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Comparing branches/development/src/brains/SimInfo.hpp (file contents):
Revision 1553 by gezelter, Fri Apr 29 17:25:12 2011 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"
# Line 166 | 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 218 | Line 222 | namespace OpenMD{
222       * @param i the iterator of molecule array
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 273 | Line 287 | namespace OpenMD{
287        return simParams_;
288      }
289  
276 –    /** Returns the velocity of center of mass of the whole system.*/
277 –    Vector3d getComVel();
278 –
279 –    /** Returns the center of the mass of the whole system.*/
280 –    Vector3d getCom();
281 –    /** Returns the center of the mass and Center of Mass velocity of
282 –        the whole system.*/
283 –    void getComAll(Vector3d& com,Vector3d& comVel);
284 –
285 –    /** Returns intertia tensor for the entire system and system
286 –        Angular Momentum.*/
287 –    void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
288 –    
289 –    /** Returns system angular momentum */
290 –    Vector3d getAngularMomentum();
291 –
292 –    /** Returns volume of system as estimated by an ellipsoid defined
293 –        by the radii of gyration*/
294 –    void getGyrationalVolume(RealType &vol);
295 –    /** Overloaded version of gyrational volume that also returns
296 –        det(I) so dV/dr can be calculated*/
297 –    void getGyrationalVolume(RealType &vol, RealType &detI);
298 –
290      void update();
291      /**
292 <     * Setup Fortran Simulation
292 >     * Do final bookkeeping before Force managers need their data.
293       */
294 <    void setupFortran();
294 >    void prepareTopology();
295  
296  
297      /** Returns the local index manager */
# Line 351 | Line 342 | namespace OpenMD{
342       * processor, these should be identical.
343       */
344      vector<int> getGlobalGroupIndices();
345 +
346          
347      string getFinalConfigFileName() {
348        return finalConfigFileName_;
# Line 410 | 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 512 | 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 519 | 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 533 | 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? */
# Line 541 | Line 538 | namespace OpenMD{
538    public:
539      bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
540      bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
541 <    bool usesMetallicAtoms() { return usesMetallicAtoms_; }
541 >    bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
542      bool usesAtomicVirial() { return usesAtomicVirial_; }
543      bool requiresPrepair() { return requiresPrepair_; }
544      bool requiresSkipCorrection() { return requiresSkipCorrection_;}
# Line 585 | Line 582 | namespace OpenMD{
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
# Line 616 | Line 631 | namespace OpenMD{
631      string restFileName_;
632          
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 */

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