def test_cubic_unit_cell_should_return_cubic_vertices_without_vector_calculation(
):
expected_vertices = [[0.00000, 0.00000, 0.00000],
[18.6400, 0.00000, 0.00000],
[0.00000, 18.6400, 0.00000],
[0.00000, 0.00000, 18.6400],
[18.6400, 18.6400, 0.00000],
[0.00000, 18.6400, 18.6400],
[18.6400, 0.00000, 18.6400],
[18.6400, 18.6400, 18.6400]]
cell = Cell([18.6400, 18.6400, 18.6400, 90.0, 90.0, 90.0])
cell.calculate_vertices()
assert np.allclose(cell.vertices, expected_vertices)
def test_triclinic_unit_cell_should_return_triclinic_vectors():
# Parameters for UVARIT_clean from CoRE database and expected results from Avogadro
expected_vectors = [[8.40900, 0.00000, 0.00000],
[2.09071, 13.32498, 0.00000],
[1.04535, 6.66249, 12.41697]]
cell = Cell([8.40900, 13.48800, 14.13020, 61.49240, 85.75740, 81.08290])
assert np.allclose(cell.vectors, expected_vectors)
def test_monoclinic_unit_cell_should_return_monoclinic_vectors():
# Parameters for OJAKOA_clean from CoRE database and expected results from Avogadro
expected_vectors = [[9.01670, 0.00000, 0.00000],
[-3.61984, 14.69194, 0.00000],
[0.00000, 0.00000, 16.82840]]
cell = Cell([9.01670, 15.13130, 16.82840, 90.00000, 90.00000, 103.84100])
assert np.allclose(cell.vectors, expected_vectors)
def test_hexagonal_unit_cell_should_return_hexagonal_vectors():
# Parameters for cm301726k_si_004_clean from CoRE database and expected results from Avogadro
expected_vectors = [[12.57380, 0.00000, 0.00000],
[-6.2869, 10.88923, 0.00000],
[0.00000, 0.00000, 14.33400]]
cell = Cell([12.57380, 12.57380, 14.33400, 90.00000, 90.00000, 120.00000])
assert np.allclose(cell.vectors, expected_vectors)
def test_tetragonal_unit_cell_should_return_tetragonal_vectors():
# Parameters for LAVTOT_clean from CoRE database and expected results from Avogadro
expected_vectors = [[10.26700, 0.00000, 0.00000],
[0.00000, 10.26700, 0.00000],
[0.00000, 0.00000, 14.46200]]
cell = Cell([10.26700, 10.26700, 14.46200, 90.0, 90.0, 90.0])
assert np.allclose(cell.vectors, expected_vectors)
def test_cubic_unit_cell_should_return_cubic_vectors():
# Parameters for ECOLEP_clean from CoRE database and expected results from Avogadro
expected_vectors = [[18.64000, 0.00000, 0.00000],
[0.00000, 18.64000, 0.00000],
[0.00000, 0.00000, 18.64000]]
cell = Cell([18.64000, 18.64000, 18.64000, 90.0, 90.0, 90.0])
assert np.allclose(cell.vectors, expected_vectors)
def test_trigonal_unit_cell_should_return_correct_cell_volume():
# Parameters for MIHHER_clean from CoRE database and expected results from Avogadro
expected_volume = 23506.4
cell = Cell([32.15390, 32.15390, 32.15390, 60.0, 60.0, 60.0])
assert np.isclose(cell.volume, expected_volume)
assert np.isclose(cell.frac_volume,
cell.volume / (cell.a * cell.b * cell.c))
def test_orthorhombic_unit_cell_should_return_orthorhombic_vectors():
# Parameters for MOGYAI_clean from CoRE database and expected results from Avogadro
expected_vectors = [[10.55690, 0.00000, 0.00000],
[0.00000, 14.84590, 0.00000],
[0.00000, 0.00000, 19.06630]]
cell = Cell([10.55690, 14.84590, 19.06630, 90.0, 90.0, 90.0])
assert np.allclose(cell.vectors, expected_vectors)
def test_triclinic_unit_cell_should_return_correct_cell_volume():
# Parameters for UVARIT_clean from CoRE database and expected results from Avogadro
expected_volume = 1391.32
cell = Cell([8.40900, 13.48800, 14.13020, 61.49240, 85.75740, 81.08290])
assert np.isclose(cell.volume, expected_volume)
assert np.isclose(cell.frac_volume,
cell.volume / (cell.a * cell.b * cell.c))
def test_monoclinic_unit_cell_should_return_correct_cell_volume():
# Parameters for OJAKOA_clean from CoRE database and expected results from Avogadro
expected_volume = 2229.31
cell = Cell([9.01670, 15.13130, 16.82840, 90.00000, 90.00000, 103.84100])
assert np.isclose(cell.volume, expected_volume)
assert np.isclose(cell.frac_volume,
cell.volume / (cell.a * cell.b * cell.c))
def test_hexagonal_unit_cell_should_return_correct_cell_volume():
# Parameters for cm301726k_si_004_clean from CoRE database and expected results from Avogadro
expected_volume = 1962.6
cell = Cell([12.57380, 12.57380, 14.33400, 90.00000, 90.00000, 120.00000])
assert np.isclose(cell.volume, expected_volume)
assert np.isclose(cell.frac_volume,
cell.volume / (cell.a * cell.b * cell.c))
def test_trigonal_unit_cell_should_return_trigonal_vectors():
# Parameters for MIHHER_clean from CoRE database and expected results from Avogadro
expected_vectors = [[32.15390, 0.00000, 0.00000],
[16.07695, 27.84609, 0.00000],
[16.07695, 9.28203, 26.25355]]
cell = Cell([32.15390, 32.15390, 32.15390, 60.0, 60.0, 60.0])
assert np.allclose(cell.vectors, expected_vectors)
def test_cubic_unit_cell_pbc():
cell = Cell([10, 10, 10, 90.0, 90.0, 90.0])
assert np.allclose([2, 2, 2], cell.car2frac([20, 20, 20]))
assert np.allclose([20, 20, 20], cell.frac2car([2, 2, 2]))
def packmol_config(structure_path, gas_path, output_path, num_molecules, boundary_tolerance, a2a_tolerance, supercell):
"""
Two tolerances: (1) boundary_tolerance is the minimum distance between a gas molecule and one of
the planes defining the boundary, (2) a2a_tolerance is the atom-to-atom tolerance defining the
minimum distance between any two atoms.
