def test_cubic_unit_cell_should_return_cubic_vertices_with_vector_calculation(
):
expected_vertices = [[0.0000, 0.0000, 0.0000], [8.4000, 0.0000, 0.0000],
[0.0000, 8.4000, 0.0000], [0.0000, 0.0000, 8.4000],
[8.4000, 8.4000, 0.0000], [0.0000, 8.4000, 8.4000],
[8.4000, 0.0000, 8.4000], [8.4000, 8.4000, 8.4000]]
cell = Cell([8.4000, 8.4000, 8.4000, 90.0, 90.0, 90.0])
cell.calculate_vectors()
cell.calculate_vertices()
assert np.allclose(cell.vertices, expected_vertices)
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