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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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#ifndef IO_GLOBALS_HPP |
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#include "types/Component.hpp" |
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#include "types/ZconsStamp.hpp" |
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#include "types/RestraintStamp.hpp" |
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#include "types/MoleculeStamp.hpp" |
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#include "utils/ParameterManager.hpp" |
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|
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namespace oopse { |
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class Globals : public DataHolder { |
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namespace OpenMD { |
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class Globals : public DataHolder { |
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public: |
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typedef std::pair<int, int> intPair; |
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|
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Globals(); |
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virtual ~Globals(); |
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DeclareParameter(ForceField, std::string); |
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DeclareParameter(TargetTemp, double); |
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DeclareParameter(Ensemble, std::string); |
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DeclareParameter(Dt, double); |
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DeclareParameter(RunTime, double); |
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DeclareParameter(InitialConfig, std::string); |
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DeclareParameter(FinalConfig, std::string); |
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DeclareParameter(SampleTime, double); |
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DeclareParameter(ResetTime, double); |
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DeclareParameter(StatusTime, double); |
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DeclareParameter(CutoffRadius, double); |
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DeclareParameter(SwitchingRadius, double); |
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DeclareParameter(Dielectric, double); |
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DeclareParameter(TempSet, bool); |
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DeclareParameter(ThermalTime, double); |
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DeclareParameter(UsePeriodicBoundaryConditions, bool); |
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DeclareParameter(TargetPressure, double); |
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DeclareParameter(TauThermostat, double); |
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DeclareParameter(TauBarostat, double); |
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DeclareParameter(ZconsTime, double); |
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DeclareParameter(ZconsTol, double); |
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DeclareParameter(ZconsForcePolicy, std::string); |
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DeclareParameter(Seed, int); |
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DeclareParameter(UseInitalTime, bool); |
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DeclareParameter(UseIntialExtendedSystemState, bool); |
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DeclareParameter(OrthoBoxTolerance, double); |
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DeclareParameter(Minimizer, std::string); |
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DeclareParameter(MinimizerMaxIter, double); |
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DeclareParameter(MinimizerWriteFrq, int); |
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DeclareParameter(MinimizerStepSize, double); |
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DeclareParameter(MinimizerFTol, double); |
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DeclareParameter(MinimizerGTol, double); |
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DeclareParameter(MinimizerLSTol, double); |
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DeclareParameter(MinimizerLSMaxIter, int); |
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DeclareParameter(ZconsGap, double); |
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DeclareParameter(ZconsFixtime, double); |
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DeclareParameter(ZconsUsingSMD, bool); |
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DeclareParameter(UseSolidThermInt, bool); |
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DeclareParameter(UseLiquidThermInt, bool); |
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DeclareParameter(ThermodynamicIntegrationLambda, double); |
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DeclareParameter(ThermodynamicIntegrationK, double); |
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DeclareParameter(ForceFieldVariant, std::string); |
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DeclareParameter(ForceFieldFileName, std::string); |
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DeclareParameter(ThermIntDistSpringConst, double); |
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DeclareParameter(ThermIntThetaSpringConst, double); |
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DeclareParameter(ThermIntOmegaSpringConst, double); |
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DeclareParameter(SurfaceTension, double); |
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DeclareParameter(PrintPressureTensor, bool); |
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DeclareParameter(ElectrostaticSummationMethod, std::string); |
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DeclareParameter(ElectrostaticScreeningMethod, std::string); |
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DeclareParameter(DampingAlpha, double); |
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DeclareParameter(CutoffPolicy, std::string); |
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DeclareParameter(SwitchingFunctionType, std::string); |
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DeclareParameter(CompressDumpFile, bool); |
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DeclareParameter(OutputForceVector, bool); |
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DeclareParameter(SkinThickness, double); |
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DeclareParameter(StatFileFormat, std::string); |
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DeclareParameter(HydroPropFile, std::string); |
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DeclareParameter(Viscosity, double); |
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DeclareParameter(BeadSize, double); |
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|
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DeclareParameter(ForceField, std::string); |
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DeclareParameter(TargetTemp, RealType); |
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DeclareParameter(Ensemble, std::string); |
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DeclareParameter(Dt, RealType); |
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DeclareParameter(RunTime, RealType); |
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DeclareParameter(FinalConfig, std::string); |
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DeclareParameter(SampleTime, RealType); |
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DeclareParameter(ResetTime, RealType); |
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DeclareParameter(StatusTime, RealType); |
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DeclareParameter(CutoffRadius, RealType); |
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DeclareParameter(SwitchingRadius, RealType); |
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DeclareParameter(TempSet, bool); |
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DeclareParameter(ThermalTime, RealType); |
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DeclareParameter(UsePeriodicBoundaryConditions, bool); |
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DeclareParameter(TargetPressure, RealType); |
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DeclareParameter(UseAtomicVirial, bool); |
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DeclareParameter(TauThermostat, RealType); |
