get_ambiguities() should not return the identity operation

3 files changed, 34 insertions, 22 deletions

diff --git a/libcrystfel/src/symmetry.c b/libcrystfel/src/symmetry.c
index 47ba088b..67298ec1 100644
--- a/libcrystfel/src/symmetry.c
+++ b/libcrystfel/src/symmetry.c
@@ -1511,6 +1511,7 @@ SymOpList *get_ambiguities(const SymOpList *source, const SymOpList *target)
 	SymOpList *tgt_reordered;
 	SymOpMask *used;
 	char *name;
+	int have_identity = 0;
 
 	n_src = num_ops(source);
 	n_tgt = num_ops(target);
@@ -1569,7 +1570,16 @@ SymOpList *get_ambiguities(const SymOpList *source, const SymOpList *target)
 			free_symoplist(src_reordered);
 			return NULL;
 		}
-		add_symop(twins, intmat_copy(src_reordered->ops[i]));
+		if ( !intmat_is_identity(src_reordered->ops[i]) ) {
+			add_symop(twins, intmat_copy(src_reordered->ops[i]));
+		} else {
+			have_identity = 1;
+		}
+
+	}
+
+	if ( !have_identity ) {
+		ERROR("WARNING: Identity not found during left coset decomp\n");
 	}
 
 	free_symopmask(used);
diff --git a/src/ambigator.c b/src/ambigator.c
index 7e1726fd..70dcb631 100644
--- a/src/ambigator.c
+++ b/src/ambigator.c
@@ -130,7 +130,7 @@ static struct flist *asymm_and_merge(RefList *in, const SymOpList *sym,
 			signed int hr, kr, lr;
 			signed int hra, kra, lra;
 
-			get_equiv(amb, NULL, 1, ha, ka, la, &hr, &kr, &lr);
+			get_equiv(amb, NULL, 0, ha, ka, la, &hr, &kr, &lr);
 			get_asymm(sym, hr, kr, lr, &hra, &kra, &lra);
 
 			/* Skip twin-proof reflections */
@@ -201,7 +201,7 @@ static struct flist *asymm_and_merge(RefList *in, const SymOpList *sym,
 			Reflection *cr;
 
 			get_indices(refl, &h, &k, &l);
-			get_equiv(amb, NULL, 1, h, k, l, &hr, &kr, &lr);
+			get_equiv(amb, NULL, 0, h, k, l, &hr, &kr, &lr);
 			get_asymm(sym, hr, kr, lr, &hra, &kra, &lra);
 
 			cr = add_refl(reidx, hra, kra, lra);
@@ -641,7 +641,9 @@ static void reindex_reflections(FILE *fh, FILE *ofh, int assignment,
 		/* See scanf() manual page about %n to see why <3 is used */
 		if ( (r < 3) && !first ) return;
 
-		get_equiv(amb, NULL, assignment, h, k, l, &h, &k, &l);
+		if ( assignment ) {
+			get_equiv(amb, NULL, 0, h, k, l, &h, &k, &l);
+		}
 
 		fprintf(ofh, "%4i %4i %4i%s", h, k, l, line+n);
 
@@ -874,7 +876,7 @@ int main(int argc, char *argv[])
 		}
 		STATUS("Ambiguity operations:\n");
 		describe_symmetry(amb);
-		if ( num_equivs(amb, NULL) != 2 ) {
+		if ( num_equivs(amb, NULL) != 1 ) {
 			ERROR("There must be only one ambiguity operator.\n");
 			ERROR("Try again with a different value for -w.\n");
 			return 1;
diff --git a/tests/ambi_check.c b/tests/ambi_check.c
index 287249eb..c25d006a 100644
--- a/tests/ambi_check.c
+++ b/tests/ambi_check.c
@@ -273,21 +273,21 @@ int main(int argc, char *argv[])
 	                     "6mm", NULL);
 
 	/* Check some easy subgroups */
-	check_subgroup("2/m",    "m",    1, 1,  2, &fail);
-	check_subgroup("mmm",    "mm2",  1, 1,  2, &fail);
-	check_subgroup("-4m2",   "-4",   1, 1,  2, &fail);
-	check_subgroup("-42m",   "-4",   1, 1,  2, &fail);
-	check_subgroup("-3m1_H", "-3_H", 1, 1,  2, &fail);
-	check_subgroup("-31m_H", "-3_H", 1, 1,  2, &fail);
-	check_subgroup("m-3m",   "-43m", 1, 1,  2, &fail);
-	check_subgroup("m-3m",   "m-3",  1, 1,  2, &fail);
-	check_subgroup("432",    "23",   1, 1,  2, &fail);
-	check_subgroup("6/m",    "-3_H", 1, 1,  2, &fail);
-	check_subgroup("4/m",    "-4",   1, 1,  2, &fail);
-	check_subgroup("622",    "321_H",  1, 1,  2, &fail);
+	check_subgroup("2/m",    "m",    1, 1,  1, &fail);
+	check_subgroup("mmm",    "mm2",  1, 1,  1, &fail);
+	check_subgroup("-4m2",   "-4",   1, 1,  1, &fail);
+	check_subgroup("-42m",   "-4",   1, 1,  1, &fail);
+	check_subgroup("-3m1_H", "-3_H", 1, 1,  1, &fail);
+	check_subgroup("-31m_H", "-3_H", 1, 1,  1, &fail);
+	check_subgroup("m-3m",   "-43m", 1, 1,  1, &fail);
+	check_subgroup("m-3m",   "m-3",  1, 1,  1, &fail);
+	check_subgroup("432",    "23",   1, 1,  1, &fail);
+	check_subgroup("6/m",    "-3_H", 1, 1,  1, &fail);
+	check_subgroup("4/m",    "-4",   1, 1,  1, &fail);
+	check_subgroup("622",    "321_H",  1, 1,  1, &fail);
 
 	/* Tetartohedral */
-	check_subgroup("6/mmm",  "-3_H", 1, 1,  4, &fail);
+	check_subgroup("6/mmm",  "-3_H", 1, 1,  3, &fail);
 
 	/* Check some things that are valid subgroups, but no valid ambiguities
 	 * exist because inversions and mirrors are not allowed */
@@ -300,10 +300,10 @@ int main(int argc, char *argv[])
 	check_subgroup("432",    "m-3",  0, 0, -1, &fail);
 
 	/* Check some pseudo-meroheral subgroups */
-	check_subgroup("3_R",  "1", 1, 1,  3, &fail);
-	check_subgroup("-3_R",  "-1", 1, 1,  3, &fail);
-	check_subgroup("6",  "2", 1, 1,  3, &fail);
-	check_subgroup("422",  "222", 1, 1,  2, &fail);
+	check_subgroup("3_R",  "1", 1, 1,  2, &fail);
+	check_subgroup("-3_R",  "-1", 1, 1,  2, &fail);
+	check_subgroup("6",  "2", 1, 1,  2, &fail);
+	check_subgroup("422",  "222", 1, 1,  1, &fail);
 
 	return fail;
 }