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);
    }

    //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) {
    BendType* bendType;
    Atom* atomA;
    Atom* atomB;
    Atom* atomC;

    //need to consider the ghost bend
    atomA = mol->getAtomAt(stamp->getA());
    atomB = mol->getAtomAt(stamp->getB());
    atomC = mol->getAtomAt(stamp->getC());

    assert( atomA && atomB && atomC);
    
    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 Bond(atomA, atomB, 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;
}    

//Constraint* MoleculeCreator::createConstraint() {

//}

}
Revision:	1733
Committed:	Fri Nov 12 06:19:04 2004 UTC (19 years, 9 months ago) by tim
File size:	9319 byte(s)
Log Message:	OOPSE = Object-Obfuscated Parallel Simulation Engine
#	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			//create constraints
105
106			//the construction of this molecule is finished
107			mol->complete();
108
109			return mol;
110			}
111
112
113			Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
114			LocalIndexManager* localIndexMan) {
115			AtomType * atomType;
116			Atom* atom;
117
118			atomType = ff->getAtomType(stamp->getType());
119
120	tim	1733	if (bondType == NULL) {
121			sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
122			stamp->getType());
123
124			painCave.isFatal = 1;
125			simError();
126			}
127
128	tim	1719	//below code still have some kind of hard-coding smell
129			if (stamp->haveOrientation()){
130			DirectionalAtom* dAtom;
131			double phi;
132			double theta;
133			double psi;
134
135			dAtom = new DirectionalAtom(atomType);
136
137			// Directional Atoms have standard unit vectors which are oriented
138			// in space using the three Euler angles. We assume the standard
139			// unit vector was originally along the z axis below.
140
141			phi = stamp->getEulerPhi() * M_PI / 180.0;
142			theta = stamp->getEulerTheta() * M_PI / 180.0;
143			psi = stamp->getEulerPsi()* M_PI / 180.0;
144
145			dAtom->setUnitFrameFromEuler(phi, theta, psi);
146			atom = dAtom;
147			}
148			else{
149			atom = new Atom(atomType);
150			}
151
152			atom->setLocalIndex(localIndexMan->getNextAtomIndex());
153			}
154
155			RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp molStamp, Molecule mol,
156			RigidBodyStamp* rbStamp,
157			LocalIndexManager* localIndexMan) {
158			Atom* atom;
159			int nAtoms;
160			Vector3d refCoor;
161			AtomStamp* atomStamp;
162
163	tim	1733	nAtoms = molStamp->getNMembers();
164	tim	1719
165			RigidBody* rb = new RigidBody();
166
167			for (int i = 0; i < nAtoms; ++i) {
168			//rbStamp->getMember(i) return the local index of current atom inside the molecule.
169			//It is not the same as local index of atom which is the index of atom at DataStorage class
170			atom = mol->getAtomAt(rbStamp->getMember(i));
171			atomStamp= molStamp->molStamp->getAtom(rbStamp->getMember(i));
172			rb->addAtom(atom, atomStamp);
173			}
174	tim	1733
175			//after all of the atoms are added, we need to calculate the reference coordinates
176	tim	1719	rb->calcRefCoords();
177	tim	1733
178			//set the local index of this rigid body, global index will be set later
179	tim	1719	rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
180	tim	1733
181			//the rule for naming rigidbody MoleculeName_RB_Integer
182			//The first part is the name of the molecule
183			//The second part is alway fixed as "RB"
184			//The third part is the index of the rigidbody defined in meta-data file
185			//For example, Butane_RB_0 is a valid rigid body name of butane molecule
186			rb->setType(mol->getType() + "_RB_" + itoa(mol.getNRigidBodies()));
187	tim	1719
188			return rb;
189			}
190
191			Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
192			BondType* bondType;
193			Atom* atomA;
194			Atom* atomB;
195
196			atomA = mol->getAtomAt(stamp->getA());
197			atomB = mol->getAtomAt(stamp->getB());
198
199			assert( atomA && atomB);
200
201			bondType = ff->getBondType(atomA, atomB);
202
203	tim	1733	if (bondType == NULL) {
204			sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
205			atomA->getType().c_str(),
206			atomB->getType().c_str());
207
208			painCave.isFatal = 1;
209			simError();
210			}
211	tim	1719	return new Bond(atomA, atomB, bondType);
212			}
213
214			Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
215	tim	1733	BendType* bendType;
216	tim	1719	Atom* atomA;
217			Atom* atomB;
218			Atom* atomC;
219
220			//need to consider the ghost bend
221			atomA = mol->getAtomAt(stamp->getA());
222			atomB = mol->getAtomAt(stamp->getB());
223			atomC = mol->getAtomAt(stamp->getC());
224
225			assert( atomA && atomB && atomC);
226
227	tim	1733	bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
228	tim	1719
229	tim	1733	if (bendType == NULL) {
230			sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
231			atomA->getType().c_str(),
232			atomB->getType().c_str(),
233			atomC->getType().c_str());
234	tim	1719
235	tim	1733	painCave.isFatal = 1;
236			simError();
237			}
238
239			return new Bond(atomA, atomB, bendType);
240
241	tim	1719	}
242
243			Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
244			TorsionType* torsionType;
245			Atom* atomA;
246			Atom* atomB;
247			Atom* atomC;
248			Atom* atomD;
249
250			atomA = mol->getAtomAt(stamp->getA());
251			atomB = mol->getAtomAt(stamp->getB());
252			atomC = mol->getAtomAt(stamp->getC());
253			atomD = mol->getAtomAt(stamp->getD());
254
255			assert(atomA && atomB && atomC && atomD);
256
257			torsionType = ff->getTosionType(atomA->getType(), atomB->getType(),
258			atomC->getType(), atomD->getType());
259
260	tim	1733	if (torsionType == NULL) {
261			sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
262			atomA->getType().c_str(),
263			atomB->getType().c_str(),
264			atomC->getType().c_str(),
265			atomD->getType().c_str());
266
267			painCave.isFatal = 1;
268			simError();
269			}
270
271	tim	1719	return new Torsion(atomA, atomB, torsionType);
272			}
273
274			CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
275			int nAtoms;
276			CutoffGroup* cg;
277			Atom* atom;
278			cg = new CutoffGroup();
279
280			nAtoms = stamp->getNMembers();
281			for (int i =0; i < nAtoms; ++i) {
282			atom = mol->getAtomAt(stamp->getMember(i));
283			assert(atom);
284			cg->addAtom(atom);
285			}
286
287			return cg;
288			}
289
290			//Constraint* MoleculeCreator::createConstraint() {
291
292			//}
293
294			}