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

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trunk/src/brains/SimInfo.hpp (file contents), Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1808 by gezelter, Mon Oct 22 20:42:10 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"
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, rigid bodies, cutoff groups, constrains).
81	<	* 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.
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
95	<	* @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 126 | 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_;
#	Line 155 | Line 163 | namespace oopse{
163		return nAtoms_;
164		}
165
166	+	/** Returns the number of effective cutoff groups on local processor */
167	+	unsigned int getNLocalCutoffGroups();
168	+
169		/** Returns the number of local bonds */
170		unsigned int getNBonds(){
171		return nBonds_;
#	Line 170 | Line 181 | namespace oopse{
181		return nTorsions_;
182		}
183
184	+	/** Returns the number of local torsions */
185	+	unsigned int getNInversions() {
186	+	return nInversions_;
187	+	}
188		/** Returns the number of local rigid bodies */
189		unsigned int getNRigidBodies() {
190		return nRigidBodies_;
#	Line 204 | Line 219 | namespace oopse{
219		*/
220		Molecule* nextMolecule(MoleculeIterator& i);
221
222	+	/** Returns the total number of fluctuating charges that are present */
223	+	int getNFluctuatingCharges() {
224	+	return nGlobalFluctuatingCharges_;
225	+	}
226	+
227		/** Returns the number of degrees of freedom */
228		int getNdf() {
229		return ndf_ - getFdf();
230		}
231
232	+	/** Returns the number of degrees of freedom (LOCAL) */
233	+	int getNdfLocal() {
234	+	return ndfLocal_;
235	+	}
236	+
237		/** Returns the number of raw degrees of freedom */
238		int getNdfRaw() {
239		return ndfRaw_;
#	Line 226 | Line 251 | namespace oopse{
251
252		int getFdf();
253
254	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
254	>	//getNZconstraint and setNZconstraint ruin the coherence of
255	>	//SimInfo class, need refactoring
256
257		/** Returns the total number of z-constraint molecules in the system */
258		int getNZconstraint() {
#	Line 257 | Line 283 | namespace oopse{
283		return simParams_;
284		}
285
260	–	/** Returns the velocity of center of mass of the whole system.*/
261	–	Vector3d getComVel();
262	–
263	–	/** Returns the center of the mass of the whole system.*/
264	–	Vector3d getCom();
265	–	/** Returns the center of the mass and Center of Mass velocity of the whole system.*/
266	–	void getComAll(Vector3d& com,Vector3d& comVel);
267	–
268	–	/** Returns intertia tensor for the entire system and system Angular Momentum.*/
269	–	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
270	–
271	–	/** Returns system angular momentum */
272	–	Vector3d getAngularMomentum();
273	–
274	–	/** main driver function to interact with fortran during the initialization and molecule migration */
286		void update();
287	+	/**
288	+	* Do final bookkeeping before Force managers need their data.
289	+	*/
290	+	void prepareTopology();
291
292	+
293		/** Returns the local index manager */
294		LocalIndexManager* getLocalIndexManager() {
295		return &localIndexMan_;
#	Line 305 | Line 321 | namespace oopse{
321		return i != molecules_.end() ? i->second : NULL;
322		}
323
324	<	RealType getRcut() {
325	<	return rcut_;
324	>	int getGlobalMolMembership(int id){
325	>	return globalMolMembership_[id];
326		}
327
328	<	RealType getRsw() {
329	<	return rsw_;
330	<	}
328	>	/**
329	>	* returns a vector which maps the local atom index on this
330	>	* processor to the global atom index.  With only one processor,
331	>	* these should be identical.
332	>	*/
333	>	vector<int> getGlobalAtomIndices();
334
335	<	RealType getList() {
336	<	return rlist_;
337	<	}
335	>	/**
336	>	* returns a vector which maps the local cutoff group index on
337	>	* this processor to the global cutoff group index.  With only one
338	>	* processor, these should be identical.
