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::addConstraintPair(ConstraintPair* cp) {
    if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) == constraintPairs_.end()) {
        constraintPairs_.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;    
} 

ConstraintPair* Molecule::beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
    i = constraintPairs_.begin();
    return (i == constraintPairs_.end()) ? NULL : *i;
}

ConstraintPair* Molecule::nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {            
    ++i;
    return (i == constraintPairs_.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;
    o << mol.getNConstraintPairs() << "constraint pairs" << std::endl;
    return o;
}

}//end namespace oopse
Revision:	1901
Committed:	Tue Jan 4 22:18:36 2005 UTC (19 years, 6 months ago) by tim
File size:	9724 byte(s)
Log Message:	constraints in progress
#	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	1901	void Molecule::addConstraintPair(ConstraintPair* cp) {
98			if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) == constraintPairs_.end()) {
99			constraintPairs_.push_back(cp);
100			}
101
102			}
103
104
105	tim	1692	void Molecule::complete() {
106
107			std::set<Atom*> rigidAtoms;
108			RigidBody* rb;
109	tim	1695	std::vector<RigidBody*>::iterator rbIter;
110	gezelter	1490
111	tim	1692
112			for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
113	tim	1695	rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
114	tim	1692	}
115	gezelter	1490
116	tim	1843	Atom* atom;
117			AtomIterator ai;
118			for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
119	tim	1844
120			if (rigidAtoms.find(*ai) == rigidAtoms.end()) {
121			//if an atom does not belong to a rigid body, it is an integrable object
122	tim	1843	integrableObjects_.push_back(*ai);
123			}
124			}
125
126	tim	1692	//find all free atoms (which do not belong to rigid bodies)
127			//performs the "difference" operation from set theory, the output range contains a copy of every
128			//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
129			//[rigidAtoms.begin(), rigidAtoms.end()).
130	tim	1843	//std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(),
131			// std::back_inserter(integrableObjects_));
132	gezelter	1490
133	tim	1843	//if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) {
134			// //Some atoms in rigidAtoms are not in allAtoms, something must be wrong
135			// sprintf(painCave.errMsg, "Atoms in rigidbody are not in the atom list of the same molecule");
136			//
137			// painCave.isFatal = 1;
138			// simError();
139			//}
140	tim	1733
141	tim	1692	integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end());
142	gezelter	1490	}
143
144	tim	1692	Atom* Molecule::beginAtom(std::vector<Atom*>::iterator& i) {
145			i = atoms_.begin();
146			return (i == atoms_.end()) ? NULL : *i;
147			}
148	gezelter	1490
149	tim	1692	Atom* Molecule::nextAtom(std::vector<Atom*>::iterator& i) {
150			++i;
151			return (i == atoms_.end()) ? NULL : *i;
152			}
153	gezelter	1490
154	tim	1692	Bond* Molecule::beginBond(std::vector<Bond*>::iterator& i) {
155			i = bonds_.begin();
156			return (i == bonds_.end()) ? NULL : *i;
157			}
158	gezelter	1490
159	tim	1692	Bond* Molecule::nextBond(std::vector<Bond*>::iterator& i) {
160			++i;
161			return (i == bonds_.end()) ? NULL : *i;
162	gezelter	1490
163	tim	1692	}
164	gezelter	1490
165
166	tim	1692	Bend* Molecule::beginBend(std::vector<Bend*>::iterator& i) {
167			i = bends_.begin();
168			return (i == bends_.end()) ? NULL : *i;
169	gezelter	1490	}
170
171	tim	1692	Bend* Molecule::nextBend(std::vector<Bend*>::iterator& i) {
172			++i;
173			return (i == bends_.end()) ? NULL : *i;
174			}
175	gezelter	1490
176	tim	1692	Torsion* Molecule::beginTorsion(std::vector<Torsion*>::iterator& i) {
177			i = torsions_.begin();
178			return (i == torsions_.end()) ? NULL : *i;
179			}
180	gezelter	1490
181	tim	1692	Torsion* Molecule::nextTorsion(std::vector<Torsion*>::iterator& i) {
182			++i;
183			return (i == torsions_.end()) ? NULL : *i;
184			}
185	gezelter	1490
186	tim	1692	RigidBody* Molecule::beginRigidBody(std::vector<RigidBody*>::iterator& i) {
187			i = rigidBodies_.begin();
188			return (i == rigidBodies_.end()) ? NULL : *i;
189			}
