SliplinkerAll.cpp

#ifndef SLIPLINKER_ALL_CPP
#define SLIPLINKER_ALL_CPP

/*
* MolMcD - Monte Carlo and Molecular Dynamics Simulator for Molecular Liquids
*
* Copyright 2010 - 2014, The Regents of the University of Minnesota
* Distributed under the terms of the GNU General Public License.
*/

#include "SliplinkerAll.h"
#include <mcMd/simulation/Simulation.h>
#include <mcMd/mcSimulation/McSystem.h>
#include <mcMd/links/LinkMaster.h>
#include <mcMd/potentials/pair/McPairPotential.h>
#include <mcMd/potentials/bond/BondPotential.h>
#include <mcMd/chemistry/Molecule.h>
#include <mcMd/chemistry/Atom.h>
#include <simp/boundary/Boundary.h>
#include <util/misc/FileMaster.h>
#include <util/space/Vector.h>
#include <util/space/Dimension.h>
#include <util/global.h>


namespace McMd
{
  
   using namespace Util;
   using namespace Simp;

   // Constructor
   SliplinkerAll::SliplinkerAll(McSystem& system) :
      SystemMove(system),
      cutoff_(0),
      mu_(0),
      speciesId_(0)
   {  setClassName("SliplinkerAll"); }

   void SliplinkerAll::readParameters(std::istream& in)
   {
      readProbability(in);
      read<double>(in, "cutoff", cutoff_);
      read<double>(in, "mu", mu_);
      read<int>(in, "speciesId", speciesId_);
      

   }


   // Create or destroy the slip-springs.
   bool SliplinkerAll::move() 
   {
     System::MoleculeIterator molIter;
     Molecule::AtomIterator   atomIter;
     Atom                    *atom0Ptr, *atom1Ptr;
     Atom*                    atomPtr;
     // Molecule                *mol0Ptr, *mol1Ptr;
     Molecule*                molIPtr;
     double                   prob, dRSq, mindRSq=cutoff_*cutoff_, rnd, norm;
     int                      i, ntrials, j, nNeighbor, idLink, iAtom, id1, id0;
     // int                      iAtom0, iAtom1, iMolecule0, iMolecule1;
     int                      n0;
     Link*                    linkPtr;
     static const int         maxNeighbor = CellList::MaxNeighbor;
     double                   cdf[maxNeighbor], energy, sum;
     int                      idneighbors[maxNeighbor];

     
     ntrials = 2 * system().simulation().atomCapacity();
     for (i=0; i < ntrials; ++i){   
       
       //Choose to create or destroy a link with prob 0.5
       if (random().uniform(0.0, 1.0) > 0.5){         
     // Try to create a link. 
     incrementNAttempt();     
     // Choose a molecule and atom at random
     molIPtr  = &(system().randomMolecule(speciesId_));
     // iMolecule0 = system().moleculeId(*molIPtr);
     iAtom = random().uniformInt(0, molIPtr->nAtom());
     atomPtr = &molIPtr->atom(iAtom);
     id0 = atomPtr->id();
     
     // Get array of neighbors
     system().pairPotential().cellList().getNeighbors(atomPtr->position(), neighbors_);
     nNeighbor = neighbors_.size();
       
     n0 = 0;
     sum = 0;
     // Loop over neighboring atoms
     for (j = 0; j < nNeighbor; ++j) {
       atom1Ptr = neighbors_[j];
       // mol1Ptr = &atom1Ptr->molecule();
       // iMolecule1 = system().moleculeId(*mol1Ptr); 
       id1 = atom1Ptr->id();
       
            // Check if atoms are the same
            if (id0 != id1){            
         // Exclude masked pairs     
         if (!atomPtr->mask().isMasked(*atom1Ptr)) {
      // Identify possible partners and calculate the cumulative distribution function
      dRSq = system().boundary().distanceSq(atomPtr->position(), atom1Ptr->position());
      if (dRSq <= mindRSq) {
        energy = system().linkPotential().energy(dRSq, 0);
        sum = sum + boltzmann(energy);
        cdf[n0] = sum;
        idneighbors[n0] = j;
        n0++;
      }    
         }
       }
     }   
       
