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 "brains/MoleculeCreator.hpp"
#include <cassert>

namespace oopse {

Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp, int stampId, int globalIndex) {
    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, currentAtomStamp);
        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(ff, mol, currentRigidBodyStamp);
        mol->addRigidBody(rb);
    }

    //create bonds
    Bond* bond;
    BondStamp* currentBondStamp;
    int nBonds = molStamp->getNBends();

    for (int i = 0; i < nBonds; ++i) {
        currentBondStamp = molStamp->getBend(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(ff, mol, currentCutoffGroupStamp);
        mol->addCutoffGroup(cutoffGroup);
    }

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

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

    typename 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.end()));

    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) {
        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 (bondType == 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 (stamp->haveOrientation()){
        DirectionalAtom* dAtom;
        double phi;
        double theta;
        double psi;
        
        dAtom = new DirectionalAtom(atomType);

        // Directional Atoms have standard unit vectors which are oriented
        // in space using the three Euler angles.  We assume the standard
        // unit vector was originally along the z axis below.

        phi = stamp->getEulerPhi() * M_PI / 180.0;
        theta = stamp->getEulerTheta() * M_PI / 180.0;
        psi = stamp->getEulerPsi()* M_PI / 180.0;

        dAtom->setUnitFrameFromEuler(phi, theta, psi);
        atom = dAtom;    
    }
    else{
        atom = new Atom(atomType);
    }

    atom->setLocalIndex(localIndexMan->getNextAtomIndex());
}

RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, Molecule* mol,
                                                                                    RigidBodyStamp* rbStamp, 
                                                                                    LocalIndexManager* localIndexMan) {
    Atom* atom;
    int nAtoms;
    Vector3d refCoor;
    AtomStamp* atomStamp;
    
    nAtoms = molStamp->getNMembers();

    RigidBody* rb = new RigidBody();
    
    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->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
    rb->setType(mol->getType() + "_RB_" + itoa(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, atomB);

    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 = currentBend->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) ;
        Atom* ghostAtom = mol->getAtomAt(ghostIndex);
        
        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->getTosionType(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, 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();
    return cg;
}
//Constraint* MoleculeCreator::createConstraint() {

