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root/OpenMD/trunk/src/brains/SimInfo.hpp

Comparing trunk/src/brains/SimInfo.hpp (file contents):
Revision 1386 by gezelter, Fri Oct 23 18:41:09 2009 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 2014 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, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 59 | Line 60
60		#include "math/Vector3.hpp"
61		#include "math/SquareMatrix3.hpp"
62		#include "types/MoleculeStamp.hpp"
63	<	#include "UseTheForce/ForceField.hpp"
63	>	#include "brains/ForceField.hpp"
64		#include "utils/PropertyMap.hpp"
65		#include "utils/LocalIndexManager.hpp"
66	+	#include "nonbonded/SwitchingFunction.hpp"
67
68	<	//another nonsense macro declaration
69	<	#define __OOPSE_C
70	<	#include "brains/fSimulation.h"
69	<
70	<	namespace oopse{
71	<
72	<	//forward decalration
68	>	using namespace std;
69	>	namespace OpenMD{
70	>	//forward declaration
71		class SnapshotManager;
72		class Molecule;
73		class SelectionManager;
74		class StuntDouble;
75	+
76		/**
77	<	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
78	<	* @brief One of the heavy weight classes of OOPSE, SimInfo maintains a list of molecules.
79	<	* The Molecule class maintains all of the concrete objects
80	<	* (atoms, bond, bend, torsions, inversions, rigid bodies, cutoff groups,
81	<	* constraints). In both the single and parallel versions, atoms and
82	<	* rigid bodies have both global and local indices.  The local index is
83	<	* not relevant to molecules or cutoff groups.
84	<	*/
77	>	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
78	>	*
79	>	* @brief One of the heavy-weight classes of OpenMD, SimInfo
80	>	* maintains objects and variables relating to the current
81	>	* simulation.  This includes the master list of Molecules.  The
82	>	* Molecule class maintains all of the concrete objects (Atoms,
83	>	* Bond, Bend, Torsions, Inversions, RigidBodies, CutoffGroups,
84	>	* Constraints). In both the single and parallel versions, Atoms and
85	>	* RigidBodies have both global and local indices.
86	>	*/
87		class SimInfo {
88		public:
89	<	typedef std::map<int, Molecule*>::iterator  MoleculeIterator;
90	<
89	>	typedef map<int, Molecule*>::iterator  MoleculeIterator;
90	>
91		/**
92		* Constructor of SimInfo
93	<	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
94	<	* second element is the total number of molecules with the same molecule stamp in the system
95	<	* @param ff pointer of a concrete ForceField instance
96	<	* @param simParams
96	<	* @note
93	>	*
94	>	* @param ff pointer to a concrete ForceField instance
95	>	*
96	>	* @param simParams pointer to the simulation parameters in a Globals object
97		*/
98		SimInfo(ForceField* ff, Globals* simParams);
99		virtual ~SimInfo();
100
101		/**
102		* Adds a molecule
103	<	* @return return true if adding successfully, return false if the molecule is already in SimInfo
104	<	* @param mol molecule to be added
103	>	*
104	>	* @return return true if adding successfully, return false if the
105	>	* molecule is already in SimInfo
106	>	*
107	>	* @param mol Molecule to be added
108		*/
109		bool addMolecule(Molecule* mol);
110
111		/**
112		* Removes a molecule from SimInfo
113	<	* @return true if removing successfully, return false if molecule is not in this SimInfo
113	>	*
114	>	* @return true if removing successfully, return false if molecule
115	>	* is not in this SimInfo
116		*/
117		bool removeMolecule(Molecule* mol);
118
#	Line 127 | Line 132 | namespace oopse{
132		}
133
134		/**
135	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
136	<	* of atoms which do not belong to the rigid bodies) in the system
135	>	* Returns the total number of integrable objects (total number of
136	>	* rigid bodies plus the total number of atoms which do not belong
137	>	* to the rigid bodies) in the system
138		*/
139		int getNGlobalIntegrableObjects() {
140		return nGlobalIntegrableObjects_;
141		}
142
143		/**
144	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
145	<	* of atoms which do not belong to the rigid bodies) in the system
144	>	* Returns the total number of integrable objects (total number of
