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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
  
 /**
  * @file MoleculeCreator.cpp
  * @author tlin
  * @date 11/04/2004
  * @time 13:44am
  * @version 1.0
  */

#include <cassert>
#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 oopse {

Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
    int stampId, int globalIndex, LocalIndexManager* localIndexMan) {

    Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
    
    //create atoms
    Atom* atom;
    AtomStamp* currentAtomStamp;
    int nAtom = molStamp->getNAtoms();
    for (int i = 0; i < nAtom; ++i) {
        currentAtomStamp = molStamp->getAtom(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->getRigidBody(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->getBond(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->getBend(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->getTorsion(i);
        torsion = createTorsion(ff, mol, currentTorsionStamp);
        mol->addTorsion(torsion);
    }

    //create cutoffGroups
    CutoffGroup* cutoffGroup;
    CutoffGroupStamp* currentCutoffGroupStamp;
    int nCutoffGroups = molStamp->getNCutoffGroups();
    for (int i = 0; i < nCutoffGroups; ++i) {
        currentCutoffGroupStamp = molStamp->getCutoffGroup(i);
        cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
        mol->addCutoffGroup(cutoffGroup);
    }

    //every free atom is a cutoff group    
    std::set<Atom*> allAtoms;
     Molecule::AtomIterator ai;

    //add all atoms into allAtoms set
    for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        allAtoms.insert(atom);
    }

    Molecule::CutoffGroupIterator ci;
    CutoffGroup* cg;
    std::set<Atom*> cutoffAtoms;    
    
    //add all of the atoms belong to cutoff groups into cutoffAtoms set
    for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {

        for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
            cutoffAtoms.insert(atom);
        }

    }       
    
    //find all free atoms (which do not belong to cutoff groups)  
    //performs the "difference" operation from set theory,  the output range contains a copy of every
    //element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in 
    //[cutoffAtoms.begin(), cutoffAtoms.end()).
    std::vector<Atom*> freeAtoms;    
    std::set_difference(allAtoms.begin(), allAtoms.end(), cutoffAtoms.begin(), cutoffAtoms.end(),
                            std::back_inserter(freeAtoms));

    if (freeAtoms.size() != allAtoms.size() - cutoffAtoms.size()) {
        //Some atoms in rigidAtoms are not in allAtoms, something must be wrong
        sprintf(painCave.errMsg, "Atoms in cutoff groups are not in the atom list of the same molecule");

        painCave.isFatal = 1;
        simError();        
    }

    //loop over the free atoms and then create one cutoff group for every single free atom
    std::vector<Atom*>::iterator fai;

    for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
        cutoffGroup = createCutoffGroup(mol, *fai);
        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());

        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->getMember(i));
        atomStamp= molStamp->getAtom(rbStamp->getMember(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 */
    rb->setType(mol->getType() + "_RB_" + toString(mol->getNRigidBodies()));
    
    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) {
    bool isGhostBend = false;
    int ghostIndex;

    
    //
    if (stamp->haveExtras()){
        LinkedAssign* extras = stamp->getExtras();
        LinkedAssign* currentExtra = extras;

        while (currentExtra != NULL){
            if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
                switch (currentExtra->getType()){
                case 0:
                    ghostIndex = currentExtra->getInt();
                    isGhostBend = true;
                    break;

                default:
                sprintf(painCave.errMsg,
                "SimSetup Error: ghostVectorSource must be an int.\n");
                painCave.isFatal = 1;
                simError();
                }
            } else{
                sprintf(painCave.errMsg,
                "SimSetup Error: unhandled bend assignment:\n");
                painCave.isFatal = 1;
                simError();
            }
            currentExtra = currentExtra->getNext();
        }
        
    }

    if (isGhostBend) {

        int indexA = stamp->getA();
        int indexB= stamp->getB();

        assert(indexA != indexB);

        int normalIndex;
        if (indexA == ghostIndex) {
            normalIndex = indexB;
        } else if (indexB == ghostIndex) {
            normalIndex = indexA;
        }
        
