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brownsys1.cpp
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brownsys1.cpp
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// implemention files for brownsys class
#include "headers/brownsys.h"
#include "dem_funcs.cpp"
using namespace std;
/////////////////////////////////////////////////////////////////////////////////////////
///// CONSTRUCTORS CONSTRUCTORS CONSTRUCTORS CONSTRUCTORS........
////////////////////////////////////////////////////////////////////////////////////////
//default, one protein system constructor
brownsys::brownsys()
{
crowds=false;
reaction=false;
Ncr=0;
double xx,yy,zz,mag,mag2; // dummies
srand (time(NULL));
//Generate random point on surface of sphere radius b, centered at origin
xx=2*(( (double) rand() / RAND_MAX + 1)-1.5);
yy=2*(( (double) rand() / RAND_MAX + 1)-1.5);
zz=2*(( (double) rand() / RAND_MAX + 1)-1.5);
mag2=xx*xx+yy*yy+zz*zz;
mag=pow(mag2,0.5);
xx=b*xx/mag;
yy=b*yy/mag;
zz=b*zz/mag;
main = protein(xx,yy,zz,M,r,false);
for(int i=0;i<dim;i++){cvel.push_back(0);cpos.push_back(0);}
crad=r;
cmass=M;
}
//N protein system constructor
brownsys::brownsys(int num)
{
Ncr=num;
crowds=true;
reaction=false;
escape=false;
double xx,yy,zz,mag,mag2; // dummies
int u,v,w,ran;
double n=ceil(pow(num,1.0/3.0));
int Np=n*n*n; // number of lattice points
int dN=Np-num; // number of lattice points which should eventually not contain crowders
double l=2*L/n; // cubic lattice spacing
vector< int > rem(dN-1);
for(int i=0;i<dim;i++){cvel.push_back(0);cpos.push_back(0);}
crad=r;
cmass=M;
//initiate random int generator
random_device rd;
srand (time(NULL));
default_random_engine gen(rd());
uniform_int_distribution<int> dist(1,Np); //random ints between 0 and Np
//done
//Generate random point on surface of sphere radius b, centered at origin
xx=2*(( (double) rand() / RAND_MAX + 1)-1.5);
yy=2*(( (double) rand() / RAND_MAX + 1)-1.5);
zz=2*(( (double) rand() / RAND_MAX + 1)-1.5);
mag2=xx*xx+yy*yy+zz*zz;
mag=pow(mag2,0.5);
xx=b*xx/mag;
yy=b*yy/mag;
zz=b*zz/mag;
main = protein(xx,yy,zz,M,r,false);
//Find indices of lattice point nearest to protein
u=round((xx+L)/l - 0.5);
v=round((yy+L)/l - 0.5);
w=round((zz+L)/l - 0.5);
//Indices found
//Generate indices of lattice points to be removed
int count=0;
while(count<dN-1){
ran=dist(gen);
if (find(rem.begin(), rem.end(), ran) == rem.end()){rem[count]=ran;count++;}
}
//Generated
int numb=1;
count=1;
// START COMPLICATED IF PROCESS TO AVOID PROTEIN
while(numb<N){
for(double k=0;k<n;k++){// k for
for(double j=0;j<n;j++){// j for
for(double i=0;i<n;i++){// i for
if (find(rem.begin(), rem.end(), count) == rem.end()){//check
if(k!=w){// k if
xx=l/2.0 + i*l-L;
yy=l/2.0 + j*l-L;
zz=l/2.0 + k*l-L;
