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# Copyright (c) 2024, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Test unrestrictied single point logfiles in cclib"""
import numpy
from skip import skipForParser
class GenericSPunTest:
"""Generic unrestricted single point unittest"""
def testnatom(self, data) -> None:
"""Is the number of atoms equal to 20?"""
assert data.natom == 20
def testatomnos(self, data) -> None:
"""Are the atomnos correct?"""
assert numpy.all([numpy.issubdtype(atomno, numpy.signedinteger) for atomno in data.atomnos])
assert data.atomnos.shape == (20,)
assert sum(data.atomnos == 6) + sum(data.atomnos == 1) == 20
@skipForParser("ADF", "???")
@skipForParser(
"DALTON",
"DALTON has a very low accuracy for the printed values of all populations (2 decimals rounded in a weird way), so let it slide for now",
)
@skipForParser("FChk", "The parser is still being developed so we skip this test")
@skipForParser("Jaguar", "???")
@skipForParser("Molcas", "Length is zero for some reason")
@skipForParser("Molpro", "???")
@skipForParser("Turbomole", "???")
def testatomcharges(self, data) -> None:
"""Are atomic charges consistent with natom?"""
for atomcharge_type in data.atomcharges:
charges = data.atomcharges[atomcharge_type]
natom = data.natom
assert (
len(charges) == natom
), f"len(atomcharges['{atomcharge_type}']) = {len(charges)}, natom = {natom}"
@skipForParser("ADF", "???")
@skipForParser(
"DALTON",
"DALTON has a very low accuracy for the printed values of all populations (2 decimals rounded in a weird way), so let it slide for now",
)
@skipForParser("FChk", "The parser is still being developed so we skip this test")
@skipForParser("Jaguar", "???")
@skipForParser("Molcas", "Length is zero for some reason")
@skipForParser("Molpro", "???")
@skipForParser("Turbomole", "???")
def testatomcharges_mulliken(self, data) -> None:
"""Do Mulliken atomic charges sum to positive one?"""
charges = data.atomcharges["mulliken"]
assert abs(sum(charges) - 1.0) < 1.0e-2
def testatomcoords(self, data) -> None:
"""Are the dimensions of atomcoords 1 x natom x 3?"""
assert data.atomcoords.shape == (1, data.natom, 3)
@skipForParser("Jaguar", "Data file does not contain enough information")
def testdimmocoeffs(self, data) -> None:
"""Are the dimensions of mocoeffs equal to 2 x nmo x nbasis?"""
if hasattr(data, "mocoeffs"):
assert isinstance(data.mocoeffs, list)
assert len(data.mocoeffs) == 2
assert data.mocoeffs[0].shape == (data.nmo, data.nbasis)
assert data.mocoeffs[1].shape == (data.nmo, data.nbasis)
@skipForParser("Jaguar", "Data file does not contain enough information")
@skipForParser("DALTON", "mocoeffs not implemented yet")
def testfornoormo(self, data) -> None:
"""Do we have NOs or MOs?"""
assert hasattr(data, "nocoeffs") or hasattr(data, "mocoeffs")
def testdimnoccnos(self, data) -> None:
"""Is the length of nooccnos equal to nmo?"""
if hasattr(data, "nooccnos"):
assert isinstance(data.nooccnos, numpy.ndarray)
# FIXME
assert data.nooccnos.shape in [(data.nmo,), (2, data.nmo)]
def testdimnocoeffs(self, data) -> None:
"""Are the dimensions of nocoeffs equal to 2 x nmo x nmo?"""
if hasattr(data, "nocoeffs"):
assert isinstance(data.nocoeffs, numpy.ndarray)
assert data.nocoeffs.shape == (2, data.nmo, data.nmo)
@skipForParser("Molcas", "The parser is still being developed so we skip this test")
def testcharge_and_mult(self, data) -> None:
"""Are the charge and multiplicity correct?"""
assert data.charge == 1
assert data.mult == 2
def testhomos(self, data) -> None:
"""Are the homos correct?"""
msg = f"{numpy.array_repr(data.homos)} != array([34,33],'i')"
numpy.testing.assert_array_equal(data.homos, numpy.array([34, 33], "i"), msg)
def testmoenergies(self, data) -> None:
"""Are the dims of the moenergies equals to 2 x nmo?"""
if hasattr(data, "moenergies"):
assert len(data.moenergies) == 2
assert len(data.moenergies[0]) == data.nmo
assert len(data.moenergies[1]) == data.nmo
@skipForParser("FChk", "Fchk files do not have a section for symmetry")
@skipForParser("Molcas", "The parser is still being developed so we skip this test")
@skipForParser("Molpro", "?")
