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-rw-r--r--.gitignore1
-rw-r--r--Makefile.am2
-rw-r--r--src/Makefile.am11
-rw-r--r--src/get_hkl.c78
-rw-r--r--src/process_hkl.c70
-rw-r--r--src/reflections.c87
-rw-r--r--src/reflections.h29
7 files changed, 205 insertions, 73 deletions
diff --git a/.gitignore b/.gitignore
index 2e09d144..0ca4d405 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,4 +11,5 @@ src/*.o
src/.deps
src/pattern_sim
src/process_hkl
+src/get_hkl
*~
diff --git a/Makefile.am b/Makefile.am
index 604c2a15..b5e1b3fe 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,4 +1,4 @@
EXTRA_DIST = configure src/cell.h src/hdf5-file.h src/image.h src/relrod.h \
src/utils.h src/diffraction.h src/detector.h src/ewald.h \
- src/sfac.h src/intensities.h
+ src/sfac.h src/intensities.h src/reflections.h
SUBDIRS = src
diff --git a/src/Makefile.am b/src/Makefile.am
index efaf09a8..81b52045 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,10 +1,15 @@
-bin_PROGRAMS = pattern_sim process_hkl
+bin_PROGRAMS = pattern_sim process_hkl get_hkl
AM_CFLAGS = -Wall
pattern_sim_SOURCES = pattern_sim.c diffraction.c utils.c image.c cell.c \
- hdf5-file.c ewald.c detector.c sfac.c intensities.c
+ hdf5-file.c ewald.c detector.c sfac.c intensities.c \
+ reflections.c
pattern_sim_LDADD = @LIBS@
-process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c
+process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
+ reflections.c
process_hkl_LDADD = @LIBS@
+
+get_hkl_SOURCES = get_hkl.c sfac.c cell.c utils.c reflections.c
+get_hkl_LDADD = @LIBS@
diff --git a/src/get_hkl.c b/src/get_hkl.c
new file mode 100644
index 00000000..907a47d4
--- /dev/null
+++ b/src/get_hkl.c
@@ -0,0 +1,78 @@
+/*
+ * get_hkl.c
+ *
+ * Small program to write out a list of h,k,l,I values given a structure
+ *
+ * (c) 2006-2009 Thomas White <thomas.white@desy.de>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdarg.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+#include <getopt.h>
+
+#include "utils.h"
+#include "sfac.h"
+#include "reflections.h"
+
+
+static void show_help(const char *s)
+{
+ printf("Syntax: %s [options]\n\n", s);
+ printf(
+"Write idealised intensity lists.\n"
+"\n"
+" -h, --help Display this help message.\n");
+}
+
+
+int main(int argc, char *argv[])
+{
+ int c;
+ double *ref;
+ struct molecule *mol;
+
+ /* Long options */
+ const struct option longopts[] = {
+ {"help", 0, NULL, 'h'},
+ {0, 0, NULL, 0}
+ };
+
+ /* Short options */
+ while ((c = getopt_long(argc, argv, "hi:e:r", longopts, NULL)) != -1) {
+
+ switch (c) {
+ case 'h' : {
+ show_help(argv[0]);
+ return 0;
+ }
+
+ case 0 : {
+ break;
+ }
+
+ default : {
+ return 1;
+ }
+ }
+
+ }
+
+ mol = load_molecule();
+ get_reflections_cached(mol, eV_to_J(2.0e3));
+ ref = ideal_intensities(mol->reflections);
+ write_reflections("results/ideal-reflections.hkl", NULL, ref, 1,
+ mol->cell);
+
+ return 0;
+}
diff --git a/src/process_hkl.c b/src/process_hkl.c
index aed9856e..9142d5c7 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -24,6 +24,7 @@
#include "utils.h"
#include "statistics.h"
#include "sfac.h"
+#include "reflections.h"
/* Number of divisions for R vs |q| graphs */
@@ -124,72 +125,6 @@ static void write_RvsQ(const char *name, double *ref, double *trueref,
}
-static void write_reflections(const char *filename, unsigned int *counts,
- double *ref, int zone_axis, UnitCell *cell)
-{
- FILE *fh;
- signed int h, k, l;
-
- fh = fopen(filename, "w");
-
- /* Write spacings and angle if zone axis pattern */
- if ( zone_axis ) {
- double a, b, c, alpha, beta, gamma;
- cell_get_parameters(cell, &a, &b, &c, &alpha, &beta, &gamma);
- 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++ ) {
