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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 1908 by gezelter, Fri Jul 19 21:25:45 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
89	<
88	<	Molecule(int stampId, int globalIndex, const std::string& molName);
89	>	Molecule(int stampId, int globalIndex, const std::string& molName, int region);
90		virtual ~Molecule();
91	<
91	>
92		/**
93		* Returns the global index of this molecule.
94		* @return  the global index of this molecule
#	Line 106 | Line 107 | namespace OpenMD{
107		int getStampId() {
108		return stampId_;
109		}
110	+	int getRegion() {
111	+	return region_;
112	+	}
113
114		/** Returns the name of the molecule */
115		std::string getType() {
#	Line 114 | Line 118 | namespace OpenMD{
118
119		/**
120		* Sets the global index of this molecule.
121	<	* @param new global index to be set
121	>	* @param index new global index to be set
122		*/
123		void setGlobalIndex(int index) {
124		globalIndex_ = index;
125		}
126	+
127	+	void setConstrainTotalCharge(bool ctc) {
128	+	constrainTotalCharge_ = ctc;
129	+	}
130
131	<
131	>	bool constrainTotalCharge() {
132	>	return constrainTotalCharge_;
133	>	}
134	>
135		/** add an atom into this molecule */
136		void addAtom(Atom* atom);
137
#	Line 193 | Line 204 | namespace OpenMD{
204		unsigned int getNConstraintPairs() {
205		return constraintPairs_.size();
206		}
207	<
207	>
208	>	/** Returns the total number of fluctuating charges in this molecule */
209	>	unsigned int getNFluctuatingCharges() {
210	>	return fluctuatingCharges_.size();
211	>	}
212	>
213		Atom* getAtomAt(unsigned int i) {
214		assert(i < atoms_.size());
215		return atoms_[i];
#	Line 303 | Line 319 | namespace OpenMD{
319		ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
320		++i;
321		return (i == constraintElems_.end()) ? NULL : *i;
322	+	}
323	+
324	+	Atom* beginFluctuatingCharge(std::vector<Atom*>::iterator& i) {
325	+	i = fluctuatingCharges_.begin();
326	+	return (i == fluctuatingCharges_.end()) ? NULL : *i;
327		}
328	+
329	+	Atom* nextFluctuatingCharge(std::vector<Atom*>::iterator& i) {
330	+	++i;
331	+	return (i == fluctuatingCharges_.end()) ? NULL : *i;
332	+	}
333	+
334
335		/**
336		* Returns the total potential energy of short range interaction
#	Line 381 | Line 408 | namespace OpenMD{
408		std::vector<CutoffGroup*> cutoffGroups_;
409		std::vector<ConstraintPair*> constraintPairs_;
410		std::vector<ConstraintElem*> constraintElems_;
411	+	std::vector<Atom*> fluctuatingCharges_;
412		int stampId_;
413	+	int region_;
414		std::string moleculeName_;
415		PropertyMap properties_;
416	+	bool constrainTotalCharge_;
417
418		};
419

Comparing trunk/src/primitives/Molecule.hpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1908 by gezelter, Fri Jul 19 21:25:45 2013 UTC

#	Line 0 | Line 1
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