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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 1665 by gezelter, Tue Nov 22 20:38:56 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]  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"
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"
68	<
69	<	namespace oopse{
70	<
71	<	//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 As one of the heavy weight class of OOPSE, SimInfo
79	<	* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
80	<	* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
81	<	* cutoff groups, constrains).
82	<	* Another major change is the index. No matter single version or parallel version,  atoms and
83	<	* rigid bodies have both global index and local index. Local index is not important to molecule as well as
84	<	* cutoff group.
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
93	>	*
94	>	* @param molStampPairs MoleculeStamp Array. The first element of
95	>	* the pair is molecule stamp, the second element is the total
96	>	* number of molecules with the same molecule stamp in the system
97	>	*
98		* @param ff pointer of a concrete ForceField instance
99	+	*
100		* @param simParams
95	–	* @note
101		*/
102	<	SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams);
102	>	SimInfo(ForceField* ff, Globals* simParams);
103		virtual ~SimInfo();
104
105		/**
106		* Adds a molecule
107	<	* @return return true if adding successfully, return false if the molecule is already in SimInfo
107	>	*
108	>	* @return return true if adding successfully, return false if the
109	>	* molecule is already in SimInfo
110	>	*
111		* @param mol molecule to be added
112		*/
113		bool addMolecule(Molecule* mol);
114
115		/**
116		* Removes a molecule from SimInfo
117	<	* @return true if removing successfully, return false if molecule is not in this SimInfo
117	>	*
118	>	* @return true if removing successfully, return false if molecule
119	>	* is not in this SimInfo
120		*/
121		bool removeMolecule(Molecule* mol);
122
#	Line 126 | Line 136 | namespace oopse{
136		}
137
138		/**
139	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
140	<	* of atoms which do not belong to the rigid bodies) in the system
139	>	* Returns the total number of integrable objects (total number of
140	>	* rigid bodies plus the total number of atoms which do not belong
141	>	* to the rigid bodies) in the system
142		*/
143		int getNGlobalIntegrableObjects() {
144		return nGlobalIntegrableObjects_;
145		}
146
147		/**
148	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
149	<	* of atoms which do not belong to the rigid bodies) in the system
148	>	* Returns the total number of integrable objects (total number of
149	>	* rigid bodies plus the total number of atoms which do not belong
150	>	* to the rigid bodies) in the system
151		*/
152		int getNGlobalRigidBodies() {
153		return nGlobalRigidBodies_;
#	Line 155 | Line 167 | namespace oopse{
167		return nAtoms_;
168		}
169
170	+	/** Returns the number of effective cutoff groups on local processor */
171	+	unsigned int getNLocalCutoffGroups();
172	+
173		/** Returns the number of local bonds */
174		unsigned int getNBonds(){
175		return nBonds_;
#	Line 170 | Line 185 | namespace oopse{
185		return nTorsions_;
186		}
187
188	+	/** Returns the number of local torsions */
189	+	unsigned int getNInversions() {
190	+	return nInversions_;
191	+	}
192		/** Returns the number of local rigid bodies */
193		unsigned int getNRigidBodies() {
194		return nRigidBodies_;
#	Line 206 | Line 225 | namespace oopse{
225
226		/** Returns the number of degrees of freedom */
227		int getNdf() {
228	<	return ndf_;
228	>	return ndf_ - getFdf();
229		}
230
231		/** Returns the number of raw degrees of freedom */
#	Line 219 | Line 238 | namespace oopse{
238		return ndfTrans_;
239		}
240
241	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
241	>	/** sets the current number of frozen degrees of freedom */
242	>	void setFdf(int fdf) {
243	>	fdf_local = fdf;
244	>	}
245	>
246	>	int getFdf();
247	>
248	>	//getNZconstraint and setNZconstraint ruin the coherence of
249	>	//SimInfo class, need refactoring
250
251		/** Returns the total number of z-constraint molecules in the system */
252		int getNZconstraint() {
#	Line 255 | Line 282 | namespace oopse{
282
283		/** Returns the center of the mass of the whole system.*/
284		Vector3d getCom();
285	+	/** Returns the center of the mass and Center of Mass velocity of
286	+	the whole system.*/
287	+	void getComAll(Vector3d& com,Vector3d& comVel);
288
289	<	/** main driver function to interact with fortran during the initialization and molecule migration */
289	>	/** Returns intertia tensor for the entire system and system
290	>	Angular Momentum.*/
291	>	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
292	>
293	>	/** Returns system angular momentum */
294	>	Vector3d getAngularMomentum();
295	>
296	>	/** Returns volume of system as estimated by an ellipsoid defined
297	>	by the radii of gyration*/
298	>	void getGyrationalVolume(RealType &vol);
299	>	/** Overloaded version of gyrational volume that also returns
300	>	det(I) so dV/dr can be calculated*/
301	>	void getGyrationalVolume(RealType &vol, RealType &detI);
302	>
303		void update();
304	+	/**
305	+	* Do final bookkeeping before Force managers need their data.
