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Comparing branches/development/src/primitives/Molecule.hpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1718 by gezelter, Thu May 24 01:29:59 2012 UTC

# Line 36 | Line 36
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]  Vardeman & Gezelter, in progress (2009).                        
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   /**
# Line 83 | 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      
87 –    
89      Molecule(int stampId, int globalIndex, const std::string& molName);
90      virtual ~Molecule();
91  
# Line 119 | Line 120 | namespace OpenMD{
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 193 | 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 304 | 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 381 | 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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