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 (21 years, 2 months ago) by tim
File size:	13248 byte(s)
Log Message:	refactory NPT integrator
#	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 "brains/MoleculeCreator.hpp"
35			#include <cassert>
36
37			namespace oopse {
38
39			Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp, int stampId, int globalIndex) {
40	tim	1733	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
41	tim	1719
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	tim	1734	//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	tim	1719	//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	tim	1733	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	tim	1719	//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	tim	1733	nAtoms = molStamp->getNMembers();
209	tim	1719
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	tim	1733
220			//after all of the atoms are added, we need to calculate the reference coordinates
221	tim	1719	rb->calcRefCoords();
222	tim	1733
223			//set the local index of this rigid body, global index will be set later
224	tim	1719	rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
225	tim	1733
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	tim	1719
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	tim	1733	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	tim	1719	return new Bond(atomA, atomB, bondType);
257			}
258
259			Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
260	tim	1774	bool isGhostBend = false;
261			int ghostIndex;
262	tim	1719
263
264	tim	1774	//
265			if (stamp->haveExtras()){
266			LinkedAssign* extras = currentBend->getExtras();
267			LinkedAssign* currentExtra = extras;
268	tim	1719
269	tim	1774	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	tim	1719
277	tim	1774	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	tim	1733	}
293
294	tim	1774	if (isGhostBend) {
295	tim	1733
296	tim	1774	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	tim	1719	}
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	tim	1733	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	tim	1719	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	tim	1734	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
397			CutoffGroup* cg;
398			cg = new CutoffGroup();
399			cg->addAtom();
400			return cg;
401			}
402	tim	1719	//Constraint* MoleculeCreator::createConstraint() {
403
404			//}
405
406			}