339	>	*/
340	>	vector<int> getGlobalGroupIndices();
341	>
342
343	<	std::string getFinalConfigFileName() {
343	>	string getFinalConfigFileName() {
344		return finalConfigFileName_;
345		}
346	<
347	<	void setFinalConfigFileName(const std::string& fileName) {
346	>
347	>	void setFinalConfigFileName(const string& fileName) {
348		finalConfigFileName_ = fileName;
349		}
350
351	<	std::string getDumpFileName() {
351	>	string getRawMetaData() {
352	>	return rawMetaData_;
353	>	}
354	>	void setRawMetaData(const string& rawMetaData) {
355	>	rawMetaData_ = rawMetaData;
356	>	}
357	>
358	>	string getDumpFileName() {
359		return dumpFileName_;
360		}
361
362	<	void setDumpFileName(const std::string& fileName) {
362	>	void setDumpFileName(const string& fileName) {
363		dumpFileName_ = fileName;
364		}
365
366	<	std::string getStatFileName() {
366	>	string getStatFileName() {
367		return statFileName_;
368		}
369
370	<	void setStatFileName(const std::string& fileName) {
370	>	void setStatFileName(const string& fileName) {
371		statFileName_ = fileName;
372		}
373
374	<	std::string getRestFileName() {
374	>	string getRestFileName() {
375		return restFileName_;
376		}
377
378	<	void setRestFileName(const std::string& fileName) {
378	>	void setRestFileName(const string& fileName) {
379		restFileName_ = fileName;
380		}
381
382		/**
383		* Sets GlobalGroupMembership
354	–	* @see #SimCreator::setGlobalIndex
384		*/
385	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
386	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
385	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
386	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
387		globalGroupMembership_ = globalGroupMembership;
388		}
389
390		/**
391		* Sets GlobalMolMembership
363	–	* @see #SimCreator::setGlobalIndex
392		*/
393	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
394	<	assert(globalMolMembership.size() == nGlobalAtoms_);
393	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
394	>	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
395		globalMolMembership_ = globalMolMembership;
396		}
397
398
399	<	bool isFortranInitialized() {
400	<	return fortranInitialized_;
399	>	bool isTopologyDone() {
400	>	return topologyDone_;
401		}
402
403		bool getCalcBoxDipole() {
404		return calcBoxDipole_;
405		}
406
407	<	//below functions are just forward functions
408	<	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
409	<	//the other hand, has-a relation need composing.
407	>	bool getUseAtomicVirial() {
408	>	return useAtomicVirial_;
409	>	}
410	>
411		/**
412		* Adds property into property map
413		* @param genData GenericData to be added into PropertyMap
#	Line 389 | Line 418 | namespace oopse{
418		* Removes property from PropertyMap by name
419		* @param propName the name of property to be removed
420		*/
421	<	void removeProperty(const std::string& propName);
421	>	void removeProperty(const string& propName);
422
423		/**
424		* clear all of the properties
#	Line 400 | Line 429 | namespace oopse{
429		* Returns all names of properties
430		* @return all names of properties
431		*/
432	<	std::vector<std::string> getPropertyNames();
432	>	vector<string> getPropertyNames();
433
434		/**
435		* Returns all of the properties in PropertyMap
436		* @return all of the properties in PropertyMap
437		*/
438	<	std::vector<GenericData*> getProperties();
438	>	vector<GenericData*> getProperties();
439
440		/**
441		* Returns property
#	Line 414 | Line 443 | namespace oopse{
443		* @return a pointer point to property with propName. If no property named propName
444		* exists, return NULL
445		*/
446	<	GenericData* getPropertyByName(const std::string& propName);
446	>	GenericData* getPropertyByName(const string& propName);
447
448		/**
449	<	* add all exclude pairs of a molecule into exclude list.
449	>	* add all special interaction pairs (including excluded
450	>	* interactions) in a molecule into the appropriate lists.
451		*/
452	<	void addExcludePairs(Molecule* mol);
452	>	void addInteractionPairs(Molecule* mol);
453
454		/**
455	<	* remove all exclude pairs which belong to a molecule from exclude list
455	>	* remove all special interaction pairs which belong to a molecule
456	>	* from the appropriate lists.
457		*/
458	+	void removeInteractionPairs(Molecule* mol);
459
460	<	void removeExcludePairs(Molecule* mol);
461	<
430	<
431	<	/** Returns the unique atom types of local processor in an array */
432	<	std::set<AtomType*> getUniqueAtomTypes();
460	>	/** Returns the set of atom types present in this simulation */
461	>	set<AtomType*> getSimulatedAtomTypes();
462
463	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
463	>	friend ostream& operator <<(ostream& o, SimInfo& info);
464
465		void getCutoff(RealType& rcut, RealType& rsw);
466
467		private:
468
469	<	/** fill up the simtype struct*/
470	<	void setupSimType();
469	>	/** fill up the simtype struct and other simulation-related variables */
470	>	void setupSimVariables();
471
443	–	/**
444	–	* Setup Fortran Simulation
445	–	* @see #setupFortranParallel
446	–	*/
447	–	void setupFortranSim();
472
449	–	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
450	–	void setupCutoff();
451	–
452	–	/** Figure out which coulombic correction method to use and pass to fortran */
453	–	void setupElectrostaticSummationMethod( int isError );
454	–
455	–	/** Figure out which polynomial type to use for the switching function */
456	–	void setupSwitchingFunction();
457	–
473		/** Determine if we need to accumulate the simulation box dipole */
474		void setupAccumulateBoxDipole();
475
#	Line 463 | Line 478 | namespace oopse{
478		void calcNdfRaw();
479		void calcNdfTrans();
480
466	–	ForceField* forceField_;
467	–	Globals* simParams_;
468	–
469	–	std::map<int, Molecule*>  molecules_; /**< Molecule array */
470	–
481		/**
482	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
483	<	* system.
