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test_atoms.py
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test_atoms.py
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# coding: utf-8
# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
# Distributed under the terms of "New BSD License", see the LICENSE file.
import unittest
import numpy as np
import os
import warnings
from pyiron.atomistics.structure.atom import Atom
from pyiron.atomistics.structure.atoms import Atoms, CrystalStructure
from pyiron.atomistics.structure.factory import StructureFactory
from pyiron.atomistics.structure.sparse_list import SparseList
from pyiron.atomistics.structure.periodic_table import PeriodicTable, ChemicalElement
from pyiron_base import FileHDFio, ProjectHDFio, Project
from ase.cell import Cell as ASECell
from ase.atoms import Atoms as ASEAtoms
class TestAtoms(unittest.TestCase):
@classmethod
def tearDownClass(cls):
file_location = os.path.dirname(os.path.abspath(__file__))
if os.path.isfile(
os.path.join(file_location, "../../static/atomistics/test_hdf")
):
os.remove(
os.path.join(file_location, "../../static/atomistics/test_hdf")
)
if os.path.isfile(
os.path.join(file_location, "../../static/atomistics/test.h5")
):
os.remove(
os.path.join(file_location, "../../static/atomistics/test.h5")
)
@classmethod
def setUpClass(cls):
C = Atom("C").element
cls.C3 = Atoms([C, C, C], positions=[[0, 0, 0], [0, 0, 2], [0, 2, 0]])
cls.C2 = Atoms(2 * [Atom("C")])
cls.struct_factory = StructureFactory()
def setUp(self):
# These atoms are reset before every test.
self.CO2 = Atoms("CO2", positions=[[0, 0, 0], [0, 0, 1.5], [0, 1.5, 0]])
def test__init__(self):
pos, cell = generate_fcc_lattice()
pse = PeriodicTable()
el = pse.element("Al")
basis = Atoms()
ase_basis = ASEAtoms()
self.assertIsInstance(ase_basis, ASEAtoms)
self.assertIsInstance(ase_basis.info, dict)
self.assertIsInstance(ase_basis.arrays, dict)
self.assertIsInstance(ase_basis.pbc, (bool, list, np.ndarray))
self.assertIsInstance(ase_basis._cellobj, ASECell)
self.assertIsInstance(basis, Atoms)
self.assertIsInstance(basis.info, dict)
self.assertIsInstance(basis.arrays, dict)
self.assertIsInstance(basis.units, dict)
self.assertIsInstance(basis.pbc, (bool, list, np.ndarray))
self.assertIsInstance(basis.indices, np.ndarray)
self.assertEqual(len(basis.positions), 0)
self.assertIsInstance(basis.species, list)
self.assertIsInstance(basis.elements, np.ndarray)
basis = Atoms(symbols="Al", positions=pos, cell=cell)
self.assertIsInstance(basis, Atoms)
self.assertEqual(basis.get_spacegroup()["Number"], 225)
basis = Atoms(elements="Al", positions=pos, cell=cell)
self.assertIsInstance(basis, Atoms)
basis = Atoms(elements=["Al"], positions=pos, cell=cell)
self.assertIsInstance(basis, Atoms)
self.assertRaises(
ValueError, Atoms, symbols="Pt", elements="Al", positions=pos, cell=cell
)
basis = Atoms(numbers=[13], positions=pos, cell=cell)
self.assertEqual(basis.get_majority_species()["symbol"], "Al")
basis = Atoms(species=[el], indices=[0], positions=pos, cell=cell)
self.assertEqual(basis.get_majority_species()["symbol"], "Al")
self.assertIsInstance(basis, Atoms)
self.assertIsInstance(basis.info, dict)
self.assertIsInstance(basis.arrays, dict)
self.assertIsInstance(basis.units, dict)
self.assertIsInstance(basis.pbc, (bool, list, np.ndarray))
self.assertIsInstance(basis.indices, np.ndarray)
self.assertIsInstance(basis.species, list)
self.assertIsInstance(basis.cell, ASECell)
self.assertIsInstance(basis.positions, np.ndarray)
self.assertIsInstance(basis.get_scaled_positions(), np.ndarray)
self.assertIsInstance(basis.elements, np.ndarray)
def test_set_species(self):
pos, cell = generate_fcc_lattice()
pse = PeriodicTable()
el = pse.element("Pt")
basis = Atoms(symbols="Al", positions=pos, cell=cell)
self.assertEqual(basis.get_chemical_formula(), "Al")
basis.set_species([el])
self.assertEqual(basis.get_chemical_formula(), "Pt")
self.assertTrue(
"Al" not in [sp.Abbreviation] for sp in basis._species_to_index_dict.keys()
)
self.assertTrue(
"Pt" in [sp.Abbreviation] for sp in basis._species_to_index_dict.keys()
)
def test_new_array(self):
pos, cell = generate_fcc_lattice()
basis = Atoms(symbols="Al", positions=pos, cell=cell)
basis.set_repeat([10, 10, 10])
spins = np.ones(len(basis))
basis.new_array(name="spins", a=spins)
self.assertTrue(np.array_equal(basis.arrays["spins"], spins))
def test_set_array(self):
pos, cell = generate_fcc_lattice()
basis = Atoms(symbols="Al", positions=pos, cell=cell)
basis.set_repeat([10, 10, 10])
spins = np.ones(len(basis), dtype=float)