145	>	* rigid bodies plus the total number of atoms which do not belong
146	>	* to the rigid bodies) in the system
147		*/
148		int getNGlobalRigidBodies() {
149		return nGlobalRigidBodies_;
150		}
151
152	<	int getNGlobalConstraints();
152	>	/** Returns the number of global bonds */
153	>	unsigned int getNGlobalBonds(){
154	>	return nGlobalBonds_;
155	>	}
156	>
157	>	/** Returns the number of global bends */
158	>	unsigned int getNGlobalBends() {
159	>	return nGlobalBends_;
160	>	}
161	>
162	>	/** Returns the number of global torsions */
163	>	unsigned int getNGlobalTorsions() {
164	>	return nGlobalTorsions_;
165	>	}
166	>
167	>	/** Returns the number of global inversions */
168	>	unsigned int getNGlobalInversions() {
169	>	return nGlobalInversions_;
170	>	}
171	>
172	>	unsigned int getNGlobalConstraints() {
173	>	if (!hasNGlobalConstraints_) calcNConstraints();
174	>	return nGlobalConstraints_;
175	>	}
176		/**
177		* Returns the number of local molecules.
178		* @return the number of local molecules
#	Line 156 | Line 186 | namespace oopse{
186		return nAtoms_;
187		}
188
189	+	/** Returns the number of effective cutoff groups on local processor */
190	+	unsigned int getNLocalCutoffGroups();
191	+
192		/** Returns the number of local bonds */
193		unsigned int getNBonds(){
194		return nBonds_;
#	Line 171 | Line 204 | namespace oopse{
204		return nTorsions_;
205		}
206
207	<	/** Returns the number of local torsions */
207	>	/** Returns the number of local inversions */
208		unsigned int getNInversions() {
209		return nInversions_;
210		}
#	Line 209 | Line 242 | namespace oopse{
242		*/
243		Molecule* nextMolecule(MoleculeIterator& i);
244
245	+	/** Returns the total number of fluctuating charges that are present */
246	+	int getNFluctuatingCharges() {
247	+	return nGlobalFluctuatingCharges_;
248	+	}
249	+
250		/** Returns the number of degrees of freedom */
251		int getNdf() {
252		return ndf_ - getFdf();
253		}
254
255	+	/** Returns the number of degrees of freedom (LOCAL) */
256	+	int getNdfLocal() {
257	+	return ndfLocal_;
258	+	}
259	+
260		/** Returns the number of raw degrees of freedom */
261		int getNdfRaw() {
262		return ndfRaw_;
#	Line 231 | Line 274 | namespace oopse{
274
275		int getFdf();
276
277	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
277	>	//getNZconstraint and setNZconstraint ruin the coherence of
278	>	//SimInfo class, need refactoring
279
280		/** Returns the total number of z-constraint molecules in the system */
281		int getNZconstraint() {
#	Line 249 | Line 293 | namespace oopse{
293		SnapshotManager* getSnapshotManager() {
294		return sman_;
295		}
296	<
296	>	/** Returns the storage layout (computed by SimCreator) */
297	>	int getStorageLayout() {
298	>	return storageLayout_;
299	>	}
300	>	/** Sets the storage layout (computed by SimCreator) */
301	>	void setStorageLayout(int sl) {
302	>	storageLayout_ = sl;
303	>	}
304	>
305		/** Sets the snapshot manager. */
306		void setSnapshotManager(SnapshotManager* sman);
307
#	Line 262 | Line 314 | namespace oopse{
314		return simParams_;
315		}
316
265	–	/** Returns the velocity of center of mass of the whole system.*/
266	–	Vector3d getComVel();
267	–
268	–	/** Returns the center of the mass of the whole system.*/
269	–	Vector3d getCom();
270	–	/** Returns the center of the mass and Center of Mass velocity of the whole system.*/
271	–	void getComAll(Vector3d& com,Vector3d& comVel);
272	–
273	–	/** Returns intertia tensor for the entire system and system Angular Momentum.*/
274	–	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
275	–
276	–	/** Returns system angular momentum */
277	–	Vector3d getAngularMomentum();
278	–
279	–	/** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/
280	–	void getGyrationalVolume(RealType &vol);
281	–	/** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/
282	–	void getGyrationalVolume(RealType &vol, RealType &detI);
283	–	/** main driver function to interact with fortran during the initialization and molecule migration */
317		void update();
318	+	/**
319	+	* Do final bookkeeping before Force managers need their data.
