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Comparing branches/development/src/io/Globals.cpp (file contents):
Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC vs.
Revision 1729 by jmarr, Wed May 30 16:08:07 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);
# Line 130 | Line 135 | Globals::Globals() {
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 +
154    DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
155    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
156    DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
157    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);
164  
139 –
140 –
165    deprecatedKeywords_.insert("nComponents");
166    deprecatedKeywords_.insert("nZconstraints");
167    deprecatedKeywords_.insert("initialConfig");
# Line 146 | Line 170 | Globals::Globals() {
170    deprecatedKeywords_.insert("thermIntOmegaSpringConst");
171    deprecatedKeywords_.insert("useSolidThermInt");  
172    deprecatedKeywords_.insert("useLiquidThermInt");
149 –  deprecatedKeywords_.insert("cutoffPolicy");
173      
174   }
175  
# Line 161 | Line 184 | void Globals::validate() {
184  
185    CheckParameter(ForceField, isNotEmpty());
186    CheckParameter(TargetTemp, isPositive());
187 <  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"));
187 >  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"));
188    CheckParameter(Dt, isPositive());
189    CheckParameter(RunTime, isPositive());
190    CheckParameter(FinalConfig, isNotEmpty());
# Line 192 | Line 215 | void Globals::validate() {
215    CheckParameter(ForceFieldVariant, isNotEmpty());
216    CheckParameter(ForceFieldFileName, isNotEmpty());
217    CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
218 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
218 >  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
219 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
220    CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
221    CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
222    CheckParameter(OrthoBoxTolerance, isPositive());  
# Line 205 | Line 229 | void Globals::validate() {
229    CheckParameter(NeighborListNeighbors, isPositive());
230    CheckParameter(RNEMD_exchangeTime, isPositive());
231    CheckParameter(RNEMD_nBins, isPositive() && isEven());
232 <  CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
209 <  CheckParameter(RNEMD_targetFlux, isNonNegative());
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"));
233    CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
234    CheckParameter(Alpha, isPositive());
235 <
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());
241    
242    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
243      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
# Line 219 | Line 247 | void Globals::validate() {
247      }
248    }
249   }
250 <  
250 >
251   bool Globals::addComponent(Component* comp) {
252      components_.push_back(comp);
253      return true;

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