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A series of Python3 script to lower the barrier of computing and simulating molecular and material systems.
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CMMDE/cmmde_gui/test/metana_02514d87e9c74c04985f.../cmmd.out

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cmmde-gui modification
2 years ago
*****************
* O R C A *
*****************
#,
###
####
#####
######
########,
,,################,,,,,
,,#################################,,
,,##########################################,,
,#########################################, ''#####,
,#############################################,, '####,
,##################################################,,,,####,
,###########'''' ''''###############################
,#####'' ,,,,##########,,,, '''####''' '####
,##' ,,,,###########################,,, '##
' ,,###'''' '''############,,,
,,##'' '''############,,,, ,,,,,,###''
,#'' '''#######################'''
' ''''####''''
,#######, #######, ,#######, ##
,#' '#, ## ## ,#' '#, #''# ###### ,####,
## ## ## ,#' ## #' '# # #' '#
## ## ####### ## ,######, #####, # #
'#, ,#' ## ## '#, ,#' ,# #, ## #, ,#
'#######' ## ## '#######' #' '# #####' # '####'
#######################################################
# -***- #
# Department of theory and spectroscopy #
# Directorship and core code : Frank Neese #
# Max Planck Institute fuer Kohlenforschung #
# Kaiser Wilhelm Platz 1 #
# D-45470 Muelheim/Ruhr #
# Germany #
# #
# All rights reserved #
# -***- #
#######################################################
Program Version 5.0.2 - RELEASE -
With contributions from (in alphabetic order):
Daniel Aravena : Magnetic Suceptibility
Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation)
Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum
Ute Becker : Parallelization
Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD
Martin Brehm : Molecular dynamics
Dmytro Bykov : SCF Hessian
Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE
Dipayan Datta : RHF DLPNO-CCSD density
Achintya Kumar Dutta : EOM-CC, STEOM-CC
Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI
Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme
Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization
Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods
Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals
Lee Huntington : MR-EOM, pCC
Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM
Marcus Kettner : VPT2
Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K
Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian
Martin Krupicka : Initial AUTO-CI
Lucas Lang : DCDCAS
Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC
Dagmar Lenk : GEPOL surface, SMD
Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization
Dimitrios Manganas : Further ROCIS development; embedding schemes
Dimitrios Pantazis : SARC Basis sets
Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients
Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS
Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient
Christoph Reimann : Effective Core Potentials
Marius Retegan : Local ZFS, SOC
Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples
Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB
Michael Roemelt : Original ROCIS implementation
Masaaki Saitow : Open-shell DLPNO-CCSD energy and density
Barbara Sandhoefer : DKH picture change effects
Avijit Sen : IP-ROCIS
Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI
Bernardo de Souza : ESD, SOC TD-DFT
Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response
Willem Van den Heuvel : Paramagnetic NMR
Boris Wezisla : Elementary symmetry handling
Frank Wennmohs : Technical directorship
We gratefully acknowledge several colleagues who have allowed us to
interface, adapt or use parts of their codes:
Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization,
C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF
Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods
Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG
Ulf Ekstrom : XCFun DFT Library
Mihaly Kallay : mrcc (arbitrary order and MRCC methods)
Jiri Pittner, Ondrej Demel : Mk-CCSD
Frank Weinhold : gennbo (NPA and NBO analysis)
Christopher J. Cramer and Donald G. Truhlar : smd solvation model
Lars Goerigk : TD-DFT with DH, B97 family of functionals
V. Asgeirsson, H. Jonsson : NEB implementation
FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT
MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM,
LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT,
nearIR, NL-DFT gradient (VV10), updates on ESD,
ML-optimized integration grids
S Lehtola, MJT Oliveira, MAL Marques : LibXC Library
Liviu Ungur et al : ANISO software
Your calculation uses the libint2 library for the computation of 2-el integrals
For citations please refer to: http://libint.valeyev.net
Your ORCA version has been built with support for libXC version: 5.1.0
For citations please refer to: https://tddft.org/programs/libxc/
This ORCA versions uses:
CBLAS interface : Fast vector & matrix operations
LAPACKE interface : Fast linear algebra routines
SCALAPACK package : Parallel linear algebra routines
Shared memory : Shared parallel matrices
BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED
Core in use : SkylakeX
Copyright (c) 2011-2014, The OpenBLAS Project
***************************************
The coordinates will be read from file: geom.xyz
***************************************
Your calculation utilizes the semiempirical GFN2-xTB method
Please cite in your paper:
C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652.
