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Comparing branches/development/src/brains/SimInfo.hpp (file contents):
Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC vs.
Revision 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC

# Line 62 | Line 62
62   #include "UseTheForce/ForceField.hpp"
63   #include "utils/PropertyMap.hpp"
64   #include "utils/LocalIndexManager.hpp"
65 < #include "nonbonded/Electrostatic.hpp"
65 > #include "nonbonded/SwitchingFunction.hpp"
66  
67   //another nonsense macro declaration
68   #define __OPENMD_C
69   #include "brains/fSimulation.h"
70  
71 + using namespace std;
72   namespace OpenMD{
72 –
73    //forward decalration
74    class SnapshotManager;
75    class Molecule;
76    class SelectionManager;
77    class StuntDouble;
78 <  class Electrostatic;
78 >
79    /**
80 <   * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
81 <   * @brief One of the heavy weight classes of OpenMD, SimInfo maintains a list of molecules.
82 <    * The Molecule class maintains all of the concrete objects
83 <    * (atoms, bond, bend, torsions, inversions, rigid bodies, cutoff groups,
84 <    * constraints). In both the single and parallel versions, atoms and
85 <    * rigid bodies have both global and local indices.  The local index is
86 <    * not relevant to molecules or cutoff groups.
87 <    */
80 >   * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
81 >   *
82 >   * @brief One of the heavy-weight classes of OpenMD, SimInfo
83 >   * maintains objects and variables relating to the current
84 >   * simulation.  This includes the master list of Molecules.  The
85 >   * Molecule class maintains all of the concrete objects (Atoms,
86 >   * Bond, Bend, Torsions, Inversions, RigidBodies, CutoffGroups,
87 >   * Constraints). In both the single and parallel versions, Atoms and
88 >   * RigidBodies have both global and local indices.
89 >   */
90    class SimInfo {
91    public:
92 <    typedef std::map<int, Molecule*>::iterator  MoleculeIterator;
93 <
92 >    typedef map<int, Molecule*>::iterator  MoleculeIterator;
93 >    
94      /**
95       * Constructor of SimInfo
96 <     * @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
97 <     * second element is the total number of molecules with the same molecule stamp in the system
96 >     *
97 >     * @param molStampPairs MoleculeStamp Array. The first element of
98 >     * the pair is molecule stamp, the second element is the total
99 >     * number of molecules with the same molecule stamp in the system
100 >     *
101       * @param ff pointer of a concrete ForceField instance
102 +     *
103       * @param simParams
98 –     * @note
104       */
105      SimInfo(ForceField* ff, Globals* simParams);
106      virtual ~SimInfo();
107  
108      /**
109       * Adds a molecule
110 <     * @return return true if adding successfully, return false if the molecule is already in SimInfo
110 >     *
111 >     * @return return true if adding successfully, return false if the
112 >     * molecule is already in SimInfo
113 >     *
114       * @param mol molecule to be added
115       */
116      bool addMolecule(Molecule* mol);
117  
118      /**
119       * Removes a molecule from SimInfo
120 <     * @return true if removing successfully, return false if molecule is not in this SimInfo
120 >     *
121 >     * @return true if removing successfully, return false if molecule
122 >     * is not in this SimInfo
123       */
124      bool removeMolecule(Molecule* mol);
125  
# Line 129 | Line 139 | namespace OpenMD{
139      }
140  
141      /**
142 <     * Returns the total number of integrable objects (total number of rigid bodies plus the total number
143 <     * of atoms which do not belong to the rigid bodies) in the system
142 >     * Returns the total number of integrable objects (total number of
143 >     * rigid bodies plus the total number of atoms which do not belong
144 >     * to the rigid bodies) in the system
145       */
146      int getNGlobalIntegrableObjects() {
147        return nGlobalIntegrableObjects_;
148      }
149  
150      /**
151 <     * Returns the total number of integrable objects (total number of rigid bodies plus the total number
152 <     * of atoms which do not belong to the rigid bodies) in the system
151 >     * Returns the total number of integrable objects (total number of
152 >     * rigid bodies plus the total number of atoms which do not belong
153 >     * to the rigid bodies) in the system
154       */
155      int getNGlobalRigidBodies() {
156        return nGlobalRigidBodies_;
# Line 233 | Line 245 | namespace OpenMD{
245  
246      int getFdf();
247      
248 <    //getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
248 >    //getNZconstraint and setNZconstraint ruin the coherence of
