From d79e90a428846d5944633bbe334cafd0ed9fc926 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Fri, 26 Mar 2010 18:23:32 +0100 Subject: Don't try to render PDBs, part III: tidy up and fix --- src/compare_hkl.c | 6 ++-- src/diffraction.c | 2 +- src/get_hkl.c | 2 +- src/indexamajig.c | 2 +- src/pattern_sim.c | 2 +- src/process_hkl.c | 13 +++------ src/sfac.c | 86 ++++++------------------------------------------------- src/sfac.h | 6 ++-- 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; in_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; in_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 */ -- cgit v1.2.3