ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/brains/SimInfo.hpp
(Generate patch)

Comparing branches/development/src/brains/SimInfo.hpp (file contents):
Revision 1549 by gezelter, Wed Apr 27 18:38:15 2011 UTC vs.
Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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 64 | Line 65
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 <  //forward decalration
70 >  //forward declaration
71    class SnapshotManager;
72    class Molecule;
73    class SelectionManager;
# Line 170 | 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 302 | Line 302 | namespace OpenMD{
302  
303      void update();
304      /**
305 <     * Setup Fortran Simulation
305 >     * Do final bookkeeping before Force managers need their data.
306       */
307 <    void setupFortran();
307 >    void prepareTopology();
308  
309  
310      /** Returns the local index manager */
# Line 355 | Line 355 | namespace OpenMD{
355       * processor, these should be identical.
356       */
357      vector<int> getGlobalGroupIndices();
358 +
359          
360      string getFinalConfigFileName() {
361        return finalConfigFileName_;
# Line 414 | Line 415 | namespace OpenMD{
415      }
416  
417  
418 <    bool isFortranInitialized() {
419 <      return fortranInitialized_;
418 >    bool isTopologyDone() {
419 >      return topologyDone_;
420      }
421          
422      bool getCalcBoxDipole() {
# Line 554 | Line 555 | namespace OpenMD{
555    private:
556      /// Data structures holding primary simulation objects
557      map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
557 –    simtype fInfo_;                   /**< A dual struct shared by C++
558 –                                         and Fortran to pass
559 –                                         information about what types
560 –                                         of calculation are
561 –                                         required */
558  
559      /// Stamps are templates for objects that are then used to create
560      /// groups of objects.  For example, a molecule stamp contains
# Line 595 | Line 591 | namespace OpenMD{
591    public:
592      vector<int> getIdentArray() { return identArray_; }
593    private:
594 +    
595 +    /**
596 +     * A vector which contains the fractional contribution of an
597 +     * atom's mass to the total mass of the cutoffGroup that atom
598 +     * belongs to.  In the case of single atom cutoff groups, the mass
599 +     * factor for that atom is 1.  For massless atoms, the factor is
600 +     * also 1.
601 +     */
602 +    vector<RealType> massFactors_;
603 +  public:
604 +    vector<RealType> getMassFactors() { return massFactors_; }
605 +
606 +    PairList* getExcludedInteractions() { return &excludedInteractions_; }
607 +    PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
608 +    PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
609 +    PairList* getOneFourInteractions() { return &oneFourInteractions_; }
610 +
611 +  private:
612                
613      /// lists to handle atoms needing special treatment in the non-bonded interactions
614      PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
# Line 625 | Line 639 | namespace OpenMD{
639      string restFileName_;
640          
641  
642 <    bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
642 >    bool topologyDone_;  /** flag to indicate whether the topology has
643 >                             been scanned and all the relevant
644 >                             bookkeeping has been done*/
645      
646      bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
647                              the simulation box dipole moment */

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines