 1 C 6.0000 0 12.011 0.950021 -2.451763 -0.016495 + 2 C 6.0000 0 12.011 -1.634724 -2.045833 -0.025978 + 3 C 6.0000 0 12.011 -2.575803 0.395518 -0.008436 + 4 C 6.0000 0 12.011 -0.931978 2.430971 0.018478 + 5 C 6.0000 0 12.011 1.652819 2.025074 0.027773 + 6 H 1.0000 0 1.008 4.610866 -0.733078 0.017686 + 7 H 1.0000 0 1.008 1.684413 -4.356833 -0.029937 + 8 H 1.0000 0 1.008 -2.917537 -3.634172 -0.047173 + 9 H 1.0000 0 1.008 -4.592843 0.712184 -0.015750 + 10 H 1.0000 0 1.008 -1.666294 4.336076 0.032339 + 11 H 1.0000 0 1.008 2.935588 3.613447 0.048512 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 19:28:19.132 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 12 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.87450535693857 + + ID Z sym. atoms + 1 6 C 1-6 + 2 1 H 7-12 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 18 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.1965611 -0.161966E+02 0.876E-04 4.93 0.0 T + 2 -16.1965611 -0.258140E-09 0.515E-04 4.93 56.0 T + 3 -16.1965611 0.267484E-10 0.814E-05 4.93 354.6 T + + *** convergence criteria satisfied after 3 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6416606 -17.4605 + ... ... ... ... + 9 2.0000 -0.4763530 -12.9622 + 10 2.0000 -0.4763503 -12.9622 + 11 2.0000 -0.4747601 -12.9189 + 12 2.0000 -0.4214018 -11.4669 + 13 2.0000 -0.4213924 -11.4667 + 14 2.0000 -0.4025298 -10.9534 + 15 2.0000 -0.4025275 -10.9533 (HOMO) + 16 -0.2211971 -6.0191 (LUMO) + 17 -0.2211902 -6.0189 + 18 -0.0899154 -2.4467 + 19 0.1180093 3.2112 + 20 0.1377152 3.7474 + ... ... ... + 30 0.6741465 18.3445 + ------------------------------------------------------------- + HL-Gap 0.1813304 Eh 4.9343 eV + Fermi-level -0.3118623 Eh -8.4862 eV + + SCC (total) 0 d, 0 h, 0 min, 0.013 sec + SCC setup ... 0 min, 0.000 sec ( 1.548%) + Dispersion ... 0 min, 0.000 sec ( 0.711%) + classical contributions ... 0 min, 0.000 sec ( 0.245%) + integral evaluation ... 0 min, 0.002 sec ( 15.290%) + iterations ... 0 min, 0.005 sec ( 43.463%) + molecular gradient ... 0 min, 0.005 sec ( 37.053%) + printout ... 0 min, 0.000 sec ( 1.551%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.879640652449 Eh :: + :: gradient norm 0.000058531220 Eh/a0 :: + :: HOMO-LUMO gap 4.934252272558 eV :: + ::.................................................:: + :: SCC energy -16.196561052560 Eh :: + :: -> isotropic ES 0.000791525912 Eh :: + :: -> anisotropic ES 0.002517595461 Eh :: + :: -> anisotropic XC 0.012388537747 Eh :: + :: -> dispersion -0.008019556015 Eh :: + :: repulsion energy 0.316913616164 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.879640652449 Eh | + | GRADIENT NORM 0.000058531220 Eh/α | + | HOMO-LUMO GAP 4.934252272558 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 19:28:19.160 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.028 sec + * cpu-time: 0 d, 0 h, 0 min, 0.027 sec + * ratio c/w: 0.969 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.013 sec + * cpu-time: 0 d, 0 h, 0 min, 0.012 sec + * ratio c/w: 0.940 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.879640652450 +------------------------- -------------------- + + *** OPTIMIZATION RUN DONE *** + +Timings for individual modules: + +Sum of individual times ... 0.268 sec (= 0.004 min) +Geometry relaxation ... 0.078 sec (= 0.001 min) 29.1 % +XTB module ... 0.190 sec (= 0.003 min) 70.9 % + ****ORCA TERMINATED NORMALLY**** 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-0.38792834851432 0.00935918376693 + H 0.89135300032527 -2.30553664453777 -0.01584172099556 + H -1.54389392375015 -1.92312101358440 -0.02496277241009 + H -2.43042795974921 0.37687130997575 -0.00833452091932 + H -0.88176466598630 2.29455258686373 0.01711318587593 + H 1.55344645105395 1.91215391126322 0.02567143521620 diff --git a/cmmde_gui/test/test/cmmd_property.txt b/cmmde_gui/test/test/cmmd_property.txt new file mode 100644 index 0000000..8f1a67f --- /dev/null +++ b/cmmde_gui/test/test/cmmd_property.txt @@ -0,0 +1,6 @@ +------------------------------------------------------------- +----------------------- !PROPERTIES! ------------------------ +------------------------------------------------------------- +# ------------------------------------------------------------- +----------------------- !GEOMETRIES! ------------------------ +# ------------------------------------------------------------- diff --git a/cmmde_gui/test/test/cmmd_trj.xyz b/cmmde_gui/test/test/cmmd_trj.xyz new file mode 100644 index 0000000..4e3bfb0 --- /dev/null +++ b/cmmde_gui/test/test/cmmd_trj.xyz @@ -0,0 +1,56 @@ +12 +Coordinates from ORCA-job cmmd E -15.878848475480 + C 1.382680 -0.221770 0.005570 + C 0.506340 -1.307050 -0.008130 + C -0.871400 -1.090590 -0.014570 + C -1.373230 0.210910 -0.004460 + C -0.496830 1.295960 0.010580 + C 0.880990 1.079530 0.014120 + H 2.456200 -0.390440 0.009600 + H 0.897240 -2.320890 -0.014140 + H -1.554150 -1.935930 -0.027090 + H -2.446570 0.379420 -0.008330 + H -0.887690 2.310030 0.019130 + H 1.563770 1.924860 0.023730 +12 +Coordinates from ORCA-job cmmd E -15.879635904820 + C 1.373483 -0.220370 0.005486 + C 0.503034 -1.298271 -0.008552 + C -0.865566 -1.083277 -0.013955 + C -1.363971 0.209460 -0.004455 + C -0.493502 1.287234 0.009972 + C 0.875165 1.072283 0.014515 + H 2.440669 -0.388048 0.009436 + H 0.891632 -2.306209 -0.015155 + H -1.544313 -1.923643 -0.025717 + H -2.431149 0.376991 -0.008298 + H -0.882040 2.295219 0.017842 + H 1.553908 1.912671 0.024891 +12 +Coordinates from ORCA-job cmmd E -15.879640611400 + C 1.372627 -0.220257 0.005473 + C 0.502734 -1.297441 -0.008692 + C -0.865051 -1.082610 -0.013787 + C -1.363089 0.209312 -0.004461 + C -0.493192 1.286428 0.009814 + C 0.874638 1.071627 0.014658 + H 2.439905 -0.387931 0.009379 + H 0.891345 -2.305478 -0.015658 + H -1.543848 -1.923054 -0.025162 + H -2.430378 0.376863 -0.008322 + H -0.881754 2.294490 0.017304 + H 1.553413 1.912091 0.025463 +12 +Coordinates from ORCA-job cmmd E -15.879640652450 + C 1.372604 -0.220263 0.005470 + C 0.502729 -1.297417 -0.008729 + C -0.865058 -1.082608 -0.013747 + C -1.363056 0.209299 -0.004464 + C -0.493181 1.286414 0.009778 + C 0.874634 1.071623 0.014697 + H 2.439965 -0.387928 0.009359 + H 0.891353 -2.305537 -0.015842 + H -1.543894 -1.923121 -0.024963 + H -2.430428 0.376871 -0.008335 + H -0.881765 2.294553 0.017113 + H 1.553446 1.912154 0.025671 diff --git a/cmmde_gui/test/test/freq/cmmd.engrad b/cmmde_gui/test/test/freq/cmmd.engrad new file mode 100644 index 0000000..b64e17f --- /dev/null +++ b/cmmde_gui/test/test/freq/cmmd.engrad @@ -0,0 +1,62 @@ +# +# Number of atoms +# + 12 +# +# The current total energy in Eh +# + -15.879640652000 +# +# The current gradient in Eh/bohr +# + 0.000013771226 + 0.000024631843 + -0.000000349193 + -0.000020533282 + -0.000020386864 + -0.000003992377 + 0.000026170877 + 0.000002260421 + 0.000004206431 + -0.000020073729 + 0.000008164410 + -0.000000079043 + 0.000005505355 + -0.000000354275 + -0.000004263306 + -0.000005810630 + -0.000008859617 + 0.000004520578 + -0.000006170100 + -0.000005864960 + 0.000000462599 + 0.000003278326 + 0.000007205240 + 0.000004296571 + -0.000001328123 + 0.000004964612 + -0.000004560781 + 0.000006218997 + -0.000001947380 + 0.000000233825 + -0.000000995619 + -0.000005122712 + 0.000004486502 + -0.000000033297 + -0.000004690718 + -0.000004961807 +# +# The atomic numbers and current coordinates in Bohr +# + 6 2.5938463 -0.4162363 0.0103377 + 6 0.9500210 -2.4517633 -0.0164952 + 6 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-1.5556081361E-01 -1.3798087256E-01 1.5472461950E-01 + 22 3.7880133540E-01 3.4859556296E-01 4.0732111568E-01 3.5601264663E-01 -4.0309615583E-01 + 23 2.6646188143E-03 2.4530571186E-03 2.8832834138E-03 2.5174089223E-03 -2.8383413845E-03 + 24 -2.5680881960E-01 -3.5713253161E-01 6.6563009716E-02 3.5308872560E-01 6.9963645676E-02 + 25 -3.1797802975E-01 -4.4158106049E-01 8.5664300386E-02 4.3690293037E-01 8.8067434024E-02 + 26 -4.2235504574E-03 -5.8897262925E-03 1.1287270026E-03 5.8096229684E-03 1.1643355578E-03 + 27 4.0006252246E-01 1.8588333209E-01 -5.3510649507E-01 1.8274019421E-01 5.4023911640E-01 + 28 -6.2806971063E-02 -3.1164417129E-02 8.3314526705E-02 -2.9584098174E-02 -8.4511154807E-02 + 29 1.4440734064E-03 6.5519572264E-04 -1.9464099598E-03 6.6495730857E-04 1.9521203675E-03 + 30 -1.4651383465E-01 1.3616577684E-01 1.5611921798E-01 -1.3766827782E-01 1.5415579272E-01 + 31 3.8011827535E-01 -3.4890982685E-01 -4.0882280606E-01 3.5525317891E-01 -4.0165463831E-01 + 32 2.7517791938E-03 -2.5263290589E-03 -2.9784634445E-03 2.5823649533E-03 -2.9091981833E-03 + 33 -2.5709989283E-01 3.5563716784E-01 -6.6412699265E-02 3.5427491318E-01 7.0082190175E-02 + 34 -3.1835548706E-01 4.3975564122E-01 -8.5478055734E-02 4.3839368084E-01 8.8229867814E-02 + 35 -4.1425721777E-03 5.7469079182E-03 -1.1033525905E-03 5.7122715218E-03 1.1431276526E-03 + 35 + 0 -3.5536804117E-02 + 1 5.5832202445E-03 + 2 -1.3787142157E-04 + 3 -1.2921710263E-02 + 4 3.3514761055E-02 + 5 2.4146234657E-04 + 6 2.2412876325E-02 + 7 2.7749572815E-02 + 8 3.7295552605E-04 + 9 3.5595538921E-02 + 10 -5.5891846303E-03 + 11 1.2503967204E-04 + 12 1.2888460229E-02 + 13 -3.3436520523E-02 + 14 -2.4167103260E-04 + 15 -2.2419036909E-02 + 16 -2.7760795894E-02 + 17 -3.5792232363E-04 + 18 4.0321612125E-01 + 19 -6.3339346162E-02 + 20 1.4865281304E-03 + 21 1.4657646370E-01 + 22 -3.8022864770E-01 + 23 -2.7309906796E-03 + 24 -2.5405909708E-01 + 25 -3.1457238497E-01 + 26 -4.1698558800E-03 + 27 -4.0396842900E-01 + 28 6.3428044678E-02 + 29 -1.4678913808E-03 + 30 -1.4617832276E-01 + 31 3.7924120388E-01 + 32 2.7251230596E-03 + 33 2.5418300319E-01 + 34 3.1474364179E-01 + 35 4.1333415890E-03 + +# +# The atoms: label mass x y z (in bohrs) +# +$atoms +12 + C 12.01100 2.593846332749 -0.416236301861 0.010337690574 + C 12.01100 0.950020996603 -2.451763295587 -0.016495234112 + C 12.01100 -1.634723625950 -2.045833471680 -0.025978173978 + C 12.01100 -2.575803392589 0.395518164552 -0.008436465229 + C 12.01100 -0.931977631006 2.430970686794 0.018477869277 + C 12.01100 1.652818942247 2.025074337392 0.027773336334 + H 1.00800 4.610866417404 -0.733078338276 0.017686294157 + H 1.00800 1.684413059264 -4.356832849896 -0.029936514172 + H 1.00800 -2.917536695713 -3.634172038064 -0.047172803398 + H 1.00800 -4.592843232151 0.712183563586 -0.015749961995 + H 1.00800 -1.666293733283 4.336075989053 0.032339234584 + H 1.00800 2.935588356204 3.613447218194 0.048511982023 + +$actual_temperature + 0.000000 + +$frequency_scale_factor + 1.000000 + +$dipole_derivatives +36 + 2.0000000000E-01 -0.0000000000E+00 0.0000000000E+00 + -0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 + 0.0000000000E+00 -0.0000000000E+00 -0.0000000000E+00 + -0.0000000000E+00 2.0000000000E-01 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 2.0000000000E-01 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 + 2.0000000000E-01 -0.0000000000E+00 0.0000000000E+00 + -0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 + 0.0000000000E+00 -0.0000000000E+00 -0.0000000000E+00 + -0.0000000000E+00 2.0000000000E-01 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 2.0000000000E-01 0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 + -2.0000000000E-01 0.0000000000E+00 -0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 + -0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 + -0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 -2.0000000000E-01 -0.0000000000E+00 + 0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 + -0.0000000000E+00 -2.0000000000E-01 -0.0000000000E+00 + -2.0000000000E-01 -2.0000000000E-01 -0.0000000000E+00 + -0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 + -2.0000000000E-01 0.0000000000E+00 -0.0000000000E+00 + 0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 + -0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 + -0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 + 0.0000000000E+00 -2.0000000000E-01 -0.0000000000E+00 + 0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 + -0.0000000000E+00 -2.0000000000E-01 -0.0000000000E+00 + -2.0000000000E-01 -2.0000000000E-01 -0.0000000000E+00 + -0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 + +# +# The IR spectrum +# wavenumber eps Int TX TY TZ +# +$ir_spectrum +36 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000 + 368.34 0.00000032 0.00163414 -0.000405 -0.000331 0.000000 + 368.35 0.00000010 0.00049393 0.000058 -0.000282 0.000000 + 578.85 0.00000000 0.00000001 0.000001 0.000001 0.000000 + 578.86 0.00000000 0.00000000 0.000000 -0.000000 0.000000 + 657.51 0.00000000 0.00000004 0.000000 0.000002 0.000000 + 692.59 0.00000391 0.01974259 0.000673 0.001143 0.000000 + 882.01 0.00000000 0.00000036 0.000002 0.000004 0.000000 + 882.03 0.00000000 0.00000049 0.000002 0.000005 0.000000 + 930.42 0.00000098 0.00493332 -0.000199 0.000537 0.000000 + 930.44 0.00000096 0.00487261 -0.000348 -0.000450 0.000000 + 936.89 0.00000000 0.00000154 0.000003 0.000010 0.000000 + 956.87 0.00039164 1.97916311 0.009098 0.006704 0.000000 + 1066.82 0.00000000 0.00000019 -0.000001 0.000003 0.000000 + 1090.46 0.00410414 20.74061755 0.029281 -0.017807 0.000000 + 1090.47 0.00022985 1.16158452 0.007902 0.001826 0.000000 + 1176.03 0.00137544 6.95092017 -0.017376 -0.007941 0.000000 + 1198.27 0.00000000 0.00000004 0.000001 0.000000 0.000000 + 1198.31 0.00000000 0.00000029 -0.000004 -0.000001 0.000000 + 1304.23 0.00000000 0.00000001 0.000000 0.000001 0.000000 + 1319.65 0.00042078 2.12645852 0.001909 -0.009791 0.000000 + 1460.44 0.00144696 7.31236348 -0.015194 0.008850 0.000000 + 1460.55 0.00193439 9.77562126 0.015248 0.013446 0.000000 + 1599.79 0.00000000 0.00000038 -0.000004 -0.000002 0.000000 + 1599.80 0.00000000 0.00000060 0.000003 0.000004 0.000000 + 3068.19 0.00141812 7.16662153 -0.006118 0.010335 0.000000 + 3071.53 0.00000012 0.00059657 0.000037 0.000103 0.000000 + 3071.62 0.00000004 0.00022530 -0.000058 0.000034 0.000000 + 3083.57 0.05333409 269.52863401 -0.034081 -0.065084 0.000000 + 3083.65 0.01495348 75.56876497 -0.036094 0.014509 0.000000 + 3092.32 0.00000001 0.00003518 0.000017 0.000020 0.000000 + + +$end + diff --git a/cmmde_gui/test/test/freq/cmmd.in b/cmmde_gui/test/test/freq/cmmd.in new file mode 100644 index 0000000..247d130 --- /dev/null +++ b/cmmde_gui/test/test/freq/cmmd.in @@ -0,0 +1,13 @@ +#CMMDE generated Orca input file +!XTB2 Numfreq +%pal + nprocs 1 +end + +*xyzfile 0 1 ../cmmd.xyz + +%freq + scalfreq 1 + Temp 298.15 + Pressure 1.0 +end diff --git a/cmmde_gui/test/test/freq/cmmd.out b/cmmde_gui/test/test/freq/cmmd.out new file mode 100644 index 0000000..46958f4 --- /dev/null +++ b/cmmde_gui/test/test/freq/cmmd.out @@ -0,0 +1,1003 @@ + + ***************** + * O R C A * + ***************** + + #, + ### + #### + ##### + ###### + ########, + ,,################,,,,, + ,,#################################,, + ,,##########################################,, + ,#########################################, ''#####, + ,#############################################,, '####, + ,##################################################,,,,####, + ,###########'''' ''''############################### + ,#####'' ,,,,##########,,,, '''####''' '#### + ,##' ,,,,###########################,,, '## + ' ,,###'''' '''############,,, + ,,##'' '''############,,,, ,,,,,,###'' + ,#'' '''#######################''' + ' ''''####'''' + ,#######, #######, ,#######, ## + ,#' '#, ## ## ,#' '#, #''# ###### ,####, + ## ## ## ,#' ## #' '# # #' '# + ## ## ####### ## ,######, #####, # # + '#, ,#' ## ## '#, ,#' ,# #, ## #, ,# + '#######' ## ## '#######' #' '# #####' # '####' + + + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship and core code : Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 5.0.2 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Marcus Kettner : VPT2 + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : Initial AUTO-CI + Lucas Lang : DCDCAS + Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, + C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT + MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, + LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, + nearIR, NL-DFT gradient (VV10), updates on ESD, + ML-optimized integration grids + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + Liviu Ungur et al : ANISO software + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 5.1.0 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + Shared memory : Shared parallel matrices + BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED + Core in use : SkylakeX + Copyright (c) 2011-2014, The OpenBLAS Project + + + + +*************************************** +The coordinates will be read from file: ../cmmd.xyz +*************************************** + + +Your calculation utilizes the semiempirical GFN2-xTB method +Please cite in your paper: +C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. + + +================================================================================ + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + +WARNING: Gradients needed for Numerical Frequencies + ===> : Setting RunTyp to EnGrad + +WARNING: Found dipole moment calculation with XTB calculation + ===> : Switching off dipole moment calculation + + +WARNING: TRAH-SCF for XTB is not implemented! + ===> : Turning TRAH off! + +================================================================================ + INPUT FILE +================================================================================ +NAME = cmmd.in +| 1> #CMMDE generated Orca input file +| 2> !XTB2 Numfreq +| 3> %pal +| 4> nprocs 1 +| 5> end +| 6> +| 7> *xyzfile 0 1 ../cmmd.xyz +| 8> +| 9> %freq +| 10> scalfreq 1 +| 11> Temp 298.15 +| 12> Pressure 1.0 +| 13> end +| 14> +| 15> ****END OF INPUT**** +================================================================================ + + ******************************* + * Energy+Gradient Calculation * + ******************************* + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 19:28:37.919 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 12 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.46546282047707 + + ID Z sym. atoms + 1 6 C 1-6 + 2 1 H 7-12 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 18 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.1804934 -0.161805E+02 0.483E+00 4.95 0.0 T + 2 -16.1958586 -0.153652E-01 0.289E+00 4.94 1.0 T + 3 -16.1962526 -0.394030E-03 0.500E-01 4.93 1.0 T + 4 -16.1965610 -0.308394E-03 0.498E-02 4.93 1.0 T + 5 -16.1965610 -0.268115E-07 0.641E-03 4.93 4.5 T + 6 -16.1965611 -0.565617E-08 0.759E-04 4.93 38.0 T + 7 -16.1965611 0.351822E-09 0.213E-04 4.93 135.2 T + + *** convergence criteria satisfied after 7 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6416603 -17.4605 + ... ... ... ... + 9 2.0000 -0.4763532 -12.9622 + 10 2.0000 -0.4763496 -12.9621 + 11 2.0000 -0.4747597 -12.9189 + 12 2.0000 -0.4214015 -11.4669 + 13 2.0000 -0.4213920 -11.4667 + 14 2.0000 -0.4025286 -10.9534 + 15 2.0000 -0.4025278 -10.9533 (HOMO) + 16 -0.2211974 -6.0191 (LUMO) + 17 -0.2211890 -6.0189 + 18 -0.0899149 -2.4467 + 19 0.1180097 3.2112 + 20 0.1377156 3.7474 + ... ... ... + 30 0.6741469 18.3445 + ------------------------------------------------------------- + HL-Gap 0.1813304 Eh 4.9343 eV + Fermi-level -0.3118626 Eh -8.4862 eV + + SCC (total) 0 d, 0 h, 0 min, 0.028 sec + SCC setup ... 0 min, 0.000 sec ( 0.506%) + Dispersion ... 0 min, 0.000 sec ( 0.278%) + classical contributions ... 0 min, 0.000 sec ( 0.100%) + integral evaluation ... 0 min, 0.002 sec ( 6.341%) + iterations ... 0 min, 0.021 sec ( 76.344%) + molecular gradient ... 0 min, 0.004 sec ( 15.617%) + printout ... 0 min, 0.000 sec ( 0.733%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.879640651996 Eh :: + :: gradient norm 0.000057843236 Eh/a0 :: + :: HOMO-LUMO gap 4.934252036755 eV :: + ::.................................................:: + :: SCC energy -16.196561052107 Eh :: + :: -> isotropic ES 0.000791437720 Eh :: + :: -> anisotropic ES 0.002517591356 Eh :: + :: -> anisotropic XC 0.012388541351 Eh :: + :: -> dispersion -0.008019563558 Eh :: + :: repulsion energy 0.316913616164 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.879640651996 Eh | + | GRADIENT NORM 0.000057843236 Eh/α | + | HOMO-LUMO GAP 4.934252036755 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 19:28:37.959 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.041 sec + * cpu-time: 0 d, 0 h, 0 min, 0.024 sec + * ratio c/w: 0.594 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.028 sec + * cpu-time: 0 d, 0 h, 0 min, 0.012 sec + * ratio c/w: 0.413 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.879640652000 +------------------------- -------------------- + + +---------------------------------------------------------------------------- + ORCA NUMERICAL FREQUENCIES +---------------------------------------------------------------------------- + +Number of atoms ... 12 +Central differences ... used +Number of displacements ... 72 +Numerical increment ... 5.000e-03 bohr +IR-spectrum generation ... on +Raman-spectrum generation ... off +Surface Crossing Hessian ... off + +The output will be reduced. Please look at the following files: +SCF program output ... >cmmd.lastscf +Integral program output ... >cmmd.lastint +Gradient program output ... >cmmd.lastgrad +Dipole moment program output ... >cmmd.lastmom +AutoCI program output ... >cmmd.lastautoci + + << Calculating on displaced geometry 1 (of 72) >> + << Calculating on displaced geometry 2 (of 72) >> + << Calculating on displaced geometry 3 (of 72) >> + << Calculating on displaced geometry 4 (of 72) >> + << Calculating on displaced geometry 5 (of 72) >> + << Calculating on displaced geometry 6 (of 72) >> + << Calculating on displaced geometry 7 (of 72) >> + << Calculating on displaced geometry 8 (of 72) >> + << Calculating on displaced geometry 9 (of 72) >> + << Calculating on displaced geometry 10 (of 72) >> + << Calculating on displaced geometry 11 (of 72) >> + << Calculating on displaced geometry 12 (of 72) >> + << Calculating on displaced geometry 13 (of 72) >> + << Calculating on displaced geometry 14 (of 72) >> + << Calculating on displaced geometry 15 (of 72) >> + << Calculating on displaced geometry 16 (of 72) >> + << Calculating on displaced geometry 17 (of 72) >> + << Calculating on displaced geometry 18 (of 72) >> + << Calculating on displaced geometry 19 (of 72) >> + << Calculating on displaced geometry 20 (of 72) >> + << Calculating on displaced geometry 21 (of 72) >> + << Calculating on displaced geometry 22 (of 72) >> + << Calculating on displaced geometry 23 (of 72) >> + << Calculating on displaced geometry 24 (of 72) >> + << Calculating on displaced geometry 25 (of 72) >> + << Calculating on displaced geometry 26 (of 72) >> + << Calculating on displaced geometry 27 (of 72) >> + << Calculating on displaced geometry 28 (of 72) >> + << Calculating on displaced geometry 29 (of 72) >> + << Calculating on displaced geometry 30 (of 72) >> + << Calculating on displaced geometry 31 (of 72) >> + << Calculating on displaced geometry 32 (of 72) >> + << Calculating on displaced geometry 33 (of 72) >> + << Calculating on displaced geometry 34 (of 72) >> + << Calculating on displaced geometry 35 (of 72) >> + << Calculating on displaced geometry 36 (of 72) >> + << Calculating on displaced geometry 37 (of 72) >> + << Calculating on displaced geometry 38 (of 72) >> + << Calculating on displaced geometry 39 (of 72) >> + << Calculating on displaced geometry 40 (of 72) >> + << Calculating on displaced geometry 41 (of 72) >> + << Calculating on displaced geometry 42 (of 72) >> + << Calculating on displaced geometry 43 (of 72) >> + << Calculating on displaced geometry 44 (of 72) >> + << Calculating on displaced geometry 45 (of 72) >> + << Calculating on displaced geometry 46 (of 72) >> + << Calculating on displaced geometry 47 (of 72) >> + << Calculating on displaced geometry 48 (of 72) >> + << Calculating on displaced geometry 49 (of 72) >> + << Calculating on displaced geometry 50 (of 72) >> + << Calculating on displaced geometry 51 (of 72) >> + << Calculating on displaced geometry 52 (of 72) >> + << Calculating on displaced geometry 53 (of 72) >> + << Calculating on displaced geometry 54 (of 72) >> + << Calculating on displaced geometry 55 (of 72) >> + << Calculating on displaced geometry 56 (of 72) >> + << Calculating on displaced geometry 57 (of 72) >> + << Calculating on displaced geometry 58 (of 72) >> + << Calculating on displaced geometry 59 (of 72) >> + << Calculating on displaced geometry 60 (of 72) >> + << Calculating on displaced geometry 61 (of 72) >> + << Calculating on displaced geometry 62 (of 72) >> + << Calculating on displaced geometry 63 (of 72) >> + << Calculating on displaced geometry 64 (of 72) >> + << Calculating on displaced geometry 65 (of 72) >> + << Calculating on displaced geometry 66 (of 72) >> + << Calculating on displaced geometry 67 (of 72) >> + << Calculating on displaced geometry 68 (of 72) >> + << Calculating on displaced geometry 69 (of 72) >> + << Calculating on displaced geometry 70 (of 72) >> + << Calculating on displaced geometry 71 (of 72) >> + << Calculating on displaced geometry 72 (of 72) >> + +----------------------- +VIBRATIONAL FREQUENCIES +----------------------- + +Scaling factor for frequencies = 1.000000000 (already applied!) + + 0: 0.00 cm**-1 + 1: 0.00 cm**-1 + 2: 0.00 cm**-1 + 3: 0.00 cm**-1 + 4: 0.00 cm**-1 + 5: 0.00 cm**-1 + 6: 368.34 cm**-1 + 7: 368.35 cm**-1 + 8: 578.85 cm**-1 + 9: 578.86 cm**-1 + 10: 657.51 cm**-1 + 11: 692.59 cm**-1 + 12: 882.01 cm**-1 + 13: 882.03 cm**-1 + 14: 930.42 cm**-1 + 15: 930.44 cm**-1 + 16: 936.89 cm**-1 + 17: 956.87 cm**-1 + 18: 1066.82 cm**-1 + 19: 1090.46 cm**-1 + 20: 1090.47 cm**-1 + 21: 1176.03 cm**-1 + 22: 1198.27 cm**-1 + 23: 1198.31 cm**-1 + 24: 1304.23 cm**-1 + 25: 1319.65 cm**-1 + 26: 1460.44 cm**-1 + 27: 1460.55 cm**-1 + 28: 1599.79 cm**-1 + 29: 1599.80 cm**-1 + 30: 3068.19 cm**-1 + 31: 3071.53 cm**-1 + 32: 3071.62 cm**-1 + 33: 3083.57 cm**-1 + 34: 3083.65 cm**-1 + 35: 3092.32 cm**-1 + + +------------ +NORMAL MODES +------------ + +These modes 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0.001164 -0.004170 + 27 0.400063 0.185883 -0.535106 0.182740 0.540239 -0.403968 + 28 -0.062807 -0.031164 0.083315 -0.029584 -0.084511 0.063428 + 29 0.001444 0.000655 -0.001946 0.000665 0.001952 -0.001468 + 30 -0.146514 0.136166 0.156119 -0.137668 0.154156 -0.146178 + 31 0.380118 -0.348910 -0.408823 0.355253 -0.401655 0.379241 + 32 0.002752 -0.002526 -0.002978 0.002582 -0.002909 0.002725 + 33 -0.257100 0.355637 -0.066413 0.354275 0.070082 0.254183 + 34 -0.318355 0.439756 -0.085478 0.438394 0.088230 0.314744 + 35 -0.004143 0.005747 -0.001103 0.005712 0.001143 0.004133 + + +----------- +IR SPECTRUM +----------- + + Mode freq eps Int T**2 TX TY TZ + cm**-1 L/(mol*cm) km/mol a.u. +---------------------------------------------------------------------------- + 6: 368.34 0.000000 0.00 0.000000 (-0.000405 -0.000331 0.000000) + 7: 368.35 0.000000 0.00 0.000000 ( 0.000058 -0.000282 0.000000) + 8: 578.85 0.000000 0.00 0.000000 ( 0.000001 0.000001 0.000000) + 9: 578.86 0.000000 0.00 0.000000 ( 0.000000 -0.000000 0.000000) + 10: 657.51 0.000000 0.00 0.000000 ( 0.000000 0.000002 0.000000) + 11: 692.59 0.000004 0.02 0.000002 ( 0.000673 0.001143 0.000000) + 12: 882.01 0.000000 0.00 0.000000 ( 0.000002 0.000004 0.000000) + 13: 882.03 0.000000 0.00 0.000000 ( 0.000002 0.000005 0.000000) + 14: 930.42 0.000001 0.00 0.000000 (-0.000199 0.000537 0.000000) + 15: 930.44 0.000001 0.00 0.000000 (-0.000348 -0.000450 0.000000) + 16: 936.89 0.000000 0.00 0.000000 ( 0.000003 0.000010 0.000000) + 17: 956.87 0.000392 1.98 0.000128 ( 0.009098 0.006704 0.000000) + 18: 1066.82 0.000000 0.00 0.000000 (-0.000001 0.000003 0.000000) + 19: 1090.46 0.004104 20.74 0.001175 ( 0.029281 -0.017807 0.000000) + 20: 1090.47 0.000230 1.16 0.000066 ( 0.007902 0.001826 0.000000) + 21: 1176.03 0.001375 6.95 0.000365 (-0.017376 -0.007941 0.000000) + 22: 1198.27 0.000000 0.00 0.000000 ( 0.000001 0.000000 0.000000) + 23: 1198.31 0.000000 0.00 0.000000 (-0.000004 -0.000001 0.000000) + 24: 1304.23 0.000000 0.00 0.000000 ( 0.000000 0.000001 0.000000) + 25: 1319.65 0.000421 2.13 0.000100 ( 0.001909 -0.009791 0.000000) + 26: 1460.44 0.001447 7.31 0.000309 (-0.015194 0.008850 0.000000) + 27: 1460.55 0.001934 9.78 0.000413 ( 0.015248 0.013446 0.000000) + 28: 1599.79 0.000000 0.00 0.000000 (-0.000004 -0.000002 0.000000) + 29: 1599.80 0.000000 0.00 0.000000 ( 0.000003 0.000004 0.000000) + 30: 3068.19 0.001418 7.17 0.000144 (-0.006118 0.010335 0.000000) + 31: 3071.53 0.000000 0.00 0.000000 ( 0.000037 0.000103 0.000000) + 32: 3071.62 0.000000 0.00 0.000000 (-0.000058 0.000034 0.000000) + 33: 3083.57 0.053334 269.53 0.005398 (-0.034081 -0.065084 0.000000) + 34: 3083.65 0.014953 75.57 0.001513 (-0.036094 0.014509 0.000000) + 35: 3092.32 0.000000 0.00 0.000000 ( 0.000017 0.000020 0.000000) + +* The epsilon (eps) is given for a Dirac delta lineshape. +** The dipole moment derivative (T) already includes vibrational overlap. + +The first frequency considered to be a vibration is 6 +The total number of vibrations considered is 30 + + +-------------------------- +THERMOCHEMISTRY AT 298.15K +-------------------------- + +Temperature ... 298.15 K +Pressure ... 1.00 atm +Total Mass ... 78.11 AMU + +Throughout the following assumptions are being made: + (1) The electronic state is orbitally nondegenerate + (2) There are no thermally accessible electronically excited states + (3) Hindered rotations indicated by low frequency modes are not + treated as such but are treated as vibrations and this may + cause some error + (4) All equations used are the standard statistical mechanics + equations for an ideal gas + (5) All vibrations are strictly harmonic + +freq. 368.34 E(vib) ... 0.21 +freq. 368.35 E(vib) ... 0.21 +freq. 578.85 E(vib) ... 0.11 +freq. 578.86 E(vib) ... 0.11 +freq. 657.51 E(vib) ... 0.08 +freq. 692.59 E(vib) ... 0.07 +freq. 882.01 E(vib) ... 0.04 +freq. 882.03 E(vib) ... 0.04 +freq. 930.42 E(vib) ... 0.03 +freq. 930.44 E(vib) ... 0.03 +freq. 936.89 E(vib) ... 0.03 +freq. 956.87 E(vib) ... 0.03 +freq. 1066.82 E(vib) ... 0.02 +freq. 1090.46 E(vib) ... 0.02 +freq. 1090.47 E(vib) ... 0.02 +freq. 1176.03 E(vib) ... 0.01 +freq. 1198.27 E(vib) ... 0.01 +freq. 1198.31 E(vib) ... 0.01 +freq. 1304.23 E(vib) ... 0.01 +freq. 1319.65 E(vib) ... 0.01 +freq. 1460.44 E(vib) ... 0.00 +freq. 1460.55 E(vib) ... 0.00 +freq. 1599.79 E(vib) ... 0.00 +freq. 1599.80 E(vib) ... 0.00 +freq. 3068.19 E(vib) ... 0.00 +freq. 3071.53 E(vib) ... 0.00 +freq. 3071.62 E(vib) ... 0.00 +freq. 3083.57 E(vib) ... 0.00 +freq. 3083.65 E(vib) ... 0.00 +freq. 3092.32 E(vib) ... 0.00 + +------------ +INNER ENERGY +------------ + +The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans) + E(el) - is the total energy from the electronic structure calculation + = E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc) + E(ZPE) - the the zero temperature vibrational energy from the frequency calculation + E(vib) - the the finite temperature correction to E(ZPE) due to population + of excited vibrational states + E(rot) - is the rotational thermal energy + E(trans)- is the translational thermal energy + +Summary of contributions to the inner energy U: +Electronic energy ... -15.87964065 Eh +Zero point energy ... 0.09750303 Eh 61.18 kcal/mol +Thermal vibrational correction ... 0.00174764 Eh 1.10 kcal/mol +Thermal rotational correction ... 