src/brains/MoleculeCreator.cpp

/*
 * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
 * 
 * Contact: oopse@oopse.org
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */
 
 /**
  * @file MoleculeCreator.cpp
  * @author tlin
  * @date 11/04/2004
  * @time 13:44am
  * @version 1.0
  */

#include <cassert>

#include "brains/MoleculeCreator.hpp"
#include "primitives/GhostBend.hpp"
#include "types/DirectionalAtomType.hpp"
#include "types/FixedBondType.hpp"
#include "utils/simError.h"
#include "utils/StringUtils.hpp"

namespace oopse {

Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
    int stampId, int globalIndex, LocalIndexManager* localIndexMan) {

    Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
    
    //create atoms
    Atom* atom;
    AtomStamp* currentAtomStamp;
    int nAtom = molStamp->getNAtoms();
    for (int i = 0; i < nAtom; ++i) {
        currentAtomStamp = molStamp->getAtom(i);
        atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
        mol->addAtom(atom);
    }

    //create rigidbodies
    RigidBody* rb;
    RigidBodyStamp * currentRigidBodyStamp;
    int nRigidbodies = molStamp->getNRigidBodies();

    for (int i = 0; i < nRigidbodies; ++i) {
        currentRigidBodyStamp = molStamp->getRigidBody(i);
        rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
        mol->addRigidBody(rb);
    }

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

    for (int i = 0; i < nBonds; ++i) {
        currentBondStamp = molStamp->getBond(i);
        bond = createBond(ff, mol, currentBondStamp);
        mol->addBond(bond);
    }

    //create bends
    Bend* bend;
    BendStamp* currentBendStamp;
    int nBends = molStamp->getNBends();
    for (int i = 0; i < nBends; ++i) {
        currentBendStamp = molStamp->getBend(i);
        bend = createBend(ff, mol, currentBendStamp);
        mol->addBend(bend);
    }

    //create torsions
    Torsion* torsion;
    TorsionStamp* currentTorsionStamp;
    int nTorsions = molStamp->getNTorsions();
    for (int i = 0; i < nTorsions; ++i) {
        currentTorsionStamp = molStamp->getTorsion(i);
        torsion = createTorsion(ff, mol, currentTorsionStamp);
        mol->addTorsion(torsion);
    }

    //create cutoffGroups
    CutoffGroup* cutoffGroup;
    CutoffGroupStamp* currentCutoffGroupStamp;
    int nCutoffGroups = molStamp->getNCutoffGroups();
    for (int i = 0; i < nCutoffGroups; ++i) {
        currentCutoffGroupStamp = molStamp->getCutoffGroup(i);
        cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
        mol->addCutoffGroup(cutoffGroup);
    }

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

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

    Molecule::CutoffGroupIterator ci;
    CutoffGroup* cg;
    std::set<Atom*> cutoffAtoms;    
    
    //add all of the atoms belong to cutoff groups into cutoffAtoms set
    for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {

        for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
            cutoffAtoms.insert(atom);
        }

    }       
    
    //find all free atoms (which do not belong to cutoff groups)  
    //performs the "difference" operation from set theory,  the output range contains a copy of every
    //element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in 
    //[cutoffAtoms.begin(), cutoffAtoms.end()).
    std::vector<Atom*> freeAtoms;    
    std::set_difference(allAtoms.begin(), allAtoms.end(), cutoffAtoms.begin(), cutoffAtoms.end(),
                            std::back_inserter(freeAtoms));

    if (freeAtoms.size() != allAtoms.size() - cutoffAtoms.size()) {
        //Some atoms in rigidAtoms are not in allAtoms, something must be wrong
        sprintf(painCave.errMsg, "Atoms in cutoff groups are not in the atom list of the same molecule");

        painCave.isFatal = 1;
        simError();        
    }

    //loop over the free atoms and then create one cutoff group for every single free atom
    std::vector<Atom*>::iterator fai;

    for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
        cutoffGroup = createCutoffGroup(mol, *fai);
        mol->addCutoffGroup(cutoffGroup);
    }
    //create constraints

    //the construction of this molecule is finished
    mol->complete();

    return mol;
}    


Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp, 
                                                                  LocalIndexManager* localIndexMan) {
    AtomType * atomType;
    Atom* atom;

    atomType =  ff->getAtomType(stamp->getType());

    if (atomType == NULL) {
        sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
                   stamp->getType());

        painCave.isFatal = 1;
        simError();
    }
    
    //below code still have some kind of hard-coding smell
    if (atomType->isDirectional()){
     
        DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
        
        if (dAtomType == NULL) {
            sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");

            painCave.isFatal = 1;
            simError();
        }

        DirectionalAtom* dAtom;
        dAtom = new DirectionalAtom(dAtomType);
        atom = dAtom;    
    }
    else{
        atom = new Atom(atomType);
    }

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

    return atom;
}

RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, Molecule* mol,
                                                                                    RigidBodyStamp* rbStamp, 
                                                                                    LocalIndexManager* localIndexMan) {
    Atom* atom;
    int nAtoms;
    Vector3d refCoor;
    AtomStamp* atomStamp;
    
    RigidBody* rb = new RigidBody();
    nAtoms = rbStamp->getNMembers();    
    for (int i = 0; i < nAtoms; ++i) {
        //rbStamp->getMember(i) return the local index of current atom inside the molecule.
        //It is not the same as local index of atom which is the index of atom at DataStorage class
        atom = mol->getAtomAt(rbStamp->getMember(i));
        atomStamp= molStamp->getAtom(rbStamp->getMember(i));    
        rb->addAtom(atom, atomStamp);
    }

    //after all of the atoms are added, we need to calculate the reference coordinates
    rb->calcRefCoords();

    //set the local index of this rigid body, global index will be set later
    rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());

    //the rule for naming rigidbody MoleculeName_RB_Integer
    //The first part is the name of the molecule
    //The second part is alway fixed as "RB"
    //The third part is the index of the rigidbody defined in meta-data file
    //For example, Butane_RB_0 is a valid rigid body name of butane molecule
    /**@todo replace itoa by lexi_cast */
    rb->setType(mol->getType() + "_RB_" + toString(mol->getNRigidBodies()));
    
    return rb;
}    

Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
    BondType* bondType;
    Atom* atomA;
    Atom* atomB;

    atomA = mol->getAtomAt(stamp->getA());
    atomB = mol->getAtomAt(stamp->getB());

    assert( atomA && atomB);
    
    bondType = ff->getBondType(atomA->getType(), atomB->getType());

    if (bondType == NULL) {
        sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
                   atomA->getType().c_str(),
                   atomB->getType().c_str());

        painCave.isFatal = 1;
        simError();
    }
    return new Bond(atomA, atomB, bondType);    
}    

Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
    bool isGhostBend = false;
    int ghostIndex;

    
    //
    if (stamp->haveExtras()){
        LinkedAssign* extras = stamp->getExtras();
        LinkedAssign* currentExtra = extras;

        while (currentExtra != NULL){
            if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
                switch (currentExtra->getType()){
                case 0:
                    ghostIndex = currentExtra->getInt();
                    isGhostBend = true;
                    break;

                default:
                sprintf(painCave.errMsg,
                "SimSetup Error: ghostVectorSource must be an int.\n");
                painCave.isFatal = 1;
                simError();
                }
            } else{
                sprintf(painCave.errMsg,
                "SimSetup Error: unhandled bend assignment:\n");
                painCave.isFatal = 1;
                simError();
            }
            currentExtra = currentExtra->getNext();
        }
        
    }

    if (isGhostBend) {

        int indexA = stamp->getA();
        int indexB= stamp->getB();

        assert(indexA != indexB);

        int normalIndex;
        if (indexA == ghostIndex) {
            normalIndex = indexB;
        } else if (indexB == ghostIndex) {
            normalIndex = indexA;
        }
        
        Atom* normalAtom = mol->getAtomAt(normalIndex) ;        
        DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
        if (ghostAtom == NULL) {
            sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
            painCave.isFatal = 1;
            simError();
        }
                
        BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");

        if (bendType == NULL) {
            sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
                       normalAtom->getType().c_str(),
                       ghostAtom->getType().c_str(),
                       "GHOST");

            painCave.isFatal = 1;
            simError();
        }
        
        return new GhostBend(normalAtom, ghostAtom, bendType);       

    } else {
            
        Atom* atomA = mol->getAtomAt(stamp->getA());
        Atom* atomB = mol->getAtomAt(stamp->getB());
        Atom* atomC = mol->getAtomAt(stamp->getC());

        assert( atomA && atomB && atomC);
        
        BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());

        if (bendType == NULL) {
            sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
                       atomA->getType().c_str(),
                       atomB->getType().c_str(),
                       atomC->getType().c_str());

            painCave.isFatal = 1;
            simError();
        }

        return new Bend(atomA, atomB, atomC, bendType);       
    }
}    

Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
    TorsionType* torsionType;
    Atom* atomA;
    Atom* atomB;
    Atom* atomC;
    Atom* atomD;

    atomA = mol->getAtomAt(stamp->getA());
    atomB = mol->getAtomAt(stamp->getB());
    atomC = mol->getAtomAt(stamp->getC());
    atomD = mol->getAtomAt(stamp->getD());

    assert(atomA && atomB && atomC && atomD);
    
    torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), 
                                                       atomC->getType(), atomD->getType());

    if (torsionType == NULL) {
        sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
                   atomA->getType().c_str(),
                   atomB->getType().c_str(),
                   atomC->getType().c_str(),
                   atomD->getType().c_str());

        painCave.isFatal = 1;
        simError();
    }
    
    return new Torsion(atomA, atomB, atomC, atomD, torsionType);       
}    

CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
    int nAtoms;
    CutoffGroup* cg;
    Atom* atom;
    cg = new CutoffGroup();
    
    nAtoms = stamp->getNMembers();
    for (int i =0; i < nAtoms; ++i) {
        atom = mol->getAtomAt(stamp->getMember(i));
        assert(atom);
        cg->addAtom(atom);
    }

    return cg;
}    

CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
    CutoffGroup* cg;
    cg  = new CutoffGroup();
    cg->addAtom(atom);
    return cg;
}

void MoleculeCreator::createConstraintPair(Molecule* mol) {

    //add bond constraints
    Molecule::BondIterator bi;
    Bond* bond;
    for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
        
        BondType* bt = bond->getBondType();
        FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);

