| 1 |
|
/* |
| 2 |
< |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 2 |
> |
* Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved. |
| 3 |
|
* |
| 4 |
|
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
|
* non-exclusive, royalty free, license to use, modify and |
| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
#include <stdlib.h> |
| 49 |
|
#include "utils/MemoryUtils.hpp" |
| 50 |
|
#include "utils/simError.h" |
| 51 |
|
|
| 52 |
< |
namespace oopse { |
| 52 |
> |
namespace OpenMD { |
| 53 |
|
Globals::Globals() { |
| 54 |
|
DefineParameter(ForceField, "forceField") |
| 55 |
|
|
| 74 |
|
DefineOptionalParameter(Seed, "seed"); |
| 75 |
|
DefineOptionalParameter(Minimizer, "minimizer"); |
| 76 |
|
DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter"); |
| 77 |
< |
DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq"); |
| 77 |
> |
DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq"); |
| 78 |
|
DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize"); |
| 79 |
|
DefineOptionalParameter(MinimizerFTol, "minimizerFTol"); |
| 80 |
|
DefineOptionalParameter(MinimizerGTol, "minimizerGTol"); |
| 99 |
|
DefineOptionalParameter(BeadSize, "beadSize"); |
| 100 |
|
DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius"); |
| 101 |
|
DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius"); |
| 102 |
– |
DefineOptionalParameter(ThermalConductivity, "thermalConductivity"); |
| 103 |
– |
DefineOptionalParameter(ThermalLength, "thermalLength"); |
| 102 |
|
DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors"); |
| 103 |
|
DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod"); |
| 104 |
|
DefineOptionalParameter(MTM_Ce, "MTM_Ce"); |
| 106 |
|
DefineOptionalParameter(MTM_Io, "MTM_Io"); |
| 107 |
|
DefineOptionalParameter(MTM_Sigma, "MTM_Sigma"); |
| 108 |
|
DefineOptionalParameter(MTM_R, "MTM_R"); |
| 109 |
< |
|
| 109 |
> |
DefineOptionalParameter(Alpha, "alpha"); |
| 110 |
|
|
| 111 |
|
|
| 112 |
|
DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true); |
| 119 |
|
DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5); |
| 120 |
|
DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0); |
| 121 |
|
DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0); |
| 122 |
+ |
DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", 0); |
| 123 |
|
DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0); |
| 124 |
|
DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY"); |
| 125 |
|
DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false); |
| 126 |
|
DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false); |
| 127 |
|
|
| 128 |
|
DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false); |
| 129 |
< |
DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0); |
| 129 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0); |
| 130 |
|
DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16); |
| 131 |
< |
DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic"); |
| 131 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16); |
| 132 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale"); |
| 133 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0); |
| 134 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_targetJzKE, "RNEMD_targetJzKE", 0.0); |
| 135 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpx, "RNEMD_targetJzpx", 0.0); |
| 136 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpy, "RNEMD_targetJzpy", 0.0); |
| 137 |
> |
DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpz, "RNEMD_targetJzpz", 0.0); |
| 138 |
|
DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all"); |
| 139 |
+ |
DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false); |
| 140 |
+ |
DefineOptionalParameterWithDefaultValue(RNEMD_outputTemperature, "RNEMD_outputTemperature", false); |
| 141 |
+ |
DefineOptionalParameterWithDefaultValue(RNEMD_outputVx, "RNEMD_outputVx", false); |
| 142 |
+ |
DefineOptionalParameterWithDefaultValue(RNEMD_outputVy, "RNEMD_outputVy", false); |
| 143 |
+ |
DefineOptionalParameterWithDefaultValue(RNEMD_outputXyzTemperature, "RNEMD_outputXyzTemperature", false); |
| 144 |
+ |
DefineOptionalParameterWithDefaultValue(RNEMD_outputRotTemperature, "RNEMD_outputRotTemperature", false); |
| 145 |
|
DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false); |
| 146 |
|
DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in"); |
| 147 |
|
DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false); |
| 148 |
+ |
DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex"); |
| 149 |
|
|
| 150 |
|
|
| 151 |
|
deprecatedKeywords_.insert("nComponents"); |
| 170 |
|
|
| 171 |
|
CheckParameter(ForceField, isNotEmpty()); |
| 172 |
|
CheckParameter(TargetTemp, isPositive()); |
| 173 |
< |
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")); |
| 173 |
> |
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")); |
| 174 |
|
CheckParameter(Dt, isPositive()); |
| 175 |
|
CheckParameter(RunTime, isPositive()); |
| 176 |
|
CheckParameter(FinalConfig, isNotEmpty()); |
| 188 |
|
CheckParameter(Seed, isPositive()); |
| 189 |
|
CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG")); |
| 190 |
|
CheckParameter(MinimizerMaxIter, isPositive()); |
| 191 |
< |
CheckParameter(MinimizerWriteFrq, isPositive()); |
| 191 |
> |
CheckParameter(MinimizerWriteFreq, isPositive()); |
| 192 |
|
CheckParameter(MinimizerStepSize, isPositive()); |
| 193 |
|
CheckParameter(MinimizerFTol, isPositive()); |
| 194 |
|
CheckParameter(MinimizerGTol, isPositive()); |
| 209 |
|
CheckParameter(DampingAlpha,isNonNegative()); |
| 210 |
|
CheckParameter(SkinThickness, isPositive()); |
| 211 |
|
CheckParameter(Viscosity, isNonNegative()); |
| 200 |
– |
CheckParameter(ThermalConductivity, isNonNegative()); |
| 201 |
– |
CheckParameter(ThermalLength, isNonNegative()); |
| 212 |
|
CheckParameter(BeadSize, isPositive()); |
| 213 |
|
CheckParameter(FrozenBufferRadius, isPositive()); |
| 214 |
|
CheckParameter(LangevinBufferRadius, isPositive()); |
| 215 |
|
CheckParameter(NeighborListNeighbors, isPositive()); |
| 216 |
< |
CheckParameter(RNEMD_swapTime, isPositive()); |
| 216 |
> |
CheckParameter(RNEMD_exchangeTime, isPositive()); |
| 217 |
|
CheckParameter(RNEMD_nBins, isPositive() && isEven()); |
| 218 |
< |
CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz")); |
| 218 |
> |
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")); |
| 219 |
> |
//CheckParameter(RNEMD_targetFlux, isNonNegative()); |
| 220 |
> |
CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape")); |
| 221 |
> |
CheckParameter(Alpha, isPositive()); |
| 222 |
|
|
| 223 |
+ |
|
| 224 |
|
for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) { |
| 225 |
|
if (!(*i)->findMoleculeStamp(moleculeStamps_)) { |
| 226 |
|
std::ostringstream oss; |
| 227 |
|
oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl; |
| 228 |
< |
throw OOPSEException(oss.str()); |
| 228 |
> |
throw OpenMDException(oss.str()); |
| 229 |
|
} |
| 230 |
|
} |
| 231 |
|
} |
| 232 |
< |
|
| 232 |
> |
|
| 233 |
|
bool Globals::addComponent(Component* comp) { |
| 234 |
|
components_.push_back(comp); |
| 235 |
|
return true; |
| 256 |
|
} else { |
| 257 |
|
std::ostringstream oss; |
| 258 |
|
oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n"; |
| 259 |
< |
throw OOPSEException(oss.str()); |
| 259 |
> |
throw OpenMDException(oss.str()); |
| 260 |
|
} |
| 261 |
|
return ret; |
| 262 |
|
} |