0.00141627 Eh 0.89 kcal/mol +Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol +----------------------------------------------------------------------- +Total thermal energy -15.77755744 Eh + + +Summary of corrections to the electronic energy: +(perhaps to be used in another calculation) +Total thermal correction 0.00458018 Eh 2.87 kcal/mol +Non-thermal (ZPE) correction 0.09750303 Eh 61.18 kcal/mol +----------------------------------------------------------------------- +Total correction 0.10208321 Eh 64.06 kcal/mol + + +-------- +ENTHALPY +-------- + +The enthalpy is H = U + kB*T + kB is Boltzmann's constant +Total free energy ... -15.77755744 Eh +Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol +----------------------------------------------------------------------- +Total Enthalpy ... -15.77661323 Eh + + +Note: Only C1 symmetry has been detected, increase convergence thresholds + if your molecule has a higher symmetry. Symmetry factor of 1.0 is + used for the rotational entropy correction. + + +Note: Rotational entropy computed according to Herzberg +Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945 +Point Group: C1, Symmetry Number: 1 +Rotational constants in cm-1: 0.192765 0.192759 0.096381 + +Vibrational entropy computed according to the QRRHO of S. Grimme +Chem.Eur.J. 2012 18 9955 + + +------- +ENTROPY +------- + +The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans)) + S(el) - electronic entropy + S(vib) - vibrational entropy + S(rot) - rotational entropy + S(trans)- translational entropy +The entropies will be listed as multiplied by the temperature to get +units of energy + +Electronic entropy ... 0.00000000 Eh 0.00 kcal/mol +Vibrational entropy ... 0.00239275 Eh 1.50 kcal/mol +Rotational entropy ... 0.01216964 Eh 7.64 kcal/mol +Translational entropy ... 0.01852142 Eh 11.62 kcal/mol +----------------------------------------------------------------------- +Final entropy term ... 0.03308382 Eh 20.76 kcal/mol + +In case the symmetry of your molecule has not been determined correctly +or in case you have a reason to use a different symmetry number we print +out the resulting rotational entropy values for sn=1,12 : + -------------------------------------------------------- +| sn= 1 | S(rot)= 0.01216964 Eh 7.64 kcal/mol| +| sn= 2 | S(rot)= 0.01151519 Eh 7.23 kcal/mol| +| sn= 3 | S(rot)= 0.01113235 Eh 6.99 kcal/mol| +| sn= 4 | S(rot)= 0.01086073 Eh 6.82 kcal/mol| +| sn= 5 | S(rot)= 0.01065004 Eh 6.68 kcal/mol| +| sn= 6 | S(rot)= 0.01047790 Eh 6.57 kcal/mol| +| sn= 7 | S(rot)= 0.01033235 Eh 6.48 kcal/mol| +| sn= 8 | S(rot)= 0.01020627 Eh 6.40 kcal/mol| +| sn= 9 | S(rot)= 0.01009507 Eh 6.33 kcal/mol| +| sn=10 | S(rot)= 0.00999559 Eh 6.27 kcal/mol| +| sn=11 | S(rot)= 0.00990560 Eh 6.22 kcal/mol| +| sn=12 | S(rot)= 0.00982344 Eh 6.16 kcal/mol| + -------------------------------------------------------- + + +------------------- +GIBBS FREE ENERGY +------------------- + +The Gibbs free energy is G = H - T*S + +Total enthalpy ... -15.77661323 Eh +Total entropy correction ... -0.03308382 Eh -20.76 kcal/mol +----------------------------------------------------------------------- +Final Gibbs free energy ... -15.80969705 Eh + +For completeness - the Gibbs free energy minus the electronic energy +G-E(el) ... 0.06994360 Eh 43.89 kcal/mol + + + +Timings for individual modules: + +Sum of individual times ... 123.425 sec (= 2.057 min) +Numerical frequency calculation ... 123.326 sec (= 2.055 min) 99.9 % +XTB module ... 0.099 sec (= 0.002 min) 0.1 % + ****ORCA TERMINATED NORMALLY**** +TOTAL RUN TIME: 0 days 0 hours 2 minutes 3 seconds 441 msec diff --git a/cmmde_gui/test/test/freq/cmmd.xtbrestart b/cmmde_gui/test/test/freq/cmmd.xtbrestart new file mode 100644 index 0000000000000000000000000000000000000000..3bb750154cb0d1085b2c9e8d4d20dde72b7858b2 GIT binary patch literal 1088 zcmXw%3rv$&7=~N!7l};dGU$*YL7BlZ+|XI%qn2yASjxSyNh@Jm9Cq342DTF@0%AmN zuImN~wG_&Lac?sejua{gB&&`{vr&W~jN1TZT!N79km*Ujy#I5~o0BL1|9cS#1Oq&K z>uv7)9|;HEr1P768(#RK1P^!Xc=Q2M2cislr~3%&VZE4Ku7V!R_lM9hRcr3E92wF);1@{%K zNi_xf9+HP=&M);?Dmw!qDh3hk45t+F9H?Wuq~xZ&^pkv4!AzcG!42z+K3?8wAk$Hc zE3cYBpD3%f=xI9G{!SX*Y@s09=Ch&X&UwGsuGRd8>KJGxHF#EMa8RxOShDIM0eSfO z-)>lEp{rZDW1;40DB;l%b*gixCnqC7T_RQi>10?e=Yj}H#&36hz@k9=7cLwhhX!~M 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THERMOCHEMISTRY_Energies + description: The Thermochemistry energies + geom. index: 0 + prop. index: 1 + Temperature (Kelvin) : 298.1500000000 + Pressure (atm) : 1.0000000000 + Total Mass (AMU) : 78.1140000000 + Spin Degeneracy : 1.0000000000 + Electronic Energy (Hartree) : -15.8796406525 + Translational Energy (Hartree) : 0.0014162714 + Rotational Energy (Hartree) : 0.0014162714 + Vibrational Energy (Hartree) : 0.0017476412 + Number of frequencies : 36 + Scaling Factor for frequencies : 1.0000000000 + Vibrational frequencies : + 0 + 0 0.000000 + 1 0.000000 + 2 0.000000 + 3 0.000000 + 4 0.000000 + 5 0.000000 + 6 368.336258 + 7 368.348959 + 8 578.848660 + 9 578.862438 + 10 657.506975 + 11 692.591921 + 12 882.009398 + 13 882.033619 + 14 930.417283 + 15 930.442016 + 16 936.893568 + 17 956.869360 + 18 1066.816359 + 19 1090.461880 + 20 1090.465889 + 21 1176.034406 + 22 1198.269618 + 23 1198.307442 + 24 1304.230477 + 25 1319.651918 + 26 1460.443190 + 27 1460.547052 + 28 1599.794493 + 29 1599.803615 + 30 3068.191339 + 31 3071.531989 + 32 3071.623795 + 33 3083.572705 + 34 3083.653376 + 35 3092.323321 + Zero Point Energy (Hartree) : 0.0975030306 + Inner Energy (Hartree) : -15.7775574379 + Enthalpy (Hartree) : -15.7766132289 + Electronic entropy : 0.0000000000 + Rotational entropy : 0.0121696430 + Vibrational entropy : 0.0023927545 + Translational entropy : 0.0121696430 + Entropy : 0.0330838193 + Gibbs Energy (Hartree) : -15.8096970482 + Is Linear : false +# ------------------------------------------------------------- +----------------------- !GEOMETRIES! ------------------------ +# ------------------------------------------------------------- diff --git a/cmmde_gui/test/test/freq/run.sh b/cmmde_gui/test/test/freq/run.sh new file mode 100644 index 0000000..f72e163 --- /dev/null +++ b/cmmde_gui/test/test/freq/run.sh @@ -0,0 +1,10 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH +export PATH=/home/adit/opt/openmpi411/bin:$PATH +export OMP_NUM_THREADS=1 +cd $PWD +$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe diff --git a/cmmde_gui/test/test/freq/slurm-2895.out b/cmmde_gui/test/test/freq/slurm-2895.out new file mode 100644 index 0000000..e69de29 diff --git a/cmmde_gui/test/test/geom.smi b/cmmde_gui/test/test/geom.smi new file mode 100644 index 0000000..17163bb --- /dev/null +++ b/cmmde_gui/test/test/geom.smi @@ -0,0 +1 @@ +c1ccccc1 diff --git a/cmmde_gui/test/test/geom.xyz b/cmmde_gui/test/test/geom.xyz new file mode 100644 index 0000000..d5cf7e8 --- /dev/null +++ b/cmmde_gui/test/test/geom.xyz @@ -0,0 +1,14 @@ +12 + +C 1.38268 -0.22177 0.00557 +C 0.50634 -1.30705 -0.00813 +C -0.87140 -1.09059 -0.01457 +C -1.37323 0.21091 -0.00446 +C -0.49683 1.29596 0.01058 +C 0.88099 1.07953 0.01412 +H 2.45620 -0.39044 0.00960 +H 0.89724 -2.32089 -0.01414 +H -1.55415 -1.93593 -0.02709 +H -2.44657 0.37942 -0.00833 +H -0.88769 2.31003 0.01913 +H 1.56377 1.92486 0.02373 diff --git a/cmmde_gui/test/test/run.sh b/cmmde_gui/test/test/run.sh new file mode 100644 index 0000000..f72e163 --- /dev/null +++ b/cmmde_gui/test/test/run.sh @@ -0,0 +1,10 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH +export PATH=/home/adit/opt/openmpi411/bin:$PATH +export OMP_NUM_THREADS=1 +cd $PWD +$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe diff --git a/cmmde_gui/test/test/run_babel.sh b/cmmde_gui/test/test/run_babel.sh new file mode 100644 index 0000000..0d5d00e --- /dev/null +++ b/cmmde_gui/test/test/run_babel.sh @@ -0,0 +1,8 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export OMP_NUM_THREADS=1 +cd $PWD +obabel geom.smi -O geom.xyz --gen3d diff --git a/cmmde_gui/test/test/slurm-2891.out b/cmmde_gui/test/test/slurm-2891.out new file mode 100644 index 0000000..b7d75ac --- /dev/null +++ b/cmmde_gui/test/test/slurm-2891.out @@ -0,0 +1 @@ +1 molecule converted diff --git a/cmmde_gui/test/test/slurm-2892.out b/cmmde_gui/test/test/slurm-2892.out new file mode 100644 index 0000000..e69de29 diff --git a/cmmde_gui/test/test/test/cmmd.engrad b/cmmde_gui/test/test/test/cmmd.engrad new file mode 100644 index 0000000..169b237 --- /dev/null +++ b/cmmde_gui/test/test/test/cmmd.engrad @@ -0,0 +1,62 @@ +# +# Number of atoms +# + 12 +# +# The current total energy in Eh +# + -15.879640652450 +# +# The current gradient in Eh/bohr +# + 0.000083151256 + 0.000032627904 + -0.000000801280 + -0.000011773444 + -0.000092719019 + -0.000008798638 + 0.000004092498 + -0.000045349095 + 0.000008265502 + -0.000095719643 + 0.000023986034 + -0.000000346361 + -0.000010542094 + 0.000056660251 + -0.000008827102 + 0.000027808309 + 0.000031909554 + 0.000010537622 + -0.000055844305 + -0.000000629739 + 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Lr*6M|v(or~Xz32? literal 0 HcmV?d00001 diff --git a/cmmde_gui/test/test/test/cmmd.in b/cmmde_gui/test/test/test/cmmd.in new file mode 100644 index 0000000..f93f575 --- /dev/null +++ b/cmmde_gui/test/test/test/cmmd.in @@ -0,0 +1,11 @@ +#CMMDE generated Orca input file +!XTB2 opt +%pal + nprocs 1 +end +%geom + maxiter 9999 +end + +*xyzfile 0 1 geom.xyz + diff --git a/cmmde_gui/test/test/test/cmmd.opt b/cmmde_gui/test/test/test/cmmd.opt new file mode 100644 index 0000000..9c9c252 --- /dev/null +++ b/cmmde_gui/test/test/test/cmmd.opt @@ -0,0 +1,789 @@ + +$orca_opt_file + +$trust + 0.300000000000 + +$epredict + 0.000000000000 + +$ediffsc + 1000.000000000000 + +$ctyp + 3 + +$coordinates + 3 36 + 2.61288653 -0.41908456 0.01052577 0.95684393 -2.46996654 -0.01536347 + -1.64670735 -2.06091642 -0.02753331 -2.59502862 0.39856214 -0.00842818 + -0.93887264 2.44900948 0.01999330 1.66482983 2.04001605 0.02668293 + 4.64154533 -0.73782467 0.01814137 1.69553788 -4.38584649 -0.02672073 + -2.93691787 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+ ########, + ,,################,,,,, + ,,#################################,, + ,,##########################################,, + ,#########################################, ''#####, + ,#############################################,, '####, + ,##################################################,,,,####, + ,###########'''' ''''############################### + ,#####'' ,,,,##########,,,, '''####''' '#### + ,##' ,,,,###########################,,, '## + ' ,,###'''' '''############,,, + ,,##'' '''############,,,, ,,,,,,###'' + ,#'' '''#######################''' + ' ''''####'''' + ,#######, #######, ,#######, ## + ,#' '#, ## ## ,#' '#, #''# ###### ,####, + ## ## ## ,#' ## #' '# # #' '# + ## ## ####### ## ,######, #####, # # + '#, ,#' ## ## '#, ,#' ,# #, ## #, ,# + '#######' ## ## '#######' #' '# #####' # '####' + + + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship and core code : Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 5.0.2 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Marcus Kettner : VPT2 + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : Initial AUTO-CI + Lucas Lang : DCDCAS + Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, + C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT + MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, + LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, + nearIR, NL-DFT gradient (VV10), updates on ESD, + ML-optimized integration grids + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + Liviu Ungur et al : ANISO software + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 5.1.0 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + Shared memory : Shared parallel matrices + BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED + Core in use : SkylakeX + Copyright (c) 2011-2014, The OpenBLAS Project + + + + +*************************************** +The coordinates will be read from file: geom.xyz +*************************************** + + +Your calculation utilizes the semiempirical GFN2-xTB method +Please cite in your paper: +C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. + + +================================================================================ + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + + +WARNING: Geometry Optimization + ===> : Switching off AutoStart + For restart on a previous wavefunction, please use MOREAD + +WARNING: Found dipole moment calculation with XTB calculation + ===> : Switching off dipole moment calculation + + +WARNING: TRAH-SCF for XTB is not implemented! + ===> : Turning TRAH off! + +================================================================================ + INPUT FILE +================================================================================ +NAME = cmmd.in +| 1> #CMMDE generated Orca input file +| 2> !XTB2 opt +| 3> %pal +| 4> nprocs 1 +| 5> end +| 6> %geom +| 7> maxiter 9999 +| 8> end +| 9> +| 10> *xyzfile 0 1 geom.xyz +| 11> +| 12> +| 13> ****END OF INPUT**** +================================================================================ + + ***************************** + * Geometry Optimization Run * + ***************************** + +Geometry optimization settings: +Update method Update .... BFGS +Choice of coordinates CoordSys .... Z-matrix Internals +Initial Hessian InHess .... Almoef's Model + +Convergence Tolerances: +Energy Change TolE .... 5.0000e-06 Eh +Max. Gradient TolMAXG .... 3.0000e-04 Eh/bohr +RMS Gradient TolRMSG .... 1.0000e-04 Eh/bohr +Max. Displacement TolMAXD .... 4.0000e-03 bohr +RMS Displacement TolRMSD .... 2.0000e-03 bohr +Strict Convergence .... False +------------------------------------------------------------------------------ + ORCA OPTIMIZATION COORDINATE SETUP +------------------------------------------------------------------------------ + +The optimization will be done in new redundant internal coordinates +Making redundant internal coordinates ... (new redundants) done +Evaluating the initial hessian ... (Almloef) done +Evaluating the coordinates ... done +Calculating the B-matrix .... done +Calculating the G-matrix .... done +Diagonalizing the G-matrix .... done +The first mode is .... 24 +The number of degrees of freedom .... 30 + + ----------------------------------------------------------------- + Redundant Internal Coordinates + + + ----------------------------------------------------------------- + Definition Initial Value Approx d2E/dq + ----------------------------------------------------------------- + 1. B(C 1,C 0) 1.3950 0.613451 + 2. B(C 2,C 1) 1.3947 0.614202 + 3. B(C 3,C 2) 1.3949 0.613576 + 4. B(C 4,C 3) 1.3949 0.613739 + 5. B(C 5,C 4) 1.3947 0.614057 + 6. B(C 5,C 0) 1.3947 0.614134 + 7. B(H 6,C 0) 1.0867 0.364496 + 8. B(H 7,C 1) 1.0866 0.364619 + 9. B(H 8,C 2) 1.0867 0.364500 + 10. B(H 9,C 3) 1.0865 0.364768 + 11. B(H 10,C 4) 1.0868 0.364328 + 12. B(H 11,C 5) 1.0867 0.364525 + 13. A(C 1,C 0,C 5) 119.9985 0.432498 + 14. A(C 1,C 0,H 6) 119.9915 0.352999 + 15. A(C 5,C 0,H 6) 120.0100 0.353066 + 16. A(C 2,C 1,H 7) 120.0112 0.353093 + 17. A(C 0,C 1,C 2) 119.9923 0.432506 + 18. A(C 0,C 1,H 7) 119.9965 0.353020 + 19. A(C 3,C 2,H 8) 119.9904 0.353012 + 20. A(C 1,C 2,H 8) 119.9986 0.353073 + 21. A(C 1,C 2,C 3) 120.0110 0.432522 + 22. A(C 4,C 3,H 9) 120.0060 0.353072 + 23. A(C 2,C 3,H 9) 120.0051 0.353056 + 24. A(C 2,C 3,C 4) 119.9889 0.432464 + 25. A(C 3,C 4,H 10) 119.9962 0.353000 + 26. A(C 3,C 4,C 5) 120.0006 0.432525 + 27. A(C 5,C 4,H 10) 120.0032 0.353031 + 28. A(C 0,C 5,C 4) 120.0085 0.432575 + 29. A(C 4,C 5,H 11) 120.0010 0.353063 + 30. A(C 0,C 5,H 11) 119.9904 0.353071 + 31. D(H 7,C 1,C 0,C 5) -179.9604 0.026008 + 32. D(H 7,C 1,C 0,H 6) 0.0383 0.026008 + 33. D(C 2,C 1,C 0,H 6) -179.9399 0.026008 + 34. D(C 2,C 1,C 0,C 5) 0.0614 0.026008 + 35. D(H 8,C 2,C 1,C 0) 179.8875 0.026075 + 36. D(C 3,C 2,C 1,C 0) -0.1354 0.026075 + 37. D(C 3,C 2,C 1,H 7) 179.8864 0.026075 + 38. D(H 8,C 2,C 1,H 7) -0.0907 0.026075 + 39. D(H 9,C 3,C 2,H 8) 0.0470 0.026019 + 40. D(H 9,C 3,C 2,C 1) -179.9301 0.026019 + 41. D(C 4,C 3,C 2,H 8) -179.9511 0.026019 + 42. D(C 4,C 3,C 2,C 1) 0.0718 0.026019 + 43. D(H 10,C 4,C 3,C 2) -179.9591 0.026033 + 44. D(C 5,C 4,C 3,H 9) -179.9323 0.026033 + 45. D(C 5,C 4,C 3,C 2) 0.0658 0.026033 + 46. D(H 10,C 4,C 3,H 9) 0.0427 0.026033 + 47. D(H 11,C 5,C 4,H 10) -0.1033 0.026062 + 48. D(C 0,C 5,C 4,H 10) 179.8851 0.026062 + 49. D(C 0,C 5,C 4,C 3) -0.1398 0.026062 + 50. D(H 11,C 5,C 0,H 6) 0.0659 0.026069 + 51. D(H 11,C 5,C 0,C 1) -179.9354 0.026069 + 52. D(H 11,C 5,C 4,C 3) 179.8717 0.026062 + 53. D(C 4,C 5,C 0,H 6) -179.9225 0.026069 + 54. D(C 4,C 5,C 0,C 1) 0.0762 0.026069 + ----------------------------------------------------------------- + +Number of atoms .... 12 +Number of degrees of freedom .... 54 + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 1 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.382680 -0.221770 0.005570 + C 0.506340 -1.307050 -0.008130 + C -0.871400 -1.090590 -0.014570 + C -1.373230 0.210910 -0.004460 + C -0.496830 1.295960 0.010580 + C 0.880990 1.079530 0.014120 + H 2.456200 -0.390440 0.009600 + H 0.897240 -2.320890 -0.014140 + H -1.554150 -1.935930 -0.027090 + H -2.446570 0.379420 -0.008330 + H -0.887690 2.310030 0.019130 + H 1.563770 1.924860 0.023730 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.612887 -0.419085 0.010526 + 1 C 6.0000 0 12.011 0.956844 -2.469967 -0.015363 + 2 C 6.0000 0 12.011 -1.646707 -2.060916 -0.027533 + 3 C 6.0000 0 12.011 -2.595029 0.398562 -0.008428 + 4 C 6.0000 0 12.011 -0.938873 2.449009 0.019993 + 5 C 6.0000 0 12.011 1.664830 2.040016 0.026683 + 6 H 1.0000 0 1.008 4.641545 -0.737825 0.018141 + 7 H 1.0000 0 1.008 1.695538 -4.385846 -0.026721 + 8 H 1.0000 0 1.008 -2.936918 -3.658378 -0.051193 + 9 H 1.0000 0 1.008 -4.623347 0.717000 -0.015741 + 10 H 1.0000 0 1.008 -1.677491 4.365324 0.036150 + 11 H 1.0000 0 1.008 2.955097 3.637458 0.044843 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 19:28:31.922 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 12 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.44737554337715 + + ID Z sym. atoms + 1 6 C 1-6 + 2 1 H 7-12 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 18 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.1615201 -0.161615E+02 0.494E+00 4.84 0.0 T + 2 -16.1767145 -0.151944E-01 0.296E+00 4.83 1.0 T + 3 -16.1770942 -0.379688E-03 0.492E-01 4.83 1.0 T + 4 -16.1774041 -0.309971E-03 0.515E-02 4.82 1.0 T + 5 -16.1774041 0.174099E-07 0.659E-03 4.82 4.4 T + 6 -16.1774041 -0.309461E-07 0.180E-03 4.82 16.0 T + 7 -16.1774042 -0.311983E-07 0.588E-04 4.82 49.1 T + 8 -16.1774042 0.808171E-10 0.178E-04 4.82 162.4 T + + *** convergence criteria satisfied after 8 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6387825 -17.3822 + ... ... ... ... + 9 2.0000 -0.4756453 -12.9430 + 10 2.0000 -0.4756384 -12.9428 + 11 2.0000 -0.4718343 -12.8393 + 12 2.0000 -0.4219300 -11.4813 + 13 2.0000 -0.4218886 -11.4802 + 14 2.0000 -0.4009568 -10.9106 + 15 2.0000 -0.4009234 -10.9097 (HOMO) + 16 -0.2236200 -6.0850 (LUMO) + 17 -0.2235509 -6.0831 + 18 -0.0961178 -2.6155 + 19 0.1107873 3.0147 + 20 0.1226310 3.3370 + ... ... ... + 30 0.6433999 17.5078 + ------------------------------------------------------------- + HL-Gap 0.1773034 Eh 4.8247 eV + Fermi-level -0.3122717 Eh -8.4973 eV + + SCC (total) 0 d, 0 h, 0 min, 0.033 sec + SCC setup ... 0 min, 0.000 sec ( 0.561%) + Dispersion ... 0 min, 0.000 sec ( 0.271%) + classical contributions ... 0 min, 0.000 sec ( 0.138%) + integral evaluation ... 0 min, 0.002 sec ( 5.498%) + iterations ... 0 min, 0.026 sec ( 79.290%) + molecular gradient ... 0 min, 0.004 sec ( 13.577%) + printout ... 0 min, 0.000 sec ( 0.624%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.878848475482 Eh :: + :: gradient norm 0.019149425975 Eh/a0 :: + :: HOMO-LUMO gap 4.824670438233 eV :: + ::.................................................:: + :: SCC energy -16.177404175194 Eh :: + :: -> isotropic ES 0.000752368509 Eh :: + :: -> anisotropic ES 0.002689473865 Eh :: + :: -> anisotropic XC 0.013008868445 Eh :: + :: -> dispersion -0.007987832843 Eh :: + :: repulsion energy 0.298548672022 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.878848475482 Eh | + | GRADIENT NORM 0.019149425975 Eh/α | + | HOMO-LUMO GAP 4.824670438233 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 19:28:31.968 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.046 sec + * cpu-time: 0 d, 0 h, 0 min, 0.026 sec + * ratio c/w: 0.555 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.033 sec + * cpu-time: 0 d, 0 h, 0 min, 0.013 sec + * ratio c/w: 0.378 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.878848475480 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 12 +Number of internal coordinates .... 54 +Current Energy .... -15.878848475 Eh +Current gradient norm .... 0.019149426 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Evaluating the initial hessian .... (Almloef) done +Projecting the Hessian .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.998622698 +Lowest eigenvalues of augmented Hessian: + -0.001470266 0.026024439 0.026025966 0.026033561 0.026041952 +Length of the computed step .... 0.052538613 +The final length of the internal step .... 