From 051077e3bcb44822713ec341a25e853fbbc1c811 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Tue, 26 Mar 2019 15:13:45 +0100
Subject: cell_tool: Add --csl

---
 libcrystfel/src/cell-utils.c | 12 ++++++------
 libcrystfel/src/cell-utils.h |  2 +-
 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);
 
-- 
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