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*> allAtoms;
    allAtoms.insert(atoms_.begin(), atoms_.end());

    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());
    }

    //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;    
} 


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;
}

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:	1782
Committed:	Wed Nov 24 20:55:03 2004 UTC (19 years, 9 months ago) by tim
File size:	7901 byte(s)
Log Message:	types and primitives get built
#	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*> allAtoms;
100			allAtoms.insert(atoms_.begin(), atoms_.end());
101	gezelter	1490
102	tim	1692	std::set<Atom*> rigidAtoms;
103			RigidBody* rb;
104	tim	1695	std::vector<RigidBody*>::iterator rbIter;
105	gezelter	1490
106	tim	1692
107			for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
108	tim	1695	rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
109	tim	1692	}
110	gezelter	1490
111	tim	1692	//find all free atoms (which do not belong to rigid bodies)
112			//performs the "difference" operation from set theory, the output range contains a copy of every
113			//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
114			//[rigidAtoms.begin(), rigidAtoms.end()).
115			std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(),
116	tim	1782	std::back_inserter(integrableObjects_));
117	gezelter	1490
118	tim	1692	if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) {
119			//Some atoms in rigidAtoms are not in allAtoms, something must be wrong
120	tim	1733	sprintf(painCave.errMsg, "Atoms in rigidbody are not in the atom list of the same molecule");
121
122			painCave.isFatal = 1;
123			simError();
124	tim	1692	}
125	gezelter	1490
126	tim	1692	integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end());
127	gezelter	1490	}
128
129	tim	1692	Atom* Molecule::beginAtom(std::vector<Atom*>::iterator& i) {
130			i = atoms_.begin();
131			return (i == atoms_.end()) ? NULL : *i;
132			}
133	gezelter	1490
134	tim	1692	Atom* Molecule::nextAtom(std::vector<Atom*>::iterator& i) {
135			++i;
136			return (i == atoms_.end()) ? NULL : *i;
137			}
138	gezelter	1490
139	tim	1692	Bond* Molecule::beginBond(std::vector<Bond*>::iterator& i) {
140			i = bonds_.begin();
141			return (i == bonds_.end()) ? NULL : *i;
142			}
143	gezelter	1490
144	tim	1692	Bond* Molecule::nextBond(std::vector<Bond*>::iterator& i) {
145			++i;
146			return (i == bonds_.end()) ? NULL : *i;
147	gezelter	1490
148	tim	1692	}
149	gezelter	1490
150
151	tim	1692	Bend* Molecule::beginBend(std::vector<Bend*>::iterator& i) {
152			i = bends_.begin();
153			return (i == bends_.end()) ? NULL : *i;
154	gezelter	1490	}
155
156	tim	1692	Bend* Molecule::nextBend(std::vector<Bend*>::iterator& i) {
157			++i;
158			return (i == bends_.end()) ? NULL : *i;
159			}
160	gezelter	1490
161	tim	1692	Torsion* Molecule::beginTorsion(std::vector<Torsion*>::iterator& i) {
162			i = torsions_.begin();
163			return (i == torsions_.end()) ? NULL : *i;
164			}
165	gezelter	1490
166	tim	1692	Torsion* Molecule::nextTorsion(std::vector<Torsion*>::iterator& i) {
167			++i;
168			return (i == torsions_.end()) ? NULL : *i;
169			}
170	gezelter	1490
171	tim	1692	RigidBody* Molecule::beginRigidBody(std::vector<RigidBody*>::iterator& i) {
172			i = rigidBodies_.begin();
173			return (i == rigidBodies_.end()) ? NULL : *i;
174			}
175	gezelter	1490
176	tim	1692	RigidBody* Molecule::nextRigidBody(std::vector<RigidBody*>::iterator& i) {
177			++i;
178			return (i == rigidBodies_.end()) ? NULL : *i;
179			}
180	gezelter	1490
181	tim	1692	StuntDouble* Molecule::beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
182			i = integrableObjects_.begin();
183			return (i == integrableObjects_.end()) ? NULL : *i;
184	gezelter	1490	}
185
186	tim	1692	StuntDouble* Molecule::nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
187			++i;
188			return (i == integrableObjects_.end()) ? NULL : *i;
189			}
190	gezelter	1490
191	tim	1692	CutoffGroup* Molecule::beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
192			i = cutoffGroups_.begin();
193			return (i == cutoffGroups_.end()) ? NULL : *i;
194	gezelter	1490	}
195
196	tim	1692	CutoffGroup* Molecule::nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
197			++i;
198			return (i == cutoffGroups_.end()) ? NULL : *i;
199			}
200	gezelter	1490
201
202	tim	1692	Vector3d Molecule::getCom() {
203			StuntDouble* sd;
204			std::vector<StuntDouble*>::iterator i;
205			Vector3d com;
206			double totalMass = 0;
207			double mass;
208
209			for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
210			mass = sd->getMass();
211			totalMass += mass;
212			com += sd->getPos() * mass;
213			}
214	gezelter	1490
215	tim	1692	com /= totalMass;
216	gezelter	1490
217	tim	1692	return com;
218			}
219	gezelter	1490
220	tim	1695	void Molecule::moveCom(const Vector3d& delta) {
221	tim	1692	StuntDouble* sd;
222			std::vector<StuntDouble*>::iterator i;
223
224			for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
225	tim	1695	sd->setPos(sd->getPos() + delta);
226	gezelter	1490	}
227
228			}
229
230	tim	1692	Vector3d Molecule::getComVel() {
231			StuntDouble* sd;
232			std::vector<StuntDouble*>::iterator i;
233			Vector3d velCom;
234			double totalMass = 0;
235			double mass;
236
237			for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
238			mass = sd->getMass();
239			totalMass += mass;
240			velCom += sd->getVel() * mass;
241	gezelter	1490	}
242
243	tim	1692	velCom /= totalMass;
244	gezelter	1490
245	tim	1692	return velCom;
246	gezelter	1490	}
247
248	tim	1695	std::ostream& operator <<(std::ostream& o, Molecule& mol) {
249	tim	1692	o << std::endl;
250			o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
251			o << mol.getNAtoms() << " atoms" << std::endl;
252			o << mol.getNBonds() << " bonds" << std::endl;
253			o << mol.getNBends() << " bends" << std::endl;
254			o << mol.getNTorsions() << " torsions" << std::endl;
255			o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
256			o << mol.getNIntegrableObjects() << "integrable objects" << std::endl;
257			o << mol.getNCutoffGroups() << "cutoff groups" << std::endl;
258	gezelter	1490
259	tim	1692	return o;
260			}
261	gezelter	1490
262	tim	1692	}//end namespace oopse