ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing:
trunk/src/brains/SimInfo.hpp (file contents), Revision 555 by chuckv, Mon May 30 14:01:52 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1577 by gezelter, Wed Jun 8 20:26:56 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 54 | Line 54
54		#include <utility>
55		#include <vector>
56
57	<	#include "brains/Exclude.hpp"
57	>	#include "brains/PairList.hpp"
58		#include "io/Globals.hpp"
59		#include "math/Vector3.hpp"
60		#include "math/SquareMatrix3.hpp"
#	Line 62 | Line 62
62		#include "UseTheForce/ForceField.hpp"
63		#include "utils/PropertyMap.hpp"
64		#include "utils/LocalIndexManager.hpp"
65	+	#include "nonbonded/SwitchingFunction.hpp"
66
67	<	//another nonsense macro declaration
68	<	#define __C
69	<	#include "brains/fSimulation.h"
69	<
70	<	namespace oopse{
71	<
72	<	//forward decalration
67	>	using namespace std;
68	>	namespace OpenMD{
69	>	//forward declaration
70		class SnapshotManager;
71		class Molecule;
72		class SelectionManager;
73	+	class StuntDouble;
74	+
75		/**
76	<	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
77	<	* @brief As one of the heavy weight class of OOPSE, SimInfo
78	<	* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
79	<	* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
80	<	* cutoff groups, constrains).
81	<	* Another major change is the index. No matter single version or parallel version,  atoms and
82	<	* rigid bodies have both global index and local index. Local index is not important to molecule as well as
83	<	* cutoff group.
76	>	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
77	>	*
78	>	* @brief One of the heavy-weight classes of OpenMD, SimInfo
79	>	* maintains objects and variables relating to the current
80	>	* simulation.  This includes the master list of Molecules.  The
81	>	* Molecule class maintains all of the concrete objects (Atoms,
82	>	* Bond, Bend, Torsions, Inversions, RigidBodies, CutoffGroups,
83	>	* Constraints). In both the single and parallel versions, Atoms and
84	>	* RigidBodies have both global and local indices.
85		*/
86		class SimInfo {
87		public:
88	<	typedef std::map<int, Molecule*>::iterator  MoleculeIterator;
89	<
88	>	typedef map<int, Molecule*>::iterator  MoleculeIterator;
89	>
90		/**
91		* Constructor of SimInfo
92	<	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
93	<	* second element is the total number of molecules with the same molecule stamp in the system
92	>	*
93	>	* @param molStampPairs MoleculeStamp Array. The first element of
94	>	* the pair is molecule stamp, the second element is the total
95	>	* number of molecules with the same molecule stamp in the system
96	>	*
97		* @param ff pointer of a concrete ForceField instance
98	<	* @param simParams
99	<	* @note
98	>	*
99	>	* @param simParams
100		*/
101	<	SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams);
101	>	SimInfo(ForceField* ff, Globals* simParams);
102		virtual ~SimInfo();
103
104		/**
105		* Adds a molecule
106	<	* @return return true if adding successfully, return false if the molecule is already in SimInfo
106	>	*
107	>	* @return return true if adding successfully, return false if the
108	>	* molecule is already in SimInfo
109	>	*
110		* @param mol molecule to be added
111		*/
112		bool addMolecule(Molecule* mol);
113
114		/**
115		* Removes a molecule from SimInfo
116	<	* @return true if removing successfully, return false if molecule is not in this SimInfo
116	>	*
117	>	* @return true if removing successfully, return false if molecule
118	>	* is not in this SimInfo
119		*/
120		bool removeMolecule(Molecule* mol);
121
#	Line 127 | Line 135 | namespace oopse{
135		}
136
137		/**
138	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
139	<	* of atoms which do not belong to the rigid bodies) in the system
138	>	* Returns the total number of integrable objects (total number of
139	>	* rigid bodies plus the total number of atoms which do not belong
