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;
    
  }
  
  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:	3432
Committed:	Mon Jul 14 12:35:58 2008 UTC (16 years, 9 months ago) by gezelter
File size:	9462 byte(s)
Log Message:	Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
#	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	gezelter	2204	std::ostream& operator <<(std::ostream& o, Molecule& mol) {
279	gezelter	1930	o << std::endl;
280			o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
281			o << mol.getNAtoms() << " atoms" << std::endl;
282			o << mol.getNBonds() << " bonds" << std::endl;
283			o << mol.getNBends() << " bends" << std::endl;
284			o << mol.getNTorsions() << " torsions" << std::endl;
285	gezelter	3432	o << mol.getNInversions() << " inversions" << std::endl;
286	gezelter	1930	o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
287			o << mol.getNIntegrableObjects() << "integrable objects" << std::endl;
288			o << mol.getNCutoffGroups() << "cutoff groups" << std::endl;
289			o << mol.getNConstraintPairs() << "constraint pairs" << std::endl;
290			return o;
291	gezelter	2204	}
292	gezelter	3320
293	gezelter	1930	}//end namespace oopse