src/primitives/Molecule.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 Molecule.cpp
 * @author    tlin
 * @date  10/28/2004
 * @version 1.0
 */ 

#include <algorithm>
#include <set>

#include "primitives/Molecule.hpp"
#include "utils/MemoryUtils.hpp"
#include "utils/simError.h"

namespace oopse {
Molecule::Molecule(int stampId, int globalIndex, const std::string& molName) 
    : stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) {

}

Molecule::~Molecule() {

    MemoryUtils::deleteVectorOfPointer(atoms_);
    MemoryUtils::deleteVectorOfPointer(bonds_);
    MemoryUtils::deleteVectorOfPointer(bends_);
    MemoryUtils::deleteVectorOfPointer(torsions_);
    MemoryUtils::deleteVectorOfPointer(rigidBodies_);
    MemoryUtils::deleteVectorOfPointer(cutoffGroups_);

    //integrableObjects_ don't own the objects
    integrableObjects_.clear();
    
}

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

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

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

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

void Molecule::addRigidBody(RigidBody *rb) {
    if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == rigidBodies_.end()) {
        rigidBodies_.push_back(rb);
    }
}

void Molecule::addCutoffGroup(CutoffGroup* cp) {
    if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) == cutoffGroups_.end()) {
        cutoffGroups_.push_back(cp);
    }

}

void Molecule::complete() {
    
    std::set<Atom*> rigidAtoms;
    RigidBody* rb;
    std::vector<RigidBody*>::iterator rbIter;

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

    Atom* atom;
    AtomIterator ai;
    for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
   
        if (rigidAtoms.find(*ai) == rigidAtoms.end()) {
            //if an atom does not belong to a rigid body, it is an integrable object
            integrableObjects_.push_back(*ai);
        }
    }

    //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
    //    sprintf(painCave.errMsg, "Atoms in rigidbody are not in the atom list of the same molecule");
    //
    //    painCave.isFatal = 1;
    //    simError();        
    //}

    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;    
} 

double Molecule::getMass() {
    StuntDouble* sd;
    std::vector<StuntDouble*>::iterator i;
    double mass = 0.0;

    for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
        mass += sd->getMass();
    }

    return mass;

}

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 Vector3d& delta) {
    StuntDouble* sd;
    std::vector<StuntDouble*>::iterator i;
    
    for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
        sd->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;
}

double Molecule::getPotential() {

    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    Molecule::BondIterator bondIter;;
    Molecule::BendIterator  bendIter;
    Molecule::TorsionIterator  torsionIter;

    double potential = 0.0;

    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;

