/** nonbonded and bonded force calculation using the verlet list */
void nsq_calculate_ia()
{
Particle *partl, *partg;
Particle *pt1, *pt2;
int p, p2, npl, npg, c;
double d[3], dist2, dist;
npl = local->n;
partl = local->part;
/* calculate bonded interactions and non bonded node-node */
for (p = 0; p < npl; p++) {
pt1 = &partl[p];
add_bonded_force(pt1);
#ifdef CONSTRAINTS
add_constraints_forces(pt1);
#endif
/* other particles, same node */
for (p2 = p + 1; p2 < npl; p2++) {
pt2 = &partl[p2];
get_mi_vector(d, pt1->r.p, pt2->r.p);
dist2 = sqrlen(d);
dist = sqrt(dist2);
#ifdef EXCLUSIONS
if (do_nonbonded(pt1, pt2))
#endif
add_non_bonded_pair_force(pt1, pt2, d, dist, dist2);
}
/* calculate with my ghosts */
for (c = 0; c < me_do_ghosts.n; c++) {
npg = me_do_ghosts.cell[c]->n;
partg = me_do_ghosts.cell[c]->part;
for (p2 = 0; p2 < npg; p2++) {
pt2 = &partg[p2];
get_mi_vector(d, pt1->r.p, pt2->r.p);
dist2 = sqrlen(d);
dist = sqrt(dist2);
#ifdef EXCLUSIONS
if (do_nonbonded(pt1, pt2))
#endif
add_non_bonded_pair_force(pt1, pt2, d, dist, dist2);
}
}
}
}
void calculate_verlet_ia()
{
int c, np, n, i;
Cell *cell;
Particle *p1, *p2, **pairs;
double dist2, vec21[3];
/* Loop local cells */
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p1 = cell->part;
np = cell->n;
/* calculate bonded interactions (loop local particles) */
for(i = 0; i < np; i++) {
add_bonded_force(&p1[i]);
#ifdef CONSTRAINTS
add_constraints_forces(&p1[i]);
#endif
add_external_potential_forces(&p1[i]);
}
/* Loop cell neighbors */
for (n = 0; n < dd.cell_inter[c].n_neighbors; n++) {
pairs = dd.cell_inter[c].nList[n].vList.pair;
np = dd.cell_inter[c].nList[n].vList.n;
/* verlet list loop */
for(i=0; i<2*np; i+=2) {
p1 = pairs[i]; /* pointer to particle 1 */
p2 = pairs[i+1]; /* pointer to particle 2 */
dist2 = distance2vec(p1->r.p, p2->r.p, vec21);
add_non_bonded_pair_force(p1, p2, vec21, sqrt(dist2), dist2);
}
}
}
}
void build_verlet_lists_and_calc_verlet_ia()
{
int c, np1, n, np2, i ,j, j_start;
Cell *cell;
IA_Neighbor *neighbor;
Particle *p1, *p2;
PairList *pl;
double dist2, vec21[3];
#ifdef VERLET_DEBUG
int estimate, sum=0;
double max_range_nonbonded2 = SQR(max_cut_nonbonded + skin);
fprintf(stderr,"%d: build_verlet_list_and_calc_verlet_ia:\n",this_node);
/* estimate number of interactions: (0.5*n_part*ia_volume*density)/n_nodes */
estimate = 0.5*n_part*(4.0/3.0*PI*pow(max_range_nonbonded2,1.5))*(n_part/(box_l[0]*box_l[1]*box_l[2]))/n_nodes;
if (!dd.use_vList) { fprintf(stderr, "%d: build_verlet_lists, but use_vList == 0\n", this_node); errexit(); }
#endif
/* Loop local cells */
for (c = 0; c < local_cells.n; c++) {
VERLET_TRACE(fprintf(stderr,"%d: cell %d with %d neighbors\n",this_node,c, dd.cell_inter[c].n_neighbors));
cell = local_cells.cell[c];
p1 = cell->part;
np1 = cell->n;
/* Loop cell neighbors */
for (n = 0; n < dd.cell_inter[c].n_neighbors; n++) {
neighbor = &dd.cell_inter[c].nList[n];
p2 = neighbor->pList->part;
np2 = neighbor->pList->n;
VERLET_TRACE(fprintf(stderr,"%d: neighbor %d contains %d parts\n",this_node,n,np2));
/* init pair list */
pl = &neighbor->vList;
pl->n = 0;
/* Loop cell particles */
for(i=0; i < np1; i++) {
j_start = 0;
/* Tasks within cell: bonded forces, store old position, avoid double counting */
if(n == 0) {
#ifdef MULTI_TIMESTEP
if (p1[i].p.smaller_timestep==current_time_step_is_small || smaller_time_step < 0.)
#endif
{
add_bonded_force(&p1[i]);
#ifdef CONSTRAINTS
add_constraints_forces(&p1[i]);
#endif
add_external_potential_forces(&p1[i]);
memcpy(p1[i].l.p_old, p1[i].r.p, 3*sizeof(double));
j_start = i+1;
}
}
/* no interaction set, no need for particle pairs */
if (max_cut_nonbonded == 0.0)
continue;
/* Loop neighbor cell particles */
for(j = j_start; j < np2; j++) {
#ifdef EXCLUSIONS
if(do_nonbonded(&p1[i], &p2[j]))
#endif
{
dist2 = distance2vec(p1[i].r.p, p2[j].r.p, vec21);
VERLET_TRACE(fprintf(stderr,"%d: pair %d %d has distance %f\n",this_node,p1[i].p.identity,p2[j].p.identity,sqrt(dist2)));
if(dist2 <= SQR(get_ia_param(p1[i].p.type, p2[j].p.type)->max_cut + skin)) {
ONEPART_TRACE(if(p1[i].p.identity==check_id) fprintf(stderr,"%d: OPT: Verlet Pair %d %d (Cells %d,%d %d,%d dist %f)\n",this_node,p1[i].p.identity,p2[j].p.identity,c,i,n,j,sqrt(dist2)));
ONEPART_TRACE(if(p2[j].p.identity==check_id) fprintf(stderr,"%d: OPT: Verlet Pair %d %d (Cells %d %d dist %f)\n",this_node,p1[i].p.identity,p2[j].p.identity,c,n,sqrt(dist2)));
add_pair(pl, &p1[i], &p2[j]);
#ifdef MULTI_TIMESTEP
if (smaller_time_step < 0.
|| (p1[i].p.smaller_timestep==0 && p2[j].p.smaller_timestep==0 && current_time_step_is_small==0)
|| (!(p1[i].p.smaller_timestep==0 && p2[j].p.smaller_timestep==0) && current_time_step_is_small==1))
#endif
{
/* calc non bonded interactions */
add_non_bonded_pair_force(&(p1[i]), &(p2[j]), vec21, sqrt(dist2), dist2);
}
}
}
}
}
resize_verlet_list(pl);
VERLET_TRACE(fprintf(stderr,"%d: neighbor %d has %d pairs\n",this_node,n,pl->n));
VERLET_TRACE(sum += pl->n);
}
