test/brains/Molecule.cpp

/*
 * Copyright (C) 2000-2009  The Open Molecular Dynamics Engine (OpenMD) project
 * 
 * Contact: gezelter@openscience.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 Molecule.cpp
 * @author    tlin
 * @date  10/28/2004
 * @version 1.0
 */ 

#include "primitives/Molecule.hpp"
#include <algorithm>

namespace OpenMD {

Molecule::~Molecule() {

    deleteVectorOfPointer(atoms_);
    deleteVectorOfPointer(bonds_);
    deleteVectorOfPointer(bends_);
    deleteVectorOfPointer(torsions_);
    deleteVectorOfPointer(rigidbodies_);
    deleteVectorOfPointer(cutoffGroups_);

    integrableObjects_.clear();
    
}

void Molecule::addAtom(Atom* atom) {
    if (atoms_.find(atom) == atoms_.end()) {
        atoms_.push_back(atom);
    }
}

void Molecule::addBond(Bond* bond) {
    if (bonds_.find(bond) == bonds_.end()) {
        bonds_.push_back(bond);
    }
}

void Molecule::addBend(Bend* bend) {
    if (bends_.find(bend) == bends_.end()) {
        bends_.push_back(bend);
    }
}

void Molecule::addTorsion(Torsion* torsion) {
    if (torsions_.find(torsion) == torsions_.end()) {
        torsions_.push_back(torsion);
    }
}

void Molecule::addRigidBody(RigidBody *rb) {
    if (rigidBodies_.find(bond) == bonds_.end()) {
        rigidBodies_.push_back(rb);
    }
}

void Molecule::addCutoffGroup(CutoffGroup* cp) {
    if (cutoffGroups_.find(bond) == bonds_.end()) {
        cutoffGroups_.push_back(cp);
    }

}

void Molecule::complete() {
    
    std::set<Atom*> allAtoms;
    allAtoms.insert(atoms_.begin(), atoms_.end());

    std::set<Atom*> rigidAtoms;
    RigidBody* rb;
    std::vector<RigidBody*> rbIter;

    
    for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
        rigidAtoms.insert(rb->beginAtomIter(), rb->endAtomIter());
    }

    //find all free atoms (which do not belong to rigid bodies)  
    //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 
    //[rigidAtoms.begin(), rigidAtoms.end()).
    std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(),
                            std::back_inserter(integrableObjects_));

    if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) {
        //Some atoms in rigidAtoms are not in allAtoms, something must be wrong
    }

    integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end());
}

Atom* Molecule::beginAtom(std::vector<Atom*>::iterator& i) {
    i = atoms_.begin();
    return (i == atoms_.end()) ? NULL : *i;
}

Atom* Molecule::nextAtom(std::vector<Atom*>::iterator& i) {
    ++i;
    return (i == atoms_.end()) ? NULL : *i;    
}

Bond* Molecule::beginBond(std::vector<Bond*>::iterator& i) {
    i = bonds_.begin();
    return (i == bonds_.end()) ? NULL : *i;
}

Bond* Molecule::nextBond(std::vector<Bond*>::iterator& i) {
    ++i;
    return (i == bonds_.end()) ? NULL : *i;    

}


Bend* Molecule::beginBend(std::vector<Bend*>::iterator& i) {
    i = bends_.begin();
    return (i == bends_.end()) ? NULL : *i;
}

Bend* Molecule::nextBend(std::vector<Bend*>::iterator& i) {
    ++i;
    return (i == bends_.end()) ? NULL : *i;    
}

Torsion* Molecule::beginTorsion(std::vector<Torsion*>::iterator& i) {
    i = torsions_.begin();
    return (i == torsions_.end()) ? NULL : *i;
}

Torsion* Molecule::nextTorsion(std::vector<Torsion*>::iterator& i) {
    ++i;
    return (i == torsions_.end()) ? NULL : *i;    
}    

