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/*
* diffraction.c
*
* Calculate diffraction patterns by Fourier methods
*
* (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 <string.h>
#include <complex.h>
#include "image.h"
#include "utils.h"
#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,
double bx, double by, double bz,
double cx, double cy, double cz)
{
struct threevec Udotq;
double f1, f2, f3;
int na = 8;
int nb = 8;
int nc = 8;
Udotq.u = (ax*q.u + ay*q.v + az*q.w)/2.0;
Udotq.v = (bx*q.u + by*q.v + bz*q.w)/2.0;
Udotq.w = (cx*q.u + cy*q.v + cz*q.w)/2.0;
if ( na > 1 ) {
f1 = sin(2.0*M_PI*(double)na*Udotq.u) / sin(2.0*M_PI*Udotq.u);
} else {
f1 = 1.0;
}
if ( nb > 1 ) {
f2 = sin(2.0*M_PI*(double)nb*Udotq.v) / sin(2.0*M_PI*Udotq.v);
} else {
f2 = 1.0;
}
if ( nc > 1 ) {
f3 = sin(2.0*M_PI*(double)nc*Udotq.w) / sin(2.0*M_PI*Udotq.w);
} else {
f3 = 1.0;
}
return f1 * f2 * f3;
}
/* 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,
double en)
{
int i;
double F = 0.0;
double s;
/* s = sin(theta)/lambda = 1/2d = (1/d)/2.0 */
s = modulus(q.u, q.v, q.w) / 2.0;
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;
ph= q.u*spec->x[j] + q.v*spec->y[j] + q.w*spec->z[j];
/* Conversion from revolutions to radians is required */
contrib += cos(2.0*M_PI*ph) + I*sin(2.0*M_PI*ph);
}
sfac = get_sfac(spec->species, s, en);
F += sfac * contrib * exp(-2.0 * spec->B[j] * s);
}
return F;
}
/* Load PDB file into a memory format suitable for efficient(ish) structure
* factor calculation */
static struct molecule *load_molecule()
{
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;
fh = fopen("molecule.pdb", "r");
if ( fh == NULL ) {
fprintf(stderr, "Couldn't open file\n");
return NULL;
}
do {
char el[4];
int j, r;
int done = 0;
float x, y, z, occ, B;
char *coords;
rval = fgets(line, 1023, fh);
/* Only interested in atoms */
if ( strncmp(line, "HETATM", 6) != 0 ) continue;
/* The following crimes against programming style
* were brought to you by Wizbit Enterprises, Inc. */
if ( line[76] == ' ' ) {
el[0] = line[77];
el[1] = '\0';
} else {
el[0] = line[76];
el[1] = line[77];
el[2] = '\0';
}
coords = line + 29;
r = sscanf(coords, "%f %f %f %f %f", &x, &y, &z, &occ, &B);
if ( r != 5 ) {
fprintf(stderr, "WTF?\n");
abort();
}
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;
spec->y[n] = y;
spec->z[n] = z;
spec->occ[n] = occ;
spec->B[n] = B;
mol->species[j]->n_atoms++;
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, 4);
spec->x[0] = x;
spec->y[0] = y;
spec->z[0] = z;
spec->occ[0] = occ;
spec->B[0] = B;
spec->n_atoms = 1;
mol->species[mol->n_species] = spec;
mol->n_species++;
}
} while ( rval != NULL );
fclose(fh);
printf("There are %i species\n", mol->n_species);
for ( i=0; i<mol->n_species; i++ ) {
printf("'%s': %i\n", mol->species[i]->species,
mol->species[i]->n_atoms);
}
return mol;
}
void get_diffraction(struct image *image, UnitCell *cell)
{
int x, y;
double ax, ay, az;
double bx, by, bz;
double cx, cy, cz;
/* Generate the array of reciprocal space vectors in image->qvecs */
get_ewald(image);
image->molecule = load_molecule();
if ( image->molecule == NULL ) return;
cell_get_cartesian(cell, &ax, &ay, &az,
&bx, &by, &bz,
&cx, &cy, &cz);
image->sfacs = malloc(image->width * image->height
* sizeof(double complex));
for ( x=0; x<image->width; x++ ) {
for ( y=0; y<image->height; y++ ) {
double f_lattice;
double complex f_molecule;
struct threevec q;
q = image->qvecs[x + image->width*y];
f_lattice = lattice_factor(q, ax,ay,az,bx,by,bz,cx,cy,cz);
f_molecule = molecule_factor(image->molecule, q,
image->xray_energy);
image->sfacs[x + image->width*y] = f_lattice * f_molecule;
}
printf("x=%i\n", x);
}
}
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