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, 234107 (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"
#include "utils/StringUtils.hpp"

namespace OpenMD {
  Molecule::Molecule(int stampId, int globalIndex, const std::string& molName, 
                     int region) : 
                                   globalIndex_(globalIndex), 
                                   stampId_(stampId),
                                   region_(region),
                                   moleculeName_(molName),
                                   constrainTotalCharge_(false) {
  }
  
  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();
    fluctuatingCharges_.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;
    Atom* atom;
    Atom* atom1;
    Atom* atom2;
    AtomIterator ai, aj;
    RigidBody* rb;
    RigidBodyIterator rbIter;
    Bond* bond;
    BondIterator bi;

    // Get list of all the atoms that are part of rigid bodies

    for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
      rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
    }
    
    // add any atom that wasn't part of a rigid body to the list of integrableObjects

    for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
      
      if (rigidAtoms.find(atom) == rigidAtoms.end()) {

        // If an atom does not belong to a rigid body, it is an
        // integrable object

        integrableObjects_.push_back(atom);
      }
    }
    
    // then add the rigid bodies themselves to the integrableObjects

    for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
      integrableObjects_.push_back(rb);
    } 

    // find the atoms that are fluctuating charges and add them to the 
    // fluctuatingCharges_ vector

    for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
      if ( atom->isFluctuatingCharge() )
        fluctuatingCharges_.push_back( atom );      
    }


    // find the electronegative atoms and add them to the
    // hBondAcceptors_ vector:
    
    for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
      AtomType* at = atom->getAtomType();
      // get the chain of base types for this atom type:
      std::vector<AtomType*> ayb = at->allYourBase();
      // use the last type in the chain of base types for the name:
      std::string bn = UpperCase(ayb[ayb.size()-1]->getName());

        if (bn.compare("O")==0 || bn.compare("N")==0
            || bn.compare("F")==0) 
          hBondAcceptors_.push_back( atom );
      
    }
    
    // find electronegative atoms that are either bonded to
    // hydrogens or are present in the same rigid bodies:
    
    for (bond = beginBond(bi); bond != NULL; bond = nextBond(bi)) {
      Atom* atom1 = bond->getAtomA();
      Atom* atom2 = bond->getAtomB();
      AtomType* at1 = atom1->getAtomType();
      AtomType* at2 = atom1->getAtomType();
      // get the chain of base types for this atom type:
      std::vector<AtomType*> ayb1 = at1->allYourBase();
      std::vector<AtomType*> ayb2 = at2->allYourBase();
      // use the last type in the chain of base types for the name:
      std::string bn1 = UpperCase(ayb1[ayb1.size()-1]->getName());
      std::string bn2 = UpperCase(ayb2[ayb2.size()-1]->getName());
      
      if (bn1.compare("H")==0) {
        if (bn2.compare("O")==0 || bn2.compare("N")==0
            || bn2.compare("F")==0) {
          HBondDonor* donor = new HBondDonor();
          donor->donorAtom = atom2;
          donor->donatedHydrogen = atom1;
          hBondDonors_.push_back( donor );
        }
      }
      if (bn2.compare("H")==0) {
        if (bn1.compare("O")==0 || bn1.compare("N")==0
            || bn1.compare("F")==0) {
          HBondDonor* donor = new HBondDonor();
          donor->donorAtom = atom1;
          donor->donatedHydrogen = atom2;
            hBondDonors_.push_back( donor );
        }
      } 
    }
    
    for (rb = beginRigidBody(rbIter); rb != NULL;
         rb = nextRigidBody(rbIter)) {
      for(atom1 = rb->beginAtom(ai); atom1 != NULL;
          atom1 = rb->nextAtom(ai)) {
        AtomType* at1 = atom1->getAtomType();
        // get the chain of base types for this atom type:
        std::vector<AtomType*> ayb1 = at1->allYourBase();
        // use the last type in the chain of base types for the name:
        std::string bn1 = UpperCase(ayb1[ayb1.size()-1]->getName());
        
        if (bn1.compare("O")==0 || bn1.compare("N")==0
            || bn1.compare("F")==0) {
          for(atom2 = rb->beginAtom(aj); atom2 != NULL;
              atom2 = rb->nextAtom(aj)) {
            AtomType* at2 = atom2->getAtomType();
            // get the chain of base types for this atom type:              
            std::vector<AtomType*> ayb2 = at2->allYourBase();
            // use the last type in the chain of base types for the name:
            std::string bn2 = UpperCase(ayb2[ayb2.size()-1]->getName());
            if (bn2.compare("H")==0) {              
              HBondDonor* donor = new HBondDonor();
              donor->donorAtom = atom1;
              donor->donatedHydrogen = atom2;
              hBondDonors_.push_back( donor );
            }
          }
        }
      }
    }
  }
  
