Tidy some things up:

	s convention
	detector geometry
	comments, help messages

src/cell.c

@@ -554,6 +554,7 @@ done:
 }
 
 
+/* Return sin(theta)/lambda = 1/2d.  Multiply by two if you want 1/d */
 double resolution(UnitCell *cell, signed int h, signed int k, signed int l)
 {
 	const double a = cell->a;

src/compare_hkl.c

@@ -28,7 +28,7 @@
 
 static void show_help(const char *s)
 {
-	printf("Syntax: %s [options] <file1.hkl> <file2.hkl>\n\n", s);
+	printf("Syntax: %s [options] -a <file1.hkl> -b <file2.hkl>\n\n", s);
 	printf(
 "Compare intensity lists.\n"
 "\n"

src/detector.c

@@ -191,6 +191,7 @@ void record_image(struct image *image, int do_water, int do_poisson,
 			return;
 		}
 
+		/* FIXME: Move to diffraction.c somehow */
 		if ( do_water ) {
 
 			struct rvec q;

src/geometry-lcls.tmp

+/* Set up detector configuration */
+image.det.n_panels = 2;
+image.det.panels = malloc(2*sizeof(struct panel));
+
+/* Upper panel */
+image.det.panels[0].min_x = 0;
+image.det.panels[0].max_x = 1023;
+image.det.panels[0].min_y = 512;
+image.det.panels[0].max_y = 1023;
+image.det.panels[0].cx = 491.9;
+image.det.panels[0].cy = 440.7;
+image.det.panels[0].clen = 67.0e-3;
+image.det.panels[0].res = 13333.3;  /* 75 micron pixel size */
+
+/* Lower panel */
+image.det.panels[1].min_x = 0;
+image.det.panels[1].max_x = 1023;
+image.det.panels[1].min_y = 0;
+image.det.panels[1].max_y = 511;
+image.det.panels[1].cx = 492.0;
+image.det.panels[1].cy = 779.7;
+image.det.panels[1].clen = 75.0e-3;
+image.det.panels[1].res = 13333.3;  /* 75 micron pixel size */

src/indexamajig.c

@@ -170,28 +170,7 @@ int main(int argc, char *argv[])
 		image.data = NULL;
 		image.indexed_cell = NULL;
 
-		/* Set up detector configuration */
-		image.det.n_panels = 2;
-		image.det.panels = malloc(2*sizeof(struct panel));
-		/* Upper panel */
-		image.det.panels[0].min_x = 0;
-		image.det.panels[0].max_x = 1023;
-		image.det.panels[0].min_y = 512;
-		image.det.panels[0].max_y = 1023;
-		image.det.panels[0].cx = 491.9;
-		image.det.panels[0].cy = 440.7;
-		image.det.panels[0].clen = 67.0e-3;
-		image.det.panels[0].res = 13333.3;  /* 75 micron pixel size */
-
-		/* Lower panel */
-		image.det.panels[1].min_x = 0;
-		image.det.panels[1].max_x = 1023;
-		image.det.panels[1].min_y = 0;
-		image.det.panels[1].max_y = 511;
-		image.det.panels[1].cx = 492.0;
-		image.det.panels[1].cy = 779.7;
-		image.det.panels[1].clen = 75.0e-3;
-		image.det.panels[1].res = 13333.3;  /* 75 micron pixel size */
+		#include "geometry-lcls.tmp"
 
 		STATUS("Processing '%s'\n", line);
 

src/pattern_sim.c

 /*
- * main.c
+ * pattern_sim.c
+ *
+ * Simulate diffraction patterns from small crystals
  *
  * (c) 2006-2010 Thomas White <taw@physics.org>
  *
@@ -227,27 +229,7 @@ int main(int argc, char *argv[])
 	image.lambda = ph_en_to_lambda(eV_to_J(2.0e3));  /* Wavelength */
 	image.molecule = load_molecule();
 
-	/* Set up detector configuration */
-	image.det.n_panels = 2;
-	image.det.panels = malloc(2*sizeof(struct panel));
-	/* Upper panel */
-	image.det.panels[0].min_x = 0;
-	image.det.panels[0].max_x = 1023;
-	image.det.panels[0].min_y = 512;
-	image.det.panels[0].max_y = 1023;
-	image.det.panels[0].cx = 491.9;
-	image.det.panels[0].cy = 440.7;
-	image.det.panels[0].clen = 67.0e-3;
-	image.det.panels[0].res = 13333.3;  /* 75 micron pixel size */
-	/* Lower panel */
-	image.det.panels[1].min_x = 0;
-	image.det.panels[1].max_x = 1023;
-	image.det.panels[1].min_y = 0;
-	image.det.panels[1].max_y = 511;
-	image.det.panels[1].cx = 492.0;
-	image.det.panels[1].cy = 779.7;
-	image.det.panels[1].clen = 75.0e-3;
-	image.det.panels[1].res = 13333.3;  /* 75 micron pixel size */
+	#include "geometry-lcls.tmp"
 
 	powder = calloc(image.width*image.height, sizeof(*powder));
 

src/process_hkl.c

@@ -78,7 +78,7 @@ static void write_RvsQ(const char *name, double *ref, double *trueref,
 	for ( h=-INDMAX; h<INDMAX; h++ ) {
 	for ( k=-INDMAX; k<INDMAX; k++ ) {
 	for ( l=-INDMAX; l<INDMAX; l++ ) {
-		double s = resolution(cell, h, k, l);
+		double s = 2.0*resolution(cell, h, k, l);
 		if ( (lookup_count(counts, h, k, l) > 0) && (s > smax) ) {
 			smax = s;
 		}
@@ -105,7 +105,7 @@ static void write_RvsQ(const char *name, double *ref, double *trueref,
 			if ( (h==0) && (k==0) && (l==0) ) continue;
 
 			c = lookup_count(counts, h, k, l);
-			s = resolution(cell, h, k, l);
+			s = 2.0*resolution(cell, h, k, l);
 			if ((s>=sbracket) && (s<sbracket+smax/RVQDV) && (c>0)) {
 
 				double obs, calc, obsi;

src/reflections.c

@@ -45,7 +45,6 @@ void write_reflections(const char *filename, unsigned int *counts,
 		fprintf(fh, "a %5.3f nm\n", a*1e9);
 		fprintf(fh, "b %5.3f nm\n", b*1e9);
 		fprintf(fh, "angle %5.3f deg\n", rad2deg(gamma));
-		fprintf(fh, "scale 10\n");
 	}
 
 	for ( h=-INDMAX; h<INDMAX; h++ ) {
@@ -65,7 +64,7 @@ void write_reflections(const char *filename, unsigned int *counts,
 		F = lookup_intensity(ref, h, k, l) / N;
 		if ( zone_axis && (l != 0) ) continue;
 
-		s = resolution(cell, h, k, l);
+		s = 2.0*resolution(cell, h, k, l);
 
 		/* h, k, l, I, sigma(I), s */
 		fprintf(fh, "%3i %3i %3i %f %f %f\n", h, k, l, F, 0.0, s/1.0e9);

src/sfac.c

@@ -456,6 +456,7 @@ double complex *get_reflections(struct molecule *mol, double en)
 		int i;
 		double s;
 
+		/* We need sin(theta)/lambda = 1/2d */
 		s = resolution(mol->cell, h, k, l);
 
 		/* Atoms are grouped by species for faster calculation */