0.052538613 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0071495997 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0141313345 RMS(Int)= 0.0071497568 + Iter 1: RMS(Cart)= 0.0000052351 RMS(Int)= 0.0000037874 + Iter 2: RMS(Cart)= 0.0000000333 RMS(Int)= 0.0000000244 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + RMS gradient 0.0039083086 0.0001000000 NO + MAX gradient 0.0109681387 0.0003000000 NO + RMS step 0.0071495997 0.0020000000 NO + MAX step 0.0178357525 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0094 Max(Angles) 0.00 + Max(Dihed) 0.10 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.3950 0.010968 -0.0094 1.3855 + 2. B(C 2,C 1) 1.3947 0.010773 -0.0093 1.3854 + 3. B(C 3,C 2) 1.3949 0.010938 -0.0094 1.3855 + 4. B(C 4,C 3) 1.3949 0.010920 -0.0094 1.3855 + 5. B(C 5,C 4) 1.3947 0.010783 -0.0093 1.3855 + 6. B(C 5,C 0) 1.3947 0.010796 -0.0093 1.3854 + 7. B(H 6,C 0) 1.0867 0.004434 -0.0064 1.0803 + 8. B(H 7,C 1) 1.0866 0.004380 -0.0063 1.0803 + 9. B(H 8,C 2) 1.0867 0.004421 -0.0064 1.0803 + 10. B(H 9,C 3) 1.0865 0.004318 -0.0062 1.0803 + 11. B(H 10,C 4) 1.0868 0.004506 -0.0065 1.0803 + 12. B(H 11,C 5) 1.0867 0.004409 -0.0064 1.0803 + 13. A(C 1,C 0,C 5) 120.00 0.000006 -0.00 120.00 + 14. A(C 1,C 0,H 6) 119.99 -0.000013 0.00 119.99 + 15. A(C 5,C 0,H 6) 120.01 0.000007 -0.00 120.01 + 16. A(C 2,C 1,H 7) 120.01 0.000017 -0.00 120.01 + 17. A(C 0,C 1,C 2) 119.99 -0.000022 0.00 120.00 + 18. A(C 0,C 1,H 7) 120.00 0.000005 -0.00 120.00 + 19. A(C 3,C 2,H 8) 119.99 -0.000005 0.00 119.99 + 20. A(C 1,C 2,H 8) 120.00 -0.000008 0.00 120.00 + 21. A(C 1,C 2,C 3) 120.01 0.000013 -0.00 120.01 + 22. A(C 4,C 3,H 9) 120.01 0.000010 -0.00 120.00 + 23. A(C 2,C 3,H 9) 120.01 0.000016 -0.00 120.00 + 24. A(C 2,C 3,C 4) 119.99 -0.000026 0.00 119.99 + 25. A(C 3,C 4,H 10) 120.00 -0.000002 0.00 120.00 + 26. A(C 3,C 4,C 5) 120.00 -0.000002 0.00 120.00 + 27. A(C 5,C 4,H 10) 120.00 0.000004 -0.00 120.00 + 28. A(C 0,C 5,C 4) 120.01 0.000030 -0.00 120.00 + 29. A(C 4,C 5,H 11) 120.00 -0.000005 0.00 120.00 + 30. A(C 0,C 5,H 11) 119.99 -0.000026 0.00 119.99 + 31. D(H 7,C 1,C 0,C 5) -179.96 0.000006 -0.01 -179.97 + 32. D(H 7,C 1,C 0,H 6) 0.04 0.000007 -0.01 0.02 + 33. D(C 2,C 1,C 0,H 6) -179.94 0.000021 -0.04 -179.98 + 34. D(C 2,C 1,C 0,C 5) 0.06 0.000020 -0.04 0.02 + 35. D(H 8,C 2,C 1,C 0) 179.89 -0.000030 0.06 179.95 + 36. D(C 3,C 2,C 1,C 0) -0.14 -0.000045 0.09 -0.04 + 37. D(C 3,C 2,C 1,H 7) 179.89 -0.000031 0.06 179.95 + 38. D(H 8,C 2,C 1,H 7) -0.09 -0.000016 0.03 -0.06 + 39. D(H 9,C 3,C 2,H 8) 0.05 0.000008 -0.02 0.03 + 40. D(H 9,C 3,C 2,C 1) -179.93 0.000023 -0.05 -179.98 + 41. D(C 4,C 3,C 2,H 8) -179.95 0.000008 -0.02 -179.97 + 42. D(C 4,C 3,C 2,C 1) 0.07 0.000024 -0.05 0.02 + 43. D(H 10,C 4,C 3,C 2) -179.96 0.000006 -0.01 -179.97 + 44. D(C 5,C 4,C 3,H 9) -179.93 0.000024 -0.05 -179.98 + 45. D(C 5,C 4,C 3,C 2) 0.07 0.000023 -0.05 0.02 + 46. D(H 10,C 4,C 3,H 9) 0.04 0.000007 -0.01 0.03 + 47. D(H 11,C 5,C 4,H 10) -0.10 -0.000019 0.04 -0.06 + 48. D(C 0,C 5,C 4,H 10) 179.89 -0.000031 0.06 179.95 + 49. D(C 0,C 5,C 4,C 3) -0.14 -0.000048 0.10 -0.04 + 50. D(H 11,C 5,C 0,H 6) 0.07 0.000014 -0.03 0.04 + 51. D(H 11,C 5,C 0,C 1) -179.94 0.000014 -0.03 -179.97 + 52. D(H 11,C 5,C 4,C 3) 179.87 -0.000036 0.07 179.95 + 53. D(C 4,C 5,C 0,H 6) -179.92 0.000025 -0.05 -179.97 + 54. D(C 4,C 5,C 0,C 1) 0.08 0.000026 -0.05 0.02 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 2 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.373483 -0.220370 0.005486 + C 0.503034 -1.298271 -0.008552 + C -0.865566 -1.083277 -0.013955 + C -1.363971 0.209460 -0.004455 + C -0.493502 1.287234 0.009972 + C 0.875165 1.072283 0.014515 + H 2.440669 -0.388048 0.009436 + H 0.891632 -2.306209 -0.015155 + H -1.544313 -1.923643 -0.025717 + H -2.431149 0.376991 -0.008298 + H -0.882040 2.295219 0.017842 + H 1.553908 1.912671 0.024891 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.595506 -0.416438 0.010368 + 1 C 6.0000 0 12.011 0.950597 -2.453376 -0.016162 + 2 C 6.0000 0 12.011 -1.635683 -2.047097 -0.026371 + 3 C 6.0000 0 12.011 -2.577532 0.395823 -0.008418 + 4 C 6.0000 0 12.011 -0.932584 2.432519 0.018844 + 5 C 6.0000 0 12.011 1.653822 2.026321 0.027429 + 6 H 1.0000 0 1.008 4.612197 -0.733305 0.017832 + 7 H 1.0000 0 1.008 1.684939 -4.358103 -0.028638 + 8 H 1.0000 0 1.008 -2.918328 -3.635159 -0.048599 + 9 H 1.0000 0 1.008 -4.594205 0.712411 -0.015681 + 10 H 1.0000 0 1.008 -1.666814 4.337335 0.033716 + 11 H 1.0000 0 1.008 2.936460 3.614423 0.047037 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 19:28:32.027 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 12 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.45328135573027 + + ID Z sym. atoms + 1 6 C 1-6 + 2 1 H 7-12 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 18 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.1955129 -0.161955E+02 0.125E-01 4.92 0.0 T + 2 -16.1955133 -0.403352E-06 0.742E-02 4.92 1.0 T + 3 -16.1955134 -0.164805E-06 0.315E-03 4.92 9.2 T + 4 -16.1955134 -0.155953E-08 0.132E-03 4.92 21.9 T + 5 -16.1955134 -0.140488E-08 0.609E-04 4.92 47.4 T + 6 -16.1955134 -0.245915E-08 0.596E-05 4.92 484.2 T + + *** convergence criteria satisfied after 6 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6413965 -17.4533 + ... ... ... ... + 9 2.0000 -0.4762976 -12.9607 + 10 2.0000 -0.4762924 -12.9606 + 11 2.0000 -0.4744819 -12.9113 + 12 2.0000 -0.4214505 -11.4683 + 13 2.0000 -0.4214244 -11.4675 + 14 2.0000 -0.4023732 -10.9491 + 15 2.0000 -0.4023625 -10.9488 (HOMO) + 16 -0.2213940 -6.0244 (LUMO) + 17 -0.2213674 -6.0237 + 18 -0.0904365 -2.4609 + 19 0.1184369 3.2228 + 20 0.1371976 3.7333 + ... ... ... + 30 0.6721149 18.2892 + ------------------------------------------------------------- + HL-Gap 0.1809685 Eh 4.9244 eV + Fermi-level -0.3118783 Eh -8.4866 eV + + SCC (total) 0 d, 0 h, 0 min, 0.012 sec + SCC setup ... 0 min, 0.000 sec ( 1.666%) + Dispersion ... 0 min, 0.000 sec ( 0.841%) + classical contributions ... 0 min, 0.000 sec ( 0.310%) + integral evaluation ... 0 min, 0.002 sec ( 16.700%) + iterations ... 0 min, 0.006 sec ( 45.262%) + molecular gradient ... 0 min, 0.004 sec ( 33.743%) + printout ... 0 min, 0.000 sec ( 1.303%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.879635904823 Eh :: + :: gradient norm 0.002431966060 Eh/a0 :: + :: HOMO-LUMO gap 4.924403565589 eV :: + ::.................................................:: + :: SCC energy -16.195513428874 Eh :: + :: -> isotropic ES 0.000795412668 Eh :: + :: -> anisotropic ES 0.002526209138 Eh :: + :: -> anisotropic XC 0.012416937729 Eh :: + :: -> dispersion -0.008017088770 Eh :: + :: repulsion energy 0.315870723599 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.879635904823 Eh | + | GRADIENT NORM 0.002431966060 Eh/α | + | HOMO-LUMO GAP 4.924403565589 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 19:28:32.053 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.025 sec + * cpu-time: 0 d, 0 h, 0 min, 0.024 sec + * ratio c/w: 0.965 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.012 sec + * cpu-time: 0 d, 0 h, 0 min, 0.012 sec + * ratio c/w: 0.944 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.879635904820 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 12 +Number of internal coordinates .... 54 +Current Energy .... -15.879635905 Eh +Current gradient norm .... 0.002431966 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999990087 +Lowest eigenvalues of augmented Hessian: + -0.000009204 0.026024381 0.026025797 0.026033356 0.026041404 +Length of the computed step .... 0.004452581 +The final length of the internal step .... 0.004452581 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0006059195 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0009627615 RMS(Int)= 0.0006059190 + Iter 1: RMS(Cart)= 0.0000000996 RMS(Int)= 0.0000001111 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0007874293 0.0000050000 NO + RMS gradient 0.0003080612 0.0001000000 NO + MAX gradient 0.0009650443 0.0003000000 NO + RMS step 0.0006059195 0.0020000000 YES + MAX step 0.0017122026 0.0040000000 YES + ........................................................ + Max(Bonds) 0.0009 Max(Angles) 0.00 + Max(Dihed) 0.03 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.3855 0.000965 -0.0009 1.3846 + 2. B(C 2,C 1) 1.3854 0.000884 -0.0008 1.3846 + 3. B(C 3,C 2) 1.3855 0.000952 -0.0009 1.3846 + 4. B(C 4,C 3) 1.3855 0.000928 -0.0009 1.3846 + 5. B(C 5,C 4) 1.3855 0.000905 -0.0008 1.3846 + 6. B(C 5,C 0) 1.3854 0.000890 -0.0008 1.3846 + 7. B(H 6,C 0) 1.0803 -0.000065 0.0001 1.0804 + 8. B(H 7,C 1) 1.0803 -0.000072 0.0001 1.0804 + 9. B(H 8,C 2) 1.0803 -0.000064 0.0001 1.0804 + 10. B(H 9,C 3) 1.0803 -0.000080 0.0001 1.0804 + 11. B(H 10,C 4) 1.0803 -0.000057 0.0001 1.0804 + 12. B(H 11,C 5) 1.0803 -0.000062 0.0001 1.0804 + 13. A(C 1,C 0,C 5) 120.00 -0.000003 0.00 120.00 + 14. A(C 1,C 0,H 6) 119.99 -0.000010 0.00 120.00 + 15. A(C 5,C 0,H 6) 120.01 0.000013 -0.00 120.01 + 16. A(C 2,C 1,H 7) 120.01 0.000017 -0.00 120.01 + 17. A(C 0,C 1,C 2) 120.00 -0.000014 0.00 120.00 + 18. A(C 0,C 1,H 7) 120.00 -0.000003 0.00 120.00 + 19. A(C 3,C 2,H 8) 119.99 -0.000015 0.00 119.99 + 20. A(C 1,C 2,H 8) 120.00 -0.000005 0.00 120.00 + 21. A(C 1,C 2,C 3) 120.01 0.000020 -0.00 120.01 + 22. A(C 4,C 3,H 9) 120.00 0.000010 -0.00 120.00 + 23. A(C 2,C 3,H 9) 120.00 0.000013 -0.00 120.00 + 24. A(C 2,C 3,C 4) 119.99 -0.000023 0.00 120.00 + 25. A(C 3,C 4,H 10) 120.00 -0.000009 0.00 120.00 + 26. A(C 3,C 4,C 5) 120.00 0.000004 -0.00 120.00 + 27. A(C 5,C 4,H 10) 120.00 0.000005 -0.00 120.00 + 28. A(C 0,C 5,C 4) 120.00 0.000016 -0.00 120.00 + 29. A(C 4,C 5,H 11) 120.00 0.000001 -0.00 120.00 + 30. A(C 0,C 5,H 11) 119.99 -0.000017 0.00 120.00 + 31. D(H 7,C 1,C 0,C 5) -179.97 0.000006 -0.01 -179.99 + 32. D(H 7,C 1,C 0,H 6) 0.02 0.000006 -0.01 0.01 + 33. D(C 2,C 1,C 0,H 6) -179.98 0.000005 -0.01 -180.00 + 34. D(C 2,C 1,C 0,C 5) 0.02 0.000006 -0.01 0.01 + 35. D(H 8,C 2,C 1,C 0) 179.95 -0.000013 0.03 179.98 + 36. D(C 3,C 2,C 1,C 0) -0.04 -0.000012 0.03 -0.01 + 37. D(C 3,C 2,C 1,H 7) 179.95 -0.000013 0.03 179.98 + 38. D(H 8,C 2,C 1,H 7) -0.06 -0.000013 0.03 -0.03 + 39. D(H 9,C 3,C 2,H 8) 0.03 0.000007 -0.02 0.01 + 40. D(H 9,C 3,C 2,C 1) -179.98 0.000007 -0.02 -179.99 + 41. D(C 4,C 3,C 2,H 8) -179.97 0.000007 -0.02 -179.99 + 42. D(C 4,C 3,C 2,C 1) 0.02 0.000007 -0.02 0.01 + 43. D(H 10,C 4,C 3,C 2) -179.97 0.000006 -0.02 -179.99 + 44. D(C 5,C 4,C 3,H 9) -179.98 0.000006 -0.01 -180.00 + 45. D(C 5,C 4,C 3,C 2) 0.02 0.000006 -0.01 0.00 + 46. D(H 10,C 4,C 3,H 9) 0.03 0.000007 -0.02 0.01 + 47. D(H 11,C 5,C 4,H 10) -0.06 -0.000015 0.03 -0.03 + 48. D(C 0,C 5,C 4,H 10) 179.95 -0.000013 0.03 179.98 + 49. D(C 0,C 5,C 4,C 3) -0.04 -0.000012 0.03 -0.01 + 50. D(H 11,C 5,C 0,H 6) 0.04 0.000009 -0.02 0.02 + 51. D(H 11,C 5,C 0,C 1) -179.97 0.000008 -0.02 -179.98 + 52. D(H 11,C 5,C 4,C 3) 179.95 -0.000014 0.03 179.98 + 53. D(C 4,C 5,C 0,H 6) -179.97 0.000007 -0.02 -179.99 + 54. D(C 4,C 5,C 0,C 1) 0.02 0.000007 -0.02 0.01 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 3 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.372627 -0.220257 0.005473 + C 0.502734 -1.297441 -0.008692 + C -0.865051 -1.082610 -0.013787 + C -1.363089 0.209312 -0.004461 + C -0.493192 1.286428 0.009814 + C 0.874638 1.071627 0.014658 + H 2.439905 -0.387931 0.009379 + H 0.891345 -2.305478 -0.015658 + H -1.543848 -1.923054 -0.025162 + H -2.430378 0.376863 -0.008322 + H -0.881754 2.294490 0.017304 + H 1.553413 1.912091 0.025463 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.593889 -0.416225 0.010342 + 1 C 6.0000 0 12.011 0.950030 -2.451808 -0.016426 + 2 C 6.0000 0 12.011 -1.634710 -2.045836 -0.026054 + 3 C 6.0000 0 12.011 -2.575864 0.395542 -0.008430 + 4 C 6.0000 0 12.011 -0.931998 2.430997 0.018545 + 5 C 6.0000 0 12.011 1.652826 2.025081 0.027700 + 6 H 1.0000 0 1.008 4.610753 -0.733083 0.017724 + 7 H 1.0000 0 1.008 1.684398 -4.356723 -0.029589 + 8 H 1.0000 0 1.008 -2.917450 -3.634045 -0.047548 + 9 H 1.0000 0 1.008 -4.592749 0.712168 -0.015726 + 10 H 1.0000 0 1.008 -1.666273 4.335957 0.032700 + 11 H 1.0000 0 1.008 2.935525 3.613329 0.048118 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 19:28:32.111 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 12 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.20220677144916 + + ID Z sym. atoms + 1 6 C 1-6 + 2 1 H 7-12 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 18 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.1966048 -0.161966E+02 0.940E-03 4.93 0.0 T + 2 -16.1966048 -0.207695E-07 0.559E-03 4.93 5.2 T + 3 -16.1966048 -0.612392E-09 0.508E-04 4.93 56.8 T + 4 -16.1966048 -0.514106E-09 0.150E-04 4.93 192.2 T + + *** convergence criteria satisfied after 4 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6416541 -17.4603 + ... ... ... ... + 9 2.0000 -0.4763535 -12.9622 + 10 2.0000 -0.4763484 -12.9621 + 11 2.0000 -0.4747520 -12.9187 + 12 2.0000 -0.4214048 -11.4670 + 13 2.0000 -0.4213893 -11.4666 + 14 2.0000 -0.4025242 -10.9532 + 15 2.0000 -0.4025215 -10.9532 (HOMO) + 16 -0.2212009 -6.0192 (LUMO) + 17 -0.2211879 -6.0188 + 18 -0.0899223 -2.4469 + 19 0.1181313 3.2145 + 20 0.1377925 3.7495 + ... ... ... + 30 0.6741822 18.3454 + ------------------------------------------------------------- + HL-Gap 0.1813206 Eh 4.9340 eV + Fermi-level -0.3118612 Eh -8.4862 eV + + SCC (total) 0 d, 0 h, 0 min, 0.011 sec + SCC setup ... 0 min, 0.000 sec ( 1.713%) + Dispersion ... 0 min, 0.000 sec ( 0.811%) + classical contributions ... 0 min, 0.000 sec ( 0.271%) + integral evaluation ... 0 min, 0.002 sec ( 18.813%) + iterations ... 0 min, 0.004 sec ( 38.743%) + molecular gradient ... 0 min, 0.004 sec ( 37.989%) + printout ... 0 min, 0.000 sec ( 1.536%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.879640611397 Eh :: + :: gradient norm 0.000229130871 Eh/a0 :: + :: HOMO-LUMO gap 4.933984539935 eV :: + ::.................................................:: + :: SCC energy -16.196604837071 Eh :: + :: -> isotropic ES 0.000792285296 Eh :: + :: -> anisotropic ES 0.002517056106 Eh :: + :: -> anisotropic XC 0.012386338819 Eh :: + :: -> dispersion -0.008019545150 Eh :: + :: repulsion energy 0.316957441898 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.879640611397 Eh | + | GRADIENT NORM 0.000229130871 Eh/α | + | HOMO-LUMO GAP 4.933984539935 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 19:28:32.137 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.026 sec + * cpu-time: 0 d, 0 h, 0 min, 0.026 sec + * ratio c/w: 0.979 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.012 sec + * cpu-time: 0 d, 0 h, 0 min, 0.011 sec + * ratio c/w: 0.954 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.879640611400 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 12 +Number of internal coordinates .... 54 +Current Energy .... -15.879640611 Eh +Current gradient norm .... 0.000229131 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999999659 +Lowest eigenvalues of augmented Hessian: + -0.000000069 0.025858500 0.026024548 0.026026832 0.026034093 +Length of the computed step .... 0.000825581 +The final length of the internal step .... 0.000825581 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0001123473 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0001364097 RMS(Int)= 0.0001123433 + Iter 1: RMS(Cart)= 0.0000000115 RMS(Int)= 0.0000000096 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0000047066 0.0000050000 YES + RMS gradient 0.0000197543 0.0001000000 YES + MAX gradient 0.0000576598 0.0003000000 YES + RMS step 0.0001123473 0.0020000000 YES + MAX step 0.0002850650 0.0040000000 YES + ........................................................ + Max(Bonds) 0.0001 Max(Angles) 0.00 + Max(Dihed) 0.02 Max(Improp) 0.00 + --------------------------------------------------------------------- + + ***********************HURRAY******************** + *** THE OPTIMIZATION HAS CONVERGED *** + ************************************************* + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + + --- Optimized Parameters --- + (Angstroem and degrees) + + Definition OldVal dE/dq Step FinalVal + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.3846 0.000030 -0.0000 1.3846 + 2. B(C 2,C 1) 1.3846 -0.000006 -0.0000 1.3846 + 3. B(C 3,C 2) 1.3846 0.000022 -0.0000 1.3846 + 4. B(C 4,C 3) 1.3846 0.000009 -0.0000 1.3846 + 5. B(C 5,C 4) 1.3846 0.000010 -0.0000 1.3846 + 6. B(C 5,C 0) 1.3846 -0.000003 -0.0000 1.3846 + 7. B(H 6,C 0) 1.0804 -0.000055 0.0001 1.0805 + 8. B(H 7,C 1) 1.0804 -0.000056 0.0001 1.0805 + 9. B(H 8,C 2) 1.0804 -0.000052 0.0001 1.0805 + 10. B(H 9,C 3) 1.0804 -0.000058 0.0001 1.0805 + 11. B(H 10,C 4) 1.0804 -0.000054 0.0001 1.0805 + 12. B(H 11,C 5) 1.0804 -0.000052 0.0001 1.0805 + 13. A(C 1,C 0,C 5) 120.00 -0.000004 0.00 120.00 + 14. A(C 1,C 0,H 6) 120.00 -0.000008 0.00 120.00 + 15. A(C 5,C 0,H 6) 120.01 0.000011 -0.00 120.00 + 16. A(C 2,C 1,H 7) 120.01 0.000012 -0.00 120.00 + 17. A(C 0,C 1,C 2) 120.00 -0.000008 0.00 120.00 + 18. A(C 0,C 1,H 7) 120.00 -0.000004 0.00 120.00 + 19. A(C 3,C 2,H 8) 119.99 -0.000013 0.00 120.00 + 20. A(C 1,C 2,H 8) 120.00 -0.000002 0.00 120.00 + 21. A(C 1,C 2,C 3) 120.01 0.000015 -0.00 120.00 + 22. A(C 4,C 3,H 9) 120.00 0.000007 -0.00 120.00 + 23. A(C 2,C 3,H 9) 120.00 0.000006 -0.00 120.00 + 24. A(C 2,C 3,C 4) 120.00 -0.000013 0.00 120.00 + 25. A(C 3,C 4,H 10) 120.00 -0.000006 0.00 120.00 + 26. A(C 3,C 4,C 5) 120.00 0.000002 -0.00 120.00 + 27. A(C 5,C 4,H 10) 120.00 0.000004 -0.00 120.00 + 28. A(C 0,C 5,C 4) 120.00 0.000008 -0.00 120.00 + 29. A(C 4,C 5,H 11) 120.00 0.000001 -0.00 120.00 + 30. A(C 0,C 5,H 11) 120.00 -0.000009 0.00 120.00 + 31. D(H 7,C 1,C 0,C 5) -179.99 0.000003 -0.01 -179.99 + 32. D(H 7,C 1,C 0,H 6) 0.01 0.000003 -0.01 0.00 + 33. D(C 2,C 1,C 0,H 6) -180.00 0.000001 -0.00 -180.00 + 34. D(C 2,C 1,C 0,C 5) 0.01 0.000001 -0.00 0.00 + 35. D(H 8,C 2,C 1,C 0) 179.98 -0.000005 0.01 179.99 + 36. D(C 3,C 2,C 1,C 0) -0.01 -0.000003 0.01 -0.00 + 37. D(C 3,C 2,C 1,H 7) 179.98 -0.000005 0.01 179.99 + 38. D(H 8,C 2,C 1,H 7) -0.03 -0.000007 0.02 -0.01 + 39. D(H 9,C 3,C 2,H 8) 0.01 0.000004 -0.01 0.01 + 40. D(H 9,C 3,C 2,C 1) -179.99 0.000002 -0.00 -180.00 + 41. D(C 4,C 3,C 2,H 8) -179.99 0.000004 -0.01 -179.99 + 42. D(C 4,C 3,C 2,C 1) 0.01 0.000002 -0.00 0.00 + 43. D(H 10,C 4,C 3,C 2) -179.99 0.000003 -0.01 -179.99 + 44. D(C 5,C 4,C 3,H 9) -180.00 0.000001 -0.00 -180.00 + 45. D(C 5,C 4,C 3,C 2) 0.00 0.000001 -0.00 0.00 + 46. D(H 10,C 4,C 3,H 9) 0.01 0.000003 -0.01 0.01 + 47. D(H 11,C 5,C 4,H 10) -0.03 -0.000007 0.02 -0.01 + 48. D(C 0,C 5,C 4,H 10) 179.98 -0.000005 0.01 179.99 + 49. D(C 0,C 5,C 4,C 3) -0.01 -0.000003 0.01 -0.00 + 50. D(H 11,C 5,C 0,H 6) 0.02 0.000004 -0.01 0.01 + 51. D(H 11,C 5,C 0,C 1) -179.98 0.000004 -0.01 -179.99 + 52. D(H 11,C 5,C 4,C 3) 179.98 -0.000005 0.01 179.99 + 53. D(C 4,C 5,C 0,H 6) -179.99 0.000002 -0.00 -180.00 + 54. D(C 4,C 5,C 0,C 1) 0.01 0.000002 -0.00 0.00 + ---------------------------------------------------------------------------- + ******************************************************* + *** FINAL ENERGY EVALUATION AT THE STATIONARY POINT *** + *** (AFTER 3 CYCLES) *** + ******************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.372604 -0.220263 0.005470 + C 0.502729 -1.297417 -0.008729 + C -0.865058 -1.082608 -0.013747 + C -1.363056 0.209299 -0.004464 + C -0.493181 1.286414 0.009778 + C 0.874634 1.071623 0.014697 + H 2.439965 -0.387928 0.009359 + H 0.891353 -2.305537 -0.015842 + H -1.543894 -1.923121 -0.024963 + H -2.430428 0.376871 -0.008335 + H -0.881765 2.294553 0.017113 + H 1.553446 1.912154 0.025671 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.593846 -0.416236 0.010338 + 1 C 6.0000 0 12.011 0.950021 -2.451763 -0.016495 + 2 C 6.0000 0 12.011 -1.634724 -2.045833 -0.025978 + 3 C 6.0000 0 12.011 -2.575803 0.395518 -0.008436 + 4 C 6.0000 0 12.011 -0.931978 2.430971 0.018478 + 5 C 6.0000 0 12.011 1.652819 2.025074 0.027773 + 6 H 1.0000 0 1.008 4.610866 -0.733078 0.017686 + 7 H 1.0000 0 1.008 1.684413 -4.356833 -0.029937 + 8 H 1.0000 0 1.008 -2.917537 -3.634172 -0.047173 + 9 H 1.0000 0 1.008 -4.592843 0.712184 -0.015750 + 10 H 1.0000 0 1.008 -1.666294 4.336076 0.032339 + 11 H 1.0000 0 1.008 2.935588 3.613447 0.048512 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/22 at 19:28:32.192 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 12 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.75526078653767 + + ID Z sym. atoms + 1 6 C 1-6 + 2 1 H 7-12 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 18 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.1965611 -0.161966E+02 0.876E-04 4.93 0.0 T + 2 -16.1965611 -0.258140E-09 0.515E-04 4.93 56.0 T + 3 -16.1965611 0.267484E-10 0.814E-05 4.93 354.6 T + + *** convergence criteria satisfied after 3 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6416606 -17.4605 + ... ... ... ... + 9 2.0000 -0.4763530 -12.9622 + 10 2.0000 -0.4763503 -12.9622 + 11 2.0000 -0.4747601 -12.9189 + 12 2.0000 -0.4214018 -11.4669 + 13 2.0000 -0.4213924 -11.4667 + 14 2.0000 -0.4025298 -10.9534 + 15 2.0000 -0.4025275 -10.9533 (HOMO) + 16 -0.2211971 -6.0191 (LUMO) + 17 -0.2211902 -6.0189 + 18 -0.0899154 -2.4467 + 19 0.1180093 3.2112 + 20 0.1377152 3.7474 + ... ... ... + 30 0.6741465 18.3445 + ------------------------------------------------------------- + HL-Gap 0.1813304 Eh 4.9343 eV + Fermi-level -0.3118623 Eh -8.4862 eV + + SCC (total) 0 d, 0 h, 0 min, 0.010 sec + SCC setup ... 0 min, 0.000 sec ( 1.392%) + Dispersion ... 0 min, 0.000 sec ( 0.808%) + classical contributions ... 0 min, 0.000 sec ( 0.280%) + integral evaluation ... 0 min, 0.002 sec ( 18.125%) + iterations ... 0 min, 0.004 sec ( 38.488%) + molecular gradient ... 0 min, 0.004 sec ( 38.876%) + printout ... 