249 >    //SimInfo class, need refactoring
250          
251      /** Returns the total number of z-constraint molecules in the system */
252      int getNZconstraint() {
# Line 269 | Line 282 | namespace OpenMD{
282  
283      /** Returns the center of the mass of the whole system.*/
284      Vector3d getCom();
285 <   /** Returns the center of the mass and Center of Mass velocity of the whole system.*/
285 >    /** Returns the center of the mass and Center of Mass velocity of
286 >        the whole system.*/
287      void getComAll(Vector3d& com,Vector3d& comVel);
288  
289 <    /** Returns intertia tensor for the entire system and system Angular Momentum.*/
289 >    /** Returns intertia tensor for the entire system and system
290 >        Angular Momentum.*/
291      void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
292      
293      /** Returns system angular momentum */
294      Vector3d getAngularMomentum();
295  
296 <    /** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/
296 >    /** Returns volume of system as estimated by an ellipsoid defined
297 >        by the radii of gyration*/
298      void getGyrationalVolume(RealType &vol);
299 <    /** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/
299 >    /** Overloaded version of gyrational volume that also returns
300 >        det(I) so dV/dr can be calculated*/
301      void getGyrationalVolume(RealType &vol, RealType &detI);
302 <    /** main driver function to interact with fortran during the initialization and molecule migration */
302 >
303      void update();
304 +    /**
305 +     * Setup Fortran Simulation
306 +     */
307 +    void setupFortran();
308  
309 +
310      /** Returns the local index manager */
311      LocalIndexManager* getLocalIndexManager() {
312        return &localIndexMan_;
# Line 318 | Line 340 | namespace OpenMD{
340  
341      int getGlobalMolMembership(int id){
342        return globalMolMembership_[id];
321 –    }
322 –
323 –    RealType getRcut() {
324 –      return rcut_;
325 –    }
326 –
327 –    RealType getRsw() {
328 –      return rsw_;
329 –    }
330 –
331 –    RealType getList() {
332 –      return rlist_;
343      }
344          
345 <    std::string getFinalConfigFileName() {
345 >    string getFinalConfigFileName() {
346        return finalConfigFileName_;
347      }
348  
349 <    void setFinalConfigFileName(const std::string& fileName) {
349 >    void setFinalConfigFileName(const string& fileName) {
350        finalConfigFileName_ = fileName;
351      }
352  
353 <    std::string getRawMetaData() {
353 >    string getRawMetaData() {
354        return rawMetaData_;
355      }
356 <    void setRawMetaData(const std::string& rawMetaData) {
356 >    void setRawMetaData(const string& rawMetaData) {
357        rawMetaData_ = rawMetaData;
358      }
359          
360 <    std::string getDumpFileName() {
360 >    string getDumpFileName() {
361        return dumpFileName_;
362      }
363          
364 <    void setDumpFileName(const std::string& fileName) {
364 >    void setDumpFileName(const string& fileName) {
365        dumpFileName_ = fileName;
366      }
367  
368 <    std::string getStatFileName() {
368 >    string getStatFileName() {
369        return statFileName_;
370      }
371          
372 <    void setStatFileName(const std::string& fileName) {
372 >    void setStatFileName(const string& fileName) {
373        statFileName_ = fileName;
374      }
375          
376 <    std::string getRestFileName() {
376 >    string getRestFileName() {
377        return restFileName_;
378      }
379          
380 <    void setRestFileName(const std::string& fileName) {
380 >    void setRestFileName(const string& fileName) {
381        restFileName_ = fileName;
382      }
383  
# Line 375 | Line 385 | namespace OpenMD{
385       * Sets GlobalGroupMembership
386       * @see #SimCreator::setGlobalIndex
387       */  
388 <    void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
388 >    void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
389        assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
390        globalGroupMembership_ = globalGroupMembership;
391      }
# Line 384 | Line 394 | namespace OpenMD{
394       * Sets GlobalMolMembership
395       * @see #SimCreator::setGlobalIndex
396       */        
397 <    void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
397 >    void setGlobalMolMembership(const vector<int>& globalMolMembership) {
398        assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
399        globalMolMembership_ = globalMolMembership;
400      }
# Line 402 | Line 412 | namespace OpenMD{
412        return useAtomicVirial_;
413      }
414  
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.
