src/brains/SimInfo.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
/**
 * @file SimInfo.cpp
 * @author    tlin
 * @date  11/02/2004
 * @version 1.0
 */

#include <algorithm>
#include <set>
#include <map>

#include "brains/SimInfo.hpp"
#include "math/Vector3.hpp"
#include "primitives/Molecule.hpp"
#include "primitives/StuntDouble.hpp"
#include "UseTheForce/fCutoffPolicy.h"
#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
#include "UseTheForce/doForces_interface.h"
#include "UseTheForce/DarkSide/neighborLists_interface.h"
#include "UseTheForce/DarkSide/electrostatic_interface.h"
#include "UseTheForce/DarkSide/switcheroo_interface.h"
#include "utils/MemoryUtils.hpp"
#include "utils/simError.h"
#include "selection/SelectionManager.hpp"
#include "io/ForceFieldOptions.hpp"
#include "UseTheForce/ForceField.hpp"


#ifdef IS_MPI
#include "UseTheForce/mpiComponentPlan.h"
#include "UseTheForce/DarkSide/simParallel_interface.h"
#endif 

namespace oopse {
  std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
    std::map<int, std::set<int> >::iterator i = container.find(index);
    std::set<int> result;
    if (i != container.end()) {
        result = i->second;
    }

    return result;
  }
  
  SimInfo::SimInfo(ForceField* ff, Globals* simParams) : 
    forceField_(ff), simParams_(simParams), 
    ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
    nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), 
    nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
    nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0), 
    nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0), 
    nConstraints_(0), sman_(NULL), fortranInitialized_(false), 
    calcBoxDipole_(false), useAtomicVirial_(true) {


      MoleculeStamp* molStamp;
      int nMolWithSameStamp;
      int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
      int nGroups = 0;      //total cutoff groups defined in meta-data file
      CutoffGroupStamp* cgStamp;    
      RigidBodyStamp* rbStamp;
      int nRigidAtoms = 0;

      std::vector<Component*> components = simParams->getComponents();
      
      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
        molStamp = (*i)->getMoleculeStamp();
        nMolWithSameStamp = (*i)->getNMol();
        
        addMoleculeStamp(molStamp, nMolWithSameStamp);

        //calculate atoms in molecules
        nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;   

        //calculate atoms in cutoff groups
        int nAtomsInGroups = 0;
        int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
        
        for (int j=0; j < nCutoffGroupsInStamp; j++) {
          cgStamp = molStamp->getCutoffGroupStamp(j);
          nAtomsInGroups += cgStamp->getNMembers();
        }

        nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;

        nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            

        //calculate atoms in rigid bodies
        int nAtomsInRigidBodies = 0;
        int nRigidBodiesInStamp = molStamp->getNRigidBodies();
        
        for (int j=0; j < nRigidBodiesInStamp; j++) {
          rbStamp = molStamp->getRigidBodyStamp(j);
          nAtomsInRigidBodies += rbStamp->getNMembers();
        }

        nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
        nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;            
        
      }

      //every free atom (atom does not belong to cutoff groups) is a cutoff 
      //group therefore the total number of cutoff groups in the system is 
      //equal to the total number of atoms minus number of atoms belong to 
      //cutoff group defined in meta-data file plus the number of cutoff 
      //groups defined in meta-data file
      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;

      //every free atom (atom does not belong to rigid bodies) is an 
      //integrable object therefore the total number of integrable objects 
      //in the system is equal to the total number of atoms minus number of 
      //atoms belong to rigid body defined in meta-data file plus the number 
      //of rigid bodies defined in meta-data file
      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms 
                                                + nGlobalRigidBodies_;
  
      nGlobalMols_ = molStampIds_.size();
      molToProcMap_.resize(nGlobalMols_);
    }

  SimInfo::~SimInfo() {
    std::map<int, Molecule*>::iterator i;
    for (i = molecules_.begin(); i != molecules_.end(); ++i) {
      delete i->second;
    }
    molecules_.clear();
       
    delete sman_;
    delete simParams_;
    delete forceField_;
  }

  int SimInfo::getNGlobalConstraints() {
    int nGlobalConstraints;
#ifdef IS_MPI
    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
                  MPI_COMM_WORLD);    
#else
    nGlobalConstraints =  nConstraints_;
#endif
    return nGlobalConstraints;
  }

  bool SimInfo::addMolecule(Molecule* mol) {
    MoleculeIterator i;

    i = molecules_.find(mol->getGlobalIndex());
    if (i == molecules_.end() ) {

      molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
        
      nAtoms_ += mol->getNAtoms();
      nBonds_ += mol->getNBonds();
      nBends_ += mol->getNBends();
      nTorsions_ += mol->getNTorsions();
      nInversions_ += mol->getNInversions();
      nRigidBodies_ += mol->getNRigidBodies();
      nIntegrableObjects_ += mol->getNIntegrableObjects();
      nCutoffGroups_ += mol->getNCutoffGroups();
      nConstraints_ += mol->getNConstraintPairs();

      addExcludePairs(mol);
        
      return true;
    } else {
      return false;
    }
  }

  bool SimInfo::removeMolecule(Molecule* mol) {
    MoleculeIterator i;
    i = molecules_.find(mol->getGlobalIndex());

