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

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trunk/src/brains/SimInfo.hpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC

#	Line 36 | Line 36
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).
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 59 | Line 60
60		#include "math/Vector3.hpp"
61		#include "math/SquareMatrix3.hpp"
62		#include "types/MoleculeStamp.hpp"
63	<	#include "UseTheForce/ForceField.hpp"
63	>	#include "brains/ForceField.hpp"
64		#include "utils/PropertyMap.hpp"
65		#include "utils/LocalIndexManager.hpp"
66	+	#include "nonbonded/SwitchingFunction.hpp"
67
68	<	//another nonsense macro declaration
67	<	#define __OPENMD_C
68	<	#include "brains/fSimulation.h"
69	<
68	>	using namespace std;
69		namespace OpenMD{
70	<
72	<	//forward decalration
70	>	//forward declaration
71		class SnapshotManager;
72		class Molecule;
73		class SelectionManager;
74		class StuntDouble;
75	+
76		/**
77	<	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
78	<	* @brief One of the heavy weight classes of OpenMD, SimInfo maintains a list of molecules.
79	<	* The Molecule class maintains all of the concrete objects
80	<	* (atoms, bond, bend, torsions, inversions, rigid bodies, cutoff groups,
81	<	* constraints). In both the single and parallel versions, atoms and
82	<	* rigid bodies have both global and local indices.  The local index is
83	<	* not relevant to molecules or cutoff groups.
84	<	*/
77	>	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
78	>	*
79	>	* @brief One of the heavy-weight classes of OpenMD, SimInfo
80	>	* maintains objects and variables relating to the current
81	>	* simulation.  This includes the master list of Molecules.  The
82	>	* Molecule class maintains all of the concrete objects (Atoms,
83	>	* Bond, Bend, Torsions, Inversions, RigidBodies, CutoffGroups,
84	>	* Constraints). In both the single and parallel versions, Atoms and
85	>	* RigidBodies have both global and local indices.
86	>	*/
87		class SimInfo {
88		public:
89	<	typedef std::map<int, Molecule*>::iterator  MoleculeIterator;
90	<
89	>	typedef map<int, Molecule*>::iterator  MoleculeIterator;
90	>
91		/**
92		* Constructor of SimInfo
93	<	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
94	<	* second element is the total number of molecules with the same molecule stamp in the system
93	>	*
94	>	* @param molStampPairs MoleculeStamp Array. The first element of
95	>	* the pair is molecule stamp, the second element is the total
96	>	* number of molecules with the same molecule stamp in the system
97	>	*
98		* @param ff pointer of a concrete ForceField instance
99	+	*
100		* @param simParams
96	–	* @note
101		*/
102		SimInfo(ForceField* ff, Globals* simParams);
103		virtual ~SimInfo();
104
105		/**
106		* Adds a molecule
107	<	* @return return true if adding successfully, return false if the molecule is already in SimInfo
107	>	*
108	>	* @return return true if adding successfully, return false if the
109	>	* molecule is already in SimInfo
110	>	*
111		* @param mol molecule to be added
112		*/
113		bool addMolecule(Molecule* mol);
114
115		/**
116		* Removes a molecule from SimInfo
117	<	* @return true if removing successfully, return false if molecule is not in this SimInfo
117	>	*
118	>	* @return true if removing successfully, return false if molecule
119	>	* is not in this SimInfo
120		*/
121		bool removeMolecule(Molecule* mol);
122
#	Line 127 | Line 136 | namespace OpenMD{
136		}
137
138		/**
139	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
140	<	* of atoms which do not belong to the rigid bodies) in the system
139	>	* Returns the total number of integrable objects (total number of
140	>	* rigid bodies plus the total number of atoms which do not belong
141	>	* to the rigid bodies) in the system
142		*/
143		int getNGlobalIntegrableObjects() {
144		return nGlobalIntegrableObjects_;
