/* find_longest_path:
* Find and return longest path in tree.
*/
static nodelist_t*
find_longest_path(Agraph_t* tree)
{
Agnode_t* n;
Agedge_t* e;
Agnode_t* common = 0;
nodelist_t* path;
nodelist_t* endPath;
int maxlength = 0;
int length;
if (agnnodes(tree) == 1) {
path = mkNodelist();
n = agfstnode(tree);
appendNodelist(path, NULL, n);
SET_ONPATH(n);
return path;
}
for(n = agfstnode(tree); n; n = agnxtnode(tree, n)) {
int count = 0;
for(e = agfstedge(tree, n); e; e = agnxtedge(tree, e, n)) {
count++;
}
if(count == 1)
measure_distance(n, n, 0, NULL);
}
/* find the branch node rooted at the longest path */
for(n = agfstnode(tree); n; n = agnxtnode(tree, n)) {
length = DISTONE(n) + DISTTWO(n);
if(length > maxlength) {
common = n;
maxlength = length;
}
}
path = mkNodelist();
for (n = LEAFONE(common); n != common; n = TPARENT(n)) {
appendNodelist(path, NULL, n);
SET_ONPATH(n);
}
appendNodelist(path, NULL, common);
SET_ONPATH(common);
if (DISTTWO(common)) { /* 2nd path might be empty */
endPath = mkNodelist();
for (n = LEAFTWO(common); n != common; n = TPARENT(n)) {
appendNodelist(endPath, NULL, n);
SET_ONPATH(n);
}
reverseAppend(path, endPath);
}
return path;
}
static void
measure_distance(Agnode_t * n, Agnode_t * ancestor, int dist,
Agnode_t * change)
{
Agnode_t *parent;
parent = TPARENT(ancestor);
if (parent == NULL)
return;
dist++;
/* check parent to see if it has other leaf paths at greater distance
than the context node.
set the path/distance of the leaf at this ancestor node */
if (DISTONE(parent) == 0) {
LEAFONE(parent) = n;
DISTONE(parent) = dist;
} else if (dist > DISTONE(parent)) {
if (LEAFONE(parent) != change) {
if (!DISTTWO(parent) || (LEAFTWO(parent) != change))
change = LEAFONE(parent);
LEAFTWO(parent) = LEAFONE(parent);
DISTTWO(parent) = DISTONE(parent);
}
LEAFONE(parent) = n;
DISTONE(parent) = dist;
} else if (dist > DISTTWO(parent)) {
LEAFTWO(parent) = n;
DISTTWO(parent) = dist;
return;
} else
return;
measure_distance(n, parent, dist, change);
}
void loop()
{
unsigned int current_distance = measure_distance();
Serial.println(current_distance);
}
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);
}