    if (i != molecules_.end() ) {

      assert(mol == i->second);
        
      nAtoms_ -= mol->getNAtoms();
      nBonds_ -= mol->getNBonds();
      nBends_ -= mol->getNBends();
      nTorsions_ -= mol->getNTorsions();
      nInversions_ -= mol->getNInversions();
      nRigidBodies_ -= mol->getNRigidBodies();
      nIntegrableObjects_ -= mol->getNIntegrableObjects();
      nCutoffGroups_ -= mol->getNCutoffGroups();
      nConstraints_ -= mol->getNConstraintPairs();

      removeExcludePairs(mol);
      molecules_.erase(mol->getGlobalIndex());

      delete mol;
        
      return true;
    } else {
      return false;
    }


  }    

        
  Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
    i = molecules_.begin();
    return i == molecules_.end() ? NULL : i->second;
  }    

  Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
    ++i;
    return i == molecules_.end() ? NULL : i->second;    
  }


  void SimInfo::calcNdf() {
    int ndf_local;
    MoleculeIterator i;
    std::vector<StuntDouble*>::iterator j;
    Molecule* mol;
    StuntDouble* integrableObject;

    ndf_local = 0;
    
    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; 
           integrableObject = mol->nextIntegrableObject(j)) {

        ndf_local += 3;

        if (integrableObject->isDirectional()) {
          if (integrableObject->isLinear()) {
            ndf_local += 2;
          } else {
            ndf_local += 3;
          }
        }
            
      }
    }
    
    // n_constraints is local, so subtract them on each processor
    ndf_local -= nConstraints_;

#ifdef IS_MPI
    MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
#else
    ndf_ = ndf_local;
#endif

    // nZconstraints_ is global, as are the 3 COM translations for the 
    // entire system:
    ndf_ = ndf_ - 3 - nZconstraint_;

  }

  int SimInfo::getFdf() {
#ifdef IS_MPI
    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
#else
    fdf_ = fdf_local;
#endif
    return fdf_;
  }
    
  void SimInfo::calcNdfRaw() {
    int ndfRaw_local;

    MoleculeIterator i;
    std::vector<StuntDouble*>::iterator j;
    Molecule* mol;
    StuntDouble* integrableObject;

    // Raw degrees of freedom that we have to set
    ndfRaw_local = 0;
    
    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j)) {

        ndfRaw_local += 3;

        if (integrableObject->isDirectional()) {
          if (integrableObject->isLinear()) {
            ndfRaw_local += 2;
          } else {
            ndfRaw_local += 3;
          }
        }
            
      }
    }
    
#ifdef IS_MPI
    MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
#else
    ndfRaw_ = ndfRaw_local;
#endif
  }

  void SimInfo::calcNdfTrans() {
    int ndfTrans_local;

    ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;


#ifdef IS_MPI
    MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
#else
    ndfTrans_ = ndfTrans_local;
#endif

    ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
 
  }

  void SimInfo::addExcludePairs(Molecule* mol) {
    std::vector<Bond*>::iterator bondIter;
    std::vector<Bend*>::iterator bendIter;
    std::vector<Torsion*>::iterator torsionIter;
    std::vector<Inversion*>::iterator inversionIter;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    Inversion* inversion;
    int a;
    int b;
    int c;
    int d;

    std::map<int, std::set<int> > atomGroups;

    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;
    Molecule::IntegrableObjectIterator ii;
    StuntDouble* integrableObject;
    
    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(ii)) {

      if (integrableObject->isRigidBody()) {
          rb = static_cast<RigidBody*>(integrableObject);
          std::vector<Atom*> atoms = rb->getAtoms();
          std::set<int> rigidAtoms;
          for (int i = 0; i < atoms.size(); ++i) {
            rigidAtoms.insert(atoms[i]->getGlobalIndex());
          }
          for (int i = 0; i < atoms.size(); ++i) {
            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
          }      
      } else {
        std::set<int> oneAtomSet;
        oneAtomSet.insert(integrableObject->getGlobalIndex());
        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
      }
    }  

    
    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
      a = bond->getAtomA()->getGlobalIndex();
      b = bond->getAtomB()->getGlobalIndex();        
      exclude_.addPair(a, b);
    }

    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
      a = bend->getAtomA()->getGlobalIndex();
      b = bend->getAtomB()->getGlobalIndex();        
      c = bend->getAtomC()->getGlobalIndex();
      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
      std::set<int> rigidSetC = getRigidSet(c, atomGroups);

      exclude_.addPairs(rigidSetA, rigidSetB);
      exclude_.addPairs(rigidSetA, rigidSetC);
      exclude_.addPairs(rigidSetB, rigidSetC);
      
      //exclude_.addPair(a, b);
      //exclude_.addPair(a, c);
      //exclude_.addPair(b, c);        
    }

