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I'm having trouble moving a vector after I iterate through it

msmit247 (2)
I have a project where I have a bunch of molecules moving around a box, I need the molecules to form a polymer if they come close to each other, if the polymer exists add a molecule to the end of the polymer until the polymer vector is > the molecule vector.
I have created everything and I believe it polymerizes, but no matter what I try I just can't get the polymer chain to move after it adds a molecule.
so I know that is a bit confusing here is my code
I hope that makes sense to everyone
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#include <iostream>
#include <vector>
#include <stdio.h>
#include <math.h>
#include <assert.h>
#include <time.h>
#include <algorithm>
using namespace std;
#include "random.h"
#include "molecule.h"
#include "polymer.h"
#include "box.h"



void Box::move()
{

	for(int i=0;i<molecules.size();i++) {
		 	molecules[i]->move();
			checkForMoleculeWrapping(molecules[i]);
			if(!checkOverlap(i)) {
			molecules[i]->goBack();
				}
				if(polymer.size()<molecules.size()) {
				checkPolymerization(i);
		}
	}
 }	

bool Box::checkOverlap(int molecule_index)
{
	vector<Molecule*>::iterator it;
	Molecule* m1;
	m1 = molecules[molecule_index];
	Molecule* m2;
	for(int i=0;i<molecules.size();i++) {
		if(i!=molecule_index) {
			m2 = molecules[i];
			if(distanceCalc(m1->getX(),m1->getY(),m1->getZ(),m2->getX(),m2->getY(),m2->getZ()) < (m1->getDiameter()/2.0 + m2->getDiameter()/2.0)) return false; //this code checks for molecule overlap
				it=find(polymer.begin(),polymer.end(),molecules[molecule_index]);	// to check if the molecules in the polymer are misbehaving all of the code below
				if(it!=polymer.end()) {
				m1=*it;
					if(it==polymer.begin()){
					m2=*it+1;
						if(distanceCalc(m1->getX(),m1->getY(),m1->getZ(),m2->getX(),m2->getY(),m2->getZ())>max_distance_between_neighboring_molecules){
						return false;
				}
			}
			else if(it==(polymer.end()-1)){
			m2=*it-1;
				if(distanceCalc(m1->getX(),m1->getY(),m1->getZ(),m2->getX(),m2->getY(),m2->getZ())>max_distance_between_neighboring_molecules){
				return false;
				}
				
			}
			else {
			m2=*it+1;
				if(distanceCalc(m1->getX(),m1->getY(),m1->getZ(),m2->getX(),m2->getY(),m2->getZ())>max_distance_between_neighboring_molecules){
				return false;
				}
			m2=*it-1;
				if(distanceCalc(m1->getX(),m1->getY(),m1->getZ(),m2->getX(),m2->getY(),m2->getZ())>max_distance_between_neighboring_molecules){
				return false;
				}
			}
		}
	}
} return true;
}
bool Box::MoleInPoly(int molecule_index){
	
	vector<Molecule*>::iterator it;
	Molecule* m1;
	m1 = polymer[molecule_index];
	Molecule* m2;
	for(int i=0;i<polymer.size();i++) {
		if(i!=molecule_index) {
			m2 = polymer[i];
			if(distanceCalc(m1->getX(),m1->getY(),m1->getZ(),m2->getX(),m2->getY(),m2->getZ()) < (m1->getDiameter() + m2->getDiameter())) return false;
			else { polymer[i]->move();}
				}
}
return true;
}
void Box::checkPolymerization(int molecule_index)
{
	vector<Molecule*>::iterator iter;