basis.set_array(name="spins", a=2 * spins, dtype=int)
self.assertTrue(np.array_equal(basis.arrays["spins"], 2 * spins))
def test_get_array(self):
pos, cell = generate_fcc_lattice()
basis = Atoms(symbols="Al", positions=pos, cell=cell)
basis.set_repeat([10, 10, 10])
spins = np.ones(len(basis), dtype=float)
basis.set_array(name="spins", a=2 * spins, dtype=int)
self.assertTrue(np.array_equal(basis.arrays["spins"], 2 * spins))
self.assertTrue(np.array_equal(basis.get_array(name="spins"), 2 * spins))
def test_add_tags(self):
self.CO2.add_tag(test_tag="a")
self.assertIsInstance(self.CO2.test_tag, SparseList)
self.assertEqual(self.CO2.test_tag[0], "a")
self.assertEqual(self.CO2.test_tag[0], self.CO2.test_tag[2])
self.assertIsInstance(self.CO2.test_tag.list(), list)
self.CO2.add_tag(selective_dynamics=[True, True, True])
self.CO2.selective_dynamics[1] = [True, False, True]
self.assertEqual(self.CO2.selective_dynamics[1], [True, False, True])
self.assertIsInstance(self.CO2.selective_dynamics.list(), list)
def test_get_tags(self):
self.CO2.add_tag(test_tag="a")
self.assertIsInstance(self.CO2.test_tag, SparseList)
self.assertIsInstance(self.CO2.get_tags(), type(dict().keys()))
def test_get_pbc(self):
self.assertTrue(np.array_equal(self.CO2.pbc, self.CO2.get_pbc()))
self.assertEqual(len(self.CO2.get_pbc()), 3)
def test_set_pbc(self):
self.CO2.set_pbc([True, True, False])
self.assertTrue(np.array_equal(self.CO2.pbc, self.CO2.get_pbc()))
self.assertTrue(np.array_equal([True, True, False], self.CO2.get_pbc()))
self.CO2.set_pbc(False)
self.assertTrue(np.array_equal([False, False, False], self.CO2.get_pbc()))
self.assertTrue(np.array_equal(self.CO2.pbc, self.CO2.get_pbc()))
def test_chemical_element(self):
conv = self.CO2.convert_element("C")
self.assertIsInstance(conv, ChemicalElement)
self.assertIsInstance(self.CO2.convert_element(conv), ChemicalElement)
self.assertIsInstance(self.CO2.convert_element(self.CO2[0]), ChemicalElement)
with self.assertRaises(ValueError):
self.assertIsInstance(self.CO2.convert_element(self.CO2), ChemicalElement)
self.assertEqual(len(self.CO2.species), 2)
def test_copy(self):
pos, cell = generate_fcc_lattice()
basis = Atoms(symbols="Al", positions=pos, cell=cell)
basis_copy = basis.copy()
basis_copy.positions[0, 0] += 5
self.assertNotEqual(basis_copy.positions[0, 0], basis.positions[0, 0])
basis_copy.cell[0, 0] += 5
self.assertNotEqual(basis_copy.cell[0, 0], basis.cell[0, 0])
basis_copy = basis.copy()
self.assertEqual(basis, basis_copy)
basis_copy[:] = "Pt"
self.assertNotEqual(basis, basis_copy)
def test_numbers_to_elements(self):
num_list = [1, 12, 13, 6]
self.assertTrue(
np.array_equal(
[el.Abbreviation for el in self.CO2.numbers_to_elements(num_list)],
["H", "Mg", "Al", "C"],
)
)
def test_scaled_pos_xyz(self):
basis = Atoms(symbols="AlAl", positions=[3 * [0], 3 * [1]], cell=2 * np.eye(3))
pos_xyz = basis.pos_xyz()
self.assertAlmostEqual(np.linalg.norm(pos_xyz[0] - np.array([0, 1])), 0)
scaled_pos_xyz = basis.scaled_pos_xyz()
self.assertAlmostEqual(
np.linalg.norm(pos_xyz[0] - basis.cell[0, 0] * scaled_pos_xyz[0]), 0
)
def test_to_hdf(self):
filename = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"../../static/atomistics/test_hdf",
)
abs_filename = os.path.abspath(filename)
hdf_obj = FileHDFio(abs_filename)
pos, cell = generate_fcc_lattice()
basis = Atoms(symbols="Al", positions=pos, cell=cell)
basis.set_repeat([2, 2, 2])
basis.to_hdf(hdf_obj, "test_structure")
self.assertTrue(
np.array_equal(hdf_obj["test_structure/positions"], basis.positions)
)
basis_new = Atoms().from_hdf(hdf_obj, "test_structure")
self.assertEqual(basis, basis_new)
def test_from_hdf(self):
filename = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"../../static/atomistics/test_hdf",
)
abs_filename = os.path.abspath(filename)
hdf_obj = FileHDFio(abs_filename)
pos, cell = generate_fcc_lattice()
basis_store = Atoms(symbols="Al", positions=pos, cell=cell)
basis_store.set_repeat([2, 2, 2])
basis_store.add_tag(selective_dynamics=[False, False, False])
basis_store.selective_dynamics[7] = [True, True, True]
basis_store.to_hdf(hdf_obj, "simple_structure")
basis = Atoms().from_hdf(hdf_obj, group_name="simple_structure")
self.assertEqual(len(basis), 8)
self.assertEqual(basis.get_majority_species()["symbol"], "Al")
self.assertEqual(basis.get_spacegroup()["Number"], 225)
self.assertTrue(basis.selective_dynamics[7][0])
self.assertFalse(basis.selective_dynamics[0][0])
basis.add_tag(selective_dynamics=[False, False, False])
basis.selective_dynamics[6] = [True, True, True]
