<filename>tests/test_crystal.py
# -*- coding: utf-8 -*-
import pickle
import socket
import os
import tempfile
import unittest
from contextlib import suppress
from copy import copy, deepcopy
from itertools import islice
from math import radians
from pathlib import Path

import numpy as np
from crystals import Atom, AtomicStructure, CenteringType, Crystal, Lattice
from crystals.affine import rotation_matrix, transform, translation_matrix
from crystals.crystal import symmetry_expansion, symmetry_reduction
from .utils import retry_test

np.random.seed(23)


def connection_available():
    """ Returns whether or not an internet connection is available """
    with suppress(OSError):
        try:
            socket.create_connection(("www.google.com", 80))
        except:
            return False
        else:
            return True
    return False


class TestSpglibMethods(unittest.TestCase):
    def test_symmetry_graphite(self):
        """ Test that Crystal.symmetry() works correctly for graphite """
        c = Crystal.from_database("C")
        info = c.symmetry(1e-1)

        supposed = {
            "international_number": 194,
            "hall_number": 488,
            "international_symbol": "P6_3/mmc",
            "international_full": "P 6_3/m 2/m 2/c",
            "hall_symbol": "-P 6c 2c",
            "hm_symbol": "P63/mmc",
            "centering": CenteringType("P"),
            "pointgroup": "6/mmm",
        }

        self.assertDictEqual(info, supposed)

    def test_primitive_for_builtins(self):
        """ Test that all built-in crystal have a primitive cell """
        for name in Crystal.builtins:
            with self.subTest(name):
                c = Crystal.from_database(name)
                prim = c.primitive(symprec=0.1)
                self.assertLessEqual(len(prim), len(c))

    def test_primitive_preserves_subclass(self):
        """ Check that Crystal returned by Crystal.primitive() preserve subclass """

        class TestCrystal(Crystal):
            pass

        c = TestCrystal.from_database("C")
        prim = c.primitive()
        self.assertEqual(TestCrystal, type(prim))

    def test_ideal_for_builtins(self):
        """ Test that all built-in crystal have an ideal cell """
        for name in Crystal.builtins:
            with self.subTest(name):
                # This will raise an error if no idealized cell is found
                c = Crystal.from_database(name).ideal()

    def test_ideal_preserves_subclass(self):
        """ Check that Crystal returned by Crystal.ideal() preserve subclass """

        class TestCrystal(Crystal):
            pass

        c = TestCrystal.from_database("C")
        ideal = c.ideal()
        self.assertEqual(TestCrystal, type(ideal))

    def test_symmetry_operations(self):
        """ Test that the symmetry operations output makes sense """
        identity = np.eye(4)

        for name in Crystal.builtins:
            with self.subTest(name):
                c = Crystal.from_database(name)
                symops = c.symmetry_operations()
                self.assertTrue(np.allclose(identity, symops[0]))

    def test_reciprocal_symmetry_operations(self):
        """ Test that the reciprocal symmetry operations output makes sense """
        identity = np.eye(4)

        for name in Crystal.builtins:
            with self.subTest(name):
                c = Crystal.from_database(name)
                symops = c.reciprocal_symmetry_operations()
                self.assertTrue(np.allclose(identity, symops[0]))


class TestCrystalSpecialMethods(unittest.TestCase):
    def test_str_vs_repr(self):
        """ Test that str and repr are workign as expected """
        for name in Crystal.builtins:
            with self.subTest(name):
                c = Crystal.from_database(name)

                # If small crystal, repr and str should be the same
                if len(c) <= 10:
                    self.assertEqual(repr(c), str(c))
                else:
                    self.assertNotEqual(repr(c), str(c))

    def test_equality(self):
        """ Test that __eq__ works as expected """
        c1 = Crystal.from_database("Pu-alpha")
        c2 = deepcopy(c1)
        self.assertEqual(c1, c2)

        c3 = Crystal.from_database("Pu-epsilon")
        self.assertNotEqual(c1, c3)


class TestCrystalConstructors(unittest.TestCase):
    def test_builtins(self):
        """ Test that all names in Crystal.builtins build without errors,
        and that Crystal.source is correctly recorded. """
        for name in Crystal.builtins:
            with self.subTest(name):
                c = Crystal.from_database(name)

                self.assertIn(name, c.source)

    def test_builtins_wrong_name(self):
        """ Test that a name not in Crystal.builtins will raise a ValueError """
        with self.assertRaises(ValueError):
            Crystal.from_database("___")

    def test_substructure_preservation(self):
        """ Test that initializing a crystal with substructures preserves the substructures """
        atoms = [Atom("Ag", [0, 0, 0]), Atom("Ag", [1, 1, 1])]
        substructures = [AtomicStructure(atoms=[Atom("U", [0, 0, 0])])]
        c = Crystal(unitcell=atoms + substructures, lattice_vectors=np.eye(3))

        self.assertEqual(len(c), 3)
        self.assertIn(substructures[0], c.substructures)

