MC.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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
  
/**
 * @file MoleculeCreator.cpp
 * @author tlin
 * @date 11/04/2004
 * @version 1.0
 */
 
#include <cassert>
#include <typeinfo>
#include <set>
 
#include "brains/MoleculeCreator.hpp"
#include "primitives/GhostBend.hpp"
#include "primitives/GhostTorsion.hpp"
#include "types/AtomType.hpp"
#include "types/FixedBondType.hpp"
#include "types/BondTypeParser.hpp"
#include "types/BendTypeParser.hpp"
#include "types/TorsionTypeParser.hpp"
#include "types/InversionTypeParser.hpp"
#include "types/UFFAdapter.hpp"
#include "types/HarmonicBondType.hpp"
#include "types/HarmonicBendType.hpp"
#include "utils/simError.h"
#include "utils/StringUtils.hpp"
#include "forcefields/UFF.hpp"
 
namespace OpenMD {
  
  Molecule* MoleculeCreator::createMolecule(ForceField* ff, 
                                            MoleculeStamp *molStamp,
                                            int stampId, int globalIndex, 
                                            LocalIndexManager* localIndexMan) {
    Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName(), 
                                 molStamp->getRegion() );
 
    //create atoms
    Atom* atom;
    AtomStamp* currentAtomStamp;
    int nAtom = molStamp->getNAtoms();
    for (int i = 0; i < nAtom; ++i) {
      currentAtomStamp = molStamp->getAtomStamp(i);
      atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
      mol->addAtom(atom);
    }
 
    //create rigidbodies
    RigidBody* rb;
    RigidBodyStamp * currentRigidBodyStamp;
    int nRigidbodies = molStamp->getNRigidBodies();
 
    for (int i = 0; i < nRigidbodies; ++i) {
      currentRigidBodyStamp = molStamp->getRigidBodyStamp(i);
      rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, 
                           localIndexMan);
      mol->addRigidBody(rb);
    }
    
    //create bonds
    Bond* bond;
    BondStamp* currentBondStamp;
    int nBonds = molStamp->getNBonds();
 
    for (int i = 0; i < nBonds; ++i) {
      currentBondStamp = molStamp->getBondStamp(i);        
      bond = createBond(ff, mol, currentBondStamp, localIndexMan);
      mol->addBond(bond);
    }
 
    //create bends
    Bend* bend;
    BendStamp* currentBendStamp;
    int nBends = molStamp->getNBends();
    for (int i = 0; i < nBends; ++i) {
      currentBendStamp = molStamp->getBendStamp(i);
      bend = createBend(ff, mol, currentBendStamp, localIndexMan);
      mol->addBend(bend);
    }
 
    //create torsions
    Torsion* torsion;
    TorsionStamp* currentTorsionStamp;
    int nTorsions = molStamp->getNTorsions();
    for (int i = 0; i < nTorsions; ++i) {
      currentTorsionStamp = molStamp->getTorsionStamp(i);
      torsion = createTorsion(ff, mol, currentTorsionStamp, localIndexMan);
      mol->addTorsion(torsion);
    }
 
    //create inversions
    Inversion* inversion;
    InversionStamp* currentInversionStamp;
    int nInversions = molStamp->getNInversions();
    for (int i = 0; i < nInversions; ++i) {
      currentInversionStamp = molStamp->getInversionStamp(i);
      inversion = createInversion(ff, mol, currentInversionStamp, 
                                  localIndexMan);
      if (inversion != NULL ) {
        mol->addInversion(inversion);
      }
    }
 
    //create cutoffGroups
    CutoffGroup* cutoffGroup;
    CutoffGroupStamp* currentCutoffGroupStamp;
    int nCutoffGroups = molStamp->getNCutoffGroups();
    for (int i = 0; i < nCutoffGroups; ++i) {
      currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i);
      cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp, 
                                      localIndexMan);
      mol->addCutoffGroup(cutoffGroup);
    }
 
    //every free atom is a cutoff group    
    std::vector<Atom*> freeAtoms;
    std::vector<Atom*>::iterator ai;
    std::vector<Atom*>::iterator fai;
 
    //add all atoms into allAtoms set
    for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) {
      freeAtoms.push_back(atom);
    }
 
    Molecule::CutoffGroupIterator ci;
    CutoffGroup* cg;
    
    for (cg = mol->beginCutoffGroup(ci); cg != NULL; 
         cg = mol->nextCutoffGroup(ci)) {
      
      for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
        //erase the atoms belong to cutoff groups from freeAtoms vector
        freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom),
                        freeAtoms.end());
      }      
    }       
    
