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Comparing branches/development/src/brains/SimInfo.hpp (file contents):
Revision 1725 by gezelter, Sat May 26 18:13:43 2012 UTC vs.
Revision 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC

# Line 35 | Line 35
35   *                                                                      
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).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 91 | Line 91 | namespace OpenMD{
91      /**
92       * Constructor of SimInfo
93       *
94 <     * @param molStampPairs MoleculeStamp Array. The first element of
95 <     * the pair is molecule stamp, the second element is the total
96 <     * number of molecules with the same molecule stamp in the system
94 >     * @param ff pointer to a concrete ForceField instance
95       *
96 <     * @param ff pointer of a concrete ForceField instance
99 <     *
100 <     * @param simParams
96 >     * @param simParams pointer to the simulation parameters in a Globals object
97       */
98      SimInfo(ForceField* ff, Globals* simParams);
99      virtual ~SimInfo();
# Line 108 | Line 104 | namespace OpenMD{
104       * @return return true if adding successfully, return false if the
105       * molecule is already in SimInfo
106       *
107 <     * @param mol molecule to be added
107 >     * @param mol Molecule to be added
108       */
109      bool addMolecule(Molecule* mol);
110  
# Line 233 | Line 229 | namespace OpenMD{
229        return ndf_ - getFdf();
230      }
231  
232 +    /** Returns the number of degrees of freedom (LOCAL) */
233 +    int getNdfLocal() {
234 +      return ndfLocal_;
235 +    }
236 +
237      /** Returns the number of raw degrees of freedom */
238      int getNdfRaw() {
239        return ndfRaw_;
# Line 269 | Line 270 | namespace OpenMD{
270      SnapshotManager* getSnapshotManager() {
271        return sman_;
272      }
273 <
273 >    /** Returns the storage layout (computed by SimCreator) */
274 >    int getStorageLayout() {
275 >      return storageLayout_;
276 >    }
277 >    /** Sets the storage layout (computed by SimCreator) */
278 >    void setStorageLayout(int sl) {
279 >      storageLayout_ = sl;
280 >    }
281 >    
282      /** Sets the snapshot manager. */
283      void setSnapshotManager(SnapshotManager* sman);
284          
# Line 281 | Line 290 | namespace OpenMD{
290      Globals* getSimParams() {
291        return simParams_;
292      }
284 –
285 –    /** Returns the velocity of center of mass of the whole system.*/
286 –    Vector3d getComVel();
287 –
288 –    /** Returns the center of the mass of the whole system.*/
289 –    Vector3d getCom();
290 –    /** Returns the center of the mass and Center of Mass velocity of
291 –        the whole system.*/
292 –    void getComAll(Vector3d& com,Vector3d& comVel);
293 –
294 –    /** Returns intertia tensor for the entire system and system
295 –        Angular Momentum.*/
296 –    void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
297 –    
298 –    /** Returns system angular momentum */
299 –    Vector3d getAngularMomentum();
293  
301 –    /** Returns volume of system as estimated by an ellipsoid defined
302 –        by the radii of gyration*/
303 –    void getGyrationalVolume(RealType &vol);
304 –    /** Overloaded version of gyrational volume that also returns
305 –        det(I) so dV/dr can be calculated*/
306 –    void getGyrationalVolume(RealType &vol, RealType &detI);
307 –
294      void update();
295      /**
296       * Do final bookkeeping before Force managers need their data.
# Line 403 | Line 389 | namespace OpenMD{
389  
390      /**
391       * Sets GlobalGroupMembership
406 –     * @see #SimCreator::setGlobalIndex
392       */  
393 <    void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
394 <      assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
395 <      globalGroupMembership_ = globalGroupMembership;
393 >    void setGlobalGroupMembership(const vector<int>& ggm) {
394 >      assert(ggm.size() == static_cast<size_t>(nGlobalAtoms_));
395 >      globalGroupMembership_ = ggm;
396      }
397  
398      /**
399       * Sets GlobalMolMembership
415 –     * @see #SimCreator::setGlobalIndex
400       */        
401 <    void setGlobalMolMembership(const vector<int>& globalMolMembership) {
402 <      assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
403 <      globalMolMembership_ = globalMolMembership;
401 >    void setGlobalMolMembership(const vector<int>& gmm) {
402 >      assert(gmm.size() == (static_cast<size_t>(nGlobalAtoms_ +
403 >                                                nGlobalRigidBodies_)));
404 >      globalMolMembership_ = gmm;
405      }
406  
407  
# Line 483 | Line 468 | namespace OpenMD{
468  
469      /** Returns the set of atom types present in this simulation */
470      set<AtomType*> getSimulatedAtomTypes();
471 +
472 +    /** Returns the global count of atoms of a particular type */
473 +    int getGlobalCountOfType(AtomType* atype);
474          
475      friend ostream& operator <<(ostream& o, SimInfo& info);
476  
# Line 535 | Line 523 | namespace OpenMD{
523        
524      /// Degress of freedom
525      int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
526 +    int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
527      int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
528      int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
529      int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
# Line 627 | Line 616 | namespace OpenMD{
616  
617      PropertyMap properties_;       /**< Generic Properties can be added */
618      SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
619 +    int storageLayout_;            /**< Bits to tell how much data to store on each object */
620  
621      /**
622       * The reason to have a local index manager is that when molecule
# Line 646 | Line 636 | namespace OpenMD{
636      string dumpFileName_;
637      string statFileName_;
638      string restFileName_;
649 –        
639  
640      bool topologyDone_;  /** flag to indicate whether the topology has
641                               been scanned and all the relevant
# Line 684 | Line 673 | namespace OpenMD{
673      
674      /**
675       * Set MolToProcMap array
687 –     * @see #SimCreator::divideMolecules
676       */
677      void setMolToProcMap(const vector<int>& molToProcMap) {
678        molToProcMap_ = molToProcMap;

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