    @unittest.skipUnless(connection_available(), "Internet connection is required.")
    def test_from_pdb(self):
        """ Test Crystal.from_pdb constructor """
        c = Crystal.from_pdb("1fbb")
        self.assertIn("1fbb", c.source)

    @unittest.skipUnless(connection_available(), "Internet connection is required.")
    def test_from_cod(self):
        """ Test building a Crystal object from the COD """
        # revision = None and latest revision should give the same Crystal
        c = Crystal.from_cod(1521124)
        c2 = Crystal.from_cod(1521124, revision=176429)

        self.assertEqual(c, c2)

    @unittest.skipUnless(connection_available(), "Internet connection is required.")
    def test_from_cod_new_dir(self):
        """ Test that a cache dir is created by Crystal.from_cod """
        with tempfile.TemporaryDirectory() as temp_dir:
            download_dir = Path(temp_dir) / "test_cod"
            self.assertFalse(download_dir.exists())
            c = Crystal.from_cod(1521124, download_dir=download_dir)
            self.assertTrue(download_dir.exists())


class TestSupercell(unittest.TestCase):
    def test_constructors(self):
        """ Test Supercell constructors for varyous 'builtin' structures """
        for name in islice(Crystal.builtins, 20):
            with self.subTest(name):
                s = Crystal.from_database(name).supercell(2, 2, 2)

                self.assertEqual(len(s), 8 * len(s.crystal))


class TestIndexedBy(unittest.TestCase):
    def test_trivial_reindexing(self):
        """ Test re-indexing a crystal by itself """
        c1 = Crystal.from_database("Pu-gamma")
        c2 = c1.indexed_by(c1)

        self.assertEqual(c1, c2)


# # The tests below are very flaky. Due to floating-point arithmetic
# # being non-deterministic, sometimes comparing atoms does not work
# # and the tests below fail.
# # Because of this, we skip tests when in a continuous integration environment
# # See here for details on environment variables:
# #   https://www.appveyor.com/docs/environment-variables/
# @unittest.skipIf(bool(os.environ.get('CI', False)), reason="Flaky tests")
class TestSymmetryReduction(unittest.TestCase):
    def test_trivial(self):
        """ Test that the symmetry_reduction function returns the unit cell when
        there is only one possibility. """
        ucell = set([Atom("H", coords=[0, 0, 0])])
        symops = [np.eye(4)]
        asym_cell = symmetry_reduction(ucell, symops)
        self.assertEqual(ucell, asym_cell)

    @retry_test(max_retries=5)
    def test_simple_translation(self):
        """ Test that symmetry_reduction works on a unitcell where two atoms are
        linked by a translation """
        symops = [np.eye(4), translation_matrix([0, 0, 1 / 2])]
        asym_cell = set([Atom("H", coords=[0, 0, 0])])
        unitcell = set(symmetry_expansion(asym_cell, symmetry_operators=symops))

        asym_cell2 = symmetry_reduction(unitcell, symops)
        self.assertEqual(asym_cell, asym_cell2)

    @retry_test(max_retries=5)
    def test_reciprocity_with_symmetry_expansion(self):
        """ Test that symmetry_reduction is reciprocal to symmetry_expansion """
        structures = ["vo2-m1", "Os", "Na"]  # , 'Nb', 'Pd', 'Zn']
        for s in structures:
            with self.subTest("Crystal " + s):
                cryst = Crystal.from_database(s)
                asym_cell = symmetry_reduction(
                    cryst.unitcell, cryst.symmetry_operations()
                )
                ucell = set(symmetry_expansion(asym_cell, cryst.symmetry_operations()))
                self.assertEqual(set(cryst.unitcell), ucell)


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

<filename>tests/test_crystal.py
# -*- coding: utf-8 -*-
import pickle
import socket
import os
import tempfile
import unittest
from contextlib import suppress
from copy import copy, deepcopy
from itertools import islice
from math import radians
from pathlib import Path

import numpy as np
from crystals import Atom, AtomicStructure, CenteringType, Crystal, Lattice
from crystals.affine import rotation_matrix, transform, translation_matrix
from crystals.crystal import symmetry_expansion, symmetry_reduction
from .utils import retry_test

np.random.seed(23)


def connection_available():
    """ Returns whether or not an internet connection is available """
    with suppress(OSError):
        try:
            socket.create_connection(("www.google.com", 80))
        except:
            return False
        else:
            return True
    return False


