void Robot::move()
{
Pos p = posAfterMove();
if (world_->canMoveTo(p)) pos_ = p;
}
bool recruit(int s, int dpxx, int dpxy, int dpxz, int cs, int axis, int turns, int dx, int dy, int dz){
/* By introducing seemingly redundant parameter dpxx, dpxy and dpxz
(which is simply the position difference between molecule s and cs),
we could be sure that the position difference would always have a change between -1 and 1,
thus avoiding the unphysical rotation near the surface due to periodic boundary conditions.
note: do not use static variables in this function unless required, because the function is recursive.
*/
ppos dpx(dpxx, dpxy, dpxz), n_dir;
mol[s].status = 2;
cluster_series[cluster_size++] = s; // use cluster_series instead of checking molecule status in loops to improve efficiency
if (turns){
switch (axis){
case 0: n_dir.set(1, 0, 0); break;
case 1: n_dir.set(0, 1, 0); break;
case 2: n_dir.set(0, 0, 1);
}
}
else{
n_dir.set(dx, dy, dz);
}
mol[s].cluster_eff_rad_diff2 = (double)mod2(dpx.crossproduct(n_dir.x, n_dir.y, n_dir.z)) / mod2(n_dir);
int i, j, k;
int s1;
int oOrnt, nOrnt;
double E0, Ef, Er;
double pf, pr;
ppos px_cnt = mol[s].px,
px_fwd = posAfterMove(dpxx, dpxy, dpxz, cs, axis, turns, dx, dy, dz),
px_rev = posAfterMove(dpxx, dpxy, dpxz, cs, axis, turns ? (4 - turns) : 0, -dx, -dy, -dz),
npx;
px_fwd.adjust();
px_rev.adjust();
mol[s].px_cnt_backup = px_cnt;
mol[s].px_fwd_dest = px_fwd;
mol[s].ornt_cnt_backup = oOrnt = mol[s].ornt;
mol[s].ornt_fwd_dest = nOrnt = orntRot[mol[s].ornt][axis][turns];
bool accept = true;
double judge_value;
if (s == 210){
i = 100;
}
for (i = -1; i <= 1; i++){
for (j = -1; j <= 1; j++){
for (k = -1; k <= 1; k++){
npx = mol[s].px.plus(i, j, k);
npx.adjust();
if ((i || j || k) && stage[npx.x][npx.y][npx.z] >= 0){ // propose a link
s1 = stage[npx.x][npx.y][npx.z];
if (px_fwd == npx){ // forward move cause overlap
switch (mol[s1].status){
case 0: // recruit and accept (temp)
if (mol[s].links >= 8){
cout << "Warning: too many links for particle " << s << endl;
break;
}
mol[s].link_with[mol[s].links] = s1;
if (px_rev == npx)mol[s].link_with_pRatio[mol[s].links] = 1; // reverse also overlap
else{ // reverse not overlap
E0 = interactEnergy(s, s1);
mol[s].put(px_rev.x, px_rev.y, px_rev.z, orntRot[oOrnt][axis][turns ? (4 - turns) : 0]);
Er = interactEnergy(s, s1);
mol[s].put(px_cnt.x, px_cnt.y, px_cnt.z, oOrnt);
pr = (Er > E0) ? (1 - exp(-(Er - E0) / k_B / T)) : 0;
mol[s].link_with_pRatio[mol[s].links] = pr / 1.0;
}
mol[s].links++;
accept = recruit(s1, dpxx + i, dpxy + j, dpxz + k, cs, axis, turns, dx, dy, dz) && accept; // "accept" must be put after "&&"
break;
case 1: // unrecruit and deny
accept = false;
break;
case 2: ;// do nothing because already recruited
}
}
else{ // forward move do not cause overlap
switch (mol[s1].status){
case 0: // try to recruit
E0 = interactEnergy(s, s1);
mol[s].put(px_fwd.x, px_fwd.y, px_fwd.z, nOrnt);
Ef = interactEnergy(s, s1);
mol[s].put(px_cnt.x, px_cnt.y, px_cnt.z, oOrnt);
pf = (Ef > E0) ? (1 - exp(-(Ef - E0) / k_B / T)) : 0;
judge_value = judge(gen);
if (judge_value < pf){ // link formed (where pf must be over 0.0)
if (mol[s].links >= 8){
cout << "Warning: too many links for particle " << s << endl;
break;
}
mol[s].link_with[mol[s].links] = s1;
if (px_rev == npx)mol[s].link_with_pRatio[mol[s].links] = 1; // reverse overlap
else{ // reverse not overlap
mol[s].put(px_rev.x, px_rev.y, px_rev.z, orntRot[oOrnt][axis][turns ? (4 - turns) : 0]);
Er = interactEnergy(s, s1);
mol[s].put(px_cnt.x, px_cnt.y, px_cnt.z, oOrnt);
pr = (Er > E0) ? (1 - exp(-(Er - E0) / k_B / T)) : 0;
mol[s].link_with_pRatio[mol[s].links] = pr / pf;
}
mol[s].links++;
accept = recruit(s1, dpxx + i, dpxy + j, dpxz + k, cs, axis, turns, dx, dy, dz) && accept; // "accept" must be put after "&&"
}
break;
case 1: case 2: ;// do nothing
}
}
//calculate energy
}
}
}
}
// do not prevent far away collisions
return accept;
}