    // loop over the free atoms and then create one cutoff group for
    // every single free atom
    
    for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
      cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan);
      mol->addCutoffGroup(cutoffGroup);
    }
 
    //create bonded constraintPairs:
    createConstraintPair(mol);
 
    //create non-bonded constraintPairs
    for (std::size_t i = 0; i < molStamp->getNConstraints(); ++i) {
      ConstraintStamp* cStamp = molStamp->getConstraintStamp(i);
      Atom* atomA;
      Atom* atomB;
      
      atomA = mol->getAtomAt(cStamp->getA());
      atomB = mol->getAtomAt(cStamp->getB());
      assert( atomA && atomB );
      
      bool printConstraintForce = false;
 
      if (cStamp->havePrintConstraintForce()) {
        printConstraintForce = cStamp->getPrintConstraintForce();
      }
 
      if (!cStamp->haveConstrainedDistance()) {
        snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                "Constraint Error: A non-bond constraint was specified\n"
                "\twithout providing a value for the constrainedDistance.\n");
        painCave.isFatal = 1;
        simError();      
      } else {
        RealType distance = cStamp->getConstrainedDistance();
        ConstraintElem* consElemA = new ConstraintElem(atomA);
        ConstraintElem* consElemB = new ConstraintElem(atomB);
        ConstraintPair* cPair = new ConstraintPair(consElemA, consElemB, 
                                                   distance,
                                                   printConstraintForce);
        mol->addConstraintPair(cPair);
      }   
    }
 
    // now create the constraint elements:
 
    createConstraintElem(mol);
    
    // Does this molecule stamp define a total constrained charge value?
    // If so, let the created molecule know about it.
    if (molStamp->haveConstrainTotalCharge() ) {
      mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() );
    }
 
    // The construction of this molecule is finished:
    mol->complete();
    
    return mol;
  }    
 
 
  Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, 
                                    AtomStamp* stamp,
                                    LocalIndexManager* localIndexMan) {
    AtomType * atomType;
    Atom* atom;
 
    atomType =  ff->getAtomType(stamp->getType());
    
    if (atomType == NULL) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH, "Can not find Matching Atom Type for[%s]",
              stamp->getType().c_str());
 
      painCave.isFatal = 1;
      simError();
    }
 
    //below code still have some kind of hard-coding smell
    if (atomType->isDirectional()){
 
      DirectionalAtom* dAtom;
      dAtom = new DirectionalAtom(atomType);
      atom = dAtom;    
    }
    else{
      atom = new Atom(atomType);
    }
 
    atom->setLocalIndex(localIndexMan->getNextAtomIndex());
 
    return atom;
  }
  
  RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, 
                                              Molecule* mol,
                                              RigidBodyStamp* rbStamp, 
                                              LocalIndexManager* localIndexMan){
    Atom* atom;
    int nAtoms;
    Vector3d refCoor;
    AtomStamp* atomStamp;
    
    RigidBody* rb = new RigidBody();
    nAtoms = rbStamp->getNMembers();    
    for (int i = 0; i < nAtoms; ++i) {
      //rbStamp->getMember(i) return the local index of current atom
      //inside the molecule.  It is not the same as local index of
      //atom which is the index of atom at DataStorage class
      atom = mol->getAtomAt(rbStamp->getMemberAt(i));
      atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i));    
      rb->addAtom(atom, atomStamp);
    }
 
    //after all of the atoms are added, we need to calculate the
    //reference coordinates
    rb->calcRefCoords();
 
    //set the local index of this rigid body, global index will be set later
    rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
 
    // The rule for naming a rigidbody is: MoleculeName_RB_Integer
    // The first part is the name of the molecule
    // The second part is always fixed as "RB"
    // The third part is the index of the rigidbody defined in meta-data file
    // For example, Butane_RB_0 is a valid rigid body name of butane molecule
 
    std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10);
    rb->setType(mol->getType() + "_RB_" + s.c_str());
    return rb;
  }    
 
  Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, 
                                    BondStamp* stamp,
                                    LocalIndexManager* localIndexMan) {
    BondTypeParser btParser;        
    BondType* bondType = NULL;
    Atom* atomA;
    Atom* atomB;
    
    atomA = mol->getAtomAt(stamp->getA());
    atomB = mol->getAtomAt(stamp->getB());
    
    assert( atomA && atomB);
 
    if (stamp->hasOverride()) {
      try {
        bondType = btParser.parseTypeAndPars(stamp->getOverrideType(),
                                             stamp->getOverridePars() );
      }
      catch( OpenMDException& e) {
        snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH, "MoleculeCreator Error: %s "
                "for molecule %s\n",
                e.what(), mol->getType().c_str() );
        painCave.isFatal = 1;
        simError();
      }
 
    } else {
      
      bondType = ff->getBondType(atomA->getType(), atomB->getType());
            
      if (bondType == NULL) {
        
        if (ff->getForceFieldOptions().getDelayedParameterCalculation()) {
              
          RealType bondorder = stamp->getBondOrder();
 
          RealType b0 = UFF::calcBondRestLength(bondorder,
                                                atomA->getAtomType(),
                                                atomB->getAtomType() );
 
          RealType kb = UFF::calcBondForceConstant(b0,
                                                   atomA->getAtomType(),
                                                   atomB->getAtomType() );
          
          bondType = new HarmonicBondType(b0, kb);
 
          ff->addBondType(atomA->getType(), atomB->getType(), bondType);
          
        } else {
          
          snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH, "Can not find Matching Bond Type for[%s, %s]",
                  atomA->getType().c_str(),
                  atomB->getType().c_str());
          
          painCave.isFatal = 1;
          simError();
        }
      }
    }
           
    Bond* bond = new Bond(atomA, atomB, bondType);
 
    //set the local index of this bond, the global index will be set later
    bond->setLocalIndex(localIndexMan->getNextBondIndex());
 
    // The rule for naming a bond is: MoleculeName_Bond_Integer
    // The first part is the name of the molecule
    // The second part is always fixed as "Bond"
    // The third part is the index of the bond defined in meta-data file
    // For example, Butane_bond_0 is a valid Bond name in a butane molecule
 
    std::string s = OpenMD_itoa(mol->getNBonds(), 10);
    bond->setName(mol->getType() + "_Bond_" + s.c_str());
    return bond;    
  }    
  
  Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, 
                                    BendStamp* stamp,
                                    LocalIndexManager* localIndexMan) {
    BendTypeParser btParser;
    BendType* bendType = NULL;
    Bend* bend = NULL;
    
    std::vector<int> bendAtoms = stamp->getMembers();
    if (bendAtoms.size() == 3) {
      Atom* atomA = mol->getAtomAt(bendAtoms[0]);
      Atom* atomB = mol->getAtomAt(bendAtoms[1]);
      Atom* atomC = mol->getAtomAt(bendAtoms[2]);
      
      assert( atomA && atomB && atomC );
 
      if (stamp->hasOverride()) {
        
        try {
          bendType = btParser.parseTypeAndPars(stamp->getOverrideType(),
                                               stamp->getOverridePars() );
        }
        catch( OpenMDException& e) {
          snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH, "MoleculeCreator Error: %s "
                  "for molecule %s\n",
                  e.what(), mol->getType().c_str() );
          painCave.isFatal = 1;
          simError();
        }
      } else {
        
        bendType = ff->getBendType(atomA->getType().c_str(), 
                                   atomB->getType().c_str(), 
                                   atomC->getType().c_str());
      
        if (bendType == NULL) {
          
          if (ff->getForceFieldOptions().getDelayedParameterCalculation()) {
            UFFAdapter uffj = UFFAdapter(atomB->getAtomType());
            RealType theta0 = uffj.getTheta0() * Constants::PI / 180.0;
 
 
            RealType bo12 = 
            RealType ktheta  = UFF:calcAngleForceConstant(theta0, bo12, bo23,
                                                          atomA->getAtomType(),
                                                          atomB->getAtomType(),
                                                          atomC->getAtomType());
            bendType = new HarmonicBendType(theta0, ktheta);
            
            ff->addBendType(atomA->getType(), atomB->getType(),
                            atomC->getType(), bendType);
            
          } else {
            
            snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH, 
                    "Can not find Matching Bend Type for[%s, %s, %s]",
                    atomA->getType().c_str(),
                    atomB->getType().c_str(),
                    atomC->getType().c_str());
            
            painCave.isFatal = 1;
            simError();
          }
        }
        
        bend = new Bend(atomA, atomB, atomC, bendType);
        