  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;
  }
  
  Vector3d Molecule::getCom(int snapshotNo) {
    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(snapshotNo) * 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;
    o << mol.getNFluctuatingCharges() << " fluctuating charges" << std::endl;
    return o;
  }
  
}//end namespace OpenMD
Revision:	2071
Committed:	Sat Mar 7 21:41:51 2015 UTC (10 years, 1 month ago) by gezelter
File size:	13896 byte(s)
Log Message:	Reducing the number of warnings when using g++ to compile.
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [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	2054	#include "utils/StringUtils.hpp"
57	gezelter	2
58	gezelter	1390	namespace OpenMD {
59	gezelter	1908	Molecule::Molecule(int stampId, int globalIndex, const std::string& molName,
60	gezelter	2071	int region) :
61	gezelter	1908	globalIndex_(globalIndex),
62	gezelter	2071	stampId_(stampId),
63			region_(region),
64			moleculeName_(molName),
65	gezelter	1908	constrainTotalCharge_(false) {
66	gezelter	1211	}
67
68	gezelter	507	Molecule::~Molecule() {
69	gezelter	1211
70	tim	398	MemoryUtils::deletePointers(atoms_);
71			MemoryUtils::deletePointers(bonds_);
72			MemoryUtils::deletePointers(bends_);
73			MemoryUtils::deletePointers(torsions_);
74	gezelter	1277	MemoryUtils::deletePointers(inversions_);
75	tim	398	MemoryUtils::deletePointers(rigidBodies_);
76			MemoryUtils::deletePointers(cutoffGroups_);
77			MemoryUtils::deletePointers(constraintPairs_);
78			MemoryUtils::deletePointers(constraintElems_);
79	gezelter	1782
80	gezelter	1211	// integrableObjects_ don't own the objects
81	gezelter	246	integrableObjects_.clear();
82	gezelter	1782	fluctuatingCharges_.clear();
83	gezelter	246
84	gezelter	507	}
85	gezelter	1211
86	gezelter	507	void Molecule::addAtom(Atom* atom) {
87	gezelter	246	if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) {
88	gezelter	507	atoms_.push_back(atom);
89	gezelter	246	}
90	gezelter	507	}
91	gezelter	1211
92	gezelter	507	void Molecule::addBond(Bond* bond) {
93	gezelter	246	if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) {
94	gezelter	507	bonds_.push_back(bond);
95	gezelter	246	}
96	gezelter	507	}
97	gezelter	1211
98	gezelter	507	void Molecule::addBend(Bend* bend) {
99	gezelter	246	if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) {
100	gezelter	507	bends_.push_back(bend);
101	gezelter	246	}
102	gezelter	507	}
103	gezelter	1211
104	gezelter	507	void Molecule::addTorsion(Torsion* torsion) {
105	gezelter	1211	if (std::find(torsions_.begin(), torsions_.end(), torsion) ==
106			torsions_.end()) {
107	gezelter	507	torsions_.push_back(torsion);
108	gezelter	246	}
109	gezelter	507	}
110	gezelter	1277
111			void Molecule::addInversion(Inversion* inversion) {
112			if (std::find(inversions_.begin(), inversions_.end(), inversion) ==
113			inversions_.end()) {
114			inversions_.push_back(inversion);
115			}
116			}
117	gezelter	1211
118	gezelter	507	void Molecule::addRigidBody(RigidBody *rb) {
119	gezelter	1211	if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) ==
120			rigidBodies_.end()) {
121	gezelter	507	rigidBodies_.push_back(rb);
122	gezelter	246	}
123	gezelter	507	}
124	gezelter	1211
125	gezelter	507	void Molecule::addCutoffGroup(CutoffGroup* cp) {
126	gezelter	1211	if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) ==
127			cutoffGroups_.end()) {
128	gezelter	507	cutoffGroups_.push_back(cp);
129	gezelter	1211	}
130	gezelter	507	}
131	gezelter	1211
132	gezelter	507	void Molecule::addConstraintPair(ConstraintPair* cp) {