================================================================================
================================================================================
WARNINGS
Please study these warnings very carefully!
================================================================================
WARNING: Geometry Optimization
===> : Switching off AutoStart
For restart on a previous wavefunction, please use MOREAD
WARNING: Found dipole moment calculation with XTB calculation
===> : Switching off dipole moment calculation
WARNING: TRAH-SCF for XTB is not implemented!
===> : Turning TRAH off!
================================================================================
INPUT FILE
================================================================================
NAME = cmmd.in
| 1> #CMMDE generated Orca input file
| 2> !XTB2 opt
| 3> %pal
| 4> nprocs 1
| 5> end
| 6> %geom
| 7> maxiter 9999
| 8> end
| 9>
| 10> *xyzfile 0 1 geom.xyz
| 11>
| 12>
| 13> ****END OF INPUT****
================================================================================
*****************************
* Geometry Optimization Run *
*****************************
Geometry optimization settings:
Update method Update .... BFGS
Choice of coordinates CoordSys .... Z-matrix Internals
Initial Hessian InHess .... Almoef's Model
Convergence Tolerances:
Energy Change TolE .... 5.0000e-06 Eh
Max. Gradient TolMAXG .... 3.0000e-04 Eh/bohr
RMS Gradient TolRMSG .... 1.0000e-04 Eh/bohr
Max. Displacement TolMAXD .... 4.0000e-03 bohr
RMS Displacement TolRMSD .... 2.0000e-03 bohr
Strict Convergence .... False
------------------------------------------------------------------------------
ORCA OPTIMIZATION COORDINATE SETUP
------------------------------------------------------------------------------
The optimization will be done in new redundant internal coordinates
Making redundant internal coordinates ... (new redundants) done
Evaluating the initial hessian ... (Almloef) done
Evaluating the coordinates ... done
Calculating the B-matrix .... done
Calculating the G-matrix .... done
Diagonalizing the G-matrix .... done
The first mode is .... 1
The number of degrees of freedom .... 9
-----------------------------------------------------------------
Redundant Internal Coordinates
-----------------------------------------------------------------
Definition Initial Value Approx d2E/dq
-----------------------------------------------------------------
1. B(H 1,C 0) 1.0922 0.357201
2. B(H 2,C 0) 1.0922 0.357201
3. B(H 3,C 0) 1.0922 0.357215
4. B(H 4,C 0) 1.0922 0.357198
5. A(H 1,C 0,H 3) 109.4713 0.290104
6. A(H 2,C 0,H 3) 109.4717 0.290104
7. A(H 1,C 0,H 4) 109.4703 0.290102
8. A(H 2,C 0,H 4) 109.4711 0.290102
9. A(H 3,C 0,H 4) 109.4718 0.290104
10. A(H 1,C 0,H 2) 109.4711 0.290102
-----------------------------------------------------------------
Number of atoms .... 5
Number of degrees of freedom .... 10
*************************************************************
* GEOMETRY OPTIMIZATION CYCLE 1 *
*************************************************************
---------------------------------
CARTESIAN COORDINATES (ANGSTROEM)
---------------------------------
C 1.042270 -0.054690 -0.072270
H 2.134470 -0.054680 -0.072270
H 0.678210 -0.652910 0.765880
H 0.678210 -0.481430 -1.009410
H 0.678210 0.970280 0.026740
----------------------------
CARTESIAN COORDINATES (A.U.)
----------------------------
NO LB ZA FRAG MASS X Y Z
0 C 6.0000 0 12.011 1.969605 -0.103349 -0.136571
1 H 1.0000 0 1.008 4.033564 -0.103330 -0.136571
2 H 1.0000 0 1.008 1.281631 -1.233821 1.447303
3 H 1.0000 0 1.008 1.281631 -0.909771 -1.907508
4 H 1.0000 0 1.008 1.281631 1.833563 0.050531
-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
| Aditya W. Sakti |
| Departemen Kimia |
| Universitas Pertamina |
-----------------------------------------------------------
* xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021
xtb is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
xtb is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
Cite this work as:
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht,
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11,
e01493. DOI: 10.1002/wcms.1493
for GFN2-xTB:
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
for GFN1-xTB:
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
for GFN0-xTB:
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
DOI: 10.26434/chemrxiv.8326202.v1
for GFN-FF:
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673.
