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:	3520
Committed:	Mon Sep 7 16:31:51 2009 UTC (15 years, 10 months ago) by cli2
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	2204	/*
2	gezelter	1930	* 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	1490
49	gezelter	1930	#include <algorithm>
50			#include <set>
51	gezelter	1490
52	tim	1492	#include "primitives/Molecule.hpp"
53	gezelter	1930	#include "utils/MemoryUtils.hpp"
54	tim	1492	#include "utils/simError.h"
55	gezelter	1490
56	gezelter	1930	namespace oopse {
57	gezelter	2204	Molecule::Molecule(int stampId, int globalIndex, const std::string& molName)
58	gezelter	1930	: stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) {
59	gezelter	3320	}
60
61	gezelter	2204	Molecule::~Molecule() {
62	gezelter	3320
63	tim	2082	MemoryUtils::deletePointers(atoms_);
64			MemoryUtils::deletePointers(bonds_);
65			MemoryUtils::deletePointers(bends_);
66			MemoryUtils::deletePointers(torsions_);
67	gezelter	3432	MemoryUtils::deletePointers(inversions_);
68	tim	2082	MemoryUtils::deletePointers(rigidBodies_);
69			MemoryUtils::deletePointers(cutoffGroups_);
70			MemoryUtils::deletePointers(constraintPairs_);
71			MemoryUtils::deletePointers(constraintElems_);
72	gezelter	3320	// integrableObjects_ don't own the objects
73	gezelter	1930	integrableObjects_.clear();
74
75	gezelter	2204	}
76	gezelter	3320
77	gezelter	2204	void Molecule::addAtom(Atom* atom) {
78	gezelter	1930	if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) {
79	gezelter	2204	atoms_.push_back(atom);
80	gezelter	1930	}
81	gezelter	2204	}
82	gezelter	3320
83	gezelter	2204	void Molecule::addBond(Bond* bond) {
84	gezelter	1930	if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) {
85	gezelter	2204	bonds_.push_back(bond);
86	gezelter	1930	}
87	gezelter	2204	}
88	gezelter	3320
89	gezelter	2204	void Molecule::addBend(Bend* bend) {
90	gezelter	1930	if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) {
91	gezelter	2204	bends_.push_back(bend);
92	gezelter	1930	}
93	gezelter	2204	}
94	gezelter	3320
95	gezelter	2204	void Molecule::addTorsion(Torsion* torsion) {
96	gezelter	3320	if (std::find(torsions_.begin(), torsions_.end(), torsion) ==
97			torsions_.end()) {
98	gezelter	2204	torsions_.push_back(torsion);
99	gezelter	1930	}
100	gezelter	2204	}
101	gezelter	3432
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	3320
109	gezelter	2204	void Molecule::addRigidBody(RigidBody *rb) {
110	gezelter	3320	if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) ==
111			rigidBodies_.end()) {
112	gezelter	2204	rigidBodies_.push_back(rb);
113	gezelter	1930	}
114	gezelter	2204	}
115	gezelter	3320
116	gezelter	2204	void Molecule::addCutoffGroup(CutoffGroup* cp) {
117	gezelter	3320	if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) ==
118			cutoffGroups_.end()) {
119	gezelter	2204	cutoffGroups_.push_back(cp);
120	gezelter	3320	}
121	gezelter	2204	}
122	gezelter	3320
123	gezelter	2204	void Molecule::addConstraintPair(ConstraintPair* cp) {
124	gezelter	3320	if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) ==
125			constraintPairs_.end()) {
126	gezelter	2204	constraintPairs_.push_back(cp);
127	gezelter	3320	}
128	gezelter	2204	}
129	gezelter	3320
130	gezelter	2204	void Molecule::addConstraintElem(ConstraintElem* cp) {
131	gezelter	3320	if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) ==
132			constraintElems_.end()) {
133	gezelter	2204	constraintElems_.push_back(cp);
134	gezelter	1930	}
135	gezelter	2204	}
136	gezelter	3320
137	gezelter	2204	void Molecule::complete() {
138	gezelter	1930
139			std::set<Atom*> rigidAtoms;
140			RigidBody* rb;
141			std::vector<RigidBody*>::iterator rbIter;
142	gezelter	1490
143	gezelter	1930
144			for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
145	gezelter	2204	rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
146	gezelter	1930	}
147	gezelter	3320
148	gezelter	1930	Atom* atom;
149			AtomIterator ai;
150			for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
151	gezelter	3320
152	gezelter	2204	if (rigidAtoms.find(*ai) == rigidAtoms.end()) {
153	gezelter	3320
154			// If an atom does not belong to a rigid body, it is an
