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/*
* basis.c
*
* Handle basis structures
*
* (c) 2007-2009 Thomas White <taw27@cam.ac.uk>
*
* dtr - Diffraction Tomography Reconstruction
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <math.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_linalg.h>
#include "reflections.h"
#include "basis.h"
#include "utils.h"
#include "displaywindow.h"
#include "reproject.h"
static void basis_print(Basis *cell)
{
printf("%12.8f %12.8f %12.8f\n",
cell->a.x/1e9, cell->a.y/1e9, cell->a.z/1e9);
printf("%12.8f %12.8f %12.8f\n",
cell->b.x/1e9, cell->b.y/1e9, cell->b.z/1e9);
printf("%12.8f %12.8f %12.8f\n",
cell->c.x/1e9, cell->c.y/1e9, cell->c.z/1e9);
}
static void cell_print(UnitCell *cell)
{
printf("%12.8f %12.8f %12.8f nm\n",
cell->a*1e9, cell->b*1e9, cell->c*1e9);
printf("%12.8f %12.8f %12.8f deg\n",
rad2deg(cell->alpha), rad2deg(cell->beta), rad2deg(cell->gamma));
}
UnitCell basis_get_cell(Basis *basis)
{
UnitCell cell;
gsl_matrix *m;
gsl_matrix *inv;
gsl_permutation *perm;
double ax, ay, az, bx, by, bz, cx, cy, cz;
int s;
printf("Reciprocal-space cell (nm^-1):\n");
basis_print(basis);
m = gsl_matrix_alloc(3, 3);
gsl_matrix_set(m, 0, 0, basis->a.x);
gsl_matrix_set(m, 0, 1, basis->b.x);
gsl_matrix_set(m, 0, 2, basis->c.x);
gsl_matrix_set(m, 1, 0, basis->a.y);
gsl_matrix_set(m, 1, 1, basis->b.y);
gsl_matrix_set(m, 1, 2, basis->c.y);
gsl_matrix_set(m, 2, 0, basis->a.z);
gsl_matrix_set(m, 2, 1, basis->b.z);
gsl_matrix_set(m, 2, 2, basis->c.z);
perm = gsl_permutation_alloc(m->size1);
inv = gsl_matrix_alloc(m->size1, m->size2);
gsl_linalg_LU_decomp(m, perm, &s);
gsl_linalg_LU_invert(m, perm, inv);
gsl_permutation_free(perm);
gsl_matrix_free(m);
gsl_matrix_transpose(inv);
ax = gsl_matrix_get(inv, 0, 0);
bx = gsl_matrix_get(inv, 0, 1);
cx = gsl_matrix_get(inv, 0, 2);
ay = gsl_matrix_get(inv, 1, 0);
by = gsl_matrix_get(inv, 1, 1);
cy = gsl_matrix_get(inv, 1, 2);
az = gsl_matrix_get(inv, 2, 0);
bz = gsl_matrix_get(inv, 2, 1);
cz = gsl_matrix_get(inv, 2, 2);
printf("Real-space cell (nm):\n");
printf("%12.8f %12.8f %12.8f\n", ax*1e9, ay*1e9, az*1e9);
printf("%12.8f %12.8f %12.8f\n", bx*1e9, by*1e9, bz*1e9);
printf("%12.8f %12.8f %12.8f\n", cx*1e9, cy*1e9, cz*1e9);
cell.a = sqrt(ax*ax + ay*ay + az*az);
cell.b = sqrt(bx*bx + by*by + bz*bz);
cell.c = sqrt(cx*cx + cy*cy + cz*cz);
cell.alpha = acos((bx*cx + by*cy + bz*cz)/(cell.b * cell.c));
cell.beta = acos((ax*cx + ay*cy + az*cz)/(cell.a * cell.c));
cell.gamma = acos((bx*ax + by*ay + bz*az)/(cell.b * cell.a));
gsl_matrix_free(inv);
printf("Cell parameters:\n");
cell_print(&cell);
return cell;
}
static int basis_do_save(Basis *cell, const char *filename)
{
FILE *fh;
UnitCell rcell;
fh = fopen(filename, "w");
fprintf(fh, "# DTR unit cell description\n");
/* A "human-readable" form */
rcell = basis_get_cell(cell);
fprintf(fh, "# a %12.8f nm\n", rcell.a*1e9);