self.assertTrue(basis.selective_dynamics[6][0])
self.assertFalse(basis.selective_dynamics[5][0])
def test_to_object(self):
filename = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"../../static/atomistics",
)
abs_filename = os.path.abspath(filename)
hdf_obj = ProjectHDFio(
project=Project(abs_filename),
file_name="test.h5"
)
pos, cell = generate_fcc_lattice()
basis_store = Atoms(symbols="Al", positions=pos, cell=cell)
basis_store.set_repeat([2, 2, 2])
basis_store.to_hdf(hdf_obj, "simple_structure")
basis = hdf_obj["simple_structure"].to_object()
self.assertEqual(len(basis), 8)
self.assertEqual(basis.get_majority_species()["symbol"], "Al")
self.assertEqual(basis.get_spacegroup()["Number"], 225)
def test_create_Fe_bcc(self):
self.pse = PeriodicTable()
self.pse.add_element("Fe", "Fe_up", spin="up", pseudo_name="GGA")
self.pse.add_element("Fe", "Fe_down", spin="down", pseudo_name="GGA")
Fe_up = self.pse.element("Fe_up")
Fe_down = self.pse.element("Fe_down")
self.Fe_bcc = Atoms(
[Fe_up, Fe_down],
scaled_positions=[[0, 0, 0], [0.25, 0.25, 0.25]],
cell=np.identity(3),
)
self.Fe_bcc.add_tag("group")
self.Fe_bcc.group[:] = 0
def test_convert_formula(self):
self.assertEqual(self.CO2.convert_formula("C"), ["C"])
self.assertEqual(self.CO2.convert_formula("C3"), ["C", "C", "C"])
self.assertEqual(self.CO2.convert_formula("CO2"), ["C", "O", "O"])
self.assertEqual(self.CO2.convert_formula("CO2Fe"), ["C", "O", "O", "Fe"])
self.assertEqual(
self.CO2.convert_formula("CO2FeF21"), ["C", "O", "O", "Fe", "F", "F"]
)
def test__getitem__(self):
self.assertEqual(self.CO2[0].symbol, "C")
self.assertEqual(self.C3[2].position.tolist(), [0, 2, 0])
self.assertTrue(
(self.C3[1:].positions == np.array([[0, 0, 2], [0, 2, 0]])).all()
)
short_basis = self.CO2[0]
self.assertIsInstance(short_basis, Atom)
short_basis = self.CO2[[0]]
self.assertIsInstance(short_basis, Atoms)
self.assertEqual(short_basis.indices[0], 0)
self.assertEqual(len(short_basis.species), 1)
short_basis = self.CO2[[2]]
self.assertIsInstance(short_basis, Atoms)
self.assertEqual(short_basis.indices[0], 0)
self.assertEqual(len(short_basis.species), 1)
basis_Mg = CrystalStructure("Mg", bravais_basis="fcc", lattice_constant=4.2)
basis_O = CrystalStructure("O", bravais_basis="fcc", lattice_constant=4.2)
basis_O.positions += [0.0, 0.0, 0.5]
basis = basis_Mg + basis_O
basis.center_coordinates_in_unit_cell()
basis.set_repeat([3, 3, 3])
mg_indices = basis.select_index("Mg")
o_indices = basis.select_index("O")
basis_new = basis[mg_indices] + basis[o_indices]
self.assertEqual(
len(basis_new._tag_list), len(basis[mg_indices]) + len(basis[o_indices])
)
self.assertEqual(basis_new.get_spacegroup()["Number"], 225)
self.assertEqual(basis[:-3], basis[0:len(basis)-3])
self.assertEqual(basis.dimension, basis[mg_indices].dimension)
self.assertTrue(np.array_equal(basis.pbc, basis[mg_indices].pbc))
self.assertRaises(IndexError, basis_new.__getitem__, [True, True, False])
self.assertEqual(basis_new, basis_new[[True] * len(basis_new)])
bool_array = np.array([True] * len(basis_new))
bool_array[[10, 20, 40]] = False
self.assertEqual(len(basis_new[bool_array]), len(basis_new) - 3)
bool_array = np.array([True] * len(basis))
bool_array[mg_indices] = False
self.assertEqual(len(basis[bool_array]), len(o_indices))
self.assertEqual(len(basis[0:10]), 10)
self.assertEqual(basis[0, 10], basis[[0, 10]])
def test_positions(self):
self.assertEqual(self.CO2[1:].positions[1:].tolist(), [[0.0, 1.5, 0.0]])
self.CO2.positions[1][0] = 5.0
self.assertEqual(self.CO2.positions[1].tolist(), [5.0, 0, 1.5])
def test_set_positions(self):
pos, cell = generate_fcc_lattice()
basis = Atoms(symbols="Al", positions=pos, cell=cell)
basis.set_positions(np.array([[2.5, 2.5, 2.5]]))
self.assertTrue(np.array_equal(basis.positions, [[2.5, 2.5, 2.5]]))
def test_set_scaled_positions(self):
pos, cell = generate_fcc_lattice()
basis = Atoms(symbols="Al", positions=pos, cell=cell, a=4.2)
basis.set_scaled_positions(np.array([[0.5, 0.5, 0.5]]))
self.assertTrue(np.array_equal(basis.get_scaled_positions(), [[0.5, 0.5, 0.5]]))
self.assertTrue(
np.array_equal(basis.positions, np.dot([[0.5, 0.5, 0.5]], basis.cell))
)
with warnings.catch_warnings(record=True):
basis.scaled_positions = np.array([[0.5, 0.5, 0.5]])
self.assertTrue(np.array_equal(basis.scaled_positions, [[0.5, 0.5, 0.5]]))
def test_cell(self):
CO = Atoms(
"CO",
positions=[[0, 0, 0], [0, 0, 2]],
cell=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
pbc=[True, True, True],
)
self.assertTrue((CO.get_cell() == np.identity(3)).all())
