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

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trunk/src/brains/SimInfo.hpp (file contents), Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1715 by gezelter, Tue May 22 21:55:31 2012 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"
#	Line 62 | Line 63
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"
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 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
96	–	* @note
101		*/
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 127 | 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 156 | 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 171 | 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 205 | Line 223 | namespace oopse{
223		*/
224		Molecule* nextMolecule(MoleculeIterator& i);
225
226	+	/** Returns the total number of fluctuating charges that are present */
227	+	int getNFluctuatingCharges() {
228	+	return nGlobalFluctuatingCharges_;
229	+	}
230	+
231		/** Returns the number of degrees of freedom */
232		int getNdf() {
233	<	return ndf_;
233	>	return ndf_ - getFdf();
234		}
235
236		/** Returns the number of raw degrees of freedom */
#	Line 220 | Line 243 | namespace oopse{
243		return ndfTrans_;
244		}
245
246	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
246	>	/** sets the current number of frozen degrees of freedom */
247	>	void setFdf(int fdf) {
248	>	fdf_local = fdf;
249	>	}
250	>
251	>	int getFdf();
252	>
253	>	//getNZconstraint and setNZconstraint ruin the coherence of
254	>	//SimInfo class, need refactoring
255
256		/** Returns the total number of z-constraint molecules in the system */
257		int getNZconstraint() {
#	Line 256 | Line 287 | namespace oopse{
287
288		/** Returns the center of the mass of the whole system.*/
289		Vector3d getCom();
290	<	/** Returns the center of the mass and Center of Mass velocity of the whole system.*/
290	>	/** Returns the center of the mass and Center of Mass velocity of
291	>	the whole system.*/
292		void getComAll(Vector3d& com,Vector3d& comVel);
293
294	<	/** Returns intertia tensor for the entire system and system Angular Momentum.*/
294	>	/** Returns intertia tensor for the entire system and system
295	>	Angular Momentum.*/
296		void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
297
298		/** Returns system angular momentum */
299		Vector3d getAngularMomentum();
300
301	<	/** main driver function to interact with fortran during the initialization and molecule migration */
301	>	/** Returns volume of system as estimated by an ellipsoid defined
302	>	by the radii of gyration*/
303	>	void getGyrationalVolume(RealType &vol);
304	>	/** Overloaded version of gyrational volume that also returns
305	>	det(I) so dV/dr can be calculated*/
306	>	void getGyrationalVolume(RealType &vol, RealType &detI);
307	>
308		void update();
309	+	/**
310	+	* Do final bookkeeping before Force managers need their data.
311	+	*/
312	+	void prepareTopology();
313
314	+
315		/** Returns the local index manager */
316		LocalIndexManager* getLocalIndexManager() {
317		return &localIndexMan_;
#	Line 297 | Line 341 | namespace oopse{
341		i = molecules_.find(index);
342
343		return i != molecules_.end() ? i->second : NULL;
300	–	}
301	–
302	–	double getRcut() {
303	–	return rcut_;
304	–	}
305	–
306	–	double getRsw() {
307	–	return rsw_;
344		}
345
346	<	double getList() {
347	<	return rlist_;
346	>	int getGlobalMolMembership(int id){
347	>	return globalMolMembership_[id];
348		}
349	+
350	+	/**
351	+	* returns a vector which maps the local atom index on this
352	+	* processor to the global atom index.  With only one processor,
353	+	* these should be identical.
354	+	*/
355	+	vector<int> getGlobalAtomIndices();
356	+
357	+	/**
358	+	* returns a vector which maps the local cutoff group index on
359	+	* this processor to the global cutoff group index.  With only one
360	+	* processor, these should be identical.
361	+	*/
362	+	vector<int> getGlobalGroupIndices();
363	+
364
365	<	std::string getFinalConfigFileName() {
365	>	string getFinalConfigFileName() {
366		return finalConfigFileName_;
367		}
368	<
369	<	void setFinalConfigFileName(const std::string& fileName) {
368	>
369	>	void setFinalConfigFileName(const string& fileName) {
370		finalConfigFileName_ = fileName;
371		}
372
373	<	std::string getDumpFileName() {
373	>	string getRawMetaData() {
374	>	return rawMetaData_;
375	>	}
376	>	void setRawMetaData(const string& rawMetaData) {
377	>	rawMetaData_ = rawMetaData;
378	>	}
379	>
380	>	string getDumpFileName() {
381		return dumpFileName_;
382		}
383
384	<	void setDumpFileName(const std::string& fileName) {
384	>	void setDumpFileName(const string& fileName) {
385		dumpFileName_ = fileName;
386		}
387
388	<	std::string getStatFileName() {
388	>	string getStatFileName() {
389		return statFileName_;
390		}
391
392	<	void setStatFileName(const std::string& fileName) {
392	>	void setStatFileName(const string& fileName) {
393		statFileName_ = fileName;
394		}
395
396	<	std::string getRestFileName() {
396	>	string getRestFileName() {
397		return restFileName_;
398		}
399
400	<	void setRestFileName(const std::string& fileName) {
400	>	void setRestFileName(const string& fileName) {
401		restFileName_ = fileName;
402		}
403
#	Line 347 | Line 405 | namespace oopse{
405		* Sets GlobalGroupMembership
406		* @see #SimCreator::setGlobalIndex
407		*/
408	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
409	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
408	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
409	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
410		globalGroupMembership_ = globalGroupMembership;
411		}
412
#	Line 356 | Line 414 | namespace oopse{
414		* Sets GlobalMolMembership
415		* @see #SimCreator::setGlobalIndex
416		*/
417	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
418	<	assert(globalMolMembership.size() == nGlobalAtoms_);
417	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
418	>	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
419		globalMolMembership_ = globalMolMembership;
420		}
421
422
423	<	bool isFortranInitialized() {
424	<	return fortranInitialized_;
423	>	bool isTopologyDone() {
424	>	return topologyDone_;
425		}
426
427	<	//below functions are just forward functions
428	<	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
429	<	//the other hand, has-a relation need composing.
427	>	bool getCalcBoxDipole() {
428	>	return calcBoxDipole_;
429	>	}
430	>
431	>	bool getUseAtomicVirial() {
432	>	return useAtomicVirial_;
433	>	}
434	>
435		/**
436		* Adds property into property map
437		* @param genData GenericData to be added into PropertyMap
#	Line 379 | Line 442 | namespace oopse{
442		* Removes property from PropertyMap by name
443		* @param propName the name of property to be removed
444		*/
445	<	void removeProperty(const std::string& propName);
445	>	void removeProperty(const string& propName);
446
447		/**
448		* clear all of the properties
#	Line 390 | Line 453 | namespace oopse{
453		* Returns all names of properties
454		* @return all names of properties
455		*/
456	<	std::vector<std::string> getPropertyNames();
456	>	vector<string> getPropertyNames();
457
458		/**
459		* Returns all of the properties in PropertyMap
460		* @return all of the properties in PropertyMap
461		*/
462	<	std::vector<GenericData*> getProperties();
462	>	vector<GenericData*> getProperties();
463
464		/**
465		* Returns property
#	Line 404 | Line 467 | namespace oopse{
467		* @return a pointer point to property with propName. If no property named propName
468		* exists, return NULL
469		*/
470	<	GenericData* getPropertyByName(const std::string& propName);
470	>	GenericData* getPropertyByName(const string& propName);
471
472		/**
473	<	* add all exclude pairs of a molecule into exclude list.
473	>	* add all special interaction pairs (including excluded
474	>	* interactions) in a molecule into the appropriate lists.
475		*/
476	<	void addExcludePairs(Molecule* mol);
476	>	void addInteractionPairs(Molecule* mol);
477
478		/**
479	<	* remove all exclude pairs which belong to a molecule from exclude list
479	>	* remove all special interaction pairs which belong to a molecule
480	>	* from the appropriate lists.
481		*/
482	+	void removeInteractionPairs(Molecule* mol);
483
484	<	void removeExcludePairs(Molecule* mol);
485	<
420	<
421	<	/** Returns the unique atom types of local processor in an array */
422	<	std::set<AtomType*> getUniqueAtomTypes();
484	>	/** Returns the set of atom types present in this simulation */
485	>	set<AtomType*> getSimulatedAtomTypes();
486
487	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
487	>	friend ostream& operator <<(ostream& o, SimInfo& info);
488
489	<	void getCutoff(double& rcut, double& rsw);
489	>	void getCutoff(RealType& rcut, RealType& rsw);
490
491		private:
492
493	<	/** fill up the simtype struct*/
494	<	void setupSimType();
493	>	/** fill up the simtype struct and other simulation-related variables */
494	>	void setupSimVariables();
495
433	–	/**
434	–	* Setup Fortran Simulation
435	–	* @see #setupFortranParallel
436	–	*/
437	–	void setupFortranSim();
496
497	<	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
498	<	void setupCutoff();
441	<
442	<	/** Figure out which coulombic correction method to use and pass to fortran */
443	<	void setupElectrostaticSummationMethod( int isError );
444	<
445	<	/** Figure out which polynomial type to use for the switching function */
446	<	void setupSwitchingFunction();
497	>	/** Determine if we need to accumulate the simulation box dipole */
498	>	void setupAccumulateBoxDipole();
499
500		/** Calculates the number of degress of freedom in the whole system */
501		void calcNdf();
502		void calcNdfRaw();
503		void calcNdfTrans();
504
453	–	ForceField* forceField_;
454	–	Globals* simParams_;
455	–
456	–	std::map<int, Molecule*>  molecules_; /**< Molecule array */
457	–
505		/**
506	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
507	<	* system.
