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

Comparing trunk/src/brains/SimInfo.hpp (file contents):
Revision 1277 by gezelter, Mon Jul 14 12:35:58 2008 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 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 54 | Line 55
55		#include <utility>
56		#include <vector>
57
58	<	#include "brains/Exclude.hpp"
58	>	#include "brains/PairList.hpp"
59		#include "io/Globals.hpp"
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 __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	+	/** 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		int getNGlobalConstraints();
173		/**
174		* Returns the number of local molecules.
#	Line 156 | Line 183 | namespace oopse{
183		return nAtoms_;
184		}
185
186	+	/** Returns the number of effective cutoff groups on local processor */
187	+	unsigned int getNLocalCutoffGroups();
188	+
189		/** Returns the number of local bonds */
190		unsigned int getNBonds(){
191		return nBonds_;
#	Line 171 | Line 201 | namespace oopse{
201		return nTorsions_;
202		}
203
204	<	/** Returns the number of local torsions */
204	>	/** Returns the number of local inversions */
205		unsigned int getNInversions() {
206		return nInversions_;
207		}
#	Line 209 | Line 239 | namespace oopse{
239		*/
240		Molecule* nextMolecule(MoleculeIterator& i);
241
242	+	/** Returns the total number of fluctuating charges that are present */
243	+	int getNFluctuatingCharges() {
244	+	return nGlobalFluctuatingCharges_;
245	+	}
246	+
247		/** Returns the number of degrees of freedom */
248		int getNdf() {
249		return ndf_ - getFdf();
250		}
251
252	+	/** Returns the number of degrees of freedom (LOCAL) */
253	+	int getNdfLocal() {
254	+	return ndfLocal_;
255	+	}
256	+
257		/** Returns the number of raw degrees of freedom */
258		int getNdfRaw() {
259		return ndfRaw_;
#	Line 231 | Line 271 | namespace oopse{
271
272		int getFdf();
273
274	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
274	>	//getNZconstraint and setNZconstraint ruin the coherence of
275	>	//SimInfo class, need refactoring
276
277		/** Returns the total number of z-constraint molecules in the system */
278		int getNZconstraint() {
#	Line 249 | Line 290 | namespace oopse{
290		SnapshotManager* getSnapshotManager() {
291		return sman_;
292		}
293	<
293	>	/** Returns the storage layout (computed by SimCreator) */
294	>	int getStorageLayout() {
295	>	return storageLayout_;
296	>	}
297	>	/** Sets the storage layout (computed by SimCreator) */
298	>	void setStorageLayout(int sl) {
299	>	storageLayout_ = sl;
300	>	}
301	>
302		/** Sets the snapshot manager. */
303		void setSnapshotManager(SnapshotManager* sman);
304
#	Line 262 | Line 311 | namespace oopse{
311		return simParams_;
312		}
313
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 */
314		void update();
315	+	/**
316	+	* Do final bookkeeping before Force managers need their data.
317	+	*/
318	+	void prepareTopology();
319
320	+
321		/** Returns the local index manager */
322		LocalIndexManager* getLocalIndexManager() {
323		return &localIndexMan_;
#	Line 314 | Line 349 | namespace oopse{
349		return i != molecules_.end() ? i->second : NULL;
350		}
351
352	<	RealType getRcut() {
353	<	return rcut_;
352	>	int getGlobalMolMembership(int id){
353	>	return globalMolMembership_[id];
354		}
355
356	<	RealType getRsw() {
357	<	return rsw_;
358	<	}
356	>	/**
357	>	* returns a vector which maps the local atom index on this
358	>	* processor to the global atom index.  With only one processor,
359	>	* these should be identical.
360	>	*/
361	>	vector<int> getGlobalAtomIndices();
362
363	<	RealType getList() {
364	<	return rlist_;
365	<	}
363	>	/**
364	>	* returns a vector which maps the local cutoff group index on
365	>	* this processor to the global cutoff group index.  With only one
366	>	* processor, these should be identical.
