| 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. |
| 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, 234107 (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 |
| 52 |
|
|
| 53 |
|
#include "types/Component.hpp" |
| 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; |
| 83 |
|
DeclareParameter(UsePeriodicBoundaryConditions, bool); |
| 84 |
|
DeclareParameter(TargetPressure, RealType); |
| 85 |
|
DeclareParameter(UseAtomicVirial, bool); |
| 86 |
+ |
DeclareParameter(UseLongRangeCorrections, bool); |
| 87 |
|
DeclareParameter(TauThermostat, RealType); |
| 88 |
|
DeclareParameter(TauBarostat, RealType); |
| 89 |
|
DeclareParameter(ZconsTime, RealType); |
| 93 |
|
DeclareParameter(UseInitalTime, bool); |
| 94 |
|
DeclareParameter(UseIntialExtendedSystemState, bool); |
| 95 |
|
DeclareParameter(OrthoBoxTolerance, RealType); |
| 90 |
– |
DeclareParameter(Minimizer, std::string); |
| 91 |
– |
DeclareParameter(MinimizerMaxIter, RealType); |
| 92 |
– |
DeclareParameter(MinimizerWriteFrq, int); |
| 93 |
– |
DeclareParameter(MinimizerStepSize, RealType); |
| 94 |
– |
DeclareParameter(MinimizerFTol, RealType); |
| 95 |
– |
DeclareParameter(MinimizerGTol, RealType); |
| 96 |
– |
DeclareParameter(MinimizerLSTol, RealType); |
| 97 |
– |
DeclareParameter(MinimizerLSMaxIter, int); |
| 96 |
|
DeclareParameter(ZconsGap, RealType); |
| 97 |
|
DeclareParameter(ZconsFixtime, RealType); |
| 98 |
|
DeclareParameter(ZconsUsingSMD, bool); |
| 99 |
< |
DeclareParameter(UseSolidThermInt, bool); |
| 102 |
< |
DeclareParameter(UseLiquidThermInt, bool); |
| 99 |
> |
DeclareParameter(UseThermodynamicIntegration, bool); |
| 100 |
|
DeclareParameter(ThermodynamicIntegrationLambda, RealType); |
| 101 |
|
DeclareParameter(ThermodynamicIntegrationK, RealType); |
| 102 |
|
DeclareParameter(ForceFieldVariant, std::string); |
| 103 |
|
DeclareParameter(ForceFieldFileName, std::string); |
| 107 |
– |
DeclareParameter(ThermIntDistSpringConst, RealType); |
| 108 |
– |
DeclareParameter(ThermIntThetaSpringConst, RealType); |
| 109 |
– |
DeclareParameter(ThermIntOmegaSpringConst, RealType); |
| 104 |
|
DeclareParameter(SurfaceTension, RealType); |
| 105 |
|
DeclareParameter(PrintPressureTensor, bool); |
| 106 |
+ |
DeclareParameter(PrintHeatFlux, bool); |
| 107 |
|
DeclareParameter(TaggedAtomPair, intPair); |
| 108 |
|
DeclareParameter(PrintTaggedPairDistance, bool); |
| 109 |
|
DeclareParameter(ElectrostaticSummationMethod, std::string); |
| 110 |
|
DeclareParameter(ElectrostaticScreeningMethod, std::string); |
| 111 |
|
DeclareParameter(DampingAlpha, RealType); |
| 112 |
|
DeclareParameter(Dielectric, RealType); |
| 113 |
< |
DeclareParameter(CutoffPolicy, std::string); |
| 113 |
> |
DeclareParameter(CutoffMethod, 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(OutputSitePotential, bool); |
| 121 |
|
DeclareParameter(SkinThickness, RealType); |
| 122 |
|
DeclareParameter(StatFileFormat, std::string); |
| 123 |
|
DeclareParameter(HydroPropFile, std::string); |
| 127 |
|
DeclareParameter(FrozenBufferRadius, RealType); |
| 128 |
|
DeclareParameter(LangevinBufferRadius, RealType); |
| 129 |
|
DeclareParameter(AccumulateBoxDipole, bool); |
| 130 |
+ |
DeclareParameter(AccumulateBoxQuadrupole, bool); |
| 131 |
|
