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root/OpenMD/branches/development/src/io/Globals.cpp
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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 945 by gezelter, Tue Apr 25 02:09:01 2006 UTC vs.
Revision 1291 by gezelter, Thu Sep 11 19:40:59 2008 UTC

# Line 57 | Line 57 | Globals::Globals() {
57    DefineOptionalParameter(Ensemble, "ensemble");
58    DefineOptionalParameter(Dt, "dt");
59    DefineOptionalParameter(RunTime, "runTime");
60 –  DefineOptionalParameter(InitialConfig, "initialConfig");
60    DefineOptionalParameter(FinalConfig, "finalConfig");
61    DefineOptionalParameter(SampleTime, "sampleTime");
62    DefineOptionalParameter(ResetTime, "resetTime");
63    DefineOptionalParameter(StatusTime, "statusTime");
64    DefineOptionalParameter(CutoffRadius, "cutoffRadius");
65    DefineOptionalParameter(SwitchingRadius, "switchingRadius");
67 –  DefineOptionalParameter(Dielectric, "dielectric");
66    DefineOptionalParameter(TempSet, "tempSet");
67    DefineOptionalParameter(ThermalTime, "thermalTime");
68 <  DefineOptionalParameter(TargetPressure, "targetPressure");
68 >  DefineOptionalParameter(TargetPressure, "targetPressure");  
69    DefineOptionalParameter(TauThermostat, "tauThermostat");
70    DefineOptionalParameter(TauBarostat, "tauBarostat");
71    DefineOptionalParameter(ZconsTime, "zconsTime");
# Line 89 | Line 87 | Globals::Globals() {
87    DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
88    DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89    DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90 +  DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91    DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
92    DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
93    DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
94    DefineOptionalParameter(SurfaceTension, "surfaceTension");
95    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
96 <  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
97 <  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
96 >  DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
97 >  DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
98    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
99    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
100    DefineOptionalParameter(HydroPropFile, "HydroPropFile");
# Line 103 | Line 102 | Globals::Globals() {
102    DefineOptionalParameter(BeadSize, "beadSize");
103    DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
104    DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
105 +  DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
106    
107 +  
108    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
109 +  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
110    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
111    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
112    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
# Line 113 | Line 115 | Globals::Globals() {
115    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
116    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
117    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
118 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
118 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
119 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
120 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
121    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
122    DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 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 <
129 <    deprecatedKeywords_.insert("nComponents");
130 <    deprecatedKeywords_.insert("nZconstraints");
128 >  deprecatedKeywords_.insert("nComponents");
129 >  deprecatedKeywords_.insert("nZconstraints");
130 >  deprecatedKeywords_.insert("initialConfig");
131      
132   }
133  
# Line 136 | Line 141 | void Globals::validate() {
141  
142    CheckParameter(ForceField, isNotEmpty());
143    CheckParameter(TargetTemp, isPositive());
144 <  CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT"));
144 >  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"));
145    CheckParameter(Dt, isPositive());
146    CheckParameter(RunTime, isPositive());
142 –  CheckParameter(InitialConfig, isNotEmpty());
147    CheckParameter(FinalConfig, isNotEmpty());
148    CheckParameter(SampleTime, isNonNegative());
149    CheckParameter(ResetTime, isNonNegative());
# Line 148 | Line 152 | void Globals::validate() {
152    CheckParameter(SwitchingRadius, isNonNegative());
153    CheckParameter(Dielectric, isPositive());
154    CheckParameter(ThermalTime,  isNonNegative());
151 –  CheckParameter(TargetPressure,  isPositive());
155    CheckParameter(TauThermostat, isPositive());
156    CheckParameter(TauBarostat, isPositive());
157    CheckParameter(ZconsTime, isPositive());
# Line 164 | Line 167 | void Globals::validate() {
167    CheckParameter(MinimizerLSMaxIter, isPositive());
168    CheckParameter(ZconsGap, isPositive());
169    CheckParameter(ZconsFixtime, isPositive());
170 <  CheckParameter(ThermodynamicIntegrationLambda, isPositive());
170 >  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
171    CheckParameter(ThermodynamicIntegrationK, isPositive());
172    CheckParameter(ForceFieldVariant, isNotEmpty());
173    CheckParameter(ForceFieldFileName, isNotEmpty());
174    CheckParameter(ThermIntDistSpringConst, isPositive());
175    CheckParameter(ThermIntThetaSpringConst, isPositive());
176    CheckParameter(ThermIntOmegaSpringConst, isPositive());
174 –  CheckParameter(SurfaceTension, isNonNegative());
177    CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
178    CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
179    CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
# Line 187 | Line 189 | void Globals::validate() {
189    CheckParameter(BeadSize, isPositive());
190    CheckParameter(FrozenBufferRadius, isPositive());
191    CheckParameter(LangevinBufferRadius, isPositive());
192 +  CheckParameter(NeighborListNeighbors, isPositive());
193 +
194    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
195      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
196          std::ostringstream oss;

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