src/brains/MoleculeCreator.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 "utils/simError.h"
#include "utils/StringUtils.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 (int 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 );
      
      RealType distance;
      bool printConstraintForce = false;

      if (!cStamp->haveConstrainedDistance()) {
        sprintf(painCave.errMsg,
                "Constraint Error: A non-bond constraint was specified\n"
                "\twithout providing a value for the constrainedDistance.\n");
        painCave.isFatal = 1;
        simError();      
      } else {
        distance = cStamp->getConstrainedDistance();
      }

      if (cStamp->havePrintConstraintForce()) {
        printConstraintForce = cStamp->getPrintConstraintForce();
      }
    
      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) {
      sprintf(painCave.errMsg, "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) {
    BondType* bondType;
    Atom* atomA;
    Atom* atomB;
    
    atomA = mol->getAtomAt(stamp->getA());
    atomB = mol->getAtomAt(stamp->getB());
    
    assert( atomA && atomB);
    
    bondType = ff->getBondType(atomA->getType(), atomB->getType());

    if (bondType == NULL) {
      sprintf(painCave.errMsg, "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) {
    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);
      
      BendType* bendType = ff->getBendType(atomA->getType().c_str(), 
                                           atomB->getType().c_str(), 
                                           atomC->getType().c_str());
      
      if (bendType == NULL) {
        sprintf(painCave.errMsg, 
                "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) {
        sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
        painCave.isFatal = 1;
        simError();
      }
                
      BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");

      if (bendType == NULL) {
        sprintf(painCave.errMsg, 
                "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) {

    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);
        
      TorsionType* torsionType = ff->getTorsionType(atomA->getType(), 
                                                    atomB->getType(), 
                                                    atomC->getType(), 
                                                    atomD->getType());
      if (torsionType == NULL) {
        sprintf(painCave.errMsg, 
                "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) {
        sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
        painCave.isFatal = 1;
        simError();
      }        
      
      TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), 
                                                    atomC->getType(), "GHOST");
      
      if (torsionType == NULL) {
        sprintf(painCave.errMsg, "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) {
    
    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);
    
    InversionType* inversionType = ff->getInversionType(atomA->getType(), 
                                                        atomB->getType(), 
                                                        atomC->getType(), 
                                                        atomD->getType());

    if (inversionType == NULL) {
      sprintf(painCave.errMsg, "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();
      return NULL;
    } else {
      
