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Home Page: https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/gcp
License: GNU Lesser General Public License v3.0
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Project URL https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/gcp is a broken link
results differ between classic and mctc
I was seeing if I could drive mctc-gcp with slight modifications of the gcp QCEngine harness. atom is fine, but molecules differ in Egcp by about an order of magnitude with the same input. It's not a simple bohr/ang issue. I don't particularly need this solved -- just FYI and stashing notes.
command=['mctc-gcp', 'gcp_geometry.xyz', '-level', 'HF/SV', '-grad']
infiles={'gcp_geometry.xyz': '10\n0 1 C4H6\nC 0.000000000000 -0.667578000000 -2.124659000000\nC 0.000000000000 0.667578000000 -2.124659000000\nH 0.923621000000 -1.232253000000 -2.126185000000\nH -0.923621000000 -1.232253000000 -2.126185000000\nH -0.923621000000 1.232253000000 -2.126185000000\nH 0.923621000000 1.232253000000 -2.126185000000\nC 0.000000000000 0.000000000000 2.900503000000\nC 0.000000000000 0.000000000000 1.693240000000\nH 0.000000000000 0.000000000000 0.627352000000\nH 0.000000000000 0.000000000000 3.963929000000\n'}
"classic" on left, mctc on right
'keywords': {}, 'keywords': {},
'model': {'basis': None, 'method': 'hf/sv'}, 'model': {'basis': None, 'method': 'hf/sv'},
'molecule': {'atom_labels': array(['', '', '', '', '', '', '', '', '', ''], dtype='<U1'), 'molecule': {'atom_labels': array(['', '', '', '', '', '', '', '', '', ''], dtype='<U1'),
'atomic_numbers': array([6, 6, 1, 1, 1, 1, 6, 6, 1, 1], dtype=int16), 'atomic_numbers': array([6, 6, 1, 1, 1, 1, 6, 6, 1, 1], dtype=int16),
'fix_com': False, 'fix_com': False,
'fix_orientation': False, 'fix_orientation': False,
'fragment_charges': [0.0, 0.0], 'fragment_charges': [0.0, 0.0],
'fragment_multiplicities': [1, 1], 'fragment_multiplicities': [1, 1],
'fragments': [array([0, 1, 2, 3, 4, 5], dtype=int32), 'fragments': [array([0, 1, 2, 3, 4, 5], dtype=int32),
array([6, 7, 8, 9], dtype=int32)], array([6, 7, 8, 9], dtype=int32)],
'geometry': array([[ 0. , -1.26153959, -4.01502362], 'geometry': array([[ 0. , -1.26153959, -4.01502362],
[ 0. , 1.26153959, -4.01502362], [ 0. , 1.26153959, -4.01502362],
[ 1.74539073, -2.32862069, -4.01790734], [ 1.74539073, -2.32862069, -4.01790734],
[-1.74539073, -2.32862069, -4.01790734], [-1.74539073, -2.32862069, -4.01790734],
[-1.74539073, 2.32862069, -4.01790734], [-1.74539073, 2.32862069, -4.01790734],
[ 1.74539073, 2.32862069, -4.01790734], [ 1.74539073, 2.32862069, -4.01790734],
[ 0. , 0. , 5.4811563 ], [ 0. , 0. , 5.4811563 ],
[ 0. , 0. , 3.19975986], [ 0. , 0. , 3.19975986],
[ 0. , 0. , 1.18552346], [ 0. , 0. , 1.18552346],
[ 0. , 0. , 7.49074019]]), [ 0. , 0. , 7.49074019]]),
'mass_numbers': array([12, 12, 1, 1, 1, 1, 12, 12, 1, 1], dtype=int16), 'mass_numbers': array([12, 12, 1, 1, 1, 1, 12, 12, 1, 1], dtype=int16),
'masses': array([12. , 12. , 1.00782503, 1.00782503, 1.00782503, 'masses': array([12. , 12. , 1.00782503, 1.00782503, 1.00782503,
1.00782503, 12. , 12. , 1.00782503, 1.00782503]), 1.00782503, 12. , 12. , 1.00782503, 1.00782503]),
'molecular_charge': 0.0, 'molecular_charge': 0.0,
'molecular_multiplicity': 1, 'molecular_multiplicity': 1,
'name': 'C4H6', 'name': 'C4H6',
'provenance': {'creator': 'QCElemental', 'provenance': {'creator': 'QCElemental',
