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-rw-r--r--src/cell.c16
-rw-r--r--src/cell.h1
-rw-r--r--src/dirax.c1
-rw-r--r--src/indexamajig.c17
-rw-r--r--src/sfac.c36
-rw-r--r--src/sfac.h3
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 */