diff options
Diffstat (limited to 'src/basis.c')
-rw-r--r-- | src/basis.c | 290 |
1 files changed, 192 insertions, 98 deletions
diff --git a/src/basis.c b/src/basis.c index 6e7aed8..37fedba 100644 --- a/src/basis.c +++ b/src/basis.c @@ -3,7 +3,7 @@ * * Handle basis structures * - * (c) 2007 Thomas White <taw27@cam.ac.uk> + * (c) 2007-2009 Thomas White <taw27@cam.ac.uk> * * dtr - Diffraction Tomography Reconstruction * @@ -21,135 +21,229 @@ #include "reflections.h" #include "basis.h" #include "utils.h" - -double basis_efom(ReflectionList *reflectionlist, Basis *basis) { - - int n_indexed, n_counted; - Reflection *cur; - - cur = reflectionlist->reflections; - n_indexed = 0; - n_counted = 0; - while ( cur ) { - - if ( cur->type == REFLECTION_NORMAL ) { - - /* Can this basis "approximately" account for this reflection? */ - double det; - double a11, a12, a13, a21, a22, a23, a31, a32, a33; - double h, k, l; - - /* Set up the coordinate transform from hkl to xyz */ - a11 = basis->a.x; a12 = basis->a.y; a13 = basis->a.z; - a21 = basis->b.x; a22 = basis->b.y; a23 = basis->b.z; - a31 = basis->c.x; a32 = basis->c.y; a33 = basis->c.z; - - /* Invert the matrix to get hkl from xyz */ - det = a11*(a22*a33 - a23*a32) - a12*(a21*a33 - a23*a31) + a13*(a21*a32 - a22*a31); - h = ((a22*a33-a23*a32)*cur->x + (a23*a31-a21*a33)*cur->y + (a21*a32-a22*a31)*cur->z) / det; - k = ((a13*a32-a12*a33)*cur->x + (a11*a33-a13*a31)*cur->y + (a12*a31-a11*a32)*cur->z) / det; - l = ((a12*a23-a13*a22)*cur->x + (a13*a21-a11*a23)*cur->y + (a11*a22-a12*a21)*cur->z) / det; - - /* Calculate the deviations in terms of |a|, |b| and |c| */ - h = fabs(h); k = fabs(k); l = fabs(l); - h -= floor(h); k -= floor(k); l -= floor(l); - if ( h == 1.0 ) h = 0.0; - if ( k == 1.0 ) k = 0.0; - if ( l == 1.0 ) l = 0.0; - - /* Define "approximately" here. Circle in basis space becomes an ellipsoid in reciprocal space */ - if ( h*h + k*k + l*l <= 0.1*0.1*0.1 ) n_indexed++; - - n_counted++; - - } - - cur = cur->next; - - } - - return (double)n_indexed / n_counted; - +#include "displaywindow.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); } -Basis basis_add(Basis u, Basis v) { - - Basis ans; - - ans.a.x = u.a.x + v.a.x; ans.a.y = u.a.y + v.a.y; ans.a.z = u.a.z + v.a.z; - ans.b.x = u.b.x + v.b.x; ans.b.y = u.b.y + v.b.y; ans.b.z = u.b.z + v.b.z; - ans.c.x = u.c.x + v.c.x; ans.c.y = u.c.y + v.c.y; ans.c.z = u.c.z + v.c.z; - - return ans; - +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)); } -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 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; - -// basis->a.x = 0.5; basis->a.y = 0.0; basis->a.z = 0.0; -// basis->b.x = 0.0; basis->b.y = 0.2; basis->b.z = 0.0; -// basis->c.x = 0.0; basis->c.y = 0.0; basis->c.z = 1.0; + 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); - + 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); - + + 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"); + + 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); + } + 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); +} |