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root/group/trunk/OOPSE-4/src/io/Globals.cpp
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Comparing trunk/OOPSE-4/src/io/Globals.cpp (file contents):
Revision 2548 by chrisfen, Thu Jan 12 04:13:46 2006 UTC vs.
Revision 3463 by chuckv, Thu Oct 16 18:25:36 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 <  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
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    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
115 +  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
116    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
117    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
118    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
# Line 108 | Line 121 | Globals::Globals() {
121    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
122    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
123    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
124 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
124 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
125 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
126 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
127    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
128    DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
129    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
130    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
131 +  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
132 +  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
133  
134 <
135 <    deprecatedKeywords_.insert("nComponents");
136 <    deprecatedKeywords_.insert("nZconstraints");
134 >  deprecatedKeywords_.insert("nComponents");
135 >  deprecatedKeywords_.insert("nZconstraints");
136 >  deprecatedKeywords_.insert("initialConfig");
137      
138   }
139  
# Line 130 | Line 147 | void Globals::validate() {
147  
148    CheckParameter(ForceField, isNotEmpty());
149    CheckParameter(TargetTemp, isPositive());
150 <  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) ||
134 <                 isEqualIgnoreCase(std::string("NVT")) ||
135 <                 isEqualIgnoreCase(std::string("NPTi")) ||
136 <                 isEqualIgnoreCase(std::string("NPTf")) ||
137 <                 isEqualIgnoreCase(std::string("NPTxyz")) );
150 >  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"));
151    CheckParameter(Dt, isPositive());
152    CheckParameter(RunTime, isPositive());
140 –  CheckParameter(InitialConfig, isNotEmpty());
153    CheckParameter(FinalConfig, isNotEmpty());
154    CheckParameter(SampleTime, isNonNegative());
155    CheckParameter(ResetTime, isNonNegative());
# Line 146 | Line 158 | void Globals::validate() {
158    CheckParameter(SwitchingRadius, isNonNegative());
159    CheckParameter(Dielectric, isPositive());
160    CheckParameter(ThermalTime,  isNonNegative());
149 –  CheckParameter(TargetPressure,  isPositive());
161    CheckParameter(TauThermostat, isPositive());
162    CheckParameter(TauBarostat, isPositive());
163    CheckParameter(ZconsTime, isPositive());
164    CheckParameter(ZconsTol, isPositive());
165    CheckParameter(Seed, isPositive());
166 <  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) ||
156 <                 isEqualIgnoreCase(std::string("CG")));
166 >  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
167    CheckParameter(MinimizerMaxIter, isPositive());
168    CheckParameter(MinimizerWriteFrq, isPositive());
169    CheckParameter(MinimizerStepSize, isPositive());
# Line 163 | Line 173 | void Globals::validate() {
173    CheckParameter(MinimizerLSMaxIter, isPositive());
174    CheckParameter(ZconsGap, isPositive());
175    CheckParameter(ZconsFixtime, isPositive());
176 <  CheckParameter(ThermodynamicIntegrationLambda, isPositive());
176 >  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
177    CheckParameter(ThermodynamicIntegrationK, isPositive());
178    CheckParameter(ForceFieldVariant, isNotEmpty());
179    CheckParameter(ForceFieldFileName, isNotEmpty());
180    CheckParameter(ThermIntDistSpringConst, isPositive());
181    CheckParameter(ThermIntThetaSpringConst, isPositive());
182    CheckParameter(ThermIntOmegaSpringConst, isPositive());
183 <  CheckParameter(SurfaceTension, isPositive());
184 <  CheckParameter(ElectrostaticSummationMethod,
185 <                 isEqualIgnoreCase(std::string("NONE")) ||
186 <                 isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) ||
177 <                 isEqualIgnoreCase(std::string("SHIFTED_FORCE")) ||
178 <                 isEqualIgnoreCase(std::string("REACTION_FIELD")));
179 <  CheckParameter(ElectrostaticScreeningMethod,
180 <                 isEqualIgnoreCase(std::string("UNDAMPED")) ||
181 <                 isEqualIgnoreCase(std::string("DAMPED")));
182 <  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) ||
183 <                 isEqualIgnoreCase(std::string("MAX")) ||
184 <                 isEqualIgnoreCase(std::string("TRADITIONAL")));
185 <  CheckParameter(SwitchingFunctionType,
186 <                 isEqualIgnoreCase(std::string("CUBIC")) ||
187 <                 isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
183 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
184 >  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
185 >  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
186 >  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
187    //CheckParameter(StatFileFormat,);    
189 –  //CheckParameter(MixingRule,);
188    CheckParameter(OrthoBoxTolerance, isPositive());  
189    CheckParameter(ThermIntDistSpringConst, isPositive());
190    CheckParameter(ThermIntThetaSpringConst, isPositive());
191    CheckParameter(ThermIntOmegaSpringConst, isPositive());
192    CheckParameter(DampingAlpha,isNonNegative());
193    CheckParameter(SkinThickness, isPositive());
194 +  CheckParameter(Viscosity, isNonNegative());
195 +  CheckParameter(BeadSize, isPositive());
196 +  CheckParameter(FrozenBufferRadius, isPositive());
197 +  CheckParameter(LangevinBufferRadius, isPositive());
198 +  CheckParameter(NeighborListNeighbors, isPositive());
199  
200    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
201      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {

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