306	+	*/
307	+	void prepareTopology();
308
309	+
310		/** Returns the local index manager */
311		LocalIndexManager* getLocalIndexManager() {
312		return &localIndexMan_;
#	Line 290 | Line 338 | namespace oopse{
338		return i != molecules_.end() ? i->second : NULL;
339		}
340
341	<	/** Calculate the maximum cutoff radius based on the atom types */
342	<	double calcMaxCutoffRadius();
295	<
296	<	double getRcut() {
297	<	return rcut_;
341	>	int getGlobalMolMembership(int id){
342	>	return globalMolMembership_[id];
343		}
344
345	<	double getRsw() {
346	<	return rsw_;
347	<	}
345	>	/**
346	>	* returns a vector which maps the local atom index on this
347	>	* processor to the global atom index.  With only one processor,
348	>	* these should be identical.
349	>	*/
350	>	vector<int> getGlobalAtomIndices();
351	>
352	>	/**
353	>	* returns a vector which maps the local cutoff group index on
354	>	* this processor to the global cutoff group index.  With only one
355	>	* processor, these should be identical.
356	>	*/
357	>	vector<int> getGlobalGroupIndices();
358	>
359
360	<	std::string getFinalConfigFileName() {
360	>	string getFinalConfigFileName() {
361		return finalConfigFileName_;
362		}
363	<
364	<	void setFinalConfigFileName(const std::string& fileName) {
363	>
364	>	void setFinalConfigFileName(const string& fileName) {
365		finalConfigFileName_ = fileName;
366		}
367
368	<	std::string getDumpFileName() {
368	>	string getRawMetaData() {
369	>	return rawMetaData_;
370	>	}
371	>	void setRawMetaData(const string& rawMetaData) {
372	>	rawMetaData_ = rawMetaData;
373	>	}
374	>
375	>	string getDumpFileName() {
376		return dumpFileName_;
377		}
378
379	<	void setDumpFileName(const std::string& fileName) {
379	>	void setDumpFileName(const string& fileName) {
380		dumpFileName_ = fileName;
381		}
382
383	<	std::string getStatFileName() {
383	>	string getStatFileName() {
384		return statFileName_;
385		}
386
387	<	void setStatFileName(const std::string& fileName) {
387	>	void setStatFileName(const string& fileName) {
388		statFileName_ = fileName;
389		}
390
391	<	std::string getRestFileName() {
391	>	string getRestFileName() {
392		return restFileName_;
393		}
394
395	<	void setRestFileName(const std::string& fileName) {
395	>	void setRestFileName(const string& fileName) {
396		restFileName_ = fileName;
397		}
398
#	Line 337 | Line 400 | namespace oopse{
400		* Sets GlobalGroupMembership
401		* @see #SimCreator::setGlobalIndex
402		*/
403	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
404	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
403	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
404	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
405		globalGroupMembership_ = globalGroupMembership;
406		}
407
#	Line 346 | Line 409 | namespace oopse{
409		* Sets GlobalMolMembership
410		* @see #SimCreator::setGlobalIndex
411		*/
412	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
413	<	assert(globalMolMembership.size() == nGlobalAtoms_);
412	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
413	>	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
414		globalMolMembership_ = globalMolMembership;
415		}
416
417
418	<	bool isFortranInitialized() {
419	<	return fortranInitialized_;
418	>	bool isTopologyDone() {
419	>	return topologyDone_;
420		}
421
422	<	//below functions are just forward functions
423	<	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
424	<	//the other hand, has-a relation need composing.
