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 "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->getNBends();

    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) {
        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:	1813
Committed:	Wed Dec 1 17:38:32 2004 UTC (19 years, 9 months ago) by tim
File size:	13528 byte(s)
Log Message:	refactory AtomType
#	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			#include "utils/simError.h"
39			#include "utils/StringUtils.hpp"
40
41	tim	1719	namespace oopse {
42
43	tim	1805	Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
44			int stampId, int globalIndex, LocalIndexManager* localIndexMan) {
45
46	tim	1733	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
47	tim	1719
48			//create atoms
49			Atom* atom;
50			AtomStamp* currentAtomStamp;
51			int nAtom = molStamp->getNAtoms();
52			for (int i = 0; i < nAtom; ++i) {
53			currentAtomStamp = molStamp->getAtom(i);
54	tim	1805	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
55	tim	1719	mol->addAtom(atom);
56			}
57
58			//create rigidbodies
59			RigidBody* rb;
60			RigidBodyStamp * currentRigidBodyStamp;
61			int nRigidbodies = molStamp->getNRigidBodies();
62
63			for (int i = 0; i < nRigidbodies; ++i) {
64			currentRigidBodyStamp = molStamp->getRigidBody(i);
65	tim	1805	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
66	tim	1719	mol->addRigidBody(rb);
67			}
68
69			//create bonds
70			Bond* bond;
71			BondStamp* currentBondStamp;
72			int nBonds = molStamp->getNBends();
73
74			for (int i = 0; i < nBonds; ++i) {
75	tim	1805	currentBondStamp = molStamp->getBond(i);
76	tim	1719	bond = createBond(ff, mol, currentBondStamp);
77			mol->addBond(bond);
78			}
79
80			//create bends
81			Bend* bend;
82			BendStamp* currentBendStamp;
83			int nBends = molStamp->getNBends();
84			for (int i = 0; i < nBends; ++i) {
85			currentBendStamp = molStamp->getBend(i);
86			bend = createBend(ff, mol, currentBendStamp);
87			mol->addBend(bend);
88			}
89
90			//create torsions
91			Torsion* torsion;
92			TorsionStamp* currentTorsionStamp;
93			int nTorsions = molStamp->getNTorsions();
94			for (int i = 0; i < nTorsions; ++i) {
95			currentTorsionStamp = molStamp->getTorsion(i);
96			torsion = createTorsion(ff, mol, currentTorsionStamp);
97			mol->addTorsion(torsion);
98			}
99
100			//create cutoffGroups
101			CutoffGroup* cutoffGroup;
102			CutoffGroupStamp* currentCutoffGroupStamp;
103			int nCutoffGroups = molStamp->getNCutoffGroups();
104			for (int i = 0; i < nCutoffGroups; ++i) {
105			currentCutoffGroupStamp = molStamp->getCutoffGroup(i);
106	tim	1805	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
107	tim	1719	mol->addCutoffGroup(cutoffGroup);
108			}
109
110	tim	1734	//every free atom is a cutoff group
111			std::set<Atom*> allAtoms;
112	tim	1805	Molecule::AtomIterator ai;
113	tim	1734
114			//add all atoms into allAtoms set
115			for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
116			allAtoms.insert(atom);
117			}
118
119	tim	1805	Molecule::CutoffGroupIterator ci;
120	tim	1734	CutoffGroup* cg;
121			std::set<Atom*> cutoffAtoms;
122
123			//add all of the atoms belong to cutoff groups into cutoffAtoms set
124			for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
125
126			for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
127			cutoffAtoms.insert(atom);
128			}
129
130			}
131
132			//find all free atoms (which do not belong to cutoff groups)
133			//performs the "difference" operation from set theory, the output range contains a copy of every
134			//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
135			//[cutoffAtoms.begin(), cutoffAtoms.end()).
