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root/OpenMD/branches/development/src/brains/SimInfo.hpp
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trunk/src/brains/SimInfo.hpp (file contents), Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1581 by gezelter, Mon Jun 13 22:13:12 2011 UTC

# 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
67 < #define __OPENMD_C
68 < #include "brains/fSimulation.h"
69 <
67 > using namespace std;
68   namespace OpenMD{
69 <
72 <  //forward decalration
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 One of the heavy weight classes of OpenMD, SimInfo maintains a list of molecules.
78 <    * The Molecule class maintains all of the concrete objects
79 <    * (atoms, bond, bend, torsions, inversions, rigid bodies, cutoff groups,
80 <    * constraints). In both the single and parallel versions, atoms and
81 <    * rigid bodies have both global and local indices.  The local index is
82 <    * not relevant to molecules or cutoff groups.
83 <    */
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 +     *
99       * @param simParams
96 –     * @note
100       */
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 OpenMD{
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 OpenMD{
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 231 | Line 244 | namespace OpenMD{
244  
245      int getFdf();
246      
247 <    //getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
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 267 | Line 281 | namespace OpenMD{
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 <    /** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/
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 det(I) so dV/dr can be calculated*/
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 <    /** main driver function to interact with fortran during the initialization and molecule migration */
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 318 | Line 341 | namespace OpenMD{
341        return globalMolMembership_[id];
342      }
343  
344 <    RealType getRcut() {
345 <      return rcut_;
346 <    }
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 <    RealType getRsw() {
352 <      return rsw_;
353 <    }
354 <
355 <    RealType getList() {
356 <      return rlist_;
357 <    }
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) {
363 >    void setFinalConfigFileName(const string& fileName) {
364        finalConfigFileName_ = fileName;
365      }
366  
367 <    std::string getRawMetaData() {
367 >    string getRawMetaData() {
368        return rawMetaData_;
369      }
370 <    void setRawMetaData(const std::string& rawMetaData) {
370 >    void setRawMetaData(const string& rawMetaData) {
371        rawMetaData_ = rawMetaData;
372      }
373          
374 <    std::string getDumpFileName() {
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 373 | Line 399 | namespace OpenMD{
399       * Sets GlobalGroupMembership
400       * @see #SimCreator::setGlobalIndex
401       */  
402 <    void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
402 >    void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
403        assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
404        globalGroupMembership_ = globalGroupMembership;
405      }
# Line 382 | Line 408 | namespace OpenMD{
408       * Sets GlobalMolMembership
409       * @see #SimCreator::setGlobalIndex
410       */        
411 <    void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
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      bool getCalcBoxDipole() {
# Line 400 | Line 426 | namespace OpenMD{
426        return useAtomicVirial_;
427      }
428  
403 –    //below functions are just forward functions
404 –    //To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
405 –    //the other hand, has-a relation need composing.
429      /**
430       * Adds property into property map
431       * @param genData GenericData to be added into PropertyMap
# Line 413 | Line 436 | namespace OpenMD{
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 424 | Line 447 | namespace OpenMD{
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 438 | Line 461 | namespace OpenMD{
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 special interaction pairs (including excluded
# Line 452 | Line 475 | namespace OpenMD{
475       */
476      void removeInteractionPairs(Molecule* mol);
477  
478 <
479 <    /** Returns the unique atom types of local processor in an array */
457 <    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(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  
468 –    /**
469 –     * Setup Fortran Simulation
470 –     * @see #setupFortranParallel
471 –     */
472 –    void setupFortranSim();
490  
474 –    /** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
475 –    void setupCutoff();
476 –
477 –    /** Figure out which coulombic correction method to use and pass to fortran */
478 –    void setupElectrostaticSummationMethod( int isError );
479 –
480 –    /** Figure out which polynomial type to use for the switching function */
481 –    void setupSwitchingFunction();
482 –
491      /** Determine if we need to accumulate the simulation box dipole */
492      void setupAccumulateBoxDipole();
493  
# Line 488 | Line 496 | namespace OpenMD{
496      void calcNdfRaw();
497      void calcNdfTrans();
498  
491 –    ForceField* forceField_;      
492 –    Globals* simParams_;
493 –
494 –    std::map<int, Molecule*>  molecules_; /**< Molecule array */
495 –
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);
501 –        
502 –    //degress of freedom
503 –    int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
504 –    int fdf_local;       /**< number of frozen degrees of freedom */
505 –    int fdf_;            /**< number of frozen degrees of freedom */
506 –    int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
507 –    int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
508 –    int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
509 –        
510 –    //number of global objects
511 –    int nGlobalMols_;       /**< number of molecules in the system */
512 –    int nGlobalAtoms_;   /**< number of atoms in the system */
513 –    int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
514 –    int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
515 –    int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
516 –    /**
517 –     * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
518 –     * corresponding content is the global index of cutoff group this atom belong to.
519 –     * It is filled by SimCreator once and only once, since it never changed during the simulation.
520 –     */
521 –    std::vector<int> globalGroupMembership_;
504  
505 <    /**
506 <     * the size of globalMolMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
507 <     * corresponding content is the global index of molecule this atom belong to.
526 <     * It is filled by SimCreator once and only once, since it is never changed during the simulation.
