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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
/**
 * @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::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 oopse
Revision:	1360
Committed:	Mon Sep 7 16:31:51 2009 UTC (15 years, 7 months ago) by cli2
Original Path:	*trunk/src/primitives/Molecule.cpp*
File size:	10102 byte(s)
Log Message:	Added new restraint infrastructure Added MolecularRestraints Added ObjectRestraints Added RestraintStamp Updated thermodynamic integration to use ObjectRestraints Added Quaternion mathematics for twist swing decompositions Significantly updated RestWriter and RestReader to use dump-like files Added selections for x, y, and z coordinates of atoms Removed monolithic Restraints class Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody Added some rotational capabilities to prinicpalAxisCalculator
#	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			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			/**
43			* @file Molecule.cpp
44			* @author tlin
45			* @date 10/28/2004
46			* @version 1.0
47			*/
48	gezelter	2
49	gezelter	246	#include <algorithm>
50			#include <set>
51	gezelter	2
52	tim	3	#include "primitives/Molecule.hpp"
53	gezelter	246	#include "utils/MemoryUtils.hpp"
54	tim	3	#include "utils/simError.h"
55	gezelter	2
56	gezelter	246	namespace oopse {
57	gezelter	507	Molecule::Molecule(int stampId, int globalIndex, const std::string& molName)
58	gezelter	246	: stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) {
59	gezelter	1211	}
60
61	gezelter	507	Molecule::~Molecule() {
62	gezelter	1211
63	tim	398	MemoryUtils::deletePointers(atoms_);
64			MemoryUtils::deletePointers(bonds_);
65			MemoryUtils::deletePointers(bends_);
66			MemoryUtils::deletePointers(torsions_);
67	gezelter	1277	MemoryUtils::deletePointers(inversions_);
68	tim	398	MemoryUtils::deletePointers(rigidBodies_);
69			MemoryUtils::deletePointers(cutoffGroups_);
70			MemoryUtils::deletePointers(constraintPairs_);
71			MemoryUtils::deletePointers(constraintElems_);
72	gezelter	1211	// integrableObjects_ don't own the objects
73	gezelter	246	integrableObjects_.clear();
74
75	gezelter	507	}
76	gezelter	1211
77	gezelter	507	void Molecule::addAtom(Atom* atom) {
78	gezelter	246	if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) {
79	gezelter	507	atoms_.push_back(atom);
80	gezelter	246	}
81	gezelter	507	}
82	gezelter	1211
83	gezelter	507	void Molecule::addBond(Bond* bond) {
84	gezelter	246	if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) {
85	gezelter	507	bonds_.push_back(bond);
86	gezelter	246	}
87	gezelter	507	}
88	gezelter	1211
89	gezelter	507	void Molecule::addBend(Bend* bend) {
90	gezelter	246	if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) {
91	gezelter	507	bends_.push_back(bend);
92	gezelter	246	}
93	gezelter	507	}
94	gezelter	1211
95	gezelter	507	void Molecule::addTorsion(Torsion* torsion) {
96	gezelter	1211	if (std::find(torsions_.begin(), torsions_.end(), torsion) ==
97			torsions_.end()) {
98	gezelter	507	torsions_.push_back(torsion);
99	gezelter	246	}
100	gezelter	507	}
101	gezelter	1277
102			void Molecule::addInversion(Inversion* inversion) {
103			if (std::find(inversions_.begin(), inversions_.end(), inversion) ==
104			inversions_.end()) {
105			inversions_.push_back(inversion);
106			}
107			}
108	gezelter	1211
109	gezelter	507	void Molecule::addRigidBody(RigidBody *rb) {
110	gezelter	1211	if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) ==
111			rigidBodies_.end()) {
112	gezelter	507	rigidBodies_.push_back(rb);
113	gezelter	246	}
114	gezelter	507	}
115	gezelter	1211
