mirror of https://github.com/phonopy/phono3py.git
Fix distance calculation in BZ
This commit is contained in:
Atsushi Togo
parent
2d30f9baf0
commit
71bb34aa4a
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@ -804,13 +804,11 @@ int64_t py_tpl_get_triplets_reciprocal_mesh_at_q(
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return num_ir;
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}
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int64_t py_tpl_get_BZ_triplets_at_q(nb::ndarray<> py_triplets,
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int64_t grid_point,
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nb::ndarray<> py_bz_grid_address,
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nb::ndarray<> py_bz_map,
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nb::ndarray<> py_map_triplets,
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nb::ndarray<> py_D_diag, nb::ndarray<> py_Q,
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int64_t bz_grid_type) {
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int64_t py_tpl_get_BZ_triplets_at_q(
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nb::ndarray<> py_triplets, int64_t grid_point,
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nb::ndarray<> py_bz_grid_address, nb::ndarray<> py_bz_map,
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nb::ndarray<> py_map_triplets, nb::ndarray<> py_D_diag, nb::ndarray<> py_Q,
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nb::ndarray<> py_reciprocal_lattice, int64_t bz_grid_type) {
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int64_t (*triplets)[3];
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int64_t (*bz_grid_address)[3];
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int64_t *bz_map;
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@ -818,6 +816,7 @@ int64_t py_tpl_get_BZ_triplets_at_q(nb::ndarray<> py_triplets,
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int64_t num_map_triplets;
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int64_t *D_diag;
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int64_t (*Q)[3];
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double (*reciprocal_lattice)[3];
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int64_t num_ir;
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triplets = (int64_t (*)[3])py_triplets.data();
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@ -827,10 +826,11 @@ int64_t py_tpl_get_BZ_triplets_at_q(nb::ndarray<> py_triplets,
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num_map_triplets = (int64_t)py_map_triplets.shape(0);
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D_diag = (int64_t *)py_D_diag.data();
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Q = (int64_t (*)[3])py_Q.data();
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reciprocal_lattice = (double (*)[3])py_reciprocal_lattice.data();
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num_ir = ph3py_get_BZ_triplets_at_q(triplets, grid_point, bz_grid_address,
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bz_map, map_triplets, num_map_triplets,
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D_diag, Q, bz_grid_type);
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num_ir = ph3py_get_BZ_triplets_at_q(
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triplets, grid_point, bz_grid_address, bz_map, map_triplets,
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num_map_triplets, D_diag, Q, reciprocal_lattice, bz_grid_type);
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return num_ir;
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}
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@ -138,7 +138,7 @@ int64_t gridsys_get_bz_grid_addresses(
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if (!niggli_reduce(niggli_lattice, GRIDSYS_NIGGLI_TOLERANCE)) {
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return 0;
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}
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if (!lagmat_inverse_matrix_d3(inv_Lr, (double(*)[3])niggli_lattice,
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if (!lagmat_inverse_matrix_d3(inv_Lr, (double (*)[3])niggli_lattice,
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GRIDSYS_NIGGLI_TOLERANCE)) {
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return 0;
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}
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@ -156,7 +156,7 @@ int64_t gridsys_get_bz_grid_addresses(
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bzgrid->bzg2grg = bzg2grg;
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bzgrid->type = bz_grid_type;
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lagmat_multiply_matrix_l3(bzgrid->Q, inv_Mpr_int, Q);
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lagmat_copy_matrix_d3(bzgrid->reclat, (double(*)[3])niggli_lattice);
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lagmat_copy_matrix_d3(bzgrid->reclat, (double (*)[3])niggli_lattice);
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for (i = 0; i < 3; i++) {
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bzgrid->D_diag[i] = D_diag[i];
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bzgrid->PS[i] = PS[i];
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@ -220,7 +220,7 @@ int64_t gridsys_get_bz_triplets_at_q(
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const int64_t (*bz_grid_addresses)[3], const int64_t *bz_map,
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const int64_t *map_triplets, const int64_t num_map_triplets,
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const int64_t D_diag[3], const int64_t Q[3][3],
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const int64_t bz_grid_type) {
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const double reciprocal_lattice[3][3], const int64_t bz_grid_type) {
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RecgridConstBZGrid *bzgrid;
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int64_t i, j, num_ir;
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@ -237,6 +237,7 @@ int64_t gridsys_get_bz_triplets_at_q(
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bzgrid->D_diag[i] = D_diag[i];
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bzgrid->PS[i] = 0;
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for (j = 0; j < 3; j++) {
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bzgrid->reclat[i][j] = reciprocal_lattice[i][j];
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bzgrid->Q[i][j] = Q[i][j];
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}
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}