'routine': 'qcelemental.molparse.from_string', 'routine': 'qcelemental.molparse.from_string',
'version': 'v0.18.0'}, 'version': 'v0.18.0'},
'real': array([ True, True, True, True, True, True, True, True, True, 'real': array([ True, True, True, True, True, True, True, True, True,
True]), True]),
'schema_name': 'qcschema_molecule', 'schema_name': 'qcschema_molecule',
'schema_version': 2, 'schema_version': 2,
'symbols': array(['C', 'C', 'H', 'H', 'H', 'H', 'C', 'C', 'H', 'H'], dtype='<U1'), 'symbols': array(['C', 'C', 'H', 'H', 'H', 'H', 'C', 'C', 'H', 'H'], dtype='<U1'),
'validated': True}, 'validated': True},
'properties': {}, 'properties': {},
'protocols': {}, 'protocols': {},
'provenance': {'cpu': 'Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz', 'provenance': {'cpu': 'Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz',
'creator': 'GCP', 'creator': 'GCP',
'hostname': 'psinet', 'hostname': 'psinet',
'qcengine_version': 'v0.18.0+12.g30ed0d2.dirty', 'qcengine_version': 'v0.18.0+12.g30ed0d2.dirty',
'routine': 'qcengine.programs.gcp.parse_output', 'routine': 'qcengine.programs.gcp.parse_output',
'username': 'psilocaluser', 'username': 'psilocaluser',
'version': '2.2', | 'version': '2.1.2',
'wall_time': 1.2454249858856201}, | 'wall_time': 1.2334864139556885},
'return_result': array([[-6.11830758e-20, -6.91724066e-05, 1.09826314e-04], | 'return_result': array([[ 2.33645568e-21, 1.88406240e-04, 9.40795164e-05],
[ 7.12044626e-20, 6.91724066e-05, 1.09826314e-04], | [-4.67291136e-21, -1.88406240e-04, 9.40795164e-05],
[-1.52546975e-03, 1.10309566e-03, 2.80148912e-05], | [ 2.63848984e-05, 6.77932735e-05, 2.46892935e-05],
[ 1.52546975e-03, 1.10309566e-03, 2.80148912e-05], | [-2.63848984e-05, 6.77932735e-05, 2.46892935e-05],
[ 1.52546975e-03, -1.10309566e-03, 2.80148912e-05], | [-2.63848984e-05, -6.77932735e-05, 2.46892935e-05],
[-1.52546975e-03, -1.10309566e-03, 2.80148912e-05], | [ 2.63848984e-05, -6.77932735e-05, 2.46892935e-05],
[-2.77691314e-24, -5.08629086e-24, 1.82372296e-04], | [ 1.14084750e-23, 6.84508500e-23, -1.57281683e-04],
[-6.06354197e-23, -1.02697054e-21, -2.59507279e-04], | [ 3.65071200e-23, 1.82535600e-22, 7.77370261e-05],
[-4.59899866e-22, 3.60801817e-21, 1.47563104e-03], | [ 0.00000000e+00, 0.00000000e+00, -2.02905480e-04],
[ 3.74257354e-26, -2.25113303e-25, -1.73020825e-03]]), | [ 0.00000000e+00, -1.14084750e-24, -4.46606984e-06]]),
'schema_name': 'qcschema_output', 'schema_name': 'qcschema_output',
'schema_version': 1, 'schema_version': 1,
'stderr': None, 'stderr': None,
'stdout': ' ___________________________________________ \n' | 'stdout': ' -------------------------------------------\n'
' \n' <
' | ** g C P ** |\n' '| ** g C P ** |\n'
' | a geometrical counterpoise correction |\n' '| a geometrical counterpoise correction |\n'
' | H.Kruse J.G.Brandenburg S.Grimme |\n' '| H.Kruse J.G.Brandenburg S.Grimme |\n'
' | Version 2.02 Nov 2016 |\n' | ' -------------------------------------------\n'
' | |\n' | 'mctc-gcp version 2.1.2\n'
' ___________________________________________ \n' <
' \n' '\n'
' Please cite work done with this code as:\n' 'Please cite work done with this code as:\n'
' H. Kruse, S. Grimme J. Chem. Phys. 136, 154101 (2012)\n' 'H. Kruse, S. Grimme J. Chem. Phys. 136, 154101 (2012)\n'
' DOI: 10.1063/1.3700154 \n' 'DOI: 10.1063/1.3700154\n'
' For the periodic version, please also cite:\n' 'For the periodic version, please also cite:\n'
