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root/OpenMD/branches/development/src/io/Globals.cpp
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Comparing branches/development/src/io/Globals.cpp (file contents):
Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC vs.
Revision 1780 by jmarr, Mon Aug 20 18:28:22 2012 UTC

# Line 52 | Line 52 | Globals::Globals() {
52  
53   namespace OpenMD {
54   Globals::Globals() {
55 +  
56 +  flucQpars_ = new FluctuatingChargeParameters();
57 +  rnemdPars_ = new RNEMDParameters();
58 +  minimizerPars_ = new MinimizerParameters();
59 +
60    DefineParameter(ForceField, "forceField")
61  
62    DefineOptionalParameter(TargetTemp, "targetTemp");
# Line 73 | Line 78 | Globals::Globals() {
78    DefineOptionalParameter(ZconsTol, "zconsTol");
79    DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
80    DefineOptionalParameter(Seed, "seed");
76 –  DefineOptionalParameter(Minimizer, "minimizer");
77 –  DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
78 –  DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq");
79 –  DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
80 –  DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
81 –  DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
82 –  DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
83 –  DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
81    DefineOptionalParameter(ZconsGap, "zconsGap");
82    DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
83    DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
# Line 91 | Line 88 | Globals::Globals() {
88    DefineOptionalParameter(DampingAlpha, "dampingAlpha");
89    DefineOptionalParameter(SurfaceTension, "surfaceTension");
90    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
91 <  DefineOptionalParameter(PrintHeatFlux, "printHeatFlux");
91 >  DefineOptionalParameter(ElectricField, "electricField");
92 >
93    DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
94    DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
95    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
# Line 120 | Line 118 | Globals::Globals() {
118    DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
119    DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
120    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false);
121 +  DefineOptionalParameterWithDefaultValue(PrintHeatFlux, "printHeatFlux", false);
122    DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false);
123    DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false);
124    DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false);
# Line 129 | Line 128 | Globals::Globals() {
128    DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
129    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
130  
132 –  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
133 –  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
134 –  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
135 –  DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
136 –  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
137 –  DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
138 –  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzKE, "RNEMD_targetJzKE", 0.0);
139 –  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpx, "RNEMD_targetJzpx", 0.0);
140 –  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpy, "RNEMD_targetJzpy", 0.0);
141 –  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpz, "RNEMD_targetJzpz", 0.0);
142 –  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
143 –  DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false);
144 –  DefineOptionalParameterWithDefaultValue(RNEMD_outputTemperature, "RNEMD_outputTemperature", false);
145 –  DefineOptionalParameterWithDefaultValue(RNEMD_outputVx, "RNEMD_outputVx", false);
146 –  DefineOptionalParameterWithDefaultValue(RNEMD_outputVy, "RNEMD_outputVy", false);
147 –  DefineOptionalParameterWithDefaultValue(RNEMD_outputXyzTemperature, "RNEMD_outputXyzTemperature", false);
148 –  DefineOptionalParameterWithDefaultValue(RNEMD_outputRotTemperature, "RNEMD_outputRotTemperature", false);
149 –
131    DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
132    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
133    DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