506	>	* Adds molecule stamp and the total number of the molecule with
507	>	* same molecule stamp in the whole system.
508		*/
509		void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
510	+
511	+	// Other classes holdingn important information
512	+	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
513	+	Globals* simParams_;     /**< provides access to simulation parameters set by user */
514	+
515	+	///  Counts of local objects
516	+	int nAtoms_;              /**< number of atoms in local processor */
517	+	int nBonds_;              /**< number of bonds in local processor */
518	+	int nBends_;              /**< number of bends in local processor */
519	+	int nTorsions_;           /**< number of torsions in local processor */
520	+	int nInversions_;         /**< number of inversions in local processor */
521	+	int nRigidBodies_;        /**< number of rigid bodies in local processor */
522	+	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
523	+	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
524	+	int nConstraints_;        /**< number of constraints in local processors */
525	+	int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */
526
527	<	//degress of freedom
528	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
529	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
530	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
468	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
469	<
470	<	//number of global objects
471	<	int nGlobalMols_;       /**< number of molecules in the system */
472	<	int nGlobalAtoms_;   /**< number of atoms in the system */
473	<	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
527	>	/// Counts of global objects
528	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
529	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
530	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
531		int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
532	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
532	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
533	>	int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
534	>
535	>
536	>	/// Degress of freedom
537	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
538	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
539	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
540	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
541	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
542	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
543	>
544	>	/// logicals
545	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
546	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
547	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
548	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
549	>	bool usesFluctuatingCharges_; /**< are there fluctuating charges? */
550	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
551	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
552	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
553	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
554	>
555	>	public:
556	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
557	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
558	>	bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
559	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
560	>	bool requiresPrepair() { return requiresPrepair_; }
561	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
562	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
563	>
564	>	private:
565	>	/// Data structures holding primary simulation objects
566	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
567	>
568	>	/// Stamps are templates for objects that are then used to create
569	>	/// groups of objects.  For example, a molecule stamp contains
570	>	/// information on how to build that molecule (i.e. the topology,
571	>	/// the atoms, the bonds, etc.)  Once the system is built, the
572	>	/// stamps are no longer useful.
573	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
574	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
575	>
576		/**
577	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
578	<	* corresponding content is the global index of cutoff group this atom belong to.
579	<	* It is filled by SimCreator once and only once, since it never changed during the simulation.
577	>	* A vector that maps between the global index of an atom, and the
578	>	* global index of cutoff group the atom belong to.  It is filled
579	>	* by SimCreator once and only once, since it never changed during
580	>	* the simulation.  It should be nGlobalAtoms_ in size.
581		*/
582	<	std::vector<int> globalGroupMembership_;
582	>	vector<int> globalGroupMembership_;
583	>	public:
584	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
585	>	private:
586
587		/**
588	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
589	<	* corresponding content is the global index of molecule this atom belong to.
590	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
588	>	* A vector that maps between the global index of an atom and the
589	>	* global index of the molecule the atom belongs to.  It is filled
590	>	* by SimCreator once and only once, since it is never changed
591	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
592		*/
593	<	std::vector<int> globalMolMembership_;
593	>	vector<int> globalMolMembership_;
594
595	<
596	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
597	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
598	<
599	<	//number of local objects
600	<	int nAtoms_;                        /**< number of atoms in local processor */
601	<	int nBonds_;                        /**< number of bonds in local processor */
602	<	int nBends_;                        /**< number of bends in local processor */
603	<	int nTorsions_;                    /**< number of torsions in local processor */
604	<	int nRigidBodies_;              /**< number of rigid bodies in local processor */
605	<	int nIntegrableObjects_;    /**< number of integrable objects in local processor */
606	<	int nCutoffGroups_;             /**< number of cutoff groups in local processor */
607	<	int nConstraints_;              /**< number of constraints in local processors */
595	>	/**
596	>	* A vector that maps between the local index of an atom and the
597	>	* index of the AtomType.
