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

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trunk/src/brains/SimInfo.hpp (file contents), Revision 764 by gezelter, Mon Nov 21 22:59:21 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1764 by gezelter, Tue Jul 3 18:32:27 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 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(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 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 degrees of freedom (LOCAL) */
237	+	int getNdfLocal() {
238	+	return ndfLocal_;
239	+	}
240	+
241		/** Returns the number of raw degrees of freedom */
242		int getNdfRaw() {
243		return ndfRaw_;
#	Line 220 | Line 248 | namespace oopse{
248		return ndfTrans_;
249		}
250
251	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
251	>	/** sets the current number of frozen degrees of freedom */
252	>	void setFdf(int fdf) {
253	>	fdf_local = fdf;
254	>	}
255	>
256	>	int getFdf();
257	>
258	>	//getNZconstraint and setNZconstraint ruin the coherence of
259	>	//SimInfo class, need refactoring
260
261		/** Returns the total number of z-constraint molecules in the system */
262		int getNZconstraint() {
#	Line 251 | Line 287 | namespace oopse{
287		return simParams_;
288		}
289
290	<	/** Returns the velocity of center of mass of the whole system.*/
291	<	Vector3d getComVel();
292	<
293	<	/** Returns the center of the mass of the whole system.*/
294	<	Vector3d getCom();
259	<	/** Returns the center of the mass and Center of Mass velocity of the whole system.*/
260	<	void getComAll(Vector3d& com,Vector3d& comVel);
261	<
262	<	/** Returns intertia tensor for the entire system and system Angular Momentum.*/
263	<	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
264	<
265	<	/** Returns system angular momentum */
266	<	Vector3d getAngularMomentum();
290	>	void update();
291	>	/**
292	>	* Do final bookkeeping before Force managers need their data.
293	>	*/
294	>	void prepareTopology();
295
268	–	/** main driver function to interact with fortran during the initialization and molecule migration */
269	–	void update();
296
297		/** Returns the local index manager */
298		LocalIndexManager* getLocalIndexManager() {
#	Line 299 | Line 325 | namespace oopse{
325		return i != molecules_.end() ? i->second : NULL;
326		}
327
328	<	double getRcut() {
329	<	return rcut_;
328	>	int getGlobalMolMembership(int id){
329	>	return globalMolMembership_[id];
330		}
331
332	<	double getRsw() {
333	<	return rsw_;
334	<	}
332	>	/**
333	>	* returns a vector which maps the local atom index on this
334	>	* processor to the global atom index.  With only one processor,
335	>	* these should be identical.
336	>	*/
337	>	vector<int> getGlobalAtomIndices();
338
339	<	double getList() {
340	<	return rlist_;
341	<	}
339	>	/**
340	>	* returns a vector which maps the local cutoff group index on
341	>	* this processor to the global cutoff group index.  With only one
342	>	* processor, these should be identical.
343	>	*/
344	>	vector<int> getGlobalGroupIndices();
345	>
346
347	<	std::string getFinalConfigFileName() {
347	>	string getFinalConfigFileName() {
348		return finalConfigFileName_;
349		}
350	<
351	<	void setFinalConfigFileName(const std::string& fileName) {
350	>
351	>	void setFinalConfigFileName(const string& fileName) {
352		finalConfigFileName_ = fileName;
353		}
354
355	<	std::string getDumpFileName() {
355	>	string getRawMetaData() {
356	>	return rawMetaData_;
357	>	}
358	>	void setRawMetaData(const string& rawMetaData) {
359	>	rawMetaData_ = rawMetaData;
360	>	}
361	>
362	>	string getDumpFileName() {
363		return dumpFileName_;
364		}
365
366	<	void setDumpFileName(const std::string& fileName) {
366	>	void setDumpFileName(const string& fileName) {
367		dumpFileName_ = fileName;
368		}
369
370	<	std::string getStatFileName() {
370	>	string getStatFileName() {
371		return statFileName_;
372		}
373
374	<	void setStatFileName(const std::string& fileName) {
374	>	void setStatFileName(const string& fileName) {
375		statFileName_ = fileName;
376		}
377
378	<	std::string getRestFileName() {
378	>	string getRestFileName() {
379		return restFileName_;
380		}
381
382	<	void setRestFileName(const std::string& fileName) {
382	>	void setRestFileName(const string& fileName) {
383		restFileName_ = fileName;
384		}
385
#	Line 347 | Line 387 | namespace oopse{
387		* Sets GlobalGroupMembership
388		* @see #SimCreator::setGlobalIndex
389		*/
390	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
391	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
390	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
391	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
392		globalGroupMembership_ = globalGroupMembership;
393		}
394
#	Line 356 | Line 396 | namespace oopse{
396		* Sets GlobalMolMembership
397		* @see #SimCreator::setGlobalIndex
398		*/
399	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
400	<	assert(globalMolMembership.size() == nGlobalAtoms_);
399	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
400	>	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
401		globalMolMembership_ = globalMolMembership;
402		}
403
404
405	<	bool isFortranInitialized() {
406	<	return fortranInitialized_;
405	>	bool isTopologyDone() {
406	>	return topologyDone_;
407		}
408
409	<	//below functions are just forward functions
410	<	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
411	<	//the other hand, has-a relation need composing.
409	>	bool getCalcBoxDipole() {
410	>	return calcBoxDipole_;
411	>	}
412	>
413	>	bool getUseAtomicVirial() {
414	>	return useAtomicVirial_;
415	>	}
416	>
417		/**
418		* Adds property into property map
419		* @param genData GenericData to be added into PropertyMap
#	Line 379 | Line 424 | namespace oopse{
424		* Removes property from PropertyMap by name
425		* @param propName the name of property to be removed
426		*/
427	<	void removeProperty(const std::string& propName);
427	>	void removeProperty(const string& propName);
428
429		/**
430		* clear all of the properties
#	Line 390 | Line 435 | namespace oopse{
435		* Returns all names of properties
436		* @return all names of properties
437		*/
438	<	std::vector<std::string> getPropertyNames();
438	>	vector<string> getPropertyNames();
439
440		/**
441		* Returns all of the properties in PropertyMap
442		* @return all of the properties in PropertyMap
443		*/
444	<	std::vector<GenericData*> getProperties();
444	>	vector<GenericData*> getProperties();
445
446		/**
447		* Returns property
#	Line 404 | Line 449 | namespace oopse{
449		* @return a pointer point to property with propName. If no property named propName
450		* exists, return NULL
451		*/
452	<	GenericData* getPropertyByName(const std::string& propName);
452	>	GenericData* getPropertyByName(const string& propName);
453
454		/**
455	<	* add all exclude pairs of a molecule into exclude list.
455	>	* add all special interaction pairs (including excluded
456	>	* interactions) in a molecule into the appropriate lists.
457		*/
458	<	void addExcludePairs(Molecule* mol);
458	>	void addInteractionPairs(Molecule* mol);
459
460		/**
461	<	* remove all exclude pairs which belong to a molecule from exclude list
461	>	* remove all special interaction pairs which belong to a molecule
462	>	* from the appropriate lists.
463		*/
464	+	void removeInteractionPairs(Molecule* mol);
465
466	<	void removeExcludePairs(Molecule* mol);
467	<
420	<
421	<	/** Returns the unique atom types of local processor in an array */
422	<	std::set<AtomType*> getUniqueAtomTypes();
466	>	/** Returns the set of atom types present in this simulation */
467	>	set<AtomType*> getSimulatedAtomTypes();
468
469	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
469	>	friend ostream& operator <<(ostream& o, SimInfo& info);
470
471	<	void getCutoff(double& rcut, double& rsw);
471	>	void getCutoff(RealType& rcut, RealType& rsw);
472
473		private:
474
475	<	/** fill up the simtype struct*/
476	<	void setupSimType();
475	>	/** fill up the simtype struct and other simulation-related variables */
476	>	void setupSimVariables();
477
433	–	/**
434	–	* Setup Fortran Simulation
435	–	* @see #setupFortranParallel
436	–	*/
437	–	void setupFortranSim();
438	–
439	–	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
440	–	void setupCutoff();
441	–
442	–	/** Figure out which coulombic correction method to use and pass to fortran */
443	–	void setupElectrostaticSummationMethod( int isError );
478
479	<	/** Figure out which polynomial type to use for the switching function */
480	<	void setupSwitchingFunction();
479	>	/** Determine if we need to accumulate the simulation box dipole */
480	>	void setupAccumulateBoxDipole();
481
482		/** Calculates the number of degress of freedom in the whole system */
483		void calcNdf();
#	Line 451 | Line 485 | namespace oopse{
485		void calcNdfTrans();
486
487		/**
488	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
489	<	* system.
