src/brains/MoleculeCreator.cpp

/*
 * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
 * 
 * Contact: oopse@oopse.org
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */
 
 /**
  * @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 "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) {
    TorsionType* torsionType;
    Atom* atomA;
    Atom* atomB;
    Atom* atomC;
    Atom* atomD;

    atomA = mol->getAtomAt(stamp->getA());
    atomB = mol->getAtomAt(stamp->getB());
    atomC = mol->getAtomAt(stamp->getC());
    atomD = mol->getAtomAt(stamp->getD());

    assert(atomA && atomB && atomC && atomD);
    
    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();
    }
    
    return new Torsion(atomA, atomB, atomC, atomD, torsionType);       
}    

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:	1907
Committed:	Thu Jan 6 22:31:07 2005 UTC (21 years, 6 months ago) by tim
File size:	15483 byte(s)
Log Message:	constraint is almost working
#	User	Rev	Content
1	tim	1719	/*
2			* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project
3			*
4			* Contact: oopse@oopse.org
5			*
6			* This program is free software; you can redistribute it and/or
7			* modify it under the terms of the GNU Lesser General Public License
8			* as published by the Free Software Foundation; either version 2.1
9			* of the License, or (at your option) any later version.
10			* All we ask is that proper credit is given for our work, which includes
11			* - but is not limited to - adding the above copyright notice to the beginning
12			* of your source code files, and to any copyright notice that you may distribute
13			* with programs based on this work.
14			*
15			* This program is distributed in the hope that it will be useful,
16			* but WITHOUT ANY WARRANTY; without even the implied warranty of
17			* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18			* GNU Lesser General Public License for more details.
19			*
20			* You should have received a copy of the GNU Lesser General Public License
21			* along with this program; if not, write to the Free Software
22			* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23			*
24			*/
25
26			/**
27			* @file MoleculeCreator.cpp
28			* @author tlin
29			* @date 11/04/2004
30			* @time 13:44am
31			* @version 1.0
32			*/
33
34			#include <cassert>
35	tim	1907	#include <set>
36	tim	1719
37	tim	1805	#include "brains/MoleculeCreator.hpp"
38			#include "primitives/GhostBend.hpp"
39	tim	1832	#include "types/DirectionalAtomType.hpp"
40	tim	1901	#include "types/FixedBondType.hpp"
41	tim	1805	#include "utils/simError.h"
42			#include "utils/StringUtils.hpp"
43
44	tim	1719	namespace oopse {
45
46	tim	1805	Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
47			int stampId, int globalIndex, LocalIndexManager* localIndexMan) {
48
49	tim	1733	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
50	tim	1719
51			//create atoms
52			Atom* atom;
53			AtomStamp* currentAtomStamp;
54			int nAtom = molStamp->getNAtoms();
55			for (int i = 0; i < nAtom; ++i) {
56			currentAtomStamp = molStamp->getAtom(i);
57	tim	1805	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
58	tim	1719	mol->addAtom(atom);
59			}
60
61			//create rigidbodies
62			RigidBody* rb;
63			RigidBodyStamp * currentRigidBodyStamp;
64			int nRigidbodies = molStamp->getNRigidBodies();
65
66			for (int i = 0; i < nRigidbodies; ++i) {
67			currentRigidBodyStamp = molStamp->getRigidBody(i);
68	tim	1805	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
69	tim	1719	mol->addRigidBody(rb);
70			}
71
72			//create bonds
73			Bond* bond;
74			BondStamp* currentBondStamp;
75	tim	1857	int nBonds = molStamp->getNBonds();
76	tim	1719
77			for (int i = 0; i < nBonds; ++i) {
78	tim	1805	currentBondStamp = molStamp->getBond(i);
79	tim	1719	bond = createBond(ff, mol, currentBondStamp);
80			mol->addBond(bond);
81			}
82
83			//create bends
84			Bend* bend;
85			BendStamp* currentBendStamp;
