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Comparing branches/development/src/io/Globals.cpp (file contents):
Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC vs.
Revision 1780 by jmarr, Mon Aug 20 18:28:22 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 +  minimizerPars_ = new MinimizerParameters();
59 +
60    DefineParameter(ForceField, "forceField")
61  
62    DefineOptionalParameter(TargetTemp, "targetTemp");
# Line 72 | Line 78 | Globals::Globals() {
78    DefineOptionalParameter(ZconsTol, "zconsTol");
79    DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
80    DefineOptionalParameter(Seed, "seed");
75 –  DefineOptionalParameter(Minimizer, "minimizer");
76 –  DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
77 –  DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq");
78 –  DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
79 –  DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
80 –  DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
81 –  DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
82 –  DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
81    DefineOptionalParameter(ZconsGap, "zconsGap");
82    DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
83    DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
# Line 90 | Line 88 | Globals::Globals() {
88    DefineOptionalParameter(DampingAlpha, "dampingAlpha");
89    DefineOptionalParameter(SurfaceTension, "surfaceTension");
90    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
91 +  DefineOptionalParameter(ElectricField, "electricField");
92 +
93    DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
94    DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
95    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
# Line 117 | Line 117 | Globals::Globals() {
117    DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
118    DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
119    DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
120 <  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
121 <  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
122 <  DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", 0);
120 >  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false);
121 >  DefineOptionalParameterWithDefaultValue(PrintHeatFlux, "printHeatFlux", 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);
129    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
130  
128 –  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
129 –  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
130 –  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
131 –  DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
132 –  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
133 –  DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
134 –  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
135 –  DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false);
136 –  DefineOptionalParameterWithDefaultValue(RNEMD_outputDimensionalTemperature, "RNEMD_outputDimensionalTemperature", false);
131    DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
132    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
133    DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
134    DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
135  
142 –
143 –
136    deprecatedKeywords_.insert("nComponents");
137    deprecatedKeywords_.insert("nZconstraints");
138    deprecatedKeywords_.insert("initialConfig");
# Line 149 | Line 141 | Globals::Globals() {
141    deprecatedKeywords_.insert("thermIntOmegaSpringConst");
142    deprecatedKeywords_.insert("useSolidThermInt");  
143    deprecatedKeywords_.insert("useLiquidThermInt");
144 +  deprecatedKeywords_.insert("minimizerMaxIter");
145 +  deprecatedKeywords_.insert("minimizerWriteFreq");
146 +  deprecatedKeywords_.insert("minimizerStepSize");
147 +  deprecatedKeywords_.insert("minimizerFTol");
148 +  deprecatedKeywords_.insert("minimizerGTol");
149 +  deprecatedKeywords_.insert("minimizerLSTol");
150 +  deprecatedKeywords_.insert("minimizerLSMaxIter");
151 +
152      
153   }
154  
# Line 179 | Line 179 | void Globals::validate() {
179    CheckParameter(ZconsTime, isPositive());
180    CheckParameter(ZconsTol, isPositive());
181    CheckParameter(Seed, isPositive());
182 –  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
183 –  CheckParameter(MinimizerMaxIter, isPositive());
184 –  CheckParameter(MinimizerWriteFreq, isPositive());
185 –  CheckParameter(MinimizerStepSize, isPositive());
186 –  CheckParameter(MinimizerFTol, isPositive());
187 –  CheckParameter(MinimizerGTol, isPositive());
188 –  CheckParameter(MinimizerLSTol, isPositive());
189 –  CheckParameter(MinimizerLSMaxIter, isPositive());
182    CheckParameter(ZconsGap, isPositive());
183    CheckParameter(ZconsFixtime, isPositive());
184    CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
# Line 206 | Line 198 | void Globals::validate() {
198    CheckParameter(FrozenBufferRadius, isPositive());
199    CheckParameter(LangevinBufferRadius, isPositive());
200    CheckParameter(NeighborListNeighbors, isPositive());
209 –  CheckParameter(RNEMD_exchangeTime, isPositive());
210 –  CheckParameter(RNEMD_nBins, isPositive() && isEven());
211 –  CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
201    CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
202    CheckParameter(Alpha, isPositive());
214 –
203    
204    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
205      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
# Line 237 | Line 225 | bool Globals::addRestraintStamp(RestraintStamp* rest)
225      return true;
226   }
227  
228 + bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
229 +  if (flucQpars_ != NULL)
230 +    delete flucQpars_;
231 +    
232 +  flucQpars_ = fqp;
233 +  return true;
234 + }
235 +
236 + bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
237 +  if (rnemdPars_ != NULL)
238 +    delete rnemdPars_;
239 +    
240 +  rnemdPars_ = rnemdPars;
241 +  return true;
242 + }
243 +
244 + bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
245 +  if (minimizerPars_ != NULL)
246 +    delete minimizerPars_;
247 +    
248 +  minimizerPars_ = miniPars;
249 +  return true;
250 + }
251 +
252   bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
253      std::string molStampName = molStamp->getName();
254      std::map<std::string, MoleculeStamp*>::iterator i;

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