class TestSpglibMethods(unittest.TestCase):
    def test_symmetry_graphite(self):
        """ Test that Crystal.symmetry() works correctly for graphite """
        c = Crystal.from_database("C")
        info = c.symmetry(1e-1)

        supposed = {
            "international_number": 194,
            "hall_number": 488,
            "international_symbol": "P6_3/mmc",
            "international_full": "P 6_3/m 2/m 2/c",
            "hall_symbol": "-P 6c 2c",
            "hm_symbol": "P63/mmc",
            "centering": CenteringType("P"),
            "pointgroup": "6/mmm",
        }

        self.assertDictEqual(info, supposed)

    def test_primitive_for_builtins(self):
        """ Test that all built-in crystal have a primitive cell """
        for name in Crystal.builtins:
            with self.subTest(name):
                c = Crystal.from_database(name)
                prim = c.primitive(symprec=0.1)
                self.assertLessEqual(len(prim), len(c))

    def test_primitive_preserves_subclass(self):
        """ Check that Crystal returned by Crystal.primitive() preserve subclass """

        class TestCrystal(Crystal):
            pass

        c = TestCrystal.from_database("C")
        prim = c.primitive()
        self.assertEqual(TestCrystal, type(prim))

    def test_ideal_for_builtins(self):
        """ Test that all built-in crystal have an ideal cell """
        for name in Crystal.builtins:
            with self.subTest(name):
                # This will raise an error if no idealized cell is found
                c = Crystal.from_database(name).ideal()

    def test_ideal_preserves_subclass(self):
        """ Check that Crystal returned by Crystal.ideal() preserve subclass """

        class TestCrystal(Crystal):
            pass

        c = TestCrystal.from_database("C")
        ideal = c.ideal()
        self.assertEqual(TestCrystal, type(ideal))

    def test_symmetry_operations(self):
        """ Test that the symmetry operations output makes sense """
        identity = np.eye(4)

        for name in Crystal.builtins:
            with self.subTest(name):
                c = Crystal.from_database(name)
                symops = c.symmetry_operations()
                self.assertTrue(np.allclose(identity, symops[0]))

    def test_reciprocal_symmetry_operations(self):
        """ Test that the reciprocal symmetry operations output makes sense """
        identity = np.eye(4)

        for name in Crystal.builtins:
            with self.subTest(name):
                c = Crystal.from_database(name)
                symops = c.reciprocal_symmetry_operations()
                self.assertTrue(np.allclose(identity, symops[0]))


class TestCrystalSpecialMethods(unittest.TestCase):
    def test_str_vs_repr(self):
        """ Test that str and repr are workign as expected """
        for name in Crystal.builtins:
            with self.subTest(name):
                c = Crystal.from_database(name)

                # If small crystal, repr and str should be the same
                if len(c) <= 10:
                    self.assertEqual(repr(c), str(c))
                else:
                    self.assertNotEqual(repr(c), str(c))

    def test_equality(self):
        """ Test that __eq__ works as expected """
        c1 = Crystal.from_database("Pu-alpha")
        c2 = deepcopy(c1)
        self.assertEqual(c1, c2)

        c3 = Crystal.from_database("Pu-epsilon")
        self.assertNotEqual(c1, c3)


class TestCrystalConstructors(unittest.TestCase):
    def test_builtins(self):
        """ Test that all names in Crystal.builtins build without errors,
        and that Crystal.source is correctly recorded. """
        for name in Crystal.builtins:
            with self.subTest(name):
                c = Crystal.from_database(name)

                self.assertIn(name, c.source)

    def test_builtins_wrong_name(self):
        """ Test that a name not in Crystal.builtins will raise a ValueError """
        with self.assertRaises(ValueError):
            Crystal.from_database("___")

    def test_substructure_preservation(self):
        """ Test that initializing a crystal with substructures preserves the substructures """
        atoms = [Atom("Ag", [0, 0, 0]), Atom("Ag", [1, 1, 1])]
        substructures = [AtomicStructure(atoms=[Atom("U", [0, 0, 0])])]
        c = Crystal(unitcell=atoms + substructures, lattice_vectors=np.eye(3))

        self.assertEqual(len(c), 3)
        self.assertIn(substructures[0], c.substructures)

    @unittest.skipUnless(connection_available(), "Internet connection is required.")
    def test_from_pdb(self):
        """ Test Crystal.from_pdb constructor """
        c = Crystal.from_pdb("1fbb")
        self.assertIn("1fbb", c.source)

    @unittest.skipUnless(connection_available(), "Internet connection is required.")
    def test_from_cod(self):
        """ Test building a Crystal object from the COD """
        # revision = None and latest revision should give the same Crystal
        c = Crystal.from_cod(1521124)
        c2 = Crystal.from_cod(1521124, revision=176429)

        self.assertEqual(c, c2)

