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root/OpenMD/trunk/src/io/Globals.hpp
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Comparing trunk/src/io/Globals.hpp (file contents):
Revision 1698 by skuang, Fri Mar 16 21:18:27 2012 UTC vs.
Revision 2034 by gezelter, Mon Nov 3 16:49:03 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).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
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   */
42  
43   #ifndef IO_GLOBALS_HPP
# Line 53 | 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 79 | 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 88 | Line 93 | namespace OpenMD {
93      DeclareParameter(UseInitalTime, bool);
94      DeclareParameter(UseIntialExtendedSystemState, bool);
95      DeclareParameter(OrthoBoxTolerance, RealType);
91 –    DeclareParameter(Minimizer, std::string);
92 –    DeclareParameter(MinimizerMaxIter, RealType);
93 –    DeclareParameter(MinimizerWriteFreq, int);
94 –    DeclareParameter(MinimizerStepSize, RealType);
95 –    DeclareParameter(MinimizerFTol, RealType);
96 –    DeclareParameter(MinimizerGTol, RealType);
97 –    DeclareParameter(MinimizerLSTol, RealType);
98 –    DeclareParameter(MinimizerLSMaxIter, int);
96      DeclareParameter(ZconsGap, RealType);
97      DeclareParameter(ZconsFixtime, RealType);
98      DeclareParameter(ZconsUsingSMD, bool);
# Line 106 | Line 103 | namespace OpenMD {
103      DeclareParameter(ForceFieldFileName, std::string);
104      DeclareParameter(SurfaceTension, RealType);
105      DeclareParameter(PrintPressureTensor, bool);
106 +    DeclareParameter(PrintHeatFlux, bool);
107      DeclareParameter(TaggedAtomPair, intPair);
108      DeclareParameter(PrintTaggedPairDistance, bool);
109      DeclareParameter(ElectrostaticSummationMethod, std::string);
110      DeclareParameter(ElectrostaticScreeningMethod, std::string);
111      DeclareParameter(DampingAlpha, RealType);
112      DeclareParameter(Dielectric, RealType);
113 +    DeclareParameter(CutoffMethod, std::string);
114      DeclareParameter(CutoffPolicy, std::string);
115      DeclareParameter(SwitchingFunctionType, std::string);
116      DeclareParameter(CompressDumpFile, bool);
117      DeclareParameter(OutputForceVector, bool);
118      DeclareParameter(OutputParticlePotential, bool);
119 +    DeclareParameter(OutputElectricField, bool);
120 +    DeclareParameter(OutputFluctuatingCharges, bool);
121 +    DeclareParameter(OutputSitePotential, bool);
122      DeclareParameter(SkinThickness, RealType);
123      DeclareParameter(StatFileFormat, std::string);    
124      DeclareParameter(HydroPropFile, std::string);
# Line 126 | Line 128 | namespace OpenMD {
128      DeclareParameter(FrozenBufferRadius, RealType);
129      DeclareParameter(LangevinBufferRadius, RealType);
130      DeclareParameter(AccumulateBoxDipole, bool);
131 +    DeclareParameter(AccumulateBoxQuadrupole, bool);
132      DeclareParameter(NeighborListNeighbors, int);
133      DeclareParameter(UseMultipleTemperatureMethod, bool);
134      DeclareParameter(MTM_Ce, RealType);
# Line 133 | Line 136 | namespace OpenMD {
136      DeclareParameter(MTM_Io, RealType);
137      DeclareParameter(MTM_Sigma, RealType);    
138      DeclareParameter(MTM_R, RealType);    
136 –    DeclareParameter(UseRNEMD, bool);
137 –    DeclareParameter(RNEMD_exchangeTime, RealType);
138 –    DeclareParameter(RNEMD_nBins, int);
139 –    DeclareParameter(RNEMD_logWidth, int);
140 –    DeclareParameter(RNEMD_exchangeType, std::string);
141 –    DeclareParameter(RNEMD_objectSelection, std::string);
142 –    DeclareParameter(RNEMD_targetFlux, RealType);
143 –    DeclareParameter(RNEMD_targetJzKE, RealType);
144 –    DeclareParameter(RNEMD_targetJzpx, RealType);
145 –    DeclareParameter(RNEMD_targetJzpy, RealType);
146 –    DeclareParameter(RNEMD_targetJzpz, RealType);
147 –    DeclareParameter(RNEMD_binShift, bool);
148 –    DeclareParameter(RNEMD_outputTemperature, bool);
149 –    DeclareParameter(RNEMD_outputVx, bool);
150 –    DeclareParameter(RNEMD_outputVy, bool);
151 –    DeclareParameter(RNEMD_outputXyzTemperature, bool);
152 –    DeclareParameter(RNEMD_outputRotTemperature, bool);
139      DeclareParameter(UseRestraints, bool);
140      DeclareParameter(Restraint_file, std::string);
141      DeclareParameter(HULL_Method, std::string);
142      DeclareParameter(Alpha, RealType);
143 <    
143 >    DeclareAlterableParameter(MDfileVersion, int);
144 >    DeclareParameter(UniformField, std::vector<RealType> );
145 >    DeclareParameter(UniformGradientStrength, RealType );
146 >    DeclareParameter(UniformGradientDirection1, std::vector<RealType> );
147 >    DeclareParameter(UniformGradientDirection2, std::vector<RealType> );
148 >
149 >    DeclareParameter(ElectricField, std::vector<RealType> );
150 >    DeclareParameter(ConstraintTime, RealType);
151 >
152    public:
153      bool addComponent(Component* comp);
154      bool addZConsStamp(ZConsStamp* zcons);
# Line 172 | Line 166 | namespace OpenMD {
166      std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
167      RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}    
168  
169 <    //std::string getRestraint_file(){
169 >    bool addFluctuatingChargeParameters(FluctuatingChargeParameters* flucqPars);
170 >    FluctuatingChargeParameters* getFluctuatingChargeParameters() {return flucQpars_;}
171 >
172 >    bool addRNEMDParameters(RNEMDParameters* rnemdPars);
173 >    RNEMDParameters* getRNEMDParameters() {return rnemdPars_;}
174 >
175 >    bool addMinimizerParameters(MinimizerParameters* miniPars);
176 >    MinimizerParameters* getMinimizerParameters() {return minimizerPars_;}
177      
178      virtual void validate();
179    private:
# Line 182 | Line 183 | namespace OpenMD {
183      std::vector<RestraintStamp*> restraints_;    
184      std::map<std::string, MoleculeStamp*> moleculeStamps_;
185      std::pair<int, int> taggedAtomPair_;
186 +    FluctuatingChargeParameters* flucQpars_;
187 +    RNEMDParameters* rnemdPars_;
188 +    MinimizerParameters* minimizerPars_;
189   };
190   }
191   #endif

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