C++ (Cpp) get_conventional_primitive Examples

Example #1

File: refinement.c Project: etp12/avogadro

/* Only the atoms corresponding to those in primitive are returned. */
static Cell * get_bravais_exact_positions_and_lattice(int * wyckoffs,
        int * equiv_atoms,
        SPGCONST Spacegroup *spacegroup,
        SPGCONST Cell * primitive,
        const double symprec)
{
    int i;
    Symmetry *conv_sym;
    Cell *bravais;
    VecDBL *exact_positions;

    /* Positions of primitive atoms are represented wrt Bravais lattice */
    bravais = get_conventional_primitive(spacegroup, primitive);
    /* Symmetries in database (wrt Bravais lattice) */
    conv_sym = get_db_symmetry(spacegroup->hall_number);
    /* Lattice vectors are set. */
    get_conventional_lattice(bravais->lattice,
                             spacegroup->holohedry,
                             spacegroup->bravais_lattice);

    /* Symmetrize atomic positions of conventional unit cell */
    exact_positions = ssm_get_exact_positions(wyckoffs,
                      equiv_atoms,
                      bravais,
                      conv_sym,
                      spacegroup->hall_number,
                      symprec);
    sym_free_symmetry(conv_sym);

    if (exact_positions->size > 0) {
        for (i = 0; i < bravais->size; i++) {
            mat_copy_vector_d3(bravais->position[i], exact_positions->vec[i]);
        }
    } else {
        cel_free_cell(bravais);
        bravais = cel_alloc_cell(0);
    }

    mat_free_VecDBL(exact_positions);

    return bravais;
}

Example #2

File: refinement.c Project: WeiLiPenguin/pymatgen

/* Return NULL if failed */
static Cell *
get_bravais_exact_positions_and_lattice(int * wyckoffs,
					int * equiv_atoms,
					SPGCONST Spacegroup *spacegroup,
					SPGCONST Cell * primitive,
					const double symprec)
{
  int i;
  int *wyckoffs_prim, *equiv_atoms_prim;
  Symmetry *conv_sym;
  Cell *bravais, *conv_prim;
  VecDBL *exact_positions;

  debug_print("get_bravais_exact_positions_and_lattice\n");

  wyckoffs_prim = NULL;
  equiv_atoms_prim = NULL;
  conv_prim = NULL;
  bravais = NULL;
  conv_sym = NULL;
  exact_positions = NULL;

  /* Symmetrize atomic positions of conventional unit cell */
  if ((wyckoffs_prim = (int*)malloc(sizeof(int) * primitive->size)) == NULL) {
    warning_print("spglib: Memory could not be allocated ");
    return NULL;
  }

  if ((equiv_atoms_prim = (int*)malloc(sizeof(int) * primitive->size)) == NULL) {
    warning_print("spglib: Memory could not be allocated ");
    free(wyckoffs_prim);
    wyckoffs_prim = NULL;
    return NULL;
  }

  for (i = 0; i < primitive->size; i++) {
    wyckoffs_prim[i] = -1;
    equiv_atoms_prim[i] = -1;
  }

  /* Positions of primitive atoms are represented wrt Bravais lattice */
  if ((conv_prim = get_conventional_primitive(spacegroup, primitive)) == NULL) {
    free(wyckoffs_prim);
    wyckoffs_prim = NULL;
    free(equiv_atoms_prim);
    equiv_atoms_prim = NULL;
    return NULL;
  }

  /* Symmetries in database (wrt Bravais lattice) */
  if ((conv_sym = spgdb_get_spacegroup_operations(spacegroup->hall_number))
      == NULL) {
    goto err;
  }

  /* Lattice vectors are set. */
  get_conventional_lattice(conv_prim->lattice, spacegroup);

  if ((exact_positions = ssm_get_exact_positions(wyckoffs_prim,
						 equiv_atoms_prim,
						 conv_prim,
						 conv_sym,
						 spacegroup->hall_number,
						 symprec)) == NULL) {
    sym_free_symmetry(conv_sym);
    conv_sym = NULL;
    goto err;
  }

  for (i = 0; i < conv_prim->size; i++) {
    mat_copy_vector_d3(conv_prim->position[i], exact_positions->vec[i]);
  }

  bravais = expand_positions(wyckoffs,
			     equiv_atoms,
			     conv_prim,
			     conv_sym,
			     wyckoffs_prim,
			     equiv_atoms_prim);

  mat_free_VecDBL(exact_positions);
  exact_positions = NULL;
  sym_free_symmetry(conv_sym);
  conv_sym = NULL;
 err:
  free(wyckoffs_prim);
  wyckoffs_prim = NULL;
  free(equiv_atoms_prim);
  equiv_atoms_prim = NULL;
  cel_free_cell(conv_prim);
  conv_prim = NULL;

  return bravais;
}