488	>	* Adds molecule stamp and the total number of the molecule with
489	>	* same molecule stamp in the whole system.
490		*/
491		void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
492
493	<	MakeStamps* stamps_;
494	<	ForceField* forceField_;
495	<	Globals* simParams_;
493	>	// Other classes holdingn important information
494	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
495	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
496
497	<	std::map<int, Molecule*>  molecules_; /**< Molecule array */
497	>	///  Counts of local objects
498	>	int nAtoms_;              /**< number of atoms in local processor */
499	>	int nBonds_;              /**< number of bonds in local processor */
500	>	int nBends_;              /**< number of bends in local processor */
501	>	int nTorsions_;           /**< number of torsions in local processor */
502	>	int nInversions_;         /**< number of inversions in local processor */
503	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
504	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
505	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
506	>	int nConstraints_;        /**< number of constraints in local processors */
507	>	int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */
508
509	<	//degress of freedom
510	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
511	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
512	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
469	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
470	<
471	<	//number of global objects
472	<	int nGlobalMols_;       /**< number of molecules in the system */
473	<	int nGlobalAtoms_;   /**< number of atoms in the system */
474	<	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
509	>	/// Counts of global objects
510	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
511	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
512	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
513		int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
514	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
514	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
515	>	int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
516	>
517	>
518	>	/// Degress of freedom
519	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
520	>	int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
521	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
522	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
523	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
524	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
525	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
526	>
527	>	/// logicals
528	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
529	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
530	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
531	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
532	>	bool usesFluctuatingCharges_; /**< are there fluctuating charges? */
533	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
534	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
535	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
536	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
537	>
538	>	public:
539	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
540	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
541	>	bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
542	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
543	>	bool requiresPrepair() { return requiresPrepair_; }
544	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
545	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
546	>
547	>	private:
548	>	/// Data structures holding primary simulation objects
549	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
550	>
551	>	/// Stamps are templates for objects that are then used to create
552	>	/// groups of objects.  For example, a molecule stamp contains
553	>	/// information on how to build that molecule (i.e. the topology,
554	>	/// the atoms, the bonds, etc.)  Once the system is built, the
555	>	/// stamps are no longer useful.
556	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
557	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
558	>
559		/**
560	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
561	<	* corresponding content is the global index of cutoff group this atom belong to.
562	<	* It is filled by SimCreator once and only once, since it never changed during the simulation.
560	>	* A vector that maps between the global index of an atom, and the
561	>	* global index of cutoff group the atom belong to.  It is filled
562	>	* by SimCreator once and only once, since it never changed during
563	>	* the simulation.  It should be nGlobalAtoms_ in size.
564		*/
565	<	std::vector<int> globalGroupMembership_;
565	>	vector<int> globalGroupMembership_;
566	>	public:
567	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
568	>	private:
569
570		/**
571	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
572	<	* corresponding content is the global index of molecule this atom belong to.
573	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
571	>	* A vector that maps between the global index of an atom and the
572	>	* global index of the molecule the atom belongs to.  It is filled
573	>	* by SimCreator once and only once, since it is never changed
574	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
575		*/
576	<	std::vector<int> globalMolMembership_;
576	>	vector<int> globalMolMembership_;
577
578	<
579	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
580	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
581	<
582	<	//number of local objects
583	<	int nAtoms_;                        /**< number of atoms in local processor */
584	<	int nBonds_;                        /**< number of bonds in local processor */
585	<	int nBends_;                        /**< number of bends in local processor */
586	<	int nTorsions_;                    /**< number of torsions in local processor */
587	<	int nRigidBodies_;              /**< number of rigid bodies in local processor */
588	<	int nIntegrableObjects_;    /**< number of integrable objects in local processor */
589	<	int nCutoffGroups_;             /**< number of cutoff groups in local processor */
590	<	int nConstraints_;              /**< number of constraints in local processors */
578	>	/**
579	>	* A vector that maps between the local index of an atom and the
580	>	* index of the AtomType.
