int i;
t_ho_params hop;
t_lj_params ljp;
+ t_tersoff_params tp;
double s,e;
memset(moldyn,0,sizeof(t_moldyn));
moldyn->mwrite=atoi(argv[++i]);
strncpy(moldyn->mfb,argv[++i],64);
break;
- case 'D':
- moldyn->dwrite=atoi(argv[++i]);
- strncpy(moldyn->dfb,argv[++i],64);
- break;
case 'S':
moldyn->swrite=atoi(argv[++i]);
strncpy(moldyn->sfb,argv[++i],64);
if(moldyn->swrite)
moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
- if(moldyn->dwrite) {
- moldyn->dfd=open(moldyn->dfb,O_WRONLY|O_CREAT|O_TRUNC);
- if(moldyn->dfd<0) {
- perror("[moldyn] dfd open");
- return moldyn->dfd;
- }
- write(moldyn->dfd,moldyn,sizeof(t_moldyn));
- moldyn->lvstat|=MOLDYN_LVSTAT_DUMP;
- }
-
if((moldyn->vwrite)&&(vis)) {
moldyn->visual=vis;
visual_init(vis,moldyn->vfb);
}
}
+ lc->dnlc=count2;
+ lc->countn=27;
+
return count2;
}
write(fd,moldyn->atom,
moldyn->count*sizeof(t_atom));
}
+ close(fd);
}
}
- if(d) {
- if(!(i%d))
- write(moldyn->dfd,moldyn->atom,
- moldyn->count*sizeof(t_atom));
-
- }
if(v) {
if(!(i%v)) {
visual_atoms(moldyn->visual,i*moldyn->tau,
/* forces depending on chosen potential */
printf("calc potential/force ...\n");
- moldyn->potential_force_function(moldyn);
+ potential_force_calc(moldyn);
+ //moldyn->potential_force_function(moldyn);
printf("done\n");
for(i=0;i<count;i++) {
*
*/
+/* generic potential and force calculation */
+
+#define CREATE_CELL_LIST(nb_list) \
+ link_cell_neighbour_index(moldyn,\
+ (atom[i].r.x+moldyn->dim.x/2)/lc->x,\
+ (atom[i].r.y+moldyn->dim.y/2)/lc->y,\
+ (atom[i].r.z+moldyn->dim.z/2)/lc->z,\
+ nb_list);
+
+
+int potential_force_calc(t_moldyn *moldyn) {
+
+ int i,count;
+ t_atom *atom;
+ t_linkcell *lc;
+ t_list neighbour[27];
+ t_list *this;
+ double u;
+
+ count=moldyn->count;
+ atom=moldyn->atom;
+ lc=&(moldyn->lc);
+
+ /* reset energy */
+ u=0.0;
+
+ for(i=0;i<count;i++) {
+
+ /* reset force */
+ v3_zero(&(atom[i].f));
+
+ /* single particle potential/force */
+ if(moldyn->status&MOLDYN_STAT_1BP)
+ moldyn->pf_func1b(moldyn,&(atom[i]));
+
+ /* 2 body pair potential/force */
+ if(moldyn->status&MOLDYN_STAT_2BP) {
+
+ CREATE_CELL_LIST(neighbour);
+
+ /*
+ * processing cell of atom i
+ * => no need to check for empty list
+ * (1 element at minimum)
+ */
+
+ this=&(neighbour[0]);
+ list_reset(this);
+ do {
+ btom=this->current->data;
+ if(btom!=&(atom[i]))
+ moldyn->pf_func2b(moldyn,
+ &(atom[i]),btom);
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+ /*
+ * direct neighbour cells
+ * => no boundary condition check necessary
+ */
+ for(j=0;j<lc->dnlc;j++) {
+ this=&(neighbour[j]);
+ list_reset(this);
+ if(this->start!=NULL) {
+ do {
+ btom=this->current->data;
+ moldyn->pf_func2b(moldyn,
+ &(atom[i]),
+ btom);
+ } while(list_next(this)!=\
+ L_NO_NEXT_ELEMENT);
+ }
+
+ /*
+ * neighbour cells due to periodic bc
+ * => check boundary conditions
+ */
+ for(j=lc->dnlc;j<lc->countn;j++) {
+ this=&(neighbour[j]);
+ list_reset(this);
+ if(this->start!=NULL) {
+ do {
+ btom=this->current->data;
+ moldyn->pf_func2b(moldyn,
+ &(atom[i]),
+ btom);
+
+ }
+
+ }
+
+ return 0;
+}
+
+
/* harmonic oscillator potential and force */
int harmonic_oscillator(t_moldyn *moldyn) {