140	>	* to the rigid bodies) in the system
141		*/
142		int getNGlobalIntegrableObjects() {
143		return nGlobalIntegrableObjects_;
144		}
145
146		/**
147	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
148	<	* of atoms which do not belong to the rigid bodies) in the system
147	>	* Returns the total number of integrable objects (total number of
148	>	* rigid bodies plus the total number of atoms which do not belong
149	>	* to the rigid bodies) in the system
150		*/
151		int getNGlobalRigidBodies() {
152		return nGlobalRigidBodies_;
#	Line 156 | Line 166 | namespace oopse{
166		return nAtoms_;
167		}
168
169	+	/** Returns the number of effective cutoff groups on local processor */
170	+	unsigned int getNLocalCutoffGroups();
171	+
172		/** Returns the number of local bonds */
173		unsigned int getNBonds(){
174		return nBonds_;
#	Line 171 | Line 184 | namespace oopse{
184		return nTorsions_;
185		}
186
187	+	/** Returns the number of local torsions */
188	+	unsigned int getNInversions() {
189	+	return nInversions_;
190	+	}
191		/** Returns the number of local rigid bodies */
192		unsigned int getNRigidBodies() {
193		return nRigidBodies_;
#	Line 207 | Line 224 | namespace oopse{
224
225		/** Returns the number of degrees of freedom */
226		int getNdf() {
227	<	return ndf_;
227	>	return ndf_ - getFdf();
228		}
229
230		/** Returns the number of raw degrees of freedom */
#	Line 220 | Line 237 | namespace oopse{
237		return ndfTrans_;
238		}
239
240	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
240	>	/** sets the current number of frozen degrees of freedom */
241	>	void setFdf(int fdf) {
242	>	fdf_local = fdf;
243	>	}
244	>
245	>	int getFdf();
246	>
247	>	//getNZconstraint and setNZconstraint ruin the coherence of
248	>	//SimInfo class, need refactoring
249
250		/** Returns the total number of z-constraint molecules in the system */
251		int getNZconstraint() {
#	Line 256 | Line 281 | namespace oopse{
281
282		/** Returns the center of the mass of the whole system.*/
283		Vector3d getCom();
284	<	/** Returns the center of the mass and Center of Mass velocity of the whole system.*/
284	>	/** Returns the center of the mass and Center of Mass velocity of
285	>	the whole system.*/
286		void getComAll(Vector3d& com,Vector3d& comVel);
287
288	<	/** Returns intertia tensor for the entire system and system Angular Momentum.*/
288	>	/** Returns intertia tensor for the entire system and system
289	>	Angular Momentum.*/
290		void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
291
292		/** Returns system angular momentum */
293		Vector3d getAngularMomentum();
294
295	<	/** main driver function to interact with fortran during the initialization and molecule migration */
295	>	/** Returns volume of system as estimated by an ellipsoid defined
296	>	by the radii of gyration*/
297	>	void getGyrationalVolume(RealType &vol);
298	>	/** Overloaded version of gyrational volume that also returns
299	>	det(I) so dV/dr can be calculated*/
300	>	void getGyrationalVolume(RealType &vol, RealType &detI);
301	>
302		void update();
303	+	/**
304	+	* Do final bookkeeping before Force managers need their data.
305	+	*/
306	+	void prepareTopology();
307
308	+
309		/** Returns the local index manager */
310		LocalIndexManager* getLocalIndexManager() {
311		return &localIndexMan_;
#	Line 297 | Line 335 | namespace oopse{
335		i = molecules_.find(index);
336
337		return i != molecules_.end() ? i->second : NULL;
300	–	}
301	–
302	–	/** Calculate the maximum cutoff radius based on the atom types */
303	–	double calcMaxCutoffRadius();
304	–
305	–	double getRcut() {
306	–	return rcut_;
338		}
339
340	<	double getRsw() {
341	<	return rsw_;
340	>	int getGlobalMolMembership(int id){
341	>	return globalMolMembership_[id];
342		}
343	+
344	+	/**
345	+	* returns a vector which maps the local atom index on this
346	+	* processor to the global atom index.  With only one processor,
347	+	* these should be identical.