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@ -272,7 +272,8 @@ int64_t gridsys_get_bz_triplets_at_q(
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int64_t (*ir_triplets)[3], const int64_t bz_grid_index,
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const int64_t (*bz_grid_addresses)[3], const int64_t *bz_map,
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const int64_t *map_triplets, const int64_t num_map_triplets,
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const int64_t D_diag[3], const int64_t Q[3][3], const int64_t bz_grid_type);
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const int64_t D_diag[3], const int64_t Q[3][3],
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const double reciprocal_lattice[3][3], const int64_t bz_grid_type);
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/**
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* @brief Return integration weight of linear tetrahedron method
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@ -411,7 +411,7 @@ int64_t ph3py_get_BZ_triplets_at_q(
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const int64_t (*bz_grid_addresses)[3], const int64_t *bz_map,
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const int64_t *map_triplets, const int64_t num_map_triplets,
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const int64_t D_diag[3], const int64_t Q[3][3],
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const int64_t bz_grid_type) {
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const double reciprocal_lattice[3][3], const int64_t bz_grid_type) {
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RecgridConstBZGrid *bzgrid;
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int64_t i, j, num_ir;
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@ -429,6 +429,7 @@ int64_t ph3py_get_BZ_triplets_at_q(
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bzgrid->PS[i] = 0;
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for (j = 0; j < 3; j++) {
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bzgrid->Q[i][j] = Q[i][j];
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bzgrid->reclat[i][j] = reciprocal_lattice[i][j];
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}
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}
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bzgrid->size = num_map_triplets;
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@ -173,7 +173,8 @@ int64_t ph3py_get_BZ_triplets_at_q(
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int64_t (*triplets)[3], const int64_t grid_point,
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const int64_t (*bz_grid_addresses)[3], const int64_t *bz_map,
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const int64_t *map_triplets, const int64_t num_map_triplets,
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const int64_t D_diag[3], const int64_t Q[3][3], const int64_t bz_grid_type);
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const int64_t D_diag[3], const int64_t Q[3][3],
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const double reciprocal_lattice[3][3], const int64_t bz_grid_type);
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int64_t ph3py_get_integration_weight(
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double *iw, char *iw_zero, const double *frequency_points,
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const int64_t num_band0, const int64_t relative_grid_address[24][4][3],
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13
c/recgrid.c
13
c/recgrid.c
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@ -193,20 +193,11 @@ double recgrid_get_tolerance_for_BZ_reduction(const RecgridBZGrid *bzgrid) {
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int64_t i, j;
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double tolerance;
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double length[3];
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double reclatQ[3][3];
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for (i = 0; i < 3; i++) {
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for (j = 0; j < 3; j++) {
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reclatQ[i][j] = bzgrid->reclat[i][0] * bzgrid->Q[0][j] +
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bzgrid->reclat[i][1] * bzgrid->Q[1][j] +
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bzgrid->reclat[i][2] * bzgrid->Q[2][j];
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}
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}
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for (i = 0; i < 3; i++) {
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length[i] = 0;
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for (j = 0; j < 3; j++) {
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length[i] += reclatQ[j][i] * reclatQ[j][i];
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length[i] += bzgrid->reclat[j][i] * bzgrid->reclat[j][i];
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}
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length[i] /= bzgrid->D_diag[i] * bzgrid->D_diag[i];
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}
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@ -233,7 +224,7 @@ RecgridMats *recgrid_alloc_RotMats(const int64_t size) {
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rotmats->size = size;
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if (size > 0) {
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if ((rotmats->mat = (int64_t(*)[3][3])malloc(sizeof(int64_t[3][3]) *
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if ((rotmats->mat = (int64_t (*)[3][3])malloc(sizeof(int64_t[3][3]) *
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size)) == NULL) {
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warning_print("Memory could not be allocated ");
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warning_print("(RecgridMats, line %d, %s).\n", __LINE__, __FILE__);
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@ -262,7 +262,7 @@ static void get_BZ_triplets_at_q_type1(int64_t (*triplets)[3],
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int64_t bzgp[3], G[3];
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int64_t bz_adrs0[3], bz_adrs1[3], bz_adrs2[3];
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const int64_t *gp_map;
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const int64_t(*bz_adrs)[3];
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const int64_t (*bz_adrs)[3];
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double d2, min_d2, tolerance;
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double LQD_inv[3][3];