self.assertTrue((CO.cell == np.identity(3)).all())
cell = CO.cell.copy()
cell[2][2] = 10.0
CO.set_cell(cell)
self.assertEqual(CO.cell[2, 2], 10.0)
self.assertAlmostEqual(CO.get_volume(), 10)
self.assertAlmostEqual(CO.get_volume(per_atom=True), 0.5 * 10)
CO.set_cell(-np.eye(3))
with self.assertRaises(ValueError):
CO.set_cell([2, 1])
dx = 1.0
r_o = [0, 0, 0]
r_h1 = [dx, 0, 0]
r_h2 = [0, dx, 0]
water = Atoms(elements=['H', 'H', 'O'], positions=[r_h1, r_h2, r_o])
self.assertEqual(water.center_coordinates_in_unit_cell(), water)
water.set_cell(np.zeros((3, 3)))
self.assertTrue(np.array_equal(water.cell, np.zeros((3, 3))))
self.assertTrue(np.array_equal(water.get_scaled_positions(), water.positions))
self.assertEqual(water.center_coordinates_in_unit_cell(), water)
def test_add(self):
COX = self.C2 + Atom("O", position=[0, 0, -2])
COX += Atom("O", position=[0, 0, -4])
COX += COX
n_objects = len(set(COX.get_species_objects()))
n_species = len(set(COX.get_chemical_elements()))
self.assertEqual(n_objects, n_species)
def test_pbc(self):
CO = Atoms(
"CO",
positions=[[0, 0, 0], [0, 0, 2]],
cell=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
pbc=[True, True, True],
)
self.assertTrue((CO.pbc == np.array([True, True, True])).all())
CO.set_pbc((True, True, False))
def test_get_masses_DOF(self):
self.assertEqual(
len(self.CO2.get_masses_dof()), len(self.CO2.positions.flatten())
)
def test_get_center_of_mass(self):
basis = Atoms(
elements="AlFe", positions=[3 * [0.5], 3 * [1.5]], cell=2 * np.eye(3)
)
mass = np.array(basis.get_masses())
self.assertAlmostEqual(
(mass[0] * 0.5 + mass[1] * 1.5) / mass.sum(), basis.get_center_of_mass()[0]
)
basis.set_repeat(2)
self.assertAlmostEqual(
(mass[0] * 0.5 + mass[1] * 1.5) / mass.sum() + 1,
basis.get_center_of_mass()[0],
)
def test_rotate(self):
unitcell = Atoms(
elements="AlFe", positions=[3 * [0], 3 * [1]], cell=2 * np.eye(3), pbc=True)
basis = unitcell.copy()
basis.rotate(a=10.0, v=[0, 0, 0.1 * np.pi])
self.assertAlmostEqual(np.arccos(basis.positions[1, :2].sum() / 2) * 180 / np.pi, 10.0)
basis = unitcell.copy()
basis.rotate(v=[0, 0, 1], a=0.1)
self.assertAlmostEqual(np.arccos(basis.positions[1, :2].sum() / 2) * 180 / np.pi, 0.1)
basis = unitcell.copy()
center_of_mass = basis.get_center_of_mass()
basis.rotate(v=[0, 0, 0.1 * np.pi], center="com")
self.assertTrue(np.allclose(basis.get_center_of_mass(), center_of_mass))
basis = unitcell.copy()
center_of_positions = basis.positions.mean(axis=0)
basis.rotate(v=[0, 0, 1], center="cop")
self.assertTrue(np.allclose(center_of_positions, basis.positions.mean(axis=0)))
basis = unitcell.copy()
position = basis.positions[1]
basis.rotate(v=[0, 0, 1], center="cou")
self.assertTrue(np.allclose(position, basis.positions[1]))
basis = unitcell.copy()
basis.rotate(v=np.random.random(3), rotate_cell=True)
self.assertAlmostEqual(basis.get_scaled_positions()[1, 0], 0.5)
basis = unitcell.copy()
basis.rotate(v=np.random.random(3), index_list=[0])
self.assertTrue(
np.allclose(unitcell.positions.flatten(), basis.positions.flatten())
)
def test_rotate_euler(self):
unitcell = Atoms(
elements="AlFe", positions=[3 * [0], 3 * [1]], cell=2 * np.eye(3)
)
basis = unitcell.copy()
basis.rotate_euler(phi=0.1 * np.pi)
self.assertAlmostEqual(np.arccos(basis.positions[1, :2].sum() / 2) / np.pi, 0.1)
basis = unitcell.copy()
center_of_mass = basis.get_center_of_mass()
basis.rotate_euler(phi=0.1 * np.pi, center="com")
self.assertTrue(np.allclose(basis.get_center_of_mass(), center_of_mass))
basis = unitcell.copy()
center_of_positions = basis.positions.mean(axis=0)
basis.rotate_euler(phi=0.1 * np.pi, center="cop")
self.assertTrue(np.allclose(center_of_positions, basis.positions.mean(axis=0)))
basis = unitcell.copy()
position = basis.positions[1]
basis.rotate_euler(phi=0.1 * np.pi, center="cou")
self.assertTrue(np.allclose(position, basis.positions[1]))
def test_set_initial_magnetic_moments(self):
pos, cell = generate_fcc_lattice()
basis = Atoms(symbols="Al", positions=pos, cell=cell, a=4.2, pbc=True)
basis *= 2
basis.set_initial_magnetic_moments(magmoms=np.ones(len(basis)))
basis = Atoms(symbols="Al", positions=pos, cell=cell, a=4.2, pbc=True)
basis.set_initial_magnetic_moments(magmoms=np.ones((len(basis), 3)))
basis = Atoms(symbols="Al", positions=pos, cell=cell, a=4.2, pbc=True)
basis *= 2
basis.set_initial_magnetic_moments(magmoms=np.ones(len(basis)))
self.assertTrue(np.allclose(basis.arrays["initial_magmoms"], np.ones(len(basis))))
# set new magnetic moments with different shape
basis.set_initial_magnetic_moments(magmoms=np.ones((len(basis), 3)))
