diff --git a/cmmde_gui/gui.py b/cmmde_gui/gui.py index 3530e26..6b8f2b3 100755 --- a/cmmde_gui/gui.py +++ b/cmmde_gui/gui.py @@ -64,9 +64,9 @@ def cmmde_gui(): job_list = [job[i] for i in job_btn.value] jobs = ",".join(job_list) - cmd = subprocess.run(["cmmde.py","-i","{}".format(editor.value),"-s","{}".format(software[software_btn.value]),"-j","{}".format(jobs),"-m","{}".format(method[method_btn.value])],capture_output=True,text=True) + cmd = subprocess.run(["cmmde.py","-i","{}".format(editor.value),"-s","{}".format(software[software_btn.value]),"-j","{}".format(jobs),"-m","{}".format(method[method_btn.value])]) #terminal.subprocess.run("cmmde.py","-i{}".format(editor.value),"-s{}".format(software[software_btn.value]), "-j{}".format(jobs), "-m{}".format(method[method_btn.value])) - TextArea.value = TextArea.value + "\n" + cmd.stdout + TextArea.value = TextArea.value + "\n" + "Perhitungan anda telah tersubmit!" # RunMessage.value = "Perhitungan telah tersubmit!" @@ -75,6 +75,11 @@ def cmmde_gui(): Run_btn.on_click(run) +# Upload structure button + + structure_input = pn.widgets.FileInput() + + # Post calculations post_calc = {'Frequency calculation':'freq', 'Radial distribution function':'rdf','Mean Square Displacement':'msd','Time-dependent calculation':'td','Thermochemistry calculation':'thermo'} post_btn = pn.widgets.Select(name="Job Selection",value='Frequency calculation', options=['Frequency calculation','Radial distribution function', 'Mean Square Displacement','Time-dependent calculation','Thermochemistry calculation']) @@ -109,7 +114,12 @@ def cmmde_gui(): Progress_btn = pn.widgets.Button(name="Check calculation",button_type='primary') Progress_btn.on_click(progress) - +# Check the output + def check_out(event): + cmd = subprocess.run(["tail","-f","cmmd.out"],capture_output=True,text=True) + cmd.stdout + checkout_btn = pn.widgets.Button(name="Check output",button_type='primary') + checkout_btn.on_click(check_out) # Visualize the results xyzview = py3Dmol.view() xyzview.setBackgroundColor('0xeeeeee') diff --git a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/slurm-3029.out b/cmmde_gui/test/.xtboptok similarity index 100% rename from cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/slurm-3029.out rename to cmmde_gui/test/.xtboptok diff --git a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.engrad b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.engrad deleted file mode 100644 index be34378..0000000 --- a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.engrad +++ /dev/null @@ -1,34 +0,0 @@ -# -# Number of atoms -# - 5 -# -# The current total energy in Eh -# - -4.175218519960 -# -# The current gradient in Eh/bohr -# - -0.000001468287 - -0.000001452748 - -0.000001409928 - 0.000099625376 - 0.000000596936 - 0.000000170656 - -0.000032985992 - -0.000054178347 - 0.000076588754 - -0.000032654559 - -0.000038682622 - -0.000084843552 - -0.000032516537 - 0.000093716782 - 0.000009494069 -# -# The atomic numbers and current coordinates in Bohr -# - 6 1.9696099 -0.1033438 -0.1365649 - 1 4.0145972 -0.1033340 -0.1365671 - 1 1.2879566 -1.2234273 1.4327440 - 1 1.2879485 -0.9023595 -1.8912376 - 1 1.2879498 1.8157567 0.0488109 diff --git a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.gbw b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.gbw deleted file mode 100644 index 0c5465d..0000000 Binary files a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.gbw and /dev/null differ diff --git a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.in b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.in deleted file mode 100644 index f93f575..0000000 --- a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.in +++ /dev/null @@ -1,11 +0,0 @@ -#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/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.opt b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.opt deleted file mode 100644 index dd83954..0000000 --- a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.opt +++ /dev/null @@ -1,164 +0,0 @@ - -$orca_opt_file - -$trust - 0.300000000000 - -$epredict - 0.000000000000 - -$ediffsc - 1000.000000000000 - -$ctyp - 3 - -$coordinates - 2 15 - 1.96960486 -0.10334912 -0.13657051 4.03356374 -0.10333023 -0.13657051 - 1.28163116 -1.23382109 1.44730345 1.28163116 -0.90977085 -1.90750846 - 1.28163116 1.83356347 0.05053128 - 1.96960809 -0.10334555 -0.13656646 4.01487809 -0.10333190 -0.13656706 - 1.28786237 -1.22358138 1.43296133 1.28785515 -0.90247073 -1.89148051 - 1.28785837 1.81602174 0.04883795 - -# 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 -$redundant_internals - 4 6 0 0 0 - 1 0 0 - 2 0 0 - 3 0 0 - 4 0 0 - 1 0 3 0 0 - 2 0 3 0 0 - 1 0 4 0 0 - 2 0 4 0 0 - 3 0 4 0 0 - 1 0 2 0 0 -$energies - 2 - -4.1749622801599999 - -4.1752184657600004 - -$gradients - 2 15 - -0.0000027886034344 -0.0000043518393354 -0.0000060472176322 0.0066850309380137 - 0.0000008881278605 0.0000000440083344 -0.0022284396811313 -0.0036618597626871 - 0.0051310474440805 -0.0022260362495245 -0.0026101268472735 -0.0057316617241839 - -0.0022277664039233 0.0062754503214355 0.0006066174894011 - -0.0000014682870466 -0.0000014527480153 -0.0000014099279061 0.0000996253756442 - 0.0000005969356365 0.0000001706562852 -0.0000329859920495 -0.0000541783471346 - 0.0000765887541975 -0.0000326545594519 -0.0000386826222359 -0.0000848435517582 - -0.0000325165370961 0.0000937167817493 0.0000094940691815 - -$redundant_coords - 2 10 - 2.0639588835553004 2.0639601244554804 2.0639392030244004 2.0639634897792400 - 1.9106339276550293 