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

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trunk/src/brains/SimInfo.hpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1569 by gezelter, Thu May 26 13:55:04 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"
61		#include "types/MoleculeStamp.hpp"
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"
68	<
69	<	namespace oopse{
70	<
71	<	//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
95	–	* @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 126 | 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 170 | 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 206 | 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 219 | 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 255 | 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
282	+	the whole system.*/
283	+	void getComAll(Vector3d& com,Vector3d& comVel);
284
285	<	/** main driver function to interact with fortran during the initialization and molecule migration */
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	>	/** 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	+	* Do final bookkeeping before Force managers need their data.
302	+	*/
303	+	void prepareTopology();
304
305	+
306		/** Returns the local index manager */
307		LocalIndexManager* getLocalIndexManager() {
308		return &localIndexMan_;
#	Line 288 | Line 332 | namespace oopse{
332		i = molecules_.find(index);
333
334		return i != molecules_.end() ? i->second : NULL;
291	–	}
292	–
293	–	/** Calculate the maximum cutoff radius based on the atom types */
294	–	double calcMaxCutoffRadius();
295	–
296	–	double getRcut() {
297	–	return rcut_;
335		}
336
337	<	double getRsw() {
338	<	return rsw_;
337	>	int getGlobalMolMembership(int id){
338	>	return globalMolMembership_[id];
339		}
340	+
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
356	<	std::string getFinalConfigFileName() {
356	>	string getFinalConfigFileName() {
357		return finalConfigFileName_;
358		}
359	<
360	<	void setFinalConfigFileName(const std::string& fileName) {
359	>
360	>	void setFinalConfigFileName(const string& fileName) {
361		finalConfigFileName_ = fileName;
362		}
363
364	<	std::string getDumpFileName() {
364	>	string getRawMetaData() {
365	>	return rawMetaData_;
366	>	}
367	>	void setRawMetaData(const string& rawMetaData) {
368	>	rawMetaData_ = rawMetaData;
369	>	}
370	>
371	>	string getDumpFileName() {
372		return dumpFileName_;
373		}
374
375	<	void setDumpFileName(const std::string& fileName) {
375	>	void setDumpFileName(const string& fileName) {
376		dumpFileName_ = fileName;
377		}
378
379	<	std::string getStatFileName() {
379	>	string getStatFileName() {
380		return statFileName_;
381		}
382
383	<	void setStatFileName(const std::string& fileName) {
383	>	void setStatFileName(const string& fileName) {
384		statFileName_ = fileName;
385		}
386
387	<	std::string getRestFileName() {
387	>	string getRestFileName() {
388		return restFileName_;
389		}
390
391	<	void setRestFileName(const std::string& fileName) {
391	>	void setRestFileName(const string& fileName) {
392		restFileName_ = fileName;
393		}
394
#	Line 337 | Line 396 | namespace oopse{
396		* Sets GlobalGroupMembership
397		* @see #SimCreator::setGlobalIndex
398		*/
399	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
400	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
399	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
400	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
401		globalGroupMembership_ = globalGroupMembership;
402		}
403
#	Line 346 | Line 405 | namespace oopse{
405		* Sets GlobalMolMembership
406		* @see #SimCreator::setGlobalIndex
407		*/
408	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
409	<	assert(globalMolMembership.size() == nGlobalAtoms_);
408	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
409	>	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
410		globalMolMembership_ = globalMolMembership;
411		}
412
413
414	<	bool isFortranInitialized() {
415	<	return fortranInitialized_;
414	>	bool isTopologyDone() {
415	>	return topologyDone_;
416		}
417
418	<	//below functions are just forward functions
419	<	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
420	<	//the other hand, has-a relation need composing.
418	>	bool getCalcBoxDipole() {
419	>	return calcBoxDipole_;
420	>	}
421	>
422	>	bool getUseAtomicVirial() {
423	>	return useAtomicVirial_;
424	>	}
425	>
426		/**
427		* Adds property into property map
428		* @param genData GenericData to be added into PropertyMap
#	Line 369 | Line 433 | namespace oopse{
433		* Removes property from PropertyMap by name
434		* @param propName the name of property to be removed
435		*/
436	<	void removeProperty(const std::string& propName);
436	>	void removeProperty(const string& propName);
437
438		/**
439		* clear all of the properties
#	Line 380 | Line 444 | namespace oopse{
444		* Returns all names of properties
445		* @return all names of properties
446		*/
447	<	std::vector<std::string> getPropertyNames();
447	>	vector<string> getPropertyNames();
448
449		/**
450		* Returns all of the properties in PropertyMap
451		* @return all of the properties in PropertyMap
452		*/
453	<	std::vector<GenericData*> getProperties();
453	>	vector<GenericData*> getProperties();
454
455		/**
456		* Returns property
#	Line 394 | Line 458 | namespace oopse{
458		* @return a pointer point to property with propName. If no property named propName
459		* exists, return NULL
460		*/
461	<	GenericData* getPropertyByName(const std::string& propName);
461	>	GenericData* getPropertyByName(const string& propName);
462
463		/**
464	<	* add all exclude pairs of a molecule into exclude list.
