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Comparing branches/development/src/brains/SimInfo.hpp (file contents):
Revision 1569 by gezelter, Thu May 26 13:55:04 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"
# 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 219 | 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 513 | 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 520 | 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 534 | 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 542 | 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_;}
# Line 598 | Line 617 | namespace OpenMD{
617      vector<RealType> massFactors_;
618    public:
619      vector<RealType> getMassFactors() { return massFactors_; }
601 –  private:
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 */

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