367	>	*/
368	>	vector<int> getGlobalGroupIndices();
369	>
370
371	<	std::string getFinalConfigFileName() {
371	>	string getFinalConfigFileName() {
372		return finalConfigFileName_;
373		}
374
375	<	void setFinalConfigFileName(const std::string& fileName) {
375	>	void setFinalConfigFileName(const string& fileName) {
376		finalConfigFileName_ = fileName;
377		}
378
379	<	std::string getRawMetaData() {
379	>	string getRawMetaData() {
380		return rawMetaData_;
381		}
382	<	void setRawMetaData(const std::string& rawMetaData) {
382	>	void setRawMetaData(const string& rawMetaData) {
383		rawMetaData_ = rawMetaData;
384		}
385
386	<	std::string getDumpFileName() {
386	>	string getDumpFileName() {
387		return dumpFileName_;
388		}
389
390	<	void setDumpFileName(const std::string& fileName) {
390	>	void setDumpFileName(const string& fileName) {
391		dumpFileName_ = fileName;
392		}
393
394	<	std::string getStatFileName() {
394	>	string getStatFileName() {
395		return statFileName_;
396		}
397
398	<	void setStatFileName(const std::string& fileName) {
398	>	void setStatFileName(const string& fileName) {
399		statFileName_ = fileName;
400		}
401
402	<	std::string getRestFileName() {
402	>	string getRestFileName() {
403		return restFileName_;
404		}
405
406	<	void setRestFileName(const std::string& fileName) {
406	>	void setRestFileName(const string& fileName) {
407		restFileName_ = fileName;
408		}
409
410		/**
411		* Sets GlobalGroupMembership
370	–	* @see #SimCreator::setGlobalIndex
412		*/
413	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
414	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
415	<	globalGroupMembership_ = globalGroupMembership;
413	>	void setGlobalGroupMembership(const vector<int>& ggm) {
414	>	assert(ggm.size() == static_cast<size_t>(nGlobalAtoms_));
415	>	globalGroupMembership_ = ggm;
416		}
417
418		/**
419		* Sets GlobalMolMembership
379	–	* @see #SimCreator::setGlobalIndex
420		*/
421	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
422	<	assert(globalMolMembership.size() == nGlobalAtoms_);
423	<	globalMolMembership_ = globalMolMembership;
421	>	void setGlobalMolMembership(const vector<int>& gmm) {
422	>	assert(gmm.size() == (static_cast<size_t>(nGlobalAtoms_ +
423	>	nGlobalRigidBodies_)));
424	>	globalMolMembership_ = gmm;
425		}
426
427
428	<	bool isFortranInitialized() {
429	<	return fortranInitialized_;
428	>	bool isTopologyDone() {
429	>	return topologyDone_;
430		}
431
432		bool getCalcBoxDipole() {
#	Line 396 | Line 437 | namespace oopse{
437		return useAtomicVirial_;
438		}
439
399	–	//below functions are just forward functions
400	–	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
401	–	//the other hand, has-a relation need composing.
440		/**
441		* Adds property into property map
442		* @param genData GenericData to be added into PropertyMap
#	Line 409 | Line 447 | namespace oopse{
447		* Removes property from PropertyMap by name
448		* @param propName the name of property to be removed
449		*/
450	<	void removeProperty(const std::string& propName);
450	>	void removeProperty(const string& propName);
451
452		/**
453		* clear all of the properties
#	Line 420 | Line 458 | namespace oopse{
458		* Returns all names of properties
459		* @return all names of properties
460		*/
461	<	std::vector<std::string> getPropertyNames();
461	>	vector<string> getPropertyNames();
462
463		/**
464		* Returns all of the properties in PropertyMap
465		* @return all of the properties in PropertyMap
466		*/
467	<	std::vector<GenericData*> getProperties();
467	>	vector<GenericData*> getProperties();
468
469		/**
470		* Returns property
#	Line 434 | Line 472 | namespace oopse{
472		* @return a pointer point to property with propName. If no property named propName
473		* exists, return NULL
474		*/
475	<	GenericData* getPropertyByName(const std::string& propName);
475	>	GenericData* getPropertyByName(const string& propName);
476
477		/**
478	<	* add all exclude pairs of a molecule into exclude list.