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@ -348,13 +348,14 @@ static void get_BZ_triplets_at_q_type2(int64_t (*triplets)[3],
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int64_t bzgp[3], G[3];
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int64_t bz_adrs0[3], bz_adrs1[3], bz_adrs2[3];
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const int64_t *gp_map;
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const int64_t(*bz_adrs)[3];
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const int64_t (*bz_adrs)[3];
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double d2, min_d2, tolerance;
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double LQD_inv[3][3];
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gp_map = bzgrid->gp_map;
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bz_adrs = bzgrid->addresses;
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get_LQD_inv(LQD_inv, bzgrid);
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/* This tolerance is used to be consistent to BZ reduction in bzgrid. */
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tolerance = recgrid_get_tolerance_for_BZ_reduction((RecgridBZGrid *)bzgrid);
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@ -423,10 +424,15 @@ static void get_LQD_inv(double LQD_inv[3][3],
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int64_t i, j, k;
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/* LQD^-1 */
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for (i = 0; i < 3; i++) {
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for (j = 0; j < 3; j++) {
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LQD_inv[i][j] = 0;
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}
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}
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for (i = 0; i < 3; i++) {
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for (j = 0; j < 3; j++) {
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for (k = 0; k < 3; k++) {
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LQD_inv[i][k] =
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LQD_inv[i][k] +=
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bzgrid->reclat[i][j] * bzgrid->Q[j][k] / bzgrid->D_diag[k];
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}
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}
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@ -39,6 +39,8 @@ from __future__ import annotations
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import warnings
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from collections.abc import Sequence
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from numpy.typing import ArrayLike, NDArray
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try:
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from spglib import SpglibDataset # type: ignore
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except ImportError:
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@ -356,6 +358,16 @@ class BZGrid:
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"""
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return self._microzone_lattice
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@property
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def reciprocal_lattice(self) -> np.ndarray:
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"""Reciprocal basis vectors of primitive cell.
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Reciprocal basis vectors of primitive cell in column vectors.
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shape=(3, 3), dtype='double', order='C'.
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"""
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return self._reciprocal_lattice
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@property
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def store_dense_gp_map(self):
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"""Return gp_map type.
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@ -1172,22 +1184,15 @@ def _relocate_BZ_grid_address(
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else:
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bz_map = np.zeros(np.prod(D_diag) * 9 + 1, dtype="int64")
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# Mpr^-1 = Lr^-1 Lp
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reclat_T = np.array(np.transpose(reciprocal_lattice), dtype="double", order="C")
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reduced_basis = get_reduced_bases(reclat_T)
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assert reduced_basis is not None, "Reduced basis is not found."
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tmat_inv = np.dot(np.linalg.inv(reduced_basis.T), reclat_T.T)
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tmat_inv_int = np.rint(tmat_inv).astype("int64")
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assert (np.abs(tmat_inv - tmat_inv_int) < 1e-5).all()
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reduced_basis, tmat_inv_int = get_reduced_bases_and_tmat_inv(reciprocal_lattice)
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num_gp = recgrid.bz_grid_addresses(
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bz_grid_addresses,
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bz_map,
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bzg2grg,
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np.array(D_diag, dtype="int64"),
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np.array(np.dot(tmat_inv_int, Q), dtype="int64", order="C"),
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np.array(tmat_inv_int @ Q, dtype="int64", order="C"),
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_PS,
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np.array(reduced_basis.T, dtype="double", order="C"),
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reduced_basis,
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store_dense_gp_map * 1 + 1,
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)
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@ -1196,6 +1201,39 @@ def _relocate_BZ_grid_address(
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return bz_grid_addresses, bz_map, bzg2grg
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def get_reduced_bases_and_tmat_inv(
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reciprocal_lattice: ArrayLike,
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) -> tuple[NDArray, NDArray]:
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"""Return reduced bases and inverse transformation matrix.
