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);
}
gint read_nwchem_geometry(gpointer scan, struct model_pak *model)
{
gint n, zmode=0, end_count=0;
gchar **buff;
struct core_pak *core;
#if DEBUG_READ_NWCHEM_GEOMETRY
printf("read_nwchem_geometry(): start\n");
#endif
// TODO - rewrite this using symbol scanning functionality
while (!scan_complete(scan))
{
buff = scan_get_tokens(scan, &n);
// zmatrix?
if (g_ascii_strncasecmp(*buff, "zmatrix", 7) == 0)
{
zmode = 1;
g_strfreev(buff);
continue;
}
if (g_ascii_strncasecmp(*buff, "variables", 9) == 0)
{
zmode = 2;
g_strfreev(buff);
continue;
}
if (g_ascii_strncasecmp(*buff, "constants", 9) == 0)
{
zmode = 3;
g_strfreev(buff);
continue;
}
// end?
if (n)
{
if (g_ascii_strncasecmp(*buff, "end", 3) == 0)
{
g_strfreev(buff);
/* if we processed zmatrix entries - expect 2 x end */
if (zmode && !end_count)
{
/* keep going until we hit a second end ... */
end_count++;
continue;
}
/* exit */
break;
}
}
/* main parse */
switch (zmode)
{
// cartesian coords
case 0:
// can cart coord line have >4 tokens?
if (n == 4)
{
if (elem_test(*buff))
{
core = core_new(*buff, NULL, model);
model->cores = g_slist_prepend(model->cores, core);
core->x[0] = str_to_float(*(buff+1));
core->x[1] = str_to_float(*(buff+2));
core->x[2] = str_to_float(*(buff+3));
#if DEBUG_READ_NWCHEM_GEOMETRY
printf("Added [%s] ", *buff);
P3VEC(": ", core->x);
#endif
}
}
break;
// zmatrix coords
case 1:
#if DEBUG_READ_NWCHEM_GEOMETRY
printf("zcoord: %s", scan_cur_line(scan));
#endif
zmat_nwchem_core_add(scan_cur_line(scan), model->zmatrix);
break;
// zmatrix vars
case 2:
#if DEBUG_READ_NWCHEM_GEOMETRY
printf("zvar: %s", scan_cur_line(scan));
#endif
zmat_var_add(scan_cur_line(scan), model->zmatrix);
break;
// zmatrix consts
case 3:
#if DEBUG_READ_NWCHEM_GEOMETRY
printf("zconst: %s", scan_cur_line(scan));
#endif
zmat_const_add(scan_cur_line(scan), model->zmatrix);
break;
}
g_strfreev(buff);
}
if (zmode)
{
#if DEBUG_READ_NWCHEM_GEOMETRY
printf("Creating zmatrix cores...\n");
#endif
zmat_angle_units_set(model->zmatrix, DEGREES);
zmat_process(model->zmatrix, model);
}
#if DEBUG_READ_NWCHEM_GEOMETRY
printf("read_nwchem_geometry(): stop\n");
#endif
return(0);
}