598	>	*/
599	>	vector<int> identArray_;
600	>	public:
601	>	vector<int> getIdentArray() { return identArray_; }
602	>	private:
603	>
604	>	/**
605	>	* A vector which contains the fractional contribution of an
606	>	* atom's mass to the total mass of the cutoffGroup that atom
607	>	* belongs to.  In the case of single atom cutoff groups, the mass
608	>	* factor for that atom is 1.  For massless atoms, the factor is
609	>	* also 1.
610	>	*/
611	>	vector<RealType> massFactors_;
612	>	public:
613	>	vector<RealType> getMassFactors() { return massFactors_; }
614
615	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
616	<	Exclude exclude_;
617	<	PropertyMap properties_;                  /**< Generic Property */
618	<	SnapshotManager* sman_;               /**< SnapshotManager */
615	>	PairList* getExcludedInteractions() { return &excludedInteractions_; }
616	>	PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
617	>	PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
618	>	PairList* getOneFourInteractions() { return &oneFourInteractions_; }
619
620	+	private:
621	+
622	+	/// lists to handle atoms needing special treatment in the non-bonded interactions
623	+	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
624	+	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
625	+	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
626	+	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
627	+
628	+	PropertyMap properties_;       /**< Generic Properties can be added */
629	+	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
630	+
631		/**
632	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
633	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
634	<	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
635	<	* to make a efficient data moving plan.
632	>	* The reason to have a local index manager is that when molecule
633	>	* is migrating to other processors, the atoms and the
634	>	* rigid-bodies will release their local indices to
635	>	* LocalIndexManager. Combining the information of molecule
636	>	* migrating to current processor, Migrator class can query the
637	>	* LocalIndexManager to make a efficient data moving plan.
638		*/
639		LocalIndexManager localIndexMan_;
640
641	<	//file names
642	<	std::string finalConfigFileName_;
643	<	std::string dumpFileName_;
644	<	std::string statFileName_;
645	<	std::string restFileName_;
641	>	// unparsed MetaData block for storing in Dump and EOR files:
642	>	string rawMetaData_;
643	>
644	>	// file names
645	>	string finalConfigFileName_;
646	>	string dumpFileName_;
647	>	string statFileName_;
648	>	string restFileName_;
649
523	–	double rcut_;       /**< cutoff radius*/
524	–	double rsw_;        /**< radius of switching function*/
525	–	double rlist_;      /**< neighbor list radius */
650
651	<	bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
652	<
653	<	#ifdef IS_MPI
654	<	//in Parallel version, we need MolToProc
651	>	bool topologyDone_;  /** flag to indicate whether the topology has
652	>	been scanned and all the relevant
653	>	bookkeeping has been done*/
654	>
655	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
656	>	the simulation box dipole moment */
657	>
658	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
659	>	Atomic Virials to calculate the pressure */
660	>
661		public:
662	+	/**
663	+	* return an integral objects by its global index. In MPI
664	+	* version, if the StuntDouble with specified global index does
665	+	* not belong to local processor, a NULL will be return.
666	+	*/
667	+	StuntDouble* getIOIndexToIntegrableObject(int index);
668	+	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
669	+
670	+	private:
671	+	vector<StuntDouble*> IOIndexToIntegrableObject;
672	+
673	+	public:
674
675		/**
676		* Finds the processor where a molecule resides
#	Line 539 | Line 681 | namespace oopse{
681		//assert(globalIndex < molToProcMap_.size());
682		return molToProcMap_[globalIndex];
683		}
684	<
684	>
685		/**
686		* Set MolToProcMap array
687		* @see #SimCreator::divideMolecules
688		*/
689	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
689	>	void setMolToProcMap(const vector<int>& molToProcMap) {
690		molToProcMap_ = molToProcMap;
691		}
692
693		private:
552	–
553	–	void setupFortranParallel();
694
695		/**
696	<	* The size of molToProcMap_ is equal to total number of molecules in the system.
697	<	*  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
698	<	* once.
696	>	* The size of molToProcMap_ is equal to total number of molecules
697	>	* in the system.  It maps a molecule to the processor on which it
698	>	* resides. it is filled by SimCreator once and only once.
699		*/
700	<	std::vector<int> molToProcMap_;
700	>	vector<int> molToProcMap_;
701
562	–	#endif
563	–
702		};
703
704	<	} //namespace oopse
704	>	} //namespace OpenMD
705		#endif //BRAINS_SIMMODEL_HPP
706

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (property svn:keywords), Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC

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