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Parameters
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----------
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reciprocal_lattice : ArrayLike
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Reciprocal lattice vectors in column vectors.
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shape=(3, 3), dtype='double'
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Returns
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-------
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reduced_basis : ndarray
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Reduced basis vectors in column vectors.
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shape=(3, 3), dtype='double', order='C'
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tmat_inv_int : ndarray
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Inverse transformation matrix in integer.
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This is used to transform reciprocal lattice vectors to
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conventional lattice vectors.
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shape=(3, 3), dtype='int64'
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"""
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# Mpr^-1 = Lr^-1 Lp
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reclat_T = np.array(np.transpose(reciprocal_lattice), dtype="double", order="C")
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reduced_basis = get_reduced_bases(reclat_T)
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assert reduced_basis is not None, "Reduced basis is not found."
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tmat_inv = np.linalg.inv(reduced_basis.T) @ reclat_T.T
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tmat_inv_int = np.rint(tmat_inv).astype("int64")
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assert (np.abs(tmat_inv - tmat_inv_int) < 1e-5).all()
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return np.array(reduced_basis.T, dtype="double", order="C"), tmat_inv_int
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def _get_ir_grid_map(
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D_diag: Union[np.ndarray, Sequence],
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grg_rotations: Union[np.ndarray, Sequence],
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@ -42,7 +42,11 @@ from phonopy.structure.tetrahedron_method import TetrahedronMethod
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from phono3py.other.tetrahedron_method import get_tetrahedra_relative_grid_address
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from phono3py.phonon.func import gaussian
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from phono3py.phonon.grid import BZGrid, get_grid_point_from_address_py
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from phono3py.phonon.grid import (
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BZGrid,
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get_grid_point_from_address_py,
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get_reduced_bases_and_tmat_inv,
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)
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if TYPE_CHECKING:
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from phono3py.phonon3.interaction import Interaction
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@ -327,14 +331,18 @@ def _get_BZ_triplets_at_q(bz_grid_index, bz_grid: BZGrid, map_triplets):
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weights[g] += 1
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ir_weights = np.extract(weights > 0, weights)
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triplets = -np.ones((len(ir_weights), 3), dtype="int64", order="C")
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reduced_basis, tmat_inv_int = get_reduced_bases_and_tmat_inv(
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bz_grid.reciprocal_lattice
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)
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num_ir_ret = phono3c.BZ_triplets_at_q(
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triplets,
