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root/OpenMD/trunk/src/io/Globals.cpp
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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC vs.
Revision 2022 by gezelter, Fri Sep 26 22:22:28 2014 UTC

# Line 35 | Line 35
35   *                                                                      
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).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 51 | Line 51 | namespace OpenMD {
51   #include "utils/simError.h"
52  
53   namespace OpenMD {
54 < Globals::Globals() {
54 >  Globals::Globals() {
55    
56 <  flucQpars_ = new FluctuatingChargeParameters();
57 <  rnemdPars_ = new RNEMDParameters();
58 <  minimizerPars_ = new MinimizerParameters();
56 >    flucQpars_ = new FluctuatingChargeParameters();
57 >    rnemdPars_ = new RNEMDParameters();
58 >    minimizerPars_ = new MinimizerParameters();
59  
60 <  DefineParameter(ForceField, "forceField")
61 <
62 <  DefineOptionalParameter(TargetTemp, "targetTemp");
63 <  DefineOptionalParameter(Ensemble, "ensemble");
64 <  DefineOptionalParameter(Dt, "dt");
65 <  DefineOptionalParameter(RunTime, "runTime");
66 <  DefineOptionalParameter(FinalConfig, "finalConfig");
67 <  DefineOptionalParameter(SampleTime, "sampleTime");
68 <  DefineOptionalParameter(ResetTime, "resetTime");
69 <  DefineOptionalParameter(StatusTime, "statusTime");
70 <  DefineOptionalParameter(CutoffRadius, "cutoffRadius");
71 <  DefineOptionalParameter(SwitchingRadius, "switchingRadius");
72 <  DefineOptionalParameter(TempSet, "tempSet");
73 <  DefineOptionalParameter(ThermalTime, "thermalTime");
74 <  DefineOptionalParameter(TargetPressure, "targetPressure");  
75 <  DefineOptionalParameter(TauThermostat, "tauThermostat");
76 <  DefineOptionalParameter(TauBarostat, "tauBarostat");
77 <  DefineOptionalParameter(ZconsTime, "zconsTime");
78 <  DefineOptionalParameter(ZconsTol, "zconsTol");
79 <  DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
80 <  DefineOptionalParameter(Seed, "seed");
81 <  DefineOptionalParameter(ZconsGap, "zconsGap");
82 <  DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
83 <  DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
84 <  DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
85 <  DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
86 <  DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
87 <  DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
88 <  DefineOptionalParameter(DampingAlpha, "dampingAlpha");
89 <  DefineOptionalParameter(SurfaceTension, "surfaceTension");
90 <  DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
91 <  DefineOptionalParameter(ElectricField, "electricField");
60 >    DefineParameter(ForceField, "forceField");
61 >    
62 >    DefineOptionalParameter(TargetTemp, "targetTemp");
63 >    DefineOptionalParameter(Ensemble, "ensemble");
64 >    DefineOptionalParameter(Dt, "dt");
65 >    DefineOptionalParameter(RunTime, "runTime");
66 >    DefineOptionalParameter(FinalConfig, "finalConfig");
67 >    DefineOptionalParameter(SampleTime, "sampleTime");
68 >    DefineOptionalParameter(ResetTime, "resetTime");
69 >    DefineOptionalParameter(StatusTime, "statusTime");
70 >    DefineOptionalParameter(CutoffRadius, "cutoffRadius");
71 >    DefineOptionalParameter(SwitchingRadius, "switchingRadius");
72 >    DefineOptionalParameter(TempSet, "tempSet");
73 >    DefineOptionalParameter(ThermalTime, "thermalTime");
74 >    DefineOptionalParameter(TargetPressure, "targetPressure");  
75 >    DefineOptionalParameter(TauThermostat, "tauThermostat");
76 >    DefineOptionalParameter(TauBarostat, "tauBarostat");
77 >    DefineOptionalParameter(ZconsTime, "zconsTime");
78 >    DefineOptionalParameter(ZconsTol, "zconsTol");
79 >    DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
80 >    DefineOptionalParameter(Seed, "seed");
81 >    DefineOptionalParameter(ZconsGap, "zconsGap");
82 >    DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
83 >    DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
84 >    DefineOptionalParameter(ThermodynamicIntegrationLambda,
85 >                            "thermodynamicIntegrationLambda");
86 >    DefineOptionalParameter(ThermodynamicIntegrationK,
87 >                            "thermodynamicIntegrationK");
88 >    DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89 >    DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90 >    DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91 >    DefineOptionalParameter(SurfaceTension, "surfaceTension");
92 >    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
93 >    DefineOptionalParameter(ElectricField, "electricField");
