A series of Python3 script to lower the barrier of computing and simulating molecular and material systems.
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*****************
* O R C A *
*****************
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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: ../cmmd.xyz
***************************************
Your calculation utilizes the semiempirical GFN-xTB method
Please cite in your paper:
S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 13, (2017), 1989.
================================================================================
================================================================================
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> !XTB1 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 2022/08/04 at 09:43:13.227
-------------------------------------------------
| 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 --gfn 1 --acc 1.000000
hostname : compute
calculation namespace : cmmd
coordinate file : cmmd_XTB.xyz
number of atoms : 71
number of electrons : 200
charge : 0
spin : 0.0
first test random number : 0.60158050573190
ID Z sym. atoms
1 6 C 1-43
2 1 H 44-71
-------------------------------------------------
| G F N 1 - x T B |
-------------------------------------------------
Reference 10.1021/acs.jctc.7b00118
* Hamiltonian:
H0-scaling (s, p, d) 1.850000 2.250000 2.000000
zeta-weighting 0.000000
* Dispersion:
s8 2.400000
a1 0.630000
a2 5.000000
s9 0.000000
* Repulsion:
kExp 1.500000
rExp 1.000000
* Coulomb:
alpha 2.000000
third order atomic
anisotropic false
* Halogen bond correction:
rad-scale 1.300000
damping 0.440000
...................................................
: SETUP :
:.................................................:
: # basis functions 228 :
: # atomic orbitals 228 :
: # shells 142 :
: # electrons 200 :
: # halogen bonds 0 :
: max. iterations 250 :
: Hamiltonian GFN1-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 0.2000000E-04 e :
: Broyden damping 0.4000000 :
...................................................
iter E dE RMSdq gap omega full diag
1 -107.8847039 -0.107885E+03 0.104E+01 1.52 0.0 T
2 -107.9625255 -0.778216E-01 0.628E+00 1.49 1.0 T
3 -107.9286345 0.338911E-01 0.684E-01 1.54 1.0 T
4 -107.9667855 -0.381510E-01 0.207E-01 1.49 1.0 T
5 -107.9716052 -0.481967E-02 0.610E-02 1.49 1.0 T
6 -107.9721688 -0.563640E-03 0.109E-02 1.49 1.1 T
7 -107.9721891 -0.203189E-04 0.279E-03 1.49 4.3 T
8 -107.9721901 -0.975196E-06 0.986E-04 1.49 12.0 T
9 -107.9721901 -0.487483E-07 0.245E-04 1.49 48.5 T
10 -107.9721901 -0.387629E-08 0.109E-04 1.49 109.2 T
11 -107.9721901 -0.763720E-09 0.575E-05 1.49 206.3 T
*** convergence criteria satisfied after 11 iterations ***
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -0.6780191 -18.4498
... ... ... ...
94 2.0000 -0.4299532 -11.6996
95 2.0000 -0.4242112 -11.5434
96 2.0000 -0.4217088 -11.4753
97 2.0000 -0.4141608 -11.2699
98 2.0000 -0.4065523 -11.0629
99 2.0000 -0.4025242 -10.9532
100 2.0000 -0.3741493 -10.1811 (HOMO)
101 -0.3193038 -8.6887 (LUMO)
102 -0.2855657 -7.7706
103 -0.2802989 -7.6273
104 -0.2694394 -7.3318
105 -0.2598322 -7.0704
... ... ...
228 0.6943955 18.8955
-------------------------------------------------------------
HL-Gap 0.0548455 Eh 1.4924 eV
Fermi-level -0.3467265 Eh -9.4349 eV
SCC (total) 0 d, 0 h, 0 min, 0.235 sec
SCC setup ... 0 min, 0.001 sec ( 0.366%)
Dispersion ... 0 min, 0.002 sec ( 0.739%)
classical contributions ... 0 min, 0.000 sec ( 0.147%)
integral evaluation ... 0 min, 0.045 sec ( 18.969%)
iterations ... 0 min, 0.073 sec ( 30.918%)
molecular gradient ... 0 min, 0.113 sec ( 47.933%)
printout ... 0 min, 0.002 sec ( 0.914%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -106.196831730665 Eh ::
:: gradient norm 0.015896196187 Eh/a0 ::
:: HOMO-LUMO gap 1.492422010339 eV ::
::.................................................::
:: SCC energy -107.972190143337 Eh ::
:: -> electrostatic 0.004053721879 Eh ::
:: repulsion energy 1.841954650940 Eh ::
:: dispersion energy -0.066596238268 Eh ::
:: halogen bond corr. 0.000000000000 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge 0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
Property printout bound to 'properties.out'
-------------------------------------------------
| TOTAL ENERGY -106.196831730665 Eh |
| GRADIENT NORM 0.015896196187 Eh/α |
| HOMO-LUMO GAP 1.492422010339 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2022/08/04 at 09:43:13.520
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.293 sec
* cpu-time: 0 d, 0 h, 0 min, 0.284 sec
* ratio c/w: 0.969 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.235 sec
* cpu-time: 0 d, 0 h, 0 min, 0.234 sec
* ratio c/w: 0.995 speedup
------------------------- --------------------
FINAL SINGLE POINT ENERGY -106.196831730670
------------------------- --------------------
----------------------------------------------------------------------------
ORCA NUMERICAL FREQUENCIES
----------------------------------------------------------------------------
Number of atoms ... 71
Central differences ... used
Number of displacements ... 426
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
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