320	+	*/
321	+	void prepareTopology();
322
323	+
324		/** Returns the local index manager */
325		LocalIndexManager* getLocalIndexManager() {
326		return &localIndexMan_;
#	Line 318 | Line 356 | namespace oopse{
356		return globalMolMembership_[id];
357		}
358
359	<	RealType getRcut() {
360	<	return rcut_;
361	<	}
359	>	/**
360	>	* returns a vector which maps the local atom index on this
361	>	* processor to the global atom index.  With only one processor,
362	>	* these should be identical.
363	>	*/
364	>	vector<int> getGlobalAtomIndices();
365
366	<	RealType getRsw() {
367	<	return rsw_;
368	<	}
366	>	/**
367	>	* returns a vector which maps the local cutoff group index on
368	>	* this processor to the global cutoff group index.  With only one
369	>	* processor, these should be identical.
370	>	*/
371	>	vector<int> getGlobalGroupIndices();
372
329	–	RealType getList() {
330	–	return rlist_;
331	–	}
373
374	<	std::string getFinalConfigFileName() {
374	>	string getFinalConfigFileName() {
375		return finalConfigFileName_;
376		}
377
378	<	void setFinalConfigFileName(const std::string& fileName) {
378	>	void setFinalConfigFileName(const string& fileName) {
379		finalConfigFileName_ = fileName;
380		}
381
382	<	std::string getRawMetaData() {
382	>	string getRawMetaData() {
383		return rawMetaData_;
384		}
385	<	void setRawMetaData(const std::string& rawMetaData) {
385	>	void setRawMetaData(const string& rawMetaData) {
386		rawMetaData_ = rawMetaData;
387		}
388
389	<	std::string getDumpFileName() {
389	>	string getDumpFileName() {
390		return dumpFileName_;
391		}
392
393	<	void setDumpFileName(const std::string& fileName) {
393	>	void setDumpFileName(const string& fileName) {
394		dumpFileName_ = fileName;
395		}
396
397	<	std::string getStatFileName() {
397	>	string getStatFileName() {
398		return statFileName_;
399		}
400
401	<	void setStatFileName(const std::string& fileName) {
401	>	void setStatFileName(const string& fileName) {
402		statFileName_ = fileName;
403		}
404
405	<	std::string getRestFileName() {
405	>	string getRestFileName() {
406		return restFileName_;
407		}
408
409	<	void setRestFileName(const std::string& fileName) {
409	>	void setRestFileName(const string& fileName) {
410		restFileName_ = fileName;
411		}
412
413		/**
414		* Sets GlobalGroupMembership
374	–	* @see #SimCreator::setGlobalIndex
415		*/
416	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
417	<	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
418	<	globalGroupMembership_ = globalGroupMembership;
416	>	void setGlobalGroupMembership(const vector<int>& ggm) {
417	>	assert(ggm.size() == static_cast<size_t>(nGlobalAtoms_));
418	>	globalGroupMembership_ = ggm;
419		}
420
421		/**
422		* Sets GlobalMolMembership
383	–	* @see #SimCreator::setGlobalIndex
423		*/
424	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
425	<	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
426	<	globalMolMembership_ = globalMolMembership;
424	>	void setGlobalMolMembership(const vector<int>& gmm) {
425	>	assert(gmm.size() == (static_cast<size_t>(nGlobalAtoms_ +
426	>	nGlobalRigidBodies_)));
427	>	globalMolMembership_ = gmm;
428		}
429
430
431	<	bool isFortranInitialized() {
432	<	return fortranInitialized_;
431	>	bool isTopologyDone() {
432	>	return topologyDone_;
433		}
434
435		bool getCalcBoxDipole() {
#	Line 400 | Line 440 | namespace oopse{
440		return useAtomicVirial_;
441		}
442
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.
