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authorThomas White <taw@physics.org>2011-07-18 18:21:30 +0200
committerThomas White <taw@physics.org>2012-02-22 15:27:33 +0100
commit599c277480ee1d3d5a1a2ffb486e855b845c0dbe (patch)
tree668685308cca58d126b11d10f98eb256c7dac0f6
parent33077f930ed81d70081a95edb7d7004390fa4047 (diff)
Compiles (with warnings)
-rw-r--r--src/compare_hkl.c19
-rw-r--r--src/diffraction.c29
-rw-r--r--src/diffraction.h3
-rw-r--r--src/get_hkl.c79
-rw-r--r--src/povray.c20
-rw-r--r--src/povray.h3
-rw-r--r--src/powder_plot.c19
-rw-r--r--src/process_hkl.c25
-rw-r--r--src/reflist-utils.c16
-rw-r--r--src/reflist-utils.h7
-rw-r--r--src/render_hkl.c34
-rw-r--r--src/symmetry.c27
-rw-r--r--src/symmetry.h27
13 files changed, 192 insertions, 116 deletions
diff --git a/src/compare_hkl.c b/src/compare_hkl.c
index 0ed48311..c8a6fde5 100644
--- a/src/compare_hkl.c
+++ b/src/compare_hkl.c
@@ -51,7 +51,7 @@ static void show_help(const char *s)
static void plot_shells(RefList *list1, double *arr2, double scale,
- UnitCell *cell, const char *sym,
+ UnitCell *cell, const SymOpList *sym,
double rmin_fix, double rmax_fix)
{
double num[NBINS];
@@ -170,7 +170,7 @@ static void plot_shells(RefList *list1, double *arr2, double scale,
signed int hs, ks, ls;
int bin;
- get_asymm(h, k, l, &hs, &ks, &ls, sym);
+ get_asymm(sym, h, k, l, &hs, &ks, &ls);
if ( lookup_count(counted, hs, ks, ls) ) continue;
set_count(counted, hs, ks, ls, 1);
@@ -259,7 +259,8 @@ int main(int argc, char *argv[])
char *ratiofile = NULL;
char *afile = NULL;
char *bfile = NULL;
- char *sym = NULL;
+ char *sym_str = NULL;
+ SymOpList *sym;
double scale, scale_r2, scale_rdig, R1, R2, R1i, Rdiff, pearson;
double scale_rintint, scale_r1i, scale_r1, scale_r1fi;
int ncom;
@@ -306,7 +307,7 @@ int main(int argc, char *argv[])
break;
case 'y' :
- sym = strdup(optarg);
+ sym_str = strdup(optarg);
break;
case 'p' :
@@ -345,9 +346,11 @@ int main(int argc, char *argv[])
return 1;
}
- if ( sym == NULL ) {
- sym = strdup("1");
+ if ( sym_str == NULL ) {
+ sym_str = strdup("1");
}
+ sym = get_pointgroup(sym_str);
+ free(sym_str);
afile = strdup(argv[optind++]);
bfile = strdup(argv[optind]);
@@ -374,12 +377,12 @@ int main(int argc, char *argv[])
/* Check that the intensities have the correct symmetry */
if ( check_list_symmetry(list1, sym) ) {
ERROR("The first input reflection list does not appear to"
- " have symmetry %s\n", sym);
+ " have symmetry %s\n", symmetry_name(sym));
return 1;
}
if ( check_list_symmetry(list2, sym) ) {
ERROR("The second input reflection list does not appear to"
- " have symmetry %s\n", sym);
+ " have symmetry %s\n", symmetry_name(sym));
return 1;
}
diff --git a/src/diffraction.c b/src/diffraction.c
index 0c90f556..aa04fd52 100644
--- a/src/diffraction.c
+++ b/src/diffraction.c
@@ -93,20 +93,21 @@ static double lattice_factor(struct rvec q, double ax, double ay, double az,
static double sym_lookup_intensity(const double *intensities,
- const unsigned char *flags, const char *sym,
+ const unsigned char *flags,
+ const SymOpList *sym,
signed int h, signed int k, signed int l)
{
int i;
double ret = 0.0;
- for ( i=0; i<num_general_equivs(sym); i++ ) {
+ for ( i=0; i<num_equivs(sym); i++ ) {
signed int he;
signed int ke;
signed int le;
double f, val;
- get_general_equiv(h, k, l, &he, &ke, &le, sym, i);
+ get_equiv(sym, i, h, k, l, &he, &ke, &le);
f = (double)lookup_flag(flags, he, ke, le);
val = lookup_intensity(intensities, he, ke, le);
@@ -120,20 +121,20 @@ static double sym_lookup_intensity(const double *intensities,
static double sym_lookup_phase(const double *phases,
- const unsigned char *flags, const char *sym,
+ const unsigned char *flags, const SymOpList *sym,
signed int h, signed int k, signed int l)
{
int i;
double ret = 0.0;
- for ( i=0; i<num_general_equivs(sym); i++ ) {
+ for ( i=0; i<num_equivs(sym); i++ ) {
signed int he;
signed int ke;
signed int le;
double f, val;
- get_general_equiv(h, k, l, &he, &ke, &le, sym, i);