1.9106418999213668 1.9106168596569035 1.9106313676756239 - 1.9106434938538384 1.9106318685398802 - 2.0452700066184040 2.0452684490353756 2.0452656178615110 2.0452697281465047 - 1.9106345549334645 1.9106391086153649 1.9106230642023705 1.9106310752882207 - 1.9106396714048268 1.9106319429665910 - -$redundant_gradients - 2 10 - 0.0066850309457483 0.0066860158599383 0.0066798162630520 0.0066867184136725 - -0.0000001823075762 0.0000008112283392 -0.0000018032042837 0.0000000849723980 - 0.0000011109061823 -0.0000000216333131 - 0.0000996253795746 0.0000994435536643 0.0000987977985070 0.0000996471539910 - 0.0000001372361801 0.0000006886868494 -0.0000012431323971 -0.0000002458445154 - 0.0000007916373290 -0.0000001286033218 - -$hessian_approx - 15 15 - 0 1 2 3 4 5 - 0 0.839467 0.000006 0.000005 -0.357182 -0.000002 0.000000 - 1 0.000006 0.839472 0.000006 0.000017 -0.136199 -0.000001 - 2 0.000005 0.000006 0.839488 0.000019 -0.000001 -0.136202 - 3 -0.357182 0.000017 0.000019 0.355990 -0.000006 -0.000002 - 4 -0.000002 -0.136199 -0.000001 -0.000006 0.102150 0.000001 - 5 0.000000 -0.000001 -0.136202 -0.000002 0.000001 0.102151 - 6 -0.160760 -0.040355 0.056523 0.000401 -0.037297 0.052261 - 7 -0.040361 -0.202511 0.092879 0.000658 0.007665 -0.010732 - 8 0.056545 0.092904 -0.266334 -0.000931 -0.010740 0.015038 - 9 -0.160765 -0.028791 -0.063217 0.000397 -0.026605 -0.058433 - 10 -0.028793 -0.169952 -0.074101 0.000470 0.003901 0.008562 - 11 -0.063228 -0.074110 -0.298935 0.001031 0.008569 0.018804 - 12 -0.160758 0.069124 0.006671 0.000393 0.063911 0.006174 - 13 0.069149 -0.330810 -0.018783 -0.001140 0.022483 0.002170 - 14 0.006679 -0.018798 -0.138016 -0.000116 0.002171 0.000210 - 6 7 8 9 10 11 - 0 -0.160760 -0.040361 0.056545 -0.160765 -0.028793 -0.063228 - 1 -0.040355 -0.202511 0.092904 -0.028791 -0.169952 -0.074110 - 2 0.056523 0.092879 -0.266334 -0.063217 -0.074101 -0.298935 - 3 0.000401 0.000658 -0.000931 0.000397 0.000470 0.001031 - 4 -0.037297 0.007665 -0.010740 -0.026605 0.003901 0.008569 - 5 0.052261 -0.010732 0.015038 -0.058433 0.008562 0.018804 - 6 0.130354 0.046348 -0.064932 0.015002 0.022930 -0.016732 - 7 0.046348 0.178307 -0.106695 0.019305 0.029523 -0.021703 - 8 -0.064932 -0.106695 0.251633 0.020811 0.031642 -0.021418 - 9 0.015002 0.019305 0.020811 0.130362 0.033066 0.072612 - 10 0.022930 0.029523 0.031642 0.033066 0.140910 0.085110 - 11 -0.016732 -0.021703 -0.021418 0.072612 0.085110 0.289060 - 12 0.015003 -0.025951 -0.011493 0.015004 -0.027673 0.006316 - 13 0.008375 -0.012984 -0.007111 0.003025 -0.004381 0.002136 - 14 -0.027120 0.046252 0.021081 0.028226 -0.051213 0.012490 - 12 13 14 - 0 -0.160758 0.069149 0.006679 - 1 0.069124 -0.330810 -0.018798 - 2 0.006671 -0.018783 -0.138016 - 3 0.000393 -0.001140 -0.000116 - 4 0.063911 0.022483 0.002171 - 5 0.006174 0.002170 0.000210 - 6 0.015003 0.008375 -0.027120 - 7 -0.025951 -0.012984 0.046252 - 8 -0.011493 -0.007111 0.021081 - 9 0.015004 0.003025 0.028226 - 10 -0.027673 -0.004381 -0.051213 - 11 0.006316 0.002136 0.012490 - 12 0.130359 -0.079410 -0.007668 - 13 -0.079410 0.325693 0.021588 - 14 -0.007668 0.021588 0.104236 - -$bmatrix - 10 15 - 0 1 2 3 4 5 - 0 -1.000000 -0.000007 0.000000 1.000000 0.000007 -0.000000 - 1 0.333328 0.547721 -0.767395 0.000000 0.000000 0.000000 - 2 0.333332 0.390720 0.858037 0.000000 0.000000 0.000000 - 3 0.333330 -0.938442 -0.090650 0.000000 0.000000 0.000000 - 4 0.460973 -0.270161 -0.593296 -0.000001 0.202623 0.444971 - 5 -0.460970 -0.648895 -0.062676 0.000000 0.000000 0.000000 - 6 0.460968 0.648889 0.062680 0.000003 -0.486668 -0.047010 - 7 -0.460964 0.270166 0.593299 0.000000 0.000000 0.000000 - 8 -0.460971 0.378729 -0.530618 0.000000 0.000000 0.000000 - 9 0.460974 -0.378720 0.530618 -0.000002 0.284042 -0.397964 - 6 7 8 9 10 11 - 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 1 -0.333328 -0.547721 0.767395 0.000000 0.000000 0.000000 - 2 0.000000 0.000000 0.000000 -0.333332 -0.390720 -0.858037 - 3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 4 0.000000 0.000000 0.000000 -0.460972 0.067538 0.148325 - 5 0.230485 0.297307 0.312315 0.230484 0.351587 -0.249639 - 6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 7 0.230482 -0.391988 -0.179665 0.000000 0.000000 0.000000 - 8 0.000000 0.000000 0.000000 0.230485 -0.419128 0.101316 - 9 -0.460972 0.094677 -0.132654 0.000000 0.000000 0.000000 - 12 13 14 - 0 0.000000 0.000000 0.000000 - 1 0.000000 0.000000 0.000000 - 2 0.000000 0.000000 0.000000 - 3 -0.333330 0.938442 0.090650 - 4 0.000000 0.000000 0.000000 - 5 0.000000 0.000000 0.000000 - 6 -0.460971 -0.162221 -0.015670 - 7 0.230482 0.121822 -0.413634 - 8 0.230486 0.040398 0.429302 - 9 0.000000 0.000000 0.000000 - diff --git a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.out b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.out deleted file mode 100644 index 3b2648a..0000000 --- a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.out +++ /dev/null @@ -1,1136 +0,0 @@ - - ***************** - * 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 0.357201 - 3. B(H 3,C 0) 1.0922 0.357215 - 4. B(H 4,C 0) 1.0922 0.357198 - 5. A(H 1,C 0,H 3) 109.4713 0.290104 - 6. A(H 2,C 0,H 3) 109.4717 0.290104 - 7. A(H 1,C 0,H 4) 109.4703 0.290102 - 8. A(H 2,C 0,H 4) 109.4711 0.290102 - 9. A(H 3,C 0,H 4) 109.4718 0.290104 - 10. A(H 1,C 0,H 2) 109.4711 0.290102 - ----------------------------------------------------------------- - -Number of atoms .... 5 -Number of degrees of freedom .... 