527 <     */
528 <    std::vector<int> globalMolMembership_;        
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 <        
531 <    std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
532 <    std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */        
533 <        
534 <    //number of local objects
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 */
# Line 541 | Line 516 | namespace OpenMD{
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 +    /// 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 (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 <    simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
536 <    PairList excludedInteractions_;      
537 <    PairList oneTwoInteractions_;      
538 <    PairList oneThreeInteractions_;      
539 <    PairList oneFourInteractions_;      
540 <    PropertyMap properties_;                  /**< Generic Property */
541 <    SnapshotManager* sman_;               /**< SnapshotManager */
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 +     * 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 +    vector<int> globalGroupMembership_;
573 +  public:
574 +    vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
575 +  private:
576 +
577 +    /**
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 +    vector<int> globalMolMembership_;
584 +
585      /**
586 <     * The reason to have a local index manager is that when molecule is migrating to other processors,
587 <     * the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
588 <     * information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
589 <     * to make a efficient data moving plan.
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 >    PairList getExcludedInteractions() { return excludedInteractions_; }
606 >    PairList getOneTwoInteractions() { return oneTwoInteractions_; }
607 >    PairList getOneThreeInteractions() { return oneThreeInteractions_; }
608 >    PairList getOneFourInteractions() { return oneFourInteractions_; }
609 >
610 >  private:
611 >              
612 >    /// lists to handle atoms needing special treatment in the non-bonded interactions
613 >    PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
614 >    PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
615 >    PairList oneThreeInteractions_;  /**< atoms sharing a Bend */    
616 >    PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
617 >
618 >    PropertyMap properties_;       /**< Generic Properties can be added */
619 >    SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
620 >
621 >    /**
622 >     * The reason to have a local index manager is that when molecule
623 >     * is migrating to other processors, the atoms and the
624 >     * rigid-bodies will release their local indices to
625 >     * LocalIndexManager. Combining the information of molecule
626 >     * migrating to current processor, Migrator class can query the
627 >     * LocalIndexManager to make a efficient data moving plan.
628       */        
629      LocalIndexManager localIndexMan_;
630  
631      // unparsed MetaData block for storing in Dump and EOR files:
632 <    std::string rawMetaData_;
632 >    string rawMetaData_;
633  
634 <    //file names
635 <    std::string finalConfigFileName_;
636 <    std::string dumpFileName_;
637 <    std::string statFileName_;
638 <    std::string restFileName_;
634 >    // file names
635 >    string finalConfigFileName_;
636 >    string dumpFileName_;
637 >    string statFileName_;
638 >    string restFileName_;
639          
570 –    RealType rcut_;       /**< cutoff radius*/
571 –    RealType rsw_;        /**< radius of switching function*/
572 –    RealType rlist_;      /**< neighbor list radius */
640  
641 <    int ljsp_; /**< use shifted potential for LJ*/
642 <    int ljsf_; /**< use shifted force for LJ*/
643 <
577 <    bool fortranInitialized_; /**< flag indicate whether fortran side
578 <                                 is initialized */
641 >    bool topologyDone_;  /** flag to indicate whether the topology has
642 >                             been scanned and all the relevant
643 >                             bookkeeping has been done*/
644      
645      bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
646                              the simulation box dipole moment */
647      
648      bool useAtomicVirial_; /**< flag to indicate whether or not we use
649                                Atomic Virials to calculate the pressure */
650 <
651 <    public:
587 <     /**
588 <      * return an integral objects by its global index. In MPI version, if the StuntDouble with specified
589 <      * global index does not belong to local processor, a NULL will be return.
590 <      */
591 <      StuntDouble* getIOIndexToIntegrableObject(int index);
592 <      void setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v);
593 <    private:
594 <      std::vector<StuntDouble*> IOIndexToIntegrableObject;
595 <  //public:
596 <    //void setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v);
650 >    
651 >  public:
652      /**
653 <     * return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
654 <     * global index does not belong to local processor, a NULL will be return.
655 <     */
656 <    //StuntDouble* getStuntDoubleFromGlobalIndex(int index);
657 <  //private:
658 <    //std::vector<StuntDouble*> sdByGlobalIndex_;
653 >     * return an integral objects by its global index. In MPI
654 >     * version, if the StuntDouble with specified global index does
655 >      * not belong to local processor, a NULL will be return.
656 >      */
657 >    StuntDouble* getIOIndexToIntegrableObject(int index);
658 >    void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
659      
660 <    //in Parallel version, we need MolToProc
660 >  private:
661 >    vector<StuntDouble*> IOIndexToIntegrableObject;
662 >    
663    public:
664                  
665      /**
# Line 614 | Line 671 | namespace OpenMD{
671        //assert(globalIndex < molToProcMap_.size());
672        return molToProcMap_[globalIndex];
673      }
674 <
674 >    
675      /**
676       * Set MolToProcMap array
677       * @see #SimCreator::divideMolecules
678       */
679 <    void setMolToProcMap(const std::vector<int>& molToProcMap) {
679 >    void setMolToProcMap(const vector<int>& molToProcMap) {
680        molToProcMap_ = molToProcMap;
681      }
682          
683    private:
627 –
628 –    void setupFortranParallel();
684          
685      /**
686       * The size of molToProcMap_ is equal to total number of molecules
687       * in the system.  It maps a molecule to the processor on which it
688       * resides. it is filled by SimCreator once and only once.
689       */        
690 <    std::vector<int> molToProcMap_;
690 >    vector<int> molToProcMap_;
691  
637 –
692    };
693  
694   } //namespace OpenMD

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