From 95f1889cd62019856308fa8f7e26ef205d00d095 Mon Sep 17 00:00:00 2001 From: Aditya Wibawa Sakti Date: Thu, 30 Jun 2022 09:09:43 +0700 Subject: [PATCH] change gui template --- README.md | 2 +- cmmde_gui/test/cmmd.engrad | 62 ++ cmmde_gui/test/cmmd.gbw | Bin 0 -> 652588 bytes cmmde_gui/test/cmmd.in | 8 + cmmde_gui/test/cmmd.opt | 789 ++++++++++++++ cmmde_gui/test/cmmd.out | 1709 ++++++++++++++++++++++++++++++ cmmde_gui/test/cmmd.xtbrestart | Bin 0 -> 1088 bytes cmmde_gui/test/cmmd.xyz | 14 + cmmde_gui/test/cmmd_property.txt | 6 + cmmde_gui/test/cmmd_trj.xyz | 56 + cmmde_gui/test/geom.smi | 1 + cmmde_gui/test/geom.xyz | 14 + cmmde_gui/test/run.sh | 10 + cmmde_gui/test/run_babel.sh | 8 + cmmde_gui/test/slurm-2745.out | 1 + cmmde_gui/test/slurm-2746.out | 0 16 files changed, 2679 insertions(+), 1 deletion(-) create mode 100644 cmmde_gui/test/cmmd.engrad create mode 100644 cmmde_gui/test/cmmd.gbw create mode 100644 cmmde_gui/test/cmmd.in create mode 100644 cmmde_gui/test/cmmd.opt create mode 100644 cmmde_gui/test/cmmd.out create mode 100644 cmmde_gui/test/cmmd.xtbrestart create mode 100644 cmmde_gui/test/cmmd.xyz create mode 100644 cmmde_gui/test/cmmd_property.txt create mode 100644 cmmde_gui/test/cmmd_trj.xyz create mode 100644 cmmde_gui/test/geom.smi create mode 100644 cmmde_gui/test/geom.xyz create mode 100644 cmmde_gui/test/run.sh create mode 100644 cmmde_gui/test/run_babel.sh create mode 100644 cmmde_gui/test/slurm-2745.out create mode 100644 cmmde_gui/test/slurm-2746.out diff --git a/README.md b/README.md index 74c9a5d..c57fa6c 100644 --- a/README.md +++ b/README.md @@ -36,7 +36,7 @@ Informasi lebih lanjut: cmmde@mki.or.id ## Installation 1. Cloning the repository: ```bash -git clone https://git.mki.or.id/CoreDev/CMMDE +git clone https://git.mki.or.id/coredev/CMMDE ``` 2. Change directory to CMMDE: ```bash diff --git a/cmmde_gui/test/cmmd.engrad b/cmmde_gui/test/cmmd.engrad new file mode 100644 index 0000000..169b237 --- /dev/null +++ b/cmmde_gui/test/cmmd.engrad @@ -0,0 +1,62 @@ +# +# Number of atoms +# + 12 +# +# The current total energy in Eh +# + -15.879640652450 +# +# The current gradient in Eh/bohr +# + 0.000083151256 + 0.000032627904 + -0.000000801280 + -0.000011773444 + -0.000092719019 + -0.000008798638 + 0.000004092498 + -0.000045349095 + 0.000008265502 + -0.000095719643 + 0.000023986034 + -0.000000346361 + -0.000010542094 + 0.000056660251 + -0.000008827102 + 0.000027808309 + 0.000031909554 + 0.000010537622 + -0.000055844305 + -0.000000629739 + 0.000001035977 + -0.000012931289 + 0.000055053936 + 0.000010215618 + 0.000028823167 + 0.000043789233 + -0.000010112181 + 0.000056885559 + -0.000009417128 + 0.000000682946 + 0.000014817015 + -0.000052034477 + 0.000010200866 + -0.000028767027 + -0.000043877452 + -0.000012052970 +# +# The atomic numbers and current coordinates in Bohr +# + 6 2.5938463 -0.4162363 0.0103377 + 6 0.9500210 -2.4517633 -0.0164952 + 6 -1.6347236 -2.0458335 -0.0259782 + 6 -2.5758034 0.3955182 -0.0084365 + 6 -0.9319776 2.4309707 0.0184779 + 6 1.6528189 2.0250743 0.0277733 + 1 4.6108664 -0.7330783 0.0176863 + 1 1.6844131 -4.3568328 -0.0299365 + 1 -2.9175367 -3.6341720 -0.0471728 + 1 -4.5928432 0.7121836 -0.0157500 + 1 -1.6662937 4.3360760 0.0323392 + 1 2.9355884 3.6134472 0.0485120 diff --git a/cmmde_gui/test/cmmd.gbw b/cmmde_gui/test/cmmd.gbw new file mode 100644 index 0000000000000000000000000000000000000000..5e63b44d30bdd1073eb9d72f6bd44017b1cfd74f GIT binary patch literal 652588 zcmeI*3z!{MeE{&gNx+C`Lx_He6tP5&MjjFZtu#C1i&u;UQLsRjWV1;Yvk!JRNRaAU z0kK8#Sv3>{DIess#TQt4xwpacQ9jhvAQ;h)r}#i{5mO)#?VUO2++^2;O)!vz`OWv; z{ok20_sluJbLQNc*}3;lsfFpWho2vxZ8)@bcFx;yiltQ$*l%HXXZwD0=5_S%*WJ^2 z^tR2ZLbcT~3KR|g-Z@>}9bNrQDkxC4|AKz)U%|F7s$8~zpZ2e4^N05DnrHv7Xa@-U zf7|?uR=@JqF5ADe=YYyXR1_eze{WkyMeASnYM1Tb*3r|a15~mrl4`L 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zuNhpusC(#Ve_yLlzwxu**&t)m;NVZrJbC#=y<_uTXFRdurw@F3vpha~ZttPLJ7rCF^f_O6-SN|E`Bi(3 zd*KB=|GHUu+eCtc&Uw!#zK~g{jun@` z{KCDLtr=`zar>;v@7^W9=SM%f^t+$9D4K3s9=9F!k-- literal 0 HcmV?d00001 diff --git a/cmmde_gui/test/cmmd.in b/cmmde_gui/test/cmmd.in new file mode 100644 index 0000000..83e0fa1 --- /dev/null +++ b/cmmde_gui/test/cmmd.in @@ -0,0 +1,8 @@ +#CMMDE generated Orca input file +!XTB2 opt +%pal + nprocs 1 +end + +*xyzfile 0 1 geom.xyz + diff --git a/cmmde_gui/test/cmmd.opt b/cmmde_gui/test/cmmd.opt new file mode 100644 index 0000000..9c9c252 --- /dev/null +++ b/cmmde_gui/test/cmmd.opt @@ -0,0 +1,789 @@ + +$orca_opt_file + +$trust + 0.300000000000 + +$epredict + 0.000000000000 + +$ediffsc + 1000.000000000000 + +$ctyp + 3 + +$coordinates + 3 36 + 2.61288653 -0.41908456 0.01052577 0.95684393 -2.46996654 -0.01536347 + -1.64670735 -2.06091642 -0.02753331 -2.59502862 0.39856214 -0.00842818 + -0.93887264 2.44900948 0.01999330 1.66482983 2.04001605 0.02668293 + 4.64154533 -0.73782467 0.01814137 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***************** + + #, + ### + #### + ##### + ###### + ########, + ,,################,,,,, + ,,#################################,, + ,,##########################################,, + ,#########################################, ''#####, + ,#############################################,, '####, + ,##################################################,,,,####, + ,###########'''' ''''############################### + ,#####'' ,,,,##########,,,, '''####''' '#### + ,##' ,,,,###########################,,, '## + ' ,,###'''' '''############,,, + ,,##'' '''############,,,, ,,,,,,###'' + ,#'' '''#######################''' + ' ''''####'''' + ,#######, #######, ,#######, ## + ,#' '#, ## ## ,#' '#, #''# ###### ,####, + ## ## ## ,#' ## #' '# # #' '# + ## ## ####### ## ,######, #####, # # + '#, ,#' ## ## '#, ,#' ,# #, ## #, ,# + '#######' ## ## '#######' #' '# #####' # '####' + + + + ####################################################### + # -***- # + # Department of theory and spectroscopy # + # Directorship and core code : Frank Neese # + # Max Planck Institute fuer Kohlenforschung # + # Kaiser Wilhelm Platz 1 # + # D-45470 Muelheim/Ruhr # + # Germany # + # # + # All rights reserved # + # -***- # + ####################################################### + + + Program Version 5.0.2 - RELEASE - + + + With contributions from (in alphabetic order): + Daniel Aravena : Magnetic Suceptibility + Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation) + Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum + Ute Becker : Parallelization + Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD + Martin Brehm : Molecular dynamics + Dmytro Bykov : SCF Hessian + Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE + Dipayan Datta : RHF DLPNO-CCSD density + Achintya Kumar Dutta : EOM-CC, STEOM-CC + Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI + Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme + Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization + Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods + Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals + Lee Huntington : MR-EOM, pCC + Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM + Marcus Kettner : VPT2 + Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K + Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian + Martin Krupicka : Initial AUTO-CI + Lucas Lang : DCDCAS + Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC + Dagmar Lenk : GEPOL surface, SMD + Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization + Dimitrios Manganas : Further ROCIS development; embedding schemes + Dimitrios Pantazis : SARC Basis sets + Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients + Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS + Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient + Christoph Reimann : Effective Core Potentials + Marius Retegan : Local ZFS, SOC + Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples + Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB + Michael Roemelt : Original ROCIS implementation + Masaaki Saitow : Open-shell DLPNO-CCSD energy and density + Barbara Sandhoefer : DKH picture change effects + Avijit Sen : IP-ROCIS + Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI + Bernardo de Souza : ESD, SOC TD-DFT + Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response + Willem Van den Heuvel : Paramagnetic NMR + Boris Wezisla : Elementary symmetry handling + Frank Wennmohs : Technical directorship + + + We gratefully acknowledge several colleagues who have allowed us to + interface, adapt or use parts of their codes: + Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization, + C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF + Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods + Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG + Ulf Ekstrom : XCFun DFT Library + Mihaly Kallay : mrcc (arbitrary order and MRCC methods) + Jiri Pittner, Ondrej Demel : Mk-CCSD + Frank Weinhold : gennbo (NPA and NBO analysis) + Christopher J. Cramer and Donald G. Truhlar : smd solvation model + Lars Goerigk : TD-DFT with DH, B97 family of functionals + V. Asgeirsson, H. Jonsson : NEB implementation + FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT + MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM, + LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT, + nearIR, NL-DFT gradient (VV10), updates on ESD, + ML-optimized integration grids + S Lehtola, MJT Oliveira, MAL Marques : LibXC Library + Liviu Ungur et al : ANISO software + + + Your calculation uses the libint2 library for the computation of 2-el integrals + For citations please refer to: http://libint.valeyev.net + + Your ORCA version has been built with support for libXC version: 5.1.0 + For citations please refer to: https://tddft.org/programs/libxc/ + + This ORCA versions uses: + CBLAS interface : Fast vector & matrix operations + LAPACKE interface : Fast linear algebra routines + SCALAPACK package : Parallel linear algebra routines + Shared memory : Shared parallel matrices + BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED + Core in use : SkylakeX + Copyright (c) 2011-2014, The OpenBLAS Project + + + + +*************************************** +The coordinates will be read from file: geom.xyz +*************************************** + + +Your calculation utilizes the semiempirical GFN2-xTB method +Please cite in your paper: +C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652. + + +================================================================================ + +================================================================================ + WARNINGS + Please study these warnings very carefully! +================================================================================ + + +WARNING: Geometry Optimization + ===> : Switching off AutoStart + For restart on a previous wavefunction, please use MOREAD + +WARNING: Found dipole moment calculation with XTB calculation + ===> : Switching off dipole moment calculation + + +WARNING: TRAH-SCF for XTB is not implemented! + ===> : Turning TRAH off! + +================================================================================ + INPUT FILE +================================================================================ +NAME = cmmd.in +| 1> #CMMDE generated Orca input file +| 2> !XTB2 opt +| 3> %pal +| 4> nprocs 1 +| 5> end +| 6> +| 7> *xyzfile 0 1 geom.xyz +| 8> +| 9> +| 10> ****END OF INPUT**** +================================================================================ + + ***************************** + * Geometry Optimization Run * + ***************************** + +Geometry optimization settings: +Update method Update .... BFGS +Choice of coordinates CoordSys .... Z-matrix Internals +Initial Hessian InHess .... Almoef's Model + +Convergence Tolerances: +Energy Change TolE .... 5.0000e-06 Eh +Max. Gradient TolMAXG .... 3.0000e-04 Eh/bohr +RMS Gradient TolRMSG .... 1.0000e-04 Eh/bohr +Max. Displacement TolMAXD .... 4.0000e-03 bohr +RMS Displacement TolRMSD .... 2.0000e-03 bohr +Strict Convergence .... False +------------------------------------------------------------------------------ + ORCA OPTIMIZATION COORDINATE SETUP +------------------------------------------------------------------------------ + +The optimization will be done in new redundant internal coordinates +Making redundant internal coordinates ... (new redundants) done +Evaluating the initial hessian ... (Almloef) done +Evaluating the coordinates ... done +Calculating the B-matrix .... done +Calculating the G-matrix .... done +Diagonalizing the G-matrix .... done +The first mode is .... 24 +The number of degrees of freedom .... 