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

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trunk/src/brains/SimInfo.hpp (file contents), Revision 604 by chrisfen, Fri Sep 16 19:00:12 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1553 by gezelter, Fri Apr 29 17:25:12 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 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 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
69	<	#include "brains/fSimulation.h"
69	<
70	<	namespace oopse{
71	<
72	<	//forward decalration
67	>	using namespace std;
68	>	namespace OpenMD{
69	>	//forward declaration
70		class SnapshotManager;
71		class Molecule;
72		class SelectionManager;
73	+	class StuntDouble;
74	+
75		/**
76	<	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
77	<	* @brief As one of the heavy weight class of OOPSE, SimInfo
78	<	* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
79	<	* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
80	<	* cutoff groups, constrains).
81	<	* Another major change is the index. No matter single version or parallel version,  atoms and
82	<	* rigid bodies have both global index and local index. Local index is not important to molecule as well as
83	<	* cutoff group.
76	>	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
77	>	*
78	>	* @brief One of the heavy-weight classes of OpenMD, SimInfo
79	>	* maintains objects and variables relating to the current
80	>	* simulation.  This includes the master list of Molecules.  The
81	>	* Molecule class maintains all of the concrete objects (Atoms,
82	>	* Bond, Bend, Torsions, Inversions, RigidBodies, CutoffGroups,
83	>	* Constraints). In both the single and parallel versions, Atoms and
84	>	* RigidBodies have both global and local indices.
85		*/
86		class SimInfo {
87		public:
88	<	typedef std::map<int, Molecule*>::iterator  MoleculeIterator;
89	<
88	>	typedef map<int, Molecule*>::iterator  MoleculeIterator;
89	>
90		/**
91		* Constructor of SimInfo
92	<	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
93	<	* second element is the total number of molecules with the same molecule stamp in the system
92	>	*
93	>	* @param molStampPairs MoleculeStamp Array. The first element of
94	>	* the pair is molecule stamp, the second element is the total
95	>	* number of molecules with the same molecule stamp in the system
96	>	*
97		* @param ff pointer of a concrete ForceField instance
98	+	*
99		* @param simParams
96	–	* @note
100		*/
101	<	SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams);
101	>	SimInfo(ForceField* ff, Globals* simParams);
102		virtual ~SimInfo();
103
104		/**
105		* Adds a molecule
106	<	* @return return true if adding successfully, return false if the molecule is already in SimInfo
106	>	*
107	>	* @return return true if adding successfully, return false if the
108	>	* molecule is already in SimInfo
109	>	*
110		* @param mol molecule to be added
111		*/
112		bool addMolecule(Molecule* mol);
113
114		/**
115		* Removes a molecule from SimInfo
116	<	* @return true if removing successfully, return false if molecule is not in this SimInfo
116	>	*
117	>	* @return true if removing successfully, return false if molecule
118	>	* is not in this SimInfo
119		*/
120		bool removeMolecule(Molecule* mol);
121
#	Line 127 | Line 135 | namespace oopse{
135		}
136
137		/**
138	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
139	<	* of atoms which do not belong to the rigid bodies) in the system
138	>	* Returns the total number of integrable objects (total number of
139	>	* rigid bodies plus the total number of atoms which do not belong
140	>	* to the rigid bodies) in the system
141		*/
142		int getNGlobalIntegrableObjects() {