@skipForParser("ORCA", "ORCA has no support for symmetry yet")
def testmosyms(self, data) -> None:
"""Are the dims of the mosyms equals to 2 x nmo?"""
shape = (len(data.mosyms), len(data.mosyms[0]))
assert shape == (2, data.nmo)
class GenericROSPTest(GenericSPunTest):
"""Customized restricted open-shell single point unittest"""
@skipForParser("DALTON", "mocoeffs not implemented yet")
@skipForParser("Molcas", "The parser is still being developed so we skip this test")
@skipForParser("Turbomole", "The parser is still being developed so we skip this test")
def testdimmocoeffs(self, data) -> None:
"""Are the dimensions of mocoeffs equal to 1 x nmo x nbasis?"""
assert isinstance(data.mocoeffs, list)
assert len(data.mocoeffs) == 1
assert data.mocoeffs[0].shape == (data.nmo, data.nbasis)
@skipForParser("Molcas", "The parser is still being developed so we skip this test")
@skipForParser("Turbomole", "The parser is still being developed so we skip this test")
def testhomos(self, data) -> None:
"""Are the HOMO indices equal to 34 and 33 (one more alpha electron
than beta electron)?
"""
msg = f"{numpy.array_repr(data.homos)} != array([34, 33], 'i')"
numpy.testing.assert_array_equal(data.homos, numpy.array([34, 33], "i"), msg)
@skipForParser("QChem", "prints 2 sets of different MO energies?")
@skipForParser("Molcas", "The parser is still being developed so we skip this test")
@skipForParser("Turbomole", "The parser is still being developed so we skip this test")
def testmoenergies(self, data) -> None:
"""Are the dims of the moenergies equals to 1 x nmo?"""
assert len(data.moenergies) == 1
assert len(data.moenergies[0]) == data.nmo
@skipForParser("Molcas", "The parser is still being developed so we skip this test")
@skipForParser("Turbomole", "The parser is still being developed so we skip this test")
def testmosyms(self, data) -> None:
"""Are the dims of the mosyms equals to 1 x nmo?"""
shape = (len(data.mosyms), len(data.mosyms[0]))
assert shape == (1, data.nmo)
class GamessUK70SPunTest(GenericSPunTest):
"""Customized unrestricted single point unittest"""
def testdimmocoeffs(self, data) -> None:
"""Are the dimensions of mocoeffs equal to 2 x (homos+6) x nbasis?"""
assert isinstance(data.mocoeffs, list)
assert len(data.mocoeffs) == 2
# This is only an issue in version 7.0 (and before?), since in the version 8.0
# logfile all eigenvectors are happily printed.
shape_alpha = (data.homos[0] + 6, data.nbasis)
shape_beta = (data.homos[1] + 6, data.nbasis)
assert data.mocoeffs[0].shape == shape_alpha
assert data.mocoeffs[1].shape == shape_beta
def testnooccnos(self, data) -> None:
"""Are natural orbital occupation numbers the right size?"""
assert data.nooccnos.shape == (data.nmo,)
class GamessUK80SPunTest(GenericSPunTest):
"""Customized unrestricted single point unittest"""
def testnooccnos(self, data) -> None:
"""Are natural orbital occupation numbers the right size?"""
assert data.nooccnos.shape == (data.nmo,)
class GaussianSPunTest(GenericSPunTest):
"""Customized unrestricted single point unittest"""
def testatomspins(self, data) -> None:
"""Are atomic spins from Mulliken population analysis consistent with
natom and sum to one (doublet)?
"""
spins = data.atomspins["mulliken"]
assert len(spins) == data.natom
assert abs(sum(spins) - 1.0) < 0.001
class JaguarSPunTest(GenericSPunTest):
"""Customized unrestricted single point unittest"""
def testmoenergies(self, data) -> None:
"""Are the dims of the moenergies equal to 2 x homos+11?"""
assert len(data.moenergies) == 2
assert len(data.moenergies[0]) == data.homos[0] + 11
assert len(data.moenergies[1]) == data.homos[1] + 11
def testmosyms(self, data) -> None:
"""Are the dims of the mosyms equals to 2 x nmo?"""
shape0 = (len(data.mosyms), len(data.mosyms[0]))
shape1 = (len(data.mosyms), len(data.mosyms[1]))
assert shape0 == (2, data.homos[0] + 11)
assert shape1 == (2, data.homos[1] + 11)
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