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, 24107 (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
 * @time 13:44am
 * @version 1.0
 */

#include <cassert>
#include <typeinfo>
#include <set>

#include "brains/MoleculeCreator.hpp"
#include "primitives/GhostBend.hpp"
#include "primitives/GhostTorsion.hpp"
#include "types/DirectionalAtomType.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());
    
    //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);
      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);
      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);
      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);
      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 constraints
    createConstraintPair(mol);
    createConstraintElem(mol);
    
    //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()){
     
      DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
        
      if (dAtomType == NULL) {
        sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");

        painCave.isFatal = 1;
        simError();
      }

      DirectionalAtom* dAtom;
      dAtom = new DirectionalAtom(dAtomType);
      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 rigidbody MoleculeName_RB_Integer
    //The first part is the name of the molecule
    //The second part is alway 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
    /**@todo replace itoa by lexi_cast */
    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) {
    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();
    }
    return new Bond(atomA, atomB, bondType);    
  }    
  
  Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, 
                                    BendStamp* stamp) {
    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);       
      
    } 
    
    return bend;
  }    

  Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, 
                                          TorsionStamp* stamp) {

    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);               
    }
    
    return torsion;
  }    

  Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol, 
                                              InversionStamp* stamp) {
    
    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);
      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;
    for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
        
      BondType* bt = bond->getBondType();

      //class Parent1 {};
      //class Child1 : public Parent {};
      //class Child2 : public Parent {};
      //Child1* ch1 = new Child1();
      //Child2* ch2 = dynamic_cast<Child2*>(ch1); 
      //the dynamic_cast is succeed in above line. A compiler bug?        

      if (typeid(FixedBondType) == typeid(*bt)) {
        FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);

        ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
        ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());            
        ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
        mol->addConstraintPair(consPair);
      }
    }