86			int nBends = molStamp->getNBends();
87			for (int i = 0; i < nBends; ++i) {
88			currentBendStamp = molStamp->getBend(i);
89			bend = createBend(ff, mol, currentBendStamp);
90			mol->addBend(bend);
91			}
92
93			//create torsions
94			Torsion* torsion;
95			TorsionStamp* currentTorsionStamp;
96			int nTorsions = molStamp->getNTorsions();
97			for (int i = 0; i < nTorsions; ++i) {
98			currentTorsionStamp = molStamp->getTorsion(i);
99			torsion = createTorsion(ff, mol, currentTorsionStamp);
100			mol->addTorsion(torsion);
101			}
102
103			//create cutoffGroups
104			CutoffGroup* cutoffGroup;
105			CutoffGroupStamp* currentCutoffGroupStamp;
106			int nCutoffGroups = molStamp->getNCutoffGroups();
107			for (int i = 0; i < nCutoffGroups; ++i) {
108			currentCutoffGroupStamp = molStamp->getCutoffGroup(i);
109	tim	1805	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
110	tim	1719	mol->addCutoffGroup(cutoffGroup);
111			}
112
113	tim	1734	//every free atom is a cutoff group
114			std::set<Atom*> allAtoms;
115	tim	1805	Molecule::AtomIterator ai;
116	tim	1734
117			//add all atoms into allAtoms set
118			for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
119			allAtoms.insert(atom);
120			}
121
122	tim	1805	Molecule::CutoffGroupIterator ci;
123	tim	1734	CutoffGroup* cg;
124			std::set<Atom*> cutoffAtoms;
125
126			//add all of the atoms belong to cutoff groups into cutoffAtoms set
127			for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
128
129			for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
130			cutoffAtoms.insert(atom);
131			}
132
133			}
134
135			//find all free atoms (which do not belong to cutoff groups)
136			//performs the "difference" operation from set theory, the output range contains a copy of every
137			//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
138			//[cutoffAtoms.begin(), cutoffAtoms.end()).
139			std::vector<Atom*> freeAtoms;
140			std::set_difference(allAtoms.begin(), allAtoms.end(), cutoffAtoms.begin(), cutoffAtoms.end(),
141	tim	1805	std::back_inserter(freeAtoms));
142	tim	1734
143			if (freeAtoms.size() != allAtoms.size() - cutoffAtoms.size()) {
144			//Some atoms in rigidAtoms are not in allAtoms, something must be wrong
145			sprintf(painCave.errMsg, "Atoms in cutoff groups are not in the atom list of the same molecule");
146
147			painCave.isFatal = 1;
148			simError();
149			}
150
151			//loop over the free atoms and then create one cutoff group for every single free atom
152			std::vector<Atom*>::iterator fai;
153
154			for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
155	tim	1842	cutoffGroup = createCutoffGroup(mol, *fai);
156	tim	1734	mol->addCutoffGroup(cutoffGroup);
157			}
158	tim	1719	//create constraints
159	tim	1907	createConstraintPair(mol);
160			createConstraintElem(mol);
161
162	tim	1719	//the construction of this molecule is finished
163			mol->complete();
164
165			return mol;
166			}
167
168
169			Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
170			LocalIndexManager* localIndexMan) {
171			AtomType * atomType;
172			Atom* atom;
173
174			atomType = ff->getAtomType(stamp->getType());
175
176	tim	1804	if (atomType == NULL) {
177	tim	1733	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
178			stamp->getType());
179
180			painCave.isFatal = 1;
181			simError();
182			}
183
184	tim	1719	//below code still have some kind of hard-coding smell
185	tim	1813	if (atomType->isDirectional()){
186
187	tim	1804	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
188	tim	1813
189	tim	1804	if (dAtomType == NULL) {
190			sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
191
192			painCave.isFatal = 1;
193			simError();
194			}
195	tim	1813
196			DirectionalAtom* dAtom;
197	tim	1804	dAtom = new DirectionalAtom(dAtomType);
198	tim	1719	atom = dAtom;
199			}
200			else{
201			atom = new Atom(atomType);
202			}
203
204			atom->setLocalIndex(localIndexMan->getNextAtomIndex());
205	tim	1805
206			return atom;
207	tim	1719	}
