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root/OpenMD/branches/development/src/brains/SimInfo.hpp

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trunk/src/brains/SimInfo.hpp (file contents), Revision 1292 by chuckv, Fri Sep 12 20:51:22 2008 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1534 by gezelter, Wed Dec 29 21:53:28 2010 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 62 | Line 62
62		#include "UseTheForce/ForceField.hpp"
63		#include "utils/PropertyMap.hpp"
64		#include "utils/LocalIndexManager.hpp"
65	+	#include "nonbonded/SwitchingFunction.hpp"
66
67		//another nonsense macro declaration
68	<	#define __OOPSE_C
68	>	#define __OPENMD_C
69		#include "brains/fSimulation.h"
70
71	<	namespace oopse{
71	>	using namespace std;
72	>	namespace OpenMD{
73	>	enum CutoffMethod {
74	>	HARD,
75	>	SWITCHING_FUNCTION,
76	>	SHIFTED_POTENTIAL,
77	>	SHIFTED_FORCE
78	>	};
79
80		//forward decalration
81		class SnapshotManager;
82		class Molecule;
83		class SelectionManager;
84		class StuntDouble;
85	+
86		/**
87	<	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
88	<	* @brief One of the heavy weight classes of OOPSE, SimInfo maintains a list of molecules.
89	<	* The Molecule class maintains all of the concrete objects
90	<	* (atoms, bond, bend, torsions, inversions, rigid bodies, cutoff groups,
91	<	* constraints). In both the single and parallel versions, atoms and
92	<	* rigid bodies have both global and local indices.  The local index is
93	<	* not relevant to molecules or cutoff groups.
94	<	*/
87	>	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
88	>	*
89	>	* @brief One of the heavy-weight classes of OpenMD, SimInfo
90	>	* maintains objects and variables relating to the current
91	>	* simulation.  This includes the master list of Molecules.  The
92	>	* Molecule class maintains all of the concrete objects (Atoms,
93	>	* Bond, Bend, Torsions, Inversions, RigidBodies, CutoffGroups,
94	>	* Constraints). In both the single and parallel versions, Atoms and
95	>	* RigidBodies have both global and local indices.
96	>	*/
97		class SimInfo {
98		public:
99	<	typedef std::map<int, Molecule*>::iterator  MoleculeIterator;
100	<
99	>	typedef map<int, Molecule*>::iterator  MoleculeIterator;
100	>
101		/**
102		* Constructor of SimInfo
103	<	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
104	<	* second element is the total number of molecules with the same molecule stamp in the system
103	>	*
104	>	* @param molStampPairs MoleculeStamp Array. The first element of
105	>	* the pair is molecule stamp, the second element is the total
106	>	* number of molecules with the same molecule stamp in the system
107	>	*
108		* @param ff pointer of a concrete ForceField instance
109	+	*
110		* @param simParams
96	–	* @note
111		*/
112		SimInfo(ForceField* ff, Globals* simParams);
113		virtual ~SimInfo();
114
115		/**
116		* Adds a molecule
117	<	* @return return true if adding successfully, return false if the molecule is already in SimInfo
117	>	*
118	>	* @return return true if adding successfully, return false if the
119	>	* molecule is already in SimInfo
120	>	*
121		* @param mol molecule to be added
122		*/
123		bool addMolecule(Molecule* mol);
124
125		/**
126		* Removes a molecule from SimInfo
127	<	* @return true if removing successfully, return false if molecule is not in this SimInfo
127	>	*
128	>	* @return true if removing successfully, return false if molecule
129	>	* is not in this SimInfo
130		*/
131		bool removeMolecule(Molecule* mol);
132
#	Line 127 | Line 146 | namespace oopse{
146		}
147
148		/**
149	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
150	<	* of atoms which do not belong to the rigid bodies) in the system
149	>	* Returns the total number of integrable objects (total number of
150	>	* rigid bodies plus the total number of atoms which do not belong
151	>	* to the rigid bodies) in the system
152		*/
153		int getNGlobalIntegrableObjects() {
154		return nGlobalIntegrableObjects_;
155		}
156
157		/**
158	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
159	<	* of atoms which do not belong to the rigid bodies) in the system
158	>	* Returns the total number of integrable objects (total number of
159	>	* rigid bodies plus the total number of atoms which do not belong
160	>	* to the rigid bodies) in the system
161		*/
162		int getNGlobalRigidBodies() {
163		return nGlobalRigidBodies_;
#	Line 231 | Line 252 | namespace oopse{
252
253		int getFdf();
254
255	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