136			std::vector<Atom*> freeAtoms;
137			std::set_difference(allAtoms.begin(), allAtoms.end(), cutoffAtoms.begin(), cutoffAtoms.end(),
138	tim	1805	std::back_inserter(freeAtoms));
139	tim	1734
140			if (freeAtoms.size() != allAtoms.size() - cutoffAtoms.size()) {
141			//Some atoms in rigidAtoms are not in allAtoms, something must be wrong
142			sprintf(painCave.errMsg, "Atoms in cutoff groups are not in the atom list of the same molecule");
143
144			painCave.isFatal = 1;
145			simError();
146			}
147
148			//loop over the free atoms and then create one cutoff group for every single free atom
149			std::vector<Atom*>::iterator fai;
150
151			for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
152			createCutoffGroup(mol, *fai);
153			mol->addCutoffGroup(cutoffGroup);
154			}
155	tim	1719	//create constraints
156
157			//the construction of this molecule is finished
158			mol->complete();
159
160			return mol;
161			}
162
163
164			Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
165			LocalIndexManager* localIndexMan) {
166			AtomType * atomType;
167			Atom* atom;
168
169			atomType = ff->getAtomType(stamp->getType());
170
171	tim	1804	if (atomType == NULL) {
172	tim	1733	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
173			stamp->getType());
174
175			painCave.isFatal = 1;
176			simError();
177			}
178
179	tim	1719	//below code still have some kind of hard-coding smell
180	tim	1813	if (atomType->isDirectional()){
181
182	tim	1804	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
183	tim	1813
184	tim	1804	if (dAtomType == NULL) {
185			sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
186
187			painCave.isFatal = 1;
188			simError();
189			}
190	tim	1813
191			DirectionalAtom* dAtom;
192	tim	1804	dAtom = new DirectionalAtom(dAtomType);
193	tim	1719	atom = dAtom;
194			}
195			else{
196			atom = new Atom(atomType);
197			}
198
199			atom->setLocalIndex(localIndexMan->getNextAtomIndex());
200	tim	1805
201			return atom;
202	tim	1719	}
203
204			RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp molStamp, Molecule mol,
205			RigidBodyStamp* rbStamp,
206			LocalIndexManager* localIndexMan) {
207			Atom* atom;
208			int nAtoms;
209			Vector3d refCoor;
210			AtomStamp* atomStamp;
211
212			RigidBody* rb = new RigidBody();
213	tim	1805	nAtoms = rbStamp->getNMembers();
214	tim	1719	for (int i = 0; i < nAtoms; ++i) {
215			//rbStamp->getMember(i) return the local index of current atom inside the molecule.
216			//It is not the same as local index of atom which is the index of atom at DataStorage class
217			atom = mol->getAtomAt(rbStamp->getMember(i));
218	tim	1805	atomStamp= molStamp->getAtom(rbStamp->getMember(i));
219	tim	1719	rb->addAtom(atom, atomStamp);
220			}
221	tim	1733
222			//after all of the atoms are added, we need to calculate the reference coordinates
223	tim	1719	rb->calcRefCoords();
224	tim	1733
225			//set the local index of this rigid body, global index will be set later
226	tim	1719	rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
227	tim	1733
228			//the rule for naming rigidbody MoleculeName_RB_Integer
229			//The first part is the name of the molecule
230			//The second part is alway fixed as "RB"
231			//The third part is the index of the rigidbody defined in meta-data file
232			//For example, Butane_RB_0 is a valid rigid body name of butane molecule
233	tim	1805	/*@todo replace itoa by lexi_cast /
234			rb->setType(mol->getType() + "_RB_" + toString(mol->getNRigidBodies()));
235	tim	1719
236			return rb;
237			}
238
239			Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
240			BondType* bondType;
241			Atom* atomA;
242			Atom* atomB;
243
244			atomA = mol->getAtomAt(stamp->getA());
245			atomB = mol->getAtomAt(stamp->getB());
246
247			assert( atomA && atomB);
248
249	tim	1805	bondType = ff->getBondType(atomA->getType(), atomB->getType());
250	tim	1719
251	tim	1733	if (bondType == NULL) {
252			sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
253			atomA->getType().c_str(),
254			atomB->getType().c_str());
255
256			painCave.isFatal = 1;
257			simError();
258			}
259	tim	1719	return new Bond(atomA, atomB, bondType);