190	gezelter	1490
191	tim	1692	RigidBody* Molecule::nextRigidBody(std::vector<RigidBody*>::iterator& i) {
192			++i;
193			return (i == rigidBodies_.end()) ? NULL : *i;
194			}
195	gezelter	1490
196	tim	1692	StuntDouble* Molecule::beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
197			i = integrableObjects_.begin();
198			return (i == integrableObjects_.end()) ? NULL : *i;
199	gezelter	1490	}
200
201	tim	1692	StuntDouble* Molecule::nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
202			++i;
203			return (i == integrableObjects_.end()) ? NULL : *i;
204			}
205	gezelter	1490
206	tim	1692	CutoffGroup* Molecule::beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
207			i = cutoffGroups_.begin();
208			return (i == cutoffGroups_.end()) ? NULL : *i;
209	gezelter	1490	}
210
211	tim	1692	CutoffGroup* Molecule::nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
212			++i;
213			return (i == cutoffGroups_.end()) ? NULL : *i;
214			}
215	gezelter	1490
216	tim	1901	ConstraintPair* Molecule::beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
217			i = constraintPairs_.begin();
218			return (i == constraintPairs_.end()) ? NULL : *i;
219			}
220
221			ConstraintPair* Molecule::nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
222			++i;
223			return (i == constraintPairs_.end()) ? NULL : *i;
224			}
225
226	tim	1843	double Molecule::getMass() {
227			StuntDouble* sd;
228			std::vector<StuntDouble*>::iterator i;
229			double mass = 0.0;
230	gezelter	1490
231	tim	1843	for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
232			mass += sd->getMass();
233			}
234
235			return mass;
236
237			}
238
239	tim	1692	Vector3d Molecule::getCom() {
240			StuntDouble* sd;
241			std::vector<StuntDouble*>::iterator i;
242			Vector3d com;
243			double totalMass = 0;
244			double mass;
245
246			for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
247			mass = sd->getMass();
248			totalMass += mass;
249			com += sd->getPos() * mass;
250			}
251	gezelter	1490
252	tim	1692	com /= totalMass;
253	gezelter	1490
254	tim	1692	return com;
255			}
256	gezelter	1490
257	tim	1695	void Molecule::moveCom(const Vector3d& delta) {
258	tim	1692	StuntDouble* sd;
259			std::vector<StuntDouble*>::iterator i;
260
261			for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
262	tim	1695	sd->setPos(sd->getPos() + delta);
263	gezelter	1490	}
264
265			}
266
267	tim	1692	Vector3d Molecule::getComVel() {
268			StuntDouble* sd;
269			std::vector<StuntDouble*>::iterator i;
270			Vector3d velCom;
271			double totalMass = 0;
272			double mass;
273
274			for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
275			mass = sd->getMass();
276			totalMass += mass;
277			velCom += sd->getVel() * mass;
278	gezelter	1490	}
279
280	tim	1692	velCom /= totalMass;
281	gezelter	1490
282	tim	1692	return velCom;
283	gezelter	1490	}
284
285	tim	1843	double Molecule::getPotential() {
286
287			Bond* bond;
288			Bend* bend;
289			Torsion* torsion;
290			Molecule::BondIterator bondIter;;
291			Molecule::BendIterator bendIter;
292			Molecule::TorsionIterator torsionIter;
293
294			double potential = 0.0;
295
296			for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
297			potential += bond->getPotential();
298			}
299
300			for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
301			potential += bend->getPotential();
302			}
303
304			for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) {
305			potential += torsion->getPotential();
306			}
307
308			return potential;
309
310			}
311
312	tim	1695	std::ostream& operator <<(std::ostream& o, Molecule& mol) {
313	tim	1692	o << std::endl;
314			o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
315			o << mol.getNAtoms() << " atoms" << std::endl;
316			o << mol.getNBonds() << " bonds" << std::endl;
317			o << mol.getNBends() << " bends" << std::endl;
318			o << mol.getNTorsions() << " torsions" << std::endl;
319			o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
320			o << mol.getNIntegrableObjects() << "integrable objects" << std::endl;
321			o << mol.getNCutoffGroups() << "cutoff groups" << std::endl;
322	tim	1901	o << mol.getNConstraintPairs() << "constraint pairs" << std::endl;
323	tim	1692	return o;
324			}
325	gezelter	1490
326	tim	1692	}//end namespace oopse