10 - - ************************************************************* - * GEOMETRY OPTIMIZATION CYCLE 1 * - ************************************************************* ---------------------------------- -CARTESIAN COORDINATES (ANGSTROEM) ---------------------------------- - C 1.042270 -0.054690 -0.072270 - H 2.134470 -0.054680 -0.072270 - H 0.678210 -0.652910 0.765880 - H 0.678210 -0.481430 -1.009410 - H 0.678210 0.970280 0.026740 - ----------------------------- -CARTESIAN COORDINATES (A.U.) ----------------------------- - NO LB ZA FRAG MASS X Y Z - 0 C 6.0000 0 12.011 1.969605 -0.103349 -0.136571 - 1 H 1.0000 0 1.008 4.033564 -0.103330 -0.136571 - 2 H 1.0000 0 1.008 1.281631 -1.233821 1.447303 - 3 H 1.0000 0 1.008 1.281631 -0.909771 -1.907508 - 4 H 1.0000 0 1.008 1.281631 1.833563 0.050531 - - ----------------------------------------------------------- - | ===================== | - | 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 2022/08/05 at 08:09:45.270 - - ------------------------------------------------- - | 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 : 0.13962921932938 - - 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 -4.2288353 -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 -4.2418549 -0.465207E-04 0.968E-02 16.85 1.0 T - 5 -4.2418548 0.611476E-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 14114.0 T - - *** convergence criteria satisfied after 7 iterations *** - - # Occupation Energy/Eh Energy/eV - ------------------------------------------------------------- - 1 2.0000 -0.5801036 -15.7854 - 2 2.0000 -0.4667180 -12.7000 - 3 2.0000 -0.4667171 -12.7000 - 4 2.0000 -0.4667162 -12.7000 (HOMO) - 5 0.1525567 4.1513 (LUMO) - 6 0.2134364 5.8079 - 7 0.2134420 5.8081 - 8 0.2134570 5.8085 - ------------------------------------------------------------- - HL-Gap 0.6192729 Eh 16.8513 eV - Fermi-level -0.1570797 Eh -4.2744 eV - - SCC (total) 0 d, 0 h, 0 min, 0.023 sec - SCC setup ... 0 min, 0.000 sec ( 0.637%) - Dispersion ... 0 min, 0.000 sec ( 0.085%) - classical contributions ... 0 min, 0.000 sec ( 0.064%) - integral evaluation ... 0 min, 0.000 sec ( 0.864%) - iterations ... 0 min, 0.022 sec ( 96.023%) - molecular gradient ... 0 min, 0.000 sec ( 1.620%) - printout ... 0 min, 0.000 sec ( 0.654%) - - ::::::::::::::::::::::::::::::::::::::::::::::::::::: - :: SUMMARY :: - ::::::::::::::::::::::::::::::::::::::::::::::::::::: - :: total energy -4.174962280159 Eh :: - :: gradient norm 0.013368794308 Eh/a0 :: - :: HOMO-LUMO gap 16.851274252485 eV :: - ::.................................................:: - :: SCC energy -4.241854917268 Eh :: - :: -> isotropic ES 0.001954142490 Eh :: - :: -> anisotropic ES 0.002520377280 Eh :: - :: -> anisotropic XC 0.003827617066 Eh :: - :: -> dispersion -0.000662667279 Eh :: - :: repulsion energy 0.066892631144 Eh :: - :: add. restraining 0.000000000000 Eh :: - :: total charge -0.000000000000 e :: - ::::::::::::::::::::::::::::::::::::::::::::::::::::: - - -Property printout bound to 'properties.out' - - ------------------------------------------------- - | TOTAL ENERGY -4.174962280159 Eh | - | GRADIENT NORM 0.013368794308 Eh/α | - | HOMO-LUMO GAP 16.851274252485 eV | - ------------------------------------------------- - ------------------------------------------------------------------------- - * finished run on 2022/08/05 at 08:09:45.304 ------------------------------------------------------------------------- - total: - * wall-time: 0 d, 0 h, 0 min, 0.035 sec - * cpu-time: 0 d, 0 h, 0 min, 0.015 sec - * ratio c/w: 0.421 speedup - SCF: - * wall-time: 0 d, 0 h, 0 min, 0.023 sec - * cpu-time: 0 d, 0 h, 0 min, 0.004 sec - * ratio c/w: 0.172 speedup - - -------------------------- -------------------- -FINAL SINGLE POINT ENERGY -4.174962280160 -------------------------- -------------------- - ------------------------------------------------------------------------------- - 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 .... -4.174962280 Eh -Current gradient norm .... 0.013368794 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 .... 0.999302325 -Lowest eigenvalues of augmented Hessian: - -0.000499645 0.290101871 0.290102101 0.290102951 0.290103802 -Length of the computed step .... 0.037373954 -The final length of the internal step .... 0.037373954 -Converting the step to cartesian space: - Initial RMS(Int)= 0.0118186819 -Transforming coordinates: - Iter 0: RMS(Cart)= 0.0096499129 RMS(Int)= 0.0118186819 - Iter 1: RMS(Cart)= 0.0000000192 RMS(Int)= 0.0000000229 -done -Storing new coordinates .... done - - .--------------------. - ----------------------|Geometry convergence|------------------------- - Item value Tolerance Converged - --------------------------------------------------------------------- - RMS gradient 0.0042275832 0.0001000000 NO - MAX gradient 0.0066867184 0.0003000000 NO - RMS step 0.0118186819 0.0020000000 NO - MAX step 0.0186937616 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 0.006686 -0.0099 1.0823 - 3. B(H 3,C 0) 1.0922 0.006680 -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 0.000001 -0.00 109.47 - 7. A(H 1,C 0,H 4) 109.47 -0.000002 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 1.042272 -0.054688 -0.072268 - H 2.124582 -0.054681 -0.072268 - H 0.681507 -0.647491 0.758290 - H 0.681504 -0.477567 -1.000928 - H 0.681505 0.960997 0.025844 - ----------------------------- -CARTESIAN COORDINATES (A.U.) ----------------------------- - NO LB ZA FRAG MASS X Y Z - 0 C 6.0000 0 12.011 1.969608 -0.103346 -0.136566 - 1 H 1.0000 0 1.008 4.014878 -0.103332 -0.136567 - 2 H 1.0000 0 1.008 1.287862 -1.223581 1.432961 - 3 H 1.0000 0 1.008 1.287855 -0.902471 -1.891481 - 4 H 1.0000 