src/primitives/Molecule.cpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
/**
 * @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::deletePointers(atoms_);
    MemoryUtils::deletePointers(bonds_);
    MemoryUtils::deletePointers(bends_);
    MemoryUtils::deletePointers(torsions_);
    MemoryUtils::deletePointers(rigidBodies_);
    MemoryUtils::deletePointers(cutoffGroups_);
    MemoryUtils::deletePointers(constraintPairs_);
    MemoryUtils::deletePointers(constraintElems_);
    //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::addConstraintPair(ConstraintPair* cp) {
    if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) == constraintPairs_.end()) {
        constraintPairs_.push_back(cp);
    }

}

void Molecule::addConstraintElem(ConstraintElem* cp) {
    if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) == constraintElems_.end()) {
        constraintElems_.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();        
    //}
    for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
      integrableObjects_.push_back(rb);
    } 
    //integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end());
}

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;
    o << mol.getNConstraintPairs() << "constraint pairs" << std::endl;
    return o;
}

}//end namespace oopse
Revision:	398
Committed:	Mon Mar 7 22:39:33 2005 UTC (20 years, 8 months ago) by tim
File size:	8678 byte(s)
Log Message:	Fixing a bug in BitSet.cpp
#	User	Rev	Content
1	gezelter	246	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			/**
43			* @file Molecule.cpp
44			* @author tlin
45			* @date 10/28/2004
46			* @version 1.0
47			*/
48	gezelter	2
49	gezelter	246	#include <algorithm>
50			#include <set>
51	gezelter	2
52	tim	3	#include "primitives/Molecule.hpp"
53	gezelter	246	#include "utils/MemoryUtils.hpp"
54	tim	3	#include "utils/simError.h"
55	gezelter	2
56	gezelter	246	namespace oopse {
57			Molecule::Molecule(int stampId, int globalIndex, const std::string& molName)
58			: stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) {
59	gezelter	2
60	gezelter	246	}
61	gezelter	2
62	gezelter	246	Molecule::~Molecule() {
63	gezelter	2
64	tim	398	MemoryUtils::deletePointers(atoms_);
65			MemoryUtils::deletePointers(bonds_);
66			MemoryUtils::deletePointers(bends_);
67			MemoryUtils::deletePointers(torsions_);
68			MemoryUtils::deletePointers(rigidBodies_);
69			MemoryUtils::deletePointers(cutoffGroups_);
70			MemoryUtils::deletePointers(constraintPairs_);
71			MemoryUtils::deletePointers(constraintElems_);
72	gezelter	246	//integrableObjects_ don't own the objects
73			integrableObjects_.clear();
74
75	gezelter	2	}
76
77	gezelter	246	void Molecule::addAtom(Atom* atom) {
78			if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) {
79			atoms_.push_back(atom);
80			}
81			}
82	gezelter	2
83	gezelter	246	void Molecule::addBond(Bond* bond) {
84			if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) {
85			bonds_.push_back(bond);
86			}
87			}
88	gezelter	2
89	gezelter	246	void Molecule::addBend(Bend* bend) {
90			if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) {
91			bends_.push_back(bend);
92			}
93			}
94	gezelter	2
95	gezelter	246	void Molecule::addTorsion(Torsion* torsion) {
96			if (std::find(torsions_.begin(), torsions_.end(), torsion) == torsions_.end()) {
97			torsions_.push_back(torsion);
98			}
99			}
100	gezelter	2
101	gezelter	246	void Molecule::addRigidBody(RigidBody *rb) {
102			if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == rigidBodies_.end()) {
103			rigidBodies_.push_back(rb);
104			}
105	gezelter	2	}
106
107	gezelter	246	void Molecule::addCutoffGroup(CutoffGroup* cp) {
108			if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) == cutoffGroups_.end()) {
109			cutoffGroups_.push_back(cp);
110			}
111	gezelter	2
112	gezelter	246	}
113	gezelter	2
114	gezelter	246	void Molecule::addConstraintPair(ConstraintPair* cp) {
115			if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) == constraintPairs_.end()) {
116			constraintPairs_.push_back(cp);
117			}
118	gezelter	2
119			}
120
121	gezelter	246	void Molecule::addConstraintElem(ConstraintElem* cp) {
122			if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) == constraintElems_.end()) {
123			constraintElems_.push_back(cp);
124			}
125	gezelter	2
126			}
127
128	gezelter	246	void Molecule::complete() {
129
130			std::set<Atom*> rigidAtoms;
131			RigidBody* rb;
132			std::vector<RigidBody*>::iterator rbIter;
133	gezelter	2
134	gezelter	246
