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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 906 by tim, Fri Mar 17 23:20:35 2006 UTC vs.
Revision 1327 by gezelter, Mon Mar 9 14:03:31 2009 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");
101    DefineOptionalParameter(Viscosity, "viscosity");
102    DefineOptionalParameter(BeadSize, "beadSize");
103 +  DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
104 +  DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
105 +  DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
106 +  DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
107 +  DefineOptionalParameter(MTM_Ce, "MTM_Ce");
108 +  DefineOptionalParameter(MTM_G, "MTM_G");
109 +  DefineOptionalParameter(MTM_Io, "MTM_Io");
110 +  DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
111 +  DefineOptionalParameter(MTM_R, "MTM_R");
112    
113 +
114 +  
115    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
116 +  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
117    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
118    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
119    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
# Line 111 | Line 122 | Globals::Globals() {
122    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
123    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
124    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
125 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
125 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
126 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
127 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
128    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
129    DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
130    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
131    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
132 +  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
133 +  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
134  
135 +  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
136 +  DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
137 +  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 15);
138 +  DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
139 +  
140  
141 <    deprecatedKeywords_.insert("nComponents");
142 <    deprecatedKeywords_.insert("nZconstraints");
141 >  deprecatedKeywords_.insert("nComponents");
142 >  deprecatedKeywords_.insert("nZconstraints");
143 >  deprecatedKeywords_.insert("initialConfig");
144      
145   }
146  
# Line 133 | Line 154 | void Globals::validate() {
154  
155    CheckParameter(ForceField, isNotEmpty());
156    CheckParameter(TargetTemp, isPositive());
157 <  CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") );
157 >  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"));
158    CheckParameter(Dt, isPositive());
159    CheckParameter(RunTime, isPositive());
139 –  CheckParameter(InitialConfig, isNotEmpty());
160    CheckParameter(FinalConfig, isNotEmpty());
161    CheckParameter(SampleTime, isNonNegative());
162    CheckParameter(ResetTime, isNonNegative());
# Line 145 | Line 165 | void Globals::validate() {
165    CheckParameter(SwitchingRadius, isNonNegative());
166    CheckParameter(Dielectric, isPositive());
167    CheckParameter(ThermalTime,  isNonNegative());
148 –  CheckParameter(TargetPressure,  isPositive());
168    CheckParameter(TauThermostat, isPositive());
169    CheckParameter(TauBarostat, isPositive());
170    CheckParameter(ZconsTime, isPositive());
# Line 161 | Line 180 | void Globals::validate() {
180    CheckParameter(MinimizerLSMaxIter, isPositive());
181    CheckParameter(ZconsGap, isPositive());
182    CheckParameter(ZconsFixtime, isPositive());
183 <  CheckParameter(ThermodynamicIntegrationLambda, isPositive());
183 >  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
184    CheckParameter(ThermodynamicIntegrationK, isPositive());
185    CheckParameter(ForceFieldVariant, isNotEmpty());
186    CheckParameter(ForceFieldFileName, isNotEmpty());
187    CheckParameter(ThermIntDistSpringConst, isPositive());
188    CheckParameter(ThermIntThetaSpringConst, isPositive());
189    CheckParameter(ThermIntOmegaSpringConst, isPositive());
171 –  CheckParameter(SurfaceTension, isPositive());
190    CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
191    CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
192    CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
# Line 180 | Line 198 | void Globals::validate() {
198    CheckParameter(ThermIntOmegaSpringConst, isPositive());
199    CheckParameter(DampingAlpha,isNonNegative());
200    CheckParameter(SkinThickness, isPositive());
201 <  CheckParameter(Viscosity,isNonNegative());
202 <  CheckParameter(BeadSize,isPositive());
201 >  CheckParameter(Viscosity, isNonNegative());
202 >  CheckParameter(BeadSize, isPositive());
203 >  CheckParameter(FrozenBufferRadius, isPositive());
204 >  CheckParameter(LangevinBufferRadius, isPositive());
205 >  CheckParameter(NeighborListNeighbors, isPositive());
206 >  CheckParameter(RNEMD_swapTime, isPositive());
207 >  CheckParameter(RNEMD_nBins, isPositive());
208 >  CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
209 >
210    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
211      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
212          std::ostringstream oss;

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