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 write_gromacs_dihedrals(FILE *fp, struct model_pak *model)
{
gint i, j, k, l, n;
gdouble angle, da;
GSList *list, *list1, *list2, *end1, *end2;
GSList *d_list, *r_list, *i_list;
struct core_pak *c[4];
struct bond_pak *bond;
struct forcefield_pak *ff, *ff_gromacs;
g_assert(model != NULL);
d_list = ff_filter_list(FF_DIHEDRAL, model->ff_list);
r_list = ff_filter_list(FF_DIHEDRAL_RB, model->ff_list);
i_list = ff_filter_list(FF_IMPROPER, model->ff_list);
/* header */
fprintf(fp, "\n[ dihedrals ]\n");
/* generate torsions for all combinations about a bond */
for (list=model->bonds ; list ; list=g_slist_next(list))
{
bond = list->data;
if (bond->type == BOND_HBOND)
continue;
c[1] = bond->atom1;
c[2] = bond->atom2;
/* get lists of connected atoms at each end */
end1 = connect_neighbours(c[1]);
end1 = g_slist_remove(end1, c[2]);
end2 = connect_neighbours(c[2]);
end2 = g_slist_remove(end2, c[1]);
/* skip bonds with no neighbour atoms */
/*
if (!end1 || !end2)
goto gromacs_dihedral_loop_done;
*/
/* enumerate four body terms */
for (list1=end1 ; list1 ; list1=g_slist_next(list1))
{
c[0] = list1->data;
for (list2=end2 ; list2 ; list2=g_slist_next(list2))
{
c[3] = list2->data;
/* search for standard dihedral potential */
ff = ff_search(c, 4, d_list);
/* search for RB dihedral */
if (!ff)
ff = ff_search(c, 4, r_list);
/* CURRENT */
/*
printf("[%s][%s][%s][%s]", c[0]->atom_label, c[1]->atom_label, c[2]->atom_label, c[3]->atom_label);
printf(" : dihedral = %f\n", measure_torsion(c));
*/
if (ff)
{
ff_gromacs = gromacs_type(ff);
i = g_slist_index(model->cores, c[0])+1;
j = g_slist_index(model->cores, c[1])+1;
k = g_slist_index(model->cores, c[2])+1;
l = g_slist_index(model->cores, c[3])+1;
/* lambda 0 */
/* print atoms and type */
fprintf(fp, "%2d %2d %2d %2d %d ", i, j, k, l, ff_gromacs->type);
/* NB: gromacs has the bond length 1st, followed by the potential parameters */
/* which is the reverse from internal/GULP format */
if (ff_gromacs->bond_expected)
fprintf(fp, "%f", ff_gromacs->bond_value);
for (n=0 ; n<ff_gromacs->data_expected ; n++)
fprintf(fp, " %f", ff_gromacs->data[n]);
/* lambda 1 */
fprintf(fp, " ");
if (ff_gromacs->bond_expected)
fprintf(fp, "%f", ff_gromacs->bond_value);
for (n=0 ; n<ff_gromacs->data_expected ; n++)
fprintf(fp, " %f", ff_gromacs->data[n]);
fprintf(fp, "\n");
g_free(ff_gromacs);
}
}
}
g_slist_free(end1);
g_slist_free(end2);
}
/* CURRENT - improper torsions (implemented as proper) */
/* FIXME - only valid for OPLS-AA */
/*
fprintf(fp, "\n[ impropers ]\n");
*/
fprintf(fp, "; Improper terms, implemented as proper torsions.\n");
/* for each atom with 3 bonds (planar) */
for (list=model->cores ; list ; list=g_slist_next(list))
{
c[0] = list->data;
list1 = connect_neighbours(c[0]);
/* CHECK - only an atom with 3 bonds can be a candidate */
if (g_slist_length(list1) == 3)
{
c[1] = list1->data;
list2 = g_slist_next(list1);
c[2] = list2->data;
list2 = g_slist_next(list2);
c[3] = list2->data;
/* TODO - want c[3] to be defined so that the c[1] - c[2] axis is */
/* orthogonal to the c[0] - c[3] direction */
/* TODO - choose c[1] & c[2] to be same type (if possible) */
/* improper torsion - only allow if angle is ~180 */
angle = measure_torsion(c);
/*
da = fabs(180.0 - fabs(angle));
*/
da = fabs(angle);
/* 10 degree tolerance */
ff = NULL;
if (da < 10.0)
ff = ff_search(c, 4, i_list);
if (ff)
{
ff_gromacs = gromacs_type(ff);
i = g_slist_index(model->cores, c[0])+1;
j = g_slist_index(model->cores, c[1])+1;
k = g_slist_index(model->cores, c[2])+1;
l = g_slist_index(model->cores, c[3])+1;
/* lambda 0 */
fprintf(fp, "%2d %2d %2d %2d 1 ", i, j, k, l);
fprintf(fp, " %f", ff_gromacs->bond_value);
for (n=0 ; n<ff_gromacs->data_current ; n++)
fprintf(fp, " %f", ff_gromacs->data[n]);
/* lambda 1 */
fprintf(fp, " %f", ff_gromacs->bond_value);
for (n=0 ; n<ff_gromacs->data_current ; n++)
fprintf(fp, " %f", ff_gromacs->data[n]);
fprintf(fp, "\n");
g_free(ff_gromacs);
}
}
g_slist_free(list1);
}
/* cleanup */
g_slist_free(d_list);
g_slist_free(r_list);
g_slist_free(i_list);
return(0);
}