    //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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	18181 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	gezelter	507	/**
44			* @file MoleculeCreator.cpp
45			* @author tlin
46			* @date 11/04/2004
47			* @time 13:44am
48			* @version 1.0
49			*/
50	gezelter	246
51			#include <cassert>
52	gezelter	809	#include <typeinfo>
53	gezelter	246	#include <set>
54
55			#include "brains/MoleculeCreator.hpp"
56			#include "primitives/GhostBend.hpp"
57	tim	273	#include "primitives/GhostTorsion.hpp"
58	gezelter	246	#include "types/DirectionalAtomType.hpp"
59			#include "types/FixedBondType.hpp"
60			#include "utils/simError.h"
61			#include "utils/StringUtils.hpp"
62
63	gezelter	1390	namespace OpenMD {
64	tim	647
65	gezelter	1277	Molecule* MoleculeCreator::createMolecule(ForceField* ff,
66			MoleculeStamp *molStamp,
67			int stampId, int globalIndex,
68			LocalIndexManager* localIndexMan) {
69	tim	770	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName());
70	gezelter	246
71			//create atoms
72			Atom* atom;
73			AtomStamp* currentAtomStamp;
74			int nAtom = molStamp->getNAtoms();
75			for (int i = 0; i < nAtom; ++i) {
76	tim	770	currentAtomStamp = molStamp->getAtomStamp(i);
77	gezelter	507	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
78			mol->addAtom(atom);
79	gezelter	246	}
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	tim	770	currentRigidBodyStamp = molStamp->getRigidBodyStamp(i);
88	gezelter	1277	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp,
89			localIndexMan);
90	gezelter	507	mol->addRigidBody(rb);
91	gezelter	246	}
92	gezelter	1277
93	gezelter	246	//create bonds
94			Bond* bond;
95			BondStamp* currentBondStamp;
96			int nBonds = molStamp->getNBonds();
97
98			for (int i = 0; i < nBonds; ++i) {
99	tim	770	currentBondStamp = molStamp->getBondStamp(i);
100	gezelter	507	bond = createBond(ff, mol, currentBondStamp);
101			mol->addBond(bond);
102	gezelter	246	}
103
104			//create bends
105			Bend* bend;
106			BendStamp* currentBendStamp;
107			int nBends = molStamp->getNBends();
108			for (int i = 0; i < nBends; ++i) {
109	tim	770	currentBendStamp = molStamp->getBendStamp(i);
110	gezelter	507	bend = createBend(ff, mol, currentBendStamp);
111			mol->addBend(bend);
112	gezelter	246	}
113
114			//create torsions
115			Torsion* torsion;
116			TorsionStamp* currentTorsionStamp;
117			int nTorsions = molStamp->getNTorsions();
118			for (int i = 0; i < nTorsions; ++i) {
119	tim	770	currentTorsionStamp = molStamp->getTorsionStamp(i);
120	gezelter	507	torsion = createTorsion(ff, mol, currentTorsionStamp);
121			mol->addTorsion(torsion);
122	gezelter	246	}
123
124	gezelter	1277	//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			if (inversion != NULL ) {
132			mol->addInversion(inversion);
133			}
134			}
135
136	gezelter	246	//create cutoffGroups
137			CutoffGroup* cutoffGroup;
138			CutoffGroupStamp* currentCutoffGroupStamp;
139			int nCutoffGroups = molStamp->getNCutoffGroups();
140			for (int i = 0; i < nCutoffGroups; ++i) {
141	tim	770	currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i);
142	gezelter	1540	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp, localIndexMan);
143	gezelter	507	mol->addCutoffGroup(cutoffGroup);
144	gezelter	246	}
145
146			//every free atom is a cutoff group
147	tim	647	std::vector<Atom*> freeAtoms;
148			std::vector<Atom*>::iterator ai;
149			std::vector<Atom*>::iterator fai;
150	gezelter	246
151			//add all atoms into allAtoms set
152	tim	647	for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) {
153			freeAtoms.push_back(atom);
154	gezelter	246	}
155
156			Molecule::CutoffGroupIterator ci;
157			CutoffGroup* cg;
158
159	gezelter	1277	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
160			cg = mol->nextCutoffGroup(ci)) {
161
162	gezelter	507	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
163	gezelter	1277	//erase the atoms belong to cutoff groups from freeAtoms vector
164			freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom),
165			freeAtoms.end());
166			}
167	gezelter	246	}
168
169	gezelter	1277	// loop over the free atoms and then create one cutoff group for
170			// every single free atom
171	tim	647
172	gezelter	246	for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
173	gezelter	1540	cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan);
174	gezelter	507	mol->addCutoffGroup(cutoffGroup);
175	gezelter	246	}
176			//create constraints
177			createConstraintPair(mol);
178			createConstraintElem(mol);
179
180			//the construction of this molecule is finished
181			mol->complete();
182	gezelter	1277
183	gezelter	246	return mol;
184	gezelter	507	}
185	gezelter	246
186
187	gezelter	1277	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol,
188			AtomStamp* stamp,
189			LocalIndexManager* localIndexMan) {
190	gezelter	246	AtomType * atomType;
191			Atom* atom;
192
193			atomType = ff->getAtomType(stamp->getType());
194	gezelter	1277
195	gezelter	246	if (atomType == NULL) {
196	gezelter	507	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
197	tim	770	stamp->getType().c_str());
198	gezelter	246
199	gezelter	507	painCave.isFatal = 1;
200			simError();
201	gezelter	246	}
202
203			//below code still have some kind of hard-coding smell
204			if (atomType->isDirectional()){
205
206	gezelter	507	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
207	gezelter	246
208	gezelter	507	if (dAtomType == NULL) {
209			sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
210	gezelter	246
211	gezelter	507	painCave.isFatal = 1;
