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

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trunk/src/brains/SimInfo.hpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1528 by gezelter, Fri Dec 17 20:11:05 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 54 | Line 54
54		#include <utility>
55		#include <vector>
56
57	<	#include "brains/Exclude.hpp"
57	>	#include "brains/PairList.hpp"
58		#include "io/Globals.hpp"
59		#include "math/Vector3.hpp"
60		#include "math/SquareMatrix3.hpp"
#	Line 64 | Line 64
64		#include "utils/LocalIndexManager.hpp"
65
66		//another nonsense macro declaration
67	<	#define __C
67	>	#define __OPENMD_C
68		#include "brains/fSimulation.h"
69
70	<	namespace oopse{
70	>	using namespace std;
71	>	namespace OpenMD{
72
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, rigid bodies, cutoff groups, constrains).
91	<	* 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.
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
95	–	* @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 126 | 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 170 | Line 192 | namespace oopse{
192		return nTorsions_;
193		}
194
195	+	/** Returns the number of local torsions */
196	+	unsigned int getNInversions() {
197	+	return nInversions_;
198	+	}
199		/** Returns the number of local rigid bodies */
200		unsigned int getNRigidBodies() {
201		return nRigidBodies_;
#	Line 226 | 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 262 | 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	<	/** main driver function to interact with fortran during the initialization and molecule migration */
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
310	>	initialization and molecule migration */
311		void update();
312
313		/** Returns the local index manager */
#	Line 305 | Line 341 | namespace oopse{
341		return i != molecules_.end() ? i->second : NULL;
342		}
343
344	<	RealType getRcut() {
345	<	return rcut_;
344	>	int getGlobalMolMembership(int id){
345	>	return globalMolMembership_[id];
346		}
347
348	<	RealType getRsw() {
349	<	return rsw_;
348	>	RealType getCutoffRadius() {
349	>	return cutoffRadius_;
350		}
351
352	<	RealType getList() {
353	<	return rlist_;
352	>	RealType getSwitchingRadius() {
353	>	return switchingRadius_;
354		}
355	+
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) {
363	>
364	>	void setFinalConfigFileName(const string& fileName) {
365		finalConfigFileName_ = fileName;
366		}
367
368	<	std::string getDumpFileName() {
368	>	string getRawMetaData() {
369	>	return rawMetaData_;
370	>	}
371	>	void setRawMetaData(const string& rawMetaData) {
372	>	rawMetaData_ = rawMetaData;
373	>	}
374	>
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 353 | Line 400 | namespace oopse{
400		* Sets GlobalGroupMembership
401		* @see #SimCreator::setGlobalIndex
402		*/
403	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
404	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
403	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
404	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
405		globalGroupMembership_ = globalGroupMembership;
406		}
407
#	Line 362 | Line 409 | namespace oopse{
409		* Sets GlobalMolMembership
410		* @see #SimCreator::setGlobalIndex
411		*/
412	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
413	<	assert(globalMolMembership.size() == nGlobalAtoms_);
412	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
413	>	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
414		globalMolMembership_ = globalMolMembership;
415		}
416
#	Line 372 | Line 419 | namespace oopse{
419		return fortranInitialized_;
420		}
421
422	<	//below functions are just forward functions
423	<	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
424	<	//the other hand, has-a relation need composing.
422	>	bool getCalcBoxDipole() {
423	>	return calcBoxDipole_;
424	>	}
425	>
426	>	bool getUseAtomicVirial() {
427	>	return useAtomicVirial_;
428	>	}
429	>
430		/**
431		* Adds property into property map
432		* @param genData GenericData to be added into PropertyMap
#	Line 385 | 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 396 | 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 410 | 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 exclude pairs of a molecule into exclude list.
468	>	* add all special interaction pairs (including excluded
469	>	* interactions) in a molecule into the appropriate lists.
470		*/
471	<	void addExcludePairs(Molecule* mol);
471	>	void addInteractionPairs(Molecule* mol);
472
473		/**
474	<	* remove all exclude pairs which belong to a molecule from exclude list
474	>	* remove all special interaction pairs which belong to a molecule
475	>	* from the appropriate lists.
476		*/
477	+	void removeInteractionPairs(Molecule* mol);
478
424	–	void removeExcludePairs(Molecule* mol);
479
426	–
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
#	Line 442 | 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();
503	<
504	<	/** Figure out which coulombic correction method to use and pass to fortran */
505	<	void setupElectrostaticSummationMethod( int isError );
506	<
501	>	/** Figure out the cutoff radius */
502	>	void setupCutoffRadius();
503	>	/** Figure out the cutoff method */
504	>	void setupCutoffMethod();
505	>	/** Figure out the switching radius */
506	>	void setupSwitchingRadius();
507	>	/** Figure out the neighbor list skin thickness */
508	>	void setupSkinThickness();
509		/** Figure out which polynomial type to use for the switching function */
510		void setupSwitchingFunction();
511
512	+	/** Determine if we need to accumulate the simulation box dipole */
513	+	void setupAccumulateBoxDipole();
514	+
515		/** Calculates the number of degress of freedom in the whole system */
516		void calcNdf();
517		void calcNdfRaw();
518		void calcNdfTrans();
519
459	–	ForceField* forceField_;
460	–	Globals* simParams_;
461	–
462	–	std::map<int, Molecule*>  molecules_; /**< Molecule array */
463	–
520		/**
521	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
522	<	* system.
521	>	* Adds molecule stamp and the total number of the molecule with
522	>	* same molecule stamp in the whole system.
523		*/
524		void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
525	+
526	+	// Other classes holdingn important information
527	+	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
528	+	Globals* simParams_;     /**< provides access to simulation parameters set by user */
529	+
530	+	///  Counts of local objects
531	+	int nAtoms_;              /**< number of atoms in local processor */
532	+	int nBonds_;              /**< number of bonds in local processor */
533	+	int nBends_;              /**< number of bends in local processor */
534	+	int nTorsions_;           /**< number of torsions in local processor */
535	+	int nInversions_;         /**< number of inversions in local processor */
536	+	int nRigidBodies_;        /**< number of rigid bodies in local processor */
537	+	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
538	+	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
539	+	int nConstraints_;        /**< number of constraints in local processors */
540
541	<	//degress of freedom
542	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
543	<	int fdf_local;       /**< number of frozen degrees of freedom */
544	<	int fdf_;            /**< number of frozen degrees of freedom */
474	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
475	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
476	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
477	<
478	<	//number of global objects
479	<	int nGlobalMols_;       /**< number of molecules in the system */
480	<	int nGlobalAtoms_;   /**< number of atoms in the system */
481	<	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
541	>	/// Counts of global objects
542	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
543	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
544	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
545		int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
546	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
546	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
547	>
548	>	/// Degress of freedom
549	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
550	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
551	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
552	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
553	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
554	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
555	>
556	>	/// logicals
557	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
558	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
559	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
560	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
561	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
562	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
563	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
564	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
565	>
566	>	/// Data structures holding primary simulation objects
567	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
568	>	simtype fInfo_;                   /**< A dual struct shared by C++
569	>	and Fortran to pass
570	>	information about what types
571	>	of calculation are
572	>	required */
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	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
584	<	* corresponding content is the global index of cutoff group this atom belong to.
585	<	* It is filled by SimCreator once and only once, since it never changed during the simulation.
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	<	std::vector<int> globalGroupMembership_;
588	>	vector<int> globalGroupMembership_;
589
590		/**
591	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
592	<	* corresponding content is the global index of molecule this atom belong to.
593	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
591	>	* A vector that maps between the global index of an atom and the
592	>	* global index of the molecule the atom belongs to.  It is filled
593	>	* by SimCreator once and only once, since it is never changed
594	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
595		*/
596	<	std::vector<int> globalMolMembership_;
596	>	vector<int> globalMolMembership_;
597	>
598	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
599	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
600	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
601	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
602	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
603
604	<
605	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
500	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
501	<
502	<	//number of local objects
503	<	int nAtoms_;                        /**< number of atoms in local processor */
504	<	int nBonds_;                        /**< number of bonds in local processor */
505	<	int nBends_;                        /**< number of bends in local processor */
506	<	int nTorsions_;                    /**< number of torsions in local processor */
507	<	int nRigidBodies_;              /**< number of rigid bodies in local processor */
508	<	int nIntegrableObjects_;    /**< number of integrable objects in local processor */
509	<	int nCutoffGroups_;             /**< number of cutoff groups in local processor */
510	<	int nConstraints_;              /**< number of constraints in local processors */
604	>	PropertyMap properties_;       /**< Generic Properties can be added */
605	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
606
512	–	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
513	–	Exclude exclude_;
514	–	PropertyMap properties_;                  /**< Generic Property */
515	–	SnapshotManager* sman_;               /**< SnapshotManager */
516	–
607		/**
608	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
609	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
610	<	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
611	<	* to make a efficient data moving plan.
608	>	* The reason to have a local index manager is that when molecule
609	>	* is migrating to other processors, the atoms and the
610	>	* rigid-bodies will release their local indices to
611	>	* LocalIndexManager. Combining the information of molecule
612	>	* migrating to current processor, Migrator class can query the
613	>	* LocalIndexManager to make a efficient data moving plan.
614		*/
615		LocalIndexManager localIndexMan_;
616
617	<	//file names
618	<	std::string finalConfigFileName_;
619	<	std::string dumpFileName_;
620	<	std::string statFileName_;
621	<	std::string restFileName_;
617	>	// unparsed MetaData block for storing in Dump and EOR files:
618	>	string rawMetaData_;
619	>
620	>	// file names
621	>	string finalConfigFileName_;
622	>	string dumpFileName_;
623	>	string statFileName_;
624	>	string restFileName_;
625
626	<	RealType rcut_;       /**< cutoff radius*/
627	<	RealType rsw_;        /**< radius of switching function*/
628	<	RealType rlist_;      /**< neighbor list radius */
626	>	RealType cutoffRadius_;         /**< cutoff radius for non-bonded interactions */
627	>	RealType switchingRadius_;      /**< inner radius of switching function */
628	>	RealType listRadius_;           /**< Verlet neighbor list radius */
629	>	RealType skinThickness_;        /**< Verlet neighbor list skin thickness */
630	>	CutoffMethod cutoffMethod_;     /**< Cutoff Method for most non-bonded interactions */
631
632	<	bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
633	<
634	<	#ifdef IS_MPI
635	<	//in Parallel version, we need MolToProc
632	>	bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
633	>
634	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
635	>	the simulation box dipole moment */
636	>
637	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
638	>	Atomic Virials to calculate the pressure */
639	>
640		public:
641	+	/**
642	+	* return an integral objects by its global index. In MPI
643	+	* version, if the StuntDouble with specified global index does
644	+	* not belong to local processor, a NULL will be return.
645	+	*/
646	+	StuntDouble* getIOIndexToIntegrableObject(int index);
647	+	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
648	+
649	+	private:
650	+	vector<StuntDouble*> IOIndexToIntegrableObject;
651	+
652	+	public:
653
654		/**
655		* Finds the processor where a molecule resides
#	Line 547 | Line 660 | namespace oopse{
660		//assert(globalIndex < molToProcMap_.size());
661		return molToProcMap_[globalIndex];
662		}
663	<
663	>
664		/**
665		* Set MolToProcMap array
666		* @see #SimCreator::divideMolecules
667		*/
668	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
668	>	void setMolToProcMap(const vector<int>& molToProcMap) {
669		molToProcMap_ = molToProcMap;
670		}
671
#	Line 561 | Line 674 | namespace oopse{
674		void setupFortranParallel();
675
676		/**
677	<	* The size of molToProcMap_ is equal to total number of molecules in the system.
678	<	*  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
679	<	* once.
677	>	* The size of molToProcMap_ is equal to total number of molecules
678	>	* in the system.  It maps a molecule to the processor on which it
679	>	* resides. it is filled by SimCreator once and only once.
680		*/
681	<	std::vector<int> molToProcMap_;
681	>	vector<int> molToProcMap_;
682
570	–	#endif
571	–
683		};
684
685	<	} //namespace oopse
685	>	} //namespace OpenMD
686		#endif //BRAINS_SIMMODEL_HPP
687

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/SimInfo.hpp (property svn:keywords), Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC

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