255	>	//getNZconstraint and setNZconstraint ruin the coherence of
256	>	//SimInfo class, need refactoring
257
258		/** Returns the total number of z-constraint molecules in the system */
259		int getNZconstraint() {
#	Line 267 | Line 289 | namespace oopse{
289
290		/** Returns the center of the mass of the whole system.*/
291		Vector3d getCom();
292	<	/** Returns the center of the mass and Center of Mass velocity of the whole system.*/
292	>	/** Returns the center of the mass and Center of Mass velocity of
293	>	the whole system.*/
294		void getComAll(Vector3d& com,Vector3d& comVel);
295
296	<	/** Returns intertia tensor for the entire system and system Angular Momentum.*/
296	>	/** Returns intertia tensor for the entire system and system
297	>	Angular Momentum.*/
298		void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
299
300		/** Returns system angular momentum */
301		Vector3d getAngularMomentum();
302
303	<	/** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/
304	<	void getGyrationalVolume(RealType &vol);
305	<	/** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/
303	>	/** Returns volume of system as estimated by an ellipsoid defined
304	>	by the radii of gyration*/
305	>	void getGyrationalVolume(RealType &vol);
306	>	/** Overloaded version of gyrational volume that also returns
307	>	det(I) so dV/dr can be calculated*/
308		void getGyrationalVolume(RealType &vol, RealType &detI);
309	<	/** main driver function to interact with fortran during the initialization and molecule migration */
309	>	/** main driver function to interact with fortran during the
310	>	initialization and molecule migration */
311		void update();
312
313		/** Returns the local index manager */
#	Line 318 | Line 345 | namespace oopse{
345		return globalMolMembership_[id];
346		}
347
348	<	RealType getRcut() {
349	<	return rcut_;
348	>	RealType getCutoffRadius() {
349	>	return cutoffRadius_;
350		}
351
352	<	RealType getRsw() {
353	<	return rsw_;
352	>	RealType getSwitchingRadius() {
353	>	return switchingRadius_;
354		}
355
356	<	RealType getList() {
357	<	return rlist_;
356	>	RealType getListRadius() {
357	>	return listRadius_;
358		}
359
360	<	std::string getFinalConfigFileName() {
360	>	string getFinalConfigFileName() {
361		return finalConfigFileName_;
362		}
363
364	<	void setFinalConfigFileName(const std::string& fileName) {
364	>	void setFinalConfigFileName(const string& fileName) {
365		finalConfigFileName_ = fileName;
366		}
367
368	<	std::string getRawMetaData() {
368	>	string getRawMetaData() {
369		return rawMetaData_;
370		}
371	<	void setRawMetaData(const std::string& rawMetaData) {
371	>	void setRawMetaData(const string& rawMetaData) {
372		rawMetaData_ = rawMetaData;
373		}
374
375	<	std::string getDumpFileName() {
375	>	string getDumpFileName() {
376		return dumpFileName_;
377		}
378
379	<	void setDumpFileName(const std::string& fileName) {
379	>	void setDumpFileName(const string& fileName) {
380		dumpFileName_ = fileName;
381		}
382
383	<	std::string getStatFileName() {
383	>	string getStatFileName() {
384		return statFileName_;
385		}
386
387	<	void setStatFileName(const std::string& fileName) {
387	>	void setStatFileName(const string& fileName) {
388		statFileName_ = fileName;
389		}
390
391	<	std::string getRestFileName() {
391	>	string getRestFileName() {
392		return restFileName_;
393		}
394
395	<	void setRestFileName(const std::string& fileName) {
395	>	void setRestFileName(const string& fileName) {
396		restFileName_ = fileName;
397		}
398
#	Line 373 | Line 400 | namespace oopse{
400		* Sets GlobalGroupMembership
401		* @see #SimCreator::setGlobalIndex
402		*/
403	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
403	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
404		assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
405		globalGroupMembership_ = globalGroupMembership;
406		}
#	Line 382 | Line 409 | namespace oopse{
409		* Sets GlobalMolMembership
410		* @see #SimCreator::setGlobalIndex
411		*/
412	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
412	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
413		assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
414		globalMolMembership_ = globalMolMembership;
415		}
#	Line 400 | Line 427 | namespace oopse{
427		return useAtomicVirial_;
428		}
429
403	–	//below functions are just forward functions
404	–	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
405	–	//the other hand, has-a relation need composing.
430		/**
431		* Adds property into property map
432		* @param genData GenericData to be added into PropertyMap
#	Line 413 | Line 437 | namespace oopse{
437		* Removes property from PropertyMap by name
438		* @param propName the name of property to be removed
439		*/
440	<	void removeProperty(const std::string& propName);
440	>	void removeProperty(const string& propName);
441
442		/**
443		* clear all of the properties
#	Line 424 | Line 448 | namespace oopse{
448		* Returns all names of properties
449		* @return all names of properties
450		*/
451	<	std::vector<std::string> getPropertyNames();
451	>	vector<string> getPropertyNames();
452
453		/**
454		* Returns all of the properties in PropertyMap
455		* @return all of the properties in PropertyMap
456		*/
457	<	std::vector<GenericData*> getProperties();
457	>	vector<GenericData*> getProperties();
458
459		/**
460		* Returns property
#	Line 438 | Line 462 | namespace oopse{
462		* @return a pointer point to property with propName. If no property named propName
463		* exists, return NULL
464		*/
465	<	GenericData* getPropertyByName(const std::string& propName);
465	>	GenericData* getPropertyByName(const string& propName);
466
467		/**
468		* add all special interaction pairs (including excluded
#	Line 454 | Line 478 | namespace oopse{
478
479
480		/** Returns the unique atom types of local processor in an array */
481	<	std::set<AtomType*> getUniqueAtomTypes();
481	>	set<AtomType*> getUniqueAtomTypes();
482	>
483	>	/** Returns the set of atom types present in this simulation */
484	>	set<AtomType*> getSimulatedAtomTypes();
485
486	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
486	>	friend ostream& operator <<(ostream& o, SimInfo& info);
487
488		void getCutoff(RealType& rcut, RealType& rsw);
489
490		private:
491
492	<	/** fill up the simtype struct*/
493	<	void setupSimType();
492	>	/** fill up the simtype struct and other simulation-related variables */
493	>	void setupSimVariables();
494
495		/**
496		* Setup Fortran Simulation
#	Line 471 | Line 498 | namespace oopse{
498		*/
499		void setupFortranSim();
500
501	<	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
502	<	void setupCutoff();
501	>	/** Figure out the cutoff radius and cutoff method */
502	>	void setupCutoffs();
503	>	/** Figure out the switching radius and polynomial type for the switching function */
504	>	void setupSwitching();
505	>	/** Figure out the simulation variables associated with electrostatics */
506	>	void setupElectrostatics();
507	>	/** Figure out the neighbor list skin thickness */
508	>	void setupNeighborlists();
509
477	–	/** Figure out which coulombic correction method to use and pass to fortran */
478	–	void setupElectrostaticSummationMethod( int isError );
479	–
480	–	/** Figure out which polynomial type to use for the switching function */
481	–	void setupSwitchingFunction();
482	–
510		/** Determine if we need to accumulate the simulation box dipole */
511		void setupAccumulateBoxDipole();
512
#	Line 488 | Line 515 | namespace oopse{
515		void calcNdfRaw();
516		void calcNdfTrans();
517
491	–	ForceField* forceField_;
492	–	Globals* simParams_;
493	–
494	–	std::map<int, Molecule*>  molecules_; /**< Molecule array */
495	–
518		/**
519	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
520	<	* system.
519	>	* Adds molecule stamp and the total number of the molecule with
520	>	* same molecule stamp in the whole system.
