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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
/**
 * @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 OpenMD {
  Molecule::Molecule(int stampId, int globalIndex, const std::string& molName) 
    : stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName), 
      constrainTotalCharge_(false) {
  }
  
  Molecule::~Molecule() {
    
    MemoryUtils::deletePointers(atoms_);
    MemoryUtils::deletePointers(bonds_);
    MemoryUtils::deletePointers(bends_);
    MemoryUtils::deletePointers(torsions_);
    MemoryUtils::deletePointers(inversions_);
    MemoryUtils::deletePointers(rigidBodies_);
    MemoryUtils::deletePointers(cutoffGroups_);
    MemoryUtils::deletePointers(constraintPairs_);
    MemoryUtils::deletePointers(constraintElems_);

    // integrableObjects_ don't own the objects
    integrableObjects_.clear();
    fluctuatingCharges_.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::addInversion(Inversion* inversion) {
    if (std::find(inversions_.begin(), inversions_.end(), inversion) == 
        inversions_.end()) {
      inversions_.push_back(inversion);
    }
  }
  
  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;
    Atom* atom;
    AtomIterator ai;
    RigidBody* rb;
    RigidBodyIterator rbIter;

    // Get list of all the atoms that are part of rigid bodies

    for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
      rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
    }
    
    // add any atom that wasn't part of a rigid body to the list of integrableObjects

    for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
      
      if (rigidAtoms.find(atom) == rigidAtoms.end()) {

        // If an atom does not belong to a rigid body, it is an
        // integrable object

        integrableObjects_.push_back(atom);
      }
    }
    
    // then add the rigid bodies themselves to the integrableObjects

    for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
      integrableObjects_.push_back(rb);
    } 

    // find the atoms that are fluctuating charges and add them to the 
    // fluctuatingCharges_ vector

    for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
      if ( atom->isFluctuatingCharge() )
        fluctuatingCharges_.push_back( atom );      
    }

  }

  RealType Molecule::getMass() {
    StuntDouble* sd;
    std::vector<StuntDouble*>::iterator i;
    RealType 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;
    RealType totalMass = 0;
    RealType 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;
    RealType totalMass = 0;
    RealType mass;
    
    for (sd = beginIntegrableObject(i); sd != NULL; sd = 
           nextIntegrableObject(i)){
      mass = sd->getMass();
      totalMass += mass;
      velCom += sd->getVel() * mass;    
    }
    
    velCom /= totalMass;
    
    return velCom;
  }

  RealType Molecule::getPotential() {

    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    Inversion* inversion;
    Molecule::BondIterator bondIter;;
    Molecule::BendIterator  bendIter;
    Molecule::TorsionIterator  torsionIter;
    Molecule::InversionIterator  inversionIter;

    RealType 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();
    }
    
    for (inversion = beginInversion(inversionIter); torsion != NULL; 
         inversion =  nextInversion(inversionIter)) {
      potential += inversion->getPotential();
    }
    
    return potential;
    
  }
  
  void Molecule::addProperty(GenericData* genData) {
    properties_.addProperty(genData);  
  }

  void Molecule::removeProperty(const std::string& propName) {
    properties_.removeProperty(propName);  
  }

  void Molecule::clearProperties() {
    properties_.clearProperties(); 
  }

  std::vector<std::string> Molecule::getPropertyNames() {
    return properties_.getPropertyNames();  
  }
      
  std::vector<GenericData*> Molecule::getProperties() { 
    return properties_.getProperties(); 
  }

  GenericData* Molecule::getPropertyByName(const std::string& propName) {
    return properties_.getPropertyByName(propName); 
  }

  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.getNInversions() << " inversions" << 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;
    o << mol.getNFluctuatingCharges() << " fluctuating charges" << std::endl;
    return o;
  }
  
