| 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"); | 
| 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_)) { |