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-rw-r--r--Makefile.am3
-rw-r--r--src/Makefile.am2
-rw-r--r--src/diffraction.c142
-rw-r--r--src/sfac.c164
-rw-r--r--src/sfac.h23
5 files changed, 191 insertions, 143 deletions
diff --git a/Makefile.am b/Makefile.am
index 9087ee19..955cc8f0 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,3 +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/utils.h src/diffraction.h src/detector.h src/ewald.h \
+ src/sfac.h
SUBDIRS = src
diff --git a/src/Makefile.am b/src/Makefile.am
index c224a2b0..1220b7f2 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -3,5 +3,5 @@ bin_PROGRAMS = pattern_sim
AM_CFLAGS = -Wall -g @CFLAGS@
pattern_sim_SOURCES = main.c diffraction.c utils.c image.c cell.c hdf5-file.c \
- ewald.c detector.c
+ ewald.c detector.c sfac.c
pattern_sim_LDADD = @LIBS@
diff --git a/src/diffraction.c b/src/diffraction.c
index e02d80f4..b5c07a71 100644
--- a/src/diffraction.c
+++ b/src/diffraction.c
@@ -21,6 +21,7 @@
#include "cell.h"
#include "ewald.h"
#include "diffraction.h"
+#include "sfac.h"
static double lattice_factor(struct threevec q, double ax, double ay, double az,
@@ -59,147 +60,6 @@ static double lattice_factor(struct threevec q, double ax, double ay, double az,
}
-/* Look up f1 and f2 for this atom at this energy (in J/photon) */
-static double complex get_f1f2(const char *n, double en)
-{
- FILE *fh;
- char filename[64];
- char line[1024];
- char *rval;
- float last_E, last_f1, last_f2;
-
- snprintf(filename, 63, "scattering-factors/%s.nff", n);
- fh = fopen(filename, "r");
- if ( fh == NULL ) {
- fprintf(stderr, "Couldn't open file '%s'\n", filename);
- return 0.0;
- }
-
- en = J_to_eV(en);
-
- /* Discard first line */
- fgets(line, 1023, fh);
-
- last_E = 0.0;
- last_f1 = 0.0;
- last_f2 = 0.0;
- do {
-
- int r;
- float E, f1, f2;
-
- rval = fgets(line, 1023, fh);
-
- r = sscanf(line, "%f %f %f", &E, &f1, &f2);
- if ( r != 3 ) {
- fprintf(stderr, "WTF?\n");
- abort();
- }
-
- /* Find the first energy greater than the required value */
- if ( E < en ) {
- /* Store old values ready for interpolation*/
- last_E = E;
- last_f1 = f1;
- last_f2 = f2;
- } else {
-
- /* Perform (linear) interpolation */
- float f;
- float actual_f1, actual_f2;
-
- f = (en - last_E) / (E - last_E);
-
- actual_f1 = last_f1 + f * (f1 - last_f1);
- actual_f2 = last_f2 + f * (f2 - last_f2);
-
- fclose(fh);
- return actual_f1 + I*actual_f2;
-
- }
-
- } while ( rval != NULL );
-
- fclose(fh);
-
- fprintf(stderr, "Couldn't find scattering factors for '%s' at %f eV!\n",
- n, en);
-
- return 0.0;
-}
-
-
-/* s = sin(theta)/lambda */
-static double get_waas_kirf(const char *n, double s)
-{
- FILE *fh;
- char *rval;
- double f;
- float a1, a2, a3, a4, a5, c, b1, b2, b3, b4, b5;
- double s2;
-
- fh = fopen("scattering-factors/f0_WaasKirf.dat", "r");
- if ( fh == NULL ) {
- fprintf(stderr, "Couldn't open f0_WaasKirf.dat\n");
- return 0.0;
- }
-
- do {
-
- int r;
- char line[1024];
- char sp[1024];
- int Z;
-
- rval = fgets(line, 1023, fh);
-
- if ( (line[0] != '#') || (line[1] != 'S') ) continue;
-
- r = sscanf(line, "#S %i %s", &Z, sp);
- if ( (r != 2) || (strcmp(sp, n) != 0) ) continue;
-
- /* Skip two lines */
- fgets(line, 1023, fh);
- fgets(line, 1023, fh);
-
- /* Read scattering coefficients */
- rval = fgets(line, 1023, fh);
- r = sscanf(line, " %f %f %f %f %f %f %f %f %f %f %f",
- &a1, &a2, &a3, &a4, &a5, &c, &b1, &b2, &b3, &b4, &b5);
- if ( r != 11 ) {
- fprintf(stderr, "Couldn't read scattering factors\n");
- return 0.0;
- }
-
- break;
-
- } while ( rval != NULL );
-
- fclose(fh);
-
- s2 = pow(s/1e10, 2.0); /* s2 is s squared in Angstroms squared */
- f = c + a1*exp(-b1*s2) + a2*exp(-b2*s2) + a3*exp(-b3*s2)
- + a4*exp(-b4*s2) + a5*exp(-b5*s2);
-
- return f;
-}
-
-
-/* Get complex scattering factors for element 'n' at energy 'en' (J/photon),
- * at resolution 's' = sin(theta)/lambda (in m^-1) */
-static double complex get_sfac(const char *n, double s, double en)
-{
- double complex f1f2;
- double fq, fq0;
-
- f1f2 = get_f1f2(n, en);
- fq = get_waas_kirf(n, s);
- fq0 = get_waas_kirf(n, 0.0);
-
- return fq - fq0 + f1f2;
-}
-
-