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bz_grid_index,
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bz_grid.addresses,
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bz_grid.gp_map,
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map_triplets,
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np.array(bz_grid.D_diag, dtype="int64"),
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bz_grid.Q,
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bz_grid.D_diag,
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np.array(tmat_inv_int @ bz_grid.Q, dtype="int64", order="C"),
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reduced_basis,
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bz_grid.store_dense_gp_map * 1 + 1,
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)
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@ -911,7 +911,7 @@ def test_get_BZ_triplets_at_q(aln_cell: PhonopyAtoms, params):
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[1, 36, 60],
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[1, 38, 59],
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[1, 41, 56],
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],
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], # 0
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[
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[1, 0, 4],
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[1, 1, 3],
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@ -937,7 +937,7 @@ def test_get_BZ_triplets_at_q(aln_cell: PhonopyAtoms, params):
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[1, 36, 60],
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[1, 38, 59],
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[1, 41, 56],
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],
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], # 1
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[
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[1, 0, 4],
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[1, 1, 3],
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@ -969,7 +969,7 @@ def test_get_BZ_triplets_at_q(aln_cell: PhonopyAtoms, params):
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[1, 39, 57],
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[1, 41, 56],
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[1, 42, 55],
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],
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], # 2
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[
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[1, 0, 4],
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[1, 1, 3],
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@ -1016,7 +1016,7 @@ def test_get_BZ_triplets_at_q(aln_cell: PhonopyAtoms, params):
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[1, 70, 26],
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[1, 72, 25],
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[1, 73, 24],
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],
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], # 3
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[
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[1, 0, 4],
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[1, 1, 3],
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@ -1150,11 +1150,11 @@ def test_get_BZ_triplets_at_q(aln_cell: PhonopyAtoms, params):
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[8, 2, 87],
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[8, 3, 86],
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[9, 4, 92],
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[8, 5, 84],
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[8, 6, 82],
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[8, 8, 81],
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[8, 10, 80],
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[8, 11, 85],
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[9, 5, 84],
|
||||
[8, 7, 82],
|
||||
[8, 9, 81],
|
||||
[9, 10, 80],
|
||||
[9, 11, 85],
|
||||
[8, 12, 78],
|
||||
[8, 13, 76],
|
||||
[8, 14, 75],
|
||||
|
|
@ -1164,23 +1164,23 @@ def test_get_BZ_triplets_at_q(aln_cell: PhonopyAtoms, params):
|