DOI: 10.1002/anie.202004239
for ALPB and GBSA implicit solvation:
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput.,
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471
for DFT-D4:
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017,
147, 034112. DOI: 10.1063/1.4993215
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher,
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122.
DOI: 10.1063/1.5090222
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys.
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A
for sTDA-xTB:
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
DOI: 10.1063/1.4959605
in the mass-spec context:
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879.
DOI: 10.1039/c7sc00601b
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133.
DOI: 10.1021/acsomega.9b02011
for metadynamics refer to:
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
DOI: 10.1021/acs.jctc.9b00143
for SPH calculations refer to:
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714
DOI: 10.1021/acs.jctc.0c01306
with help from (in alphabetical order)
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman
C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer
J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher
M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber
* started run on 2022/08/05 at 08:09:45.270
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000
hostname : compute
calculation namespace : cmmd
coordinate file : cmmd_XTB.xyz
number of atoms : 5
number of electrons : 8
charge : 0
spin : 0.0
first test random number : 0.13962921932938
ID Z sym. atoms
1 6 C 1
2 1 H 2-5
-------------------------------------------------
| G F N 2 - x T B |
-------------------------------------------------
Reference 10.1021/acs.jctc.8b01176
* Hamiltonian:
H0-scaling (s, p, d) 1.850000 2.230000 2.230000
zeta-weighting 0.500000
* Dispersion:
s8 2.700000
a1 0.520000
a2 5.000000
s9 5.000000
* Repulsion:
kExp 1.500000 1.000000
rExp 1.000000
* Coulomb:
alpha 2.000000
third order shell-resolved
anisotropic true
a3 3.000000
a5 4.000000
cn-shift 1.200000
cn-exp 4.000000
max-rad 5.000000
...................................................
: SETUP :
:.................................................:
: # basis functions 8 :
: # atomic orbitals 8 :
: # shells 6 :
: # electrons 8 :
: max. iterations 250 :
: Hamiltonian GFN2-xTB :
: restarted? false :
: GBSA solvation false :
: PC potential false :
: electronic temp. 300.0000000 K :
: accuracy 1.0000000 :
: -> integral cutoff 0.2500000E+02 :
: -> integral neglect 0.1000000E-07 :
: -> SCF convergence 0.1000000E-05 Eh :
: -> wf. convergence 0.1000000E-03 e :
: Broyden damping 0.4000000 :
...................................................
iter E dE RMSdq gap omega full diag
1 -4.2288353 -0.422884E+01 0.246E+00 17.25 0.0 T
2 -4.2416604 -0.128252E-01 0.917E-01 17.07 1.0 T
3 -4.2418083 -0.147906E-03 0.503E-01 16.97 1.0 T
4 -4.2418549 -0.465207E-04 0.968E-02 16.85 1.0 T
5 -4.2418548 0.611476E-07 0.615E-03 16.85 7.3 T
6 -4.2418549 -0.109447E-06 0.181E-04 16.85 247.0 T
7 -4.2418549 -0.991518E-10 0.317E-06 16.85 14114.0 T
*** convergence criteria satisfied after 7 iterations ***
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -0.5801036 -15.7854
2 2.0000 -0.4667180 -12.7000
3 2.0000 -0.4667171 -12.7000
4 2.0000 -0.4667162 -12.7000 (HOMO)
5 0.1525567 4.1513 (LUMO)
6 0.2134364 5.8079
7 0.2134420 5.8081
8 0.2134570 5.8085
-------------------------------------------------------------
HL-Gap 0.6192729 Eh 16.8513 eV
Fermi-level -0.1570797 Eh -4.2744 eV
SCC (total) 0 d, 0 h, 0 min, 0.023 sec
SCC setup ... 0 min, 0.000 sec ( 0.637%)
Dispersion ... 0 min, 0.000 sec ( 0.085%)
classical contributions ... 0 min, 0.000 sec ( 0.064%)
integral evaluation ... 0 min, 0.000 sec ( 0.864%)
iterations ... 0 min, 0.022 sec ( 96.023%)
molecular gradient ... 0 min, 0.000 sec ( 1.620%)
printout ... 0 min, 0.000 sec ( 0.654%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -4.174962280159 Eh ::
:: gradient norm 0.013368794308 Eh/a0 ::
:: HOMO-LUMO gap 16.851274252485 eV ::
::.................................................::
:: SCC energy -4.241854917268 Eh ::
:: -> isotropic ES 0.001954142490 Eh ::
:: -> anisotropic ES 0.002520377280 Eh ::