415      /**
416       * Adds property into property map
417       * @param genData GenericData to be added into PropertyMap
# Line 415 | Line 422 | namespace OpenMD{
422       * Removes property from PropertyMap by name
423       * @param propName the name of property to be removed
424       */
425 <    void removeProperty(const std::string& propName);
425 >    void removeProperty(const string& propName);
426  
427      /**
428       * clear all of the properties
# Line 426 | Line 433 | namespace OpenMD{
433       * Returns all names of properties
434       * @return all names of properties
435       */
436 <    std::vector<std::string> getPropertyNames();
436 >    vector<string> getPropertyNames();
437  
438      /**
439       * Returns all of the properties in PropertyMap
440       * @return all of the properties in PropertyMap
441       */      
442 <    std::vector<GenericData*> getProperties();
442 >    vector<GenericData*> getProperties();
443  
444      /**
445       * Returns property
# Line 440 | Line 447 | namespace OpenMD{
447       * @return a pointer point to property with propName. If no property named propName
448       * exists, return NULL
449       */      
450 <    GenericData* getPropertyByName(const std::string& propName);
450 >    GenericData* getPropertyByName(const string& propName);
451  
452      /**
453       * add all special interaction pairs (including excluded
# Line 454 | Line 461 | namespace OpenMD{
461       */
462      void removeInteractionPairs(Molecule* mol);
463  
464 <
465 <    /** Returns the unique atom types of local processor in an array */
459 <    std::set<AtomType*> getUniqueAtomTypes();
464 >    /** Returns the set of atom types present in this simulation */
465 >    set<AtomType*> getSimulatedAtomTypes();
466          
467 <    friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
467 >    friend ostream& operator <<(ostream& o, SimInfo& info);
468  
469      void getCutoff(RealType& rcut, RealType& rsw);
470          
471    private:
472  
473 <    /** fill up the simtype struct*/
474 <    void setupSimType();
473 >    /** fill up the simtype struct and other simulation-related variables */
474 >    void setupSimVariables();
475  
470 –    /**
471 –     * Setup Fortran Simulation
472 –     * @see #setupFortranParallel
473 –     */
474 –    void setupFortranSim();
476  
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 –
477      /** Determine if we need to accumulate the simulation box dipole */
478      void setupAccumulateBoxDipole();
479  
# Line 490 | Line 482 | namespace OpenMD{
482      void calcNdfRaw();
483      void calcNdfTrans();
484  
493 –    ForceField* forceField_;      
494 –    Globals* simParams_;
495 –
496 –    std::map<int, Molecule*>  molecules_; /**< Molecule array */
497 –
485      /**
486 <     * Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
487 <     * system.
486 >     * Adds molecule stamp and the total number of the molecule with
487 >     * same molecule stamp in the whole system.
488       */
489      void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
490 <        
491 <    //degress of freedom
492 <    int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
493 <    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_;
490 >
491 >    // Other classes holdingn important information
492 >    ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
493 >    Globals* simParams_;     /**< provides access to simulation parameters set by user */
494  
495 <    /**
526 <     * the size of globalMolMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
527 <     * 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_;        
531 <
532 <        
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
495 >    ///  Counts of local objects
496      int nAtoms_;              /**< number of atoms in local processor */
497      int nBonds_;              /**< number of bonds in local processor */
498      int nBends_;              /**< number of bends in local processor */
# Line 543 | Line 502 | namespace OpenMD{
502      int nIntegrableObjects_;  /**< number of integrable objects in local processor */
503      int nCutoffGroups_;       /**< number of cutoff groups in local processor */
504      int nConstraints_;        /**< number of constraints in local processors */
505 +        
506 +    /// Counts of global objects
507 +    int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
508 +    int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
509 +    int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
510 +    int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
511 +    int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
512 +      
513 +    /// Degress of freedom
514 +    int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
515 +    int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
516 +    int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
517 +    int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
518 +    int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
519 +    int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
520  
521 <    simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
522 <    PairList excludedInteractions_;      
523 <    PairList oneTwoInteractions_;      
524 <    PairList oneThreeInteractions_;      
525 <    PairList oneFourInteractions_;      
526 <    PropertyMap properties_;                  /**< Generic Property */
527 <    SnapshotManager* sman_;               /**< SnapshotManager */
521 >    /// logicals
522 >    bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
523 >    bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
524 >    bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
525 >    bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
526 >    bool usesAtomicVirial_;       /**< are we computing atomic virials? */
527 >    bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
528 >    bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
529 >    bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
530  
531 +  public:
532 +    bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
533 +    bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
534 +    bool usesMetallicAtoms() { return usesMetallicAtoms_; }
535 +
536 +  private:
537 +    /// Data structures holding primary simulation objects
538 +    map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
539 +    simtype fInfo_;                   /**< A dual struct shared by C++
540 +                                         and Fortran to pass
541 +                                         information about what types
542 +                                         of calculation are
543 +                                         required */
544 +
545 +    /// Stamps are templates for objects that are then used to create
546 +    /// groups of objects.  For example, a molecule stamp contains
547 +    /// information on how to build that molecule (i.e. the topology,
548 +    /// the atoms, the bonds, etc.)  Once the system is built, the
549 +    /// stamps are no longer useful.
