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

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trunk/src/brains/SimInfo.hpp (file contents), Revision 1287 by gezelter, Wed Sep 10 18:11:32 2008 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1546 by gezelter, Sun Apr 10 15:16:39 2011 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 __C
68	>	#define __OPENMD_C
69		#include "brains/fSimulation.h"
70
71	<	namespace oopse{
72	<
71	>	using namespace std;
72	>	namespace OpenMD{
73		//forward decalration
74		class SnapshotManager;
75		class Molecule;
76		class SelectionManager;
77		class StuntDouble;
78	+
79		/**
80	<	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
81	<	* @brief One of the heavy weight classes of OOPSE, SimInfo maintains a list of molecules.
82	<	* The Molecule class maintains all of the concrete objects
83	<	* (atoms, bond, bend, torsions, inversions, rigid bodies, cutoff groups,
84	<	* constraints). In both the single and parallel versions, atoms and
85	<	* rigid bodies have both global and local indices.  The local index is
86	<	* not relevant to molecules or cutoff groups.
87	<	*/
80	>	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
81	>	*
82	>	* @brief One of the heavy-weight classes of OpenMD, SimInfo
83	>	* maintains objects and variables relating to the current
84	>	* simulation.  This includes the master list of Molecules.  The
85	>	* Molecule class maintains all of the concrete objects (Atoms,
86	>	* Bond, Bend, Torsions, Inversions, RigidBodies, CutoffGroups,
87	>	* Constraints). In both the single and parallel versions, Atoms and
88	>	* RigidBodies have both global and local indices.
89	>	*/
90		class SimInfo {
91		public:
92	<	typedef std::map<int, Molecule*>::iterator  MoleculeIterator;
93	<
92	>	typedef map<int, Molecule*>::iterator  MoleculeIterator;
93	>
94		/**
95		* Constructor of SimInfo
96	<	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
97	<	* second element is the total number of molecules with the same molecule stamp in the system
96	>	*
97	>	* @param molStampPairs MoleculeStamp Array. The first element of
98	>	* the pair is molecule stamp, the second element is the total
99	>	* number of molecules with the same molecule stamp in the system
100	>	*
101		* @param ff pointer of a concrete ForceField instance
102	+	*
103		* @param simParams
96	–	* @note
104		*/
105		SimInfo(ForceField* ff, Globals* simParams);
106		virtual ~SimInfo();
107
108		/**
109		* Adds a molecule
110	<	* @return return true if adding successfully, return false if the molecule is already in SimInfo
110	>	*
111	>	* @return return true if adding successfully, return false if the
112	>	* molecule is already in SimInfo
113	>	*
114		* @param mol molecule to be added
115		*/
116		bool addMolecule(Molecule* mol);
117
118		/**
119		* Removes a molecule from SimInfo
120	<	* @return true if removing successfully, return false if molecule is not in this SimInfo
120	>	*
121	>	* @return true if removing successfully, return false if molecule
122	>	* is not in this SimInfo
123		*/
124		bool removeMolecule(Molecule* mol);
125
#	Line 127 | Line 139 | namespace oopse{
139		}
140
141		/**
142	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
143	<	* of atoms which do not belong to the rigid bodies) in the system
142	>	* Returns the total number of integrable objects (total number of
143	>	* rigid bodies plus the total number of atoms which do not belong
144	>	* to the rigid bodies) in the system
145		*/
146		int getNGlobalIntegrableObjects() {
147		return nGlobalIntegrableObjects_;
148		}
149
150		/**
151	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
152	<	* of atoms which do not belong to the rigid bodies) in the system
151	>	* Returns the total number of integrable objects (total number of
152	>	* rigid bodies plus the total number of atoms which do not belong
153	>	* to the rigid bodies) in the system
154		*/
155		int getNGlobalRigidBodies() {
156		return nGlobalRigidBodies_;
#	Line 231 | Line 245 | namespace oopse{
245
246		int getFdf();
247
248	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
248	>	//getNZconstraint and setNZconstraint ruin the coherence of
249	>	//SimInfo class, need refactoring
250
251		/** Returns the total number of z-constraint molecules in the system */
252		int getNZconstraint() {
#	Line 267 | Line 282 | namespace oopse{
282
283		/** Returns the center of the mass of the whole system.*/
284		Vector3d getCom();
285	<	/** Returns the center of the mass and Center of Mass velocity of the whole system.*/
285	>	/** Returns the center of the mass and Center of Mass velocity of
286	>	the whole system.*/
287		void getComAll(Vector3d& com,Vector3d& comVel);
288
289	<	/** Returns intertia tensor for the entire system and system Angular Momentum.*/
289	>	/** Returns intertia tensor for the entire system and system
290	>	Angular Momentum.*/
291		void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
292
293		/** Returns system angular momentum */
294		Vector3d getAngularMomentum();
295
296	<	/** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/
296	>	/** Returns volume of system as estimated by an ellipsoid defined
297	>	by the radii of gyration*/
298		void getGyrationalVolume(RealType &vol);
299	<	/** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/
299	>	/** Overloaded version of gyrational volume that also returns
300	>	det(I) so dV/dr can be calculated*/
301		void getGyrationalVolume(RealType &vol, RealType &detI);
302	<	/** main driver function to interact with fortran during the initialization and molecule migration */
302	>
303		void update();
304	+	/**
305	+	* Setup Fortran Simulation
306	+	*/
307	+	void setupFortran();
308
309	+
310		/** Returns the local index manager */
311		LocalIndexManager* getLocalIndexManager() {
312		return &localIndexMan_;
#	Line 314 | Line 338 | namespace oopse{
338		return i != molecules_.end() ? i->second : NULL;
339		}
340
341	<	RealType getRcut() {
342	<	return rcut_;
341	>	int getGlobalMolMembership(int id){
342	>	return globalMolMembership_[id];
343		}
320	–
321	–	RealType getRsw() {
322	–	return rsw_;
323	–	}
324	–
325	–	RealType getList() {
326	–	return rlist_;
327	–	}
344
345	<	std::string getFinalConfigFileName() {
345	>	string getFinalConfigFileName() {
346		return finalConfigFileName_;
347		}
348
349	<	void setFinalConfigFileName(const std::string& fileName) {
349	>	void setFinalConfigFileName(const string& fileName) {
350		finalConfigFileName_ = fileName;
351		}
352
353	<	std::string getRawMetaData() {
353	>	string getRawMetaData() {
354		return rawMetaData_;
355		}
356	<	void setRawMetaData(const std::string& rawMetaData) {
356	>	void setRawMetaData(const string& rawMetaData) {
357		rawMetaData_ = rawMetaData;
358		}
359
360	<	std::string getDumpFileName() {
360	>	string getDumpFileName() {
361		return dumpFileName_;
362		}
363
364	<	void setDumpFileName(const std::string& fileName) {
364	>	void setDumpFileName(const string& fileName) {
365		dumpFileName_ = fileName;
366		}
367
368	<	std::string getStatFileName() {
368	>	string getStatFileName() {
369		return statFileName_;
370		}
371
372	<	void setStatFileName(const std::string& fileName) {
372	>	void setStatFileName(const string& fileName) {
373		statFileName_ = fileName;
374		}
375
376	<	std::string getRestFileName() {
376	>	string getRestFileName() {
377		return restFileName_;
378		}
379
380	<	void setRestFileName(const std::string& fileName) {
380	>	void setRestFileName(const string& fileName) {
381		restFileName_ = fileName;
382		}
383
#	Line 369 | Line 385 | namespace oopse{
385		* Sets GlobalGroupMembership
386		* @see #SimCreator::setGlobalIndex
387		*/
388	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
388	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
389		assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
390		globalGroupMembership_ = globalGroupMembership;
391		}
#	Line 378 | Line 394 | namespace oopse{
394		* Sets GlobalMolMembership
395		* @see #SimCreator::setGlobalIndex
396		*/
397	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
397	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
398		assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
399		globalMolMembership_ = globalMolMembership;
400		}
#	Line 396 | Line 412 | namespace oopse{
412		return useAtomicVirial_;
413		}
414
399	–	//below functions are just forward functions
400	–	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
401	–	//the other hand, has-a relation need composing.
415		/**
416		* Adds property into property map
417		* @param genData GenericData to be added into PropertyMap
#	Line 409 | Line 422 | namespace oopse{
422		* Removes property from PropertyMap by name
423		* @param propName the name of property to be removed
424		*/
425	<	void removeProperty(const std::string& propName);
425	>	void removeProperty(const string& propName);
426
427		/**
428		* clear all of the properties
#	Line 420 | Line 433 | namespace oopse{
433		* Returns all names of properties
434		* @return all names of properties
435		*/
436	<	std::vector<std::string> getPropertyNames();
436	>	vector<string> getPropertyNames();
437
438		/**
439		* Returns all of the properties in PropertyMap
440		* @return all of the properties in PropertyMap
441		*/
442	<	std::vector<GenericData*> getProperties();
442	>	vector<GenericData*> getProperties();
443
444		/**
445		* Returns property
#	Line 434 | Line 447 | namespace oopse{
447		* @return a pointer point to property with propName. If no property named propName
448		* exists, return NULL
449		*/
450	<	GenericData* getPropertyByName(const std::string& propName);
450	>	GenericData* getPropertyByName(const string& propName);
451
452		/**
453		* add all special interaction pairs (including excluded
#	Line 448 | Line 461 | namespace oopse{
461		*/
462		void removeInteractionPairs(Molecule* mol);
463
464	<
465	<	/** Returns the unique atom types of local processor in an array */
453	<	std::set<AtomType*> getUniqueAtomTypes();
464	>	/** Returns the set of atom types present in this simulation */
465	>	set<AtomType*> getSimulatedAtomTypes();
466
467	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
467	>	friend ostream& operator <<(ostream& o, SimInfo& info);
468
469		void getCutoff(RealType& rcut, RealType& rsw);
470
471		private:
472
473	<	/** fill up the simtype struct*/
474	<	void setupSimType();
473	>	/** fill up the simtype struct and other simulation-related variables */
474	>	void setupSimVariables();
475
464	–	/**
465	–	* Setup Fortran Simulation
466	–	* @see #setupFortranParallel
467	–	*/
468	–	void setupFortranSim();
476
470	–	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
471	–	void setupCutoff();
472	–
473	–	/** Figure out which coulombic correction method to use and pass to fortran */
474	–	void setupElectrostaticSummationMethod( int isError );
475	–
476	–	/** Figure out which polynomial type to use for the switching function */
477	–	void setupSwitchingFunction();
478	–
477		/** Determine if we need to accumulate the simulation box dipole */
478		void setupAccumulateBoxDipole();
479
#	Line 484 | Line 482 | namespace oopse{
482		void calcNdfRaw();
483		void calcNdfTrans();
484
487	–	ForceField* forceField_;
488	–	Globals* simParams_;
489	–
490	–	std::map<int, Molecule*>  molecules_; /**< Molecule array */
491	–
485		/**
486	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
487	<	* system.
486	>	* Adds molecule stamp and the total number of the molecule with
487	>	* same molecule stamp in the whole system.
488		*/
489		void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
490	<
491	<	//degress of freedom
492	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
493	<	int fdf_local;       /**< number of frozen degrees of freedom */
501	<	int fdf_;            /**< number of frozen degrees of freedom */
502	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
503	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
504	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
505	<
506	<	//number of global objects
507	<	int nGlobalMols_;       /**< number of molecules in the system */
508	<	int nGlobalAtoms_;   /**< number of atoms in the system */
509	<	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
510	<	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
511	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
512	<	/**
513	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
514	<	* corresponding content is the global index of cutoff group this atom belong to.
515	<	* It is filled by SimCreator once and only once, since it never changed during the simulation.
516	<	*/
517	<	std::vector<int> globalGroupMembership_;
490	>
491	>	// Other classes holdingn important information
492	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
493	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
494
495	<	/**
520	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
521	<	* corresponding content is the global index of molecule this atom belong to.
522	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
523	<	*/
524	<	std::vector<int> globalMolMembership_;
525	<
526	<
527	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
528	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
529	<
530	<	//number of local objects
495	>	///  Counts of local objects
496		int nAtoms_;              /**< number of atoms in local processor */
497		int nBonds_;              /**< number of bonds in local processor */
498		int nBends_;              /**< number of bends in local processor */
#	Line 537 | Line 502 | namespace oopse{
502		int nIntegrableObjects_;  /**< number of integrable objects in local processor */
503		int nCutoffGroups_;       /**< number of cutoff groups in local processor */
504		int nConstraints_;        /**< number of constraints in local processors */
505	+
506	+	/// Counts of global objects
507	+	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
508	+	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
509	+	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
510	+	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
511	+	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
512	+
513	+	/// Degress of freedom
514	+	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
515	+	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
516	+	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
517	+	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
518	+	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
519	+	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
520
521	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
522	<	PairList excludedInteractions_;
523	<	PairList oneTwoInteractions_;
524	<	PairList oneThreeInteractions_;
525	<	PairList oneFourInteractions_;
526	<	PropertyMap properties_;                  /**< Generic Property */
527	<	SnapshotManager* sman_;               /**< SnapshotManager */
521	>	/// logicals
522	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
523	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
524	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
525	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
526	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
527	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
528	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
529	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
530
531	+	public:
532	+	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
533	+	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
534	+	bool usesMetallicAtoms() { return usesMetallicAtoms_; }
535	+	bool usesAtomicVirial() { return usesAtomicVirial_; }
536	+	bool requiresPrepair() { return requiresPrepair_; }
537	+	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
538	+	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
539	+
540	+	private:
541	+	/// Data structures holding primary simulation objects
542	+	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
543	+	simtype fInfo_;                   /**< A dual struct shared by C++
544	+	and Fortran to pass
545	+	information about what types
546	+	of calculation are
547	+	required */
548	+
549	+	/// Stamps are templates for objects that are then used to create
550	+	/// groups of objects.  For example, a molecule stamp contains
551	+	/// information on how to build that molecule (i.e. the topology,
552	+	/// the atoms, the bonds, etc.)  Once the system is built, the
553	+	/// stamps are no longer useful.
554	+	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
555	+	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
556	+
557	+	/**
558	+	* A vector that maps between the global index of an atom, and the
559	+	* global index of cutoff group the atom belong to.  It is filled
560	+	* by SimCreator once and only once, since it never changed during
561	+	* the simulation.  It should be nGlobalAtoms_ in size.
562	+	*/
563	+	vector<int> globalGroupMembership_;
564	+
565	+	/**
566	+	* A vector that maps between the global index of an atom and the
567	+	* global index of the molecule the atom belongs to.  It is filled
568	+	* by SimCreator once and only once, since it is never changed
569	+	* during the simulation. It shoudl be nGlobalAtoms_ in size.
570	+	*/
571	+	vector<int> globalMolMembership_;
572	+
573		/**
574	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
575	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
576	<	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
577	<	* to make a efficient data moving plan.
574	>	* A vector that maps between the local index of an atom and the
575	>	* index of the AtomType.
576	>	*/
577	>	vector<int> identArray_;
578	>	public:
579	>	vector<int> getIdentArray() { return identArray_; }
580	>	private:
581	>
582	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
583	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
584	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
585	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
586	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
587	>
588	>	PropertyMap properties_;       /**< Generic Properties can be added */
589	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
590	>
591	>	/**
592	>	* The reason to have a local index manager is that when molecule
593	>	* is migrating to other processors, the atoms and the
594	>	* rigid-bodies will release their local indices to
595	>	* LocalIndexManager. Combining the information of molecule
596	>	* migrating to current processor, Migrator class can query the
597	>	* LocalIndexManager to make a efficient data moving plan.
598		*/
599		LocalIndexManager localIndexMan_;
600
601		// unparsed MetaData block for storing in Dump and EOR files:
602	<	std::string rawMetaData_;
602	>	string rawMetaData_;
603
604	<	//file names
605	<	std::string finalConfigFileName_;
606	<	std::string dumpFileName_;
607	<	std::string statFileName_;
608	<	std::string restFileName_;
604	>	// file names
605	>	string finalConfigFileName_;
606	>	string dumpFileName_;
607	>	string statFileName_;
608	>	string restFileName_;
609
566	–	RealType rcut_;       /**< cutoff radius*/
567	–	RealType rsw_;        /**< radius of switching function*/
568	–	RealType rlist_;      /**< neighbor list radius */
610
611	<	bool ljsp_; /**< use shifted potential for LJ*/
571	<	bool ljsf_; /**< use shifted force for LJ*/
572	<
573	<	bool fortranInitialized_; /**< flag indicate whether fortran side
574	<	is initialized */
611	>	bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
612
613		bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
614		the simulation box dipole moment */
615
616		bool useAtomicVirial_; /**< flag to indicate whether or not we use
617		Atomic Virials to calculate the pressure */
618	<
619	<	public:
583	<	/**
584	<	* return an integral objects by its global index. In MPI version, if the StuntDouble with specified
585	<	* global index does not belong to local processor, a NULL will be return.
586	<	*/
587	<	StuntDouble* getIOIndexToIntegrableObject(int index);
588	<	void setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v);
589	<	private:
590	<	std::vector<StuntDouble*> IOIndexToIntegrableObject;
591	<	//public:
592	<	//void setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v);
618	>
619	>	public:
620		/**
621	<	* return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
622	<	* global index does not belong to local processor, a NULL will be return.
623	<	*/
624	<	//StuntDouble* getStuntDoubleFromGlobalIndex(int index);
625	<	//private:
626	<	//std::vector<StuntDouble*> sdByGlobalIndex_;
621	>	* return an integral objects by its global index. In MPI
622	>	* version, if the StuntDouble with specified global index does
623	>	* not belong to local processor, a NULL will be return.
624	>	*/
625	>	StuntDouble* getIOIndexToIntegrableObject(int index);
626	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
627
628	<	//in Parallel version, we need MolToProc
628	>	private:
629	>	vector<StuntDouble*> IOIndexToIntegrableObject;
630	>
631		public:
632
633		/**
#	Line 610 | Line 639 | namespace oopse{
639		//assert(globalIndex < molToProcMap_.size());
640		return molToProcMap_[globalIndex];
641		}
642	<
642	>
643		/**
644		* Set MolToProcMap array
645		* @see #SimCreator::divideMolecules
646		*/
647	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
647	>	void setMolToProcMap(const vector<int>& molToProcMap) {
648		molToProcMap_ = molToProcMap;
649		}
650
651		private:
623	–
624	–	void setupFortranParallel();
652
653		/**
654		* The size of molToProcMap_ is equal to total number of molecules
655		* in the system.  It maps a molecule to the processor on which it
656		* resides. it is filled by SimCreator once and only once.
657		*/
658	<	std::vector<int> molToProcMap_;
658	>	vector<int> molToProcMap_;
659
633	–
660		};
661
662	<	} //namespace oopse
662	>	} //namespace OpenMD
663		#endif //BRAINS_SIMMODEL_HPP
664

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 1287 by gezelter, Wed Sep 10 18:11:32 2008 UTC vs.
branches/development/src/brains/SimInfo.hpp (property svn:keywords), Revision 1546 by gezelter, Sun Apr 10 15:16:39 2011 UTC

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