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/*
* cell.c
*
* Unit Cell Calculations
*
* (c) 2007-2009 Thomas White <thomas.white@desy.de>
*
* template_index - Indexing diffraction patterns by template matching
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <math.h>
#include <stdlib.h>
#include <stdio.h>
#include "cell.h"
#include "utils.h"
/* Update the cartesian representation from the crystallographic one */
static void cell_update_cartesian(UnitCell *cell)
{
double tmp, V, cosalphastar, cstar;
if ( !cell ) return;
/* a in terms of x, y and z
* +a (cryst) is defined to lie along +x (cart) */
cell->ax = cell->a;
cell->ay = 0.0;
cell->az = 0.0;
/* b in terms of x, y and z
* b (cryst) is defined to lie in the xy (cart) plane */
cell->bx = cell->b*cos(cell->gamma);
cell->by = cell->b*sin(cell->gamma);
cell->bz = 0.0;
tmp = cos(cell->alpha)*cos(cell->alpha)
- cos(cell->beta)*cos(cell->beta)
- cos(cell->gamma)*cos(cell->gamma)
+ 2.0*cos(cell->alpha)*cos(cell->beta)*cos(cell->gamma);
V = cell->a * cell->b * cell->c * sqrt(1.0 - tmp);
cosalphastar = cos(cell->beta)*cos(cell->gamma) - cos(cell->alpha);
cosalphastar /= sin(cell->beta)*sin(cell->gamma);
cstar = (cell->a * cell->b * sin(cell->gamma))/V;
/* c in terms of x, y and z */
cell->cx = cell->c*cos(cell->beta);
cell->cy = -cell->c*sin(cell->beta)*cosalphastar;
cell->cz = 1.0/cstar;
}
/* Update the crystallographic representation from the cartesian one */
static void cell_update_crystallographic(UnitCell *cell)
{
if ( !cell ) return;
cell->a = modulus(cell->ax, cell->ay, cell->az);
cell->b = modulus(cell->bx, cell->by, cell->bz);
cell->c = modulus(cell->cx, cell->cy, cell->cz);
cell->alpha = angle_between(cell->bx, cell->by, cell->bz,
cell->cx, cell->cy, cell->cz);
cell->beta = angle_between(cell->ax, cell->ay, cell->az,
cell->cx, cell->cy, cell->cz);
cell->gamma = angle_between(cell->ax, cell->ay, cell->az,
cell->bx, cell->by, cell->bz);
printf("a=%f nm\n", cell->a);
printf("b=%f nm\n", cell->b);
printf("c=%f nm\n", cell->c);
printf("alpha = %f deg\n", rad2deg(cell->alpha));
printf(" beta = %f deg\n", rad2deg(cell->beta));
printf("gamma = %f deg\n", rad2deg(cell->gamma));
}
UnitCell *cell_new()
{
UnitCell *cell;
cell = malloc(sizeof(UnitCell));
if ( !cell ) return NULL;
cell->a = 1.0;
cell->b = 1.0;
cell->c = 1.0;
cell->alpha = M_PI_2;
cell->beta = M_PI_2;
cell->gamma = M_PI_2;
cell_update_cartesian(cell);
return cell;
}
void cell_set_parameters(UnitCell *cell, double a, double b, double c,
double alpha, double beta, double gamma)
{
if ( !cell ) return;
cell->a = a;
cell->b = b;
cell->c = c;
cell->alpha = alpha;
cell->beta = beta;
cell->gamma = gamma;
cell_update_cartesian(cell);
}
void cell_set_cartesian(UnitCell *cell,
double ax, double ay, double az,
double bx, double by, double bz,
double cx, double cy, double cz)
{
if ( !cell ) return;
cell->ax = ax; cell->ay = ay; cell->az = az;
cell->bx = bx; cell->by = by; cell->bz = bz;
cell->cx = cx; cell->cy = cy; cell->cz = cz;
cell_update_crystallographic(cell);
}
UnitCell *cell_new_from_parameters(double a, double b, double c,
double alpha, double beta, double gamma)
{
UnitCell *cell;
cell = cell_new();
if ( !cell ) return NULL;
cell_set_parameters(cell, a, b, c, alpha, beta, gamma);
return cell;
}
void cell_get_cartesian(UnitCell *cell,
double *ax, double *ay, double *az,
double *bx, double *by, double *bz,
double *cx, double *cy, double *cz)
{
if ( !cell ) return;
*ax = cell->ax; *ay = cell->ay; *az = cell->az;
*bx = cell->bx; *by = cell->by; *bz = cell->bz;
*cx = cell->cx; *cy = cell->cy; *cz = cell->cz;
}
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