94 >    DefineOptionalParameter(UniformField, "uniformField");
95 >    //DefineOptionalParameter(PeriodicField, "periodicField");
96 >    //DefineOptionalParameter(PeriodicFieldStrength, "periodicFieldStrength");
97 >    
98  
99 <  DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
100 <  DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
101 <  DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
102 <  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
103 <  DefineOptionalParameter(Viscosity, "viscosity");
104 <  DefineOptionalParameter(BeadSize, "beadSize");
105 <  DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
106 <  DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
107 <  DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
108 <  DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
109 <  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
110 <  DefineOptionalParameter(MTM_Ce, "MTM_Ce");
111 <  DefineOptionalParameter(MTM_G, "MTM_G");
112 <  DefineOptionalParameter(MTM_Io, "MTM_Io");
113 <  DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
114 <  DefineOptionalParameter(MTM_R, "MTM_R");
115 <  DefineOptionalParameter(Alpha, "alpha");
99 >    DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
100 >    DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
101 >    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
102 >    DefineOptionalParameter(HydroPropFile, "HydroPropFile");
103 >    DefineOptionalParameter(Viscosity, "viscosity");
104 >    DefineOptionalParameter(BeadSize, "beadSize");
105 >    DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
106 >    DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
107 >    DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
108 >    DefineOptionalParameter(UseMultipleTemperatureMethod,
109 >                            "useMultipleTemperatureMethod");
110 >    DefineOptionalParameter(ElectrostaticSummationMethod,
111 >                            "electrostaticSummationMethod");
112 >    DefineOptionalParameter(MTM_Ce, "MTM_Ce");
113 >    DefineOptionalParameter(MTM_G, "MTM_G");
114 >    DefineOptionalParameter(MTM_Io, "MTM_Io");
115 >    DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
116 >    DefineOptionalParameter(MTM_R, "MTM_R");
117 >    DefineOptionalParameter(Alpha, "alpha");
118 >    DefineOptionalParameter(ConstraintTime, "constraintTime");
119  
120    
121 <  DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
122 <  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
123 <  DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
124 <  DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
125 <  DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
126 <  DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
127 <  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
128 <  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
129 <  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false);
130 <  DefineOptionalParameterWithDefaultValue(PrintHeatFlux, "printHeatFlux", false);
131 <  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false);
132 <  DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false);
133 <  DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false);
134 <  DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", false);
135 <  DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
136 <  DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
137 <  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
138 <  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
121 >    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions,
122 >                                            "usePeriodicBoundaryConditions",
123 >                                            true);
124 >    DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial",
125 >                                            true);
126 >    DefineOptionalParameterWithDefaultValue(UseLongRangeCorrections,
127 >                                            "useLongRangeCorrections", true);
128 >    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime",
129 >                                            false);
130 >    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState,
131 >                                            "useInitialExtendedSystemState",
132 >                                            false);
133 >    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance,
134 >                                            "orthoBoxTolerance", 1E-6);  
135 >    DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod",
136 >                                            "SHIFTED_FORCE");
137 >    DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod,
