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root/OpenMD/trunk/src/io/Globals.cpp
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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1610 by gezelter, Fri Aug 12 14:37:25 2011 UTC

# Line 1 | Line 1
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
# Line 74 | Line 74 | Globals::Globals() {
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");
# Line 99 | Line 99 | Globals::Globals() {
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");
# Line 108 | Line 106 | Globals::Globals() {
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);
# Line 121 | Line 119 | Globals::Globals() {
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);
# Line 133 | Line 132 | Globals::Globals() {
132    DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
133    DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
134    DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
135 +  DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false);
136 +  DefineOptionalParameterWithDefaultValue(RNEMD_outputDimensionalTemperature, "RNEMD_outputDimensionalTemperature", false);
137    DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
138    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
139    DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
140 +  DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
141  
142  
143    deprecatedKeywords_.insert("nComponents");
# Line 160 | Line 162 | void Globals::validate() {
162  
163    CheckParameter(ForceField, isNotEmpty());
164    CheckParameter(TargetTemp, isPositive());
165 <  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"));
165 >  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"));
166    CheckParameter(Dt, isPositive());
167    CheckParameter(RunTime, isPositive());
168    CheckParameter(FinalConfig, isNotEmpty());
# Line 178 | Line 180 | void Globals::validate() {
180    CheckParameter(Seed, isPositive());
181    CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
182    CheckParameter(MinimizerMaxIter, isPositive());
183 <  CheckParameter(MinimizerWriteFrq, isPositive());
183 >  CheckParameter(MinimizerWriteFreq, isPositive());
184    CheckParameter(MinimizerStepSize, isPositive());
185    CheckParameter(MinimizerFTol, isPositive());
186    CheckParameter(MinimizerGTol, isPositive());
# Line 199 | Line 201 | void Globals::validate() {
201    CheckParameter(DampingAlpha,isNonNegative());
202    CheckParameter(SkinThickness, isPositive());
203    CheckParameter(Viscosity, isNonNegative());
202 –  CheckParameter(ThermalConductivity, isNonNegative());
203 –  CheckParameter(ThermalLength, isNonNegative());
204    CheckParameter(BeadSize, isPositive());
205    CheckParameter(FrozenBufferRadius, isPositive());
206    CheckParameter(LangevinBufferRadius, isPositive());
# Line 208 | Line 208 | void Globals::validate() {
208    CheckParameter(RNEMD_exchangeTime, isPositive());
209    CheckParameter(RNEMD_nBins, isPositive() && isEven());
210    CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
211 <  CheckParameter(RNEMD_targetFlux, isNonNegative());
211 >  //CheckParameter(RNEMD_targetFlux, isNonNegative());
212 >  CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
213 >  CheckParameter(Alpha, isPositive());
214  
215 +  
216    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
217      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
218          std::ostringstream oss;

Comparing trunk/src/io/Globals.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1610 by gezelter, Fri Aug 12 14:37:25 2011 UTC

# Line 0 | Line 1
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