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Comparing branches/development/src/io/Globals.hpp (file contents):
Revision 1723 by gezelter, Thu May 24 20:59:54 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 54 | Line 54
54   #include "types/ZconsStamp.hpp"
55   #include "types/RestraintStamp.hpp"
56   #include "types/MoleculeStamp.hpp"
57 + #include "flucq/FluctuatingChargeParameters.hpp"
58 + #include "rnemd/RNEMDParameters.hpp"
59 + #include "optimization/MinimizerParameters.hpp"
60   #include "utils/ParameterManager.hpp"
61  
62   namespace OpenMD {
# Line 80 | Line 83 | namespace OpenMD {
83      DeclareParameter(UsePeriodicBoundaryConditions, bool);
84      DeclareParameter(TargetPressure, RealType);
85      DeclareParameter(UseAtomicVirial, bool);
86 +    DeclareParameter(UseLongRangeCorrections, bool);
87      DeclareParameter(TauThermostat, RealType);
88      DeclareParameter(TauBarostat, RealType);
89      DeclareParameter(ZconsTime, RealType);
# Line 89 | Line 93 | namespace OpenMD {
93      DeclareParameter(UseInitalTime, bool);
94      DeclareParameter(UseIntialExtendedSystemState, bool);
95      DeclareParameter(OrthoBoxTolerance, RealType);
92 –    DeclareParameter(Minimizer, std::string);
93 –    DeclareParameter(MinimizerMaxIter, RealType);
94 –    DeclareParameter(MinimizerWriteFreq, int);
95 –    DeclareParameter(MinimizerStepSize, RealType);
96 –    DeclareParameter(MinimizerFTol, RealType);
97 –    DeclareParameter(MinimizerGTol, RealType);
98 –    DeclareParameter(MinimizerLSTol, RealType);
99 –    DeclareParameter(MinimizerLSMaxIter, int);
96      DeclareParameter(ZconsGap, RealType);
97      DeclareParameter(ZconsFixtime, RealType);
98      DeclareParameter(ZconsUsingSMD, bool);
# Line 138 | Line 134 | namespace OpenMD {
134      DeclareParameter(MTM_Io, RealType);
135      DeclareParameter(MTM_Sigma, RealType);    
136      DeclareParameter(MTM_R, RealType);    
141 –    DeclareParameter(UseRNEMD, bool);
142 –    DeclareParameter(RNEMD_exchangeTime, RealType);
143 –    DeclareParameter(RNEMD_nBins, int);
144 –    DeclareParameter(RNEMD_logWidth, int);
145 –    DeclareParameter(RNEMD_exchangeType, std::string);
146 –    DeclareParameter(RNEMD_objectSelection, std::string);
147 –    DeclareParameter(RNEMD_targetFlux, RealType);
148 –    DeclareParameter(RNEMD_targetJzKE, RealType);
149 –    DeclareParameter(RNEMD_targetJzpx, RealType);
150 –    DeclareParameter(RNEMD_targetJzpy, RealType);
151 –    DeclareParameter(RNEMD_targetJzpz, RealType);
152 –    DeclareParameter(RNEMD_binShift, bool);
153 –    DeclareParameter(RNEMD_outputTemperature, bool);
154 –    DeclareParameter(RNEMD_outputVx, bool);
155 –    DeclareParameter(RNEMD_outputVy, bool);
156 –    DeclareParameter(RNEMD_outputXyzTemperature, bool);
157 –    DeclareParameter(RNEMD_outputRotTemperature, bool);
137      DeclareParameter(UseRestraints, bool);
138      DeclareParameter(Restraint_file, std::string);
139      DeclareParameter(HULL_Method, std::string);
140      DeclareParameter(Alpha, RealType);
162 –    DeclareParameter(FlucQPropagator, std::string);
163 –    DeclareParameter(FlucQFriction, RealType);    
164 –    DeclareParameter(FlucQTolerance, RealType);    
165 –    DeclareParameter(FlucQMaxIterations, int);    
166 –    DeclareParameter(FlucQTargetTemp, RealType);
167 –    DeclareParameter(FlucQtauThermostat, RealType);
141      DeclareAlterableParameter(MDfileVersion, int);
142 +    DeclareParameter(ElectricField, OpenMD::Vector3d);
143  
144    public:
145      bool addComponent(Component* comp);
# Line 183 | Line 157 | namespace OpenMD {
157      int getNRestraintStamps() {return restraints_.size();}
158      std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
159      RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}    
160 +
161 +    bool addFluctuatingChargeParameters(FluctuatingChargeParameters* flucqPars);
162 +    FluctuatingChargeParameters* getFluctuatingChargeParameters() {return flucQpars_;}
163 +
164 +    bool addRNEMDParameters(RNEMDParameters* rnemdPars);
165 +    RNEMDParameters* getRNEMDParameters() {return rnemdPars_;}
166 +
167 +    bool addMinimizerParameters(MinimizerParameters* miniPars);
168 +    MinimizerParameters* getMinimizerParameters() {return minimizerPars_;}
169      
170      virtual void validate();
171    private:
# Line 192 | Line 175 | namespace OpenMD {
175      std::vector<RestraintStamp*> restraints_;    
176      std::map<std::string, MoleculeStamp*> moleculeStamps_;
177      std::pair<int, int> taggedAtomPair_;
178 +    FluctuatingChargeParameters* flucQpars_;
179 +    RNEMDParameters* rnemdPars_;
180 +    MinimizerParameters* minimizerPars_;
181   };
182   }
183   #endif

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