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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 927 by tim, Fri Mar 31 18:09:22 2006 UTC vs.
Revision 1126 by gezelter, Fri Apr 6 21:53:43 2007 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");
97 –  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
98 –  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
96    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
97    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
98    DefineOptionalParameter(HydroPropFile, "HydroPropFile");
99    DefineOptionalParameter(Viscosity, "viscosity");
100    DefineOptionalParameter(BeadSize, "beadSize");
101 +  DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
102 +  DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
103 +  DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
104 +  DefineOptionalParameter(TempDepViscosityA,"tempDepViscosityA");
105 +  DefineOptionalParameter(TempDepViscosityB,"tempDepViscosityB");
106 +  DefineOptionalParameter(TempDepViscosityC,"tempDepViscosityC");
107 +  DefineOptionalParameter(TempDepViscosityD,"tempDepViscosityD");
108 +
109    
110    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
111 +  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
112    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
113    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
114    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
# Line 111 | Line 117 | Globals::Globals() {
117    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
118    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
119    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
120 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
120 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
121 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
122 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
123    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
124    DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
125    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
126    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
127 +  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
128 +  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
129  
130 <
131 <    deprecatedKeywords_.insert("nComponents");
132 <    deprecatedKeywords_.insert("nZconstraints");
130 >  deprecatedKeywords_.insert("nComponents");
131 >  deprecatedKeywords_.insert("nZconstraints");
132 >  deprecatedKeywords_.insert("initialConfig");
133      
134   }
135  
# Line 133 | Line 143 | void Globals::validate() {
143  
144    CheckParameter(ForceField, isNotEmpty());
145    CheckParameter(TargetTemp, isPositive());
146 <  CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("NPRT"));
146 >  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"));
147    CheckParameter(Dt, isPositive());
148    CheckParameter(RunTime, isPositive());
139 –  CheckParameter(InitialConfig, isNotEmpty());
149    CheckParameter(FinalConfig, isNotEmpty());
150    CheckParameter(SampleTime, isNonNegative());
151    CheckParameter(ResetTime, isNonNegative());
# Line 145 | Line 154 | void Globals::validate() {
154    CheckParameter(SwitchingRadius, isNonNegative());
155    CheckParameter(Dielectric, isPositive());
156    CheckParameter(ThermalTime,  isNonNegative());
148 –  CheckParameter(TargetPressure,  isPositive());
157    CheckParameter(TauThermostat, isPositive());
158    CheckParameter(TauBarostat, isPositive());
159    CheckParameter(ZconsTime, isPositive());
# Line 161 | Line 169 | void Globals::validate() {
169    CheckParameter(MinimizerLSMaxIter, isPositive());
170    CheckParameter(ZconsGap, isPositive());
171    CheckParameter(ZconsFixtime, isPositive());
172 <  CheckParameter(ThermodynamicIntegrationLambda, isPositive());
172 >  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
173    CheckParameter(ThermodynamicIntegrationK, isPositive());
174    CheckParameter(ForceFieldVariant, isNotEmpty());
175    CheckParameter(ForceFieldFileName, isNotEmpty());
176    CheckParameter(ThermIntDistSpringConst, isPositive());
177    CheckParameter(ThermIntThetaSpringConst, isPositive());
178    CheckParameter(ThermIntOmegaSpringConst, isPositive());
171 –  CheckParameter(SurfaceTension, isNonNegative());
179    CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
180    CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
181    CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
# Line 180 | Line 187 | void Globals::validate() {
187    CheckParameter(ThermIntOmegaSpringConst, isPositive());
188    CheckParameter(DampingAlpha,isNonNegative());
189    CheckParameter(SkinThickness, isPositive());
190 <  CheckParameter(Viscosity,isNonNegative());
191 <  CheckParameter(BeadSize,isPositive());
190 >  CheckParameter(Viscosity, isNonNegative());
191 >  CheckParameter(BeadSize, isPositive());
192 >  CheckParameter(FrozenBufferRadius, isPositive());
193 >  CheckParameter(LangevinBufferRadius, isPositive());
194 >  CheckParameter(NeighborListNeighbors, isPositive());
195 >
196    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
197      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
198          std::ostringstream oss;

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