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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 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
Revision 1355 by gezelter, Mon Jul 20 17:50:40 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");
# Line 103 | Line 102 | Globals::Globals() {
102    DefineOptionalParameter(BeadSize, "beadSize");
103    DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
104    DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
105 +  DefineOptionalParameter(ThermalConductivity, "thermalConductivity");
106 +  DefineOptionalParameter(ThermalLength, "thermalLength");
107 +  DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
108 +  DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
109 +  DefineOptionalParameter(MTM_Ce, "MTM_Ce");
110 +  DefineOptionalParameter(MTM_G, "MTM_G");
111 +  DefineOptionalParameter(MTM_Io, "MTM_Io");
112 +  DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
113 +  DefineOptionalParameter(MTM_R, "MTM_R");
114    
115 +
116 +  
117    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
118 +  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
119    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
120    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
121    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
# Line 113 | Line 124 | Globals::Globals() {
124    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
125    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
126    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
127 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
127 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
128 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
129 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
130    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
131    DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
132    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
# Line 121 | Line 134 | Globals::Globals() {
134    DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
135    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
136  
137 +  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
138 +  DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
139 +  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
140 +  DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
141 +  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
142 +  DefineOptionalParameterWithDefaultValue(UseRestraints, "UseRestraints", false);
143 +  DefineOptionalParameterWithDefaultValue(Restraint_objectSelection, "Restraint_objectSelection", "select all");
144 +  DefineOptionalParameterWithDefaultValue(Restraint_type, "Restraint_type", "positional");
145 +  DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
146 +  DefineOptionalParameterWithDefaultValue(Restraint_DisplacementSpringConstant, "Restraint_DisplacementSpringConstant", 0.0);
147 +  DefineOptionalParameterWithDefaultValue(Restraint_RollSpringConstant, "Restraint_RollSpringConstant", 0.0);   // phi
148 +  DefineOptionalParameterWithDefaultValue(Restraint_PitchSpringConstant, "Restraint_PitchSpringConstant", 0.0); // theta
149 +  DefineOptionalParameterWithDefaultValue(Restraint_YawSpringConstant, "Restraint_YawSpringConstant", 0.0);     // psi
150 +  
151  
152 <    deprecatedKeywords_.insert("nComponents");
153 <    deprecatedKeywords_.insert("nZconstraints");
152 >  deprecatedKeywords_.insert("nComponents");
153 >  deprecatedKeywords_.insert("nZconstraints");
154 >  deprecatedKeywords_.insert("initialConfig");
155      
156   }
157  
# Line 137 | Line 165 | void Globals::validate() {
165  
166    CheckParameter(ForceField, isNotEmpty());
167    CheckParameter(TargetTemp, isPositive());
168 <  CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT"));
168 >  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"));
169    CheckParameter(Dt, isPositive());
170    CheckParameter(RunTime, isPositive());
143 –  CheckParameter(InitialConfig, isNotEmpty());
171    CheckParameter(FinalConfig, isNotEmpty());
172    CheckParameter(SampleTime, isNonNegative());
173    CheckParameter(ResetTime, isNonNegative());
# Line 149 | Line 176 | void Globals::validate() {
176    CheckParameter(SwitchingRadius, isNonNegative());
177    CheckParameter(Dielectric, isPositive());
178    CheckParameter(ThermalTime,  isNonNegative());
152 –  CheckParameter(TargetPressure,  isPositive());
179    CheckParameter(TauThermostat, isPositive());
180    CheckParameter(TauBarostat, isPositive());
181    CheckParameter(ZconsTime, isPositive());
# Line 172 | Line 198 | void Globals::validate() {
198    CheckParameter(ThermIntDistSpringConst, isPositive());
199    CheckParameter(ThermIntThetaSpringConst, isPositive());
200    CheckParameter(ThermIntOmegaSpringConst, isPositive());
175 –  CheckParameter(SurfaceTension, isNonNegative());
201    CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
202    CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
203    CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
# Line 185 | Line 210 | void Globals::validate() {
210    CheckParameter(DampingAlpha,isNonNegative());
211    CheckParameter(SkinThickness, isPositive());
212    CheckParameter(Viscosity, isNonNegative());
213 +  CheckParameter(ThermalConductivity, isNonNegative());
214 +  CheckParameter(ThermalLength, isNonNegative());
215    CheckParameter(BeadSize, isPositive());
216    CheckParameter(FrozenBufferRadius, isPositive());
217    CheckParameter(LangevinBufferRadius, isPositive());
218 +  CheckParameter(NeighborListNeighbors, isPositive());
219 +  CheckParameter(RNEMD_swapTime, isPositive());
220 +  CheckParameter(RNEMD_nBins, isPositive() && isEven());
221 +  CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
222 +  CheckParameter(Restraint_DisplacementSpringConstant, isNonNegative());
223 +  CheckParameter(Restraint_RollSpringConstant, isNonNegative());
224 +  CheckParameter(Restraint_PitchSpringConstant, isNonNegative());
225 +  CheckParameter(Restraint_YawSpringConstant, isNonNegative());
226 +  CheckParameter(Restraint_type, isEqualIgnoreCase("P") || isEqualIgnoreCase("O") || isEqualIgnoreCase("P+O") || isEqualIgnoreCase("RMSD_P") || isEqualIgnoreCase("RMSD_O") || isEqualIgnoreCase("RMSD_P+RMSD_O"));
227 +
228    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
229      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
230          std::ostringstream oss;

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