0 1.008 1.287858 1.816022 0.048838 - - ----------------------------------------------------------- - | ===================== | - | 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 2022/08/05 at 08:09:45.347 - - ------------------------------------------------- - | 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 : 0.17259154546392 - - 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 -0.729517E-05 0.561E-02 17.34 1.0 T - 3 -4.2473846 -0.259690E-06 0.204E-02 17.34 2.2 T - 4 -4.2473847 -0.370480E-07 0.422E-03 17.35 10.6 T - 5 -4.2473847 -0.969713E-11 0.246E-05 17.35 1817.8 T - 6 -4.2473847 -0.112799E-11 0.111E-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 -0.4674471 -12.7199 - 4 2.0000 -0.4674466 -12.7199 (HOMO) - 5 0.1699963 4.6258 (LUMO) - 6 0.2290144 6.2318 - 7 0.2290179 6.2319 - 8 0.2290219 6.2320 - ------------------------------------------------------------- - HL-Gap 0.6374429 Eh 17.3457 eV - Fermi-level -0.1487251 Eh -4.0470 eV - - SCC (total) 0 d, 0 h, 0 min, 0.004 sec - SCC setup ... 0 min, 0.000 sec ( 3.196%) - Dispersion ... 0 min, 0.000 sec ( 0.577%) - classical contributions ... 0 min, 0.000 sec ( 0.302%) - integral evaluation ... 0 min, 0.000 sec ( 4.630%) - iterations ... 0 min, 0.003 sec ( 78.655%) - molecular gradient ... 0 min, 0.000 sec ( 9.015%) - printout ... 0 min, 0.000 sec ( 3.368%) - - ::::::::::::::::::::::::::::::::::::::::::::::::::::: - :: SUMMARY :: - ::::::::::::::::::::::::::::::::::::::::::::::::::::: - :: total energy -4.175218465758 Eh :: - :: gradient norm 0.000198777395 Eh/a0 :: - :: HOMO-LUMO gap 17.345703353999 eV :: - ::.................................................:: - :: SCC energy -4.247384681031 Eh :: - :: -> isotropic ES 0.002034388498 Eh :: - :: -> anisotropic ES 0.002324462858 Eh :: - :: -> anisotropic XC 0.003588679991 Eh :: - :: -> dispersion -0.000661035657 Eh :: - :: repulsion energy 0.072166209677 Eh :: - :: add. restraining 0.000000000000 Eh :: - :: total charge -0.000000000000 e :: - ::::::::::::::::::::::::::::::::::::::::::::::::::::: - - -Property printout bound to 'properties.out' - - ------------------------------------------------- - | TOTAL ENERGY -4.175218465758 Eh | - | GRADIENT NORM 0.000198777395 Eh/α | - | HOMO-LUMO GAP 17.345703353999 eV | - ------------------------------------------------- - ------------------------------------------------------------------------- - * finished run on 2022/08/05 at 08:09:45.361 ------------------------------------------------------------------------- - 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: 0.957 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: 0.869 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 .... 0.000198777 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 0.290101865 0.290102092 0.290102928 0.290103801 -Length of the computed step .... 0.000564067 -The final length of the internal step .... 0.000564067 -Converting the step to cartesian space: - Initial RMS(Int)= 0.0001783736 -Transforming coordinates: - Iter 0: RMS(Cart)= 0.0001456389 RMS(Int)= 0.0001783736 - Iter 1: RMS(Cart)= 0.0000000002 RMS(Int)= 0.0000000003 -done -Storing new coordinates .... done - - .--------------------. - ----------------------|Geometry convergence|------------------------- - Item value Tolerance Converged - --------------------------------------------------------------------- - Energy change -0.0002561856 0.0000050000 NO - RMS gradient 0.0000628550 0.0001000000 YES - MAX gradient 0.0000996472 0.0003000000 YES - RMS step 0.0001783736 0.0020000000 YES - MAX step 0.0002827846 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 0.000001 -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 1.042273 -0.054687 -0.072267 - H 2.124433 -0.054682 -0.072268 - H 0.681557 -0.647410 0.758175 - H 0.681553 -0.477508 -1.000800 - H 0.681554 0.960857 0.025830 - ----------------------------- -CARTESIAN COORDINATES (A.U.) ----------------------------- - NO LB ZA FRAG MASS X Y Z - 0 C 6.0000 0 12.011 1.969610 -0.103344 -0.136565 - 1 H 1.0000 0 1.008 4.014597 -0.103334 -0.136567 - 2 H 1.0000 0 1.008 1.287957 -1.223427 1.432744 - 3 H 1.0000 0 1.008 1.287949 -0.902359 -1.891238 - 4 H 1.0000 0 1.008 1.287950 1.815757 0.048811 - - ----------------------------------------------------------- - | ===================== | - | 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 2022/08/05 at 08:09:45.391 - - ------------------------------------------------- - | 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 : 0.68691715133107 - - 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 -0.163779E-08 0.849E-04 17.35 52.7 T - 3 -4.2474673 -0.599876E-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 -0.4674559 -12.7201 - 3 2.0000 -0.4674556 -12.7201 - 4 2.0000 -0.4674553 -12.7201 (HOMO) - 5 0.1702655 4.6332 (LUMO) - 6 0.2292565 6.2384 - 7 0.2292586 6.2384 - 8 0.2292605 6.2385 - ------------------------------------------------------------- - HL-Gap 0.6377208 Eh 17.3533 eV - Fermi-level -0.1485949 Eh -4.0435 eV - - SCC (total) 0 d, 0 h, 0 min, 0.004 sec - SCC setup ... 0 min, 0.000 sec ( 2.747%) - Dispersion ... 0 min, 0.000 sec ( 0.433%) - classical contributions ... 0 min, 0.000 sec ( 0.331%) - integral evaluation ... 0 min, 0.000 sec ( 4.565%) - iterations ... 0 min, 0.003 sec ( 79.096%) - molecular gradient ... 0 min, 0.000 sec ( 9.086%) - printout ... 