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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 1715 by gezelter, Tue May 22 21:55:31 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 92 | Line 93 | Globals::Globals() {
93    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
94    DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
95    DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
95 –  DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
96    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
97    DefineOptionalParameter(HydroPropFile, "HydroPropFile");
98    DefineOptionalParameter(Viscosity, "viscosity");
# Line 101 | Line 101 | Globals::Globals() {
101    DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
102    DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
103    DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
104 +  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
105    DefineOptionalParameter(MTM_Ce, "MTM_Ce");
106    DefineOptionalParameter(MTM_G, "MTM_G");
107    DefineOptionalParameter(MTM_Io, "MTM_Io");
# Line 114 | Line 115 | Globals::Globals() {
115    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
116    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
117    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
118 <  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
118 >  DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
119    DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
120 <  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
121 <  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
122 <  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
120 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
121 >  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false);
122 >  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false);
123 >  DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false);
124 >  DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false);
125 >  DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", false);
126    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
127    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
128    DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
# Line 131 | Line 135 | Globals::Globals() {
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);
140    DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
141    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
142    DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
143    DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
144 <
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);
150  
151    deprecatedKeywords_.insert("nComponents");
152    deprecatedKeywords_.insert("nZconstraints");
# Line 159 | Line 170 | void Globals::validate() {
170  
171    CheckParameter(ForceField, isNotEmpty());
172    CheckParameter(TargetTemp, isPositive());
173 <  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"));
173 >  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"));
174    CheckParameter(Dt, isPositive());
175    CheckParameter(RunTime, isPositive());
176    CheckParameter(FinalConfig, isNotEmpty());
# Line 189 | Line 200 | void Globals::validate() {
200    CheckParameter(ThermodynamicIntegrationK, isPositive());
201    CheckParameter(ForceFieldVariant, isNotEmpty());
202    CheckParameter(ForceFieldFileName, isNotEmpty());
203 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
193 <  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
203 >  CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
204    CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
205 +  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
206 +  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
207    CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
196 –  //CheckParameter(StatFileFormat,);    
208    CheckParameter(OrthoBoxTolerance, isPositive());  
209    CheckParameter(DampingAlpha,isNonNegative());
210    CheckParameter(SkinThickness, isPositive());
# Line 205 | Line 216 | void Globals::validate() {
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"));
208 –  CheckParameter(RNEMD_targetFlux, isNonNegative());
219    CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
220    CheckParameter(Alpha, isPositive());
221 <
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());
227    
228    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
229      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
# Line 218 | Line 233 | void Globals::validate() {
233      }
234    }
235   }
236 <  
236 >
237   bool Globals::addComponent(Component* comp) {
238      components_.push_back(comp);
239      return true;

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