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
#	Content
1	/*
2	* 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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	/**
44	* @file Molecule.cpp
45	* @author tlin
46	* @date 10/28/2004
47	* @version 1.0
48	*/
49
50	#include <algorithm>
51	#include <set>
52
53	#include "primitives/Molecule.hpp"
54	#include "utils/MemoryUtils.hpp"
55	#include "utils/simError.h"
56
57	namespace OpenMD {
58	Molecule::Molecule(int stampId, int globalIndex, const std::string& molName)
59	: stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) {
60	}
61
62	Molecule::~Molecule() {
63
64	MemoryUtils::deletePointers(atoms_);
65	MemoryUtils::deletePointers(bonds_);
66	MemoryUtils::deletePointers(bends_);
67	MemoryUtils::deletePointers(torsions_);
68	MemoryUtils::deletePointers(inversions_);
69	MemoryUtils::deletePointers(rigidBodies_);
70	MemoryUtils::deletePointers(cutoffGroups_);
71	MemoryUtils::deletePointers(constraintPairs_);
72	MemoryUtils::deletePointers(constraintElems_);
73	// integrableObjects_ don't own the objects
74	integrableObjects_.clear();
75
76	}
77
78	void Molecule::addAtom(Atom* atom) {
79	if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) {
80	atoms_.push_back(atom);
81	}
82	}
83
84	void Molecule::addBond(Bond* bond) {
85	if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) {
86	bonds_.push_back(bond);
87	}
88	}
89
90	void Molecule::addBend(Bend* bend) {
91	if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) {
92	bends_.push_back(bend);
93	}
94	}
95
96	void Molecule::addTorsion(Torsion* torsion) {
97	if (std::find(torsions_.begin(), torsions_.end(), torsion) ==
98	torsions_.end()) {
99	torsions_.push_back(torsion);
100	}
101	}
102
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
110	void Molecule::addRigidBody(RigidBody *rb) {
111	if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) ==
112	rigidBodies_.end()) {
113	rigidBodies_.push_back(rb);
114	}
115	}
116
117	void Molecule::addCutoffGroup(CutoffGroup* cp) {
118	if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) ==
119	cutoffGroups_.end()) {
120	cutoffGroups_.push_back(cp);
121	}
122	}
123
124	void Molecule::addConstraintPair(ConstraintPair* cp) {
125	if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) ==
126	constraintPairs_.end()) {
127	constraintPairs_.push_back(cp);
128	}
129	}
130
131	void Molecule::addConstraintElem(ConstraintElem* cp) {
132	if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) ==
133	constraintElems_.end()) {
134	constraintElems_.push_back(cp);
135	}
136	}
137
138	void Molecule::complete() {
139
140	std::set<Atom*> rigidAtoms;
141	RigidBody* rb;
142	std::vector<RigidBody*>::iterator rbIter;
143
144
145	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
146	rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
147	}
148
149	Atom* atom;
150	AtomIterator ai;
151	for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
152
153	if (rigidAtoms.find(*ai) == rigidAtoms.end()) {
154
155	// If an atom does not belong to a rigid body, it is an
156	// integrable object
157
158	integrableObjects_.push_back(*ai);
159	}
160	}
161
162	//find all free atoms (which do not belong to rigid bodies)
163	// 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	//std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(),
168	// std::back_inserter(integrableObjects_));
169
170	//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	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	}
182
183	RealType Molecule::getMass() {
184	StuntDouble* sd;
185	std::vector<StuntDouble*>::iterator i;
186	RealType mass = 0.0;
187
188	for (sd = beginIntegrableObject(i); sd != NULL; sd =
189	nextIntegrableObject(i)){
190	mass += sd->getMass();
191	}
192
193	return mass;
194	}
195
196	Vector3d Molecule::getCom() {
197	StuntDouble* sd;
198	std::vector<StuntDouble*>::iterator i;
199	Vector3d com;
200	RealType totalMass = 0;
201	RealType mass;
202
203	for (sd = beginIntegrableObject(i); sd != NULL; sd =
204	nextIntegrableObject(i)){
205	mass = sd->getMass();
206	totalMass += mass;
207	com += sd->getPos() * mass;
208	}
209
210	com /= totalMass;
211
212	return com;
213	}
214
215	void Molecule::moveCom(const Vector3d& delta) {
216	StuntDouble* sd;
217	std::vector<StuntDouble*>::iterator i;
218
219	for (sd = beginIntegrableObject(i); sd != NULL; sd =
220	nextIntegrableObject(i)){
221	sd->setPos(sd->getPos() + delta);
222	}
223	}
224
225	Vector3d Molecule::getComVel() {
226	StuntDouble* sd;
227	std::vector<StuntDouble*>::iterator i;
228	Vector3d velCom;
229	RealType totalMass = 0;
230	RealType mass;
231
232	for (sd = beginIntegrableObject(i); sd != NULL; sd =
233	nextIntegrableObject(i)){
234	mass = sd->getMass();
235	totalMass += mass;
236	velCom += sd->getVel() * mass;
237	}
238
239	velCom /= totalMass;
240
241	return velCom;
242	}
243
244	RealType Molecule::getPotential() {
245
246	Bond* bond;
247	Bend* bend;
248	Torsion* torsion;
249	Inversion* inversion;
250	Molecule::BondIterator bondIter;;
251	Molecule::BendIterator bendIter;
252	Molecule::TorsionIterator torsionIter;
253	Molecule::InversionIterator inversionIter;
254
255	RealType potential = 0.0;
256
257	for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
258	potential += bond->getPotential();
259	}
260
261	for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
262	potential += bend->getPotential();
263	}
264
265	for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion =
266	nextTorsion(torsionIter)) {
267	potential += torsion->getPotential();
268	}
269
270	for (inversion = beginInversion(inversionIter); torsion != NULL;
271	inversion = nextInversion(inversionIter)) {
272	potential += inversion->getPotential();
273	}
274
275	return potential;
276
277	}
278
279	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	std::ostream& operator <<(std::ostream& o, Molecule& mol) {
307	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	o << mol.getNInversions() << " inversions" << std::endl;
314	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	}
320
321	}//end namespace OpenMD