        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();
        }
        
        return new GhostBend(normalAtom, ghostAtom, bendType);       

    } else {
            
        Atom* atomA = mol->getAtomAt(stamp->getA());
        Atom* atomB = mol->getAtomAt(stamp->getB());
        Atom* atomC = mol->getAtomAt(stamp->getC());

        assert( atomA && atomB && atomC);
        
        BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());

        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();
        }

        return new Bend(atomA, atomB, atomC, bendType);       
    }
}    

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

    Atom* atomA = mol->getAtomAt(stamp->getA());
    Atom* atomB = mol->getAtomAt(stamp->getB());
    Atom* atomC = mol->getAtomAt(stamp->getC());
    Torsion* torsion;

    if (stamp->getD() != -1) {
        Atom* atomD = mol->getAtomAt(stamp->getD());

        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*>(atomC);
        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;
}    

CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
    int nAtoms;
    CutoffGroup* cg;
    Atom* atom;
    cg = new CutoffGroup();
    
    nAtoms = stamp->getNMembers();
    for (int i =0; i < nAtoms; ++i) {
        atom = mol->getAtomAt(stamp->getMember(i));
        assert(atom);
        cg->addAtom(atom);
    }

    return cg;
}    

CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
    CutoffGroup* cg;
    cg  = new CutoffGroup();
    cg->addAtom(atom);
    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:	1957
Committed:	Tue Jan 25 17:45:23 2005 UTC (19 years, 5 months ago) by tim
File size:	17465 byte(s)
Log Message:	(1) complete section parser's error message (2) add GhostTorsion (3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor
#	User	Rev	Content
1	gezelter	1930	/*
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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			/**
43			* @file MoleculeCreator.cpp
44			* @author tlin
45			* @date 11/04/2004
46			* @time 13:44am
47			* @version 1.0
48			*/
49
50			#include <cassert>
51			#include <set>
52
53			#include "brains/MoleculeCreator.hpp"
54			#include "primitives/GhostBend.hpp"
55	tim	1957	#include "primitives/GhostTorsion.hpp"
56	gezelter	1930	#include "types/DirectionalAtomType.hpp"
57			#include "types/FixedBondType.hpp"
58			#include "utils/simError.h"
59			#include "utils/StringUtils.hpp"
60
61			namespace oopse {
62
63			Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
64			int stampId, int globalIndex, LocalIndexManager* localIndexMan) {
65
66			Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
67
68			//create atoms
69			Atom* atom;
70			AtomStamp* currentAtomStamp;
71			int nAtom = molStamp->getNAtoms();
72			for (int i = 0; i < nAtom; ++i) {
73			currentAtomStamp = molStamp->getAtom(i);
74			atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
75			mol->addAtom(atom);
76			}
77
78			//create rigidbodies
79			RigidBody* rb;
80			RigidBodyStamp * currentRigidBodyStamp;
81			int nRigidbodies = molStamp->getNRigidBodies();
82
83			for (int i = 0; i < nRigidbodies; ++i) {
84			currentRigidBodyStamp = molStamp->getRigidBody(i);
85			rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
86			mol->addRigidBody(rb);
87			}
88
89			//create bonds
90			Bond* bond;
91			BondStamp* currentBondStamp;
92			int nBonds = molStamp->getNBonds();
93
94			for (int i = 0; i < nBonds; ++i) {
95			currentBondStamp = molStamp->getBond(i);
96			bond = createBond(ff, mol, currentBondStamp);
97			mol->addBond(bond);
98			}
99
100			//create bends
101			Bend* bend;
102			BendStamp* currentBendStamp;
103			int nBends = molStamp->getNBends();
104			for (int i = 0; i < nBends; ++i) {
105			currentBendStamp = molStamp->getBend(i);
106			bend = createBend(ff, mol, currentBendStamp);
107			mol->addBend(bend);
108			}
109
