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# fmt: off
"""Test Prism"""
from math import sqrt
import numpy as np
import pytest
from ase import Atoms
from ase.calculators.lammps import Prism
from ase.calculators.lammps.coordinatetransform import (
calc_box_parameters,
calc_reduced_cell,
)
def make_array(structure: str) -> np.ndarray:
"""Make array for the given structure"""
if structure == "sc":
array = np.array([
[1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, 0.0, 1.0],
])
elif structure == "bcc":
array = np.array([
[-0.5, +0.5, +0.5],
[+0.5, -0.5, +0.5],
[+0.5, +0.5, -0.5],
])
elif structure == "fcc":
array = np.array([
[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.0],
])
elif structure == "hcp":
covera = sqrt(8.0 / 3.0)
array = np.array([
[0.5, -0.5 * sqrt(3.0), 0.0],
[0.5, +0.5 * sqrt(3.0), 0.0],
[0.0, 0.0, covera],
])
else:
raise ValueError(structure)
return array
class TestCalcBoxParameters:
"""Test calc_box_parameters"""
def test_sc(self):
"""Test sc"""
array = make_array("sc")
box = calc_box_parameters(array)
box_ref = np.array([1.0, 1.0, 1.0, 0.0, 0.0, 0.0])
np.testing.assert_allclose(box, box_ref)
def test_bcc(self):
"""Test bcc"""
array = make_array("bcc")
box = calc_box_parameters(array)
box_ref = np.array([
+0.8660254038, # +sqrt(3) / 2
+0.8164965809, # +sqrt(6) / 3
+0.7071067812, # +sqrt(2) / 2
-0.2886751346, # -sqrt(3) / 6
-0.2886751346, # -sqrt(3) / 6
-0.4082482905, # -sqrt(6) / 6
])
np.testing.assert_allclose(box, box_ref)
def test_fcc(self):
"""Test fcc"""
array = make_array("fcc")
box = calc_box_parameters(array)
box_ref = np.array([
+0.7071067812, # +sqrt(2) / 2
+0.6123724357, # +sqrt(6) / 4
+0.5773502692, # +sqrt(3) / 3
+0.3535533906, # +sqrt(2) / 4
+0.3535533906, # +sqrt(2) / 4
+0.2041241452, # +sqrt(6) / 12
])
np.testing.assert_allclose(box, box_ref)
def test_hcp(self):
"""Test hcp"""
covera = sqrt(8.0 / 3.0)
array = make_array("hcp")
box = calc_box_parameters(array)
box_ref = np.array([1.0, 0.5 * sqrt(3.0), covera, -0.5, 0.0, 0.0])
np.testing.assert_allclose(box, box_ref)
class TestReducedCell:
"""Test reduced cell"""
def test_small(self):
"""Test small tilt"""
original = ((3.0, 0.0, 0.0), (-1.0, 3.0, 0.0), (0.0, 0.0, 3.0))
reduced_ref = ((3.0, 0.0, 0.0), (-1.0, 3.0, 0.0), (0.0, 0.0, 3.0))
self.check(original, reduced_ref)
def test_large(self):
"""Test large tilt"""
original = ((3.0, 0.0, 0.0), (2.0, 3.0, 0.0), (0.0, 0.0, 3.0))
reduced_ref = ((3.0, 0.0, 0.0), (-1.0, 3.0, 0.0), (0.0, 0.0, 3.0))
self.check(original, reduced_ref)
def test_very_large(self):
"""Test very large tilt"""
original = ((3.0, 0.0, 0.0), (5.0, 3.0, 0.0), (0.0, 0.0, 3.0))
reduced_ref = ((3.0, 0.0, 0.0), (-1.0, 3.0, 0.0), (0.0, 0.0, 3.0))
self.check(original, reduced_ref)
def test_xz_and_yz_0(self):
"""Test if the update of yz also modifies xz correctly"""
original = ((3.0, 0.0, 0.0), (1.0, 3.0, 0.0), (0.0, 2.0, 3.0))
# The third vector should be updated as c -> c - b
reduced_ref = ((3.0, 0.0, 0.0), (1.0, 3.0, 0.0), (-1.0, -1.0, 3.0))
self.check(original, reduced_ref)
def test_xz_and_yz_1(self):
"""Test if the update of yz also modifies xz correctly"""
original = ((3.0, 0.0, 0.0), (1.0, 3.0, 0.0), (-1.0, 2.0, 3.0))
# The third vector should be updated as c -> c - b -> c - b + a
reduced_ref = ((3.0, 0.0, 0.0), (1.0, 3.0, 0.0), (1.0, -1.0, 3.0))
self.check(original, reduced_ref)
def check(self, original: np.ndarray, reduced_ref: np.ndarray):
"""Check"""
reduced = calc_reduced_cell(np.array(original), pbc=(True, True, True))
np.testing.assert_allclose(reduced, reduced_ref)
@pytest.mark.parametrize("wrap", (False, True))
@pytest.mark.parametrize("reduce_cell", (False, True))
@pytest.mark.parametrize("pbc", (False, True))
@pytest.mark.parametrize("structure", ("sc", "bcc", "fcc", "hcp"))
def test_vectors(structure: str, pbc: bool, reduce_cell: bool, wrap: bool):
"""Test if vector conversion works as expected"""
array = make_array(structure)
rng = np.random.default_rng(42)
positions = 20.0 * rng.random((10, 3)) - 10.0
atoms = Atoms(positions=positions, cell=array, pbc=pbc)
prism = Prism(array, pbc=pbc, reduce_cell=reduce_cell)
vectors_ref = atoms.get_positions(wrap=(wrap or reduce_cell))
vectors = prism.vector_to_lammps(vectors_ref, wrap=wrap)
vectors = prism.vector_to_ase(vectors, wrap=wrap)
np.testing.assert_allclose(vectors, vectors_ref)
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