133	gezelter	1211	if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) ==
134			constraintPairs_.end()) {
135	gezelter	507	constraintPairs_.push_back(cp);
136	gezelter	1211	}
137	gezelter	507	}
138	gezelter	1211
139	gezelter	507	void Molecule::addConstraintElem(ConstraintElem* cp) {
140	gezelter	1211	if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) ==
141			constraintElems_.end()) {
142	gezelter	507	constraintElems_.push_back(cp);
143	gezelter	246	}
144	gezelter	507	}
145	gezelter	1211
146	gezelter	507	void Molecule::complete() {
147	gezelter	246
148			std::set<Atom*> rigidAtoms;
149	gezelter	1782	Atom* atom;
150	gezelter	2052	Atom* atom1;
151			Atom* atom2;
152			AtomIterator ai, aj;
153	gezelter	246	RigidBody* rb;
154	gezelter	1782	RigidBodyIterator rbIter;
155	gezelter	2052	Bond* bond;
156			BondIterator bi;
157	gezelter	2
158	gezelter	1782	// Get list of all the atoms that are part of rigid bodies
159
160	gezelter	246	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
161	gezelter	507	rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
162	gezelter	246	}
163	gezelter	1211
164	gezelter	1782	// add any atom that wasn't part of a rigid body to the list of integrableObjects
165
166	gezelter	246	for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
167	gezelter	1211
168	gezelter	1782	if (rigidAtoms.find(atom) == rigidAtoms.end()) {
169	gezelter	1211
170			// If an atom does not belong to a rigid body, it is an
171			// integrable object
172
173	gezelter	1782	integrableObjects_.push_back(atom);
174	gezelter	507	}
175	gezelter	246	}
176	gezelter	1211
177	gezelter	1782	// then add the rigid bodies themselves to the integrableObjects
178	gezelter	2
179	tim	372	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
180			integrableObjects_.push_back(rb);
181			}
182	gezelter	1782
183			// find the atoms that are fluctuating charges and add them to the
184			// fluctuatingCharges_ vector
185
186			for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
187			if ( atom->isFluctuatingCharge() )
188			fluctuatingCharges_.push_back( atom );
189			}
190
191	gezelter	2052
192			// find the electronegative atoms and add them to the
193			// hBondAcceptors_ vector:
194
195			for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
196			AtomType* at = atom->getAtomType();
197			// get the chain of base types for this atom type:
198			std::vector<AtomType*> ayb = at->allYourBase();
199			// use the last type in the chain of base types for the name:
200	gezelter	2054	std::string bn = UpperCase(ayb[ayb.size()-1]->getName());
201
202			if (bn.compare("O")==0 \|\| bn.compare("N")==0
203			\|\| bn.compare("F")==0)
204			hBondAcceptors_.push_back( atom );
205	gezelter	2053
206	gezelter	2052	}
207
208	gezelter	2053	// find electronegative atoms that are either bonded to
209			// hydrogens or are present in the same rigid bodies:
210
211	gezelter	2052	for (bond = beginBond(bi); bond != NULL; bond = nextBond(bi)) {
212			Atom* atom1 = bond->getAtomA();
213			Atom* atom2 = bond->getAtomB();
214			AtomType* at1 = atom1->getAtomType();
215			AtomType* at2 = atom1->getAtomType();
216			// get the chain of base types for this atom type:
217			std::vector<AtomType*> ayb1 = at1->allYourBase();
218			std::vector<AtomType*> ayb2 = at2->allYourBase();
219			// use the last type in the chain of base types for the name:
220	gezelter	2054	std::string bn1 = UpperCase(ayb1[ayb1.size()-1]->getName());
221			std::string bn2 = UpperCase(ayb2[ayb2.size()-1]->getName());
222	gezelter	2053
223			if (bn1.compare("H")==0) {
