Tidy up and fix

src/diffraction.c

@@ -129,7 +129,7 @@ static double complex water_factor(struct threevec q, double en)
 
 	/* Density of water molecules */
 	molecules_per_m3 = WATER_DENSITY * (AVOGADRO / WATER_MOLAR_MASS);
-	
+
 	/* Number of water molecules per slice */
 	molecules_per_m = (2*rb*2*rc) * molecules_per_m3 / N_WATER_SLICES;
 
@@ -168,8 +168,11 @@ void get_diffraction(struct image *image, UnitCell *cell)
 
 	/* Generate the array of reciprocal space vectors in image->qvecs */
 	get_ewald(image);
-	image->molecule = load_molecule();
-	if ( image->molecule == NULL ) return;
+
+	if ( image->molecule == NULL ) {
+		image->molecule = load_molecule();
+		if ( image->molecule == NULL ) return;
+	}
 
 	cell_get_cartesian(cell, &ax, &ay, &az,
 		                 &bx, &by, &bz,

src/ewald.c

@@ -55,32 +55,32 @@ void get_ewald(struct image *image)
 {
 	int x, y;
 	double k;  /* Wavenumber */
-	
+
 	k = 1/image->lambda;
-	
+
 	image->qvecs = malloc(image->width * image->height
 	                       * sizeof(struct threevec));
-	
+
 	image->twotheta = malloc(image->width * image->height
 	                       * sizeof(double));
-	
+
 	for ( x=0; x<image->width; x++ ) {
 	for ( y=0; y<image->height; y++ ) {
-	
+
 		double rx, ry, r;
 		double twothetax, twothetay, twotheta;
 		double qx, qy, qz;
 		struct threevec q;
-		
+
 		/* Calculate q vectors for Ewald sphere */
 		rx = ((double)x - image->x_centre) / image->resolution;
 		ry = ((double)y - image->y_centre) / image->resolution;
 		r = sqrt(pow(rx, 2.0) + pow(ry, 2.0));
-		
+
 		twothetax = atan2(rx, image->camera_len);
-		twothetay = atan2(ry, image->camera_len);	
+		twothetay = atan2(ry, image->camera_len);
 		twotheta = atan2(r, image->camera_len);
-		
+
 		qx = k * sin(twothetax);
 		qy = k * sin(twothetay);
 		qz = k - k * cos(twotheta);
@@ -89,11 +89,8 @@ void get_ewald(struct image *image)
 		image->qvecs[x + image->width*y] = quat_rot(q,
 		                                            image->orientation);
 
-		image->qvecs[x + image->width*y].u = qx;
-		image->qvecs[x + image->width*y].v = qy;
-		image->qvecs[x + image->width*y].w = qz;
 		image->twotheta[x + image->width*y] = twotheta;
-	
+
 	}
 	}
 }

src/main.c

@@ -67,6 +67,21 @@ int main(int argc, char *argv[])
 	                                deg2rad(90.0),
 	                                deg2rad(120.0));
 
+	/* Define image parameters */
+	image.width = 512;
+	image.height = 512;
+	image.fmode = FORMULATION_CLEN;
+	image.x_centre = 255.5;
+	image.y_centre = 255.5;
+	image.camera_len = 0.2;  /* 20 cm */
+	image.resolution = 5120; /* 512 pixels in 10 cm */
+	image.xray_energy = eV_to_J(2.0e3); /* 2 keV energy */
+	image.lambda = ph_en_to_lambda(image.xray_energy);  /* Wavelength */
+	image.molecule = NULL;
+
+	/* Splurge a few useful numbers */
+	printf("Wavelength is %f nm\n", image.lambda/1.0e-9);
+
 again:
 
 	/* Read quaternion from stdin */
@@ -102,23 +117,12 @@ again:
 
 	} while ( !done );
 
-	/* Define image parameters */
-	image.width = 512;
-	image.height = 512;
-	image.fmode = FORMULATION_CLEN;
-	image.x_centre = 255.5;
-	image.y_centre = 255.5;
-	image.camera_len = 0.2;  /* 20 cm */
-	image.resolution = 5120; /* 512 pixels in 10 cm */
-	image.xray_energy = eV_to_J(2.0e3); /* 2 keV energy */
-	image.lambda = ph_en_to_lambda(image.xray_energy);  /* Wavelength */
+	/* Ensure no residual information */
 	image.qvecs = NULL;
 	image.sfacs = NULL;
 	image.data = NULL;
 	image.twotheta = NULL;
-
-	/* Splurge a few useful numbers */
-	printf("Wavelength is %f nm\n", image.lambda/1.0e-9);
+	image.hdr = NULL;
 
 	get_diffraction(&image, cell);
 	record_image(&image);
@@ -128,6 +132,14 @@ again:
 
 	/* Write the output file */
 	hdf5_write(filename, image.data, image.width, image.height);
-	printf("Mock write: %i\n", number-1);
+
+	/* Clean up */
+	free(image.data);
+	free(image.qvecs);
+	free(image.hdr);
+	free(image.sfacs);
+	free(image.twotheta);
+
+	/* Do it all again */
 	goto again;
 }