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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 1032 by gezelter, Fri Sep 1 19:16:02 2006 UTC vs.
Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC

# Line 57 | Line 57 | Globals::Globals() {
57    DefineOptionalParameter(Ensemble, "ensemble");
58    DefineOptionalParameter(Dt, "dt");
59    DefineOptionalParameter(RunTime, "runTime");
60 –  //DefineOptionalParameter(InitialConfig, "initialConfig");
60    DefineOptionalParameter(FinalConfig, "finalConfig");
61    DefineOptionalParameter(SampleTime, "sampleTime");
62    DefineOptionalParameter(ResetTime, "resetTime");
63    DefineOptionalParameter(StatusTime, "statusTime");
64    DefineOptionalParameter(CutoffRadius, "cutoffRadius");
65    DefineOptionalParameter(SwitchingRadius, "switchingRadius");
67 –  DefineOptionalParameter(Dielectric, "dielectric");
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 89 | Line 87 | Globals::Globals() {
87    DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
88    DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89    DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90 <  DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
93 <  DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
94 <  DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
90 >  DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91    DefineOptionalParameter(SurfaceTension, "surfaceTension");
92    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
93 <  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
94 <  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
93 >  DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
94 >  DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
95    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
96    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
97    DefineOptionalParameter(HydroPropFile, "HydroPropFile");
# Line 103 | 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);  
119 <  DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
120 <  DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
121 <  DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
114 <  DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
115 <  DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
116 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
119 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
120 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
121 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
122    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
123    DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
124    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
# Line 121 | Line 126 | Globals::Globals() {
126    DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
127    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
128  
129 +  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
130 +  DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
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);
135 +  DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
136 +  DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
137  
138 <    deprecatedKeywords_.insert("nComponents");
139 <    deprecatedKeywords_.insert("nZconstraints");
140 <    deprecatedKeywords_.insert("initialConfig");
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 138 | Line 158 | void Globals::validate() {
158  
159    CheckParameter(ForceField, isNotEmpty());
160    CheckParameter(TargetTemp, isPositive());
161 <  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"));
161 >  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"));
162    CheckParameter(Dt, isPositive());
163    CheckParameter(RunTime, isPositive());
144 –  //CheckParameter(InitialConfig, isNotEmpty());
164    CheckParameter(FinalConfig, isNotEmpty());
165    CheckParameter(SampleTime, isNonNegative());
166    CheckParameter(ResetTime, isNonNegative());
# Line 150 | Line 169 | void Globals::validate() {
169    CheckParameter(SwitchingRadius, isNonNegative());
170    CheckParameter(Dielectric, isPositive());
171    CheckParameter(ThermalTime,  isNonNegative());
153 –  //  CheckParameter(TargetPressure,  isPositive());
172    CheckParameter(TauThermostat, isPositive());
173    CheckParameter(TauBarostat, isPositive());
174    CheckParameter(ZconsTime, isPositive());
# Line 170 | Line 188 | void Globals::validate() {
188    CheckParameter(ThermodynamicIntegrationK, isPositive());
189    CheckParameter(ForceFieldVariant, isNotEmpty());
190    CheckParameter(ForceFieldFileName, isNotEmpty());
173 –  CheckParameter(ThermIntDistSpringConst, isPositive());
174 –  CheckParameter(ThermIntThetaSpringConst, isPositive());
175 –  CheckParameter(ThermIntOmegaSpringConst, isPositive());
176 –  //  CheckParameter(SurfaceTension, isNonNegative());
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());  
183 –  CheckParameter(ThermIntDistSpringConst, isPositive());
184 –  CheckParameter(ThermIntThetaSpringConst, isPositive());
185 –  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());
205 +  CheckParameter(NeighborListNeighbors, isPositive());
206 +  CheckParameter(RNEMD_swapTime, isPositive());
207 +  CheckParameter(RNEMD_nBins, isPositive() && isEven());
208 +  CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
209 +
210    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
211      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
212          std::ostringstream oss;
# Line 208 | 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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