added pair correlation calc code

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index ad4f900..2e0e468 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -2057,6 +2057,13 @@ int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
        }
 
        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)");
@@ -2103,49 +2110,130 @@ int pair_correlation_init(t_moldyn *moldyn,double dr) {
        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;