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# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, 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"""
@skipForParser('Turbomole','The parser is still being developed so we skip this test')
def testnatom(self):
"""Is the number of atoms equal to 20?"""
self.assertEqual(self.data.natom, 20)
@skipForParser('Turbomole','The parser is still being developed so we skip this test')
def testatomnos(self):
"""Are the atomnos correct?"""
self.assertTrue(numpy.alltrue([numpy.issubdtype(atomno, numpy.signedinteger)
for atomno in self.data.atomnos]))
self.assertEqual(self.data.atomnos.shape, (20,) )
self.assertEqual(sum(self.data.atomnos==6) + sum(self.data.atomnos==1), 20)
@skipForParser('Turbomole','The parser is still being developed so we skip this test')
def testatomcoords(self):
"""Are the dimensions of atomcoords 1 x natom x 3?"""
self.assertEqual(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"):
self.assertIsInstance(self.data.mocoeffs, list)
self.assertEqual(len(self.data.mocoeffs), 2)
self.assertEqual(self.data.mocoeffs[0].shape,
(self.data.nmo, self.data.nbasis))
self.assertEqual(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?"""
self.assertTrue(
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"):
self.assertIsInstance(self.data.nsooccnos, list)
self.assertIsInstance(self.data.nsooccnos[0], list)
self.assertIsInstance(self.data.nsooccnos[1], list)
self.assertEqual(len(self.data.nsooccnos), 2)
self.assertEqual(len(self.data.nsooccnos[0]), self.data.nmo)
self.assertEqual(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"):
self.assertIsInstance(self.data.nsocoeffs, list)
self.assertIsInstance(self.data.nsocoeffs[0], numpy.ndarray)
self.assertIsInstance(self.data.nsocoeffs[1], numpy.ndarray)
self.assertEqual(len(self.data.nsocoeffs), 2)
self.assertEqual(self.data.nsocoeffs[0].shape, (self.data.nmo, self.data.nmo))
self.assertEqual(self.data.nsocoeffs[1].shape, (self.data.nmo, 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 testcharge_and_mult(self):
"""Are the charge and multiplicity correct?"""
self.assertEqual(self.data.charge, 1)
self.assertEqual(self.data.mult, 2)
@skipForParser('Turbomole','The parser is still being developed so we skip this test')
def testhomos(self):
"""Are the homos correct?"""
msg = "%s != array([34,33],'i')" % numpy.array_repr(self.data.homos)
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"):
self.assertEqual(len(self.data.moenergies), 2)
self.assertEqual(len(self.data.moenergies[0]), self.data.nmo)
self.assertEqual(len(self.data.moenergies[1]), self.data.nmo)
@skipForParser('Molcas','The parser is still being developed so we skip this test')
@skipForParser('Molpro', '?')
@skipForParser('ORCA', 'ORCA has no support for symmetry yet')
@skipForParser('Turbomole','The parser is still being developed so we skip this test')
def testmosyms(self):
"""Are the dims of the mosyms equals to 2 x nmo?"""
shape = (len(self.data.mosyms), len(self.data.mosyms[0]))
self.assertEqual(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?"""
self.assertEqual(type(self.data.mocoeffs), type([]))
self.assertEqual(len(self.data.mocoeffs), 1)
self.assertEqual(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 = "%s != array([34, 33], 'i')" % numpy.array_repr(self.data.homos)
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?"""
self.assertEqual(len(self.data.moenergies), 1)
self.assertEqual(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]))
self.assertEqual(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?"""
self.assertEqual(type(self.data.mocoeffs), type([]))
self.assertEqual(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)
self.assertEqual(self.data.mocoeffs[0].shape, shape_alpha)
self.assertEqual(self.data.mocoeffs[1].shape, shape_beta)
def testnooccnos(self):
"""Are natural orbital occupation numbers the right size?"""
self.assertEqual(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?"""
self.assertEqual(self.data.nooccnos.shape, (self.data.nmo, ))
class GaussianSPunTest(GenericSPunTest):
"""Customized unrestricted single point unittest"""
def testatomnos(self):
"""Does atomnos have the right dimension (20)?"""
size = len(self.data.atomnos)
self.assertEqual(size, 20)
class JaguarSPunTest(GenericSPunTest):
"""Customized unrestricted single point unittest"""
def testmoenergies(self):
"""Are the dims of the moenergies equal to 2 x homos+11?"""
self.assertEqual(len(self.data.moenergies), 2)
self.assertEqual(len(self.data.moenergies[0]), self.data.homos[0]+11)
self.assertEqual(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]))
self.assertEqual(shape0, (2, self.data.homos[0]+11))
self.assertEqual(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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