143		return nGlobalIntegrableObjects_;
144		}
145
146		/**
147	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
148	<	* of atoms which do not belong to the rigid bodies) in the system
147	>	* Returns the total number of integrable objects (total number of
148	>	* rigid bodies plus the total number of atoms which do not belong
149	>	* to the rigid bodies) in the system
150		*/
151		int getNGlobalRigidBodies() {
152		return nGlobalRigidBodies_;
#	Line 171 | Line 181 | namespace oopse{
181		return nTorsions_;
182		}
183
184	+	/** Returns the number of local torsions */
185	+	unsigned int getNInversions() {
186	+	return nInversions_;
187	+	}
188		/** Returns the number of local rigid bodies */
189		unsigned int getNRigidBodies() {
190		return nRigidBodies_;
#	Line 207 | Line 221 | namespace oopse{
221
222		/** Returns the number of degrees of freedom */
223		int getNdf() {
224	<	return ndf_;
224	>	return ndf_ - getFdf();
225		}
226
227		/** Returns the number of raw degrees of freedom */
#	Line 220 | Line 234 | namespace oopse{
234		return ndfTrans_;
235		}
236
237	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
237	>	/** sets the current number of frozen degrees of freedom */
238	>	void setFdf(int fdf) {
239	>	fdf_local = fdf;
240	>	}
241	>
242	>	int getFdf();
243	>
244	>	//getNZconstraint and setNZconstraint ruin the coherence of
245	>	//SimInfo class, need refactoring
246
247		/** Returns the total number of z-constraint molecules in the system */
248		int getNZconstraint() {
#	Line 256 | Line 278 | namespace oopse{
278
279		/** Returns the center of the mass of the whole system.*/
280		Vector3d getCom();
281	<	/** Returns the center of the mass and Center of Mass velocity of the whole system.*/
281	>	/** Returns the center of the mass and Center of Mass velocity of
282	>	the whole system.*/
283		void getComAll(Vector3d& com,Vector3d& comVel);
284
285	<	/** Returns intertia tensor for the entire system and system Angular Momentum.*/
285	>	/** Returns intertia tensor for the entire system and system
286	>	Angular Momentum.*/
287		void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
288
289		/** Returns system angular momentum */
290		Vector3d getAngularMomentum();
291
292	<	/** main driver function to interact with fortran during the initialization and molecule migration */
292	>	/** Returns volume of system as estimated by an ellipsoid defined
293	>	by the radii of gyration*/
294	>	void getGyrationalVolume(RealType &vol);
295	>	/** Overloaded version of gyrational volume that also returns
296	>	det(I) so dV/dr can be calculated*/
297	>	void getGyrationalVolume(RealType &vol, RealType &detI);
298	>
299		void update();
300	+	/**
301	+	* Setup Fortran Simulation
302	+	*/
303	+	void setupFortran();
304
305	+
306		/** Returns the local index manager */
307		LocalIndexManager* getLocalIndexManager() {
308		return &localIndexMan_;
#	Line 299 | Line 334 | namespace oopse{
334		return i != molecules_.end() ? i->second : NULL;
335		}
336
337	<	/** Calculate the maximum cutoff radius based on the atom types */
338	<	double calcMaxCutoffRadius();
304	<
305	<	double getRcut() {
306	<	return rcut_;
337	>	int getGlobalMolMembership(int id){
338	>	return globalMolMembership_[id];
339		}
340
341	<	double getRsw() {
342	<	return rsw_;
343	<	}
341	>	/**
342	>	* returns a vector which maps the local atom index on this
343	>	* processor to the global atom index.  With only one processor,
344	>	* these should be identical.
345	>	*/
346	>	vector<int> getGlobalAtomIndices();
347	>
348	>	/**
349	>	* returns a vector which maps the local cutoff group index on
350	>	* this processor to the global cutoff group index.  With only one
351	>	* processor, these should be identical.