208
209			RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp molStamp, Molecule mol,
210			RigidBodyStamp* rbStamp,
211			LocalIndexManager* localIndexMan) {
212			Atom* atom;
213			int nAtoms;
214			Vector3d refCoor;
215			AtomStamp* atomStamp;
216
217			RigidBody* rb = new RigidBody();
218	tim	1805	nAtoms = rbStamp->getNMembers();
219	tim	1719	for (int i = 0; i < nAtoms; ++i) {
220			//rbStamp->getMember(i) return the local index of current atom inside the molecule.
221			//It is not the same as local index of atom which is the index of atom at DataStorage class
222			atom = mol->getAtomAt(rbStamp->getMember(i));
223	tim	1805	atomStamp= molStamp->getAtom(rbStamp->getMember(i));
224	tim	1719	rb->addAtom(atom, atomStamp);
225			}
226	tim	1733
227			//after all of the atoms are added, we need to calculate the reference coordinates
228	tim	1719	rb->calcRefCoords();
229	tim	1733
230			//set the local index of this rigid body, global index will be set later
231	tim	1719	rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
232	tim	1733
233			//the rule for naming rigidbody MoleculeName_RB_Integer
234			//The first part is the name of the molecule
235			//The second part is alway fixed as "RB"
236			//The third part is the index of the rigidbody defined in meta-data file
237			//For example, Butane_RB_0 is a valid rigid body name of butane molecule
238	tim	1805	/*@todo replace itoa by lexi_cast /
239			rb->setType(mol->getType() + "_RB_" + toString(mol->getNRigidBodies()));
240	tim	1719
241			return rb;
242			}
243
244			Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
245			BondType* bondType;
246			Atom* atomA;
247			Atom* atomB;
248
249			atomA = mol->getAtomAt(stamp->getA());
250			atomB = mol->getAtomAt(stamp->getB());
251
252			assert( atomA && atomB);
253
254	tim	1805	bondType = ff->getBondType(atomA->getType(), atomB->getType());
255	tim	1719
256	tim	1733	if (bondType == NULL) {
257			sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
258			atomA->getType().c_str(),
259			atomB->getType().c_str());
260
261			painCave.isFatal = 1;
262			simError();
263			}
264	tim	1719	return new Bond(atomA, atomB, bondType);
265			}
266
267			Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
268	tim	1774	bool isGhostBend = false;
269			int ghostIndex;
270	tim	1719
271
272	tim	1774	//
273			if (stamp->haveExtras()){
274	tim	1805	LinkedAssign* extras = stamp->getExtras();
275	tim	1774	LinkedAssign* currentExtra = extras;
276	tim	1719
277	tim	1774	while (currentExtra != NULL){
278			if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
279			switch (currentExtra->getType()){
280			case 0:
281			ghostIndex = currentExtra->getInt();
282			isGhostBend = true;
283			break;
284	tim	1719
285	tim	1774	default:
286			sprintf(painCave.errMsg,
287			"SimSetup Error: ghostVectorSource must be an int.\n");
288			painCave.isFatal = 1;
289			simError();
290			}
291			} else{
292			sprintf(painCave.errMsg,
293			"SimSetup Error: unhandled bend assignment:\n");
294			painCave.isFatal = 1;
295			simError();
296			}
297			currentExtra = currentExtra->getNext();
298			}
299
300	tim	1733	}
301
302	tim	1774	if (isGhostBend) {
303	tim	1733
304	tim	1774	int indexA = stamp->getA();
305			int indexB= stamp->getB();
306
307			assert(indexA != indexB);
308
309			int normalIndex;
310			if (indexA == ghostIndex) {
311			normalIndex = indexB;
312			} else if (indexB == ghostIndex) {
313			normalIndex = indexA;
314			}
315
316	tim	1805	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
317			DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
318			if (ghostAtom == NULL) {
319			sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
320			painCave.isFatal = 1;
321			simError();
322			}
323
324	tim	1774	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
325
326			if (bendType == NULL) {
327			sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
328			normalAtom->getType().c_str(),
329			ghostAtom->getType().c_str(),
