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Comparing branches/development/src/io/Globals.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include <stdlib.h>
# Line 51 | 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 90 | Line 95 | Globals::Globals() {
95    DefineOptionalParameter(DampingAlpha, "dampingAlpha");
96    DefineOptionalParameter(SurfaceTension, "surfaceTension");
97    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
98 +  DefineOptionalParameter(PrintHeatFlux, "printHeatFlux");
99    DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
100    DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
95 –  DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
101    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
102    DefineOptionalParameter(HydroPropFile, "HydroPropFile");
103    DefineOptionalParameter(Viscosity, "viscosity");
# Line 101 | Line 106 | Globals::Globals() {
106    DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
107    DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
108    DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
109 +  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
110    DefineOptionalParameter(MTM_Ce, "MTM_Ce");
111    DefineOptionalParameter(MTM_G, "MTM_G");
112    DefineOptionalParameter(MTM_Io, "MTM_Io");
# Line 114 | Line 120 | Globals::Globals() {
120    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
121    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
122    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
123 <  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
123 >  DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
124    DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
125 <  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
126 <  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
127 <  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
125 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
126 >  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false);
127 >  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false);
128 >  DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false);
129 >  DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false);
130 >  DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", false);
131    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
132    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
133    DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
134    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
135  
127 –  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
128 –  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
129 –  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
130 –  DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
131 –  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
132 –  DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
133 –  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
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");
140  
139 –
141    deprecatedKeywords_.insert("nComponents");
142    deprecatedKeywords_.insert("nZconstraints");
143    deprecatedKeywords_.insert("initialConfig");
# Line 159 | Line 160 | void Globals::validate() {
160  
161    CheckParameter(ForceField, isNotEmpty());
162    CheckParameter(TargetTemp, isPositive());
163 <  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"));
163 >  CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || isEqualIgnoreCase("LANGEVINHULL") || isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD"));
164    CheckParameter(Dt, isPositive());
165    CheckParameter(RunTime, isPositive());
166    CheckParameter(FinalConfig, isNotEmpty());
# Line 189 | Line 190 | void Globals::validate() {
190    CheckParameter(ThermodynamicIntegrationK, isPositive());
191    CheckParameter(ForceFieldVariant, isNotEmpty());
192    CheckParameter(ForceFieldFileName, isNotEmpty());
193 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
193 <  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
193 >  CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
194    CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
195 +  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
196 +  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
197    CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
196 –  //CheckParameter(StatFileFormat,);    
198    CheckParameter(OrthoBoxTolerance, isPositive());  
199    CheckParameter(DampingAlpha,isNonNegative());
200    CheckParameter(SkinThickness, isPositive());
# Line 202 | Line 203 | void Globals::validate() {
203    CheckParameter(FrozenBufferRadius, isPositive());
204    CheckParameter(LangevinBufferRadius, isPositive());
205    CheckParameter(NeighborListNeighbors, isPositive());
205 –  CheckParameter(RNEMD_exchangeTime, isPositive());
206 –  CheckParameter(RNEMD_nBins, isPositive() && isEven());
207 –  CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
208 –  CheckParameter(RNEMD_targetFlux, isNonNegative());
206    CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
207    CheckParameter(Alpha, isPositive());
211 –
208    
209    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
210      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
# Line 218 | Line 214 | void Globals::validate() {
214      }
215    }
216   }
217 <  
217 >
218   bool Globals::addComponent(Component* comp) {
219      components_.push_back(comp);
220      return true;
# Line 234 | 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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