crowders.push_back(protein(xx,yy,zz,Mc,rc,true));
numb++;}// end k if
else if(j!=v){// j if
xx=l/2.0 + i*l-L;
yy=l/2.0 + j*l-L;
zz=l/2.0 + k*l-L;
crowders.push_back(protein(xx,yy,zz,Mc,rc,true));
numb++;}// end j if
else if(i!=u){// i if
xx=l/2.0 + i*l-L;
yy=l/2.0 + j*l-L;
zz=l/2.0 + k*l-L;
crowders.push_back(protein(xx,yy,zz,Mc,rc,true));
numb++;}// end i if
}//end check
count++;
}}}}
}
///////////////////////////////////////////////////////////////////////////////////////////
////// MEMBERS MEMBERS MEMBERS MEMBERS MEMBERS////////////
////////////////////////////////////////////////////////////////////////////////////////
// need getr function for protein class
void brownsys::startNNs(double cut)
{
vector<int> nns;
vector<int> nnns;
vector<double> dumby;
double xx, yy, zz, x, y, z,mag,mag2;
dumby=main.getv("coords");
xx=dumby[0];yy=dumby[1];zz=dumby[2];
bool NN;
//NNs of main
for(int u=0; u<Ncr; u++)
{
dumby=crowders[u].getv("coords");
x=dumby[0];y=dumby[1];z=dumby[2];
mag2=x*x+y*y+z*z;
mag=pow(mag2,0.5);
if(mag<cut){nearcntr.push_back(u);} //NNs of central protein
NN=false;
mag2=(xx-x)*(xx-x)+(yy-y)*(yy-y)+(zz-z)*(zz-z);
mag=pow(mag2,0.5);
// CAN IMPROVE THIS BY NESTING ELSE [DONE, ELSES NESTED]
if(mag<cut){nns.push_back(u);NN=true;}
else{
x-=2*L;
mag2=(xx-x)*(xx-x)+(yy-y)*(yy-y)+(zz-z)*(zz-z);
mag=pow(mag2,0.5);
if(mag<cut){nns.push_back(u+Ncr);NN=true;}
else{
x+=4*L;
mag2=(xx-x)*(xx-x)+(yy-y)*(yy-y)+(zz-z)*(zz-z);
mag=pow(mag2,0.5);
if(mag<cut){nns.push_back(u+2*Ncr);NN=true;}
else{
x-=2*L;
y-=2*L;
mag2=(xx-x)*(xx-x)+(yy-y)*(yy-y)+(zz-z)*(zz-z);
mag=pow(mag2,0.5);
if(mag<cut){nns.push_back(u+3*Ncr);NN=true;}
else{
y+=4*L;
mag2=(xx-x)*(xx-x)+(yy-y)*(yy-y)+(zz-z)*(zz-z);
mag=pow(mag2,0.5);
if(mag<cut){nns.push_back(u+4*Ncr);NN=true;}
else{
y-=2*L;
z-=2*L;
mag2=(xx-x)*(xx-x)+(yy-y)*(yy-y)+(zz-z)*(zz-z);
mag=pow(mag2,0.5);
if(mag<cut){nns.push_back(u+5*Ncr);NN=true;}
else{
z+=4*L;
mag2=(xx-x)*(xx-x)+(yy-y)*(yy-y)+(zz-z)*(zz-z);
mag=pow(mag2,0.5);
if(mag<cut){nns.push_back(u+6*Ncr);NN=true;}
if(!NN){nnns.push_back(u);}
}}}}}}//ends all 6 elses
}
sort(nearcntr.begin(),nearcntr.end());
main.setNNs(nns, nnns);
for(int u=0; u<Ncr; u++) //can improve by linking. UNFINISHED
{
vector<int> nns;
vector<int> nnns;
dumby=crowders[u].getv("coords");
xx=dumby[0];yy=dumby[1];zz=dumby[2];
for(int v=0; v<Ncr; v++){NN=false;
if(u!=v)
{
dumby=crowders[v].getv("coords");
x=dumby[0];y=dumby[1];z=dumby[2];
mag2=(xx-x)*(xx-x)+(yy-y)*(yy-y)+(zz-z)*(zz-z);
mag=pow(mag2,0.5);
if(mag<cut){nns.push_back(v);NN=true;}
else{
x-=2*L;
mag2=(xx-x)*(xx-x)+(yy-y)*(yy-y)+(zz-z)*(zz-z);
mag=pow(mag2,0.5);
if(mag<cut){nns.push_back(v+Ncr);NN=true;}
else{
x+=4*L;
mag2=(xx-x)*(xx-x)+(yy-y)*(yy-y)+(zz-z)*(zz-z);
mag=pow(mag2,0.5);
if(mag<cut){nns.push_back(v+2*Ncr);NN=true;}
else{
x-=2*L;