464	>	* add all special interaction pairs (including excluded
465	>	* interactions) in a molecule into the appropriate lists.
466		*/
467	<	void addExcludePairs(Molecule* mol);
467	>	void addInteractionPairs(Molecule* mol);
468
469		/**
470	<	* remove all exclude pairs which belong to a molecule from exclude list
470	>	* remove all special interaction pairs which belong to a molecule
471	>	* from the appropriate lists.
472		*/
473	+	void removeInteractionPairs(Molecule* mol);
474
475	<	void removeExcludePairs(Molecule* mol);
476	<
410	<
411	<	/** Returns the unique atom types of local processor in an array */
412	<	std::set<AtomType*> getUniqueAtomTypes();
475	>	/** Returns the set of atom types present in this simulation */
476	>	set<AtomType*> getSimulatedAtomTypes();
477
478	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
478	>	friend ostream& operator <<(ostream& o, SimInfo& info);
479
480	<	void getCutoff(double& rcut, double& rsw);
480	>	void getCutoff(RealType& rcut, RealType& rsw);
481
482		private:
483
484	<	/** fill up the simtype struct*/
485	<	void setupSimType();
484	>	/** fill up the simtype struct and other simulation-related variables */
485	>	void setupSimVariables();
486
423	–	/**
424	–	* Setup Fortran Simulation
425	–	* @see #setupFortranParallel
426	–	*/
427	–	void setupFortranSim();
487
488	<	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
489	<	void setupCutoff();
488	>	/** Determine if we need to accumulate the simulation box dipole */
489	>	void setupAccumulateBoxDipole();
490
491		/** Calculates the number of degress of freedom in the whole system */
492		void calcNdf();
#	Line 435 | Line 494 | namespace oopse{
494		void calcNdfTrans();
495
496		/**
497	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
498	<	* system.
497	>	* Adds molecule stamp and the total number of the molecule with
498	>	* same molecule stamp in the whole system.
499		*/
500		void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
501
502	<	MakeStamps* stamps_;
503	<	ForceField* forceField_;
504	<	Globals* simParams_;
502	>	// Other classes holdingn important information
503	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
504	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
505
506	<	std::map<int, Molecule*>  molecules_; /**< Molecule array */
506	>	///  Counts of local objects
507	>	int nAtoms_;              /**< number of atoms in local processor */
508	>	int nBonds_;              /**< number of bonds in local processor */
509	>	int nBends_;              /**< number of bends in local processor */
510	>	int nTorsions_;           /**< number of torsions in local processor */
511	>	int nInversions_;         /**< number of inversions in local processor */
512	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
513	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
514	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
515	>	int nConstraints_;        /**< number of constraints in local processors */
516
517	<	//degress of freedom
518	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
519	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
520	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
453	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
454	<
455	<	//number of global objects
456	<	int nGlobalMols_;       /**< number of molecules in the system */
457	<	int nGlobalAtoms_;   /**< number of atoms in the system */
458	<	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
517	>	/// Counts of global objects
518	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
519	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
520	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
521		int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
522	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
522	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
523	>
524	>	/// Degress of freedom
525	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
526	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
527	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
528	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
529	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
530	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
531	>
532	>	/// logicals
533	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
534	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
535	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
536	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
537	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
538	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
539	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
540	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
541	>
542	>	public:
543	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
544	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
545	>	bool usesMetallicAtoms() { return usesMetallicAtoms_; }
546	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
547	>	bool requiresPrepair() { return requiresPrepair_; }
548	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
549	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
550	>
551	>	private:
552	>	/// Data structures holding primary simulation objects
553	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
554	>
555	>	/// Stamps are templates for objects that are then used to create
556	>	/// groups of objects.  For example, a molecule stamp contains
557	>	/// information on how to build that molecule (i.e. the topology,
558	>	/// the atoms, the bonds, etc.)  Once the system is built, the
559	>	/// stamps are no longer useful.
560	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
561	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
562	>
563		/**
564	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
565	<	* corresponding content is the global index of cutoff group this atom belong to.
566	<	* It is filled by SimCreator once and only once, since it never changed during the simulation.
564	>	* A vector that maps between the global index of an atom, and the
565	>	* global index of cutoff group the atom belong to.  It is filled
566	>	* by SimCreator once and only once, since it never changed during
567	>	* the simulation.  It should be nGlobalAtoms_ in size.
568		*/
569	<	std::vector<int> globalGroupMembership_;
569	>	vector<int> globalGroupMembership_;
570	>	public:
571	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
572	>	private:
573
574		/**
575	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
576	<	* corresponding content is the global index of molecule this atom belong to.