RigidBody* Molecule::beginRigidBody(std::vector<RigidBody*>::iterator& i) {
    i = rigidBodies_.begin();
    return (i == rigidBodies_.end()) ? NULL : *i;
}

RigidBody* Molecule::nextRigidBody(std::vector<RigidBody*>::iterator& i) {
    ++i;
    return (i == rigidBodies_.end()) ? NULL : *i;    
}

StuntDouble* Molecule::beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
    i = integrableObjects_.begin();
    return (i == integrableObjects_.end()) ? NULL : *i;
}

StuntDouble* Molecule::nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
    ++i;
    return (i == integrableObjects_.end()) ? NULL : *i;    
}    

CutoffGroup* Molecule::beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
    i = cutoffGroups_.begin();
    return (i == cutoffGroups_.end()) ? NULL : *i;
}

CutoffGroup* Molecule::nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {            
    ++i;
    return (i == cutoffGroups_.end()) ? NULL : *i;    
} 

void Molecule::calcForces() {
    RigidBody* rb;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    std::vector<RigidBody*> rbIter;
    std::vector<Bond*> bondIter;;
    std::vector<Bend*> bendIter;
    std::vector<Torsion*> torsionIter;

    for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
        rb->updateAtoms();
    }

    for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
        bond->calcForce();
    }

    for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
        bend->calcForce();
    }

    for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) {
        torsion->calcForce();
    }
    
}

double Molecule::getPotential() {
    //RigidBody* rb;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    //std::vector<RigidBody*> rbIter;
    std::vector<Bond*> bondIter;;
    std::vector<Bend*> bendIter;
    std::vector<Torsion*> torsionIter;

    double potential = 0;
    
    //for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
    //    rb->updateAtoms();
    //}

    for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
        potential += bond->getPotential();
    }

    for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
        potential += bend->getPotential();
    }

    for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) {
        potential += torsion->getPotential();
    }
    
    return potential;
}

Vector3d Molecule::getCom() {
    StuntDouble* sd;
    std::vector<StuntDouble*>::iterator i;
    Vector3d com;
    double totalMass = 0;
    double mass;
    
    for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
        mass = sd->getMass();
        totalMass += mass;
        com += sd->getPos() * mass;    
    }

    com /= totalMass;

    return com;
}

void Molecule::moveCom(const Vetor3d& delta) {
    StuntDouble* sd;
    std::vector<StuntDouble*>::iterator i;
    
    for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
        s->setPos(sd->getPos() + delta);
    }

}

Vector3d Molecule::getComVel() {
    StuntDouble* sd;
    std::vector<StuntDouble*>::iterator i;
    Vector3d velCom;
    double totalMass = 0;
    double mass;
    
    for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
        mass = sd->getMass();
        totalMass += mass;
        velCom += sd->getVel() * mass;    
    }

    velCom /= totalMass;

    return velCom;
}

std::ostream& operator <<(std::ostream& o, const Molecule& mol) {
    o << std::endl;
    o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
    o << mol.getNAtoms() << " atoms" << std::endl;
    o << mol.getNBonds() << " bonds" << std::endl;
    o << mol.getNBends() << " bends" << std::endl;
    o << mol.getNTorsions() << " torsions" << std::endl;
    o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
    o << mol.getNIntegrableObjects() << "integrable objects" << std::endl;
    o << mol.getNCutoffGroups() << "cutoff groups" << std::endl;

