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, 234107 (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, 
                     int region) : stampId_(stampId),
                                   globalIndex_(globalIndex), 
                                   moleculeName_(molName), 
                                   region_(region),
                                   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:	1908
Committed:	Fri Jul 19 21:25:45 2013 UTC (11 years, 9 months ago) by gezelter
File size:	10095 byte(s)
Log Message:	Added infrastructure for region-constrained fluctuating charges.
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [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	1908	Molecule::Molecule(int stampId, int globalIndex, const std::string& molName,
59			int region) : stampId_(stampId),
60			globalIndex_(globalIndex),
61			moleculeName_(molName),
62			region_(region),
63			constrainTotalCharge_(false) {
64	gezelter	1211	}
65
66	gezelter	507	Molecule::~Molecule() {
67	gezelter	1211
68	tim	398	MemoryUtils::deletePointers(atoms_);
69			MemoryUtils::deletePointers(bonds_);
70			MemoryUtils::deletePointers(bends_);
71			MemoryUtils::deletePointers(torsions_);
72	gezelter	1277	MemoryUtils::deletePointers(inversions_);
73	tim	398	MemoryUtils::deletePointers(rigidBodies_);
74			MemoryUtils::deletePointers(cutoffGroups_);
75			MemoryUtils::deletePointers(constraintPairs_);
76			MemoryUtils::deletePointers(constraintElems_);
77	gezelter	1782
78	gezelter	1211	// integrableObjects_ don't own the objects
79	gezelter	246	integrableObjects_.clear();
80	gezelter	1782	fluctuatingCharges_.clear();
81	gezelter	246
82	gezelter	507	}
83	gezelter	1211
84	gezelter	507	void Molecule::addAtom(Atom* atom) {
85	gezelter	246	if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) {
86	gezelter	507	atoms_.push_back(atom);
87	gezelter	246	}
88	gezelter	507	}
89	gezelter	1211
90	gezelter	507	void Molecule::addBond(Bond* bond) {
91	gezelter	246	if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) {
92	gezelter	507	bonds_.push_back(bond);
93	gezelter	246	}
94	gezelter	507	}
95	gezelter	1211
96	gezelter	507	void Molecule::addBend(Bend* bend) {
97	gezelter	246	if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) {
98	gezelter	507	bends_.push_back(bend);
99	gezelter	246	}
100	gezelter	507	}
101	gezelter	1211
102	gezelter	507	void Molecule::addTorsion(Torsion* torsion) {
103	gezelter	1211	if (std::find(torsions_.begin(), torsions_.end(), torsion) ==
104			torsions_.end()) {
105	gezelter	507	torsions_.push_back(torsion);
106	gezelter	246	}
107	gezelter	507	}
108	gezelter	1277
109			void Molecule::addInversion(Inversion* inversion) {
110			if (std::find(inversions_.begin(), inversions_.end(), inversion) ==
111			inversions_.end()) {
112			inversions_.push_back(inversion);
113			}
114			}
115	gezelter	1211
116	gezelter	507	void Molecule::addRigidBody(RigidBody *rb) {
117	gezelter	1211	if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) ==
118			rigidBodies_.end()) {
119	gezelter	507	rigidBodies_.push_back(rb);
120	gezelter	246	}
121	gezelter	507	}
122	gezelter	1211
123	gezelter	507	void Molecule::addCutoffGroup(CutoffGroup* cp) {
124	gezelter	1211	if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) ==
125			cutoffGroups_.end()) {
126	gezelter	507	cutoffGroups_.push_back(cp);
127	gezelter	1211	}
128	gezelter	507	}
129	gezelter	1211
130	gezelter	507	void Molecule::addConstraintPair(ConstraintPair* cp) {
131	gezelter	1211	if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) ==
132			constraintPairs_.end()) {
133	gezelter	507	constraintPairs_.push_back(cp);
134	gezelter	1211	}
135	gezelter	507	}
136	gezelter	1211
137	gezelter	507	void Molecule::addConstraintElem(ConstraintElem* cp) {
138	gezelter	1211	if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) ==
139			constraintElems_.end()) {
140	gezelter	507	constraintElems_.push_back(cp);
141	gezelter	246	}
142	gezelter	507	}
143	gezelter	1211
144	gezelter	507	void Molecule::complete() {
145	gezelter	246
146			std::set<Atom*> rigidAtoms;
147	gezelter	1782	Atom* atom;
148			AtomIterator ai;
149	gezelter	246	RigidBody* rb;
150	gezelter	1782	RigidBodyIterator rbIter;
151	gezelter	2
152	gezelter	1782	// Get list of all the atoms that are part of rigid bodies
153
154	gezelter	246	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
155	gezelter	507	rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
156	gezelter	246	}
157	gezelter	1211
158	gezelter	1782	// add any atom that wasn't part of a rigid body to the list of integrableObjects
159
160	gezelter	246	for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
161	gezelter	1211
162	gezelter	1782	if (rigidAtoms.find(atom) == rigidAtoms.end()) {
163	gezelter	1211
164			// If an atom does not belong to a rigid body, it is an
165			// integrable object
166
167	gezelter	1782	integrableObjects_.push_back(atom);
168	gezelter	507	}
169	gezelter	246	}
170	gezelter	1211
171	gezelter	1782	// then add the rigid bodies themselves to the integrableObjects
172	gezelter	2
173	tim	372	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