      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;
    }
  }
  

  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));
      }      
    }
  }
}
Revision:	1979
Committed:	Sat Apr 5 20:56:01 2014 UTC (11 years, 6 months ago) by gezelter
File size:	22148 byte(s)
Log Message:	* Changed the stdDev printouts in RNEMD stats to the 95% confidence intervals * Added the ability to specify non-bonded constraints in a molecule * Added the ability to do selection offsets in the pAngle staticProps module
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	/**
44	* @file MoleculeCreator.cpp
45	* @author tlin
46	* @date 11/04/2004
47	* @version 1.0
48	*/
49
50	#include <cassert>
51	#include <typeinfo>
52	#include <set>
53
54	#include "brains/MoleculeCreator.hpp"
55	#include "primitives/GhostBend.hpp"
56	#include "primitives/GhostTorsion.hpp"
57	#include "types/AtomType.hpp"
58	#include "types/FixedBondType.hpp"
59	#include "utils/simError.h"
60	#include "utils/StringUtils.hpp"
61
62	namespace OpenMD {
63
64	Molecule* MoleculeCreator::createMolecule(ForceField* ff,
65	MoleculeStamp *molStamp,
66	int stampId, int globalIndex,
67	LocalIndexManager* localIndexMan) {
68	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName(),
69	molStamp->getRegion() );
70
71	//create atoms
72	Atom* atom;
73	AtomStamp* currentAtomStamp;
74	int nAtom = molStamp->getNAtoms();
75	for (int i = 0; i < nAtom; ++i) {
76	currentAtomStamp = molStamp->getAtomStamp(i);
77	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
78	mol->addAtom(atom);
79	}
80
81	//create rigidbodies
82	RigidBody* rb;
83	RigidBodyStamp * currentRigidBodyStamp;
84	int nRigidbodies = molStamp->getNRigidBodies();
85
86	for (int i = 0; i < nRigidbodies; ++i) {
87	currentRigidBodyStamp = molStamp->getRigidBodyStamp(i);
88	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp,
89	localIndexMan);
90	mol->addRigidBody(rb);
91	}
92
93	//create bonds
94	Bond* bond;
95	BondStamp* currentBondStamp;
96	int nBonds = molStamp->getNBonds();
97
98	for (int i = 0; i < nBonds; ++i) {
99	currentBondStamp = molStamp->getBondStamp(i);
100	bond = createBond(ff, mol, currentBondStamp, localIndexMan);
101	mol->addBond(bond);
102	}
103
104	//create bends
105	Bend* bend;
106	BendStamp* currentBendStamp;
107	int nBends = molStamp->getNBends();
108	for (int i = 0; i < nBends; ++i) {
109	currentBendStamp = molStamp->getBendStamp(i);
110	bend = createBend(ff, mol, currentBendStamp, localIndexMan);
111	mol->addBend(bend);
112	}
113
114	//create torsions
115	Torsion* torsion;
116	TorsionStamp* currentTorsionStamp;
117	int nTorsions = molStamp->getNTorsions();
118	for (int i = 0; i < nTorsions; ++i) {
119	currentTorsionStamp = molStamp->getTorsionStamp(i);
120	torsion = createTorsion(ff, mol, currentTorsionStamp, localIndexMan);
121	mol->addTorsion(torsion);
122	}
123
124	//create inversions
125	Inversion* inversion;
126	InversionStamp* currentInversionStamp;
127	int nInversions = molStamp->getNInversions();
128	for (int i = 0; i < nInversions; ++i) {
129	currentInversionStamp = molStamp->getInversionStamp(i);
130	inversion = createInversion(ff, mol, currentInversionStamp,
131	localIndexMan);
132	if (inversion != NULL ) {
133	mol->addInversion(inversion);
134	}
135	}
136
137	//create cutoffGroups
138	CutoffGroup* cutoffGroup;
139	CutoffGroupStamp* currentCutoffGroupStamp;
140	int nCutoffGroups = molStamp->getNCutoffGroups();
141	for (int i = 0; i < nCutoffGroups; ++i) {
142	currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i);
143	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp,
144	localIndexMan);
145	mol->addCutoffGroup(cutoffGroup);
146	}
147
148	//every free atom is a cutoff group
149	std::vector<Atom*> freeAtoms;
150	std::vector<Atom*>::iterator ai;
151	std::vector<Atom*>::iterator fai;
152
153	//add all atoms into allAtoms set
154	for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) {
155	freeAtoms.push_back(atom);
156	}
157
158	Molecule::CutoffGroupIterator ci;
159	CutoffGroup* cg;
160
161	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
162	cg = mol->nextCutoffGroup(ci)) {
163
164	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
165	//erase the atoms belong to cutoff groups from freeAtoms vector
166	freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom),
167	freeAtoms.end());
168	}
169	}
170
171	// loop over the free atoms and then create one cutoff group for
172	// every single free atom
173
174	for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
175	cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan);
176	mol->addCutoffGroup(cutoffGroup);
177	}