352	>	*/
353	>	vector<int> getGlobalGroupIndices();
354
355	<	std::string getFinalConfigFileName() {
355	>	string getFinalConfigFileName() {
356		return finalConfigFileName_;
357		}
358	<
359	<	void setFinalConfigFileName(const std::string& fileName) {
358	>
359	>	void setFinalConfigFileName(const string& fileName) {
360		finalConfigFileName_ = fileName;
361		}
362
363	<	std::string getDumpFileName() {
363	>	string getRawMetaData() {
364	>	return rawMetaData_;
365	>	}
366	>	void setRawMetaData(const string& rawMetaData) {
367	>	rawMetaData_ = rawMetaData;
368	>	}
369	>
370	>	string getDumpFileName() {
371		return dumpFileName_;
372		}
373
374	<	void setDumpFileName(const std::string& fileName) {
374	>	void setDumpFileName(const string& fileName) {
375		dumpFileName_ = fileName;
376		}
377
378	<	std::string getStatFileName() {
378	>	string getStatFileName() {
379		return statFileName_;
380		}
381
382	<	void setStatFileName(const std::string& fileName) {
382	>	void setStatFileName(const string& fileName) {
383		statFileName_ = fileName;
384		}
385
386	<	std::string getRestFileName() {
386	>	string getRestFileName() {
387		return restFileName_;
388		}
389
390	<	void setRestFileName(const std::string& fileName) {
390	>	void setRestFileName(const string& fileName) {
391		restFileName_ = fileName;
392		}
393
#	Line 346 | Line 395 | namespace oopse{
395		* Sets GlobalGroupMembership
396		* @see #SimCreator::setGlobalIndex
397		*/
398	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
399	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
398	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
399	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
400		globalGroupMembership_ = globalGroupMembership;
401		}
402
#	Line 355 | Line 404 | namespace oopse{
404		* Sets GlobalMolMembership
405		* @see #SimCreator::setGlobalIndex
406		*/
407	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
408	<	assert(globalMolMembership.size() == nGlobalAtoms_);
407	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
408	>	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
409		globalMolMembership_ = globalMolMembership;
410		}
411
#	Line 365 | Line 414 | namespace oopse{
414		return fortranInitialized_;
415		}
416
417	<	//below functions are just forward functions
418	<	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
419	<	//the other hand, has-a relation need composing.
417	>	bool getCalcBoxDipole() {
418	>	return calcBoxDipole_;
419	>	}
420	>
421	>	bool getUseAtomicVirial() {
422	>	return useAtomicVirial_;
423	>	}
424	>
425		/**
426		* Adds property into property map
427		* @param genData GenericData to be added into PropertyMap
#	Line 378 | Line 432 | namespace oopse{
432		* Removes property from PropertyMap by name
433		* @param propName the name of property to be removed
434		*/
435	<	void removeProperty(const std::string& propName);
435	>	void removeProperty(const string& propName);
436
437		/**
438		* clear all of the properties
#	Line 389 | Line 443 | namespace oopse{
443		* Returns all names of properties
444		* @return all names of properties
445		*/
446	<	std::vector<std::string> getPropertyNames();
446	>	vector<string> getPropertyNames();
447
448		/**
449		* Returns all of the properties in PropertyMap
450		* @return all of the properties in PropertyMap
451		*/
452	<	std::vector<GenericData*> getProperties();
452	>	vector<GenericData*> getProperties();
453
454		/**
455		* Returns property
#	Line 403 | Line 457 | namespace oopse{
457		* @return a pointer point to property with propName. If no property named propName
458		* exists, return NULL
459		*/
460	<	GenericData* getPropertyByName(const std::string& propName);
460	>	GenericData* getPropertyByName(const string& propName);
461
462		/**
463	<	* add all exclude pairs of a molecule into exclude list.
463	>	* add all special interaction pairs (including excluded
464	>	* interactions) in a molecule into the appropriate lists.
465		*/
466	<	void addExcludePairs(Molecule* mol);
466	>	void addInteractionPairs(Molecule* mol);
467
468		/**
469	<	* remove all exclude pairs which belong to a molecule from exclude list
469	>	* remove all special interaction pairs which belong to a molecule
470	>	* from the appropriate lists.
471		*/
472	+	void removeInteractionPairs(Molecule* mol);
473
474	<	void removeExcludePairs(Molecule* mol);
475	<
419	<
420	<	/** Returns the unique atom types of local processor in an array */
421	<	std::set<AtomType*> getUniqueAtomTypes();
474	>	/** Returns the set of atom types present in this simulation */
475	>	set<AtomType*> getSimulatedAtomTypes();
476
477	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
477	>	friend ostream& operator <<(ostream& o, SimInfo& info);
478
479	<	void getCutoff(double& rcut, double& rsw);
479	>	void getCutoff(RealType& rcut, RealType& rsw);
480
481		private:
482
483	<	/** fill up the simtype struct*/
484	<	void setupSimType();
483	>	/** fill up the simtype struct and other simulation-related variables */
484	>	void setupSimVariables();
485
432	–	/**
433	–	* Setup Fortran Simulation
434	–	* @see #setupFortranParallel
435	–	*/
436	–	void setupFortranSim();
486
487	<	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
488	<	void setupCutoff();
487	>	/** Determine if we need to accumulate the simulation box dipole */
488	>	void setupAccumulateBoxDipole();
489
441	–	/** Figure out which coulombic correction method to use and pass to fortran */
442	–	void setupElectrostaticSummationMethod( int isError );
443	–
490		/** Calculates the number of degress of freedom in the whole system */
491		void calcNdf();
492		void calcNdfRaw();
493		void calcNdfTrans();
494
495		/**
496	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
497	<	* system.
