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authorThomas White <taw@physics.org>2018-02-02 17:44:43 +0100
committerThomas White <taw@physics.org>2018-02-27 17:12:42 +0100
commitd2a12ab3570b05ea3ad9719191c01d732bf1b580 (patch)
tree8adf1140361d9b55e4720dbddd487da45228c45a
parenta759c6c61b09cbb56c6f8c2bca862bbbc08bf49c (diff)
See if pattern fits better in other orientation
-rw-r--r--src/post-refinement.c106
1 files changed, 106 insertions, 0 deletions
diff --git a/src/post-refinement.c b/src/post-refinement.c
index f85b7832..e65ecf9e 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -381,6 +381,110 @@ static int check_angle_shifts(gsl_vector *cur, gsl_vector *initial,
}
+static RefList *reindex_reflections(RefList *input, SymOpList *amb,
+ SymOpList *sym)
+{
+ RefList *n;
+ Reflection *refl;
+ RefListIterator *iter;
+
+ n = reflist_new();
+
+ for ( refl = first_refl(input, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) )
+ {
+ signed int h, k, l;
+ Reflection *rn;
+
+ get_indices(refl, &h, &k, &l);
+ get_equiv(amb, NULL, 0, h, k, l, &h, &k, &l);
+ get_asymm(sym, h, k, l, &h, &k, &l);
+ rn = add_refl(n, h, k, l);
+ copy_data(rn, refl);
+
+ get_symmetric_indices(rn, &h, &k, &l);
+ get_equiv(amb, NULL, 0, h, k, l, &h, &k, &l);
+ set_symmetric_indices(rn, h, k, l);
+ }
+
+ return n;
+}
+
+
+static void reindex_cell(UnitCell *cell, SymOpList *amb)
+{
+ signed int h, k, l;
+ struct rvec na, nb, nc;
+ struct rvec as, bs, cs;
+
+ cell_get_reciprocal(cell, &as.u, &as.v, &as.w,
+ &bs.u, &bs.v, &bs.w,
+ &cs.u, &cs.v, &cs.w);
+
+ get_equiv(amb, NULL, 0, 1, 0, 0, &h, &k, &l);
+ na.u = as.u*h + bs.u*k + cs.u*l;
+ na.v = as.v*h + bs.v*k + cs.v*l;
+ na.w = as.w*h + bs.w*k + cs.w*l;
+
+ get_equiv(amb, NULL, 0, 0, 1, 0, &h, &k, &l);
+ nb.u = as.u*h + bs.u*k + cs.u*l;
+ nb.v = as.v*h + bs.v*k + cs.v*l;
+ nb.w = as.w*h + bs.w*k + cs.w*l;
+
+ get_equiv(amb, NULL, 0, 0, 0, 1, &h, &k, &l);
+ nc.u = as.u*h + bs.u*k + cs.u*l;
+ nc.v = as.v*h + bs.v*k + cs.v*l;
+ nc.w = as.w*h + bs.w*k + cs.w*l;
+
+ cell_set_reciprocal(cell, na.u, na.v, na.w,
+ nb.u, nb.v, nb.w,
+ nc.u, nc.v, nc.w);
+}
+
+
+void try_reindex(Crystal *crin, const RefList *full)
+{
+ RefList *list;
+ Crystal *cr;
+ UnitCell *cell;
+ SymOpList *amb;
+ SymOpList *sym;
+ double residual_original, residual_flipped;
+
+ amb = parse_symmetry_operations("k,h,-l");
+ sym = get_pointgroup("m-3");
+
+ residual_original = residual(crin, full, 0, NULL, NULL, 0);
+
+ cr = crystal_copy(crin);
+
+ cell = cell_new_from_cell(crystal_get_cell(crin));
+ if ( cell == NULL ) return;
+ reindex_cell(cell, amb);
+ crystal_set_cell(cr, cell);
+
+ list = reindex_reflections(crystal_get_reflections(crin), amb, sym);
+ crystal_set_reflections(cr, list);
+
+ update_predictions(cr);
+ calculate_partialities(cr, PMODEL_XSPHERE);
+
+ residual_flipped = residual(cr, full, 0, NULL, NULL, 1);
+
+ if ( residual_flipped < residual_original ) {
+ crystal_set_cell(crin, cell);
+ crystal_set_reflections(crin, list);
+ } else {
+ cell_free(crystal_get_cell(cr));
+ reflist_free(crystal_get_reflections(cr));
+ crystal_free(cr);
+ }
+
+ free_symoplist(amb);
+}
+
+
static void do_pr_refine(Crystal *cr, const RefList *full,
PartialityModel pmodel, int verbose, int serial,
int cycle)
@@ -402,6 +506,8 @@ static void do_pr_refine(Crystal *cr, const RefList *full,
const int write_logs = 1;
FILE *fh = NULL;
+ try_reindex(cr, full);
+
residual_start = residual(cr, full, 0, NULL, NULL, 0);
residual_free_start = residual(cr, full, 1, NULL, NULL, 0);