30 + + ----------------------------------------------------------------- + Redundant Internal Coordinates + + + ----------------------------------------------------------------- + Definition Initial Value Approx d2E/dq + ----------------------------------------------------------------- + 1. B(C 1,C 0) 1.3950 0.613451 + 2. B(C 2,C 1) 1.3947 0.614202 + 3. B(C 3,C 2) 1.3949 0.613576 + 4. B(C 4,C 3) 1.3949 0.613739 + 5. B(C 5,C 4) 1.3947 0.614057 + 6. B(C 5,C 0) 1.3947 0.614134 + 7. B(H 6,C 0) 1.0867 0.364496 + 8. B(H 7,C 1) 1.0866 0.364619 + 9. B(H 8,C 2) 1.0867 0.364500 + 10. B(H 9,C 3) 1.0865 0.364768 + 11. B(H 10,C 4) 1.0868 0.364328 + 12. B(H 11,C 5) 1.0867 0.364525 + 13. A(C 1,C 0,C 5) 119.9985 0.432498 + 14. A(C 1,C 0,H 6) 119.9915 0.352999 + 15. A(C 5,C 0,H 6) 120.0100 0.353066 + 16. A(C 2,C 1,H 7) 120.0112 0.353093 + 17. A(C 0,C 1,C 2) 119.9923 0.432506 + 18. A(C 0,C 1,H 7) 119.9965 0.353020 + 19. A(C 3,C 2,H 8) 119.9904 0.353012 + 20. A(C 1,C 2,H 8) 119.9986 0.353073 + 21. A(C 1,C 2,C 3) 120.0110 0.432522 + 22. A(C 4,C 3,H 9) 120.0060 0.353072 + 23. A(C 2,C 3,H 9) 120.0051 0.353056 + 24. A(C 2,C 3,C 4) 119.9889 0.432464 + 25. A(C 3,C 4,H 10) 119.9962 0.353000 + 26. A(C 3,C 4,C 5) 120.0006 0.432525 + 27. A(C 5,C 4,H 10) 120.0032 0.353031 + 28. A(C 0,C 5,C 4) 120.0085 0.432575 + 29. A(C 4,C 5,H 11) 120.0010 0.353063 + 30. A(C 0,C 5,H 11) 119.9904 0.353071 + 31. D(H 7,C 1,C 0,C 5) -179.9604 0.026008 + 32. D(H 7,C 1,C 0,H 6) 0.0383 0.026008 + 33. D(C 2,C 1,C 0,H 6) -179.9399 0.026008 + 34. D(C 2,C 1,C 0,C 5) 0.0614 0.026008 + 35. D(H 8,C 2,C 1,C 0) 179.8875 0.026075 + 36. D(C 3,C 2,C 1,C 0) -0.1354 0.026075 + 37. D(C 3,C 2,C 1,H 7) 179.8864 0.026075 + 38. D(H 8,C 2,C 1,H 7) -0.0907 0.026075 + 39. D(H 9,C 3,C 2,H 8) 0.0470 0.026019 + 40. D(H 9,C 3,C 2,C 1) -179.9301 0.026019 + 41. D(C 4,C 3,C 2,H 8) -179.9511 0.026019 + 42. D(C 4,C 3,C 2,C 1) 0.0718 0.026019 + 43. D(H 10,C 4,C 3,C 2) -179.9591 0.026033 + 44. D(C 5,C 4,C 3,H 9) -179.9323 0.026033 + 45. D(C 5,C 4,C 3,C 2) 0.0658 0.026033 + 46. D(H 10,C 4,C 3,H 9) 0.0427 0.026033 + 47. D(H 11,C 5,C 4,H 10) -0.1033 0.026062 + 48. D(C 0,C 5,C 4,H 10) 179.8851 0.026062 + 49. D(C 0,C 5,C 4,C 3) -0.1398 0.026062 + 50. D(H 11,C 5,C 0,H 6) 0.0659 0.026069 + 51. D(H 11,C 5,C 0,C 1) -179.9354 0.026069 + 52. D(H 11,C 5,C 4,C 3) 179.8717 0.026062 + 53. D(C 4,C 5,C 0,H 6) -179.9225 0.026069 + 54. D(C 4,C 5,C 0,C 1) 0.0762 0.026069 + ----------------------------------------------------------------- + +Number of atoms .... 12 +Number of degrees of freedom .... 54 + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 1 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.382680 -0.221770 0.005570 + C 0.506340 -1.307050 -0.008130 + C -0.871400 -1.090590 -0.014570 + C -1.373230 0.210910 -0.004460 + C -0.496830 1.295960 0.010580 + C 0.880990 1.079530 0.014120 + H 2.456200 -0.390440 0.009600 + H 0.897240 -2.320890 -0.014140 + H -1.554150 -1.935930 -0.027090 + H -2.446570 0.379420 -0.008330 + H -0.887690 2.310030 0.019130 + H 1.563770 1.924860 0.023730 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.612887 -0.419085 0.010526 + 1 C 6.0000 0 12.011 0.956844 -2.469967 -0.015363 + 2 C 6.0000 0 12.011 -1.646707 -2.060916 -0.027533 + 3 C 6.0000 0 12.011 -2.595029 0.398562 -0.008428 + 4 C 6.0000 0 12.011 -0.938873 2.449009 0.019993 + 5 C 6.0000 0 12.011 1.664830 2.040016 0.026683 + 6 H 1.0000 0 1.008 4.641545 -0.737825 0.018141 + 7 H 1.0000 0 1.008 1.695538 -4.385846 -0.026721 + 8 H 1.0000 0 1.008 -2.936918 -3.658378 -0.051193 + 9 H 1.0000 0 1.008 -4.623347 0.717000 -0.015741 + 10 H 1.0000 0 1.008 -1.677491 4.365324 0.036150 + 11 H 1.0000 0 1.008 2.955097 3.637458 0.044843 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/06/26 at 09:13:01.051 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 12 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.05298797103908 + + ID Z sym. atoms + 1 6 C 1-6 + 2 1 H 7-12 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 18 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.1615201 -0.161615E+02 0.494E+00 4.84 0.0 T + 2 -16.1767145 -0.151944E-01 0.296E+00 4.83 1.0 T + 3 -16.1770942 -0.379688E-03 0.492E-01 4.83 1.0 T + 4 -16.1774041 -0.309971E-03 0.515E-02 4.82 1.0 T + 5 -16.1774041 0.174099E-07 0.659E-03 4.82 4.4 T + 6 -16.1774041 -0.309461E-07 0.180E-03 4.82 16.0 T + 7 -16.1774042 -0.311983E-07 0.588E-04 4.82 49.1 T + 8 -16.1774042 0.808171E-10 0.178E-04 4.82 162.4 T + + *** convergence criteria satisfied after 8 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6387825 -17.3822 + ... ... ... ... + 9 2.0000 -0.4756453 -12.9430 + 10 2.0000 -0.4756384 -12.9428 + 11 2.0000 -0.4718343 -12.8393 + 12 2.0000 -0.4219300 -11.4813 + 13 2.0000 -0.4218886 -11.4802 + 14 2.0000 -0.4009568 -10.9106 + 15 2.0000 -0.4009234 -10.9097 (HOMO) + 16 -0.2236200 -6.0850 (LUMO) + 17 -0.2235509 -6.0831 + 18 -0.0961178 -2.6155 + 19 0.1107873 3.0147 + 20 0.1226310 3.3370 + ... ... ... + 30 0.6433999 17.5078 + ------------------------------------------------------------- + HL-Gap 0.1773034 Eh 4.8247 eV + Fermi-level -0.3122717 Eh -8.4973 eV + + SCC (total) 0 d, 0 h, 0 min, 0.049 sec + SCC setup ... 0 min, 0.001 sec ( 1.090%) + Dispersion ... 0 min, 0.000 sec ( 0.181%) + classical contributions ... 0 min, 0.000 sec ( 0.985%) + integral evaluation ... 0 min, 0.003 sec ( 5.776%) + iterations ... 0 min, 0.041 sec ( 83.251%) + molecular gradient ... 0 min, 0.004 sec ( 8.364%) + printout ... 0 min, 0.000 sec ( 0.330%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.878848475482 Eh :: + :: gradient norm 0.019149425975 Eh/a0 :: + :: HOMO-LUMO gap 4.824670438233 eV :: + ::.................................................:: + :: SCC energy -16.177404175194 Eh :: + :: -> isotropic ES 0.000752368509 Eh :: + :: -> anisotropic ES 0.002689473865 Eh :: + :: -> anisotropic XC 0.013008868445 Eh :: + :: -> dispersion -0.007987832843 Eh :: + :: repulsion energy 0.298548672022 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.878848475482 Eh | + | GRADIENT NORM 0.019149425975 Eh/α | + | HOMO-LUMO GAP 4.824670438233 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/06/26 at 09:13:01.140 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.088 sec + * cpu-time: 0 d, 0 h, 0 min, 0.032 sec + * ratio c/w: 0.362 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.049 sec + * cpu-time: 0 d, 0 h, 0 min, 0.014 sec + * ratio c/w: 0.295 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.878848475480 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 12 +Number of internal coordinates .... 