422	>	bool getCalcBoxDipole() {
423	>	return calcBoxDipole_;
424	>	}
425	>
426	>	bool getUseAtomicVirial() {
427	>	return useAtomicVirial_;
428	>	}
429	>
430		/**
431		* Adds property into property map
432		* @param genData GenericData to be added into PropertyMap
#	Line 369 | Line 437 | namespace oopse{
437		* Removes property from PropertyMap by name
438		* @param propName the name of property to be removed
439		*/
440	<	void removeProperty(const std::string& propName);
440	>	void removeProperty(const string& propName);
441
442		/**
443		* clear all of the properties
#	Line 380 | Line 448 | namespace oopse{
448		* Returns all names of properties
449		* @return all names of properties
450		*/
451	<	std::vector<std::string> getPropertyNames();
451	>	vector<string> getPropertyNames();
452
453		/**
454		* Returns all of the properties in PropertyMap
455		* @return all of the properties in PropertyMap
456		*/
457	<	std::vector<GenericData*> getProperties();
457	>	vector<GenericData*> getProperties();
458
459		/**
460		* Returns property
#	Line 394 | Line 462 | namespace oopse{
462		* @return a pointer point to property with propName. If no property named propName
463		* exists, return NULL
464		*/
465	<	GenericData* getPropertyByName(const std::string& propName);
465	>	GenericData* getPropertyByName(const string& propName);
466
467		/**
468	<	* add all exclude pairs of a molecule into exclude list.
468	>	* add all special interaction pairs (including excluded
469	>	* interactions) in a molecule into the appropriate lists.
470		*/
471	<	void addExcludePairs(Molecule* mol);
471	>	void addInteractionPairs(Molecule* mol);
472
473		/**
474	<	* remove all exclude pairs which belong to a molecule from exclude list
474	>	* remove all special interaction pairs which belong to a molecule
475	>	* from the appropriate lists.
476		*/
477	+	void removeInteractionPairs(Molecule* mol);
478
479	<	void removeExcludePairs(Molecule* mol);
480	<
410	<
411	<	/** Returns the unique atom types of local processor in an array */
412	<	std::set<AtomType*> getUniqueAtomTypes();
479	>	/** Returns the set of atom types present in this simulation */
480	>	set<AtomType*> getSimulatedAtomTypes();
481
482	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
482	>	friend ostream& operator <<(ostream& o, SimInfo& info);
483
484	<	void getCutoff(double& rcut, double& rsw);
484	>	void getCutoff(RealType& rcut, RealType& rsw);
485
486		private:
487
488	<	/** fill up the simtype struct*/
489	<	void setupSimType();
488	>	/** fill up the simtype struct and other simulation-related variables */
489	>	void setupSimVariables();
490
423	–	/**
424	–	* Setup Fortran Simulation
425	–	* @see #setupFortranParallel
426	–	*/
427	–	void setupFortranSim();
491
492	<	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
493	<	void setupCutoff();
492	>	/** Determine if we need to accumulate the simulation box dipole */
493	>	void setupAccumulateBoxDipole();
494
495		/** Calculates the number of degress of freedom in the whole system */
496		void calcNdf();
#	Line 435 | Line 498 | namespace oopse{
498		void calcNdfTrans();
499
500		/**
501	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
502	<	* system.
501	>	* Adds molecule stamp and the total number of the molecule with
502	>	* same molecule stamp in the whole system.
