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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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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#include <stdlib.h> |
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#include "utils/MemoryUtils.hpp" |
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#include "utils/simError.h" |
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|
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namespace oopse { |
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namespace OpenMD { |
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Globals::Globals() { |
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DefineParameter(ForceField, "forceField") |
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|
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DefineOptionalParameter(Ensemble, "ensemble"); |
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DefineOptionalParameter(Dt, "dt"); |
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DefineOptionalParameter(RunTime, "runTime"); |
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DefineOptionalParameter(InitialConfig, "initialConfig"); |
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DefineOptionalParameter(FinalConfig, "finalConfig"); |
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DefineOptionalParameter(SampleTime, "sampleTime"); |
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DefineOptionalParameter(ResetTime, "resetTime"); |
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DefineOptionalParameter(StatusTime, "statusTime"); |
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DefineOptionalParameter(CutoffRadius, "cutoffRadius"); |
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DefineOptionalParameter(SwitchingRadius, "switchingRadius"); |
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DefineOptionalParameter(Dielectric, "dielectric"); |
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DefineOptionalParameter(TempSet, "tempSet"); |
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DefineOptionalParameter(ThermalTime, "thermalTime"); |
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DefineOptionalParameter(TargetPressure, "targetPressure"); |
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DefineOptionalParameter(TargetPressure, "targetPressure"); |
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DefineOptionalParameter(TauThermostat, "tauThermostat"); |
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DefineOptionalParameter(TauBarostat, "tauBarostat"); |
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DefineOptionalParameter(ZconsTime, "zconsTime"); |
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DefineOptionalParameter(Seed, "seed"); |
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DefineOptionalParameter(Minimizer, "minimizer"); |
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DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter"); |
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DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq"); |
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DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq"); |
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DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize"); |
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DefineOptionalParameter(MinimizerFTol, "minimizerFTol"); |
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DefineOptionalParameter(MinimizerGTol, "minimizerGTol"); |
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DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK"); |
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DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant"); |
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DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName"); |
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DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst"); |
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DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst"); |
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DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst"); |
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DefineOptionalParameter(DampingAlpha, "dampingAlpha"); |
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DefineOptionalParameter(SurfaceTension, "surfaceTension"); |
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DefineOptionalParameter(PrintPressureTensor, "printPressureTensor"); |
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DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod"); |
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DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod"); |
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DefineOptionalParameter(CutoffPolicy, "cutoffPolicy"); |
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DefineOptionalParameter(PrintHeatFlux, "printHeatFlux"); |
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DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair"); |
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DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance"); |
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DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType"); |
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DefineOptionalParameter(HydroPropFile, "HydroPropFile"); |
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DefineOptionalParameter(Viscosity, "viscosity"); |
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DefineOptionalParameter(BeadSize, "beadSize"); |
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DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius"); |
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DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius"); |
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DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors"); |
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DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod"); |
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DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod"); |
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DefineOptionalParameter(MTM_Ce, "MTM_Ce"); |
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DefineOptionalParameter(MTM_G, "MTM_G"); |
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DefineOptionalParameter(MTM_Io, "MTM_Io"); |
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DefineOptionalParameter(MTM_Sigma, "MTM_Sigma"); |
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DefineOptionalParameter(MTM_R, "MTM_R"); |
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DefineOptionalParameter(Alpha, "alpha"); |
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|
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|
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DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true); |
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DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true); |
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DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false); |
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DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false); |
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DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6); |
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DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false); |
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DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false); |
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DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0); |
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DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5); |
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DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5); |
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DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2); |
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DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0); |
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DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0); |
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DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE"); |
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DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED"); |
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DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0); |
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DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false); |
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DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false); |
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DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false); |
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DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false); |
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DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", false); |
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DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0); |
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DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY"); |
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DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false); |
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DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false); |
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|
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DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false); |
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DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0); |
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DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16); |
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DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16); |
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DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale"); |
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DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0); |
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DefineOptionalParameterWithDefaultValue(RNEMD_targetJzKE, "RNEMD_targetJzKE", 0.0); |
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DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpx, "RNEMD_targetJzpx", 0.0); |
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DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpy, "RNEMD_targetJzpy", 0.0); |
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DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpz, "RNEMD_targetJzpz", 0.0); |
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DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all"); |
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DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false); |
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DefineOptionalParameterWithDefaultValue(RNEMD_outputTemperature, "RNEMD_outputTemperature", false); |
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DefineOptionalParameterWithDefaultValue(RNEMD_outputVx, "RNEMD_outputVx", false); |
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DefineOptionalParameterWithDefaultValue(RNEMD_outputVy, "RNEMD_outputVy", false); |
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// James put this in. |
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DefineOptionalParameterWithDefaultValue(RNEMD_outputDen, "RNEMD_outputDen", false); |
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DefineOptionalParameterWithDefaultValue(RNEMD_outputAh, "RNEMD_outputAh", false); |
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DefineOptionalParameterWithDefaultValue(RNEMD_outputVz, "RNEMD_outputVz", false); |
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DefineOptionalParameterWithDefaultValue(RNEMD_outputXyzTemperature, "RNEMD_outputXyzTemperature", false); |
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DefineOptionalParameterWithDefaultValue(RNEMD_outputRotTemperature, "RNEMD_outputRotTemperature", false); |
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|
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deprecatedKeywords_.insert("nComponents"); |
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deprecatedKeywords_.insert("nZconstraints"); |
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DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false); |
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DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in"); |
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DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false); |
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DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex"); |
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DefineOptionalParameterWithDefaultValue(FlucQPropagator, "flucQ.propagator", "NVT"); |
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DefineOptionalParameterWithDefaultValue(FlucQFriction, "flucQ.friction", 1600.0); |
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DefineOptionalParameterWithDefaultValue(FlucQTolerance, "flucQ.tolerance", 1.0e-6); |
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DefineOptionalParameterWithDefaultValue(FlucQMaxIterations, "flucQ.maxIterations", 100); |
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DefineOptionalParameterWithDefaultValue(FlucQTargetTemp, "flucQ.targetTemp", 1.0e-6); |
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DefineOptionalParameterWithDefaultValue(FlucQtauThermostat, "flucQ.tauThermostat", 10.0); |
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deprecatedKeywords_.insert("nComponents"); |
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deprecatedKeywords_.insert("nZconstraints"); |
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deprecatedKeywords_.insert("initialConfig"); |
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deprecatedKeywords_.insert("thermIntDistSpringConst"); |
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deprecatedKeywords_.insert("thermIntThetaSpringConst"); |
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deprecatedKeywords_.insert("thermIntOmegaSpringConst"); |
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deprecatedKeywords_.insert("useSolidThermInt"); |
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deprecatedKeywords_.insert("useLiquidThermInt"); |
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} |
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Globals::~Globals() { |
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MemoryUtils::deletePointers(components_); |
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MemoryUtils::deletePointers(zconstraints_); |
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MemoryUtils::deletePointers(restraints_); |
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} |
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void Globals::validate() { |
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CheckParameter(ForceField, isNotEmpty()); |
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CheckParameter(TargetTemp, isPositive()); |
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CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT") || isEqualIgnoreCase("LANGEVINDYNAMICS") ); |
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CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT") || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || isEqualIgnoreCase("LANGEVINHULL") || isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD")); |
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CheckParameter(Dt, isPositive()); |
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CheckParameter(RunTime, isPositive()); |
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CheckParameter(InitialConfig, isNotEmpty()); |
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CheckParameter(FinalConfig, isNotEmpty()); |
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CheckParameter(SampleTime, isNonNegative()); |
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CheckParameter(ResetTime, isNonNegative()); |
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CheckParameter(SwitchingRadius, isNonNegative()); |
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CheckParameter(Dielectric, isPositive()); |