478	>	* add all special interaction pairs (including excluded
479	>	* interactions) in a molecule into the appropriate lists.
480		*/
481	<	void addExcludePairs(Molecule* mol);
481	>	void addInteractionPairs(Molecule* mol);
482
483		/**
484	<	* remove all exclude pairs which belong to a molecule from exclude list
484	>	* remove all special interaction pairs which belong to a molecule
485	>	* from the appropriate lists.
486		*/
487	+	void removeInteractionPairs(Molecule* mol);
488
489	<	void removeExcludePairs(Molecule* mol);
489	>	/** Returns the set of atom types present in this simulation */
490	>	set<AtomType*> getSimulatedAtomTypes();
491
492	<
493	<	/** Returns the unique atom types of local processor in an array */
452	<	std::set<AtomType*> getUniqueAtomTypes();
492	>	/** Returns the global count of atoms of a particular type */
493	>	int getGlobalCountOfType(AtomType* atype);
494
495	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
495	>	friend ostream& operator <<(ostream& o, SimInfo& info);
496
497		void getCutoff(RealType& rcut, RealType& rsw);
498
499		private:
500
501	<	/** fill up the simtype struct*/
502	<	void setupSimType();
462	<
463	<	/**
464	<	* Setup Fortran Simulation
465	<	* @see #setupFortranParallel
466	<	*/
467	<	void setupFortranSim();
468	<
469	<	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
470	<	void setupCutoff();
501	>	/** fill up the simtype struct and other simulation-related variables */
502	>	void setupSimVariables();
503
472	–	/** Figure out which coulombic correction method to use and pass to fortran */
473	–	void setupElectrostaticSummationMethod( int isError );
504
475	–	/** Figure out which polynomial type to use for the switching function */
476	–	void setupSwitchingFunction();
477	–
505		/** Determine if we need to accumulate the simulation box dipole */
506		void setupAccumulateBoxDipole();
507
#	Line 483 | Line 510 | namespace oopse{
510		void calcNdfRaw();
511		void calcNdfTrans();
512
486	–	ForceField* forceField_;
487	–	Globals* simParams_;
488	–
489	–	std::map<int, Molecule*>  molecules_; /**< Molecule array */
490	–
513		/**
514	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
515	<	* system.
514	>	* Adds molecule stamp and the total number of the molecule with
515	>	* same molecule stamp in the whole system.
516		*/
517		void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
496	–
497	–	//degress of freedom
498	–	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
499	–	int fdf_local;       /**< number of frozen degrees of freedom */
500	–	int fdf_;            /**< number of frozen degrees of freedom */
501	–	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
502	–	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
503	–	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
504	–
505	–	//number of global objects
506	–	int nGlobalMols_;       /**< number of molecules in the system */
507	–	int nGlobalAtoms_;   /**< number of atoms in the system */
508	–	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
509	–	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
510	–	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
511	–	/**
512	–	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
513	–	* corresponding content is the global index of cutoff group this atom belong to.
514	–	* It is filled by SimCreator once and only once, since it never changed during the simulation.
515	–	*/
516	–	std::vector<int> globalGroupMembership_;
518
519	<	/**
520	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
521	<	* corresponding content is the global index of molecule this atom belong to.
