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phonopy/c/spglib/primitive.c

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/* Copyright (C) 2008 Atsushi Togo */
/* All rights reserved. */
/* This file is part of spglib. */
/* Redistribution and use in source and binary forms, with or without */
/* modification, are permitted provided that the following conditions */
/* are met: */
/* * Redistributions of source code must retain the above copyright */
/* notice, this list of conditions and the following disclaimer. */
/* * Redistributions in binary form must reproduce the above copyright */
/* notice, this list of conditions and the following disclaimer in */
/* the documentation and/or other materials provided with the */
/* distribution. */
/* * Neither the name of the phonopy project nor the names of its */
/* contributors may be used to endorse or promote products derived */
/* from this software without specific prior written permission. */
/* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS */
/* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT */
/* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS */
/* FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE */
/* COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, */
/* INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, */
/* BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; */
/* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER */
/* CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT */
/* LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN */
/* ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE */
/* POSSIBILITY OF SUCH DAMAGE. */
#include <stdio.h>
#include <stdlib.h>
#include "cell.h"
#include "delaunay.h"
#include "mathfunc.h"
#include "primitive.h"
#include "symmetry.h"
#include "debug.h"
#define REDUCE_RATE 0.95
#define NUM_ATTEMPT 20
static Primitive * get_primitive(SPGCONST Cell * cell, const double symprec);
static Cell * get_cell_with_smallest_lattice(SPGCONST Cell * cell,
const double symprec);
static Cell * get_primitive_cell(int * mapping_table,
SPGCONST Cell * cell,
const VecDBL * pure_trans,
const double symprec);
static int get_primitive_lattice_vectors_iterative(double prim_lattice[3][3],
SPGCONST Cell * cell,
const VecDBL * pure_trans,
const double symprec);
static int get_primitive_lattice_vectors(double prim_lattice[3][3],
const VecDBL * vectors,
SPGCONST Cell * cell,
const double symprec);
static VecDBL * get_translation_candidates(const VecDBL * pure_trans);
/* return NULL if failed */
Primitive * prm_alloc_primitive(const int size)
{
Primitive *primitive;
int i, j;
primitive = NULL;
if ((primitive = (Primitive*) malloc(sizeof(Primitive))) == NULL) {
warning_print("spglib: Memory could not be allocated ");
return NULL;
}
primitive->cell = NULL;
primitive->mapping_table = NULL;
primitive->size = size;
primitive->tolerance = 0;
for (i = 0; i < 3; i++) {
for (j = 0; j < 3; j++) {
primitive->t_mat[i][j] = 0;
}
}
if (size > 0) {
if ((primitive->mapping_table = (int*) malloc(sizeof(int) * size)) == NULL) {
warning_print("spglib: Memory could not be allocated ");
warning_print("(Primitive, line %d, %s).\n", __LINE__, __FILE__);
free(primitive);
primitive = NULL;
return NULL;
}
}
for (i = 0; i < size; i++) {
primitive->mapping_table[i] = -1;
}
return primitive;
}
void prm_free_primitive(Primitive * primitive)
{
if (primitive != NULL) {
if (primitive->mapping_table != NULL) {
free(primitive->mapping_table);
primitive->mapping_table = NULL;
}
if (primitive->cell != NULL) {
cel_free_cell(primitive->cell);
primitive->cell = NULL;
}
free(primitive);
}
}
/* Return NULL if failed */
Primitive * prm_get_primitive(SPGCONST Cell * cell, const double symprec)
{
return get_primitive(cell, symprec);
}
/* Return NULL if failed */
static Primitive * get_primitive(SPGCONST Cell * cell, const double symprec)
