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root/OpenMD/branches/development/src/primitives/Molecule.hpp
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Comparing branches/development/src/primitives/Molecule.hpp (file contents):
Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC vs.
Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

# Line 84 | Line 84 | namespace OpenMD{
84      typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
85      typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
86      typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
87 +    typedef std::vector<Atom*>::iterator FluctuatingChargeIterator;
88      
88 –    
89      Molecule(int stampId, int globalIndex, const std::string& molName);
90      virtual ~Molecule();
91  
# Line 115 | Line 115 | namespace OpenMD{
115      
116      /**
117       * Sets the global index of this molecule.
118 <     * @param new global index to be set
118 >     * @param index new global index to be set
119       */
120      void setGlobalIndex(int index) {
121        globalIndex_ = index;
122      }
123 +
124 +    void setConstrainTotalCharge(bool ctc) {
125 +      constrainTotalCharge_ = ctc;
126 +    }
127      
128 <    
128 >    bool constrainTotalCharge() {
129 >      return constrainTotalCharge_;
130 >    }
131 >
132      /** add an atom into this molecule */
133      void addAtom(Atom* atom);
134      
# Line 194 | Line 201 | namespace OpenMD{
201      unsigned int getNConstraintPairs() {
202        return constraintPairs_.size();
203      }
204 <    
204 >
205 >    /** Returns the total number of fluctuating charges in this molecule */
206 >    unsigned int getNFluctuatingCharges() {
207 >      return fluctuatingCharges_.size();
208 >    }
209 >
210      Atom* getAtomAt(unsigned int i) {
211        assert(i < atoms_.size());
212        return atoms_[i];
# Line 305 | Line 317 | namespace OpenMD{
317        ++i;
318        return (i == constraintElems_.end()) ? NULL : *i;    
319      }
320 +
321 +    Atom* beginFluctuatingCharge(std::vector<Atom*>::iterator& i) {
322 +      i = fluctuatingCharges_.begin();
323 +      return (i == fluctuatingCharges_.end()) ? NULL : *i;
324 +    }
325 +    
326 +    Atom* nextFluctuatingCharge(std::vector<Atom*>::iterator& i) {
327 +      ++i;
328 +      return (i == fluctuatingCharges_.end()) ? NULL : *i;    
329 +    }
330 +
331          
332      /**
333       * Returns the total potential energy of short range interaction
# Line 382 | Line 405 | namespace OpenMD{
405      std::vector<CutoffGroup*> cutoffGroups_;
406      std::vector<ConstraintPair*> constraintPairs_;
407      std::vector<ConstraintElem*> constraintElems_;
408 +    std::vector<Atom*> fluctuatingCharges_;
409      int stampId_;
410      std::string moleculeName_;
411      PropertyMap properties_;
412 +    bool constrainTotalCharge_;
413  
414    };
415  

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