}//end namespace OpenMD
Revision:	1718
Committed:	Thu May 24 01:29:59 2012 UTC (12 years, 11 months ago) by gezelter
File size:	9913 byte(s)
Log Message:	Adding fluctuating charges, still a work in progress
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43			/**
44			* @file Molecule.cpp
45			* @author tlin
46			* @date 10/28/2004
47			* @version 1.0
48			*/
49	gezelter	2
50	gezelter	246	#include <algorithm>
51			#include <set>
52	gezelter	2
53	tim	3	#include "primitives/Molecule.hpp"
54	gezelter	246	#include "utils/MemoryUtils.hpp"
55	tim	3	#include "utils/simError.h"
56	gezelter	2
57	gezelter	1390	namespace OpenMD {
58	gezelter	507	Molecule::Molecule(int stampId, int globalIndex, const std::string& molName)
59	gezelter	1718	: stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName),
60			constrainTotalCharge_(false) {
61	gezelter	1211	}
62
63	gezelter	507	Molecule::~Molecule() {
64	gezelter	1211
65	tim	398	MemoryUtils::deletePointers(atoms_);
66			MemoryUtils::deletePointers(bonds_);
67			MemoryUtils::deletePointers(bends_);
68			MemoryUtils::deletePointers(torsions_);
69	gezelter	1277	MemoryUtils::deletePointers(inversions_);
70	tim	398	MemoryUtils::deletePointers(rigidBodies_);
71			MemoryUtils::deletePointers(cutoffGroups_);
72			MemoryUtils::deletePointers(constraintPairs_);
73			MemoryUtils::deletePointers(constraintElems_);
74	gezelter	1715
75	gezelter	1211	// integrableObjects_ don't own the objects
76	gezelter	246	integrableObjects_.clear();
77	gezelter	1715	fluctuatingCharges_.clear();
78	gezelter	246
79	gezelter	507	}
80	gezelter	1211
81	gezelter	507	void Molecule::addAtom(Atom* atom) {
82	gezelter	246	if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) {
83	gezelter	507	atoms_.push_back(atom);
84	gezelter	246	}
85	gezelter	507	}
86	gezelter	1211
87	gezelter	507	void Molecule::addBond(Bond* bond) {
88	gezelter	246	if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) {
89	gezelter	507	bonds_.push_back(bond);
90	gezelter	246	}
91	gezelter	507	}
92	gezelter	1211
93	gezelter	507	void Molecule::addBend(Bend* bend) {
94	gezelter	246	if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) {
95	gezelter	507	bends_.push_back(bend);
96	gezelter	246	}
97	gezelter	507	}
98	gezelter	1211
99	gezelter	507	void Molecule::addTorsion(Torsion* torsion) {
100	gezelter	1211	if (std::find(torsions_.begin(), torsions_.end(), torsion) ==
101			torsions_.end()) {
102	gezelter	507	torsions_.push_back(torsion);
103	gezelter	246	}
104	gezelter	507	}
105	gezelter	1277
106			void Molecule::addInversion(Inversion* inversion) {
107			if (std::find(inversions_.begin(), inversions_.end(), inversion) ==
108			inversions_.end()) {
109			inversions_.push_back(inversion);
110			}
111			}
112	gezelter	1211
113	gezelter	507	void Molecule::addRigidBody(RigidBody *rb) {
114	gezelter	1211	if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) ==
115			rigidBodies_.end()) {
116	gezelter	507	rigidBodies_.push_back(rb);
117	gezelter	246	}
118	gezelter	507	}
119	gezelter	1211
120	gezelter	507	void Molecule::addCutoffGroup(CutoffGroup* cp) {
121	gezelter	1211	if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) ==
122			cutoffGroups_.end()) {
123	gezelter	507	cutoffGroups_.push_back(cp);
124	gezelter	1211	}
125	gezelter	507	}
126	gezelter	1211
127	gezelter	507	void Molecule::addConstraintPair(ConstraintPair* cp) {
128	gezelter	1211	if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) ==
129			constraintPairs_.end()) {
130	gezelter	507	constraintPairs_.push_back(cp);
131	gezelter	1211	}
132	gezelter	507	}
133	gezelter	1211
134	gezelter	507	void Molecule::addConstraintElem(ConstraintElem* cp) {
135	gezelter	1211	if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) ==
136			constraintElems_.end()) {
137	gezelter	507	constraintElems_.push_back(cp);
138	gezelter	246	}
139	gezelter	507	}
140	gezelter	1211
141	gezelter	507	void Molecule::complete() {
142	gezelter	246
143			std::set<Atom*> rigidAtoms;
144	gezelter	1715	Atom* atom;
145			AtomIterator ai;
146	gezelter	246	RigidBody* rb;
147	gezelter	1715	RigidBodyIterator rbIter;
148	gezelter	2
149	gezelter	1715	// Get list of all the atoms that are part of rigid bodies
150
151	gezelter	246	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
152	gezelter	507	rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
153	gezelter	246	}
154	gezelter	1211
155	gezelter	1715	// add any atom that wasn't part of a rigid body to the list of integrableObjects
156
157	gezelter	246	for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
158	gezelter	1211
159	gezelter	1715	if (rigidAtoms.find(atom) == rigidAtoms.end()) {
160	gezelter	1211
161			// If an atom does not belong to a rigid body, it is an
162			// integrable object
163
164	gezelter	1715	integrableObjects_.push_back(atom);
165	gezelter	507	}
166	gezelter	246	}
167	gezelter	1211
168	gezelter	1715	// then add the rigid bodies themselves to the integrableObjects
169	gezelter	2
170	tim	372	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
171			integrableObjects_.push_back(rb);
172			}
173	gezelter	1715
