aboutsummaryrefslogtreecommitdiff
path: root/src/sfac.c
diff options
context:
space:
mode:
Diffstat (limited to 'src/sfac.c')
-rw-r--r--src/sfac.c542
1 files changed, 0 insertions, 542 deletions
diff --git a/src/sfac.c b/src/sfac.c
deleted file mode 100644
index 8b69f2e3..00000000
--- a/src/sfac.c
+++ /dev/null
@@ -1,542 +0,0 @@
-/*
- * sfac.c
- *
- * Scattering factors
- *
- * (c) 2006-2010 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-
-#include <stdlib.h>
-#include <math.h>
-#include <stdio.h>
-#include <complex.h>
-#include <string.h>
-#include <ctype.h>
-
-#include "utils.h"
-#include "sfac.h"
-
-
-#define N_MEMO 1024
-
-
-/* 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;
- static char *memo_n[N_MEMO];
- static int memo_eV[N_MEMO];
- static double complex memo_res[N_MEMO];
- static int n_memo = 0;
- int eV;
- int i;
-
- eV = (int)rint(J_to_eV(en));
-
- for ( i=0; i<n_memo; i++ ) {
- if ( (memo_eV[i] == eV) && (strcmp(memo_n[i], n) == 0) ) {
- return memo_res[i];
- }
- }
-
- snprintf(filename, 63, DATADIR"/crystfel/%s.nff", n);
- fh = fopen(filename, "r");
- if ( fh == NULL ) {
- ERROR("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 ) {
- STATUS("I couldn't understand a line in the f1f2 "
- "tables\n");
- continue;
- }
- /* 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;
- double complex res;
-
- 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);
-
- res = actual_f1 + I*actual_f2;
-
- memo_n[n_memo] = strdup(n);
- memo_eV[n_memo] = eV;
- memo_res[n_memo++] = res;
- n_memo = n_memo % N_MEMO;
-
- return res;
-
- }
-
- } while ( rval != NULL );
-
- fclose(fh);
-
- ERROR("Couldn't find scattering factors for '%s' at %f eV!\n", n, en);
-
- return 0.0;
-}
-
-
-struct waas_kirf_factors {
- char *n;
- float a1;
- float a2;
- float a3;
- float a4;
- float a5;
- float b1;
- float b2;
- float b3;
- float b4;
- float b5;
- float c;
-};
-
-/* s = sin(theta)/lambda in metres^-1*/
-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;
- int i;
- static struct waas_kirf_factors waaskirfcache[N_MEMO];
- int found;
- static int n_waaskirfcache = 0;
-
- found = 0;
- for ( i=0; i<n_waaskirfcache; i++ ) {
- if ( strcmp(waaskirfcache[i].n, n) == 0 ) {
-
- found = 1;
-
- a1 = waaskirfcache[n_waaskirfcache].a1;
- a2 = waaskirfcache[n_waaskirfcache].a2;
- a3 = waaskirfcache[n_waaskirfcache].a3;
- a4 = waaskirfcache[n_waaskirfcache].a4;
- a5 = waaskirfcache[n_waaskirfcache].a5;
- b1 = waaskirfcache[n_waaskirfcache].b1;
- b2 = waaskirfcache[n_waaskirfcache].b2;
- b3 = waaskirfcache[n_waaskirfcache].b3;
- b4 = waaskirfcache[n_waaskirfcache].b4;
- b5 = waaskirfcache[n_waaskirfcache].b5;
- c = waaskirfcache[n_waaskirfcache].c;
-
- break;
- }
- }
-
- if ( !found ) {
-
- fh = fopen(DATADIR"/crystfel/f0_WaasKirf.dat", "r");
- if ( fh == NULL ) {
- ERROR("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 ) {
- ERROR("Couldn't read scattering "
- "factors (WaasKirf)\n");
- return 0.0;
- }
-
- break;
-
- } while ( rval != NULL );
-
- fclose(fh);
-
- waaskirfcache[n_waaskirfcache].a1 = a1;
- waaskirfcache[n_waaskirfcache].a2 = a2;
- waaskirfcache[n_waaskirfcache].a3 = a3;
- waaskirfcache[n_waaskirfcache].a4 = a4;
- waaskirfcache[n_waaskirfcache].a5 = a5;
- waaskirfcache[n_waaskirfcache].c = c;