     // If at least 1 candidate has been found.  
     if (n0 > 0) {
       // Choose a partner with probability cdf[j]/cdf[n0-1]
       j = 0;
       rnd = random().uniform(0.0, 1.0);
       norm = 1.0/cdf[n0-1];
       while (rnd > cdf[j]*norm ){
         j = j + 1;
       }     
       atom1Ptr = neighbors_[idneighbors[j]];        
       // Create a slip-link between the selected atoms with probability = prob
       prob = 2.0 * (system().linkMaster().nLink() + 1.0);
       prob = system().simulation().atomCapacity() * boltzmann(-mu_) * cdf[n0-1]/ prob ;
       //prob = 2.0 * system().nMolecule(speciesId_) * boltzmann(-mu_) * cdf[n0-1]/ prob ;         
       if (system().simulation().random().uniform(0.0, 1.0) < prob) {        
         system().linkMaster().addLink(*atomPtr, *atom1Ptr, 0); 
         incrementNAccept();      
       }      
     }    
       }
       else {
     // Try to destroy a link
     incrementNAttempt();
     // Choose a link at random
     if (system().linkMaster().nLink() > 0){
       idLink = random().uniformInt(0, system().linkMaster().nLink());

       // Indentify the atoms for this link.
       linkPtr = &(system().linkMaster().link(idLink));
       atom0Ptr = &(linkPtr->atom0());
       // mol0Ptr = &atom0Ptr->molecule();
       // iMolecule0 = system().moleculeId(*mol0Ptr);
       // iAtom0 = atom0Ptr->indexInMolecule();     
       atom1Ptr = &(linkPtr->atom1());
       // mol1Ptr = &atom1Ptr->molecule();
       // iMolecule1 = system().moleculeId(*mol1Ptr);
       // iAtom1 = atom1Ptr->indexInMolecule();

       // Try to delete the slip-spring   
       dRSq = system().boundary().distanceSq(atom0Ptr->position(), atom1Ptr->position());
       // try to delete the link if the bond is smaller than the cutoff
       if (dRSq <= mindRSq) {    
         // Get array of neighbors
         system().pairPotential().cellList().getNeighbors(atom0Ptr->position(), neighbors_);
         nNeighbor = neighbors_.size();
         id0 = atom0Ptr->id();
         n0 = 0;
         sum = 0;
         // Loop over neighboring atoms
         for (j = 0; j < nNeighbor; ++j) {
      atom1Ptr = neighbors_[j];
      // mol1Ptr = &atom1Ptr->molecule();
      // iMolecule1 = system().moleculeId(*mol1Ptr);
           id1 = atom1Ptr->id();
       
                // Check if atoms are the same
                if (id0 != id1){                   
        // Exclude masked pairs      
        if (!atom0Ptr->mask().isMasked(*atom1Ptr)) {
          // Identify possible partners and calculate the cumulative distribution function
          dRSq = system().boundary().distanceSq(atom0Ptr->position(), atom1Ptr->position());
          if (dRSq <= mindRSq) {
            energy = system().linkPotential().energy(dRSq, 0);
            //energy = 0.5*dRSq;
            sum = sum + boltzmann(energy);
            cdf[n0] = sum;
            idneighbors[n0] = j;
            n0++;
          }    
        }
           }
         }    
         // Destroy the slip-link between the selected atoms with probability = prob     
         //prob = 2.0 * system().nMolecule(speciesId_) * boltzmann(-mu_) * cdf[n0-1];  
         prob = system().simulation().atomCapacity() * boltzmann(-mu_) * cdf[n0-1];     
         prob = 2.0 * system().linkMaster().nLink() / prob;                
         if (system().simulation().random().uniform(0.0, 1.0) < prob) {        
                system().linkMaster().removeLink(idLink); 
      incrementNAccept();  
         }  
       }
          }
       }
     }
     return true;
   }

}
#endif