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) : stampId_(stampId),
                                   globalIndex_(globalIndex), 
                                   moleculeName_(molName), 
                                   region_(region),
                                   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:	2054
Committed:	Tue Jan 13 20:14:57 2015 UTC (10 years, 3 months ago) by gezelter
File size:	13917 byte(s)
Log Message:	check for atom names in lower cases for hydrogen bond donors/acceptors
#	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			int region) : stampId_(stampId),
61			globalIndex_(globalIndex),
62			moleculeName_(molName),
63			region_(region),
64			constrainTotalCharge_(false) {
65	gezelter	1211	}
66
67	gezelter	507	Molecule::~Molecule() {
68	gezelter	1211
69	tim	398	MemoryUtils::deletePointers(atoms_);
70			MemoryUtils::deletePointers(bonds_);
71			MemoryUtils::deletePointers(bends_);
72			MemoryUtils::deletePointers(torsions_);
73	gezelter	1277	MemoryUtils::deletePointers(inversions_);
74	tim	398	MemoryUtils::deletePointers(rigidBodies_);
75			MemoryUtils::deletePointers(cutoffGroups_);
76			MemoryUtils::deletePointers(constraintPairs_);
77			MemoryUtils::deletePointers(constraintElems_);
78	gezelter	1782
79	gezelter	1211	// integrableObjects_ don't own the objects
80	gezelter	246	integrableObjects_.clear();
81	gezelter	1782	fluctuatingCharges_.clear();
82	gezelter	246
83	gezelter	507	}
84	gezelter	1211
85	gezelter	507	void Molecule::addAtom(Atom* atom) {
86	gezelter	246	if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) {
87	gezelter	507	atoms_.push_back(atom);
88	gezelter	246	}
89	gezelter	507	}
90	gezelter	1211
91	gezelter	507	void Molecule::addBond(Bond* bond) {
92	gezelter	246	if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) {
93	gezelter	507	bonds_.push_back(bond);
94	gezelter	246	}
95	gezelter	507	}
96	gezelter	1211
97	gezelter	507	void Molecule::addBend(Bend* bend) {
98	gezelter	246	if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) {
99	gezelter	507	bends_.push_back(bend);
100	gezelter	246	}
101	gezelter	507	}
102	gezelter	1211
103	gezelter	507	void Molecule::addTorsion(Torsion* torsion) {
104	gezelter	1211	if (std::find(torsions_.begin(), torsions_.end(), torsion) ==
105			torsions_.end()) {
106	gezelter	507	torsions_.push_back(torsion);
107	gezelter	246	}
108	gezelter	507	}
109	gezelter	1277
110			void Molecule::addInversion(Inversion* inversion) {
111			if (std::find(inversions_.begin(), inversions_.end(), inversion) ==
112			inversions_.end()) {
113			inversions_.push_back(inversion);
114			}
115			}
116	gezelter	1211
117	gezelter	507	void Molecule::addRigidBody(RigidBody *rb) {
118	gezelter	1211	if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) ==
119			rigidBodies_.end()) {
120	gezelter	507	rigidBodies_.push_back(rb);
121	gezelter	246	}
122	gezelter	507	}
123	gezelter	1211
124	gezelter	507	void Molecule::addCutoffGroup(CutoffGroup* cp) {
125	gezelter	1211	if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) ==
126			cutoffGroups_.end()) {
127	gezelter	507	cutoffGroups_.push_back(cp);
128	gezelter	1211	}
129	gezelter	507	}
130	gezelter	1211
131	gezelter	507	void Molecule::addConstraintPair(ConstraintPair* cp) {
132	gezelter	1211	if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) ==
133			constraintPairs_.end()) {
134	gezelter	507	constraintPairs_.push_back(cp);
135	gezelter	1211	}
136	gezelter	507	}
137	gezelter	1211
