test_supercell.py

#!/usr/bin/env python
##############################################################################
#
# diffpy.structure  by DANSE Diffraction group
#                   Simon J. L. Billinge
#                   (c) 2008 trustees of the Michigan State University.
#                   All rights reserved.
#
# File coded by:    Pavol Juhas
#
# See AUTHORS.txt for a list of people who contributed.
# See LICENSE_DANSE.txt for license information.
#
##############################################################################
"""Unit tests for supercell.py."""

import unittest

import pytest

from diffpy.structure import Structure
from diffpy.structure.expansion import supercell

# ----------------------------------------------------------------------------


class TestSuperCell(unittest.TestCase):
    @pytest.fixture(autouse=True)
    def prepare_fixture(self, datafile):
        self.datafile = datafile

    stru_cdse = None
    stru_ni = None

    def setUp(self):
        # load test structures once
        if TestSuperCell.stru_cdse is None:
            cdsefile = self.datafile("CdSe_bulk.stru")
            TestSuperCell.stru_cdse = Structure(filename=cdsefile)
        if TestSuperCell.stru_ni is None:
            nifile = self.datafile("Ni.stru")
            TestSuperCell.stru_ni = Structure(filename=nifile)
        # bring them to the instance
        self.stru_cdse = TestSuperCell.stru_cdse
        self.stru_ni = TestSuperCell.stru_ni
        return

    def tearDown(self):
        return

    def test_exceptions(self):
        """Check argument checking of supercell."""
        self.assertRaises(ValueError, supercell, self.stru_ni, (0, 1, 1))
        self.assertRaises(ValueError, supercell, self.stru_ni, (0, 1))
        self.assertRaises(TypeError, supercell, list(self.stru_ni), (1, 1, 1))
        return

    def test_ni_supercell(self):
        """Check supercell expansion for Ni."""
        ni_123 = supercell(self.stru_ni, (1, 2, 3))
        self.assertEqual(6 * len(self.stru_ni), len(ni_123))
        a, b, c = self.stru_ni.lattice.cell_parms()[:3]
        a1, b2, c3 = ni_123.lattice.cell_parms()[:3]
        self.assertAlmostEqual(a, a1, 8)
        self.assertAlmostEqual(b * 2, b2, 8)
        self.assertAlmostEqual(c * 3, c3, 8)
        x, y, z = self.stru_ni[-1].xyz
        x1, y2, z3 = ni_123[-1 * 2 * 3].xyz
        self.assertAlmostEqual(x / 1, x1, 8)
        self.assertAlmostEqual(y / 2, y2, 8)
        self.assertAlmostEqual(z / 3, z3, 8)
        return

    def test_cdse_supercell(self):
        """Check supercell expansion for CdSe."""
        cdse_222 = supercell(self.stru_cdse, (2, 2, 2))
        # new atoms should be grouped together
        elems = sum([8 * [a.element] for a in self.stru_cdse], [])
        elems_222 = [a.element for a in cdse_222]
        self.assertEqual(elems, elems_222)
        return


# End of class TestRoutines

# ----------------------------------------------------------------------------

if __name__ == "__main__":
    unittest.main()