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root/OpenMD/branches/development/src/brains/SimInfo.hpp
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Comparing branches/development/src/brains/SimInfo.hpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1553 by gezelter, Fri Apr 29 17:25:12 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 231 | Line 241 | namespace OpenMD{
241  
242      int getFdf();
243      
244 <    //getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
244 >    //getNZconstraint and setNZconstraint ruin the coherence of
245 >    //SimInfo class, need refactoring
246          
247      /** Returns the total number of z-constraint molecules in the system */
248      int getNZconstraint() {
# Line 267 | Line 278 | namespace OpenMD{
278  
279      /** Returns the center of the mass of the whole system.*/
280      Vector3d getCom();
281 <   /** Returns the center of the mass and Center of Mass velocity of the whole system.*/
281 >    /** Returns the center of the mass and Center of Mass velocity of
282 >        the whole system.*/
283      void getComAll(Vector3d& com,Vector3d& comVel);
284  
285 <    /** Returns intertia tensor for the entire system and system Angular Momentum.*/
285 >    /** Returns intertia tensor for the entire system and system
286 >        Angular Momentum.*/
287      void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
288      
289      /** Returns system angular momentum */
290      Vector3d getAngularMomentum();
291  
292 <    /** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/
292 >    /** Returns volume of system as estimated by an ellipsoid defined
293 >        by the radii of gyration*/
294      void getGyrationalVolume(RealType &vol);
295 <    /** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/
295 >    /** Overloaded version of gyrational volume that also returns
296 >        det(I) so dV/dr can be calculated*/
297      void getGyrationalVolume(RealType &vol, RealType &detI);
298 <    /** main driver function to interact with fortran during the initialization and molecule migration */
298 >
299      void update();
300 +    /**
301 +     * Setup Fortran Simulation
302 +     */
303 +    void setupFortran();
304  
305 +
306      /** Returns the local index manager */
307      LocalIndexManager* getLocalIndexManager() {
308        return &localIndexMan_;
# Line 318 | Line 338 | namespace OpenMD{
338        return globalMolMembership_[id];
339      }
340  
341 <    RealType getRcut() {
342 <      return rcut_;
343 <    }
344 <
345 <    RealType getRsw() {
346 <      return rsw_;
347 <    }
348 <
349 <    RealType getList() {
350 <      return rlist_;
351 <    }
341 >    /**
342 >     * returns a vector which maps the local atom index on this
343 >     * processor to the global atom index.  With only one processor,
344 >     * these should be identical.
345 >     */
346 >    vector<int> getGlobalAtomIndices();
347 >
348 >    /**
349 >     * returns a vector which maps the local cutoff group index on
350 >     * this processor to the global cutoff group index.  With only one
351 >     * processor, these should be identical.
352 >     */
353 >    vector<int> getGlobalGroupIndices();
354          
355 <    std::string getFinalConfigFileName() {
355 >    string getFinalConfigFileName() {
356        return finalConfigFileName_;
357      }
358  
359 <    void setFinalConfigFileName(const std::string& fileName) {
359 >    void setFinalConfigFileName(const string& fileName) {
360        finalConfigFileName_ = fileName;
361      }
362  
363 <    std::string getRawMetaData() {
363 >    string getRawMetaData() {
364        return rawMetaData_;
365      }
366 <    void setRawMetaData(const std::string& rawMetaData) {
366 >    void setRawMetaData(const string& rawMetaData) {
367        rawMetaData_ = rawMetaData;
368      }
369          
370 <    std::string getDumpFileName() {
370 >    string getDumpFileName() {
371        return dumpFileName_;
372      }
373          
374 <    void setDumpFileName(const std::string& fileName) {
374 >    void setDumpFileName(const string& fileName) {
375        dumpFileName_ = fileName;
376      }
377  
378 <    std::string getStatFileName() {
378 >    string getStatFileName() {
379        return statFileName_;
380      }
381          
382 <    void setStatFileName(const std::string& fileName) {
382 >    void setStatFileName(const string& fileName) {
383        statFileName_ = fileName;
384      }
385          
386 <    std::string getRestFileName() {
386 >    string getRestFileName() {
387        return restFileName_;
388      }
389          
390 <    void setRestFileName(const std::string& fileName) {
390 >    void setRestFileName(const string& fileName) {
391        restFileName_ = fileName;
392      }
393  
# Line 373 | Line 395 | namespace OpenMD{
395       * Sets GlobalGroupMembership
396       * @see #SimCreator::setGlobalIndex
397       */  
398 <    void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
398 >    void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
399        assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
400        globalGroupMembership_ = globalGroupMembership;
401      }
# Line 382 | Line 404 | namespace OpenMD{
404       * Sets GlobalMolMembership
405       * @see #SimCreator::setGlobalIndex
406       */        
407 <    void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
407 >    void setGlobalMolMembership(const vector<int>& globalMolMembership) {
408        assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
409        globalMolMembership_ = globalMolMembership;
410      }
# Line 400 | Line 422 | namespace OpenMD{
422        return useAtomicVirial_;
423      }
424  
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.