self.assertTrue(np.allclose(basis.arrays["initial_magmoms"], np.ones((len(basis), 3))))
with self.assertRaises(ValueError):
basis.set_initial_magnetic_moments(magmoms=np.ones(4))
def test_get_parent_basis(self):
periodic_table = PeriodicTable()
periodic_table.add_element(parent_element="O", new_element="O_up")
O_up = periodic_table.element("O_up")
O_basis = Atoms(
[O_up], cell=10.0 * np.eye(3), scaled_positions=[[0.5, 0.5, 0.5]]
)
O_simple = Atoms(
["O"], cell=10.0 * np.eye(3), scaled_positions=[[0.5, 0.5, 0.5]]
)
O_parent = O_basis.get_parent_basis()
self.assertNotEqual(O_basis, O_parent)
self.assertEqual(O_simple, O_parent)
self.assertEqual(O_parent[0].symbol, "O")
periodic_table.add_element(parent_element="O", new_element="O_down")
O_down = periodic_table.element("O_down")
O_basis = Atoms(
[O_up, O_down],
cell=10.0 * np.eye(3),
scaled_positions=[[0, 0, 0], [0.5, 0.5, 0.5]],
)
O_simple = Atoms(
["O", "O"], cell=10.0 * np.eye(3), scaled_positions=[[0., 0., 0.], [0.5, 0.5, 0.5]]
)
O_parent = O_basis.get_parent_basis()
self.assertNotEqual(O_basis, O_parent)
self.assertEqual(O_simple, O_parent)
self.assertEqual(O_parent.get_chemical_formula(), "O2")
self.assertEqual(len(O_basis.species), 2)
self.assertEqual(len(O_simple.species), 1)
self.assertEqual(len(O_parent.species), 1)
def test_profiling(self):
num = 1000
C100 = Atoms(num * ["C"], positions=[(0, 0, 0) for _ in range(num)])
self.assertEqual(len(C100), num)
def test_Au(self):
a = 4.05 # Gold lattice constant
b = a / 2.0
fcc = Atoms(["Au"], cell=[(0, b, b), (b, 0, b), (b, b, 0)], pbc=True)
# print fcc
# print "volume: ", fcc.get_volume()
def test_set_absolute(self):
a = 4.05 # Gold lattice constant
b = a / 2.0
positions = np.array([(0.5, 0.4, 0.0)])
fcc = Atoms(
symbols=["Au"],
scaled_positions=positions,
cell=[(0, b, b), (b, 0, b), (b, b, 0)],
pbc=True,
)
# fcc.set_absolute()
# print fcc.positions
# fcc.set_relative()
self.assertTrue(np.linalg.norm(fcc.get_scaled_positions() - positions) < 1e-10)
def test_set_relative(self):
lattice = CrystalStructure(
element="Al", bravais_basis="fcc", lattice_constants=4
)
basis_relative = lattice.copy()
cell = basis_relative.cell.copy()
cell[0, 0] = 6
basis_relative.set_cell(cell, True)
basis_absolute = lattice.copy()
cell = basis_absolute.cell.copy()
cell[0, 0] = 6
basis_absolute.set_cell(cell)
self.assertAlmostEqual(
basis_relative.positions[-1, 0] * 1.5, basis_absolute.positions[-1, 0]
)
basis = lattice.copy()
self.assertAlmostEqual(
basis.get_scaled_positions(wrap=False)[-1, 0],
basis_relative.get_scaled_positions(wrap=False)[-1, 0],
)
cell = basis.cell.copy()
cell[0, 0] = 6
basis.set_cell(cell)
self.assertAlmostEqual(basis.positions[-1, 0], basis_absolute.positions[-1, 0])
basis = lattice.copy()
basis_relative = lattice.copy()
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
basis_relative.set_relative()
self.assertEqual(len(w), 1)
self.assertIsInstance(w[-1].message, DeprecationWarning)
basis.positions[-1, 0] = 0.5
basis_relative.positions[-1, 0] = 0.5
self.assertAlmostEqual(basis.positions[-1, 0], basis_relative.positions[-1, 0])
basis.set_cell(3 * np.ones(3))
self.assertAlmostEqual(basis.get_volume(), 27)
basis.set_cell(np.append(np.ones(3), 90 - np.random.random(3)).flatten())
self.assertLess(basis.get_volume(), 1)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
basis_absolute.set_absolute()
self.assertEqual(len(w), 1)
self.assertIsInstance(w[-1].message, DeprecationWarning)
def test_repeat(self):
basis_Mg = CrystalStructure("Mg", bravais_basis="fcc", lattice_constant=4.2)
basis_O = CrystalStructure("O", bravais_basis="fcc", lattice_constant=4.2)
basis_O.set_scaled_positions(basis_O.get_scaled_positions() + [0.0, 0.0, 0.5])
with self.assertRaises(ValueError):
basis_O.set_repeat(5.0)
with self.assertRaises(AssertionError):
basis_O.set_repeat([2, 2])
basis = basis_Mg + basis_O
basis.center_coordinates_in_unit_cell()
basis.add_tag(selective_dynamics=[True, True, True])
basis.selective_dynamics[basis.select_index("O")] = [False, False, False]
len_before = len(basis)
sel_dyn_before = np.array(basis.selective_dynamics.list())
self.assertTrue(
np.alltrue(
np.logical_not(
np.alltrue(sel_dyn_before[basis.select_index("O")], axis=1)
)
)
)
self.assertTrue(
np.alltrue(np.alltrue(sel_dyn_before[basis.select_index("Mg")], axis=1))
)
basis.set_repeat([3, 3, 2])
sel_dyn_after = np.array(basis.selective_dynamics.list())
len_after = len(basis)
self.assertEqual(basis.get_spacegroup()["Number"], 225)
self.assertEqual(len_before * 18, len_after)
self.assertEqual(len(sel_dyn_before) * 18, len(sel_dyn_after))