:: -> anisotropic XC 0.003827617066 Eh ::
:: -> dispersion -0.000662667279 Eh ::
:: repulsion energy 0.066892631144 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge -0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
Property printout bound to 'properties.out'
-------------------------------------------------
| TOTAL ENERGY -4.174962280159 Eh |
| GRADIENT NORM 0.013368794308 Eh/α |
| HOMO-LUMO GAP 16.851274252485 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2022/08/05 at 08:09:45.304
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.035 sec
* cpu-time: 0 d, 0 h, 0 min, 0.015 sec
* ratio c/w: 0.421 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.023 sec
* cpu-time: 0 d, 0 h, 0 min, 0.004 sec
* ratio c/w: 0.172 speedup
------------------------- --------------------
FINAL SINGLE POINT ENERGY -4.174962280160
------------------------- --------------------
------------------------------------------------------------------------------
ORCA GEOMETRY RELAXATION STEP
------------------------------------------------------------------------------
Reading the OPT-File .... done
Getting information on internals .... done
Copying old internal coords+grads .... done
Making the new internal coordinates .... (new redundants).... done
Validating the new internal coordinates .... (new redundants).... done
Calculating the B-matrix .... done
Calculating the G,G- and P matrices .... done
Transforming gradient to internals .... done
Projecting the internal gradient .... done
Number of atoms .... 5
Number of internal coordinates .... 10
Current Energy .... -4.174962280 Eh
Current gradient norm .... 0.013368794 Eh/bohr
Maximum allowed component of the step .... 0.300
Current trust radius .... 0.300
Evaluating the initial hessian .... (Almloef) done
Projecting the Hessian .... done
Forming the augmented Hessian .... done
Diagonalizing the augmented Hessian .... done
Last element of RFO vector .... 0.999302325
Lowest eigenvalues of augmented Hessian:
-0.000499645 0.290101871 0.290102101 0.290102951 0.290103802
Length of the computed step .... 0.037373954
The final length of the internal step .... 0.037373954
Converting the step to cartesian space:
Initial RMS(Int)= 0.0118186819
Transforming coordinates:
Iter 0: RMS(Cart)= 0.0096499129 RMS(Int)= 0.0118186819
Iter 1: RMS(Cart)= 0.0000000192 RMS(Int)= 0.0000000229
done
Storing new coordinates .... done
.--------------------.
----------------------|Geometry convergence|-------------------------
Item value Tolerance Converged
---------------------------------------------------------------------
RMS gradient 0.0042275832 0.0001000000 NO
MAX gradient 0.0066867184 0.0003000000 NO
RMS step 0.0118186819 0.0020000000 NO
MAX step 0.0186937616 0.0040000000 NO
........................................................
Max(Bonds) 0.0099 Max(Angles) 0.00
Max(Dihed) 0.00 Max(Improp) 0.00
---------------------------------------------------------------------
The optimization has not yet converged - more geometry cycles are needed
---------------------------------------------------------------------------
Redundant Internal Coordinates
(Angstroem and degrees)
Definition Value dE/dq Step New-Value
----------------------------------------------------------------------------
1. B(H 1,C 0) 1.0922 0.006685 -0.0099 1.0823
2. B(H 2,C 0) 1.0922 0.006686 -0.0099 1.0823
3. B(H 3,C 0) 1.0922 0.006680 -0.0099 1.0823
4. B(H 4,C 0) 1.0922 0.006687 -0.0099 1.0823
5. A(H 1,C 0,H 3) 109.47 -0.000000 0.00 109.47
6. A(H 2,C 0,H 3) 109.47 0.000001 -0.00 109.47
7. A(H 1,C 0,H 4) 109.47 -0.000002 0.00 109.47
8. A(H 2,C 0,H 4) 109.47 0.000000 -0.00 109.47
9. A(H 3,C 0,H 4) 109.47 0.000001 -0.00 109.47
10. A(H 1,C 0,H 2) 109.47 -0.000000 0.00 109.47
----------------------------------------------------------------------------
*************************************************************
* GEOMETRY OPTIMIZATION CYCLE 2 *
*************************************************************
---------------------------------
CARTESIAN COORDINATES (ANGSTROEM)
---------------------------------
C 1.042272 -0.054688 -0.072268
H 2.124582 -0.054681 -0.072268
H 0.681507 -0.647491 0.758290
H 0.681504 -0.477567 -1.000928
H 0.681505 0.960997 0.025844
----------------------------
CARTESIAN COORDINATES (A.U.)
