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Box.cpp
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#include <vector>
#include <stdio.h>
#include <time.h>
#include <assert.h>
#include <math.h>
using namespace std;
#include "Random.h"
#include "Bead.h"
#include "Polymer.h"
#include "Box.h"
void Box::addPolymer(Polymer* pol) {
polymers.push_back(pol);
}
void Box::movePolymers(){
for (int i=0 ; i<polymers.size();i++) {
for (int j = 0; j<polymers[i]->size(); j++ ) {
polymers[i] ->move(j);
if (checkPolymerMove(i,j)) {
acceptPolymerMove();
}
else {
rejectPolymerMove(i, j );
}
}
}
}
bool Box::checkPolymerMove(int polymer_index, int bead_index) { //Here, bead_index is only a local variable but not the 'index'/SetIndex in class Bead.
double distanceA, distanceB, angle;
Bead* bead_moved;
Bead* bead_next, *bead_pre;// bead pre and bead next
Bead* bead_prepre;
Bead* bead_nextnext; // bead pre pre, bead next next
bead_moved = polymers[polymer_index] ->getBead(bead_index);
periodic(bead_moved); // apply preriodic BC
if (positiveZ(polymers[polymer_index], bead_moved)) {
return false;
}
// Neighbours
if (bead_index == 0 ) {
bead_next = polymers[polymer_index] ->getBead(bead_index+1);
distanceA = periodicDistance(bead_next, bead_moved);
if (distanceA < (bead_next->getDiameter()/2.0 + bead_moved -> getDiameter()/2.0) ) return false;
if (distanceA > 1.2) return false;
if (polymers[polymer_index]->getStiff()) { //angle constrain
bead_nextnext = polymers[polymer_index] ->getBead(bead_index+2);
angle = calAngle(bead_moved, bead_next, bead_nextnext);
if (angle < 3.0) return false;
}
}
else if (bead_index== polymers[polymer_index]->size()-1) {
bead_pre = polymers[polymer_index] ->getBead(bead_index-1);
distanceA = periodicDistance(bead_pre, bead_moved);
if (distanceA < (bead_pre->getDiameter()/2.0 +bead_moved -> getDiameter()/2.0) ) return false;
if (distanceA >1.2) return false;
if (polymers[polymer_index]->getStiff()) { //angle constrain
bead_prepre = polymers[polymer_index] ->getBead(bead_index-2);
angle = calAngle(bead_moved, bead_pre, bead_prepre);
if (angle < 3.0) return false;
}
}
else {
bead_pre = polymers[polymer_index] ->getBead(bead_index-1);
bead_next = polymers[polymer_index] ->getBead(bead_index+1);
distanceA = periodicDistance(bead_pre, bead_moved);
distanceB = periodicDistance(bead_next, bead_moved);
if (distanceA < (bead_pre->getDiameter()/2.0 +bead_moved -> getDiameter()/2.0) ) return false;
if (distanceA >1.2) return false;
if (distanceB < (bead_next->getDiameter()/2.0 +bead_moved -> getDiameter()/2.0) ) return false;
if (distanceB >1.2) return false;
// The constrain for stiff polymers
if (polymers[polymer_index]->getStiff()) {
angle = calAngle(bead_pre, bead_moved, bead_next);
if (angle < 3.0) return false;
if (bead_index== 1){
bead_nextnext = polymers[polymer_index] ->getBead(bead_index+2);
angle = calAngle(bead_moved, bead_next, bead_nextnext);
if (angle < 3.0) return false;
}
else if (bead_index == polymers[polymer_index]->size()-2 ){
bead_prepre = polymers[polymer_index] ->getBead(bead_index-2);
angle = calAngle(bead_moved, bead_pre, bead_prepre);
if (angle < 3.0) return false;
}
else {
bead_nextnext = polymers[polymer_index] ->getBead(bead_index+2);
bead_prepre = polymers[polymer_index] ->getBead(bead_index-2);
angle = calAngle(bead_moved, bead_pre, bead_prepre);
if (angle < 3.0) return false;
angle = calAngle(bead_moved, bead_next, bead_nextnext);
if (angle < 3.0) return false;
}
}
}
//crosslinked special neighbor
vector <Bead*> CrosslinkedNeighbors;
CrosslinkedNeighbors = bead_moved->getSpecialNeighbors();
for (int i=0 ; i < CrosslinkedNeighbors.size(); i++)
{
if (periodicDistance(bead_moved, CrosslinkedNeighbors[i]) > 1.2 ) {return false;}
}
//non neighbour
Bead* bead;
for (int i=0 ; i<polymers.size();i++) {
for (int j = 0; j<polymers[i]->size(); j++ ) {
if (i != polymer_index && j != bead_index) {
bead = polymers[i] -> getBead(j);
if( periodicDistance(bead, bead_moved) < (bead->getDiameter()/2.0 + bead_moved->getDiameter()/2.0) )
return false;
}
}
}
return true;
}
void Box::rejectPolymerMove(int i , int j){
polymers[i]->moveBack(j) ;
}
void Box::periodic(Bead* b ) {
if(b->getX() < -x/2.0) b->setPosition(b->getX()+x, b->getY(), b->getZ() );
if(b->getY() < -y/2.0) b->setPosition(b->getX(), b->getY()+y, b->getZ() );
if(b->getZ() < -z/2.0) b->setPosition(b->getX(), b->getY(), b->getZ()+z );
if(b->getX() >= x/2.0) b->setPosition(b->getX()-x, b->getY(), b->getZ() );
if(b->getY() >= y/2.0) b->setPosition(b->getX(), b->getY()-y, b->getZ() );
if(b->getZ() >= z/2.0) b->setPosition(b->getX(), b->getY(), b->getZ()-z );
}
double Box::periodicDistance(Bead* B1, Bead* B2 ) {
double dx, dy, dz;
dx = fabs (B1->getX() - B2->getX());
dy = fabs (B1->getY() - B2->getY());
dz = fabs (B1->getZ() - B2->getZ());
if(dx > 0.5*x) { dx = x- dx; }
if(dy > 0.5*y) { dy = y- dy ; }
if(dz > 0.5*z) { dz = z- dz; }
return sqrt(pow (dx,2.0)+ pow(dy,2.0)+pow(dz, 2.0));
}
double Box::calAngle(Bead* B_p, Bead* B_m, Bead* B_n) {
double dist_A, dist_B, dist_C, angle_cal;
dist_A = periodicDistance(B_p, B_m);
dist_B = periodicDistance(B_m, B_n);
dist_C = periodicDistance(B_p, B_n);
angle_cal = acos ( (pow(dist_A, 2.0) + pow(dist_B, 2.0) - pow(dist_C,2.0))/(2* dist_A *dist_B) );
return angle_cal;
}
bool Box::positiveZ(Polymer* P, Bead* BB){
if (P->getStiff() ) {
BB->setPosition(BB->getX(), BB->getY(), 0);
return false;
}
else if (BB->getZ()>=0) {return false;}
else return true;
}