443		/**
444		* Adds property into property map
445		* @param genData GenericData to be added into PropertyMap
#	Line 413 | Line 450 | namespace oopse{
450		* Removes property from PropertyMap by name
451		* @param propName the name of property to be removed
452		*/
453	<	void removeProperty(const std::string& propName);
453	>	void removeProperty(const string& propName);
454
455		/**
456		* clear all of the properties
#	Line 424 | Line 461 | namespace oopse{
461		* Returns all names of properties
462		* @return all names of properties
463		*/
464	<	std::vector<std::string> getPropertyNames();
464	>	vector<string> getPropertyNames();
465
466		/**
467		* Returns all of the properties in PropertyMap
468		* @return all of the properties in PropertyMap
469		*/
470	<	std::vector<GenericData*> getProperties();
470	>	vector<GenericData*> getProperties();
471
472		/**
473		* Returns property
#	Line 438 | Line 475 | namespace oopse{
475		* @return a pointer point to property with propName. If no property named propName
476		* exists, return NULL
477		*/
478	<	GenericData* getPropertyByName(const std::string& propName);
478	>	GenericData* getPropertyByName(const string& propName);
479
480		/**
481		* add all special interaction pairs (including excluded
#	Line 452 | Line 489 | namespace oopse{
489		*/
490		void removeInteractionPairs(Molecule* mol);
491
492	+	/** Returns the set of atom types present in this simulation */
493	+	set<AtomType*> getSimulatedAtomTypes();
494
495	<	/** Returns the unique atom types of local processor in an array */
496	<	std::set<AtomType*> getUniqueAtomTypes();
495	>	/** Returns the global count of atoms of a particular type */
496	>	int getGlobalCountOfType(AtomType* atype);
497
498	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
498	>	friend ostream& operator <<(ostream& o, SimInfo& info);
499
500		void getCutoff(RealType& rcut, RealType& rsw);
501
502		private:
503
504	<	/** fill up the simtype struct*/
505	<	void setupSimType();
504	>	/** fill up the simtype struct and other simulation-related variables */
505	>	void setupSimVariables();
506
468	–	/**
469	–	* Setup Fortran Simulation
470	–	* @see #setupFortranParallel
471	–	*/
472	–	void setupFortranSim();
507
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	–
508		/** Determine if we need to accumulate the simulation box dipole */
509		void setupAccumulateBoxDipole();
510
#	Line 487 | Line 512 | namespace oopse{
512		void calcNdf();
513		void calcNdfRaw();
514		void calcNdfTrans();
515	+	void calcNConstraints();
516
491	–	ForceField* forceField_;
492	–	Globals* simParams_;
493	–
494	–	std::map<int, Molecule*>  molecules_; /**< Molecule array */
495	–
517		/**
518	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
519	<	* system.
518	>	* Adds molecule stamp and the total number of the molecule with
519	>	* same molecule stamp in the whole system.
520		*/
521		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_;
522
523	<	/**
524	<	* the size of globalMolMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
525	<	* corresponding content is the global index of molecule this atom belong to.
