+
+ /*
+ * bond detection should usually be done by potential
+ * functions. brrrrr! EVIL!
+ *
+ * todo: potentials need to export a 'find_bonds' function!
+ */
+
+ // bonds between atoms
+ if(!(atom[i].attr&ATOM_ATTR_VB))
+ continue;
+ 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,
+ neighbour);
+ for(j=0;j<27;j++) {
+ list_reset_f(&neighbour[j]);
+ if(neighbour[j].start==NULL)
+ continue;
+ bc=j<lc->dnlc?0:1;
+ do {
+ btom=neighbour[j].current->data;
+ if(btom==&atom[i]) // skip identical atoms
+ continue;
+ //if(btom<&atom[i]) // skip half of them
+ // continue;
+ v3_sub(&dist,&(atom[i].r),&(btom->r));
+ if(bc) check_per_bound(moldyn,&dist);
+ d2=v3_absolute_square(&dist);
+ brand=atom[i].brand;
+ if(brand==btom->brand) {
+ if(d2>moldyn->bondlen[brand])
+ continue;
+ }
+ else {
+ if(d2>moldyn->bondlen[2])
+ continue;
+ }
+ dprintf(fd,"# [B] %f %f %f %f %f %f\n",
+ atom[i].r.x,atom[i].r.y,atom[i].r.z,
+ btom->r.x,btom->r.y,btom->r.z);
+ } while(list_next_f(&neighbour[j])!=L_NO_NEXT_ELEMENT);
+ }
+ }
+
+ // boundaries