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root/OpenMD/branches/development/src/primitives/Molecule.hpp

Comparing:
trunk/src/primitives/Molecule.hpp (file contents), Revision 1211 by gezelter, Wed Jan 23 16:38:22 2008 UTC vs.
branches/development/src/primitives/Molecule.hpp (file contents), Revision 1715 by gezelter, Tue May 22 21:55:31 2012 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, 24107 (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 58 | Line 59
59		#include "primitives/Bond.hpp"
60		#include "primitives/Bend.hpp"
61		#include "primitives/Torsion.hpp"
62	+	#include "primitives/Inversion.hpp"
63		#include "primitives/CutoffGroup.hpp"
64	+	#include "utils/PropertyMap.hpp"
65
66	<	namespace oopse{
66	>	namespace OpenMD{
67
68		class Constraint;
69
#	Line 75 | Line 78 | namespace oopse{
78		typedef std::vector<Bond*>::iterator BondIterator;
79		typedef std::vector<Bend*>::iterator BendIterator;
80		typedef std::vector<Torsion*>::iterator TorsionIterator;
81	+	typedef std::vector<Inversion*>::iterator InversionIterator;
82		typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
83		typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
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
84	–
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 117 | Line 121 | namespace oopse{
121		globalIndex_ = index;
122		}
123
124	+	void setConstrainedCharge(RealType cc) {
125	+	constrainedCharge_ = cc;
126	+	}
127	+
128	+	RealType getConstrainedCharge() {
129	+	return constrainedCharge_;
130	+	}
131
132		/** add an atom into this molecule */
133		void addAtom(Atom* atom);
#	Line 129 | Line 140 | namespace oopse{
140
141		/** add a torsion into this molecule*/
142		void addTorsion(Torsion* torsion);
143	+
144	+	/** add an improper torsion into this molecule*/
145	+	void addInversion(Inversion* inversion);
146
147		/** add a rigidbody into this molecule */
148		void addRigidBody(RigidBody *rb);
#	Line 162 | Line 176 | namespace oopse{
176		unsigned int getNTorsions() {
177		return torsions_.size();
178		}
179	+
180	+	/** Returns the total number of improper torsions in this molecule */
181	+	unsigned int getNInversions() {
182	+	return inversions_.size();
183	+	}
184
185		/** Returns the total number of rigid bodies in this molecule */
186		unsigned int getNRigidBodies() {
#	Line 182 | Line 201 | namespace oopse{
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 232 | Line 256 | namespace oopse{
256		Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
257		++i;
258		return (i == torsions_.end()) ? NULL : *i;
259	+	}
260	+
261	+	Inversion* beginInversion(std::vector<Inversion*>::iterator& i) {
262	+	i = inversions_.begin();
263	+	return (i == inversions_.end()) ? NULL : *i;
264	+	}
265	+
266	+	Inversion* nextInversion(std::vector<Inversion*>::iterator& i) {
267	+	++i;
268	+	return (i == inversions_.end()) ? NULL : *i;
269		}
270
271		RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
#	Line 283 | Line 317 | namespace oopse{
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
334		* of this molecule
#	Line 307 | Line 352 | namespace oopse{
352		}
353
354		friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
355	+
356	+	//below functions are just forward functions
357	+	/**
358	+	* Adds property into property map
359	+	* @param genData GenericData to be added into PropertyMap
360	+	*/
361	+	void addProperty(GenericData* genData);
362	+
363	+	/**
364	+	* Removes property from PropertyMap by name
365	+	* @param propName the name of property to be removed
366	+	*/
367	+	void removeProperty(const std::string& propName);
368	+
369	+	/**
370	+	* clear all of the properties
371	+	*/
372	+	void clearProperties();
373	+
374	+	/**
375	+	* Returns all names of properties
376	+	* @return all names of properties
377	+	*/
378	+	std::vector<std::string> getPropertyNames();
379	+
380	+	/**
381	+	* Returns all of the properties in PropertyMap
382	+	* @return all of the properties in PropertyMap
383	+	*/
384	+	std::vector<GenericData*> getProperties();
385	+
386	+	/**
387	+	* Returns property
388	+	* @param propName name of property
389	+	* @return a pointer point to property with propName. If no property named propName
390	+	* exists, return NULL
391	+	*/
392	+	GenericData* getPropertyByName(const std::string& propName);
393
394		private:
395
#	Line 316 | Line 399 | namespace oopse{
399		std::vector<Bond*> bonds_;
400		std::vector<Bend*> bends_;
401		std::vector<Torsion*> torsions_;
402	+	std::vector<Inversion*> inversions_;
403		std::vector<RigidBody*> rigidBodies_;
404		std::vector<StuntDouble*> integrableObjects_;
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	+	RealType constrainedCharge_;
413	+
414		};
415
416	<	} //namespace oopse
416	>	} //namespace OpenMD
417		#endif //

Comparing:
trunk/src/primitives/Molecule.hpp (property svn:keywords), Revision 1211 by gezelter, Wed Jan 23 16:38:22 2008 UTC vs.
branches/development/src/primitives/Molecule.hpp (property svn:keywords), Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC

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