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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 1729 by jmarr, Wed May 30 16:08:07 2012 UTC vs.
Revision 1744 by gezelter, Tue Jun 5 18:07:08 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 +
59    DefineParameter(ForceField, "forceField")
60  
61    DefineOptionalParameter(TargetTemp, "targetTemp");
# Line 129 | Line 133 | Globals::Globals() {
133    DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
134    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
135  
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 –  // James put this in.
148 –  DefineOptionalParameterWithDefaultValue(RNEMD_outputDen, "RNEMD_outputDen", false);
149 –  DefineOptionalParameterWithDefaultValue(RNEMD_outputAh, "RNEMD_outputAh", false);
150 –  DefineOptionalParameterWithDefaultValue(RNEMD_outputVz, "RNEMD_outputVz", false);  
151 –  DefineOptionalParameterWithDefaultValue(RNEMD_outputXyzTemperature, "RNEMD_outputXyzTemperature", false);
152 –  DefineOptionalParameterWithDefaultValue(RNEMD_outputRotTemperature, "RNEMD_outputRotTemperature", false);
153 –
136    DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
137    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
138    DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
139    DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
158 –  DefineOptionalParameterWithDefaultValue(FlucQPropagator, "flucQ.propagator", "NVT");
159 –  DefineOptionalParameterWithDefaultValue(FlucQFriction, "flucQ.friction", 1600.0);    
160 –  DefineOptionalParameterWithDefaultValue(FlucQTolerance, "flucQ.tolerance", 1.0e-6);    
161 –  DefineOptionalParameterWithDefaultValue(FlucQMaxIterations, "flucQ.maxIterations", 100);    
162 –  DefineOptionalParameterWithDefaultValue(FlucQTargetTemp, "flucQ.targetTemp", 1.0e-6);
163 –  DefineOptionalParameterWithDefaultValue(FlucQtauThermostat, "flucQ.tauThermostat", 10.0);
140  
141    deprecatedKeywords_.insert("nComponents");
142    deprecatedKeywords_.insert("nZconstraints");
# Line 227 | Line 203 | void Globals::validate() {
203    CheckParameter(FrozenBufferRadius, isPositive());
204    CheckParameter(LangevinBufferRadius, isPositive());
205    CheckParameter(NeighborListNeighbors, isPositive());
230 –  CheckParameter(RNEMD_exchangeTime, isPositive());
231 –  CheckParameter(RNEMD_nBins, isPositive() && isEven());
232 –  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"));
206    CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
207    CheckParameter(Alpha, isPositive());
235 –  CheckParameter(FlucQPropagator, isEqualIgnoreCase("NVT") || isEqualIgnoreCase("Langevin") || isEqualIgnoreCase("Minimizer") || isEqualIgnoreCase("Exact") );
236 –  CheckParameter(FlucQFriction, isNonNegative());    
237 –  CheckParameter(FlucQTolerance, isPositive());    
238 –  CheckParameter(FlucQMaxIterations, isPositive());    
239 –  CheckParameter(FlucQTargetTemp,  isNonNegative());
240 –  CheckParameter(FlucQtauThermostat, isPositive());
208    
209    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
210      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
# Line 263 | Line 230 | bool Globals::addRestraintStamp(RestraintStamp* rest)
230      return true;
231   }
232  
233 + bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
234 +  if (flucQpars_ != NULL)
235 +    delete flucQpars_;
236 +    
237 +  flucQpars_ = fqp;
238 +  return true;
239 + }
240 +
241 + bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
242 +  if (rnemdPars_ != NULL)
243 +    delete rnemdPars_;
244 +    
245 +  rnemdPars_ = rnemdPars;
246 +  return true;
247 + }
248 +
249   bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
250      std::string molStampName = molStamp->getName();
251      std::map<std::string, MoleculeStamp*>::iterator i;

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