174			// find the atoms that are fluctuating charges and add them to the
175			// fluctuatingCharges_ vector
176
177			for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
178			if ( atom->isFluctuatingCharge() )
179			fluctuatingCharges_.push_back( atom );
180			}
181
182	gezelter	507	}
183	gezelter	2
184	tim	963	RealType Molecule::getMass() {
185	gezelter	246	StuntDouble* sd;
186			std::vector<StuntDouble*>::iterator i;
187	tim	963	RealType mass = 0.0;
188	gezelter	1211
189			for (sd = beginIntegrableObject(i); sd != NULL; sd =
190			nextIntegrableObject(i)){
191	gezelter	507	mass += sd->getMass();
192	gezelter	246	}
193	gezelter	1211
194			return mass;
195	gezelter	507	}
196	gezelter	2
197	gezelter	507	Vector3d Molecule::getCom() {
198	gezelter	246	StuntDouble* sd;
199			std::vector<StuntDouble*>::iterator i;
200			Vector3d com;
201	tim	963	RealType totalMass = 0;
202			RealType mass;
203	gezelter	246
204	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
205			nextIntegrableObject(i)){
206	gezelter	507	mass = sd->getMass();
207			totalMass += mass;
208			com += sd->getPos() * mass;
209	gezelter	2	}
210	gezelter	1211
211	gezelter	246	com /= totalMass;
212	gezelter	2
213	gezelter	246	return com;
214	gezelter	507	}
215	gezelter	2
216	gezelter	507	void Molecule::moveCom(const Vector3d& delta) {
217	gezelter	246	StuntDouble* sd;
218			std::vector<StuntDouble*>::iterator i;
219
220	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
221			nextIntegrableObject(i)){
222	gezelter	507	sd->setPos(sd->getPos() + delta);
223	gezelter	1211	}
224	gezelter	507	}
225	gezelter	2
226	gezelter	507	Vector3d Molecule::getComVel() {
227	gezelter	246	StuntDouble* sd;
228			std::vector<StuntDouble*>::iterator i;
229			Vector3d velCom;
230	tim	963	RealType totalMass = 0;
231			RealType mass;
232	gezelter	246
233	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
234			nextIntegrableObject(i)){
235	gezelter	507	mass = sd->getMass();
236			totalMass += mass;
237			velCom += sd->getVel() * mass;
238	gezelter	246	}
239	gezelter	1211
240	gezelter	246	velCom /= totalMass;
241	gezelter	1211
242	gezelter	246	return velCom;
243	gezelter	507	}
244	gezelter	2
245	tim	963	RealType Molecule::getPotential() {
246	gezelter	2
247	gezelter	246	Bond* bond;
248			Bend* bend;
249			Torsion* torsion;
250	gezelter	1277	Inversion* inversion;
251	gezelter	246	Molecule::BondIterator bondIter;;
252			Molecule::BendIterator bendIter;
253			Molecule::TorsionIterator torsionIter;
254	gezelter	1277	Molecule::InversionIterator inversionIter;
255	gezelter	2
256	tim	963	RealType potential = 0.0;
257	gezelter	2
258	gezelter	246	for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
259	gezelter	507	potential += bond->getPotential();
260	gezelter	246	}
261	gezelter	2
262	gezelter	246	for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
263	gezelter	507	potential += bend->getPotential();
264	gezelter	2	}
265
266	gezelter	1211	for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion =
267			nextTorsion(torsionIter)) {
268	gezelter	507	potential += torsion->getPotential();
269	gezelter	2	}
270	gezelter	1211
271	gezelter	1277	for (inversion = beginInversion(inversionIter); torsion != NULL;
272			inversion = nextInversion(inversionIter)) {
273			potential += inversion->getPotential();
274			}
275
276	gezelter	246	return potential;
277	gezelter	1211
278	gezelter	507	}
279	gezelter	1211
280	cli2	1360	void Molecule::addProperty(GenericData* genData) {
281			properties_.addProperty(genData);
282			}
283
284			void Molecule::removeProperty(const std::string& propName) {
285			properties_.removeProperty(propName);
286			}
287
288			void Molecule::clearProperties() {
289			properties_.clearProperties();
290			}
291
292			std::vector<std::string> Molecule::getPropertyNames() {
293			return properties_.getPropertyNames();
294			}
295
296			std::vector<GenericData*> Molecule::getProperties() {
297			return properties_.getProperties();
298			}
299
300			GenericData* Molecule::getPropertyByName(const std::string& propName) {
301			return properties_.getPropertyByName(propName);
302			}
303
304	gezelter	507	std::ostream& operator <<(std::ostream& o, Molecule& mol) {
305	gezelter	246	o << std::endl;
306			o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
307			o << mol.getNAtoms() << " atoms" << std::endl;
308			o << mol.getNBonds() << " bonds" << std::endl;
309			o << mol.getNBends() << " bends" << std::endl;
310			o << mol.getNTorsions() << " torsions" << std::endl;
311	gezelter	1277	o << mol.getNInversions() << " inversions" << std::endl;
312	gezelter	246	o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
313	gezelter	1715	o << mol.getNIntegrableObjects() << " integrable objects" << std::endl;
314			o << mol.getNCutoffGroups() << " cutoff groups" << std::endl;
315			o << mol.getNConstraintPairs() << " constraint pairs" << std::endl;
316			o << mol.getNFluctuatingCharges() << " fluctuating charges" << std::endl;
317	gezelter	246	return o;
318	gezelter	507	}
319	gezelter	1211
320	gezelter	1390	}//end namespace OpenMD