496	>	* Adds molecule stamp and the total number of the molecule with
497	>	* same molecule stamp in the whole system.
498		*/
499		void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
500
501	<	MakeStamps* stamps_;
502	<	ForceField* forceField_;
503	<	Globals* simParams_;
501	>	// Other classes holdingn important information
502	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
503	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
504
505	<	std::map<int, Molecule*>  molecules_; /**< Molecule array */
505	>	///  Counts of local objects
506	>	int nAtoms_;              /**< number of atoms in local processor */
507	>	int nBonds_;              /**< number of bonds in local processor */
508	>	int nBends_;              /**< number of bends in local processor */
509	>	int nTorsions_;           /**< number of torsions in local processor */
510	>	int nInversions_;         /**< number of inversions in local processor */
511	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
512	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
513	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
514	>	int nConstraints_;        /**< number of constraints in local processors */
515
516	<	//degress of freedom
517	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
518	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
519	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
465	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
466	<
467	<	//number of global objects
468	<	int nGlobalMols_;       /**< number of molecules in the system */
469	<	int nGlobalAtoms_;   /**< number of atoms in the system */
470	<	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
516	>	/// Counts of global objects
517	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
518	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
519	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
520		int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
521	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
521	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
522	>
523	>	/// Degress of freedom
524	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
525	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
526	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
527	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
528	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
529	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
530	>
531	>	/// logicals
532	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
533	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
534	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
535	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
536	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
537	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
538	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
539	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
540	>
541	>	public:
542	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
543	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
544	>	bool usesMetallicAtoms() { return usesMetallicAtoms_; }
545	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
546	>	bool requiresPrepair() { return requiresPrepair_; }
547	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
548	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
549	>
550	>	private:
551	>	/// Data structures holding primary simulation objects
552	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
553	>
554	>	/// Stamps are templates for objects that are then used to create
555	>	/// groups of objects.  For example, a molecule stamp contains
556	>	/// information on how to build that molecule (i.e. the topology,
557	>	/// the atoms, the bonds, etc.)  Once the system is built, the
558	>	/// stamps are no longer useful.
559	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
560	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
561	>
562		/**
563	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
564	<	* corresponding content is the global index of cutoff group this atom belong to.
565	<	* It is filled by SimCreator once and only once, since it never changed during the simulation.
563	>	* A vector that maps between the global index of an atom, and the
564	>	* global index of cutoff group the atom belong to.  It is filled
565	>	* by SimCreator once and only once, since it never changed during
566	>	* the simulation.  It should be nGlobalAtoms_ in size.
567		*/
568	<	std::vector<int> globalGroupMembership_;
568	>	vector<int> globalGroupMembership_;
569	>	public:
570	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
571	>	private:
572
573		/**
574	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
575	<	* corresponding content is the global index of molecule this atom belong to.
576	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
574	>	* A vector that maps between the global index of an atom and the
575	>	* global index of the molecule the atom belongs to.  It is filled
576	>	* by SimCreator once and only once, since it is never changed
577	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
578		*/
579	<	std::vector<int> globalMolMembership_;
579	>	vector<int> globalMolMembership_;
580
581	<
582	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
583	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
584	<
585	<	//number of local objects
586	<	int nAtoms_;                        /**< number of atoms in local processor */
587	<	int nBonds_;                        /**< number of bonds in local processor */
588	<	int nBends_;                        /**< number of bends in local processor */
589	<	int nTorsions_;                    /**< number of torsions in local processor */
590	<	int nRigidBodies_;              /**< number of rigid bodies in local processor */
591	<	int nIntegrableObjects_;    /**< number of integrable objects in local processor */
592	<	int nCutoffGroups_;             /**< number of cutoff groups in local processor */
593	<	int nConstraints_;              /**< number of constraints in local processors */
581	>	/**
582	>	* A vector that maps between the local index of an atom and the
583	>	* index of the AtomType.