    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
      a = torsion->getAtomA()->getGlobalIndex();
      b = torsion->getAtomB()->getGlobalIndex();        
      c = torsion->getAtomC()->getGlobalIndex();        
      d = torsion->getAtomD()->getGlobalIndex();        
      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
      std::set<int> rigidSetD = getRigidSet(d, atomGroups);

      exclude_.addPairs(rigidSetA, rigidSetB);
      exclude_.addPairs(rigidSetA, rigidSetC);
      exclude_.addPairs(rigidSetA, rigidSetD);
      exclude_.addPairs(rigidSetB, rigidSetC);
      exclude_.addPairs(rigidSetB, rigidSetD);
      exclude_.addPairs(rigidSetC, rigidSetD);

      /*
      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
         
      
      exclude_.addPair(a, b);
      exclude_.addPair(a, c);
      exclude_.addPair(a, d);
      exclude_.addPair(b, c);
      exclude_.addPair(b, d);
      exclude_.addPair(c, d);        
      */
    }

    for (inversion= mol->beginInversion(inversionIter); inversion != NULL; 
         inversion = mol->nextInversion(inversionIter)) {
      a = inversion->getAtomA()->getGlobalIndex();
      b = inversion->getAtomB()->getGlobalIndex();        
      c = inversion->getAtomC()->getGlobalIndex();        
      d = inversion->getAtomD()->getGlobalIndex();        
      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
      std::set<int> rigidSetD = getRigidSet(d, atomGroups);

      exclude_.addPairs(rigidSetA, rigidSetB);
      exclude_.addPairs(rigidSetA, rigidSetC);
      exclude_.addPairs(rigidSetA, rigidSetD);
      exclude_.addPairs(rigidSetB, rigidSetC);
      exclude_.addPairs(rigidSetB, rigidSetD);
      exclude_.addPairs(rigidSetC, rigidSetD);

      /*
      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
         
      
      exclude_.addPair(a, b);
      exclude_.addPair(a, c);
      exclude_.addPair(a, d);
      exclude_.addPair(b, c);
      exclude_.addPair(b, d);
      exclude_.addPair(c, d);        
      */
    }

    for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
      std::vector<Atom*> atoms = rb->getAtoms();
      for (int i = 0; i < atoms.size() -1 ; ++i) {
        for (int j = i + 1; j < atoms.size(); ++j) {
          a = atoms[i]->getGlobalIndex();
          b = atoms[j]->getGlobalIndex();
          exclude_.addPair(a, b);
        }
      }
    }        

  }

  void SimInfo::removeExcludePairs(Molecule* mol) {
    std::vector<Bond*>::iterator bondIter;
    std::vector<Bend*>::iterator bendIter;
    std::vector<Torsion*>::iterator torsionIter;
    std::vector<Inversion*>::iterator inversionIter;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    Inversion* inversion;
    int a;
    int b;
    int c;
    int d;

    std::map<int, std::set<int> > atomGroups;

    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;
    Molecule::IntegrableObjectIterator ii;
    StuntDouble* integrableObject;
    
    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(ii)) {

      if (integrableObject->isRigidBody()) {
          rb = static_cast<RigidBody*>(integrableObject);
          std::vector<Atom*> atoms = rb->getAtoms();
          std::set<int> rigidAtoms;
          for (int i = 0; i < atoms.size(); ++i) {
            rigidAtoms.insert(atoms[i]->getGlobalIndex());
          }
          for (int i = 0; i < atoms.size(); ++i) {
            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
          }      
      } else {
        std::set<int> oneAtomSet;
        oneAtomSet.insert(integrableObject->getGlobalIndex());
        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
      }
    }  

    
    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
      a = bond->getAtomA()->getGlobalIndex();
      b = bond->getAtomB()->getGlobalIndex();        
      exclude_.removePair(a, b);
    }

    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
      a = bend->getAtomA()->getGlobalIndex();
      b = bend->getAtomB()->getGlobalIndex();        
      c = bend->getAtomC()->getGlobalIndex();

      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
      std::set<int> rigidSetC = getRigidSet(c, atomGroups);

      exclude_.removePairs(rigidSetA, rigidSetB);
      exclude_.removePairs(rigidSetA, rigidSetC);
      exclude_.removePairs(rigidSetB, rigidSetC);
      
      //exclude_.removePair(a, b);
      //exclude_.removePair(a, c);
      //exclude_.removePair(b, c);        
    }

    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
      a = torsion->getAtomA()->getGlobalIndex();
      b = torsion->getAtomB()->getGlobalIndex();        
      c = torsion->getAtomC()->getGlobalIndex();        
      d = torsion->getAtomD()->getGlobalIndex();        

      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
      std::set<int> rigidSetD = getRigidSet(d, atomGroups);

      exclude_.removePairs(rigidSetA, rigidSetB);
      exclude_.removePairs(rigidSetA, rigidSetC);
      exclude_.removePairs(rigidSetA, rigidSetD);
      exclude_.removePairs(rigidSetB, rigidSetC);
      exclude_.removePairs(rigidSetB, rigidSetD);
      exclude_.removePairs(rigidSetC, rigidSetD);

