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-rw-r--r--src/sfac.c86
1 files changed, 8 insertions, 78 deletions
diff --git a/src/sfac.c b/src/sfac.c
index dd722cc8..00bbd6ba 100644
--- a/src/sfac.c
+++ b/src/sfac.c
@@ -304,8 +304,8 @@ static void centre_molecule(struct molecule *mol)
}
- //STATUS("Molecule was shifted by %5.3f, %5.3f, %5.3f nm\n",
- // mol->xc*1e9, mol->yc*1e9, mol->zc*1e9);
+ STATUS("The atoms were shifted by %5.3f, %5.3f, %5.3f nm\n",
+ mol->xc*1e9, mol->yc*1e9, mol->zc*1e9);
}
@@ -462,7 +462,7 @@ struct molecule *load_molecule()
centre_molecule(mol);
- STATUS("There are %i species\n", mol->n_species); fflush(stderr);
+ STATUS("There are %i species:\n", mol->n_species); fflush(stderr);
for ( i=0; i<mol->n_species; i++ ) {
STATUS("%3s : %6i\n", mol->species[i]->species,
mol->species[i]->n_atoms);
@@ -490,31 +490,9 @@ void free_molecule(struct molecule *mol)
}
-struct molecule *copy_molecule(struct molecule *orig)
+double *get_reflections(struct molecule *mol, double en)
{
- 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;
+ double *reflections;
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
@@ -525,7 +503,7 @@ double complex *get_reflections(struct molecule *mol, double en)
&bsx, &bsy, &bsz,
&csx, &csy, &csz);
- reflections = new_list_sfac();
+ reflections = new_list_intensity();
for ( h=-INDMAX; h<=INDMAX; h++ ) {
for ( k=-INDMAX; k<=INDMAX; k++ ) {
@@ -572,61 +550,13 @@ double complex *get_reflections(struct molecule *mol, double en)
}
- set_sfac(reflections, h, k, l, F);
+ set_intensity(reflections, h, k, l, pow(cabs(F), 2.0));
}
progress_bar((k+INDMAX)+IDIM*(h+INDMAX), IDIM*IDIM-1,
- "Calculating structure factors");
+ "Calculating reflection intensities");
}
}
return reflections;
}
-
-
-void get_reflections_cached(struct molecule *mol, double en)
-{
- char s[1024];
- FILE *fh;
- size_t r;
-
- /* Add 0.5 to improve rounding */
- snprintf(s, 1023, "reflections-%ieV.cache", (int)(J_to_eV(en)+0.5));
- fh = fopen(s, "rb");
- if ( fh == NULL ) {
- STATUS("No cache file found (looked for %s)\n", s);
- goto calc;
- }
-
- mol->reflections = new_list_sfac();
- r = fread(mol->reflections, sizeof(double complex), IDIM*IDIM*IDIM, fh);
- if ( r < IDIM*IDIM*IDIM ) {
- STATUS("Found cache file (%s), but failed to read"
- " (got %lli items, wanted %i).\n",
- s, (long long)r, IDIM*IDIM*IDIM);
- goto calc;
- }
-
- STATUS("Read structure factors (at Bragg positions) from %s\n", s);
- return;
-
-calc:
- STATUS("Calculating structure factors at Bragg positions...\n");
- mol->reflections = get_reflections(mol, en);
- fh = fopen(s, "wb");
- if ( fh == NULL ) {
- STATUS("Failed to write cache file (%s)\n", s);
- return;
- }
-
- r = fwrite(mol->reflections, sizeof(double complex),
- IDIM*IDIM*IDIM, fh);
- if ( r < IDIM*IDIM*IDIM ) {
- STATUS("Failed to write cache file (%s)\n", s);
- return;
- }
- fclose(fh);
-
- STATUS("Successfully saved structure factors at Bragg positions to"
- " file %s\n", s);
-}