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gezelter |
404 |
/* |
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gezelter |
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* Copyright (c) 2005 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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* 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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* 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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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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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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gezelter |
2 |
#include <stdlib.h> |
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#include <stdio.h> |
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#include <string.h> |
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tim |
665 |
#include <string> |
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gezelter |
2 |
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tim |
3 |
#include "io/Globals.hpp" |
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tim |
816 |
#include "io/ParamConstraint.hpp" |
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#include "utils/MemoryUtils.hpp" |
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tim |
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#include "utils/simError.h" |
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gezelter |
2 |
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tim |
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namespace oopse { |
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Globals::Globals() { |
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tim |
665 |
DefineParameter(ForceField, "forceField") |
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DefineOptionalParameter(TargetTemp, "targetTemp"); |
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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(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(TempSet, "tempSet"); |
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DefineOptionalParameter(ThermalTime, "thermalTime"); |
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gezelter |
1126 |
DefineOptionalParameter(TargetPressure, "targetPressure"); |
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tim |
665 |
DefineOptionalParameter(TauThermostat, "tauThermostat"); |
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DefineOptionalParameter(TauBarostat, "tauBarostat"); |
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DefineOptionalParameter(ZconsTime, "zconsTime"); |
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DefineOptionalParameter(ZconsTol, "zconsTol"); |
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DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy"); |
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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(MinimizerStepSize, "minimizerStepSize"); |
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DefineOptionalParameter(MinimizerFTol, "minimizerFTol"); |
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DefineOptionalParameter(MinimizerGTol, "minimizerGTol"); |
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DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol"); |
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DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter"); |
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DefineOptionalParameter(ZconsGap, "zconsGap"); |
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DefineOptionalParameter(ZconsFixtime, "zconsFixtime"); |
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DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD"); |
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DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda"); |
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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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gezelter |
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DefineOptionalParameter(DampingAlpha, "dampingAlpha"); |
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tim |
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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(SurfaceTension, "surfaceTension"); |
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DefineOptionalParameter(PrintPressureTensor, "printPressureTensor"); |
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gezelter |
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DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair"); |
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DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance"); |
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tim |
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DefineOptionalParameter(CutoffPolicy, "cutoffPolicy"); |
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chrisfen |
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DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType"); |
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tim |
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DefineOptionalParameter(HydroPropFile, "HydroPropFile"); |
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tim |
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DefineOptionalParameter(Viscosity, "viscosity"); |
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DefineOptionalParameter(BeadSize, "beadSize"); |
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gezelter |
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DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius"); |
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DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius"); |
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gezelter |
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DefineOptionalParameter(ThermalConductivity, "thermalConductivity"); |
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DefineOptionalParameter(ThermalLength, "thermalLength"); |
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chuckv |
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DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors"); |
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chuckv |
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DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod"); |
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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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tim |
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gezelter |
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chuckv |
1147 |
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tim |
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DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true); |
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gezelter |
1126 |
DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true); |
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tim |
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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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chrisfen |
666 |
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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gezelter |
1078 |
DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE"); |
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DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED"); |
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chrisfen |
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DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5); |
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tim |
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DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0); |
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chrisfen |
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DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0); |
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tim |
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DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0); |
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tim |
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DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY"); |
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gezelter |
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DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false); |
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chrisfen |
998 |
DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false); |
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tim |
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gezelter |
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DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false); |
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DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0); |
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skuang |
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DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16); |
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gezelter |
1327 |
DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic"); |
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gezelter |
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DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all"); |
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gezelter |