    return o;
}

}//end namespace OpenMD
Revision:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (15 years, 3 months ago) by chuckv
File size:	8759 byte(s)
Log Message:	Creating busticated version of OpenMD
#	Content
1	/*
2	* Copyright (C) 2000-2009 The Open Molecular Dynamics Engine (OpenMD) project
3	*
4	* Contact: gezelter@openscience.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 Molecule.cpp
28	* @author tlin
29	* @date 10/28/2004
30	* @version 1.0
31	*/
32
33	#include "primitives/Molecule.hpp"
34	#include <algorithm>
35
36	namespace OpenMD {
37
38	Molecule::~Molecule() {
39
40	deleteVectorOfPointer(atoms_);
41	deleteVectorOfPointer(bonds_);
42	deleteVectorOfPointer(bends_);
43	deleteVectorOfPointer(torsions_);
44	deleteVectorOfPointer(rigidbodies_);
45	deleteVectorOfPointer(cutoffGroups_);
46
47	integrableObjects_.clear();
48
49	}
50
51	void Molecule::addAtom(Atom* atom) {
52	if (atoms_.find(atom) == atoms_.end()) {
53	atoms_.push_back(atom);
54	}
55	}
56
57	void Molecule::addBond(Bond* bond) {
58	if (bonds_.find(bond) == bonds_.end()) {
59	bonds_.push_back(bond);
60	}
61	}
62
63	void Molecule::addBend(Bend* bend) {
64	if (bends_.find(bend) == bends_.end()) {
65	bends_.push_back(bend);
66	}
67	}
68
69	void Molecule::addTorsion(Torsion* torsion) {
70	if (torsions_.find(torsion) == torsions_.end()) {
71	torsions_.push_back(torsion);
72	}
73	}
74
75	void Molecule::addRigidBody(RigidBody *rb) {
76	if (rigidBodies_.find(bond) == bonds_.end()) {
77	rigidBodies_.push_back(rb);
78	}
79	}
80
81	void Molecule::addCutoffGroup(CutoffGroup* cp) {
82	if (cutoffGroups_.find(bond) == bonds_.end()) {
83	cutoffGroups_.push_back(cp);
84	}
85
86	}
87
88	void Molecule::complete() {
89
90	std::set<Atom*> allAtoms;
91	allAtoms.insert(atoms_.begin(), atoms_.end());
92
93	std::set<Atom*> rigidAtoms;
94	RigidBody* rb;
95	std::vector<RigidBody*> rbIter;
96
97
98	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
99	rigidAtoms.insert(rb->beginAtomIter(), rb->endAtomIter());
100	}
101
102	//find all free atoms (which do not belong to rigid bodies)
103	//performs the "difference" operation from set theory, the output range contains a copy of every
104	//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
105	//[rigidAtoms.begin(), rigidAtoms.end()).
106	std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(),
107	std::back_inserter(integrableObjects_));
108
109	if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) {
110	//Some atoms in rigidAtoms are not in allAtoms, something must be wrong
111	}
112
113	integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end());
114	}
115
116	Atom* Molecule::beginAtom(std::vector<Atom*>::iterator& i) {
117	i = atoms_.begin();
118	return (i == atoms_.end()) ? NULL : *i;
119	}
120
121	Atom* Molecule::nextAtom(std::vector<Atom*>::iterator& i) {
122	++i;
123	return (i == atoms_.end()) ? NULL : *i;
124	}
125
126	Bond* Molecule::beginBond(std::vector<Bond*>::iterator& i) {
127	i = bonds_.begin();
128	return (i == bonds_.end()) ? NULL : *i;
129	}
130
131	Bond* Molecule::nextBond(std::vector<Bond*>::iterator& i) {
132	++i;
133	return (i == bonds_.end()) ? NULL : *i;
134
135	}
136
137
138	Bend* Molecule::beginBend(std::vector<Bend*>::iterator& i) {
139	i = bends_.begin();
140	return (i == bends_.end()) ? NULL : *i;
141	}
142
143	Bend* Molecule::nextBend(std::vector<Bend*>::iterator& i) {
144	++i;
145	return (i == bends_.end()) ? NULL : *i;
146	}
147
148	Torsion* Molecule::beginTorsion(std::vector<Torsion*>::iterator& i) {
149	i = torsions_.begin();
150	return (i == torsions_.end()) ? NULL : *i;
151	}
152
153	Torsion* Molecule::nextTorsion(std::vector<Torsion*>::iterator& i) {
154	++i;
155	return (i == torsions_.end()) ? NULL : *i;
156	}
157
158	RigidBody* Molecule::beginRigidBody(std::vector<RigidBody*>::iterator& i) {
159	i = rigidBodies_.begin();