138	gezelter	507	void Molecule::addConstraintElem(ConstraintElem* cp) {
139	gezelter	1211	if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) ==
140			constraintElems_.end()) {
141	gezelter	507	constraintElems_.push_back(cp);
142	gezelter	246	}
143	gezelter	507	}
144	gezelter	1211
145	gezelter	507	void Molecule::complete() {
146	gezelter	246
147			std::set<Atom*> rigidAtoms;
148	gezelter	1782	Atom* atom;
149	gezelter	2052	Atom* atom1;
150			Atom* atom2;
151			AtomIterator ai, aj;
152	gezelter	246	RigidBody* rb;
153	gezelter	1782	RigidBodyIterator rbIter;
154	gezelter	2052	Bond* bond;
155			BondIterator bi;
156	gezelter	2
157	gezelter	1782	// Get list of all the atoms that are part of rigid bodies
158
159	gezelter	246	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
160	gezelter	507	rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
161	gezelter	246	}
162	gezelter	1211
163	gezelter	1782	// add any atom that wasn't part of a rigid body to the list of integrableObjects
164
165	gezelter	246	for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
166	gezelter	1211
167	gezelter	1782	if (rigidAtoms.find(atom) == rigidAtoms.end()) {
168	gezelter	1211
169			// If an atom does not belong to a rigid body, it is an
170			// integrable object
171
172	gezelter	1782	integrableObjects_.push_back(atom);
173	gezelter	507	}
174	gezelter	246	}
175	gezelter	1211
176	gezelter	1782	// then add the rigid bodies themselves to the integrableObjects
177	gezelter	2
178	tim	372	for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
179			integrableObjects_.push_back(rb);
180			}
181	gezelter	1782
182			// find the atoms that are fluctuating charges and add them to the
183			// fluctuatingCharges_ vector
184
185			for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
186			if ( atom->isFluctuatingCharge() )
187			fluctuatingCharges_.push_back( atom );
188			}
189
190	gezelter	2052
191			// find the electronegative atoms and add them to the
192			// hBondAcceptors_ vector:
193
194			for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
195			AtomType* at = atom->getAtomType();
196			// get the chain of base types for this atom type:
197			std::vector<AtomType*> ayb = at->allYourBase();
198			// use the last type in the chain of base types for the name:
199	gezelter	2054	std::string bn = UpperCase(ayb[ayb.size()-1]->getName());
200
201			if (bn.compare("O")==0 \|\| bn.compare("N")==0
202			\|\| bn.compare("F")==0)
203			hBondAcceptors_.push_back( atom );
204	gezelter	2053
205	gezelter	2052	}
206
207	gezelter	2053	// find electronegative atoms that are either bonded to
208			// hydrogens or are present in the same rigid bodies:
209
210	gezelter	2052	for (bond = beginBond(bi); bond != NULL; bond = nextBond(bi)) {
211			Atom* atom1 = bond->getAtomA();
212			Atom* atom2 = bond->getAtomB();
213			AtomType* at1 = atom1->getAtomType();
214			AtomType* at2 = atom1->getAtomType();
215			// get the chain of base types for this atom type:
216			std::vector<AtomType*> ayb1 = at1->allYourBase();
217			std::vector<AtomType*> ayb2 = at2->allYourBase();
218			// use the last type in the chain of base types for the name:
219	gezelter	2054	std::string bn1 = UpperCase(ayb1[ayb1.size()-1]->getName());
220			std::string bn2 = UpperCase(ayb2[ayb2.size()-1]->getName());
221	gezelter	2053
222			if (bn1.compare("H")==0) {
223			if (bn2.compare("O")==0 \|\| bn2.compare("N")==0
224			\|\| bn2.compare("F")==0) {
225			HBondDonor* donor = new HBondDonor();
226			donor->donorAtom = atom2;
