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Iteration loop is made to loosen crystal structure geometry tolerance until match for finding atomic permutation by symmetry

This commit is contained in:
Atsushi Togo 2019-10-12 13:21:43 +09:00
parent fb5254a90e
commit 61f29b8a51
2 changed files with 24 additions and 7 deletions
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7
c/_phonopy.c
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@ -358,7 +358,11 @@ static PyObject * py_compute_permutation(PyObject *self, PyObject *args)
num_pos,
symprec);
return Py_BuildValue("i", is_found);
if (is_found) {
Py_RETURN_TRUE;
} else {
Py_RETURN_FALSE;
}
}
static PyObject * py_gsv_copy_smallest_vectors(PyObject *self, PyObject *args)
@ -1563,7 +1567,6 @@ static int compute_permutation(int * rot_atom,
for (i = 0; i < num_pos; i++) {
if (rot_atom[i] < 0) {
printf("Encounter some problem in compute_permutation.\n");
return 0;
}
}

24
phonopy/structure/cells.py
View File

@ -857,11 +857,25 @@ def _compute_permutation_c(positions_a, # scaled positions
try:
import phonopy._phonopy as phonoc
is_found = phonoc.compute_permutation(permutation,
lattice,
positions_a,
positions_b,
symprec)
tolerance = symprec
for _ in range(20):
is_found = phonoc.compute_permutation(permutation,
lattice,
positions_a,
positions_b,
tolerance)
if is_found:
break
else:
tolerance *= 1.05
if tolerance / symprec > 1.5:
import warnings
msg = ("Crystal structure is distorted in a tricky way so that "
"phonopy could not handle the crystal symmetry properly. "
"It is recommended to symmetrize crystal structure well "
"and then re-start phonon calculation from scratch.")
warnings.warn(msg)
if not is_found:
permutation_error()