- waaskirfcache[n_waaskirfcache].b1 = b1;
- waaskirfcache[n_waaskirfcache].b2 = b2;
- waaskirfcache[n_waaskirfcache].b3 = b3;
- waaskirfcache[n_waaskirfcache].b4 = b4;
- waaskirfcache[n_waaskirfcache].b5 = b5;
- waaskirfcache[n_waaskirfcache++].n = strdup(n);
- n_waaskirfcache = n_waaskirfcache % N_MEMO; /* Unlikely */
-
- }
-
- s2 = pow(s/1e10, 2.0); /* s2 is s squared in Angstroms^-2 */
- 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;
-
- /* Anomalous part (point-like K-shell electrons only) */
- f1f2 = get_f1f2(n, en);
-
- /* Atomic form factor part (not complex-valued) */
- fq = get_waas_kirf(n, s) - get_waas_kirf(n, 0.0);
-
- return fq + f1f2;
-}
-
-
-static void centre_molecule(struct molecule *mol)
-{
- int i;
- double tx = 0.0;
- double ty = 0.0;
- double tz = 0.0;
- double total = 0.0;
-
- /* Atoms are grouped by species for faster calculation */
- for ( i=0; i<mol->n_species; i++ ) {
-
- struct mol_species *spec;
- int j;
-
- spec = mol->species[i];
-
- for ( j=0; j<spec->n_atoms; j++ ) {
-
- double sfac = get_waas_kirf(spec->species, 0.0);
-
- tx += spec->x[j] * sfac;
- ty += spec->y[j] * sfac;
- tz += spec->z[j] * sfac;
- total += sfac;
-
- }
-
- }
-
- mol->xc = tx / total;
- mol->yc = ty / total;
- mol->zc = tz / total;
-
- for ( i=0; i<mol->n_species; i++ ) {
-
- struct mol_species *spec;
- int j;
-
- spec = mol->species[i];
-
- for ( j=0; j<spec->n_atoms; j++ ) {
-
- spec->x[j] -= mol->xc;
- spec->y[j] -= mol->yc;
- spec->z[j] -= mol->zc;
-
- }
-
- }
-
- STATUS("The atoms were shifted by %5.3f, %5.3f, %5.3f nm\n",
- mol->xc*1e9, mol->yc*1e9, mol->zc*1e9);
-}
-
-
-/* Load PDB file into a memory format suitable for efficient(ish) structure
- * factor calculation */
-struct molecule *load_molecule(const char *filename)
-{
- struct molecule *mol;
- FILE *fh;
- char line[1024];
- char *rval;
- int i;
-
- mol = malloc(sizeof(struct molecule));
- if ( mol == NULL ) return NULL;
- mol->n_species = 0;
- mol->reflections = NULL;
- mol->cell = NULL;
-
- fh = fopen(filename, "r");
- if ( fh == NULL ) {
- ERROR("Couldn't open PDB file\n");
- return NULL;
- }
-
- do {
-
- int j, r;
- int done = 0;
- char xs[8];
- char ys[8];
- char zs[8];
- char occs[6];
- char Bs[6];
- char el[3];
- float xf, yf, zf, occf, Bf;
- double x, y, z, occ, B;
-
- rval = fgets(line, 1023, fh);
-
- /* Only interested in atoms */
- if ( (strncmp(line, "HETATM", 6) != 0)
- && (strncmp(line, "ATOM ", 6) != 0) ) continue;
-
- chomp(line);
- if ( strlen(line) != 80 ) {
- STATUS("Line does not have the correct length (%i):\n",
- (int)strlen(line));
- STATUS("'%s'\n", line);
- continue;
- }
-
- /* Separate out fixed-width fields */
- memcpy(xs, line+30, 5); xs[7] = '\0';
- memcpy(ys, line+38, 5); ys[7] = '\0';
- memcpy(zs, line+46, 5); zs[7] = '\0';
- memcpy(occs, line+54, 5); occs[5] = '\0';
- memcpy(Bs, line+60, 5); Bs[5] = '\0';
- memcpy(el, line+76, 2); el[2] = '\0';
-
- /* Convert fields */
- r = sscanf(xs, "%f", &xf);
- r += sscanf(ys, "%f", &yf);
- r += sscanf(zs, "%f", &zf);
- r += sscanf(occs, "%f", &occf);
- r += sscanf(Bs, "%f", &Bf);
- if ( el[0] == ' ' ) {
- el[0] = el[1];
- el[1] = '\0';
- } else {
- el[1] = tolower(el[1]);
- }
-
- /* Promote to double precision */