584	>	*/
585	>	vector<int> identArray_;
586	>	public:
587	>	vector<int> getIdentArray() { return identArray_; }
588	>	private:
589	>
590	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
591	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
592	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
593	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
594	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
595
596	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
597	<	Exclude exclude_;
503	<	PropertyMap properties_;                  /**< Generic Property */
504	<	SnapshotManager* sman_;               /**< SnapshotManager */
596	>	PropertyMap properties_;       /**< Generic Properties can be added */
597	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
598
599		/**
600	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
601	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
602	<	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
603	<	* to make a efficient data moving plan.
600	>	* The reason to have a local index manager is that when molecule
601	>	* is migrating to other processors, the atoms and the
602	>	* rigid-bodies will release their local indices to
603	>	* LocalIndexManager. Combining the information of molecule
604	>	* migrating to current processor, Migrator class can query the
605	>	* LocalIndexManager to make a efficient data moving plan.
606		*/
607		LocalIndexManager localIndexMan_;
608
609	<	//file names
610	<	std::string finalConfigFileName_;
611	<	std::string dumpFileName_;
612	<	std::string statFileName_;
613	<	std::string restFileName_;
609	>	// unparsed MetaData block for storing in Dump and EOR files:
610	>	string rawMetaData_;
611	>
612	>	// file names
613	>	string finalConfigFileName_;
614	>	string dumpFileName_;
615	>	string statFileName_;
616	>	string restFileName_;
617
520	–	double rcut_;       /**< cutoff radius*/
521	–	double rsw_;        /**< radius of switching function*/
618
619	<	bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
620	<
621	<	#ifdef IS_MPI
622	<	//in Parallel version, we need MolToProc
619	>	bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
620	>
621	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
622	>	the simulation box dipole moment */
623	>
624	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
625	>	Atomic Virials to calculate the pressure */
626	>
627		public:
628	+	/**
629	+	* return an integral objects by its global index. In MPI
630	+	* version, if the StuntDouble with specified global index does
631	+	* not belong to local processor, a NULL will be return.
632	+	*/
633	+	StuntDouble* getIOIndexToIntegrableObject(int index);
634	+	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
635	+
636	+	private:
637	+	vector<StuntDouble*> IOIndexToIntegrableObject;
638	+
639	+	public:
640
641		/**
642		* Finds the processor where a molecule resides
#	Line 535 | Line 647 | namespace oopse{
647		//assert(globalIndex < molToProcMap_.size());
648		return molToProcMap_[globalIndex];
649		}
650	<
650	>
651		/**
652		* Set MolToProcMap array
653		* @see #SimCreator::divideMolecules
654		*/
655	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
655	>	void setMolToProcMap(const vector<int>& molToProcMap) {
656		molToProcMap_ = molToProcMap;
657		}
658
659		private:
548	–
549	–	void setupFortranParallel();
660
661		/**
662	<	* The size of molToProcMap_ is equal to total number of molecules in the system.
663	<	*  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
664	<	* once.
662	>	* The size of molToProcMap_ is equal to total number of molecules
663	>	* in the system.  It maps a molecule to the processor on which it
664	>	* resides. it is filled by SimCreator once and only once.
665		*/
666	<	std::vector<int> molToProcMap_;
666	>	vector<int> molToProcMap_;
667
558	–	#endif
559	–
668		};
669
670	<	} //namespace oopse
670	>	} //namespace OpenMD
671		#endif //BRAINS_SIMMODEL_HPP
672

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 604 by chrisfen, Fri Sep 16 19:00:12 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (property svn:keywords), Revision 1553 by gezelter, Fri Apr 29 17:25:12 2011 UTC

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