ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/io/Globals.hpp
(Generate patch)

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 1665 by gezelter, Tue Nov 22 20:38:56 2011 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 112 | Line 113 | namespace oopse {
113      DeclareParameter(ElectrostaticScreeningMethod, std::string);
114      DeclareParameter(DampingAlpha, RealType);
115      DeclareParameter(Dielectric, RealType);
116 +    DeclareParameter(CutoffMethod, std::string);
117      DeclareParameter(CutoffPolicy, std::string);
118      DeclareParameter(SwitchingFunctionType, std::string);
119      DeclareParameter(CompressDumpFile, bool);
120      DeclareParameter(OutputForceVector, bool);
121 +    DeclareParameter(OutputParticlePotential, bool);
122      DeclareParameter(SkinThickness, RealType);
123      DeclareParameter(StatFileFormat, std::string);    
124      DeclareParameter(HydroPropFile, std::string);
125      DeclareParameter(Viscosity, RealType);
126      DeclareParameter(BeadSize, RealType);  
124 –    DeclareParameter(ThermalConductivity, RealType);
125 –    DeclareParameter(ThermalLength, RealType);
127      DeclareParameter(UseSphericalBoundaryConditions, bool);
128      DeclareParameter(FrozenBufferRadius, RealType);
129      DeclareParameter(LangevinBufferRadius, RealType);
# Line 141 | Line 142 | namespace oopse {
142      DeclareParameter(RNEMD_exchangeType, std::string);
143      DeclareParameter(RNEMD_objectSelection, std::string);
144      DeclareParameter(RNEMD_targetFlux, RealType);
145 +    DeclareParameter(RNEMD_binShift, bool);
146 +    DeclareParameter(RNEMD_outputDimensionalTemperature, bool);
147      DeclareParameter(UseRestraints, bool);
148      DeclareParameter(Restraint_file, std::string);
149 +    DeclareParameter(HULL_Method, std::string);
150 +    DeclareParameter(Alpha, RealType);
151 +    DeclareAlterableParameter(MDfileVersion, int);
152      
153    public:
154      bool addComponent(Component* comp);
# Line 160 | Line 166 | namespace oopse {
166      int getNRestraintStamps() {return restraints_.size();}
167      std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
168      RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}    
163 –
164 –    //std::string getRestraint_file(){
169      
170      virtual void validate();
171    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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

# Line 0 | Line 1
1 + Author Id Revision Date

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines