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Comparing trunk/src/primitives/Molecule.hpp (file contents):
Revision 1407 by cli2, Wed Jan 20 16:04:40 2010 UTC vs.
Revision 2052 by gezelter, Fri Jan 9 19:06:35 2015 UTC

# Line 35 | Line 35
35   *                                                                      
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
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 62 | Line 63
63   #include "primitives/CutoffGroup.hpp"
64   #include "utils/PropertyMap.hpp"
65  
66 +
67   namespace OpenMD{
68  
69    class Constraint;
70 <
70 >  
71    /**
72     * @class Molecule Molecule.hpp "primitives/Molecule.hpp"
73     * @brief
# Line 73 | Line 75 | namespace OpenMD{
75    class Molecule {
76    public:
77  
78 +    struct HBondDonor {
79 +      Atom* donorAtom;
80 +      Atom* donatedHydrogen;
81 +    };
82 +
83      typedef std::vector<Atom*>::iterator AtomIterator;
84      typedef std::vector<Bond*>::iterator BondIterator;
85      typedef std::vector<Bend*>::iterator BendIterator;
# Line 83 | Line 90 | namespace OpenMD{
90      typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
91      typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
92      typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
93 <    
94 <    
95 <    Molecule(int stampId, int globalIndex, const std::string& molName);
93 >    typedef std::vector<Atom*>::iterator FluctuatingChargeIterator;
94 >    typedef std::vector<HBondDonor*>::iterator HBondDonorIterator;
95 >    typedef std::vector<Atom*>::iterator HBondAcceptorIterator;
96 >
97 >    Molecule(int stampId, int globalIndex, const std::string& molName, int region);
98      virtual ~Molecule();
99  
100      /**
# Line 106 | Line 115 | namespace OpenMD{
115      int getStampId() {
116        return stampId_;
117      }
118 +    int getRegion() {
119 +      return region_;
120 +    }
121      
122      /** Returns the name of the molecule */
123      std::string getType() {
# Line 114 | Line 126 | namespace OpenMD{
126      
127      /**
128       * Sets the global index of this molecule.
129 <     * @param new global index to be set
129 >     * @param index new global index to be set
130       */
131      void setGlobalIndex(int index) {
132        globalIndex_ = index;
133      }
134 +
135 +    void setConstrainTotalCharge(bool ctc) {
136 +      constrainTotalCharge_ = ctc;
137 +    }
138      
139 <    
139 >    bool constrainTotalCharge() {
140 >      return constrainTotalCharge_;
141 >    }
142 >
143      /** add an atom into this molecule */
144      void addAtom(Atom* atom);
145      
# Line 193 | Line 212 | namespace OpenMD{
212      unsigned int getNConstraintPairs() {
213        return constraintPairs_.size();
214      }
215 +
216 +    /** Returns the total number of fluctuating charges in this molecule */
217 +    unsigned int getNFluctuatingCharges() {
218 +      return fluctuatingCharges_.size();
219 +    }
220 +    /** Returns the total number of Hydrogen Bond donors in this molecule */
221 +    unsigned int getNHBondDonors() {
222 +      return hBondDonors_.size();
223 +    }
224      
225 +    /** Returns the total number of Hydrogen Bond acceptors in this molecule */
226 +    unsigned int getNHBondAcceptors() {
227 +      return hBondAcceptors_.size();
228 +    }
229 +
230      Atom* getAtomAt(unsigned int i) {
231        assert(i < atoms_.size());
232        return atoms_[i];
# Line 303 | Line 336 | namespace OpenMD{
336      ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {            
337        ++i;
338        return (i == constraintElems_.end()) ? NULL : *i;    
339 +    }
340 +
341 +    Atom* beginFluctuatingCharge(std::vector<Atom*>::iterator& i) {
342 +      i = fluctuatingCharges_.begin();
343 +      return (i == fluctuatingCharges_.end()) ? NULL : *i;
344      }
345 +    
346 +    Atom* nextFluctuatingCharge(std::vector<Atom*>::iterator& i) {
347 +      ++i;
348 +      return (i == fluctuatingCharges_.end()) ? NULL : *i;    
349 +    }
350 +
351 +    HBondDonor* beginHBondDonor(std::vector<HBondDonor*>::iterator& i) {
352 +      i = hBondDonors_.begin();
353 +      return (i == hBondDonors_.end()) ? NULL : *i;
354 +    }
355 +    
356 +    HBondDonor* nextHBondDonor(std::vector<HBondDonor*>::iterator& i) {
357 +      ++i;
358 +      return (i == hBondDonors_.end()) ? NULL : *i;    
359 +    }
360 +    
361 +    Atom* beginHBondAcceptor(std::vector<Atom*>::iterator& i) {
362 +      i = hBondAcceptors_.begin();
363 +      return (i == hBondAcceptors_.end()) ? NULL : *i;
364 +    }
365 +    
366 +    Atom* nextHBondAcceptor(std::vector<Atom*>::iterator& i) {
367 +      ++i;
368 +      return (i == hBondAcceptors_.end()) ? NULL : *i;    
369 +    }
370 +
371          
372      /**
373       * Returns the total potential energy of short range interaction
# Line 314 | Line 378 | namespace OpenMD{
378      /** get total mass of this molecule */        
379      RealType getMass();
380      
381 <    /** return the center of mass of this molecule */
381 >    /**
382 >     * Returns the current center of mass position of this molecule.
383 >     *
384 >     * @return the center of mass position of this molecule.
385 >     */    
386      Vector3d getCom();
387      
388 +    /**
389 +     * Returns the center of mass position of this molecule in
390 +     * specified snapshot
391 +     *
392 +     * @return the center of mass position of this molecule
393 +     * @param snapshotNo
394 +     */    
395 +    Vector3d getCom(int snapshotNo);
396 +
397 +    
398      /** Moves the center of this molecule */
399      void moveCom(const Vector3d& delta);
400      
# Line 381 | Line 459 | namespace OpenMD{
459      std::vector<CutoffGroup*> cutoffGroups_;
460      std::vector<ConstraintPair*> constraintPairs_;
461      std::vector<ConstraintElem*> constraintElems_;
462 +    std::vector<Atom*> fluctuatingCharges_;
463 +    std::vector<HBondDonor*> hBondDonors_;
464 +    std::vector<Atom*> hBondAcceptors_;
465 +    
466      int stampId_;
467 +    int region_;
468      std::string moleculeName_;
469      PropertyMap properties_;
470 +    bool constrainTotalCharge_;
471  
472    };
473  

Comparing trunk/src/primitives/Molecule.hpp (property svn:keywords):
Revision 1407 by cli2, Wed Jan 20 16:04:40 2010 UTC vs.
Revision 2052 by gezelter, Fri Jan 9 19:06:35 2015 UTC

# Line 0 | Line 1
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