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grimme-lab / gcp

Geometrical Counter-Poise Correction
https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/gcp
GNU Lesser General Public License v3.0
11 stars 6 forks source link

results differ between classic and mctc #8

Closed loriab closed 3 years ago

loriab commented 3 years ago

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).
awvwgk commented 3 years ago

Okay, I have to track down which email send me the faulty version, this line clearly is wrong:

https://github.com/grimme-lab/gcp/blob/97e8a4e3209bdcab50a003b02051f28cc229d624/src/gcp.f90#L75

awvwgk commented 3 years ago

Thanks a lot, @loriab. What a shock in the morning, I will create a new release and update the cf package shortly.

awvwgk commented 3 years ago

New conda package is up

loriab commented 3 years ago

Thank you very much. All the QCEngine test cases pass now. I have a derived harness working locally that I'll PR once some other things get merged.