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 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: Old DensityContainer found on disk!
Will remove this file -
If you want to keep old densities, please start your calculation with a different basename.
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 2022/04/28 at 11:27:40.328
-------------------------------------------------
| 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 : 2
number of electrons : 12
charge : 0
spin : 0.0
first test random number : 0.84096853316258
ID Z sym. atoms
1 8 O 1, 2
-------------------------------------------------
| 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 4 :
: # electrons 12 :
: 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 -7.9155572 -0.791556E+01 0.407E+00 0.00 0.0 T
2 -7.9155697 -0.125362E-04 0.246E+00 0.00 1.0 T
3 -7.9155792 -0.944533E-05 0.542E-02 0.00 1.3 T
4 -7.9155792 -0.302522E-08 0.166E-02 0.00 4.3 T
5 -7.9155792 -0.836504E-10 0.345E-05 0.00 2049.3 T
6 -7.9155792 0.355271E-14 0.271E-07 0.00 100000.0 T
*** convergence criteria satisfied after 6 iterations ***
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -0.8284027 -22.5420
2 2.0000 -0.7371506 -20.0589
3 2.0000 -0.6631440 -18.0451
4 2.0000 -0.6631440 -18.0451
5 2.0000 -0.6374674 -17.3464
6 1.0000 -0.4399644 -11.9720 (HOMO)
7 1.0000 -0.4399644 -11.9720 (LUMO)
8 0.1444079 3.9295
-------------------------------------------------------------
HL-Gap 0.0000000 Eh 0.0000 eV
Fermi-level -0.4399644 Eh -11.9720 eV
SCC (total) 0 d, 0 h, 0 min, 0.050 sec
SCC setup ... 0 min, 0.000 sec ( 0.151%)
Dispersion ... 0 min, 0.000 sec ( 0.040%)
classical contributions ... 0 min, 0.000 sec ( 0.017%)
integral evaluation ... 0 min, 0.000 sec ( 0.294%)
iterations ... 0 min, 0.050 sec ( 98.980%)
molecular gradient ... 0 min, 0.000 sec ( 0.333%)
printout ... 0 min, 0.000 sec ( 0.168%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -7.906649846778 Eh ::
:: gradient norm 0.018481649479 Eh/a0 ::
:: HOMO-LUMO gap 0.000000000015 eV ::
::.................................................::
:: SCC energy -7.915579172539 Eh ::
:: -> isotropic ES -0.000237652172 Eh ::
:: -> anisotropic ES 0.003738001563 Eh ::
:: -> anisotropic XC -0.007283115557 Eh ::
:: -> dispersion -0.000194539012 Eh ::
:: repulsion energy 0.008929325760 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge 0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
Property printout bound to 'properties.out'
-------------------------------------------------
| TOTAL ENERGY -7.906649846778 Eh |
| GRADIENT NORM 0.018481649479 Eh/α |
| HOMO-LUMO GAP 0.000000000015 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2022/04/28 at 11:27:40.387
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.059 sec
* cpu-time: 0 d, 0 h, 0 min, 0.012 sec
* ratio c/w: 0.196 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.050 sec
* cpu-time: 0 d, 0 h, 0 min, 0.003 sec
* ratio c/w: 0.058 speedup
------------------------- --------------------
FINAL SINGLE POINT ENERGY -7.906649846780
------------------------- --------------------
----------------------------------------------------------------------------
ORCA NUMERICAL FREQUENCIES
----------------------------------------------------------------------------
Number of atoms ... 2
Central differences ... used
Number of displacements ... 12
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 12) >>
<< Calculating on displaced geometry 2 (of 12) >>
<< Calculating on displaced geometry 3 (of 12) >>
<< Calculating on displaced geometry 4 (of 12) >>
<< Calculating on displaced geometry 5 (of 12) >>
<< Calculating on displaced geometry 6 (of 12) >>
<< Calculating on displaced geometry 7 (of 12) >>
<< Calculating on displaced geometry 8 (of 12) >>
<< Calculating on displaced geometry 9 (of 12) >>
<< Calculating on displaced geometry 10 (of 12) >>
<< Calculating on displaced geometry 11 (of 12) >>
<< Calculating on displaced geometry 12 (of 12) >>
-----------------------
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: 1673.23 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 0.707107
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 -0.707107
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
-----------
IR SPECTRUM
-----------
Mode freq eps Int T**2 TX TY TZ
cm**-1 L/(mol*cm) km/mol a.u.
----------------------------------------------------------------------------
5: 1673.23 0.000000 0.00 0.000000 ( 0.000000 0.000000 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 5
The total number of vibrations considered is 1
--------------------------
THERMOCHEMISTRY AT 298.15K
--------------------------
Temperature ... 298.15 K
Pressure ... 1.00 atm
Total Mass ... 32.00 AMU
The molecule is recognized as being linear
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. 1673.23 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 ... -7.90664985 Eh
Zero point energy ... 0.00381191 Eh 2.39 kcal/mol
Thermal vibrational correction ... 0.00000238 Eh 0.00 kcal/mol
Thermal rotational correction ... 0.00094418 Eh 0.59 kcal/mol
Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol
-----------------------------------------------------------------------
Total thermal energy -7.90047511 Eh
Summary of corrections to the electronic energy:
(perhaps to be used in another calculation)
Total thermal correction 0.00236283 Eh 1.48 kcal/mol
Non-thermal (ZPE) correction 0.00381191 Eh 2.39 kcal/mol
-----------------------------------------------------------------------
Total correction 0.00617474 Eh 3.87 kcal/mol
--------
ENTHALPY
--------
The enthalpy is H = U + kB*T
kB is Boltzmann's constant
Total free energy ... -7.90047511 Eh
Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol
-----------------------------------------------------------------------
Total Enthalpy ... -7.89953090 Eh
Note: Rotational entropy computed according to Herzberg
Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945
Point Group: Dinfh, Symmetry Number: 2
Rotational constants in cm-1: 0.000000 1.459941 1.459941
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 ... 0.00000267 Eh 0.00 kcal/mol
Rotational entropy ... 0.00496853 Eh 3.12 kcal/mol
Translational entropy ... 0.01725741 Eh 10.83 kcal/mol
-----------------------------------------------------------------------
Final entropy term ... 0.02222861 Eh 13.95 kcal/mol
-------------------
GIBBS FREE ENERGY
-------------------
The Gibbs free energy is G = H - T*S
Total enthalpy ... -7.89953090 Eh
Total entropy correction ... -0.02222861 Eh -13.95 kcal/mol
-----------------------------------------------------------------------
Final Gibbs free energy ... -7.92175951 Eh
For completeness - the Gibbs free energy minus the electronic energy
G-E(el) ... -0.01510966 Eh -9.48 kcal/mol
Timings for individual modules:
Sum of individual times ... 30.549 sec (= 0.509 min)
Numerical frequency calculation ... 30.380 sec (= 0.506 min) 99.4 %
XTB module ... 0.169 sec (= 0.003 min) 0.6 %
****ORCA TERMINATED NORMALLY****
TOTAL RUN TIME: 0 days 0 hours 0 minutes 30 seconds 827 msec