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Comparing branches/development/src/io/Globals.cpp (file contents):
Revision 1616 by gezelter, Tue Aug 30 15:45:35 2011 UTC vs.
Revision 1711 by gezelter, Sat May 19 02:58:35 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 117 | Line 118 | Globals::Globals() {
118    DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
119    DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
120    DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
121 <  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
122 <  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
121 >  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false);
122 >  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false);
123 >  DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false);
124    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
125    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
126    DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
# Line 131 | Line 133 | Globals::Globals() {
133    DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
134    DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
135    DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
136 +  DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false);
137 +  DefineOptionalParameterWithDefaultValue(RNEMD_outputDimensionalTemperature, "RNEMD_outputDimensionalTemperature", false);
138    DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
139    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
140    DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
# Line 160 | Line 164 | void Globals::validate() {
164  
165    CheckParameter(ForceField, isNotEmpty());
166    CheckParameter(TargetTemp, isPositive());
167 <  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"));
167 >  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"));
168    CheckParameter(Dt, isPositive());
169    CheckParameter(RunTime, isPositive());
170    CheckParameter(FinalConfig, isNotEmpty());
# Line 206 | Line 210 | void Globals::validate() {
210    CheckParameter(RNEMD_exchangeTime, isPositive());
211    CheckParameter(RNEMD_nBins, isPositive() && isEven());
212    CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
209 –  CheckParameter(RNEMD_targetFlux, isNonNegative());
213    CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
214    CheckParameter(Alpha, isPositive());
215  

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