521		*/
522		void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
523	<
524	<	//degress of freedom
525	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
526	<	int fdf_local;       /**< number of frozen degrees of freedom */
505	<	int fdf_;            /**< number of frozen degrees of freedom */
506	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
507	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
508	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
509	<
510	<	//number of global objects
511	<	int nGlobalMols_;       /**< number of molecules in the system */
512	<	int nGlobalAtoms_;   /**< number of atoms in the system */
513	<	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
514	<	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
515	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
516	<	/**
517	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
518	<	* corresponding content is the global index of cutoff group this atom belong to.
519	<	* It is filled by SimCreator once and only once, since it never changed during the simulation.
520	<	*/
521	<	std::vector<int> globalGroupMembership_;
523	>
524	>	// Other classes holdingn important information
525	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
526	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
527
528	<	/**
524	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
525	<	* corresponding content is the global index of molecule this atom belong to.
526	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
527	<	*/
528	<	std::vector<int> globalMolMembership_;
529	<
530	<
531	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
532	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
533	<
534	<	//number of local objects
528	>	///  Counts of local objects
529		int nAtoms_;              /**< number of atoms in local processor */
530		int nBonds_;              /**< number of bonds in local processor */
531		int nBends_;              /**< number of bends in local processor */
#	Line 541 | Line 535 | namespace oopse{
535		int nIntegrableObjects_;  /**< number of integrable objects in local processor */
536		int nCutoffGroups_;       /**< number of cutoff groups in local processor */
537		int nConstraints_;        /**< number of constraints in local processors */
538	+
539	+	/// Counts of global objects
540	+	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
541	+	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
542	+	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
543	+	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
544	+	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
545	+
546	+	/// Degress of freedom
547	+	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
548	+	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
549	+	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
550	+	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
551	+	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
552	+	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
553
554	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
555	<	PairList excludedInteractions_;
556	<	PairList oneTwoInteractions_;
557	<	PairList oneThreeInteractions_;
558	<	PairList oneFourInteractions_;
559	<	PropertyMap properties_;                  /**< Generic Property */
560	<	SnapshotManager* sman_;               /**< SnapshotManager */
554	>	/// logicals
555	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
556	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
557	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
558	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
559	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
560	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
561	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
562	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
563
564	+	/// Data structures holding primary simulation objects
565	+	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
566	+	simtype fInfo_;                   /**< A dual struct shared by C++
567	+	and Fortran to pass
568	+	information about what types
569	+	of calculation are
570	+	required */
571	+
572	+	/// Stamps are templates for objects that are then used to create
573	+	/// groups of objects.  For example, a molecule stamp contains
574	+	/// information on how to build that molecule (i.e. the topology,
575	+	/// the atoms, the bonds, etc.)  Once the system is built, the
576	+	/// stamps are no longer useful.
577	+	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
578	+	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
579	+
580	+	/**
581	+	* A vector that maps between the global index of an atom, and the
582	+	* global index of cutoff group the atom belong to.  It is filled
583	+	* by SimCreator once and only once, since it never changed during
584	+	* the simulation.  It should be nGlobalAtoms_ in size.
585	+	*/
586	+	vector<int> globalGroupMembership_;
587	+
588	+	/**
589	+	* A vector that maps between the global index of an atom and the
590	+	* global index of the molecule the atom belongs to.  It is filled
591	+	* by SimCreator once and only once, since it is never changed
592	+	* during the simulation. It shoudl be nGlobalAtoms_ in size.
593	+	*/
594	+	vector<int> globalMolMembership_;
595	+
596	+	/// lists to handle atoms needing special treatment in the non-bonded interactions
597	+	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
598	+	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
599	+	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
600	+	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
601	+
602	+	PropertyMap properties_;       /**< Generic Properties can be added */
603	+	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
604	+
605		/**
606	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
607	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
608	<	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
609	<	* to make a efficient data moving plan.
606	>	* The reason to have a local index manager is that when molecule
607	>	* is migrating to other processors, the atoms and the
608	>	* rigid-bodies will release their local indices to
609	>	* LocalIndexManager. Combining the information of molecule
610	>	* migrating to current processor, Migrator class can query the
611	>	* LocalIndexManager to make a efficient data moving plan.
612		*/
613		LocalIndexManager localIndexMan_;
614
615		// unparsed MetaData block for storing in Dump and EOR files:
616	<	std::string rawMetaData_;
616	>	string rawMetaData_;
617
618	<	//file names
619	<	std::string finalConfigFileName_;
620	<	std::string dumpFileName_;
621	<	std::string statFileName_;
622	<	std::string restFileName_;
618	>	// file names
619	>	string finalConfigFileName_;
620	>	string dumpFileName_;
621	>	string statFileName_;
622	>	string restFileName_;
623
624	<	RealType rcut_;       /**< cutoff radius*/
625	<	RealType rsw_;        /**< radius of switching function*/
626	<	RealType rlist_;      /**< neighbor list radius */
624	>	RealType cutoffRadius_;         /**< cutoff radius for non-bonded interactions */
625	>	RealType switchingRadius_;      /**< inner radius of switching function */
626	>	RealType listRadius_;           /**< Verlet neighbor list radius */
627	>	RealType skinThickness_;        /**< Verlet neighbor list skin thickness */
628	>	CutoffMethod cutoffMethod_;     /**< Cutoff Method for most non-bonded interactions */
629	>	SwitchingFunctionType sft_;     /**< Type of switching function in use */
630
631	<	bool ljsp_; /**< use shifted potential for LJ*/
575	<	bool ljsf_; /**< use shifted force for LJ*/
576	<
577	<	bool fortranInitialized_; /**< flag indicate whether fortran side
578	<	is initialized */
631	>	bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
632
633		bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
634		the simulation box dipole moment */
635
636		bool useAtomicVirial_; /**< flag to indicate whether or not we use
637		Atomic Virials to calculate the pressure */
638	<
639	<	public:
587	<	/**
588	<	* return an integral objects by its global index. In MPI version, if the StuntDouble with specified
589	<	* global index does not belong to local processor, a NULL will be return.
590	<	*/
591	<	StuntDouble* getIOIndexToIntegrableObject(int index);
592	<	void setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v);
593	<	private:
594	<	std::vector<StuntDouble*> IOIndexToIntegrableObject;
595	<	//public:
596	<	//void setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v);
638	>
639	>	public:
640		/**
641	<	* return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
642	<	* global index does not belong to local processor, a NULL will be return.
643	<	*/
644	<	//StuntDouble* getStuntDoubleFromGlobalIndex(int index);
645	<	//private:
646	<	//std::vector<StuntDouble*> sdByGlobalIndex_;
641	>	* return an integral objects by its global index. In MPI
642	>	* version, if the StuntDouble with specified global index does
643	>	* not belong to local processor, a NULL will be return.
644	>	*/
645	>	StuntDouble* getIOIndexToIntegrableObject(int index);
646	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
647
648	<	//in Parallel version, we need MolToProc
648	>	private:
649	>	vector<StuntDouble*> IOIndexToIntegrableObject;
650	>
651		public:
652
653		/**
#	Line 614 | Line 659 | namespace oopse{
659		//assert(globalIndex < molToProcMap_.size());
660		return molToProcMap_[globalIndex];
661		}
662	<
662	>
663		/**
664		* Set MolToProcMap array
665		* @see #SimCreator::divideMolecules
666		*/
667	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
667	>	void setMolToProcMap(const vector<int>& molToProcMap) {
668		molToProcMap_ = molToProcMap;
669		}
670
#	Line 632 | Line 677 | namespace oopse{
677		* in the system.  It maps a molecule to the processor on which it
678		* resides. it is filled by SimCreator once and only once.
679		*/
680	<	std::vector<int> molToProcMap_;
680	>	vector<int> molToProcMap_;
681
637	–
682		};
683
684	<	} //namespace oopse
684	>	} //namespace OpenMD
685		#endif //BRAINS_SIMMODEL_HPP
686

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 1292 by chuckv, Fri Sep 12 20:51:22 2008 UTC vs.
branches/development/src/brains/SimInfo.hpp (property svn:keywords), Revision 1534 by gezelter, Wed Dec 29 21:53:28 2010 UTC

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