      /*
      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());

      
      exclude_.removePair(a, b);
      exclude_.removePair(a, c);
      exclude_.removePair(a, d);
      exclude_.removePair(b, c);
      exclude_.removePair(b, d);
      exclude_.removePair(c, d);        
      */
    }

    for (inversion= mol->beginInversion(inversionIter); inversion != NULL; inversion = mol->nextInversion(inversionIter)) {
      a = inversion->getAtomA()->getGlobalIndex();
      b = inversion->getAtomB()->getGlobalIndex();        
      c = inversion->getAtomC()->getGlobalIndex();        
      d = inversion->getAtomD()->getGlobalIndex();        

      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
      std::set<int> rigidSetD = getRigidSet(d, atomGroups);

      exclude_.removePairs(rigidSetA, rigidSetB);
      exclude_.removePairs(rigidSetA, rigidSetC);
      exclude_.removePairs(rigidSetA, rigidSetD);
      exclude_.removePairs(rigidSetB, rigidSetC);
      exclude_.removePairs(rigidSetB, rigidSetD);
      exclude_.removePairs(rigidSetC, rigidSetD);

      /*
      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());

      
      exclude_.removePair(a, b);
      exclude_.removePair(a, c);
      exclude_.removePair(a, d);
      exclude_.removePair(b, c);
      exclude_.removePair(b, d);
      exclude_.removePair(c, d);        
      */
    }

    for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
      std::vector<Atom*> atoms = rb->getAtoms();
      for (int i = 0; i < atoms.size() -1 ; ++i) {
        for (int j = i + 1; j < atoms.size(); ++j) {
          a = atoms[i]->getGlobalIndex();
          b = atoms[j]->getGlobalIndex();
          exclude_.removePair(a, b);
        }
      }
    }        

  }


  void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
    int curStampId;

    //index from 0
    curStampId = moleculeStamps_.size();

    moleculeStamps_.push_back(molStamp);
    molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
  }

  void SimInfo::update() {

    setupSimType();

#ifdef IS_MPI
    setupFortranParallel();
#endif

    setupFortranSim();

    //setup fortran force field
    /** @deprecate */    
    int isError = 0;
    
    setupCutoff();
    
    setupElectrostaticSummationMethod( isError );
    setupSwitchingFunction();
    setupAccumulateBoxDipole();

    if(isError){
      sprintf( painCave.errMsg,
               "ForceField error: There was an error initializing the forceField in fortran.\n" );
      painCave.isFatal = 1;
      simError();
    }

    calcNdf();
    calcNdfRaw();
    calcNdfTrans();

    fortranInitialized_ = true;
  }

  std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::AtomIterator ai;
    Atom* atom;
    std::set<AtomType*> atomTypes;

    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {

      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        atomTypes.insert(atom->getAtomType());
      }
        
    }

    return atomTypes;        
  }

  void SimInfo::setupSimType() {
    std::set<AtomType*>::iterator i;
    std::set<AtomType*> atomTypes;
    atomTypes = getUniqueAtomTypes();
    
    int useLennardJones = 0;
    int useElectrostatic = 0;
    int useEAM = 0;
    int useSC = 0;
    int useCharge = 0;
    int useDirectional = 0;
    int useDipole = 0;
    int useGayBerne = 0;
    int useSticky = 0;
    int useStickyPower = 0;
    int useShape = 0; 
    int useFLARB = 0; //it is not in AtomType yet
    int useDirectionalAtom = 0;    
    int useElectrostatics = 0;
    //usePBC and useRF are from simParams
    int usePBC = simParams_->getUsePeriodicBoundaryConditions();
    int useRF;
    int useSF;
    int useSP;
    int useBoxDipole;

    std::string myMethod;

    // set the useRF logical
    useRF = 0;
    useSF = 0;
    useSP = 0;


    if (simParams_->haveElectrostaticSummationMethod()) {
      std::string myMethod = simParams_->getElectrostaticSummationMethod();
      toUpper(myMethod);
      if (myMethod == "REACTION_FIELD"){
        useRF = 1;
      } else if (myMethod == "SHIFTED_FORCE"){
        useSF = 1;
      } else if (myMethod == "SHIFTED_POTENTIAL"){
        useSP = 1;
      }
    }
    
    if (simParams_->haveAccumulateBoxDipole()) 
      if (simParams_->getAccumulateBoxDipole())
        useBoxDipole = 1;

    useAtomicVirial_ = simParams_->getUseAtomicVirial();

    //loop over all of the atom types
    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
      useLennardJones |= (*i)->isLennardJones();
      useElectrostatic |= (*i)->isElectrostatic();
      useEAM |= (*i)->isEAM();
      useSC |= (*i)->isSC();
      useCharge |= (*i)->isCharge();
      useDirectional |= (*i)->isDirectional();
      useDipole |= (*i)->isDipole();
      useGayBerne |= (*i)->isGayBerne();
      useSticky |= (*i)->isSticky();
      useStickyPower |= (*i)->isStickyPower();
      useShape |= (*i)->isShape(); 
    }

    if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
      useDirectionalAtom = 1;
    }

    if (useCharge || useDipole) {
      useElectrostatics = 1;
    }

#ifdef IS_MPI    
    int temp;

    temp = usePBC;
    MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useDirectionalAtom;
    MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useLennardJones;
    MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useElectrostatics;
    MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useCharge;
    MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useDipole;
    MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useSticky;
    MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useStickyPower;
    MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
    
    temp = useGayBerne;
    MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useEAM;
    MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useSC;
    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
    
    temp = useShape;
    MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);   

    temp = useFLARB;
    MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useRF;
    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useSF;
    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);   

    temp = useSP;
    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);

    temp = useBoxDipole;
    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); 

    temp = useAtomicVirial_;
    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); 