145		}
146
147		/**
148	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
149	<	* of atoms which do not belong to the rigid bodies) in the system
148	>	* Returns the total number of integrable objects (total number of
149	>	* rigid bodies plus the total number of atoms which do not belong
150	>	* to the rigid bodies) in the system
151		*/
152		int getNGlobalRigidBodies() {
153		return nGlobalRigidBodies_;
#	Line 156 | Line 167 | namespace OpenMD{
167		return nAtoms_;
168		}
169
170	+	/** Returns the number of effective cutoff groups on local processor */
171	+	unsigned int getNLocalCutoffGroups();
172	+
173		/** Returns the number of local bonds */
174		unsigned int getNBonds(){
175		return nBonds_;
#	Line 209 | Line 223 | namespace OpenMD{
223		*/
224		Molecule* nextMolecule(MoleculeIterator& i);
225
226	+	/** Returns the total number of fluctuating charges that are present */
227	+	int getNFluctuatingCharges() {
228	+	return nGlobalFluctuatingCharges_;
229	+	}
230	+
231		/** Returns the number of degrees of freedom */
232		int getNdf() {
233		return ndf_ - getFdf();
234		}
235
236	+	/** Returns the number of degrees of freedom (LOCAL) */
237	+	int getNdfLocal() {
238	+	return ndfLocal_;
239	+	}
240	+
241		/** Returns the number of raw degrees of freedom */
242		int getNdfRaw() {
243		return ndfRaw_;
#	Line 231 | Line 255 | namespace OpenMD{
255
256		int getFdf();
257
258	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
258	>	//getNZconstraint and setNZconstraint ruin the coherence of
259	>	//SimInfo class, need refactoring
260
261		/** Returns the total number of z-constraint molecules in the system */
262		int getNZconstraint() {
#	Line 267 | Line 292 | namespace OpenMD{
292
293		/** Returns the center of the mass of the whole system.*/
294		Vector3d getCom();
295	<	/** Returns the center of the mass and Center of Mass velocity of the whole system.*/
295	>	/** Returns the center of the mass and Center of Mass velocity of
296	>	the whole system.*/
297		void getComAll(Vector3d& com,Vector3d& comVel);
298
299	<	/** Returns intertia tensor for the entire system and system Angular Momentum.*/
299	>	/** Returns intertia tensor for the entire system and system
300	>	Angular Momentum.*/
301		void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
302
303		/** Returns system angular momentum */
304		Vector3d getAngularMomentum();
305
306	<	/** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/
306	>	/** Returns volume of system as estimated by an ellipsoid defined
307	>	by the radii of gyration*/
308		void getGyrationalVolume(RealType &vol);
309	<	/** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/
309	>	/** Overloaded version of gyrational volume that also returns
310	>	det(I) so dV/dr can be calculated*/
311		void getGyrationalVolume(RealType &vol, RealType &detI);
312	<	/** main driver function to interact with fortran during the initialization and molecule migration */
312	>
313		void update();
314	+	/**
315	+	* Do final bookkeeping before Force managers need their data.
316	+	*/
317	+	void prepareTopology();
318
319	+
320		/** Returns the local index manager */
321		LocalIndexManager* getLocalIndexManager() {
322		return &localIndexMan_;
#	Line 318 | Line 352 | namespace OpenMD{
352		return globalMolMembership_[id];
353		}
354
355	<	RealType getRcut() {
356	<	return rcut_;
357	<	}
358	<
359	<	RealType getRsw() {
360	<	return rsw_;
327	<	}
355	>	/**
356	>	* returns a vector which maps the local atom index on this
357	>	* processor to the global atom index.  With only one processor,
358	>	* these should be identical.
359	>	*/
360	>	vector<int> getGlobalAtomIndices();
361
362	<	RealType getList() {
363	<	return rlist_;
364	<	}
362	>	/**
363	>	* returns a vector which maps the local cutoff group index on
364	>	* this processor to the global cutoff group index.  With only one
365	>	* processor, these should be identical.
