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 (19 years, 6 months ago) by tim
File size:	15483 byte(s)
Log Message:	constraint is almost working
#	Content
1	/*
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	#include <set>
36
37	#include "brains/MoleculeCreator.hpp"
38	#include "primitives/GhostBend.hpp"
39	#include "types/DirectionalAtomType.hpp"
40	#include "types/FixedBondType.hpp"
41	#include "utils/simError.h"
42	#include "utils/StringUtils.hpp"
43
44	namespace oopse {
45
46	Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
47	int stampId, int globalIndex, LocalIndexManager* localIndexMan) {
48
49	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
50
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	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
58	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	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
69	mol->addRigidBody(rb);
70	}
71
72	//create bonds
73	Bond* bond;
74	BondStamp* currentBondStamp;
75	int nBonds = molStamp->getNBonds();
76
77	for (int i = 0; i < nBonds; ++i) {
78	currentBondStamp = molStamp->getBond(i);
79	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	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
110	mol->addCutoffGroup(cutoffGroup);
111	}
112
113	//every free atom is a cutoff group
114	std::set<Atom*> allAtoms;
115	Molecule::AtomIterator ai;
116
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	Molecule::CutoffGroupIterator ci;
123	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	std::back_inserter(freeAtoms));
142
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	cutoffGroup = createCutoffGroup(mol, *fai);
156	mol->addCutoffGroup(cutoffGroup);
157	}
158	//create constraints
159	createConstraintPair(mol);
160	createConstraintElem(mol);
161
162	//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	if (atomType == NULL) {
177	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
178	stamp->getType());
179
180	painCave.isFatal = 1;
181	simError();
182	}
183
184	//below code still have some kind of hard-coding smell
185	if (atomType->isDirectional()){
186
187	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
188
189	if (dAtomType == NULL) {
190	sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
191
192	painCave.isFatal = 1;
193	simError();
194	}
195
196	DirectionalAtom* dAtom;
197	dAtom = new DirectionalAtom(dAtomType);
198	atom = dAtom;
199	}
200	else{
201	atom = new Atom(atomType);
202	}
203
204	atom->setLocalIndex(localIndexMan->getNextAtomIndex());
205
206	return atom;
207	}
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	nAtoms = rbStamp->getNMembers();
219	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	atomStamp= molStamp->getAtom(rbStamp->getMember(i));
224	rb->addAtom(atom, atomStamp);
225	}
226
227	//after all of the atoms are added, we need to calculate the reference coordinates
228	rb->calcRefCoords();
229
230	//set the local index of this rigid body, global index will be set later
231	rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
232
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	/*@todo replace itoa by lexi_cast /
239	rb->setType(mol->getType() + "_RB_" + toString(mol->getNRigidBodies()));
240
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	bondType = ff->getBondType(atomA->getType(), atomB->getType());
255
256	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	return new Bond(atomA, atomB, bondType);
265	}
266
267	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
268	bool isGhostBend = false;
269	int ghostIndex;
270
271
272	//
273	if (stamp->haveExtras()){
274	LinkedAssign* extras = stamp->getExtras();
275	LinkedAssign* currentExtra = extras;
276
277	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
285	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	}
301
302	if (isGhostBend) {
303
304	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	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	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
336	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	}
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	torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
377	atomC->getType(), atomD->getType());
378
379	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	return new Torsion(atomA, atomB, atomC, atomD, torsionType);
391	}
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	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
410	CutoffGroup* cg;
411	cg = new CutoffGroup();
412	cg->addAtom(atom);
413	return cg;
414	}
415
416	void MoleculeCreator::createConstraintPair(Molecule* mol) {
417
418	//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	//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	mol->addConstraintPair(consPair);
439	}
440	}
441
442	//rigidbody -- rigidbody constraint is not support yet
443	}
444
445	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	}
467
468	}