double mindist(IntList *set1, IntList *set2)
{
double mindist, pt[3];
int i, j, in_set;
mindist = SQR(box_l[0] + box_l[1] + box_l[2]);
updatePartCfg(WITHOUT_BONDS);
for (j=0; j<n_part-1; j++) {
pt[0] = partCfg[j].r.p[0];
pt[1] = partCfg[j].r.p[1];
pt[2] = partCfg[j].r.p[2];
/* check which sets particle j belongs to
bit 0: set1, bit1: set2
*/
in_set = 0;
if (!set1 || intlist_contains(set1, partCfg[j].p.type))
in_set = 1;
if (!set2 || intlist_contains(set2, partCfg[j].p.type))
in_set |= 2;
if (in_set == 0)
continue;
for (i=j+1; i<n_part; i++)
/* accept a pair if particle j is in set1 and particle i in set2 or vice versa. */
if (((in_set & 1) && (!set2 || intlist_contains(set2, partCfg[i].p.type))) ||
((in_set & 2) && (!set1 || intlist_contains(set1, partCfg[i].p.type))))
mindist = dmin(mindist, min_distance2(pt, partCfg[i].r.p));
}
mindist = sqrt(mindist);
return mindist;
}
void calc_part_distribution(int *p1_types, int n_p1, int *p2_types, int n_p2,
double r_min, double r_max, int r_bins, int log_flag,
double *low, double *dist)
{
int i,j,t1,t2,ind,cnt=0;
double inv_bin_width=0.0;
double min_dist,min_dist2=0.0,start_dist2,act_dist2;
start_dist2 = SQR(box_l[0] + box_l[1] + box_l[2]);
/* bin preparation */
*low = 0.0;
for(i=0;i<r_bins;i++) dist[i] = 0.0;
if(log_flag == 1) inv_bin_width = (double)r_bins/(log(r_max)-log(r_min));
else inv_bin_width = (double)r_bins / (r_max-r_min);
/* particle loop: p1_types*/
for(i=0; i<n_part; i++) {
for(t1=0; t1<n_p1; t1++) {
if(partCfg[i].p.type == p1_types[t1]) {
min_dist2 = start_dist2;
/* particle loop: p2_types*/
for(j=0; j<n_part; j++) {
if(j != i) {
for(t2=0; t2<n_p2; t2++) {
if(partCfg[j].p.type == p2_types[t2]) {
act_dist2 = min_distance2(partCfg[i].r.p, partCfg[j].r.p);
if(act_dist2 < min_dist2) { min_dist2 = act_dist2; }
}
}
}
}
min_dist = sqrt(min_dist2);
if(min_dist <= r_max) {
if(min_dist >= r_min) {
/* calculate bin index */
if(log_flag == 1) ind = (int) ((log(min_dist) - log(r_min))*inv_bin_width);
else ind = (int) ((min_dist - r_min)*inv_bin_width);
if(ind >= 0 && ind < r_bins) {
dist[ind] += 1.0;
}
}
else {
*low += 1.0;
}
}
cnt++;
}
}
}
/* normalization */
*low /= (double)cnt;
for(i=0;i<r_bins;i++) dist[i] /= (double)cnt;
}
/**
* updates the histogram
*/
void updateHistogram() {
double max_distance2 = 2. * (L/2.) * (L/2.);
double distance2;
int historyIndex;
#pragma omp parallel for
for(int i=0; i<Nx*Ny; i++) {
for(int j=0; j<i; j++) {
// get the minimal distance
distance2 = min_distance2(discs[i], discs[j]);
// increment the histogram value that this corresponds to
historyIndex = (distance2/max_distance2) * (M-1);
assert(historyIndex < M && historyIndex >= 0);
histogram[historyIndex]++;
}
}
}
int aggregation(double dist_criteria2, int min_contact, int s_mol_id, int f_mol_id, int *head_list, int *link_list, int *agg_id_list, int *agg_num, int *agg_size, int *agg_max, int *agg_min, int *agg_avg, int *agg_std, int charge)
{
int c, np, n, i;
Particle *p1, *p2, **pairs;
double dist2;
int target1;
int p1molid, p2molid;
int *contact_num, ind;
if (min_contact > 1) {
contact_num = (int *) malloc(n_molecules*n_molecules *sizeof(int));
for (i = 0; i < n_molecules *n_molecules; i++) contact_num[i]=0;
} else {
contact_num = (int *) 0; /* Just to keep the compiler happy */
}
on_observable_calc();
build_verlet_lists();
for (i = s_mol_id; i <= f_mol_id; i++) {
head_list[i]=i;
link_list[i]=-1;
agg_id_list[i]=i;
agg_size[i]=0;
}
/* Loop local cells */
for (c = 0; c < local_cells.n; c++) {
/* 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 */
p1molid = p1->p.mol_id;
p2molid = p2->p.mol_id;
if (((p1molid <= f_mol_id) && (p1molid >= s_mol_id)) && ((p2molid <= f_mol_id) && (p2molid >= s_mol_id))) {
if (agg_id_list[p1molid] != agg_id_list[p2molid]) {
dist2 = min_distance2(p1->r.p, p2->r.p);
#ifdef ELECTROSTATICS
if (charge && (p1->p.q * p2->p.q >= 0)) {continue;}
#endif
if (dist2 < dist_criteria2) {
if ( p1molid > p2molid ) { ind=p1molid*n_molecules + p2molid;}
else { ind=p2molid*n_molecules +p1molid;}
if (min_contact > 1) {
contact_num[ind] ++;
if (contact_num[ind] >= min_contact) {
merge_aggregate_lists( head_list, agg_id_list, p1molid, p2molid, link_list);
}
} else {
merge_aggregate_lists( head_list, agg_id_list, p1molid, p2molid, link_list);
}
}
}
}
}
}
}
/* count number of aggregates
find aggregate size
find max and find min size, and std */
for (i = s_mol_id ; i <= f_mol_id ; i++) {
if (head_list[i] != -2) {
(*agg_num)++;
agg_size[*agg_num -1]++;
target1= head_list[i];
while( link_list[target1] != -1) {
target1= link_list[target1];
agg_size[*agg_num -1]++;
}
}
}
for (i = 0 ; i < *agg_num; i++) {
*agg_avg += agg_size[i];
*agg_std += agg_size[i] * agg_size[i];
if (*agg_min > agg_size[i]) { *agg_min = agg_size[i]; }
if (*agg_max < agg_size[i]) { *agg_max = agg_size[i]; }
}
return 0;
}
/** returns the minimal distance between two positions in the perhaps periodic
simulation box.
* \param pos1 Position one.
* \param pos2 Position two.
*/
inline double min_distance(double pos1[3], double pos2[3]) {
return sqrt(min_distance2(pos1, pos2));
}