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Comparing:
trunk/src/io/Globals.hpp (file contents), Revision 1367 by skuang, Mon Oct 19 13:35:42 2009 UTC vs.
branches/development/src/io/Globals.hpp (file contents), Revision 1723 by gezelter, Thu May 24 20:59:54 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 55 | Line 56
56   #include "types/MoleculeStamp.hpp"
57   #include "utils/ParameterManager.hpp"
58  
59 < namespace oopse {
59 > namespace OpenMD {
60    class Globals : public DataHolder {
61    public:
62      typedef std::pair<int, int> intPair;
# Line 90 | Line 91 | namespace oopse {
91      DeclareParameter(OrthoBoxTolerance, RealType);
92      DeclareParameter(Minimizer, std::string);
93      DeclareParameter(MinimizerMaxIter, RealType);
94 <    DeclareParameter(MinimizerWriteFrq, int);
94 >    DeclareParameter(MinimizerWriteFreq, int);
95      DeclareParameter(MinimizerStepSize, RealType);
96      DeclareParameter(MinimizerFTol, RealType);
97      DeclareParameter(MinimizerGTol, RealType);
# Line 106 | Line 107 | namespace oopse {
107      DeclareParameter(ForceFieldFileName, std::string);
108      DeclareParameter(SurfaceTension, RealType);
109      DeclareParameter(PrintPressureTensor, bool);
110 +    DeclareParameter(PrintHeatFlux, bool);
111      DeclareParameter(TaggedAtomPair, intPair);
112      DeclareParameter(PrintTaggedPairDistance, bool);
113      DeclareParameter(ElectrostaticSummationMethod, std::string);
114      DeclareParameter(ElectrostaticScreeningMethod, std::string);
115      DeclareParameter(DampingAlpha, RealType);
116      DeclareParameter(Dielectric, RealType);
117 +    DeclareParameter(CutoffMethod, std::string);
118      DeclareParameter(CutoffPolicy, std::string);
119      DeclareParameter(SwitchingFunctionType, std::string);
120      DeclareParameter(CompressDumpFile, bool);
121      DeclareParameter(OutputForceVector, bool);
122 +    DeclareParameter(OutputParticlePotential, bool);
123 +    DeclareParameter(OutputElectricField, bool);
124 +    DeclareParameter(OutputFluctuatingCharges, bool);
125      DeclareParameter(SkinThickness, RealType);
126      DeclareParameter(StatFileFormat, std::string);    
127      DeclareParameter(HydroPropFile, std::string);
128      DeclareParameter(Viscosity, RealType);
129      DeclareParameter(BeadSize, RealType);  
124 –    DeclareParameter(ThermalConductivity, RealType);
125 –    DeclareParameter(ThermalLength, RealType);
130      DeclareParameter(UseSphericalBoundaryConditions, bool);
131      DeclareParameter(FrozenBufferRadius, RealType);
132      DeclareParameter(LangevinBufferRadius, RealType);
# Line 141 | Line 145 | namespace oopse {
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);
158      DeclareParameter(UseRestraints, bool);
159      DeclareParameter(Restraint_file, std::string);
160 <    
160 >    DeclareParameter(HULL_Method, std::string);
161 >    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);
168 >    DeclareAlterableParameter(MDfileVersion, int);
169 >
170    public:
171      bool addComponent(Component* comp);
172      bool addZConsStamp(ZConsStamp* zcons);
# Line 160 | Line 183 | namespace oopse {
183      int getNRestraintStamps() {return restraints_.size();}
184      std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
185      RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}    
163 –
164 –    //std::string getRestraint_file(){
186      
187      virtual void validate();
188    private:

Comparing:
trunk/src/io/Globals.hpp (property svn:keywords), Revision 1367 by skuang, Mon Oct 19 13:35:42 2009 UTC vs.
branches/development/src/io/Globals.hpp (property svn:keywords), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC

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