260			}
261
262			Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
263	tim	1774	bool isGhostBend = false;
264			int ghostIndex;
265	tim	1719
266
267	tim	1774	//
268			if (stamp->haveExtras()){
269	tim	1805	LinkedAssign* extras = stamp->getExtras();
270	tim	1774	LinkedAssign* currentExtra = extras;
271	tim	1719
272	tim	1774	while (currentExtra != NULL){
273			if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
274			switch (currentExtra->getType()){
275			case 0:
276			ghostIndex = currentExtra->getInt();
277			isGhostBend = true;
278			break;
279	tim	1719
280	tim	1774	default:
281			sprintf(painCave.errMsg,
282			"SimSetup Error: ghostVectorSource must be an int.\n");
283			painCave.isFatal = 1;
284			simError();
285			}
286			} else{
287			sprintf(painCave.errMsg,
288			"SimSetup Error: unhandled bend assignment:\n");
289			painCave.isFatal = 1;
290			simError();
291			}
292			currentExtra = currentExtra->getNext();
293			}
294
295	tim	1733	}
296
297	tim	1774	if (isGhostBend) {
298	tim	1733
299	tim	1774	int indexA = stamp->getA();
300			int indexB= stamp->getB();
301
302			assert(indexA != indexB);
303
304			int normalIndex;
305			if (indexA == ghostIndex) {
306			normalIndex = indexB;
307			} else if (indexB == ghostIndex) {
308			normalIndex = indexA;
309			}
310
311	tim	1805	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
312			DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
313			if (ghostAtom == NULL) {
314			sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
315			painCave.isFatal = 1;
316			simError();
317			}
318
319	tim	1774	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
320
321			if (bendType == NULL) {
322			sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
323			normalAtom->getType().c_str(),
324			ghostAtom->getType().c_str(),
325			"GHOST");
326
327			painCave.isFatal = 1;
328			simError();
329			}
330	tim	1805
331	tim	1774	return new GhostBend(normalAtom, ghostAtom, bendType);
332
333			} else {
334
335			Atom* atomA = mol->getAtomAt(stamp->getA());
336			Atom* atomB = mol->getAtomAt(stamp->getB());
337			Atom* atomC = mol->getAtomAt(stamp->getC());
338
339			assert( atomA && atomB && atomC);
340
341			BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
342
343			if (bendType == NULL) {
344			sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
345			atomA->getType().c_str(),
346			atomB->getType().c_str(),
347			atomC->getType().c_str());
348
349			painCave.isFatal = 1;
350			simError();
351			}
352
353			return new Bend(atomA, atomB, atomC, bendType);
354			}
355	tim	1719	}
356
357			Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
358			TorsionType* torsionType;
359			Atom* atomA;
360			Atom* atomB;
361			Atom* atomC;
362			Atom* atomD;
363
364			atomA = mol->getAtomAt(stamp->getA());
365			atomB = mol->getAtomAt(stamp->getB());
366			atomC = mol->getAtomAt(stamp->getC());
367			atomD = mol->getAtomAt(stamp->getD());
368
369			assert(atomA && atomB && atomC && atomD);
370
371	tim	1805	torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
372	tim	1719	atomC->getType(), atomD->getType());
373
374	tim	1733	if (torsionType == NULL) {
375			sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
376			atomA->getType().c_str(),
377			atomB->getType().c_str(),
378			atomC->getType().c_str(),
379			atomD->getType().c_str());
380
381			painCave.isFatal = 1;
382			simError();
383			}
384
385	tim	1805	return new Torsion(atomA, atomB, atomC, atomD, torsionType);
386	tim	1719	}
387
388			CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
389			int nAtoms;
390			CutoffGroup* cg;
391			Atom* atom;
392			cg = new CutoffGroup();
393
394			nAtoms = stamp->getNMembers();
395			for (int i =0; i < nAtoms; ++i) {
396			atom = mol->getAtomAt(stamp->getMember(i));
397			assert(atom);
398			cg->addAtom(atom);
399			}
400
401			return cg;
402			}
403
404	tim	1734	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
405			CutoffGroup* cg;
406			cg = new CutoffGroup();
407	tim	1805	cg->addAtom(atom);
408	tim	1734	return cg;
409			}
410	tim	1719	//Constraint* MoleculeCreator::createConstraint() {
411
412			//}
413
414			}