}

std::ostream& operator <<(std::ostream& o, 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 oopse
Revision:	1844
Committed:	Fri Dec 3 22:36:06 2004 UTC (19 years, 7 months ago) by tim
File size:	9092 byte(s)
Log Message:	NVE is running
#	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 Molecule.cpp
28	* @author tlin
29	* @date 10/28/2004
30	* @version 1.0
31	*/
32
33	#include <algorithm>
34	#include <set>
35
36	#include "primitives/Molecule.hpp"
37	#include "utils/MemoryUtils.hpp"
38	#include "utils/simError.h"
39
40	namespace oopse {
41	Molecule::Molecule(int stampId, int globalIndex, const std::string& molName)
42	: stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) {
43
44	}
45
46	Molecule::~Molecule() {
47
48	MemoryUtils::deleteVectorOfPointer(atoms_);
49	MemoryUtils::deleteVectorOfPointer(bonds_);
50	MemoryUtils::deleteVectorOfPointer(bends_);
51	MemoryUtils::deleteVectorOfPointer(torsions_);
52	MemoryUtils::deleteVectorOfPointer(rigidBodies_);
53	MemoryUtils::deleteVectorOfPointer(cutoffGroups_);
54
55	//integrableObjects_ don't own the objects
56	integrableObjects_.clear();
57
58	}
59
60	void Molecule::addAtom(Atom* atom) {
61	if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) {
62	atoms_.push_back(atom);
63	}
64	}
65
66	void Molecule::addBond(Bond* bond) {
67	if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) {
68	bonds_.push_back(bond);
69	}
70	}
71
72	void Molecule::addBend(Bend* bend) {
73	if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) {
74	bends_.push_back(bend);
75	}
76	}
77
78	void Molecule::addTorsion(Torsion* torsion) {
79	if (std::find(torsions_.begin(), torsions_.end(), torsion) == torsions_.end()) {
80	torsions_.push_back(torsion);
81	}
82	}
83
84	void Molecule::addRigidBody(RigidBody *rb) {
85	if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == rigidBodies_.end()) {
86	rigidBodies_.push_back(rb);
87	}
88	}
89
90	void Molecule::addCutoffGroup(CutoffGroup* cp) {
91	if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) == cutoffGroups_.end()) {
92	cutoffGroups_.push_back(cp);
93	}
94
95	}
96
97	void Molecule::complete() {
98
99	std::set<Atom*> rigidAtoms;
100	RigidBody* rb;
101	std::vector<RigidBody*>::iterator rbIter;
102
103
104	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
105	rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
106	}
107
108	Atom* atom;
109	AtomIterator ai;
110	for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
111
112	if (rigidAtoms.find(*ai) == rigidAtoms.end()) {
113	//if an atom does not belong to a rigid body, it is an integrable object
114	integrableObjects_.push_back(*ai);
115	}
116	}
117
118	//find all free atoms (which do not belong to rigid bodies)
119	//performs the "difference" operation from set theory, the output range contains a copy of every
120	//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
121	//[rigidAtoms.begin(), rigidAtoms.end()).
122	//std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(),
123	// std::back_inserter(integrableObjects_));
124
125	//if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) {
126	// //Some atoms in rigidAtoms are not in allAtoms, something must be wrong
127	// sprintf(painCave.errMsg, "Atoms in rigidbody are not in the atom list of the same molecule");
128	//
129	// painCave.isFatal = 1;
130	// simError();
131	//}
132
133	integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end());
134	}
135
136	Atom* Molecule::beginAtom(std::vector<Atom*>::iterator& i) {
137	i = atoms_.begin();
138	return (i == atoms_.end()) ? NULL : *i;
139	}
140
141	Atom* Molecule::nextAtom(std::vector<Atom*>::iterator& i) {
142	++i;
143	return (i == atoms_.end()) ? NULL : *i;
144	}
145
146	Bond* Molecule::beginBond(std::vector<Bond*>::iterator& i) {
147	i = bonds_.begin();
148	return (i == bonds_.end()) ? NULL : *i;
149	}
150
151	Bond* Molecule::nextBond(std::vector<Bond*>::iterator& i) {
152	++i;
153	return (i == bonds_.end()) ? NULL : *i;
154
155	}
156
157
158	Bend* Molecule::beginBend(std::vector<Bend*>::iterator& i) {
159	i = bends_.begin();
160	return (i == bends_.end()) ? NULL : *i;
161	}
162
163	Bend* Molecule::nextBend(std::vector<Bend*>::iterator& i) {
164	++i;
165	return (i == bends_.end()) ? NULL : *i;
166	}
167
168	Torsion* Molecule::beginTorsion(std::vector<Torsion*>::iterator& i) {
169	i = torsions_.begin();
170	return (i == torsions_.end()) ? NULL : *i;
171	}
172
173	Torsion* Molecule::nextTorsion(std::vector<Torsion*>::iterator& i) {
174	++i;
175	return (i == torsions_.end()) ? NULL : *i;
176	}
177
178	RigidBody* Molecule::beginRigidBody(std::vector<RigidBody*>::iterator& i) {
179	i = rigidBodies_.begin();
180	return (i == rigidBodies_.end()) ? NULL : *i;
181	}
182
183	RigidBody* Molecule::nextRigidBody(std::vector<RigidBody*>::iterator& i) {
184	++i;
185	return (i == rigidBodies_.end()) ? NULL : *i;
186	}
187
188	StuntDouble* Molecule::beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
189	i = integrableObjects_.begin();
190	return (i == integrableObjects_.end()) ? NULL : *i;
191	}
192
193	StuntDouble* Molecule::nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
194	++i;
195	return (i == integrableObjects_.end()) ? NULL : *i;
196	}
197
198	CutoffGroup* Molecule::beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
199	i = cutoffGroups_.begin();
200	return (i == cutoffGroups_.end()) ? NULL : *i;
201	}
202
203	CutoffGroup* Molecule::nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
204	++i;
205	return (i == cutoffGroups_.end()) ? NULL : *i;
206	}
207
208	double Molecule::getMass() {
209	StuntDouble* sd;
210	std::vector<StuntDouble*>::iterator i;
211	double mass = 0.0;
212
213	for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
214	mass += sd->getMass();
215	}
216
217	return mass;
218
219	}
220
221	Vector3d Molecule::getCom() {
222	StuntDouble* sd;
223	std::vector<StuntDouble*>::iterator i;
224	Vector3d com;
225	double totalMass = 0;
226	double mass;
227
228	for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
229	mass = sd->getMass();
230	totalMass += mass;
231	com += sd->getPos() * mass;
232	}
233
234	com /= totalMass;
235
236	return com;
237	}
238
239	void Molecule::moveCom(const Vector3d& delta) {
240	StuntDouble* sd;
241	std::vector<StuntDouble*>::iterator i;
242
243	for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
244	sd->setPos(sd->getPos() + delta);
245	}
246
247	}
248
249	Vector3d Molecule::getComVel() {
250	StuntDouble* sd;
251	std::vector<StuntDouble*>::iterator i;
252	Vector3d velCom;
253	double totalMass = 0;
254	double mass;
255
256	for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
257	mass = sd->getMass();
258	totalMass += mass;
259	velCom += sd->getVel() * mass;
260	}
261
262	velCom /= totalMass;
263
264	return velCom;
265	}
266
267	double Molecule::getPotential() {
268
269	Bond* bond;
270	Bend* bend;
271	Torsion* torsion;
272	Molecule::BondIterator bondIter;;
273	Molecule::BendIterator bendIter;
274	Molecule::TorsionIterator torsionIter;
275
276	double potential = 0.0;
277
278	for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
279	potential += bond->getPotential();
280	}
281
282	for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
283	potential += bend->getPotential();
284	}
285
286	for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) {
287	potential += torsion->getPotential();
288	}
289
290	return potential;
291
292	}
293
294	std::ostream& operator <<(std::ostream& o, Molecule& mol) {
295	o << std::endl;
296	o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
297	o << mol.getNAtoms() << " atoms" << std::endl;
298	o << mol.getNBonds() << " bonds" << std::endl;
299	o << mol.getNBends() << " bends" << std::endl;
300	o << mol.getNTorsions() << " torsions" << std::endl;
301	o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
302	o << mol.getNIntegrableObjects() << "integrable objects" << std::endl;
303	o << mol.getNCutoffGroups() << "cutoff groups" << std::endl;
304
305	return o;
306	}
307
308	}//end namespace oopse