366	>	*/
367	>	vector<int> getGlobalGroupIndices();
368	>
369
370	<	std::string getFinalConfigFileName() {
370	>	string getFinalConfigFileName() {
371		return finalConfigFileName_;
372		}
373
374	<	void setFinalConfigFileName(const std::string& fileName) {
374	>	void setFinalConfigFileName(const string& fileName) {
375		finalConfigFileName_ = fileName;
376		}
377
378	<	std::string getRawMetaData() {
378	>	string getRawMetaData() {
379		return rawMetaData_;
380		}
381	<	void setRawMetaData(const std::string& rawMetaData) {
381	>	void setRawMetaData(const string& rawMetaData) {
382		rawMetaData_ = rawMetaData;
383		}
384
385	<	std::string getDumpFileName() {
385	>	string getDumpFileName() {
386		return dumpFileName_;
387		}
388
389	<	void setDumpFileName(const std::string& fileName) {
389	>	void setDumpFileName(const string& fileName) {
390		dumpFileName_ = fileName;
391		}
392
393	<	std::string getStatFileName() {
393	>	string getStatFileName() {
394		return statFileName_;
395		}
396
397	<	void setStatFileName(const std::string& fileName) {
397	>	void setStatFileName(const string& fileName) {
398		statFileName_ = fileName;
399		}
400
401	<	std::string getRestFileName() {
401	>	string getRestFileName() {
402		return restFileName_;
403		}
404
405	<	void setRestFileName(const std::string& fileName) {
405	>	void setRestFileName(const string& fileName) {
406		restFileName_ = fileName;
407		}
408
#	Line 373 | Line 410 | namespace OpenMD{
410		* Sets GlobalGroupMembership
411		* @see #SimCreator::setGlobalIndex
412		*/
413	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
413	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
414		assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
415		globalGroupMembership_ = globalGroupMembership;
416		}
#	Line 382 | Line 419 | namespace OpenMD{
419		* Sets GlobalMolMembership
420		* @see #SimCreator::setGlobalIndex
421		*/
422	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
422	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
423		assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
424		globalMolMembership_ = globalMolMembership;
425		}
426
427
428	<	bool isFortranInitialized() {
429	<	return fortranInitialized_;
428	>	bool isTopologyDone() {
429	>	return topologyDone_;
430		}
431
432		bool getCalcBoxDipole() {
#	Line 400 | Line 437 | namespace OpenMD{
437		return useAtomicVirial_;
438		}
439
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.
440		/**
441		* Adds property into property map
442		* @param genData GenericData to be added into PropertyMap
#	Line 413 | Line 447 | namespace OpenMD{
447		* Removes property from PropertyMap by name
448		* @param propName the name of property to be removed
449		*/
450	<	void removeProperty(const std::string& propName);
450	>	void removeProperty(const string& propName);
451
452		/**
453		* clear all of the properties
#	Line 424 | Line 458 | namespace OpenMD{
458		* Returns all names of properties
459		* @return all names of properties
460		*/
461	<	std::vector<std::string> getPropertyNames();
461	>	vector<string> getPropertyNames();
462
463		/**
464		* Returns all of the properties in PropertyMap
465		* @return all of the properties in PropertyMap
466		*/
467	<	std::vector<GenericData*> getProperties();
467	>	vector<GenericData*> getProperties();
468
469		/**
470		* Returns property
#	Line 438 | Line 472 | namespace OpenMD{
472		* @return a pointer point to property with propName. If no property named propName
473		* exists, return NULL
474		*/
475	<	GenericData* getPropertyByName(const std::string& propName);
475	>	GenericData* getPropertyByName(const string& propName);
476
477		/**
478		* add all special interaction pairs (including excluded
#	Line 452 | Line 486 | namespace OpenMD{
486		*/
487		void removeInteractionPairs(Molecule* mol);
488
489	<
490	<	/** Returns the unique atom types of local processor in an array */
457	<	std::set<AtomType*> getUniqueAtomTypes();
489	>	/** Returns the set of atom types present in this simulation */
490	>	set<AtomType*> getSimulatedAtomTypes();
491
492	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
492	>	friend ostream& operator <<(ostream& o, SimInfo& info);
493
494		void getCutoff(RealType& rcut, RealType& rsw);
495
496		private:
497
498	<	/** fill up the simtype struct*/
499	<	void setupSimType();
498	>	/** fill up the simtype struct and other simulation-related variables */
499	>	void setupSimVariables();
500
468	–	/**
469	–	* Setup Fortran Simulation
470	–	* @see #setupFortranParallel
471	–	*/
472	–	void setupFortranSim();
501
474	–	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
475	–	void setupCutoff();
476	–
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	–
502		/** Determine if we need to accumulate the simulation box dipole */
503		void setupAccumulateBoxDipole();
504
#	Line 488 | Line 507 | namespace OpenMD{
507		void calcNdfRaw();
508		void calcNdfTrans();
509
491	–	ForceField* forceField_;
492	–	Globals* simParams_;
493	–
494	–	std::map<int, Molecule*>  molecules_; /**< Molecule array */
495	–
510		/**
511	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
512	<	* system.