#endif

    fInfo_.SIM_uses_PBC = usePBC;    
    fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
    fInfo_.SIM_uses_LennardJones = useLennardJones;
    fInfo_.SIM_uses_Electrostatics = useElectrostatics;    
    fInfo_.SIM_uses_Charges = useCharge;
    fInfo_.SIM_uses_Dipoles = useDipole;
    fInfo_.SIM_uses_Sticky = useSticky;
    fInfo_.SIM_uses_StickyPower = useStickyPower;
    fInfo_.SIM_uses_GayBerne = useGayBerne;
    fInfo_.SIM_uses_EAM = useEAM;
    fInfo_.SIM_uses_SC = useSC;
    fInfo_.SIM_uses_Shapes = useShape;
    fInfo_.SIM_uses_FLARB = useFLARB;
    fInfo_.SIM_uses_RF = useRF;
    fInfo_.SIM_uses_SF = useSF;
    fInfo_.SIM_uses_SP = useSP;
    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
  }

  void SimInfo::setupFortranSim() {
    int isError;
    int nExclude;
    std::vector<int> fortranGlobalGroupMembership;
    
    nExclude = exclude_.getSize();
    isError = 0;

    //globalGroupMembership_ is filled by SimCreator    
    for (int i = 0; i < nGlobalAtoms_; i++) {
      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
    }

    //calculate mass ratio of cutoff group
    std::vector<RealType> mfact;
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::CutoffGroupIterator ci;
    CutoffGroup* cg;
    Molecule::AtomIterator ai;
    Atom* atom;
    RealType totalMass;

    //to avoid memory reallocation, reserve enough space for mfact
    mfact.reserve(getNCutoffGroups());
    
    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {

        totalMass = cg->getMass();
        for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
          // Check for massless groups - set mfact to 1 if true
          if (totalMass != 0)
            mfact.push_back(atom->getMass()/totalMass);
          else
            mfact.push_back( 1.0 );
        }

      }       
    }

    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
    std::vector<int> identArray;

    //to avoid memory reallocation, reserve enough space identArray
    identArray.reserve(getNAtoms());
    
    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        identArray.push_back(atom->getIdent());
      }
    }    

    //fill molMembershipArray
    //molMembershipArray is filled by SimCreator    
    std::vector<int> molMembershipArray(nGlobalAtoms_);
    for (int i = 0; i < nGlobalAtoms_; i++) {
      molMembershipArray[i] = globalMolMembership_[i] + 1;
    }
    
    //setup fortran simulation
    int nGlobalExcludes = 0;
    int* globalExcludes = NULL; 
    int* excludeList = exclude_.getExcludeList();
    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], 
                   &nExclude, excludeList , &nGlobalExcludes, globalExcludes, 
                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_, 
                   &fortranGlobalGroupMembership[0], &isError); 
    
    if( isError ){
      
      sprintf( painCave.errMsg,
               "There was an error setting the simulation information in fortran.\n" );
      painCave.isFatal = 1;
      painCave.severity = OOPSE_ERROR;
      simError();
    }
    
    
    sprintf( checkPointMsg,
             "succesfully sent the simulation information to fortran.\n");
    
    errorCheckPoint();
    
    // Setup number of neighbors in neighbor list if present
    if (simParams_->haveNeighborListNeighbors()) {
      int nlistNeighbors = simParams_->getNeighborListNeighbors();
      setNeighbors(&nlistNeighbors);
    }
   

  }


  void SimInfo::setupFortranParallel() {
#ifdef IS_MPI    
    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
    std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
    std::vector<int> localToGlobalCutoffGroupIndex;
    SimInfo::MoleculeIterator mi;
    Molecule::AtomIterator ai;
    Molecule::CutoffGroupIterator ci;
    Molecule* mol;
    Atom* atom;
    CutoffGroup* cg;
    mpiSimData parallelData;
    int isError;

    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {

      //local index(index in DataStorge) of atom is important
      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
      }

      //local index of cutoff group is trivial, it only depends on the order of travesing
      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
      }        
        
    }

    //fill up mpiSimData struct
    parallelData.nMolGlobal = getNGlobalMolecules();
    parallelData.nMolLocal = getNMolecules();
    parallelData.nAtomsGlobal = getNGlobalAtoms();
    parallelData.nAtomsLocal = getNAtoms();
    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
    parallelData.nGroupsLocal = getNCutoffGroups();
    parallelData.myNode = worldRank;
    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));

    //pass mpiSimData struct and index arrays to fortran
    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
                    &localToGlobalCutoffGroupIndex[0], &isError);

    if (isError) {
      sprintf(painCave.errMsg,
              "mpiRefresh errror: fortran didn't like something we gave it.\n");
      painCave.isFatal = 1;
      simError();
    }

    sprintf(checkPointMsg, " mpiRefresh successful.\n");
    errorCheckPoint();