y-=2*L;
mag2=(xx-x)*(xx-x)+(yy-y)*(yy-y)+(zz-z)*(zz-z);
mag=pow(mag2,0.5);
if(mag<cut){nns.push_back(v+3*Ncr);NN=true;}
else{
y+=4*L;
mag2=(xx-x)*(xx-x)+(yy-y)*(yy-y)+(zz-z)*(zz-z);
mag=pow(mag2,0.5);
if(mag<cut){nns.push_back(v+4*Ncr);NN=true;}
else{
y-=2*L;
z-=2*L;
mag2=(xx-x)*(xx-x)+(yy-y)*(yy-y)+(zz-z)*(zz-z);
mag=pow(mag2,0.5);
if(mag<cut){nns.push_back(v+5*Ncr);NN=true;}
else{
z+=4*L;
mag2=(xx-x)*(xx-x)+(yy-y)*(yy-y)+(zz-z)*(zz-z);
mag=pow(mag2,0.5);
if(mag<cut){nns.push_back(v+6*Ncr);NN=true;}
}}}}}} //end all 6 elses
if(!NN){nnns.push_back(u);}
}// end if u!=v
}// end for v
crowders[u].setNNs(nns,nnns);
}// end for u
}// ends function
void brownsys::updateNNs(double cut)
{
vector<double> pos1, pos2;
double dx,dy,dz,mag2,mag,xx,yy,zz;
vector<int> NNs;
vector<int> nNNs;
int index;
int index2;
//update main
pos1=main.getv("coords");
NNs=main.getNNs(true);
nNNs=main.getNNs(false);
int NNnum=NNs.size();
int cnum=nearcntr.size();
int nNNnum=nNNs.size();
if(cnum!=0)
{int i=0;
while(i<cnum) //Updates near center list
{
pos2=crowders[nearcntr[i]].getv("coords");
xx=pos2[0];yy=pos2[1];zz=pos2[2];
mag2=xx*xx+yy*yy+zz*zz;
mag=pow(mag2,0.5);
if(mag>cut){nearcntr.erase(nearcntr.begin()+i);cnum-=1;}
else{i++;}
}
sort (nearcntr.begin(),nearcntr.end());
}
cnum=nearcntr.size();
int count=0;
for(int i=0;i<Ncr;i++)
{
if(cnum==0)
{
pos2=crowders[i].getv("coords");
mag2=pos2[0]*pos2[0]+pos2[1]*pos2[1]+pos2[2]*pos2[2];
mag=pow(mag2,0.5);
if(mag<cut){nearcntr.push_back(i);}
}
else if(i != nearcntr[count]) //assumes nearcntr is sorted
{
pos2=crowders[i].getv("coords");
mag2=pos2[0]*pos2[0]+pos2[1]*pos2[1]+pos2[2]*pos2[2];
mag=pow(mag2,0.5);
if(mag<cut){nearcntr.push_back(i);}
}
else
{
count++;
if(count==cnum){cnum=0;}
}
}
sort(nearcntr.begin(),nearcntr.end());
for(int i=0; i<NNnum; i++) // Main removal loop
{
index=NNs[i];
if(index<Ncr)
{
pos2=crowders[index].getv("coords");
mag2=(pos1[0]-pos2[0])*(pos1[0]-pos2[0])+(pos1[1]-pos2[1])*(pos1[1]-pos2[1])+(pos1[2]-pos2[2])*(pos1[2]-pos2[2]);
mag=pow(mag2,0.5);
if(mag>cut){NNs.erase(NNs.begin()+i);nNNs.push_back(index);NNnum-=1;i-=1;}
}
else if(index>=Ncr && index<2*Ncr) //-x border
{
index2=index-Ncr;
pos2=crowders[index2].getv("coords");
pos2[0]-=2*L;
mag2=(pos1[0]-pos2[0])*(pos1[0]-pos2[0])+(pos1[1]-pos2[1])*(pos1[1]-pos2[1])+(pos1[2]-pos2[2])*(pos1[2]-pos2[2]);
mag=pow(mag2,0.5);
if(mag>cut){NNs.erase(NNs.begin()+i);nNNs.push_back(index);NNnum-=1;i-=1;}
}
else if(index>=2*Ncr && index<3*Ncr) //+x border
{
index2=index-2*Ncr;
pos2=crowders[index2].getv("coords");
pos2[0]+=2*L;
mag2=(pos1[0]-pos2[0])*(pos1[0]-pos2[0])+(pos1[1]-pos2[1])*(pos1[1]-pos2[1])+(pos1[2]-pos2[2])*(pos1[2]-pos2[2]);
mag=pow(mag2,0.5);
if(mag>cut){NNs.erase(NNs.begin()+i);nNNs.push_back(index);NNnum-=1;i-=1;}
}
