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Comparing branches/development/src/io/Globals.cpp (file contents):
Revision 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC vs.
Revision 1746 by gezelter, Wed Jun 6 02:18:54 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(PrintHeatFlux, "printHeatFlux");
92    DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
93    DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
94    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
# Line 117 | Line 116 | Globals::Globals() {
116    DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
117    DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
118    DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
119 <  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
120 <  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
119 >  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false);
120 >  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false);
121 >  DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false);
122 >  DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false);
123 >  DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", 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);
127    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
128  
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");
129    DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
130    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
131    DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
132    DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
133  
139 –
140 –
134    deprecatedKeywords_.insert("nComponents");
135    deprecatedKeywords_.insert("nZconstraints");
136    deprecatedKeywords_.insert("initialConfig");
# Line 146 | Line 139 | Globals::Globals() {
139    deprecatedKeywords_.insert("thermIntOmegaSpringConst");
140    deprecatedKeywords_.insert("useSolidThermInt");  
141    deprecatedKeywords_.insert("useLiquidThermInt");
142 +  deprecatedKeywords_.insert("minimizerMaxIter");
143 +  deprecatedKeywords_.insert("minimizerWriteFreq");
144 +  deprecatedKeywords_.insert("minimizerStepSize");
145 +  deprecatedKeywords_.insert("minimizerFTol");
146 +  deprecatedKeywords_.insert("minimizerGTol");
147 +  deprecatedKeywords_.insert("minimizerLSTol");
148 +  deprecatedKeywords_.insert("minimizerLSMaxIter");
149 +
150      
151   }
152  
# Line 160 | Line 161 | void Globals::validate() {
161  
162    CheckParameter(ForceField, isNotEmpty());
163    CheckParameter(TargetTemp, isPositive());
164 <  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"));
164 >  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"));
165    CheckParameter(Dt, isPositive());
166    CheckParameter(RunTime, isPositive());
167    CheckParameter(FinalConfig, isNotEmpty());
# Line 176 | Line 177 | void Globals::validate() {
177    CheckParameter(ZconsTime, isPositive());
178    CheckParameter(ZconsTol, isPositive());
179    CheckParameter(Seed, isPositive());
179 –  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
180 –  CheckParameter(MinimizerMaxIter, isPositive());
181 –  CheckParameter(MinimizerWriteFreq, isPositive());
182 –  CheckParameter(MinimizerStepSize, isPositive());
183 –  CheckParameter(MinimizerFTol, isPositive());
184 –  CheckParameter(MinimizerGTol, isPositive());
185 –  CheckParameter(MinimizerLSTol, isPositive());
186 –  CheckParameter(MinimizerLSMaxIter, isPositive());
180    CheckParameter(ZconsGap, isPositive());
181    CheckParameter(ZconsFixtime, isPositive());
182    CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
# Line 192 | Line 185 | void Globals::validate() {
185    CheckParameter(ForceFieldFileName, isNotEmpty());
186    CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
187    CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
188 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
188 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
189    CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
190    CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
191    CheckParameter(OrthoBoxTolerance, isPositive());  
# Line 203 | Line 196 | void Globals::validate() {
196    CheckParameter(FrozenBufferRadius, isPositive());
197    CheckParameter(LangevinBufferRadius, isPositive());
198    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());
199    CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
200    CheckParameter(Alpha, isPositive());
212 –
201    
202    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
203      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
# Line 219 | Line 207 | void Globals::validate() {
207      }
208    }
209   }
210 <  
210 >
211   bool Globals::addComponent(Component* comp) {
212      components_.push_back(comp);
213      return true;
# Line 235 | Line 223 | bool Globals::addRestraintStamp(RestraintStamp* rest)
223      return true;
224   }
225  
226 + bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
227 +  if (flucQpars_ != NULL)
228 +    delete flucQpars_;
229 +    
230 +  flucQpars_ = fqp;
231 +  return true;
232 + }
233 +
234 + bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
235 +  if (rnemdPars_ != NULL)
236 +    delete rnemdPars_;
237 +    
238 +  rnemdPars_ = rnemdPars;
239 +  return true;
240 + }
241 +
242 + bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
243 +  if (minimizerPars_ != NULL)
244 +    delete minimizerPars_;
245 +    
246 +  minimizerPars_ = miniPars;
247 +  return true;
248 + }
249 +
250   bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
251      std::string molStampName = molStamp->getName();
252      std::map<std::string, MoleculeStamp*>::iterator i;

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