+ get_equiv(sym, i, h, k, l, &he, &ke, &le);
f = (double)lookup_flag(flags, he, ke, le);
val = lookup_phase(phases, he, ke, le);
@@ -147,7 +148,7 @@ static double sym_lookup_phase(const double *phases,
static double interpolate_linear(const double *ref, const unsigned char *flags,
- const char *sym, float hd,
+ const SymOpList *sym, float hd,
signed int k, signed int l)
{
signed int h;
@@ -170,7 +171,7 @@ static double interpolate_linear(const double *ref, const unsigned char *flags,
static double interpolate_bilinear(const double *ref,
- const unsigned char *flags, const char *sym,
+ const unsigned char *flags, const SymOpList *sym,
float hd, float kd, signed int l)
{
signed int k;
@@ -190,7 +191,7 @@ static double interpolate_bilinear(const double *ref,
static double interpolate_intensity(const double *ref,
- const unsigned char *flags, const char *sym,
+ const unsigned char *flags, const SymOpList *sym,
float hd, float kd, float ld)
{
signed int l;
@@ -212,7 +213,7 @@ static double interpolate_intensity(const double *ref,
static double complex interpolate_phased_linear(const double *ref,
const double *phases,
const unsigned char *flags,
- const char *sym,
+ const SymOpList *sym,
float hd,
signed int k, signed int l)
{
@@ -252,7 +253,7 @@ static double complex interpolate_phased_linear(const double *ref,
static double complex interpolate_phased_bilinear(const double *ref,
const double *phases,
const unsigned char *flags,
- const char *sym,
+ const SymOpList *sym,
float hd, float kd,
signed int l)
{
@@ -275,7 +276,7 @@ static double complex interpolate_phased_bilinear(const double *ref,
static double interpolate_phased_intensity(const double *ref,
const double *phases,
const unsigned char *flags,
- const char *sym,
+ const SymOpList *sym,
float hd, float kd, float ld)
{
signed int l;
@@ -302,7 +303,7 @@ static double molecule_factor(const double *intensities, const double *phases,
double ax, double ay, double az,
double bx, double by, double bz,
double cx, double cy, double cz,
- GradientMethod m, const char *sym)
+ GradientMethod m, const SymOpList *sym)
{
float hd, kd, ld;
signed int h, k, l;
@@ -345,7 +346,7 @@ static double molecule_factor(const double *intensities, const double *phases,
void get_diffraction(struct image *image, int na, int nb, int nc,
const double *intensities, const double *phases,
const unsigned char *flags, UnitCell *cell,
- GradientMethod m, const char *sym)
+ GradientMethod m, const SymOpList *sym)
{
unsigned int fs, ss;
double ax, ay, az;
diff --git a/src/diffraction.h b/src/diffraction.h
index 14a84197..f71d3cce 100644
--- a/src/diffraction.h
+++ b/src/diffraction.h
@@ -18,6 +18,7 @@
#include "image.h"
#include "cell.h"
+#include "symmetry.h"
typedef enum {
GRADIENT_MOSAIC,
@@ -28,6 +29,6 @@ typedef enum {
extern void get_diffraction(struct image *image, int na, int nb, int nc,
const double *intensities, const double *phases,
const unsigned char *flags, UnitCell *cell,
- GradientMethod m, const char *sym);
+ GradientMethod m, const SymOpList *sym);
#endif /* DIFFRACTION_H */
diff --git a/src/get_hkl.c b/src/get_hkl.c
index cb2ef3fb..72e1c2a3 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -141,14 +141,16 @@ static RefList *template_reflections(RefList *list, RefList *template)
static RefList *twin_reflections(RefList *in,
- const char *holo, const char *mero)
+ const SymOpList *holo, const SymOpList *mero)
{
Reflection *refl;
RefListIterator *iter;
RefList *out;
- if ( num_general_equivs(holo) < num_general_equivs(mero) ) {
- ERROR("%s is not a subgroup of %s!\n", mero, holo);
+ /* FIXME: Check properly by coset decomposition */
+ if ( num_equivs(holo) < num_equivs(mero) ) {
+ ERROR("%s is not a subgroup of %s!\n", symmetry_name(mero),
+ symmetry_name(holo));
return NULL;
}
@@ -170,19 +172,19 @@ static RefList *twin_reflections(RefList *in,
* only once for each reflection in the holohedral group, which
* contains fewer reflections.