else if(index>=3*Ncr && index<4*Ncr) //-y border
{
index2=index-3*Ncr;
pos2=crowders[index2].getv("coords");
pos2[1]-=2*L;
mag2=(pos1[0]-pos2[0])*(pos1[0]-pos2[0])+(pos1[1]-pos2[1])*(pos1[1]-pos2[1])+(pos1[2]-pos2[2])*(pos1[2]-pos2[2]);
mag=pow(mag2,0.5);
if(mag>cut){NNs.erase(NNs.begin()+i);nNNs.push_back(index);NNnum-=1;i-=1;}
}
else if(index>=4*Ncr && index<5*Ncr) //+y border
{
index2=index-4*Ncr;
pos2=crowders[index2].getv("coords");
pos2[1]+=2*L;
mag2=(pos1[0]-pos2[0])*(pos1[0]-pos2[0])+(pos1[1]-pos2[1])*(pos1[1]-pos2[1])+(pos1[2]-pos2[2])*(pos1[2]-pos2[2]);
mag=pow(mag2,0.5);
if(mag>cut){NNs.erase(NNs.begin()+i);nNNs.push_back(index);NNnum-=1;i-=1;}
}
else if(index>=5*Ncr && index<6*Ncr) //-z border
{
index2=index-5*Ncr;
pos2=crowders[index2].getv("coords");
pos2[2]-=2*L;
mag2=(pos1[0]-pos2[0])*(pos1[0]-pos2[0])+(pos1[1]-pos2[1])*(pos1[1]-pos2[1])+(pos1[2]-pos2[2])*(pos1[2]-pos2[2]);
mag=pow(mag2,0.5);
if(mag>cut){NNs.erase(NNs.begin()+i);nNNs.push_back(index);NNnum-=1;i-=1;}
}
else if(index>=6*Ncr && index<7*Ncr) //+z border
{
index2=index-6*Ncr;
pos2=crowders[index2].getv("coords");
pos2[2]+=2*L;
mag2=(pos1[0]-pos2[0])*(pos1[0]-pos2[0])+(pos1[1]-pos2[1])*(pos1[1]-pos2[1])+(pos1[2]-pos2[2])*(pos1[2]-pos2[2]);
mag=pow(mag2,0.5);
if(mag>cut){NNs.erase(NNs.begin()+i);nNNs.push_back(index);NNnum-=1;i-=1;}
}
} // ends the NN removal for loop
for(int i=0; i<nNNnum; i++) //CAN MAKE THIS BETTER BY LINKING PARTICLES FOR WHICH IVE ALREADY FOUND NNS
{
index=nNNs[i];
pos2=crowders[index].getv("coords");
dx=pos1[0]-pos2[0];
dy=pos1[1]-pos2[1];
dz=pos1[2]-pos2[2];
if(dx<cut)
{if(pow(dx*dx+dy*dy,0.5)<cut)
{if(pow(dx*dx+dy*dy+dz*dz,0.5)<cut){NNs.push_back(index);nNNs.erase(nNNs.begin()+i);nNNnum-=1;i-=1;}
}}//all ifs ended
else if(dx<cut-2*L) // -x boundary
{dx+=2*L; if(pow(dx*dx+dy*dy,0.5)<cut)
{if(pow(dx*dx+dy*dy+dz*dz,0.5)<cut){NNs.push_back(index+Ncr);nNNs.erase(nNNs.begin()+i);nNNnum-=1;i-=1;}
}}//-x ifs ended
else if(dx>2*L-cut) // +x boundary
{dx-=2*L; if(pow(dx*dx+dy*dy,0.5)<cut)
{if(pow(dx*dx+dy*dy+dz*dz,0.5)<cut){NNs.push_back(index+2*Ncr);nNNs.erase(nNNs.begin()+i);nNNnum-=1;i-=1;}
}}//+x ifs ended
else if(dy<cut-2*L) // -y boundary
{dy+=2*L; if(pow(dx*dx+dy*dy,0.5)<cut)
{if(pow(dx*dx+dy*dy+dz*dz,0.5)<cut){NNs.push_back(index+3*Ncr);nNNs.erase(nNNs.begin()+i);nNNnum-=1;i-=1;}
}}//-y ifs ended
else if(dy>2*L-cut) // +y boundary
{dy-=2*L; if(pow(dx*dx+dy*dy,0.5)<cut)
{if(pow(dx*dx+dy*dy+dz*dz,0.5)<cut){NNs.push_back(index+4*Ncr);nNNs.erase(nNNs.begin()+i);nNNnum-=1;i-=1;}
}}//+y ifs ended
else if(dz<cut-2*L) // -z boundary
{dz+=2*L; if(pow(dz*dz+dy*dy,0.5)<cut)
{if(pow(dx*dx+dy*dy+dz*dz,0.5)<cut){NNs.push_back(index+5*Ncr);nNNs.erase(nNNs.begin()+i);nNNnum-=1;i-=1;}
}}//-z ifs ended
else if(dz>2*L-cut) // +z boundary