/* Return structure factor for molecule 'mol' at energy en' (J/photon) at
* scattering vector 'q' */
static double complex molecule_factor(struct molecule *mol, struct threevec q,
diff --git a/src/sfac.c b/src/sfac.c
new file mode 100644
index 00000000..4c3dabd3
--- /dev/null
+++ b/src/sfac.c
@@ -0,0 +1,164 @@
+/*
+ * sfac.c
+ *
+ * Scattering factors
+ *
+ * (c) 2007-2009 Thomas White <thomas.white@desy.de>
+ *
+ * pattern_sim - Simulate diffraction patterns from small crystals
+ *
+ */
+
+
+#include <stdlib.h>
+#include <math.h>
+#include <stdio.h>
+#include <complex.h>
+#include <string.h>
+
+#include "utils.h"
+#include "sfac.h"
+
+
+/* Look up f1 and f2 for this atom at this energy (in J/photon) */
+static double complex get_f1f2(const char *n, double en)
+{
+ FILE *fh;
+ char filename[64];
+ char line[1024];
+ char *rval;
+ double last_E, last_f1, last_f2;
+
+ snprintf(filename, 63, "scattering-factors/%s.nff", n);
+ fh = fopen(filename, "r");
+ if ( fh == NULL ) {
+ fprintf(stderr, "Couldn't open file '%s'\n", filename);
+ return 0.0;
+ }
+
+ en = J_to_eV(en);
+
+ /* Discard first line */
+ fgets(line, 1023, fh);
+
+ last_E = 0.0;
+ last_f1 = 0.0;
+ last_f2 = 0.0;
+ do {
+
+ int r;
+ double E, f1, f2;
+ float E_f, f1_f, f2_f;
+
+ rval = fgets(line, 1023, fh);
+
+ r = sscanf(line, "%f %f %f", &E_f, &f1_f, &f2_f);
+ if ( r != 3 ) {
+ fprintf(stderr, "WTF?\n");
+ abort();
+ }
+ /* Promote to double precision */
+ E = E_f; f1 = f1_f; f2 = f2_f;
+
+ /* Find the first energy greater than the required value */
+ if ( E < en ) {
+ /* Store old values ready for interpolation*/
+ last_E = E;
+ last_f1 = f1;
+ last_f2 = f2;
+ } else {
+
+ /* Perform (linear) interpolation */
+ double f;
+ double actual_f1, actual_f2;
+
+ f = (en - last_E) / (E - last_E);
+
+ actual_f1 = last_f1 + f * (f1 - last_f1);
+ actual_f2 = last_f2 + f * (f2 - last_f2);
+
+ fclose(fh);
+ return actual_f1 + I*actual_f2;
+
+ }
+
+ } while ( rval != NULL );
+
+ fclose(fh);
+
+ fprintf(stderr, "Couldn't find scattering factors for '%s' at %f eV!\n",
+ n, en);
+
+ return 0.0;
+}
+
+
+/* s = sin(theta)/lambda */
+static double get_waas_kirf(const char *n, double s)
+{
+ FILE *fh;
+ char *rval;
+ double f;
+ float a1, a2, a3, a4, a5, c, b1, b2, b3, b4, b5;
+ double s2;
+
+ fh = fopen("scattering-factors/f0_WaasKirf.dat", "r");
+ if ( fh == NULL ) {
+ fprintf(stderr, "Couldn't open f0_WaasKirf.dat\n");
+ return 0.0;
+ }
+
+ do {
+
+ int r;
+ char line[1024];
+ char sp[1024];
+ int Z;
+
+ rval = fgets(line, 1023, fh);
+
+ if ( (line[0] != '#') || (line[1] != 'S') ) continue;
+
+ r = sscanf(line, "#S %i %s", &Z, sp);
+ if ( (r != 2) || (strcmp(sp, n) != 0) ) continue;
+
+ /* Skip two lines */
+ fgets(line, 1023, fh);
+ fgets(line, 1023, fh);
+
+ /* Read scattering coefficients */
+ rval = fgets(line, 1023, fh);
+ r = sscanf(line, " %f %f %f %f %f %f %f %f %f %f %f",
+ &a1, &a2, &a3, &a4, &a5, &c, &b1, &b2, &b3, &b4, &b5);
+ if ( r != 11 ) {
+ fprintf(stderr, "Couldn't read scattering factors\n");
+ return 0.0;
+ }
+
+ break;
+
+ } while ( rval != NULL );
+
+ fclose(fh);
+
+ s2 = pow(s/1e10, 2.0); /* s2 is s squared in Angstroms squared */
+ f = c + a1*exp(-b1*s2) + a2*exp(-b2*s2) + a3*exp(-b3*s2)
+ + a4*exp(-b4*s2) + a5*exp(-b5*s2);
+
+ return f;
+}
+
+
+/* Get complex scattering factors for element 'n' at energy 'en' (J/photon),
+ * at resolution 's' = sin(theta)/lambda (in m^-1) */
+double complex get_sfac(const char *n, double s, double en)
+{
+ double complex f1f2;
+ double fq, fq0;
+
+ f1f2 = get_f1f2(n, en);
+ fq = get_waas_kirf(n, s);
+ fq0 = get_waas_kirf(n, 0.0);
+
+ return fq - fq0 + f1f2;
+}
diff --git a/src/sfac.h b/src/sfac.h
new file mode 100644
index 00000000..afa84f84
--- /dev/null
+++ b/src/sfac.h
@@ -0,0 +1,23 @@
+/*
+ * sfac.h
+ *
+ * Scattering factors
+ *
+ * (c) 2007-2009 Thomas White <thomas.white@desy.de>
+ *
+ * pattern_sim - Simulate diffraction patterns from small crystals
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#ifndef SFAC_H
+#define SFAC_H
+
+#include <complex.h>
+
+extern double complex get_sfac(const char *n, double s, double en);
+
+#endif /* SFAC_H */
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-11 07:33:56 +0000