- /* reset energy counter */
- u=0.0;
-
- for(i=0;i<count;i++) {
- /* reset force */
- v3_zero(&(atom[i].f));
-
- /* determine cell + neighbours */
- ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
- nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
- nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
- c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
-
- /* processing cell of atom i */
- this=&(neighbour[0]);
- list_reset(this); /* list has 1 element at minimum */
- do {
- btom=this->current->data;
- if(btom==&(atom[i]))
- continue;
- v3_sub(&distance,&(atom[i].r),&(btom->r));
- d=v3_absolute_square(&distance); /* 1/r^2 */
- if(d<=moldyn->cutoff_square) {
- d=1.0/d; /* 1/r^2 */
- h2=d*d; /* 1/r^4 */
- h2*=d; /* 1/r^6 */
- h1=h2*h2; /* 1/r^12 */
- u+=eps*(sig12*h1-sig6*h2);
- h2*=d; /* 1/r^8 */
- h1*=d; /* 1/r^14 */
- h2*=6*sig6;
- h1*=12*sig12;
- d=+h1-h2;
- d*=eps;
- v3_scale(&force,&distance,d);
- v3_add(&(atom[i].f),&(atom[i].f),&force);
- }
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
-
- /* neighbours not doing boundary condition overflow */
- for(j=1;j<c;j++) {
- this=&(neighbour[j]);
- list_reset(this); /* there might not be a single atom */
- if(this->start!=NULL) {
-
- do {
- btom=this->current->data;
- v3_sub(&distance,&(atom[i].r),&(btom->r));
- d=v3_absolute_square(&distance); /* r^2 */
- if(d<=moldyn->cutoff_square) {
- d=1.0/d; /* 1/r^2 */
- h2=d*d; /* 1/r^4 */
- h2*=d; /* 1/r^6 */
- h1=h2*h2; /* 1/r^12 */
- u+=eps*(sig12*h1-sig6*h2);
- h2*=d; /* 1/r^8 */
- h1*=d; /* 1/r^14 */
- h2*=6*sig6;
- h1*=12*sig12;
- d=+h1-h2;
- d*=eps;
- v3_scale(&force,&distance,d);
- v3_add(&(atom[i].f),&(atom[i].f),
- &force);
- }
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
-
- }
- }
-
- /* neighbours due to boundary conditions */
- for(j=c;j<27;j++) {
- this=&(neighbour[j]);
- list_reset(this); /* check boundary conditions */
- if(this->start!=NULL) {
-
- do {
- btom=this->current->data;
- v3_sub(&distance,&(atom[i].r),&(btom->r));
- v3_per_bound(&distance,&(moldyn->dim));
- d=v3_absolute_square(&distance); /* r^2 */
- if(d<=moldyn->cutoff_square) {
- d=1.0/d; /* 1/r^2 */
- h2=d*d; /* 1/r^4 */
- h2*=d; /* 1/r^6 */
- h1=h2*h2; /* 1/r^12 */
- u+=eps*(sig12*h1-sig6*h2);
- h2*=d; /* 1/r^8 */
- h1*=d; /* 1/r^14 */
- h2*=6*sig6;
- h1*=12*sig12;
- d=+h1-h2;
- d*=eps;
- v3_scale(&force,&distance,d);
- v3_add(&(atom[i].f),&(atom[i].f),
- &force);
- }
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
-
- }
- }
+ v3_sub(&distance,&(aj->r),&(ai->r));
+ if(bc) check_per_bound(moldyn,&distance);
+ d=v3_absolute_square(&distance); /* 1/r^2 */
+ if(d<=moldyn->cutoff_square) {
+ d=1.0/d; /* 1/r^2 */
+ h2=d*d; /* 1/r^4 */
+ h2*=d; /* 1/r^6 */
+ h1=h2*h2; /* 1/r^12 */
+ /* energy is eps*..., but we will add this twice ... */
+ moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
+ h2*=d; /* 1/r^8 */
+ h1*=d; /* 1/r^14 */
+ h2*=6*sig6;
+ h1*=12*sig12;
+ d=+h1-h2;
+ d*=eps;
+ v3_scale(&force,&distance,-1.0*d); /* f = - grad E */
+ v3_add(&(ai->f),&(ai->f),&force);