{dz-=2*L; if(pow(dx*dx+dy*dy,0.5)<cut)
{if(pow(dx*dx+dy*dy+dz*dz,0.5)<cut){NNs.push_back(index+6*Ncr);nNNs.erase(nNNs.begin()+i);nNNnum-=1;i-=1;}
}}//+z ifs ended
} // ends NN addition loop for MAIN
main.setNNs(NNs, nNNs);
//////////////////////////////////////////////////////////////////////////////////
////////////////////////////////// NN update for every crowder
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
for(int j=0; j<Ncr; j++){ //STARTS REMOVAL LOOP
pos1=crowders[j].getv("coords");
NNs=crowders[j].getNNs(true);
nNNs=crowders[j].getNNs(false);
NNnum=NNs.size();
nNNnum=nNNs.size();
for(int i=0; i<NNnum; i++) // Main removal loop
{
index=NNs[i];
if(index<Ncr)
{
pos2=crowders[index].getv("coords");
mag2=(pos1[0]-pos2[0])*(pos1[0]-pos2[0])+(pos1[1]-pos2[1])*(pos1[1]-pos2[1])+(pos1[2]-pos2[2])*(pos1[2]-pos2[2]);
mag=pow(mag2,0.5);
if(mag>cut){NNs.erase(NNs.begin()+i);nNNs.push_back(index);NNnum-=1;i-=1;}
}
else if(index>=Ncr && index<2*Ncr) //-x border
{
index2=index-Ncr;
pos2=crowders[index2].getv("coords");
pos2[0]-=2*L;
mag2=(pos1[0]-pos2[0])*(pos1[0]-pos2[0])+(pos1[1]-pos2[1])*(pos1[1]-pos2[1])+(pos1[2]-pos2[2])*(pos1[2]-pos2[2]);
mag=pow(mag2,0.5);
if(mag>cut){NNs.erase(NNs.begin()+i);nNNs.push_back(index);NNnum-=1;i-=1;}
}
else if(index>=2*Ncr && index<3*Ncr) //+x border
{
index2=index-2*Ncr;
pos2=crowders[index2].getv("coords");
pos2[0]+=2*L;
mag2=(pos1[0]-pos2[0])*(pos1[0]-pos2[0])+(pos1[1]-pos2[1])*(pos1[1]-pos2[1])+(pos1[2]-pos2[2])*(pos1[2]-pos2[2]);
mag=pow(mag2,0.5);
if(mag>cut){NNs.erase(NNs.begin()+i);nNNs.push_back(index);NNnum-=1;i-=1;}
}
else if(index>=3*Ncr && index<4*Ncr) //-y border
{
index2=index-3*Ncr;
pos2=crowders[index2].getv("coords");
pos2[1]-=2*L;
mag2=(pos1[0]-pos2[0])*(pos1[0]-pos2[0])+(pos1[1]-pos2[1])*(pos1[1]-pos2[1])+(pos1[2]-pos2[2])*(pos1[2]-pos2[2]);
mag=pow(mag2,0.5);
if(mag>cut){NNs.erase(NNs.begin()+i);nNNs.push_back(index);NNnum-=1;i-=1;}
}
else if(index>=4*Ncr && index<5*Ncr) //+y border
{
index2=index-4*Ncr;
pos2=crowders[index2].getv("coords");
pos2[1]+=2*L;
mag2=(pos1[0]-pos2[0])*(pos1[0]-pos2[0])+(pos1[1]-pos2[1])*(pos1[1]-pos2[1])+(pos1[2]-pos2[2])*(pos1[2]-pos2[2]);
mag=pow(mag2,0.5);
if(mag>cut){NNs.erase(NNs.begin()+i);nNNs.push_back(index);NNnum-=1;i-=1;}
}
else if(index>=5*Ncr && index<6*Ncr) //-z border
{
index2=index-5*Ncr;
pos2=crowders[index2].getv("coords");
pos2[2]-=2*L;
mag2=(pos1[0]-pos2[0])*(pos1[0]-pos2[0])+(pos1[1]-pos2[1])*(pos1[1]-pos2[1])+(pos1[2]-pos2[2])*(pos1[2]-pos2[2]);
mag=pow(mag2,0.5);
if(mag>cut){NNs.erase(NNs.begin()+i);nNNs.push_back(index);NNnum-=1;i-=1;}
}
else if(index>=6*Ncr && index<7*Ncr) //+z border
{
index2=index-6*Ncr;
pos2=crowders[index2].getv("coords");
pos2[2]+=2*L;
mag2=(pos1[0]-pos2[0])*(pos1[0]-pos2[0])+(pos1[1]-pos2[1])*(pos1[1]-pos2[1])+(pos1[2]-pos2[2])*(pos1[2]-pos2[2]);