227			donor->donatedHydrogen = atom1;
228			hBondDonors_.push_back( donor );
229	gezelter	2052	}
230			}
231	gezelter	2053	if (bn2.compare("H")==0) {
232			if (bn1.compare("O")==0 \|\| bn1.compare("N")==0
233			\|\| bn1.compare("F")==0) {
234			HBondDonor* donor = new HBondDonor();
235			donor->donorAtom = atom1;
236			donor->donatedHydrogen = atom2;
237	gezelter	2052	hBondDonors_.push_back( donor );
238			}
239	gezelter	2053	}
240	gezelter	2052	}
241	gezelter	2053
242			for (rb = beginRigidBody(rbIter); rb != NULL;
243			rb = nextRigidBody(rbIter)) {
244			for(atom1 = rb->beginAtom(ai); atom1 != NULL;
245			atom1 = rb->nextAtom(ai)) {
246	gezelter	2052	AtomType* at1 = atom1->getAtomType();
247			// get the chain of base types for this atom type:
248			std::vector<AtomType*> ayb1 = at1->allYourBase();
249			// use the last type in the chain of base types for the name:
250	gezelter	2054	std::string bn1 = UpperCase(ayb1[ayb1.size()-1]->getName());
251	gezelter	2053
252			if (bn1.compare("O")==0 \|\| bn1.compare("N")==0
253			\|\| bn1.compare("F")==0) {
254			for(atom2 = rb->beginAtom(aj); atom2 != NULL;
255			atom2 = rb->nextAtom(aj)) {
256			AtomType* at2 = atom2->getAtomType();
257			// get the chain of base types for this atom type:
258			std::vector<AtomType*> ayb2 = at2->allYourBase();
259			// use the last type in the chain of base types for the name:
260	gezelter	2054	std::string bn2 = UpperCase(ayb2[ayb2.size()-1]->getName());
261	gezelter	2053	if (bn2.compare("H")==0) {
262			HBondDonor* donor = new HBondDonor();
263			donor->donorAtom = atom1;
264			donor->donatedHydrogen = atom2;
265			hBondDonors_.push_back( donor );
266	gezelter	2052	}
267			}
268			}
269			}
270	gezelter	2053	}
271	gezelter	507	}
272	gezelter	2053
273	tim	963	RealType Molecule::getMass() {
274	gezelter	246	StuntDouble* sd;
275			std::vector<StuntDouble*>::iterator i;
276	tim	963	RealType mass = 0.0;
277	gezelter	1211
278			for (sd = beginIntegrableObject(i); sd != NULL; sd =
279			nextIntegrableObject(i)){
280	gezelter	507	mass += sd->getMass();
281	gezelter	246	}
282	gezelter	1211
283			return mass;
284	gezelter	507	}
285	gezelter	2
286	gezelter	507	Vector3d Molecule::getCom() {
287	gezelter	246	StuntDouble* sd;
288			std::vector<StuntDouble*>::iterator i;
289			Vector3d com;
290	tim	963	RealType totalMass = 0;
291			RealType mass;
292	gezelter	246
293	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
294			nextIntegrableObject(i)){
295	gezelter	507	mass = sd->getMass();
296			totalMass += mass;
297			com += sd->getPos() * mass;
298	gezelter	2	}
299	gezelter	1211
300	gezelter	246	com /= totalMass;
301	gezelter	2
302	gezelter	246	return com;
303	gezelter	507	}
304	gezelter	2052
305			Vector3d Molecule::getCom(int snapshotNo) {
306			StuntDouble* sd;
307			std::vector<StuntDouble*>::iterator i;
308			Vector3d com;
309			RealType totalMass = 0;
310			RealType mass;
311
312			for (sd = beginIntegrableObject(i); sd != NULL; sd =
313			nextIntegrableObject(i)){
314			mass = sd->getMass();
315			totalMass += mass;
316			com += sd->getPos(snapshotNo) * mass;
317			}
318
319			com /= totalMass;
320	gezelter	2
321	gezelter	2052	return com;
322			}
323
324	gezelter	507	void Molecule::moveCom(const Vector3d& delta) {
325	gezelter	246	StuntDouble* sd;
326			std::vector<StuntDouble*>::iterator i;
327
328	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
329			nextIntegrableObject(i)){
330	gezelter	507	sd->setPos(sd->getPos() + delta);
331	gezelter	1211	}
332	gezelter	507	}
