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, 9 months ago) by tim
File size:	9092 byte(s)
Log Message:	NVE is running
#	User	Rev	Content
1	tim	1692	/*
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	gezelter	1490
26	tim	1692	/**
27			* @file Molecule.cpp
28			* @author tlin
29			* @date 10/28/2004
30			* @version 1.0
31			*/
32	gezelter	1490
33	tim	1692	#include <algorithm>
34	tim	1695	#include <set>
35	gezelter	1490
36	tim	1695	#include "primitives/Molecule.hpp"
37			#include "utils/MemoryUtils.hpp"
38	tim	1782	#include "utils/simError.h"
39	tim	1695
40	tim	1692	namespace oopse {
41	tim	1733	Molecule::Molecule(int stampId, int globalIndex, const std::string& molName)
42			: stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) {
43	gezelter	1490
44	tim	1733	}
45
46	tim	1692	Molecule::~Molecule() {
47	gezelter	1490
48	tim	1695	MemoryUtils::deleteVectorOfPointer(atoms_);
49			MemoryUtils::deleteVectorOfPointer(bonds_);
50			MemoryUtils::deleteVectorOfPointer(bends_);
51			MemoryUtils::deleteVectorOfPointer(torsions_);
52			MemoryUtils::deleteVectorOfPointer(rigidBodies_);
53			MemoryUtils::deleteVectorOfPointer(cutoffGroups_);
54	gezelter	1490
55	tim	1695	//integrableObjects_ don't own the objects
56	tim	1692	integrableObjects_.clear();
57
58	gezelter	1490	}
59
60	tim	1692	void Molecule::addAtom(Atom* atom) {
61	tim	1695	if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) {
62	tim	1692	atoms_.push_back(atom);
63			}
64			}
65	gezelter	1490
66	tim	1692	void Molecule::addBond(Bond* bond) {
67	tim	1695	if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) {
68	tim	1692	bonds_.push_back(bond);
69			}
70			}
71	gezelter	1490
72	tim	1692	void Molecule::addBend(Bend* bend) {
73	tim	1695	if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) {
74	tim	1692	bends_.push_back(bend);
75			}
76			}
77	gezelter	1490
78	tim	1692	void Molecule::addTorsion(Torsion* torsion) {
79	tim	1695	if (std::find(torsions_.begin(), torsions_.end(), torsion) == torsions_.end()) {
80	tim	1692	torsions_.push_back(torsion);
81			}
82			}
83	gezelter	1490
84	tim	1692	void Molecule::addRigidBody(RigidBody *rb) {
85	tim	1695	if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == rigidBodies_.end()) {
86	tim	1692	rigidBodies_.push_back(rb);
87			}
88	gezelter	1490	}
89
90	tim	1692	void Molecule::addCutoffGroup(CutoffGroup* cp) {
91	tim	1695	if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) == cutoffGroups_.end()) {
92	tim	1692	cutoffGroups_.push_back(cp);
93			}
94	gezelter	1490
95	tim	1692	}
96	gezelter	1490
97	tim	1692	void Molecule::complete() {
98
99			std::set<Atom*> rigidAtoms;
100			RigidBody* rb;
101	tim	1695	std::vector<RigidBody*>::iterator rbIter;
102	gezelter	1490
103	tim	1692
104			for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
105	tim	1695	rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
106	tim	1692	}
107	gezelter	1490
108	tim	1843	Atom* atom;
109			AtomIterator ai;
110			for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
111	tim	1844
112			if (rigidAtoms.find(*ai) == rigidAtoms.end()) {
113			//if an atom does not belong to a rigid body, it is an integrable object
114	tim	1843	integrableObjects_.push_back(*ai);
115			}
116			}
117
118	tim	1692	//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	tim	1843	//std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(),
123			// std::back_inserter(integrableObjects_));
124	gezelter	1490
125	tim	1843	//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	tim	1733
133	tim	1692	integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end());
134	gezelter	1490	}
135
136	tim	1692	Atom* Molecule::beginAtom(std::vector<Atom*>::iterator& i) {
137			i = atoms_.begin();
138			return (i == atoms_.end()) ? NULL : *i;
139			}
140	gezelter	1490
141	tim	1692	Atom* Molecule::nextAtom(std::vector<Atom*>::iterator& i) {
142			++i;
143			return (i == atoms_.end()) ? NULL : *i;
144			}
145	gezelter	1490
146	tim	1692	Bond* Molecule::beginBond(std::vector<Bond*>::iterator& i) {
147			i = bonds_.begin();
148			return (i == bonds_.end()) ? NULL : *i;
149			}
150	gezelter	1490
151	tim	1692	Bond* Molecule::nextBond(std::vector<Bond*>::iterator& i) {
152			++i;
153			return (i == bonds_.end()) ? NULL : *i;
154	gezelter	1490
155	tim	1692	}
156	gezelter	1490
157
158	tim	1692	Bend* Molecule::beginBend(std::vector<Bend*>::iterator& i) {
159			i = bends_.begin();
160			return (i == bends_.end()) ? NULL : *i;
161	gezelter	1490	}
162
163	tim	1692	Bend* Molecule::nextBend(std::vector<Bend*>::iterator& i) {
164			++i;
165			return (i == bends_.end()) ? NULL : *i;
166			}
167	gezelter	1490
168	tim	1692	Torsion* Molecule::beginTorsion(std::vector<Torsion*>::iterator& i) {
169			i = torsions_.begin();
170			return (i == torsions_.end()) ? NULL : *i;
171			}
172	gezelter	1490
173	tim	1692	Torsion* Molecule::nextTorsion(std::vector<Torsion*>::iterator& i) {
174			++i;
175			return (i == torsions_.end()) ? NULL : *i;
176			}
177	gezelter	1490
178	tim	1692	RigidBody* Molecule::beginRigidBody(std::vector<RigidBody*>::iterator& i) {
179			i = rigidBodies_.begin();
180			return (i == rigidBodies_.end()) ? NULL : *i;
181			}
182	gezelter	1490
183	tim	1692	RigidBody* Molecule::nextRigidBody(std::vector<RigidBody*>::iterator& i) {
184			++i;
185			return (i == rigidBodies_.end()) ? NULL : *i;
186			}
187	gezelter	1490
188	tim	1692	StuntDouble* Molecule::beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
189			i = integrableObjects_.begin();
190			return (i == integrableObjects_.end()) ? NULL : *i;
191	gezelter	1490	}
192
193	tim	1692	StuntDouble* Molecule::nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
194			++i;
195			return (i == integrableObjects_.end()) ? NULL : *i;
196			}
197	gezelter	1490
198	tim	1692	CutoffGroup* Molecule::beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
199			i = cutoffGroups_.begin();
200			return (i == cutoffGroups_.end()) ? NULL : *i;
201	gezelter	1490	}
202
203	tim	1692	CutoffGroup* Molecule::nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
204			++i;
205			return (i == cutoffGroups_.end()) ? NULL : *i;
206			}
207	gezelter	1490
208	tim	1843	double Molecule::getMass() {
209			StuntDouble* sd;
210			std::vector<StuntDouble*>::iterator i;
211			double mass = 0.0;
212	gezelter	1490
213	tim	1843	for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
214			mass += sd->getMass();
215			}
216
217			return mass;
218
219			}
220
221	tim	1692	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	gezelter	1490
234	tim	1692	com /= totalMass;
235	gezelter	1490
236	tim	1692	return com;
237			}
238	gezelter	1490
239	tim	1695	void Molecule::moveCom(const Vector3d& delta) {
240	tim	1692	StuntDouble* sd;
241			std::vector<StuntDouble*>::iterator i;
242
243			for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
244	tim	1695	sd->setPos(sd->getPos() + delta);
245	gezelter	1490	}
246
247			}
248
249	tim	1692	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	gezelter	1490	}
261
262	tim	1692	velCom /= totalMass;
263	gezelter	1490
264	tim	1692	return velCom;
265	gezelter	1490	}
266
267	tim	1843	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	tim	1695	std::ostream& operator <<(std::ostream& o, Molecule& mol) {
295	tim	1692	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	gezelter	1490
305	tim	1692	return o;
306			}
307	gezelter	1490
308	tim	1692	}//end namespace oopse