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 (stamp->haveOrientation()){
        DirectionalAtom* dAtom;
        double phi;
        double theta;
        double psi;

        DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
        if (dAtomType == NULL) {
            sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");

            painCave.isFatal = 1;
            simError();
        }
        
        dAtom = new DirectionalAtom(dAtomType);

        // 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());

    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:	1805
Committed:	Tue Nov 30 20:50:47 2004 UTC (19 years, 8 months ago) by tim
File size:	14008 byte(s)
Log Message:	brains get built, io is next
#	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 "utils/simError.h"
39	#include "utils/StringUtils.hpp"
40
41	namespace oopse {
42
43	Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
44	int stampId, int globalIndex, LocalIndexManager* localIndexMan) {
45
46	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
47
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	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
55	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	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
66	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	currentBondStamp = molStamp->getBond(i);
76	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	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
107	mol->addCutoffGroup(cutoffGroup);
108	}
109
110	//every free atom is a cutoff group
111	std::set<Atom*> allAtoms;
112	Molecule::AtomIterator ai;
113
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	Molecule::CutoffGroupIterator ci;
120	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	std::back_inserter(freeAtoms));
139
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	//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	if (atomType == NULL) {
172	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
173	stamp->getType());
174
175	painCave.isFatal = 1;
176	simError();
177	}
178
179	//below code still have some kind of hard-coding smell
180	if (stamp->haveOrientation()){
181	DirectionalAtom* dAtom;
182	double phi;
183	double theta;
184	double psi;
185
186	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
187	if (dAtomType == NULL) {
188	sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
189
190	painCave.isFatal = 1;
191	simError();
192	}
193
194	dAtom = new DirectionalAtom(dAtomType);
195
196	// Directional Atoms have standard unit vectors which are oriented
197	// in space using the three Euler angles. We assume the standard
198	// unit vector was originally along the z axis below.
199
200	phi = stamp->getEulerPhi() * M_PI / 180.0;
201	theta = stamp->getEulerTheta() * M_PI / 180.0;
202	psi = stamp->getEulerPsi()* M_PI / 180.0;
203
204	dAtom->setUnitFrameFromEuler(phi, theta, psi);
205	atom = dAtom;
206	}
207	else{
208	atom = new Atom(atomType);
209	}
210
211	atom->setLocalIndex(localIndexMan->getNextAtomIndex());
212
213	return atom;
214	}
215
216	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp molStamp, Molecule mol,
217	RigidBodyStamp* rbStamp,
218	LocalIndexManager* localIndexMan) {
219	Atom* atom;
220	int nAtoms;
221	Vector3d refCoor;
222	AtomStamp* atomStamp;
223
224	RigidBody* rb = new RigidBody();
225	nAtoms = rbStamp->getNMembers();
226	for (int i = 0; i < nAtoms; ++i) {
227	//rbStamp->getMember(i) return the local index of current atom inside the molecule.
228	//It is not the same as local index of atom which is the index of atom at DataStorage class
229	atom = mol->getAtomAt(rbStamp->getMember(i));
230	atomStamp= molStamp->getAtom(rbStamp->getMember(i));
231	rb->addAtom(atom, atomStamp);
232	}
233
234	//after all of the atoms are added, we need to calculate the reference coordinates
235	rb->calcRefCoords();
236
237	//set the local index of this rigid body, global index will be set later
238	rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
239
240	//the rule for naming rigidbody MoleculeName_RB_Integer
241	//The first part is the name of the molecule
242	//The second part is alway fixed as "RB"
243	//The third part is the index of the rigidbody defined in meta-data file
244	//For example, Butane_RB_0 is a valid rigid body name of butane molecule
245	/*@todo replace itoa by lexi_cast /