503		*/
504		void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
505
506	<	MakeStamps* stamps_;
507	<	ForceField* forceField_;
508	<	Globals* simParams_;
506	>	// Other classes holdingn important information
507	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
508	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
509
510	<	std::map<int, Molecule*>  molecules_; /**< Molecule array */
510	>	///  Counts of local objects
511	>	int nAtoms_;              /**< number of atoms in local processor */
512	>	int nBonds_;              /**< number of bonds in local processor */
513	>	int nBends_;              /**< number of bends in local processor */
514	>	int nTorsions_;           /**< number of torsions in local processor */
515	>	int nInversions_;         /**< number of inversions in local processor */
516	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
517	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
518	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
519	>	int nConstraints_;        /**< number of constraints in local processors */
520
521	<	//degress of freedom
522	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
523	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
524	<	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 */
521	>	/// Counts of global objects
522	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
523	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
524	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
525		int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
526	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
526	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
527	>
528	>	/// Degress of freedom
529	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
530	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
531	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
532	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
533	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
534	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
535	>
536	>	/// logicals
537	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
538	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
539	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
540	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
541	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
542	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
543	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
544	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
545	>
546	>	public:
547	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
548	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
549	>	bool usesMetallicAtoms() { return usesMetallicAtoms_; }
550	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
551	>	bool requiresPrepair() { return requiresPrepair_; }
552	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
553	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
554	>
555	>	private:
556	>	/// Data structures holding primary simulation objects
557	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
558	>
559	>	/// Stamps are templates for objects that are then used to create
560	>	/// groups of objects.  For example, a molecule stamp contains
561	>	/// information on how to build that molecule (i.e. the topology,
562	>	/// the atoms, the bonds, etc.)  Once the system is built, the
563	>	/// stamps are no longer useful.
564	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
565	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
566	>
567		/**
568	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
569	<	* corresponding content is the global index of cutoff group this atom belong to.
570	<	* It is filled by SimCreator once and only once, since it never changed during the simulation.
568	>	* A vector that maps between the global index of an atom, and the
569	>	* global index of cutoff group the atom belong to.  It is filled
570	>	* by SimCreator once and only once, since it never changed during
571	>	* the simulation.  It should be nGlobalAtoms_ in size.
572		*/
573	<	std::vector<int> globalGroupMembership_;
573	>	vector<int> globalGroupMembership_;
574	>	public:
575	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
576	>	private:
577
578		/**
579	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
580	<	* corresponding content is the global index of molecule this atom belong to.
581	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
579	>	* A vector that maps between the global index of an atom and the
580	>	* global index of the molecule the atom belongs to.  It is filled
581	>	* by SimCreator once and only once, since it is never changed
582	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
583		*/
584	<	std::vector<int> globalMolMembership_;
584	>	vector<int> globalMolMembership_;
585
586	<
587	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
588	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
589	<
590	<	//number of local objects
591	<	int nAtoms_;                        /**< number of atoms in local processor */
592	<	int nBonds_;                        /**< number of bonds in local processor */
593	<	int nBends_;                        /**< number of bends in local processor */
594	<	int nTorsions_;                    /**< number of torsions in local processor */
595	<	int nRigidBodies_;              /**< number of rigid bodies in local processor */
596	<	int nIntegrableObjects_;    /**< number of integrable objects in local processor */
597	<	int nCutoffGroups_;             /**< number of cutoff groups in local processor */
598	<	int nConstraints_;              /**< number of constraints in local processors */
586	>	/**
587	>	* A vector that maps between the local index of an atom and the
588	>	* index of the AtomType.
589	>	*/
590	>	vector<int> identArray_;
591	>	public:
592	>	vector<int> getIdentArray() { return identArray_; }
593	>	private:
594	>
595	>	/**
596	>	* A vector which contains the fractional contribution of an
597	>	* atom's mass to the total mass of the cutoffGroup that atom
598	>	* belongs to.  In the case of single atom cutoff groups, the mass
599	>	* factor for that atom is 1.  For massless atoms, the factor is
600	>	* also 1.