#endif
  }

  void SimInfo::setupCutoff() {           
    
    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();

    // Check the cutoff policy
    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default

    // Set LJ shifting bools to false
    ljsp_ = false;
    ljsf_ = false;

    std::string myPolicy;
    if (forceFieldOptions_.haveCutoffPolicy()){
      myPolicy = forceFieldOptions_.getCutoffPolicy();
    }else if (simParams_->haveCutoffPolicy()) {
      myPolicy = simParams_->getCutoffPolicy();
    }

    if (!myPolicy.empty()){
      toUpper(myPolicy);
      if (myPolicy == "MIX") {
        cp = MIX_CUTOFF_POLICY;
      } else {
        if (myPolicy == "MAX") {
          cp = MAX_CUTOFF_POLICY;
        } else {
          if (myPolicy == "TRADITIONAL") {            
            cp = TRADITIONAL_CUTOFF_POLICY;
          } else {
            // throw error        
            sprintf( painCave.errMsg,
                     "SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
            painCave.isFatal = 1;
            simError();
          }     
        }           
      }
    }           
    notifyFortranCutoffPolicy(&cp);

    // Check the Skin Thickness for neighborlists
    RealType skin;
    if (simParams_->haveSkinThickness()) {
      skin = simParams_->getSkinThickness();
      notifyFortranSkinThickness(&skin);
    }            
        
    // Check if the cutoff was set explicitly:
    if (simParams_->haveCutoffRadius()) {
      rcut_ = simParams_->getCutoffRadius();
      if (simParams_->haveSwitchingRadius()) {
        rsw_  = simParams_->getSwitchingRadius();
      } else {
        if (fInfo_.SIM_uses_Charges | 
            fInfo_.SIM_uses_Dipoles | 
            fInfo_.SIM_uses_RF) {
          
          rsw_ = 0.85 * rcut_;
          sprintf(painCave.errMsg,
                  "SimCreator Warning: No value was set for the switchingRadius.\n"
                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
        painCave.isFatal = 0;
        simError();
        } else {
          rsw_ = rcut_;
          sprintf(painCave.errMsg,
                  "SimCreator Warning: No value was set for the switchingRadius.\n"
                  "\tOOPSE will use the same value as the cutoffRadius.\n"
                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
          painCave.isFatal = 0;
          simError();
        }
      }

      if (simParams_->haveElectrostaticSummationMethod()) {
        std::string myMethod = simParams_->getElectrostaticSummationMethod();
        toUpper(myMethod);
        
        if (myMethod == "SHIFTED_POTENTIAL") {
          ljsp_ = true;
        } else if (myMethod == "SHIFTED_FORCE") {
          ljsf_ = true;
        }
      }
      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
      
    } else {
      
      // For electrostatic atoms, we'll assume a large safe value:
      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
        sprintf(painCave.errMsg,
                "SimCreator Warning: No value was set for the cutoffRadius.\n"
                "\tOOPSE will use a default value of 15.0 angstroms"
                "\tfor the cutoffRadius.\n");
        painCave.isFatal = 0;
        simError();
        rcut_ = 15.0;
      
        if (simParams_->haveElectrostaticSummationMethod()) {
          std::string myMethod = simParams_->getElectrostaticSummationMethod();
          toUpper(myMethod);
      
      // For the time being, we're tethering the LJ shifted behavior to the
      // electrostaticSummationMethod keyword options
          if (myMethod == "SHIFTED_POTENTIAL") {
            ljsp_ = true;
          } else if (myMethod == "SHIFTED_FORCE") {
            ljsf_ = true;
          }
          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
            if (simParams_->haveSwitchingRadius()){
              sprintf(painCave.errMsg,
                      "SimInfo Warning: A value was set for the switchingRadius\n"
                      "\teven though the electrostaticSummationMethod was\n"
                      "\tset to %s\n", myMethod.c_str());
              painCave.isFatal = 1;
              simError();            
            } 
          }
        }
      
        if (simParams_->haveSwitchingRadius()){
          rsw_ = simParams_->getSwitchingRadius();
        } else {        
          sprintf(painCave.errMsg,
                  "SimCreator Warning: No value was set for switchingRadius.\n"
                  "\tOOPSE will use a default value of\n"
                  "\t0.85 * cutoffRadius for the switchingRadius\n");
          painCave.isFatal = 0;
          simError();
          rsw_ = 0.85 * rcut_;
        }

        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);

      } else {
        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
        // We'll punt and let fortran figure out the cutoffs later.
        
        notifyFortranYouAreOnYourOwn();