----------------------------
NO LB ZA FRAG MASS X Y Z
0 C 6.0000 0 12.011 1.969608 -0.103346 -0.136566
1 H 1.0000 0 1.008 4.014878 -0.103332 -0.136567
2 H 1.0000 0 1.008 1.287862 -1.223581 1.432961
3 H 1.0000 0 1.008 1.287855 -0.902471 -1.891481
4 H 1.0000 0 1.008 1.287858 1.816022 0.048838
-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
| Aditya W. Sakti |
| Departemen Kimia |
| Universitas Pertamina |
-----------------------------------------------------------
* xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021
xtb is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
xtb is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
Cite this work as:
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht,
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11,
e01493. DOI: 10.1002/wcms.1493
for GFN2-xTB:
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
for GFN1-xTB:
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
for GFN0-xTB:
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
DOI: 10.26434/chemrxiv.8326202.v1
for GFN-FF:
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673.
DOI: 10.1002/anie.202004239
for ALPB and GBSA implicit solvation:
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput.,
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471
for DFT-D4:
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017,
147, 034112. DOI: 10.1063/1.4993215
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher,
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122.
DOI: 10.1063/1.5090222
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys.
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A
for sTDA-xTB:
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
DOI: 10.1063/1.4959605
in the mass-spec context:
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879.
DOI: 10.1039/c7sc00601b
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133.
DOI: 10.1021/acsomega.9b02011
for metadynamics refer to:
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
DOI: 10.1021/acs.jctc.9b00143
for SPH calculations refer to:
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714
DOI: 10.1021/acs.jctc.0c01306
with help from (in alphabetical order)
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman
C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer
J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher
M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber
* started run on 2022/08/05 at 08:09:45.347
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000
hostname : compute
calculation namespace : cmmd
coordinate file : cmmd_XTB.xyz
number of atoms : 5
number of electrons : 8
charge : 0
spin : 0.0
first test random number : 0.17259154546392
ID Z sym. atoms
1 6 C 1
2 1 H 2-5
-------------------------------------------------
| G F N 2 - x T B |
-------------------------------------------------
Reference 10.1021/acs.jctc.8b01176
* Hamiltonian:
H0-scaling (s, p, d) 1.850000 2.230000 2.230000
zeta-weighting 0.500000
* Dispersion:
s8 2.700000
a1 0.520000
a2 5.000000
s9 5.000000
* Repulsion:
kExp 1.500000 1.000000
rExp 1.000000
* Coulomb:
alpha 2.000000
third order shell-resolved
anisotropic true
a3 3.000000
a5 4.000000
cn-shift 1.200000
cn-exp 4.000000
max-rad 5.000000
q/qsh data taken from xtbrestart
CAMM data taken from xtbrestart
...................................................
: SETUP :
:.................................................:
: # basis functions 8 :
: # atomic orbitals 8 :
: # shells 6 :
: # electrons 8 :
: max. iterations 250 :
: Hamiltonian GFN2-xTB :
: restarted? true :
: GBSA solvation false :
: PC potential false :
: electronic temp. 300.0000000 K :
: accuracy 1.0000000 :
: -> integral cutoff 0.2500000E+02 :
: -> integral neglect 0.1000000E-07 :
: -> SCF convergence 0.1000000E-05 Eh :
: -> wf. convergence 0.1000000E-03 e :
: Broyden damping 0.4000000 :
...................................................
