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) {
  }
  
  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();
    
  }
  
  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;
    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();        
    //}
    for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
      integrableObjects_.push_back(rb);
    } 
    //integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end());
  }

  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;
    return o;
  }
  
}//end namespace OpenMD
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	10211 byte(s)
Log Message:	updated copyright notices
#	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	246	: stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) {
60	gezelter	1211	}
61
62	gezelter	507	Molecule::~Molecule() {
63	gezelter	1211
64	tim	398	MemoryUtils::deletePointers(atoms_);
65			MemoryUtils::deletePointers(bonds_);
66			MemoryUtils::deletePointers(bends_);
67			MemoryUtils::deletePointers(torsions_);
68	gezelter	1277	MemoryUtils::deletePointers(inversions_);
69	tim	398	MemoryUtils::deletePointers(rigidBodies_);
70			MemoryUtils::deletePointers(cutoffGroups_);
71			MemoryUtils::deletePointers(constraintPairs_);
72			MemoryUtils::deletePointers(constraintElems_);
73	gezelter	1211	// integrableObjects_ don't own the objects
74	gezelter	246	integrableObjects_.clear();
75
76	gezelter	507	}
77	gezelter	1211
78	gezelter	507	void Molecule::addAtom(Atom* atom) {
79	gezelter	246	if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) {
80	gezelter	507	atoms_.push_back(atom);
81	gezelter	246	}
82	gezelter	507	}
83	gezelter	1211
84	gezelter	507	void Molecule::addBond(Bond* bond) {
85	gezelter	246	if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) {
86	gezelter	507	bonds_.push_back(bond);
87	gezelter	246	}
88	gezelter	507	}
89	gezelter	1211
90	gezelter	507	void Molecule::addBend(Bend* bend) {
91	gezelter	246	if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) {
92	gezelter	507	bends_.push_back(bend);
93	gezelter	246	}
94	gezelter	507	}
95	gezelter	1211
96	gezelter	507	void Molecule::addTorsion(Torsion* torsion) {
97	gezelter	1211	if (std::find(torsions_.begin(), torsions_.end(), torsion) ==
98			torsions_.end()) {
99	gezelter	507	torsions_.push_back(torsion);
100	gezelter	246	}
101	gezelter	507	}
102	gezelter	1277
103			void Molecule::addInversion(Inversion* inversion) {
104			if (std::find(inversions_.begin(), inversions_.end(), inversion) ==
105			inversions_.end()) {
106			inversions_.push_back(inversion);
107			}
108			}
109	gezelter	1211
110	gezelter	507	void Molecule::addRigidBody(RigidBody *rb) {
111	gezelter	1211	if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) ==
112			rigidBodies_.end()) {
113	gezelter	507	rigidBodies_.push_back(rb);
114	gezelter	246	}
115	gezelter	507	}
116	gezelter	1211
117	gezelter	507	void Molecule::addCutoffGroup(CutoffGroup* cp) {
118	gezelter	1211	if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) ==
119			cutoffGroups_.end()) {
120	gezelter	507	cutoffGroups_.push_back(cp);
121	gezelter	1211	}
122	gezelter	507	}
123	gezelter	1211
124	gezelter	507	void Molecule::addConstraintPair(ConstraintPair* cp) {
125	gezelter	1211	if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) ==
126			constraintPairs_.end()) {
127	gezelter	507	constraintPairs_.push_back(cp);
128	gezelter	1211	}
129	gezelter	507	}
130	gezelter	1211
131	gezelter	507	void Molecule::addConstraintElem(ConstraintElem* cp) {
132	gezelter	1211	if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) ==
133			constraintElems_.end()) {
134	gezelter	507	constraintElems_.push_back(cp);
135	gezelter	246	}
136	gezelter	507	}
137	gezelter	1211
138	gezelter	507	void Molecule::complete() {
139	gezelter	246
140			std::set<Atom*> rigidAtoms;
141			RigidBody* rb;
142			std::vector<RigidBody*>::iterator rbIter;
143	gezelter	2
144	gezelter	246
145			for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
146	gezelter	507	rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
147	gezelter	246	}
148	gezelter	1211
149	gezelter	246	Atom* atom;
150			AtomIterator ai;
151			for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
152	gezelter	1211
153	gezelter	507	if (rigidAtoms.find(*ai) == rigidAtoms.end()) {
154	gezelter	1211
155			// If an atom does not belong to a rigid body, it is an
156			// integrable object
157
158	gezelter	507	integrableObjects_.push_back(*ai);
159			}
160	gezelter	246	}
161	gezelter	1211
162	gezelter	246	//find all free atoms (which do not belong to rigid bodies)
163	gezelter	1211	// performs the "difference" operation from set theory, the output
164			// range contains a copy of every element that is contained in
165			// [allAtoms.begin(), allAtoms.end()) and not contained in
166			// [rigidAtoms.begin(), rigidAtoms.end()).
167	gezelter	246	//std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(),
168			// std::back_inserter(integrableObjects_));
169	gezelter	2
170	gezelter	246	//if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) {
