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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 1423 by gezelter, Tue Mar 30 15:05:13 2010 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 136 | Line 134 | Globals::Globals() {
134    DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
135    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
136    DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
137 +  DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
138  
139  
140    deprecatedKeywords_.insert("nComponents");
# Line 178 | Line 177 | void Globals::validate() {
177    CheckParameter(Seed, isPositive());
178    CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
179    CheckParameter(MinimizerMaxIter, isPositive());
180 <  CheckParameter(MinimizerWriteFrq, isPositive());
180 >  CheckParameter(MinimizerWriteFreq, isPositive());
181    CheckParameter(MinimizerStepSize, isPositive());
182    CheckParameter(MinimizerFTol, isPositive());
183    CheckParameter(MinimizerGTol, isPositive());
# Line 199 | Line 198 | void Globals::validate() {
198    CheckParameter(DampingAlpha,isNonNegative());
199    CheckParameter(SkinThickness, isPositive());
200    CheckParameter(Viscosity, isNonNegative());
202 –  CheckParameter(ThermalConductivity, isNonNegative());
203 –  CheckParameter(ThermalLength, isNonNegative());
201    CheckParameter(BeadSize, isPositive());
202    CheckParameter(FrozenBufferRadius, isPositive());
203    CheckParameter(LangevinBufferRadius, isPositive());
# Line 209 | Line 206 | void Globals::validate() {
206    CheckParameter(RNEMD_nBins, isPositive() && isEven());
207    CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
208    CheckParameter(RNEMD_targetFlux, isNonNegative());
209 +  CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
210 +  CheckParameter(Alpha, isPositive());
211  
212 +  
213    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
214      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
215          std::ostringstream oss;

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