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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 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1078 by gezelter, Wed Oct 18 21:58:48 2006 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");
# 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");
97 –  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
98 –  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
96    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
97    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
98 <  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
98 >  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
99 >  DefineOptionalParameter(Viscosity, "viscosity");
100 >  DefineOptionalParameter(BeadSize, "beadSize");
101 >  DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
102 >  DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
103 >  
104    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
105    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
106    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
# Line 108 | Line 110 | Globals::Globals() {
110    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
111    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
112    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
113 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
113 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
114 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
115 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
116    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
117    DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
118    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
119    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
120 +  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
121 +  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
122  
123 <
124 <    deprecatedKeywords_.insert("nComponents");
125 <    deprecatedKeywords_.insert("nZconstraints");
123 >  deprecatedKeywords_.insert("nComponents");
124 >  deprecatedKeywords_.insert("nZconstraints");
125 >  deprecatedKeywords_.insert("initialConfig");
126      
127   }
128  
129   Globals::~Globals() {
130 <
131 <
130 >    MemoryUtils::deletePointers(components_);
131 >    MemoryUtils::deletePointers(zconstraints_);
132   }
133  
134   void Globals::validate() {
# Line 130 | Line 136 | void Globals::validate() {
136  
137    CheckParameter(ForceField, isNotEmpty());
138    CheckParameter(TargetTemp, isPositive());
139 <  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) || isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf")) || isEqualIgnoreCase(std::string("NPTxyz")) );
139 >  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"));
140    CheckParameter(Dt, isPositive());
141    CheckParameter(RunTime, isPositive());
136 –  CheckParameter(InitialConfig, isNotEmpty());
142    CheckParameter(FinalConfig, isNotEmpty());
143    CheckParameter(SampleTime, isNonNegative());
144    CheckParameter(ResetTime, isNonNegative());
# Line 142 | Line 147 | void Globals::validate() {
147    CheckParameter(SwitchingRadius, isNonNegative());
148    CheckParameter(Dielectric, isPositive());
149    CheckParameter(ThermalTime,  isNonNegative());
145 –  CheckParameter(TargetPressure,  isPositive());
150    CheckParameter(TauThermostat, isPositive());
151    CheckParameter(TauBarostat, isPositive());
152    CheckParameter(ZconsTime, isPositive());
153    CheckParameter(ZconsTol, isPositive());
154    CheckParameter(Seed, isPositive());
155 <  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
155 >  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
156    CheckParameter(MinimizerMaxIter, isPositive());
157    CheckParameter(MinimizerWriteFrq, isPositive());
158    CheckParameter(MinimizerStepSize, isPositive());
# Line 158 | Line 162 | void Globals::validate() {
162    CheckParameter(MinimizerLSMaxIter, isPositive());
163    CheckParameter(ZconsGap, isPositive());
164    CheckParameter(ZconsFixtime, isPositive());
165 <  CheckParameter(ThermodynamicIntegrationLambda, isPositive());
165 >  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
166    CheckParameter(ThermodynamicIntegrationK, isPositive());
167    CheckParameter(ForceFieldVariant, isNotEmpty());
168    CheckParameter(ForceFieldFileName, isNotEmpty());
169    CheckParameter(ThermIntDistSpringConst, isPositive());
170    CheckParameter(ThermIntThetaSpringConst, isPositive());
171    CheckParameter(ThermIntOmegaSpringConst, isPositive());
172 <  CheckParameter(SurfaceTension, isPositive());
173 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE")) || isEqualIgnoreCase(std::string("REACTION_FIELD")));
174 <  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED")));
175 <  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")));
172 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
173 >  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
174 >  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
175 >  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
176    //CheckParameter(StatFileFormat,);    
174 –  //CheckParameter(MixingRule,);
177    CheckParameter(OrthoBoxTolerance, isPositive());  
178    CheckParameter(ThermIntDistSpringConst, isPositive());
179    CheckParameter(ThermIntThetaSpringConst, isPositive());
180    CheckParameter(ThermIntOmegaSpringConst, isPositive());
181    CheckParameter(DampingAlpha,isNonNegative());
182    CheckParameter(SkinThickness, isPositive());
183 <
183 >  CheckParameter(Viscosity, isNonNegative());
184 >  CheckParameter(BeadSize, isPositive());
185 >  CheckParameter(FrozenBufferRadius, isPositive());
186 >  CheckParameter(LangevinBufferRadius, isPositive());
187    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
188      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
189 <        std::cout << "Globals Error: can not find molecule stamp for component" << std::endl;
189 >        std::ostringstream oss;
190 >        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
191 >        throw OOPSEException(oss.str());          
192      }
193    }
194   }
# Line 205 | Line 212 | bool Globals::addMoleculeStamp(MoleculeStamp* molStamp
212          moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
213          ret = true;
214      } else {
215 <
215 >        std::ostringstream oss;
216 >        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
217 >        throw OOPSEException(oss.str());  
218      }
219      return ret;
220   }

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