| 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"); |
| 136 |
|
|
| 137 |
|
DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false); |
| 138 |
|
DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0); |
| 139 |
< |
DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 15); |
| 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"); |
| 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()); |
| 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_)) { |