0 min, 0.000 sec ( 3.490%) - - ::::::::::::::::::::::::::::::::::::::::::::::::::::: - :: SUMMARY :: - ::::::::::::::::::::::::::::::::::::::::::::::::::::: - :: total energy -4.175218519964 Eh :: - :: gradient norm 0.000005516518 Eh/a0 :: - :: HOMO-LUMO gap 17.353265796625 eV :: - ::.................................................:: - :: SCC energy -4.247467308161 Eh :: - :: -> isotropic ES 0.002035507818 Eh :: - :: -> anisotropic ES 0.002321507905 Eh :: - :: -> anisotropic XC 0.003585039049 Eh :: - :: -> dispersion -0.000661012503 Eh :: - :: repulsion energy 0.072248782606 Eh :: - :: add. restraining 0.000000000000 Eh :: - :: total charge 0.000000000000 e :: - ::::::::::::::::::::::::::::::::::::::::::::::::::::: - - -Property printout bound to 'properties.out' - - ------------------------------------------------- - | TOTAL ENERGY -4.175218519964 Eh | - | GRADIENT NORM 0.000005516518 Eh/α | - | HOMO-LUMO GAP 17.353265796625 eV | - ------------------------------------------------- - ------------------------------------------------------------------------- - * finished run on 2022/08/05 at 08:09:45.405 ------------------------------------------------------------------------- - 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: 0.957 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: 0.849 speedup - - -------------------------- -------------------- -FINAL SINGLE POINT ENERGY -4.175218519960 -------------------------- -------------------- - - *** OPTIMIZATION RUN DONE *** - -Timings for individual modules: - -Sum of individual times ... 0.151 sec (= 0.003 min) -Geometry relaxation ... 0.039 sec (= 0.001 min) 26.0 % -XTB module ... 0.112 sec (= 0.002 min) 74.0 % - ****ORCA TERMINATED NORMALLY**** -TOTAL RUN TIME: 0 days 0 hours 0 minutes 0 seconds 249 msec diff --git a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.xtbrestart b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.xtbrestart deleted file mode 100644 index 2e49831..0000000 Binary files a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.xtbrestart and /dev/null differ diff --git a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.xyz b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.xyz deleted file mode 100644 index 131ad4a..0000000 --- a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.xyz +++ /dev/null @@ -1,7 +0,0 @@ -5 -Coordinates from ORCA-job cmmd - C 1.04227269060310 -0.05468719364080 -0.07226703535934 - H 2.12443335379334 -0.05468200026993 -0.07226820060049 - H 0.68155725235486 -0.64740982631557 0.75817547407569 - H 0.68155300087124 -0.47750805702477 -1.00079985809395 - H 0.68155370237746 0.96085707725107 0.02582961997808 diff --git a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd_property.txt b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd_property.txt deleted file mode 100644 index 8f1a67f..0000000 --- a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd_property.txt +++ /dev/null @@ -1,6 +0,0 @@ -------------------------------------------------------------- ------------------------ !PROPERTIES! ------------------------ -------------------------------------------------------------- -# ------------------------------------------------------------- ------------------------ !GEOMETRIES! ------------------------ -# ------------------------------------------------------------- diff --git a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd_trj.xyz b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd_trj.xyz deleted file mode 100644 index c35d5ce..0000000 --- a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd_trj.xyz +++ /dev/null @@ -1,21 +0,0 @@ -5 -Coordinates from ORCA-job cmmd E -4.174962280160 - C 1.042270 -0.054690 -0.072270 - H 2.134470 -0.054680 -0.072270 - H 0.678210 -0.652910 0.765880 - H 0.678210 -0.481430 -1.009410 - H 0.678210 0.970280 0.026740 -5 -Coordinates from ORCA-job cmmd E -4.175218465760 - C 1.042272 -0.054688 -0.072268 - H 2.124582 -0.054681 -0.072268 - H 0.681507 -0.647491 0.758290 - H 0.681504 -0.477567 -1.000928 - H 0.681505 0.960997 0.025844 -5 -Coordinates from ORCA-job cmmd E -4.175218519960 - C 1.042273 -0.054687 -0.072267 - H 2.124433 -0.054682 -0.072268 - H 0.681557 -0.647410 0.758175 - H 0.681553 -0.477508 -1.000800 - H 0.681554 0.960857 0.025830 diff --git a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.engrad b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.engrad deleted file mode 100644 index e8a99f7..0000000 --- a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.engrad +++ /dev/null @@ -1,34 +0,0 @@ -# -# Number of atoms -# - 5 -# -# The current total energy in Eh -# - -4.175218519970 -# -# The current gradient in Eh/bohr -# - 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2 0.0000000000E+00 6.8379081575E-04 -3.1937815854E-02 1.2483986839E-01 -2.1042842766E-06 - 3 0.0000000000E+00 -4.8958509759E-02 3.3463985344E-02 8.8286458306E-03 -2.4474256739E-06 - 4 0.0000000000E+00 3.4965092692E-01 4.7965845299E-01 1.2080417716E-01 4.8163341852E-01 - 5 0.0000000000E+00 -3.2185549380E-03 1.5013119824E-01 -5.8686871577E-01 1.3444934690E-01 - 6 0.0000000000E+00 3.6320544779E-01 -3.5086958291E-01 -2.6753226731E-01 -1.6060826546E-01 - 7 0.0000000000E+00 1.3368615134E-01 4.5875836547E-01 -1.7221936430E-01 -3.4960191712E-01 - 8 0.0000000000E+00 2.9946405912E-01 1.7951912997E-01 -1.7634254451E-01 -3.1928324596E-01 - 9 0.0000000000E+00 3.8523460216E-01 -4.1267227574E-01 8.8852833333E-02 -3.0351961154E-01 - 10 0.0000000000E+00 2.2142626156E-01 3.9231247427E-01 3.2953390855E-01 -3.0367097945E-01 - 11 0.0000000000E+00 -2.8494402080E-01 -4.1806165335E-02 -1.2850248619E-01 2.5618530386E-01 - 12 0.0000000000E+00 5.5433107230E-01 -1.2697906740E-01 -5.6276459837E-02 4.6415321872E-01 - 13 