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 "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;
}
//Constraint* MoleculeCreator::createConstraint() {

//}

}
Revision:	1857
Committed:	Mon Dec 6 20:15:02 2004 UTC (19 years, 7 months ago) by tim
File size:	13583 byte(s)
Log Message:	short range interaction for butane is correct.Still something wrong with long range one
#	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
36	#include "brains/MoleculeCreator.hpp"
37	#include "primitives/GhostBend.hpp"
38	#include "types/DirectionalAtomType.hpp"
39	#include "utils/simError.h"
40	#include "utils/StringUtils.hpp"
41
42	namespace oopse {
43
44	Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
45	int stampId, int globalIndex, LocalIndexManager* localIndexMan) {
46
47	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
48
49	//create atoms
50	Atom* atom;
51	AtomStamp* currentAtomStamp;
52	int nAtom = molStamp->getNAtoms();
53	for (int i = 0; i < nAtom; ++i) {
54	currentAtomStamp = molStamp->getAtom(i);
55	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
56	mol->addAtom(atom);
57	}
58
59	//create rigidbodies
60	RigidBody* rb;
61	RigidBodyStamp * currentRigidBodyStamp;
62	int nRigidbodies = molStamp->getNRigidBodies();
63
64	for (int i = 0; i < nRigidbodies; ++i) {
65	currentRigidBodyStamp = molStamp->getRigidBody(i);
66	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
67	mol->addRigidBody(rb);
68	}
69
70	//create bonds
71	Bond* bond;
72	BondStamp* currentBondStamp;
73	int nBonds = molStamp->getNBonds();
74
75	for (int i = 0; i < nBonds; ++i) {
76	currentBondStamp = molStamp->getBond(i);
77	bond = createBond(ff, mol, currentBondStamp);
78	mol->addBond(bond);
79	}
80
81	//create bends
82	Bend* bend;
83	BendStamp* currentBendStamp;
84	int nBends = molStamp->getNBends();
85	for (int i = 0; i < nBends; ++i) {
86	currentBendStamp = molStamp->getBend(i);
87	bend = createBend(ff, mol, currentBendStamp);
88	mol->addBend(bend);
89	}
90
91	//create torsions
92	Torsion* torsion;
93	TorsionStamp* currentTorsionStamp;
94	int nTorsions = molStamp->getNTorsions();
95	for (int i = 0; i < nTorsions; ++i) {
96	currentTorsionStamp = molStamp->getTorsion(i);
97	torsion = createTorsion(ff, mol, currentTorsionStamp);
98	mol->addTorsion(torsion);
99	}
100
101	//create cutoffGroups
102	CutoffGroup* cutoffGroup;
103	CutoffGroupStamp* currentCutoffGroupStamp;
104	int nCutoffGroups = molStamp->getNCutoffGroups();
105	for (int i = 0; i < nCutoffGroups; ++i) {
106	currentCutoffGroupStamp = molStamp->getCutoffGroup(i);
107	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
108	mol->addCutoffGroup(cutoffGroup);
109	}
110
111	//every free atom is a cutoff group
112	std::set<Atom*> allAtoms;
113	Molecule::AtomIterator ai;
114
115	//add all atoms into allAtoms set
116	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
117	allAtoms.insert(atom);
118	}
119
120	Molecule::CutoffGroupIterator ci;
121	CutoffGroup* cg;
122	std::set<Atom*> cutoffAtoms;
123
124	//add all of the atoms belong to cutoff groups into cutoffAtoms set
125	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
126
127	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
128	cutoffAtoms.insert(atom);
129	}
130
131	}
132
133	//find all free atoms (which do not belong to cutoff groups)
134	//performs the "difference" operation from set theory, the output range contains a copy of every
135	//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
136	//[cutoffAtoms.begin(), cutoffAtoms.end()).