330			"GHOST");
331
332			painCave.isFatal = 1;
333			simError();
334			}
335	tim	1805
336	tim	1774	return new GhostBend(normalAtom, ghostAtom, bendType);
337
338			} else {
339
340			Atom* atomA = mol->getAtomAt(stamp->getA());
341			Atom* atomB = mol->getAtomAt(stamp->getB());
342			Atom* atomC = mol->getAtomAt(stamp->getC());
343
344			assert( atomA && atomB && atomC);
345
346			BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
347
348			if (bendType == NULL) {
349			sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
350			atomA->getType().c_str(),
351			atomB->getType().c_str(),
352			atomC->getType().c_str());
353
354			painCave.isFatal = 1;
355			simError();
356			}
357
358			return new Bend(atomA, atomB, atomC, bendType);
359			}
360	tim	1719	}
361
362			Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
363			TorsionType* torsionType;
364			Atom* atomA;
365			Atom* atomB;
366			Atom* atomC;
367			Atom* atomD;
368
369			atomA = mol->getAtomAt(stamp->getA());
370			atomB = mol->getAtomAt(stamp->getB());
371			atomC = mol->getAtomAt(stamp->getC());
372			atomD = mol->getAtomAt(stamp->getD());
373
374			assert(atomA && atomB && atomC && atomD);
375
376	tim	1805	torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
377	tim	1719	atomC->getType(), atomD->getType());
378
379	tim	1733	if (torsionType == NULL) {
380			sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
381			atomA->getType().c_str(),
382			atomB->getType().c_str(),
383			atomC->getType().c_str(),
384			atomD->getType().c_str());
385
386			painCave.isFatal = 1;
387			simError();
388			}
389
390	tim	1805	return new Torsion(atomA, atomB, atomC, atomD, torsionType);
391	tim	1719	}
392
393			CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
394			int nAtoms;
395			CutoffGroup* cg;
396			Atom* atom;
397			cg = new CutoffGroup();
398
399			nAtoms = stamp->getNMembers();
400			for (int i =0; i < nAtoms; ++i) {
401			atom = mol->getAtomAt(stamp->getMember(i));
402			assert(atom);
403			cg->addAtom(atom);
404			}
405
406			return cg;
407			}
408
409	tim	1734	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
410			CutoffGroup* cg;
411			cg = new CutoffGroup();
412	tim	1805	cg->addAtom(atom);
413	tim	1734	return cg;
414			}
415	tim	1719
416	tim	1901	void MoleculeCreator::createConstraintPair(Molecule* mol) {
417	tim	1719
418	tim	1901	//add bond constraints
419			Molecule::BondIterator bi;
420			Bond* bond;
421			for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
422
423			BondType* bt = bond->getBondType();
424
425	tim	1907	//class Parent1 {};
426			//class Child1 : public Parent {};
427			//class Child2 : public Parent {};
428			//Child1* ch1 = new Child1();
429			//Child2* ch2 = dynamic_cast<Child2*>(ch1);
430			//the dynamic_cast is succeed in above line. A compiler bug?
431
432			if (typeid(FixedBondType) == typeid(*bt)) {
433			FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
434
435			ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
436			ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
437			ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
438	tim	1901	mol->addConstraintPair(consPair);
439			}
440			}
441
442			//rigidbody -- rigidbody constraint is not support yet
443	tim	1719	}
444	tim	1901
445	tim	1907	void MoleculeCreator::createConstraintElem(Molecule* mol) {
446
447			ConstraintPair* consPair;
448			Molecule::ConstraintPairIterator cpi;
449			std::set<StuntDouble*> sdSet;
450			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
451
452			StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
453			if (sdSet.find(sdA) == sdSet.end()){
454			sdSet.insert(sdA);
455			mol->addConstraintElem(new ConstraintElem(sdA));
456			}
457
458			StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
459			if (sdSet.find(sdB) == sdSet.end()){
460			sdSet.insert(sdB);
461			mol->addConstraintElem(new ConstraintElem(sdB));
462			}
463
464			}
465
466	tim	1901	}
467	tim	1907
468			}