Tidy up, fix things

5 files changed, 98 insertions, 58 deletions

diff --git a/src/cell.c b/src/cell.c
index 5e8b1ce6..6fc29e56 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -206,3 +206,33 @@ void cell_get_reciprocal(UnitCell *cell,
 	*bsz = gsl_matrix_get(inv, 2, 1);
 	*csz = gsl_matrix_get(inv, 2, 2);
 }
+
+
+double resolution(UnitCell *cell, signed int h, signed int k, signed int l)
+{
+	const double a = cell->a;
+	const double b = cell->b;
+	const double c = cell->c;
+	const double alpha = cell->alpha;
+	const double beta = cell->beta;
+	const double gamma = cell->gamma;
+
+	const double Vsq = a*a*b*b*c*c*(1 - cos(alpha)*cos(alpha)
+	                                  - cos(beta)*cos(beta)
+	                                  - cos(gamma)*cos(gamma)
+				          + 2*cos(alpha)*cos(beta)*cos(gamma) );
+
+	const double S11 = b*b*c*c*sin(alpha)*sin(alpha);
+	const double S22 = a*a*c*c*sin(beta)*sin(beta);
+	const double S33 = a*a*b*b*sin(gamma)*sin(gamma);
+	const double S12 = a*b*c*c*(cos(alpha)*cos(beta) - cos(gamma));
+	const double S23 = a*a*b*c*(cos(beta)*cos(gamma) - cos(alpha));
+	const double S13 = a*b*b*c*(cos(gamma)*cos(alpha) - cos(beta));
+
+	const double brackets = S11*h*h + S22*k*k + S33*l*l
+	                         + 2*S12*h*k + 2*S23*k*l + 2*S13*h*l;
+	const double oneoverdsq = brackets / Vsq;
+	const double oneoverd = sqrt(oneoverdsq);
+
+	return oneoverd / 2;
+}
diff --git a/src/cell.h b/src/cell.h
index b2203561..860cce05 100644
--- a/src/cell.h
+++ b/src/cell.h
@@ -62,4 +62,7 @@ extern void cell_get_reciprocal(UnitCell *cell,
                                double *bsx, double *bsy, double *bsz,
                                double *csx, double *csy, double *csz);
 
+extern double resolution(UnitCell *cell,
+                         signed int h, signed int k, signed int l);
+
 #endif	/* CELL_H */
diff --git a/src/diffraction.c b/src/diffraction.c
index e112e7ce..9a9e31b6 100644
--- a/src/diffraction.c
+++ b/src/diffraction.c
@@ -84,6 +84,7 @@ static double complex molecule_factor(struct molecule *mol, struct threevec q,
 {
 	double hd, kd, ld;
 	signed int h, k, l;
+	double complex r;
 
 	hd = q.u * ax + q.v * ay + q.w * az;
 	kd = q.u * bx + q.v * by + q.w * bz;
@@ -92,7 +93,9 @@ static double complex molecule_factor(struct molecule *mol, struct threevec q,
 	k = (signed int)nearbyint(kd);
 	l = (signed int)nearbyint(ld);
 
-	return get_integral(mol->reflections, h, k, l);
+	r = get_integral(mol->reflections, h, k, l);
+
+	return r;
 }
 
 
@@ -102,51 +105,6 @@ static double complex water_factor(struct threevec q, double en)
 }
 
 
-static void get_reflections_cached(struct molecule *mol, double en)
-{
-	char s[1024];
-	FILE *fh;
-	size_t r;
-
-	snprintf(s, 1023, "reflections-%ieV.cache", (int)J_to_eV(en));
-	fh = fopen(s, "rb");
-	if ( fh == NULL ) {
-		printf("No cache file found (looked for %s)\n", s);
-		goto calc;
-	}
-
-	mol->reflections = reflist_new();
-	r = fread(mol->reflections, sizeof(double complex), IDIM*IDIM*IDIM, fh);
-	if ( r <  IDIM*IDIM*IDIM ) {
-		printf("Found cache file (%s), but failed to read.\n", s);
-		goto calc;
-	}
-
-	printf("Read structure factors (at Bragg positions) from %s\n", s);
-	return;
-
-calc:
-	printf("Calculating structure factors at Bragg positions...\n");
-	mol->reflections = get_reflections(mol, en);
-	fh = fopen(s, "wb");
-	if ( fh == NULL ) {
-		printf("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 ) {
-		printf("Failed to write cache file (%s)\n", s);
-		return;
-	}
-	fclose(fh);
-
-	printf("Successfully saved structure factors at Bragg positions to"
-	       " file %s\n", s);
-}
-
-
 void get_diffraction(struct image *image)
 {
 	int x, y;
@@ -189,14 +147,8 @@ void get_diffraction(struct image *image)
 		f_molecule = molecule_factor(image->molecule, q,
 		                             ax,ay,az,bx,by,bz,cx,cy,cz);
 
-		/* Nasty approximation follows */
-		if ( y == image->height/2 ) {
-			f_water = water_factor(q, image->xray_energy);
-		} else {
-			f_water = 0.0;
-		}
-
-		val = (f_molecule) + f_water;
+		f_water = water_factor(q, image->xray_energy);
+		val = (f_molecule * f_lattice) + f_water;
 		image->sfacs[x + image->width*y] = val;
 
 	}
diff --git a/src/sfac.c b/src/sfac.c
index 7257bf01..7bf30f82 100644
--- a/src/sfac.c
+++ b/src/sfac.c
@@ -175,7 +175,7 @@ static double get_waas_kirf(const char *n, double s)
 
 	fclose(fh);
 
-	s2 = pow(s/1e10, 2.0);  /* s2 is s squared in Angstroms squared */
+	s2 = pow(s/1e10, 2.0);  /* s2 is s squared in Angstroms^-2 */
 	f = c + a1*exp(-b1*s2) + a2*exp(-b2*s2) + a3*exp(-b3*s2)
 	      + a4*exp(-b4*s2) + a5*exp(-b5*s2);
 
@@ -390,6 +390,8 @@ double complex *get_reflections(struct molecule *mol, double en)
 	double bsx, bsy, bsz;
 	double csx, csy, csz;
 	signed int h, k, l;
+	//double tscat = 0.0;
+	//double F00;
 
 	cell_get_reciprocal(mol->cell, &asx, &asy, &asz,
 	                               &bsx, &bsy, &bsz,
@@ -401,10 +403,12 @@ double complex *get_reflections(struct molecule *mol, double en)
 	for ( k=-INDMAX; k<=INDMAX; k++ ) {
 	for ( l=-INDMAX; l<=INDMAX; l++ ) {
 
-		double complex F;
+		double complex F = 0.0;
 		int i;
 		double s;
 
+		s = resolution(mol->cell, h, k, l);
+
 		/* Atoms are grouped by species for faster calculation */
 		for ( i=0; i<mol->n_species; i++ ) {
 
@@ -426,8 +430,7 @@ double complex *get_reflections(struct molecule *mol, double en)
 				ph = u*spec->x[j] + v*spec->y[j] + w*spec->z[j];
 
 				/* Conversion from revolutions to radians */
-				contrib += cos(-2.0*M_PI*ph)
-				                          + I*sin(-2.0*M_PI*ph);
+				contrib += cexp(-2.0*M_PI*I*ph);
 
 			}
 
@@ -437,12 +440,63 @@ double complex *get_reflections(struct molecule *mol, double en)
 		}
 
 		integrate_reflection(reflections, h, k, l, F);
+		//if ( (h!=0) || (k!=0) || (l!=0) ) {
+		//	tscat += cabs(F);
+		//} else {
+		//	F00 = cabs(F);
+		//}
 
 	}
 	}
 	progress_bar((h+INDMAX+1), 2*INDMAX);
 	}
 	printf("\n");
+	//printf("Total scattered = %f, F000 = %f\n", tscat, F00);
 
 	return reflections;
 }
+
+
+void get_reflections_cached(struct molecule *mol, double en)
+{
+	char s[1024];
+	FILE *fh;
+	size_t r;
+
+	snprintf(s, 1023, "reflections-%ieV.cache", (int)J_to_eV(en));
+	fh = fopen(s, "rb");
+	if ( fh == NULL ) {
+		printf("No cache file found (looked for %s)\n", s);
+		goto calc;
+	}
+
+	mol->reflections = reflist_new();
+	r = fread(mol->reflections, sizeof(double complex), IDIM*IDIM*IDIM, fh);
+	if ( r <  IDIM*IDIM*IDIM ) {
+		printf("Found cache file (%s), but failed to read.\n", s);
+		goto calc;
+	}
+
+	printf("Read structure factors (at Bragg positions) from %s\n", s);
+	return;
+
+calc:
+	printf("Calculating structure factors at Bragg positions...\n");
+	mol->reflections = get_reflections(mol, en);
+	fh = fopen(s, "wb");
+	if ( fh == NULL ) {
+		printf("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 ) {
+		printf("Failed to write cache file (%s)\n", s);
+		return;
+	}
+	fclose(fh);
+
+	printf("Successfully saved structure factors at Bragg positions to"
+	       " file %s\n", s);
+}
diff --git a/src/sfac.h b/src/sfac.h
index fc4b2bd9..131a05e8 100644
--- a/src/sfac.h
+++ b/src/sfac.h
@@ -55,5 +55,6 @@ struct molecule
 extern double complex get_sfac(const char *n, double s, double en);
 extern struct molecule *load_molecule(void);
 extern double complex *get_reflections(struct molecule *mol, double en);
+extern void get_reflections_cached(struct molecule *mol, double en);
 
 #endif	/* SFAC_H */