54 +Current Energy .... -15.878848475 Eh +Current gradient norm .... 0.019149426 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Evaluating the initial hessian .... (Almloef) done +Projecting the Hessian .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.998622698 +Lowest eigenvalues of augmented Hessian: + -0.001470266 0.026024439 0.026025966 0.026033561 0.026041952 +Length of the computed step .... 0.052538613 +The final length of the internal step .... 0.052538613 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0071495997 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0141313345 RMS(Int)= 0.0071497568 + Iter 1: RMS(Cart)= 0.0000052351 RMS(Int)= 0.0000037874 + Iter 2: RMS(Cart)= 0.0000000333 RMS(Int)= 0.0000000244 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + RMS gradient 0.0039083086 0.0001000000 NO + MAX gradient 0.0109681387 0.0003000000 NO + RMS step 0.0071495997 0.0020000000 NO + MAX step 0.0178357525 0.0040000000 NO + ........................................................ + Max(Bonds) 0.0094 Max(Angles) 0.00 + Max(Dihed) 0.10 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.3950 0.010968 -0.0094 1.3855 + 2. B(C 2,C 1) 1.3947 0.010773 -0.0093 1.3854 + 3. B(C 3,C 2) 1.3949 0.010938 -0.0094 1.3855 + 4. B(C 4,C 3) 1.3949 0.010920 -0.0094 1.3855 + 5. B(C 5,C 4) 1.3947 0.010783 -0.0093 1.3855 + 6. B(C 5,C 0) 1.3947 0.010796 -0.0093 1.3854 + 7. B(H 6,C 0) 1.0867 0.004434 -0.0064 1.0803 + 8. B(H 7,C 1) 1.0866 0.004380 -0.0063 1.0803 + 9. B(H 8,C 2) 1.0867 0.004421 -0.0064 1.0803 + 10. B(H 9,C 3) 1.0865 0.004318 -0.0062 1.0803 + 11. B(H 10,C 4) 1.0868 0.004506 -0.0065 1.0803 + 12. B(H 11,C 5) 1.0867 0.004409 -0.0064 1.0803 + 13. A(C 1,C 0,C 5) 120.00 0.000006 -0.00 120.00 + 14. A(C 1,C 0,H 6) 119.99 -0.000013 0.00 119.99 + 15. A(C 5,C 0,H 6) 120.01 0.000007 -0.00 120.01 + 16. A(C 2,C 1,H 7) 120.01 0.000017 -0.00 120.01 + 17. A(C 0,C 1,C 2) 119.99 -0.000022 0.00 120.00 + 18. A(C 0,C 1,H 7) 120.00 0.000005 -0.00 120.00 + 19. A(C 3,C 2,H 8) 119.99 -0.000005 0.00 119.99 + 20. A(C 1,C 2,H 8) 120.00 -0.000008 0.00 120.00 + 21. A(C 1,C 2,C 3) 120.01 0.000013 -0.00 120.01 + 22. A(C 4,C 3,H 9) 120.01 0.000010 -0.00 120.00 + 23. A(C 2,C 3,H 9) 120.01 0.000016 -0.00 120.00 + 24. A(C 2,C 3,C 4) 119.99 -0.000026 0.00 119.99 + 25. A(C 3,C 4,H 10) 120.00 -0.000002 0.00 120.00 + 26. A(C 3,C 4,C 5) 120.00 -0.000002 0.00 120.00 + 27. A(C 5,C 4,H 10) 120.00 0.000004 -0.00 120.00 + 28. A(C 0,C 5,C 4) 120.01 0.000030 -0.00 120.00 + 29. A(C 4,C 5,H 11) 120.00 -0.000005 0.00 120.00 + 30. A(C 0,C 5,H 11) 119.99 -0.000026 0.00 119.99 + 31. D(H 7,C 1,C 0,C 5) -179.96 0.000006 -0.01 -179.97 + 32. D(H 7,C 1,C 0,H 6) 0.04 0.000007 -0.01 0.02 + 33. D(C 2,C 1,C 0,H 6) -179.94 0.000021 -0.04 -179.98 + 34. D(C 2,C 1,C 0,C 5) 0.06 0.000020 -0.04 0.02 + 35. D(H 8,C 2,C 1,C 0) 179.89 -0.000030 0.06 179.95 + 36. D(C 3,C 2,C 1,C 0) -0.14 -0.000045 0.09 -0.04 + 37. D(C 3,C 2,C 1,H 7) 179.89 -0.000031 0.06 179.95 + 38. D(H 8,C 2,C 1,H 7) -0.09 -0.000016 0.03 -0.06 + 39. D(H 9,C 3,C 2,H 8) 0.05 0.000008 -0.02 0.03 + 40. D(H 9,C 3,C 2,C 1) -179.93 0.000023 -0.05 -179.98 + 41. D(C 4,C 3,C 2,H 8) -179.95 0.000008 -0.02 -179.97 + 42. D(C 4,C 3,C 2,C 1) 0.07 0.000024 -0.05 0.02 + 43. D(H 10,C 4,C 3,C 2) -179.96 0.000006 -0.01 -179.97 + 44. D(C 5,C 4,C 3,H 9) -179.93 0.000024 -0.05 -179.98 + 45. D(C 5,C 4,C 3,C 2) 0.07 0.000023 -0.05 0.02 + 46. D(H 10,C 4,C 3,H 9) 0.04 0.000007 -0.01 0.03 + 47. D(H 11,C 5,C 4,H 10) -0.10 -0.000019 0.04 -0.06 + 48. D(C 0,C 5,C 4,H 10) 179.89 -0.000031 0.06 179.95 + 49. D(C 0,C 5,C 4,C 3) -0.14 -0.000048 0.10 -0.04 + 50. D(H 11,C 5,C 0,H 6) 0.07 0.000014 -0.03 0.04 + 51. D(H 11,C 5,C 0,C 1) -179.94 0.000014 -0.03 -179.97 + 52. D(H 11,C 5,C 4,C 3) 179.87 -0.000036 0.07 179.95 + 53. D(C 4,C 5,C 0,H 6) -179.92 0.000025 -0.05 -179.97 + 54. D(C 4,C 5,C 0,C 1) 0.08 0.000026 -0.05 0.02 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 2 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.373483 -0.220370 0.005486 + C 0.503034 -1.298271 -0.008552 + C -0.865566 -1.083277 -0.013955 + C -1.363971 0.209460 -0.004455 + C -0.493502 1.287234 0.009972 + C 0.875165 1.072283 0.014515 + H 2.440669 -0.388048 0.009436 + H 0.891632 -2.306209 -0.015155 + H -1.544313 -1.923643 -0.025717 + H -2.431149 0.376991 -0.008298 + H -0.882040 2.295219 0.017842 + H 1.553908 1.912671 0.024891 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.595506 -0.416438 0.010368 + 1 C 6.0000 0 12.011 0.950597 -2.453376 -0.016162 + 2 C 6.0000 0 12.011 -1.635683 -2.047097 -0.026371 + 3 C 6.0000 0 12.011 -2.577532 0.395823 -0.008418 + 4 C 6.0000 0 12.011 -0.932584 2.432519 0.018844 + 5 C 6.0000 0 12.011 1.653822 2.026321 0.027429 + 6 H 1.0000 0 1.008 4.612197 -0.733305 0.017832 + 7 H 1.0000 0 1.008 1.684939 -4.358103 -0.028638 + 8 H 1.0000 0 1.008 -2.918328 -3.635159 -0.048599 + 9 H 1.0000 0 1.008 -4.594205 0.712411 -0.015681 + 10 H 1.0000 0 1.008 -1.666814 4.337335 0.033716 + 11 H 1.0000 0 1.008 2.936460 3.614423 0.047037 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/06/26 at 09:13:01.200 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 12 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.21772167094409 + + ID Z sym. atoms + 1 6 C 1-6 + 2 1 H 7-12 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 18 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.1955129 -0.161955E+02 0.125E-01 4.92 0.0 T + 2 -16.1955133 -0.403352E-06 0.742E-02 4.92 1.0 T + 3 -16.1955134 -0.164805E-06 0.315E-03 4.92 9.2 T + 4 -16.1955134 -0.155953E-08 0.132E-03 4.92 21.9 T + 5 -16.1955134 -0.140488E-08 0.609E-04 4.92 47.4 T + 6 -16.1955134 -0.245915E-08 0.596E-05 4.92 484.2 T + + *** convergence criteria satisfied after 6 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6413965 -17.4533 + ... ... ... ... + 9 2.0000 -0.4762976 -12.9607 + 10 2.0000 -0.4762924 -12.9606 + 11 2.0000 -0.4744819 -12.9113 + 12 2.0000 -0.4214505 -11.4683 + 13 2.0000 -0.4214244 -11.4675 + 14 2.0000 -0.4023732 -10.9491 + 15 2.0000 -0.4023625 -10.9488 (HOMO) + 16 -0.2213940 -6.0244 (LUMO) + 17 -0.2213674 -6.0237 + 18 -0.0904365 -2.4609 + 19 0.1184369 3.2228 + 20 0.1371976 3.7333 + ... ... ... + 30 0.6721149 18.2892 + ------------------------------------------------------------- + HL-Gap 0.1809685 Eh 4.9244 eV + Fermi-level -0.3118783 Eh -8.4866 eV + + SCC (total) 0 d, 0 h, 0 min, 0.012 sec + SCC setup ... 