511	>	* Adds molecule stamp and the total number of the molecule with
512	>	* same molecule stamp in the whole system.
513		*/
514		void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
515	<
516	<	//degress of freedom
517	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
518	<	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_;
515	>
516	>	// Other classes holdingn important information
517	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
518	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
519
520	<	/**
524	<	* the size of globalMolMembership_  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
520	>	///  Counts of local objects
521		int nAtoms_;              /**< number of atoms in local processor */
522		int nBonds_;              /**< number of bonds in local processor */
523		int nBends_;              /**< number of bends in local processor */
#	Line 541 | Line 527 | namespace OpenMD{
527		int nIntegrableObjects_;  /**< number of integrable objects in local processor */
528		int nCutoffGroups_;       /**< number of cutoff groups in local processor */
529		int nConstraints_;        /**< number of constraints in local processors */
530	+	int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */
531	+
532	+	/// Counts of global objects
533	+	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
534	+	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
535	+	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
536	+	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
537	+	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
538	+	int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
539	+
540	+
541	+	/// Degress of freedom
542	+	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
543	+	int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
544	+	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
545	+	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
546	+	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
547	+	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
548	+	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
549
550	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
551	<	PairList excludedInteractions_;
552	<	PairList oneTwoInteractions_;
553	<	PairList oneThreeInteractions_;
554	<	PairList oneFourInteractions_;
555	<	PropertyMap properties_;                  /**< Generic Property */
556	<	SnapshotManager* sman_;               /**< SnapshotManager */
550	>	/// logicals
551	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
552	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
553	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
554	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
555	>	bool usesFluctuatingCharges_; /**< are there fluctuating charges? */
556	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
557	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
558	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
559	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
560
561	+	public:
562	+	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
563	+	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
564	+	bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
565	+	bool usesAtomicVirial() { return usesAtomicVirial_; }
566	+	bool requiresPrepair() { return requiresPrepair_; }
567	+	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
568	+	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
569	+
570	+	private:
571	+	/// Data structures holding primary simulation objects
572	+	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
573	+
574	+	/// Stamps are templates for objects that are then used to create
575	+	/// groups of objects.  For example, a molecule stamp contains
576	+	/// information on how to build that molecule (i.e. the topology,
577	+	/// the atoms, the bonds, etc.)  Once the system is built, the
578	+	/// stamps are no longer useful.
579	+	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
580	+	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
581	+
582	+	/**
583	+	* A vector that maps between the global index of an atom, and the
584	+	* global index of cutoff group the atom belong to.  It is filled
585	+	* by SimCreator once and only once, since it never changed during
586	+	* the simulation.  It should be nGlobalAtoms_ in size.
587	+	*/
588	+	vector<int> globalGroupMembership_;
589	+	public:
590	+	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
591	+	private:
592	+
593	+	/**
594	+	* A vector that maps between the global index of an atom and the
595	+	* global index of the molecule the atom belongs to.  It is filled
596	+	* by SimCreator once and only once, since it is never changed
597	+	* during the simulation. It shoudl be nGlobalAtoms_ in size.
598	+	*/
599	+	vector<int> globalMolMembership_;
600	+
601		/**
602	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
603	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
604	<	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
605	<	* to make a efficient data moving plan.
602	>	* A vector that maps between the local index of an atom and the
603	>	* index of the AtomType.
604	>	*/
605	>	vector<int> identArray_;
606	>	public:
607	>	vector<int> getIdentArray() { return identArray_; }
608	>	private:
609	>
610	>	/**
611	>	* A vector which contains the fractional contribution of an
612	>	* atom's mass to the total mass of the cutoffGroup that atom
613	>	* belongs to.  In the case of single atom cutoff groups, the mass
614	>	* factor for that atom is 1.  For massless atoms, the factor is
615	>	* also 1.
