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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 the Moments method in cclib"""
import unittest
from unittest import mock
import numpy as np
from numpy.testing import assert_equal, assert_almost_equal
from cclib.method import Moments
import pytest
class TestIdealizedInputs(unittest.TestCase):
linear_dipole_attrs = {
'atomcoords': np.array([[[-1, 0, 0], [ 1, 0, 0]]]),
'atomcharges': {'mulliken': [-1, 1]},
'atomnos': [1, 1]
}
@mock.patch('cclib.parser.ccData', spec=True)
def test_dipole_moment(self, mock):
mock.configure_mock(**self.linear_dipole_attrs)
x = Moments(mock).calculate()[1]
assert_almost_equal(x / 4.80320425, [2, 0, 0])
@unittest.skip("This does not pass for some reason.")
@mock.patch('cclib.parser.ccData', spec=True)
def test_nonzero_quadrupole_moment(self, mock):
mock.atomcoords = np.array([[
[-1, 0, 0],
[0, 0, 0],
[1, 0, 0]]])
# The periods are for Python2.
mock.atomcharges = {'mulliken': [1/2., -1., 1/2.]}
mock.atomnos = np.ones(mock.atomcoords.shape[1])
x = Moments(mock).calculate()
assert np.count_nonzero(x[1]) == 0
assert_almost_equal(x[2] / 4.80320423, [1, 0, 0, -0.5, 0, -0.5])
@mock.patch('cclib.parser.ccData', spec=True)
def test_zero_moments(self, mock):
mock.atomcoords = np.array([[
[-2, 0, 0],
[-1, 0, 0],
[0, 0, 0],
[1, 0, 0],
[2, 0, 0]]])
# The periods are for Python2.
mock.atomcharges = {'mulliken': [-1/8., 1/2., -3/4., 1/2., -1/8.]}
mock.atomnos = np.ones(mock.atomcoords.shape[1])
x = Moments(mock).calculate()
assert np.count_nonzero(x[1]) == 0
assert np.count_nonzero(x[2]) == 0
@mock.patch('cclib.parser.ccData', spec=True)
def test_invariant_to_origin_dislacement(self, mock):
mock.configure_mock(**self.linear_dipole_attrs)
x = Moments(mock).calculate(origin=[0, 0, 0])[1]
y = Moments(mock).calculate(origin=[1, 1, 1])[1]
assert_equal(x, y)
@mock.patch('cclib.parser.ccData', spec=True)
def test_variant_to_origin_dislacement(self, mock):
attrs = dict(self.linear_dipole_attrs, **{
'atomcharges': {'mulliken': [-1, 2]}
})
mock.configure_mock(**attrs)
x = Moments(mock).calculate(origin=[0, 0, 0])[1]
y = Moments(mock).calculate(origin=[1, 1, 1])[1]
assert not np.array_equal(x, y)
@mock.patch('cclib.parser.ccData', spec=True)
def test_origin_at_center_of_nuclear_charge(self, mock):
mock.configure_mock(**self.linear_dipole_attrs)
x = Moments(mock).calculate()[0]
assert_equal(x, [0, 0, 0])
@mock.patch('cclib.parser.ccData', spec=True)
def test_origin_at_center_of_mass(self, mock):
mock.configure_mock(**self.linear_dipole_attrs)
mock.atommasses = np.ones(mock.atomcoords.shape[1])
x = Moments(mock).calculate(origin='mass')[0]
assert_equal(x, [0, 0, 0])
@mock.patch('cclib.parser.ccData', spec=True)
def test_user_provided_origin(self, mock):
mock.configure_mock(**self.linear_dipole_attrs)
x = Moments(mock).calculate(origin=[1, 1, 1])
assert_almost_equal(x[0], [1, 1, 1])
@mock.patch('cclib.parser.ccData', spec=True)
def test_user_provided_masses(self, mock):
mock.configure_mock(**self.linear_dipole_attrs)
x = Moments(mock).calculate(masses=[1, 3], origin='mass')
assert_almost_equal(x[0], [0.5, 0, 0])
@mock.patch('cclib.parser.ccData', spec=True)
def test_not_providing_masses(self, mock):
mock.configure_mock(**self.linear_dipole_attrs)
# Replace with the refex version when Python2 is dropped.
# with self.assertRaisesRegex(ValueError, 'masses'):
with pytest.raises(ValueError):
Moments(mock).calculate(origin='mass')
@mock.patch('cclib.parser.ccData', spec=True)
def test_results_storing(self, mock):
mock.configure_mock(**self.linear_dipole_attrs)
mock.atomcharges.update({'lowdin': [-0.5, 0.5]})
m = Moments(mock)
m.calculate(population='mulliken')
m.calculate(population='lowdin')
a, b = m.results['mulliken'][1], m.results['lowdin'][1]
assert not np.array_equal(a, b)
if __name__ == '__main__':
suite = unittest.makeSuite(TestIdealizedInputs)
unittest.TextTestRunner(verbosity=2).run(suite)
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