self.assertTrue(
np.alltrue(
np.logical_not(
np.alltrue(sel_dyn_after[basis.select_index("O")], axis=1)
)
)
)
self.assertTrue(
np.alltrue(np.alltrue(sel_dyn_after[basis.select_index("Mg")], axis=1))
)
basis = basis_Mg + basis_O
basis.add_tag(spin=None)
basis.spin[basis.select_index("Mg")] = 1
basis.spin[basis.select_index("O")] = -1
self.assertTrue(
np.array_equal(
basis.spin[basis.select_index("Mg")].list(),
1 * np.ones(len(basis.select_index("Mg"))),
)
)
self.assertTrue(
np.array_equal(
basis.spin[basis.select_index("O")].list(),
-1 * np.ones(len(basis.select_index("O"))),
)
)
basis.set_repeat(2)
self.assertTrue(
np.array_equal(
basis.spin[basis.select_index("Mg")].list(),
1 * np.ones(len(basis.select_index("Mg"))),
)
)
self.assertTrue(
np.array_equal(
basis.spin[basis.select_index("O")].list(),
-1 * np.ones(len(basis.select_index("O"))),
)
)
basis = basis_Mg + basis_O
basis.add_tag(spin=None)
# Indices set as int
Mg_indices = np.array(basis.select_index("Mg"), dtype=int).tolist()
for ind in Mg_indices:
basis.spin[ind] = 1
O_indices = np.array(basis.select_index("O"), dtype=int).tolist()
for ind in O_indices:
basis.spin[ind] = -1
basis.set_repeat(2)
self.assertTrue(
np.array_equal(
basis.spin[basis.select_index("Mg")].list(),
1 * np.ones(len(basis.select_index("Mg"))),
)
)
self.assertTrue(
np.array_equal(
basis.spin[basis.select_index("O")].list(),
-1 * np.ones(len(basis.select_index("O"))),
)
)
# Indices set as numpy.int
Mg_indices = np.array(basis.select_index("Mg"), dtype=np.int)
for ind in Mg_indices:
basis.spin[ind] = 1
O_indices = np.array(basis.select_index("O"), dtype=np.int)
for ind in O_indices:
basis.spin[ind] = -1
basis.set_repeat(2)
self.assertTrue(
np.array_equal(
basis.spin[basis.select_index("Mg")].list(),
1 * np.ones(len(basis.select_index("Mg"))),
)
)
self.assertTrue(
np.array_equal(
basis.spin[basis.select_index("O")].list(),
-1 * np.ones(len(basis.select_index("O"))),
)
)
self.assertEqual(8 * len(self.CO2), len(self.CO2.repeat(np.int64(2))))
def test_get_distance(self):
cell = 2.2 * np.identity(3)
NaCl = Atoms("NaCl", scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)], cell=cell)
self.assertAlmostEqual(NaCl.get_distance(0, 1), 2.2 * 0.5 * np.sqrt(3))
self.assertAlmostEqual(NaCl.get_distance(0, [0, 0, 0.5]), 0.5)
self.assertAlmostEqual(NaCl.get_distance([0, 0, 0], [0, 0, 0.5]), 0.5)
def test_find_neighbors_by_vector(self):
basis = Atoms(symbols=2*["Fe"],
scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)],
cell=np.identity(3),
pbc=True)
id_lst = basis.find_neighbors_by_vector([0, 0, 1],
num_neighbors=14)
self.assertEqual(len(np.unique(np.unique(id_lst, return_counts=True)[1])), 1)
def test_get_neighborhood(self):
basis = Atoms(
"FeFe", scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)], cell=np.identity(3), pbc=True
)
neigh = basis.get_neighborhood([0, 0, 0.1])
self.assertEqual(neigh.distances[0], 0.1)
def test_get_neighbors(self):
basis = Atoms(symbols="FeFe", positions=[3 * [0], 3 * [1]], cell=2 * np.eye(3), pbc=True)
neigh = basis.get_neighbors(num_neighbors=58)
self.assertAlmostEqual(neigh.distances[0][0], np.sqrt(3))
counts = np.unique(neigh.shells[0], return_counts=True)
self.assertTrue(np.array_equal(counts[0], np.arange(5)+1))
self.assertTrue(np.array_equal(counts[1], np.array([ 8, 6, 12, 24, 8])))
basis = Atoms(symbols="FeFe", positions=[3 * [0], 3 * [1]], cell=2 * np.eye(3), pbc=True)
basis.pbc = np.array([True, False, False])
neigh = basis.get_neighbors(num_neighbors=10)
self.assertAlmostEqual(neigh.distances[0][0], np.sqrt(3))
self.assertAlmostEqual(neigh.distances[0][2], 2)
self.assertAlmostEqual(neigh.distances[0][4], np.sqrt(11))
self.assertAlmostEqual(neigh.distances[0][6], 4)
self.assertAlmostEqual(neigh.distances[0][8], np.sqrt(27))
basis.pbc = True
basis.set_repeat(2)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
neigh = basis.get_neighbors(width_buffer=0.1)
self.assertGreaterEqual(len(w), 1)
with self.assertRaises(ValueError):
neigh = basis.get_neighbors(width_buffer=0.001, num_neighbors=100)
basis = Atoms(symbols="FeFe", positions=[3 * [0], 3 * [1]], cell=2 * np.eye(3))
neigh = basis.get_neighbors(num_neighbors=1)
def test_get_neighbors_by_distance(self):
basis = Atoms(symbols="FeFeFe", positions=[3 * [0], 3 * [1], [0, 0, 1]], cell=2 * np.eye(3), pbc=True)
neigh = basis.get_neighbors_by_distance(1.5)
self.assertEqual(len(neigh.distances[0]), 2)
self.assertEqual(len(neigh.distances[1]), 4)
self.assertEqual(len(neigh.distances[2]), 6)
self.assertEqual(neigh.distances[0][0], 1.)
