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-rw-r--r--src/compare_hkl.c6
-rw-r--r--src/diffraction.c2
-rw-r--r--src/get_hkl.c2
-rw-r--r--src/indexamajig.c2
-rw-r--r--src/pattern_sim.c2
-rw-r--r--src/process_hkl.c13
-rw-r--r--src/sfac.c86
-rw-r--r--src/sfac.h6
8 files changed, 22 insertions, 97 deletions
diff --git a/src/compare_hkl.c b/src/compare_hkl.c
index 2d7dd284..68920a55 100644
--- a/src/compare_hkl.c
+++ b/src/compare_hkl.c
@@ -44,7 +44,7 @@ int main(int argc, char *argv[])
double *ref1;
double *ref2;
double *out;
- struct molecule *mol;
+ UnitCell *cell;
char *outfile = NULL;
char *afile = NULL;
char *bfile = NULL;
@@ -97,7 +97,7 @@ int main(int argc, char *argv[])
return 1;
}
- mol = load_molecule();
+ cell = load_cell_from_pdb("molecule.pdb");
ref1 = read_reflections(afile);
if ( ref1 == NULL ) {
ERROR("Couldn't open file '%s'\n", afile);
@@ -127,7 +127,7 @@ int main(int argc, char *argv[])
}
}
- write_reflections(outfile, NULL, out, 1, mol->cell);
+ write_reflections(outfile, NULL, out, 1, cell);
return 0;
}
diff --git a/src/diffraction.c b/src/diffraction.c
index c47920f5..a0c3a9a1 100644
--- a/src/diffraction.c
+++ b/src/diffraction.c
@@ -223,7 +223,7 @@ void get_diffraction(struct image *image, int na, int nb, int nc,
na, nb, nc);
if ( intensities == NULL ) {
- I_molecule = 10000.0;
+ I_molecule = 1.0e10;
} else {
I_molecule = molecule_factor(intensities, q,
ax,ay,az,bx,by,bz,cx,cy,cz);
diff --git a/src/get_hkl.c b/src/get_hkl.c
index 5e5331b4..ec2b898e 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -153,7 +153,7 @@ int main(int argc, char *argv[])
}
mol = load_molecule();
- get_reflections_cached(mol, eV_to_J(1790.0));
+ ideal_ref = get_reflections(mol, eV_to_J(1790.0));
counts = new_list_count();
diff --git a/src/indexamajig.c b/src/indexamajig.c
index e0871fe7..c99a2b8b 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -208,7 +208,7 @@ int main(int argc, char *argv[])
{"no-match", 0, &config_nomatch, 1},
{"verbose", 0, &config_verbose, 1},
{"alternate", 0, &config_alternate, 1},
- {"intensities", 0, NULL, 'q'},
+ {"intensities", 1, NULL, 'q'},
{0, 0, NULL, 0}
};
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 2ff12226..55b92c0e 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -175,7 +175,7 @@ int main(int argc, char *argv[])
{"no-images", 0, &config_noimages, 1},
{"no-water", 0, &config_nowater, 1},
{"no-noise", 0, &config_nonoise, 1},
- {"intensities", 0, NULL, 'i'},
+ {"intensities", 1, NULL, 'i'},
{"powder", 0, &config_powder, 1},
{0, 0, NULL, 0}
};
diff --git a/src/process_hkl.c b/src/process_hkl.c
index 53ac1169..7b1035bc 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -187,7 +187,7 @@ int main(int argc, char *argv[])
double *ref, *trueref = NULL;
unsigned int *counts;
char *rval;
- struct molecule *mol = NULL;
+ UnitCell *cell;
int config_maxonly = 0;
int config_every = 1000;
int config_rvsq = 0;
@@ -276,8 +276,7 @@ int main(int argc, char *argv[])
ref = new_list_intensity();
counts = new_list_count();
-
- mol = load_molecule();
+ cell = load_cell_from_pdb("molecule.pdb");
if ( strcmp(filename, "-") == 0 ) {
fh = stdin;
@@ -307,7 +306,7 @@ int main(int argc, char *argv[])
if (config_every && (n_patterns % config_every == 0)) {
process_reflections(ref, trueref, counts,
- n_patterns, mol->cell,
+ n_patterns, cell,
config_rvsq,
config_zoneaxis);
}
@@ -341,20 +340,16 @@ int main(int argc, char *argv[])
fclose(fh);
if ( trueref != NULL ) {
- process_reflections(ref, trueref, counts, n_patterns, mol->cell,
+ process_reflections(ref, trueref, counts, n_patterns, cell,
config_rvsq, config_zoneaxis);
}
if ( output != NULL ) {
- UnitCell *cell = NULL;
- if ( mol != NULL ) cell = mol->cell;
write_reflections(output, counts, ref, 0, cell);
}
if ( config_zoneaxis ) {
char name[64];
- UnitCell *cell = NULL;
- if ( mol != NULL ) cell = mol->cell;
snprintf(name, 63, "ZA-%u.dat", n_patterns);
write_reflections(name, counts, ref, 1, cell);
}
diff --git a/src/sfac.c b/src/sfac.c
