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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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#include <stdlib.h> |
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#include "utils/MemoryUtils.hpp" |
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#include "utils/simError.h" |
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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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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(BeadSize, "beadSize"); |
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DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius"); |
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DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius"); |
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DefineOptionalParameter(ThermalConductivity, "thermalConductivity"); |
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DefineOptionalParameter(ThermalLength, "thermalLength"); |
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DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors"); |
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DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod"); |
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DefineOptionalParameter(MTM_Ce, "MTM_Ce"); |
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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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DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true); |
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DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false); |
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DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false); |
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DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0); |
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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_swapType, "RNEMD_swapType", "Kinetic"); |
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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_objectSelection, "RNEMD_objectSelection", "select all"); |
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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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deprecatedKeywords_.insert("nComponents"); |
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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(DampingAlpha,isNonNegative()); |
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CheckParameter(SkinThickness, isPositive()); |
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CheckParameter(Viscosity, isNonNegative()); |
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CheckParameter(ThermalConductivity, isNonNegative()); |
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CheckParameter(ThermalLength, 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_swapTime, isPositive()); |
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CheckParameter(RNEMD_exchangeTime, isPositive()); |
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CheckParameter(RNEMD_nBins, isPositive() && isEven()); |
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CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz")); |
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CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale")); |
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CheckParameter(RNEMD_targetFlux, isNonNegative()); |
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CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape")); |
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CheckParameter(Alpha, isPositive()); |
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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; |
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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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throw OpenMDException(oss.str()); |
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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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} else { |
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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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throw OpenMDException(oss.str()); |
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} |
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return ret; |
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} |