178
179	//create bonded constraintPairs:
180	createConstraintPair(mol);
181
182	//create non-bonded constraintPairs
183	for (int i = 0; i < molStamp->getNConstraints(); ++i) {
184	ConstraintStamp* cStamp = molStamp->getConstraintStamp(i);
185	Atom* atomA;
186	Atom* atomB;
187
188	atomA = mol->getAtomAt(cStamp->getA());
189	atomB = mol->getAtomAt(cStamp->getB());
190	assert( atomA && atomB );
191
192	RealType distance;
193	bool printConstraintForce = false;
194
195	if (!cStamp->haveConstrainedDistance()) {
196	sprintf(painCave.errMsg,
197	"Constraint Error: A non-bond constraint was specified\n"
198	"\twithout providing a value for the constrainedDistance.\n");
199	painCave.isFatal = 1;
200	simError();
201	} else {
202	distance = cStamp->getConstrainedDistance();
203	}
204
205	if (cStamp->havePrintConstraintForce()) {
206	printConstraintForce = cStamp->getPrintConstraintForce();
207	}
208
209	ConstraintElem* consElemA = new ConstraintElem(atomA);
210	ConstraintElem* consElemB = new ConstraintElem(atomB);
211	ConstraintPair* cPair = new ConstraintPair(consElemA, consElemB, distance,
212	printConstraintForce);
213	mol->addConstraintPair(cPair);
214	}
215
216	// now create the constraint elements:
217
218	createConstraintElem(mol);
219
220	// Does this molecule stamp define a total constrained charge value?
221	// If so, let the created molecule know about it.
222
223	if (molStamp->haveConstrainTotalCharge() ) {
224	mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() );
225	}
226
227	//the construction of this molecule is finished
228	mol->complete();
229
230	return mol;
231	}
232
233
234	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol,
235	AtomStamp* stamp,
236	LocalIndexManager* localIndexMan) {
237	AtomType * atomType;
238	Atom* atom;
239
240	atomType = ff->getAtomType(stamp->getType());
241
242	if (atomType == NULL) {
243	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
244	stamp->getType().c_str());
245
246	painCave.isFatal = 1;
247	simError();
248	}
249
250	//below code still have some kind of hard-coding smell
251	if (atomType->isDirectional()){
252
253	DirectionalAtom* dAtom;
254	dAtom = new DirectionalAtom(atomType);
255	atom = dAtom;
256	}
257	else{
258	atom = new Atom(atomType);
259	}
260
261	atom->setLocalIndex(localIndexMan->getNextAtomIndex());
262
263	return atom;
264	}
265
266	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp,
267	Molecule* mol,
268	RigidBodyStamp* rbStamp,
269	LocalIndexManager* localIndexMan){
270	Atom* atom;
271	int nAtoms;
272	Vector3d refCoor;
273	AtomStamp* atomStamp;
274
275	RigidBody* rb = new RigidBody();
276	nAtoms = rbStamp->getNMembers();
277	for (int i = 0; i < nAtoms; ++i) {
278	//rbStamp->getMember(i) return the local index of current atom
279	//inside the molecule. It is not the same as local index of
280	//atom which is the index of atom at DataStorage class
281	atom = mol->getAtomAt(rbStamp->getMemberAt(i));
282	atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i));
283	rb->addAtom(atom, atomStamp);
284	}
285
286	//after all of the atoms are added, we need to calculate the
287	//reference coordinates
288	rb->calcRefCoords();
289
290	//set the local index of this rigid body, global index will be set later
291	rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
292
293	// The rule for naming a rigidbody is: MoleculeName_RB_Integer
294	// The first part is the name of the molecule
295	// The second part is always fixed as "RB"
296	// The third part is the index of the rigidbody defined in meta-data file
297	// For example, Butane_RB_0 is a valid rigid body name of butane molecule
298
299	std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10);
300	rb->setType(mol->getType() + "_RB_" + s.c_str());
301	return rb;
302	}
303
304	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol,
305	BondStamp* stamp,
306	LocalIndexManager* localIndexMan) {
307	BondType* bondType;
308	Atom* atomA;
309	Atom* atomB;
310
311	atomA = mol->getAtomAt(stamp->getA());
312	atomB = mol->getAtomAt(stamp->getB());
313
314	assert( atomA && atomB);
315
316	bondType = ff->getBondType(atomA->getType(), atomB->getType());
317
318	if (bondType == NULL) {
319	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
320	atomA->getType().c_str(),
321	atomB->getType().c_str());
322
323	painCave.isFatal = 1;
324	simError();
325	}
326	Bond* bond = new Bond(atomA, atomB, bondType);
327
328	//set the local index of this bond, the global index will be set later
329	bond->setLocalIndex(localIndexMan->getNextBondIndex());
330
331	// The rule for naming a bond is: MoleculeName_Bond_Integer