iter E dE RMSdq gap omega full diag
1 -4.2473771 -0.424738E+01 0.106E-01 17.33 0.0 T
2 -4.2473844 -0.729517E-05 0.561E-02 17.34 1.0 T
3 -4.2473846 -0.259690E-06 0.204E-02 17.34 2.2 T
4 -4.2473847 -0.370480E-07 0.422E-03 17.35 10.6 T
5 -4.2473847 -0.969713E-11 0.246E-05 17.35 1817.8 T
6 -4.2473847 -0.112799E-11 0.111E-07 17.35 100000.0 T
*** convergence criteria satisfied after 6 iterations ***
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -0.5818102 -15.8319
2 2.0000 -0.4674475 -12.7199
3 2.0000 -0.4674471 -12.7199
4 2.0000 -0.4674466 -12.7199 (HOMO)
5 0.1699963 4.6258 (LUMO)
6 0.2290144 6.2318
7 0.2290179 6.2319
8 0.2290219 6.2320
-------------------------------------------------------------
HL-Gap 0.6374429 Eh 17.3457 eV
Fermi-level -0.1487251 Eh -4.0470 eV
SCC (total) 0 d, 0 h, 0 min, 0.004 sec
SCC setup ... 0 min, 0.000 sec ( 3.196%)
Dispersion ... 0 min, 0.000 sec ( 0.577%)
classical contributions ... 0 min, 0.000 sec ( 0.302%)
integral evaluation ... 0 min, 0.000 sec ( 4.630%)
iterations ... 0 min, 0.003 sec ( 78.655%)
molecular gradient ... 0 min, 0.000 sec ( 9.015%)
printout ... 0 min, 0.000 sec ( 3.368%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -4.175218465758 Eh ::
:: gradient norm 0.000198777395 Eh/a0 ::
:: HOMO-LUMO gap 17.345703353999 eV ::
::.................................................::
:: SCC energy -4.247384681031 Eh ::
:: -> isotropic ES 0.002034388498 Eh ::
:: -> anisotropic ES 0.002324462858 Eh ::
:: -> anisotropic XC 0.003588679991 Eh ::
:: -> dispersion -0.000661035657 Eh ::
:: repulsion energy 0.072166209677 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge -0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
Property printout bound to 'properties.out'
-------------------------------------------------
| TOTAL ENERGY -4.175218465758 Eh |
| GRADIENT NORM 0.000198777395 Eh/α |
| HOMO-LUMO GAP 17.345703353999 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2022/08/05 at 08:09:45.361
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.014 sec
* cpu-time: 0 d, 0 h, 0 min, 0.014 sec
* ratio c/w: 0.957 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.004 sec
* cpu-time: 0 d, 0 h, 0 min, 0.003 sec
* ratio c/w: 0.869 speedup
------------------------- --------------------
FINAL SINGLE POINT ENERGY -4.175218465760
------------------------- --------------------
------------------------------------------------------------------------------
ORCA GEOMETRY RELAXATION STEP
------------------------------------------------------------------------------
Reading the OPT-File .... done
Getting information on internals .... done
Copying old internal coords+grads .... done
Making the new internal coordinates .... (new redundants).... done
Validating the new internal coordinates .... (new redundants).... done
Calculating the B-matrix .... done
Calculating the G,G- and P matrices .... done
Transforming gradient to internals .... done
Projecting the internal gradient .... done
Number of atoms .... 5
Number of internal coordinates .... 10
Current Energy .... -4.175218466 Eh
Current gradient norm .... 0.000198777 Eh/bohr
Maximum allowed component of the step .... 0.300
Current trust radius .... 0.300
Updating the Hessian (BFGS) .... done
Forming the augmented Hessian .... done
Diagonalizing the augmented Hessian .... done
Last element of RFO vector .... 0.999999841
Lowest eigenvalues of augmented Hessian:
-0.000000112 0.290101865 0.290102092 0.290102928 0.290103801
Length of the computed step .... 0.000564067
The final length of the internal step .... 0.000564067
Converting the step to cartesian space:
Initial RMS(Int)= 0.0001783736
Transforming coordinates:
Iter 0: RMS(Cart)= 0.0001456389 RMS(Int)= 0.0001783736
Iter 1: RMS(Cart)= 0.0000000002 RMS(Int)= 0.0000000003
done
Storing new coordinates .... done
.--------------------.
----------------------|Geometry convergence|-------------------------
Item value Tolerance Converged
---------------------------------------------------------------------
Energy change -0.0002561856 0.0000050000 NO
RMS gradient 0.0000628550 0.0001000000 YES
MAX gradient 0.0000996472 0.0003000000 YES
RMS step 0.0001783736 0.0020000000 YES
MAX step 0.0002827846 0.0040000000 YES
........................................................
