/* Compute A = B * C * D where A, B, C, D are square matrices of the same dimension, and C is diagonal. Allow B, C, D to be complex valued but assume their product is real valued (as when B,C,D represent diagonalization of A). C is described by a vector representing its diagonal elements. A temp matrix can optionally be passed in to improve efficiency. */ void zmat_mult_real_diag(Matrix *A, Zmatrix *B, Zvector *C, Zmatrix *D, Zmatrix *scratch) { int i, j; int size = C->size; Zmatrix *tmp; if (!(A->nrows == A->ncols && A->nrows == B->nrows && B->nrows == B->ncols && B->nrows == C->size && C->size == D->nrows && D->nrows == D->ncols)) die("ERROR zmat_mult_real_diag: bad dimensions\n"); if (scratch == NULL) tmp= zmat_new(size, size); else { if (!(scratch->nrows == size && scratch->ncols == size)) die("ERROR zmat_mult_real_diag: scratch has wrong size\n"); tmp = scratch; } /* first compute tmp = C*D */ for (i = 0; i < size; i++) for (j = 0; j < size; j++) zmat_set(tmp, i, j, z_mul(zvec_get(C, i), zmat_get(D, i, j))); /* now compute A = B*tmp */ zmat_mult_real(A, B, tmp); if (scratch == NULL) zmat_free(tmp); }
Zmatrix *zmat_create_copy(Zmatrix *src) { Zmatrix *dest = zmat_new(src->nrows, src->ncols); zmat_copy(dest, src); return dest; }
Zmatrix *zmat_new_from_file(FILE *F, int nrows, int ncols) { Zmatrix *m = zmat_new(nrows, ncols); zmat_read(m, F); return m; }
void zmat_build(void) { gint i, j, k, n, type; gdouble r, a, d, x[4][3], v[3]; gdouble zaxis[3] = {0.0, 0.0, 1.0}; gchar *line; GSList *list, *species; struct zmat_pak *zmat; struct core_pak *core[4] = {NULL, NULL, NULL, NULL}; struct model_pak *model; model = sysenv.active_model; if (!model) return; /* CURRENT - using selection as our list of cores to generate a zmatrix from */ if (!model->selection) { gui_text_show(WARNING, "ZMATRIX: please select a molecule.\n"); return; } /* destroy old zmatrix */ /* TODO - prompt if non null */ zmat_free(model->zmatrix); zmat = model->zmatrix = zmat_new(); zmat_angle_units_set(model->zmatrix, DEGREES); /* setup SIESTA species type */ species = fdf_species_build(model); /* sort the list so it follows molecular connectivity */ model->selection = zmat_connect_sort(model->selection); n=0; for (list=model->selection ; list ; list=g_slist_next(list)) { /* current atom/zmatrix line init */ core[0] = list->data; type = fdf_species_index(core[0]->atom_label, species); line = NULL; zmat->zcores = g_slist_append(zmat->zcores, core[0]); /* build a ZMATRIX line for processing */ switch (n) { case 0: if (core[0]) { ARR3SET(x[0], core[0]->x); vecmat(model->latmat, x[0]); } line = g_strdup_printf("%d 0 0 0 %f %f %f 0 0 0\n", type, x[0][0], x[0][1], x[0][2]); break; case 1: if (core[0]) { ARR3SET(x[0], core[0]->x); vecmat(model->latmat, x[0]); } if (core[1]) { ARR3SET(x[1], core[1]->x); vecmat(model->latmat, x[1]); } r = measure_distance(x[0], x[1]); /* angle with z axis */ ARR3SET(v, x[0]); ARR3SUB(v, x[1]); a = R2D * via(v, zaxis, 3); /* angle between xy projection and x axis */ d = R2D * angle_x_compute(v[0], v[1]); line = g_strdup_printf("%d 1 0 0 %f %f %f 0 0 0\n", type, r, a, d); break; case 2: /* coords init */ for (i=3 ; i-- ; ) { if (core[i]) { ARR3SET(x[i], core[i]->x); vecmat(model->latmat, x[i]); } else g_assert_not_reached(); } r = measure_distance(x[0], x[1]); a = measure_angle(x[0], x[1], x[2]); /* create a fake core -> 1 unit displaced in the z direction */ g_assert(core[3] == NULL); core[3] = core_new("x", NULL, model); ARR3SET(core[3]->rx, core[2]->rx); ARR3ADD(core[3]->rx, zaxis); d = measure_torsion(core); core_free(core[3]); line = g_strdup_printf("%d 2 1 0 %f %f %f 0 0 0\n", type,r,a,d); break; default: /* connectivity test */ if (!zmat_bond_check(core[0], core[1])) { #if DEBUG_ZMAT_BUILD printf("[%d] non-connected atoms [%f]\n", n, measure_distance(x[0], x[1])); #endif /* need to build a new connectivity chain starting from core[0] */ core[1] = core[2] = core[3] = NULL; if (!zmat_connect_find(n, core, zmat)) { gui_text_show(WARNING, "ZMATRIX: bad connectivity (molecule will be incomplete)\n"); goto zmat_build_done; } } /* coords init */ for (i=3 ; i-- ; ) { if (core[i]) { ARR3SET(x[i], core[i]->x); vecmat(model->latmat, x[i]); } else g_assert_not_reached(); } r = measure_distance(x[0], x[1]); a = measure_angle(x[0], x[1], x[2]); d = measure_torsion(core); /* NB: indexing starts from 0, siesta starts from 1 (naturally) */ i = 1+g_slist_index(zmat->zcores, core[1]); j = 1+g_slist_index(zmat->zcores, core[2]); k = 1+g_slist_index(zmat->zcores, core[3]); line = g_strdup_printf("%d %d %d %d %f %f %f 0 0 0\n", type,i,j,k,r,a,d); } /* process a successfully constructed ZMATRIX line */ if (line) { zmat_core_add(line, model->zmatrix); g_free(line); } /* shuffle */ core[3] = core[2]; core[2] = core[1]; core[1] = core[0]; n++; } zmat_build_done: /* do the species typing */ zmat_type(model->zmatrix, species); free_slist(species); }