521	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
522	<	*/
523	<	std::vector<int> globalMolMembership_;
519	>	// Other classes holdingn important information
520	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
521	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
522
523	<
526	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
527	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
528	<
529	<	//number of local objects
523	>	///  Counts of local objects
524		int nAtoms_;              /**< number of atoms in local processor */
525		int nBonds_;              /**< number of bonds in local processor */
526		int nBends_;              /**< number of bends in local processor */
#	Line 536 | Line 530 | namespace oopse{
530		int nIntegrableObjects_;  /**< number of integrable objects in local processor */
531		int nCutoffGroups_;       /**< number of cutoff groups in local processor */
532		int nConstraints_;        /**< number of constraints in local processors */
533	+	int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */
534	+
535	+	/// Counts of global objects
536	+	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
537	+	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
538	+	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
539	+	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
540	+	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
541	+	int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
542	+	int nGlobalBonds_;              /**< number of bonds in the system */
543	+	int nGlobalBends_;              /**< number of bends in the system */
544	+	int nGlobalTorsions_;           /**< number of torsions in the system */
545	+	int nGlobalInversions_;         /**< number of inversions in the system */
546	+
547	+	/// Degress of freedom
548	+	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
549	+	int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
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	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
557	<	Exclude exclude_;
558	<	PropertyMap properties_;                  /**< Generic Property */
559	<	SnapshotManager* sman_;               /**< SnapshotManager */
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 usesFluctuatingCharges_; /**< are there fluctuating charges? */
562	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
563	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
564	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
565	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
566
567	+	public:
568	+	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
569	+	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
570	+	bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
571	+	bool usesAtomicVirial() { return usesAtomicVirial_; }
572	+	bool requiresPrepair() { return requiresPrepair_; }
573	+	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
574	+	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
575	+
576	+	private:
577	+	/// Data structures holding primary simulation objects
578	+	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
579	+
580	+	/// Stamps are templates for objects that are then used to create
581	+	/// groups of objects.  For example, a molecule stamp contains
582	+	/// information on how to build that molecule (i.e. the topology,
583	+	/// the atoms, the bonds, etc.)  Once the system is built, the
584	+	/// stamps are no longer useful.
585	+	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
586	+	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
587	+
588	+	/**
589	+	* A vector that maps between the global index of an atom, and the
590	+	* global index of cutoff group the atom belong to.  It is filled
591	+	* by SimCreator once and only once, since it never changed during
592	+	* the simulation.  It should be nGlobalAtoms_ in size.
593	+	*/
594	+	vector<int> globalGroupMembership_;
595	+	public:
596	+	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
597	+	private:
598	+
599	+	/**
600	+	* A vector that maps between the global index of an atom and the
601	+	* global index of the molecule the atom belongs to.  It is filled
602	+	* by SimCreator once and only once, since it is never changed
603	+	* during the simulation. It shoudl be nGlobalAtoms_ in size.
604	+	*/
605	+	vector<int> globalMolMembership_;
606	+
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	>	* A vector that maps between the local index of an atom and the
609	>	* index of the AtomType.
610	>	*/
611	>	vector<int> identArray_;
612	>	public:
613	>	vector<int> getIdentArray() { return identArray_; }
614	>
615	>	/**
616	>	* A vector that contains information about the local region of an
617	>	* atom (used for fluctuating charges, etc.)
618	>	*/
619	>	private:
620	>	vector<int> regions_;
621	>	public:
622	>	vector<int> getRegions() { return regions_; }
623	>	private:
624	>	/**
625	>	* A vector which contains the fractional contribution of an
626	>	* atom's mass to the total mass of the cutoffGroup that atom
627	>	* belongs to.  In the case of single atom cutoff groups, the mass
628	>	* factor for that atom is 1.  For massless atoms, the factor is
629	>	* also 1.
630	>	*/
631	>	vector<RealType> massFactors_;
632	>	public:
633	>	vector<RealType> getMassFactors() { return massFactors_; }
634	>
635	>	PairList* getExcludedInteractions() { return &excludedInteractions_; }
636	>	PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
637	>	PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
638	>	PairList* getOneFourInteractions() { return &oneFourInteractions_; }
639	>
640	>	private:
641	>
642	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
643	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
644	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
645	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
646	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
647	>
648	>	PropertyMap properties_;       /**< Generic Properties can be added */
649	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
650	>	int storageLayout_;            /**< Bits to tell how much data to store on each object */
651	>
652	>	/**
653	>	* The reason to have a local index manager is that when molecule
654	>	* is migrating to other processors, the atoms and the
655	>	* rigid-bodies will release their local indices to
656	>	* LocalIndexManager. Combining the information of molecule
657	>	* migrating to current processor, Migrator class can query the
658	>	* LocalIndexManager to make a efficient data moving plan.