' J. G. Brandenburg, M. Alessio, B. Civalleri, M. F. Peintinger\n' 'J. G. Brandenburg, M. Alessio, B. Civalleri, M. F. Peintinger\n'
' T. Bredow, S.Grimme J. Phys. Chem. A 117, 9282-9292 (2013).\n' 'T. Bredow, S.Grimme J. Phys. Chem. A 117, 9282-9292 (2013).\n'
' DOI: 10.1021/jp406658y \n' 'DOI: 10.1021/jp406658y\n'
' \n' '\n'
' \n' ' \n'
' reading... XYZ file [angst]: gcp_geometry.xyz\n' <
' \n' <
' level hf/sv basis: SV (Ahlrichs)\n' ' level hf/sv basis: SV (Ahlrichs)\n'
' Nbf 48\n' ' Nbf 48\n'
' Atoms 10\n' ' Atoms 10\n'
' \n' ' \n'
' Parameters: \n' ' Parameters: \n'
' sigma 0.1724\n' ' sigma 0.1724\n'
' eta 1.2804\n' ' eta 1.2804\n'
' alpha 0.8568\n' ' alpha 0.8568\n'
' beta 1.2342\n' ' beta 1.2342\n'
> ' dmp_scal 4.0000\n'
> ' dmp_exp 6.0000\n'
' \n' ' \n'
' \n' ' \n'
' element parameters hf/sv\n' ' element parameters hf/sv\n'
' elem emiss nbas elem emiss nbas elem emiss ' ' elem emiss nbas elem emiss nbas elem emiss '
'nbas\n' 'nbas\n'
' h 0.00904 2 he 0.00884 2 li 0.20419 ' ' h 0.00904 2 he 0.00884 2 li 0.20419 '
'3\n' '3\n'
' be 0.10775 3 b 0.04953 9 c 0.05548 ' ' be 0.10775 3 b 0.04953 9 c 0.05548 '
'9\n' '9\n'
' n 0.07282 9 o 0.10085 9 f 0.13403 ' ' n 0.07282 9 o 0.10085 9 f 0.13403 '
'9\n' '9\n'
' ne 0.17422 9 na 0.31562 7 mg 0.26112 ' ' ne 0.17422 9 na 0.31562 7 mg 0.26112 '
'7\n' '7\n'
' al 0.16857 13 si 0.15229 13 p 0.14691 ' ' al 0.16857 13 si 0.15229 13 p 0.14691 '
'13\n' '13\n'
' s 0.16825 13 cl 0.18788 13 ar 0.21116 ' ' s 0.16825 13 cl 0.18788 13 ar 0.21116 '
'13\n' '13\n'
' k 0.37425 11 ca 0.46097 11 sc 0.44489 ' ' k 0.37425 11 ca 0.46097 11 sc 0.44489 '
'21\n' '21\n'
' ti 0.40499 21 v 0.37841 21 cr 0.37344 ' ' ti 0.40499 21 v 0.37841 21 cr 0.37344 '
'21\n' '21\n'
' mn 0.36125 21 fe 0.36001 21 co 0.36293 ' ' mn 0.36125 21 fe 0.36001 21 co 0.36293 '
'21\n' '21\n'
' ni 0.24380 21 cu 0.40530 21 zn 0.39651 ' ' ni 0.24380 21 cu 0.40530 21 zn 0.39651 '
'21\n' '21\n'
' ga 0.36267 27 ge 0.36046 27 as 0.36336 ' ' ga 0.36267 27 ge 0.36046 27 as 0.36336 '
'27\n' '27\n'
' se 0.38417 27 br 0.39970 27 kr 0.41731 ' ' se 0.38417 27 br 0.39970 27 kr 0.41731 '
'27\n' '27\n'
' \n' ' \n'
' \n' ' \n'
' cutoffs: \n' ' cutoffs: \n'
' distance [bohr] 60.0\n' ' distance [bohr] 60.0\n'
' noise [a.u.] 2.2E-16\n' ' noise [a.u.] 2.2E-16\n'
' SR-damping F\n' | ' SR-damping T\n'
' \n' ' \n'
' # ON sites Nvirt Emiss BSSE [kcal/mol]\n' ' # ON sites Nvirt Emiss BSSE [kcal/mol]\n'
' 1 6 9 6.0 0.0555 2.8760\n' | ' 1 6 9 6.0 0.0555 0.3915\n'
' 2 6 9 6.0 0.0555 2.8760\n' | ' 2 6 9 6.0 0.0555 0.3915\n'
' 3 1 9 1.5 0.0090 0.1846\n' | ' 3 1 9 1.5 0.0090 0.0729\n'
' 4 1 9 1.5 0.0090 0.1846\n' | ' 4 1 9 1.5 0.0090 0.0729\n'
' 5 1 9 1.5 0.0090 0.1846\n' | ' 5 1 9 1.5 0.0090 0.0729\n'
' 6 1 9 1.5 0.0090 0.1846\n' | ' 6 1 9 1.5 0.0090 0.0729\n'
' 7 6 9 6.0 0.0555 1.6288\n' | ' 7 6 9 6.0 0.0555 0.1542\n'
' 8 6 9 6.0 0.0555 1.6586\n' | ' 8 6 9 6.0 0.0555 0.1870\n'
' 9 1 9 1.5 0.0090 0.1346\n' | ' 9 1 9 1.5 0.0090 0.0455\n'
' 10 1 9 1.5 0.0090 0.1033\n' | ' 10 1 9 1.5 0.0090 0.0154\n'
'cpu-time for gradient 0.0 s\n' 'cpu-time for gradient 0.0 s\n'
' \n' '\n'
' ** gCP correction ** \n' '** gCP correction ** \n'
' Egcp: 0.0159608596 / (a.u.) || 10.0156 / (kcal/mol)\n' | ' Egcp: 0.0023531419 / (a.u.) || 1.4766 / (kcal/mol)\n'
' \n' '\n'
' |G|= 1.463203748874275E-002\n' | ' |G|= 1.4828316340119714E-003\n'
