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root/OpenMD/trunk/src/io/Globals.cpp
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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 1698 by skuang, Fri Mar 16 21:18:27 2012 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 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(CutoffPolicy, "cutoffPolicy");
95    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
96    DefineOptionalParameter(HydroPropFile, "HydroPropFile");
97    DefineOptionalParameter(Viscosity, "viscosity");
# Line 101 | Line 100 | Globals::Globals() {
100    DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
101    DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
102    DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
103 +  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
104    DefineOptionalParameter(MTM_Ce, "MTM_Ce");
105    DefineOptionalParameter(MTM_G, "MTM_G");
106    DefineOptionalParameter(MTM_Io, "MTM_Io");
# Line 114 | Line 114 | Globals::Globals() {
114    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
115    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
116    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
117 <  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
117 >  DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
118    DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
119 <  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
120 <  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
121 <  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
122 <  DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", 0);
119 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
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_targetJzKE, "RNEMD_targetJzKE", 0.0);
135 –  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpx, "RNEMD_targetJzpx", 0.0);
136 –  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpy, "RNEMD_targetJzpy", 0.0);
137 –  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpz, "RNEMD_targetJzpz", 0.0);
138 –  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
139 –  DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false);
140 –  DefineOptionalParameterWithDefaultValue(RNEMD_outputTemperature, "RNEMD_outputTemperature", false);
141 –  DefineOptionalParameterWithDefaultValue(RNEMD_outputVx, "RNEMD_outputVx", false);
142 –  DefineOptionalParameterWithDefaultValue(RNEMD_outputVy, "RNEMD_outputVy", false);
143 –  DefineOptionalParameterWithDefaultValue(RNEMD_outputXyzTemperature, "RNEMD_outputXyzTemperature", false);
144 –  DefineOptionalParameterWithDefaultValue(RNEMD_outputRotTemperature, "RNEMD_outputRotTemperature", 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  
150 –
136    deprecatedKeywords_.insert("nComponents");
137    deprecatedKeywords_.insert("nZconstraints");
138    deprecatedKeywords_.insert("initialConfig");
# Line 156 | 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 186 | Line 179 | void Globals::validate() {
179    CheckParameter(ZconsTime, isPositive());
180    CheckParameter(ZconsTol, isPositive());
181    CheckParameter(Seed, isPositive());
189 –  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
190 –  CheckParameter(MinimizerMaxIter, isPositive());
191 –  CheckParameter(MinimizerWriteFreq, isPositive());
192 –  CheckParameter(MinimizerStepSize, isPositive());
193 –  CheckParameter(MinimizerFTol, isPositive());
194 –  CheckParameter(MinimizerGTol, isPositive());
195 –  CheckParameter(MinimizerLSTol, isPositive());
196 –  CheckParameter(MinimizerLSMaxIter, isPositive());
182    CheckParameter(ZconsGap, isPositive());
183    CheckParameter(ZconsFixtime, isPositive());
184    CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
185    CheckParameter(ThermodynamicIntegrationK, isPositive());
186    CheckParameter(ForceFieldVariant, isNotEmpty());
187    CheckParameter(ForceFieldFileName, isNotEmpty());
188 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
204 <  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
188 >  CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
189    CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
190 +  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
191 +  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
192    CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
207 –  //CheckParameter(StatFileFormat,);    
193    CheckParameter(OrthoBoxTolerance, isPositive());  
194    CheckParameter(DampingAlpha,isNonNegative());
195    CheckParameter(SkinThickness, isPositive());
# Line 213 | Line 198 | void Globals::validate() {
198    CheckParameter(FrozenBufferRadius, isPositive());
199    CheckParameter(LangevinBufferRadius, isPositive());
200    CheckParameter(NeighborListNeighbors, isPositive());
216 –  CheckParameter(RNEMD_exchangeTime, isPositive());
217 –  CheckParameter(RNEMD_nBins, isPositive() && isEven());
218 –  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"));
219 –  //CheckParameter(RNEMD_targetFlux, isNonNegative());
201    CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
202    CheckParameter(Alpha, isPositive());
222 –
203    
204    for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
205      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
# Line 229 | Line 209 | void Globals::validate() {
209      }
210    }
211   }
212 <  
212 >
213   bool Globals::addComponent(Component* comp) {
214      components_.push_back(comp);
215      return true;
# Line 245 | 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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