Use IntegerMatrix for all unit cell transformations

Get rid of UnitCellTransformation, a thin wrapper which didn't do
anything.

2 files changed, 115 insertions, 78 deletions

diff --git a/tests/centering_check.c b/tests/centering_check.c
index 887311dd..774af66b 100644
--- a/tests/centering_check.c
+++ b/tests/centering_check.c
@@ -61,7 +61,7 @@ static int check_centering(double a, double b, double c,
 {
 	UnitCell *cell, *cref;
 	UnitCell *n;
-	UnitCellTransformation *t;
+	IntegerMatrix *t;
 	int fail = 0;
 	int i;
 	double asx, asy, asz;
@@ -88,12 +88,17 @@ static int check_centering(double a, double b, double c,
 	check_cell(cell, "Input");
 	n = uncenter_cell(cell, &t);
 	if ( n != NULL ) {
-		STATUS("Transformation was:\n");
-		tfn_print(t);
+		STATUS("The back transformation is:\n");
+		intmat_print(t);
 		if ( check_cell(n, "Output") ) fail = 1;
-		if ( !fail ) cell_print(n);
+		if ( intmat_is_identity(t) && ((cen=='P') || (cen=='R')) ) {
+			STATUS("Identity, as expected.\n");
+		} else {
+			cell_print(n);
+		}
 	} else {
-		fail = 1;
+		STATUS("*************  Could not uncenter.\n");
+		return 1;
 	}
 
 	cell_get_reciprocal(cell, &asx, &asy, &asz,
@@ -299,10 +304,6 @@ int main(int argc, char *argv[])
 	fail += check_centering(20e-10, 20e-10, 40e-10, 90.0, 90.0, 120.0,
 	                        L_HEXAGONAL, 'H', 'c', rng);
 
-	/* Cubic P */
-	fail += check_centering(30e-10, 30e-10, 30e-10, 90.0, 90.0, 90.0,
-	                        L_CUBIC, 'P', '*', rng);
-
 	/* Cubic I */
 	fail += check_centering(30e-10, 30e-10, 30e-10, 90.0, 90.0, 90.0,
 	                        L_CUBIC, 'I', '*', rng);
diff --git a/tests/transformation_check.c b/tests/transformation_check.c
index 2e7e7378..2eb01aa6 100644
--- a/tests/transformation_check.c
+++ b/tests/transformation_check.c
@@ -37,6 +37,7 @@
 
 #include <cell.h>
 #include <cell-utils.h>
+#include <symmetry.h>
 
 
 #define MAX_REFLS (10*1024)
@@ -134,17 +135,44 @@ static int compare_rvecs(struct rvec *a, int na, struct rvec *b, int nb)
 }
 
 
-static int check_transformation(UnitCell *cell, UnitCellTransformation *tfn,
+static int check_same_reflections(UnitCell *cell, UnitCell *cnew)
+{
+	struct rvec *vecs;
+	struct rvec *tvecs;
+	int na, nb;
+
+	/* Check that the two cells predict the same reflections */
+	vecs = all_refls(cell, 1e9, &na);
+	tvecs = all_refls(cnew, 1e9, &nb);
+	if ( compare_rvecs(vecs, na, tvecs, nb)
+	    || compare_rvecs(tvecs, nb, vecs, na) )
+	{
+		ERROR("******* Transformed cell didn't predict the same reflections\n");
+		//printf("---\n");
+		//for ( i=0; i<na; i++ ) {
+		//	printf("%e %e %e\n", vecs[i].u, vecs[i].v, vecs[i].w);
+		//}
+		//printf("---\n");
+		//for ( i=0; i<nb; i++ ) {
+		//	printf("%e %e %e\n", tvecs[i].u, tvecs[i].v, tvecs[i].w);
+		//}
+		return 1;
+	} else {
+		STATUS("The cells predict the same reflections.\n");
+	}
+	free(vecs);
+	free(tvecs);
+	return 0;
+}
+
+
+static int check_transformation(UnitCell *cell, IntegerMatrix *tfn,
                                 int pred_test, UnitCell *ct)
 {
 	UnitCell *cnew, *cback;
-	UnitCellTransformation *inv;
 	double a[9], b[9];
 	int i;
 	int fail = 0;
-	struct rvec *vecs;
-	struct rvec *tvecs;
-	int na, nb;
 