	Molecule* m1;
	Molecule* m2;
	m1 = molecules[molecule_index];
	if(polymer.empty()) {                         
		for(int i=0;i<molecules.size();i++) {
			if(i!=molecule_index) {
				m2 = molecules[molecule_index];
				if(distanceCalc(m1->getX(),m1->getY(),m1->getZ(),m2->getX(),m2->getY(),m2->getZ()) < max_distance_between_neighboring_molecules) {
					polymer.push_back(m1);
					polymer.push_back(m2);
				}
			}
		}
	}
	else {
		// is m1 in the polymer?
		iter = find(polymer.begin(),polymer.end(),m1);
		if(iter!=polymer.end()) {
			if( m1==polymer.back()){// m1 is in the polmyer
			  // is m1 an end?
				for(int i=0;i<molecules.size();i++){				  
					 if(find(polymer.begin(),polymer.end(),molecules[i])==polymer.end()){
						if(	distanceCalc(molecules[i]->getX(),molecules[i]->getY(),molecules[i]->getZ(),polymer.back()->getX(),polymer.back()->getY(),polymer.back()->getZ())<max_distance_between_neighboring_molecules){
							polymer.push_back(molecules[i]);
						}
					 }
				}
			}
			else if( iter == polymer.begin()) {
				for(int i=0;i<molecules.size();i++){				  
					 if(find(polymer.begin(),polymer.end(),molecules[i])==polymer.end()){
						if(	distanceCalc(molecules[i]->getX(),molecules[i]->getY(),molecules[i]->getZ(),polymer.back()->getX(),polymer.back()->getY(),polymer.back()->getZ())<max_distance_between_neighboring_molecules){
							polymer.insert(polymer.begin(),molecules[i]);
						}
					 }
				}
			}
		}                        
		else {
			if(distanceCalc(m1->getX(),m1->getY(),m1->getZ(),(*polymer.begin())->getX(),(*polymer.begin())->getY(),(*polymer.begin())->getZ())<max_distance_between_neighboring_molecules)                                        // is the distance between m1 and polymer.end()-1 < 1.2 then add m1 to back
				polymer.insert(polymer.begin(),m1);		
			else{
			  if(distanceCalc(m1->getX(),m1->getY(),m1->getZ(),(*polymer.end()-1)->getX(),(*polymer.end()-1)->getY(),(*polymer.end()-1)->getZ())<max_distance_between_neighboring_molecules)
		       polymer.push_back(m1);
			}
		}
	}
}

double Box::distanceCalc(double _x1, double _y1, double _z1, double _x2, double _y2, double _z2) 
{
	double dx,dy,dz;
	dx = fabs(_x1-_x2);
	dy = fabs(_y1-_y2);
	dz = fabs(_z1-_z2);
	if(dx > 0.5*x) { dx = dx - x; }
	if(dy > 0.5*y) { dy = dy - y; }
	if(dz > 0.5*z) { dz = dz - z; }
	return sqrt( pow( dx,2.0 ) + pow( dy,2.0 ) + pow( dz,2.0 ) );
}

void Box::checkForMoleculeWrapping(Molecule* m)
{
	if(m->getX() < -x/2.0) m->setPosition(m->getX()+x,m->getY(),m->getZ());
	if(m->getY() < -y/2.0) m->setPosition(m->getX(),m->getY()+y,m->getZ());
	if(m->getZ() < -z/2.0) m->setPosition(m->getX(),m->getY(),m->getZ()+z);
	if(m->getX() > x/2.0) m->setPosition(m->getX()-x,m->getY(),m->getZ());
	if(m->getY() > y/2.0) m->setPosition(m->getX(),m->getY()-y,m->getZ());
	if(m->getZ() > z/2.0) m->setPosition(m->getX(),m->getY(),m->getZ()-z);
}	

/*
void Box::movePoly()   // new function to see if I can move the entire polymer
{
	vector<Molecule*>::iterator k;
	for(k=polymer.begin();k!=polymer.end();k++){
		for(int i=0;i<polymer.size();i++){
		if(k!=polymer.begin()){
			polymer[i]->setPosition(polymer[i-1]->getX(),polymer[i-1]->getY(),polymer[i-1]->getZ());
		}
		else if (k==polymer.begin()){
			polymer[i]->setPosition(polymer[i]->getX()-x/2.0,polymer[i]->getY()-y/2.0,polymer[i]->getZ()-z/2.0);
		}
		}
	}
		/*
	vector<Molecule*> polymer(copypolymer);
	for(int i=0;i<polymer.size();i++){
		
		//d=polymer[i]->getDiameter();
		//xi=polymer[i]->getX();
		//yi=polymer[i]->getY();
		//zi=polymer[i]->getZ();
		for(int j=0;j<copypolymer.size();j++){
			if(distanceCalc(polymer[i]->getX(),polymer[i]->getY(),polymer[i]->getZ(),copypolymer[j]->getX(),copypolymer[j]->getY(),copypolymer[j]->getZ())==0){
				copypolymer[j+1]=polymer[i];
				//polymer[i]->move();
			}
		}
	} 

}


*/
Last edited on
Aceix (1118)
please use code tags: http://www.cplusplus.com/articles/jEywvCM9/

Aceix.
msmit247 (2)
thanks, sorry am new didn't have time to read the rules
... p.s. I added the new function MoleInPoly() and it seems to be moving now, I can't view the .vtf file it outputs in main because of windows, so I can't be sure of it working entirely. I really appreciate any help :)
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