|||
[9, 22, 67],
|
||||
[8, 24, 65],
|
||||
[8, 27, 62],
|
||||
[8, 29, 66],
|
||||
[9, 30, 66],
|
||||
[8, 31, 58],
|
||||
[8, 32, 57],
|
||||
[8, 40, 50],
|
||||
[8, 48, 48],
|
||||
],
|
||||
], # 0
|
||||
[
|
||||
[8, 0, 89],
|
||||
[8, 1, 88],
|
||||
[8, 2, 87],
|
||||
[8, 3, 86],
|
||||
[9, 4, 92],
|
||||
[8, 5, 84],
|
||||
[8, 6, 82],
|
||||
[8, 8, 81],
|
||||
[8, 10, 80],
|
||||
[8, 11, 85],
|
||||
[9, 5, 84],
|
||||
[8, 7, 82],
|
||||
[8, 9, 81],
|
||||
[9, 10, 80],
|
||||
[9, 11, 85],
|
||||
[8, 12, 78],
|
||||
[8, 13, 76],
|
||||
[8, 14, 75],
|
||||
|
|
@ -1190,23 +1190,23 @@ def test_get_BZ_triplets_at_q(aln_cell: PhonopyAtoms, params):
|
|||
[9, 22, 67],
|
||||
[8, 24, 65],
|
||||
[8, 27, 62],
|
||||
[8, 29, 66],
|
||||
[9, 30, 66],
|
||||
[8, 31, 58],
|
||||
[8, 32, 57],
|
||||
[8, 40, 50],
|
||||
[8, 48, 48],
|
||||
],
|
||||
], # 1
|
||||
[
|
||||
[8, 0, 89],
|
||||
[8, 1, 88],
|
||||
[8, 2, 87],
|
||||
[8, 3, 86],
|
||||
[9, 4, 92],
|
||||
[8, 5, 84],
|
||||
[8, 6, 82],
|
||||
[8, 8, 81],
|
||||
[8, 10, 80],
|
||||
[8, 11, 85],
|
||||
[9, 5, 84],
|
||||
[8, 7, 82],
|
||||
[8, 9, 81],
|
||||
[9, 10, 80],
|
||||
[9, 11, 85],
|
||||
[8, 12, 78],
|
||||
[8, 13, 76],
|
||||
[8, 14, 75],
|
||||
|
|
@ -1219,7 +1219,7 @@ def test_get_BZ_triplets_at_q(aln_cell: PhonopyAtoms, params):
|
|||
[8, 24, 65],
|
||||
[8, 25, 64],
|
||||
[8, 27, 62],
|
||||
[8, 29, 66],
|
||||
[9, 30, 66],
|
||||
[8, 31, 58],
|
||||
[8, 32, 57],
|
||||
[8, 33, 56],
|
||||
|
|
@ -1227,7 +1227,7 @@ def test_get_BZ_triplets_at_q(aln_cell: PhonopyAtoms, params):
|
|||
[8, 40, 50],
|
||||
[9, 41, 49],
|
||||
[9, 42, 54],
|
||||
[8, 43, 46],
|
||||
[8, 43, 47],
|
||||
[8, 44, 45],
|
||||
[8, 48, 48],
|
||||
[8, 50, 40],
|
||||
|
|
@ -1240,20 +1240,20 @@ def test_get_BZ_triplets_at_q(aln_cell: PhonopyAtoms, params):
|
|||
[8, 71, 19],
|
||||
[9, 72, 18],
|
||||
[8, 79, 17],
|
||||
[8, 81, 8],
|
||||
[8, 81, 9],
|
||||
[8, 89, 0],
|
||||
],
|
||||
], # 2
|
||||
[
|
||||
[8, 0, 89],
|
||||
[8, 1, 88],
|
||||
[8, 2, 87],
|
||||
[8, 3, 86],
|
||||
[9, 4, 92],
|
||||
[8, 5, 84],
|
||||
[8, 6, 82],
|
||||
[8, 8, 81],
|
||||
[8, 10, 80],
|
||||
[8, 11, 85],
|
||||
[9, 5, 84],
|
||||
[8, 7, 82],
|
||||
[8, 9, 81],
|
||||
[9, 10, 80],
|
||||
[9, 11, 85],
|
||||
[8, 12, 78],
|
||||
[8, 13, 76],
|
||||
[8, 14, 75],
|
||||
|
|
@ -1266,7 +1266,7 @@ def test_get_BZ_triplets_at_q(aln_cell: PhonopyAtoms, params):
|
|||
[8, 24, 65],
|
||||
[8, 25, 64],
|
||||
[8, 27, 62],
|
||||
[8, 29, 66],
|
||||
[9, 30, 66],
|
||||
[8, 31, 58],
|
||||
[8, 32, 57],
|
||||
[8, 33, 56],
|
||||
|
|
@ -1274,7 +1274,7 @@ def test_get_BZ_triplets_at_q(aln_cell: PhonopyAtoms, params):
|
|||
[8, 40, 50],
|
||||
[9, 41, 49],
|
||||
[9, 42, 54],
|
||||
[8, 43, 46],
|
||||
[8, 43, 47],
|
||||
[8, 44, 45],
|
||||
[8, 48, 48],
|
||||
[8, 50, 40],
|
||||
|
|
@ -1287,9 +1287,9 @@ def test_get_BZ_triplets_at_q(aln_cell: PhonopyAtoms, params):
|
|||
[8, 71, 19],
|
||||
[9, 72, 18],
|
||||
[8, 79, 17],
|
||||
[8, 81, 8],
|
||||
[8, 81, 9],
|
||||
[8, 89, 0],
|
||||
],
|
||||
], # 3
|
||||
[
|
||||
[7, 0, 28],
|
||||
[8, 1, 27],
|
||||
|
|
@ -1794,22 +1794,23 @@ def test_get_BZ_triplets_at_q(aln_cell: PhonopyAtoms, params):
|
|||
ir_weights_with_zeros = np.zeros(45, dtype=int)
|
||||
ir_weights_with_zeros[: len(ir_weights)] = ir_weights
|
||||
|
||||
# print("[")
|
||||
# for tp in ir_triplets:
|
||||
# print("[%d, %d, %d]," % tuple(tp))
|
||||
# print("],")
|
||||
|
||||
np.testing.assert_equal(ref_triplets[i][params[3]], ir_triplets)
|
||||
np.testing.assert_equal(ref_ir_weights[i][params[3]], ir_weights)
|
||||
if i == 1 and params[0]:
|
||||
# if i == 1 and params[0]:
|
||||
# print("{")
|
||||
# for j, tp in enumerate(triplets_with_zeros):
|
||||
# print("%d, %d, %d, " % tuple(tp), end="")
|
||||
# if (j + 1) % 5 == 0:
|
||||
# print("&")
|
||||
print(", ".join(["%d" % x for x in ir_weights_with_zeros]))
|
||||
# print(", ".join(["%d" % x for x in ir_weights_with_zeros]))
|
||||
# print("},")
|
||||
# print(len(ir_triplets))
|
||||
# print("[")
|
||||
# print("[")
|
||||
# for tp in ir_triplets:
|
||||
# print("[%d, %d, %d]," % tuple(tp))
|
||||
# print("],")
|
||||
# print("]")
|
||||
# print("[")
|
||||
# print(",".join(["%d" % x for x in ir_weights]))
|
||||
|
|
|
|||
Loading…
Reference in New Issue