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DefineOptionalParameterWithDefaultValue(UseRestraints, "UseRestraints", false); |
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DefineOptionalParameterWithDefaultValue(Restraint_objectSelection, "Restraint_objectSelection", "select all"); |
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DefineOptionalParameterWithDefaultValue(Restraint_type, "Restraint_type", "positional"); |
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DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in"); |
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DefineOptionalParameterWithDefaultValue(Restraint_DisplacementSpringConstant, "Restraint_DisplacementSpringConstant", 0.0); |
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DefineOptionalParameterWithDefaultValue(Restraint_RollSpringConstant, "Restraint_RollSpringConstant", 0.0); // phi |
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DefineOptionalParameterWithDefaultValue(Restraint_PitchSpringConstant, "Restraint_PitchSpringConstant", 0.0); // theta |
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DefineOptionalParameterWithDefaultValue(Restraint_YawSpringConstant, "Restraint_YawSpringConstant", 0.0); // psi |
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gezelter |
1327 |
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gezelter |
1078 |
deprecatedKeywords_.insert("nComponents"); |
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deprecatedKeywords_.insert("nZconstraints"); |
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deprecatedKeywords_.insert("initialConfig"); |
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gezelter |
2 |
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} |
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tim |
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Globals::~Globals() { |
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tim |
816 |
MemoryUtils::deletePointers(components_); |
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MemoryUtils::deletePointers(zconstraints_); |
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gezelter |
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} |
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tim |
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void Globals::validate() { |
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DataHolder::validate(); |
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gezelter |
2 |
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tim |
672 |
CheckParameter(ForceField, isNotEmpty()); |
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CheckParameter(TargetTemp, isPositive()); |
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chuckv |
1293 |
CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT") || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || isEqualIgnoreCase("SMIPD")); |
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tim |
672 |
CheckParameter(Dt, isPositive()); |
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CheckParameter(RunTime, isPositive()); |
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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(StatusTime, isNonNegative()); |
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CheckParameter(CutoffRadius, isPositive()); |
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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(TauThermostat, isPositive()); |
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CheckParameter(TauBarostat, isPositive()); |
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CheckParameter(ZconsTime, isPositive()); |
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CheckParameter(ZconsTol, isPositive()); |
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CheckParameter(Seed, isPositive()); |
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tim |
850 |
CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG")); |
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tim |
672 |
CheckParameter(MinimizerMaxIter, isPositive()); |
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CheckParameter(MinimizerWriteFrq, 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(MinimizerLSTol, 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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chrisfen |
979 |
CheckParameter(ThermodynamicIntegrationLambda, isNonNegative()); |
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tim |
672 |
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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tim |
850 |
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(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL")); |
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CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL")); |
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tim |
672 |
//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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chrisfen |
716 |
CheckParameter(DampingAlpha,isNonNegative()); |
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tim |
672 |
CheckParameter(SkinThickness, isPositive()); |
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gezelter |
945 |
CheckParameter(Viscosity, isNonNegative()); |
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gezelter |
1355 |
CheckParameter(ThermalConductivity, isNonNegative()); |
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CheckParameter(ThermalLength, isNonNegative()); |
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gezelter |
945 |
CheckParameter(BeadSize, isPositive()); |
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CheckParameter(FrozenBufferRadius, isPositive()); |
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CheckParameter(LangevinBufferRadius, isPositive()); |
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chuckv |
1095 |
CheckParameter(NeighborListNeighbors, isPositive()); |
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gezelter |
1327 |
CheckParameter(RNEMD_swapTime, isPositive()); |
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skuang |
1341 |
CheckParameter(RNEMD_nBins, isPositive() && isEven()); |
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gezelter |
1327 |
CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz")); |
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gezelter |
1354 |
CheckParameter(Restraint_DisplacementSpringConstant, isNonNegative()); |
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CheckParameter(Restraint_RollSpringConstant, isNonNegative()); |
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CheckParameter(Restraint_PitchSpringConstant, isNonNegative()); |
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CheckParameter(Restraint_YawSpringConstant, isNonNegative()); |
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CheckParameter(Restraint_type, isEqualIgnoreCase("P") || isEqualIgnoreCase("O") || isEqualIgnoreCase("P+O") || isEqualIgnoreCase("RMSD_P") || isEqualIgnoreCase("RMSD_O") || isEqualIgnoreCase("RMSD_P+RMSD_O")); |
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chuckv |
1095 |
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tim |
770 |
for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) { |
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if (!(*i)->findMoleculeStamp(moleculeStamps_)) { |
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tim |
845 |
std::ostringstream oss; |
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oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl; |
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throw OOPSEException(oss.str()); |
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tim |
770 |
} |
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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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} |
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gezelter |
2 |
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tim |
770 |
bool Globals::addZConsStamp(ZConsStamp* zcons) { |
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zconstraints_.push_back(zcons); |
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return true; |
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gezelter |
2 |
} |
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tim |
770 |
bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) { |
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std::string molStampName = molStamp->getName(); |
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std::map<std::string, MoleculeStamp*>::iterator i; |
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bool ret = false; |
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i = moleculeStamps_.find(molStampName); |
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if (i == moleculeStamps_.end()) { |
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moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp)); |
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ret = true; |
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} else { |
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tim |
845 |
std::ostringstream oss; |
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oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n"; |
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throw OOPSEException(oss.str()); |
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tim |
770 |
} |
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return ret; |
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gezelter |
2 |
} |
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tim |
770 |
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} |
