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Comparing branches/development/src/io/Globals.hpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1780 by jmarr, Mon Aug 20 18:28:22 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   #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 88 | Line 92 | namespace OpenMD {
92      DeclareParameter(UseInitalTime, bool);
93      DeclareParameter(UseIntialExtendedSystemState, bool);
94      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);
95      DeclareParameter(ZconsGap, RealType);
96      DeclareParameter(ZconsFixtime, RealType);
97      DeclareParameter(ZconsUsingSMD, bool);
# Line 106 | Line 102 | namespace OpenMD {
102      DeclareParameter(ForceFieldFileName, std::string);
103      DeclareParameter(SurfaceTension, RealType);
104      DeclareParameter(PrintPressureTensor, bool);
105 +    DeclareParameter(PrintHeatFlux, bool);
106      DeclareParameter(TaggedAtomPair, intPair);
107      DeclareParameter(PrintTaggedPairDistance, bool);
108      DeclareParameter(ElectrostaticSummationMethod, std::string);
109      DeclareParameter(ElectrostaticScreeningMethod, std::string);
110      DeclareParameter(DampingAlpha, RealType);
111      DeclareParameter(Dielectric, RealType);
112 +    DeclareParameter(CutoffMethod, std::string);
113      DeclareParameter(CutoffPolicy, std::string);
114      DeclareParameter(SwitchingFunctionType, std::string);
115      DeclareParameter(CompressDumpFile, bool);
116      DeclareParameter(OutputForceVector, bool);
117 +    DeclareParameter(OutputParticlePotential, bool);
118 +    DeclareParameter(OutputElectricField, bool);
119 +    DeclareParameter(OutputFluctuatingCharges, bool);
120      DeclareParameter(SkinThickness, RealType);
121      DeclareParameter(StatFileFormat, std::string);    
122      DeclareParameter(HydroPropFile, std::string);
# Line 132 | Line 133 | namespace OpenMD {
133      DeclareParameter(MTM_Io, RealType);
134      DeclareParameter(MTM_Sigma, RealType);    
135      DeclareParameter(MTM_R, RealType);    
135 –    DeclareParameter(UseRNEMD, bool);
136 –    DeclareParameter(RNEMD_exchangeTime, RealType);
137 –    DeclareParameter(RNEMD_nBins, int);
138 –    DeclareParameter(RNEMD_logWidth, int);
139 –    DeclareParameter(RNEMD_exchangeType, std::string);
140 –    DeclareParameter(RNEMD_objectSelection, std::string);
141 –    DeclareParameter(RNEMD_targetFlux, RealType);
136      DeclareParameter(UseRestraints, bool);
137      DeclareParameter(Restraint_file, std::string);
138      DeclareParameter(HULL_Method, std::string);
139      DeclareParameter(Alpha, RealType);
140 <    
140 >    DeclareAlterableParameter(MDfileVersion, int);
141 >    DeclareParameter(ElectricField, OpenMD::Vector3d);
142 >
143    public:
144      bool addComponent(Component* comp);
145      bool addZConsStamp(ZConsStamp* zcons);
# Line 161 | Line 157 | namespace OpenMD {
157      std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
158      RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}    
159  
160 <    //std::string getRestraint_file(){
160 >    bool addFluctuatingChargeParameters(FluctuatingChargeParameters* flucqPars);
161 >    FluctuatingChargeParameters* getFluctuatingChargeParameters() {return flucQpars_;}
162 >
163 >    bool addRNEMDParameters(RNEMDParameters* rnemdPars);
164 >    RNEMDParameters* getRNEMDParameters() {return rnemdPars_;}
165 >
166 >    bool addMinimizerParameters(MinimizerParameters* miniPars);
167 >    MinimizerParameters* getMinimizerParameters() {return minimizerPars_;}
168      
169      virtual void validate();
170    private:
# Line 171 | Line 174 | namespace OpenMD {
174      std::vector<RestraintStamp*> restraints_;    
175      std::map<std::string, MoleculeStamp*> moleculeStamps_;
176      std::pair<int, int> taggedAtomPair_;
177 +    FluctuatingChargeParameters* flucQpars_;
178 +    RNEMDParameters* rnemdPars_;
179 +    MinimizerParameters* minimizerPars_;
180   };
181   }
182   #endif

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