138 >                                            "electrostaticScreeningMethod",
139 >                                            "DAMPED");
140 >    DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
141 >    DefineOptionalParameterWithDefaultValue(CompressDumpFile,
142 >                                            "compressDumpFile", false);
143 >    DefineOptionalParameterWithDefaultValue(PrintHeatFlux, "printHeatFlux",
144 >                                            false);
145 >    DefineOptionalParameterWithDefaultValue(OutputForceVector,
146 >                                            "outputForceVector", false);
147 >    DefineOptionalParameterWithDefaultValue(OutputParticlePotential,
148 >                                            "outputParticlePotential", false);
149 >    DefineOptionalParameterWithDefaultValue(OutputElectricField,
150 >                                            "outputElectricField", false);
151 >    DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges,
152 >                                            "outputFluctuatingCharges", false);
153 >    DefineOptionalParameterWithDefaultValue(OutputSitePotential,
154 >                                            "outputSitePotential", false);
155 >    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness",
156 >                                            1.0);
157 >    DefineOptionalParameterWithDefaultValue(StatFileFormat,
158 >                                            "statFileFormat",
159 >                                            "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
160 >    DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions,
161 >                                            "useSphericalBoundaryConditions",
162 >                                            false);
163 >    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole,
164 >                                            "accumulateBoxDipole", false);
165 >    DefineOptionalParameterWithDefaultValue(AccumulateBoxQuadrupole,
166 >                                            "accumulateBoxQuadrupole", false);
167 >    DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints",
168 >                                            false);
169 >    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file",
170 >                                            "idealCrystal.in");
171 >    DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration,
172 >                                            "useThermodynamicIntegration",
173 >                                            false);
174 >    DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
175  
176 <  DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
177 <  DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
178 <  DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
179 <  DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
176 >    deprecatedKeywords_.insert("nComponents");
177 >    deprecatedKeywords_.insert("nZconstraints");
178 >    deprecatedKeywords_.insert("initialConfig");
179 >    deprecatedKeywords_.insert("thermIntDistSpringConst");
180 >    deprecatedKeywords_.insert("thermIntThetaSpringConst");
181 >    deprecatedKeywords_.insert("thermIntOmegaSpringConst");
182 >    deprecatedKeywords_.insert("useSolidThermInt");  
183 >    deprecatedKeywords_.insert("useLiquidThermInt");
184 >    deprecatedKeywords_.insert("minimizerMaxIter");
185 >    deprecatedKeywords_.insert("minimizerWriteFreq");
186 >    deprecatedKeywords_.insert("minimizerStepSize");
187 >    deprecatedKeywords_.insert("minimizerFTol");
188 >    deprecatedKeywords_.insert("minimizerGTol");
189 >    deprecatedKeywords_.insert("minimizerLSTol");
190 >    deprecatedKeywords_.insert("minimizerLSMaxIter");
191 >    deprecatedKeywords_.insert("electricField");
192  
136 –  deprecatedKeywords_.insert("nComponents");
137 –  deprecatedKeywords_.insert("nZconstraints");
138 –  deprecatedKeywords_.insert("initialConfig");
139 –  deprecatedKeywords_.insert("thermIntDistSpringConst");
140 –  deprecatedKeywords_.insert("thermIntThetaSpringConst");
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 –
193      
194 < }
194 >  }
195  
196 < Globals::~Globals() {
196 >  Globals::~Globals() {
197      MemoryUtils::deletePointers(components_);
198      MemoryUtils::deletePointers(zconstraints_);
199      MemoryUtils::deletePointers(restraints_);
200 < }
200 >    delete flucQpars_;
201 >    delete rnemdPars_;
202 >    delete minimizerPars_;
203 >  }
204  
205 < void Globals::validate() {
206 <  DataHolder::validate();
205 >  void Globals::validate() {
206 >    DataHolder::validate();
207  
208 <  CheckParameter(ForceField, isNotEmpty());