171			// //Some atoms in rigidAtoms are not in allAtoms, something must be wrong
172			// sprintf(painCave.errMsg, "Atoms in rigidbody are not in the atom list of the same molecule");
173			//
174			// painCave.isFatal = 1;
175			// simError();
176			//}
177	tim	372	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
178			integrableObjects_.push_back(rb);
179			}
180			//integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end());
181	gezelter	507	}
182	gezelter	2
183	tim	963	RealType Molecule::getMass() {
184	gezelter	246	StuntDouble* sd;
185			std::vector<StuntDouble*>::iterator i;
186	tim	963	RealType mass = 0.0;
187	gezelter	1211
188			for (sd = beginIntegrableObject(i); sd != NULL; sd =
189			nextIntegrableObject(i)){
190	gezelter	507	mass += sd->getMass();
191	gezelter	246	}
192	gezelter	1211
193			return mass;
194	gezelter	507	}
195	gezelter	2
196	gezelter	507	Vector3d Molecule::getCom() {
197	gezelter	246	StuntDouble* sd;
198			std::vector<StuntDouble*>::iterator i;
199			Vector3d com;
200	tim	963	RealType totalMass = 0;
201			RealType mass;
202	gezelter	246
203	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
204			nextIntegrableObject(i)){
205	gezelter	507	mass = sd->getMass();
206			totalMass += mass;
207			com += sd->getPos() * mass;
208	gezelter	2	}
209	gezelter	1211
210	gezelter	246	com /= totalMass;
211	gezelter	2
212	gezelter	246	return com;
213	gezelter	507	}
214	gezelter	2
215	gezelter	507	void Molecule::moveCom(const Vector3d& delta) {
216	gezelter	246	StuntDouble* sd;
217			std::vector<StuntDouble*>::iterator i;
218
219	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
220			nextIntegrableObject(i)){
221	gezelter	507	sd->setPos(sd->getPos() + delta);
222	gezelter	1211	}
223	gezelter	507	}
224	gezelter	2
225	gezelter	507	Vector3d Molecule::getComVel() {
226	gezelter	246	StuntDouble* sd;
227			std::vector<StuntDouble*>::iterator i;
228			Vector3d velCom;
229	tim	963	RealType totalMass = 0;
230			RealType mass;
231	gezelter	246
232	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
233			nextIntegrableObject(i)){
234	gezelter	507	mass = sd->getMass();
235			totalMass += mass;
236			velCom += sd->getVel() * mass;
237	gezelter	246	}
238	gezelter	1211
239	gezelter	246	velCom /= totalMass;
240	gezelter	1211
241	gezelter	246	return velCom;
242	gezelter	507	}
243	gezelter	2
244	tim	963	RealType Molecule::getPotential() {
245	gezelter	2
246	gezelter	246	Bond* bond;
247			Bend* bend;
248			Torsion* torsion;
249	gezelter	1277	Inversion* inversion;
250	gezelter	246	Molecule::BondIterator bondIter;;
251			Molecule::BendIterator bendIter;
252			Molecule::TorsionIterator torsionIter;
253	gezelter	1277	Molecule::InversionIterator inversionIter;
254	gezelter	2
255	tim	963	RealType potential = 0.0;
256	gezelter	2
257	gezelter	246	for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
258	gezelter	507	potential += bond->getPotential();
259	gezelter	246	}
260	gezelter	2
261	gezelter	246	for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
262	gezelter	507	potential += bend->getPotential();
263	gezelter	2	}
264
265	gezelter	1211	for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion =
266			nextTorsion(torsionIter)) {
267	gezelter	507	potential += torsion->getPotential();
268	gezelter	2	}
269	gezelter	1211
270	gezelter	1277	for (inversion = beginInversion(inversionIter); torsion != NULL;
271			inversion = nextInversion(inversionIter)) {
272			potential += inversion->getPotential();
273			}
274
275	gezelter	246	return potential;
276	gezelter	1211
277	gezelter	507	}
278	gezelter	1211
279	cli2	1360	void Molecule::addProperty(GenericData* genData) {
280			properties_.addProperty(genData);
281			}
282
283			void Molecule::removeProperty(const std::string& propName) {
284			properties_.removeProperty(propName);
285			}
286
287			void Molecule::clearProperties() {
288			properties_.clearProperties();
289			}
290
291			std::vector<std::string> Molecule::getPropertyNames() {
292			return properties_.getPropertyNames();
293			}
294
295			std::vector<GenericData*> Molecule::getProperties() {
296			return properties_.getProperties();
297			}
298
299			GenericData* Molecule::getPropertyByName(const std::string& propName) {
300			return properties_.getPropertyByName(propName);
301			}
302
303
304
305
306	gezelter	507	std::ostream& operator <<(std::ostream& o, Molecule& mol) {
307	gezelter	246	o << std::endl;
308			o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
309			o << mol.getNAtoms() << " atoms" << std::endl;
310			o << mol.getNBonds() << " bonds" << std::endl;
311			o << mol.getNBends() << " bends" << std::endl;
312			o << mol.getNTorsions() << " torsions" << std::endl;
313	gezelter	1277	o << mol.getNInversions() << " inversions" << std::endl;
314	gezelter	246	o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
315			o << mol.getNIntegrableObjects() << "integrable objects" << std::endl;
316			o << mol.getNCutoffGroups() << "cutoff groups" << std::endl;
317			o << mol.getNConstraintPairs() << "constraint pairs" << std::endl;
318			return o;
319	gezelter	507	}
320	gezelter	1211
321	gezelter	1390	}//end namespace OpenMD