616	>	*/
617	>	vector<RealType> massFactors_;
618	>	public:
619	>	vector<RealType> getMassFactors() { return massFactors_; }
620	>
621	>	PairList* getExcludedInteractions() { return &excludedInteractions_; }
622	>	PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
623	>	PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
624	>	PairList* getOneFourInteractions() { return &oneFourInteractions_; }
625	>
626	>	private:
627	>
628	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
629	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
630	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
631	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
632	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
633	>
634	>	PropertyMap properties_;       /**< Generic Properties can be added */
635	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
636	>
637	>	/**
638	>	* The reason to have a local index manager is that when molecule
639	>	* is migrating to other processors, the atoms and the
640	>	* rigid-bodies will release their local indices to
641	>	* LocalIndexManager. Combining the information of molecule
642	>	* migrating to current processor, Migrator class can query the
643	>	* LocalIndexManager to make a efficient data moving plan.
644		*/
645		LocalIndexManager localIndexMan_;
646
647		// unparsed MetaData block for storing in Dump and EOR files:
648	<	std::string rawMetaData_;
648	>	string rawMetaData_;
649
650	<	//file names
651	<	std::string finalConfigFileName_;
652	<	std::string dumpFileName_;
653	<	std::string statFileName_;
654	<	std::string restFileName_;
650	>	// file names
651	>	string finalConfigFileName_;
652	>	string dumpFileName_;
653	>	string statFileName_;
654	>	string restFileName_;
655
570	–	RealType rcut_;       /**< cutoff radius*/
571	–	RealType rsw_;        /**< radius of switching function*/
572	–	RealType rlist_;      /**< neighbor list radius */
656
657	<	int ljsp_; /**< use shifted potential for LJ*/
658	<	int ljsf_; /**< use shifted force for LJ*/
659	<
577	<	bool fortranInitialized_; /**< flag indicate whether fortran side
578	<	is initialized */
657	>	bool topologyDone_;  /** flag to indicate whether the topology has
658	>	been scanned and all the relevant
659	>	bookkeeping has been done*/
660
661		bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
662		the simulation box dipole moment */
663
664		bool useAtomicVirial_; /**< flag to indicate whether or not we use
665		Atomic Virials to calculate the pressure */
666	<
667	<	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);
666	>
667	>	public:
668		/**
669	<	* return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
670	<	* global index does not belong to local processor, a NULL will be return.
671	<	*/
672	<	//StuntDouble* getStuntDoubleFromGlobalIndex(int index);
673	<	//private:
674	<	//std::vector<StuntDouble*> sdByGlobalIndex_;
669	>	* return an integral objects by its global index. In MPI
670	>	* version, if the StuntDouble with specified global index does
671	>	* not belong to local processor, a NULL will be return.
672	>	*/
673	>	StuntDouble* getIOIndexToIntegrableObject(int index);
674	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
675
676	<	//in Parallel version, we need MolToProc
676	>	private:
677	>	vector<StuntDouble*> IOIndexToIntegrableObject;
678	>
679		public:
680
681		/**
#	Line 614 | Line 687 | namespace OpenMD{
687		//assert(globalIndex < molToProcMap_.size());
688		return molToProcMap_[globalIndex];
689		}
690	<
690	>
691		/**
692		* Set MolToProcMap array
693		* @see #SimCreator::divideMolecules
694		*/
695	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
695	>	void setMolToProcMap(const vector<int>& molToProcMap) {
696		molToProcMap_ = molToProcMap;
697		}
698
699		private:
627	–
628	–	void setupFortranParallel();
700
701		/**
702		* The size of molToProcMap_ is equal to total number of molecules
703		* in the system.  It maps a molecule to the processor on which it
704		* resides. it is filled by SimCreator once and only once.
705		*/
706	<	std::vector<int> molToProcMap_;
706	>	vector<int> molToProcMap_;
707
637	–
708		};
709
710		} //namespace OpenMD

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/brains/SimInfo.hpp (property svn:keywords), Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC

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