monomer_dynamics.cpp

/*
This function is responsible for giving monomers a random displacement at each
time step and for executing any other movements due to systematic forces.

Algorithm: loop over all cells(loop over all monomers in cell(check for and execute interactions))
*/

void monomer_dynamics(bool init, unsigned long long step)
{ 
int icounter, jcounter, kcounter;
int ix, jy, kz;
int ix2, jy2, kz2;
int ii, jj, kk;
int dd;
int mm, nn;
int ll;//for bind site
bool avoid, same_cell;


//loop over all cells
for(ii = 0; ii < N[0]; ii++)
{
 for(jj = 0; jj < N[1]; jj++)
 {
   for(kk = 0; kk < N[2]; kk++)
   {
//start the loop over all monomers in cell
nn = get_firstmonoincell(ii,jj,kk);

while(nn != EMPTY)
{
//loop over nearby cells
icounter = 0;
for(ix2 = (ii - 1 + N[0])%N[0]; icounter < 3; ix2 = (ix2+1)%N[0], icounter++)
{
 ix = ix2;

 jcounter = 0;
 for(jy2 = (jj - 1 + N[1])%N[1]; jcounter < 3; jy2 = (jy2+1)%N[1], jcounter++)
 {
  jy = jy2;

  kcounter = 0;
  for(kz2 = kk; kcounter < 2; kz2 = (kz2+1)%N[2], kcounter++)
  {
      same_cell = false;

      kz = kz2;
      if(kz == kk)
      {
      if(jy2 == (jj-1+N[1])%N[1] || (jy == jj && ix2 == (ii-1+N[0])%N[0]))
      {
         continue;
      }

        if(jy == jj)
        if(ix == ii)
           same_cell = true;

      }

//compare all monomers mm in particular nearby cell to monomer nn
    mm = get_firstmonoincell(ix,jy,kz);

    while(mm != LAST)
    {
        avoid = false;
        if(same_cell)
        if(mm <= nn)
          avoid = true;

	if(MODIFIED_SHELL_EXC_VOL)
	{//in this case, don't execute excl vol interactions between shell monos
	   if((mm >= NUMBER_IN_POLYMER) && (nn >= NUMBER_IN_POLYMER))
		avoid = true;
	}

//apply systematic forces/torques first, if applicable
      if(!avoid)
      {     
       (mono_list[nn]).sys_force(&mono_list[mm]);


	if((nn < NUMBER_IN_POLYMER)&&(mm<NUMBER_IN_POLYMER))
		binding_func(nn, mm);
 
       } //avoid
       mm = get_monolinklist(mm);
    }//bracket closes while(mm !=-1)
  }//kz loop
 }//jy loop
}//closes for loop over ix
// Brownian motion


	if(!init)
	{
	 if(THERMAL)
           (mono_list[nn]).translational_brownian_move(step);

	 if(COMPRESS)
	 {
		compress(nn);
         }

	 if(nn >= NUMBER_IN_POLYMER)
	 {
//excess feature commented out         
//        (mono_list[nn]).outward_pressure();

		if(!COMPRESS)
		if(mono_list[nn].get_load_mono())
		{
		  (mono_list[nn]).load();
		}
	 }// if(nn >= NUMBER_IN_POLYMER)
	}//!init

nn = get_monolinklist(nn);

}//bracket closes while(nn != -1)
}//bracket closes for(kk = 0; kk < N[2]; kk++)
}//bracket closes for(jj = 0; jj < N[1]; jj++)
}//bracket closes for(ii = 0; ii < N[0]; ii++)
 

}