mag=pow(mag2,0.5);
if(mag>cut){NNs.erase(NNs.begin()+i);nNNs.push_back(index);NNnum-=1;i-=1;}
}
} // ends the i removal loops
for(int i=0; i<nNNnum; i++) //CAN MAKE THIS BETTER BY LINKING PARTICLES FOR WHICH IVE ALREADY FOUND NNS
{
index=nNNs[i];
pos2=crowders[index].getv("coords");
dx=pos1[0]-pos2[0];
dy=pos1[1]-pos2[1];
dz=pos1[2]-pos2[2];
if(dx<cut)
{if(pow(dx*dx+dy*dy,0.5)<cut)
{if(pow(dx*dx+dy*dy+dz*dz,0.5)<cut){NNs.push_back(index);nNNs.erase(nNNs.begin()+i);nNNnum-=1;i-=1;}
}}//all ifs ended
else if(dx<cut-2*L) // -x boundary
{dx+=2*L; if(pow(dx*dx+dy*dy,0.5)<cut)
{if(pow(dx*dx+dy*dy+dz*dz,0.5)<cut){NNs.push_back(index+Ncr);nNNs.erase(nNNs.begin()+i);nNNnum-=1;i-=1;}
}}//-x ifs ended
else if(dx>2*L-cut) // +x boundary
{dx-=2*L; if(pow(dx*dx+dy*dy,0.5)<cut)
{if(pow(dx*dx+dy*dy+dz*dz,0.5)<cut){NNs.push_back(index+2*Ncr);nNNs.erase(nNNs.begin()+i);nNNnum-=1;i-=1;}
}}//+x ifs ended
else if(dy<cut-2*L) // -y boundary
{dy+=2*L; if(pow(dx*dx+dy*dy,0.5)<cut)
{if(pow(dx*dx+dy*dy+dz*dz,0.5)<cut){NNs.push_back(index+3*Ncr);nNNs.erase(nNNs.begin()+i);nNNnum-=1;i-=1;}
}}//-y ifs ended
else if(dy>2*L-cut) // +y boundary
{dy-=2*L; if(pow(dx*dx+dy*dy,0.5)<cut)
{if(pow(dx*dx+dy*dy+dz*dz,0.5)<cut){NNs.push_back(index+4*Ncr);nNNs.erase(nNNs.begin()+i);nNNnum-=1;i-=1;}
}}//+y ifs ended
else if(dz<cut-2*L) // -z boundary
{dz+=2*L; if(pow(dz*dz+dy*dy,0.5)<cut)
{if(pow(dx*dx+dy*dy+dz*dz,0.5)<cut){NNs.push_back(index+5*Ncr);nNNs.erase(nNNs.begin()+i);nNNnum-=1;i-=1;}
}}//-z ifs ended
else if(dz>2*L-cut) // +z boundary
{dz-=2*L; if(pow(dx*dx+dy*dy,0.5)<cut)
{if(pow(dx*dx+dy*dy+dz*dz,0.5)<cut){NNs.push_back(index+6*Ncr);nNNs.erase(nNNs.begin()+i);nNNnum-=1;i-=1;}
}}//+z ifs ended
} // ends i addition loop
} // ends j loop for crowder nearest neighbor update
}
void brownsys::moveall(mt19937& gen, normal_distribution<> distro)
{
del_t=h; // del_t is the time remaining, t1 is the time until an event
//bool mainmove, cmove, col, resolved, secondary = false;
double v,tp,tm,t, t1, mag2, mag;
int index, index1, index2, nnNum;
double rad2, rad, vdr, crvdr, v2, vc2, r2, R, reactime=0;
vector<double> move(3), mvVel(3), pos1(3), pos2(3), npos(3), npos2(3), dr(3);
vector<int> nearest, nearest2;
vector<double> PBCvec;
bool collision, resolved = false;
t1=del_t;
/////////////// COLLISION RESOLUTION STUFF
vector<double> rhat(3), vperp(3), vpar(3), v1f(3), v2f(3);
double m1,m2,R1,R2;
bool ismain;
/*
for now:
- Move main
- move center
- move crowders
later:
- move them all randomly with checks
*/
/////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////////
//Move main
/////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////////
nearest=main.getNNs(true);
pos1=main.getv("coords");
mag2=0;
for(int k=0;k<3;k++)
