ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/brains/SimInfo.hpp
(Generate patch)

Comparing branches/development/src/brains/SimInfo.hpp (file contents):
Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC vs.
Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
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 62 | Line 63
63   #include "UseTheForce/ForceField.hpp"
64   #include "utils/PropertyMap.hpp"
65   #include "utils/LocalIndexManager.hpp"
66 < #include "nonbonded/Electrostatic.hpp"
66 > #include "nonbonded/SwitchingFunction.hpp"
67  
68 < //another nonsense macro declaration
68 < #define __OPENMD_C
69 < #include "brains/fSimulation.h"
70 <
68 > using namespace std;
69   namespace OpenMD{
70 <
73 <  //forward decalration
70 >  //forward declaration
71    class SnapshotManager;
72    class Molecule;
73    class SelectionManager;
74    class StuntDouble;
75 <  class Electrostatic;
75 >
76    /**
77 <   * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
78 <   * @brief One of the heavy weight classes of OpenMD, SimInfo maintains a list of molecules.
79 <    * The Molecule class maintains all of the concrete objects
80 <    * (atoms, bond, bend, torsions, inversions, rigid bodies, cutoff groups,
81 <    * constraints). 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.
84 <    */
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
98 –     * @note
101       */
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 129 | Line 136 | namespace OpenMD{
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 158 | Line 167 | namespace OpenMD{
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 211 | Line 223 | namespace OpenMD{
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_ - getFdf();
# Line 233 | Line 250 | namespace OpenMD{
250  
251      int getFdf();
252      
253 <    //getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
253 >    //getNZconstraint and setNZconstraint ruin the coherence of
254 >    //SimInfo class, need refactoring
255          
256      /** Returns the total number of z-constraint molecules in the system */
257      int getNZconstraint() {
# Line 269 | Line 287 | namespace OpenMD{
287  
288      /** Returns the center of the mass of the whole system.*/
289      Vector3d getCom();
290 <   /** Returns the center of the mass and Center of Mass velocity of the whole system.*/
290 >    /** Returns the center of the mass and Center of Mass velocity of
291 >        the whole system.*/
292      void getComAll(Vector3d& com,Vector3d& comVel);
293  
294 <    /** Returns intertia tensor for the entire system and system Angular Momentum.*/
294 >    /** Returns intertia tensor for the entire system and system
295 >        Angular Momentum.*/
296      void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
297      
298      /** Returns system angular momentum */
299      Vector3d getAngularMomentum();
300  
301 <    /** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/
301 >    /** Returns volume of system as estimated by an ellipsoid defined
302 >        by the radii of gyration*/
303      void getGyrationalVolume(RealType &vol);
304 <    /** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/
304 >    /** Overloaded version of gyrational volume that also returns
305 >        det(I) so dV/dr can be calculated*/
306      void getGyrationalVolume(RealType &vol, RealType &detI);
307 <    /** main driver function to interact with fortran during the initialization and molecule migration */
307 >
308      void update();
309 +    /**
310 +     * Do final bookkeeping before Force managers need their data.
311 +     */
312 +    void prepareTopology();
313  
314 +
315      /** Returns the local index manager */
316      LocalIndexManager* getLocalIndexManager() {
317        return &localIndexMan_;
# Line 320 | Line 347 | namespace OpenMD{
347        return globalMolMembership_[id];
348      }
349  
350 <    RealType getRcut() {
351 <      return rcut_;
352 <    }
350 >    /**
351 >     * returns a vector which maps the local atom index on this
352 >     * processor to the global atom index.  With only one processor,
353 >     * these should be identical.
354 >     */
355 >    vector<int> getGlobalAtomIndices();
356  
357 <    RealType getRsw() {
358 <      return rsw_;
359 <    }
357 >    /**
358 >     * returns a vector which maps the local cutoff group index on
359 >     * this processor to the global cutoff group index.  With only one
360 >     * processor, these should be identical.