self.assertAlmostEqual(neigh.distances[1][0], np.sqrt(2))
self.assertEqual(neigh.distances[2][0], 1.)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
neigh = basis.get_neighbors_by_distance(cutoff_radius=1.5, num_neighbors=5)
self.assertGreaterEqual(len(w), 1)
self.assertEqual(len(neigh.distances[2]), 5)
with self.assertRaises(ValueError):
basis.get_neighbors_by_distance(width_buffer=-1)
# Check with large cell with few atoms
dx = 0.7
r_O = [0, 0, 0]
r_H1 = [dx, dx, 0]
r_H2 = [-dx, dx, 0]
unit_cell = 10 * np.eye(3)
water = Atoms(elements=['H', 'H', 'O'], positions=[r_H1, r_H2, r_O], cell=unit_cell, pbc=True)
self.assertIsInstance(water.get_neighbors_by_distance(1.3).indices, list)
water_new = water[[0, 1]]
self.assertTrue(np.array_equal(water_new.get_neighbors_by_distance(1.3).indices, [np.array([]), np.array([])]))
def test_get_number_of_neighbors_in_sphere(self):
basis = Atoms(symbols="FeFeFe", positions=[3 * [0], 3 * [1], [0, 0, 1]], cell=2 * np.eye(3), pbc=True)
num_neighbors_per_atom = basis.get_numbers_of_neighbors_in_sphere(cutoff_radius=2,
width_buffer=0)
self.assertEqual(num_neighbors_per_atom[0], 10)
self.assertEqual(num_neighbors_per_atom[1], 12)
self.assertEqual(num_neighbors_per_atom[2], 6)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
num_neighbors_per_atom = basis.get_numbers_of_neighbors_in_sphere(cutoff_radius=1.5, num_neighbors=5)
self.assertGreaterEqual(len(w), 1)
self.assertEqual(num_neighbors_per_atom[2], 5)
with self.assertRaises(ValueError):
basis.get_numbers_of_neighbors_in_sphere(width_buffer=-1)
def test_get_shell_matrix(self):
structure = CrystalStructure(elements='Fe', lattice_constants=2.83, bravais_basis='bcc')
shell_mat_atoms = structure.get_shell_matrix(num_neighbors=8)
neigh = structure.get_neighbors(num_neighbors=8)
self.assertEqual(shell_mat_atoms[0].sum(), neigh.get_shell_matrix()[0].sum())
def test_center_coordinates(self):
cell = 2.2 * np.identity(3)
NaCl = Atoms("NaCl", scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)], cell=cell)
NaCl.set_repeat([3, 3, 3])
NaCl.positions += [2.2, 2.2, 2.2]
NaCl.center_coordinates_in_unit_cell(origin=-0.5)
self.assertTrue(-0.5 <= np.min(NaCl.get_scaled_positions()))
self.assertTrue(np.max(NaCl.get_scaled_positions() < 0.5))
NaCl.center_coordinates_in_unit_cell(origin=0.0)
self.assertTrue(0 <= np.min(NaCl.positions))
self.assertTrue(np.max(NaCl.get_scaled_positions() < 1))
@unittest.skip("skip ovito because it is not installed in the test environment")
def test_analyse_ovito_cna_adaptive(self):
basis = Atoms(
"FeFe", scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)], cell=np.identity(3)
)
basis.analyse_ovito_cna_adaptive()["CommonNeighborAnalysis.counts.BCC"] == 2
@unittest.skip("skip ovito because it is not installed in the test environment")
def test_analyse_ovito_centro_symmetry(self):
basis = Atoms(
"FeFe", scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)], cell=np.identity(3)
)
self.assertTrue(
all(basis.analyse_ovito_centro_symmetry() == np.array([0.75, 0.75]))
)
@unittest.skip("skip ovito because it is not installed in the test environment")
def test_analyse_ovito_voronoi_volume(self):
basis = Atoms(
"FeFe", scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)], cell=np.identity(3)
)
self.assertTrue(
all(basis.analyse_ovito_centro_symmetry() == np.array([0.5, 0.5]))
)
@unittest.skip("skip nglview because it is not installed in the test environment")
def test_plot3d(self):
basis = Atoms(
"FeFe", scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)], cell=np.identity(3)
)
view = basis.plot3d()
@staticmethod
def test_plot3d_plotly():
basis = Atoms(
"FeFe", scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)], cell=np.identity(3)
)
basis.plot3d(mode='plotly')
def test_group_points_by_symmetry(self):
basis = Atoms("FeFe", positions=[3 * [0], 3 * [1]], cell=2 * np.eye(3))
self.assertEqual(len(basis.group_points_by_symmetry([3 * [0.5], 3 * [1.5]])), 1)
self.assertEqual(len(basis.group_points_by_symmetry([3 * [0.5], 3 * [1.4]])), 2)
def test_get_equivalent_voronoi_vertices(self):
basis = Atoms("FeFe", positions=[3 * [0], 3 * [1]], cell=2 * np.eye(3), pbc=True)
vert = basis.get_equivalent_voronoi_vertices()
self.assertEqual(len(vert), 1)
self.assertGreater(
np.min(np.linalg.norm(vert[0] - basis.positions[0], axis=-1)), 0.5
)
self.assertGreater(
np.min(np.linalg.norm(vert[0] - basis.positions[1], axis=-1)), 0.5
)
def test_find_mic(self):
cell = 0.1*(np.random.random((3,3))-0.5)+np.eye(3)
basis = Atoms("Fe", positions=[3*[0.5]], cell=cell, pbc=True)
v = 2*np.random.random(3)-1
r = np.linalg.inv(cell.T).dot(v)
r -= np.rint(r)
self.assertTrue(np.isclose(
r[0]*cell[0]+r[1]*cell[1]+r[2]*cell[2],
basis.find_mic(v, vectors=True)
).all())
for v in [np.ones(3), np.ones((3,3)), np.ones((3,3,3))]:
self.assertTrue(np.array_equal(basis.find_mic(v).shape, v.shape))
def test_get_distances_array(self):
basis = Atoms("FeFe", positions=[3*[0], 3*[0.9]], cell=np.identity(3), pbc=True)
