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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 1147 by chuckv, Wed Jul 4 04:47:53 2007 UTC vs.
Revision 1367 by skuang, Mon Oct 19 13:35:42 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");
94 +  DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
95    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
96    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
97    DefineOptionalParameter(HydroPropFile, "HydroPropFile");
# Line 100 | 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");
107 +  DefineOptionalParameter(MTM_G, "MTM_G");
108 +  DefineOptionalParameter(MTM_Io, "MTM_Io");
109 +  DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
110 +  DefineOptionalParameter(MTM_R, "MTM_R");
111    
112 +
113    
114    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
115    DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
116    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
117    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
118    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
111 –  DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
112 –  DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
113 –  DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
114 –  DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
115 –  DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
119    DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
120    DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
121    DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
# Line 123 | Line 126 | Globals::Globals() {
126    DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
127    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
128  
129 +  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
130 +  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
131 +  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
132 +  DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
133 +  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
134 +  DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
135 +  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
136 +  DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
137 +  DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
138 +  DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
139 +
140 +
141    deprecatedKeywords_.insert("nComponents");
142    deprecatedKeywords_.insert("nZconstraints");
143    deprecatedKeywords_.insert("initialConfig");
144 +  deprecatedKeywords_.insert("thermIntDistSpringConst");
145 +  deprecatedKeywords_.insert("thermIntThetaSpringConst");
146 +  deprecatedKeywords_.insert("thermIntOmegaSpringConst");
147 +  deprecatedKeywords_.insert("useSolidThermInt");  
148 +  deprecatedKeywords_.insert("useLiquidThermInt");
149      
150   }
151  
152   Globals::~Globals() {
153      MemoryUtils::deletePointers(components_);
154      MemoryUtils::deletePointers(zconstraints_);
155 +    MemoryUtils::deletePointers(restraints_);
156   }
157  
158   void Globals::validate() {
# Line 139 | Line 160 | void Globals::validate() {
160  
161    CheckParameter(ForceField, isNotEmpty());
162    CheckParameter(TargetTemp, isPositive());
163 <  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"));
163 >  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"));
164    CheckParameter(Dt, isPositive());
165    CheckParameter(RunTime, isPositive());
166    CheckParameter(FinalConfig, isNotEmpty());
# Line 169 | Line 190 | void Globals::validate() {
190    CheckParameter(ThermodynamicIntegrationK, isPositive());
191    CheckParameter(ForceFieldVariant, isNotEmpty());
192    CheckParameter(ForceFieldFileName, isNotEmpty());
172 –  CheckParameter(ThermIntDistSpringConst, isPositive());
173 –  CheckParameter(ThermIntThetaSpringConst, isPositive());
174 –  CheckParameter(ThermIntOmegaSpringConst, isPositive());
193    CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
194    CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
195    CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
196    CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
197    //CheckParameter(StatFileFormat,);    
198    CheckParameter(OrthoBoxTolerance, isPositive());  
181 –  CheckParameter(ThermIntDistSpringConst, isPositive());
182 –  CheckParameter(ThermIntThetaSpringConst, isPositive());
183 –  CheckParameter(ThermIntOmegaSpringConst, isPositive());
199    CheckParameter(DampingAlpha,isNonNegative());
200    CheckParameter(SkinThickness, isPositive());
201    CheckParameter(Viscosity, isNonNegative());
202 +  CheckParameter(ThermalConductivity, isNonNegative());
203 +  CheckParameter(ThermalLength, isNonNegative());
204    CheckParameter(BeadSize, isPositive());
205    CheckParameter(FrozenBufferRadius, isPositive());
206    CheckParameter(LangevinBufferRadius, isPositive());
207    CheckParameter(NeighborListNeighbors, isPositive());
208 +  CheckParameter(RNEMD_exchangeTime, isPositive());
209 +  CheckParameter(RNEMD_nBins, isPositive() && isEven());
210 +  CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
211 +  CheckParameter(RNEMD_targetFlux, isNonNegative());
212  
213    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
214      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
# Line 197 | Line 218 | void Globals::validate() {
218      }
219    }
220   }
221 <    
221 >  
222   bool Globals::addComponent(Component* comp) {
223      components_.push_back(comp);
224      return true;
# Line 208 | Line 229 | bool Globals::addZConsStamp(ZConsStamp* zcons) {
229      return true;
230   }
231  
232 + bool Globals::addRestraintStamp(RestraintStamp* rest) {
233 +    restraints_.push_back(rest);
234 +    return true;
235 + }
236 +
237   bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
238      std::string molStampName = molStamp->getName();
239      std::map<std::string, MoleculeStamp*>::iterator i;

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