*/
- get_asymm(h, k, l, &h, &k, &l, holo);
+ get_asymm(holo, h, k, l, &h, &k, &l);
if ( find_refl(out, h, k, l) != NULL ) continue;
total = 0.0;
sigma = 0.0;
skip = 0;
- n = num_equivs(h, k, l, holo);
+ n = num_equivs(holo);
for ( j=0; j<n; j++ ) {
signed int he, ke, le;
signed int hu, ku, lu;
- get_equiv(h, k, l, &he, &ke, &le, holo, j);
+ get_equiv(holo, j, h, k, l, &he, &ke, &le);
/* Do we have this reflection?
* We might not have the particular (merohedral)
@@ -196,7 +198,8 @@ static RefList *twin_reflections(RefList *in,
"reflection (or an equivalent in %s), "
"which I don't have. %i %i %i won't "
"appear in the output\n",
- h, k, l, he, ke, le, mero, h, k, l);
+ h, k, l, he, ke, le, symmetry_name(mero),
+ h, k, l);
skip = 1;
break;
}
@@ -220,15 +223,17 @@ static RefList *twin_reflections(RefList *in,
}
-static RefList *expand_reflections(RefList *in,
- const char *target, const char *initial)
+static RefList *expand_reflections(RefList *in, const SymOpList *target,
+ const SymOpList *initial)
{
Reflection *refl;
RefListIterator *iter;
RefList *out;
- if ( num_general_equivs(target) > num_general_equivs(initial) ) {
- ERROR("%s is not a subgroup of %s!\n", initial, target);
+ /* FIXME: Check properly */
+ if ( num_equivs(target) > num_equivs(initial) ) {
+ ERROR("%s is not a subgroup of %s!\n", symmetry_name(initial),
+ symmetry_name(target));
return NULL;
}
@@ -245,7 +250,7 @@ static RefList *expand_reflections(RefList *in,
get_indices(refl, &h, &k, &l);
intensity = get_intensity(refl);
- n = num_equivs(h, k, l, initial);
+ n = num_equivs(initial);
/* For each equivalent in the higher symmetry group */
for ( j=0; j<n; j++ ) {
@@ -254,10 +259,10 @@ static RefList *expand_reflections(RefList *in,
Reflection *new;
/* Get the equivalent */
- get_equiv(h, k, l, &he, &ke, &le, initial, j);
+ get_equiv(initial, j, h, k, l, &he, &ke, &le);
/* Put it into the asymmetric unit for the target */
- get_asymm(he, ke, le, &he, &ke, &le, target);
+ get_asymm(target, he, ke, le, &he, &ke, &le);
/* Make sure the intensity is in the right place */
new = add_refl(out, he, ke, le);
@@ -277,9 +282,12 @@ int main(int argc, char *argv[])
int config_noise = 0;
int config_poisson = 0;
int config_multi = 0;
- char *holo = NULL;
- char *mero = NULL;
- char *expand = NULL;
+ char *holo_str = NULL;
+ char *mero_str = NULL;
+ char *expand_str = NULL;
+ SymOpList *holo;
+ SymOpList *mero;
+ SymOpList *expand;
char *input_file = NULL;
char *template = NULL;
char *output = NULL;
@@ -327,15 +335,15 @@ int main(int argc, char *argv[])
break;
case 'y' :
- mero = strdup(optarg);
+ mero_str = strdup(optarg);
break;
case 'w' :
- holo = strdup(optarg);
+ holo_str = strdup(optarg);
break;
case 'e' :
- expand = strdup(optarg);
+ expand_str = strdup(optarg);
break;
case 'b' :
@@ -359,7 +367,7 @@ int main(int argc, char *argv[])
}
- if ( (holo != NULL) && (expand != NULL) ) {
+ if ( (holo_str != NULL) && (expand_str != NULL) ) {
ERROR("You cannot 'twin' and 'expand' at the same time.\n");
ERROR("Decide which one you want to do first.\n");
return 1;
@@ -379,11 +387,30 @@ int main(int argc, char *argv[])
return 1;
}
+ if ( holo_str != NULL ) {
+ holo = get_pointgroup(holo_str);
+ free(holo_str);
+ } else {
+ holo = NULL;
+ }
+ if ( mero_str != NULL ) {
+ mero = get_pointgroup(mero_str);
+ free(mero_str);
+ } else {
+ mero = NULL;
+ }
+ if ( expand_str != NULL ) {
+ expand = get_pointgroup(expand_str);
+ free(expand_str);
+ } else {
+ expand = NULL;
+ }
+
input = read_reflections(input_file);
free(input_file);
if ( check_list_symmetry(input, mero) ) {
ERROR("The input reflection list does not appear to"
- " have symmetry %s\n", mero);
+ " have symmetry %s\n", symmetry_name(mero));
return 1;
}
@@ -402,7 +429,8 @@ int main(int argc, char *argv[])
if ( holo != NULL ) {
RefList *new;
- STATUS("Twinning from %s into %s\n", mero, holo);
