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Comparing trunk/src/primitives/Molecule.hpp (file contents):
Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
Revision 2052 by gezelter, Fri Jan 9 19:06:35 2015 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
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, 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
65	–	namespace oopse{
66
67	<	class Constraint;
67	>	namespace OpenMD{
68
69	+	class Constraint;
70	+
71		/**
72		* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
73		* @brief
#	Line 73 | Line 75 | namespace oopse{
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 oopse{
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	<
99	>
100		/**
101		* Returns the global index of this molecule.
102		* @return  the global index of this molecule
#	Line 106 | Line 115 | namespace oopse{
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 oopse{
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 192 | Line 211 | namespace oopse{
211		/** Returns the total number of constraints in this molecule */
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 304 | Line 337 | namespace oopse{
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 oopse{
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 oopse{
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
474	<	} //namespace oopse
474	>	} //namespace OpenMD
475		#endif //

Comparing trunk/src/primitives/Molecule.hpp (property svn:keywords):
Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
Revision 2052 by gezelter, Fri Jan 9 19:06:35 2015 UTC

#	Line 0 | Line 1
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