 	STATUS("-----------------------\n");
 	if ( ct == NULL ) {
@@ -154,32 +182,15 @@ static int check_transformation(UnitCell *cell, UnitCellTransformation *tfn,
 	}
 	cback = cell_transform_inverse(cnew, tfn);
 
+	STATUS("----> Before transformation:\n");
 	cell_print(cell);
-	tfn_print(tfn);
+	STATUS("----> The transformation matrix:\n");
+	intmat_print(tfn);
+	STATUS("----> After transformation:\n");
 	cell_print(cnew);
 
 	if ( pred_test ) {
-		/* Check that the two cells predict the same reflections */
-		vecs = all_refls(cell, 1e9, &na);
-		tvecs = all_refls(cnew, 1e9, &nb);
-		if ( compare_rvecs(vecs, na, tvecs, nb)
-		  || compare_rvecs(tvecs, nb, vecs, na) )
-		{
-			ERROR("Transformed cell didn't predict the same reflections\n");
-			//printf("---\n");
-			//for ( i=0; i<na; i++ ) {
-			//	printf("%e %e %e\n", vecs[i].u, vecs[i].v, vecs[i].w);
-			//}
-			//printf("---\n");
-			//for ( i=0; i<nb; i++ ) {
-			//	printf("%e %e %e\n", tvecs[i].u, tvecs[i].v, tvecs[i].w);
-			//}
-			return 1;
-		} else {
-			STATUS("The cells predict the same reflections.\n");
-		}
-		free(vecs);
-		free(tvecs);
+		check_same_reflections(cell, cnew);
 	} else {
 		STATUS("Cells not expected to predict the same reflections.\n");
 	}
@@ -193,18 +204,17 @@ static int check_transformation(UnitCell *cell, UnitCellTransformation *tfn,
 	                          &b[6], &b[7], &b[8]);
 	for ( i=0; i<9; i++ ) {
 		if ( !tolerance(a[i], b[i]) ) {
+			//STATUS("%e %e\n", a[i], b[i]);
 			fail = 1;
-			STATUS("%e %e\n", a[i], b[i]);
 		}
 	}
 
 	if ( fail ) {
-		ERROR("Original cell not recovered after transformation:\n");
-		cell_print(cell);
-		tfn_print(tfn);
-		inv = tfn_inverse(tfn);
-		tfn_print(inv);
+		ERROR("******* Original cell not recovered after transformation:\n");
+		STATUS("----> After transformation and transformation back:\n");
 		cell_print(cback);
+	} else {
+		STATUS("The original cell was recovered after inverse transform.\n");
 	}
 
 	return fail;
@@ -214,22 +224,48 @@ static int check_transformation(UnitCell *cell, UnitCellTransformation *tfn,
 static int check_uncentering(UnitCell *cell)
 {
 	UnitCell *ct;
-	UnitCellTransformation *tr;
+	IntegerMatrix *tr;
+	int fail = 0;
+
+	STATUS("-----------------------\n");
+
+	STATUS("----> Before transformation:\n");
+	cell_print(cell);
 
 	ct = uncenter_cell(cell, &tr);
-	return check_transformation(cell, tr, 1, ct);
+	if ( ct == NULL ) return 1;
+
+	STATUS("----> The primitive unit cell:\n");
+	cell_print(ct);
+
+	STATUS("----> The matrix to put the centering back:\n");
+	intmat_print(tr);
+
+	fail = check_same_reflections(cell, ct);
+	cell_free(ct);
+
+	return fail;
 }
 
 
-static int check_identity(UnitCell *cell, UnitCellTransformation *tfn)
+static int check_identity(UnitCell *cell, IntegerMatrix *tfn)
 {
 	UnitCell *cnew;
 	double a[9], b[9];
 	int i;
 	int fail = 0;
 
+	STATUS("-----------------------\n");
+
 	cnew = cell_transform(cell, tfn);
 