+ STATUS("Twinning from %s into %s\n", symmetry_name(mero),
+ symmetry_name(holo));
new = twin_reflections(input, holo, mero);
/* Replace old with new */
@@ -418,7 +446,8 @@ int main(int argc, char *argv[])
if ( expand != NULL ) {
RefList *new;
- STATUS("Expanding from %s into %s\n", mero, expand);
+ STATUS("Expanding from %s into %s\n", symmetry_name(mero),
+ symmetry_name(expand));
new = expand_reflections(input, expand, mero);
/* Replace old with new */
@@ -442,7 +471,7 @@ int main(int argc, char *argv[])
get_indices(refl, &h, &k, &l);
inty = get_intensity(refl);
- inty *= (double)num_equivs(h, k, l, mero);
+ inty *= (double)num_equivs(mero);
set_int(refl, inty);
}
diff --git a/src/povray.c b/src/povray.c
index 660f1c59..9fb267f4 100644
--- a/src/povray.c
+++ b/src/povray.c
@@ -30,7 +30,7 @@
int povray_render_animation(UnitCell *cell, RefList *list, unsigned int nproc,
- const char *sym, int wght, double boost,
+ const SymOpList *sym, int wght, double boost,
double scale_top)
{
FILE *fh;
@@ -174,8 +174,10 @@ int povray_render_animation(UnitCell *cell, RefList *list, unsigned int nproc,
float val;
signed int h, k, l;
+ SymOpList *sp;
get_indices(refl, &h, &k, &l);
+ sp = special_position(sym, h, k, l);
switch ( wght ) {
case WGHT_I :
@@ -187,7 +189,7 @@ int povray_render_animation(UnitCell *cell, RefList *list, unsigned int nproc,
break;
case WGHT_COUNTS :
val = get_redundancy(refl);
- val /= (float)num_equivs(h, k, l, sym);
+ val /= (double)num_equivs(sp);
break;
case WGHT_RAWCOUNTS :
val = get_redundancy(refl);
@@ -199,6 +201,8 @@ int povray_render_animation(UnitCell *cell, RefList *list, unsigned int nproc,
if ( val > max ) max = val;
+ free_symoplist(sp);
+
}
max /= boost;
@@ -216,8 +220,12 @@ int povray_render_animation(UnitCell *cell, RefList *list, unsigned int nproc,
int s;
float val, p, r, g, b, trans;
int j;
+ SymOpList *sp;
+ int neq;
get_indices(refl, &h, &k, &l);
+ sp = special_position(sym, h, k, l);
+ neq = num_equivs(sp);
switch ( wght ) {
case WGHT_I :
@@ -229,7 +237,7 @@ int povray_render_animation(UnitCell *cell, RefList *list, unsigned int nproc,
break;
case WGHT_COUNTS :
val = get_redundancy(refl);
- val /= (float)num_equivs(h, k, l, sym);
+ val /= (double)neq;
break;
case WGHT_RAWCOUNTS :
val = get_redundancy(refl);
@@ -281,12 +289,12 @@ int povray_render_animation(UnitCell *cell, RefList *list, unsigned int nproc,
trans = 1.0-(val/max);
/* For each equivalent */
- for ( j=0; j<num_equivs(h, k, l, sym); j++ ) {
+ for ( j=0; j<neq; j++ ) {
signed int he, ke, le;
float x, y, z;
- get_equiv(h, k, l, &he, &ke, &le, sym, j);
+ get_equiv(sp, j, h, k, l, &he, &ke, &le);
x = asx*he + bsx*ke + csx*le;
y = asy*he + bsy*ke + csy*le;
@@ -303,6 +311,8 @@ int povray_render_animation(UnitCell *cell, RefList *list, unsigned int nproc,
}
+ free_symoplist(sp);
+
}
fprintf(fh, "\n");
diff --git a/src/povray.h b/src/povray.h
index 9dbf109d..f91c141c 100644
--- a/src/povray.h
+++ b/src/povray.h
@@ -18,9 +18,10 @@
#include "reflist.h"
#include "cell.h"
+#include "symmetry.h"
extern int povray_render_animation(UnitCell *cell, RefList *list,
- unsigned int nproc, const char *sym,
+ unsigned int nproc, const SymOpList *sym,
int wght, double boost, double scale_top);
#endif /* POVRAY_H */
diff --git a/src/powder_plot.c b/src/powder_plot.c
index 7d12f31b..6065da07 100644
--- a/src/powder_plot.c
+++ b/src/powder_plot.c
@@ -305,7 +305,8 @@ static unsigned int process_h5(struct image *image, struct histogram_info *info,
}
-static unsigned int process_hkl(struct image *image, char *sym, UnitCell *cell,
+static unsigned int process_hkl(struct image *image, const SymOpList *sym,
+ UnitCell *cell,
struct histogram_info *info,
struct bin_stats *histdata,
int q_scaling, int use_redundancy)
@@ -329,7 +330,9 @@ static unsigned int process_hkl(struct image *image, char *sym, UnitCell *cell,