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CheckParameter(ThermalTime, isNonNegative()); |
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CheckParameter(TargetPressure, isPositive()); |
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CheckParameter(TauThermostat, isPositive()); |
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CheckParameter(TauBarostat, isPositive()); |
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CheckParameter(ZconsTime, isPositive()); |
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CheckParameter(Seed, isPositive()); |
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CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG")); |
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CheckParameter(MinimizerMaxIter, isPositive()); |
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CheckParameter(MinimizerWriteFrq, isPositive()); |
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CheckParameter(MinimizerWriteFreq, isPositive()); |
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CheckParameter(MinimizerStepSize, isPositive()); |
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CheckParameter(MinimizerFTol, isPositive()); |
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CheckParameter(MinimizerGTol, isPositive()); |
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CheckParameter(MinimizerLSMaxIter, isPositive()); |
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CheckParameter(ZconsGap, isPositive()); |
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CheckParameter(ZconsFixtime, isPositive()); |
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CheckParameter(ThermodynamicIntegrationLambda, isPositive()); |
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CheckParameter(ThermodynamicIntegrationLambda, isNonNegative()); |
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CheckParameter(ThermodynamicIntegrationK, isPositive()); |
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CheckParameter(ForceFieldVariant, isNotEmpty()); |
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CheckParameter(ForceFieldFileName, isNotEmpty()); |
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CheckParameter(ThermIntDistSpringConst, isPositive()); |
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CheckParameter(ThermIntThetaSpringConst, isPositive()); |
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CheckParameter(ThermIntOmegaSpringConst, isPositive()); |
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CheckParameter(SurfaceTension, isPositive()); |
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CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD")); |
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CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED")); |
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CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE")); |
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CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL")); |
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CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD")); |
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CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED")); |
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CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL")); |
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//CheckParameter(StatFileFormat,); |
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CheckParameter(OrthoBoxTolerance, isPositive()); |
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CheckParameter(ThermIntDistSpringConst, isPositive()); |
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CheckParameter(ThermIntThetaSpringConst, isPositive()); |
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CheckParameter(ThermIntOmegaSpringConst, isPositive()); |
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CheckParameter(DampingAlpha,isNonNegative()); |
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CheckParameter(SkinThickness, isPositive()); |
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|
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> |
CheckParameter(Viscosity, isNonNegative()); |
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> |
CheckParameter(BeadSize, isPositive()); |
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> |
CheckParameter(FrozenBufferRadius, isPositive()); |
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> |
CheckParameter(LangevinBufferRadius, isPositive()); |
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> |
CheckParameter(NeighborListNeighbors, isPositive()); |
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> |
CheckParameter(RNEMD_exchangeTime, isPositive()); |
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> |
CheckParameter(RNEMD_nBins, isPositive() && isEven()); |
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> |
CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("KineticScaleVAM") || isEqualIgnoreCase("KineticScaleAM") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale") || isEqualIgnoreCase("ShiftScaleV") || isEqualIgnoreCase("ShiftScaleVAM")); |
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> |
CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape")); |
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> |
CheckParameter(Alpha, isPositive()); |
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> |
CheckParameter(FlucQPropagator, isEqualIgnoreCase("NVT") || isEqualIgnoreCase("Langevin") || isEqualIgnoreCase("Minimizer") || isEqualIgnoreCase("Exact") ); |
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> |
CheckParameter(FlucQFriction, isNonNegative()); |
| 237 |
> |
CheckParameter(FlucQTolerance, isPositive()); |
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> |
CheckParameter(FlucQMaxIterations, isPositive()); |
| 239 |
> |
CheckParameter(FlucQTargetTemp, isNonNegative()); |
| 240 |
> |
CheckParameter(FlucQtauThermostat, isPositive()); |
| 241 |
> |
|
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for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) { |
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if (!(*i)->findMoleculeStamp(moleculeStamps_)) { |
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std::ostringstream oss; |
| 245 |
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oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl; |
| 246 |
< |
throw OOPSEException(oss.str()); |
| 246 |
> |
throw OpenMDException(oss.str()); |
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} |
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} |
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} |
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|
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|
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bool Globals::addComponent(Component* comp) { |
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components_.push_back(comp); |
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return true; |
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return true; |
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} |
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|
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+ |
bool Globals::addRestraintStamp(RestraintStamp* rest) { |
| 262 |
+ |
restraints_.push_back(rest); |
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+ |
return true; |
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+ |
} |
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+ |
|
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bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) { |
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std::string molStampName = molStamp->getName(); |
| 268 |
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std::map<std::string, MoleculeStamp*>::iterator i; |
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} else { |
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std::ostringstream oss; |
| 276 |
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oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n"; |
| 277 |
< |
throw OOPSEException(oss.str()); |
| 277 |
> |
throw OpenMDException(oss.str()); |
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} |
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return ret; |
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} |