550 +    vector<int> molStampIds_;                /**< stamp id for molecules in the system */
551 +    vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */        
552 +
553 +    /**
554 +     * A vector that maps between the global index of an atom, and the
555 +     * global index of cutoff group the atom belong to.  It is filled
556 +     * by SimCreator once and only once, since it never changed during
557 +     * the simulation.  It should be nGlobalAtoms_ in size.
558 +     */
559 +    vector<int> globalGroupMembership_;
560 +
561 +    /**
562 +     * A vector that maps between the global index of an atom and the
563 +     * global index of the molecule the atom belongs to.  It is filled
564 +     * by SimCreator once and only once, since it is never changed
565 +     * during the simulation. It shoudl be nGlobalAtoms_ in size.
566 +     */
567 +    vector<int> globalMolMembership_;
568 +
569      /**
570 <     * The reason to have a local index manager is that when molecule is migrating to other processors,
571 <     * the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
572 <     * information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
573 <     * to make a efficient data moving plan.
570 >     * A vector that maps between the local index of an atom and the
571 >     * index of the AtomType.
572 >     */
573 >    vector<int> identArray_;
574 >    vector<int> getIdentArray() { return identArray_; }
575 >    
576 >              
577 >    /// lists to handle atoms needing special treatment in the non-bonded interactions
578 >    PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
579 >    PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
580 >    PairList oneThreeInteractions_;  /**< atoms sharing a Bend */    
581 >    PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
582 >
583 >    PropertyMap properties_;       /**< Generic Properties can be added */
584 >    SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
585 >
586 >    /**
587 >     * The reason to have a local index manager is that when molecule
588 >     * is migrating to other processors, the atoms and the
589 >     * rigid-bodies will release their local indices to
590 >     * LocalIndexManager. Combining the information of molecule
591 >     * migrating to current processor, Migrator class can query the
592 >     * LocalIndexManager to make a efficient data moving plan.
593       */        
594      LocalIndexManager localIndexMan_;
595  
596      // unparsed MetaData block for storing in Dump and EOR files:
597 <    std::string rawMetaData_;
597 >    string rawMetaData_;
598  
599 <    //file names
600 <    std::string finalConfigFileName_;
601 <    std::string dumpFileName_;
602 <    std::string statFileName_;
603 <    std::string restFileName_;
599 >    // file names
600 >    string finalConfigFileName_;
601 >    string dumpFileName_;
602 >    string statFileName_;
603 >    string restFileName_;
604          
572 –    RealType rcut_;       /**< cutoff radius*/
573 –    RealType rsw_;        /**< radius of switching function*/
574 –    RealType rlist_;      /**< neighbor list radius */
605  
576 –    int ljsp_; /**< use shifted potential for LJ*/
577 –    int ljsf_; /**< use shifted force for LJ*/
578 –
606      bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
607      
608      bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
# Line 583 | Line 610 | namespace OpenMD{
610      
611      bool useAtomicVirial_; /**< flag to indicate whether or not we use
612                                Atomic Virials to calculate the pressure */
613 <
614 <    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);
613 >    
614 >  public:
615      /**
616 <     * return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
617 <     * global index does not belong to local processor, a NULL will be return.
618 <     */
619 <    //StuntDouble* getStuntDoubleFromGlobalIndex(int index);
620 <  //private:
621 <    //std::vector<StuntDouble*> sdByGlobalIndex_;
616 >     * return an integral objects by its global index. In MPI
617 >     * version, if the StuntDouble with specified global index does
618 >      * not belong to local processor, a NULL will be return.
619 >      */
620 >    StuntDouble* getIOIndexToIntegrableObject(int index);
621 >    void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
622      
623 <    //in Parallel version, we need MolToProc
623 >  private:
624 >    vector<StuntDouble*> IOIndexToIntegrableObject;
625 >    
626    public:
627                  
628      /**
# Line 615 | Line 634 | namespace OpenMD{
634        //assert(globalIndex < molToProcMap_.size());
635        return molToProcMap_[globalIndex];
636      }
637 <
637 >    
638      /**
639       * Set MolToProcMap array
640       * @see #SimCreator::divideMolecules
641       */
642 <    void setMolToProcMap(const std::vector<int>& molToProcMap) {
642 >    void setMolToProcMap(const vector<int>& molToProcMap) {
643        molToProcMap_ = molToProcMap;
644      }
645          
646    private:
628 –
629 –    void setupFortranParallel();
647          
648      /**
649       * The size of molToProcMap_ is equal to total number of molecules
650       * in the system.  It maps a molecule to the processor on which it
651       * resides. it is filled by SimCreator once and only once.
652       */        
653 <    std::vector<int> molToProcMap_;
653 >    vector<int> molToProcMap_;
654  
638 –
655    };
656  
657   } //namespace OpenMD

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