if ( use_redundancy ) {
redundancy = get_redundancy(refl);
} else {
- redundancy = num_equivs(h, k, l, sym);
+ SymOpList *sp = special_position(sym, h, k, l);
+ redundancy = num_equivs(sp);
+ free_symoplist(sp);
}
/* Multiply by 2 to get 1/d (in m^-1) */
@@ -734,6 +737,7 @@ int main(int argc, char *argv[])
struct hdfile *hdfile = NULL;
struct bin_stats *histdata = NULL;
struct histogram_info hist_info;
+ SymOpList *sym;
/* Default settings */
hist_info.histsize = 100;
@@ -765,7 +769,7 @@ int main(int argc, char *argv[])
char *pdb = NULL;
char *output = NULL;
char *datatype = NULL;
- char *sym = NULL;
+ char *sym_str = NULL;
/* Long options */
const struct option longopts[] = {
@@ -823,7 +827,7 @@ int main(int argc, char *argv[])
break;
case 'y' :
- sym = strdup(optarg);
+ sym_str = strdup(optarg);
break;
case 's' :
@@ -1040,9 +1044,11 @@ int main(int argc, char *argv[])
}
free(pdb);
- if ( sym == NULL ) {
- sym = strdup("1");
+ if ( sym_str == NULL ) {
+ sym_str = strdup("1");
}
+ sym = get_pointgroup(sym_str);
+ free(sym_str);
/* Set up histogram info*/
if (hist_info.q_min <= 0.0 ) {
@@ -1173,7 +1179,6 @@ int main(int argc, char *argv[])
if ( image.beam != NULL ) free(image.beam);
fclose(fh);
free(histdata);
- free(sym);
return 0;
}
diff --git a/src/process_hkl.c b/src/process_hkl.c
index 731344cb..06c5a54b 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -118,7 +118,7 @@ static void plot_histogram(double *vals, int n)
static void merge_pattern(RefList *model, RefList *new, int max_only,
- const char *sym,
+ const SymOpList *sym,
double *hist_vals, signed int hist_h,
signed int hist_k, signed int hist_l, int *hist_n,
int pass)
@@ -138,7 +138,7 @@ static void merge_pattern(RefList *model, RefList *new, int max_only,
get_indices(refl, &h, &k, &l);
/* Put into the asymmetric unit for the target group */
- get_asymm(h, k, l, &h, &k, &l, sym);
+ get_asymm(sym, h, k, l, &h, &k, &l);
model_version = find_refl(model, h, k, l);
if ( model_version == NULL ) {
@@ -209,7 +209,7 @@ enum {
};
-static void scale_intensities(RefList *model, RefList *new, const char *sym)
+static void scale_intensities(RefList *model, RefList *new, const SymOpList *sym)
{
double s;
double top = 0.0;
@@ -235,7 +235,7 @@ static void scale_intensities(RefList *model, RefList *new, const char *sym)
model_version = find_refl(model, h, k, l);
if ( model_version == NULL ) continue;
- get_asymm(h, k, l, &hu, &ku, &lu, sym);
+ get_asymm(sym, h, k, l, &hu, &ku, &lu);
i1 = get_intensity(model_version);
i2 = get_intensity(refl);
@@ -294,7 +294,7 @@ static void scale_intensities(RefList *model, RefList *new, const char *sym)
static void merge_all(FILE *fh, RefList *model,
int config_maxonly, int config_scale, int config_sum,
int config_startafter, int config_stopafter,
- const char *sym,
+ const SymOpList *sym,
int n_total_patterns,
double *hist_vals, signed int hist_h,
signed int hist_k, signed int hist_l,
@@ -416,7 +416,8 @@ int main(int argc, char *argv[])
int config_sum = 0;
int config_scale = 0;
unsigned int n_total_patterns;
- char *sym = NULL;
+ char *sym_str = NULL;
+ SymOpList *sym;
char *pdb = NULL;
char *histo = NULL;
signed int hist_h, hist_k, hist_l;
@@ -473,7 +474,7 @@ int main(int argc, char *argv[])
break;
case 'y' :
- sym = strdup(optarg);
+ sym_str = strdup(optarg);
break;
case 'g' :
@@ -518,7 +519,9 @@ int main(int argc, char *argv[])
cell = NULL;
}
- if ( sym == NULL ) sym = strdup("1");
+ if ( sym_str == NULL ) sym_str = strdup("1");
+ sym = get_pointgroup(sym_str);
+ free(sym_str);
/* Open the data stream */
if ( strcmp(filename, "-") == 0 ) {
@@ -550,13 +553,13 @@ int main(int argc, char *argv[])
ERROR("Invalid indices for '--histogram'\n");
return 1;
}
- space_for_hist = n_total_patterns * num_general_equivs(sym);
+ space_for_hist = n_total_patterns * num_equivs(sym);
hist_vals = malloc(space_for_hist * sizeof(double));
free(histo);
STATUS("Histogramming %i %i %i -> ", hist_h, hist_k, hist_l);
/* Put into the asymmetric cell for the target group */
- get_asymm(hist_h, hist_k, hist_l,
- &hist_h, &hist_k, &hist_l, sym);
+ get_asymm(sym, hist_h, hist_k, hist_l,
+ &hist_h, &hist_k, &hist_l);
STATUS("%i %i %i\n", hist_h, hist_k, hist_l);
}
diff --git a/src/reflist-utils.c b/src/reflist-utils.c
index 016fa317..c0784dbb 100644
--- a/src/reflist-utils.c
+++ b/src/reflist-utils.c
@@ -104,7 +104,7 @@ unsigned char *flags_from_list(RefList *list)
}
-int check_list_symmetry(RefList *list, const char *sym)
+int check_list_symmetry(RefList *list, const SymOpList *sym)
{
unsigned char *flags;
Reflection *refl;
@@ -122,10 +122,10 @@ int check_list_symmetry(RefList *list, const char *sym)
get_indices(refl, &h, &k, &l);
- for ( j=0; j<num_equivs(h, k, l, sym); j++ ) {
+ for ( j=0; j<num_equivs(sym); j++ ) {
signed int he, ke, le;
- get_equiv(h, k, l, &he, &ke, &le, sym, j);
+ get_equiv(sym, j, h, k, l, &he, &ke, &le);
if ( abs(he) > INDMAX ) continue;
if ( abs(le) > INDMAX ) continue;
@@ -149,17 +149,17 @@ int check_list_symmetry(RefList *list, const char *sym)
int find_equiv_in_list(RefList *list, signed int h, signed int k,
- signed int l, const char *sym, signed int *hu,
+ signed int l, const SymOpList *sym, signed int *hu,
signed int *ku, signed int *lu)
{
int i;
int found = 0;
- for ( i=0; i<num_equivs(h, k, l, sym); i++ ) {
+ for ( i=0; i<num_equivs( sym); i++ ) {
signed int he, ke, le;
Reflection *f;
- get_equiv(h, k, l, &he, &ke, &le, sym, i);
+ get_equiv(sym, i, h, k, l, &he, &ke, &le);
f = find_refl(list, he, ke, le);
/* There must only be one equivalent. If there are more, it
@@ -362,7 +362,7 @@ RefList *read_reflections(const char *filename)
}
-RefList *asymmetric_indices(RefList *in, const char *sym)
+RefList *asymmetric_indices(RefList *in, const SymOpList *sym)
{
Reflection *refl;
RefListIterator *iter;
@@ -380,7 +380,7 @@ RefList *asymmetric_indices(RefList *in, const char *sym)
get_indices(refl, &h, &k, &l);
- get_asymm(h, k, l, &ha, &ka, &la, sym);
+ get_asymm(sym, h, k, l, &ha, &ka, &la);
cr = add_refl(new, ha, ka, la);
assert(cr != NULL);
diff --git a/src/reflist-utils.h b/src/reflist-utils.h
index 775e375a..59aa6172 100644
--- a/src/reflist-utils.h
+++ b/src/reflist-utils.h
@@ -19,6 +19,7 @@
#include "reflist.h"
#include "cell.h"
+#include "symmetry.h"
#define REFLECTION_END_MARKER "End of reflections"
@@ -36,11 +37,11 @@ extern double *intensities_from_list(RefList *list);
extern double *phases_from_list(RefList *list);
extern unsigned char *flags_from_list(RefList *list);
-extern int check_list_symmetry(RefList *list, const char *sym);
+extern int check_list_symmetry(RefList *list, const SymOpList *sym);
extern int find_equiv_in_list(RefList *list, signed int h, signed int k,
- signed int l, const char *sym, signed int *hu,
+ signed int l, const SymOpList *sym, signed int *hu,
signed int *ku, signed int *lu);
-extern RefList *asymmetric_indices(RefList *in, const char *sym);
+extern RefList *asymmetric_indices(RefList *in, const SymOpList *sym);
#endif /* REFLIST_UTILS_H */
diff --git a/src/render_hkl.c b/src/render_hkl.c
index 58784e2f..823b6f1a 100644
--- a/src/render_hkl.c
+++ b/src/render_hkl.c
@@ -85,7 +85,7 @@ static void show_help(const char *s)
static void draw_circles(signed int xh, signed int xk, signed int xl,
signed int yh, signed int yk, signed int yl,
signed int zh, signed int zk, signed int zl,
- RefList *list, const char *sym,
+ RefList *list, const SymOpList *sym,
cairo_t *dctx, int wght, double boost, int colscale,
UnitCell *cell, double radius, double theta,
double as, double bs, double cx, double cy,
@@ -110,15 +110,19 @@ static void draw_circles(signed int xh, signed int xk, signed int xl,
