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Comparing trunk/src/brains/SimInfo.hpp (file contents):
Revision 604 by chrisfen, Fri Sep 16 19:00:12 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
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).                        
40   */
41  
42   /**
# Line 54 | Line 54
54   #include <utility>
55   #include <vector>
56  
57 < #include "brains/Exclude.hpp"
57 > #include "brains/PairList.hpp"
58   #include "io/Globals.hpp"
59   #include "math/Vector3.hpp"
60   #include "math/SquareMatrix3.hpp"
# Line 64 | Line 64
64   #include "utils/LocalIndexManager.hpp"
65  
66   //another nonsense macro declaration
67 < #define __C
67 > #define __OPENMD_C
68   #include "brains/fSimulation.h"
69  
70 < namespace oopse{
70 > namespace OpenMD{
71  
72    //forward decalration
73    class SnapshotManager;
74    class Molecule;
75    class SelectionManager;
76 +  class StuntDouble;
77    /**
78     * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
79 <   * @brief As one of the heavy weight class of OOPSE, SimInfo
80 <   * One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
81 <   * And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
82 <   * cutoff groups, constrains).
83 <   * Another major change is the index. No matter single version or parallel version,  atoms and
84 <   * rigid bodies have both global index and local index. Local index is not important to molecule as well as
85 <   * cutoff group.
85 <   */
79 >   * @brief One of the heavy weight classes of OpenMD, SimInfo maintains a list of molecules.
80 >    * The Molecule class maintains all of the concrete objects
81 >    * (atoms, bond, bend, torsions, inversions, rigid bodies, cutoff groups,
82 >    * constraints). In both the single and parallel versions, atoms and
83 >    * rigid bodies have both global and local indices.  The local index is
84 >    * not relevant to molecules or cutoff groups.
85 >    */
86    class SimInfo {
87    public:
88      typedef std::map<int, Molecule*>::iterator  MoleculeIterator;
# Line 95 | Line 95 | namespace oopse{
95       * @param simParams
96       * @note
97       */
98 <    SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams);
98 >    SimInfo(ForceField* ff, Globals* simParams);
99      virtual ~SimInfo();
100  
101      /**
# Line 171 | Line 171 | namespace oopse{
171        return nTorsions_;
172      }
173  
174 +    /** Returns the number of local torsions */        
175 +    unsigned int getNInversions() {
176 +      return nInversions_;
177 +    }
178      /** Returns the number of local rigid bodies */        
179      unsigned int getNRigidBodies() {
180        return nRigidBodies_;
# Line 207 | Line 211 | namespace oopse{
211  
212      /** Returns the number of degrees of freedom */
213      int getNdf() {
214 <      return ndf_;
214 >      return ndf_ - getFdf();
215      }
216  
217      /** Returns the number of raw degrees of freedom */
# Line 220 | Line 224 | namespace oopse{
224        return ndfTrans_;
225      }
226  
227 +    /** sets the current number of frozen degrees of freedom */
228 +    void setFdf(int fdf) {
229 +      fdf_local = fdf;
230 +    }
231 +
232 +    int getFdf();
233 +    
234      //getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
235          
236      /** Returns the total number of z-constraint molecules in the system */
# Line 265 | Line 276 | namespace oopse{
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 */
284      void update();
285  
# Line 299 | Line 314 | namespace oopse{
314        return i != molecules_.end() ? i->second : NULL;
315      }
316  
317 <    /** Calculate the maximum cutoff radius based on the atom types */
318 <    double calcMaxCutoffRadius();
317 >    int getGlobalMolMembership(int id){
318 >      return globalMolMembership_[id];
319 >    }
320  
321 <    double getRcut() {
321 >    RealType getRcut() {
322        return rcut_;
323      }
324  
325 <    double getRsw() {
325 >    RealType getRsw() {
326        return rsw_;
327      }
328 +
329 +    RealType getList() {
330 +      return rlist_;
331 +    }
332          
333      std::string getFinalConfigFileName() {
334        return finalConfigFileName_;
335      }
336 <        
336 >
337      void setFinalConfigFileName(const std::string& fileName) {
338        finalConfigFileName_ = fileName;
339      }
340  
341 +    std::string getRawMetaData() {
342 +      return rawMetaData_;
343 +    }
344 +    void setRawMetaData(const std::string& rawMetaData) {
345 +      rawMetaData_ = rawMetaData;
346 +    }
347 +        
348      std::string getDumpFileName() {
349        return dumpFileName_;
350      }
# Line 347 | Line 374 | namespace oopse{
374       * @see #SimCreator::setGlobalIndex
375       */  
376      void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
377 <      assert(globalGroupMembership.size() == nGlobalAtoms_);
377 >      assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
378        globalGroupMembership_ = globalGroupMembership;
379      }
380  
# Line 356 | Line 383 | namespace oopse{
383       * @see #SimCreator::setGlobalIndex
384       */        
385      void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
386 <      assert(globalMolMembership.size() == nGlobalAtoms_);
386 >      assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
387        globalMolMembership_ = globalMolMembership;
388      }
389  
# Line 365 | Line 392 | namespace oopse{
392        return fortranInitialized_;
393      }
394          
395 +    bool getCalcBoxDipole() {
396 +      return calcBoxDipole_;
397 +    }
398 +
399 +    bool getUseAtomicVirial() {
400 +      return useAtomicVirial_;
401 +    }
402 +
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.
# Line 406 | Line 441 | namespace oopse{
441      GenericData* getPropertyByName(const std::string& propName);
442  
443      /**
444 <     * add all exclude pairs of a molecule into exclude list.
444 >     * add all special interaction pairs (including excluded
445 >     * interactions) in a molecule into the appropriate lists.