526	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
527	<	*/
528	<	std::vector<int> globalMolMembership_;
523	>	// Other classes holdingn important information
524	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
525	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
526
527	<
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
527	>	///  Counts of local objects
528		int nAtoms_;              /**< number of atoms in local processor */
529		int nBonds_;              /**< number of bonds in local processor */
530		int nBends_;              /**< number of bends in local processor */
#	Line 541 | Line 534 | namespace oopse{
534		int nIntegrableObjects_;  /**< number of integrable objects in local processor */
535		int nCutoffGroups_;       /**< number of cutoff groups in local processor */
536		int nConstraints_;        /**< number of constraints in local processors */
537	+	int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */
538	+
539	+	/// Counts of global objects
540	+	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
541	+	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
542	+	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
543	+	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
544	+	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
545	+	int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
546	+	int nGlobalBonds_;              /**< number of bonds in the system */
547	+	int nGlobalBends_;              /**< number of bends in the system */
548	+	int nGlobalTorsions_;           /**< number of torsions in the system */
549	+	int nGlobalInversions_;         /**< number of inversions in the system */
550	+	int nGlobalConstraints_;        /**< number of constraints in the system */
551	+	bool hasNGlobalConstraints_;
552
553	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
554	<	PairList excludedInteractions_;
555	<	PairList oneTwoInteractions_;
556	<	PairList oneThreeInteractions_;
557	<	PairList oneFourInteractions_;
558	<	PropertyMap properties_;                  /**< Generic Property */
559	<	SnapshotManager* sman_;               /**< SnapshotManager */
553	>	/// Degress of freedom
554	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
555	>	int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
556	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
557	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
558	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
559	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
560	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
561
562	+	/// logicals
563	+	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
564	+	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
565	+	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
566	+	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
567	+	bool usesFluctuatingCharges_; /**< are there fluctuating charges? */
568	+	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
569	+	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
570	+	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
571	+	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
572	+
573	+	public:
574	+	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
575	+	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
576	+	bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
577	+	bool usesAtomicVirial() { return usesAtomicVirial_; }
578	+	bool requiresPrepair() { return requiresPrepair_; }
579	+	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
580	+	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
581	+
582	+	private:
583	+	/// Data structures holding primary simulation objects
584	+	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
585	+
586	+	/// Stamps are templates for objects that are then used to create
587	+	/// groups of objects.  For example, a molecule stamp contains
588	+	/// information on how to build that molecule (i.e. the topology,
589	+	/// the atoms, the bonds, etc.)  Once the system is built, the
590	+	/// stamps are no longer useful.
591	+	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
592	+	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
593	+
594	+	/**
595	+	* A vector that maps between the global index of an atom, and the
596	+	* global index of cutoff group the atom belong to.  It is filled
597	+	* by SimCreator once and only once, since it never changed during
598	+	* the simulation.  It should be nGlobalAtoms_ in size.
599	+	*/
600	+	vector<int> globalGroupMembership_;
601	+	public:
602	+	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
603	+	private:
604	+
605	+	/**
606	+	* A vector that maps between the global index of an atom and the
607	+	* global index of the molecule the atom belongs to.  It is filled
608	+	* by SimCreator once and only once, since it is never changed
609	+	* during the simulation. It shoudl be nGlobalAtoms_ in size.
610	+	*/
611	+	vector<int> globalMolMembership_;
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	>	* A vector that maps between the local index of an atom and the
615	>	* index of the AtomType.
616	>	*/
617	>	vector<int> identArray_;
618	>	public:
619	>	vector<int> getIdentArray() { return identArray_; }
620	>
621	>	/**
622	>	* A vector that contains information about the local region of an
623	>	* atom (used for fluctuating charges, etc.)
624	>	*/
625	>	private:
626	>	vector<int> regions_;
627	>	public:
628	>	vector<int> getRegions() { return regions_; }
629	>	private:
630	>	/**
631	>	* A vector which contains the fractional contribution of an
632	>	* atom's mass to the total mass of the cutoffGroup that atom
633	>	* belongs to.  In the case of single atom cutoff groups, the mass
634	>	* factor for that atom is 1.  For massless atoms, the factor is
635	>	* also 1.
