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, 8 months ago) by tim
File size:	9319 byte(s)
Log Message:	OOPSE = Object-Obfuscated Parallel Simulation Engine
#	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 "brains/MoleculeCreator.hpp"
35	#include <cassert>
36
37	namespace oopse {
38
39	Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp, int stampId, int globalIndex) {
40	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
41
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	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	//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	nAtoms = molStamp->getNMembers();
164
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
175	//after all of the atoms are added, we need to calculate the reference coordinates
176	rb->calcRefCoords();
177
178	//set the local index of this rigid body, global index will be set later
179	rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
180
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
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	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	return new Bond(atomA, atomB, bondType);
212	}
213
214	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
215	BendType* bendType;
216	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	bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
228
229	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
235	painCave.isFatal = 1;
236	simError();
237	}
238
239	return new Bond(atomA, atomB, bendType);
240
241	}
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	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	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	}