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 "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

    //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();
        FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);

        //found a constraint pair
        if (fbt != NULL) {
            ConstraintPair* consPair = new ConstraintPair(bond->getAtomA(), bond->getAtomB(), fbt->getEquilibriumBondLength());
            mol->addConstraintPair(consPair);
        }
        
    }

    //rigidbody -- rigidbody constraint is not support yet
        
}

}
Revision:	1901
Committed:	Tue Jan 4 22:18:36 2005 UTC (19 years, 6 months ago) by tim
File size:	14223 byte(s)
Log Message:	constraints in progress
#	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
36	tim	1805	#include "brains/MoleculeCreator.hpp"
37			#include "primitives/GhostBend.hpp"
38	tim	1832	#include "types/DirectionalAtomType.hpp"
39	tim	1901	#include "types/FixedBondType.hpp"
40	tim	1805	#include "utils/simError.h"
41			#include "utils/StringUtils.hpp"
42
43	tim	1719	namespace oopse {
44
45	tim	1805	Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
46			int stampId, int globalIndex, LocalIndexManager* localIndexMan) {
47
48	tim	1733	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
49	tim	1719
50			//create atoms
51			Atom* atom;
52			AtomStamp* currentAtomStamp;
53			int nAtom = molStamp->getNAtoms();
54			for (int i = 0; i < nAtom; ++i) {
55			currentAtomStamp = molStamp->getAtom(i);
56	tim	1805	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
57	tim	1719	mol->addAtom(atom);
58			}
59
60			//create rigidbodies
61			RigidBody* rb;
62			RigidBodyStamp * currentRigidBodyStamp;
63			int nRigidbodies = molStamp->getNRigidBodies();
64
65			for (int i = 0; i < nRigidbodies; ++i) {
66			currentRigidBodyStamp = molStamp->getRigidBody(i);
67	tim	1805	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
68	tim	1719	mol->addRigidBody(rb);
69			}
70
71			//create bonds
72			Bond* bond;
73			BondStamp* currentBondStamp;
74	tim	1857	int nBonds = molStamp->getNBonds();
75	tim	1719
76			for (int i = 0; i < nBonds; ++i) {
77	tim	1805	currentBondStamp = molStamp->getBond(i);
78	tim	1719	bond = createBond(ff, mol, currentBondStamp);
79			mol->addBond(bond);
80			}
81
82			//create bends
83			Bend* bend;
84			BendStamp* currentBendStamp;
85			int nBends = molStamp->getNBends();
86			for (int i = 0; i < nBends; ++i) {
87			currentBendStamp = molStamp->getBend(i);
88			bend = createBend(ff, mol, currentBendStamp);
89			mol->addBend(bend);
90			}
91
92			//create torsions
93			Torsion* torsion;
94			TorsionStamp* currentTorsionStamp;
95			int nTorsions = molStamp->getNTorsions();
96			for (int i = 0; i < nTorsions; ++i) {
97			currentTorsionStamp = molStamp->getTorsion(i);
98			torsion = createTorsion(ff, mol, currentTorsionStamp);
99			mol->addTorsion(torsion);
100			}
101
102			//create cutoffGroups
103			CutoffGroup* cutoffGroup;
104			CutoffGroupStamp* currentCutoffGroupStamp;
105			int nCutoffGroups = molStamp->getNCutoffGroups();
106			for (int i = 0; i < nCutoffGroups; ++i) {
107			currentCutoffGroupStamp = molStamp->getCutoffGroup(i);
108	tim	1805	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
109	tim	1719	mol->addCutoffGroup(cutoffGroup);
110			}
111
112	tim	1734	//every free atom is a cutoff group
113			std::set<Atom*> allAtoms;
114	tim	1805	Molecule::AtomIterator ai;
115	tim	1734
116			//add all atoms into allAtoms set
117			for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
118			allAtoms.insert(atom);
119			}
120
121	tim	1805	Molecule::CutoffGroupIterator ci;
122	tim	1734	CutoffGroup* cg;
123			std::set<Atom*> cutoffAtoms;
124
125			//add all of the atoms belong to cutoff groups into cutoffAtoms set
126			for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
127
128			for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
129			cutoffAtoms.insert(atom);
130			}
131
132			}
133
134			//find all free atoms (which do not belong to cutoff groups)
135			//performs the "difference" operation from set theory, the output range contains a copy of every
136			//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
137			//[cutoffAtoms.begin(), cutoffAtoms.end()).
138			std::vector<Atom*> freeAtoms;
139			std::set_difference(allAtoms.begin(), allAtoms.end(), cutoffAtoms.begin(), cutoffAtoms.end(),
140	tim	1805	std::back_inserter(freeAtoms));