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DeclareParameter(TauBarostat, RealType); |
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DeclareParameter(ZconsTime, RealType); |
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DeclareParameter(ZconsTol, RealType); |
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DeclareParameter(ZconsForcePolicy, std::string); |
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DeclareParameter(Seed, unsigned long int); |
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DeclareParameter(UseInitalTime, bool); |
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DeclareParameter(UseIntialExtendedSystemState, bool); |
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DeclareParameter(OrthoBoxTolerance, RealType); |
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DeclareParameter(Minimizer, std::string); |
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DeclareParameter(MinimizerMaxIter, RealType); |
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DeclareParameter(MinimizerWriteFreq, int); |
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DeclareParameter(MinimizerStepSize, RealType); |
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DeclareParameter(MinimizerFTol, RealType); |
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DeclareParameter(MinimizerGTol, RealType); |
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DeclareParameter(MinimizerLSTol, RealType); |
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DeclareParameter(MinimizerLSMaxIter, int); |
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DeclareParameter(ZconsGap, RealType); |
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DeclareParameter(ZconsFixtime, RealType); |
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DeclareParameter(ZconsUsingSMD, bool); |
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DeclareParameter(UseThermodynamicIntegration, bool); |
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DeclareParameter(ThermodynamicIntegrationLambda, RealType); |
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DeclareParameter(ThermodynamicIntegrationK, RealType); |
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DeclareParameter(ForceFieldVariant, std::string); |
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DeclareParameter(ForceFieldFileName, std::string); |
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DeclareParameter(SurfaceTension, RealType); |
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DeclareParameter(PrintPressureTensor, bool); |
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DeclareParameter(TaggedAtomPair, intPair); |
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DeclareParameter(PrintTaggedPairDistance, bool); |
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DeclareParameter(ElectrostaticSummationMethod, std::string); |
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DeclareParameter(ElectrostaticScreeningMethod, std::string); |
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DeclareParameter(DampingAlpha, RealType); |
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DeclareParameter(Dielectric, RealType); |
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DeclareParameter(CutoffPolicy, std::string); |
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DeclareParameter(SwitchingFunctionType, std::string); |
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DeclareParameter(CompressDumpFile, bool); |
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DeclareParameter(OutputForceVector, bool); |
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DeclareParameter(SkinThickness, RealType); |
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DeclareParameter(StatFileFormat, std::string); |
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DeclareParameter(HydroPropFile, std::string); |
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DeclareParameter(Viscosity, RealType); |
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DeclareParameter(BeadSize, RealType); |
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DeclareParameter(UseSphericalBoundaryConditions, bool); |
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DeclareParameter(FrozenBufferRadius, RealType); |
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DeclareParameter(LangevinBufferRadius, RealType); |
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DeclareParameter(AccumulateBoxDipole, bool); |
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DeclareParameter(NeighborListNeighbors, int); |
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DeclareParameter(UseMultipleTemperatureMethod, bool); |
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DeclareParameter(MTM_Ce, RealType); |
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DeclareParameter(MTM_G, RealType); |
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DeclareParameter(MTM_Io, RealType); |
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DeclareParameter(MTM_Sigma, RealType); |
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DeclareParameter(MTM_R, RealType); |
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DeclareParameter(UseRNEMD, bool); |
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DeclareParameter(RNEMD_exchangeTime, RealType); |
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DeclareParameter(RNEMD_nBins, int); |
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DeclareParameter(RNEMD_logWidth, int); |
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DeclareParameter(RNEMD_exchangeType, std::string); |
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DeclareParameter(RNEMD_objectSelection, std::string); |
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DeclareParameter(RNEMD_targetFlux, RealType); |
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DeclareParameter(UseRestraints, bool); |
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DeclareParameter(Restraint_file, std::string); |
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DeclareParameter(HULL_Method, std::string); |
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DeclareParameter(Alpha, RealType); |
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|
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public: |
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bool addComponent(Component* comp); |
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bool addZConsStamp(ZConsStamp* zcons); |
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bool addRestraintStamp(RestraintStamp* rest); |
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bool addMoleculeStamp(MoleculeStamp* molStamp); |
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int getNComponents() {return components_.size();} |
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std::vector<Component*> getComponents() {return components_;} |
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Component* getComponentAt(int index) {return components_.at(index);} |
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int getNZconsStamps() {return zconstraints_.size();} |
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std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;} |
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ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);} |
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int getNRestraintStamps() {return restraints_.size();} |
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std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;} |
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RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);} |
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|
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//std::string getRestraint_file(){ |
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virtual void validate(); |
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private: |
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void parseHydroPropFile(const std::string& filename); |
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std::vector<Component*> components_; |
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std::vector<ZConsStamp*> zconstraints_; |
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std::vector<RestraintStamp*> restraints_; |
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std::map<std::string, MoleculeStamp*> moleculeStamps_; |
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std::pair<int, int> taggedAtomPair_; |
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}; |
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} |
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#endif |
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