160	return (i == rigidBodies_.end()) ? NULL : *i;
161	}
162
163	RigidBody* Molecule::nextRigidBody(std::vector<RigidBody*>::iterator& i) {
164	++i;
165	return (i == rigidBodies_.end()) ? NULL : *i;
166	}
167
168	StuntDouble* Molecule::beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
169	i = integrableObjects_.begin();
170	return (i == integrableObjects_.end()) ? NULL : *i;
171	}
172
173	StuntDouble* Molecule::nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
174	++i;
175	return (i == integrableObjects_.end()) ? NULL : *i;
176	}
177
178	CutoffGroup* Molecule::beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
179	i = cutoffGroups_.begin();
180	return (i == cutoffGroups_.end()) ? NULL : *i;
181	}
182
183	CutoffGroup* Molecule::nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
184	++i;
185	return (i == cutoffGroups_.end()) ? NULL : *i;
186	}
187
188	void Molecule::calcForces() {
189	RigidBody* rb;
190	Bond* bond;
191	Bend* bend;
192	Torsion* torsion;
193	std::vector<RigidBody*> rbIter;
194	std::vector<Bond*> bondIter;;
195	std::vector<Bend*> bendIter;
196	std::vector<Torsion*> torsionIter;
197
198	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
199	rb->updateAtoms();
200	}
201
202	for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
203	bond->calcForce();
204	}
205
206	for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
207	bend->calcForce();
208	}
209
210	for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) {
211	torsion->calcForce();
212	}
213
214	}
215
216	double Molecule::getPotential() {
217	//RigidBody* rb;
218	Bond* bond;
219	Bend* bend;
220	Torsion* torsion;
221	//std::vector<RigidBody*> rbIter;
222	std::vector<Bond*> bondIter;;
223	std::vector<Bend*> bendIter;
224	std::vector<Torsion*> torsionIter;
225
226	double potential = 0;
227
228	//for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
229	// rb->updateAtoms();
230	//}
231
232	for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
233	potential += bond->getPotential();
234	}
235
236	for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
237	potential += bend->getPotential();
238	}
239
240	for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) {
241	potential += torsion->getPotential();
242	}
243
244	return potential;
245	}
246
247	Vector3d Molecule::getCom() {
248	StuntDouble* sd;
249	std::vector<StuntDouble*>::iterator i;
250	Vector3d com;
251	double totalMass = 0;
252	double mass;
253
254	for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
255	mass = sd->getMass();
256	totalMass += mass;
257	com += sd->getPos() * mass;
258	}
259
260	com /= totalMass;
261
262	return com;
263	}
264
265	void Molecule::moveCom(const Vetor3d& delta) {
266	StuntDouble* sd;
267	std::vector<StuntDouble*>::iterator i;
268
269	for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
270	s->setPos(sd->getPos() + delta);
271	}
272
273	}
274
275	Vector3d Molecule::getComVel() {
276	StuntDouble* sd;
277	std::vector<StuntDouble*>::iterator i;
278	Vector3d velCom;
279	double totalMass = 0;
280	double mass;
281
282	for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
283	mass = sd->getMass();
284	totalMass += mass;
285	velCom += sd->getVel() * mass;
286	}
287
288	velCom /= totalMass;
289
290	return velCom;
291	}
292
293	std::ostream& operator <<(std::ostream& o, const Molecule& mol) {
294	o << std::endl;
295	o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
296	o << mol.getNAtoms() << " atoms" << std::endl;
297	o << mol.getNBonds() << " bonds" << std::endl;
298	o << mol.getNBends() << " bends" << std::endl;
299	o << mol.getNTorsions() << " torsions" << std::endl;
300	o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
301	o << mol.getNIntegrableObjects() << "integrable objects" << std::endl;
302	o << mol.getNCutoffGroups() << "cutoff groups" << std::endl;
303
304	return o;
305	}
306
307	}//end namespace OpenMD