"""
cell = Cell(supercell)
cell.calculate_vertices()
pts = cell.vertices
# would typically use vertices of (0,1,3), (2,4,5), (0,3,2), (1,6,4), (0,1,2), (3,5,6)
# but only need the second in each pair because the planes are parallel. Since the first plane
# will always have d = 0, we only need the second plane to define the triclinic bounds.
# We can then bound the box using each plane twice, one where the plane > 0 and one where
# the plane < d. Since we are normalizing the plane coefficients so that d is equal to the
# appropriate unit cell lengths, d should be in units of angstroms. We can then add a tolerance
# by just using plane > 1 or plane < d - 1 (for a one angstrom tolerance).
plane_coefficients = []
p = Plane(pts[2], pts[4], pts[5])
n = p.d / cell.b # normalize by length of b
a, b, c, d = (p.a / n, p.b / n, p.c / n, p.d / n)
print("Using plane: %+.2fx %+.2fy %+.2fz = %.2f" % (a, b, c, d))
plane_coefficients += [a, b, c, 0 + boundary_tolerance, a, b, c, d - boundary_tolerance]
p = Plane(pts[1], pts[6], pts[4])
n = p.d / cell.a # normalize by length of a
a, b, c, d = (p.a / n, p.b / n, p.c / n, p.d / n)
print("Using plane: %+.2fx %+.2fy %+.2fz = %.2f" % (a, b, c, d))
plane_coefficients += [a, b, c, 0 + boundary_tolerance, a, b, c, d - boundary_tolerance]
p = Plane(pts[3], pts[5], pts[6])
n = p.d / cell.c # normalize by length of c
a, b, c, d = (p.a / n, p.b / n, p.c / n, p.d / n)
print("Using plane: %+.2fx %+.2fy %+.2fz = %.2f" % (a, b, c, d))
plane_coefficients += [a, b, c, 0 + boundary_tolerance, a, b, c, d - boundary_tolerance]
random_seed = random.randint(0,999999999)
s = """
tolerance %10.5f
seed %d
output %s
filetype xyz
structure %s
filetype xyz
number 1
fixed 0 0 0 0 0 0
end structure
structure %s
number %d
over plane %10.5f %10.5f %10.5f %10.5f
below plane %10.5f %10.5f %10.5f %10.5f
over plane %10.5f %10.5f %10.5f %10.5f
below plane %10.5f %10.5f %10.5f %10.5f
over plane %10.5f %10.5f %10.5f %10.5f
below plane %10.5f %10.5f %10.5f %10.5f
end structure
""" % (a2a_tolerance, random_seed, output_path, structure_path, gas_path, num_molecules, *plane_coefficients)
return s
def test_cubic_unit_cell_should_return_correct_cell_volume():
# Parameters for ECOLEP_clean from CoRE database and expected results from Avogadro
expected_volume = 6476.46
cell = Cell([18.64000, 18.64000, 18.64000, 90.0, 90.0, 90.0])
assert np.isclose(cell.volume, expected_volume)
assert np.isclose(cell.frac_volume, 1)
def test_tetragonal_unit_cell_should_return_correct_cell_volume():
# Parameters for LAVTOT_clean from CoRE database and expected results from Avogadro
expected_volume = 1524.46
cell = Cell([10.26700, 10.26700, 14.46200, 90.0, 90.0, 90.0])
assert np.isclose(cell.volume, expected_volume)
assert np.isclose(cell.frac_volume, 1)
def test_orthorhombic_unit_cell_should_return_correct_cell_volume():
# Parameters for MOGYAI_clean from CoRE database and expected results from Avogadro
expected_volume = 2988.2
cell = Cell([10.55690, 14.84590, 19.06630, 90.0, 90.0, 90.0])
assert np.isclose(cell.volume, expected_volume)
assert np.isclose(cell.frac_volume, 1)