0 min, 0.000 sec ( 1.305%) + Dispersion ... 0 min, 0.000 sec ( 0.706%) + classical contributions ... 0 min, 0.000 sec ( 0.251%) + integral evaluation ... 0 min, 0.002 sec ( 16.094%) + iterations ... 0 min, 0.005 sec ( 43.762%) + molecular gradient ... 0 min, 0.004 sec ( 36.333%) + printout ... 0 min, 0.000 sec ( 1.452%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.879635904823 Eh :: + :: gradient norm 0.002431966060 Eh/a0 :: + :: HOMO-LUMO gap 4.924403565589 eV :: + ::.................................................:: + :: SCC energy -16.195513428874 Eh :: + :: -> isotropic ES 0.000795412668 Eh :: + :: -> anisotropic ES 0.002526209138 Eh :: + :: -> anisotropic XC 0.012416937729 Eh :: + :: -> dispersion -0.008017088770 Eh :: + :: repulsion energy 0.315870723599 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.879635904823 Eh | + | GRADIENT NORM 0.002431966060 Eh/α | + | HOMO-LUMO GAP 4.924403565589 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/06/26 at 09:13:01.225 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.025 sec + * cpu-time: 0 d, 0 h, 0 min, 0.024 sec + * ratio c/w: 0.972 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.012 sec + * cpu-time: 0 d, 0 h, 0 min, 0.011 sec + * ratio c/w: 0.941 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.879635904820 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 12 +Number of internal coordinates .... 54 +Current Energy .... -15.879635905 Eh +Current gradient norm .... 0.002431966 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999990087 +Lowest eigenvalues of augmented Hessian: + -0.000009204 0.026024381 0.026025797 0.026033356 0.026041404 +Length of the computed step .... 0.004452581 +The final length of the internal step .... 0.004452581 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0006059195 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0009627615 RMS(Int)= 0.0006059190 + Iter 1: RMS(Cart)= 0.0000000996 RMS(Int)= 0.0000001111 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0007874293 0.0000050000 NO + RMS gradient 0.0003080612 0.0001000000 NO + MAX gradient 0.0009650443 0.0003000000 NO + RMS step 0.0006059195 0.0020000000 YES + MAX step 0.0017122026 0.0040000000 YES + ........................................................ + Max(Bonds) 0.0009 Max(Angles) 0.00 + Max(Dihed) 0.03 Max(Improp) 0.00 + --------------------------------------------------------------------- + +The optimization has not yet converged - more geometry cycles are needed + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + (Angstroem and degrees) + + Definition Value dE/dq Step New-Value + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.3855 0.000965 -0.0009 1.3846 + 2. B(C 2,C 1) 1.3854 0.000884 -0.0008 1.3846 + 3. B(C 3,C 2) 1.3855 0.000952 -0.0009 1.3846 + 4. B(C 4,C 3) 1.3855 0.000928 -0.0009 1.3846 + 5. B(C 5,C 4) 1.3855 0.000905 -0.0008 1.3846 + 6. B(C 5,C 0) 1.3854 0.000890 -0.0008 1.3846 + 7. B(H 6,C 0) 1.0803 -0.000065 0.0001 1.0804 + 8. B(H 7,C 1) 1.0803 -0.000072 0.0001 1.0804 + 9. B(H 8,C 2) 1.0803 -0.000064 0.0001 1.0804 + 10. B(H 9,C 3) 1.0803 -0.000080 0.0001 1.0804 + 11. B(H 10,C 4) 1.0803 -0.000057 0.0001 1.0804 + 12. B(H 11,C 5) 1.0803 -0.000062 0.0001 1.0804 + 13. A(C 1,C 0,C 5) 120.00 -0.000003 0.00 120.00 + 14. A(C 1,C 0,H 6) 119.99 -0.000010 0.00 120.00 + 15. A(C 5,C 0,H 6) 120.01 0.000013 -0.00 120.01 + 16. A(C 2,C 1,H 7) 120.01 0.000017 -0.00 120.01 + 17. A(C 0,C 1,C 2) 120.00 -0.000014 0.00 120.00 + 18. A(C 0,C 1,H 7) 120.00 -0.000003 0.00 120.00 + 19. A(C 3,C 2,H 8) 119.99 -0.000015 0.00 119.99 + 20. A(C 1,C 2,H 8) 120.00 -0.000005 0.00 120.00 + 21. A(C 1,C 2,C 3) 120.01 0.000020 -0.00 120.01 + 22. A(C 4,C 3,H 9) 120.00 0.000010 -0.00 120.00 + 23. A(C 2,C 3,H 9) 120.00 0.000013 -0.00 120.00 + 24. A(C 2,C 3,C 4) 119.99 -0.000023 0.00 120.00 + 25. A(C 3,C 4,H 10) 120.00 -0.000009 0.00 120.00 + 26. A(C 3,C 4,C 5) 120.00 0.000004 -0.00 120.00 + 27. A(C 5,C 4,H 10) 120.00 0.000005 -0.00 120.00 + 28. A(C 0,C 5,C 4) 120.00 0.000016 -0.00 120.00 + 29. A(C 4,C 5,H 11) 120.00 0.000001 -0.00 120.00 + 30. A(C 0,C 5,H 11) 119.99 -0.000017 0.00 120.00 + 31. D(H 7,C 1,C 0,C 5) -179.97 0.000006 -0.01 -179.99 + 32. D(H 7,C 1,C 0,H 6) 0.02 0.000006 -0.01 0.01 + 33. D(C 2,C 1,C 0,H 6) -179.98 0.000005 -0.01 -180.00 + 34. D(C 2,C 1,C 0,C 5) 0.02 0.000006 -0.01 0.01 + 35. D(H 8,C 2,C 1,C 0) 179.95 -0.000013 0.03 179.98 + 36. D(C 3,C 2,C 1,C 0) -0.04 -0.000012 0.03 -0.01 + 37. D(C 3,C 2,C 1,H 7) 179.95 -0.000013 0.03 179.98 + 38. D(H 8,C 2,C 1,H 7) -0.06 -0.000013 0.03 -0.03 + 39. D(H 9,C 3,C 2,H 8) 0.03 0.000007 -0.02 0.01 + 40. D(H 9,C 3,C 2,C 1) -179.98 0.000007 -0.02 -179.99 + 41. D(C 4,C 3,C 2,H 8) -179.97 0.000007 -0.02 -179.99 + 42. D(C 4,C 3,C 2,C 1) 0.02 0.000007 -0.02 0.01 + 43. D(H 10,C 4,C 3,C 2) -179.97 0.000006 -0.02 -179.99 + 44. D(C 5,C 4,C 3,H 9) -179.98 0.000006 -0.01 -180.00 + 45. D(C 5,C 4,C 3,C 2) 0.02 0.000006 -0.01 0.00 + 46. D(H 10,C 4,C 3,H 9) 0.03 0.000007 -0.02 0.01 + 47. D(H 11,C 5,C 4,H 10) -0.06 -0.000015 0.03 -0.03 + 48. D(C 0,C 5,C 4,H 10) 179.95 -0.000013 0.03 179.98 + 49. D(C 0,C 5,C 4,C 3) -0.04 -0.000012 0.03 -0.01 + 50. D(H 11,C 5,C 0,H 6) 0.04 0.000009 -0.02 0.02 + 51. D(H 11,C 5,C 0,C 1) -179.97 0.000008 -0.02 -179.98 + 52. D(H 11,C 5,C 4,C 3) 179.95 -0.000014 0.03 179.98 + 53. D(C 4,C 5,C 0,H 6) -179.97 0.000007 -0.02 -179.99 + 54. D(C 4,C 5,C 0,C 1) 0.02 0.000007 -0.02 0.01 + ---------------------------------------------------------------------------- + + ************************************************************* + * GEOMETRY OPTIMIZATION CYCLE 3 * + ************************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.372627 -0.220257 0.005473 + C 0.502734 -1.297441 -0.008692 + C -0.865051 -1.082610 -0.013787 + C -1.363089 0.209312 -0.004461 + C -0.493192 1.286428 0.009814 + C 0.874638 1.071627 0.014658 + H 2.439905 -0.387931 0.009379 + H 0.891345 -2.305478 -0.015658 + H -1.543848 -1.923054 -0.025162 + H -2.430378 0.376863 -0.008322 + H -0.881754 2.294490 0.017304 + H 1.553413 1.912091 0.025463 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.593889 -0.416225 0.010342 + 1 C 6.0000 0 12.011 0.950030 -2.451808 -0.016426 + 2 C 6.0000 0 12.011 -1.634710 -2.045836 -0.026054 + 3 C 