Change horribly confusing names of unit cell comparison functions

cells_are_similar -> compare_cell_parameters_and_orientation
compare_cells -> compare_reindexed_cell_parameters_and_orientation
cell_tool.c:cells_the_same -> cellutils.c:compare_cell_parameters

All comparisons now done in real space, checking that centering is the
same, and without uncentering anything.

2 files changed, 9 insertions, 32 deletions

diff --git a/src/cell_tool.c b/src/cell_tool.c
index 1a2f33fb..ee82f332 100644
--- a/src/cell_tool.c
+++ b/src/cell_tool.c
@@ -68,30 +68,6 @@ static void show_help(const char *s)
 }
 
 
-static int cells_the_same(UnitCell *cell1, UnitCell *cell2, float ltl, float atl)
-{
-	double a1, b1, c1, al1, be1, ga1;
-	double a2, b2, c2, al2, be2, ga2;
-	UnitCellTransformation *tfn1, *tfn2;
-
-	/* Centering must match: we don't arbitrarte primitive vs centered,
-	 * different cell choices etc */
-	if ( cell_get_centering(cell1) != cell_get_centering(cell2) ) return 0;
-
-	cell_get_parameters(cell1, &a1, &b1, &c1, &al1, &be1, &ga1);
-	cell_get_parameters(cell2, &a2, &b2, &c2, &al2, &be2, &ga2);
-
-	if ( !within_tolerance(a1, a2, ltl) ) return 0;
-	if ( !within_tolerance(b1, b2, ltl) ) return 0;
-	if ( !within_tolerance(c1, c2, ltl) ) return 0;
-	if ( fabs(al1-al2) > atl ) return 0;
-	if ( fabs(be1-be2) > atl ) return 0;
-	if ( fabs(ga1-ga2) > atl ) return 0;
-
-	return 1;
-}
-
-
 static int comparecells(UnitCell *cell, const char *comparecell,
                         double ltl, double atl)
 {
@@ -146,7 +122,7 @@ static int comparecells(UnitCell *cell, const char *comparecell,
 		tfn = tfn_from_intmat(m);
 		nc = cell_transform(cell, tfn);
 
-		if ( cells_the_same(cell2, nc, ltl, atl) ) {
+		if ( compare_cell_parameters(cell2, nc, ltl, atl) ) {
 			STATUS("-----------------------------------------------"
 			       "-------------------------------------------\n");
 			cell_print(nc);
@@ -327,7 +303,7 @@ static int find_ambi(UnitCell *cell, SymOpList *sym, double ltl, double atl)
 		tfn = tfn_from_intmat(m);
 		nc = cell_transform(cell, tfn);
 
-		if ( cells_the_same(cell, nc, ltl, atl) ) {
+		if ( compare_cell_parameters(cell, nc, ltl, atl) ) {
 			if ( !intmat_is_identity(m) ) add_symop(ops, m);
 			STATUS("-----------------------------------------------"
 			       "-------------------------------------------\n");
diff --git a/src/whirligig.c b/src/whirligig.c
index f5a435c2..54ade40a 100644
--- a/src/whirligig.c
+++ b/src/whirligig.c
@@ -309,9 +309,9 @@ static IntegerMatrix *try_all(struct window *win, int n1, int n2,
 	for ( i=0; i<i1->n_crystals; i++ ) {
 	for ( j=0; j<i2->n_crystals; j++ ) {
 
-		if ( compare_cells(crystal_get_cell(i1->crystals[i]),
-		                   crystal_get_cell(i2->crystals[j]),
-		                   0.1, deg2rad(5.0), &m) )
+		if ( compare_reindexed_cell_parameters_and_orientation(crystal_get_cell(i1->crystals[i]),
+		                                                       crystal_get_cell(i2->crystals[j]),
+		                                                       0.1, deg2rad(5.0), &m) )
 		{
 			if ( !crystal_used(win, n1, i)
 			  && !crystal_used(win, n2, j) )
@@ -377,9 +377,10 @@ static int try_join(struct window *win, int sn)
 	for ( j=0; j<win->img[win->join_ptr].n_crystals; j++ ) {
 		Crystal *cr2;
 		cr2 = win->img[win->join_ptr].crystals[j];
-		if ( compare_cells(ref, crystal_get_cell(cr2),
-		                   0.1, deg2rad(5.0),
-		                   &win->mat[sn][win->join_ptr]) ) {
+		if ( compare_reindexed_cell_parameters_and_orientation(ref, crystal_get_cell(cr2),
+		                                                       0.1, deg2rad(5.0),
+		                                                       &win->mat[sn][win->join_ptr]) )
+		{
 			win->ser[sn][win->join_ptr] = j;
 			cell_free(ref);
 			return 1;