Max(Bonds) 0.0001 Max(Angles) 0.00
Max(Dihed) 0.00 Max(Improp) 0.00
---------------------------------------------------------------------
Everything but the energy has converged. However, the energy
appears to be close enough to convergence to make sure that the
final evaluation at the new geometry represents the equilibrium energy.
Convergence will therefore be signaled now
***********************HURRAY********************
*** THE OPTIMIZATION HAS CONVERGED ***
*************************************************
---------------------------------------------------------------------------
Redundant Internal Coordinates
--- Optimized Parameters ---
(Angstroem and degrees)
Definition OldVal dE/dq Step FinalVal
----------------------------------------------------------------------------
1. B(H 1,C 0) 1.0823 0.000100 -0.0001 1.0822
2. B(H 2,C 0) 1.0823 0.000099 -0.0001 1.0822
3. B(H 3,C 0) 1.0823 0.000099 -0.0001 1.0822
4. B(H 4,C 0) 1.0823 0.000100 -0.0001 1.0822
5. A(H 1,C 0,H 3) 109.47 0.000000 -0.00 109.47
6. A(H 2,C 0,H 3) 109.47 0.000001 -0.00 109.47
7. A(H 1,C 0,H 4) 109.47 -0.000001 0.00 109.47
8. A(H 2,C 0,H 4) 109.47 -0.000000 0.00 109.47
9. A(H 3,C 0,H 4) 109.47 0.000001 -0.00 109.47
10. A(H 1,C 0,H 2) 109.47 -0.000000 0.00 109.47
----------------------------------------------------------------------------
*******************************************************
*** FINAL ENERGY EVALUATION AT THE STATIONARY POINT ***
*** (AFTER 2 CYCLES) ***
*******************************************************
---------------------------------
CARTESIAN COORDINATES (ANGSTROEM)
---------------------------------
C 1.042273 -0.054687 -0.072267
H 2.124433 -0.054682 -0.072268
H 0.681557 -0.647410 0.758175
H 0.681553 -0.477508 -1.000800
H 0.681554 0.960857 0.025830
----------------------------
CARTESIAN COORDINATES (A.U.)
----------------------------
NO LB ZA FRAG MASS X Y Z
0 C 6.0000 0 12.011 1.969610 -0.103344 -0.136565
1 H 1.0000 0 1.008 4.014597 -0.103334 -0.136567
2 H 1.0000 0 1.008 1.287957 -1.223427 1.432744
3 H 1.0000 0 1.008 1.287949 -0.902359 -1.891238
4 H 1.0000 0 1.008 1.287950 1.815757 0.048811
-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
| Aditya W. Sakti |
| Departemen Kimia |
| Universitas Pertamina |
-----------------------------------------------------------
* xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021
xtb is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
xtb is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
Cite this work as:
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht,
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11,
e01493. DOI: 10.1002/wcms.1493
for GFN2-xTB:
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
for GFN1-xTB:
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
for GFN0-xTB:
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
DOI: 10.26434/chemrxiv.8326202.v1
for GFN-FF:
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673.
DOI: 10.1002/anie.202004239
for ALPB and GBSA implicit solvation:
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput.,
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471
for DFT-D4:
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017,
147, 034112. DOI: 10.1063/1.4993215
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher,
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122.
DOI: 10.1063/1.5090222
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys.
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A
for sTDA-xTB:
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
DOI: 10.1063/1.4959605
in the mass-spec context:
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879.
DOI: 10.1039/c7sc00601b
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133.
DOI: 10.1021/acsomega.9b02011
for metadynamics refer to:
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
DOI: 10.1021/acs.jctc.9b00143
for SPH calculations refer to:
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714
DOI: 10.1021/acs.jctc.0c01306
with help from (in alphabetical order)
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman
C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer
J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher
M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber
* started run on 2022/08/05 at 08:09:45.391
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000
hostname : compute
calculation namespace : cmmd
coordinate file : cmmd_XTB.xyz
number of atoms : 5
number of electrons : 8
charge : 0
spin : 0.0
first test random number : 0.68691715133107
ID Z sym. atoms
1 6 C 1
2 1 H 2-5
-------------------------------------------------
| G F N 2 - x T B |
-------------------------------------------------
Reference 10.1021/acs.jctc.8b01176
* Hamiltonian:
H0-scaling (s, p, d) 1.850000 2.230000 2.230000
zeta-weighting 0.500000
* Dispersion:
s8 2.700000
a1 0.520000
a2 5.000000
s9 5.000000
* Repulsion:
kExp 1.500000 1.000000
rExp 1.000000
* Coulomb:
alpha 2.000000
third order shell-resolved
anisotropic true
a3 3.000000
a5 4.000000
cn-shift 1.200000
cn-exp 4.000000
max-rad 5.000000
q/qsh data taken from xtbrestart
CAMM data taken from xtbrestart
...................................................
