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Comparing trunk/src/brains/SimInfo.hpp (file contents):
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC vs.
Revision 2022 by gezelter, Fri Sep 26 22:22:28 2014 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 153 | Line 149 | namespace OpenMD{
149        return nGlobalRigidBodies_;
150      }
151  
152 <    int getNGlobalConstraints();
152 >    /** Returns the number of global bonds */        
153 >    unsigned int getNGlobalBonds(){
154 >      return nGlobalBonds_;
155 >    }
156 >
157 >    /** Returns the number of global bends */        
158 >    unsigned int getNGlobalBends() {
159 >      return nGlobalBends_;
160 >    }
161 >
162 >    /** Returns the number of global torsions */        
163 >    unsigned int getNGlobalTorsions() {
164 >      return nGlobalTorsions_;
165 >    }
166 >
167 >    /** Returns the number of global inversions */        
168 >    unsigned int getNGlobalInversions() {
169 >      return nGlobalInversions_;
170 >    }
171 >
172 >    unsigned int getNGlobalConstraints() {
173 >      if (!hasNGlobalConstraints_) calcNConstraints();
174 >      return nGlobalConstraints_;
175 >    }
176      /**
177       * Returns the number of local molecules.
178       * @return the number of local molecules
# Line 185 | Line 204 | namespace OpenMD{
204        return nTorsions_;
205      }
206  
207 <    /** Returns the number of local torsions */        
207 >    /** Returns the number of local inversions */        
208      unsigned int getNInversions() {
209        return nInversions_;
210      }
# Line 274 | Line 293 | namespace OpenMD{
293      SnapshotManager* getSnapshotManager() {
294        return sman_;
295      }
296 <
296 >    /** Returns the storage layout (computed by SimCreator) */
297 >    int getStorageLayout() {
298 >      return storageLayout_;
299 >    }
300 >    /** Sets the storage layout (computed by SimCreator) */
301 >    void setStorageLayout(int sl) {
302 >      storageLayout_ = sl;
303 >    }
304 >    
305      /** Sets the snapshot manager. */
306      void setSnapshotManager(SnapshotManager* sman);
307          
# Line 385 | Line 412 | namespace OpenMD{
412  
413      /**
414       * Sets GlobalGroupMembership
388 –     * @see #SimCreator::setGlobalIndex
415       */  
416 <    void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
417 <      assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
418 <      globalGroupMembership_ = globalGroupMembership;
416 >    void setGlobalGroupMembership(const vector<int>& ggm) {
417 >      assert(ggm.size() == static_cast<size_t>(nGlobalAtoms_));
418 >      globalGroupMembership_ = ggm;
419      }
420  
421      /**
422       * Sets GlobalMolMembership
397 –     * @see #SimCreator::setGlobalIndex
423       */        
424 <    void setGlobalMolMembership(const vector<int>& globalMolMembership) {
425 <      assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
426 <      globalMolMembership_ = globalMolMembership;
424 >    void setGlobalMolMembership(const vector<int>& gmm) {
425 >      assert(gmm.size() == (static_cast<size_t>(nGlobalAtoms_ +
426 >                                                nGlobalRigidBodies_)));
427 >      globalMolMembership_ = gmm;
428      }
429  
430  
# Line 409 | Line 435 | namespace OpenMD{
435      bool getCalcBoxDipole() {
436        return calcBoxDipole_;
437      }
438 +    bool getCalcBoxQuadrupole() {
439 +      return calcBoxQuadrupole_;
440 +    }
441  
442      bool getUseAtomicVirial() {
443        return useAtomicVirial_;
# Line 465 | Line 494 | namespace OpenMD{
494  
495      /** Returns the set of atom types present in this simulation */
496      set<AtomType*> getSimulatedAtomTypes();
497 +
498 +    /** Returns the global count of atoms of a particular type */
499 +    int getGlobalCountOfType(AtomType* atype);
500          
501      friend ostream& operator <<(ostream& o, SimInfo& info);
502  
# Line 476 | Line 508 | namespace OpenMD{
508      void setupSimVariables();
509  
510  
479 –    /** Determine if we need to accumulate the simulation box dipole */
480 –    void setupAccumulateBoxDipole();
481 –
511      /** Calculates the number of degress of freedom in the whole system */
512      void calcNdf();
513      void calcNdfRaw();
514      void calcNdfTrans();
515 +    void calcNConstraints();
516  
517      /**
518       * Adds molecule stamp and the total number of the molecule with
# Line 513 | Line 543 | namespace OpenMD{
543      int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
544      int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
545      int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
546 <    
547 <      
546 >    int nGlobalBonds_;              /**< number of bonds in the system */
547 >    int nGlobalBends_;              /**< number of bends in the system */
548 >    int nGlobalTorsions_;           /**< number of torsions in the system */
549 >    int nGlobalInversions_;         /**< number of inversions in the system */
550 >    int nGlobalConstraints_;        /**< number of constraints in the system */
551 >    bool hasNGlobalConstraints_;
552 >
553      /// Degress of freedom
554      int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
555      int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
# Line 582 | Line 617 | namespace OpenMD{
617      vector<int> identArray_;
618    public:
619      vector<int> getIdentArray() { return identArray_; }
620 +
621 +    /**
622 +     * A vector that contains information about the local region of an
623 +     * atom (used for fluctuating charges, etc.)
624 +     */
625    private:
626 <    
626 >    vector<int> regions_;
627 >  public:
628 >    vector<int> getRegions() { return regions_; }
629 >  private:
630      /**
631       * A vector which contains the fractional contribution of an
632       * atom's mass to the total mass of the cutoffGroup that atom
# Line 610 | Line 653 | namespace OpenMD{
653  
654      PropertyMap properties_;       /**< Generic Properties can be added */
655      SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
656 +    int storageLayout_;            /**< Bits to tell how much data to store on each object */
657  
658      /**
659       * The reason to have a local index manager is that when molecule
# Line 629 | Line 673 | namespace OpenMD{
673      string dumpFileName_;
674      string statFileName_;
675      string restFileName_;
632 –        
676  
677      bool topologyDone_;  /** flag to indicate whether the topology has
678                               been scanned and all the relevant
# Line 637 | Line 680 | namespace OpenMD{
680      
681      bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
682                              the simulation box dipole moment */
683 +    bool calcBoxQuadrupole_; /**< flag to indicate whether or not we calculate
684 +                                the simulation box quadrupole moment */
685      
686      bool useAtomicVirial_; /**< flag to indicate whether or not we use
687                                Atomic Virials to calculate the pressure */
# Line 667 | Line 712 | namespace OpenMD{
712      
713      /**
714       * Set MolToProcMap array
670 –     * @see #SimCreator::divideMolecules
715       */
716      void setMolToProcMap(const vector<int>& molToProcMap) {
717        molToProcMap_ = molToProcMap;

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