348	+	*/
349	+	vector<int> getGlobalAtomIndices();
350	+
351	+	/**
352	+	* returns a vector which maps the local cutoff group index on
353	+	* this processor to the global cutoff group index.  With only one
354	+	* processor, these should be identical.
355	+	*/
356	+	vector<int> getGlobalGroupIndices();
357	+
358
359	<	std::string getFinalConfigFileName() {
359	>	string getFinalConfigFileName() {
360		return finalConfigFileName_;
361		}
362	<
363	<	void setFinalConfigFileName(const std::string& fileName) {
362	>
363	>	void setFinalConfigFileName(const string& fileName) {
364		finalConfigFileName_ = fileName;
365		}
366
367	<	std::string getDumpFileName() {
367	>	string getRawMetaData() {
368	>	return rawMetaData_;
369	>	}
370	>	void setRawMetaData(const string& rawMetaData) {
371	>	rawMetaData_ = rawMetaData;
372	>	}
373	>
374	>	string getDumpFileName() {
375		return dumpFileName_;
376		}
377
378	<	void setDumpFileName(const std::string& fileName) {
378	>	void setDumpFileName(const string& fileName) {
379		dumpFileName_ = fileName;
380		}
381
382	<	std::string getStatFileName() {
382	>	string getStatFileName() {
383		return statFileName_;
384		}
385
386	<	void setStatFileName(const std::string& fileName) {
386	>	void setStatFileName(const string& fileName) {
387		statFileName_ = fileName;
388		}
389
390	<	std::string getRestFileName() {
390	>	string getRestFileName() {
391		return restFileName_;
392		}
393
394	<	void setRestFileName(const std::string& fileName) {
394	>	void setRestFileName(const string& fileName) {
395		restFileName_ = fileName;
396		}
397
#	Line 346 | Line 399 | namespace oopse{
399		* Sets GlobalGroupMembership
400		* @see #SimCreator::setGlobalIndex
401		*/
402	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
403	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
402	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
403	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
404		globalGroupMembership_ = globalGroupMembership;
405		}
406
#	Line 355 | Line 408 | namespace oopse{
408		* Sets GlobalMolMembership
409		* @see #SimCreator::setGlobalIndex
410		*/
411	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
412	<	assert(globalMolMembership.size() == nGlobalAtoms_);
411	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
412	>	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
413		globalMolMembership_ = globalMolMembership;
414		}
415
416
417	<	bool isFortranInitialized() {
418	<	return fortranInitialized_;
417	>	bool isTopologyDone() {
418	>	return topologyDone_;
419		}
420
421	<	//below functions are just forward functions
422	<	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
423	<	//the other hand, has-a relation need composing.
421	>	bool getCalcBoxDipole() {
422	>	return calcBoxDipole_;
423	>	}
424	>
425	>	bool getUseAtomicVirial() {
426	>	return useAtomicVirial_;
427	>	}
428	>
429		/**
430		* Adds property into property map
431		* @param genData GenericData to be added into PropertyMap
#	Line 378 | Line 436 | namespace oopse{
436		* Removes property from PropertyMap by name
437		* @param propName the name of property to be removed
438		*/
439	<	void removeProperty(const std::string& propName);
439	>	void removeProperty(const string& propName);
440
441		/**
442		* clear all of the properties
#	Line 389 | Line 447 | namespace oopse{
447		* Returns all names of properties
448		* @return all names of properties
449		*/
450	<	std::vector<std::string> getPropertyNames();
450	>	vector<string> getPropertyNames();
451
452		/**
453		* Returns all of the properties in PropertyMap
454		* @return all of the properties in PropertyMap
455		*/
456	<	std::vector<GenericData*> getProperties();
456	>	vector<GenericData*> getProperties();
457
458		/**
459		* Returns property
#	Line 403 | Line 461 | namespace oopse{
461		* @return a pointer point to property with propName. If no property named propName
462		* exists, return NULL
463		*/
464	<	GenericData* getPropertyByName(const std::string& propName);
464	>	GenericData* getPropertyByName(const string& propName);
465
466		/**
467	<	* add all exclude pairs of a molecule into exclude list.
