diff options
| -rw-r--r-- | libcrystfel/src/cell-utils.c | 12 | ||||
| -rw-r--r-- | libcrystfel/src/cell-utils.h | 2 | ||||
| -rw-r--r-- | src/cell_tool.c | 11 |
3 files changed, 15 insertions, 10 deletions
diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c index 2a3bcfa2..847ddb55 100644 --- a/libcrystfel/src/cell-utils.c +++ b/libcrystfel/src/cell-utils.c @@ -1875,7 +1875,7 @@ static int cmpcand(const void *av, const void *bv) static Rational *find_candidates(double len, double *a, double *b, double *c, - double ltl, int *pncand) + double ltl, int csl, int *pncand) { Rational *r; struct cand *cands; @@ -1890,7 +1890,7 @@ static Rational *find_candidates(double len, double *a, double *b, double *c, cands = malloc(max_cand * sizeof(struct cand)); if ( cands == NULL ) return NULL; - rat = rtnl_list(-5, 5, 1, 4, &nrat); + rat = rtnl_list(-5, 5, 1, csl ? 4 : 1, &nrat); if ( rat == NULL ) return NULL; for ( ia=0; ia<nrat; ia++ ) { @@ -1999,7 +1999,7 @@ static double g6_distance(double a1, double b1, double c1, * */ int compare_reindexed_cell_parameters(UnitCell *cell_in, UnitCell *reference_in, - double ltl, double atl, + double ltl, double atl, int csl, RationalMatrix **pmb) { UnitCell *cell; @@ -2036,9 +2036,9 @@ int compare_reindexed_cell_parameters(UnitCell *cell_in, UnitCell *reference_in, &cv[0], &cv[1], &cv[2]); /* Find vectors in 'cell' with lengths close to a, b and c */ - cand_a = find_candidates(a, av, bv, cv, ltl, &ncand_a); - cand_b = find_candidates(b, av, bv, cv, ltl, &ncand_b); - cand_c = find_candidates(c, av, bv, cv, ltl, &ncand_c); + cand_a = find_candidates(a, av, bv, cv, ltl, csl, &ncand_a); + cand_b = find_candidates(b, av, bv, cv, ltl, csl, &ncand_b); + cand_c = find_candidates(c, av, bv, cv, ltl, csl, &ncand_c); if ( (ncand_a==0) || (ncand_b==0) || (ncand_c==0) ) { *pmb = NULL; diff --git a/libcrystfel/src/cell-utils.h b/libcrystfel/src/cell-utils.h index a97f2bfb..79c98e61 100644 --- a/libcrystfel/src/cell-utils.h +++ b/libcrystfel/src/cell-utils.h @@ -97,7 +97,7 @@ extern int compare_reindexed_cell_parameters_and_orientation(UnitCell *a, IntegerMatrix **pmb); extern int compare_reindexed_cell_parameters(UnitCell *cell, UnitCell *reference, - double ltl, double atl, + double ltl, double atl, int csl, RationalMatrix **pmb); #ifdef __cplusplus diff --git a/src/cell_tool.c b/src/cell_tool.c index 652df885..cd457f25 100644 --- a/src/cell_tool.c +++ b/src/cell_tool.c @@ -67,12 +67,13 @@ static void show_help(const char *s) " --tolerance=<tol> Set the tolerances for cell comparison.\n" " Default: 5,1.5 (axis percentage, angle deg).\n" " --highres=n Resolution limit (Angstroms) for --rings\n" +" --csl Allow --compare to find coincidence site lattice relationships.\n" ); } static int comparecells(UnitCell *cell, const char *comparecell, - double ltl, double atl) + double ltl, double atl, int csl) { UnitCell *cell2; RationalMatrix *m; @@ -90,7 +91,7 @@ static int comparecells(UnitCell *cell, const char *comparecell, cell_print(cell2); STATUS("------------------> The comparison results:\n"); - if ( !compare_reindexed_cell_parameters(cell, cell2, ltl, atl, &m) ) { + if ( !compare_reindexed_cell_parameters(cell, cell2, ltl, atl, csl, &m) ) { STATUS("No relationship found between lattices.\n"); return 0; } else { @@ -425,6 +426,7 @@ int main(int argc, char *argv[]) float highres; double rmax = 1/(2.0e-10); char *trans_str = NULL; + int csl = 0; /* Long options */ const struct option longopts[] = { @@ -440,8 +442,10 @@ int main(int argc, char *argv[]) {"rings", 0, &mode, CT_RINGS}, {"compare-cell", 1, NULL, 3}, {"cell-choices", 0, &mode, CT_CHOICES}, + {"transform", 1, NULL, 4}, {"highres", 1, NULL, 5}, + {"csl", 0, &csl, 1}, {0, 0, NULL, 0} }; @@ -568,7 +572,8 @@ int main(int argc, char *argv[]) if ( mode == CT_FINDAMBI ) return find_ambi(cell, sym, ltl, atl); if ( mode == CT_UNCENTER ) return uncenter(cell, out_file); if ( mode == CT_RINGS ) return all_rings(cell, sym, rmax); - if ( mode == CT_COMPARE ) return comparecells(cell, comparecell, ltl, atl); + if ( mode == CT_COMPARE ) return comparecells(cell, comparecell, + ltl, atl, csl); if ( mode == CT_TRANSFORM ) return transform(cell, trans_str, out_file); if ( mode == CT_CHOICES ) return cell_choices(cell); |