self.assertAlmostEqual(basis.get_distances_array(mic=False)[0, 1], 0.9*np.sqrt(3))
self.assertTrue(np.allclose(basis.get_distances_array(p1=0.5*np.ones(3)),
basis.get_distances_array(p2=0.5*np.ones(3))))
self.assertTrue(np.allclose(basis.get_distances_array(vectors=True)[0, 1], -0.1*np.ones(3)))
def test_repeat_points(self):
basis = Atoms("Fe", positions=np.random.rand(3).reshape(-1, 3), cell=np.identity(3))
basis.cell[0, 1] = 0.01
with self.assertRaises(ValueError):
basis.repeat_points([0, 0, 0], [2 ,2])
with self.assertRaises(ValueError):
basis.repeat_points([0, 0], 2)
v = np.random.rand(3)
w = basis.repeat_points(v, 3)
v += np.array([1, 0.01, 0])
self.assertAlmostEqual(np.linalg.norm(w-v, axis=-1).min(), 0)
v = np.random.rand(6).reshape(-1, 3)
self.assertEqual(basis.repeat_points(v, 2).shape, (8, 2, 3))
def test_get_extended_positions(self):
basis = Atoms("FeFe", positions=[[0.01, 0, 0], [0.5, 0.5, 0.5]], cell=np.identity(3), pbc=True)
with self.assertRaises(ValueError):
basis.get_extended_positions(-0.1)
self.assertTrue(np.array_equal(basis.get_extended_positions(0), basis.positions))
def test_get_equivalent_points(self):
basis = Atoms("FeFe", positions=[[0.01, 0, 0], [0.5, 0.5, 0.5]], cell=np.identity(3))
arr = basis.get_equivalent_points([0, 0, 0.5])
self.assertAlmostEqual(np.linalg.norm(arr-np.array([0.51, 0.5, 0]), axis=-1).min(), 0)
def test_cluster_analysis(self):
basis = CrystalStructure("Al", bravais_basis="fcc", lattice_constants=4.2).repeat(10)
key, counts = basis.cluster_analysis(id_list=[0,1], return_cluster_sizes=True)
self.assertTrue(np.array_equal(key[1], [0,1]))
self.assertEqual(counts[0], 2)
key, counts = basis.cluster_analysis(id_list=[0,int(len(basis)/2)], return_cluster_sizes=True)
self.assertTrue(np.array_equal(key[1], [0]))
self.assertEqual(counts[0], 1)
def test_get_bonds(self):
basis = CrystalStructure("Al", bravais_basis="fcc", lattice_constants=4.2).repeat(5)
bonds = basis.get_bonds()
neigh = basis.get_neighbors()
self.assertTrue(np.array_equal(np.sort(bonds[0]['Al'][0]),
np.sort(neigh.indices[0, neigh.shells[0]==1])))
def test_get_symmetr(self):
cell = 2.2 * np.identity(3)
Al = Atoms("AlAl", scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)], cell=cell)
with self.assertRaises(ValueError):
Al.symmetrize_vectors(1)
v = np.random.rand(6).reshape(-1, 3)
self.assertAlmostEqual(np.linalg.norm(Al.symmetrize_vectors(v)), 0)
Al.positions[0,0] += 0.01
w = Al.symmetrize_vectors(v, force_update=True)
self.assertAlmostEqual(np.absolute(w[:,0]).sum(), np.linalg.norm(w, axis=-1).sum())
def test_get_symmetry(self):
cell = 2.2 * np.identity(3)
Al = Atoms("AlAl", positions=[(0, 0, 0), (0.5, 0.5, 0.5)], cell=cell).repeat(2)
self.assertEqual(len(set(Al.get_symmetry()["equivalent_atoms"])), 1)
self.assertEqual(len(Al.get_symmetry()["translations"]), 96)
self.assertEqual(
len(Al.get_symmetry()["translations"]), len(Al.get_symmetry()["rotations"])
)
def test_get_voronoi_vertices(self):
cell = 2.2 * np.identity(3)
Al = Atoms("AlAl", scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)], cell=cell, pbc=True)
pos, box = Al._get_voronoi_vertices()
self.assertEqual(len(pos), 14)
def test_get_parent_symbols(self):
self.assertTrue(np.array_equal(self.CO2.get_parent_symbols(), ["C", "O", "O"]))
self.assertTrue(
np.array_equal(
self.CO2.get_parent_symbols(), self.CO2.get_chemical_symbols()
)
)
cell = np.eye(3) * 10.0
pse = PeriodicTable()
pse.add_element("O", "O_up", spin="up")
o_up = pse.element("O_up")
basis = Atoms([o_up], scaled_positions=[[0.27, 0.27, 0.27]], cell=cell)
self.assertTrue(np.array_equal(basis.get_parent_symbols(), ["O"]))
self.assertFalse(
np.array_equal(basis.get_parent_symbols(), basis.get_chemical_symbols())
)
def test_get_chemical_symbols(self):
self.assertTrue(
np.array_equal(self.CO2.get_chemical_symbols(), ["C", "O", "O"])
)
cell = np.eye(3) * 10.0
pse = PeriodicTable()
pse.add_element("O", "O_up", spin="up")
o_up = pse.element("O_up")
basis = Atoms([o_up], scaled_positions=[[0.27, 0.27, 0.27]], cell=cell)
self.assertTrue(np.array_equal(basis.get_chemical_symbols(), ["O_up"]))
def test_get_symmetry_dataset(self):
cell = 2.2 * np.identity(3)
Al_sc = Atoms("AlAl", scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)], cell=cell)
Al_sc.set_repeat([2, 2, 2])
self.assertEqual(Al_sc.get_symmetry_dataset()["number"], 229)
def test_get_space_group(self):
cell = 2.2 * np.identity(3)
Al_sc = Atoms("AlAl", scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)], cell=cell)
self.assertEqual(Al_sc.get_spacegroup()["InternationalTableSymbol"], "Im-3m")
self.assertEqual(Al_sc.get_spacegroup()["Number"], 229)
cell = 4.2 * (0.5 * np.ones((3, 3)) - 0.5 * np.eye(3))
Al_fcc = Atoms("Al", scaled_positions=[(0, 0, 0)], cell=cell)
self.assertEqual(Al_fcc.get_spacegroup()["InternationalTableSymbol"], "Fm-3m")
self.assertEqual(Al_fcc.get_spacegroup()["Number"], 225)
a = 3.18
c = 1.623 * a
cell = np.eye(3)
cell[0, 0] = a
cell[2, 2] = c
cell[1, 0] = -a / 2.0