- x = xf; y = yf; z = zf; occ = occf; B = Bf;
-
- for ( j=0; j<mol->n_species; j++ ) {
-
- struct mol_species *spec;
- int n;
-
- spec = mol->species[j];
-
- if ( strcmp(spec->species, el) != 0 ) continue;
-
- n = mol->species[j]->n_atoms;
-
- spec->x[n] = x*1.0e-10; /* Convert to m */
- spec->y[n] = y*1.0e-10;
- spec->z[n] = z*1.0e-10;
- spec->occ[n] = occ;
- spec->B[n] = B*1.0e-20; /* Convert to m^2 */
- mol->species[j]->n_atoms++;
- if ( mol->species[j]->n_atoms == MAX_ATOMS ) {
- ERROR("Too many atoms of type '%s'!\n", el);
- exit(1);
- }
-
- done = 1;
-
- }
-
- if ( !done ) {
-
- /* Need to create record for this species */
- struct mol_species *spec;
-
- spec = malloc(sizeof(struct mol_species));
-
- memcpy(spec->species, el, 1+strlen(el));
- spec->x[0] = x*1.0e-10; /* Convert to m */
- spec->y[0] = y*1.0e-10;
- spec->z[0] = z*1.0e-10;
- spec->occ[0] = occ;
- spec->B[0] = B*1.0e-20; /* Convert to m^2 */
- spec->n_atoms = 1;
-
- mol->species[mol->n_species] = spec;
- mol->n_species++;
-
- }
-
- } while ( rval != NULL );
-
- fclose(fh);
-
- centre_molecule(mol);
-
- 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);
- }
-
- mol->cell = load_cell_from_pdb(filename);
- if ( mol->cell == NULL ) {
- ERROR("No unit cell found in PDB file\n");
- return NULL;
- }
-
- return mol;
-}
-
-
-void free_molecule(struct molecule *mol)
-{
- int i;
-
- for ( i=0; i<mol->n_species; i++ ) {
- free(mol->species[i]);
- }
-
- free(mol->cell);
- free(mol);
-}
-
-
-double *get_reflections(struct molecule *mol, double en, double res,
- double *phases, ReflItemList *items)
-{
- double *reflections;
- double asx, asy, asz;
- double bsx, bsy, bsz;
- double csx, csy, csz;
- signed int h, k, l;
- const int do_thermal = 1;
-
- cell_get_reciprocal(mol->cell, &asx, &asy, &asz,
- &bsx, &bsy, &bsz,
- &csx, &csy, &csz);
-
- reflections = new_list_intensity();
-
- for ( h=-INDMAX; h<=INDMAX; h++ ) {
- for ( k=-INDMAX; k<=INDMAX; k++ ) {
- for ( l=-INDMAX; l<=INDMAX; l++ ) {
-
- double complex F = 0.0;
- int i;
- double s, oneoverd;
-
- /* We need sin(theta)/lambda = 1/2d */
- s = resolution(mol->cell, h, k, l);
- oneoverd = 2.0 * s;
- if ( oneoverd > res ) continue;
-
- /* Atoms are grouped by species for faster calculation */
- for ( i=0; i<mol->n_species; i++ ) {
-
- double complex sfac;
- double complex contrib = 0.0;
- struct mol_species *spec;
- int j;
-
- spec = mol->species[i];
-
- for ( j=0; j<spec->n_atoms; j++ ) {
-
- double ph, u, v, w;
- double complex cpart;
-
- u = h*asx + k*bsx + l*csx;
- v = h*asy + k*bsy + l*csy;
- w = h*asz + k*bsz + l*csz;
-
- ph = u*spec->x[j] + v*spec->y[j] + w*spec->z[j];
-
- /* Conversion from revolutions to radians */
- cpart = cexp(-2.0*M_PI*I*ph);
- if ( do_thermal ) {
- cpart *= exp(-2.0 * spec->B[j] * s * s);
- }
- contrib += cpart;
-
- }
-
- sfac = get_sfac(spec->species, s, en);
- F += sfac * contrib;
-
- }
-
- set_intensity(reflections, h, k, l, pow(cabs(F), 2.0));
- if ( phases != NULL ) set_phase(phases, h, k, l, carg(F));
- if ( items != NULL ) add_item(items, h, k, l);
-
- }
- progress_bar((k+INDMAX)+IDIM*(h+INDMAX), IDIM*IDIM-1,
- "Calculating reflection intensities");
- }
- }
-
- return reflections;
-}
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-14 01:32:20 +0000