{
int i, attempt;
double tolerance;
double inv_lat[3][3];
Primitive *primitive;
VecDBL * pure_trans;
debug_print("get_primitive (tolerance = %f):\n", symprec);
primitive = NULL;
pure_trans = NULL;
if ((primitive = prm_alloc_primitive(cell->size)) == NULL) {
goto notfound;
}
tolerance = symprec;
for (attempt = 0; attempt < NUM_ATTEMPT; attempt++) {
debug_print("get_primitive (attempt = %d):\n", attempt);
if ((pure_trans = sym_get_pure_translation(cell, tolerance)) == NULL) {
goto cont;
}
if (pure_trans->size == 1) {
if ((primitive->cell = get_cell_with_smallest_lattice(cell, tolerance))
!= NULL) {
for (i = 0; i < cell->size; i++) {
primitive->mapping_table[i] = i;
}
goto found;
}
} else {
if ((primitive->cell = get_primitive_cell(primitive->mapping_table,
cell,
pure_trans,
tolerance)) != NULL) {
goto found;
}
}
mat_free_VecDBL(pure_trans);
pure_trans = NULL;
cont:
tolerance *= REDUCE_RATE;
warning_print("spglib: Reduce tolerance to %f ", tolerance);
warning_print("(line %d, %s).\n", __LINE__, __FILE__);
}
prm_free_primitive(primitive);
primitive = NULL;
notfound:
return NULL;
found:
primitive->tolerance = tolerance;
mat_inverse_matrix_d3(inv_lat, cell->lattice, 0);
mat_multiply_matrix_d3(primitive->t_mat, primitive->cell->lattice, inv_lat);
mat_free_VecDBL(pure_trans);
pure_trans = NULL;
return primitive;
}
/* Return NULL if failed */
static Cell * get_cell_with_smallest_lattice(SPGCONST Cell * cell,
const double symprec)
{
int i, j;
double min_lat[3][3], trans_mat[3][3], inv_lat[3][3];
Cell * smallest_cell;
debug_print("get_cell_with_smallest_lattice:\n");
smallest_cell = NULL;
if (!del_delaunay_reduce(min_lat, cell->lattice, symprec)) {
return NULL;
}
mat_inverse_matrix_d3(inv_lat, min_lat, 0);
mat_multiply_matrix_d3(trans_mat, inv_lat, cell->lattice);
if ((smallest_cell = cel_alloc_cell(cell->size)) == NULL) {
return NULL;
}
mat_copy_matrix_d3(smallest_cell->lattice, min_lat);
for (i = 0; i < cell->size; i++) {
smallest_cell->types[i] = cell->types[i];
mat_multiply_matrix_vector_d3(smallest_cell->position[i],
trans_mat, cell->position[i]);
for (j = 0; j < 3; j++) {
smallest_cell->position[i][j] = mat_Dmod1(smallest_cell->position[i][j]);
}
}
return smallest_cell;
}
/* Return NULL if failed */
static Cell * get_primitive_cell(int * mapping_table,
SPGCONST Cell * cell,
const VecDBL * pure_trans,
const double symprec)
{
int multi;
double prim_lat[3][3], smallest_lat[3][3];
Cell * primitive_cell;
debug_print("get_primitive_cell:\n");
primitive_cell = NULL;
/* Primitive lattice vectors are searched. */
/* To be consistent, sometimes tolerance is decreased iteratively. */
/* The descreased tolerance is stored in 'static double tolerance'. */
multi = get_primitive_lattice_vectors_iterative(prim_lat,
cell,
pure_trans,
symprec);
if (! multi) {
goto not_found;
}
if (! del_delaunay_reduce(smallest_lat, prim_lat, symprec)) {
goto not_found;
}
/* Fit atoms into new primitive cell */
if ((primitive_cell = cel_trim_cell(mapping_table,
smallest_lat,
cell,
symprec)) == NULL) {
goto not_found;
}
/* found */
return primitive_cell;
not_found:
warning_print("spglib: Primitive cell could not be found ");
warning_print("(line %d, %s).\n", __LINE__, __FILE__);
return NULL;
}
/* Return 0 if failed */
static int get_primitive_lattice_vectors_iterative(double prim_lattice[3][3],
SPGCONST Cell * cell,
const VecDBL * pure_trans,
const double symprec)
{
int i, multi, attempt;
double tolerance;
VecDBL * vectors, * pure_trans_reduced, *tmp_vec;
vectors = NULL;
pure_trans_reduced = NULL;
tmp_vec = NULL;
tolerance = symprec;
if ((pure_trans_reduced = mat_alloc_VecDBL(pure_trans->size)) == NULL) {
goto fail;
}
for (i = 0; i < pure_trans->size; i++) {
mat_copy_vector_d3(pure_trans_reduced->vec[i], pure_trans->vec[i]);
}
for (attempt = 0; attempt < NUM_ATTEMPT; attempt++) {
multi = pure_trans_reduced->size;
if ((vectors = get_translation_candidates(pure_trans_reduced)) == NULL) {
mat_free_VecDBL(pure_trans_reduced);
pure_trans_reduced = NULL;
goto fail;
}
/* Lattice of primitive cell is found among pure translation vectors */
if (get_primitive_lattice_vectors(prim_lattice,
vectors,
cell,
tolerance)) {
mat_free_VecDBL(vectors);
vectors = NULL;
mat_free_VecDBL(pure_trans_reduced);
pure_trans_reduced = NULL;
goto found;
} else {
if ((tmp_vec = mat_alloc_VecDBL(multi)) == NULL) {
mat_free_VecDBL(vectors);
vectors = NULL;
mat_free_VecDBL(pure_trans_reduced);
pure_trans_reduced = NULL;
goto fail;
}
for (i = 0; i < multi; i++) {
mat_copy_vector_d3(tmp_vec->vec[i], pure_trans_reduced->vec[i]);
}
mat_free_VecDBL(pure_trans_reduced);
pure_trans_reduced = NULL;
pure_trans_reduced = sym_reduce_pure_translation(cell,
tmp_vec,
tolerance);
mat_free_VecDBL(tmp_vec);
tmp_vec = NULL;
mat_free_VecDBL(vectors);
vectors = NULL;
if (pure_trans_reduced == NULL) {
goto fail;
}
warning_print("spglib: Tolerance is reduced to %f (%d), ",
tolerance, attempt);
warning_print("num_pure_trans = %d\n", pure_trans_reduced->size);
tolerance *= REDUCE_RATE;
}
}
mat_free_VecDBL(pure_trans_reduced);
pure_trans_reduced = NULL;
fail:
return 0;
found:
return multi;
}
/* Return 0 if failed */
static int get_primitive_lattice_vectors(double prim_lattice[3][3],
const VecDBL * vectors,
SPGCONST Cell * cell,
const double symprec)
{
int i, j, k, size;
double initial_volume, volume;
double relative_lattice[3][3], min_vectors[3][3], tmp_lattice[3][3];
double inv_mat_dbl[3][3];
int inv_mat_int[3][3];
debug_print("get_primitive_lattice_vectors:\n");
size = vectors->size;
initial_volume = mat_Dabs(mat_get_determinant_d3(cell->lattice));
/* check volumes of all possible lattices, find smallest volume */
for (i = 0; i < size; i++) {
for (j = i + 1; j < size; j++) {
for (k = j + 1; k < size; k++) {
mat_multiply_matrix_vector_d3(tmp_lattice[0],
cell->lattice,
vectors->vec[i]);
mat_multiply_matrix_vector_d3(tmp_lattice[1],
cell->lattice,
vectors->vec[j]);
mat_multiply_matrix_vector_d3(tmp_lattice[2],
cell->lattice,
vectors->vec[k]);
volume = mat_Dabs(mat_get_determinant_d3(tmp_lattice));
if (volume > symprec) {
if (mat_Nint(initial_volume / volume) == size-2) {
mat_copy_vector_d3(min_vectors[0], vectors->vec[i]);
mat_copy_vector_d3(min_vectors[1], vectors->vec[j]);
mat_copy_vector_d3(min_vectors[2], vectors->vec[k]);
goto ret;
}
}
}
}
}
/* Not found */
warning_print("spglib: Primitive lattice vectors cound not be found ");
warning_print("(line %d, %s).\n", __LINE__, __FILE__);
return 0;
/* Found */
ret:
for (i = 0; i < 3; i++) {
for (j = 0; j < 3; j++) {
relative_lattice[j][i] = min_vectors[i][j];
}
}
mat_inverse_matrix_d3(inv_mat_dbl, relative_lattice, 0);
mat_cast_matrix_3d_to_3i(inv_mat_int, inv_mat_dbl);
if (abs(mat_get_determinant_i3(inv_mat_int)) == size-2) {
mat_cast_matrix_3i_to_3d(inv_mat_dbl, inv_mat_int);
mat_inverse_matrix_d3(relative_lattice, inv_mat_dbl, 0);
} else {
warning_print("spglib: Primitive lattice cleaning is incomplete ");
warning_print("(line %d, %s).\n", __LINE__, __FILE__);
}
mat_multiply_matrix_d3(prim_lattice, cell->lattice, relative_lattice);
return 1;
}
static VecDBL * get_translation_candidates(const VecDBL * pure_trans)
{
int i, j, multi;
VecDBL * vectors;
vectors = NULL;
multi = pure_trans->size;
if ((vectors = mat_alloc_VecDBL(multi + 2)) == NULL) {
return NULL;
}
/* store pure translations in original cell */
/* as trial primitive lattice vectors */
for (i = 0; i < multi - 1; i++) {
mat_copy_vector_d3(vectors->vec[i], pure_trans->vec[i + 1]);
}
/* store lattice translations of original cell */
/* as trial primitive lattice vectors */
for (i = 0; i < 3; i++) {
for (j = 0; j < 3; j++) {
if (i == j) {
vectors->vec[i+multi-1][j] = 1;
} else {
vectors->vec[i+multi-1][j] = 0;
}
}
}
return vectors;
}
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