}
size=moldyn->count*sizeof(t_atom);
+
+ moldyn->atom=(t_atom *)malloc(size);
+ if(moldyn->atom==NULL) {
+ perror("[moldyn] load save file malloc (atoms)");
+ return -1;
+ }
+
cnt=read(fd,moldyn->atom,size);
if(cnt!=size) {
perror("[moldyn] load save file read (atoms)");
return 0;
}
-int calculate_pair_correlation(t_moldyn *moldyn,double dr) {
+int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
int slots;
- int *stat;
- int i;
+ double *stat;
+ int i,j;
t_linkcell *lc;
t_list neighbour[27];
t_atom *itom,*jtom;
t_list *this;
+ unsigned char bc;
+ t_3dvec dist;
+ double d,norm;
+ int o,s;
+ unsigned char ibrand;
lc=&(moldyn->lc);
slots=(int)(moldyn->cutoff/dr);
+ o=2*slots;
- stat=(int *)malloc(3*slots*sizeof(int));
- if(stat==NULL) {
- perror("[moldyn] pair correlation malloc");
- return -1;
+ if(ptr!=NULL) {
+ stat=(double *)ptr;
+ }
+ else {
+ stat=(double *)malloc(3*slots*sizeof(double));
+ if(stat==NULL) {
+ perror("[moldyn] pair correlation malloc");
+ return -1;
+ }
}
+ memset(stat,0,3*slots*sizeof(double));
+
link_cell_init(moldyn,VERBOSE);
-
- for(i=0;i<lc->cells;i++) {
- /* check for atoms */
- itom=lc->subcell[i].current->data;
- if(itom==NULL)
- continue;
- /* pick first atom and do neighbour indexing */
+ itom=moldyn->atom;
+
+ for(i=0;i<moldyn->count;i++) {
+ /* neighbour indexing */
link_cell_neighbour_index(moldyn,
- (itom->r.x+moldyn->dim.x/2)/lc->x,
- (itom->r.y+moldyn->dim.y/2)/lc->x,
- (itom->r.z+moldyn->dim.z/2)/lc->x,
+ (itom[i].r.x+moldyn->dim.x/2)/lc->x,
+ (itom[i].r.y+moldyn->dim.y/2)/lc->x,
+ (itom[i].r.z+moldyn->dim.z/2)/lc->x,
neighbour);
- /* calculation of g(r) */
- do {
- itom=lc->subcell[i].current->data;
-// GO ON HERE ...
- } while(list_next_f(this)!=L_NO_NEXT_ELEMENT););
+ /* brand of atom i */
+ ibrand=itom[i].brand;
+
+ for(j=0;j<27;j++) {
+ /* prepare the neighbour cell list */
+ this=&(neighbour[j]);
+ list_reset_f(this);
+
+ /* check for atoms */
+ if(this->start==NULL)
+ continue;
+
+ /* boundary check */
+ bc=(j<lc->dnlc)?0:1;
+
+ do {
+ jtom=this->current->data;
+
+
+ if(jtom==&(itom[i]))
+ continue;
+
+ /* only count pairs once */
+ if(itom[i].tag>jtom->tag)
+ continue;
+
+ /*
+ * pair correlation calc
+ */
+
+ /* distance */
+ v3_sub(&dist,&(jtom->r),&(itom[i].r));
+ if(bc) check_per_bound(moldyn,&dist);
+ d=v3_absolute_square(&dist);
+ /* ignore if greater cutoff */
+ if(d>moldyn->cutoff_square)
+ continue;
+
+ /* fill the slots */
+ d=sqrt(d);
+ s=(int)(d/dr);
+
+ if(ibrand!=jtom->brand) {
+ /* mixed */
+ stat[s]+=1;
+ }
+ else {
+ /* type a - type a bonds */
+ if(ibrand==0)
+ stat[s+slots]+=1;
+ else
+ /* type b - type b bonds */
+ stat[s+o]+=1;
+ }
+
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+ }
}
+ /* normalization */
+ for(i=1;i<slots;i++) {
+ /*
+ * normalization: 4 pi r r dr
+ * here: not double counting pairs -> 2 pi r r dr
+ */
+ norm=2*M_PI*moldyn->count*(i*dr*i*dr)*dr;
+ stat[i]/=norm;
+ stat[slots+i]/=norm;
+ stat[o+i]/=norm;
+ }
+
+ if(ptr==NULL) {
+ /* todo: store/print pair correlation function */
+ free(stat);
+ }
+
+ free(moldyn->atom);
+
link_cell_shutdown(moldyn);
return 0;