From 274a5e2803eb3afe0d53b27c6078ef4495d587a0 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Wed, 17 Mar 2010 14:09:49 +0100
Subject: Fix various memory leaks and tidy a few things

---
 src/cell.c        | 16 ++++++++++++++++
 src/cell.h        |  1 +
 src/dirax.c       |  1 +
 src/indexamajig.c | 17 +++++++++++++----
 src/sfac.c        | 36 ++++++++++++++++++++++++++++++++++++
 src/sfac.h        |  3 +++
 6 files changed, 70 insertions(+), 4 deletions(-)

diff --git a/src/cell.c b/src/cell.c
index 5747ed63..408b5bf3 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -262,11 +262,25 @@ static UnitCell *cell_new_from_axes(struct rvec as, struct rvec bs,
 	cell->cy = gsl_matrix_get(inv, 2, 1);
 	cell->cz = gsl_matrix_get(inv, 2, 2);
 
+	gsl_matrix_free(inv);
+
 	cell_update_crystallographic(cell);
 	return cell;
 }
 
 
+UnitCell *cell_new_from_cell(UnitCell *orig)
+{
+	UnitCell *new;
+
+	new = malloc(sizeof(UnitCell));
+
+	*new = *orig;
+
+	return new;
+}
+
+
 void cell_get_cartesian(UnitCell *cell,
                         double *ax, double *ay, double *az,
                         double *bx, double *by, double *bz,
@@ -321,6 +335,8 @@ void cell_get_reciprocal(UnitCell *cell,
 	*asz = gsl_matrix_get(inv, 2, 0);
 	*bsz = gsl_matrix_get(inv, 2, 1);
 	*csz = gsl_matrix_get(inv, 2, 2);
+
+	gsl_matrix_free(inv);
 }
 
 
diff --git a/src/cell.h b/src/cell.h
index 4c74b283..5a534268 100644
--- a/src/cell.h
+++ b/src/cell.h
@@ -39,6 +39,7 @@ typedef struct {
 } UnitCell;
 
 extern UnitCell *cell_new(void);
+extern UnitCell *cell_new_from_cell(UnitCell *orig);
 
 /* Lengths in m, angles in radians */
 extern UnitCell *cell_new_from_parameters(double a, double b, double c,
diff --git a/src/dirax.c b/src/dirax.c
index d18d1fa6..49e16921 100644
--- a/src/dirax.c
+++ b/src/dirax.c
@@ -421,6 +421,7 @@ void run_dirax(struct image *image)
 
 	close(image->dirax_pty);
 	close(saved_stderr);
+	free(image->dirax_rbuffer);
 	wait(&status);
 
 	return;
diff --git a/src/indexamajig.c b/src/indexamajig.c
index f3cb05fc..7c227cb1 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -114,6 +114,7 @@ static struct image *get_simage(struct image *template, int alternate)
 		panels[1].res = 13333.3;   /* 75 microns/pixel */
 
 		image->det.panels = panels;
+
 	} else {
 
 		/* Copy pointer to old geometry */
@@ -123,8 +124,9 @@ static struct image *get_simage(struct image *template, int alternate)
 
 	image->lambda = ph_en_to_lambda(eV_to_J(1.8e3));
 
-	image->molecule = template->molecule;
-	image->molecule->cell = template->indexed_cell;
+	image->molecule = copy_molecule(template->molecule);
+	free(image->molecule->cell);
+	image->molecule->cell = cell_new_from_cell(template->indexed_cell);
 
 	return image;
 }
@@ -241,8 +243,9 @@ int main(int argc, char *argv[])
 
 	if ( indm_str == NULL ) {
 		STATUS("You didn't specify an indexing method, so I won't"
-		       " try to index anything.  If that isn't what you\n"
-		       " wanted, re-run with --indexing=<method>.\n");
+		       " try to index anything.\n"
+		       "If that isn't what you wanted, re-run with"
+		       " --indexing=<method>.\n");
 		indm = INDEXING_NONE;
 	} else if ( strcmp(indm_str, "none") == 0 ) {
 		indm = INDEXING_NONE;
@@ -252,6 +255,7 @@ int main(int argc, char *argv[])
 		ERROR("Unrecognised indexing method '%s'\n", indm_str);
 		return 1;
 	}
+	free(indm_str);
 
 	image.molecule = load_molecule();
 	if ( image.molecule == NULL ) {
@@ -342,8 +346,12 @@ int main(int argc, char *argv[])
 		/* Finished with alternate image */
 		if ( simage->twotheta != NULL ) free(simage->twotheta);
 		if ( simage->data != NULL ) free(simage->data);
+		free_molecule(simage->molecule);
 		free(simage);
 
+		/* Only free cell if found */
+		free(image.indexed_cell);
+
 done:
 		free(image.data);
 		free(image.det.panels);
@@ -354,6 +362,7 @@ done:
 	} while ( rval != NULL );
 
 	fclose(fh);
+	free_molecule(image.molecule);
 
 	STATUS("There were %i images.\n", n_images);
 	STATUS("%i hits were found.\n", n_hits);
diff --git a/src/sfac.c b/src/sfac.c
index 0e8b9382..81e381b3 100644
--- a/src/sfac.c
+++ b/src/sfac.c
@@ -323,6 +323,7 @@ struct molecule *load_molecule()
 	if ( mol == NULL ) return NULL;
 	mol->n_species = 0;
 	mol->reflections = NULL;
+	mol->cell = NULL;
 
 	fh = fopen("molecule.pdb", "r");
 	if ( fh == NULL ) {
@@ -443,6 +444,41 @@ struct molecule *load_molecule()
 }
 
 
+void free_molecule(struct molecule *mol)
+{
+	int i;
+
+	for ( i=0; i<mol->n_species; i++ ) {
+		free(mol->species[i]);
+	}
+
+	free(mol->cell);
+	free(mol);
+}
+
+
+struct molecule *copy_molecule(struct molecule *orig)
+{
+	struct molecule *new;
+	int i;
+
+	new = malloc(sizeof(*new));
+	*new = *orig;
+
+	/* Now sort out pointers */
+	for ( i=0; i<orig->n_species; i++ ) {
+		new->species[i] = malloc(sizeof(struct mol_species));
+		memcpy(new->species[i], orig->species[i],
+		       sizeof(struct mol_species));
+	}
+
+	new->cell = cell_new_from_cell(orig->cell);
+	new->reflections = NULL;
+
+	return new;
+}
+
+
 double complex *get_reflections(struct molecule *mol, double en)
 {
 	double complex *reflections;
diff --git a/src/sfac.h b/src/sfac.h
index d1424fc7..000b859f 100644
--- a/src/sfac.h
+++ b/src/sfac.h
@@ -54,7 +54,10 @@ struct molecule
 
 extern double complex get_sfac(const char *n, double s, double en);
 extern struct molecule *load_molecule(void);
+extern void free_molecule(struct molecule *mol);
+extern struct molecule *copy_molecule(struct molecule *orig);
 extern double complex *get_reflections(struct molecule *mol, double en);
 extern void get_reflections_cached(struct molecule *mol, double en);
 
+
 #endif	/* SFAC_H */
-- 
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