482	>	* Adds molecule stamp and the total number of the molecule with
483	>	* same molecule stamp in the whole system.
484		*/
485		void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
486	+
487	+	// Other classes holdingn important information
488	+	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
489	+	Globals* simParams_;     /**< provides access to simulation parameters set by user */
490	+
491	+	///  Counts of local objects
492	+	int nAtoms_;              /**< number of atoms in local processor */
493	+	int nBonds_;              /**< number of bonds in local processor */
494	+	int nBends_;              /**< number of bends in local processor */
495	+	int nTorsions_;           /**< number of torsions in local processor */
496	+	int nInversions_;         /**< number of inversions in local processor */
497	+	int nRigidBodies_;        /**< number of rigid bodies in local processor */
498	+	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
499	+	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
500	+	int nConstraints_;        /**< number of constraints in local processors */
501	+	int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */
502
503	<	//degress of freedom
504	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
505	<	int fdf_local;       /**< number of frozen degrees of freedom */
506	<	int fdf_;            /**< number of frozen degrees of freedom */
481	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
482	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
483	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
484	<
485	<	//number of global objects
486	<	int nGlobalMols_;       /**< number of molecules in the system */
487	<	int nGlobalAtoms_;   /**< number of atoms in the system */
488	<	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
503	>	/// Counts of global objects
504	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
505	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
506	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
507		int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
508	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
508	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
509	>	int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
510	>
511	>
512	>	/// Degress of freedom
513	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
514	>	int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
515	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
516	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
517	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
518	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
519	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
520	>
521	>	/// logicals
522	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
523	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
524	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
525	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
526	>	bool usesFluctuatingCharges_; /**< are there fluctuating charges? */
527	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
528	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
529	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
530	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
531	>
532	>	public:
533	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
534	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
535	>	bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
536	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
537	>	bool requiresPrepair() { return requiresPrepair_; }
538	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
539	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
540	>
541	>	private:
542	>	/// Data structures holding primary simulation objects
543	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
544	>
545	>	/// Stamps are templates for objects that are then used to create
546	>	/// groups of objects.  For example, a molecule stamp contains
547	>	/// information on how to build that molecule (i.e. the topology,
548	>	/// the atoms, the bonds, etc.)  Once the system is built, the
549	>	/// stamps are no longer useful.
550	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
551	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
552	>
553		/**
554	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
555	<	* corresponding content is the global index of cutoff group this atom belong to.
556	<	* It is filled by SimCreator once and only once, since it never changed during the simulation.
554	>	* A vector that maps between the global index of an atom, and the
555	>	* global index of cutoff group the atom belong to.  It is filled
556	>	* by SimCreator once and only once, since it never changed during
557	>	* the simulation.  It should be nGlobalAtoms_ in size.
558		*/
559	<	std::vector<int> globalGroupMembership_;
559	>	vector<int> globalGroupMembership_;
560	>	public:
561	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
562	>	private:
563
564		/**
565	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
566	<	* corresponding content is the global index of molecule this atom belong to.
567	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
565	>	* A vector that maps between the global index of an atom and the
566	>	* global index of the molecule the atom belongs to.  It is filled
567	>	* by SimCreator once and only once, since it is never changed
568	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
569		*/
570	<	std::vector<int> globalMolMembership_;
570	>	vector<int> globalMolMembership_;
571
572	<
573	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
574	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
575	<
576	<	//number of local objects
577	<	int nAtoms_;                        /**< number of atoms in local processor */
578	<	int nBonds_;                        /**< number of bonds in local processor */
579	<	int nBends_;                        /**< number of bends in local processor */
580	<	int nTorsions_;                    /**< number of torsions in local processor */
581	<	int nRigidBodies_;              /**< number of rigid bodies in local processor */
582	<	int nIntegrableObjects_;    /**< number of integrable objects in local processor */
583	<	int nCutoffGroups_;             /**< number of cutoff groups in local processor */
584	<	int nConstraints_;              /**< number of constraints in local processors */
572	>	/**
573	>	* A vector that maps between the local index of an atom and the
574	>	* index of the AtomType.