467	>	* add all special interaction pairs (including excluded
468	>	* interactions) in a molecule into the appropriate lists.
469		*/
470	<	void addExcludePairs(Molecule* mol);
470	>	void addInteractionPairs(Molecule* mol);
471
472		/**
473	<	* remove all exclude pairs which belong to a molecule from exclude list
473	>	* remove all special interaction pairs which belong to a molecule
474	>	* from the appropriate lists.
475		*/
476	+	void removeInteractionPairs(Molecule* mol);
477
478	<	void removeExcludePairs(Molecule* mol);
479	<
419	<
420	<	/** Returns the unique atom types of local processor in an array */
421	<	std::set<AtomType*> getUniqueAtomTypes();
478	>	/** Returns the set of atom types present in this simulation */
479	>	set<AtomType*> getSimulatedAtomTypes();
480
481	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
481	>	friend ostream& operator <<(ostream& o, SimInfo& info);
482
483	<	void getCutoff(double& rcut, double& rsw);
483	>	void getCutoff(RealType& rcut, RealType& rsw);
484
485		private:
486
487	<	/** fill up the simtype struct*/
488	<	void setupSimType();
487	>	/** fill up the simtype struct and other simulation-related variables */
488	>	void setupSimVariables();
489
432	–	/**
433	–	* Setup Fortran Simulation
434	–	* @see #setupFortranParallel
435	–	*/
436	–	void setupFortranSim();
490
491	<	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
492	<	void setupCutoff();
491	>	/** Determine if we need to accumulate the simulation box dipole */
492	>	void setupAccumulateBoxDipole();
493
494		/** Calculates the number of degress of freedom in the whole system */
495		void calcNdf();
#	Line 444 | Line 497 | namespace oopse{
497		void calcNdfTrans();
498
499		/**
500	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
501	<	* system.
500	>	* Adds molecule stamp and the total number of the molecule with
501	>	* same molecule stamp in the whole system.
502		*/
503		void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
504
505	<	MakeStamps* stamps_;
506	<	ForceField* forceField_;
507	<	Globals* simParams_;
505	>	// Other classes holdingn important information
506	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
507	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
508
509	<	std::map<int, Molecule*>  molecules_; /**< Molecule array */
509	>	///  Counts of local objects
510	>	int nAtoms_;              /**< number of atoms in local processor */
511	>	int nBonds_;              /**< number of bonds in local processor */
512	>	int nBends_;              /**< number of bends in local processor */
513	>	int nTorsions_;           /**< number of torsions in local processor */
514	>	int nInversions_;         /**< number of inversions in local processor */
515	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
516	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
517	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
518	>	int nConstraints_;        /**< number of constraints in local processors */
519
520	<	//degress of freedom
521	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
522	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
523	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
462	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
463	<
464	<	//number of global objects
465	<	int nGlobalMols_;       /**< number of molecules in the system */
466	<	int nGlobalAtoms_;   /**< number of atoms in the system */
467	<	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
520	>	/// Counts of global objects
521	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
522	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
523	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
524		int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
525	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
525	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
526	>
527	>	/// Degress of freedom
528	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
529	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
530	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
531	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
532	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
533	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
534	>
535	>	/// logicals
536	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
537	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
538	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
539	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
540	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
541	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
542	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
543	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
544	>
545	>	public:
546	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
547	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
548	>	bool usesMetallicAtoms() { return usesMetallicAtoms_; }
549	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
550	>	bool requiresPrepair() { return requiresPrepair_; }
551	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
552	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
553	>
554	>	private:
555	>	/// Data structures holding primary simulation objects
556	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
557	>
558	>	/// Stamps are templates for objects that are then used to create
559	>	/// groups of objects.  For example, a molecule stamp contains
560	>	/// information on how to build that molecule (i.e. the topology,
561	>	/// the atoms, the bonds, etc.)  Once the system is built, the
562	>	/// stamps are no longer useful.
