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Revision 1530 by gezelter, Tue Dec 28 21:47:55 2010 UTC vs.
Revision 1725 by gezelter, Sat May 26 18:13:43 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  
67 – //another nonsense macro declaration
68 – #define __OPENMD_C
69 – #include "brains/fSimulation.h"
70 –
68   using namespace std;
69   namespace OpenMD{
70 <  enum CutoffMethod {
74 <    HARD,
75 <    SWITCHING_FUNCTION,
76 <    SHIFTED_POTENTIAL,
77 <    SHIFTED_FORCE
78 <  };
79 <
80 <  //forward decalration
70 >  //forward declaration
71    class SnapshotManager;
72    class Molecule;
73    class SelectionManager;
# Line 176 | Line 166 | namespace OpenMD{
166      unsigned int getNAtoms() {
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(){
# Line 230 | 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 306 | Line 304 | namespace OpenMD{
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
310 <        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 345 | Line 347 | namespace OpenMD{
347        return globalMolMembership_[id];
348      }
349  
350 <    RealType getCutoffRadius() {
351 <      return cutoffRadius_;
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 getSwitchingRadius() {
358 <      return switchingRadius_;
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  
356 –    RealType getListRadius() {
357 –      return listRadius_;
358 –    }
364          
365      string getFinalConfigFileName() {
366        return finalConfigFileName_;
# Line 415 | Line 420 | namespace OpenMD{
420      }
421  
422  
423 <    bool isFortranInitialized() {
424 <      return fortranInitialized_;
423 >    bool isTopologyDone() {
424 >      return topologyDone_;
425      }
426          
427      bool getCalcBoxDipole() {
# Line 476 | Line 481 | namespace OpenMD{
481       */
482      void removeInteractionPairs(Molecule* mol);
483  
479 –
480 –    /** Returns the unique atom types of local processor in an array */
481 –    set<AtomType*> getUniqueAtomTypes();
482 –
484      /** Returns the set of atom types present in this simulation */
485      set<AtomType*> getSimulatedAtomTypes();
486          
# Line 492 | Line 493 | namespace OpenMD{
493      /** fill up the simtype struct and other simulation-related variables */
494      void setupSimVariables();
495  
495 –    /**
496 –     * Setup Fortran Simulation
497 –     * @see #setupFortranParallel
498 –     */
499 –    void setupFortranSim();
496  
501 –    /** Figure out the cutoff radius and cutoff method */
502 –    void setupCutoffs();
503 –    /** Figure out the switching radius and polynomial type for the switching function */
504 –    void setupSwitching();
505 –    /** Figure out the simulation variables associated with electrostatics */
506 –    void setupElectrostatics();  
507 –    /** Figure out the neighbor list skin thickness */
508 –    void setupNeighborlists();
509 –
497      /** Determine if we need to accumulate the simulation box dipole */
498      void setupAccumulateBoxDipole();
499  
# Line 535 | 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) */
# Line 542 | Line 530 | namespace OpenMD{
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) */
# Line 556 | Line 546 | namespace OpenMD{
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 <    simtype fInfo_;                   /**< A dual struct shared by C++
567 <                                         and Fortran to pass
568 <                                         information about what types
569 <                                         of calculation are
570 <                                         required */
571 <    
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,
# Line 584 | Line 580 | namespace OpenMD{
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
# Line 591 | Line 590 | namespace OpenMD{
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_;        
593 >    vector<int> globalMolMembership_;
594 >
595 >    /**
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 */
# Line 621 | Line 647 | namespace OpenMD{
647      string statFileName_;
648      string restFileName_;
649          
624 –    RealType cutoffRadius_;         /**< cutoff radius for non-bonded interactions */
625 –    RealType switchingRadius_;      /**< inner radius of switching function */
626 –    RealType listRadius_;           /**< Verlet neighbor list radius */
627 –    RealType skinThickness_;        /**< Verlet neighbor list skin thickness */    
628 –    CutoffMethod cutoffMethod_;     /**< Cutoff Method for most non-bonded interactions */
650  
651 <    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 */
# Line 668 | Line 691 | namespace OpenMD{
691      }
692          
693    private:
671 –
672 –    void setupFortranParallel();
694          
695      /**
696       * The size of molToProcMap_ is equal to total number of molecules

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