575	>	*/
576	>	vector<int> identArray_;
577	>	public:
578	>	vector<int> getIdentArray() { return identArray_; }
579	>	private:
580	>
581	>	/**
582	>	* A vector which contains the fractional contribution of an
583	>	* atom's mass to the total mass of the cutoffGroup that atom
584	>	* belongs to.  In the case of single atom cutoff groups, the mass
585	>	* factor for that atom is 1.  For massless atoms, the factor is
586	>	* also 1.
587	>	*/
588	>	vector<RealType> massFactors_;
589	>	public:
590	>	vector<RealType> getMassFactors() { return massFactors_; }
591
592	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
593	<	Exclude exclude_;
594	<	PropertyMap properties_;                  /**< Generic Property */
595	<	SnapshotManager* sman_;               /**< SnapshotManager */
592	>	PairList* getExcludedInteractions() { return &excludedInteractions_; }
593	>	PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
594	>	PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
595	>	PairList* getOneFourInteractions() { return &oneFourInteractions_; }
596
597	+	private:
598	+
599	+	/// lists to handle atoms needing special treatment in the non-bonded interactions
600	+	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
601	+	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
602	+	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
603	+	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
604	+
605	+	PropertyMap properties_;       /**< Generic Properties can be added */
606	+	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
607	+
608		/**
609	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
610	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
611	<	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
612	<	* to make a efficient data moving plan.
609	>	* The reason to have a local index manager is that when molecule
610	>	* is migrating to other processors, the atoms and the
611	>	* rigid-bodies will release their local indices to
612	>	* LocalIndexManager. Combining the information of molecule
613	>	* migrating to current processor, Migrator class can query the
614	>	* LocalIndexManager to make a efficient data moving plan.
615		*/
616		LocalIndexManager localIndexMan_;
617
618	<	//file names
619	<	std::string finalConfigFileName_;
620	<	std::string dumpFileName_;
621	<	std::string statFileName_;
622	<	std::string restFileName_;
618	>	// unparsed MetaData block for storing in Dump and EOR files:
619	>	string rawMetaData_;
620	>
621	>	// file names
622	>	string finalConfigFileName_;
623	>	string dumpFileName_;
624	>	string statFileName_;
625	>	string restFileName_;
626
538	–	RealType rcut_;       /**< cutoff radius*/
539	–	RealType rsw_;        /**< radius of switching function*/
540	–	RealType rlist_;      /**< neighbor list radius */
627
628	<	bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
629	<
630	<	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate the simulation box dipole moment */
631	<
632	<	#ifdef IS_MPI
633	<	//in Parallel version, we need MolToProc
628	>	bool topologyDone_;  /** flag to indicate whether the topology has
629	>	been scanned and all the relevant
630	>	bookkeeping has been done*/
631	>
632	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
633	>	the simulation box dipole moment */
634	>
635	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
636	>	Atomic Virials to calculate the pressure */
637	>
638		public:
639	+	/**
640	+	* return an integral objects by its global index. In MPI
641	+	* version, if the StuntDouble with specified global index does
642	+	* not belong to local processor, a NULL will be return.
643	+	*/
644	+	StuntDouble* getIOIndexToIntegrableObject(int index);
645	+	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
646	+
647	+	private:
648	+	vector<StuntDouble*> IOIndexToIntegrableObject;
649	+
650	+	public:
651
652		/**
653		* Finds the processor where a molecule resides
#	Line 556 | Line 658 | namespace oopse{
658		//assert(globalIndex < molToProcMap_.size());
659		return molToProcMap_[globalIndex];
660		}
661	<
661	>
662		/**
663		* Set MolToProcMap array
562	–	* @see #SimCreator::divideMolecules
664		*/
665	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
665	>	void setMolToProcMap(const vector<int>& molToProcMap) {
666		molToProcMap_ = molToProcMap;
667		}
668
669		private:
569	–
570	–	void setupFortranParallel();
670
671		/**
672	<	* The size of molToProcMap_ is equal to total number of molecules in the system.
673	<	*  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
674	<	* once.
672	>	* The size of molToProcMap_ is equal to total number of molecules
673	>	* in the system.  It maps a molecule to the processor on which it
674	>	* resides. it is filled by SimCreator once and only once.
675		*/
676	<	std::vector<int> molToProcMap_;
676	>	vector<int> molToProcMap_;
677
579	–	#endif
580	–
678		};
679
680	<	} //namespace oopse
680	>	} //namespace OpenMD
681		#endif //BRAINS_SIMMODEL_HPP
682

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
branches/development/src/brains/SimInfo.hpp (property svn:keywords), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

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