581	>	*/
582	>	vector<int> identArray_;
583	>	public:
584	>	vector<int> getIdentArray() { return identArray_; }
585	>	private:
586	>
587	>	/**
588	>	* A vector which contains the fractional contribution of an
589	>	* atom's mass to the total mass of the cutoffGroup that atom
590	>	* belongs to.  In the case of single atom cutoff groups, the mass
591	>	* factor for that atom is 1.  For massless atoms, the factor is
592	>	* also 1.
593	>	*/
594	>	vector<RealType> massFactors_;
595	>	public:
596	>	vector<RealType> getMassFactors() { return massFactors_; }
597
598	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
599	<	Exclude exclude_;
600	<	PropertyMap properties_;                  /**< Generic Property */
601	<	SnapshotManager* sman_;               /**< SnapshotManager */
598	>	PairList* getExcludedInteractions() { return &excludedInteractions_; }
599	>	PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
600	>	PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
601	>	PairList* getOneFourInteractions() { return &oneFourInteractions_; }
602
603	+	private:
604	+
605	+	/// lists to handle atoms needing special treatment in the non-bonded interactions
606	+	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
607	+	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
608	+	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
609	+	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
610	+
611	+	PropertyMap properties_;       /**< Generic Properties can be added */
612	+	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
613	+
614		/**
615	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
616	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
617	<	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
618	<	* to make a efficient data moving plan.
615	>	* The reason to have a local index manager is that when molecule
616	>	* is migrating to other processors, the atoms and the
617	>	* rigid-bodies will release their local indices to
618	>	* LocalIndexManager. Combining the information of molecule
619	>	* migrating to current processor, Migrator class can query the
620	>	* LocalIndexManager to make a efficient data moving plan.
621		*/
622		LocalIndexManager localIndexMan_;
623
624	<	//file names
625	<	std::string finalConfigFileName_;
626	<	std::string dumpFileName_;
627	<	std::string statFileName_;
628	<	std::string restFileName_;
624	>	// unparsed MetaData block for storing in Dump and EOR files:
625	>	string rawMetaData_;
626	>
627	>	// file names
628	>	string finalConfigFileName_;
629	>	string dumpFileName_;
630	>	string statFileName_;
631	>	string restFileName_;
632
524	–	double rcut_;       /**< cutoff radius*/
525	–	double rsw_;        /**< radius of switching function*/
526	–	double rlist_;      /**< neighbor list radius */
633
634	<	bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
635	<
636	<	#ifdef IS_MPI
637	<	//in Parallel version, we need MolToProc
634	>	bool topologyDone_;  /** flag to indicate whether the topology has
635	>	been scanned and all the relevant
636	>	bookkeeping has been done*/
637	>
638	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
639	>	the simulation box dipole moment */
640	>
641	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
642	>	Atomic Virials to calculate the pressure */
643	>
644		public:
645	+	/**
646	+	* return an integral objects by its global index. In MPI
647	+	* version, if the StuntDouble with specified global index does
648	+	* not belong to local processor, a NULL will be return.
649	+	*/
650	+	StuntDouble* getIOIndexToIntegrableObject(int index);
651	+	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
652	+
653	+	private:
654	+	vector<StuntDouble*> IOIndexToIntegrableObject;
655	+
656	+	public:
657
658		/**
659		* Finds the processor where a molecule resides
#	Line 540 | Line 664 | namespace oopse{
664		//assert(globalIndex < molToProcMap_.size());
665		return molToProcMap_[globalIndex];
666		}
667	<
667	>
668		/**
669		* Set MolToProcMap array
670		* @see #SimCreator::divideMolecules
671		*/
672	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
672	>	void setMolToProcMap(const vector<int>& molToProcMap) {
673		molToProcMap_ = molToProcMap;
674		}
675
676		private:
553	–
554	–	void setupFortranParallel();
677
678		/**
679	<	* The size of molToProcMap_ is equal to total number of molecules in the system.
680	<	*  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
681	<	* once.
679	>	* The size of molToProcMap_ is equal to total number of molecules
680	>	* in the system.  It maps a molecule to the processor on which it
681	>	* resides. it is filled by SimCreator once and only once.
682		*/
683	<	std::vector<int> molToProcMap_;
683	>	vector<int> molToProcMap_;
684
563	–	#endif
564	–
685		};
686
687	<	} //namespace oopse
687	>	} //namespace OpenMD
688		#endif //BRAINS_SIMMODEL_HPP
689

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 764 by gezelter, Mon Nov 21 22:59:21 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (property svn:keywords), Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

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