636	>	*/
637	>	vector<RealType> massFactors_;
638	>	public:
639	>	vector<RealType> getMassFactors() { return massFactors_; }
640	>
641	>	PairList* getExcludedInteractions() { return &excludedInteractions_; }
642	>	PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
643	>	PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
644	>	PairList* getOneFourInteractions() { return &oneFourInteractions_; }
645	>
646	>	private:
647	>
648	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
649	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
650	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
651	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
652	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
653	>
654	>	PropertyMap properties_;       /**< Generic Properties can be added */
655	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
656	>	int storageLayout_;            /**< Bits to tell how much data to store on each object */
657	>
658	>	/**
659	>	* The reason to have a local index manager is that when molecule
660	>	* is migrating to other processors, the atoms and the
661	>	* rigid-bodies will release their local indices to
662	>	* LocalIndexManager. Combining the information of molecule
663	>	* migrating to current processor, Migrator class can query the
664	>	* LocalIndexManager to make a efficient data moving plan.
665		*/
666		LocalIndexManager localIndexMan_;
667
668		// unparsed MetaData block for storing in Dump and EOR files:
669	<	std::string rawMetaData_;
669	>	string rawMetaData_;
670
671	<	//file names
672	<	std::string finalConfigFileName_;
673	<	std::string dumpFileName_;
674	<	std::string statFileName_;
675	<	std::string restFileName_;
569	<
570	<	RealType rcut_;       /**< cutoff radius*/
571	<	RealType rsw_;        /**< radius of switching function*/
572	<	RealType rlist_;      /**< neighbor list radius */
671	>	// file names
672	>	string finalConfigFileName_;
673	>	string dumpFileName_;
674	>	string statFileName_;
675	>	string restFileName_;
676
677	<	int ljsp_; /**< use shifted potential for LJ*/
678	<	int ljsf_; /**< use shifted force for LJ*/
679	<
577	<	bool fortranInitialized_; /**< flag indicate whether fortran side
578	<	is initialized */
677	>	bool topologyDone_;  /** flag to indicate whether the topology has
678	>	been scanned and all the relevant
679	>	bookkeeping has been done*/
680
681		bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
682		the simulation box dipole moment */
683
684		bool useAtomicVirial_; /**< flag to indicate whether or not we use
685		Atomic Virials to calculate the pressure */
686	<
687	<	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);
686	>
687	>	public:
688		/**
689	<	* return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
690	<	* global index does not belong to local processor, a NULL will be return.
691	<	*/
692	<	//StuntDouble* getStuntDoubleFromGlobalIndex(int index);
693	<	//private:
694	<	//std::vector<StuntDouble*> sdByGlobalIndex_;
689	>	* return an integral objects by its global index. In MPI
690	>	* version, if the StuntDouble with specified global index does
691	>	* not belong to local processor, a NULL will be return.
692	>	*/
693	>	StuntDouble* getIOIndexToIntegrableObject(int index);
694	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
695
696	<	//in Parallel version, we need MolToProc
696	>	private:
697	>	vector<StuntDouble*> IOIndexToIntegrableObject;
698	>
699		public:
700
701		/**
#	Line 614 | Line 707 | namespace oopse{
707		//assert(globalIndex < molToProcMap_.size());
708		return molToProcMap_[globalIndex];
709		}
710	<
710	>
711		/**
712		* Set MolToProcMap array
620	–	* @see #SimCreator::divideMolecules
713		*/
714	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
714	>	void setMolToProcMap(const vector<int>& molToProcMap) {
715		molToProcMap_ = molToProcMap;
716		}
717
718		private:
627	–
628	–	void setupFortranParallel();
719
720		/**
721		* The size of molToProcMap_ is equal to total number of molecules
722		* in the system.  It maps a molecule to the processor on which it
723		* resides. it is filled by SimCreator once and only once.
724		*/
725	<	std::vector<int> molToProcMap_;
725	>	vector<int> molToProcMap_;
726
637	–
727		};
728
729	<	} //namespace oopse
729	>	} //namespace OpenMD
730		#endif //BRAINS_SIMMODEL_HPP
731

Comparing trunk/src/brains/SimInfo.hpp (property svn:keywords):
Revision 1386 by gezelter, Fri Oct 23 18:41:09 2009 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 2014 UTC

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