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root/OpenMD/trunk/src/io/Globals.cpp
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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 789 by tim, Mon Dec 5 23:37:56 2005 UTC vs.
Revision 1293 by chuckv, Sun Sep 14 01:32:26 2008 UTC

# Line 45 | Line 45
45   #include <string>
46  
47   #include "io/Globals.hpp"
48 + #include "io/ParamConstraint.hpp"
49 + #include "utils/MemoryUtils.hpp"
50   #include "utils/simError.h"
51  
50 – #include "io/ParamConstraint.hpp"
51 –
52   namespace oopse {
53   Globals::Globals() {
54    DefineParameter(ForceField, "forceField")
# 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(DampingAlpha, "dampingAlpha");
91    DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
92    DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
93    DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
94    DefineOptionalParameter(SurfaceTension, "surfaceTension");
95    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
96 <  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
97 <  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
96 >  DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
97 >  DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
98    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
99    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
100 <  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
100 >  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
101 >  DefineOptionalParameter(Viscosity, "viscosity");
102 >  DefineOptionalParameter(BeadSize, "beadSize");
103 >  DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
104 >  DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
105 >  DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
106 >  
107 >  
108    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
109 +  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
110    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
111    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
112    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
# Line 108 | Line 115 | Globals::Globals() {
115    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
116    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
117    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
118 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
118 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
119 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
120 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
121    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
122    DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
123    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
124    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
125 +  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
126 +  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
127  
128 <
129 <    deprecatedKeywords_.insert("nComponents");
130 <    deprecatedKeywords_.insert("nZconstraints");
128 >  deprecatedKeywords_.insert("nComponents");
129 >  deprecatedKeywords_.insert("nZconstraints");
130 >  deprecatedKeywords_.insert("initialConfig");
131      
132   }
133  
134   Globals::~Globals() {
135 <
136 <
135 >    MemoryUtils::deletePointers(components_);
136 >    MemoryUtils::deletePointers(zconstraints_);
137   }
138  
139   void Globals::validate() {
# Line 130 | Line 141 | void Globals::validate() {
141  
142    CheckParameter(ForceField, isNotEmpty());
143    CheckParameter(TargetTemp, isPositive());
144 <  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) || isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf")) || isEqualIgnoreCase(std::string("NPTxyz")) );
144 >  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"));
145    CheckParameter(Dt, isPositive());
146    CheckParameter(RunTime, isPositive());
136 –  CheckParameter(InitialConfig, isNotEmpty());
147    CheckParameter(FinalConfig, isNotEmpty());
148    CheckParameter(SampleTime, isNonNegative());
149    CheckParameter(ResetTime, isNonNegative());
# Line 142 | Line 152 | void Globals::validate() {
152    CheckParameter(SwitchingRadius, isNonNegative());
153    CheckParameter(Dielectric, isPositive());
154    CheckParameter(ThermalTime,  isNonNegative());
145 –  CheckParameter(TargetPressure,  isPositive());
155    CheckParameter(TauThermostat, isPositive());
156    CheckParameter(TauBarostat, isPositive());
157    CheckParameter(ZconsTime, isPositive());
158    CheckParameter(ZconsTol, isPositive());
159    CheckParameter(Seed, isPositive());
160 <  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
160 >  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
161    CheckParameter(MinimizerMaxIter, isPositive());
162    CheckParameter(MinimizerWriteFrq, isPositive());
163    CheckParameter(MinimizerStepSize, isPositive());
# Line 158 | Line 167 | void Globals::validate() {
167    CheckParameter(MinimizerLSMaxIter, isPositive());
168    CheckParameter(ZconsGap, isPositive());
169    CheckParameter(ZconsFixtime, isPositive());
170 <  CheckParameter(ThermodynamicIntegrationLambda, isPositive());
170 >  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
171    CheckParameter(ThermodynamicIntegrationK, isPositive());
172    CheckParameter(ForceFieldVariant, isNotEmpty());
173    CheckParameter(ForceFieldFileName, isNotEmpty());
174    CheckParameter(ThermIntDistSpringConst, isPositive());
175    CheckParameter(ThermIntThetaSpringConst, isPositive());
176    CheckParameter(ThermIntOmegaSpringConst, isPositive());
177 <  CheckParameter(SurfaceTension, isPositive());
178 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE")) || isEqualIgnoreCase(std::string("REACTION_FIELD")));
179 <  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED")));
180 <  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
172 <  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase(std::string("CUBIC")) || isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
177 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
178 >  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
179 >  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
180 >  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
181    //CheckParameter(StatFileFormat,);    
174 –  //CheckParameter(MixingRule,);
182    CheckParameter(OrthoBoxTolerance, isPositive());  
183    CheckParameter(ThermIntDistSpringConst, isPositive());
184    CheckParameter(ThermIntThetaSpringConst, isPositive());
185    CheckParameter(ThermIntOmegaSpringConst, isPositive());
186    CheckParameter(DampingAlpha,isNonNegative());
187    CheckParameter(SkinThickness, isPositive());
188 +  CheckParameter(Viscosity, isNonNegative());
189 +  CheckParameter(BeadSize, isPositive());
190 +  CheckParameter(FrozenBufferRadius, isPositive());
191 +  CheckParameter(LangevinBufferRadius, isPositive());
192 +  CheckParameter(NeighborListNeighbors, isPositive());
193  
194    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
195      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
196 <        std::cout << "Globals Error: can not find molecule stamp for component" << std::endl;
196 >        std::ostringstream oss;
197 >        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
198 >        throw OOPSEException(oss.str());          
199      }
200    }
201   }
# Line 205 | Line 219 | bool Globals::addMoleculeStamp(MoleculeStamp* molStamp
219          moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
220          ret = true;
221      } else {
222 <        std::cout << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
222 >        std::ostringstream oss;
223 >        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
224 >        throw OOPSEException(oss.str());  
225      }
226      return ret;
227   }

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