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root/OpenMD/trunk/src/primitives/Molecule.hpp

Comparing trunk/src/primitives/Molecule.hpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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 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	<
91	>
92		/**
93		* Returns the global index of this molecule.
94		* @return  the global index of this molecule
#	Line 114 | 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 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

Comparing trunk/src/primitives/Molecule.hpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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