DeclareParameter(NeighborListNeighbors, int); |
| 132 |
|
DeclareParameter(UseMultipleTemperatureMethod, bool); |
| 133 |
|
DeclareParameter(MTM_Ce, RealType); |
| 135 |
|
DeclareParameter(MTM_Io, RealType); |
| 136 |
|
DeclareParameter(MTM_Sigma, RealType); |
| 137 |
|
DeclareParameter(MTM_R, RealType); |
| 138 |
< |
DeclareParameter(UseRNEMD, bool); |
| 139 |
< |
DeclareParameter(RNEMD_swapTime, RealType); |
| 140 |
< |
DeclareParameter(RNEMD_nBins, int); |
| 141 |
< |
DeclareParameter(RNEMD_swapType, std::string); |
| 142 |
< |
DeclareParameter(RNEMD_objectSelection, std::string); |
| 143 |
< |
|
| 138 |
> |
DeclareParameter(UseRestraints, bool); |
| 139 |
> |
DeclareParameter(Restraint_file, std::string); |
| 140 |
> |
DeclareParameter(HULL_Method, std::string); |
| 141 |
> |
DeclareParameter(Alpha, RealType); |
| 142 |
> |
DeclareAlterableParameter(MDfileVersion, int); |
| 143 |
> |
DeclareParameter(UniformField, std::vector<RealType> ); |
| 144 |
> |
DeclareParameter(UniformGradientStrength, RealType ); |
| 145 |
> |
DeclareParameter(UniformGradientDirection1, std::vector<RealType> ); |
| 146 |
> |
DeclareParameter(UniformGradientDirection2, std::vector<RealType> ); |
| 147 |
> |
|
| 148 |
> |
DeclareParameter(ElectricField, std::vector<RealType> ); |
| 149 |
> |
DeclareParameter(ConstraintTime, RealType); |
| 150 |
> |
|
| 151 |
|
public: |
| 152 |
|
bool addComponent(Component* comp); |
| 153 |
|
bool addZConsStamp(ZConsStamp* zcons); |
| 154 |
+ |
bool addRestraintStamp(RestraintStamp* rest); |
| 155 |
|
bool addMoleculeStamp(MoleculeStamp* molStamp); |
| 156 |
|
int getNComponents() {return components_.size();} |
| 157 |
|
std::vector<Component*> getComponents() {return components_;} |
| 160 |
|
int getNZconsStamps() {return zconstraints_.size();} |
| 161 |
|
std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;} |
| 162 |
|
ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);} |
| 163 |
+ |
|
| 164 |
+ |
int getNRestraintStamps() {return restraints_.size();} |
| 165 |
+ |
std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;} |
| 166 |
+ |
RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);} |
| 167 |
+ |
|
| 168 |
+ |
bool addFluctuatingChargeParameters(FluctuatingChargeParameters* flucqPars); |
| 169 |
+ |
FluctuatingChargeParameters* getFluctuatingChargeParameters() {return flucQpars_;} |
| 170 |
+ |
|
| 171 |
+ |
bool addRNEMDParameters(RNEMDParameters* rnemdPars); |
| 172 |
+ |
RNEMDParameters* getRNEMDParameters() {return rnemdPars_;} |
| 173 |
+ |
|
| 174 |
+ |
bool addMinimizerParameters(MinimizerParameters* miniPars); |
| 175 |
+ |
MinimizerParameters* getMinimizerParameters() {return minimizerPars_;} |
| 176 |
|
|
| 177 |
|
virtual void validate(); |
| 178 |
|
private: |
| 179 |
|
|
| 180 |
|
std::vector<Component*> components_; |
| 181 |
|
std::vector<ZConsStamp*> zconstraints_; |
| 182 |
+ |
std::vector<RestraintStamp*> restraints_; |
| 183 |
|
std::map<std::string, MoleculeStamp*> moleculeStamps_; |
| 184 |
|
std::pair<int, int> taggedAtomPair_; |
| 185 |
+ |
FluctuatingChargeParameters* flucQpars_; |
| 186 |
+ |
RNEMDParameters* rnemdPars_; |
| 187 |
+ |
MinimizerParameters* minimizerPars_; |
| 188 |
|
}; |
| 189 |
|
} |
| 190 |
|
#endif |
| 166 |
– |
|
