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

    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:	246
Committed:	Wed Jan 12 22:41:40 2005 UTC (20 years, 9 months ago) by gezelter
File size:	8606 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	Content
1	/*
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
49	#include <algorithm>
50	#include <set>
51
52	#include "primitives/Molecule.hpp"
53	#include "utils/MemoryUtils.hpp"
54	#include "utils/simError.h"
55
56	namespace oopse {
57	Molecule::Molecule(int stampId, int globalIndex, const std::string& molName)
58	: stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) {
59
60	}
61
62	Molecule::~Molecule() {
63
64	MemoryUtils::deleteVectorOfPointer(atoms_);
65	MemoryUtils::deleteVectorOfPointer(bonds_);
66	MemoryUtils::deleteVectorOfPointer(bends_);
67	MemoryUtils::deleteVectorOfPointer(torsions_);
68	MemoryUtils::deleteVectorOfPointer(rigidBodies_);
69	MemoryUtils::deleteVectorOfPointer(cutoffGroups_);
70	MemoryUtils::deleteVectorOfPointer(constraintPairs_);
71	MemoryUtils::deleteVectorOfPointer(constraintElems_);
72	//integrableObjects_ don't own the objects
73	integrableObjects_.clear();
74
75	}
76
77	void Molecule::addAtom(Atom* atom) {
78	if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) {
79	atoms_.push_back(atom);
80	}
81	}
82
83	void Molecule::addBond(Bond* bond) {
84	if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) {
85	bonds_.push_back(bond);
86	}
87	}
88
89	void Molecule::addBend(Bend* bend) {
90	if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) {
91	bends_.push_back(bend);
92	}
93	}
94
95	void Molecule::addTorsion(Torsion* torsion) {
96	if (std::find(torsions_.begin(), torsions_.end(), torsion) == torsions_.end()) {
97	torsions_.push_back(torsion);
98	}
99	}
100
101	void Molecule::addRigidBody(RigidBody *rb) {
102	if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == rigidBodies_.end()) {
103	rigidBodies_.push_back(rb);
104	}
105	}
106
107	void Molecule::addCutoffGroup(CutoffGroup* cp) {
108	if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) == cutoffGroups_.end()) {
109	cutoffGroups_.push_back(cp);
110	}
111
112	}
113
114	void Molecule::addConstraintPair(ConstraintPair* cp) {
115	if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) == constraintPairs_.end()) {
116	constraintPairs_.push_back(cp);
117	}
118
119	}
120
121	void Molecule::addConstraintElem(ConstraintElem* cp) {
122	if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) == constraintElems_.end()) {
123	constraintElems_.push_back(cp);
124	}
125
126	}
127
128	void Molecule::complete() {
129
130	std::set<Atom*> rigidAtoms;
131	RigidBody* rb;
132	std::vector<RigidBody*>::iterator rbIter;
133
134
135	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
136	rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
137	}
138
139	Atom* atom;
140	AtomIterator ai;
141	for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
142
143	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
149	//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
156	//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
164	integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end());
165	}
166
167	double Molecule::getMass() {
168	StuntDouble* sd;
169	std::vector<StuntDouble*>::iterator i;
170	double mass = 0.0;
171
172	for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
173	mass += sd->getMass();
174	}
175
176	return mass;
177
178	}
179
180	Vector3d Molecule::getCom() {
181	StuntDouble* sd;
182	std::vector<StuntDouble*>::iterator i;
183	Vector3d com;
184	double totalMass = 0;
185	double mass;
186
187	for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
188	mass = sd->getMass();
189	totalMass += mass;
190	com += sd->getPos() * mass;
191	}
192
193	com /= totalMass;
194
195	return com;
196	}
197
198	void Molecule::moveCom(const Vector3d& delta) {
199	StuntDouble* sd;
200	std::vector<StuntDouble*>::iterator i;
201
202	for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
203	sd->setPos(sd->getPos() + delta);
204	}
205
206	}
207
208	Vector3d Molecule::getComVel() {
209	StuntDouble* sd;
210	std::vector<StuntDouble*>::iterator i;
211	Vector3d velCom;
212	double totalMass = 0;
213	double mass;
214
215	for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
216	mass = sd->getMass();
217	totalMass += mass;
218	velCom += sd->getVel() * mass;
219	}
220
221	velCom /= totalMass;
222
223	return velCom;
224	}
225
226	double Molecule::getPotential() {
227
228	Bond* bond;
229	Bend* bend;
230	Torsion* torsion;
231	Molecule::BondIterator bondIter;;
232	Molecule::BendIterator bendIter;
233	Molecule::TorsionIterator torsionIter;
234
235	double potential = 0.0;
236
237	for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
238	potential += bond->getPotential();
239	}
240
241	for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
242	potential += bend->getPotential();
243	}
244
245	for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) {
246	potential += torsion->getPotential();
247	}
248
249	return potential;
250
251	}
252
253	std::ostream& operator <<(std::ostream& o, Molecule& mol) {
254	o << std::endl;
255	o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
256	o << mol.getNAtoms() << " atoms" << std::endl;
257	o << mol.getNBonds() << " bonds" << std::endl;
258	o << mol.getNBends() << " bends" << std::endl;
259	o << mol.getNTorsions() << " torsions" << std::endl;
260	o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
261	o << mol.getNIntegrableObjects() << "integrable objects" << std::endl;
262	o << mol.getNCutoffGroups() << "cutoff groups" << std::endl;
263	o << mol.getNConstraintPairs() << "constraint pairs" << std::endl;
264	return o;
265	}
266
267	}//end namespace oopse