361 >     */
362 >    vector<int> getGlobalGroupIndices();
363  
331 –    RealType getList() {
332 –      return rlist_;
333 –    }
364          
365 <    std::string getFinalConfigFileName() {
365 >    string getFinalConfigFileName() {
366        return finalConfigFileName_;
367      }
368  
369 <    void setFinalConfigFileName(const std::string& fileName) {
369 >    void setFinalConfigFileName(const string& fileName) {
370        finalConfigFileName_ = fileName;
371      }
372  
373 <    std::string getRawMetaData() {
373 >    string getRawMetaData() {
374        return rawMetaData_;
375      }
376 <    void setRawMetaData(const std::string& rawMetaData) {
376 >    void setRawMetaData(const string& rawMetaData) {
377        rawMetaData_ = rawMetaData;
378      }
379          
380 <    std::string getDumpFileName() {
380 >    string getDumpFileName() {
381        return dumpFileName_;
382      }
383          
384 <    void setDumpFileName(const std::string& fileName) {
384 >    void setDumpFileName(const string& fileName) {
385        dumpFileName_ = fileName;
386      }
387  
388 <    std::string getStatFileName() {
388 >    string getStatFileName() {
389        return statFileName_;
390      }
391          
392 <    void setStatFileName(const std::string& fileName) {
392 >    void setStatFileName(const string& fileName) {
393        statFileName_ = fileName;
394      }
395          
396 <    std::string getRestFileName() {
396 >    string getRestFileName() {
397        return restFileName_;
398      }
399          
400 <    void setRestFileName(const std::string& fileName) {
400 >    void setRestFileName(const string& fileName) {
401        restFileName_ = fileName;
402      }
403  
# Line 375 | Line 405 | namespace OpenMD{
405       * Sets GlobalGroupMembership
406       * @see #SimCreator::setGlobalIndex
407       */  
408 <    void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
408 >    void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
409        assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
410        globalGroupMembership_ = globalGroupMembership;
411      }
# Line 384 | Line 414 | namespace OpenMD{
414       * Sets GlobalMolMembership
415       * @see #SimCreator::setGlobalIndex
416       */        
417 <    void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
417 >    void setGlobalMolMembership(const vector<int>& globalMolMembership) {
418        assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
419        globalMolMembership_ = globalMolMembership;
420      }
421  
422  
423 <    bool isFortranInitialized() {
424 <      return fortranInitialized_;
423 >    bool isTopologyDone() {
424 >      return topologyDone_;
425      }
426          
427      bool getCalcBoxDipole() {
# Line 402 | Line 432 | namespace OpenMD{
432        return useAtomicVirial_;
433      }
434  
405 –    //below functions are just forward functions
406 –    //To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
407 –    //the other hand, has-a relation need composing.
