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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 1715 by gezelter, Tue May 22 21:55:31 2012 UTC vs.
Revision 1746 by gezelter, Wed Jun 6 02:18:54 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");
92    DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
93    DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
94    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
# Line 128 | Line 126 | Globals::Globals() {
126    DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
127    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
128  
131 –  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
132 –  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
133 –  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
134 –  DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
135 –  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
136 –  DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
137 –  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
138 –  DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false);
139 –  DefineOptionalParameterWithDefaultValue(RNEMD_outputDimensionalTemperature, "RNEMD_outputDimensionalTemperature", false);
129    DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
130    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
131    DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
132    DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
144 –  DefineOptionalParameterWithDefaultValue(FlucQPropagator, "flucQ.propagator", "NVT");
145 –  DefineOptionalParameterWithDefaultValue(FlucQFriction, "flucQ.friction", 1600.0);    
146 –  DefineOptionalParameterWithDefaultValue(FlucQTolerance, "flucQ.tolerance", 1.0e-6);    
147 –  DefineOptionalParameterWithDefaultValue(FlucQMaxIterations, "flucQ.maxIterations", 100);    
148 –  DefineOptionalParameterWithDefaultValue(FlucQTargetTemp, "flucQ.targetTemp", 1.0e-6);
149 –  DefineOptionalParameterWithDefaultValue(FlucQtauThermostat, "flucQ.tauThermostat", 10.0);
133  
134    deprecatedKeywords_.insert("nComponents");
135    deprecatedKeywords_.insert("nZconstraints");
# Line 156 | Line 139 | Globals::Globals() {
139    deprecatedKeywords_.insert("thermIntOmegaSpringConst");
140    deprecatedKeywords_.insert("useSolidThermInt");  
141    deprecatedKeywords_.insert("useLiquidThermInt");
142 +  deprecatedKeywords_.insert("minimizerMaxIter");
143 +  deprecatedKeywords_.insert("minimizerWriteFreq");
144 +  deprecatedKeywords_.insert("minimizerStepSize");
145 +  deprecatedKeywords_.insert("minimizerFTol");
146 +  deprecatedKeywords_.insert("minimizerGTol");
147 +  deprecatedKeywords_.insert("minimizerLSTol");
148 +  deprecatedKeywords_.insert("minimizerLSMaxIter");
149 +
150      
151   }
152  
# Line 186 | Line 177 | void Globals::validate() {
177    CheckParameter(ZconsTime, isPositive());
178    CheckParameter(ZconsTol, isPositive());
179    CheckParameter(Seed, isPositive());
189 –  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
190 –  CheckParameter(MinimizerMaxIter, isPositive());
191 –  CheckParameter(MinimizerWriteFreq, isPositive());
192 –  CheckParameter(MinimizerStepSize, isPositive());
193 –  CheckParameter(MinimizerFTol, isPositive());
194 –  CheckParameter(MinimizerGTol, isPositive());
195 –  CheckParameter(MinimizerLSTol, isPositive());
196 –  CheckParameter(MinimizerLSMaxIter, isPositive());
180    CheckParameter(ZconsGap, isPositive());
181    CheckParameter(ZconsFixtime, isPositive());
182    CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
# Line 213 | Line 196 | void Globals::validate() {
196    CheckParameter(FrozenBufferRadius, isPositive());
197    CheckParameter(LangevinBufferRadius, isPositive());
198    CheckParameter(NeighborListNeighbors, isPositive());
216 –  CheckParameter(RNEMD_exchangeTime, isPositive());
217 –  CheckParameter(RNEMD_nBins, isPositive() && isEven());
218 –  CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
199    CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
200    CheckParameter(Alpha, isPositive());
221 –  CheckParameter(FlucQPropagator, isEqualIgnoreCase("NVT") || isEqualIgnoreCase("Langevin") || isEqualIgnoreCase("Minimizer") || isEqualIgnoreCase("Exact") );
222 –  CheckParameter(FlucQFriction, isNonNegative());    
223 –  CheckParameter(FlucQTolerance, isPositive());    
224 –  CheckParameter(FlucQMaxIterations, isPositive());    
225 –  CheckParameter(FlucQTargetTemp,  isNonNegative());
226 –  CheckParameter(FlucQtauThermostat, isPositive());
201    
202    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
203      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
# Line 249 | Line 223 | bool Globals::addRestraintStamp(RestraintStamp* rest)
223      return true;
224   }
225  
226 + bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
227 +  if (flucQpars_ != NULL)
228 +    delete flucQpars_;
229 +    
230 +  flucQpars_ = fqp;
231 +  return true;
232 + }
233 +
234 + bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
235 +  if (rnemdPars_ != NULL)
236 +    delete rnemdPars_;
237 +    
238 +  rnemdPars_ = rnemdPars;
239 +  return true;
240 + }
241 +
242 + bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
243 +  if (minimizerPars_ != NULL)
244 +    delete minimizerPars_;
245 +    
246 +  minimizerPars_ = miniPars;
247 +  return true;
248 + }
249 +
250   bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
251      std::string molStampName = molStamp->getName();
252      std::map<std::string, MoleculeStamp*>::iterator i;

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