- for ( k=-INDMAX; k<INDMAX; k++ ) {
- for ( l=-INDMAX; l<INDMAX; l++ ) {
-
- int N;
- double F;
-
- if ( counts ) {
- N = lookup_count(counts, h, k, l);
- if ( N == 0 ) continue;
- } else {
- N = 1;
- }
-
- F = lookup_intensity(ref, h, k, l) / N;
- if ( zone_axis && (l != 0) ) continue;
-
- fprintf(fh, "%3i %3i %3i %f\n", h, k, l, F);
-
- }
- }
- }
- fclose(fh);
-}
-
-
-static double *ideal_intensities(double complex *sfac)
-{
- double *ref;
- signed int h, k, l;
-
- ref = new_list_intensity();
-
- /* Generate ideal reflections from complex structure factors */
- for ( h=-INDMAX; h<=INDMAX; h++ ) {
- for ( k=-INDMAX; k<=INDMAX; k++ ) {
- for ( l=-INDMAX; l<=INDMAX; l++ ) {
- double complex F = lookup_sfac(sfac, h, k, l);
- double intensity = pow(cabs(F), 2.0);
- set_intensity(ref, h, k, l, intensity);
- }
- }
- }
-
- return ref;
-}
-
-
static void process_reflections(double *ref, double *trueref,
unsigned int *counts, unsigned int n_patterns,
UnitCell *cell, int do_rvsq, int do_zoneaxis)
@@ -315,9 +250,6 @@ int main(int argc, char *argv[])
counts = new_list_count();
trueref = ideal_intensities(mol->reflections);
- write_reflections("results/ideal-reflections.hkl", NULL, trueref, 1,
- mol->cell);
-
if ( strcmp(filename, "-") == 0 ) {
fh = stdin;
} else {
diff --git a/src/reflections.c b/src/reflections.c
new file mode 100644
index 00000000..5790b543
--- /dev/null
+++ b/src/reflections.c
@@ -0,0 +1,87 @@
+/*
+ * reflections.c
+ *
+ * Utilities for handling reflections
+ *
+ * (c) 2007-2009 Thomas White <thomas.white@desy.de>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+
+#include <stdlib.h>
+#include <math.h>
+#include <stdio.h>
+#include <complex.h>
+#include <string.h>
+
+#include "utils.h"
+#include "cell.h"
+#include "reflections.h"
+
+
+void write_reflections(const char *filename, unsigned int *counts,
+ double *ref, int zone_axis, UnitCell *cell)
+{
+ FILE *fh;
+ signed int h, k, l;
+
+ fh = fopen(filename, "w");
+
+ /* Write spacings and angle if zone axis pattern */
+ if ( zone_axis ) {
+ double a, b, c, alpha, beta, gamma;
+ cell_get_parameters(cell, &a, &b, &c, &alpha, &beta, &gamma);
+ 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++ ) {
+ for ( k=-INDMAX; k<INDMAX; k++ ) {
+ for ( l=-INDMAX; l<INDMAX; l++ ) {
+
+ int N;
+ double F;
+
+ if ( counts ) {
+ N = lookup_count(counts, h, k, l);
+ if ( N == 0 ) continue;
+ } else {
+ N = 1;
+ }
+
+ F = lookup_intensity(ref, h, k, l) / N;
+ if ( zone_axis && (l != 0) ) continue;
+
+ fprintf(fh, "%3i %3i %3i %f\n", h, k, l, F);
+
+ }
+ }
+ }
+ fclose(fh);
+}
+
+
+double *ideal_intensities(double complex *sfac)
+{
+ double *ref;
+ signed int h, k, l;
+
+ ref = new_list_intensity();
+
+ /* Generate ideal reflections from complex structure factors */
+ for ( h=-INDMAX; h<=INDMAX; h++ ) {
+ for ( k=-INDMAX; k<=INDMAX; k++ ) {
+ for ( l=-INDMAX; l<=INDMAX; l++ ) {
+ double complex F = lookup_sfac(sfac, h, k, l);
+ double intensity = pow(cabs(F), 2.0);
+ set_intensity(ref, h, k, l, intensity);
+ }
+ }
+ }
+
+ return ref;
+}
diff --git a/src/reflections.h b/src/reflections.h
new file mode 100644
index 00000000..ac35ae1e
--- /dev/null
+++ b/src/reflections.h
@@ -0,0 +1,29 @@
+/*
+ * reflections.h
+ *
+ * Utilities for handling reflections
+ *
+ * (c) 2007-2009 Thomas White <thomas.white@desy.de>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#ifndef REFLECTIONS_H
+#define REFLECTIONS_H
+
+
+#include "cell.h"
+
+
+extern void write_reflections(const char *filename, unsigned int *counts,
+ double *ref, int zone_axis, UnitCell *cell);
+
+extern double *ideal_intensities(double complex *sfac);
+
+
+#endif /* REFLECTIONS_H */
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-16 15:38:35 +0000