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results differ between classic and mctc #8

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loriab opened this issue Feb 24, 2021 · 4 comments · Fixed by #9
Closed

results differ between classic and mctc #8

loriab opened this issue Feb 24, 2021 · 4 comments · Fixed by #9
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bug Something isn't working

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@loriab
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loriab commented Feb 24, 2021

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
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awvwgk commented Feb 24, 2021

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

gcp/src/gcp.f90

Line 75 in 97e8a4e

damp=.true.

@awvwgk awvwgk mentioned this issue Feb 24, 2021
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awvwgk commented Feb 24, 2021

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

@awvwgk awvwgk added the bug Something isn't working label Feb 24, 2021
@awvwgk awvwgk closed this as completed in #9 Feb 24, 2021
@awvwgk awvwgk mentioned this issue Feb 24, 2021
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awvwgk commented Feb 24, 2021

New conda package is up

@loriab
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loriab commented Feb 24, 2021

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.

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Fix bug which unconditionally enables damping awvwgk/gcp
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@loriab @awvwgk