fprintf(fh, "# b %12.8f nm\n", rcell.b*1e9);
fprintf(fh, "# c %12.8f nm\n", rcell.c*1e9);
fprintf(fh, "# alpha %12.8f deg\n", rad2deg(rcell.alpha));
fprintf(fh, "# beta %12.8f deg\n", rad2deg(rcell.beta));
fprintf(fh, "# gamma %12.8f deg\n", rad2deg(rcell.gamma));
/* The useful form */
fprintf(fh, "a %12.8f %12.8f %12.8f\n",
cell->a.x, cell->a.y, cell->a.z);
fprintf(fh, "b %12.8f %12.8f %12.8f\n",
cell->b.x, cell->b.y, cell->b.z);
fprintf(fh, "c %12.8f %12.8f %12.8f\n",
cell->c.x, cell->c.y, cell->c.z);
fclose(fh);
return 0;
}
static gint basis_save_response(GtkWidget *widget, gint response,
ControlContext *ctx)
{
if ( response == GTK_RESPONSE_ACCEPT ) {
char *filename;
filename = gtk_file_chooser_get_filename(
GTK_FILE_CHOOSER(widget));
if ( basis_do_save(ctx->cell, filename) ) {
displaywindow_error("Failed to save unit cell.",
ctx->dw);
}
g_free(filename);
}
gtk_widget_destroy(widget);
return 0;
}
void basis_save(ControlContext *ctx)
{
GtkWidget *save;
save = gtk_file_chooser_dialog_new("Save Unit Cell to File",
GTK_WINDOW(ctx->dw->window),
GTK_FILE_CHOOSER_ACTION_SAVE,
GTK_STOCK_CANCEL, GTK_RESPONSE_CANCEL,
GTK_STOCK_SAVE, GTK_RESPONSE_ACCEPT,
NULL);
g_signal_connect(G_OBJECT(save), "response",
G_CALLBACK(basis_save_response), ctx);
gtk_widget_show_all(save);
}
static int basis_do_load(Basis *cell, const char *filename)
{
FILE *fh;
float x, y, z;
int got_a = 0;
int got_b = 0;
int got_c = 0;
fh = fopen(filename, "r");
while ( !feof(fh) ) {
char line[256];
if ( fgets(line, 255, fh) != NULL ) {
if ( sscanf(line, "a %f %f %f\n", &x, &y, &z) == 3 ) {
cell->a.x = x; cell->a.y = y; cell->a.z = z;
got_a = 1;
}
if ( sscanf(line, "b %f %f %f\n", &x, &y, &z) == 3 ) {
cell->b.x = x; cell->b.y = y; cell->b.z = z;
got_b = 1;
}
if ( sscanf(line, "c %f %f %f\n", &x, &y, &z) == 3 ) {
cell->c.x = x; cell->c.y = y; cell->c.z = z;
got_c = 1;
}
}
}
fclose(fh);
return !(got_a && got_b && got_c);
}
static gint basis_load_response(GtkWidget *widget, gint response,
ControlContext *ctx)
{
if ( response == GTK_RESPONSE_ACCEPT ) {
char *filename;
filename = gtk_file_chooser_get_filename(
GTK_FILE_CHOOSER(widget));
if ( ctx->cell ) {
free(ctx->cell);
}
ctx->cell = malloc(sizeof(Basis));
if ( basis_do_load(ctx->cell, filename) ) {
displaywindow_error("Failed to load unit cell.",
ctx->dw);
} else {
displaywindow_update(ctx->dw);
reproject_lattice_changed(ctx);
}
g_free(filename);
}
gtk_widget_destroy(widget);
return 0;
}
void basis_load(ControlContext *ctx)
{
GtkWidget *load;
load = gtk_file_chooser_dialog_new("Load Unit Cell from File",
GTK_WINDOW(ctx->dw->window),
GTK_FILE_CHOOSER_ACTION_OPEN,
GTK_STOCK_CANCEL, GTK_RESPONSE_CANCEL,
GTK_STOCK_SAVE, GTK_RESPONSE_ACCEPT,
NULL);
g_signal_connect(G_OBJECT(load), "response",
G_CALLBACK(basis_load_response), ctx);
gtk_widget_show_all(load);
}
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