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Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 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 59 | Line 60
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
67 < #define __OPENMD_C
68 < #include "brains/fSimulation.h"
69 <
68 > using namespace std;
69   namespace OpenMD{
70 <
72 <  //forward decalration
70 >  //forward declaration
71    class SnapshotManager;
72    class Molecule;
73    class SelectionManager;
74    class StuntDouble;
75 +
76    /**
77 <   * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
78 <   * @brief One of the heavy weight classes of 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
96 –     * @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 127 | 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 156 | 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 209 | 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();
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 231 | Line 255 | namespace OpenMD{
255  
256      int getFdf();
257      
258 <    //getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
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 262 | Line 287 | namespace OpenMD{
287        return simParams_;
288      }
289  
265 –    /** Returns the velocity of center of mass of the whole system.*/
266 –    Vector3d getComVel();
267 –
268 –    /** Returns the center of the mass of the whole system.*/
269 –    Vector3d getCom();
270 –   /** Returns the center of the mass and Center of Mass velocity of the whole system.*/
271 –    void getComAll(Vector3d& com,Vector3d& comVel);
272 –
273 –    /** Returns intertia tensor for the entire system and system Angular Momentum.*/
274 –    void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
275 –    
276 –    /** Returns system angular momentum */
277 –    Vector3d getAngularMomentum();
278 –
279 –    /** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/
280 –    void getGyrationalVolume(RealType &vol);
281 –    /** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/
282 –    void getGyrationalVolume(RealType &vol, RealType &detI);
283 –    /** main driver function to interact with fortran during the initialization and molecule migration */
290      void update();
291 +    /**
292 +     * Do final bookkeeping before Force managers need their data.
293 +     */
294 +    void prepareTopology();
295  
296 +
297      /** Returns the local index manager */
298      LocalIndexManager* getLocalIndexManager() {
299        return &localIndexMan_;
# Line 318 | Line 329 | namespace OpenMD{
329        return globalMolMembership_[id];
330      }
331  
332 <    RealType getRcut() {
333 <      return rcut_;
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 <    RealType getRsw() {
340 <      return rsw_;
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  
329 –    RealType getList() {
330 –      return rlist_;
331 –    }
346          
347 <    std::string getFinalConfigFileName() {
347 >    string getFinalConfigFileName() {
348        return finalConfigFileName_;
349      }
350  
351 <    void setFinalConfigFileName(const std::string& fileName) {
351 >    void setFinalConfigFileName(const string& fileName) {
352        finalConfigFileName_ = fileName;
353      }
354  
355 <    std::string getRawMetaData() {
355 >    string getRawMetaData() {
356        return rawMetaData_;
357      }
358 <    void setRawMetaData(const std::string& rawMetaData) {
358 >    void setRawMetaData(const string& rawMetaData) {
359        rawMetaData_ = rawMetaData;
360      }
361          
362 <    std::string getDumpFileName() {
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 373 | Line 387 | namespace OpenMD{
387       * Sets GlobalGroupMembership
388       * @see #SimCreator::setGlobalIndex
389       */  
390 <    void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
390 >    void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
391        assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
392        globalGroupMembership_ = globalGroupMembership;
393      }
# Line 382 | Line 396 | namespace OpenMD{
396       * Sets GlobalMolMembership
397       * @see #SimCreator::setGlobalIndex
398       */        
399 <    void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
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      bool getCalcBoxDipole() {
# Line 400 | Line 414 | namespace OpenMD{
414        return useAtomicVirial_;
415      }
416  
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.
417      /**
418       * Adds property into property map
419       * @param genData GenericData to be added into PropertyMap
# Line 413 | Line 424 | namespace OpenMD{
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 424 | Line 435 | namespace OpenMD{
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 438 | Line 449 | namespace OpenMD{
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 special interaction pairs (including excluded
# Line 452 | Line 463 | namespace OpenMD{
463       */
464      void removeInteractionPairs(Molecule* mol);
465  
466 <
467 <    /** Returns the unique atom types of local processor in an array */
457 <    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(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  
468 –    /**
469 –     * Setup Fortran Simulation
470 –     * @see #setupFortranParallel
471 –     */
472 –    void setupFortranSim();
478  
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 –
479      /** Determine if we need to accumulate the simulation box dipole */
480      void setupAccumulateBoxDipole();
481  
# Line 488 | Line 484 | namespace OpenMD{
484      void calcNdfRaw();
485      void calcNdfTrans();
486  
491 –    ForceField* forceField_;      
492 –    Globals* simParams_;
493 –
494 –    std::map<int, Molecule*>  molecules_; /**< Molecule array */
495 –
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);
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_;
492  
493 <    /**
494 <     * the size of globalMolMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
495 <     * 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_;        
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 <        
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
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 */
# Line 541 | Line 504 | namespace OpenMD{
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 +    /// 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 (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 <    simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
528 <    PairList excludedInteractions_;      
529 <    PairList oneTwoInteractions_;      
530 <    PairList oneThreeInteractions_;      
531 <    PairList oneFourInteractions_;      
532 <    PropertyMap properties_;                  /**< Generic Property */
533 <    SnapshotManager* sman_;               /**< SnapshotManager */
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 +     * 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 +    vector<int> globalGroupMembership_;
566 +  public:
567 +    vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
568 +  private:
569 +
570 +    /**
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 +    vector<int> globalMolMembership_;
577 +
578      /**
579 <     * The reason to have a local index manager is that when molecule is migrating to other processors,
580 <     * the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
581 <     * information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
582 <     * to make a efficient data moving plan.
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 >    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
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      // unparsed MetaData block for storing in Dump and EOR files:
625 <    std::string rawMetaData_;
625 >    string rawMetaData_;
626  
627 <    //file names
628 <    std::string finalConfigFileName_;
629 <    std::string dumpFileName_;
630 <    std::string statFileName_;
631 <    std::string restFileName_;
627 >    // file names
628 >    string finalConfigFileName_;
629 >    string dumpFileName_;
630 >    string statFileName_;
631 >    string restFileName_;
632          
570 –    RealType rcut_;       /**< cutoff radius*/
571 –    RealType rsw_;        /**< radius of switching function*/
572 –    RealType rlist_;      /**< neighbor list radius */
633  
634 <    int ljsp_; /**< use shifted potential for LJ*/
635 <    int ljsf_; /**< use shifted force for LJ*/
636 <
577 <    bool fortranInitialized_; /**< flag indicate whether fortran side
578 <                                 is initialized */
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:
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);
643 >    
644 >  public:
645      /**
646 <     * return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
647 <     * global index does not belong to local processor, a NULL will be return.
648 <     */
649 <    //StuntDouble* getStuntDoubleFromGlobalIndex(int index);
650 <  //private:
651 <    //std::vector<StuntDouble*> sdByGlobalIndex_;
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 <    //in Parallel version, we need MolToProc
653 >  private:
654 >    vector<StuntDouble*> IOIndexToIntegrableObject;
655 >    
656    public:
657                  
658      /**
# Line 614 | Line 664 | namespace OpenMD{
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:
627 –
628 –    void setupFortranParallel();
677          
678      /**
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  
637 –
685    };
686  
687   } //namespace OpenMD

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