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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.
"""Unit tests for wfx writer."""
import os
import unittest
import numpy as np
import cclib
from cclib.io.filewriter import MissingAttributeError
from cclib.io.wfxwriter import _section
from cclib.io.wfxwriter import _list_format
__filedir__ = os.path.dirname(__file__)
__filepath__ = os.path.realpath(__filedir__)
__datadir__ = os.path.join(__filepath__, "..", "..")
class WFXTest(unittest.TestCase):
def test_missing_attribute_error(self):
"""Check if MissingAttributeError is raised as expected."""
fpath = os.path.join(__datadir__,
"data/GAMESS/basicGAMESS-US2017/C_bigbasis.out")
required_attrs = ('atomcoords', 'atomnos', 'gbasis', 'charge',
'homos', 'mult', 'mocoeffs')
for attr in required_attrs:
data = cclib.io.ccread(fpath)
delattr(data, attr)
# WFX files cannot be written if required attrs are missing.
with self.assertRaises(MissingAttributeError):
cclib.io.wfxwriter.WFXWriter(data)
def test_no_of_prims(self):
"""Check if number of primitives are calculated correctly."""
num_orb = {'s':1, 'p':3, 'd':6, 'f':10, 'g':15, 'h':21}
gamessdir = os.path.join(__datadir__,
"data/GAMESS/basicGAMESS-US2017")
filenames = ["C_bigbasis.out", "dvb_un_sp.out"]
filepaths = [os.path.join(gamessdir, fn) for fn in filenames]
for fpath in filepaths:
data = cclib.io.ccread(fpath)
wfx = cclib.io.wfxwriter.WFXWriter(data)
no_prims_writer = wfx._no_of_prims()
no_prims_ccdata = 0
for atom in data.gbasis:
for prims in atom:
no_prims_ccdata += num_orb[prims[0].lower()]\
* len(prims[1])
self.assertEqual(no_prims_writer, no_prims_ccdata)
def test_mo_normalization(self):
"""Check if MO section is printed correctly."""
fpath = os.path.join(__datadir__,
"data/GAMESS/basicGAMESS-US2017/C_bigbasis.out")
data = cclib.io.ccread(fpath)
wfx = cclib.io.wfxwriter.WFXWriter(data)
normalized_mocoeffs = wfx._normalized_mocoeffs()
if len(data.homos) > 1:
self.assertEqual(len(normalized_mocoeffs), wfx._no_electrons())
else:
self.assertEqual(len(normalized_mocoeffs), wfx._no_of_mos())
self.assertEqual(len(normalized_mocoeffs[0]), wfx._no_of_prims())
def test_mo_normalization_dat(self):
"""Check if MOs are normalized as expected."""
fpath = os.path.join(__datadir__,
"data/GAMESS/basicGAMESS-US2017/dvb_sp.out")
data = cclib.io.ccread(fpath)
wfx = cclib.io.wfxwriter.WFXWriter(data)
normalized_mocoeffs_wfx = wfx._normalized_mocoeffs()
datfile = os.path.join(__datadir__,
"data/GAMESS/basicGAMESS-US2017/dvb_sp.dat")
with open(datfile) as file:
content = iter(file.readlines())
normalized_mocoeffs_dat = []
line = next(content)
while 'TOP OF INPUT FILE FOR BADER' not in line:
line = next(content)
while 'END OF INPUT FILE FOR BADER' not in line:
if 'MO' in line and 'OCC NO' in line and 'ORB. ENERGY' in line:
line = next(content)
mo = []
while 'MO' not in line and 'END DATA' not in line:
mo.extend([float(x) for x in line.rsplit()])
line = next(content)
normalized_mocoeffs_dat.append(mo)
else:
line = next(content)
for mo1, mo2 in zip(normalized_mocoeffs_dat, normalized_mocoeffs_wfx):
for coeff1, coeff2 in zip(mo1, mo2):
self.assertTrue(-0.09 <= abs(coeff1) - abs(coeff2) <= 0.09)
def test_programs(self):
"""Check other programs against reference data."""
ref_file = "data/GAMESS/basicGAMESS-US2017/dvb_sp.out"
# Skipping ORCA test until https://github.com/cclib/cclib/pull/394 is
# merged.
programs = {
#'ORCA': "data/ORCA/basicORCA4.0/dvb_sp.out",
'NWChem': "data/NWChem/basicNWChem6.5/dvb_sp_hf.out",
'Psi4': "data/Psi4/basicPsi4-1.0/dvb_sp_rhf.out",
'GAMESS-UK': "data/GAMESS-UK/basicGAMESS-UK8.0/dvb_sp_hf.out",
'Firefly': "data/GAMESS/basicFirefly8.0/dvb_sp.out",
}
fpath_ref = os.path.join(__datadir__, ref_file)
data_ref = cclib.io.ccread(fpath_ref)
wfx_ref = cclib.io.wfxwriter.WFXWriter(data_ref)
norm_mat_ref = wfx_ref._norm_mat()[0]
mos_ref = wfx_ref._no_of_mos()
for name in programs:
fpath_prog = os.path.join(__datadir__, programs[name])
data_prog = cclib.io.ccread(fpath_prog)
wfx_prog = cclib.io.wfxwriter.WFXWriter(data_prog)
norm_mat_prog = wfx_prog._norm_mat()[0]
mos_prog = wfx_prog._no_of_mos()
# Check if normalization matrix are matching.
self.assertAlmostEqual(max(np.array(norm_mat_prog) -
np.array(norm_mat_ref)), 0, places=5)
# Check if number of orbitals to be printed are as expected.
self.assertEqual(mos_prog, mos_ref)
def test_section_printing(self):
"""Check if wfx section printing works as expected."""
float_section = _section('Test Section', 123.456)
expected = ['<Test Section>', ' 123.456', '</Test Section>']
self.assertEqual(float_section, expected)
list_section = _section('Test Section', ['1', '2'])
expected = ['<Test Section>', '1', '2', '</Test Section>']
self.assertEqual(list_section, expected)
str_section = _section('Test Section', 'Test Data')
expected = ['<Test Section>', ' Test Data', '</Test Section>']
self.assertEqual(str_section, expected)
def test_list_format(self):
"""Check if list formatting works as expected."""
odd_list = _list_format([1, 2, 3], 2, '%8.1E')
odd_expected = [' 1.0E+00 2.0E+00', ' 3.0E+00']
self.assertEqual(odd_list, odd_expected)
even_list = _list_format([1, 2, 3, 4], 2, '%8.1E')
even_expected = [' 1.0E+00 2.0E+00', ' 3.0E+00 4.0E+00']
self.assertEqual(even_list, even_expected)
if __name__ == "__main__":
unittest.main()
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