+/*
+ * numerical tricks
+ */
+
+/* linked list / cell method */
+
+int link_cell_init(t_moldyn *moldyn) {
+
+ t_linkcell *lc;
+ int i;
+ int fd;
+
+ fd=open("/dev/null",O_WRONLY);
+
+ lc=&(moldyn->lc);
+
+ /* partitioning the md cell */
+ lc->nx=moldyn->dim.x/moldyn->cutoff;
+ lc->x=moldyn->dim.x/lc->nx;
+ lc->ny=moldyn->dim.y/moldyn->cutoff;
+ lc->y=moldyn->dim.y/lc->ny;
+ lc->nz=moldyn->dim.z/moldyn->cutoff;
+ lc->z=moldyn->dim.z/lc->nz;
+
+ lc->cells=lc->nx*lc->ny*lc->nz;
+ lc->subcell=malloc(lc->cells*sizeof(t_list));
+
+ printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+
+ for(i=0;i<lc->cells;i++)
+ //list_init(&(lc->subcell[i]),1);
+ list_init(&(lc->subcell[i]),fd);
+
+ link_cell_update(moldyn);
+
+ return 0;
+}
+
+int link_cell_update(t_moldyn *moldyn) {
+
+ int count,i,j,k;
+ int nx,ny,nz;
+ t_atom *atom;
+ t_linkcell *lc;
+
+ atom=moldyn->atom;
+ lc=&(moldyn->lc);
+
+ nx=lc->nx;
+ ny=lc->ny;
+ nz=lc->nz;
+
+ for(i=0;i<lc->cells;i++)
+ list_destroy(&(moldyn->lc.subcell[i]));
+
+ for(count=0;count<moldyn->count;count++) {
+ i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
+ j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
+ k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
+ list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+ &(atom[count]));
+ }
+
+ return 0;
+}
+
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
+
+ t_linkcell *lc;
+ int a;
+ int count1,count2;
+ int ci,cj,ck;
+ int nx,ny,nz;
+ int x,y,z;
+ u8 bx,by,bz;
+
+ lc=&(moldyn->lc);
+ nx=lc->nx;
+ ny=lc->ny;
+ nz=lc->nz;
+ count1=1;
+ count2=27;
+ a=nx*ny;
+
+ cell[0]=lc->subcell[i+j*nx+k*a];
+ for(ci=-1;ci<=1;ci++) {
+ bx=0;
+ x=i+ci;
+ if((x<0)||(x>=nx)) {
+ x=(x+nx)%nx;
+ bx=1;
+ }
+ for(cj=-1;cj<=1;cj++) {
+ by=0;
+ y=j+cj;
+ if((y<0)||(y>=ny)) {
+ y=(y+ny)%ny;
+ by=1;
+ }
+ for(ck=-1;ck<=1;ck++) {
+ bz=0;
+ z=k+ck;
+ if((z<0)||(z>=nz)) {
+ z=(z+nz)%nz;
+ bz=1;
+ }
+ if(!(ci|cj|ck)) continue;
+ if(bx|by|bz) {
+ cell[--count2]=lc->subcell[x+y*nx+z*a];
+ }
+ else {
+ cell[count1++]=lc->subcell[x+y*nx+z*a];
+ }
+ }
+ }
+ }
+
+ lc->dnlc=count1;
+ lc->countn=27;
+
+ return count2;
+}
+
+int link_cell_shutdown(t_moldyn *moldyn) {
+
+ int i;
+ t_linkcell *lc;
+
+ lc=&(moldyn->lc);
+
+ for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
+ list_shutdown(&(moldyn->lc.subcell[i]));
+
+ return 0;
+}
+
+int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
+
+ int count;
+ void *ptr;
+ t_moldyn_schedule *schedule;
+
+ schedule=&(moldyn->schedule);
+ count=++(schedule->content_count);
+
+ ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
+ if(!ptr) {
+ perror("[moldyn] realloc (runs)");
+ return -1;
+ }
+ moldyn->schedule.runs=ptr;
+ moldyn->schedule.runs[count-1]=runs;
+
+ ptr=realloc(schedule->tau,count*sizeof(double));
+ if(!ptr) {
+ perror("[moldyn] realloc (tau)");
+ return -1;
+ }
+ moldyn->schedule.tau=ptr;
+ moldyn->schedule.tau[count-1]=tau;
+
+ return 0;
+}
+
+int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
+
+ moldyn->schedule.hook=hook;
+ moldyn->schedule.hook_params=hook_params;
+
+ return 0;
+}