425      /**
426       * Adds property into property map
427       * @param genData GenericData to be added into PropertyMap
# Line 413 | Line 432 | namespace OpenMD{
432       * Removes property from PropertyMap by name
433       * @param propName the name of property to be removed
434       */
435 <    void removeProperty(const std::string& propName);
435 >    void removeProperty(const string& propName);
436  
437      /**
438       * clear all of the properties
# Line 424 | Line 443 | namespace OpenMD{
443       * Returns all names of properties
444       * @return all names of properties
445       */
446 <    std::vector<std::string> getPropertyNames();
446 >    vector<string> getPropertyNames();
447  
448      /**
449       * Returns all of the properties in PropertyMap
450       * @return all of the properties in PropertyMap
451       */      
452 <    std::vector<GenericData*> getProperties();
452 >    vector<GenericData*> getProperties();
453  
454      /**
455       * Returns property
# Line 438 | Line 457 | namespace OpenMD{
457       * @return a pointer point to property with propName. If no property named propName
458       * exists, return NULL
459       */      
460 <    GenericData* getPropertyByName(const std::string& propName);
460 >    GenericData* getPropertyByName(const string& propName);
461  
462      /**
463       * add all special interaction pairs (including excluded
# Line 452 | Line 471 | namespace OpenMD{
471       */
472      void removeInteractionPairs(Molecule* mol);
473  
474 <
475 <    /** Returns the unique atom types of local processor in an array */
457 <    std::set<AtomType*> getUniqueAtomTypes();
474 >    /** Returns the set of atom types present in this simulation */
475 >    set<AtomType*> getSimulatedAtomTypes();
476          
477 <    friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
477 >    friend ostream& operator <<(ostream& o, SimInfo& info);
478  
479      void getCutoff(RealType& rcut, RealType& rsw);
480          
481    private:
482  
483 <    /** fill up the simtype struct*/
484 <    void setupSimType();
483 >    /** fill up the simtype struct and other simulation-related variables */
484 >    void setupSimVariables();
485  
468 –    /**
469 –     * Setup Fortran Simulation
470 –     * @see #setupFortranParallel
471 –     */
472 –    void setupFortranSim();
486  
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 –
487      /** Determine if we need to accumulate the simulation box dipole */
488      void setupAccumulateBoxDipole();
489  
# Line 488 | Line 492 | namespace OpenMD{
492      void calcNdfRaw();
493      void calcNdfTrans();
494  
491 –    ForceField* forceField_;      
492 –    Globals* simParams_;
493 –
494 –    std::map<int, Molecule*>  molecules_; /**< Molecule array */
495 –
495      /**
496 <     * Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
497 <     * system.
496 >     * Adds molecule stamp and the total number of the molecule with
497 >     * same molecule stamp in the whole system.
498       */
499      void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
500 <        
501 <    //degress of freedom
502 <    int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
503 <    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_;
500 >
501 >    // Other classes holdingn important information
502 >    ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
503 >    Globals* simParams_;     /**< provides access to simulation parameters set by user */
504  
505 <    /**
524 <     * the size of globalMolMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
525 <     * 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_;        
529 <
530 <        
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
505 >    ///  Counts of local objects
506      int nAtoms_;              /**< number of atoms in local processor */
507      int nBonds_;              /**< number of bonds in local processor */
508      int nBends_;              /**< number of bends in local processor */
# Line 541 | Line 512 | namespace OpenMD{
512      int nIntegrableObjects_;  /**< number of integrable objects in local processor */
513      int nCutoffGroups_;       /**< number of cutoff groups in local processor */
514      int nConstraints_;        /**< number of constraints in local processors */
515 +        
516 +    /// Counts of global objects
517 +    int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
518 +    int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
519 +    int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
520 +    int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
521 +    int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
522 +      
523 +    /// Degress of freedom
524 +    int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
525 +    int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
526 +    int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
527 +    int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
528 +    int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
529 +    int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
530  
531 <    simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
532 <    PairList excludedInteractions_;      
533 <    PairList oneTwoInteractions_;      
534 <    PairList oneThreeInteractions_;      
535 <    PairList oneFourInteractions_;      
536 <    PropertyMap properties_;                  /**< Generic Property */
537 <    SnapshotManager* sman_;               /**< SnapshotManager */
531 >    /// logicals
532 >    bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
533 >    bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
534 >    bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
535 >    bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
536 >    bool usesAtomicVirial_;       /**< are we computing atomic virials? */
537 >    bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
538 >    bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
539 >    bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
540  
541 +  public:
542 +    bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
543 +    bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
544 +    bool usesMetallicAtoms() { return usesMetallicAtoms_; }
545 +    bool usesAtomicVirial() { return usesAtomicVirial_; }
546 +    bool requiresPrepair() { return requiresPrepair_; }
547 +    bool requiresSkipCorrection() { return requiresSkipCorrection_;}
548 +    bool requiresSelfCorrection() { return requiresSelfCorrection_;}
549 +
550 +  private:
551 +    /// Data structures holding primary simulation objects
552 +    map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
553 +
554 +    /// Stamps are templates for objects that are then used to create
555 +    /// groups of objects.  For example, a molecule stamp contains
556 +    /// information on how to build that molecule (i.e. the topology,
557 +    /// the atoms, the bonds, etc.)  Once the system is built, the
558 +    /// stamps are no longer useful.