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

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

}
Revision:	1901
Committed:	Tue Jan 4 22:18:36 2005 UTC (19 years, 7 months ago) by tim
File size:	14223 byte(s)
Log Message:	constraints in progress
#	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 "types/FixedBondType.hpp"
40	#include "utils/simError.h"
41	#include "utils/StringUtils.hpp"
42
43	namespace oopse {
44
45	Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
46	int stampId, int globalIndex, LocalIndexManager* localIndexMan) {
47
48	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
49
50	//create atoms
51	Atom* atom;
52	AtomStamp* currentAtomStamp;
53	int nAtom = molStamp->getNAtoms();
54	for (int i = 0; i < nAtom; ++i) {
55	currentAtomStamp = molStamp->getAtom(i);
56	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
57	mol->addAtom(atom);
58	}
59
60	//create rigidbodies
61	RigidBody* rb;
62	RigidBodyStamp * currentRigidBodyStamp;
63	int nRigidbodies = molStamp->getNRigidBodies();
64
65	for (int i = 0; i < nRigidbodies; ++i) {
66	currentRigidBodyStamp = molStamp->getRigidBody(i);
67	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
68	mol->addRigidBody(rb);
69	}
70
71	//create bonds
72	Bond* bond;
73	BondStamp* currentBondStamp;
74	int nBonds = molStamp->getNBonds();
75
76	for (int i = 0; i < nBonds; ++i) {
77	currentBondStamp = molStamp->getBond(i);
78	bond = createBond(ff, mol, currentBondStamp);
79	mol->addBond(bond);
80	}
81
82	//create bends
83	Bend* bend;
84	BendStamp* currentBendStamp;
85	int nBends = molStamp->getNBends();
86	for (int i = 0; i < nBends; ++i) {
87	currentBendStamp = molStamp->getBend(i);
88	bend = createBend(ff, mol, currentBendStamp);
89	mol->addBend(bend);
90	}
91
92	//create torsions
93	Torsion* torsion;
94	TorsionStamp* currentTorsionStamp;
95	int nTorsions = molStamp->getNTorsions();
96	for (int i = 0; i < nTorsions; ++i) {
97	currentTorsionStamp = molStamp->getTorsion(i);
98	torsion = createTorsion(ff, mol, currentTorsionStamp);
99	mol->addTorsion(torsion);
100	}
101
102	//create cutoffGroups
103	CutoffGroup* cutoffGroup;
104	CutoffGroupStamp* currentCutoffGroupStamp;
105	int nCutoffGroups = molStamp->getNCutoffGroups();
106	for (int i = 0; i < nCutoffGroups; ++i) {
107	currentCutoffGroupStamp = molStamp->getCutoffGroup(i);
108	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
109	mol->addCutoffGroup(cutoffGroup);
110	}
111
112	//every free atom is a cutoff group
113	std::set<Atom*> allAtoms;
114	Molecule::AtomIterator ai;
115
116	//add all atoms into allAtoms set
117	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
118	allAtoms.insert(atom);
119	}
120
121	Molecule::CutoffGroupIterator ci;
122	CutoffGroup* cg;
123	std::set<Atom*> cutoffAtoms;
124
125	//add all of the atoms belong to cutoff groups into cutoffAtoms set
126	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
127
128	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
129	cutoffAtoms.insert(atom);
130	}
131
132	}
133
134	//find all free atoms (which do not belong to cutoff groups)
135	//performs the "difference" operation from set theory, the output range contains a copy of every
136	//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
137	//[cutoffAtoms.begin(), cutoffAtoms.end()).
138	std::vector<Atom*> freeAtoms;
139	std::set_difference(allAtoms.begin(), allAtoms.end(), cutoffAtoms.begin(), cutoffAtoms.end(),
140	std::back_inserter(freeAtoms));
141
142	if (freeAtoms.size() != allAtoms.size() - cutoffAtoms.size()) {
143	//Some atoms in rigidAtoms are not in allAtoms, something must be wrong
144	sprintf(painCave.errMsg, "Atoms in cutoff groups are not in the atom list of the same molecule");
145
146	painCave.isFatal = 1;
147	simError();
148	}
149
150	//loop over the free atoms and then create one cutoff group for every single free atom
151	std::vector<Atom*>::iterator fai;
152
153	for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
154	cutoffGroup = createCutoffGroup(mol, *fai);
155	mol->addCutoffGroup(cutoffGroup);
156	}
157	//create constraints
158
159	//the construction of this molecule is finished
160	mol->complete();
161
162	return mol;
163	}
164
165
166	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
167	LocalIndexManager* localIndexMan) {
168	AtomType * atomType;
169	Atom* atom;
170
171	atomType = ff->getAtomType(stamp->getType());
172
173	if (atomType == NULL) {
174	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
175	stamp->getType());
176
177	painCave.isFatal = 1;
178	simError();
179	}
180
181	//below code still have some kind of hard-coding smell
182	if (atomType->isDirectional()){
183
184	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
185
186	if (dAtomType == NULL) {
187	sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
188
189	painCave.isFatal = 1;
190	simError();
191	}
192
193	DirectionalAtom* dAtom;
194	dAtom = new DirectionalAtom(dAtomType);
195	atom = dAtom;
196	}
197	else{
198	atom = new Atom(atomType);
199	}
200
201	atom->setLocalIndex(localIndexMan->getNextAtomIndex());
202
203	return atom;
204	}
205
206	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp molStamp, Molecule mol,
207	RigidBodyStamp* rbStamp,
208	LocalIndexManager* localIndexMan) {
209	Atom* atom;
210	int nAtoms;
211	Vector3d refCoor;
212	AtomStamp* atomStamp;
213
214	RigidBody* rb = new RigidBody();
215	nAtoms = rbStamp->getNMembers();
216	for (int i = 0; i < nAtoms; ++i) {
217	//rbStamp->getMember(i) return the local index of current atom inside the molecule.
218	//It is not the same as local index of atom which is the index of atom at DataStorage class
