void delete_duplicate_cores(struct model_pak *model)
{
gdouble vec[3];
GSList *list1, *list2, *za_list;
gpointer zone;
struct core_pak *core1, *core2;
struct shel_pak *s1, *s2;
/* checks */
g_assert(model != NULL);
g_assert(model->zone_array != NULL);
#if DEBUG_REMOVE_DUPLICATES
printf("Initial cores: %d\n", g_slist_length(model->cores));
printf("Initial shels: %d\n", g_slist_length(model->shels));
#endif
/* enumerate all cores */
for (list1=model->cores ; list1 ; list1=g_slist_next(list1))
{
core1 = list1->data;
if (core1->status & DELETED)
continue;
/* enumerate cores in current locality */
zone = zone_get(core1->x, model->zone_array);
#if DEBUG_REMOVE_DUPLICATES_MORE
printf(" + %s [%p] : [%p] :", core1->atom_label, core1, zone);
P3VEC(" ", core1->x);
#endif
/* should use zone_area_cores() as a very small coord difference */
/* can result in cores being put in different (neighbouring) zones */
/*
for (list2=zone_cores(zone) ; list2 ; list2=g_slist_next(list2))
*/
za_list = zone_area_cores(1, zone, model->zone_array);
for (list2=za_list ; list2 ; list2=g_slist_next(list2))
{
core2 = list2->data;
if (core2->status & DELETED)
continue;
/* avoid double counting */
if (core1 >= core2)
continue;
if (core1->atom_code != core2->atom_code)
continue;
#if DEBUG_REMOVE_DUPLICATES_MORE
printf(" - %s :", core2->atom_label);
P3VEC(" ", core2->x);
#endif
/* compute and test the minimum separation */
ARR3SET(vec, core1->x);
ARR3SUB(vec, core2->x);
fractional_min(vec, model->periodic);
if (VEC3MAGSQ(vec) < FRACTION_TOLERANCE)
{
/* delete core2, unless primary AND core1 is non primary */
if (core2->primary && !core1->primary)
{
core1->status |= DELETED;
/* FIXME - this may be a problem since we start the core2 loop */
/* requiring that core1 be undeleted */
#if DEBUG_REMOVE_DUPLICATES_MORE
printf(" * rm 1\n");
#endif
}
else
{
core2->status |= DELETED;
#if DEBUG_REMOVE_DUPLICATES_MORE
printf(" * rm 2\n");
#endif
}
}
}
g_slist_free(za_list);
}
/* commit before searching for duplicate shells, as a commit */
/* will delete some attached shells */
delete_commit(model);
for (list1=model->shels ; list1 ; list1=g_slist_next(list1))
{
s1 = list1->data;
if (s1->status & DELETED)
continue;
/* NEW - enumerate shells in the current locality */
zone = zone_get(s1->x, model->zone_array);
for (list2=zone_shells(zone) ; list2 ; list2=g_slist_next(list2))
{
s2 = list2->data;
if (s2->status & DELETED)
continue;
if (s1 == s2)
continue;
ARR3SET(vec, s1->x);
ARR3SUB(vec, s2->x);
/* adjust for periodicity */
fractional_min(vec, model->periodic);
if (VEC3MAGSQ(vec) < FRACTION_TOLERANCE)
{
/* delete shell2, unless primary AND shell1 is non primary */
if (s2->primary && !s1->primary)
s1->status |= DELETED;
else
s2->status |= DELETED;
}
}
}
delete_commit(model);
#if DEBUG_REMOVE_DUPLICATES
printf("Final cores: %d\n", g_slist_length(model->cores));
printf("Final shels: %d\n", g_slist_length(model->shels));
#endif
}
gint region_move_atom(struct core_pak *core, gint direction,
struct model_pak *data)
{
gint flag, primary, secondary, mov[2];
gdouble vec[3], tmp[3], d[3];
GSList *list;
struct core_pak *comp;
#if DEBUG_REGION_SWITCH_ATOM
printf(" model: %s\n", data->basename);
printf(" periodicity: %d\n", data->periodic);
printf(" hkl: %f %f %f\n", data->surface.miller[0],
data->surface.miller[1], data->surface.miller[2]);
printf(" dhkl: %f\n", data->surface.dspacing);
printf("region sizes: %f %f\n", data->surface.region[0], data->surface.region[1]);
printf(" moving: ");
if (direction == UP)
printf("UP\n");
else
printf("DOWN\n");
#endif
/* checks */
g_return_val_if_fail(data != NULL, 1);
g_return_val_if_fail(data->periodic == 2, 1);
if (data->surface.region[0] < 1)
{
gui_text_show(ERROR, "region 1 is empty.\n");
return(1);
}
/* setup region switching labels */
