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Comparing branches/development/src/io/Globals.cpp (file contents):
Revision 1613 by gezelter, Thu Aug 18 20:18:19 2011 UTC vs.
Revision 1731 by gezelter, Thu May 31 12:25:30 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 90 | Line 91 | Globals::Globals() {
91    DefineOptionalParameter(DampingAlpha, "dampingAlpha");
92    DefineOptionalParameter(SurfaceTension, "surfaceTension");
93    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
94 +  DefineOptionalParameter(PrintHeatFlux, "printHeatFlux");
95    DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
96    DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
97    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
# Line 117 | Line 119 | Globals::Globals() {
119    DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
120    DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
121    DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
122 <  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
123 <  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
122 >  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false);
123 >  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false);
124 >  DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false);
125 >  DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false);
126 >  DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", false);
127    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
128    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
129    DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
130    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
131  
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");
132    DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
133    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
134    DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
135    DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
136  
139 –
140 –
137    deprecatedKeywords_.insert("nComponents");
138    deprecatedKeywords_.insert("nZconstraints");
139    deprecatedKeywords_.insert("initialConfig");
# Line 160 | Line 156 | void Globals::validate() {
156  
157    CheckParameter(ForceField, isNotEmpty());
158    CheckParameter(TargetTemp, isPositive());
159 <  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"));
159 >  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"));
160    CheckParameter(Dt, isPositive());
161    CheckParameter(RunTime, isPositive());
162    CheckParameter(FinalConfig, isNotEmpty());
# Line 192 | Line 188 | void Globals::validate() {
188    CheckParameter(ForceFieldFileName, isNotEmpty());
189    CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
190    CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
191 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
191 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
192    CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
193    CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
194    CheckParameter(OrthoBoxTolerance, isPositive());  
# Line 203 | Line 199 | void Globals::validate() {
199    CheckParameter(FrozenBufferRadius, isPositive());
200    CheckParameter(LangevinBufferRadius, isPositive());
201    CheckParameter(NeighborListNeighbors, isPositive());
206 –  CheckParameter(RNEMD_exchangeTime, isPositive());
207 –  CheckParameter(RNEMD_nBins, isPositive() && isEven());
208 –  CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
209 –  CheckParameter(RNEMD_targetFlux, isNonNegative());
202    CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
203    CheckParameter(Alpha, isPositive());
212 –
204    
205    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
206      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
# Line 235 | Line 226 | bool Globals::addRestraintStamp(RestraintStamp* rest)
226      return true;
227   }
228  
229 + bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
230 +  if (flucQpars_ != NULL)
231 +    delete flucQpars_;
232 +    
233 +  flucQpars_ = fqp;
234 +  return true;
235 + }
236 +
237 + bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
238 +  if (rnemdPars_ != NULL)
239 +    delete rnemdPars_;
240 +    
241 +  rnemdPars_ = rnemdPars;
242 +  return true;
243 + }
244 +
245   bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
246      std::string molStampName = molStamp->getName();
247      std::map<std::string, MoleculeStamp*>::iterator i;

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