224			if (bn2.compare("O")==0 \|\| bn2.compare("N")==0
225			\|\| bn2.compare("F")==0) {
226			HBondDonor* donor = new HBondDonor();
227			donor->donorAtom = atom2;
228			donor->donatedHydrogen = atom1;
229			hBondDonors_.push_back( donor );
230	gezelter	2052	}
231			}
232	gezelter	2053	if (bn2.compare("H")==0) {
233			if (bn1.compare("O")==0 \|\| bn1.compare("N")==0
234			\|\| bn1.compare("F")==0) {
235			HBondDonor* donor = new HBondDonor();
236			donor->donorAtom = atom1;
237			donor->donatedHydrogen = atom2;
238	gezelter	2052	hBondDonors_.push_back( donor );
239			}
240	gezelter	2053	}
241	gezelter	2052	}
242	gezelter	2053
243			for (rb = beginRigidBody(rbIter); rb != NULL;
244			rb = nextRigidBody(rbIter)) {
245			for(atom1 = rb->beginAtom(ai); atom1 != NULL;
246			atom1 = rb->nextAtom(ai)) {
247	gezelter	2052	AtomType* at1 = atom1->getAtomType();
248			// get the chain of base types for this atom type:
249			std::vector<AtomType*> ayb1 = at1->allYourBase();
250			// use the last type in the chain of base types for the name:
251	gezelter	2054	std::string bn1 = UpperCase(ayb1[ayb1.size()-1]->getName());
252	gezelter	2053
253			if (bn1.compare("O")==0 \|\| bn1.compare("N")==0
254			\|\| bn1.compare("F")==0) {
255			for(atom2 = rb->beginAtom(aj); atom2 != NULL;
256			atom2 = rb->nextAtom(aj)) {
257			AtomType* at2 = atom2->getAtomType();
258			// get the chain of base types for this atom type:
259			std::vector<AtomType*> ayb2 = at2->allYourBase();
260			// use the last type in the chain of base types for the name:
261	gezelter	2054	std::string bn2 = UpperCase(ayb2[ayb2.size()-1]->getName());
262	gezelter	2053	if (bn2.compare("H")==0) {
263			HBondDonor* donor = new HBondDonor();
264			donor->donorAtom = atom1;
265			donor->donatedHydrogen = atom2;
266			hBondDonors_.push_back( donor );
267	gezelter	2052	}
268			}
269			}
270			}
271	gezelter	2053	}
272	gezelter	507	}
273	gezelter	2053
274	tim	963	RealType Molecule::getMass() {
275	gezelter	246	StuntDouble* sd;
276			std::vector<StuntDouble*>::iterator i;
277	tim	963	RealType mass = 0.0;
278	gezelter	1211
279			for (sd = beginIntegrableObject(i); sd != NULL; sd =
280			nextIntegrableObject(i)){
281	gezelter	507	mass += sd->getMass();
282	gezelter	246	}
283	gezelter	1211
284			return mass;
285	gezelter	507	}
286	gezelter	2
287	gezelter	507	Vector3d Molecule::getCom() {
288	gezelter	246	StuntDouble* sd;
289			std::vector<StuntDouble*>::iterator i;
290			Vector3d com;
291	tim	963	RealType totalMass = 0;
292			RealType mass;
293	gezelter	246
294	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
295			nextIntegrableObject(i)){
296	gezelter	507	mass = sd->getMass();
297			totalMass += mass;
298			com += sd->getPos() * mass;
299	gezelter	2	}
300	gezelter	1211
301	gezelter	246	com /= totalMass;
302	gezelter	2
303	gezelter	246	return com;
304	gezelter	507	}
305	gezelter	2052
306			Vector3d Molecule::getCom(int snapshotNo) {
307			StuntDouble* sd;
308			std::vector<StuntDouble*>::iterator i;
309			Vector3d com;
310			RealType totalMass = 0;
311			RealType mass;
312
313			for (sd = beginIntegrableObject(i); sd != NULL; sd =
314			nextIntegrableObject(i)){
315			mass = sd->getMass();
316			totalMass += mass;
317			com += sd->getPos(snapshotNo) * mass;
318			}
319
320			com /= totalMass;
321	gezelter	2
322	gezelter	2052	return com;
323			}
324
325	gezelter	507	void Molecule::moveCom(const Vector3d& delta) {
326	gezelter	246	StuntDouble* sd;
327			std::vector<StuntDouble*>::iterator i;
328
329	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
330			nextIntegrableObject(i)){