      }
    }
  }

  void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
     
    int errorOut;
    int esm =  NONE;
    int sm = UNDAMPED;
    RealType alphaVal;
    RealType dielectric;
    
    errorOut = isError;

    if (simParams_->haveElectrostaticSummationMethod()) {
      std::string myMethod = simParams_->getElectrostaticSummationMethod();
      toUpper(myMethod);
      if (myMethod == "NONE") {
        esm = NONE;
      } else {
        if (myMethod == "SWITCHING_FUNCTION") {
          esm = SWITCHING_FUNCTION;
        } else {
          if (myMethod == "SHIFTED_POTENTIAL") {
            esm = SHIFTED_POTENTIAL;
          } else {
            if (myMethod == "SHIFTED_FORCE") {            
              esm = SHIFTED_FORCE;
            } else {
              if (myMethod == "REACTION_FIELD") {
                esm = REACTION_FIELD;
                dielectric = simParams_->getDielectric();
                if (!simParams_->haveDielectric()) {
                  // throw warning
                  sprintf( painCave.errMsg,
                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
                  painCave.isFatal = 0;
                  simError();
                }
              } else {
                // throw error        
                sprintf( painCave.errMsg,
                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
                         "\t(Input file specified %s .)\n"
                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
                         "\t\"shifted_potential\", \"shifted_force\", or \n"
                         "\t\"reaction_field\".\n", myMethod.c_str() );
                painCave.isFatal = 1;
                simError();
              }     
            }           
          }
        }
      }
    }
    
    if (simParams_->haveElectrostaticScreeningMethod()) {
      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
      toUpper(myScreen);
      if (myScreen == "UNDAMPED") {
        sm = UNDAMPED;
      } else {
        if (myScreen == "DAMPED") {
          sm = DAMPED;
          if (!simParams_->haveDampingAlpha()) {
            // first set a cutoff dependent alpha value
            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
            alphaVal = 0.5125 - rcut_* 0.025;
            // for values rcut > 20.5, alpha is zero
            if (alphaVal < 0) alphaVal = 0;

            // throw warning
            sprintf( painCave.errMsg,
                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
            painCave.isFatal = 0;
            simError();
          } else {
            alphaVal = simParams_->getDampingAlpha();
          }
          
        } else {
          // throw error        
          sprintf( painCave.errMsg,
                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
                   "\t(Input file specified %s .)\n"
                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
                   "or \"damped\".\n", myScreen.c_str() );
          painCave.isFatal = 1;
          simError();
        }
      }
    }
    
    // let's pass some summation method variables to fortran
    setElectrostaticSummationMethod( &esm );
    setFortranElectrostaticMethod( &esm );
    setScreeningMethod( &sm );
    setDampingAlpha( &alphaVal );
    setReactionFieldDielectric( &dielectric );
    initFortranFF( &errorOut );
  }

  void SimInfo::setupSwitchingFunction() {    
    int ft = CUBIC;

    if (simParams_->haveSwitchingFunctionType()) {
      std::string funcType = simParams_->getSwitchingFunctionType();
      toUpper(funcType);
      if (funcType == "CUBIC") {
        ft = CUBIC;
      } else {
        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
          ft = FIFTH_ORDER_POLY;
        } else {
          // throw error        
          sprintf( painCave.errMsg,
                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
          painCave.isFatal = 1;
          simError();
        }           
      }
    }

    // send switching function notification to switcheroo
    setFunctionType(&ft);

  }

  void SimInfo::setupAccumulateBoxDipole() {    

    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
    if ( simParams_->haveAccumulateBoxDipole() ) 
      if ( simParams_->getAccumulateBoxDipole() ) {
        setAccumulateBoxDipole();
        calcBoxDipole_ = true;
      }

  }

  void SimInfo::addProperty(GenericData* genData) {
    properties_.addProperty(genData);  
  }

  void SimInfo::removeProperty(const std::string& propName) {
    properties_.removeProperty(propName);  
  }

  void SimInfo::clearProperties() {
    properties_.clearProperties(); 
  }

  std::vector<std::string> SimInfo::getPropertyNames() {
    return properties_.getPropertyNames();  
  }
      
  std::vector<GenericData*> SimInfo::getProperties() { 
    return properties_.getProperties(); 
  }

  GenericData* SimInfo::getPropertyByName(const std::string& propName) {
    return properties_.getPropertyByName(propName); 
  }

  void SimInfo::setSnapshotManager(SnapshotManager* sman) {
    if (sman_ == sman) {
      return;
    }    
    delete sman_;
    sman_ = sman;

    Molecule* mol;
    RigidBody* rb;
    Atom* atom;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    Molecule::AtomIterator atomIter;;
 
    for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
        
      for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
        atom->setSnapshotManager(sman_);
      }
        
      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
        rb->setSnapshotManager(sman_);
      }
    }    
    
  }

  Vector3d SimInfo::getComVel(){ 
    SimInfo::MoleculeIterator i;
    Molecule* mol;

    Vector3d comVel(0.0);
    RealType totalMass = 0.0;
    
 
    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
      RealType mass = mol->getMass();
      totalMass += mass;
      comVel += mass * mol->getComVel();
    }  

#ifdef IS_MPI
    RealType tmpMass = totalMass;
    Vector3d tmpComVel(comVel);    
    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
#endif

    comVel /= totalMass;

    return comVel;
  }

  Vector3d SimInfo::getCom(){ 
    SimInfo::MoleculeIterator i;
    Molecule* mol;

    Vector3d com(0.0);
    RealType totalMass = 0.0;
     
    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
      RealType mass = mol->getMass();
      totalMass += mass;
      com += mass * mol->getCom();
    }  