0.0000000000E+00 1.8158410278E-01 -1.1485574868E-01 2.8082622332E-02 1.7174845695E-01 - 14 0.0000000000E+00 -1.9449312243E-02 9.2716458384E-02 -5.9583750281E-01 -7.1326330842E-02 - 10 11 12 13 14 - 0 2.6627445365E-07 -9.2465528650E-05 -1.2392804697E-02 -1.5777178984E-02 -8.4952426649E-02 - 1 7.6420126515E-07 -6.0382317016E-05 -3.8001795953E-02 -7.6080830644E-02 1.9673297139E-02 - 2 -1.1373327037E-06 2.8933120330E-05 7.7600466571E-02 -3.9777771804E-02 -3.9330151542E-03 - 3 1.2399571826E-06 -4.9908209222E-01 1.2262267864E-01 1.5594148384E-01 8.3825091479E-01 - 4 -1.3444228464E-01 -3.0339721201E-05 -1.7574466793E-02 -3.5184448973E-02 9.1012344449E-03 - 5 4.8159367532E-01 1.4242294503E-05 3.5887637599E-02 -1.8395850186E-02 -1.8197234278E-03 - 6 4.4320256200E-01 1.6691715919E-01 2.8491106346E-01 4.9042483503E-02 1.0534938301E-02 - 7 -2.2968569630E-01 2.7432124992E-01 4.6000479877E-01 5.7387058460E-02 9.0971785732E-02 - 8 2.8572925384E-02 -3.8436939116E-01 -6.3323291108E-01 -1.4810466961E-01 -1.1652870621E-01 - 9 -3.6069470191E-01 1.6672499246E-01 -1.6969360392E-01 2.3044093055E-01 4.3166124965E-02 - 10 3.4582583817E-01 1.9545046246E-01 -2.0976549547E-01 2.4347887274E-01 1.0575001080E-01 - 11 -1.7352728000E-02 4.2929823266E-01 -3.8616812782E-01 5.9357259509E-01 2.1043489954E-01 - 12 -8.2512272887E-02 1.6654172972E-01 -9.0171509999E-02 -2.4742916696E-01 1.2031349464E-01 - 13 1.8293036796E-02 -4.6902187661E-01 2.2015219841E-01 6.4087293927E-01 -4.4024363806E-01 - 14 -4.9280032062E-01 -4.5287841445E-02 5.8851492583E-02 4.6906909965E-02 -4.5221941107E-02 - -# -# The atoms: label mass x y z (in bohrs) -# -$atoms -5 - C 12.01100 1.969609942105 -0.103343819014 -0.136564905340 - H 1.00800 4.014597228437 -0.103334004965 -0.136567107326 - H 1.00800 1.287956551539 -1.223427268146 1.432744007459 - H 1.00800 1.287948517399 -0.902359454518 -1.891237646665 - H 1.00800 1.287949843053 1.815756729845 0.048810907902 - -$actual_temperature - 0.000000 - -$frequency_scale_factor - 1.000000 - -$dipole_derivatives -15 - -0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 - 0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 - 0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 - -2.0000000000E-01 0.0000000000E+00 0.0000000000E+00 - 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 - 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 - 0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 - -0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 - 0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 - 0.0000000000E+00 -0.0000000000E+00 -0.0000000000E+00 - -0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00 - -0.0000000000E+00 -0.0000000000E+00 -0.0000000000E+00 - 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 - 0.0000000000E+00 -2.0000000000E-01 -0.0000000000E+00 - 0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00 - -# -# The IR spectrum -# wavenumber eps Int TX TY TZ -# -$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 0.00022921 1.15834033 0.001870 -0.006937 0.000000 - 1385.81 0.00009275 0.46870034 -0.001278 0.004388 0.000000 - 1385.82 0.00000562 0.02838005 -0.000337 -0.001073 0.000000 - 1557.27 0.00022581 1.14113331 0.000000 -0.006727 0.000000 - 1557.28 0.00000256 0.01294560 -0.000000 -0.000716 0.000000 - 3090.01 0.00359073 18.14609414 0.013877 0.013041 0.000000 - 3103.92 0.00044880 2.26803333 -0.003269 -0.005868 0.000000 - 3103.94 0.00307453 15.53740262 -0.004157 -0.017083 0.000000 - 3103.96 0.00633569 32.01796816 -0.022344 0.011735 0.000000 - - -$end - diff --git a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.in b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.in deleted file mode 100644 index 247d130..0000000 --- a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.in +++ /dev/null @@ -1,13 +0,0 @@ -#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/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.out b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.out deleted file mode 100644 index 1b262da..0000000 --- a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.out +++ /dev/null @@ -1,711 +0,0 @@ - - ***************** - * 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 2022/08/05 at 08:10:00.277 - - ------------------------------------------------- - | 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 : 0.76798836703338 - - 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 10340.8 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 -0.4674580 -12.7202 - 4 2.0000 -0.4674577 -12.7202 (HOMO) - 5 0.1702647 4.6331 (LUMO) - 6 0.2292553 6.2384 - 7 0.2292573 6.2384 - 8 0.2292593 6.2385 - ------------------------------------------------------------- - HL-Gap 0.6377224 Eh 17.3533 eV - Fermi-level -0.1485965 Eh -4.0435 eV - - SCC (total) 0 d, 0 h, 0 min, 0.020 sec - SCC setup ... 0 min, 0.000 sec ( 0.578%) - Dispersion ... 0 min, 0.000 sec ( 0.119%) - classical contributions ... 0 min, 0.000 sec ( 0.083%) - integral evaluation ... 0 min, 0.000 sec ( 0.958%) - iterations ... 0 min, 0.019 sec ( 95.735%) - molecular gradient ... 0 min, 0.000 sec ( 1.769%) - printout ... 0 min, 0.000 sec ( 0.706%) - - ::::::::::::::::::::::::::::::::::::::::::::::::::::: - :: SUMMARY :: - ::::::::::::::::::::::::::::::::::::::::::::::::::::: - :: total energy -4.175218519973 Eh :: - :: gradient norm 0.000006772752 Eh/a0 :: - :: HOMO-LUMO gap 17.353310653954 eV :: - ::.................................................:: - :: SCC energy -4.247467308169 Eh :: - :: -> isotropic ES 0.002035567931 Eh :: - :: -> anisotropic ES 0.002321540934 Eh :: - :: -> anisotropic XC 0.003585096737 Eh :: - :: -> dispersion -0.000661011606 Eh :: - :: repulsion energy 0.072248782606 Eh :: - :: add. restraining 0.000000000000 Eh :: - :: total charge -0.000000000000 e :: - ::::::::::::::::::::::::::::::::::::::::::::::::::::: - - -Property printout bound to 'properties.out' - - ------------------------------------------------- - | TOTAL ENERGY -4.175218519973 Eh | - | GRADIENT NORM 0.000006772752 Eh/α | - | HOMO-LUMO GAP 17.353310653954 eV | - ------------------------------------------------- - ------------------------------------------------------------------------- - * finished run on 2022/08/05 at 08:10:00.308 ------------------------------------------------------------------------- - total: - * wall-time: 0 d, 0 h, 0 min, 0.031 sec - * cpu-time: 0 d, 0 h, 0 min, 0.014 sec - * ratio c/w: 0.453 speedup - SCF: - * wall-time: 0 d, 0 h, 0 min, 0.020 sec - * cpu-time: 0 d, 0 h, 0 min, 0.003 sec - * ratio c/w: 0.166 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 -0.105224 0.071927 0.018977 -0.000002 0.000000 -0.000092 - 1 -0.074385 -0.102040 -0.025697 -0.000009 0.000001 -0.000060 - 2 0.000684 -0.031938 0.124840 -0.000002 -0.000001 0.000029 - 3 -0.048959 0.033464 0.008829 -0.000002 0.000001 -0.499082 - 4 0.349651 0.479658 0.120804 0.481633 -0.134442 -0.000030 - 5 -0.003219 0.150131 -0.586869 0.134449 0.481594 0.000014 - 6 0.363205 -0.350870 -0.267532 -0.160608 0.443203 0.166917 - 7 0.133686 0.458758 -0.172219 -0.349602 -0.229686 0.274321 - 8 0.299464 0.179519 -0.176343 -0.319283 0.028573 -0.384369 - 9 0.385235 -0.412672 0.088853 -0.303520 -0.360695 0.166725 - 10 0.221426 0.392312 0.329534 -0.303671 0.345826 0.195450 - 11 -0.284944 -0.041806 -0.128502 0.256185 -0.017353 0.429298 - 12 0.554331 -0.126979 -0.056276 0.464153 -0.082512 0.166542 - 13 0.181584 -0.114856 0.028083 0.171748 0.018293 -0.469022 - 14 -0.019449 0.092716 -0.595838 -0.071326 -0.492800 -0.045288 - 12 13 14 - 0 -0.012393 -0.015777 -0.084952 - 1 -0.038002 -0.076081 0.019673 - 2 0.077600 -0.039778 -0.003933 - 3 0.122623 0.155941 0.838251 - 4 -0.017574 -0.035184 0.009101 - 5 0.035888 -0.018396 -0.001820 - 6 0.284911 0.049042 0.010535 - 7 0.460005 0.057387 0.090972 - 8 -0.633233 -0.148105 -0.116529 - 9 -0.169694 0.230441 0.043166 - 10 -0.209765 0.243479 0.105750 - 11 -0.386168 0.593573 0.210435 - 12 -0.090172 -0.247429 0.120313 - 13 0.220152 0.640873 -0.440244 - 14 0.058851 0.046907 -0.045222 - - ------------ -IR SPECTRUM ------------ - - Mode freq eps Int T**2 TX TY TZ - cm**-1 L/(mol*cm) km/mol a.u. ----------------------------------------------------------------------------- - 6: 1385.80 0.000229 1.16 0.000052 ( 0.001870 -0.006937 0.000000) - 7: 1385.81 0.000093 0.47 0.000021 (-0.001278 0.004388 0.000000) - 8: 1385.82 0.000006 0.03 0.000001 (-0.000337 -0.001073 0.000000) - 9: 1557.27 0.000226 1.14 0.000045 ( 0.000000 -0.006727 0.000000) - 10: 1557.28 0.000003 0.01 0.000001 (-0.000000 -0.000716 0.000000) - 11: 3090.01 0.003591 18.15 0.000363 ( 0.013877 0.013041 0.000000) - 12: 3103.92 0.000449 2.27 0.000045 (-0.003269 -0.005868 0.000000) - 13: 3103.94 0.003075 15.54 0.000309 (-0.004157 -0.017083 0.000000) - 14: 3103.96 0.006336 32.02 0.000637 (-0.022344 0.011735 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: 5.355317 5.355310 5.355299 - -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 ... 51.424 sec (= 0.857 min) -Numerical frequency calculation ... 51.346 sec (= 0.856 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 463 msec diff --git a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.xtbrestart b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.xtbrestart deleted file mode 100644 index 6656072..0000000 Binary files a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.xtbrestart and /dev/null differ diff --git a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd_property.txt b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd_property.txt deleted file mode 100644 index 5081b06..0000000 --- a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd_property.txt +++ /dev/null @@ -1,48 +0,0 @@ -------------------------------------------------------------- ------------------------ !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 1385.801368 - 7 1385.807055 - 8 1385.818393 - 9 1557.267394 - 10 1557.277196 - 11 3090.006345 - 12 3103.917565 - 13 3103.936793 - 14 3103.955476 - Zero Point Energy (Hartree) : 0.0448201860 - Inner Energy (Hartree) : -4.1275343906 - 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) : -4.1476937452 - Is Linear : false -# ------------------------------------------------------------- ------------------------ !GEOMETRIES! ------------------------ -# ------------------------------------------------------------- diff --git a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/run.sh b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/run.sh deleted file mode 100644 index f72e163..0000000 --- a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/run.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/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/metana_02514d87e9c74c04985fb73ba2b46a97/geom.smi b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/geom.smi deleted file mode 100644 index 3cc58df..0000000 --- a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/geom.smi +++ /dev/null @@ -1 +0,0 @@ -C diff --git a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/geom.xyz b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/geom.xyz deleted file mode 100644 index ecd66c5..0000000 --- a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/geom.xyz +++ /dev/null @@ -1,7 +0,0 @@ -5 - -C 1.04227 -0.05469 -0.07227 -H 2.13447 -0.05468 -0.07227 -H 0.67821 -0.65291 0.76588 -H 0.67821 -0.48143 -1.00941 -H 0.67821 0.97028 0.02674 diff --git a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/run.sh b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/run.sh deleted file mode 100644 index f72e163..0000000 --- a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/run.