141	tim	1734
142			if (freeAtoms.size() != allAtoms.size() - cutoffAtoms.size()) {
143			//Some atoms in rigidAtoms are not in allAtoms, something must be wrong
144			sprintf(painCave.errMsg, "Atoms in cutoff groups are not in the atom list of the same molecule");
145
146			painCave.isFatal = 1;
147			simError();
148			}
149
150			//loop over the free atoms and then create one cutoff group for every single free atom
151			std::vector<Atom*>::iterator fai;
152
153			for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
154	tim	1842	cutoffGroup = createCutoffGroup(mol, *fai);
155	tim	1734	mol->addCutoffGroup(cutoffGroup);
156			}
157	tim	1719	//create constraints
158
159			//the construction of this molecule is finished
160			mol->complete();
161
162			return mol;
163			}
164
165
166			Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
167			LocalIndexManager* localIndexMan) {
168			AtomType * atomType;
169			Atom* atom;
170
171			atomType = ff->getAtomType(stamp->getType());
172
173	tim	1804	if (atomType == NULL) {
174	tim	1733	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
175			stamp->getType());
176
177			painCave.isFatal = 1;
178			simError();
179			}
180
181	tim	1719	//below code still have some kind of hard-coding smell
182	tim	1813	if (atomType->isDirectional()){
183
184	tim	1804	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
185	tim	1813
186	tim	1804	if (dAtomType == NULL) {
187			sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
188
189			painCave.isFatal = 1;
190			simError();
191			}
192	tim	1813
193			DirectionalAtom* dAtom;
194	tim	1804	dAtom = new DirectionalAtom(dAtomType);
195	tim	1719	atom = dAtom;
196			}
197			else{
198			atom = new Atom(atomType);
199			}
200
201			atom->setLocalIndex(localIndexMan->getNextAtomIndex());
202	tim	1805
203			return atom;
204	tim	1719	}
205
206			RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp molStamp, Molecule mol,
207			RigidBodyStamp* rbStamp,
208			LocalIndexManager* localIndexMan) {
209			Atom* atom;
210			int nAtoms;
211			Vector3d refCoor;
212			AtomStamp* atomStamp;
213
214			RigidBody* rb = new RigidBody();
215	tim	1805	nAtoms = rbStamp->getNMembers();
216	tim	1719	for (int i = 0; i < nAtoms; ++i) {
217			//rbStamp->getMember(i) return the local index of current atom inside the molecule.
218			//It is not the same as local index of atom which is the index of atom at DataStorage class
219			atom = mol->getAtomAt(rbStamp->getMember(i));
220	tim	1805	atomStamp= molStamp->getAtom(rbStamp->getMember(i));
221	tim	1719	rb->addAtom(atom, atomStamp);
222			}
223	tim	1733
224			//after all of the atoms are added, we need to calculate the reference coordinates
225	tim	1719	rb->calcRefCoords();
226	tim	1733
227			//set the local index of this rigid body, global index will be set later
228	tim	1719	rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
229	tim	1733
230			//the rule for naming rigidbody MoleculeName_RB_Integer
231			//The first part is the name of the molecule
232			//The second part is alway fixed as "RB"
233			//The third part is the index of the rigidbody defined in meta-data file
234			//For example, Butane_RB_0 is a valid rigid body name of butane molecule
235	tim	1805	/*@todo replace itoa by lexi_cast /
236			rb->setType(mol->getType() + "_RB_" + toString(mol->getNRigidBodies()));
237	tim	1719
238			return rb;
239			}
240
241			Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
242			BondType* bondType;
243			Atom* atomA;
244			Atom* atomB;
245
246			atomA = mol->getAtomAt(stamp->getA());
247			atomB = mol->getAtomAt(stamp->getB());
248
249			assert( atomA && atomB);
250
251	tim	1805	bondType = ff->getBondType(atomA->getType(), atomB->getType());
252	tim	1719
253	tim	1733	if (bondType == NULL) {
254			sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
255			atomA->getType().c_str(),
256			atomB->getType().c_str());
257
258			painCave.isFatal = 1;
259			simError();
260			}
261	tim	1719	return new Bond(atomA, atomB, bondType);
262			}
263
264			Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
265	tim	1774	bool isGhostBend = false;
266			int ghostIndex;
267	tim	1719
268
269	tim	1774	//
270			if (stamp->haveExtras()){
271	tim	1805	LinkedAssign* extras = stamp->getExtras();
272	tim	1774	LinkedAssign* currentExtra = extras;
273	tim	1719
274	tim	1774	while (currentExtra != NULL){
