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Comparing branches/development/src/integrators/Integrator.hpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 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 52 | Line 53
53  
54   #include "brains/ForceManager.hpp"
55   #include "restraints/ThermoIntegrationForceManager.hpp"
56 + #include "brains/Stats.hpp"
57   #include "io/DumpWriter.hpp"
58   #include "io/StatWriter.hpp"
59 + #include "integrators/RotationAlgorithm.hpp"
60 + #include "flucq/FluctuatingChargePropagator.hpp"
61   #include "integrators/Velocitizer.hpp"
62 < #include "integrators/RNEMD.hpp"
62 > #include "rnemd/RNEMD.hpp"
63 > #include "constraints/Rattle.hpp"
64  
65   namespace OpenMD {
66  
# Line 75 | Line 80 | namespace OpenMD {
80        doIntegrate();
81      }
82  
83 <    void update() {
84 <      doUpdate();
83 >    void updateSizes() {
84 >      doUpdateSizes();
85 >      flucQ_->updateSizes();
86      }
87  
88      void setForceManager(ForceManager* forceMan) {
# Line 85 | Line 91 | namespace OpenMD {
91          delete forceMan_;
92        }
93        forceMan_ = forceMan;
94 +      // forward this on:
95 +      if (flucQ_ != NULL) {
96 +        flucQ_->setForceManager(forceMan_);
97 +      }
98      }
99  
100      void setVelocitizer(Velocitizer* velocitizer) {
# Line 94 | Line 104 | namespace OpenMD {
104        velocitizer_ = velocitizer;
105      }
106  
107 +    void setFluctuatingChargePropagator(FluctuatingChargePropagator* prop) {
108 +      if (prop != flucQ_ && flucQ_ != NULL){            
109 +        delete flucQ_;
110 +      }            
111 +      flucQ_ = prop;
112 +      if (forceMan_ != NULL) {
113 +        flucQ_->setForceManager(forceMan_);
114 +      }
115 +    }
116 +
117 +    void setRotationAlgorithm(RotationAlgorithm* algo) {
118 +      if (algo != rotAlgo_ && rotAlgo_ != NULL){            
119 +        delete rotAlgo_;
120 +      }
121 +            
122 +      rotAlgo_ = algo;
123 +    }
124 +
125      void setRNEMD(RNEMD* rnemd) {
126        if (rnemd_ != rnemd && rnemd_  != NULL) {
127          delete rnemd_;
# Line 107 | Line 135 | namespace OpenMD {
135  
136      virtual void doIntegrate() = 0;
137  
138 <    virtual void doUpdate() {}
138 >    virtual void doUpdateSizes() {}
139          
140      void saveConservedQuantity() {
141 <      currentSnapshot_->statData[Stats::CONSERVED_QUANTITY] = calcConservedQuantity();
141 >      snap->setConservedQuantity( calcConservedQuantity() );
142      }
143          
144      SimInfo* info_;
145      Globals* simParams;
146      ForceManager* forceMan_;
147 +    RotationAlgorithm* rotAlgo_;
148 +    FluctuatingChargePropagator* flucQ_;
149 +    Rattle* rattle_;
150 +    Velocitizer* velocitizer_;
151 +    RNEMD* rnemd_;
152 +
153      bool needPotential;
154      bool needStress;
155      bool needReset;    
122 –    Velocitizer* velocitizer_;
123 –    RNEMD* rnemd_;
156      bool needVelocityScaling;
157      RealType targetScalingTemp;
158  
159      bool useRNEMD;    
160      
161 +    Stats* stats;
162      DumpWriter* dumpWriter;
163      StatWriter* statWriter;
164      Thermo thermo;
# Line 138 | Line 171 | namespace OpenMD {
171      RealType RNEMD_exchangeTime;
172      RealType dt;
173  
174 <    Snapshot* currentSnapshot_; //During the integration, the address of currentSnapshot Will not change
174 >    Snapshot* snap; // During the integration, the address of snap Will not change
175  
176          
177    private:

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