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Revision 1570 by gezelter, Thu May 26 21:56:04 2011 UTC vs.
Revision 1848 by gezelter, Mon Feb 4 21:13:46 2013 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 90 | Line 91 | namespace OpenMD{
91      /**
92       * Constructor of SimInfo
93       *
94 <     * @param molStampPairs MoleculeStamp Array. The first element of
94 <     * the pair is molecule stamp, the second element is the total
95 <     * 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
98 <     *
99 <     * @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 107 | 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 166 | Line 163 | namespace OpenMD{
163        return nAtoms_;
164      }
165  
166 +    /** Returns the number of effective cutoff groups on local processor */
167 +    unsigned int getNLocalCutoffGroups();
168 +
169      /** Returns the number of local bonds */        
170      unsigned int getNBonds(){
171        return nBonds_;
# Line 219 | Line 219 | namespace OpenMD{
219       */
220      Molecule* nextMolecule(MoleculeIterator& i);
221  
222 +    /** Returns the total number of fluctuating charges that are present */
223 +    int getNFluctuatingCharges() {
224 +      return nGlobalFluctuatingCharges_;
225 +    }
226 +
227      /** Returns the number of degrees of freedom */
228      int getNdf() {
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 260 | 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 273 | Line 291 | namespace OpenMD{
291        return simParams_;
292      }
293  
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 –
294      void update();
295      /**
296       * Do final bookkeeping before Force managers need their data.
# Line 394 | Line 389 | namespace OpenMD{
389  
390      /**
391       * Sets GlobalGroupMembership
397 –     * @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
406 –     * @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 513 | Line 507 | namespace OpenMD{
507      int nIntegrableObjects_;  /**< number of integrable objects in local processor */
508      int nCutoffGroups_;       /**< number of cutoff groups in local processor */
509      int nConstraints_;        /**< number of constraints in local processors */
510 +    int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */
511          
512      /// Counts of global objects
513      int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
# Line 520 | Line 515 | namespace OpenMD{
515      int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
516      int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
517      int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
518 +    int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
519 +    
520        
521      /// Degress of freedom
522      int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
523 +    int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
524      int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
525      int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
526      int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
# Line 534 | Line 532 | namespace OpenMD{
532      bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
533      bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
534      bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
535 +    bool usesFluctuatingCharges_; /**< are there fluctuating charges? */
536      bool usesAtomicVirial_;       /**< are we computing atomic virials? */
537      bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
538      bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
# Line 542 | Line 541 | namespace OpenMD{
541    public:
542      bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
543      bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
544 <    bool usesMetallicAtoms() { return usesMetallicAtoms_; }
544 >    bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
545      bool usesAtomicVirial() { return usesAtomicVirial_; }
546      bool requiresPrepair() { return requiresPrepair_; }
547      bool requiresSkipCorrection() { return requiresSkipCorrection_;}
# Line 599 | Line 598 | namespace OpenMD{
598    public:
599      vector<RealType> getMassFactors() { return massFactors_; }
600  
601 <    PairList getExcludedInteractions() { return excludedInteractions_; }
602 <    PairList getOneTwoInteractions() { return oneTwoInteractions_; }
603 <    PairList getOneThreeInteractions() { return oneThreeInteractions_; }
604 <    PairList getOneFourInteractions() { return oneFourInteractions_; }
601 >    PairList* getExcludedInteractions() { return &excludedInteractions_; }
602 >    PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
603 >    PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
604 >    PairList* getOneFourInteractions() { return &oneFourInteractions_; }
605  
606    private:
608 –
607                
608      /// lists to handle atoms needing special treatment in the non-bonded interactions
609      PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
# Line 615 | Line 613 | namespace OpenMD{
613  
614      PropertyMap properties_;       /**< Generic Properties can be added */
615      SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
616 +    int storageLayout_;            /**< Bits to tell how much data to store on each object */
617  
618      /**
619       * The reason to have a local index manager is that when molecule
# Line 634 | Line 633 | namespace OpenMD{
633      string dumpFileName_;
634      string statFileName_;
635      string restFileName_;
637 –        
636  
637      bool topologyDone_;  /** flag to indicate whether the topology has
638                               been scanned and all the relevant
# Line 672 | Line 670 | namespace OpenMD{
670      
671      /**
672       * Set MolToProcMap array
675 –     * @see #SimCreator::divideMolecules
673       */
674      void setMolToProcMap(const vector<int>& molToProcMap) {
675        molToProcMap_ = molToProcMap;

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