435      /**
436       * Adds property into property map
437       * @param genData GenericData to be added into PropertyMap
# Line 415 | Line 442 | namespace OpenMD{
442       * Removes property from PropertyMap by name
443       * @param propName the name of property to be removed
444       */
445 <    void removeProperty(const std::string& propName);
445 >    void removeProperty(const string& propName);
446  
447      /**
448       * clear all of the properties
# Line 426 | Line 453 | namespace OpenMD{
453       * Returns all names of properties
454       * @return all names of properties
455       */
456 <    std::vector<std::string> getPropertyNames();
456 >    vector<string> getPropertyNames();
457  
458      /**
459       * Returns all of the properties in PropertyMap
460       * @return all of the properties in PropertyMap
461       */      
462 <    std::vector<GenericData*> getProperties();
462 >    vector<GenericData*> getProperties();
463  
464      /**
465       * Returns property
# Line 440 | Line 467 | namespace OpenMD{
467       * @return a pointer point to property with propName. If no property named propName
468       * exists, return NULL
469       */      
470 <    GenericData* getPropertyByName(const std::string& propName);
470 >    GenericData* getPropertyByName(const string& propName);
471  
472      /**
473       * add all special interaction pairs (including excluded
# Line 454 | Line 481 | namespace OpenMD{
481       */
482      void removeInteractionPairs(Molecule* mol);
483  
484 <
485 <    /** Returns the unique atom types of local processor in an array */
459 <    std::set<AtomType*> getUniqueAtomTypes();
484 >    /** Returns the set of atom types present in this simulation */
485 >    set<AtomType*> getSimulatedAtomTypes();
486          
487 <    friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
487 >    friend ostream& operator <<(ostream& o, SimInfo& info);
488  
489      void getCutoff(RealType& rcut, RealType& rsw);
490          
491    private:
492  
493 <    /** fill up the simtype struct*/
494 <    void setupSimType();
493 >    /** fill up the simtype struct and other simulation-related variables */
494 >    void setupSimVariables();
495  
470 –    /**
471 –     * Setup Fortran Simulation
472 –     * @see #setupFortranParallel
473 –     */
474 –    void setupFortranSim();
496  
476 –    /** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
477 –    void setupCutoff();
478 –
479 –    /** Figure out which coulombic correction method to use and pass to fortran */
480 –    void setupElectrostaticSummationMethod( int isError );
481 –
482 –    /** Figure out which polynomial type to use for the switching function */
483 –    void setupSwitchingFunction();
484 –
497      /** Determine if we need to accumulate the simulation box dipole */
498      void setupAccumulateBoxDipole();
499  
# Line 490 | Line 502 | namespace OpenMD{
502      void calcNdfRaw();
503      void calcNdfTrans();
504  
493 –    ForceField* forceField_;      
494 –    Globals* simParams_;
495 –
496 –    std::map<int, Molecule*>  molecules_; /**< Molecule array */
497 –
505      /**
506 <     * Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
507 <     * system.
506 >     * Adds molecule stamp and the total number of the molecule with
507 >     * same molecule stamp in the whole system.
508       */
509      void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
503 –        
504 –    //degress of freedom
505 –    int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
506 –    int fdf_local;       /**< number of frozen degrees of freedom */
507 –    int fdf_;            /**< number of frozen degrees of freedom */
508 –    int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
509 –    int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
510 –    int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
511 –        
512 –    //number of global objects
513 –    int nGlobalMols_;       /**< number of molecules in the system */
514 –    int nGlobalAtoms_;   /**< number of atoms in the system */
515 –    int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
516 –    int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
517 –    int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
518 –    /**
519 –     * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
520 –     * corresponding content is the global index of cutoff group this atom belong to.
521 –     * It is filled by SimCreator once and only once, since it never changed during the simulation.
522 –     */
523 –    std::vector<int> globalGroupMembership_;
510  
511 <    /**
512 <     * the size of globalMolMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
513 <     * corresponding content is the global index of molecule this atom belong to.
528 <     * It is filled by SimCreator once and only once, since it is never changed during the simulation.
529 <     */
530 <    std::vector<int> globalMolMembership_;        
511 >    // Other classes holdingn important information
512 >    ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
513 >    Globals* simParams_;     /**< provides access to simulation parameters set by user */
514  
515 <        
533 <    std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
534 <    std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */        
535 <        
536 <    //number of local objects
515 >    ///  Counts of local objects
516      int nAtoms_;              /**< number of atoms in local processor */
517      int nBonds_;              /**< number of bonds in local processor */
518      int nBends_;              /**< number of bends in local processor */
# Line 543 | Line 522 | namespace OpenMD{
522      int nIntegrableObjects_;  /**< number of integrable objects in local processor */
523      int nCutoffGroups_;       /**< number of cutoff groups in local processor */
524      int nConstraints_;        /**< number of constraints in local processors */
525 +    int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */
526 +        
527 +    /// Counts of global objects
528 +    int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
529 +    int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
530 +    int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
531 +    int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
532 +    int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
533 +    int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
534 +    
535 +      
536 +    /// Degress of freedom
537 +    int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
538 +    int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
539 +    int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
540 +    int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
541 +    int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
542 +    int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
543  
544 <    simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
545 <    PairList excludedInteractions_;      
546 <    PairList oneTwoInteractions_;      
547 <    PairList oneThreeInteractions_;      
548 <    PairList oneFourInteractions_;      
549 <    PropertyMap properties_;                  /**< Generic Property */
550 <    SnapshotManager* sman_;               /**< SnapshotManager */
544 >    /// logicals
545 >    bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
546 >    bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
547 >    bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
548 >    bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
549 >    bool usesFluctuatingCharges_; /**< are there fluctuating charges? */
550 >    bool usesAtomicVirial_;       /**< are we computing atomic virials? */
551 >    bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
552 >    bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
553 >    bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
554  
555 +  public:
556 +    bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
557 +    bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
558 +    bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
559 +    bool usesAtomicVirial() { return usesAtomicVirial_; }
560 +    bool requiresPrepair() { return requiresPrepair_; }
561 +    bool requiresSkipCorrection() { return requiresSkipCorrection_;}
562 +    bool requiresSelfCorrection() { return requiresSelfCorrection_;}
563 +
564 +  private:
565 +    /// Data structures holding primary simulation objects
566 +    map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
567 +
568 +    /// Stamps are templates for objects that are then used to create
569 +    /// groups of objects.  For example, a molecule stamp contains
570 +    /// information on how to build that molecule (i.e. the topology,
571 +    /// the atoms, the bonds, etc.)  Once the system is built, the
572 +    /// stamps are no longer useful.
573 +    vector<int> molStampIds_;                /**< stamp id for molecules in the system */
574 +    vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */        
575 +
576 +    /**
577 +     * A vector that maps between the global index of an atom, and the
578 +     * global index of cutoff group the atom belong to.  It is filled
579 +     * by SimCreator once and only once, since it never changed during
580 +     * the simulation.  It should be nGlobalAtoms_ in size.
581 +     */
582 +    vector<int> globalGroupMembership_;
583 +  public:
584 +    vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
585 +  private:
586 +
587 +    /**
588 +     * A vector that maps between the global index of an atom and the
589 +     * global index of the molecule the atom belongs to.  It is filled
590 +     * by SimCreator once and only once, since it is never changed
591 +     * during the simulation. It shoudl be nGlobalAtoms_ in size.
592 +     */
593 +    vector<int> globalMolMembership_;
594 +
595      /**
596 <     * The reason to have a local index manager is that when molecule is migrating to other processors,
597 <     * the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
598 <     * information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
599 <     * to make a efficient data moving plan.
596 >     * A vector that maps between the local index of an atom and the
597 >     * index of the AtomType.
598 >     */
599 >    vector<int> identArray_;
600 >  public:
601 >    vector<int> getIdentArray() { return identArray_; }
602 >  private:
603 >    
604 >    /**
605 >     * A vector which contains the fractional contribution of an
606 >     * atom's mass to the total mass of the cutoffGroup that atom
607 >     * belongs to.  In the case of single atom cutoff groups, the mass
608 >     * factor for that atom is 1.  For massless atoms, the factor is
609 >     * also 1.
610 >     */
611 >    vector<RealType> massFactors_;
612 >  public:
613 >    vector<RealType> getMassFactors() { return massFactors_; }
614 >
615 >    PairList* getExcludedInteractions() { return &excludedInteractions_; }
616 >    PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
617 >    PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
618 >    PairList* getOneFourInteractions() { return &oneFourInteractions_; }
619 >
620 >  private:
621 >              
622 >    /// lists to handle atoms needing special treatment in the non-bonded interactions
623 >    PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
624 >    PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
625 >    PairList oneThreeInteractions_;  /**< atoms sharing a Bend */    
626 >    PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
627 >
628 >    PropertyMap properties_;       /**< Generic Properties can be added */
629 >    SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
630 >
631 >    /**
632 >     * The reason to have a local index manager is that when molecule
633 >     * is migrating to other processors, the atoms and the
634 >     * rigid-bodies will release their local indices to
635 >     * LocalIndexManager. Combining the information of molecule
636 >     * migrating to current processor, Migrator class can query the
637 >     * LocalIndexManager to make a efficient data moving plan.
