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Comparing:
trunk/src/io/Globals.hpp (file contents), Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
branches/development/src/io/Globals.hpp (file contents), Revision 1746 by gezelter, Wed Jun 6 02:18:54 2012 UTC

# Line 1 | Line 1
1   /*
2 < * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2 > * Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
5   * non-exclusive, royalty free, license to use, modify and
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
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]  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 oopse {
62 > namespace OpenMD {
63    class Globals : public DataHolder {
64    public:
65      typedef std::pair<int, int> intPair;
# Line 88 | Line 92 | namespace oopse {
92      DeclareParameter(UseInitalTime, bool);
93      DeclareParameter(UseIntialExtendedSystemState, bool);
94      DeclareParameter(OrthoBoxTolerance, RealType);
91 –    DeclareParameter(Minimizer, std::string);
92 –    DeclareParameter(MinimizerMaxIter, RealType);
93 –    DeclareParameter(MinimizerWriteFrq, 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 oopse {
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);
123      DeclareParameter(Viscosity, RealType);
124      DeclareParameter(BeadSize, RealType);  
124 –    DeclareParameter(ThermalConductivity, RealType);
125 –    DeclareParameter(ThermalLength, RealType);
125      DeclareParameter(UseSphericalBoundaryConditions, bool);
126      DeclareParameter(FrozenBufferRadius, RealType);
127      DeclareParameter(LangevinBufferRadius, RealType);
# Line 134 | Line 133 | namespace oopse {
133      DeclareParameter(MTM_Io, RealType);
134      DeclareParameter(MTM_Sigma, RealType);    
135      DeclareParameter(MTM_R, RealType);    
137 –    DeclareParameter(UseRNEMD, bool);
138 –    DeclareParameter(RNEMD_swapTime, RealType);
139 –    DeclareParameter(RNEMD_nBins, int);
140 –    DeclareParameter(RNEMD_swapType, std::string);
141 –    DeclareParameter(RNEMD_objectSelection, std::string);
136      DeclareParameter(UseRestraints, bool);
137      DeclareParameter(Restraint_file, std::string);
138 +    DeclareParameter(HULL_Method, std::string);
139 +    DeclareParameter(Alpha, RealType);
140 +    DeclareAlterableParameter(MDfileVersion, int);
141  
145 –    
142    public:
143      bool addComponent(Component* comp);
144      bool addZConsStamp(ZConsStamp* zcons);
# Line 160 | Line 156 | namespace oopse {
156      std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
157      RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}    
158  
159 <    //std::string getRestraint_file(){
159 >    bool addFluctuatingChargeParameters(FluctuatingChargeParameters* flucqPars);
160 >    FluctuatingChargeParameters* getFluctuatingChargeParameters() {return flucQpars_;}
161 >
162 >    bool addRNEMDParameters(RNEMDParameters* rnemdPars);
163 >    RNEMDParameters* getRNEMDParameters() {return rnemdPars_;}
164 >
165 >    bool addMinimizerParameters(MinimizerParameters* miniPars);
166 >    MinimizerParameters* getMinimizerParameters() {return minimizerPars_;}
167      
168      virtual void validate();
169    private:
# Line 170 | Line 173 | namespace oopse {
173      std::vector<RestraintStamp*> restraints_;    
174      std::map<std::string, MoleculeStamp*> moleculeStamps_;
175      std::pair<int, int> taggedAtomPair_;
176 +    FluctuatingChargeParameters* flucQpars_;
177 +    RNEMDParameters* rnemdPars_;
178 +    MinimizerParameters* minimizerPars_;
179   };
180   }
181   #endif
176 –

Comparing:
trunk/src/io/Globals.hpp (property svn:keywords), Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
branches/development/src/io/Globals.hpp (property svn:keywords), Revision 1746 by gezelter, Wed Jun 6 02:18:54 2012 UTC

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