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Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC vs.
Revision 1764 by gezelter, Tue Jul 3 18:32:27 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  
66 – //another nonsense macro declaration
67 – #define __OPENMD_C
68 – #include "brains/fSimulation.h"
69 –
68   using namespace std;
69   namespace OpenMD{
70 <
73 <  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 177 | 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 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();
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 284 | Line 287 | namespace OpenMD{
287        return simParams_;
288      }
289  
287 –    /** Returns the velocity of center of mass of the whole system.*/
288 –    Vector3d getComVel();
289 –
290 –    /** Returns the center of the mass of the whole system.*/
291 –    Vector3d getCom();
292 –    /** Returns the center of the mass and Center of Mass velocity of
293 –        the whole system.*/
294 –    void getComAll(Vector3d& com,Vector3d& comVel);
295 –
296 –    /** Returns intertia tensor for the entire system and system
297 –        Angular Momentum.*/
298 –    void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
299 –    
300 –    /** Returns system angular momentum */
301 –    Vector3d getAngularMomentum();
302 –
303 –    /** Returns volume of system as estimated by an ellipsoid defined
304 –        by the radii of gyration*/
305 –    void getGyrationalVolume(RealType &vol);
306 –    /** Overloaded version of gyrational volume that also returns
307 –        det(I) so dV/dr can be calculated*/
308 –    void getGyrationalVolume(RealType &vol, RealType &detI);
309 –    /** main driver function to interact with fortran during the
310 –        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 345 | Line 329 | namespace OpenMD{
329        return globalMolMembership_[id];
330      }
331  
332 <    RealType getCutoffRadius() {
333 <      return cutoffRadius_;
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 getSwitchingRadius() {
340 <      return switchingRadius_;
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  
356 –    RealType getListRadius() {
357 –      return listRadius_;
358 –    }
346          
347      string getFinalConfigFileName() {
348        return finalConfigFileName_;
# Line 415 | Line 402 | namespace OpenMD{
402      }
403  
404  
405 <    bool isFortranInitialized() {
406 <      return fortranInitialized_;
405 >    bool isTopologyDone() {
406 >      return topologyDone_;
407      }
408          
409      bool getCalcBoxDipole() {
# Line 475 | Line 462 | namespace OpenMD{
462       * from the appropriate lists.
463       */
464      void removeInteractionPairs(Molecule* mol);
478 –
479 –
480 –    /** Returns the unique atom types of local processor in an array */
481 –    set<AtomType*> getUniqueAtomTypes();
465  
466      /** Returns the set of atom types present in this simulation */
467      set<AtomType*> getSimulatedAtomTypes();
# Line 489 | Line 472 | namespace OpenMD{
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  
495 –    /**
496 –     * Setup Fortran Simulation
497 –     * @see #setupFortranParallel
498 –     */
499 –    void setupFortranSim();
478  
501 –    /** Figure out the cutoff radius */
502 –    void setupCutoffRadius();
503 –    /** Figure out the cutoff method */
504 –    void setupCutoffMethod();
505 –    /** Figure out the switching radius */
506 –    void setupSwitchingRadius();
507 –    /** Figure out the neighbor list skin thickness */
508 –    void setupSkinThickness();
509 –    /** Figure out which polynomial type to use for the switching function */
510 –    void setupSwitchingFunction();
511 –
479      /** Determine if we need to accumulate the simulation box dipole */
480      void setupAccumulateBoxDipole();
481  
# Line 537 | 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) */
# Line 544 | Line 512 | namespace OpenMD{
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) */
# Line 558 | Line 529 | namespace OpenMD{
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 <    simtype fInfo_;                   /**< A dual struct shared by C++
569 <                                         and Fortran to pass
570 <                                         information about what types
571 <                                         of calculation are
572 <                                         required */
573 <    
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,
# Line 586 | Line 563 | namespace OpenMD{
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
# Line 593 | Line 573 | namespace OpenMD{
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_;        
576 >    vector<int> globalMolMembership_;
577 >
578 >    /**
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 */
# Line 623 | Line 630 | namespace OpenMD{
630      string statFileName_;
631      string restFileName_;
632          
626 –    RealType cutoffRadius_;         /**< cutoff radius for non-bonded interactions */
627 –    RealType switchingRadius_;      /**< inner radius of switching function */
628 –    RealType listRadius_;           /**< Verlet neighbor list radius */
629 –    RealType skinThickness_;        /**< Verlet neighbor list skin thickness */    
630 –    CutoffMethod cutoffMethod_;     /**< Cutoff Method for most non-bonded interactions */
633  
634 <    bool fortranInitialized_; /** flag to indicate whether the fortran side 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 */
# Line 670 | Line 674 | namespace OpenMD{
674      }
675          
676    private:
673 –
674 –    void setupFortranParallel();
677          
678      /**
679       * The size of molToProcMap_ is equal to total number of molecules

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