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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 1078 by gezelter, Wed Oct 18 21:58:48 2006 UTC vs.
Revision 1354 by gezelter, Mon Jun 15 20:12:09 2009 UTC

# Line 65 | Line 65 | Globals::Globals() {
65    DefineOptionalParameter(SwitchingRadius, "switchingRadius");
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 93 | Line 93 | Globals::Globals() {
93    DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
94    DefineOptionalParameter(SurfaceTension, "surfaceTension");
95    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
96 +  DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
97 +  DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
98    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
99    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
100    DefineOptionalParameter(HydroPropFile, "HydroPropFile");
# Line 100 | Line 102 | Globals::Globals() {
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 120 | Line 132 | Globals::Globals() {
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", 16);
138 +  DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
139 +  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
140 +  DefineOptionalParameterWithDefaultValue(UseRestraints, "UseRestraints", false);
141 +  DefineOptionalParameterWithDefaultValue(Restraint_objectSelection, "Restraint_objectSelection", "select all");
142 +  DefineOptionalParameterWithDefaultValue(Restraint_type, "Restraint_type", "positional");
143 +  DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
144 +  DefineOptionalParameterWithDefaultValue(Restraint_DisplacementSpringConstant, "Restraint_DisplacementSpringConstant", 0.0);
145 +  DefineOptionalParameterWithDefaultValue(Restraint_RollSpringConstant, "Restraint_RollSpringConstant", 0.0);   // phi
146 +  DefineOptionalParameterWithDefaultValue(Restraint_PitchSpringConstant, "Restraint_PitchSpringConstant", 0.0); // theta
147 +  DefineOptionalParameterWithDefaultValue(Restraint_YawSpringConstant, "Restraint_YawSpringConstant", 0.0);     // psi
148 +  
149 +
150    deprecatedKeywords_.insert("nComponents");
151    deprecatedKeywords_.insert("nZconstraints");
152    deprecatedKeywords_.insert("initialConfig");
# Line 136 | Line 163 | void Globals::validate() {
163  
164    CheckParameter(ForceField, isNotEmpty());
165    CheckParameter(TargetTemp, isPositive());
166 <  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"));
166 >  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"));
167    CheckParameter(Dt, isPositive());
168    CheckParameter(RunTime, isPositive());
169    CheckParameter(FinalConfig, isNotEmpty());
# Line 184 | Line 211 | void Globals::validate() {
211    CheckParameter(BeadSize, isPositive());
212    CheckParameter(FrozenBufferRadius, isPositive());
213    CheckParameter(LangevinBufferRadius, isPositive());
214 +  CheckParameter(NeighborListNeighbors, isPositive());
215 +  CheckParameter(RNEMD_swapTime, isPositive());
216 +  CheckParameter(RNEMD_nBins, isPositive() && isEven());
217 +  CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
218 +  CheckParameter(Restraint_DisplacementSpringConstant, isNonNegative());
219 +  CheckParameter(Restraint_RollSpringConstant, isNonNegative());
220 +  CheckParameter(Restraint_PitchSpringConstant, isNonNegative());
221 +  CheckParameter(Restraint_YawSpringConstant, isNonNegative());
222 +  CheckParameter(Restraint_type, isEqualIgnoreCase("P") || isEqualIgnoreCase("O") || isEqualIgnoreCase("P+O") || isEqualIgnoreCase("RMSD_P") || isEqualIgnoreCase("RMSD_O") || isEqualIgnoreCase("RMSD_P+RMSD_O"));
223 +
224    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
225      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
226          std::ostringstream oss;

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