//}

}
Revision:	1774
Committed:	Tue Nov 23 23:12:23 2004 UTC (19 years, 7 months ago) by tim
File size:	13248 byte(s)
Log Message:	refactory NPT integrator
#	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 "brains/MoleculeCreator.hpp"
35	#include <cassert>
36
37	namespace oopse {
38
39	Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp, int stampId, int globalIndex) {
40	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
41
42	//create atoms
43	Atom* atom;
44	AtomStamp* currentAtomStamp;
45	int nAtom = molStamp->getNAtoms();
46	for (int i = 0; i < nAtom; ++i) {
47	currentAtomStamp = molStamp->getAtom(i);
48	atom = createAtom(ff, currentAtomStamp);
49	mol->addAtom(atom);
50	}
51
52	//create rigidbodies
53	RigidBody* rb;
54	RigidBodyStamp * currentRigidBodyStamp;
55	int nRigidbodies = molStamp->getNRigidBodies();
56
57	for (int i = 0; i < nRigidbodies; ++i) {
58	currentRigidBodyStamp = molStamp->getRigidBody(i);
59	rb = createRigidBody(ff, mol, currentRigidBodyStamp);
60	mol->addRigidBody(rb);
61	}
62
63	//create bonds
64	Bond* bond;
65	BondStamp* currentBondStamp;
66	int nBonds = molStamp->getNBends();
67
68	for (int i = 0; i < nBonds; ++i) {
69	currentBondStamp = molStamp->getBend(i);
70	bond = createBond(ff, mol, currentBondStamp);
71	mol->addBond(bond);
72	}
73
74	//create bends
75	Bend* bend;
76	BendStamp* currentBendStamp;
77	int nBends = molStamp->getNBends();
78	for (int i = 0; i < nBends; ++i) {
79	currentBendStamp = molStamp->getBend(i);
80	bend = createBend(ff, mol, currentBendStamp);
81	mol->addBend(bend);
82	}
83
84	//create torsions
85	Torsion* torsion;
86	TorsionStamp* currentTorsionStamp;
87	int nTorsions = molStamp->getNTorsions();
88	for (int i = 0; i < nTorsions; ++i) {
89	currentTorsionStamp = molStamp->getTorsion(i);
90	torsion = createTorsion(ff, mol, currentTorsionStamp);
91	mol->addTorsion(torsion);
92	}
93
94	//create cutoffGroups
95	CutoffGroup* cutoffGroup;
96	CutoffGroupStamp* currentCutoffGroupStamp;
97	int nCutoffGroups = molStamp->getNCutoffGroups();
98	for (int i = 0; i < nCutoffGroups; ++i) {
99	currentCutoffGroupStamp = molStamp->getCutoffGroup(i);
100	cutoffGroup = createCutoffGroup(ff, mol, currentCutoffGroupStamp);
101	mol->addCutoffGroup(cutoffGroup);
102	}
103
104	//every free atom is a cutoff group
105	std::set<Atom*> allAtoms;
106	typename Molecule::AtomIterator ai;
107
108	//add all atoms into allAtoms set
109	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
110	allAtoms.insert(atom);
111	}
112
113	typename Molecule::CutoffGroupIterator ci;
114	CutoffGroup* cg;
115	std::set<Atom*> cutoffAtoms;
116
117	//add all of the atoms belong to cutoff groups into cutoffAtoms set
118	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
119
120	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
121	cutoffAtoms.insert(atom);
122	}
123
124	}
125
126	//find all free atoms (which do not belong to cutoff groups)
127	//performs the "difference" operation from set theory, the output range contains a copy of every
128	//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
129	//[cutoffAtoms.begin(), cutoffAtoms.end()).
130	std::vector<Atom*> freeAtoms;
131	std::set_difference(allAtoms.begin(), allAtoms.end(), cutoffAtoms.begin(), cutoffAtoms.end(),
132	std::back_inserter(freeAtoms.end()));
133
134	if (freeAtoms.size() != allAtoms.size() - cutoffAtoms.size()) {
135	//Some atoms in rigidAtoms are not in allAtoms, something must be wrong
136	sprintf(painCave.errMsg, "Atoms in cutoff groups are not in the atom list of the same molecule");
137
138	painCave.isFatal = 1;
139	simError();
140	}
141
142	//loop over the free atoms and then create one cutoff group for every single free atom
143	std::vector<Atom*>::iterator fai;
144
145	for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
146	createCutoffGroup(mol, *fai);
147	mol->addCutoffGroup(cutoffGroup);
148	}
149	//create constraints
150
151	//the construction of this molecule is finished
152	mol->complete();
153
154	return mol;
155	}
156
157
158	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
159	LocalIndexManager* localIndexMan) {
160	AtomType * atomType;
161	Atom* atom;
162
163	atomType = ff->getAtomType(stamp->getType());
164
165	if (bondType == NULL) {
166	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
167	stamp->getType());
168
169	painCave.isFatal = 1;
170	simError();
171	}
172
173	//below code still have some kind of hard-coding smell
174	if (stamp->haveOrientation()){
175	DirectionalAtom* dAtom;
176	double phi;
177	double theta;
178	double psi;
179
180	dAtom = new DirectionalAtom(atomType);
181
182	// Directional Atoms have standard unit vectors which are oriented
183	// in space using the three Euler angles. We assume the standard
184	// unit vector was originally along the z axis below.
185
186	phi = stamp->getEulerPhi() * M_PI / 180.0;
187	theta = stamp->getEulerTheta() * M_PI / 180.0;
188	psi = stamp->getEulerPsi()* M_PI / 180.0;
189
190	dAtom->setUnitFrameFromEuler(phi, theta, psi);
191	atom = dAtom;
192	}
193	else{
194	atom = new Atom(atomType);
195	}
196
197	atom->setLocalIndex(localIndexMan->getNextAtomIndex());
198	}
199
200	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp molStamp, Molecule mol,
201	RigidBodyStamp* rbStamp,
202	LocalIndexManager* localIndexMan) {
203	Atom* atom;