#ifdef IS_MPI
    RealType tmpMass = totalMass;
    Vector3d tmpCom(com);    
    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
#endif

    com /= totalMass;

    return com;

  }        

  std::ostream& operator <<(std::ostream& o, SimInfo& info) {

    return o;
  }
   
   
   /* 
   Returns center of mass and center of mass velocity in one function call.
   */
   
   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){ 
      SimInfo::MoleculeIterator i;
      Molecule* mol;
      
    
      RealType totalMass = 0.0;
    

      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
         RealType mass = mol->getMass();
         totalMass += mass;
         com += mass * mol->getCom();
         comVel += mass * mol->getComVel();           
      }  
      
#ifdef IS_MPI
      RealType tmpMass = totalMass;
      Vector3d tmpCom(com);  
      Vector3d tmpComVel(comVel);
      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
#endif
      
      com /= totalMass;
      comVel /= totalMass;
   }        
   
   /* 
   Return intertia tensor for entire system and angular momentum Vector.


       [  Ixx -Ixy  -Ixz ]
  J =| -Iyx  Iyy  -Iyz |
       [ -Izx -Iyz   Izz ]
    */

   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
      
 
      RealType xx = 0.0;
      RealType yy = 0.0;
      RealType zz = 0.0;
      RealType xy = 0.0;
      RealType xz = 0.0;
      RealType yz = 0.0;
      Vector3d com(0.0);
      Vector3d comVel(0.0);
      
      getComAll(com, comVel);
      
      SimInfo::MoleculeIterator i;
      Molecule* mol;
      
      Vector3d thisq(0.0);
      Vector3d thisv(0.0);

      RealType thisMass = 0.0;
     
      
      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
        
         thisq = mol->getCom()-com;
         thisv = mol->getComVel()-comVel;
         thisMass = mol->getMass();
         // Compute moment of intertia coefficients.
         xx += thisq[0]*thisq[0]*thisMass;
         yy += thisq[1]*thisq[1]*thisMass;
         zz += thisq[2]*thisq[2]*thisMass;
         
         // compute products of intertia
         xy += thisq[0]*thisq[1]*thisMass;
         xz += thisq[0]*thisq[2]*thisMass;
         yz += thisq[1]*thisq[2]*thisMass;
            
         angularMomentum += cross( thisq, thisv ) * thisMass;
            
      }  
      
      
      inertiaTensor(0,0) = yy + zz;
      inertiaTensor(0,1) = -xy;
      inertiaTensor(0,2) = -xz;
      inertiaTensor(1,0) = -xy;
      inertiaTensor(1,1) = xx + zz;
      inertiaTensor(1,2) = -yz;
      inertiaTensor(2,0) = -xz;
      inertiaTensor(2,1) = -yz;
      inertiaTensor(2,2) = xx + yy;
      
#ifdef IS_MPI
      Mat3x3d tmpI(inertiaTensor);
      Vector3d tmpAngMom;
      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
#endif
               
      return;
   }

   //Returns the angular momentum of the system
   Vector3d SimInfo::getAngularMomentum(){
      
      Vector3d com(0.0);
      Vector3d comVel(0.0);
      Vector3d angularMomentum(0.0);
      
      getComAll(com,comVel);
      
      SimInfo::MoleculeIterator i;
      Molecule* mol;
      
      Vector3d thisr(0.0);
      Vector3d thisp(0.0);
      
      RealType thisMass;
      
      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {         
        thisMass = mol->getMass(); 
        thisr = mol->getCom()-com;
        thisp = (mol->getComVel()-comVel)*thisMass;
         
        angularMomentum += cross( thisr, thisp );
         
      }  
       
#ifdef IS_MPI
      Vector3d tmpAngMom;
      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
#endif
      
      return angularMomentum;
   }
   
  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
    return IOIndexToIntegrableObject.at(index);
  }
  
  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
    IOIndexToIntegrableObject= v;
  }

  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes 
     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to 
     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
  */
  void SimInfo::getGyrationalVolume(RealType &volume){
    Mat3x3d intTensor;
    RealType det;
    Vector3d dummyAngMom; 
    RealType sysconstants;
    RealType geomCnst;

    geomCnst = 3.0/2.0;
    /* Get the inertial tensor and angular momentum for free*/
    getInertiaTensor(intTensor,dummyAngMom);
    
    det = intTensor.determinant();
    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
    return;
  }

  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
    Mat3x3d intTensor;
    Vector3d dummyAngMom; 
    RealType sysconstants;
    RealType geomCnst;

    geomCnst = 3.0/2.0;
    /* Get the inertial tensor and angular momentum for free*/
    getInertiaTensor(intTensor,dummyAngMom);
    
    detI = intTensor.determinant();
    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
    return;
  }
/*
   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
      assert( v.size() == nAtoms_ + nRigidBodies_);
      sdByGlobalIndex_ = v;
    }

    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
      //assert(index < nAtoms_ + nRigidBodies_);
      return sdByGlobalIndex_.at(index);
    }   
*/   
}//end namespace oopse

Revision:	1277
Committed:	Mon Jul 14 12:35:58 2008 UTC (17 years, 3 months ago) by gezelter
File size:	52437 byte(s)
Log Message:	Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.