212			simError();
213			}
214	gezelter	246
215	gezelter	507	DirectionalAtom* dAtom;
216			dAtom = new DirectionalAtom(dAtomType);
217			atom = dAtom;
218	gezelter	246	}
219			else{
220	gezelter	507	atom = new Atom(atomType);
221	gezelter	246	}
222
223			atom->setLocalIndex(localIndexMan->getNextAtomIndex());
224
225			return atom;
226	gezelter	507	}
227	gezelter	1277
228			RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp,
229			Molecule* mol,
230	gezelter	507	RigidBodyStamp* rbStamp,
231			LocalIndexManager* localIndexMan) {
232	gezelter	246	Atom* atom;
233			int nAtoms;
234			Vector3d refCoor;
235			AtomStamp* atomStamp;
236
237			RigidBody* rb = new RigidBody();
238			nAtoms = rbStamp->getNMembers();
239			for (int i = 0; i < nAtoms; ++i) {
240	gezelter	1277	//rbStamp->getMember(i) return the local index of current atom
241			//inside the molecule. It is not the same as local index of
242			//atom which is the index of atom at DataStorage class
243	tim	770	atom = mol->getAtomAt(rbStamp->getMemberAt(i));
244			atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i));
245	gezelter	507	rb->addAtom(atom, atomStamp);
246	gezelter	246	}
247
248	gezelter	1277	//after all of the atoms are added, we need to calculate the
249			//reference coordinates
250	gezelter	246	rb->calcRefCoords();
251
252			//set the local index of this rigid body, global index will be set later
253			rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
254
255			//the rule for naming rigidbody MoleculeName_RB_Integer
256			//The first part is the name of the molecule
257			//The second part is alway fixed as "RB"
258			//The third part is the index of the rigidbody defined in meta-data file
259			//For example, Butane_RB_0 is a valid rigid body name of butane molecule
260			/*@todo replace itoa by lexi_cast /
261	gezelter	1390	std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10);
262	gezelter	403	rb->setType(mol->getType() + "_RB_" + s.c_str());
263	tim	292
264	gezelter	246	return rb;
265	gezelter	507	}
266	gezelter	246
267	gezelter	1277	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol,
268			BondStamp* stamp) {
269	gezelter	246	BondType* bondType;
270			Atom* atomA;
271			Atom* atomB;
272	gezelter	1277
273	gezelter	246	atomA = mol->getAtomAt(stamp->getA());
274			atomB = mol->getAtomAt(stamp->getB());
275	gezelter	1277
276	gezelter	246	assert( atomA && atomB);
277
278			bondType = ff->getBondType(atomA->getType(), atomB->getType());
279
280			if (bondType == NULL) {
281	gezelter	507	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
282			atomA->getType().c_str(),
283			atomB->getType().c_str());
284	gezelter	1277
285	gezelter	507	painCave.isFatal = 1;
286			simError();
287	gezelter	246	}
288			return new Bond(atomA, atomB, bondType);
289	gezelter	507	}
290	gezelter	1277
291			Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol,
292			BendStamp* stamp) {
293	tim	770	Bend* bend = NULL;
294			std::vector<int> bendAtoms = stamp->getMembers();
295			if (bendAtoms.size() == 3) {
296			Atom* atomA = mol->getAtomAt(bendAtoms[0]);
297			Atom* atomB = mol->getAtomAt(bendAtoms[1]);
298			Atom* atomC = mol->getAtomAt(bendAtoms[2]);
299	gezelter	1277
300	tim	770	assert( atomA && atomB && atomC);
301	gezelter	1277
302			BendType* bendType = ff->getBendType(atomA->getType().c_str(),
303			atomB->getType().c_str(),
304			atomC->getType().c_str());
305
306	tim	770	if (bendType == NULL) {
307			sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
308			atomA->getType().c_str(),
309			atomB->getType().c_str(),
310			atomC->getType().c_str());
311	gezelter	1277
312	tim	770	painCave.isFatal = 1;
313			simError();
314	gezelter	507	}
315	gezelter	1277
316	tim	770	bend = new Bend(atomA, atomB, atomC, bendType);
317			} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
318			int ghostIndex = stamp->getGhostVectorSource();
319			int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1];
320	gezelter	507	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
321			DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
322			if (ghostAtom == NULL) {
323			sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
324			painCave.isFatal = 1;
325			simError();
326			}
327	gezelter	246
328	gezelter	507	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
329	gezelter	246
330	gezelter	507	if (bendType == NULL) {
331			sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
332			normalAtom->getType().c_str(),
333			ghostAtom->getType().c_str(),
334			"GHOST");
335	gezelter	246
336	gezelter	507	painCave.isFatal = 1;
337			simError();
338			}
339	gezelter	1277
340	tim	770	bend = new GhostBend(normalAtom, ghostAtom, bendType);
341	gezelter	1277
342	tim	770	}
343
344			return bend;
345			}
346	gezelter	246
347	gezelter	1277	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol,
348			TorsionStamp* stamp) {
349	gezelter	246
350	tim	770	Torsion* torsion = NULL;
351			std::vector<int> torsionAtoms = stamp->getMembers();
352			if (torsionAtoms.size() < 3) {
353			return torsion;
354	gezelter	246	}
355
356	tim	770	Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
357			Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
358			Atom* atomC = mol->getAtomAt(torsionAtoms[2]);
359	gezelter	246
360	tim	770	if (torsionAtoms.size() == 4) {
361			Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
362	gezelter	246
363	gezelter	507	assert(atomA && atomB && atomC && atomD);
364	tim	273
365	gezelter	1277	TorsionType* torsionType = ff->getTorsionType(atomA->getType(),
366			atomB->getType(),
367			atomC->getType(),
368			atomD->getType());