110			//create torsions
111			Torsion* torsion;
112			TorsionStamp* currentTorsionStamp;
113			int nTorsions = molStamp->getNTorsions();
114			for (int i = 0; i < nTorsions; ++i) {
115			currentTorsionStamp = molStamp->getTorsion(i);
116			torsion = createTorsion(ff, mol, currentTorsionStamp);
117			mol->addTorsion(torsion);
118			}
119
120			//create cutoffGroups
121			CutoffGroup* cutoffGroup;
122			CutoffGroupStamp* currentCutoffGroupStamp;
123			int nCutoffGroups = molStamp->getNCutoffGroups();
124			for (int i = 0; i < nCutoffGroups; ++i) {
125			currentCutoffGroupStamp = molStamp->getCutoffGroup(i);
126			cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
127			mol->addCutoffGroup(cutoffGroup);
128			}
129
130			//every free atom is a cutoff group
131			std::set<Atom*> allAtoms;
132			Molecule::AtomIterator ai;
133
134			//add all atoms into allAtoms set
135			for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
136			allAtoms.insert(atom);
137			}
138
139			Molecule::CutoffGroupIterator ci;
140			CutoffGroup* cg;
141			std::set<Atom*> cutoffAtoms;
142
143			//add all of the atoms belong to cutoff groups into cutoffAtoms set
144			for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
145
146			for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
147			cutoffAtoms.insert(atom);
148			}
149
150			}
151
152			//find all free atoms (which do not belong to cutoff groups)
153			//performs the "difference" operation from set theory, the output range contains a copy of every
154			//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
155			//[cutoffAtoms.begin(), cutoffAtoms.end()).
156			std::vector<Atom*> freeAtoms;
157			std::set_difference(allAtoms.begin(), allAtoms.end(), cutoffAtoms.begin(), cutoffAtoms.end(),
158			std::back_inserter(freeAtoms));
159
160			if (freeAtoms.size() != allAtoms.size() - cutoffAtoms.size()) {
161			//Some atoms in rigidAtoms are not in allAtoms, something must be wrong
162			sprintf(painCave.errMsg, "Atoms in cutoff groups are not in the atom list of the same molecule");
163
164			painCave.isFatal = 1;
165			simError();
166			}
167
168			//loop over the free atoms and then create one cutoff group for every single free atom
169			std::vector<Atom*>::iterator fai;
170
171			for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
172			cutoffGroup = createCutoffGroup(mol, *fai);
173			mol->addCutoffGroup(cutoffGroup);
174			}
175			//create constraints
176			createConstraintPair(mol);
177			createConstraintElem(mol);
178
179			//the construction of this molecule is finished
180			mol->complete();
181
182			return mol;
183			}
184
185
186			Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
187			LocalIndexManager* localIndexMan) {
188			AtomType * atomType;
189			Atom* atom;
190
191			atomType = ff->getAtomType(stamp->getType());
192
193			if (atomType == NULL) {
194			sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
195			stamp->getType());
196
197			painCave.isFatal = 1;
198			simError();
199			}
200
201			//below code still have some kind of hard-coding smell
202			if (atomType->isDirectional()){
203
204			DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
205
206			if (dAtomType == NULL) {
207			sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
208
209			painCave.isFatal = 1;
210			simError();
211			}
212
213			DirectionalAtom* dAtom;
214			dAtom = new DirectionalAtom(dAtomType);
215			atom = dAtom;
216			}
217			else{
218			atom = new Atom(atomType);
219			}
220
221			atom->setLocalIndex(localIndexMan->getNextAtomIndex());
222
223			return atom;
224			}
225
226			RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp molStamp, Molecule mol,
227			RigidBodyStamp* rbStamp,
228			LocalIndexManager* localIndexMan) {
229			Atom* atom;
230			int nAtoms;
231			Vector3d refCoor;
232			AtomStamp* atomStamp;
233
234			RigidBody* rb = new RigidBody();
235			nAtoms = rbStamp->getNMembers();
236			for (int i = 0; i < nAtoms; ++i) {
237			//rbStamp->getMember(i) return the local index of current atom inside the molecule.
238			//It is not the same as local index of atom which is the index of atom at DataStorage class
239			atom = mol->getAtomAt(rbStamp->getMember(i));
240			atomStamp= molStamp->getAtom(rbStamp->getMember(i));
241			rb->addAtom(atom, atomStamp);
242			}
243
244			//after all of the atoms are added, we need to calculate the reference coordinates
245			rb->calcRefCoords();
246
247			//set the local index of this rigid body, global index will be set later
248			rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
249
250			//the rule for naming rigidbody MoleculeName_RB_Integer
251			//The first part is the name of the molecule
252			//The second part is alway fixed as "RB"
253			//The third part is the index of the rigidbody defined in meta-data file
254			//For example, Butane_RB_0 is a valid rigid body name of butane molecule
255			/*@todo replace itoa by lexi_cast /
256			rb->setType(mol->getType() + "_RB_" + toString(mol->getNRigidBodies()));
257
258			return rb;
259			}
260
261			Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
262			BondType* bondType;
263			Atom* atomA;
264			Atom* atomB;
265
266			atomA = mol->getAtomAt(stamp->getA());
267			atomB = mol->getAtomAt(stamp->getB());
268
269			assert( atomA && atomB);
270
271			bondType = ff->getBondType(atomA->getType(), atomB->getType());
272
273			if (bondType == NULL) {
274			sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
275			atomA->getType().c_str(),
276			atomB->getType().c_str());
277
278			painCave.isFatal = 1;
279			simError();
280			}
281			return new Bond(atomA, atomB, bondType);
282			}
283
284			Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
285			bool isGhostBend = false;
286			int ghostIndex;
287
288
289			//
290			if (stamp->haveExtras()){
291			LinkedAssign* extras = stamp->getExtras();
292			LinkedAssign* currentExtra = extras;
293
294			while (currentExtra != NULL){
295			if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
296			switch (currentExtra->getType()){
297			case 0:
298			ghostIndex = currentExtra->getInt();
299			isGhostBend = true;
300			break;
301
302			default:
303			sprintf(painCave.errMsg,
304			"SimSetup Error: ghostVectorSource must be an int.\n");
305			painCave.isFatal = 1;
306			simError();
307			}
308			} else{
309			sprintf(painCave.errMsg,
310			"SimSetup Error: unhandled bend assignment:\n");
311			painCave.isFatal = 1;
312			simError();
313			}
314			currentExtra = currentExtra->getNext();
315			}
316
317			}
318
319			if (isGhostBend) {
320
321			int indexA = stamp->getA();
322			int indexB= stamp->getB();
323
324			assert(indexA != indexB);
325
326			int normalIndex;
327			if (indexA == ghostIndex) {
328			normalIndex = indexB;
329			} else if (indexB == ghostIndex) {
330			normalIndex = indexA;
331			}
332
333			Atom* normalAtom = mol->getAtomAt(normalIndex) ;
334			DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
335			if (ghostAtom == NULL) {
336			sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
337			painCave.isFatal = 1;
338			simError();
339			}
340
341			BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
342
343			if (bendType == NULL) {
344			sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
345			normalAtom->getType().c_str(),
346			ghostAtom->getType().c_str(),
347			"GHOST");
348
349			painCave.isFatal = 1;
350			simError();
351			}
352
353			return new GhostBend(normalAtom, ghostAtom, bendType);
354
355			} else {
356
357			Atom* atomA = mol->getAtomAt(stamp->getA());
358			Atom* atomB = mol->getAtomAt(stamp->getB());
359			Atom* atomC = mol->getAtomAt(stamp->getC());
360
361			assert( atomA && atomB && atomC);
362
363			BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
364
365			if (bendType == NULL) {
366			sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
367			atomA->getType().c_str(),
368			atomB->getType().c_str(),
369			atomC->getType().c_str());
370
371			painCave.isFatal = 1;
372			simError();
373			}
374
375			return new Bend(atomA, atomB, atomC, bendType);
376			}
377			}
378
379			Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
380
381	tim	1957	Atom* atomA = mol->getAtomAt(stamp->getA());
382			Atom* atomB = mol->getAtomAt(stamp->getB());
383			Atom* atomC = mol->getAtomAt(stamp->getC());
384			Torsion* torsion;
385	gezelter	1930
386	tim	1957	if (stamp->getD() != -1) {
387			Atom* atomD = mol->getAtomAt(stamp->getD());
388	gezelter	1930
389	tim	1957	assert(atomA && atomB && atomC && atomD);
390
391			TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
392			atomC->getType(), atomD->getType());
393	gezelter	1930
394	tim	1957	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			atomD->getType().c_str());
400
401			painCave.isFatal = 1;
402			simError();
403			}
404
405			torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
406	gezelter	1930	}
407	tim	1957	else {
408
409			DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(atomC);
410			if (dAtom == NULL) {
411			sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
412			painCave.isFatal = 1;
413			simError();
414			}
415
416			TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
417			atomC->getType(), "GHOST");
418
419			if (torsionType == NULL) {
420			sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
421			atomA->getType().c_str(),
422			atomB->getType().c_str(),
423			atomC->getType().c_str(),
424			"GHOST");
425
426			painCave.isFatal = 1;
427			simError();
428			}
429
430			torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
431			}
432
433			return torsion;
434	gezelter	1930	}
435
436			CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
437			int nAtoms;
438			CutoffGroup* cg;
439			Atom* atom;
440			cg = new CutoffGroup();
441
442			nAtoms = stamp->getNMembers();
443			for (int i =0; i < nAtoms; ++i) {
444			atom = mol->getAtomAt(stamp->getMember(i));
445			assert(atom);
446			cg->addAtom(atom);
447			}
448
449			return cg;
450			}
451
452			CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
453			CutoffGroup* cg;
454			cg = new CutoffGroup();
455			cg->addAtom(atom);
456			return cg;
457			}
458
459			void MoleculeCreator::createConstraintPair(Molecule* mol) {
460
461			//add bond constraints
462			Molecule::BondIterator bi;
463			Bond* bond;
464			for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
465
466			BondType* bt = bond->getBondType();
467
468			//class Parent1 {};
469			//class Child1 : public Parent {};
470			//class Child2 : public Parent {};
471			//Child1* ch1 = new Child1();
472			//Child2* ch2 = dynamic_cast<Child2*>(ch1);
473			//the dynamic_cast is succeed in above line. A compiler bug?
474
475			if (typeid(FixedBondType) == typeid(*bt)) {
476			FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
477
478			ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
479			ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
480			ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
481			mol->addConstraintPair(consPair);
482			}
483			}
484
485			//rigidbody -- rigidbody constraint is not support yet
486			}
487
488			void MoleculeCreator::createConstraintElem(Molecule* mol) {
489
490			ConstraintPair* consPair;
491			Molecule::ConstraintPairIterator cpi;
492			std::set<StuntDouble*> sdSet;
493			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
494
495			StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
496			if (sdSet.find(sdA) == sdSet.end()){
497			sdSet.insert(sdA);
498			mol->addConstraintElem(new ConstraintElem(sdA));
499			}
500
501			StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
502			if (sdSet.find(sdB) == sdSet.end()){
503			sdSet.insert(sdB);
504			mol->addConstraintElem(new ConstraintElem(sdB));
505			}
506
507			}
508
509			}
510
511			}