446       */
447 <    void addExcludePairs(Molecule* mol);
447 >    void addInteractionPairs(Molecule* mol);
448  
449      /**
450 <     * remove all exclude pairs which belong to a molecule from exclude list
450 >     * remove all special interaction pairs which belong to a molecule
451 >     * from the appropriate lists.
452       */
453 +    void removeInteractionPairs(Molecule* mol);
454  
417 –    void removeExcludePairs(Molecule* mol);
455  
419 –
456      /** Returns the unique atom types of local processor in an array */
457      std::set<AtomType*> getUniqueAtomTypes();
458          
459      friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
460  
461 <    void getCutoff(double& rcut, double& rsw);
461 >    void getCutoff(RealType& rcut, RealType& rsw);
462          
463    private:
464  
# Line 441 | Line 477 | namespace oopse{
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 +
483 +    /** Determine if we need to accumulate the simulation box dipole */
484 +    void setupAccumulateBoxDipole();
485 +
486      /** Calculates the number of degress of freedom in the whole system */
487      void calcNdf();
488      void calcNdfRaw();
489      void calcNdfTrans();
490  
491 +    ForceField* forceField_;      
492 +    Globals* simParams_;
493 +
494 +    std::map<int, Molecule*>  molecules_; /**< Molecule array */
495 +
496      /**
497       * Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
498       * system.
499       */
500      void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
454 –
455 –    MakeStamps* stamps_;
456 –    ForceField* forceField_;      
457 –    Globals* simParams_;
458 –
459 –    std::map<int, Molecule*>  molecules_; /**< Molecule array */
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 */
# Line 478 | Line 521 | namespace oopse{
521      std::vector<int> globalGroupMembership_;
522  
523      /**
524 <     * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
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       */
# Line 489 | Line 532 | namespace oopse{
532      std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */        
533          
534      //number of local objects
535 <    int nAtoms_;                        /**< number of atoms in local processor */
536 <    int nBonds_;                        /**< number of bonds in local processor */
537 <    int nBends_;                        /**< number of bends in local processor */
538 <    int nTorsions_;                    /**< number of torsions in local processor */
539 <    int nRigidBodies_;              /**< number of rigid bodies in local processor */
540 <    int nIntegrableObjects_;    /**< number of integrable objects in local processor */
541 <    int nCutoffGroups_;             /**< number of cutoff groups in local processor */
542 <    int nConstraints_;              /**< number of constraints in local processors */
535 >    int nAtoms_;              /**< number of atoms in local processor */
536 >    int nBonds_;              /**< number of bonds in local processor */
537 >    int nBends_;              /**< number of bends in local processor */
538 >    int nTorsions_;           /**< number of torsions in local processor */
539 >    int nInversions_;         /**< number of inversions in local processor */
540 >    int nRigidBodies_;        /**< number of rigid bodies in local processor */
541 >    int nIntegrableObjects_;  /**< number of integrable objects in local processor */
542 >    int nCutoffGroups_;       /**< number of cutoff groups in local processor */
543 >    int nConstraints_;        /**< number of constraints in local processors */
544  
545      simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
546 <    Exclude exclude_;      
546 >    PairList excludedInteractions_;      
547 >    PairList oneTwoInteractions_;      
548 >    PairList oneThreeInteractions_;      
549 >    PairList oneFourInteractions_;      
550      PropertyMap properties_;                  /**< Generic Property */
551      SnapshotManager* sman_;               /**< SnapshotManager */
552  
# Line 511 | Line 558 | namespace oopse{
558       */        
559      LocalIndexManager localIndexMan_;
560  
561 +    // unparsed MetaData block for storing in Dump and EOR files:
562 +    std::string rawMetaData_;
563 +
564      //file names
565      std::string finalConfigFileName_;
566      std::string dumpFileName_;
567      std::string statFileName_;
568      std::string restFileName_;
569          
570 <    double rcut_;       /**< cutoff radius*/
571 <    double rsw_;        /**< radius of switching function*/
570 >    RealType rcut_;       /**< cutoff radius*/
571 >    RealType rsw_;        /**< radius of switching function*/
572 >    RealType rlist_;      /**< neighbor list radius */
573  
574 <    bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
574 >    int ljsp_; /**< use shifted potential for LJ*/
575 >    int ljsf_; /**< use shifted force for LJ*/
576  
577 < #ifdef IS_MPI
577 >    bool fortranInitialized_; /**< flag indicate whether fortran side
578 >                                 is initialized */
579 >    
580 >    bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
581 >                            the simulation box dipole moment */
582 >    
583 >    bool useAtomicVirial_; /**< flag to indicate whether or not we use
584 >                              Atomic Virials to calculate the pressure */
585 >
586 >    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);
597 >    /**
598 >     * return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
599 >     * global index does not belong to local processor, a NULL will be return.
600 >     */
601 >    //StuntDouble* getStuntDoubleFromGlobalIndex(int index);
602 >  //private:
603 >    //std::vector<StuntDouble*> sdByGlobalIndex_;
604 >    
605      //in Parallel version, we need MolToProc
606    public:
607                  
# Line 549 | Line 628 | namespace oopse{
628      void setupFortranParallel();
629          
630      /**
631 <     * The size of molToProcMap_ is equal to total number of molecules in the system.
632 <     *  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
633 <     * once.
631 >     * The size of molToProcMap_ is equal to total number of molecules
632 >     * in the system.  It maps a molecule to the processor on which it
633 >     * resides. it is filled by SimCreator once and only once.
634       */        
635      std::vector<int> molToProcMap_;
636  
558 – #endif
637  
638    };
639  
640 < } //namespace oopse
640 > } //namespace OpenMD
641   #endif //BRAINS_SIMMODEL_HPP
642  

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