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Comparing branches/development/src/brains/SimInfo.hpp (file contents):
Revision 1547 by gezelter, Mon Apr 11 18:44:16 2011 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 <  //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 223 | 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 302 | Line 307 | namespace OpenMD{
307  
308      void update();
309      /**
310 <     * Setup Fortran Simulation
310 >     * Do final bookkeeping before Force managers need their data.
311       */
312 <    void setupFortran();
312 >    void prepareTopology();
313  
314  
315      /** Returns the local index manager */
# Line 341 | Line 346 | namespace OpenMD{
346      int getGlobalMolMembership(int id){
347        return globalMolMembership_[id];
348      }
349 +
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 +    /**
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 +
364          
365      string getFinalConfigFileName() {
366        return finalConfigFileName_;
# Line 400 | 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 502 | 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 509 | 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 523 | 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? */
# Line 531 | Line 555 | namespace OpenMD{
555    public:
556      bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
557      bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
558 <    bool usesMetallicAtoms() { return usesMetallicAtoms_; }
558 >    bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
559      bool usesAtomicVirial() { return usesAtomicVirial_; }
560      bool requiresPrepair() { return requiresPrepair_; }
561      bool requiresSkipCorrection() { return requiresSkipCorrection_;}
# Line 540 | Line 564 | namespace OpenMD{
564    private:
565      /// Data structures holding primary simulation objects
566      map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
543 –    simtype fInfo_;                   /**< A dual struct shared by C++
544 –                                         and Fortran to pass
545 –                                         information about what types
546 –                                         of calculation are
547 –                                         required */
567  
568      /// Stamps are templates for objects that are then used to create
569      /// groups of objects.  For example, a molecule stamp contains
# Line 581 | Line 600 | namespace OpenMD{
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 611 | Line 648 | namespace OpenMD{
648      string restFileName_;
649          
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 */

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