333	gezelter	2
334	gezelter	507	Vector3d Molecule::getComVel() {
335	gezelter	246	StuntDouble* sd;
336			std::vector<StuntDouble*>::iterator i;
337			Vector3d velCom;
338	tim	963	RealType totalMass = 0;
339			RealType mass;
340	gezelter	246
341	gezelter	1211	for (sd = beginIntegrableObject(i); sd != NULL; sd =
342			nextIntegrableObject(i)){
343	gezelter	507	mass = sd->getMass();
344			totalMass += mass;
345			velCom += sd->getVel() * mass;
346	gezelter	246	}
347	gezelter	1211
348	gezelter	246	velCom /= totalMass;
349	gezelter	1211
350	gezelter	246	return velCom;
351	gezelter	507	}
352	gezelter	2
353	tim	963	RealType Molecule::getPotential() {
354	gezelter	2
355	gezelter	246	Bond* bond;
356			Bend* bend;
357			Torsion* torsion;
358	gezelter	1277	Inversion* inversion;
359	gezelter	246	Molecule::BondIterator bondIter;;
360			Molecule::BendIterator bendIter;
361			Molecule::TorsionIterator torsionIter;
362	gezelter	1277	Molecule::InversionIterator inversionIter;
363	gezelter	2
364	tim	963	RealType potential = 0.0;
365	gezelter	2
366	gezelter	246	for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
367	gezelter	507	potential += bond->getPotential();
368	gezelter	246	}
369	gezelter	2
370	gezelter	246	for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
371	gezelter	507	potential += bend->getPotential();
372	gezelter	2	}
373
374	gezelter	1211	for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion =
375			nextTorsion(torsionIter)) {
376	gezelter	507	potential += torsion->getPotential();
377	gezelter	2	}
378	gezelter	1211
379	gezelter	1277	for (inversion = beginInversion(inversionIter); torsion != NULL;
380			inversion = nextInversion(inversionIter)) {
381			potential += inversion->getPotential();
382			}
383
384	gezelter	246	return potential;
385	gezelter	1211
386	gezelter	507	}
387	gezelter	1211
388	cli2	1360	void Molecule::addProperty(GenericData* genData) {
389			properties_.addProperty(genData);
390			}
391
392			void Molecule::removeProperty(const std::string& propName) {
393			properties_.removeProperty(propName);
394			}
395
396			void Molecule::clearProperties() {
397			properties_.clearProperties();
398			}
399
400			std::vector<std::string> Molecule::getPropertyNames() {
401			return properties_.getPropertyNames();
402			}
403
404			std::vector<GenericData*> Molecule::getProperties() {
405			return properties_.getProperties();
406			}
407
408			GenericData* Molecule::getPropertyByName(const std::string& propName) {
409			return properties_.getPropertyByName(propName);
410			}
411
412	gezelter	507	std::ostream& operator <<(std::ostream& o, Molecule& mol) {
413	gezelter	246	o << std::endl;
414			o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
415			o << mol.getNAtoms() << " atoms" << std::endl;
416			o << mol.getNBonds() << " bonds" << std::endl;
417			o << mol.getNBends() << " bends" << std::endl;
418			o << mol.getNTorsions() << " torsions" << std::endl;
419	gezelter	1277	o << mol.getNInversions() << " inversions" << std::endl;
420	gezelter	246	o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
421	gezelter	1782	o << mol.getNIntegrableObjects() << " integrable objects" << std::endl;
422			o << mol.getNCutoffGroups() << " cutoff groups" << std::endl;
423			o << mol.getNConstraintPairs() << " constraint pairs" << std::endl;
424			o << mol.getNFluctuatingCharges() << " fluctuating charges" << std::endl;
425	gezelter	246	return o;
426	gezelter	507	}
427	gezelter	1211
428	gezelter	1390	}//end namespace OpenMD