' no gradient file found to add G(gcp)!\n' ' no gradient file found to add G(gcp)!\n'
' hence written to file gcp_gradient\n' | ' hence written to file gcp_gradient\n',
'cpu-time for gCP 0.0 s\n' <
' \n' <
' normal termination of gCP\n', <
'success': True, 'success': True,
'wavefunction': None} 'wavefunction': None}
{'CURRENT ENERGY': '0.0159608596', 'GCP CORRECTION ENERGY': '0.0159608596', 'HF/SV GCP CORRECTION ENERGY': '0.0159608596', 'CURRENT GRADIENT': [-6.1 | {'CURRENT ENERGY': '0.0023531419', 'GCP CORRECTION ENERGY': '0.0023531419', 'HF/SV GCP CORRECTION ENERGY': '0.0023531419', 'CURRENT GRADIENT': [2.33
==================================================================================================================================================== | ----------------------------------------------------------------------------------------------------------------------------------------------------
FAILED qcengine/programs/tests/test_dftd3_mp2d.py::test_gcp[inp0-qcmol] - assert 0 | ERROR root:testing.py:20 test_gcp.............................................FAILED
> ERROR root:testing.py:21 test_gcp: computed value (0.002353142) does not match (0.015960860) to atol=1e-07 by difference (-0.013607718).
`-hess` flag seems to be ignored
No additional output is written when the -hess flag is specified. I've tried for a few methods using the condaforge mctc-gcp version 2.3.1.
Package for conda-forge
This project should be packaged for conda-forge at some point.
Include legacy command-line interface in build
The old command line interface of gcp is still available at https://github.com/grimme-lab/gcp/tree/main/old but currently not build.
For projects interfacing gcp via command line the legacy command line interface might be a useful fallback (e.g. see MolSSI/QCEngine#278) until an actual API is provided (see #5) or the new command line interface is adapted in dependent projects.
Provide flag to enable damping for all methods
The bug in #8 showed large deviations between individual GCP corrections, yet relative GCP corrections were largely unaffected. For some systems we checked the difference and found an improvement with enabled damping.
To further investigate this a command line option could be added to enable the damping for other GCP corrected methods than the 3c methods.
Provide C API
The GCP library should provide a C API using iso_c_binding to provide better access than just the command line interface for non-Fortran project. This would allow to create a Python API based on the CFFI wrapper as well.
HSE-3c parameterization differs from reference
From the supporting information of the original HSE-3c paper (Phys. Chem. Chem. Phys., 2016,18, 15519-15523 DOI), the gCP parameters for HSE-3c should be:
sigma = 1.00000
eta = 1.40858
alpha = 0.29083
beta = 1.95260
In the code, slightly different values are used:
p(1)=1.00000d0 ! sigma
p(2)=1.32378d0 ! eta
p(3)=0.28314d0 ! alpha
p(4)=1.94527d0 ! beta
Is this a bug or some later update to the HSE-3c parameters?
Number of declared basis functions seems inconsistent with the basis
See e.g. line https://github.com/grimme-lab/gcp/blob/98fcfe5b42cd62b14b5d4e73995601fe06878fba/src/gcp.f90#L1167C1-L1167C6
which states that there are 10 basis functions for Li and Be. Yet the def2-msvp has only 9 basis functions for these atoms. There is no inconsistency for these atoms in the cc-pvdz basis.
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