+	STATUS("----> Before identity transformation:\n");
+	cell_print(cell);
+	STATUS("----> The identity transformation matrix:\n");
+	intmat_print(tfn);
+	STATUS("----> After identity transformation:\n");
+	cell_print(cnew);
+
 	cell_get_cartesian(cell, &a[0], &a[1], &a[2],
 	                         &a[3], &a[4], &a[5],
 	                         &a[6], &a[7], &a[8]);
@@ -239,14 +275,14 @@ static int check_identity(UnitCell *cell, UnitCellTransformation *tfn)
 	for ( i=0; i<9; i++ ) {
 		if ( !within_tolerance(a[i], b[i], 0.1) ) {
 			fail = 1;
-			STATUS("%e %e\n", a[i], b[i]);
+			//STATUS("%e %e\n", a[i], b[i]);
 		}
 	}
 
 	if ( fail ) {
-		ERROR("Original cell not recovered after transformation:\n");
+		ERROR("Original cell not recovered after identity transformation:\n");
 		cell_print(cell);
-		tfn_print(tfn);
+		intmat_print(tfn);
 		cell_print(cnew);
 	}
 
@@ -258,7 +294,8 @@ int main(int argc, char *argv[])
 {
 	int fail = 0;
 	UnitCell *cell, *cref;
-	UnitCellTransformation *tfn;
+	IntegerMatrix *tfn;
+	IntegerMatrix *part1, *part2;
 	gsl_rng *rng;
 
 	rng = gsl_rng_alloc(gsl_rng_mt19937);
@@ -273,53 +310,52 @@ int main(int argc, char *argv[])
 	if ( cell == NULL ) return 1;
 	cell_free(cref);
 
+	tfn = intmat_identity(3);
+
 	/* Permutation of axes */
-	tfn = tfn_identity();
 	if ( tfn == NULL ) return 1;
-	tfn_combine(tfn, tfn_vector(0,1,0),
-	                 tfn_vector(0,0,1),
-	                 tfn_vector(1,0,0));
+	intmat_set_all_3x3(tfn, 0,1,0,
+	                        0,0,1,
+	                        1,0,0);
 	fail += check_transformation(cell, tfn, 1, NULL);
-	tfn_free(tfn);
 
 	/* Doubling of cell in one direction */
-	tfn = tfn_identity();
 	if ( tfn == NULL ) return 1;
-	tfn_combine(tfn, tfn_vector(2,0,0),
-	                 tfn_vector(0,1,0),
-	                 tfn_vector(0,0,1));
+	intmat_set_all_3x3(tfn, 2,0,0,
+	                        0,1,0,
+	                        0,0,1);
 	fail += check_transformation(cell, tfn, 0, NULL);
-	tfn_free(tfn);
 
-	/* Diagonal supercell */
-	tfn = tfn_identity();
+	/* Shearing */
 	if ( tfn == NULL ) return 1;
-	tfn_combine(tfn, tfn_vector(1,1,0),
-	                 tfn_vector(0,1,0),
-	                 tfn_vector(0,0,1));
+	intmat_set_all_3x3(tfn, 1,1,0,
+	                        0,1,0,
+	                        0,0,1);
 	fail += check_transformation(cell, tfn, 1, NULL);
-	tfn_free(tfn);
 
 	/* Crazy */
-	tfn = tfn_identity();
 	if ( tfn == NULL ) return 1;
-	tfn_combine(tfn, tfn_vector(1,1,0),
-	                 tfn_vector(0,1,0),
-	                 tfn_vector(0,1,1));
+	intmat_set_all_3x3(tfn, 1,1,0,
+	                        0,1,0,
+	                        0,1,1);
 	fail += check_transformation(cell, tfn, 0, NULL);
-	tfn_free(tfn);
 
 	/* Identity in two parts */
-	tfn = tfn_identity();
+	part1 = intmat_identity(3);
+	part2 = intmat_identity(3);
 	if ( tfn == NULL ) return 1;
-	tfn_combine(tfn, tfn_vector(0,0,1),
-	                 tfn_vector(0,1,0),
-	                 tfn_vector(-1,0,0));
-	tfn_combine(tfn,  tfn_vector(0,0,-1),
-	                  tfn_vector(0,1,0),
-	                  tfn_vector(1,0,0));
+	intmat_set_all_3x3(part1, 0,0,1,
+	                        0,1,0,
+	                        -1,0,0);
+	intmat_set_all_3x3(part2,  0,0,-1,
+	                         0,1,0,
+	                         1,0,0);
+	tfn = intmat_intmat_mult(part1, part2);
 	fail += check_identity(cell, tfn);
-	tfn_free(tfn);
+	intmat_free(part1);
+	intmat_free(part2);
+
+	intmat_free(tfn);
 
 	/* Check some uncentering transformations */
 	cref = cell_new_from_parameters(50e-10, 50e-10, 50e-10,