0 min, 0.000 sec ( 1.929%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.879640652449 Eh :: + :: gradient norm 0.000058531220 Eh/a0 :: + :: HOMO-LUMO gap 4.934252272558 eV :: + ::.................................................:: + :: SCC energy -16.196561052560 Eh :: + :: -> isotropic ES 0.000791525912 Eh :: + :: -> anisotropic ES 0.002517595461 Eh :: + :: -> anisotropic XC 0.012388537747 Eh :: + :: -> dispersion -0.008019556015 Eh :: + :: repulsion energy 0.316913616164 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.879640652449 Eh | + | GRADIENT NORM 0.000058531220 Eh/α | + | HOMO-LUMO GAP 4.934252272558 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/22 at 19:28:32.216 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.023 sec + * cpu-time: 0 d, 0 h, 0 min, 0.023 sec + * ratio c/w: 0.978 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.011 sec + * cpu-time: 0 d, 0 h, 0 min, 0.010 sec + * ratio c/w: 0.951 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.879640652450 +------------------------- -------------------- + + *** OPTIMIZATION RUN DONE *** + +Timings for individual modules: + +Sum of individual times ... 0.275 sec (= 0.005 min) +Geometry relaxation ... 0.086 sec (= 0.001 min) 31.2 % +XTB module ... 0.189 sec (= 0.003 min) 68.8 % + ****ORCA TERMINATED NORMALLY**** 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-0.38792834851432 0.00935918376693 + H 0.89135300032527 -2.30553664453777 -0.01584172099556 + H -1.54389392375015 -1.92312101358440 -0.02496277241009 + H -2.43042795974921 0.37687130997575 -0.00833452091932 + H -0.88176466598630 2.29455258686373 0.01711318587593 + H 1.55344645105395 1.91215391126322 0.02567143521620 diff --git a/cmmde_gui/test/test/test/cmmd_property.txt b/cmmde_gui/test/test/test/cmmd_property.txt new file mode 100644 index 0000000..8f1a67f --- /dev/null +++ b/cmmde_gui/test/test/test/cmmd_property.txt @@ -0,0 +1,6 @@ +------------------------------------------------------------- +----------------------- !PROPERTIES! ------------------------ +------------------------------------------------------------- +# ------------------------------------------------------------- +----------------------- !GEOMETRIES! ------------------------ +# ------------------------------------------------------------- diff --git a/cmmde_gui/test/test/test/cmmd_trj.xyz b/cmmde_gui/test/test/test/cmmd_trj.xyz new file mode 100644 index 0000000..4e3bfb0 --- /dev/null +++ b/cmmde_gui/test/test/test/cmmd_trj.xyz @@ -0,0 +1,56 @@ +12 +Coordinates from ORCA-job cmmd E -15.878848475480 + C 1.382680 -0.221770 0.005570 + C 0.506340 -1.307050 -0.008130 + C -0.871400 -1.090590 -0.014570 + C -1.373230 0.210910 -0.004460 + C -0.496830 1.295960 0.010580 + C 0.880990 1.079530 0.014120 + H 2.456200 -0.390440 0.009600 + H 0.897240 -2.320890 -0.014140 + H -1.554150 -1.935930 -0.027090 + H -2.446570 0.379420 -0.008330 + H -0.887690 2.310030 0.019130 + H 1.563770 1.924860 0.023730 +12 +Coordinates from ORCA-job cmmd E -15.879635904820 + C 1.373483 -0.220370 0.005486 + C 0.503034 -1.298271 -0.008552 + C -0.865566 -1.083277 -0.013955 + C -1.363971 0.209460 -0.004455 + C -0.493502 1.287234 0.009972 + C 0.875165 1.072283 0.014515 + H 2.440669 -0.388048 0.009436 + H 0.891632 -2.306209 -0.015155 + H -1.544313 -1.923643 -0.025717 + H -2.431149 0.376991 -0.008298 + H -0.882040 2.295219 0.017842 + H 1.553908 1.912671 0.024891 +12 +Coordinates from ORCA-job cmmd E -15.879640611400 + C 1.372627 -0.220257 0.005473 + C 0.502734 -1.297441 -0.008692 + C -0.865051 -1.082610 -0.013787 + C -1.363089 0.209312 -0.004461 + C -0.493192 1.286428 0.009814 + C 0.874638 1.071627 0.014658 + H 2.439905 -0.387931 0.009379 + H 0.891345 -2.305478 -0.015658 + H -1.543848 -1.923054 -0.025162 + H -2.430378 0.376863 -0.008322 + H -0.881754 2.294490 0.017304 + H 1.553413 1.912091 0.025463 +12 +Coordinates from ORCA-job cmmd E -15.879640652450 + C 1.372604 -0.220263 0.005470 + C 0.502729 -1.297417 -0.008729 + C -0.865058 -1.082608 -0.013747 + C -1.363056 0.209299 -0.004464 + C -0.493181 1.286414 0.009778 + C 0.874634 1.071623 0.014697 + H 2.439965 -0.387928 0.009359 + H 0.891353 -2.305537 -0.015842 + H -1.543894 -1.923121 -0.024963 + H -2.430428 0.376871 -0.008335 + H -0.881765 2.294553 0.017113 + H 1.553446 1.912154 0.025671 diff --git a/cmmde_gui/test/test/test/geom.smi b/cmmde_gui/test/test/test/geom.smi new file mode 100644 index 0000000..17163bb --- /dev/null +++ b/cmmde_gui/test/test/test/geom.smi @@ -0,0 +1 @@ +c1ccccc1 diff --git a/cmmde_gui/test/test/test/geom.xyz b/cmmde_gui/test/test/test/geom.xyz new file mode 100644 index 0000000..d5cf7e8 --- /dev/null +++ b/cmmde_gui/test/test/test/geom.xyz @@ -0,0 +1,14 @@ +12 + +C 1.38268 -0.22177 0.00557 +C 0.50634 -1.30705 -0.00813 +C -0.87140 -1.09059 -0.01457 +C -1.37323 0.21091 -0.00446 +C -0.49683 1.29596 0.01058 +C 0.88099 1.07953 0.01412 +H 2.45620 -0.39044 0.00960 +H 0.89724 -2.32089 -0.01414 +H -1.55415 -1.93593 -0.02709 +H -2.44657 0.37942 -0.00833 +H -0.88769 2.31003 0.01913 +H 1.56377 1.92486 0.02373 diff --git a/cmmde_gui/test/test/test/run.sh b/cmmde_gui/test/test/test/run.sh new file mode 100644 index 0000000..f72e163 --- /dev/null +++ b/cmmde_gui/test/test/test/run.sh @@ -0,0 +1,10 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH +export PATH=/home/adit/opt/openmpi411/bin:$PATH +export OMP_NUM_THREADS=1 +cd $PWD +$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe diff --git a/cmmde_gui/test/test/test/run_babel.sh b/cmmde_gui/test/test/test/run_babel.sh new file mode 100644 index 0000000..0d5d00e --- /dev/null +++ b/cmmde_gui/test/test/test/run_babel.sh @@ -0,0 +1,8 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export OMP_NUM_THREADS=1 +cd $PWD +obabel geom.smi -O geom.xyz --gen3d diff --git a/cmmde_gui/test/test/test/slurm-2893.out b/cmmde_gui/test/test/test/slurm-2893.out new file mode 100644 index 0000000..b7d75ac --- /dev/null +++ b/cmmde_gui/test/test/test/slurm-2893.out @@ -0,0 +1 @@ +1 molecule converted diff --git a/cmmde_gui/test/test/test/slurm-2894.out b/cmmde_gui/test/test/test/slurm-2894.out new file mode 100644 index 0000000..e69de29 diff --git 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a/lib/cmmde_xtb.py +++ b/lib/cmmde_xtb.py @@ -1,6 +1,6 @@ # CMMDE function for xTB standalone program import os -def xtb(job,geom,nproc,product,temperature,nrun,npoint,anopt,kpush,kpull,ppull,alp,distance,angle,dihedral,scanmode,maxiter,scan,solvent): +def xtb(job,geom,nproc,product,temperature,nrun,npoint,anopt,kpush,kpull,ppull,alp,distance,angle,dihedral,scanmode,maxiter,scan,solvent,charge,mult,method): with open('run.sh','w') as fout: print("""#!/bin/bash #SBATCH --nodes=1 @@ -9,31 +9,40 @@ def xtb(job,geom,nproc,product,temperature,nrun,npoint,anopt,kpush,kpull,ppull,a #SBATCH --time=168:0:0 export OMP_NUM_THREADS={} cd $PWD""".format(nproc),file=fout) + meth = '' + if 'GFN-FF' in method or 'gfnff' in method: + meth += '--gfnff' + if 'XTB2' in method or 'xtb2' in method: + meth += '--gfn2' + if 'XTB1' in method or 'xtb1' in method: + meth += '--gfn1' + if 'XTB0' in method or 'xtb0' in method: + meth += '--gfn0' if 'opt' in job: if solvent != 'none': - print("$XTB_COMMAND {} --opt -P {} --alpb {} > xtb.out".format(geom,nproc,solvent),file=fout) + print("$XTB_COMMAND {} --opt -P {} --alpb {} --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,solvent,charge,mult-1,meth),file=fout) else: - print("$XTB_COMMAND {} --opt -P {} > xtb.out".format(geom,nproc),file=fout) + print("$XTB_COMMAND {} --opt -P {} --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,charge,mult-1,meth),file=fout) if 'freq' in job: if solvent != 'none': - print("$XTB_COMMAND {} --hess -P {} --input cmmd.in --alpb {} > xtb.out".format(geom,nproc,solvent), file=fout) + print("$XTB_COMMAND {} --hess -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,solvent,charge,mult-1,meth), file=fout) else: - print("$XTB_COMMAND {} --hess -P {} --input cmmd.in > xtb.out".format(geom,nproc), file=fout) + print("$XTB_COMMAND {} --hess -P {} --input cmmd.in --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,charge,mult-1,meth), file=fout) if 'opt' in job and 'freq' in job: if solvent != 'none': - print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in --alpb {} > xtb.out".format(geom,nproc,solvent),file=fout) + print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,solvent,charge, mult-1,meth),file=fout) else: - print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in > xtb.out".format(geom,nproc),file=fout) + print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,charge,mult-1,meth),file=fout) if 'path' in job: if solvent != 'none': - print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} --alpb {} > xtb.out".format(geom,product,nproc,solvent),file=fout) + print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} --alpb {} --chrg {} --uhf {} ,method > xtb.out".format(geom,product,nproc,solvent,charge,mult-1,meth),file=fout) else: - print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} > xtb.out".format(geom,product,nproc),file=fout) + print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} --chrg {} --uhf {} {} > xtb.out".format(geom,product,nproc,charge,mult-1,meth),file=fout) if 'scan' in job: if solvent != 'none': - print("$XTB_COMMAND {} --opt -P {} --input cmmd.in --alpb {} > xtb.out".format(geom,nproc,solvent), file=fout) + print("$XTB_COMMAND {} --opt -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,solvent,charge,mult-1,meth), file=fout) else: - print("$XTB_COMMAND {} --opt -P {} --input cmmd.in > xtb.out".format(geom,nproc), file=fout) + print("$XTB_COMMAND {} --opt -P {} --input cmmd.in --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,charge,mult-1,meth), file=fout) if 'freq' in job: with open('cmmd.in', 'w') as f: print("""$thermo @@ -55,18 +64,24 @@ $end""".format(nrun,npoint,anopt,kpush,kpull,ppull,alp),file=f) with open("cmmd.in",'w') as f: print("$constrain",file=f) if distance != 'None': - print("distance: {}".format(distance),file=f) + distance = distance.split(";") + for index, i in enumerate(distance): + print("distance: {}".format(i),file=f) if angle != 'None': - print("angle: {}".format(angle),file=f) + angle = angle.split(";") + for index, i in enumerate(angle): + print("angle: {}".format(i),file=f) if dihedral != 'None': - print("dihedral: {}".format(dihedral),file=f) + dihedral = dihedral.split(";") + for index, i in enumerate(dihedral): + print("dihedral: {}".format(i),file=f) print("$scan",file=f) if scanmode != 'None': print("mode = {}".format(scanmode),file=f) scan = scan.split(";") for index, i in enumerate(scan): print("{}: {}".format(index+1,i),file=f) - print("""$opt + print("""$opt maxcycle = {}""".format(maxiter),file=f)