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# -*- coding: utf-8 -*-
#
# Copyright (c) 2023, 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 os
import unittest
import numpy
from skip import skipForParser
from skip import skipForLogfile
__filedir__ = os.path.realpath(os.path.dirname(__file__))
class GenericSPunTest(unittest.TestCase):
"""Generic unrestricted single point unittest"""
def testnatom(self):
"""Is the number of atoms equal to 20?"""
assert self.data.natom == 20
def testatomnos(self):
"""Are the atomnos correct?"""
assert numpy.alltrue([numpy.issubdtype(atomno, numpy.signedinteger)
for atomno in self.data.atomnos])
assert self.data.atomnos.shape == (20,)
assert sum(self.data.atomnos == 6) + sum(self.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):
"""Are atomic charges consistent with natom?"""
for atomcharge_type in self.data.atomcharges:
charges = self.data.atomcharges[atomcharge_type]
natom = self.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):
"""Do Mulliken atomic charges sum to positive one?"""
charges = self.data.atomcharges["mulliken"]
assert abs(sum(charges)-1.0) < 1.0e-2
def testatomcoords(self):
"""Are the dimensions of atomcoords 1 x natom x 3?"""
assert self.data.atomcoords.shape == (1,self.data.natom,3)
@skipForParser('Jaguar', 'Data file does not contain enough information')
def testdimmocoeffs(self):
"""Are the dimensions of mocoeffs equal to 2 x nmo x nbasis?"""
if hasattr(self.data, "mocoeffs"):
assert isinstance(self.data.mocoeffs, list)
assert len(self.data.mocoeffs) == 2
assert self.data.mocoeffs[0].shape == (self.data.nmo, self.data.nbasis)
assert self.data.mocoeffs[1].shape == (self.data.nmo, self.data.nbasis)
@skipForParser('Jaguar', 'Data file does not contain enough information')
@skipForParser('DALTON', 'mocoeffs not implemented yet')
def testfornsoormo(self):
"""Do we have NSOs or MOs?"""
assert hasattr(self.data, "nsocoeffs") or hasattr(self.data, "mocoeffs")
def testdimnsoccnos(self):
"""Are the dimensions of nsooccnos equal to 2 x nmo?"""
if hasattr(self.data, "nsooccnos"):
assert isinstance(self.data.nsooccnos, list)
assert isinstance(self.data.nsooccnos[0], list)
assert isinstance(self.data.nsooccnos[1], list)
assert len(self.data.nsooccnos) == 2
assert len(self.data.nsooccnos[0]) == self.data.nmo
assert len(self.data.nsooccnos[1]) == self.data.nmo
def testdimnsocoeffs(self):
"""Are the dimensions of nsocoeffs equal to 2 x nmo x nmo?"""
if hasattr(self.data, "nsocoeffs"):
assert isinstance(self.data.nsocoeffs, list)
assert isinstance(self.data.nsocoeffs[0], numpy.ndarray)
assert isinstance(self.data.nsocoeffs[1], numpy.ndarray)
assert len(self.data.nsocoeffs) == 2
assert self.data.nsocoeffs[0].shape == (self.data.nmo, self.data.nmo)
assert self.data.nsocoeffs[1].shape == (self.data.nmo, self.data.nmo)
@skipForParser('Molcas','The parser is still being developed so we skip this test')
def testcharge_and_mult(self):
"""Are the charge and multiplicity correct?"""
assert self.data.charge == 1
assert self.data.mult == 2
def testhomos(self):
"""Are the homos correct?"""
msg = f"{numpy.array_repr(self.data.homos)} != array([34,33],'i')"
numpy.testing.assert_array_equal(self.data.homos, numpy.array([34,33],"i"), msg)
def testmoenergies(self):
"""Are the dims of the moenergies equals to 2 x nmo?"""
if hasattr(self.data, "moenergies"):
assert len(self.data.moenergies) == 2
assert len(self.data.moenergies[0]) == self.data.nmo
assert len(self.data.moenergies[1]) == self.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):
"""Are the dims of the mosyms equals to 2 x nmo?"""
shape = (len(self.data.mosyms), len(self.data.mosyms[0]))
assert shape == (2, self.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):
"""Are the dimensions of mocoeffs equal to 1 x nmo x nbasis?"""
assert isinstance(self.data.mocoeffs, list)
assert len(self.data.mocoeffs) == 1
assert self.data.mocoeffs[0].shape == (self.data.nmo, self.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):
"""Are the HOMO indices equal to 34 and 33 (one more alpha electron
than beta electron)?
"""
msg = f"{numpy.array_repr(self.data.homos)} != array([34, 33], 'i')"
numpy.testing.assert_array_equal(self.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):
"""Are the dims of the moenergies equals to 1 x nmo?"""
assert len(self.data.moenergies) == 1
assert len(self.data.moenergies[0]) == self.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):
"""Are the dims of the mosyms equals to 1 x nmo?"""
shape = (len(self.data.mosyms), len(self.data.mosyms[0]))
assert shape == (1, self.data.nmo)
class GamessUK70SPunTest(GenericSPunTest):
"""Customized unrestricted single point unittest"""
def testdimmocoeffs(self):
"""Are the dimensions of mocoeffs equal to 2 x (homos+6) x nbasis?"""
assert isinstance(self.data.mocoeffs, list)
assert len(self.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 = (self.data.homos[0]+6, self.data.nbasis)
shape_beta = (self.data.homos[1]+6, self.data.nbasis)
assert self.data.mocoeffs[0].shape == shape_alpha
assert self.data.mocoeffs[1].shape == shape_beta
def testnooccnos(self):
"""Are natural orbital occupation numbers the right size?"""
assert self.data.nooccnos.shape == (self.data.nmo, )
class GamessUK80SPunTest(GenericSPunTest):
"""Customized unrestricted single point unittest"""
def testnooccnos(self):
"""Are natural orbital occupation numbers the right size?"""
assert self.data.nooccnos.shape == (self.data.nmo, )
class GaussianSPunTest(GenericSPunTest):
"""Customized unrestricted single point unittest"""
def testatomspins(self):
"""Are atomic spins from Mulliken population analysis consistent with
natom and sum to one (doublet)?
"""
spins = self.data.atomspins['mulliken']
assert len(spins) == self.data.natom
assert abs(sum(spins)-1.0) < 0.001
class JaguarSPunTest(GenericSPunTest):
"""Customized unrestricted single point unittest"""
def testmoenergies(self):
"""Are the dims of the moenergies equal to 2 x homos+11?"""
assert len(self.data.moenergies) == 2
assert len(self.data.moenergies[0]) == self.data.homos[0]+11
assert len(self.data.moenergies[1]) == self.data.homos[1]+11
def testmosyms(self):
"""Are the dims of the mosyms equals to 2 x nmo?"""
shape0 = (len(self.data.mosyms), len(self.data.mosyms[0]))
shape1 = (len(self.data.mosyms), len(self.data.mosyms[1]))
assert shape0 == (2, self.data.homos[0]+11)
assert shape1 == (2, self.data.homos[1]+11)
if __name__=="__main__":
import sys
sys.path.insert(1, os.path.join(__filedir__, ".."))
from test_data import DataSuite
suite = DataSuite(['SPun'])
suite.testall()
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