double u, v, val, res;
signed int ha, ka, la;
int xi, yi;
- int i;
+ int i, n;
+ SymOpList *sp;
get_indices(refl, &ha, &ka, &la);
- for ( i=0; i<num_equivs(ha, ka, la, sym); i++ ) {
+ sp = special_position(sym, ha, ka, la);
+ n = num_equivs(sp);
+
+ for ( i=0; i<n; i++ ) {
signed int h, k, l;
- get_equiv(ha, ka, la, &h, &k, &l, sym, i);
+ get_equiv(sp, i, ha, ka, la, &h, &k, &l);
/* Is the reflection in the zone? */
if ( h*zh + k*zk + l*zl != 0 ) continue;
@@ -136,7 +140,7 @@ static void draw_circles(signed int xh, signed int xk, signed int xl,
break;
case WGHT_COUNTS :
val = get_redundancy(refl);
- val /= (float)num_equivs(h, k, l, sym);
+ val /= (double)n;
break;
case WGHT_RAWCOUNTS :
val = get_redundancy(refl);
@@ -190,6 +194,8 @@ static void draw_circles(signed int xh, signed int xk, signed int xl,
}
+ free_symoplist(sp);
+
}
}
@@ -245,7 +251,8 @@ static void render_overlined_indices(cairo_t *dctx,
static void render_za(UnitCell *cell, RefList *list,
- double boost, const char *sym, int wght, int colscale,
+ double boost, const SymOpList *sym, int wght,
+ int colscale,
signed int xh, signed int xk, signed int xl,
signed int yh, signed int yk, signed int yl,
const char *outfile, double scale_top)
@@ -558,7 +565,8 @@ int main(int argc, char *argv[])
char *pdb = NULL;
int r = 0;
double boost = 1.0;
- char *sym = NULL;
+ char *sym_str = NULL;
+ SymOpList *sym;
char *weighting = NULL;
int wght;
int colscale;
@@ -612,7 +620,7 @@ int main(int argc, char *argv[])
break;
case 'y' :
- sym = strdup(optarg);
+ sym_str = strdup(optarg);
break;
case 'w' :
@@ -664,9 +672,11 @@ int main(int argc, char *argv[])
return 1;
}
- if ( sym == NULL ) {
- sym = strdup("1");
+ if ( sym_str == NULL ) {
+ sym_str = strdup("1");
}
+ sym = get_pointgroup(sym_str);
+ free(sym_str);
if ( weighting == NULL ) {
weighting = strdup("I");
@@ -755,7 +765,7 @@ int main(int argc, char *argv[])
}
if ( check_list_symmetry(list, sym) ) {
ERROR("The input reflection list does not appear to"
- " have symmetry %s\n", sym);
+ " have symmetry %s\n", symmetry_name(sym));
return 1;
}
@@ -770,7 +780,7 @@ int main(int argc, char *argv[])
}
free(pdb);
- free(sym);
+ free_symoplist(sym);
reflist_free(list);
if ( outfile != NULL ) free(outfile);
diff --git a/src/symmetry.c b/src/symmetry.c
index 42c66193..f09b3e9c 100644
--- a/src/symmetry.c
+++ b/src/symmetry.c
@@ -78,6 +78,7 @@ struct _symoplist
struct sym_op *ops;
int n_ops;
int max_ops;
+ char *name;
};
@@ -97,6 +98,7 @@ static SymOpList *new_symoplist()
new->max_ops = 16;
new->n_ops = 0;
new->ops = NULL;
+ new->name = NULL;
alloc_ops(new);
return new;
}
@@ -118,6 +120,7 @@ void free_symoplist(SymOpList *ops)
free(ops->ops[i].l);
}
if ( ops->ops != NULL ) free(ops->ops);
+ if ( ops->name != NULL ) free(ops->name);
free(ops);
}
@@ -253,6 +256,7 @@ static SymOpList *make_1bar()
{
SymOpList *new = new_symoplist();
add_symop(new, v(-1,0,0,0), v(0,-1,0,0), v(0,0,0,-1)); /* -I */
+ new->name = strdup("-1");
return new;
}
@@ -260,6 +264,7 @@ static SymOpList *make_1bar()
static SymOpList *make_1()
{
SymOpList *new = new_symoplist();
+ new->name = strdup("1");
return new;
}
@@ -271,6 +276,7 @@ static SymOpList *make_2m()
SymOpList *new = new_symoplist();
add_symop(new, v(-1,0,0,0), v(0,1,0,0), v(0,0,0,-1)); /* 2 */
add_symop(new, v(1,0,0,0), v(0,-1,0,0), v(0,0,0,1)); /* m */
+ new->name = strdup("2/m");
return NULL;
}
@@ -279,6 +285,7 @@ static SymOpList *make_2()
{
SymOpList *new = new_symoplist();
add_symop(new, v(-1,0,0,0), v(0,1,0,0), v(0,0,0,-1)); /* 2 */
+ new->name = strdup("2");
return NULL;
}
@@ -287,6 +294,7 @@ static SymOpList *make_m()
{
SymOpList *new = new_symoplist();
add_symop(new, v(1,0,0,0), v(0,-1,0,0), v(0,0,0,1)); /* m */
+ new->name = strdup("m");
return NULL;
}
@@ -299,6 +307,7 @@ static SymOpList *make_mmm()
add_symop(new, v(-1,0,0,0), v(0,-1,0,0), v(0,0,0,1)); /* 2 */
add_symop(new, v(-1,0,0,0), v(0,1,0,0), v(0,0,0,-1)); /* 2 */
add_symop(new, v(1,0,0,0), v(0,-1,0,0), v(0,0,0,1)); /* m */
+ new->name = strdup("mmm");
return NULL;
}
@@ -308,6 +317,7 @@ static SymOpList *make_222()
SymOpList *new = new_symoplist();
add_symop(new, v(-1,0,0,0), v(0,-1,0,0), v(0,0,0,1)); /* 2 */
add_symop(new, v(-1,0,0,0), v(0,1,0,0), v(0,0,0,-1)); /* 2 */
+ new->name = strdup("222");
return NULL;
}
@@ -317,6 +327,7 @@ static SymOpList *make_mm2()
SymOpList *new = new_symoplist();
add_symop(new, v(-1,0,0,0), v(0,-1,0,0), v(0,0,0,1)); /* 2 */
add_symop(new, v(1,0,0,0), v(0,-1,0,0), v(0,0,0,1)); /* m */
+ new->name = strdup("mm2");
return NULL;
}
@@ -455,7 +466,7 @@ SymOpList *get_pointgroup(const char *sym)
}
-static void do_op(struct sym_op *op,
+static void do_op(const struct sym_op *op,
signed int h, signed int k, signed int l,
signed int *he, signed int *ke, signed int *le)
{
@@ -485,7 +496,7 @@ static void do_op(struct sym_op *op,
* given reflection is a special high-symmetry one), call special_position()
* first to get a "specialised" SymOpList and use that instead.
**/
-void get_equiv(SymOpList *ops, int idx,
+void get_equiv(const SymOpList *ops, int idx,
signed int h, signed int k, signed int l,
signed int *he, signed int *ke, signed int *le)
{
@@ -531,7 +542,7 @@ void get_equiv(SymOpList *ops, int idx,
*
* Returns: the "specialised" %SymOpList.
**/
-SymOpList *special_position(SymOpList *ops,
+SymOpList *special_position(const SymOpList *ops,
signed int h, signed int k, signed int l)
{
int i, n;
@@ -554,7 +565,7 @@ SymOpList *special_position(SymOpList *ops,
}
-void get_asymm(SymOpList *ops, int idx,
+void get_asymm(const SymOpList *ops,
signed int h, signed int k, signed int l,
signed int *hp, signed int *kp, signed int *lp)
{
@@ -595,7 +606,7 @@ void get_asymm(SymOpList *ops, int idx,
*
* To count the number of possibilities, use num_ops() on the result.
*/
-SymOpList *get_twins(SymOpList *source, SymOpList *target)
+SymOpList *get_twins(const SymOpList *source, const SymOpList *target)
{
int n_src, n_tgt;
int i;
@@ -611,3 +622,9 @@ SymOpList *get_twins(SymOpList *source, SymOpList *target)
return twins;
}
+
+
+const char *symmetry_name(const SymOpList *ops)
+{
+ return ops->name;
+}
diff --git a/src/symmetry.h b/src/symmetry.h
index 23c00160..4dcaae06 100644
--- a/src/symmetry.h
+++ b/src/symmetry.h
@@ -28,26 +28,21 @@ extern void free_symoplist(SymOpList *ops);
extern SymOpList *get_pointgroup(const char *sym);
-extern SymOpList *special_position(SymOpList *ops,
- signed int h, signed int k, signed int l);
-
-extern void get_asymm(signed int h, signed int k, signed int l,
- signed int *hp, signed int *kp, signed int *lp,
- const char *sym);
+extern const char *symmetry_name(const SymOpList *ops);
-extern int num_equivs(signed int h, signed int k, signed int l,
- const char *sym);
+extern SymOpList *special_position(const SymOpList *ops,
+ signed int h, signed int k, signed int l);
-extern int num_general_equivs(const char *sym);
+extern void get_asymm(const SymOpList *ops,
+ signed int h, signed int k, signed int l,
+ signed int *hp, signed int *kp, signed int *lp);
-extern void get_equiv(signed int h, signed int k, signed int l,
- signed int *he, signed int *ke, signed int *le,
- const char *sym, int idx);
+extern int num_equivs(const SymOpList *ops);
-extern void get_general_equiv(signed int h, signed int k, signed int l,
- signed int *he, signed int *ke, signed int *le,
- const char *sym, int idx);
+extern void get_equiv(const SymOpList *ops, int idx,
+ signed int h, signed int k, signed int l,
+ signed int *he, signed int *ke, signed int *le);
-extern SymOpList *get_twins(SymOpList *source, SymOpList *target);
+extern SymOpList *get_twins(const SymOpList *source, const SymOpList *target);
#endif /* SYMMETRY_H */