638       */        
639      LocalIndexManager localIndexMan_;
640  
641      // unparsed MetaData block for storing in Dump and EOR files:
642 <    std::string rawMetaData_;
642 >    string rawMetaData_;
643  
644 <    //file names
645 <    std::string finalConfigFileName_;
646 <    std::string dumpFileName_;
647 <    std::string statFileName_;
648 <    std::string restFileName_;
644 >    // file names
645 >    string finalConfigFileName_;
646 >    string dumpFileName_;
647 >    string statFileName_;
648 >    string restFileName_;
649          
572 –    RealType rcut_;       /**< cutoff radius*/
573 –    RealType rsw_;        /**< radius of switching function*/
574 –    RealType rlist_;      /**< neighbor list radius */
650  
651 <    int ljsp_; /**< use shifted potential for LJ*/
652 <    int ljsf_; /**< use shifted force for LJ*/
653 <
579 <    bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
651 >    bool topologyDone_;  /** flag to indicate whether the topology has
652 >                             been scanned and all the relevant
653 >                             bookkeeping has been done*/
654      
655      bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
656                              the simulation box dipole moment */
657      
658      bool useAtomicVirial_; /**< flag to indicate whether or not we use
659                                Atomic Virials to calculate the pressure */
660 <
661 <    public:
588 <     /**
589 <      * return an integral objects by its global index. In MPI version, if the StuntDouble with specified
590 <      * global index does not belong to local processor, a NULL will be return.
591 <      */
592 <      StuntDouble* getIOIndexToIntegrableObject(int index);
593 <      void setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v);
594 <    private:
595 <      std::vector<StuntDouble*> IOIndexToIntegrableObject;
596 <  //public:
597 <    //void setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v);
660 >    
661 >  public:
662      /**
663 <     * return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
664 <     * global index does not belong to local processor, a NULL will be return.
665 <     */
666 <    //StuntDouble* getStuntDoubleFromGlobalIndex(int index);
667 <  //private:
668 <    //std::vector<StuntDouble*> sdByGlobalIndex_;
663 >     * return an integral objects by its global index. In MPI
664 >     * version, if the StuntDouble with specified global index does
665 >      * not belong to local processor, a NULL will be return.
666 >      */
667 >    StuntDouble* getIOIndexToIntegrableObject(int index);
668 >    void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
669      
670 <    //in Parallel version, we need MolToProc
670 >  private:
671 >    vector<StuntDouble*> IOIndexToIntegrableObject;
672 >    
673    public:
674                  
675      /**
# Line 615 | Line 681 | namespace OpenMD{
681        //assert(globalIndex < molToProcMap_.size());
682        return molToProcMap_[globalIndex];
683      }
684 <
684 >    
685      /**
686       * Set MolToProcMap array
687       * @see #SimCreator::divideMolecules
688       */
689 <    void setMolToProcMap(const std::vector<int>& molToProcMap) {
689 >    void setMolToProcMap(const vector<int>& molToProcMap) {
690        molToProcMap_ = molToProcMap;
691      }
692          
693    private:
628 –
629 –    void setupFortranParallel();
694          
695      /**
696       * The size of molToProcMap_ is equal to total number of molecules
697       * in the system.  It maps a molecule to the processor on which it
698       * resides. it is filled by SimCreator once and only once.
699       */        
700 <    std::vector<int> molToProcMap_;
700 >    vector<int> molToProcMap_;
701  
638 –
702    };
703  
704   } //namespace OpenMD

Diff Legend

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