6.0000 0 12.011 -2.575864 0.395542 -0.008430 + 4 C 6.0000 0 12.011 -0.931998 2.430997 0.018545 + 5 C 6.0000 0 12.011 1.652826 2.025081 0.027700 + 6 H 1.0000 0 1.008 4.610753 -0.733083 0.017724 + 7 H 1.0000 0 1.008 1.684398 -4.356723 -0.029589 + 8 H 1.0000 0 1.008 -2.917450 -3.634045 -0.047548 + 9 H 1.0000 0 1.008 -4.592749 0.712168 -0.015726 + 10 H 1.0000 0 1.008 -1.666273 4.335957 0.032700 + 11 H 1.0000 0 1.008 2.935525 3.613329 0.048118 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/06/26 at 09:13:01.284 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 12 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.62916046083203 + + ID Z sym. atoms + 1 6 C 1-6 + 2 1 H 7-12 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 18 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.1966048 -0.161966E+02 0.940E-03 4.93 0.0 T + 2 -16.1966048 -0.207695E-07 0.559E-03 4.93 5.2 T + 3 -16.1966048 -0.612392E-09 0.508E-04 4.93 56.8 T + 4 -16.1966048 -0.514106E-09 0.150E-04 4.93 192.2 T + + *** convergence criteria satisfied after 4 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6416541 -17.4603 + ... ... ... ... + 9 2.0000 -0.4763535 -12.9622 + 10 2.0000 -0.4763484 -12.9621 + 11 2.0000 -0.4747520 -12.9187 + 12 2.0000 -0.4214048 -11.4670 + 13 2.0000 -0.4213893 -11.4666 + 14 2.0000 -0.4025242 -10.9532 + 15 2.0000 -0.4025215 -10.9532 (HOMO) + 16 -0.2212009 -6.0192 (LUMO) + 17 -0.2211879 -6.0188 + 18 -0.0899223 -2.4469 + 19 0.1181313 3.2145 + 20 0.1377925 3.7495 + ... ... ... + 30 0.6741822 18.3454 + ------------------------------------------------------------- + HL-Gap 0.1813206 Eh 4.9340 eV + Fermi-level -0.3118612 Eh -8.4862 eV + + SCC (total) 0 d, 0 h, 0 min, 0.033 sec + SCC setup ... 0 min, 0.000 sec ( 0.483%) + Dispersion ... 0 min, 0.000 sec ( 0.248%) + classical contributions ... 0 min, 0.000 sec ( 0.090%) + integral evaluation ... 0 min, 0.002 sec ( 5.454%) + iterations ... 0 min, 0.027 sec ( 80.057%) + molecular gradient ... 0 min, 0.004 sec ( 13.098%) + printout ... 0 min, 0.000 sec ( 0.532%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.879640611397 Eh :: + :: gradient norm 0.000229130871 Eh/a0 :: + :: HOMO-LUMO gap 4.933984539935 eV :: + ::.................................................:: + :: SCC energy -16.196604837071 Eh :: + :: -> isotropic ES 0.000792285296 Eh :: + :: -> anisotropic ES 0.002517056106 Eh :: + :: -> anisotropic XC 0.012386338819 Eh :: + :: -> dispersion -0.008019545150 Eh :: + :: repulsion energy 0.316957441898 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.879640611397 Eh | + | GRADIENT NORM 0.000229130871 Eh/α | + | HOMO-LUMO GAP 4.933984539935 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/06/26 at 09:13:01.331 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.047 sec + * cpu-time: 0 d, 0 h, 0 min, 0.026 sec + * ratio c/w: 0.549 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.033 sec + * cpu-time: 0 d, 0 h, 0 min, 0.012 sec + * ratio c/w: 0.371 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.879640611400 +------------------------- -------------------- + +------------------------------------------------------------------------------ + ORCA GEOMETRY RELAXATION STEP +------------------------------------------------------------------------------ + +Reading the OPT-File .... done +Getting information on internals .... done +Copying old internal coords+grads .... done +Making the new internal coordinates .... (new redundants).... done +Validating the new internal coordinates .... (new redundants).... done +Calculating the B-matrix .... done +Calculating the G,G- and P matrices .... done +Transforming gradient to internals .... done +Projecting the internal gradient .... done +Number of atoms .... 12 +Number of internal coordinates .... 54 +Current Energy .... -15.879640611 Eh +Current gradient norm .... 0.000229131 Eh/bohr +Maximum allowed component of the step .... 0.300 +Current trust radius .... 0.300 +Updating the Hessian (BFGS) .... done +Forming the augmented Hessian .... done +Diagonalizing the augmented Hessian .... done +Last element of RFO vector .... 0.999999659 +Lowest eigenvalues of augmented Hessian: + -0.000000069 0.025858500 0.026024548 0.026026832 0.026034093 +Length of the computed step .... 0.000825581 +The final length of the internal step .... 0.000825581 +Converting the step to cartesian space: + Initial RMS(Int)= 0.0001123473 +Transforming coordinates: + Iter 0: RMS(Cart)= 0.0001364097 RMS(Int)= 0.0001123433 + Iter 1: RMS(Cart)= 0.0000000115 RMS(Int)= 0.0000000096 +done +Storing new coordinates .... done + + .--------------------. + ----------------------|Geometry convergence|------------------------- + Item value Tolerance Converged + --------------------------------------------------------------------- + Energy change -0.0000047066 0.0000050000 YES + RMS gradient 0.0000197543 0.0001000000 YES + MAX gradient 0.0000576598 0.0003000000 YES + RMS step 0.0001123473 0.0020000000 YES + MAX step 0.0002850650 0.0040000000 YES + ........................................................ + Max(Bonds) 0.0001 Max(Angles) 0.00 + Max(Dihed) 0.02 Max(Improp) 0.00 + --------------------------------------------------------------------- + + ***********************HURRAY******************** + *** THE OPTIMIZATION HAS CONVERGED *** + ************************************************* + + + --------------------------------------------------------------------------- + Redundant Internal Coordinates + + --- Optimized Parameters --- + (Angstroem and degrees) + + Definition OldVal dE/dq Step FinalVal + ---------------------------------------------------------------------------- + 1. B(C 1,C 0) 1.3846 0.000030 -0.0000 1.3846 + 2. B(C 2,C 1) 1.3846 -0.000006 -0.0000 1.3846 + 3. B(C 3,C 2) 1.3846 0.000022 -0.0000 1.3846 + 4. B(C 4,C 3) 1.3846 0.000009 -0.0000 1.3846 + 5. B(C 5,C 4) 1.3846 0.000010 -0.0000 1.3846 + 6. B(C 5,C 0) 1.3846 -0.000003 -0.0000 1.3846 + 7. B(H 6,C 0) 1.0804 -0.000055 0.0001 1.0805 + 8. B(H 7,C 1) 1.0804 -0.000056 0.0001 1.0805 + 9. B(H 8,C 2) 1.0804 -0.000052 0.0001 1.0805 + 10. B(H 9,C 3) 1.0804 -0.000058 0.0001 1.0805 + 11. B(H 10,C 4) 1.0804 -0.000054 0.0001 1.0805 + 12. B(H 11,C 5) 1.0804 -0.000052 0.0001 1.0805 + 13. A(C 1,C 0,C 5) 120.00 -0.000004 0.00 120.00 + 14. A(C 1,C 0,H 6) 120.00 -0.000008 0.00 120.00 + 15. A(C 5,C 0,H 6) 120.01 0.000011 -0.00 120.00 + 16. A(C 2,C 1,H 7) 120.01 0.000012 -0.00 120.00 + 17. A(C 0,C 1,C 2) 120.00 -0.000008 0.00 120.00 + 18. A(C 0,C 1,H 7) 120.00 -0.000004 0.00 120.00 + 19. A(C 3,C 2,H 8) 119.99 -0.000013 0.00 120.00 + 20. A(C 1,C 2,H 8) 120.00 -0.000002 0.00 120.00 + 21. A(C 1,C 2,C 3) 120.01 0.000015 -0.00 120.00 + 22. A(C 4,C 3,H 9) 120.00 0.000007 -0.00 120.00 + 23. A(C 2,C 3,H 9) 120.00 0.000006 -0.00 120.00 + 24. A(C 2,C 3,C 4) 120.00 -0.000013 0.00 120.00 + 25. A(C 3,C 4,H 10) 120.00 -0.000006 0.00 120.00 + 26. A(C 3,C 4,C 5) 120.00 0.000002 -0.00 120.00 + 27. A(C 5,C 4,H 10) 120.00 0.000004 -0.00 120.00 + 28. A(C 0,C 5,C 4) 120.00 0.000008 -0.00 120.00 + 29. A(C 4,C 5,H 11) 120.00 0.000001 -0.00 120.00 + 30. A(C 0,C 5,H 11) 120.00 -0.000009 0.00 120.00 + 31. D(H 7,C 1,C 0,C 5) -179.99 0.000003 -0.01 -179.99 + 32. D(H 7,C 1,C 0,H 6) 0.01 0.000003 -0.01 0.00 + 33. D(C 2,C 1,C 0,H 6) -180.00 0.000001 -0.00 -180.00 + 34. D(C 2,C 1,C 0,C 5) 0.01 0.000001 -0.00 0.00 + 35. D(H 8,C 2,C 1,C 0) 179.98 -0.000005 0.01 179.99 + 36. D(C 3,C 2,C 1,C 0) -0.01 -0.000003 0.01 -0.00 + 37. D(C 3,C 2,C 1,H 7) 179.98 -0.000005 0.01 179.99 + 38. D(H 8,C 2,C 1,H 7) -0.03 -0.000007 0.02 -0.01 + 39. D(H 9,C 3,C 2,H 8) 0.01 0.000004 -0.01 0.01 + 40. D(H 9,C 3,C 2,C 1) -179.99 0.000002 -0.00 -180.00 + 41. D(C 4,C 3,C 2,H 8) -179.99 0.000004 -0.01 -179.99 + 42. D(C 4,C 3,C 2,C 1) 0.01 0.000002 -0.00 0.00 + 43. D(H 10,C 4,C 3,C 2) -179.99 0.000003 -0.01 -179.99 + 44. D(C 5,C 4,C 3,H 9) -180.00 0.000001 -0.00 -180.00 + 45. D(C 5,C 4,C 3,C 2) 0.00 0.000001 -0.00 0.00 + 46. D(H 10,C 4,C 3,H 9) 0.01 0.000003 -0.01 0.01 + 47. D(H 11,C 5,C 4,H 10) -0.03 -0.000007 0.02 -0.01 + 48. D(C 0,C 5,C 4,H 10) 179.98 -0.000005 0.01 179.99 + 49. D(C 0,C 5,C 4,C 3) -0.01 -0.000003 0.01 -0.00 + 50. D(H 11,C 5,C 0,H 6) 0.02 0.000004 -0.01 0.01 + 51. D(H 11,C 5,C 0,C 1) -179.98 0.000004 -0.01 -179.99 + 52. D(H 11,C 5,C 4,C 3) 179.98 -0.000005 0.01 179.99 + 53. D(C 4,C 5,C 0,H 6) -179.99 0.000002 -0.00 -180.00 + 54. D(C 4,C 5,C 0,C 1) 0.01 0.000002 -0.00 0.00 + ---------------------------------------------------------------------------- + ******************************************************* + *** FINAL ENERGY EVALUATION AT THE STATIONARY POINT *** + *** (AFTER 3 CYCLES) *** + ******************************************************* +--------------------------------- +CARTESIAN COORDINATES (ANGSTROEM) +--------------------------------- + C 1.372604 -0.220263 0.005470 + C 0.502729 -1.297417 -0.008729 + C -0.865058 -1.082608 -0.013747 + C -1.363056 0.209299 -0.004464 + C -0.493181 1.286414 0.009778 + C 0.874634 1.071623 0.014697 + H 2.439965 -0.387928 0.009359 + H 0.891353 -2.305537 -0.015842 + H -1.543894 -1.923121 -0.024963 + H -2.430428 0.376871 -0.008335 + H -0.881765 2.294553 0.017113 + H 1.553446 1.912154 0.025671 + +---------------------------- +CARTESIAN COORDINATES (A.U.) +---------------------------- + NO LB ZA FRAG MASS X Y Z + 0 C 6.0000 0 12.011 2.593846 -0.416236 0.010338 + 1 C 6.0000 0 12.011 0.950021 -2.451763 -0.016495 + 2 C 6.0000 0 12.011 -1.634724 -2.045833 -0.025978 + 3 C 6.0000 0 12.011 -2.575803 0.395518 -0.008436 + 4 C 6.0000 0 12.011 -0.931978 2.430971 0.018478 + 5 C 6.0000 0 12.011 1.652819 2.025074 0.027773 + 6 H 1.0000 0 1.008 4.610866 -0.733078 0.017686 + 7 H 1.0000 0 1.008 1.684413 -4.356833 -0.029937 + 8 H 1.0000 0 1.008 -2.917537 -3.634172 -0.047173 + 9 H 1.0000 0 1.008 -4.592843 0.712184 -0.015750 + 10 H 1.0000 0 1.008 -1.666294 4.336076 0.032339 + 11 H 1.0000 0 1.008 2.935588 3.613447 0.048512 + + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + | Aditya W. Sakti | + | Departemen Kimia | + | Universitas Pertamina | + ----------------------------------------------------------- + + * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman + C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer + J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher + M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/06/26 at 09:13:01.384 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000 + hostname : compute + calculation namespace : cmmd + coordinate file : cmmd_XTB.xyz + number of atoms : 12 + number of electrons : 30 + charge : 0 + spin : 0.0 + first test random number : 0.26850588191834 + + ID Z sym. atoms + 1 6 C 1-6 + 2 1 H 7-12 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 30 : + : # atomic orbitals 30 : + : # shells 18 : + : # electrons 30 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -16.1965611 -0.161966E+02 0.876E-04 4.93 0.0 T + 2 -16.1965611 -0.258140E-09 0.515E-04 4.93 56.0 T + 3 -16.1965611 0.267484E-10 0.814E-05 4.93 354.6 T + + *** convergence criteria satisfied after 3 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6416606 -17.4605 + ... ... ... ... + 9 2.0000 -0.4763530 -12.9622 + 10 2.0000 -0.4763503 -12.9622 + 11 2.0000 -0.4747601 -12.9189 + 12 2.0000 -0.4214018 -11.4669 + 13 2.0000 -0.4213924 -11.4667 + 14 2.0000 -0.4025298 -10.9534 + 15 2.0000 -0.4025275 -10.9533 (HOMO) + 16 -0.2211971 -6.0191 (LUMO) + 17 -0.2211902 -6.0189 + 18 -0.0899154 -2.4467 + 19 0.1180093 3.2112 + 20 0.1377152 3.7474 + ... ... ... + 30 0.6741465 18.3445 + ------------------------------------------------------------- + HL-Gap 0.1813304 Eh 4.9343 eV + Fermi-level -0.3118623 Eh -8.4862 eV + + SCC (total) 0 d, 0 h, 0 min, 0.027 sec + SCC setup ... 0 min, 0.000 sec ( 0.523%) + Dispersion ... 0 min, 0.000 sec ( 0.301%) + classical contributions ... 0 min, 0.000 sec ( 0.107%) + integral evaluation ... 0 min, 0.002 sec ( 7.369%) + iterations ... 0 min, 0.021 sec ( 74.824%) + molecular gradient ... 0 min, 0.004 sec ( 16.188%) + printout ... 0 min, 0.000 sec ( 0.641%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -15.879640652449 Eh :: + :: gradient norm 0.000058531220 Eh/a0 :: + :: HOMO-LUMO gap 4.934252272558 eV :: + ::.................................................:: + :: SCC energy -16.196561052560 Eh :: + :: -> isotropic ES 0.000791525912 Eh :: + :: -> anisotropic ES 0.002517595461 Eh :: + :: -> anisotropic XC 0.012388537747 Eh :: + :: -> dispersion -0.008019556015 Eh :: + :: repulsion energy 0.316913616164 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + +Property printout bound to 'properties.out' + + ------------------------------------------------- + | TOTAL ENERGY -15.879640652449 Eh | + | GRADIENT NORM 0.000058531220 Eh/α | + | HOMO-LUMO GAP 4.934252272558 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/06/26 at 09:13:01.425 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.041 sec + * cpu-time: 0 d, 0 h, 0 min, 0.024 sec + * ratio c/w: 0.580 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.028 sec + * cpu-time: 0 d, 0 h, 0 min, 0.011 sec + * ratio c/w: 0.383 speedup + + +------------------------- -------------------- +FINAL SINGLE POINT ENERGY -15.879640652450 +------------------------- -------------------- + + *** OPTIMIZATION RUN DONE *** + +Timings for individual modules: + +Sum of individual times ... 0.381 sec (= 0.006 min) +Geometry relaxation ... 0.109 sec (= 0.002 min) 28.6 % +XTB module ... 0.272 sec (= 0.005 min) 71.4 % + ****ORCA TERMINATED NORMALLY**** 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z-JGLEDXLb7$2Rex7$8#OnzX1cuY$72m5;tUkO9}b1?bLRCu%Y7Go|sJ-=#Og>6{t*0*s=cAu=W=31*i|U(Bxvj>-4_~K(9VPL zOA9ZgFq2A%Ov^an;YBe(oLb;X?B-99f$$^Cm3qyS1oL*cwMV!wR~~TQwp|J*M^^f~ zH@IkbfVE$J#8p^w;EEiA>EJOX_ij{0LVVuU&zSNSwA|lb`;SpA>{|4;WUEQ|wK{9G zJX{8aNA8%3U($g%w3B9O$bd)gB0%{3Uw*GA%V(u9rT*Jyp@0Lgo6}~}vCnh?spUEa z!f(kn6ulV<)1B{$H*kMFNYApvK8{Xa0)tI1+EmR79k5Sq09izY(!upSJ;%?KgoUCP LOZ&0U)*t#0&Kmr~ literal 0 HcmV?d00001 diff --git a/cmmde_gui/test/cmmd.xyz b/cmmde_gui/test/cmmd.xyz new file mode 100644 index 0000000..1b107ed --- /dev/null +++ b/cmmde_gui/test/cmmd.xyz @@ -0,0 +1,14 @@ +12 +Coordinates from ORCA-job cmmd + C 1.37260436112356 -0.22026276421215 0.00547047023826 + C 0.50272945880886 -1.29741725617100 -0.00872890193775 + C -0.86505848472206 -1.08260844519038 -0.01374705758241 + C -1.36305644841968 0.20929919814959 -0.00446438511787 + C -0.49318132097366 1.28641428149678 0.00977806727944 + C 0.87463411368352 1.07162318446095 0.01469701658624 + H 2.43996541860591 -0.38792834851432 0.00935918376693 + H 0.89135300032527 -2.30553664453777 -0.01584172099556 + H -1.54389392375015 -1.92312101358440 -0.02496277241009 + H -2.43042795974921 0.37687130997575 -0.00833452091932 + H -0.88176466598630 2.29455258686373 0.01711318587593 + H 1.55344645105395 1.91215391126322 0.02567143521620 diff --git a/cmmde_gui/test/cmmd_property.txt b/cmmde_gui/test/cmmd_property.txt new file mode 100644 index 0000000..8f1a67f --- /dev/null +++ b/cmmde_gui/test/cmmd_property.txt @@ -0,0 +1,6 @@ +------------------------------------------------------------- +----------------------- !PROPERTIES! ------------------------ +------------------------------------------------------------- +# ------------------------------------------------------------- +----------------------- !GEOMETRIES! ------------------------ +# ------------------------------------------------------------- diff --git a/cmmde_gui/test/cmmd_trj.xyz b/cmmde_gui/test/cmmd_trj.xyz new file mode 100644 index 0000000..4e3bfb0 --- /dev/null +++ b/cmmde_gui/test/cmmd_trj.xyz @@ -0,0 +1,56 @@ +12 +Coordinates from ORCA-job cmmd E -15.878848475480 + C 1.382680 -0.221770 0.005570 + C 0.506340 -1.307050 -0.008130 + C -0.871400 -1.090590 -0.014570 + C -1.373230 0.210910 -0.004460 + C -0.496830 1.295960 0.010580 + C 0.880990 1.079530 0.014120 + H 2.456200 -0.390440 0.009600 + H 0.897240 -2.320890 -0.014140 + H -1.554150 -1.935930 -0.027090 + H -2.446570 0.379420 -0.008330 + H -0.887690 2.310030 0.019130 + H 1.563770 1.924860 0.023730 +12 +Coordinates from ORCA-job cmmd E -15.879635904820 + C 1.373483 -0.220370 0.005486 + C 0.503034 -1.298271 -0.008552 + C -0.865566 -1.083277 -0.013955 + C -1.363971 0.209460 -0.004455 + C -0.493502 1.287234 0.009972 + C 0.875165 1.072283 0.014515 + H 2.440669 -0.388048 0.009436 + H 0.891632 -2.306209 -0.015155 + H -1.544313 -1.923643 -0.025717 + H -2.431149 0.376991 -0.008298 + H -0.882040 2.295219 0.017842 + H 1.553908 1.912671 0.024891 +12 +Coordinates from ORCA-job cmmd E -15.879640611400 + C 1.372627 -0.220257 0.005473 + C 0.502734 -1.297441 -0.008692 + C -0.865051 -1.082610 -0.013787 + C -1.363089 0.209312 -0.004461 + C -0.493192 1.286428 0.009814 + C 0.874638 1.071627 0.014658 + H 2.439905 -0.387931 0.009379 + H 0.891345 -2.305478 -0.015658 + H -1.543848 -1.923054 -0.025162 + H -2.430378 0.376863 -0.008322 + H -0.881754 2.294490 0.017304 + H 1.553413 1.912091 0.025463 +12 +Coordinates from ORCA-job cmmd E -15.879640652450 + C 1.372604 -0.220263 0.005470 + C 0.502729 -1.297417 -0.008729 + C -0.865058 -1.082608 -0.013747 + C -1.363056 0.209299 -0.004464 + C -0.493181 1.286414 0.009778 + C 0.874634 1.071623 0.014697 + H 2.439965 -0.387928 0.009359 + H 0.891353 -2.305537 -0.015842 + H -1.543894 -1.923121 -0.024963 + H -2.430428 0.376871 -0.008335 + H -0.881765 2.294553 0.017113 + H 1.553446 1.912154 0.025671 diff --git a/cmmde_gui/test/geom.smi b/cmmde_gui/test/geom.smi new file mode 100644 index 0000000..17163bb --- /dev/null +++ b/cmmde_gui/test/geom.smi @@ -0,0 +1 @@ +c1ccccc1 diff --git a/cmmde_gui/test/geom.xyz b/cmmde_gui/test/geom.xyz new file mode 100644 index 0000000..d5cf7e8 --- /dev/null +++ b/cmmde_gui/test/geom.xyz @@ -0,0 +1,14 @@ +12 + +C 1.38268 -0.22177 0.00557 +C 0.50634 -1.30705 -0.00813 +C -0.87140 -1.09059 -0.01457 +C -1.37323 0.21091 -0.00446 +C -0.49683 1.29596 0.01058 +C 0.88099 1.07953 0.01412 +H 2.45620 -0.39044 0.00960 +H 0.89724 -2.32089 -0.01414 +H -1.55415 -1.93593 -0.02709 +H -2.44657 0.37942 -0.00833 +H -0.88769 2.31003 0.01913 +H 1.56377 1.92486 0.02373 diff --git a/cmmde_gui/test/run.sh b/cmmde_gui/test/run.sh new file mode 100644 index 0000000..f72e163 --- /dev/null +++ b/cmmde_gui/test/run.sh @@ -0,0 +1,10 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH +export PATH=/home/adit/opt/openmpi411/bin:$PATH +export OMP_NUM_THREADS=1 +cd $PWD +$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe diff --git a/cmmde_gui/test/run_babel.sh b/cmmde_gui/test/run_babel.sh new file mode 100644 index 0000000..0d5d00e --- /dev/null +++ b/cmmde_gui/test/run_babel.sh @@ -0,0 +1,8 @@ +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=1 +#SBATCH --time=168:0:0 +export OMP_NUM_THREADS=1 +cd $PWD +obabel geom.smi -O geom.xyz --gen3d diff --git a/cmmde_gui/test/slurm-2745.out b/cmmde_gui/test/slurm-2745.out new file mode 100644 index 0000000..b7d75ac --- /dev/null +++ b/cmmde_gui/test/slurm-2745.out @@ -0,0 +1 @@ +1 molecule converted diff --git a/cmmde_gui/test/slurm-2746.out b/cmmde_gui/test/slurm-2746.out new file mode 100644 index 0000000..e69de29