: SETUP :
:.................................................:
: # basis functions 8 :
: # atomic orbitals 8 :
: # shells 6 :
: # electrons 8 :
: max. iterations 250 :
: Hamiltonian GFN2-xTB :
: restarted? true :
: GBSA solvation false :
: PC potential false :
: electronic temp. 300.0000000 K :
: accuracy 1.0000000 :
: -> integral cutoff 0.2500000E+02 :
: -> integral neglect 0.1000000E-07 :
: -> SCF convergence 0.1000000E-05 Eh :
: -> wf. convergence 0.1000000E-03 e :
: Broyden damping 0.4000000 :
...................................................
iter E dE RMSdq gap omega full diag
1 -4.2474673 -0.424747E+01 0.161E-03 17.35 0.0 T
2 -4.2474673 -0.163779E-08 0.849E-04 17.35 52.7 T
3 -4.2474673 -0.599876E-10 0.305E-04 17.35 146.8 T
*** convergence criteria satisfied after 3 iterations ***
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -0.5818333 -15.8325
2 2.0000 -0.4674559 -12.7201
3 2.0000 -0.4674556 -12.7201
4 2.0000 -0.4674553 -12.7201 (HOMO)
5 0.1702655 4.6332 (LUMO)
6 0.2292565 6.2384
7 0.2292586 6.2384
8 0.2292605 6.2385
-------------------------------------------------------------
HL-Gap 0.6377208 Eh 17.3533 eV
Fermi-level -0.1485949 Eh -4.0435 eV
SCC (total) 0 d, 0 h, 0 min, 0.004 sec
SCC setup ... 0 min, 0.000 sec ( 2.747%)
Dispersion ... 0 min, 0.000 sec ( 0.433%)
classical contributions ... 0 min, 0.000 sec ( 0.331%)
integral evaluation ... 0 min, 0.000 sec ( 4.565%)
iterations ... 0 min, 0.003 sec ( 79.096%)
molecular gradient ... 0 min, 0.000 sec ( 9.086%)
printout ... 0 min, 0.000 sec ( 3.490%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -4.175218519964 Eh ::
:: gradient norm 0.000005516518 Eh/a0 ::
:: HOMO-LUMO gap 17.353265796625 eV ::
::.................................................::
:: SCC energy -4.247467308161 Eh ::
:: -> isotropic ES 0.002035507818 Eh ::
:: -> anisotropic ES 0.002321507905 Eh ::
:: -> anisotropic XC 0.003585039049 Eh ::
:: -> dispersion -0.000661012503 Eh ::
:: repulsion energy 0.072248782606 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge 0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
Property printout bound to 'properties.out'
-------------------------------------------------
| TOTAL ENERGY -4.175218519964 Eh |
| GRADIENT NORM 0.000005516518 Eh/α |
| HOMO-LUMO GAP 17.353265796625 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2022/08/05 at 08:09:45.405
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.014 sec
* cpu-time: 0 d, 0 h, 0 min, 0.014 sec
* ratio c/w: 0.957 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.004 sec
* cpu-time: 0 d, 0 h, 0 min, 0.003 sec
* ratio c/w: 0.849 speedup
------------------------- --------------------
FINAL SINGLE POINT ENERGY -4.175218519960
------------------------- --------------------
*** OPTIMIZATION RUN DONE ***
Timings for individual modules:
Sum of individual times ... 0.151 sec (= 0.003 min)
Geometry relaxation ... 0.039 sec (= 0.001 min) 26.0 %
XTB module ... 0.112 sec (= 0.002 min) 74.0 %
****ORCA TERMINATED NORMALLY****
TOTAL RUN TIME: 0 days 0 hours 0 minutes 0 seconds 249 msec