559 +    vector<int> molStampIds_;                /**< stamp id for molecules in the system */
560 +    vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */        
561 +
562 +    /**
563 +     * A vector that maps between the global index of an atom, and the
564 +     * global index of cutoff group the atom belong to.  It is filled
565 +     * by SimCreator once and only once, since it never changed during
566 +     * the simulation.  It should be nGlobalAtoms_ in size.
567 +     */
568 +    vector<int> globalGroupMembership_;
569 +  public:
570 +    vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
571 +  private:
572 +
573 +    /**
574 +     * A vector that maps between the global index of an atom and the
575 +     * global index of the molecule the atom belongs to.  It is filled
576 +     * by SimCreator once and only once, since it is never changed
577 +     * during the simulation. It shoudl be nGlobalAtoms_ in size.
578 +     */
579 +    vector<int> globalMolMembership_;
580 +
581      /**
582 <     * The reason to have a local index manager is that when molecule is migrating to other processors,
583 <     * the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
584 <     * information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
585 <     * to make a efficient data moving plan.
582 >     * A vector that maps between the local index of an atom and the
583 >     * index of the AtomType.
584 >     */
585 >    vector<int> identArray_;
586 >  public:
587 >    vector<int> getIdentArray() { return identArray_; }
588 >  private:
589 >              
590 >    /// lists to handle atoms needing special treatment in the non-bonded interactions
591 >    PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
592 >    PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
593 >    PairList oneThreeInteractions_;  /**< atoms sharing a Bend */    
594 >    PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
595 >
596 >    PropertyMap properties_;       /**< Generic Properties can be added */
597 >    SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
598 >
599 >    /**
600 >     * The reason to have a local index manager is that when molecule
601 >     * is migrating to other processors, the atoms and the
602 >     * rigid-bodies will release their local indices to
603 >     * LocalIndexManager. Combining the information of molecule
604 >     * migrating to current processor, Migrator class can query the
605 >     * LocalIndexManager to make a efficient data moving plan.
606       */        
607      LocalIndexManager localIndexMan_;
608  
609      // unparsed MetaData block for storing in Dump and EOR files:
610 <    std::string rawMetaData_;
610 >    string rawMetaData_;
611  
612 <    //file names
613 <    std::string finalConfigFileName_;
614 <    std::string dumpFileName_;
615 <    std::string statFileName_;
616 <    std::string restFileName_;
612 >    // file names
613 >    string finalConfigFileName_;
614 >    string dumpFileName_;
615 >    string statFileName_;
616 >    string restFileName_;
617          
570 –    RealType rcut_;       /**< cutoff radius*/
571 –    RealType rsw_;        /**< radius of switching function*/
572 –    RealType rlist_;      /**< neighbor list radius */
618  
619 <    int ljsp_; /**< use shifted potential for LJ*/
575 <    int ljsf_; /**< use shifted force for LJ*/
576 <
577 <    bool fortranInitialized_; /**< flag indicate whether fortran side
578 <                                 is initialized */
619 >    bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
620      
621      bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
622                              the simulation box dipole moment */
623      
624      bool useAtomicVirial_; /**< flag to indicate whether or not we use
625                                Atomic Virials to calculate the pressure */
626 <
627 <    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);
626 >    
627 >  public:
628      /**
629 <     * return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
630 <     * global index does not belong to local processor, a NULL will be return.
631 <     */
632 <    //StuntDouble* getStuntDoubleFromGlobalIndex(int index);
633 <  //private:
634 <    //std::vector<StuntDouble*> sdByGlobalIndex_;
629 >     * return an integral objects by its global index. In MPI
630 >     * version, if the StuntDouble with specified global index does
631 >      * not belong to local processor, a NULL will be return.
632 >      */
633 >    StuntDouble* getIOIndexToIntegrableObject(int index);
634 >    void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
635      
636 <    //in Parallel version, we need MolToProc
636 >  private:
637 >    vector<StuntDouble*> IOIndexToIntegrableObject;
638 >    
639    public:
640                  
641      /**
# Line 614 | Line 647 | namespace OpenMD{
647        //assert(globalIndex < molToProcMap_.size());
648        return molToProcMap_[globalIndex];
649      }
650 <
650 >    
651      /**
652       * Set MolToProcMap array
653       * @see #SimCreator::divideMolecules
654       */
655 <    void setMolToProcMap(const std::vector<int>& molToProcMap) {
655 >    void setMolToProcMap(const vector<int>& molToProcMap) {
656        molToProcMap_ = molToProcMap;
657      }
658          
659    private:
627 –
628 –    void setupFortranParallel();
660          
661      /**
662       * The size of molToProcMap_ is equal to total number of molecules
663       * in the system.  It maps a molecule to the processor on which it
664       * resides. it is filled by SimCreator once and only once.
665       */        
666 <    std::vector<int> molToProcMap_;
666 >    vector<int> molToProcMap_;
667  
637 –
668    };
669  
670   } //namespace OpenMD

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