275			if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
276			switch (currentExtra->getType()){
277			case 0:
278			ghostIndex = currentExtra->getInt();
279			isGhostBend = true;
280			break;
281	tim	1719
282	tim	1774	default:
283			sprintf(painCave.errMsg,
284			"SimSetup Error: ghostVectorSource must be an int.\n");
285			painCave.isFatal = 1;
286			simError();
287			}
288			} else{
289			sprintf(painCave.errMsg,
290			"SimSetup Error: unhandled bend assignment:\n");
291			painCave.isFatal = 1;
292			simError();
293			}
294			currentExtra = currentExtra->getNext();
295			}
296
297	tim	1733	}
298
299	tim	1774	if (isGhostBend) {
300	tim	1733
301	tim	1774	int indexA = stamp->getA();
302			int indexB= stamp->getB();
303
304			assert(indexA != indexB);
305
306			int normalIndex;
307			if (indexA == ghostIndex) {
308			normalIndex = indexB;
309			} else if (indexB == ghostIndex) {
310			normalIndex = indexA;
311			}
312
313	tim	1805	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
314			DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
315			if (ghostAtom == NULL) {
316			sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
317			painCave.isFatal = 1;
318			simError();
319			}
320
321	tim	1774	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
322
323			if (bendType == NULL) {
324			sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
325			normalAtom->getType().c_str(),
326			ghostAtom->getType().c_str(),
327			"GHOST");
328
329			painCave.isFatal = 1;
330			simError();
331			}
332	tim	1805
333	tim	1774	return new GhostBend(normalAtom, ghostAtom, bendType);
334
335			} else {
336
337			Atom* atomA = mol->getAtomAt(stamp->getA());
338			Atom* atomB = mol->getAtomAt(stamp->getB());
339			Atom* atomC = mol->getAtomAt(stamp->getC());
340
341			assert( atomA && atomB && atomC);
342
343			BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
344
345			if (bendType == NULL) {
346			sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
347			atomA->getType().c_str(),
348			atomB->getType().c_str(),
349			atomC->getType().c_str());
350
351			painCave.isFatal = 1;
352			simError();
353			}
354
355			return new Bend(atomA, atomB, atomC, bendType);
356			}
357	tim	1719	}
358
359			Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
360			TorsionType* torsionType;
361			Atom* atomA;
362			Atom* atomB;
363			Atom* atomC;
364			Atom* atomD;
365
366			atomA = mol->getAtomAt(stamp->getA());
367			atomB = mol->getAtomAt(stamp->getB());
368			atomC = mol->getAtomAt(stamp->getC());
369			atomD = mol->getAtomAt(stamp->getD());
370
371			assert(atomA && atomB && atomC && atomD);
372
373	tim	1805	torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
374	tim	1719	atomC->getType(), atomD->getType());
375
376	tim	1733	if (torsionType == NULL) {
377			sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
378			atomA->getType().c_str(),
379			atomB->getType().c_str(),
380			atomC->getType().c_str(),
381			atomD->getType().c_str());
382
383			painCave.isFatal = 1;
384			simError();
385			}
386
387	tim	1805	return new Torsion(atomA, atomB, atomC, atomD, torsionType);
388	tim	1719	}
389
390			CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
391			int nAtoms;
392			CutoffGroup* cg;
393			Atom* atom;
394			cg = new CutoffGroup();
395
396			nAtoms = stamp->getNMembers();
397			for (int i =0; i < nAtoms; ++i) {
398			atom = mol->getAtomAt(stamp->getMember(i));
399			assert(atom);
400			cg->addAtom(atom);
401			}
402
403			return cg;
404			}
405
406	tim	1734	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
407			CutoffGroup* cg;
408			cg = new CutoffGroup();
409	tim	1805	cg->addAtom(atom);
410	tim	1734	return cg;
411			}
412	tim	1719
413	tim	1901	void MoleculeCreator::createConstraintPair(Molecule* mol) {
414	tim	1719
415	tim	1901	//add bond constraints
416			Molecule::BondIterator bi;
417			Bond* bond;
418			for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
419
420			BondType* bt = bond->getBondType();
421			FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
422
423			//found a constraint pair
424			if (fbt != NULL) {
425			ConstraintPair* consPair = new ConstraintPair(bond->getAtomA(), bond->getAtomB(), fbt->getEquilibriumBondLength());
426			mol->addConstraintPair(consPair);
427			}
428
429			}
430
431			//rigidbody -- rigidbody constraint is not support yet
432
433	tim	1719	}
434	tim	1901
435			}