135			for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
136			rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
137			}
138	gezelter	2
139	gezelter	246	Atom* atom;
140			AtomIterator ai;
141			for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
142	gezelter	2
143	gezelter	246	if (rigidAtoms.find(*ai) == rigidAtoms.end()) {
144			//if an atom does not belong to a rigid body, it is an integrable object
145			integrableObjects_.push_back(*ai);
146			}
147			}
148	gezelter	2
149	gezelter	246	//find all free atoms (which do not belong to rigid bodies)
150			//performs the "difference" operation from set theory, the output range contains a copy of every
151			//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
152			//[rigidAtoms.begin(), rigidAtoms.end()).
153			//std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(),
154			// std::back_inserter(integrableObjects_));
155	gezelter	2
156	gezelter	246	//if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) {
157			// //Some atoms in rigidAtoms are not in allAtoms, something must be wrong
158			// sprintf(painCave.errMsg, "Atoms in rigidbody are not in the atom list of the same molecule");
159			//
160			// painCave.isFatal = 1;
161			// simError();
162			//}
163	tim	372	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
164			integrableObjects_.push_back(rb);
165			}
166			//integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end());
167	gezelter	2	}
168
169	gezelter	246	double Molecule::getMass() {
170			StuntDouble* sd;
171			std::vector<StuntDouble*>::iterator i;
172			double mass = 0.0;
173	gezelter	2
174	gezelter	246	for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
175			mass += sd->getMass();
176			}
177	gezelter	2
178	gezelter	246	return mass;
179	gezelter	2
180			}
181
182	gezelter	246	Vector3d Molecule::getCom() {
183			StuntDouble* sd;
184			std::vector<StuntDouble*>::iterator i;
185			Vector3d com;
186			double totalMass = 0;
187			double mass;
188
189			for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
190			mass = sd->getMass();
191			totalMass += mass;
192			com += sd->getPos() * mass;
193	gezelter	2	}
194
195	gezelter	246	com /= totalMass;
196	gezelter	2
197	gezelter	246	return com;
198			}
199	gezelter	2
200	gezelter	246	void Molecule::moveCom(const Vector3d& delta) {
201			StuntDouble* sd;
202			std::vector<StuntDouble*>::iterator i;
203
204			for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
205			sd->setPos(sd->getPos() + delta);
206	gezelter	2	}
207
208			}
209
210	gezelter	246	Vector3d Molecule::getComVel() {
211			StuntDouble* sd;
212			std::vector<StuntDouble*>::iterator i;
213			Vector3d velCom;
214			double totalMass = 0;
215			double mass;
216
217			for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
218			mass = sd->getMass();
219			totalMass += mass;
220			velCom += sd->getVel() * mass;
221			}
222	gezelter	2
223	gezelter	246	velCom /= totalMass;
224	gezelter	2
225	gezelter	246	return velCom;
226			}
227	gezelter	2
228	gezelter	246	double Molecule::getPotential() {
229	gezelter	2
230	gezelter	246	Bond* bond;
231			Bend* bend;
232			Torsion* torsion;
233			Molecule::BondIterator bondIter;;
234			Molecule::BendIterator bendIter;
235			Molecule::TorsionIterator torsionIter;
236	gezelter	2
237	gezelter	246	double potential = 0.0;
238	gezelter	2
239	gezelter	246	for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
240			potential += bond->getPotential();
241			}
242	gezelter	2
243	gezelter	246	for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
244			potential += bend->getPotential();
245	gezelter	2	}
246
247	gezelter	246	for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) {
248			potential += torsion->getPotential();
249	gezelter	2	}
250
251	gezelter	246	return potential;
252	gezelter	2
253			}
254
255	gezelter	246	std::ostream& operator <<(std::ostream& o, Molecule& mol) {
256			o << std::endl;
257			o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
258			o << mol.getNAtoms() << " atoms" << std::endl;
259			o << mol.getNBonds() << " bonds" << std::endl;
260			o << mol.getNBends() << " bends" << std::endl;
261			o << mol.getNTorsions() << " torsions" << std::endl;
262			o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
263			o << mol.getNIntegrableObjects() << "integrable objects" << std::endl;
264			o << mol.getNCutoffGroups() << "cutoff groups" << std::endl;
265			o << mol.getNConstraintPairs() << "constraint pairs" << std::endl;
266			return o;
267			}
268	gezelter	2
269	gezelter	246	}//end namespace oopse