134    DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
154 –  DefineOptionalParameterWithDefaultValue(FlucQPropagator, "flucQ.propagator", "NVT");
155 –  DefineOptionalParameterWithDefaultValue(FlucQFriction, "flucQ.friction", 1600.0);    
156 –  DefineOptionalParameterWithDefaultValue(FlucQTolerance, "flucQ.tolerance", 1.0e-6);    
157 –  DefineOptionalParameterWithDefaultValue(FlucQMaxIterations, "flucQ.maxIterations", 100);    
158 –  DefineOptionalParameterWithDefaultValue(FlucQTargetTemp, "flucQ.targetTemp", 1.0e-6);
159 –  DefineOptionalParameterWithDefaultValue(FlucQtauThermostat, "flucQ.tauThermostat", 10.0);
135  
136    deprecatedKeywords_.insert("nComponents");
137    deprecatedKeywords_.insert("nZconstraints");
# Line 166 | Line 141 | Globals::Globals() {
141    deprecatedKeywords_.insert("thermIntOmegaSpringConst");
142    deprecatedKeywords_.insert("useSolidThermInt");  
143    deprecatedKeywords_.insert("useLiquidThermInt");
144 +  deprecatedKeywords_.insert("minimizerMaxIter");
145 +  deprecatedKeywords_.insert("minimizerWriteFreq");
146 +  deprecatedKeywords_.insert("minimizerStepSize");
147 +  deprecatedKeywords_.insert("minimizerFTol");
148 +  deprecatedKeywords_.insert("minimizerGTol");
149 +  deprecatedKeywords_.insert("minimizerLSTol");
150 +  deprecatedKeywords_.insert("minimizerLSMaxIter");
151 +
152      
153   }
154  
# Line 196 | Line 179 | void Globals::validate() {
179    CheckParameter(ZconsTime, isPositive());
180    CheckParameter(ZconsTol, isPositive());
181    CheckParameter(Seed, isPositive());
199 –  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
200 –  CheckParameter(MinimizerMaxIter, isPositive());
201 –  CheckParameter(MinimizerWriteFreq, isPositive());
202 –  CheckParameter(MinimizerStepSize, isPositive());
203 –  CheckParameter(MinimizerFTol, isPositive());
204 –  CheckParameter(MinimizerGTol, isPositive());
205 –  CheckParameter(MinimizerLSTol, isPositive());
206 –  CheckParameter(MinimizerLSMaxIter, isPositive());
182    CheckParameter(ZconsGap, isPositive());
183    CheckParameter(ZconsFixtime, isPositive());
184    CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
# Line 223 | Line 198 | void Globals::validate() {
198    CheckParameter(FrozenBufferRadius, isPositive());
199    CheckParameter(LangevinBufferRadius, isPositive());
200    CheckParameter(NeighborListNeighbors, isPositive());
226 –  CheckParameter(RNEMD_exchangeTime, isPositive());
227 –  CheckParameter(RNEMD_nBins, isPositive() && isEven());
228 –  CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("KineticScaleVAM") || isEqualIgnoreCase("KineticScaleAM") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale") || isEqualIgnoreCase("ShiftScaleV") || isEqualIgnoreCase("ShiftScaleVAM"));
201    CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
202    CheckParameter(Alpha, isPositive());
231 –  CheckParameter(FlucQPropagator, isEqualIgnoreCase("NVT") || isEqualIgnoreCase("Langevin") || isEqualIgnoreCase("Minimizer") || isEqualIgnoreCase("Exact") );
232 –  CheckParameter(FlucQFriction, isNonNegative());    
233 –  CheckParameter(FlucQTolerance, isPositive());    
234 –  CheckParameter(FlucQMaxIterations, isPositive());    
235 –  CheckParameter(FlucQTargetTemp,  isNonNegative());
236 –  CheckParameter(FlucQtauThermostat, isPositive());
203    
204    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
205      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
# Line 259 | Line 225 | bool Globals::addRestraintStamp(RestraintStamp* rest)
225      return true;
226   }
227  
228 + bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
229 +  if (flucQpars_ != NULL)
230 +    delete flucQpars_;
231 +    
232 +  flucQpars_ = fqp;
233 +  return true;
234 + }
235 +
236 + bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
237 +  if (rnemdPars_ != NULL)
238 +    delete rnemdPars_;
239 +    
240 +  rnemdPars_ = rnemdPars;
241 +  return true;
242 + }
243 +
244 + bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
245 +  if (minimizerPars_ != NULL)
246 +    delete minimizerPars_;
247 +    
248 +  minimizerPars_ = miniPars;
249 +  return true;
250 + }
251 +
252   bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
253      std::string molStampName = molStamp->getName();
254      std::map<std::string, MoleculeStamp*>::iterator i;

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