331	gezelter	507	sd->setPos(sd->getPos() + delta);
332	gezelter	1211	}
333	gezelter	507	}
334	gezelter	2
335	gezelter	507	Vector3d Molecule::getComVel() {
336	gezelter	246	StuntDouble* sd;
337			std::vector<StuntDouble*>::iterator i;
338			Vector3d velCom;
339	tim	963	RealType totalMass = 0;
340			RealType mass;
341	gezelter	246
342	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
343			nextIntegrableObject(i)){
344	gezelter	507	mass = sd->getMass();
345			totalMass += mass;
346			velCom += sd->getVel() * mass;
347	gezelter	246	}
348	gezelter	1211
349	gezelter	246	velCom /= totalMass;
350	gezelter	1211
351	gezelter	246	return velCom;
352	gezelter	507	}
353	gezelter	2
354	tim	963	RealType Molecule::getPotential() {
355	gezelter	2
356	gezelter	246	Bond* bond;
357			Bend* bend;
358			Torsion* torsion;
359	gezelter	1277	Inversion* inversion;
360	gezelter	246	Molecule::BondIterator bondIter;;
361			Molecule::BendIterator bendIter;
362			Molecule::TorsionIterator torsionIter;
363	gezelter	1277	Molecule::InversionIterator inversionIter;
364	gezelter	2
365	tim	963	RealType potential = 0.0;
366	gezelter	2
367	gezelter	246	for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
368	gezelter	507	potential += bond->getPotential();
369	gezelter	246	}
370	gezelter	2
371	gezelter	246	for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
372	gezelter	507	potential += bend->getPotential();
373	gezelter	2	}
374
375	gezelter	1211	for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion =
376			nextTorsion(torsionIter)) {
377	gezelter	507	potential += torsion->getPotential();
378	gezelter	2	}
379	gezelter	1211
380	gezelter	1277	for (inversion = beginInversion(inversionIter); torsion != NULL;
381			inversion = nextInversion(inversionIter)) {
382			potential += inversion->getPotential();
383			}
384
385	gezelter	246	return potential;
386	gezelter	1211
387	gezelter	507	}
388	gezelter	1211
389	cli2	1360	void Molecule::addProperty(GenericData* genData) {
390			properties_.addProperty(genData);
391			}
392
393			void Molecule::removeProperty(const std::string& propName) {
394			properties_.removeProperty(propName);
395			}
396
397			void Molecule::clearProperties() {
398			properties_.clearProperties();
399			}
400
401			std::vector<std::string> Molecule::getPropertyNames() {
402			return properties_.getPropertyNames();
403			}
404
405			std::vector<GenericData*> Molecule::getProperties() {
406			return properties_.getProperties();
407			}
408
409			GenericData* Molecule::getPropertyByName(const std::string& propName) {
410			return properties_.getPropertyByName(propName);
411			}
412
413	gezelter	507	std::ostream& operator <<(std::ostream& o, Molecule& mol) {
414	gezelter	246	o << std::endl;
415			o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
416			o << mol.getNAtoms() << " atoms" << std::endl;
417			o << mol.getNBonds() << " bonds" << std::endl;
418			o << mol.getNBends() << " bends" << std::endl;
419			o << mol.getNTorsions() << " torsions" << std::endl;
420	gezelter	1277	o << mol.getNInversions() << " inversions" << std::endl;
421	gezelter	246	o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
422	gezelter	1782	o << mol.getNIntegrableObjects() << " integrable objects" << std::endl;
423			o << mol.getNCutoffGroups() << " cutoff groups" << std::endl;
424			o << mol.getNConstraintPairs() << " constraint pairs" << std::endl;
425			o << mol.getNFluctuatingCharges() << " fluctuating charges" << std::endl;
426	gezelter	246	return o;
427	gezelter	507	}
428	gezelter	1211
429	gezelter	1390	}//end namespace OpenMD