659		*/
660		LocalIndexManager localIndexMan_;
661
662		// unparsed MetaData block for storing in Dump and EOR files:
663	<	std::string rawMetaData_;
663	>	string rawMetaData_;
664
665	<	//file names
666	<	std::string finalConfigFileName_;
667	<	std::string dumpFileName_;
668	<	std::string statFileName_;
669	<	std::string restFileName_;
561	<
562	<	RealType rcut_;       /**< cutoff radius*/
563	<	RealType rsw_;        /**< radius of switching function*/
564	<	RealType rlist_;      /**< neighbor list radius */
665	>	// file names
666	>	string finalConfigFileName_;
667	>	string dumpFileName_;
668	>	string statFileName_;
669	>	string restFileName_;
670
671	<	bool ljsp_; /**< use shifted potential for LJ*/
672	<	bool ljsf_; /**< use shifted force for LJ*/
673	<
569	<	bool fortranInitialized_; /**< flag indicate whether fortran side
570	<	is initialized */
671	>	bool topologyDone_;  /** flag to indicate whether the topology has
672	>	been scanned and all the relevant
673	>	bookkeeping has been done*/
674
675		bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
676		the simulation box dipole moment */
677
678		bool useAtomicVirial_; /**< flag to indicate whether or not we use
679		Atomic Virials to calculate the pressure */
680	<
681	<	public:
579	<	/**
580	<	* return an integral objects by its global index. In MPI version, if the StuntDouble with specified
581	<	* global index does not belong to local processor, a NULL will be return.
582	<	*/
583	<	StuntDouble* getIOIndexToIntegrableObject(int index);
584	<	void setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v);
585	<	private:
586	<	std::vector<StuntDouble*> IOIndexToIntegrableObject;
587	<	//public:
588	<	//void setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v);
680	>
681	>	public:
682		/**
683	<	* return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
684	<	* global index does not belong to local processor, a NULL will be return.
685	<	*/
686	<	//StuntDouble* getStuntDoubleFromGlobalIndex(int index);
687	<	//private:
688	<	//std::vector<StuntDouble*> sdByGlobalIndex_;
683	>	* return an integral objects by its global index. In MPI
684	>	* version, if the StuntDouble with specified global index does
685	>	* not belong to local processor, a NULL will be return.
686	>	*/
687	>	StuntDouble* getIOIndexToIntegrableObject(int index);
688	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
689
690	<	//in Parallel version, we need MolToProc
690	>	private:
691	>	vector<StuntDouble*> IOIndexToIntegrableObject;
692	>
693		public:
694
695		/**
#	Line 606 | Line 701 | namespace oopse{
701		//assert(globalIndex < molToProcMap_.size());
702		return molToProcMap_[globalIndex];
703		}
704	<
704	>
705		/**
706		* Set MolToProcMap array
612	–	* @see #SimCreator::divideMolecules
707		*/
708	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
708	>	void setMolToProcMap(const vector<int>& molToProcMap) {
709		molToProcMap_ = molToProcMap;
710		}
711
712		private:
619	–
620	–	void setupFortranParallel();
713
714		/**
715		* The size of molToProcMap_ is equal to total number of molecules
716		* in the system.  It maps a molecule to the processor on which it
717		* resides. it is filled by SimCreator once and only once.
718		*/
719	<	std::vector<int> molToProcMap_;
719	>	vector<int> molToProcMap_;
720
629	–
721		};
722
723	<	} //namespace oopse
723	>	} //namespace OpenMD
724		#endif //BRAINS_SIMMODEL_HPP
725

Comparing trunk/src/brains/SimInfo.hpp (property svn:keywords):
Revision 1277 by gezelter, Mon Jul 14 12:35:58 2008 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

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