ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing:
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 1549 by gezelter, Wed Apr 27 18:38:15 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 __OOPSE_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 318 | Line 342 | namespace oopse{
342		return globalMolMembership_[id];
343		}
344
345	<	RealType getRcut() {
346	<	return rcut_;
347	<	}
345	>	/**
346	>	* returns a vector which maps the local atom index on this
347	>	* processor to the global atom index.  With only one processor,
348	>	* these should be identical.
349	>	*/
350	>	vector<int> getGlobalAtomIndices();
351
352	<	RealType getRsw() {
353	<	return rsw_;
354	<	}
355	<
356	<	RealType getList() {
357	<	return rlist_;
331	<	}
352	>	/**
353	>	* returns a vector which maps the local cutoff group index on
354	>	* this processor to the global cutoff group index.  With only one
355	>	* processor, these should be identical.
356	>	*/
357	>	vector<int> getGlobalGroupIndices();
358
359	<	std::string getFinalConfigFileName() {
359	>	string getFinalConfigFileName() {
360		return finalConfigFileName_;
361		}
362
363	<	void setFinalConfigFileName(const std::string& fileName) {
363	>	void setFinalConfigFileName(const string& fileName) {
364		finalConfigFileName_ = fileName;
365		}
366
367	<	std::string getRawMetaData() {
367	>	string getRawMetaData() {
368		return rawMetaData_;
369		}
370	<	void setRawMetaData(const std::string& rawMetaData) {
370	>	void setRawMetaData(const string& rawMetaData) {
371		rawMetaData_ = rawMetaData;
372		}
373
374	<	std::string getDumpFileName() {
374	>	string getDumpFileName() {
375		return dumpFileName_;
376		}
377
378	<	void setDumpFileName(const std::string& fileName) {
378	>	void setDumpFileName(const string& fileName) {
379		dumpFileName_ = fileName;
380		}
381
382	<	std::string getStatFileName() {
382	>	string getStatFileName() {
383		return statFileName_;
384		}
385
386	<	void setStatFileName(const std::string& fileName) {
386	>	void setStatFileName(const string& fileName) {
387		statFileName_ = fileName;
388		}
389
390	<	std::string getRestFileName() {
390	>	string getRestFileName() {
391		return restFileName_;
392		}
393
394	<	void setRestFileName(const std::string& fileName) {
394	>	void setRestFileName(const string& fileName) {
395		restFileName_ = fileName;
396		}
397
#	Line 373 | Line 399 | namespace oopse{
399		* Sets GlobalGroupMembership
400		* @see #SimCreator::setGlobalIndex
401		*/
402	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
402	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
403		assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
404		globalGroupMembership_ = globalGroupMembership;
405		}
#	Line 382 | Line 408 | namespace oopse{
408		* Sets GlobalMolMembership
409		* @see #SimCreator::setGlobalIndex
410		*/
411	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
411	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
412		assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
413		globalMolMembership_ = globalMolMembership;
414		}
#	Line 400 | Line 426 | namespace oopse{
426		return useAtomicVirial_;
427		}
428
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.
429		/**
430		* Adds property into property map
431		* @param genData GenericData to be added into PropertyMap
#	Line 413 | Line 436 | namespace oopse{
436		* Removes property from PropertyMap by name
437		* @param propName the name of property to be removed
438		*/
439	<	void removeProperty(const std::string& propName);
439	>	void removeProperty(const string& propName);
440
441		/**
442		* clear all of the properties
#	Line 424 | Line 447 | namespace oopse{
447		* Returns all names of properties
448		* @return all names of properties
449		*/
450	<	std::vector<std::string> getPropertyNames();
450	>	vector<string> getPropertyNames();
451
452		/**
453		* Returns all of the properties in PropertyMap
454		* @return all of the properties in PropertyMap
455		*/
456	<	std::vector<GenericData*> getProperties();
456	>	vector<GenericData*> getProperties();
457
458		/**
459		* Returns property
#	Line 438 | Line 461 | namespace oopse{
461		* @return a pointer point to property with propName. If no property named propName
462		* exists, return NULL
463		*/
464	<	GenericData* getPropertyByName(const std::string& propName);
464	>	GenericData* getPropertyByName(const string& propName);
465
466		/**
467		* add all special interaction pairs (including excluded
#	Line 452 | Line 475 | namespace oopse{
475		*/
476		void removeInteractionPairs(Molecule* mol);
477
478	<
479	<	/** Returns the unique atom types of local processor in an array */
457	<	std::set<AtomType*> getUniqueAtomTypes();
478	>	/** Returns the set of atom types present in this simulation */
479	>	set<AtomType*> getSimulatedAtomTypes();
480
481	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
481	>	friend ostream& operator <<(ostream& o, SimInfo& info);
482
483		void getCutoff(RealType& rcut, RealType& rsw);
484
485		private:
486
487	<	/** fill up the simtype struct*/
488	<	void setupSimType();
487	>	/** fill up the simtype struct and other simulation-related variables */
488	>	void setupSimVariables();
489
468	–	/**
469	–	* Setup Fortran Simulation
470	–	* @see #setupFortranParallel
471	–	*/
472	–	void setupFortranSim();
490
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	–
491		/** Determine if we need to accumulate the simulation box dipole */
492		void setupAccumulateBoxDipole();
493
#	Line 488 | Line 496 | namespace oopse{
496		void calcNdfRaw();
497		void calcNdfTrans();
498
491	–	ForceField* forceField_;
492	–	Globals* simParams_;
493	–
494	–	std::map<int, Molecule*>  molecules_; /**< Molecule array */
495	–
499		/**
500	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
501	<	* system.
500	>	* Adds molecule stamp and the total number of the molecule with
501	>	* same molecule stamp in the whole system.
502		*/
503		void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
501	–
502	–	//degress of freedom
503	–	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
504	–	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_;
504
505	<	/**
506	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
507	<	* 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_;
505	>	// Other classes holdingn important information
506	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
507	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
508
509	<
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
509	>	///  Counts of local objects
510		int nAtoms_;              /**< number of atoms in local processor */
511		int nBonds_;              /**< number of bonds in local processor */
512		int nBends_;              /**< number of bends in local processor */
#	Line 541 | Line 516 | namespace oopse{
516		int nIntegrableObjects_;  /**< number of integrable objects in local processor */
517		int nCutoffGroups_;       /**< number of cutoff groups in local processor */
518		int nConstraints_;        /**< number of constraints in local processors */
519	+
520	+	/// Counts of global objects
521	+	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
522	+	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
523	+	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
524	+	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
525	+	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
526	+
527	+	/// Degress of freedom
528	+	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
529	+	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
530	+	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
531	+	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
532	+	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
533	+	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
534
535	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
536	<	PairList excludedInteractions_;
537	<	PairList oneTwoInteractions_;
538	<	PairList oneThreeInteractions_;
539	<	PairList oneFourInteractions_;
540	<	PropertyMap properties_;                  /**< Generic Property */
541	<	SnapshotManager* sman_;               /**< SnapshotManager */
535	>	/// logicals
536	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
537	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
538	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
539	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
540	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
541	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
542	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
543	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
544
545	+	public:
546	+	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
547	+	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
548	+	bool usesMetallicAtoms() { return usesMetallicAtoms_; }
549	+	bool usesAtomicVirial() { return usesAtomicVirial_; }
550	+	bool requiresPrepair() { return requiresPrepair_; }
551	+	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
552	+	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
553	+
554	+	private:
555	+	/// Data structures holding primary simulation objects
556	+	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
557	+	simtype fInfo_;                   /**< A dual struct shared by C++
558	+	and Fortran to pass
559	+	information about what types
560	+	of calculation are
561	+	required */
562	+
563	+	/// Stamps are templates for objects that are then used to create
564	+	/// groups of objects.  For example, a molecule stamp contains
565	+	/// information on how to build that molecule (i.e. the topology,
566	+	/// the atoms, the bonds, etc.)  Once the system is built, the
567	+	/// stamps are no longer useful.
568	+	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
569	+	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
570	+
571	+	/**
572	+	* A vector that maps between the global index of an atom, and the
573	+	* global index of cutoff group the atom belong to.  It is filled
574	+	* by SimCreator once and only once, since it never changed during
575	+	* the simulation.  It should be nGlobalAtoms_ in size.
576	+	*/
577	+	vector<int> globalGroupMembership_;
578	+	public:
579	+	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
580	+	private:
581	+
582	+	/**
583	+	* A vector that maps between the global index of an atom and the
584	+	* global index of the molecule the atom belongs to.  It is filled
585	+	* by SimCreator once and only once, since it is never changed
586	+	* during the simulation. It shoudl be nGlobalAtoms_ in size.
587	+	*/
588	+	vector<int> globalMolMembership_;
589	+
590		/**
591	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
592	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
593	<	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
594	<	* to make a efficient data moving plan.
591	>	* A vector that maps between the local index of an atom and the
592	>	* index of the AtomType.
593	>	*/
594	>	vector<int> identArray_;
595	>	public:
596	>	vector<int> getIdentArray() { return identArray_; }
597	>	private:
598	>
599	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
600	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
601	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
602	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
603	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
604	>
605	>	PropertyMap properties_;       /**< Generic Properties can be added */
606	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
607	>
608	>	/**
609	>	* The reason to have a local index manager is that when molecule
610	>	* is migrating to other processors, the atoms and the
611	>	* rigid-bodies will release their local indices to
612	>	* LocalIndexManager. Combining the information of molecule
613	>	* migrating to current processor, Migrator class can query the
614	>	* LocalIndexManager to make a efficient data moving plan.
615		*/
616		LocalIndexManager localIndexMan_;
617
618		// unparsed MetaData block for storing in Dump and EOR files:
619	<	std::string rawMetaData_;
619	>	string rawMetaData_;
620
621	<	//file names
622	<	std::string finalConfigFileName_;
623	<	std::string dumpFileName_;
624	<	std::string statFileName_;
625	<	std::string restFileName_;
621	>	// file names
622	>	string finalConfigFileName_;
623	>	string dumpFileName_;
624	>	string statFileName_;
625	>	string restFileName_;
626
570	–	RealType rcut_;       /**< cutoff radius*/
571	–	RealType rsw_;        /**< radius of switching function*/
572	–	RealType rlist_;      /**< neighbor list radius */
627
628	<	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 */
628	>	bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
629
630		bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
631		the simulation box dipole moment */
632
633		bool useAtomicVirial_; /**< flag to indicate whether or not we use
634		Atomic Virials to calculate the pressure */
635	<
636	<	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);
635	>
636	>	public:
637		/**
638	<	* return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
639	<	* global index does not belong to local processor, a NULL will be return.
640	<	*/
641	<	//StuntDouble* getStuntDoubleFromGlobalIndex(int index);
642	<	//private:
643	<	//std::vector<StuntDouble*> sdByGlobalIndex_;
638	>	* return an integral objects by its global index. In MPI
639	>	* version, if the StuntDouble with specified global index does
640	>	* not belong to local processor, a NULL will be return.
641	>	*/
642	>	StuntDouble* getIOIndexToIntegrableObject(int index);
643	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
644
645	<	//in Parallel version, we need MolToProc
645	>	private:
646	>	vector<StuntDouble*> IOIndexToIntegrableObject;
647	>
648		public:
649
650		/**
#	Line 614 | Line 656 | namespace oopse{
656		//assert(globalIndex < molToProcMap_.size());
657		return molToProcMap_[globalIndex];
658		}
659	<
659	>
660		/**
661		* Set MolToProcMap array
662		* @see #SimCreator::divideMolecules
663		*/
664	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
664	>	void setMolToProcMap(const vector<int>& molToProcMap) {
665		molToProcMap_ = molToProcMap;
666		}
667
668		private:
627	–
628	–	void setupFortranParallel();
669
670		/**
671		* The size of molToProcMap_ is equal to total number of molecules
672		* in the system.  It maps a molecule to the processor on which it
673		* resides. it is filled by SimCreator once and only once.
674		*/
675	<	std::vector<int> molToProcMap_;
675	>	vector<int> molToProcMap_;
676
637	–
677		};
678
679	<	} //namespace oopse
679	>	} //namespace OpenMD
680		#endif //BRAINS_SIMMODEL_HPP
681

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 1549 by gezelter, Wed Apr 27 18:38:15 2011 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines