}
/* display progress */
- if(!(moldyn->total_steps%10)) {
+ //if(!(moldyn->total_steps%10)) {
/* get current time */
gettimeofday(&t2,NULL);
/* copy over time */
t1=t2;
- }
+ //}
/* increase absolute time */
moldyn->time+=moldyn->tau;
* restore function
*/
+int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
+
+ int fd;
+ int cnt,size;
+
+ fd=open(file,O_RDONLY);
+ if(fd<0) {
+ perror("[moldyn] load save file open");
+ return fd;
+ }
+
+ size=sizeof(t_moldyn);
+ cnt=read(fd,moldyn,size);
+ if(cnt!=size) {
+ perror("[moldyn] load save file read (moldyn)");
+ return cnt;
+ }
+
+ 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 cnt;
+ }
+
+ // hooks
+
+ return 0;
+}
+
int moldyn_load(t_moldyn *moldyn) {
// later ...
}
}
+int pair_correlation_init(t_moldyn *moldyn,double dr) {
+
+
+ return 0;
+}
+
+int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
+
+ int slots;
+ 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;
+
+ 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);
+
+ itom=moldyn->atom;
+
+ for(i=0;i<moldyn->count;i++) {
+ /* neighbour indexing */
+ link_cell_neighbour_index(moldyn,
+ (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);
+
+ /* 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;
+}
+
int analyze_bonds(t_moldyn *moldyn) {