137	std::vector<Atom*> freeAtoms;
138	std::set_difference(allAtoms.begin(), allAtoms.end(), cutoffAtoms.begin(), cutoffAtoms.end(),
139	std::back_inserter(freeAtoms));
140
141	if (freeAtoms.size() != allAtoms.size() - cutoffAtoms.size()) {
142	//Some atoms in rigidAtoms are not in allAtoms, something must be wrong
143	sprintf(painCave.errMsg, "Atoms in cutoff groups are not in the atom list of the same molecule");
144
145	painCave.isFatal = 1;
146	simError();
147	}
148
149	//loop over the free atoms and then create one cutoff group for every single free atom
150	std::vector<Atom*>::iterator fai;
151
152	for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
153	cutoffGroup = createCutoffGroup(mol, *fai);
154	mol->addCutoffGroup(cutoffGroup);
155	}
156	//create constraints
157
158	//the construction of this molecule is finished
159	mol->complete();
160
161	return mol;
162	}
163
164
165	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
166	LocalIndexManager* localIndexMan) {
167	AtomType * atomType;
168	Atom* atom;
169
170	atomType = ff->getAtomType(stamp->getType());
171
172	if (atomType == NULL) {
173	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
174	stamp->getType());
175
176	painCave.isFatal = 1;
177	simError();
178	}
179
180	//below code still have some kind of hard-coding smell
181	if (atomType->isDirectional()){
182
183	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
184
185	if (dAtomType == NULL) {
186	sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
187
188	painCave.isFatal = 1;
189	simError();
190	}
191
192	DirectionalAtom* dAtom;
193	dAtom = new DirectionalAtom(dAtomType);
194	atom = dAtom;
195	}
196	else{
197	atom = new Atom(atomType);
198	}
199
200	atom->setLocalIndex(localIndexMan->getNextAtomIndex());
201
202	return atom;
203	}
204
205	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp molStamp, Molecule mol,
206	RigidBodyStamp* rbStamp,
207	LocalIndexManager* localIndexMan) {
208	Atom* atom;
209	int nAtoms;
210	Vector3d refCoor;
211	AtomStamp* atomStamp;
212
213	RigidBody* rb = new RigidBody();
214	nAtoms = rbStamp->getNMembers();
215	for (int i = 0; i < nAtoms; ++i) {
216	//rbStamp->getMember(i) return the local index of current atom inside the molecule.
217	//It is not the same as local index of atom which is the index of atom at DataStorage class
218	atom = mol->getAtomAt(rbStamp->getMember(i));
219	atomStamp= molStamp->getAtom(rbStamp->getMember(i));
220	rb->addAtom(atom, atomStamp);
221	}
222
223	//after all of the atoms are added, we need to calculate the reference coordinates
224	rb->calcRefCoords();
225
226	//set the local index of this rigid body, global index will be set later
227	rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
228
229	//the rule for naming rigidbody MoleculeName_RB_Integer
230	//The first part is the name of the molecule
231	//The second part is alway fixed as "RB"
232	//The third part is the index of the rigidbody defined in meta-data file
233	//For example, Butane_RB_0 is a valid rigid body name of butane molecule
234	/*@todo replace itoa by lexi_cast /
235	rb->setType(mol->getType() + "_RB_" + toString(mol->getNRigidBodies()));
236
237	return rb;
238	}
239
240	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
241	BondType* bondType;
242	Atom* atomA;
243	Atom* atomB;
244
245	atomA = mol->getAtomAt(stamp->getA());
246	atomB = mol->getAtomAt(stamp->getB());
247
248	assert( atomA && atomB);
249
250	bondType = ff->getBondType(atomA->getType(), atomB->getType());
251
252	if (bondType == NULL) {
253	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
254	atomA->getType().c_str(),
255	atomB->getType().c_str());
256
257	painCave.isFatal = 1;
258	simError();
259	}