116	gezelter	507	void Molecule::addCutoffGroup(CutoffGroup* cp) {
117	gezelter	1211	if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) ==
118			cutoffGroups_.end()) {
119	gezelter	507	cutoffGroups_.push_back(cp);
120	gezelter	1211	}
121	gezelter	507	}
122	gezelter	1211
123	gezelter	507	void Molecule::addConstraintPair(ConstraintPair* cp) {
124	gezelter	1211	if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) ==
125			constraintPairs_.end()) {
126	gezelter	507	constraintPairs_.push_back(cp);
127	gezelter	1211	}
128	gezelter	507	}
129	gezelter	1211
130	gezelter	507	void Molecule::addConstraintElem(ConstraintElem* cp) {
131	gezelter	1211	if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) ==
132			constraintElems_.end()) {
133	gezelter	507	constraintElems_.push_back(cp);
134	gezelter	246	}
135	gezelter	507	}
136	gezelter	1211
137	gezelter	507	void Molecule::complete() {
138	gezelter	246
139			std::set<Atom*> rigidAtoms;
140			RigidBody* rb;
141			std::vector<RigidBody*>::iterator rbIter;
142	gezelter	2
143	gezelter	246
144			for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
145	gezelter	507	rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
146	gezelter	246	}
147	gezelter	1211
148	gezelter	246	Atom* atom;
149			AtomIterator ai;
150			for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
151	gezelter	1211
152	gezelter	507	if (rigidAtoms.find(*ai) == rigidAtoms.end()) {
153	gezelter	1211
154			// If an atom does not belong to a rigid body, it is an
155			// integrable object
156
157	gezelter	507	integrableObjects_.push_back(*ai);
158			}
159	gezelter	246	}
160	gezelter	1211
161	gezelter	246	//find all free atoms (which do not belong to rigid bodies)
162	gezelter	1211	// performs the "difference" operation from set theory, the output
163			// range contains a copy of every element that is contained in
164			// [allAtoms.begin(), allAtoms.end()) and not contained in
165			// [rigidAtoms.begin(), rigidAtoms.end()).
166	gezelter	246	//std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(),
167			// std::back_inserter(integrableObjects_));
168	gezelter	2
169	gezelter	246	//if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) {
170			// //Some atoms in rigidAtoms are not in allAtoms, something must be wrong
171			// sprintf(painCave.errMsg, "Atoms in rigidbody are not in the atom list of the same molecule");
172			//
173			// painCave.isFatal = 1;
174			// simError();
175			//}
176	tim	372	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
177			integrableObjects_.push_back(rb);
178			}
179			//integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end());
180	gezelter	507	}
181	gezelter	2
182	tim	963	RealType Molecule::getMass() {
183	gezelter	246	StuntDouble* sd;
184			std::vector<StuntDouble*>::iterator i;
185	tim	963	RealType mass = 0.0;
186	gezelter	1211
187			for (sd = beginIntegrableObject(i); sd != NULL; sd =
188			nextIntegrableObject(i)){
189	gezelter	507	mass += sd->getMass();
190	gezelter	246	}
191	gezelter	1211
192			return mass;
193	gezelter	507	}
194	gezelter	2
195	gezelter	507	Vector3d Molecule::getCom() {
196	gezelter	246	StuntDouble* sd;
197			std::vector<StuntDouble*>::iterator i;
198			Vector3d com;
199	tim	963	RealType totalMass = 0;
200			RealType mass;
201	gezelter	246
202	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
203			nextIntegrableObject(i)){
204	gezelter	507	mass = sd->getMass();
205			totalMass += mass;
206			com += sd->getPos() * mass;
207	gezelter	2	}
208	gezelter	1211
209	gezelter	246	com /= totalMass;
210	gezelter	2
211	gezelter	246	return com;
212	gezelter	507	}
213	gezelter	2
214	gezelter	507	void Molecule::moveCom(const Vector3d& delta) {