    @unittest.skipUnless(connection_available(), "Internet connection is required.")
    def test_from_cod_new_dir(self):
        """ Test that a cache dir is created by Crystal.from_cod """
        with tempfile.TemporaryDirectory() as temp_dir:
            download_dir = Path(temp_dir) / "test_cod"
            self.assertFalse(download_dir.exists())
            c = Crystal.from_cod(1521124, download_dir=download_dir)
            self.assertTrue(download_dir.exists())


class TestSupercell(unittest.TestCase):
    def test_constructors(self):
        """ Test Supercell constructors for varyous 'builtin' structures """
        for name in islice(Crystal.builtins, 20):
            with self.subTest(name):
                s = Crystal.from_database(name).supercell(2, 2, 2)

                self.assertEqual(len(s), 8 * len(s.crystal))


class TestIndexedBy(unittest.TestCase):
    def test_trivial_reindexing(self):
        """ Test re-indexing a crystal by itself """
        c1 = Crystal.from_database("Pu-gamma")
        c2 = c1.indexed_by(c1)

        self.assertEqual(c1, c2)


# # The tests below are very flaky. Due to floating-point arithmetic
# # being non-deterministic, sometimes comparing atoms does not work
# # and the tests below fail.
# # Because of this, we skip tests when in a continuous integration environment
# # See here for details on environment variables:
# #   https://www.appveyor.com/docs/environment-variables/
# @unittest.skipIf(bool(os.environ.get('CI', False)), reason="Flaky tests")
class TestSymmetryReduction(unittest.TestCase):
    def test_trivial(self):
        """ Test that the symmetry_reduction function returns the unit cell when
        there is only one possibility. """
        ucell = set([Atom("H", coords=[0, 0, 0])])
        symops = [np.eye(4)]
        asym_cell = symmetry_reduction(ucell, symops)
        self.assertEqual(ucell, asym_cell)

    @retry_test(max_retries=5)
    def test_simple_translation(self):
        """ Test that symmetry_reduction works on a unitcell where two atoms are
        linked by a translation """
        symops = [np.eye(4), translation_matrix([0, 0, 1 / 2])]
        asym_cell = set([Atom("H", coords=[0, 0, 0])])
        unitcell = set(symmetry_expansion(asym_cell, symmetry_operators=symops))

        asym_cell2 = symmetry_reduction(unitcell, symops)
        self.assertEqual(asym_cell, asym_cell2)

    @retry_test(max_retries=5)
    def test_reciprocity_with_symmetry_expansion(self):
        """ Test that symmetry_reduction is reciprocal to symmetry_expansion """
        structures = ["vo2-m1", "Os", "Na"]  # , 'Nb', 'Pd', 'Zn']
        for s in structures:
            with self.subTest("Crystal " + s):
                cryst = Crystal.from_database(s)
                asym_cell = symmetry_reduction(
                    cryst.unitcell, cryst.symmetry_operations()
                )
                ucell = set(symmetry_expansion(asym_cell, cryst.symmetry_operations()))
                self.assertEqual(set(cryst.unitcell), ucell)


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

# -*- coding: utf-8 -*- Returns whether or not an internet connection is available Test that Crystal.symmetry() works correctly for graphite Test that all built-in crystal have a primitive cell Check that Crystal returned by Crystal.primitive() preserve subclass Test that all built-in crystal have an ideal cell # This will raise an error if no idealized cell is found Check that Crystal returned by Crystal.ideal() preserve subclass Test that the symmetry operations output makes sense Test that the reciprocal symmetry operations output makes sense Test that str and repr are workign as expected # If small crystal, repr and str should be the same Test that __eq__ works as expected Test that all names in Crystal.builtins build without errors,         and that Crystal.source is correctly recorded. Test that a name not in Crystal.builtins will raise a ValueError Test that initializing a crystal with substructures preserves the substructures Test Crystal.from_pdb constructor Test building a Crystal object from the COD # revision = None and latest revision should give the same Crystal Test that a cache dir is created by Crystal.from_cod Test Supercell constructors for varyous 'builtin' structures Test re-indexing a crystal by itself # # The tests below are very flaky. Due to floating-point arithmetic # # being non-deterministic, sometimes comparing atoms does not work # # and the tests below fail. # # Because of this, we skip tests when in a continuous integration environment # # See here for details on environment variables: # #   https://www.appveyor.com/docs/environment-variables/ # @unittest.skipIf(bool(os.environ.get('CI', False)), reason="Flaky tests") Test that the symmetry_reduction function returns the unit cell when         there is only one possibility. Test that symmetry_reduction works on a unitcell where two atoms are         linked by a translation Test that symmetry_reduction is reciprocal to symmetry_expansion # , 'Nb', 'Pd', 'Zn']