219	atom = mol->getAtomAt(rbStamp->getMember(i));
220	atomStamp= molStamp->getAtom(rbStamp->getMember(i));
221	rb->addAtom(atom, atomStamp);
222	}
223
224	//after all of the atoms are added, we need to calculate the reference coordinates
225	rb->calcRefCoords();
226
227	//set the local index of this rigid body, global index will be set later
228	rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
229
230	//the rule for naming rigidbody MoleculeName_RB_Integer
231	//The first part is the name of the molecule
232	//The second part is alway fixed as "RB"
233	//The third part is the index of the rigidbody defined in meta-data file
234	//For example, Butane_RB_0 is a valid rigid body name of butane molecule
235	/*@todo replace itoa by lexi_cast /
236	rb->setType(mol->getType() + "_RB_" + toString(mol->getNRigidBodies()));
237
238	return rb;
239	}
240
241	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
242	BondType* bondType;
243	Atom* atomA;
244	Atom* atomB;
245
246	atomA = mol->getAtomAt(stamp->getA());
247	atomB = mol->getAtomAt(stamp->getB());
248
249	assert( atomA && atomB);
250
251	bondType = ff->getBondType(atomA->getType(), atomB->getType());
252
253	if (bondType == NULL) {
254	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
255	atomA->getType().c_str(),
256	atomB->getType().c_str());
257
258	painCave.isFatal = 1;
259	simError();
260	}
261	return new Bond(atomA, atomB, bondType);
262	}
263
264	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
265	bool isGhostBend = false;
266	int ghostIndex;
267
268
269	//
270	if (stamp->haveExtras()){
271	LinkedAssign* extras = stamp->getExtras();
272	LinkedAssign* currentExtra = extras;
273
274	while (currentExtra != NULL){
275	if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
276	switch (currentExtra->getType()){
277	case 0:
278	ghostIndex = currentExtra->getInt();
279	isGhostBend = true;
280	break;
281
282	default:
283	sprintf(painCave.errMsg,
284	"SimSetup Error: ghostVectorSource must be an int.\n");
285	painCave.isFatal = 1;
286	simError();
287	}
288	} else{
289	sprintf(painCave.errMsg,
290	"SimSetup Error: unhandled bend assignment:\n");
291	painCave.isFatal = 1;
292	simError();
293	}
294	currentExtra = currentExtra->getNext();
295	}
296
297	}
298
299	if (isGhostBend) {
300
301	int indexA = stamp->getA();
302	int indexB= stamp->getB();
303
304	assert(indexA != indexB);
305
306	int normalIndex;
307	if (indexA == ghostIndex) {
308	normalIndex = indexB;
309	} else if (indexB == ghostIndex) {
310	normalIndex = indexA;
311	}
312
313	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
314	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
315	if (ghostAtom == NULL) {
316	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
317	painCave.isFatal = 1;
318	simError();
319	}
320
321	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
322
323	if (bendType == NULL) {
324	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
325	normalAtom->getType().c_str(),
326	ghostAtom->getType().c_str(),
327	"GHOST");
328
329	painCave.isFatal = 1;
330	simError();
331	}
332
333	return new GhostBend(normalAtom, ghostAtom, bendType);
334
335	} else {
336
337	Atom* atomA = mol->getAtomAt(stamp->getA());
338	Atom* atomB = mol->getAtomAt(stamp->getB());
339	Atom* atomC = mol->getAtomAt(stamp->getC());
340
341	assert( atomA && atomB && atomC);
342
343	BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
344
345	if (bendType == NULL) {
346	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
347	atomA->getType().c_str(),
348	atomB->getType().c_str(),
349	atomC->getType().c_str());
350
351	painCave.isFatal = 1;
352	simError();
353	}
354
355	return new Bend(atomA, atomB, atomC, bendType);
356	}
357	}
358
359	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
360	TorsionType* torsionType;
361	Atom* atomA;
362	Atom* atomB;
363	Atom* atomC;
364	Atom* atomD;
365
366	atomA = mol->getAtomAt(stamp->getA());
367	atomB = mol->getAtomAt(stamp->getB());
368	atomC = mol->getAtomAt(stamp->getC());
369	atomD = mol->getAtomAt(stamp->getD());
370
371	assert(atomA && atomB && atomC && atomD);
372
373	torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
374	atomC->getType(), atomD->getType());
375
376	if (torsionType == NULL) {
377	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
378	atomA->getType().c_str(),
379	atomB->getType().c_str(),
380	atomC->getType().c_str(),
381	atomD->getType().c_str());
382
383	painCave.isFatal = 1;
384	simError();
385	}
386
387	return new Torsion(atomA, atomB, atomC, atomD, torsionType);
388	}
389
390	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
391	int nAtoms;
392	CutoffGroup* cg;
393	Atom* atom;
394	cg = new CutoffGroup();
395
396	nAtoms = stamp->getNMembers();
397	for (int i =0; i < nAtoms; ++i) {
398	atom = mol->getAtomAt(stamp->getMember(i));
399	assert(atom);
400	cg->addAtom(atom);
401	}
402
403	return cg;
404	}
405
406	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
407	CutoffGroup* cg;
408	cg = new CutoffGroup();
409	cg->addAtom(atom);
410	return cg;
411	}
412
413	void MoleculeCreator::createConstraintPair(Molecule* mol) {
414
415	//add bond constraints
416	Molecule::BondIterator bi;
417	Bond* bond;
418	for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
419
420	BondType* bt = bond->getBondType();
421	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
422
423	//found a constraint pair
424	if (fbt != NULL) {
425	ConstraintPair* consPair = new ConstraintPair(bond->getAtomA(), bond->getAtomB(), fbt->getEquilibriumBondLength());
426	mol->addConstraintPair(consPair);
427	}
428
429	}
430
431	//rigidbody -- rigidbody constraint is not support yet
432
433	}
434
435	}