if (direction == UP)
{
primary = REGION1A;
secondary = REGION2A;
}
else
{
primary = REGION2A;
secondary = REGION1A;
}
/* get fractional depth translation vector */
ARR3SET(vec, data->surface.depth_vec);
vecmat(data->ilatmat, vec);
/* calculate offset to region boundary */
ARR3SET(tmp, vec);
if (direction == DOWN)
{
VEC3MUL(tmp, data->surface.region[0]);
VEC3MUL(tmp, -1.0);
}
else
{
if (data->surface.region[1] == 0)
{
VEC3MUL(tmp, data->surface.region[0]);
}
else
{
VEC3MUL(tmp, data->surface.region[1]);
}
}
/* if region 2 is empty, just move core to the bottom */
if (data->surface.region[1] == 0.0)
{
ARR3ADD(core->x, tmp);
if (core->shell)
{
ARR3ADD((core->shell)->x, tmp);
}
atom_colour_scheme(data->colour_scheme, core, data);
return(0);
}
/* get coordinates of target atom */
ARR3ADD(tmp, core->x);
#if DEBUG_REGION_SWITCH_ATOM
P3VEC(" translation: ", vec);
P3VEC(" target coords: ", tmp);
#endif
/* find the target */
flag=0;
for (list=data->cores ; list ; list=g_slist_next(list))
{
comp = list->data;
/* only atoms of the same type need apply */
if (core->atom_code != comp->atom_code)
continue;
/* get difference vector */
ARR3SET(d, comp->x);
ARR3SUB(d, tmp);
/* pbc constraint */
while(d[0] < -FRACTION_TOLERANCE)
d[0] += 1.0;
while(d[0] > 0.5)
d[0] -= 1.0;
while(d[1] < -FRACTION_TOLERANCE)
d[1] += 1.0;
while(d[1] > 0.5)
d[1] -= 1.0;
/* test difference vector's magnitude */
if (VEC3MAGSQ(d) < FRACTION_TOLERANCE)
{
/* change its labelling */
#if DEBUG_REGION_SWITCH_ATOM
printf("Matched core: %p\n", comp);
#endif
comp->region = secondary;
if (comp->shell)
{
(comp->shell)->region = secondary;
}
atom_colour_scheme(data->colour_scheme, comp, data);
flag++;
break;
}
}
if (!flag)
{
gui_text_show(ERROR, "Failed to find a boundary image.\n");
return(1);
}
/* now move selected atom to bottom of region 2 */
ARR3SET(tmp, vec);
VEC3MUL(tmp, (data->surface.region[0] + data->surface.region[1]));
if (direction == UP)
VEC3MUL(tmp, -1.0);
ARR3SUB(core->x, tmp);
core->region = primary;
/* pbc constrain */
fractional_clamp(core->x, mov, 2);
if (core->shell)
{
ARR3SUB((core->shell)->x, tmp);
ARR2ADD((core->shell)->x, mov);
(core->shell)->region = primary;
}
atom_colour_scheme(data->colour_scheme, core, data);
return(0);
}
gint surf_sysabs(struct model_pak *data, gint h, gint k, gint l)
{
gint i, flag;
gint f1[3] /*, f2[3]*/;
gdouble dp, dummy, vec[3], df[3];
#if DEBUG_FACET_ABSENT
printf("testing %d %d %d\n", h, k, l);
#endif
/* apply the symmetry matrices (skip identity) */
VEC3SET(f1, h, k, l);
for (i=1 ; i<data->sginfo.order ; i++)
{
/* NEW - identity + translation alone is insufficent */
if (matrix_is_identity(*(data->sginfo.matrix+i)))
continue;
VEC3SET(vec, h, k, l);
vecmat(*(data->sginfo.matrix+i), vec);
flag = 0;
/* not needed - we've expanded all symmetry operations (incl. inversion) */
/* test f1 . m = -f1 */
/*
ARR3SET(df, f1);
ARR3ADD(df, vec);
if (VEC3MAGSQ(df) < FRACTION_TOLERANCE)
if (data->sginfo.inversion)
flag++;
*/
/* test f1 . m = f1 */
ARR3SET(df, f1);
ARR3SUB(df, vec);
if (VEC3MAGSQ(df) < POSITION_TOLERANCE)
flag++;
if (flag)
{
#if DEBUG_FACET_ABSENT
printf("symop [%d] satisfies 1st absence condition.\n", i);
P3MAT("matrix:", *(data->sginfo.matrix+i));
P3VEC("offset:", *(data->sginfo.offset+i));
#endif
/* test if <f1,t> = non-integer */
ARR3SET(vec, *(data->sginfo.offset+i));
ARR3MUL(vec, f1);
dp = fabs(vec[0] + vec[1] + vec[2]);
if (modf(dp, &dummy) > POSITION_TOLERANCE)
{
#if DEBUG_FACET_ABSENT
printf("symop [%d] [%f %f %f] satisfies 2nd absence condition.\n",
i, *(*(data->sginfo.offset+i)+0), *(*(data->sginfo.offset+i)+1),
*(*(data->sginfo.offset+i)+2));
printf("facet is extinct.\n");
#endif
return(TRUE);
}
}
}
#if DEBUG_FACET_ABSENT
printf(">>> Not absent\n");
#endif
return(FALSE);
}