{
move[k]=distro(gen); mvVel[k]=move[k]/h;npos[k]=move[k]+pos1[k];
mag2+=npos[k]*npos[k]; v2+=mvVel[k]*mvVel[k]; vdr+=mvVel[k]*pos1[k];
r2+=pos1[k]*pos1[k];
}
mag=pow(mag2,0.5);
// REACTION
if(mag<crad+main.getp("radius"))
{
rad2=vdr*vdr - v2*(r2-(crad+main.getp("radius")));
if(rad2>0)
{
rad=pow(rad2,0.5);
}
else
{
cout<<"err: negative in radical"<<endl;
}
tm=(-1.0*vdr - rad)/v2;
tp=(-1.0*vdr + rad)/v2;
if(tm<0)
{
t=tp;
}
else
{
t=tm;
}
if(t<del_t)
{
reaction=true;
t1=t;
cout<<"potential reaction"<<endl;
}
else
{
cout<<"err: time is greater than time step"<<endl;
}
} // closes reaction loop
// ESCAPE
else if(mag > q)
{
rad2=vdr*vdr - v2*(r2-q*q);
if(rad2>0)
{
rad=pow(rad2,0.5);
}
else
{
cout<<"err: negative in radical"<<endl;
}
tm=(-1.0*vdr - rad)/v2;
tp=(-1.0*vdr + rad)/v2;
if(tm<0)
{
t=tp;
}
else
{
t=tm;
}
if(t<del_t)
{
escape=true;
t1=t;
cout<<"potential escape"<<endl;
}
else
{
cout<<"err: time is greater than time step"<<endl;
}
} // closes escape loop
// collisions with crowders
R = main.getp("radius")+crowders[nearest[k]%Ncr].getp("radius");
for(int k=0;k<nearest.size();k++)
{
vdr, mag2=0;
pos2=crowders[nearest[k]%Ncr].getv("coords");
PBCvec=PBCswitch(Ncr, nearest[k]);
for(int i=0;i<3;i++) //
{
pos2[i]+=PBCvec[i]*L; // position of potential collidee
dr[i]=pos2[i]-pos1[i];
mag2+=dr[i]*dr[i]; // dist^2 between particles
vdr+=mvVel[i]*dr[i];
}
mag=pow(mag2,0.5);
if(mag<R)
{
rad2 = vdr*vdr - v2*(mag2-R*R);
if(rad2>0)
{
rad=pow(rad2,0.5);
}
else
{
cout<<"err: negative in radical"<<endl;
}
tm = (vdr - rad)/v2;
tp = (vdr + rad)/v2;
if(tm<0)
{
t=tp;
}
else
{
t=tm;
}
if(t<t1)
{
t1 = t;
reaction, escape = false;
collision=true;
index=nearest[k];
}
} // closes crowder collision loop
} // closes NN loop
if(escape)
{
cout<<"No reaction"<<endl;
}
else if(reaction)
{
cout<<"Reaction"<<endl;
}
else if(collision)
{
index2=index;
index1=-1; // use -1 to indicate that its main
ismain=true;
R1=main.getp("radius");
R2=crowders[index%Ncr].getp("radius");
m1=main.getp("mass");
m2=crowders[index%Ncr].getp("mass");
pos2=crowders[index%Ncr].getv("coords");
PBCvec=PBCswitch(Ncr, index);
del_t=del_t-t1; // remaining time, move forward to t1 seconds
while(!resolved)
{
vdr=0;
crvdr=0;
v2,vc2,mag2=0;
collision=false;
for(int k=0;k<3;k++)
{
pos1[k]+=mvVel[k]*t1; // update new position
rhat[k]=((pos2[k]+PBCvec[k]*L)-npos[k])/R; // unit vector from 1 to 2
vperp[k]=mvVel[k]*rhat[k]; // normal component
vpar[k]=mvVel[k]-vperp[k]; // tangent component
v1f[k]=vpar[k] + vperp[k]*(m1-m2)/(m1+m2); // final vel of main
v2f[k]=vperp[k]*2*m1/(m1+m2); // final vel of crowder
// update some stuff to check for secondaries
npos[k]=pos1[k]+v1f[k]*del_t;
npos2[k]=pos2[k] + v2f[k]*del_t;
v2+=v1f[k]*v1f[k];
vc2+=v2f[k]*v2f[k];
mag2+=npos[k]*npos[k];
vdr+=pos1[k]*v1f[k];
