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Revision 1544 by gezelter, Fri Mar 18 19:31:52 2011 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  
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();
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 */
# Line 302 | Line 312 | namespace OpenMD{
312  
313      void update();
314      /**
315 <     * Setup Fortran Simulation
315 >     * Do final bookkeeping before Force managers need their data.
316       */
317 <    void setupFortran();
317 >    void prepareTopology();
318  
319  
320      /** Returns the local index manager */
# Line 341 | Line 351 | namespace OpenMD{
351      int getGlobalMolMembership(int id){
352        return globalMolMembership_[id];
353      }
354 +
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 +    /**
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 +
369          
370      string getFinalConfigFileName() {
371        return finalConfigFileName_;
# Line 400 | 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 502 | 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 509 | 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 523 | 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? */
# Line 531 | Line 561 | namespace OpenMD{
561    public:
562      bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
563      bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
564 <    bool usesMetallicAtoms() { return usesMetallicAtoms_; }
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 */
539 –    simtype fInfo_;                   /**< A dual struct shared by C++
540 –                                         and Fortran to pass
541 –                                         information about what types
542 –                                         of calculation are
543 –                                         required */
573  
574      /// Stamps are templates for objects that are then used to create
575      /// groups of objects.  For example, a molecule stamp contains
# Line 557 | 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 571 | Line 603 | namespace OpenMD{
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 603 | Line 654 | namespace OpenMD{
654      string restFileName_;
655          
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 */

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