index dd722cc8..00bbd6ba 100644
--- a/src/sfac.c
+++ b/src/sfac.c
@@ -304,8 +304,8 @@ static void centre_molecule(struct molecule *mol)
}
- //STATUS("Molecule was shifted by %5.3f, %5.3f, %5.3f nm\n",
- // mol->xc*1e9, mol->yc*1e9, mol->zc*1e9);
+ STATUS("The atoms were shifted by %5.3f, %5.3f, %5.3f nm\n",
+ mol->xc*1e9, mol->yc*1e9, mol->zc*1e9);
}
@@ -462,7 +462,7 @@ struct molecule *load_molecule()
centre_molecule(mol);
- STATUS("There are %i species\n", mol->n_species); fflush(stderr);
+ STATUS("There are %i species:\n", mol->n_species); fflush(stderr);
for ( i=0; i<mol->n_species; i++ ) {
STATUS("%3s : %6i\n", mol->species[i]->species,
mol->species[i]->n_atoms);
@@ -490,31 +490,9 @@ void free_molecule(struct molecule *mol)
}
-struct molecule *copy_molecule(struct molecule *orig)
+double *get_reflections(struct molecule *mol, double en)
{
- struct molecule *new;
- int i;
-
- new = malloc(sizeof(*new));
- *new = *orig;
-
- /* Now sort out pointers */
- for ( i=0; i<orig->n_species; i++ ) {
- new->species[i] = malloc(sizeof(struct mol_species));
- memcpy(new->species[i], orig->species[i],
- sizeof(struct mol_species));
- }
-
- new->cell = cell_new_from_cell(orig->cell);
- new->reflections = NULL;
-
- return new;
-}
-
-
-double complex *get_reflections(struct molecule *mol, double en)
-{
- double complex *reflections;
+ double *reflections;
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
@@ -525,7 +503,7 @@ double complex *get_reflections(struct molecule *mol, double en)
&bsx, &bsy, &bsz,
&csx, &csy, &csz);
- reflections = new_list_sfac();
+ reflections = new_list_intensity();
for ( h=-INDMAX; h<=INDMAX; h++ ) {
for ( k=-INDMAX; k<=INDMAX; k++ ) {
@@ -572,61 +550,13 @@ double complex *get_reflections(struct molecule *mol, double en)
}
- set_sfac(reflections, h, k, l, F);
+ set_intensity(reflections, h, k, l, pow(cabs(F), 2.0));
}
progress_bar((k+INDMAX)+IDIM*(h+INDMAX), IDIM*IDIM-1,
- "Calculating structure factors");
+ "Calculating reflection intensities");
}
}
return reflections;
}
-
-
-void get_reflections_cached(struct molecule *mol, double en)
-{
- char s[1024];
- FILE *fh;
- size_t r;
-
- /* Add 0.5 to improve rounding */
- snprintf(s, 1023, "reflections-%ieV.cache", (int)(J_to_eV(en)+0.5));
- fh = fopen(s, "rb");
- if ( fh == NULL ) {
- STATUS("No cache file found (looked for %s)\n", s);
- goto calc;
- }
-
- mol->reflections = new_list_sfac();
- r = fread(mol->reflections, sizeof(double complex), IDIM*IDIM*IDIM, fh);
- if ( r < IDIM*IDIM*IDIM ) {
- STATUS("Found cache file (%s), but failed to read"
- " (got %lli items, wanted %i).\n",
- s, (long long)r, IDIM*IDIM*IDIM);
- goto calc;
- }
-
- STATUS("Read structure factors (at Bragg positions) from %s\n", s);
- return;
-
-calc:
- STATUS("Calculating structure factors at Bragg positions...\n");
- mol->reflections = get_reflections(mol, en);
- fh = fopen(s, "wb");
- if ( fh == NULL ) {
- STATUS("Failed to write cache file (%s)\n", s);
- return;
- }
-
- r = fwrite(mol->reflections, sizeof(double complex),
- IDIM*IDIM*IDIM, fh);
- if ( r < IDIM*IDIM*IDIM ) {
- STATUS("Failed to write cache file (%s)\n", s);
- return;
- }
- fclose(fh);
-
- STATUS("Successfully saved structure factors at Bragg positions to"
- " file %s\n", s);
-}
diff --git a/src/sfac.h b/src/sfac.h
index fea97022..1367abbd 100644
--- a/src/sfac.h
+++ b/src/sfac.h
@@ -55,12 +55,12 @@ struct molecule
};
+/* This is so that the water background calculation can use it */
extern double complex get_sfac(const char *n, double s, double en);
+
extern struct molecule *load_molecule(void);
extern void free_molecule(struct molecule *mol);
-extern struct molecule *copy_molecule(struct molecule *orig);
-extern double complex *get_reflections(struct molecule *mol, double en);
-extern void get_reflections_cached(struct molecule *mol, double en);
+extern double *get_reflections(struct molecule *mol, double en);
#endif /* SFAC_H */
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-10 15:34:35 +0000