crvdr+=pos2[k]+v2f[k];
}
t1=del_t;
if(ismain)
{
//check reaction
mag=pow(mag2,0.5);
if(mag<crad+R1)
{
rad2=vdr*vdr - v2*(r2-(crad+main.getp("radius")));
if(rad2>0)
{
rad=pow(rad2,0.5);
}
else
{
cout<<"err: negative in radical"<<endl;
}
tm=(-1.0*vdr - rad)/v2;
tp=(-1.0*vdr + rad)/v2;
if(tm<0)
{
t=tp;
}
else
{
t=tm;
}
if(t<del_t)
{
reaction=true;
t1=t;
cout<<"potential reaction"<<endl;
}
else
{
cout<<"err: time is greater than time step"<<endl;
}
} // closes reaction loop
// ESCAPE
else if(mag > q)
{
rad2=vdr*vdr - v2*(r2-q*q);
if(rad2>0)
{
rad=pow(rad2,0.5);
}
else
{
cout<<"err: negative in radical"<<endl;
}
tm=(-1.0*vdr - rad)/v2;
tp=(-1.0*vdr + rad)/v2;
if(tm<0)
{
t=tp;
}
else if(tm>0)
{
t=tm;
}
else
{
cout<<"err: negative times"<<endl;
}
if(t<del_t)
{
escape=true;
t1=t;
cout<<"potential escape"<<endl;
}
else
{
cout<<"err: time is greater than remaining time"<<endl;
}
} // closes escape loop
} // closes ismain if
//check secondary collision for particle 1, use pos2 as dumby
if(index1==-1){nearest=main.getNNs(true);}
else{nearest=crowders[index1%Ncr]}
for(int i=0;i<nearest.size();i++)
{
pos2=crowders[nearest[i]%Ncr].getv("coords");
PBCvec=PBCswitch(Ncr, nearest[i]);
R=main.getp("radius")+crowders[nearest[i]%Ncr].getp("radius");
for(int i=0;i<3;i++) //
{
pos2[i]+=PBCvec[i]*L; // position of potential collidee
dr[i]=pos2[i]-pos1[i];
mag2+=dr[i]*dr[i]; // dist^2 between particles
vdr+=mvVel[i]*dr[i];
}
mag=pow(mag2,0.5);
if(mag<R)
{
rad2=(vdr*vdr - v2*(mag2-R*R))/v2;
if(rad2>0)
{
rad=pow(rad2,0.5);
tm=(vdr-rad)/v2;
tp=(vdr+rad)/v2;
if(tm<0)
{
t=tp;
}
else
{
t=tm;
}
if(t<t1)
{
t1=t;
reaction, escape=false;
secondary=true;
}
}
} // close time calculation if
} // close main nn loop
if(secondary)
{
// set up to continue while
}
else if(reaction || escape)
{
resolved=true;
}
}//closes secondary resolution
}
else
{
main.setpos(npos);
}
////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////
/////////////// MOVE CENTER ////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////
for(int k=0;k<3;k++)
{
move[k]=distro(gen); mvVel[k]=move[k]/h; npos[k]=move[k];
}
// reaction
pos1=main.getv("coords");
mag2=0;
for(int k=0;k<3;k++)
{
mag2+=(npos[k]-pos1[k])*(npos[k]-pos1[k]);
}
mag=pow(mag2,0.5);
if(mag<main.getp("radius")+crad)
{
// store time and compare with crowder collisions
}
// check for collision with crowders
for(int k=0; k<nearcntr.size(); k++)
{
mag2=0;
pos2=crowders[k].getv("coords");
for(int i=0;i<3;i++)
{
mag2+=(pos2[k]-npos[k])*(pos2[k]-npos[k]);
}
mag=pow(mag2,0.5);
if(mag<crad+crowders[k].getp("radius"))
{
// RESOLVE
}
}
// update ALL positions, check for escape THEN check PBCs
//////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
// MOVE CROWDERS /////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////