332	// The first part is the name of the molecule
333	// The second part is always fixed as "Bond"
334	// The third part is the index of the bond defined in meta-data file
335	// For example, Butane_bond_0 is a valid Bond name in a butane molecule
336
337	std::string s = OpenMD_itoa(mol->getNBonds(), 10);
338	bond->setName(mol->getType() + "_Bond_" + s.c_str());
339	return bond;
340	}
341
342	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol,
343	BendStamp* stamp,
344	LocalIndexManager* localIndexMan) {
345	Bend* bend = NULL;
346	std::vector<int> bendAtoms = stamp->getMembers();
347	if (bendAtoms.size() == 3) {
348	Atom* atomA = mol->getAtomAt(bendAtoms[0]);
349	Atom* atomB = mol->getAtomAt(bendAtoms[1]);
350	Atom* atomC = mol->getAtomAt(bendAtoms[2]);
351
352	assert( atomA && atomB && atomC);
353
354	BendType* bendType = ff->getBendType(atomA->getType().c_str(),
355	atomB->getType().c_str(),
356	atomC->getType().c_str());
357
358	if (bendType == NULL) {
359	sprintf(painCave.errMsg,
360	"Can not find Matching Bend Type for[%s, %s, %s]",
361	atomA->getType().c_str(),
362	atomB->getType().c_str(),
363	atomC->getType().c_str());
364
365	painCave.isFatal = 1;
366	simError();
367	}
368
369	bend = new Bend(atomA, atomB, atomC, bendType);
370	} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
371	int ghostIndex = stamp->getGhostVectorSource();
372	int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1];
373	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
374	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
375	if (ghostAtom == NULL) {
376	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
377	painCave.isFatal = 1;
378	simError();
379	}
380
381	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
382
383	if (bendType == NULL) {
384	sprintf(painCave.errMsg,
385	"Can not find Matching Bend Type for[%s, %s, %s]",
386	normalAtom->getType().c_str(),
387	ghostAtom->getType().c_str(),
388	"GHOST");
389
390	painCave.isFatal = 1;
391	simError();
392	}
393
394	bend = new GhostBend(normalAtom, ghostAtom, bendType);
395
396	}
397
398	//set the local index of this bend, the global index will be set later
399	bend->setLocalIndex(localIndexMan->getNextBendIndex());
400
401	// The rule for naming a bend is: MoleculeName_Bend_Integer
402	// The first part is the name of the molecule
403	// The second part is always fixed as "Bend"
404	// The third part is the index of the bend defined in meta-data file
405	// For example, Butane_Bend_0 is a valid Bend name in a butane molecule
406
407	std::string s = OpenMD_itoa(mol->getNBends(), 10);
408	bend->setName(mol->getType() + "_Bend_" + s.c_str());
409	return bend;
410	}
411
412	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol,
413	TorsionStamp* stamp,
414	LocalIndexManager* localIndexMan) {
415
416	Torsion* torsion = NULL;
417	std::vector<int> torsionAtoms = stamp->getMembers();
418	if (torsionAtoms.size() < 3) {
419	return torsion;
420	}
421
422	Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
423	Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
424	Atom* atomC = mol->getAtomAt(torsionAtoms[2]);
425
426	if (torsionAtoms.size() == 4) {
427	Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
428
429	assert(atomA && atomB && atomC && atomD);
430
431	TorsionType* torsionType = ff->getTorsionType(atomA->getType(),
432	atomB->getType(),
433	atomC->getType(),
434	atomD->getType());
435	if (torsionType == NULL) {
436	sprintf(painCave.errMsg,
437	"Can not find Matching Torsion Type for[%s, %s, %s, %s]",
438	atomA->getType().c_str(),
439	atomB->getType().c_str(),
440	atomC->getType().c_str(),
441	atomD->getType().c_str());
442
443	painCave.isFatal = 1;
444	simError();
445	}
446
447	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
448	}
449	else {
450
451	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
452	if (dAtom == NULL) {
453	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
454	painCave.isFatal = 1;
455	simError();
456	}
457
458	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
459	atomC->getType(), "GHOST");
460
461	if (torsionType == NULL) {
462	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
463	atomA->getType().c_str(),
464	atomB->getType().c_str(),
465	atomC->getType().c_str(),
466	"GHOST");
467
468	painCave.isFatal = 1;
469	simError();
470	}
471
472	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
473	}
474
475	//set the local index of this torsion, the global index will be set later
476	torsion->setLocalIndex(localIndexMan->getNextTorsionIndex());
477
478	// The rule for naming a torsion is: MoleculeName_Torsion_Integer
479	// The first part is the name of the molecule
480	// The second part is always fixed as "Torsion"
481	// The third part is the index of the torsion defined in meta-data file
482	// For example, Butane_Torsion_0 is a valid Torsion name in a
483	// butane molecule
484
485	std::string s = OpenMD_itoa(mol->getNTorsions(), 10);
486	torsion->setName(mol->getType() + "_Torsion_" + s.c_str());
487	return torsion;
488	}
489
490	Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol,
491	InversionStamp* stamp,
492	LocalIndexManager* localIndexMan) {
493
494	Inversion* inversion = NULL;
495	int center = stamp->getCenter();
496	std::vector<int> satellites = stamp->getSatellites();
497	if (satellites.size() != 3) {
498	return inversion;
499	}
500
501	Atom* atomA = mol->getAtomAt(center);
502	Atom* atomB = mol->getAtomAt(satellites[0]);
503	Atom* atomC = mol->getAtomAt(satellites[1]);
504	Atom* atomD = mol->getAtomAt(satellites[2]);
505
506	assert(atomA && atomB && atomC && atomD);
507
508	InversionType* inversionType = ff->getInversionType(atomA->getType(),
509	atomB->getType(),
510	atomC->getType(),
511	atomD->getType());
512
513	if (inversionType == NULL) {
514	sprintf(painCave.errMsg, "No Matching Inversion Type for[%s, %s, %s, %s]\n"
515	"\t(May not be a problem: not all inversions are parametrized)\n",
516	atomA->getType().c_str(),
517	atomB->getType().c_str(),
518	atomC->getType().c_str(),
519	atomD->getType().c_str());
520
521	painCave.isFatal = 0;
522	painCave.severity = OPENMD_INFO;
523	simError();
524	return NULL;
525	} else {
526
527	inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType);
528
529	// set the local index of this inversion, the global index will
530	// be set later
531	inversion->setLocalIndex(localIndexMan->getNextInversionIndex());
532
533	// The rule for naming an inversion is: MoleculeName_Inversion_Integer
534	// The first part is the name of the molecule
535	// The second part is always fixed as "Inversion"
536	// The third part is the index of the inversion defined in meta-data file
537	// For example, Benzene_Inversion_0 is a valid Inversion name in a
538	// Benzene molecule
539
540	std::string s = OpenMD_itoa(mol->getNInversions(), 10);
541	inversion->setName(mol->getType() + "_Inversion_" + s.c_str());
542	return inversion;
543	}
544	}
545
546
547	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol,
548	CutoffGroupStamp* stamp,
549	LocalIndexManager* localIndexMan) {
550	int nAtoms;
551	CutoffGroup* cg;
552	Atom* atom;
553	cg = new CutoffGroup();
554
555	nAtoms = stamp->getNMembers();
556	for (int i =0; i < nAtoms; ++i) {
557	atom = mol->getAtomAt(stamp->getMemberAt(i));
558	assert(atom);
559	cg->addAtom(atom);
560	}
561
562	//set the local index of this cutoffGroup, global index will be set later
563	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
564
565	return cg;
566	}
567
568	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom,
569	LocalIndexManager* localIndexMan) {
570	CutoffGroup* cg;
571	cg = new CutoffGroup();
572	cg->addAtom(atom);
573
574	//set the local index of this cutoffGroup, global index will be set later
575	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
576
577	return cg;
578	}
579
580	void MoleculeCreator::createConstraintPair(Molecule* mol) {
581
582	//add bond constraints
583	Molecule::BondIterator bi;
584	Bond* bond;
585	ConstraintPair* cPair;
586
587	for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
588
589	BondType* bt = bond->getBondType();
590
591	if (typeid(FixedBondType) == typeid(*bt)) {
592	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
593
594	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
595	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
596	cPair = new ConstraintPair(consElemA, consElemB,
597	fbt->getEquilibriumBondLength(), false);
598	mol->addConstraintPair(cPair);
599	}
600	}
601
602	//rigidbody -- rigidbody constraint is not support yet
603	}
604
605	void MoleculeCreator::createConstraintElem(Molecule* mol) {
606
607	ConstraintPair* consPair;
608	Molecule::ConstraintPairIterator cpi;
609	std::set<StuntDouble*> sdSet;
610	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
611	consPair = mol->nextConstraintPair(cpi)) {
612
613	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
614	if (sdSet.find(sdA) == sdSet.end()){
615	sdSet.insert(sdA);
616	mol->addConstraintElem(new ConstraintElem(sdA));
617	}
618
619	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
620	if (sdSet.find(sdB) == sdSet.end()){
621	sdSet.insert(sdB);
622	mol->addConstraintElem(new ConstraintElem(sdB));
623	}
624	}
625	}
626	}