204	int nAtoms;
205	Vector3d refCoor;
206	AtomStamp* atomStamp;
207
208	nAtoms = molStamp->getNMembers();
209
210	RigidBody* rb = new RigidBody();
211
212	for (int i = 0; i < nAtoms; ++i) {
213	//rbStamp->getMember(i) return the local index of current atom inside the molecule.
214	//It is not the same as local index of atom which is the index of atom at DataStorage class
215	atom = mol->getAtomAt(rbStamp->getMember(i));
216	atomStamp= molStamp->molStamp->getAtom(rbStamp->getMember(i));
217	rb->addAtom(atom, atomStamp);
218	}
219
220	//after all of the atoms are added, we need to calculate the reference coordinates
221	rb->calcRefCoords();
222
223	//set the local index of this rigid body, global index will be set later
224	rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
225
226	//the rule for naming rigidbody MoleculeName_RB_Integer
227	//The first part is the name of the molecule
228	//The second part is alway fixed as "RB"
229	//The third part is the index of the rigidbody defined in meta-data file
230	//For example, Butane_RB_0 is a valid rigid body name of butane molecule
231	rb->setType(mol->getType() + "_RB_" + itoa(mol.getNRigidBodies()));
232
233	return rb;
234	}
235
236	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
237	BondType* bondType;
238	Atom* atomA;
239	Atom* atomB;
240
241	atomA = mol->getAtomAt(stamp->getA());
242	atomB = mol->getAtomAt(stamp->getB());
243
244	assert( atomA && atomB);
245
246	bondType = ff->getBondType(atomA, atomB);
247
248	if (bondType == NULL) {
249	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
250	atomA->getType().c_str(),
251	atomB->getType().c_str());
252
253	painCave.isFatal = 1;
254	simError();
255	}
256	return new Bond(atomA, atomB, bondType);
257	}
258
259	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
260	bool isGhostBend = false;
261	int ghostIndex;
262
263
264	//
265	if (stamp->haveExtras()){
266	LinkedAssign* extras = currentBend->getExtras();
267	LinkedAssign* currentExtra = extras;
268
269	while (currentExtra != NULL){
270	if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
271	switch (currentExtra->getType()){
272	case 0:
273	ghostIndex = currentExtra->getInt();
274	isGhostBend = true;
275	break;
276
277	default:
278	sprintf(painCave.errMsg,
279	"SimSetup Error: ghostVectorSource must be an int.\n");
280	painCave.isFatal = 1;
281	simError();
282	}
283	} else{
284	sprintf(painCave.errMsg,
285	"SimSetup Error: unhandled bend assignment:\n");
286	painCave.isFatal = 1;
287	simError();
288	}
289	currentExtra = currentExtra->getNext();
290	}
291
292	}
293
294	if (isGhostBend) {
295
296	int indexA = stamp->getA();
297	int indexB= stamp->getB();
298
299	assert(indexA != indexB);
300
301	int normalIndex;
302	if (indexA == ghostIndex) {
303	normalIndex = indexB;
304	} else if (indexB == ghostIndex) {
305	normalIndex = indexA;
306	}
307
308	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
309	Atom* ghostAtom = mol->getAtomAt(ghostIndex);
310
311	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
312
313	if (bendType == NULL) {
314	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
315	normalAtom->getType().c_str(),
316	ghostAtom->getType().c_str(),
317	"GHOST");
318
319	painCave.isFatal = 1;
320	simError();
321	}
322
323	return new GhostBend(normalAtom, ghostAtom, bendType);
324
325	} else {
326
327	Atom* atomA = mol->getAtomAt(stamp->getA());
328	Atom* atomB = mol->getAtomAt(stamp->getB());
329	Atom* atomC = mol->getAtomAt(stamp->getC());
330
331	assert( atomA && atomB && atomC);
332
333	BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
334
335	if (bendType == NULL) {
336	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
337	atomA->getType().c_str(),
338	atomB->getType().c_str(),
339	atomC->getType().c_str());
340
341	painCave.isFatal = 1;
342	simError();
343	}
344
345	return new Bend(atomA, atomB, atomC, bendType);
346	}
347	}
348
349	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
350	TorsionType* torsionType;
351	Atom* atomA;
352	Atom* atomB;
353	Atom* atomC;
354	Atom* atomD;
355
356	atomA = mol->getAtomAt(stamp->getA());
357	atomB = mol->getAtomAt(stamp->getB());
358	atomC = mol->getAtomAt(stamp->getC());
359	atomD = mol->getAtomAt(stamp->getD());
360
361	assert(atomA && atomB && atomC && atomD);
362
363	torsionType = ff->getTosionType(atomA->getType(), atomB->getType(),
364	atomC->getType(), atomD->getType());
365
366	if (torsionType == NULL) {
367	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
368	atomA->getType().c_str(),
369	atomB->getType().c_str(),
370	atomC->getType().c_str(),
371	atomD->getType().c_str());
372
373	painCave.isFatal = 1;
374	simError();
375	}
376
377	return new Torsion(atomA, atomB, torsionType);
378	}
379
380	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
381	int nAtoms;
382	CutoffGroup* cg;
383	Atom* atom;
384	cg = new CutoffGroup();
385
386	nAtoms = stamp->getNMembers();
387	for (int i =0; i < nAtoms; ++i) {
388	atom = mol->getAtomAt(stamp->getMember(i));
389	assert(atom);
390	cg->addAtom(atom);
391	}
392
393	return cg;
394	}
395
396	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
397	CutoffGroup* cg;
398	cg = new CutoffGroup();
399	cg->addAtom();
400	return cg;
401	}
402	//Constraint* MoleculeCreator::createConstraint() {
403
404	//}
405
406	}