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authorThomas White <taw@physics.org>2009-11-19 16:14:02 +0100
committerThomas White <taw@physics.org>2009-11-19 16:14:02 +0100
commitcc261b60d06a475f40995e14e83cdd4189b92b0b (patch)
treebcad019fb90843c1a4208e35d778704cb8f71428 /src
parenta90da1791f73b8b9ddcca28e1865c6ae17a78db2 (diff)
Make molecular transform work
Diffstat (limited to 'src')
-rw-r--r--src/diffraction.c3
-rw-r--r--src/sfac.c16
2 files changed, 10 insertions, 9 deletions
diff --git a/src/diffraction.c b/src/diffraction.c
index 0fd8dea9..87f2a5f7 100644
--- a/src/diffraction.c
+++ b/src/diffraction.c
@@ -80,12 +80,13 @@ static double complex molecule_factor(struct molecule *mol, struct threevec q,
double en)
{
int i;
- double F = 0.0;
+ double complex F = 0.0;
double s;
/* s = sin(theta)/lambda = 1/2d = (1/d)/2.0 */
s = modulus(q.u, q.v, q.w) / 2.0;
+ /* Atoms are grouped by species for faster calculation */
for ( i=0; i<mol->n_species; i++ ) {
double complex sfac;
diff --git a/src/sfac.c b/src/sfac.c
index ffe98f11..b8e2119f 100644
--- a/src/sfac.c
+++ b/src/sfac.c
@@ -268,11 +268,11 @@ struct molecule *load_molecule()
n = mol->species[j]->n_atoms;
- spec->x[n] = x;
- spec->y[n] = y;
- spec->z[n] = z;
+ spec->x[n] = x*1.0e-10; /* Convert to nm */
+ spec->y[n] = y*1.0e-10;
+ spec->z[n] = z*1.0e-10;
spec->occ[n] = occ;
- spec->B[n] = B;
+ spec->B[n] = B*1.0e-20; /* Convert to m^2 */
mol->species[j]->n_atoms++;
done = 1;
@@ -287,11 +287,11 @@ struct molecule *load_molecule()
spec = malloc(sizeof(struct mol_species));
memcpy(spec->species, el, 4);
- spec->x[0] = x;
- spec->y[0] = y;
- spec->z[0] = z;
+ spec->x[0] = x*1.0e-10; /* Convert to nm */
+ spec->y[0] = y*1.0e-10;
+ spec->z[0] = z*1.0e-10;
spec->occ[0] = occ;
- spec->B[0] = B;
+ spec->B[0] = B*1.0e-20; /* Convert to nm^2 */
spec->n_atoms = 1;
mol->species[mol->n_species] = spec;