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Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC vs.
Revision 1744 by gezelter, Tue Jun 5 18:07:08 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 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();
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 306 | Line 309 | namespace OpenMD{
309      /** Overloaded version of gyrational volume that also returns
310          det(I) so dV/dr can be calculated*/
311      void getGyrationalVolume(RealType &vol, RealType &detI);
312 <    /** main driver function to interact with fortran during the
310 <        initialization and molecule migration */
312 >
313      void update();
314 +    /**
315 +     * Do final bookkeeping before Force managers need their data.
316 +     */
317 +    void prepareTopology();
318 +
319  
320      /** Returns the local index manager */
321      LocalIndexManager* getLocalIndexManager() {
# Line 345 | Line 352 | namespace OpenMD{
352        return globalMolMembership_[id];
353      }
354  
355 <    RealType getCutoffRadius() {
356 <      return cutoffRadius_;
357 <    }
355 >    /**
356 >     * returns a vector which maps the local atom index on this
357 >     * processor to the global atom index.  With only one processor,
358 >     * these should be identical.
359 >     */
360 >    vector<int> getGlobalAtomIndices();
361  
362 <    RealType getSwitchingRadius() {
363 <      return switchingRadius_;
364 <    }
362 >    /**
363 >     * returns a vector which maps the local cutoff group index on
364 >     * this processor to the global cutoff group index.  With only one
365 >     * processor, these should be identical.
366 >     */
367 >    vector<int> getGlobalGroupIndices();
368  
356 –    RealType getListRadius() {
357 –      return listRadius_;
358 –    }
369          
370      string getFinalConfigFileName() {
371        return finalConfigFileName_;
# Line 415 | Line 425 | namespace OpenMD{
425      }
426  
427  
428 <    bool isFortranInitialized() {
429 <      return fortranInitialized_;
428 >    bool isTopologyDone() {
429 >      return topologyDone_;
430      }
431          
432      bool getCalcBoxDipole() {
# Line 476 | Line 486 | namespace OpenMD{
486       */
487      void removeInteractionPairs(Molecule* mol);
488  
479 –
480 –    /** Returns the unique atom types of local processor in an array */
481 –    set<AtomType*> getUniqueAtomTypes();
482 –
489      /** Returns the set of atom types present in this simulation */
490      set<AtomType*> getSimulatedAtomTypes();
491          
# Line 489 | Line 495 | namespace OpenMD{
495          
496    private:
497  
498 <    /** fill up the simtype struct*/
499 <    void setupSimType();
494 <
495 <    /**
496 <     * Setup Fortran Simulation
497 <     * @see #setupFortranParallel
498 <     */
499 <    void setupFortranSim();
498 >    /** fill up the simtype struct and other simulation-related variables */
499 >    void setupSimVariables();
500  
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();
501  
502      /** Determine if we need to accumulate the simulation box dipole */
503      void setupAccumulateBoxDipole();
# Line 537 | Line 527 | namespace OpenMD{
527      int nIntegrableObjects_;  /**< number of integrable objects in local processor */
528      int nCutoffGroups_;       /**< number of cutoff groups in local processor */
529      int nConstraints_;        /**< number of constraints in local processors */
530 +    int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */
531          
532      /// Counts of global objects
533      int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
# Line 544 | Line 535 | namespace OpenMD{
535      int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
536      int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
537      int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
538 +    int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
539 +    
540        
541      /// Degress of freedom
542      int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
543 +    int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
544      int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
545      int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
546      int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
# Line 558 | Line 552 | namespace OpenMD{
552      bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
553      bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
554      bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
555 +    bool usesFluctuatingCharges_; /**< are there fluctuating charges? */
556      bool usesAtomicVirial_;       /**< are we computing atomic virials? */
557      bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
558      bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
559      bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
560  
561 +  public:
562 +    bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
563 +    bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
564 +    bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
565 +    bool usesAtomicVirial() { return usesAtomicVirial_; }
566 +    bool requiresPrepair() { return requiresPrepair_; }
567 +    bool requiresSkipCorrection() { return requiresSkipCorrection_;}
568 +    bool requiresSelfCorrection() { return requiresSelfCorrection_;}
569 +
570 +  private:
571      /// Data structures holding primary simulation objects
572      map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
573 <    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 <    
573 >
574      /// Stamps are templates for objects that are then used to create
575      /// groups of objects.  For example, a molecule stamp contains
576      /// information on how to build that molecule (i.e. the topology,
# Line 586 | Line 586 | namespace OpenMD{
586       * the simulation.  It should be nGlobalAtoms_ in size.
587       */
588      vector<int> globalGroupMembership_;
589 +  public:
590 +    vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
591 +  private:
592  
593      /**
594       * A vector that maps between the global index of an atom and the
# Line 593 | Line 596 | namespace OpenMD{
596       * by SimCreator once and only once, since it is never changed
597       * during the simulation. It shoudl be nGlobalAtoms_ in size.
598       */
599 <    vector<int> globalMolMembership_;        
599 >    vector<int> globalMolMembership_;
600 >
601 >    /**
602 >     * A vector that maps between the local index of an atom and the
603 >     * index of the AtomType.
604 >     */
605 >    vector<int> identArray_;
606 >  public:
607 >    vector<int> getIdentArray() { return identArray_; }
608 >  private:
609 >    
610 >    /**
611 >     * A vector which contains the fractional contribution of an
612 >     * atom's mass to the total mass of the cutoffGroup that atom
613 >     * belongs to.  In the case of single atom cutoff groups, the mass
614 >     * factor for that atom is 1.  For massless atoms, the factor is
615 >     * also 1.
616 >     */
617 >    vector<RealType> massFactors_;
618 >  public:
619 >    vector<RealType> getMassFactors() { return massFactors_; }
620 >
621 >    PairList* getExcludedInteractions() { return &excludedInteractions_; }
622 >    PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
623 >    PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
624 >    PairList* getOneFourInteractions() { return &oneFourInteractions_; }
625 >
626 >  private:
627                
628      /// lists to handle atoms needing special treatment in the non-bonded interactions
629      PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
# Line 623 | Line 653 | namespace OpenMD{
653      string statFileName_;
654      string restFileName_;
655          
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 */
656  
657 <    bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
657 >    bool topologyDone_;  /** flag to indicate whether the topology has
658 >                             been scanned and all the relevant
659 >                             bookkeeping has been done*/
660      
661      bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
662                              the simulation box dipole moment */
# Line 670 | Line 697 | namespace OpenMD{
697      }
698          
699    private:
673 –
674 –    void setupFortranParallel();
700          
701      /**
702       * The size of molToProcMap_ is equal to total number of molecules

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