        
      } else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
        int ghostIndex = stamp->getGhostVectorSource();
        int normalIndex = ghostIndex != bendAtoms[0] ?
          bendAtoms[0] : bendAtoms[1]; 
        Atom* normalAtom = mol->getAtomAt(normalIndex) ;        
        DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
        if (ghostAtom == NULL) {
          snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH, "Can not cast Atom to DirectionalAtom");
          painCave.isFatal = 1;
          simError();
        }
        
        if (stamp->hasOverride()) {
          
          try {
            bendType = btParser.parseTypeAndPars(stamp->getOverrideType(),
                                                 stamp->getOverridePars() );
          }
          catch( OpenMDException& e) {
            snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH, "MoleculeCreator Error: %s "
                    "for molecule %s\n",
                    e.what(), mol->getType().c_str() );
            painCave.isFatal = 1;
            simError();
          }
        } else {
          
          bendType = ff->getBendType(normalAtom->getType(),
                                     ghostAtom->getType(),
                                     "GHOST");
          
          if (bendType == NULL) {
            snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH, 
                    "Can not find Matching Bend Type for[%s, %s, %s]",
                    normalAtom->getType().c_str(),
                    ghostAtom->getType().c_str(),
                    "GHOST");
            
            painCave.isFatal = 1;
            simError();
          }
        }
        
        bend = new GhostBend(normalAtom, ghostAtom, bendType);       
        
      }
    }
    //set the local index of this bend, the global index will be set later
    bend->setLocalIndex(localIndexMan->getNextBendIndex());
    
    // The rule for naming a bend is: MoleculeName_Bend_Integer
    // The first part is the name of the molecule
    // The second part is always fixed as "Bend"
    // The third part is the index of the bend defined in meta-data file
    // For example, Butane_Bend_0 is a valid Bend name in a butane molecule
    
    std::string s = OpenMD_itoa(mol->getNBends(), 10);
    bend->setName(mol->getType() + "_Bend_" + s.c_str());    
    return bend;
  }
 
 
    Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, 
                                            TorsionStamp* stamp,
                                            LocalIndexManager* localIndexMan) {
 
      TorsionTypeParser ttParser;
      TorsionType* torsionType = NULL;
      Torsion* torsion = NULL;
 
      std::vector<int> torsionAtoms = stamp->getMembers();
      if (torsionAtoms.size() < 3) {
        return torsion;
      }
 
      Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
      Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
      Atom* atomC = mol->getAtomAt(torsionAtoms[2]);
 
      if (torsionAtoms.size() == 4) {
        Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
 
        assert(atomA && atomB && atomC && atomD );
 
        if (stamp->hasOverride()) {
        
          try {
            torsionType = ttParser.parseTypeAndPars(stamp->getOverrideType(),
                                                    stamp->getOverridePars() );
          }
          catch( OpenMDException& e) {
            snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH, "MoleculeCreator Error: %s "
                    "for molecule %s\n",
                    e.what(), mol->getType().c_str() );
            painCave.isFatal = 1;
            simError();
          }
        } else {
 
        
          torsionType = ff->getTorsionType(atomA->getType(), 
                                           atomB->getType(), 
                                           atomC->getType(), 
                                           atomD->getType());
          if (torsionType == NULL) {
            snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH, 
                    "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
                    atomA->getType().c_str(),
                    atomB->getType().c_str(),
                    atomC->getType().c_str(),
                    atomD->getType().c_str());
          
            painCave.isFatal = 1;
            simError();
          }
        }
      
        torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);       
      } else {
      
        DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
        if (dAtom == NULL) {
          snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH, "Can not cast Atom to DirectionalAtom");
          painCave.isFatal = 1;
          simError();
        }        
 
        if (stamp->hasOverride()) {
        
          try {
            torsionType = ttParser.parseTypeAndPars(stamp->getOverrideType(),
                                                    stamp->getOverridePars() );
          }
          catch( OpenMDException& e) {
            snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH, "MoleculeCreator Error: %s "
                    "for molecule %s\n",
                    e.what(), mol->getType().c_str() );
            painCave.isFatal = 1;
            simError();
          }
        } else {              
          torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), 
                                           atomC->getType(), "GHOST");
      
          if (torsionType == NULL) {
            snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                    "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
                    atomA->getType().c_str(),
                    atomB->getType().c_str(),
                    atomC->getType().c_str(),
                    "GHOST");
          
            painCave.isFatal = 1;
            simError();
          }
        }
 
        torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);               
      }
 
      //set the local index of this torsion, the global index will be set later
      torsion->setLocalIndex(localIndexMan->getNextTorsionIndex());
    
      // The rule for naming a torsion is: MoleculeName_Torsion_Integer
      // The first part is the name of the molecule
      // The second part is always fixed as "Torsion"
      // The third part is the index of the torsion defined in meta-data file
      // For example, Butane_Torsion_0 is a valid Torsion name in a
      // butane molecule
 
      std::string s = OpenMD_itoa(mol->getNTorsions(), 10);
      torsion->setName(mol->getType() + "_Torsion_" + s.c_str());
      return torsion;
    }    
 
    Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol, 
                                                InversionStamp* stamp,
                                                LocalIndexManager* localIndexMan) {
 
