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Comparing trunk/src/io/Globals.hpp (file contents):
Revision 1354 by gezelter, Mon Jun 15 20:12:09 2009 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
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]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   #ifndef IO_GLOBALS_HPP
# Line 51 | Line 51
51  
52   #include "types/Component.hpp"
53   #include "types/ZconsStamp.hpp"
54 + #include "types/RestraintStamp.hpp"
55   #include "types/MoleculeStamp.hpp"
56   #include "utils/ParameterManager.hpp"
57  
58 < namespace oopse {
58 > namespace OpenMD {
59    class Globals : public DataHolder {
60    public:
61      typedef std::pair<int, int> intPair;
# Line 98 | Line 99 | namespace oopse {
99      DeclareParameter(ZconsGap, RealType);
100      DeclareParameter(ZconsFixtime, RealType);
101      DeclareParameter(ZconsUsingSMD, bool);
102 <    DeclareParameter(UseSolidThermInt, bool);
102 <    DeclareParameter(UseLiquidThermInt, bool);
102 >    DeclareParameter(UseThermodynamicIntegration, bool);
103      DeclareParameter(ThermodynamicIntegrationLambda, RealType);
104      DeclareParameter(ThermodynamicIntegrationK, RealType);
105      DeclareParameter(ForceFieldVariant, std::string);
106      DeclareParameter(ForceFieldFileName, std::string);
107 –    DeclareParameter(ThermIntDistSpringConst, RealType);
108 –    DeclareParameter(ThermIntThetaSpringConst, RealType);
109 –    DeclareParameter(ThermIntOmegaSpringConst, RealType);
107      DeclareParameter(SurfaceTension, RealType);
108      DeclareParameter(PrintPressureTensor, bool);
109      DeclareParameter(TaggedAtomPair, intPair);
# Line 124 | Line 121 | namespace oopse {
121      DeclareParameter(HydroPropFile, std::string);
122      DeclareParameter(Viscosity, RealType);
123      DeclareParameter(BeadSize, RealType);  
124 +    DeclareParameter(ThermalConductivity, RealType);
125 +    DeclareParameter(ThermalLength, RealType);
126      DeclareParameter(UseSphericalBoundaryConditions, bool);
127      DeclareParameter(FrozenBufferRadius, RealType);
128      DeclareParameter(LangevinBufferRadius, RealType);
# Line 136 | Line 135 | namespace oopse {
135      DeclareParameter(MTM_Sigma, RealType);    
136      DeclareParameter(MTM_R, RealType);    
137      DeclareParameter(UseRNEMD, bool);
138 <    DeclareParameter(RNEMD_swapTime, RealType);
138 >    DeclareParameter(RNEMD_exchangeTime, RealType);
139      DeclareParameter(RNEMD_nBins, int);
140 <    DeclareParameter(RNEMD_swapType, std::string);
140 >    DeclareParameter(RNEMD_logWidth, int);
141 >    DeclareParameter(RNEMD_exchangeType, std::string);
142      DeclareParameter(RNEMD_objectSelection, std::string);
143 +    DeclareParameter(RNEMD_targetFlux, RealType);
144      DeclareParameter(UseRestraints, bool);
144 –    DeclareParameter(Restraint_objectSelection, std::string);
145 –    DeclareParameter(Restraint_type, std::string);
145      DeclareParameter(Restraint_file, std::string);
147 –    DeclareParameter(Restraint_DisplacementSpringConstant, RealType);
148 –    DeclareParameter(Restraint_RollSpringConstant, RealType);  // phi
149 –    DeclareParameter(Restraint_PitchSpringConstant, RealType); // theta
150 –    DeclareParameter(Restraint_YawSpringConstant, RealType);   // psi
146      
147    public:
148      bool addComponent(Component* comp);
149      bool addZConsStamp(ZConsStamp* zcons);
150 +    bool addRestraintStamp(RestraintStamp* rest);
151      bool addMoleculeStamp(MoleculeStamp* molStamp);
152      int getNComponents() {return components_.size();}
153      std::vector<Component*> getComponents() {return components_;}
# Line 160 | Line 156 | namespace oopse {
156      int getNZconsStamps() {return zconstraints_.size();}
157      std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;}
158      ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);}    
159 +
160 +    int getNRestraintStamps() {return restraints_.size();}
161 +    std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
162 +    RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}    
163 +
164 +    //std::string getRestraint_file(){
165      
166      virtual void validate();
167    private:
168      
169      std::vector<Component*> components_;
170      std::vector<ZConsStamp*> zconstraints_;    
171 +    std::vector<RestraintStamp*> restraints_;    
172      std::map<std::string, MoleculeStamp*> moleculeStamps_;
173      std::pair<int, int> taggedAtomPair_;
174   };
175   }
176   #endif
174 –

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