369	gezelter	507	if (torsionType == NULL) {
370			sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
371			atomA->getType().c_str(),
372			atomB->getType().c_str(),
373			atomC->getType().c_str(),
374			atomD->getType().c_str());
375	gezelter	1277
376	gezelter	507	painCave.isFatal = 1;
377			simError();
378			}
379	gezelter	1277
380	gezelter	507	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
381	gezelter	246	}
382	tim	273	else {
383	gezelter	1277
384	tim	770	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
385	gezelter	507	if (dAtom == NULL) {
386			sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
387			painCave.isFatal = 1;
388			simError();
389			}
390	gezelter	1277
391	gezelter	507	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
392			atomC->getType(), "GHOST");
393	gezelter	1277
394	gezelter	507	if (torsionType == NULL) {
395			sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
396			atomA->getType().c_str(),
397			atomB->getType().c_str(),
398			atomC->getType().c_str(),
399			"GHOST");
400	gezelter	1277
401	gezelter	507	painCave.isFatal = 1;
402			simError();
403			}
404	gezelter	1277
405	gezelter	507	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
406	tim	273	}
407	gezelter	1277
408	tim	273	return torsion;
409	gezelter	507	}
410	gezelter	246
411	gezelter	1277	Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol,
412			InversionStamp* stamp) {
413
414			Inversion* inversion = NULL;
415			int center = stamp->getCenter();
416			std::vector<int> satellites = stamp->getSatellites();
417			if (satellites.size() != 3) {
418			return inversion;
419			}
420
421			Atom* atomA = mol->getAtomAt(center);
422			Atom* atomB = mol->getAtomAt(satellites[0]);
423			Atom* atomC = mol->getAtomAt(satellites[1]);
424			Atom* atomD = mol->getAtomAt(satellites[2]);
425
426			assert(atomA && atomB && atomC && atomD);
427
428			InversionType* inversionType = ff->getInversionType(atomA->getType(),
429			atomB->getType(),
430			atomC->getType(),
431			atomD->getType());
432
433			if (inversionType == NULL) {
434			sprintf(painCave.errMsg, "No Matching Inversion Type for[%s, %s, %s, %s]\n"
435			"\t(May not be a problem: not all inversions are parametrized)\n",
436			atomA->getType().c_str(),
437			atomB->getType().c_str(),
438			atomC->getType().c_str(),
439			atomD->getType().c_str());
440
441			painCave.isFatal = 0;
442	gezelter	1390	painCave.severity = OPENMD_INFO;
443	gezelter	1277	simError();
444			return NULL;
445			} else {
446
447			inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType);
448			return inversion;
449			}
450			}
451
452
453	gezelter	1540	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol,
454			CutoffGroupStamp* stamp,
455			LocalIndexManager* localIndexMan) {
456	gezelter	246	int nAtoms;
457			CutoffGroup* cg;
458			Atom* atom;
459			cg = new CutoffGroup();
460
461			nAtoms = stamp->getNMembers();
462			for (int i =0; i < nAtoms; ++i) {
463	tim	770	atom = mol->getAtomAt(stamp->getMemberAt(i));
464	gezelter	507	assert(atom);
465			cg->addAtom(atom);
466	gezelter	246	}
467	gezelter	1540
468			//set the local index of this cutoffGroup, global index will be set later
469			cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
470
471	gezelter	246	return cg;
472	gezelter	507	}
473	gezelter	1540
474			CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom,
475			LocalIndexManager* localIndexMan) {
476	gezelter	246	CutoffGroup* cg;
477			cg = new CutoffGroup();
478			cg->addAtom(atom);
479	gezelter	1540
480			//set the local index of this cutoffGroup, global index will be set later
481			cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
482
483	gezelter	246	return cg;
484	gezelter	507	}
485	gezelter	246
486	gezelter	507	void MoleculeCreator::createConstraintPair(Molecule* mol) {
487	gezelter	246
488			//add bond constraints
489			Molecule::BondIterator bi;
490			Bond* bond;
491			for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
492
493	gezelter	507	BondType* bt = bond->getBondType();
494	gezelter	246
495	gezelter	507	//class Parent1 {};
496			//class Child1 : public Parent {};
497			//class Child2 : public Parent {};
498			//Child1* ch1 = new Child1();
499			//Child2* ch2 = dynamic_cast<Child2*>(ch1);
500			//the dynamic_cast is succeed in above line. A compiler bug?
501	gezelter	246
502	gezelter	507	if (typeid(FixedBondType) == typeid(*bt)) {
503			FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
504	gezelter	246
505	gezelter	507	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
506			ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
507			ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
508			mol->addConstraintPair(consPair);
509			}
510	gezelter	246	}
511
512			//rigidbody -- rigidbody constraint is not support yet
513	gezelter	507	}
514	gezelter	246
515	gezelter	507	void MoleculeCreator::createConstraintElem(Molecule* mol) {
516	gezelter	246
517			ConstraintPair* consPair;
518			Molecule::ConstraintPairIterator cpi;
519			std::set<StuntDouble*> sdSet;
520			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
521
522	gezelter	507	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
523			if (sdSet.find(sdA) == sdSet.end()){
524			sdSet.insert(sdA);
525			mol->addConstraintElem(new ConstraintElem(sdA));
526			}
527	gezelter	246
528	gezelter	507	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
529			if (sdSet.find(sdB) == sdSet.end()){
530			sdSet.insert(sdB);
531			mol->addConstraintElem(new ConstraintElem(sdB));
532			}
533	gezelter	246
534			}
535
536	gezelter	507	}
537	gezelter	246
538			}