601	>	*/
602	>	vector<RealType> massFactors_;
603	>	public:
604	>	vector<RealType> getMassFactors() { return massFactors_; }
605
606	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
607	<	Exclude exclude_;
608	<	PropertyMap properties_;                  /**< Generic Property */
609	<	SnapshotManager* sman_;               /**< SnapshotManager */
606	>	PairList* getExcludedInteractions() { return &excludedInteractions_; }
607	>	PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
608	>	PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
609	>	PairList* getOneFourInteractions() { return &oneFourInteractions_; }
610
611	+	private:
612	+
613	+	/// lists to handle atoms needing special treatment in the non-bonded interactions
614	+	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
615	+	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
616	+	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
617	+	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
618	+
619	+	PropertyMap properties_;       /**< Generic Properties can be added */
620	+	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
621	+
622		/**
623	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
624	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
625	<	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
626	<	* to make a efficient data moving plan.
623	>	* The reason to have a local index manager is that when molecule
624	>	* is migrating to other processors, the atoms and the
625	>	* rigid-bodies will release their local indices to
626	>	* LocalIndexManager. Combining the information of molecule
627	>	* migrating to current processor, Migrator class can query the
628	>	* LocalIndexManager to make a efficient data moving plan.
629		*/
630		LocalIndexManager localIndexMan_;
631
632	<	//file names
633	<	std::string finalConfigFileName_;
634	<	std::string dumpFileName_;
635	<	std::string statFileName_;
636	<	std::string restFileName_;
632	>	// unparsed MetaData block for storing in Dump and EOR files:
633	>	string rawMetaData_;
634	>
635	>	// file names
636	>	string finalConfigFileName_;
637	>	string dumpFileName_;
638	>	string statFileName_;
639	>	string restFileName_;
640
508	–	double rcut_;       /**< cutoff radius*/
509	–	double rsw_;        /**< radius of switching function*/
641
642	<	bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
643	<
644	<	#ifdef IS_MPI
645	<	//in Parallel version, we need MolToProc
642	>	bool topologyDone_;  /** flag to indicate whether the topology has
643	>	been scanned and all the relevant
644	>	bookkeeping has been done*/
645	>
646	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
647	>	the simulation box dipole moment */
648	>
649	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
650	>	Atomic Virials to calculate the pressure */
651	>
652		public:
653	+	/**
654	+	* return an integral objects by its global index. In MPI
655	+	* version, if the StuntDouble with specified global index does
656	+	* not belong to local processor, a NULL will be return.
657	+	*/
658	+	StuntDouble* getIOIndexToIntegrableObject(int index);
659	+	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
660	+
661	+	private:
662	+	vector<StuntDouble*> IOIndexToIntegrableObject;
663	+
664	+	public:
665
666		/**
667		* Finds the processor where a molecule resides
#	Line 523 | Line 672 | namespace oopse{
672		//assert(globalIndex < molToProcMap_.size());
673		return molToProcMap_[globalIndex];
674		}
675	<
675	>
676		/**
677		* Set MolToProcMap array
678		* @see #SimCreator::divideMolecules
679		*/
680	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
680	>	void setMolToProcMap(const vector<int>& molToProcMap) {
681		molToProcMap_ = molToProcMap;
682		}
683
684		private:
536	–
537	–	void setupFortranParallel();
685
686		/**
687	<	* The size of molToProcMap_ is equal to total number of molecules in the system.
688	<	*  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
689	<	* once.
687	>	* The size of molToProcMap_ is equal to total number of molecules
688	>	* in the system.  It maps a molecule to the processor on which it
689	>	* resides. it is filled by SimCreator once and only once.
690		*/
691	<	std::vector<int> molToProcMap_;
691	>	vector<int> molToProcMap_;
692
546	–	#endif
547	–
693		};
694
695	<	} //namespace oopse
695	>	} //namespace OpenMD
696		#endif //BRAINS_SIMMODEL_HPP
697

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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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