246	rb->setType(mol->getType() + "_RB_" + toString(mol->getNRigidBodies()));
247
248	return rb;
249	}
250
251	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
252	BondType* bondType;
253	Atom* atomA;
254	Atom* atomB;
255
256	atomA = mol->getAtomAt(stamp->getA());
257	atomB = mol->getAtomAt(stamp->getB());
258
259	assert( atomA && atomB);
260
261	bondType = ff->getBondType(atomA->getType(), atomB->getType());
262
263	if (bondType == NULL) {
264	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
265	atomA->getType().c_str(),
266	atomB->getType().c_str());
267
268	painCave.isFatal = 1;
269	simError();
270	}
271	return new Bond(atomA, atomB, bondType);
272	}
273
274	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
275	bool isGhostBend = false;
276	int ghostIndex;
277
278
279	//
280	if (stamp->haveExtras()){
281	LinkedAssign* extras = stamp->getExtras();
282	LinkedAssign* currentExtra = extras;
283
284	while (currentExtra != NULL){
285	if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
286	switch (currentExtra->getType()){
287	case 0:
288	ghostIndex = currentExtra->getInt();
289	isGhostBend = true;
290	break;
291
292	default:
293	sprintf(painCave.errMsg,
294	"SimSetup Error: ghostVectorSource must be an int.\n");
295	painCave.isFatal = 1;
296	simError();
297	}
298	} else{
299	sprintf(painCave.errMsg,
300	"SimSetup Error: unhandled bend assignment:\n");
301	painCave.isFatal = 1;
302	simError();
303	}
304	currentExtra = currentExtra->getNext();
305	}
306
307	}
308
309	if (isGhostBend) {
310
311	int indexA = stamp->getA();
312	int indexB= stamp->getB();
313
314	assert(indexA != indexB);
315
316	int normalIndex;
317	if (indexA == ghostIndex) {
318	normalIndex = indexB;
319	} else if (indexB == ghostIndex) {
320	normalIndex = indexA;
321	}
322
323	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
324	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
325	if (ghostAtom == NULL) {
326	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
327	painCave.isFatal = 1;
328	simError();
329	}
330
331	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
332
333	if (bendType == NULL) {
334	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
335	normalAtom->getType().c_str(),
336	ghostAtom->getType().c_str(),
337	"GHOST");
338
339	painCave.isFatal = 1;
340	simError();
341	}
342
343	return new GhostBend(normalAtom, ghostAtom, bendType);
344
345	} else {
346
347	Atom* atomA = mol->getAtomAt(stamp->getA());
348	Atom* atomB = mol->getAtomAt(stamp->getB());
349	Atom* atomC = mol->getAtomAt(stamp->getC());
350
351	assert( atomA && atomB && atomC);
352
353	BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
354
355	if (bendType == NULL) {
356	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
357	atomA->getType().c_str(),
358	atomB->getType().c_str(),
359	atomC->getType().c_str());
360
361	painCave.isFatal = 1;
362	simError();
363	}
364
365	return new Bend(atomA, atomB, atomC, bendType);
366	}
367	}
368
369	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
370	TorsionType* torsionType;
371	Atom* atomA;
372	Atom* atomB;
373	Atom* atomC;
374	Atom* atomD;
375
376	atomA = mol->getAtomAt(stamp->getA());
377	atomB = mol->getAtomAt(stamp->getB());
378	atomC = mol->getAtomAt(stamp->getC());
379	atomD = mol->getAtomAt(stamp->getD());
380
381	assert(atomA && atomB && atomC && atomD);
382
383	torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
384	atomC->getType(), atomD->getType());
385
386	if (torsionType == NULL) {
387	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
388	atomA->getType().c_str(),
389	atomB->getType().c_str(),
390	atomC->getType().c_str(),
391	atomD->getType().c_str());
392
393	painCave.isFatal = 1;
394	simError();
395	}
396
397	return new Torsion(atomA, atomB, atomC, atomD, torsionType);
398	}
399
400	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
401	int nAtoms;
402	CutoffGroup* cg;
403	Atom* atom;
404	cg = new CutoffGroup();
405
406	nAtoms = stamp->getNMembers();
407	for (int i =0; i < nAtoms; ++i) {
408	atom = mol->getAtomAt(stamp->getMember(i));
409	assert(atom);
410	cg->addAtom(atom);
411	}
412
413	return cg;
414	}
415
416	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
417	CutoffGroup* cg;
418	cg = new CutoffGroup();
419	cg->addAtom(atom);
420	return cg;
421	}
422	//Constraint* MoleculeCreator::createConstraint() {
423
424	//}
425
426	}