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/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/metana_02514d87e9c74c04985fb73ba2b46a97/run_babel.sh b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/run_babel.sh deleted file mode 100644 index 0d5d00e..0000000 --- a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/run_babel.sh +++ /dev/null @@ -1,8 +0,0 @@ -#!/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/metana_02514d87e9c74c04985fb73ba2b46a97/slurm-3027.out b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/slurm-3027.out deleted file mode 100644 index b7d75ac..0000000 --- a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/slurm-3027.out +++ /dev/null @@ -1 +0,0 @@ -1 molecule converted diff --git a/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/slurm-3028.out b/cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/slurm-3028.out deleted file mode 100644 index e69de29..0000000 diff --git a/lib/__pycache__/cmmde_xtb.cpython-39.pyc b/lib/__pycache__/cmmde_xtb.cpython-39.pyc index cc15f64..290b0bd 100644 Binary files a/lib/__pycache__/cmmde_xtb.cpython-39.pyc and b/lib/__pycache__/cmmde_xtb.cpython-39.pyc differ diff --git a/lib/cmmde_xtb.py b/lib/cmmde_xtb.py index 35427a2..a99a6de 100644 --- a/lib/cmmde_xtb.py +++ b/lib/cmmde_xtb.py @@ -20,34 +20,34 @@ cd $PWD""".format(nproc),file=fout) meth += '--gfn0' if 'opt' in job: if solvent != 'none': - print("$XTB_COMMAND {} --opt -P {} --alpb {} --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,solvent,charge,mult-1,meth),file=fout) + print("$XTB_COMMAND {} --opt -P {} --alpb {} --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,solvent,charge,mult-1,meth),file=fout) else: - print("$XTB_COMMAND {} --opt -P {} --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,charge,mult-1,meth),file=fout) + print("$XTB_COMMAND {} --opt -P {} --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,charge,mult-1,meth),file=fout) if 'fix' in job: if solvent != 'none': - print("$XTB_COMMAND {} --opt -P {} --alpb {} --chrg {} --uhf {} {} --input cmmd.in > xtb.out".format(geom,nproc,solvent,charge,mult-1,meth),file=fout) + print("$XTB_COMMAND {} --opt -P {} --alpb {} --chrg {} --uhf {} {} --input cmmd.in > cmmd.out".format(geom,nproc,solvent,charge,mult-1,meth),file=fout) else: - print("$XTB_COMMAND {} --opt -P {} --chrg {} --uhf {} {} --input cmmd.in > xtb.out".format(geom,nproc,charge,mult-1,meth),file=fout) + print("$XTB_COMMAND {} --opt -P {} --chrg {} --uhf {} {} --input cmmd.in > cmmd.out".format(geom,nproc,charge,mult-1,meth),file=fout) if 'freq' in job: if solvent != 'none': - print("$XTB_COMMAND {} --hess -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,solvent,charge,mult-1,meth), file=fout) + print("$XTB_COMMAND {} --hess -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,solvent,charge,mult-1,meth), file=fout) else: - print("$XTB_COMMAND {} --hess -P {} --input cmmd.in --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,charge,mult-1,meth), file=fout) + print("$XTB_COMMAND {} --hess -P {} --input cmmd.in --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,charge,mult-1,meth), file=fout) if 'opt' in job and 'freq' in job: if solvent != 'none': - print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,solvent,charge, mult-1,meth),file=fout) + print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,solvent,charge, mult-1,meth),file=fout) else: - print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,charge,mult-1,meth),file=fout) + print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,charge,mult-1,meth),file=fout) if 'path' in job: if solvent != 'none': - print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} --alpb {} --chrg {} --uhf {} ,method > xtb.out".format(geom,product,nproc,solvent,charge,mult-1,meth),file=fout) + print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} --alpb {} --chrg {} --uhf {} ,method > cmmd.out".format(geom,product,nproc,solvent,charge,mult-1,meth),file=fout) else: - print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} --chrg {} --uhf {} {} > xtb.out".format(geom,product,nproc,charge,mult-1,meth),file=fout) + print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} --chrg {} --uhf {} {} > cmmd.out".format(geom,product,nproc,charge,mult-1,meth),file=fout) if 'scan' in job: if solvent != 'none': - print("$XTB_COMMAND {} --opt -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,solvent,charge,mult-1,meth), file=fout) + print("$XTB_COMMAND {} --opt -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,solvent,charge,mult-1,meth), file=fout) else: - print("$XTB_COMMAND {} --opt -P {} --input cmmd.in --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,charge,mult-1,meth), file=fout) + print("$XTB_COMMAND {} --opt -P {} --input cmmd.in --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,charge,mult-1,meth), file=fout) if 'freq' in job: with open('cmmd.in', 'w') as f: print("""$thermo @@ -112,3 +112,5 @@ $end""".format(nrun,npoint,anopt,kpush,kpull,ppull,alp),file=f) os.system('sbatch run.sh') + +