577	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
575	>	* A vector that maps between the global index of an atom and the
576	>	* global index of the molecule the atom belongs to.  It is filled
577	>	* by SimCreator once and only once, since it is never changed
578	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
579		*/
580	<	std::vector<int> globalMolMembership_;
580	>	vector<int> globalMolMembership_;
581
582	<
583	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
584	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
585	<
586	<	//number of local objects
587	<	int nAtoms_;                        /**< number of atoms in local processor */
588	<	int nBonds_;                        /**< number of bonds in local processor */
589	<	int nBends_;                        /**< number of bends in local processor */
590	<	int nTorsions_;                    /**< number of torsions in local processor */
591	<	int nRigidBodies_;              /**< number of rigid bodies in local processor */
592	<	int nIntegrableObjects_;    /**< number of integrable objects in local processor */
593	<	int nCutoffGroups_;             /**< number of cutoff groups in local processor */
594	<	int nConstraints_;              /**< number of constraints in local processors */
582	>	/**
583	>	* A vector that maps between the local index of an atom and the
584	>	* index of the AtomType.
585	>	*/
586	>	vector<int> identArray_;
587	>	public:
588	>	vector<int> getIdentArray() { return identArray_; }
589	>	private:
590	>
591	>	/**
592	>	* A vector which contains the fractional contribution of an
593	>	* atom's mass to the total mass of the cutoffGroup that atom
594	>	* belongs to.  In the case of single atom cutoff groups, the mass
595	>	* factor for that atom is 1.  For massless atoms, the factor is
596	>	* also 1.
597	>	*/
598	>	vector<RealType> massFactors_;
599	>	public:
600	>	vector<RealType> getMassFactors() { return massFactors_; }
601	>	private:
602
603	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
604	<	Exclude exclude_;
605	<	PropertyMap properties_;                  /**< Generic Property */
606	<	SnapshotManager* sman_;               /**< SnapshotManager */
603	>
604	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
605	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
606	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
607	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
608	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
609
610	+	PropertyMap properties_;       /**< Generic Properties can be added */
611	+	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
612	+
613		/**
614	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
615	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
616	<	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
617	<	* to make a efficient data moving plan.
614	>	* The reason to have a local index manager is that when molecule
615	>	* is migrating to other processors, the atoms and the
616	>	* rigid-bodies will release their local indices to
617	>	* LocalIndexManager. Combining the information of molecule
618	>	* migrating to current processor, Migrator class can query the
619	>	* LocalIndexManager to make a efficient data moving plan.
620		*/
621		LocalIndexManager localIndexMan_;
622
623	<	//file names
624	<	std::string finalConfigFileName_;
625	<	std::string dumpFileName_;
626	<	std::string statFileName_;
627	<	std::string restFileName_;
623	>	// unparsed MetaData block for storing in Dump and EOR files:
624	>	string rawMetaData_;
625	>
626	>	// file names
627	>	string finalConfigFileName_;
628	>	string dumpFileName_;
629	>	string statFileName_;
630	>	string restFileName_;
631
508	–	double rcut_;       /**< cutoff radius*/
509	–	double rsw_;        /**< radius of switching function*/
632
633	<	bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
634	<
635	<	#ifdef IS_MPI
636	<	//in Parallel version, we need MolToProc
633	>	bool topologyDone_;  /** flag to indicate whether the topology has
634	>	been scanned and all the relevant
635	>	bookkeeping has been done*/
636	>
637	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
638	>	the simulation box dipole moment */
639	>
640	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
641	>	Atomic Virials to calculate the pressure */
642	>
643		public:
644	+	/**
645	+	* return an integral objects by its global index. In MPI
646	+	* version, if the StuntDouble with specified global index does
647	+	* not belong to local processor, a NULL will be return.
648	+	*/
649	+	StuntDouble* getIOIndexToIntegrableObject(int index);
650	+	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
651	+
652	+	private:
653	+	vector<StuntDouble*> IOIndexToIntegrableObject;
654	+
655	+	public:
656
657		/**
658		* Finds the processor where a molecule resides
#	Line 523 | Line 663 | namespace oopse{
663		//assert(globalIndex < molToProcMap_.size());
664		return molToProcMap_[globalIndex];
665		}
666	<
666	>
667		/**
668		* Set MolToProcMap array
669		* @see #SimCreator::divideMolecules
670		*/
671	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
671	>	void setMolToProcMap(const vector<int>& molToProcMap) {
672		molToProcMap_ = molToProcMap;
673		}
674
675		private:
536	–
537	–	void setupFortranParallel();
676
677		/**
678	<	* The size of molToProcMap_ is equal to total number of molecules in the system.
679	<	*  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
680	<	* once.
678	>	* The size of molToProcMap_ is equal to total number of molecules
679	>	* in the system.  It maps a molecule to the processor on which it
680	>	* resides. it is filled by SimCreator once and only once.
681		*/
682	<	std::vector<int> molToProcMap_;
682	>	vector<int> molToProcMap_;
683
546	–	#endif
547	–
684		};
685
686	<	} //namespace oopse
686	>	} //namespace OpenMD
687		#endif //BRAINS_SIMMODEL_HPP
688

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (property svn:keywords), Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC

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