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forcefit displacement matrix implementation in C

This commit is contained in:
Atsushi Togo 2013-08-26 22:42:44 +09:00
parent d6ac90f7d6
commit 62aa1645d0
2 changed files with 19 additions and 16 deletions
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19
anharmonic/force_fit/fc4.py
View File

@ -101,8 +101,9 @@ class FC4Fit:
site_syms_cart = np.double([similarity_transformation(self._lattice, sym)
for sym in site_symmetry])
triplets_c, num_triplets = self._create_displacement_triplets_for_c(
disp_triplets)
(disp_triplets_rearranged,
num_triplets) = self._create_displacement_triplets_for_c(disp_triplets)
max_num_disp = np.amax(num_triplets[:, :, :, 1])
for second_atom_num in range(self._num_atom):
print second_atom_num + 1
@ -114,10 +115,11 @@ class FC4Fit:
rot_disps_set.append(self._create_displacement_matrix_c(
second_atom_num,
third_atom_num,
triplets_c,
disp_triplets_rearranged,
num_triplets,
site_syms_cart,
rot_map_syms))
rot_map_syms,
max_num_disp))
except ImportError:
rot_disps_set.append(self._create_displacement_matrix(
second_atom_num,
@ -167,7 +169,6 @@ class FC4Fit:
column_num,
1e-13,
info)
inv_disps_set = []
inv_disps_set = [
inv_disps[i, :row_nums[i] * column_num].reshape(column_num, -1)
for i in range(self._num_atom)]
@ -250,11 +251,13 @@ class FC4Fit:
disp_triplets,
num_disps,
site_syms_cart,
rot_map_syms):
rot_map_syms,
max_num_disp):
import anharmonic._forcefit as forcefit
num_row_elem = 27 * 10 + 9 * 6 + 3 * 3 + 1
disp_matrix_tmp = np.zeros((len(disp_triplets) * len(site_syms_cart),
num_row_elem), dtype='double')
disp_matrix_tmp = np.zeros(
(len(num_disps) * max_num_disp * len(site_syms_cart), num_row_elem),
dtype='double')
num_elems = forcefit.displacement_matrix_fc4(disp_matrix_tmp,
second_atom_num,
third_atom_num,

16
c/_forcefit.c
View File

@ -5,7 +5,7 @@
static PyObject * py_phonopy_pinv(PyObject *self, PyObject *args);
static PyObject * py_phonopy_pinv_mt(PyObject *self, PyObject *args);
static PyObject * py_displacement_matrix_fc4(PyObject *self, PyObject *args);
void get_tensor1(double sym_u[9], const double u[9], const double *sym);
void get_tensor1(double sym_u[9], const double *u, const double *sym);
int set_tensor2(double *disp_matrix, const double u[9]);
int set_tensor3(double *disp_matrix, const double u[9]);
@ -115,7 +115,7 @@ static PyObject * py_displacement_matrix_fc4(PyObject *self, PyObject *args)
const int *rot_map_syms = (int*)rot_map_syms_py->data;
int i, j, k, l, rot_num2, rot_num3, address, num_disp, count;
double u[9], sym_u[9];
double sym_u[9];
count = 0;
for (i = 0; i < num_first_disps; i++) {
@ -131,10 +131,9 @@ static PyObject * py_displacement_matrix_fc4(PyObject *self, PyObject *args)
for (k = 0; k < num_disp; k++) {
disp_matrix[count] = -1;
count++;
for (l = 0; l < 9; l++) {
u[l] = disp_triplets[address + k * 9 + l];
}
get_tensor1(sym_u, u, site_syms_cart + j * 9);
get_tensor1(sym_u,
disp_triplets + (address + k) * 9,
site_syms_cart + j * 9);
for (l = 0; l < 9; l++) {
disp_matrix[count] = sym_u[l];
count++;
@ -147,14 +146,15 @@ static PyObject * py_displacement_matrix_fc4(PyObject *self, PyObject *args)
return PyInt_FromLong((long) count);
}
void get_tensor1(double sym_u[9], const double u[9], const double *sym)
void get_tensor1(double sym_u[9], const double *u, const double *sym)
{
int i, j, k;
for (i = 0; i < 3; i++) {
for (j = 0; j < 3; j++) {
sym_u[i * 3 + j] = 0;
for (k = 0; k < 3; k++) {
sym_u[i * 3 + j] = sym[j * 3 + k] * u[i * 3 + k];
sym_u[i * 3 + j] += sym[j * 3 + k] * u[i * 3 + k];
}
}
}