209 <  CheckParameter(TargetTemp, isPositive());
210 <  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"));
211 <  CheckParameter(Dt, isPositive());
212 <  CheckParameter(RunTime, isPositive());
213 <  CheckParameter(FinalConfig, isNotEmpty());
214 <  CheckParameter(SampleTime, isNonNegative());
215 <  CheckParameter(ResetTime, isNonNegative());
216 <  CheckParameter(StatusTime, isNonNegative());
217 <  CheckParameter(CutoffRadius, isPositive());
218 <  CheckParameter(SwitchingRadius, isNonNegative());
219 <  CheckParameter(Dielectric, isPositive());
220 <  CheckParameter(ThermalTime,  isNonNegative());
221 <  CheckParameter(TauThermostat, isPositive());
222 <  CheckParameter(TauBarostat, isPositive());
223 <  CheckParameter(ZconsTime, isPositive());
224 <  CheckParameter(ZconsTol, isPositive());
225 <  CheckParameter(Seed, isPositive());
226 <  CheckParameter(ZconsGap, isPositive());
227 <  CheckParameter(ZconsFixtime, isPositive());
228 <  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
229 <  CheckParameter(ThermodynamicIntegrationK, isPositive());
230 <  CheckParameter(ForceFieldVariant, isNotEmpty());
231 <  CheckParameter(ForceFieldFileName, isNotEmpty());
232 <  CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
233 <  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
234 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
235 <  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
236 <  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
237 <  CheckParameter(OrthoBoxTolerance, isPositive());  
238 <  CheckParameter(DampingAlpha,isNonNegative());
239 <  CheckParameter(SkinThickness, isPositive());
240 <  CheckParameter(Viscosity, isNonNegative());
241 <  CheckParameter(BeadSize, isPositive());
242 <  CheckParameter(FrozenBufferRadius, isPositive());
243 <  CheckParameter(LangevinBufferRadius, isPositive());
244 <  CheckParameter(NeighborListNeighbors, isPositive());
245 <  CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
246 <  CheckParameter(Alpha, isPositive());
208 >    CheckParameter(ForceField, isNotEmpty());
209 >    CheckParameter(TargetTemp, isPositive());
210 >    CheckParameter(Ensemble, isEqualIgnoreCase("NVE") ||
211 >                   isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") ||
212 >                   isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") ||
213 >                   isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT")  ||
214 >                   isEqualIgnoreCase("NPA") ||
215 >                   isEqualIgnoreCase("LANGEVINDYNAMICS") ||
216 >                   isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") ||
217 >                   isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") ||
218 >                   isEqualIgnoreCase("NGT") ||
219 >                   isEqualIgnoreCase("LANGEVINHULL") ||
220 >                   isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD"));
221 >    CheckParameter(Dt, isPositive());
222 >    CheckParameter(RunTime, isPositive());
223 >    CheckParameter(FinalConfig, isNotEmpty());
224 >    CheckParameter(SampleTime, isNonNegative());
225 >    CheckParameter(ResetTime, isNonNegative());
226 >    CheckParameter(StatusTime, isNonNegative());
227 >    CheckParameter(CutoffRadius, isPositive());
228 >    CheckParameter(SwitchingRadius, isNonNegative());
229 >    CheckParameter(Dielectric, isPositive());
230 >    CheckParameter(ThermalTime,  isNonNegative());
231 >    CheckParameter(TauThermostat, isPositive());
232 >    CheckParameter(TauBarostat, isPositive());
233 >    CheckParameter(ZconsTime, isPositive());
234 >    CheckParameter(ZconsTol, isPositive());
235 >    CheckParameter(Seed, isPositive());
236 >    CheckParameter(ZconsGap, isPositive());
237 >    CheckParameter(ZconsFixtime, isPositive());
238 >    CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
239 >    CheckParameter(ThermodynamicIntegrationK, isPositive());
240 >    CheckParameter(ForceFieldVariant, isNotEmpty());
241 >    CheckParameter(ForceFieldFileName, isNotEmpty());
242 >    CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") ||
243 >                   isEqualIgnoreCase("SWITCHED") ||
244 >                   isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
245 >                   isEqualIgnoreCase("SHIFTED_FORCE") ||
246 >                   isEqualIgnoreCase("TAYLOR_SHIFTED") ||
247 >                   isEqualIgnoreCase("EWALD_FULL"));
248 >    CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") ||
249 >                   isEqualIgnoreCase("MAX") ||
250 >                   isEqualIgnoreCase("TRADITIONAL"));
251 >    CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") ||
