From cc261b60d06a475f40995e14e83cdd4189b92b0b Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 19 Nov 2009 16:14:02 +0100
Subject: Make molecular transform work

---
 src/diffraction.c |  3 ++-
 src/sfac.c        | 16 ++++++++--------
 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;
-- 
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