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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 1354 by gezelter, Mon Jun 15 20:12:09 2009 UTC vs.
Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC

# Line 88 | Line 88 | Globals::Globals() {
88    DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89    DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90    DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91 –  DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
92 –  DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
93 –  DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
91    DefineOptionalParameter(SurfaceTension, "surfaceTension");
92    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
93    DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
# Line 102 | Line 99 | Globals::Globals() {
99    DefineOptionalParameter(BeadSize, "beadSize");
100    DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
101    DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
102 +  DefineOptionalParameter(ThermalConductivity, "thermalConductivity");
103 +  DefineOptionalParameter(ThermalLength, "thermalLength");
104    DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
105    DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
106    DefineOptionalParameter(MTM_Ce, "MTM_Ce");
# Line 117 | Line 116 | Globals::Globals() {
116    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
117    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
118    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
120 –  DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
121 –  DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
122 –  DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
123 –  DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
124 –  DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
119    DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
120    DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
121    DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
# Line 137 | Line 131 | Globals::Globals() {
131    DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
132    DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
133    DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
134 <  DefineOptionalParameterWithDefaultValue(UseRestraints, "UseRestraints", false);
141 <  DefineOptionalParameterWithDefaultValue(Restraint_objectSelection, "Restraint_objectSelection", "select all");
142 <  DefineOptionalParameterWithDefaultValue(Restraint_type, "Restraint_type", "positional");
134 >  DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
135    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
136 <  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 <  
136 >  DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
137  
138 +
139    deprecatedKeywords_.insert("nComponents");
140    deprecatedKeywords_.insert("nZconstraints");
141    deprecatedKeywords_.insert("initialConfig");
142 +  deprecatedKeywords_.insert("thermIntDistSpringConst");
143 +  deprecatedKeywords_.insert("thermIntThetaSpringConst");
144 +  deprecatedKeywords_.insert("thermIntOmegaSpringConst");
145 +  deprecatedKeywords_.insert("useSolidThermInt");  
146 +  deprecatedKeywords_.insert("useLiquidThermInt");
147      
148   }
149  
150   Globals::~Globals() {
151      MemoryUtils::deletePointers(components_);
152      MemoryUtils::deletePointers(zconstraints_);
153 +    MemoryUtils::deletePointers(restraints_);
154   }
155  
156   void Globals::validate() {
# Line 193 | Line 188 | void Globals::validate() {
188    CheckParameter(ThermodynamicIntegrationK, isPositive());
189    CheckParameter(ForceFieldVariant, isNotEmpty());
190    CheckParameter(ForceFieldFileName, isNotEmpty());
196 –  CheckParameter(ThermIntDistSpringConst, isPositive());
197 –  CheckParameter(ThermIntThetaSpringConst, isPositive());
198 –  CheckParameter(ThermIntOmegaSpringConst, isPositive());
191    CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
192    CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
193    CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
194    CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
195    //CheckParameter(StatFileFormat,);    
196    CheckParameter(OrthoBoxTolerance, isPositive());  
205 –  CheckParameter(ThermIntDistSpringConst, isPositive());
206 –  CheckParameter(ThermIntThetaSpringConst, isPositive());
207 –  CheckParameter(ThermIntOmegaSpringConst, isPositive());
197    CheckParameter(DampingAlpha,isNonNegative());
198    CheckParameter(SkinThickness, isPositive());
199    CheckParameter(Viscosity, isNonNegative());
200 +  CheckParameter(ThermalConductivity, isNonNegative());
201 +  CheckParameter(ThermalLength, isNonNegative());
202    CheckParameter(BeadSize, isPositive());
203    CheckParameter(FrozenBufferRadius, isPositive());
204    CheckParameter(LangevinBufferRadius, isPositive());
# Line 215 | Line 206 | void Globals::validate() {
206    CheckParameter(RNEMD_swapTime, isPositive());
207    CheckParameter(RNEMD_nBins, isPositive() && isEven());
208    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"));
209  
210    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
211      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
# Line 240 | Line 226 | bool Globals::addZConsStamp(ZConsStamp* zcons) {
226      return true;
227   }
228  
229 + bool Globals::addRestraintStamp(RestraintStamp* rest) {
230 +    restraints_.push_back(rest);
231 +    return true;
232 + }
233 +
234   bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
235      std::string molStampName = molStamp->getName();
236      std::map<std::string, MoleculeStamp*>::iterator i;

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