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root/OpenMD/branches/development/src/io/Globals.cpp
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Comparing branches/development/src/io/Globals.cpp (file contents):
Revision 1714 by gezelter, Sat May 19 18:12:46 2012 UTC vs.
Revision 1729 by jmarr, Wed May 30 16:08:07 2012 UTC

# Line 91 | Line 91 | Globals::Globals() {
91    DefineOptionalParameter(DampingAlpha, "dampingAlpha");
92    DefineOptionalParameter(SurfaceTension, "surfaceTension");
93    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
94 +  DefineOptionalParameter(PrintHeatFlux, "printHeatFlux");
95    DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
96    DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
97    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
# Line 134 | Line 135 | Globals::Globals() {
135    DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
136    DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
137    DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
138 +  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzKE, "RNEMD_targetJzKE", 0.0);
139 +  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpx, "RNEMD_targetJzpx", 0.0);
140 +  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpy, "RNEMD_targetJzpy", 0.0);
141 +  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpz, "RNEMD_targetJzpz", 0.0);
142    DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
143    DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false);
144 <  DefineOptionalParameterWithDefaultValue(RNEMD_outputDimensionalTemperature, "RNEMD_outputDimensionalTemperature", false);
144 >  DefineOptionalParameterWithDefaultValue(RNEMD_outputTemperature, "RNEMD_outputTemperature", false);
145 >  DefineOptionalParameterWithDefaultValue(RNEMD_outputVx, "RNEMD_outputVx", false);
146 >  DefineOptionalParameterWithDefaultValue(RNEMD_outputVy, "RNEMD_outputVy", false);
147 >  // James put this in.
148 >  DefineOptionalParameterWithDefaultValue(RNEMD_outputDen, "RNEMD_outputDen", false);
149 >  DefineOptionalParameterWithDefaultValue(RNEMD_outputAh, "RNEMD_outputAh", false);
150 >  DefineOptionalParameterWithDefaultValue(RNEMD_outputVz, "RNEMD_outputVz", false);  
151 >  DefineOptionalParameterWithDefaultValue(RNEMD_outputXyzTemperature, "RNEMD_outputXyzTemperature", false);
152 >  DefineOptionalParameterWithDefaultValue(RNEMD_outputRotTemperature, "RNEMD_outputRotTemperature", false);
153 >
154    DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
155    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
156    DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
157    DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
158 <
158 >  DefineOptionalParameterWithDefaultValue(FlucQPropagator, "flucQ.propagator", "NVT");
159 >  DefineOptionalParameterWithDefaultValue(FlucQFriction, "flucQ.friction", 1600.0);    
160 >  DefineOptionalParameterWithDefaultValue(FlucQTolerance, "flucQ.tolerance", 1.0e-6);    
161 >  DefineOptionalParameterWithDefaultValue(FlucQMaxIterations, "flucQ.maxIterations", 100);    
162 >  DefineOptionalParameterWithDefaultValue(FlucQTargetTemp, "flucQ.targetTemp", 1.0e-6);
163 >  DefineOptionalParameterWithDefaultValue(FlucQtauThermostat, "flucQ.tauThermostat", 10.0);
164  
146 –
165    deprecatedKeywords_.insert("nComponents");
166    deprecatedKeywords_.insert("nZconstraints");
167    deprecatedKeywords_.insert("initialConfig");
# Line 211 | Line 229 | void Globals::validate() {
229    CheckParameter(NeighborListNeighbors, isPositive());
230    CheckParameter(RNEMD_exchangeTime, isPositive());
231    CheckParameter(RNEMD_nBins, isPositive() && isEven());
232 <  CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
232 >  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"));
233    CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
234    CheckParameter(Alpha, isPositive());
235 <
235 >  CheckParameter(FlucQPropagator, isEqualIgnoreCase("NVT") || isEqualIgnoreCase("Langevin") || isEqualIgnoreCase("Minimizer") || isEqualIgnoreCase("Exact") );
236 >  CheckParameter(FlucQFriction, isNonNegative());    
237 >  CheckParameter(FlucQTolerance, isPositive());    
238 >  CheckParameter(FlucQMaxIterations, isPositive());    
239 >  CheckParameter(FlucQTargetTemp,  isNonNegative());
240 >  CheckParameter(FlucQtauThermostat, isPositive());
241    
242    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
243      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {

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