563	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
564	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
565	>
566		/**
567	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
568	<	* corresponding content is the global index of cutoff group this atom belong to.
569	<	* It is filled by SimCreator once and only once, since it never changed during the simulation.
567	>	* A vector that maps between the global index of an atom, and the
568	>	* global index of cutoff group the atom belong to.  It is filled
569	>	* by SimCreator once and only once, since it never changed during
570	>	* the simulation.  It should be nGlobalAtoms_ in size.
571		*/
572	<	std::vector<int> globalGroupMembership_;
572	>	vector<int> globalGroupMembership_;
573	>	public:
574	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
575	>	private:
576
577		/**
578	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
579	<	* corresponding content is the global index of molecule this atom belong to.
580	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
578	>	* A vector that maps between the global index of an atom and the
579	>	* global index of the molecule the atom belongs to.  It is filled
580	>	* by SimCreator once and only once, since it is never changed
581	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
582		*/
583	<	std::vector<int> globalMolMembership_;
583	>	vector<int> globalMolMembership_;
584
585	<
586	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
587	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
588	<
589	<	//number of local objects
590	<	int nAtoms_;                        /**< number of atoms in local processor */
591	<	int nBonds_;                        /**< number of bonds in local processor */
592	<	int nBends_;                        /**< number of bends in local processor */
593	<	int nTorsions_;                    /**< number of torsions in local processor */
594	<	int nRigidBodies_;              /**< number of rigid bodies in local processor */
595	<	int nIntegrableObjects_;    /**< number of integrable objects in local processor */
596	<	int nCutoffGroups_;             /**< number of cutoff groups in local processor */
597	<	int nConstraints_;              /**< number of constraints in local processors */
585	>	/**
586	>	* A vector that maps between the local index of an atom and the
587	>	* index of the AtomType.
588	>	*/
589	>	vector<int> identArray_;
590	>	public:
591	>	vector<int> getIdentArray() { return identArray_; }
592	>	private:
593	>
594	>	/**
595	>	* A vector which contains the fractional contribution of an
596	>	* atom's mass to the total mass of the cutoffGroup that atom
597	>	* belongs to.  In the case of single atom cutoff groups, the mass
598	>	* factor for that atom is 1.  For massless atoms, the factor is
599	>	* also 1.
600	>	*/
601	>	vector<RealType> massFactors_;
602	>	public:
603	>	vector<RealType> getMassFactors() { return massFactors_; }
604
605	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
606	<	Exclude exclude_;
607	<	PropertyMap properties_;                  /**< Generic Property */
608	<	SnapshotManager* sman_;               /**< SnapshotManager */
605	>	PairList getExcludedInteractions() { return excludedInteractions_; }
606	>	PairList getOneTwoInteractions() { return oneTwoInteractions_; }
607	>	PairList getOneThreeInteractions() { return oneThreeInteractions_; }
608	>	PairList getOneFourInteractions() { return oneFourInteractions_; }
609
610	+	private:
611	+
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
517	–	double rcut_;       /**< cutoff radius*/
518	–	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 532 | 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:
545	–
546	–	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
555	–	#endif
556	–
693		};
694
695	<	} //namespace oopse
695	>	} //namespace OpenMD
696		#endif //BRAINS_SIMMODEL_HPP
697

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 555 by chuckv, Mon May 30 14:01:52 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (property svn:keywords), Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines