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Minor clean-up

This commit is contained in:
Atsushi Togo 2018-06-13 15:29:31 +02:00
parent 95ac66c680
commit f12122dc9f
1 changed files with 16 additions and 15 deletions
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31
phonopy/structure/cells.py
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@ -491,16 +491,15 @@ def get_reduced_bases(lattice,
def _get_smallest_vectors(supercell, primitive, symprec=1e-5):
p2s_map = primitive.get_primitive_to_supercell_map()
s_pos = supercell.get_scaled_positions()
p_pos = s_pos[list(p2s_map)]
supercell_pos = supercell.get_scaled_positions()
primitive_pos = supercell_pos[p2s_map]
supercell_bases = supercell.get_cell()
primitive_bases = primitive.get_cell()
svecs, multi = get_smallest_vectors(
supercell_bases, s_pos, p_pos, symprec=symprec)
svecs = np.array(np.dot(svecs,
np.dot(supercell_bases,
np.linalg.inv(primitive_bases))),
dtype='double', order='C')
supercell_bases, supercell_pos, primitive_pos, symprec=symprec)
svecs = np.array(
np.dot(svecs, np.dot(supercell_bases, np.linalg.inv(primitive_bases))),
dtype='double', order='C')
return svecs, multi
def get_smallest_vectors(supercell_bases,
@ -526,7 +525,7 @@ def get_smallest_vectors(supercell_bases,
supercell_bases : ndarray
Supercell basis vectors as row vectors, (a, b, c)^T. Must be order='C'.
dtype='double'
shape=(3,3)
shape=(3, 3)
supercell_pos : array_like
Atomic positions in fractional coordinates of supercell.
dtype='double'
@ -554,13 +553,17 @@ def get_smallest_vectors(supercell_bases,
"""
reduced_bases = get_reduced_bases(supercell_bases, tolerance=symprec)
trans_mat_float = np.dot(supercell_bases, np.linalg.inv(reduced_bases))
trans_mat = np.rint(trans_mat_float).astype(int)
assert (np.abs(trans_mat_float - trans_mat) < 1e-8).all()
trans_mat_inv_float = np.linalg.inv(trans_mat)
trans_mat_inv = np.rint(trans_mat_inv_float).astype(int)
assert (np.abs(trans_mat_inv_float - trans_mat_inv) < 1e-8).all()
# Reduce all positions into the cell formed by the reduced bases.
supercell_fracs = np.dot(np.dot(supercell_pos, supercell_bases),
np.linalg.inv(reduced_bases))
supercell_fracs = np.dot(supercell_pos, trans_mat)
supercell_fracs -= np.rint(supercell_fracs)
primitive_fracs = np.dot(np.dot(primitive_pos, supercell_bases),
np.linalg.inv(reduced_bases))
primitive_fracs = np.dot(primitive_pos, trans_mat)
primitive_fracs -= np.rint(primitive_fracs)
# For each vector, we will need to consider all nearby images in the reduced bases.
@ -607,9 +610,7 @@ def get_smallest_vectors(supercell_bases,
# by the primitive cell.
#
# shape: (size_super, size_prim, 27, 3)
candidate_vectors = np.array(np.dot(
candidate_fracs,
reduced_bases.dot(np.linalg.inv(supercell_bases))),
candidate_vectors = np.array(np.dot(candidate_fracs, trans_mat_inv),
dtype='double', order='C')
# The last final bits are done in C.