      InversionTypeParser itParser;
      InversionType* inversionType = NULL;
      Inversion* inversion = NULL;
    
      int center = stamp->getCenter();
      std::vector<int> satellites = stamp->getSatellites();
      if (satellites.size() != 3) {
        return inversion;
      }
 
      Atom* atomA = mol->getAtomAt(center);
      Atom* atomB = mol->getAtomAt(satellites[0]);
      Atom* atomC = mol->getAtomAt(satellites[1]);
      Atom* atomD = mol->getAtomAt(satellites[2]);
      
      assert(atomA && atomB && atomC && atomD);
 
      if (stamp->hasOverride()) {
      
        try {
          inversionType = itParser.parseTypeAndPars(stamp->getOverrideType(),
                                                    stamp->getOverridePars() );
        }
        catch( OpenMDException& e) {
          snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH, "MoleculeCreator Error: %s "
                  "for molecule %s\n",
                  e.what(), mol->getType().c_str() );
          painCave.isFatal = 1;
          simError();
        }
      } else {
      
        inversionType = ff->getInversionType(atomA->getType(), 
                                             atomB->getType(), 
                                             atomC->getType(), 
                                             atomD->getType());
      
        if (inversionType == NULL) {
          snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                  "No Matching Inversion Type for[%s, %s, %s, %s]\n"
                  "\t(May not be a problem: not all inversions are parametrized)\n",
                  atomA->getType().c_str(),
                  atomB->getType().c_str(),
                  atomC->getType().c_str(),
                  atomD->getType().c_str());
        
          painCave.isFatal = 0;
          painCave.severity = OPENMD_INFO;
          simError();
        }
      }
      if (inversionType != NULL) {
      
        inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType);
      
        // set the local index of this inversion, the global index will
        // be set later
        inversion->setLocalIndex(localIndexMan->getNextInversionIndex());
      
        // The rule for naming an inversion is: MoleculeName_Inversion_Integer
        // The first part is the name of the molecule
        // The second part is always fixed as "Inversion"
        // The third part is the index of the inversion defined in meta-data file
        // For example, Benzene_Inversion_0 is a valid Inversion name in a
        // Benzene molecule
 
        std::string s = OpenMD_itoa(mol->getNInversions(), 10);
        inversion->setName(mol->getType() + "_Inversion_" + s.c_str());
        return inversion;
      } else {
        return NULL;
      }
    }
  
 
    CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, 
                                                    CutoffGroupStamp* stamp,
                                                    LocalIndexManager* localIndexMan) {
      int nAtoms;
      CutoffGroup* cg;
      Atom* atom;
      cg = new CutoffGroup();
    
      nAtoms = stamp->getNMembers();
      for (int i =0; i < nAtoms; ++i) {
        atom = mol->getAtomAt(stamp->getMemberAt(i));
        assert(atom);
        cg->addAtom(atom);
      }
    
      //set the local index of this cutoffGroup, global index will be set later
      cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
    
      return cg;
    }    
  
    CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom,
                                                    LocalIndexManager* localIndexMan) {
      CutoffGroup* cg;
      cg  = new CutoffGroup();
      cg->addAtom(atom);
 
      //set the local index of this cutoffGroup, global index will be set later
      cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
 
      return cg;
    }
 
    void MoleculeCreator::createConstraintPair(Molecule* mol) {
 
      //add bond constraints
      Molecule::BondIterator bi;
      Bond* bond;
      ConstraintPair* cPair;
 
      for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
        
        BondType* bt = bond->getBondType();
 
        if (typeid(FixedBondType) == typeid(*bt)) {
          FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
 
          ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
          ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());            
          cPair = new ConstraintPair(consElemA, consElemB, 
                                     fbt->getEquilibriumBondLength(), false);
          mol->addConstraintPair(cPair);
        }
      }
 
      //rigidbody -- rigidbody constraint is not support yet
    }
 
    void MoleculeCreator::createConstraintElem(Molecule* mol) {
 
      ConstraintPair* consPair;
      Molecule::ConstraintPairIterator cpi;
      std::set<StuntDouble*> sdSet;
      for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; 
           consPair = mol->nextConstraintPair(cpi)) {
 
        StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();            
        if (sdSet.find(sdA) == sdSet.end()){
          sdSet.insert(sdA);
          mol->addConstraintElem(new ConstraintElem(sdA));
        }
      
        StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();            
        if (sdSet.find(sdB) == sdSet.end()){
          sdSet.insert(sdB);
          mol->addConstraintElem(new ConstraintElem(sdB));
        }      
      }
    }
  }