252 >                   isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") ||
253 >                   isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
254 >                   isEqualIgnoreCase("SHIFTED_FORCE") ||
255 >                   isEqualIgnoreCase("REACTION_FIELD") ||
256 >                   isEqualIgnoreCase("TAYLOR_SHIFTED"));
257 >    CheckParameter(ElectrostaticScreeningMethod,
258 >                   isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
259 >    CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") ||
260 >                   isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
261 >    CheckParameter(OrthoBoxTolerance, isPositive());  
262 >    CheckParameter(DampingAlpha,isNonNegative());
263 >    CheckParameter(SkinThickness, isPositive());
264 >    CheckParameter(Viscosity, isNonNegative());
265 >    CheckParameter(BeadSize, isPositive());
266 >    CheckParameter(FrozenBufferRadius, isPositive());
267 >    CheckParameter(LangevinBufferRadius, isPositive());
268 >    CheckParameter(NeighborListNeighbors, isPositive());
269 >    CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") ||
270 >                   isEqualIgnoreCase("AlphaShape"));
271 >    CheckParameter(Alpha, isPositive());
272    
273 <  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
274 <    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
273 >    for(std::vector<Component*>::iterator i = components_.begin();
274 >        i != components_.end(); ++i) {
275 >      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
276          std::ostringstream oss;
277 <        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
277 >        oss << "Globals Error: can not find molecule stamp for component "
278 >            << (*i)->getType() << std::endl;
279          throw OpenMDException(oss.str());          
280 +      }
281      }
282    }
283 < }
284 <
213 < bool Globals::addComponent(Component* comp) {
283 >  
284 >  bool Globals::addComponent(Component* comp) {
285      components_.push_back(comp);
286      return true;
287 < }
287 >  }
288  
289 < bool Globals::addZConsStamp(ZConsStamp* zcons) {
289 >  bool Globals::addZConsStamp(ZConsStamp* zcons) {
290      zconstraints_.push_back(zcons);
291      return true;
292 < }
292 >  }
293  
294 < bool Globals::addRestraintStamp(RestraintStamp* rest) {
294 >  bool Globals::addRestraintStamp(RestraintStamp* rest) {
295      restraints_.push_back(rest);
296      return true;
297 < }
297 >  }
298  
299 < bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
300 <  if (flucQpars_ != NULL)
301 <    delete flucQpars_;
299 >  bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
300 >    if (flucQpars_ != NULL)
301 >      delete flucQpars_;
302      
303 <  flucQpars_ = fqp;
304 <  return true;
305 < }
303 >    flucQpars_ = fqp;
304 >    return true;
305 >  }
306  
307 < bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
308 <  if (rnemdPars_ != NULL)
309 <    delete rnemdPars_;
307 >  bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
308 >    if (rnemdPars_ != NULL)
309 >      delete rnemdPars_;
310      
311 <  rnemdPars_ = rnemdPars;
312 <  return true;
313 < }
311 >    rnemdPars_ = rnemdPars;
312 >    return true;
313 >  }
314  
315 < bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
316 <  if (minimizerPars_ != NULL)
317 <    delete minimizerPars_;
315 >  bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
316 >    if (minimizerPars_ != NULL)
317 >      delete minimizerPars_;
318      
319 <  minimizerPars_ = miniPars;
320 <  return true;
321 < }
319 >    minimizerPars_ = miniPars;
320 >    return true;
321 >  }
322  
323 < bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
323 >  bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
324      std::string molStampName = molStamp->getName();
325      std::map<std::string, MoleculeStamp*>::iterator i;
326      bool ret = false;
327      i = moleculeStamps_.find(molStampName);
328      if (i == moleculeStamps_.end()) {
329 <        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
330 <        ret = true;
329 >      moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
330 >      ret = true;
331      } else {
332 <        std::ostringstream oss;
333 <        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
334 <        throw OpenMDException(oss.str());  
332 >      std::ostringstream oss;
333 >      oss << "Globals Error: Molecule Stamp " << molStamp->getName()
334 >          << "appears multiple times\n";
335 >      throw OpenMDException(oss.str());  
336      }
337      return ret;
338 +  }
339   }
267 –
268 –
269 – }

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