260	return new Bond(atomA, atomB, bondType);
261	}
262
263	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
264	bool isGhostBend = false;
265	int ghostIndex;
266
267
268	//
269	if (stamp->haveExtras()){
270	LinkedAssign* extras = stamp->getExtras();
271	LinkedAssign* currentExtra = extras;
272
273	while (currentExtra != NULL){
274	if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
275	switch (currentExtra->getType()){
276	case 0:
277	ghostIndex = currentExtra->getInt();
278	isGhostBend = true;
279	break;
280
281	default:
282	sprintf(painCave.errMsg,
283	"SimSetup Error: ghostVectorSource must be an int.\n");
284	painCave.isFatal = 1;
285	simError();
286	}
287	} else{
288	sprintf(painCave.errMsg,
289	"SimSetup Error: unhandled bend assignment:\n");
290	painCave.isFatal = 1;
291	simError();
292	}
293	currentExtra = currentExtra->getNext();
294	}
295
296	}
297
298	if (isGhostBend) {
299
300	int indexA = stamp->getA();
301	int indexB= stamp->getB();
302
303	assert(indexA != indexB);
304
305	int normalIndex;
306	if (indexA == ghostIndex) {
307	normalIndex = indexB;
308	} else if (indexB == ghostIndex) {
309	normalIndex = indexA;
310	}
311
312	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
313	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
314	if (ghostAtom == NULL) {
315	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
316	painCave.isFatal = 1;
317	simError();
318	}
319
320	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
321
322	if (bendType == NULL) {
323	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
324	normalAtom->getType().c_str(),
325	ghostAtom->getType().c_str(),
326	"GHOST");
327
328	painCave.isFatal = 1;
329	simError();
330	}
331
332	return new GhostBend(normalAtom, ghostAtom, bendType);
333
334	} else {
335
336	Atom* atomA = mol->getAtomAt(stamp->getA());
337	Atom* atomB = mol->getAtomAt(stamp->getB());
338	Atom* atomC = mol->getAtomAt(stamp->getC());
339
340	assert( atomA && atomB && atomC);
341
342	BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
343
344	if (bendType == NULL) {
345	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
346	atomA->getType().c_str(),
347	atomB->getType().c_str(),
348	atomC->getType().c_str());
349
350	painCave.isFatal = 1;
351	simError();
352	}
353
354	return new Bend(atomA, atomB, atomC, bendType);
355	}
356	}
357
358	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
359	TorsionType* torsionType;
360	Atom* atomA;
361	Atom* atomB;
362	Atom* atomC;
363	Atom* atomD;
364
365	atomA = mol->getAtomAt(stamp->getA());
366	atomB = mol->getAtomAt(stamp->getB());
367	atomC = mol->getAtomAt(stamp->getC());
368	atomD = mol->getAtomAt(stamp->getD());
369
370	assert(atomA && atomB && atomC && atomD);
371
372	torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
373	atomC->getType(), atomD->getType());
374
375	if (torsionType == NULL) {
376	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
377	atomA->getType().c_str(),
378	atomB->getType().c_str(),
379	atomC->getType().c_str(),
380	atomD->getType().c_str());
381
382	painCave.isFatal = 1;
383	simError();
384	}
385
386	return new Torsion(atomA, atomB, atomC, atomD, torsionType);
387	}
388
389	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
390	int nAtoms;
391	CutoffGroup* cg;
392	Atom* atom;
393	cg = new CutoffGroup();
394
395	nAtoms = stamp->getNMembers();
396	for (int i =0; i < nAtoms; ++i) {
397	atom = mol->getAtomAt(stamp->getMember(i));
398	assert(atom);
399	cg->addAtom(atom);
400	}
401
402	return cg;
403	}
404
405	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
406	CutoffGroup* cg;
407	cg = new CutoffGroup();
408	cg->addAtom(atom);
409	return cg;
410	}
411	//Constraint* MoleculeCreator::createConstraint() {
412
413	//}
414
415	}