215	gezelter	246	StuntDouble* sd;
216			std::vector<StuntDouble*>::iterator i;
217
218	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
219			nextIntegrableObject(i)){
220	gezelter	507	sd->setPos(sd->getPos() + delta);
221	gezelter	1211	}
222	gezelter	507	}
223	gezelter	2
224	gezelter	507	Vector3d Molecule::getComVel() {
225	gezelter	246	StuntDouble* sd;
226			std::vector<StuntDouble*>::iterator i;
227			Vector3d velCom;
228	tim	963	RealType totalMass = 0;
229			RealType mass;
230	gezelter	246
231	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
232			nextIntegrableObject(i)){
233	gezelter	507	mass = sd->getMass();
234			totalMass += mass;
235			velCom += sd->getVel() * mass;
236	gezelter	246	}
237	gezelter	1211
238	gezelter	246	velCom /= totalMass;
239	gezelter	1211
240	gezelter	246	return velCom;
241	gezelter	507	}
242	gezelter	2
243	tim	963	RealType Molecule::getPotential() {
244	gezelter	2
245	gezelter	246	Bond* bond;
246			Bend* bend;
247			Torsion* torsion;
248	gezelter	1277	Inversion* inversion;
249	gezelter	246	Molecule::BondIterator bondIter;;
250			Molecule::BendIterator bendIter;
251			Molecule::TorsionIterator torsionIter;
252	gezelter	1277	Molecule::InversionIterator inversionIter;
253	gezelter	2
254	tim	963	RealType potential = 0.0;
255	gezelter	2
256	gezelter	246	for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
257	gezelter	507	potential += bond->getPotential();
258	gezelter	246	}
259	gezelter	2
260	gezelter	246	for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
261	gezelter	507	potential += bend->getPotential();
262	gezelter	2	}
263
264	gezelter	1211	for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion =
265			nextTorsion(torsionIter)) {
266	gezelter	507	potential += torsion->getPotential();
267	gezelter	2	}
268	gezelter	1211
269	gezelter	1277	for (inversion = beginInversion(inversionIter); torsion != NULL;
270			inversion = nextInversion(inversionIter)) {
271			potential += inversion->getPotential();
272			}
273
274	gezelter	246	return potential;
275	gezelter	1211
276	gezelter	507	}
277	gezelter	1211
278	cli2	1360	void Molecule::addProperty(GenericData* genData) {
279			properties_.addProperty(genData);
280			}
281
282			void Molecule::removeProperty(const std::string& propName) {
283			properties_.removeProperty(propName);
284			}
285
286			void Molecule::clearProperties() {
287			properties_.clearProperties();
288			}
289
290			std::vector<std::string> Molecule::getPropertyNames() {
291			return properties_.getPropertyNames();
292			}
293
294			std::vector<GenericData*> Molecule::getProperties() {
295			return properties_.getProperties();
296			}
297
298			GenericData* Molecule::getPropertyByName(const std::string& propName) {
299			return properties_.getPropertyByName(propName);
300			}
301
302
303
304
305	gezelter	507	std::ostream& operator <<(std::ostream& o, Molecule& mol) {
306	gezelter	246	o << std::endl;
307			o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
308			o << mol.getNAtoms() << " atoms" << std::endl;
309			o << mol.getNBonds() << " bonds" << std::endl;
310			o << mol.getNBends() << " bends" << std::endl;
311			o << mol.getNTorsions() << " torsions" << std::endl;
312	gezelter	1277	o << mol.getNInversions() << " inversions" << std::endl;
313	gezelter	246	o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
314			o << mol.getNIntegrableObjects() << "integrable objects" << std::endl;
315			o << mol.getNCutoffGroups() << "cutoff groups" << std::endl;
316			o << mol.getNConstraintPairs() << "constraint pairs" << std::endl;
317			return o;
318	gezelter	507	}
319	gezelter	1211
320	gezelter	246	}//end namespace oopse