174			integrableObjects_.push_back(rb);
175			}
176	gezelter	1782
177			// find the atoms that are fluctuating charges and add them to the
178			// fluctuatingCharges_ vector
179
180			for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
181			if ( atom->isFluctuatingCharge() )
182			fluctuatingCharges_.push_back( atom );
183			}
184
185	gezelter	507	}
186	gezelter	2
187	tim	963	RealType Molecule::getMass() {
188	gezelter	246	StuntDouble* sd;
189			std::vector<StuntDouble*>::iterator i;
190	tim	963	RealType mass = 0.0;
191	gezelter	1211
192			for (sd = beginIntegrableObject(i); sd != NULL; sd =
193			nextIntegrableObject(i)){
194	gezelter	507	mass += sd->getMass();
195	gezelter	246	}
196	gezelter	1211
197			return mass;
198	gezelter	507	}
199	gezelter	2
200	gezelter	507	Vector3d Molecule::getCom() {
201	gezelter	246	StuntDouble* sd;
202			std::vector<StuntDouble*>::iterator i;
203			Vector3d com;
204	tim	963	RealType totalMass = 0;
205			RealType mass;
206	gezelter	246
207	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
208			nextIntegrableObject(i)){
209	gezelter	507	mass = sd->getMass();
210			totalMass += mass;
211			com += sd->getPos() * mass;
212	gezelter	2	}
213	gezelter	1211
214	gezelter	246	com /= totalMass;
215	gezelter	2
216	gezelter	246	return com;
217	gezelter	507	}
218	gezelter	2
219	gezelter	507	void Molecule::moveCom(const Vector3d& delta) {
220	gezelter	246	StuntDouble* sd;
221			std::vector<StuntDouble*>::iterator i;
222
223	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
224			nextIntegrableObject(i)){
225	gezelter	507	sd->setPos(sd->getPos() + delta);
226	gezelter	1211	}
227	gezelter	507	}
228	gezelter	2
229	gezelter	507	Vector3d Molecule::getComVel() {
230	gezelter	246	StuntDouble* sd;
231			std::vector<StuntDouble*>::iterator i;
232			Vector3d velCom;
233	tim	963	RealType totalMass = 0;
234			RealType mass;
235	gezelter	246
236	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
237			nextIntegrableObject(i)){
238	gezelter	507	mass = sd->getMass();
239			totalMass += mass;
240			velCom += sd->getVel() * mass;
241	gezelter	246	}
242	gezelter	1211
243	gezelter	246	velCom /= totalMass;
244	gezelter	1211
245	gezelter	246	return velCom;
246	gezelter	507	}
247	gezelter	2
248	tim	963	RealType Molecule::getPotential() {
249	gezelter	2
250	gezelter	246	Bond* bond;
251			Bend* bend;
252			Torsion* torsion;
253	gezelter	1277	Inversion* inversion;
254	gezelter	246	Molecule::BondIterator bondIter;;
255			Molecule::BendIterator bendIter;
256			Molecule::TorsionIterator torsionIter;
257	gezelter	1277	Molecule::InversionIterator inversionIter;
258	gezelter	2
259	tim	963	RealType potential = 0.0;
260	gezelter	2
261	gezelter	246	for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
262	gezelter	507	potential += bond->getPotential();
263	gezelter	246	}
264	gezelter	2
265	gezelter	246	for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
266	gezelter	507	potential += bend->getPotential();
267	gezelter	2	}
268
269	gezelter	1211	for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion =
270			nextTorsion(torsionIter)) {
271	gezelter	507	potential += torsion->getPotential();
272	gezelter	2	}
273	gezelter	1211
274	gezelter	1277	for (inversion = beginInversion(inversionIter); torsion != NULL;
275			inversion = nextInversion(inversionIter)) {
276			potential += inversion->getPotential();
277			}
278
279	gezelter	246	return potential;
280	gezelter	1211
281	gezelter	507	}
282	gezelter	1211
283	cli2	1360	void Molecule::addProperty(GenericData* genData) {
284			properties_.addProperty(genData);
285			}
286
287			void Molecule::removeProperty(const std::string& propName) {
288			properties_.removeProperty(propName);
289			}
290
291			void Molecule::clearProperties() {
292			properties_.clearProperties();
293			}
294
295			std::vector<std::string> Molecule::getPropertyNames() {
296			return properties_.getPropertyNames();
297			}
298
299			std::vector<GenericData*> Molecule::getProperties() {
300			return properties_.getProperties();
301			}
302
303			GenericData* Molecule::getPropertyByName(const std::string& propName) {
304			return properties_.getPropertyByName(propName);
305			}
306
307	gezelter	507	std::ostream& operator <<(std::ostream& o, Molecule& mol) {
308	gezelter	246	o << std::endl;
309			o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
310			o << mol.getNAtoms() << " atoms" << std::endl;
311			o << mol.getNBonds() << " bonds" << std::endl;
312			o << mol.getNBends() << " bends" << std::endl;
313			o << mol.getNTorsions() << " torsions" << std::endl;
314	gezelter	1277	o << mol.getNInversions() << " inversions" << std::endl;
315	gezelter	246	o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
316	gezelter	1782	o << mol.getNIntegrableObjects() << " integrable objects" << std::endl;
317			o << mol.getNCutoffGroups() << " cutoff groups" << std::endl;
318			o << mol.getNConstraintPairs() << " constraint pairs" << std::endl;
319			o << mol.getNFluctuatingCharges() << " fluctuating charges" << std::endl;
320	gezelter	246	return o;
321	gezelter	507	}
322	gezelter	1211
323	gezelter	1390	}//end namespace OpenMD