155			// integrable object
156
157	gezelter	2204	integrableObjects_.push_back(*ai);
158			}
159	gezelter	1930	}
160	gezelter	3320
161	gezelter	1930	//find all free atoms (which do not belong to rigid bodies)
162	gezelter	3320	// 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	1930	//std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(),
167			// std::back_inserter(integrableObjects_));
168	gezelter	1490
169	gezelter	1930	//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	2056	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	2204	}
181	gezelter	1490
182	tim	2759	RealType Molecule::getMass() {
183	gezelter	1930	StuntDouble* sd;
184			std::vector<StuntDouble*>::iterator i;
185	tim	2759	RealType mass = 0.0;
186	gezelter	3320
187			for (sd = beginIntegrableObject(i); sd != NULL; sd =
188			nextIntegrableObject(i)){
189	gezelter	2204	mass += sd->getMass();
190	gezelter	1930	}
191	gezelter	3320
192			return mass;
193	gezelter	2204	}
194	gezelter	1490
195	gezelter	2204	Vector3d Molecule::getCom() {
196	gezelter	1930	StuntDouble* sd;
197			std::vector<StuntDouble*>::iterator i;
198			Vector3d com;
199	tim	2759	RealType totalMass = 0;
200			RealType mass;
201	gezelter	1930
202	gezelter	3320	for (sd = beginIntegrableObject(i); sd != NULL; sd =
203			nextIntegrableObject(i)){
204	gezelter	2204	mass = sd->getMass();
205			totalMass += mass;
206			com += sd->getPos() * mass;
207	gezelter	1490	}
208	gezelter	3320
209	gezelter	1930	com /= totalMass;
210	gezelter	1490
211	gezelter	1930	return com;
212	gezelter	2204	}
213	gezelter	1490
214	gezelter	2204	void Molecule::moveCom(const Vector3d& delta) {
215	gezelter	1930	StuntDouble* sd;
216			std::vector<StuntDouble*>::iterator i;
217
218	gezelter	3320	for (sd = beginIntegrableObject(i); sd != NULL; sd =
219			nextIntegrableObject(i)){
220	gezelter	2204	sd->setPos(sd->getPos() + delta);
221	gezelter	3320	}
222	gezelter	2204	}
223	gezelter	1490
224	gezelter	2204	Vector3d Molecule::getComVel() {
225	gezelter	1930	StuntDouble* sd;
226			std::vector<StuntDouble*>::iterator i;
227			Vector3d velCom;
228	tim	2759	RealType totalMass = 0;
229			RealType mass;
230	gezelter	1930
231	gezelter	3320	for (sd = beginIntegrableObject(i); sd != NULL; sd =
232			nextIntegrableObject(i)){
233	gezelter	2204	mass = sd->getMass();
234			totalMass += mass;
235			velCom += sd->getVel() * mass;
236	gezelter	1930	}
237	gezelter	3320
238	gezelter	1930	velCom /= totalMass;
239	gezelter	3320
240	gezelter	1930	return velCom;
241	gezelter	2204	}
242	gezelter	1490
243	tim	2759	RealType Molecule::getPotential() {
244	gezelter	1490
245	gezelter	1930	Bond* bond;
246			Bend* bend;
247			Torsion* torsion;
248	gezelter	3432	Inversion* inversion;
249	gezelter	1930	Molecule::BondIterator bondIter;;
250			Molecule::BendIterator bendIter;
251			Molecule::TorsionIterator torsionIter;
252	gezelter	3432	Molecule::InversionIterator inversionIter;
253	gezelter	1490
254	tim	2759	RealType potential = 0.0;
255	gezelter	1490
256	gezelter	1930	for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
257	gezelter	2204	potential += bond->getPotential();
258	gezelter	1930	}
259	gezelter	1490
260	gezelter	1930	for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
261	gezelter	2204	potential += bend->getPotential();
262	gezelter	1490	}
263
264	gezelter	3320	for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion =
265			nextTorsion(torsionIter)) {
266	gezelter	2204	potential += torsion->getPotential();
267	gezelter	1490	}
268	gezelter	3320
269	gezelter	3432	for (inversion = beginInversion(inversionIter); torsion != NULL;
270			inversion = nextInversion(inversionIter)) {
271			potential += inversion->getPotential();
272			}
273
274	gezelter	1930	return potential;
275	gezelter	3320
276	gezelter	2204	}
277	gezelter	3320
278	cli2	3520	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	2204	std::ostream& operator <<(std::ostream& o, Molecule& mol) {
306	gezelter	1930	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	3432	o << mol.getNInversions() << " inversions" << std::endl;
313	gezelter	1930	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	2204	}
319	gezelter	3320
320	gezelter	1930	}//end namespace oopse