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root/OpenMD/trunk/src/io/Globals.cpp
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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 1610 by gezelter, Fri Aug 12 14:37:25 2011 UTC vs.
Revision 2011 by gezelter, Wed Aug 6 19:27:37 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).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
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   */
42  
43   #include <stdlib.h>
# Line 50 | Line 51 | namespace OpenMD {
51   #include "utils/simError.h"
52  
53   namespace OpenMD {
54 < Globals::Globals() {
54 <  DefineParameter(ForceField, "forceField")
55 <
56 <  DefineOptionalParameter(TargetTemp, "targetTemp");
57 <  DefineOptionalParameter(Ensemble, "ensemble");
58 <  DefineOptionalParameter(Dt, "dt");
59 <  DefineOptionalParameter(RunTime, "runTime");
60 <  DefineOptionalParameter(FinalConfig, "finalConfig");
61 <  DefineOptionalParameter(SampleTime, "sampleTime");
62 <  DefineOptionalParameter(ResetTime, "resetTime");
63 <  DefineOptionalParameter(StatusTime, "statusTime");
64 <  DefineOptionalParameter(CutoffRadius, "cutoffRadius");
65 <  DefineOptionalParameter(SwitchingRadius, "switchingRadius");
66 <  DefineOptionalParameter(TempSet, "tempSet");
67 <  DefineOptionalParameter(ThermalTime, "thermalTime");
68 <  DefineOptionalParameter(TargetPressure, "targetPressure");  
69 <  DefineOptionalParameter(TauThermostat, "tauThermostat");
70 <  DefineOptionalParameter(TauBarostat, "tauBarostat");
71 <  DefineOptionalParameter(ZconsTime, "zconsTime");
72 <  DefineOptionalParameter(ZconsTol, "zconsTol");
73 <  DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
74 <  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");
83 <  DefineOptionalParameter(ZconsGap, "zconsGap");
84 <  DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
85 <  DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
86 <  DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
87 <  DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
88 <  DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89 <  DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90 <  DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91 <  DefineOptionalParameter(SurfaceTension, "surfaceTension");
92 <  DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
93 <  DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
94 <  DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
95 <  DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
96 <  DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
97 <  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
98 <  DefineOptionalParameter(Viscosity, "viscosity");
99 <  DefineOptionalParameter(BeadSize, "beadSize");
100 <  DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
101 <  DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
102 <  DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
103 <  DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
104 <  DefineOptionalParameter(MTM_Ce, "MTM_Ce");
105 <  DefineOptionalParameter(MTM_G, "MTM_G");
106 <  DefineOptionalParameter(MTM_Io, "MTM_Io");
107 <  DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
108 <  DefineOptionalParameter(MTM_R, "MTM_R");
109 <  DefineOptionalParameter(Alpha, "alpha");
110 <
54 >  Globals::Globals() {
55    
56 <  DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
57 <  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
58 <  DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
115 <  DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
116 <  DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
117 <  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "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);
123 <  DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
124 <  DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
125 <  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
126 <  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
56 >    flucQpars_ = new FluctuatingChargeParameters();
57 >    rnemdPars_ = new RNEMDParameters();
58 >    minimizerPars_ = new MinimizerParameters();
59  
60 <  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
61 <  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
62 <  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
63 <  DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
64 <  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
65 <  DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
66 <  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
67 <  DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false);
68 <  DefineOptionalParameterWithDefaultValue(RNEMD_outputDimensionalTemperature, "RNEMD_outputDimensionalTemperature", false);
69 <  DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
70 <  DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
71 <  DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
72 <  DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
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  
95 +    DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
96 +    DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
97 +    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
98 +    DefineOptionalParameter(HydroPropFile, "HydroPropFile");
99 +    DefineOptionalParameter(Viscosity, "viscosity");
100 +    DefineOptionalParameter(BeadSize, "beadSize");
101 +    DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
102 +    DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
103 +    DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
104 +    DefineOptionalParameter(UseMultipleTemperatureMethod,
105 +                            "useMultipleTemperatureMethod");
106 +    DefineOptionalParameter(ElectrostaticSummationMethod,
107 +                            "electrostaticSummationMethod");
108 +    DefineOptionalParameter(MTM_Ce, "MTM_Ce");
109 +    DefineOptionalParameter(MTM_G, "MTM_G");
110 +    DefineOptionalParameter(MTM_Io, "MTM_Io");
111 +    DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
112 +    DefineOptionalParameter(MTM_R, "MTM_R");
113 +    DefineOptionalParameter(Alpha, "alpha");
114 +    DefineOptionalParameter(ConstraintTime, "constraintTime");
115  
116 <  deprecatedKeywords_.insert("nComponents");
117 <  deprecatedKeywords_.insert("nZconstraints");
118 <  deprecatedKeywords_.insert("initialConfig");
119 <  deprecatedKeywords_.insert("thermIntDistSpringConst");
120 <  deprecatedKeywords_.insert("thermIntThetaSpringConst");
121 <  deprecatedKeywords_.insert("thermIntOmegaSpringConst");
122 <  deprecatedKeywords_.insert("useSolidThermInt");  
123 <  deprecatedKeywords_.insert("useLiquidThermInt");
124 <    
125 < }
116 >  
117 >    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions,
118 >                                            "usePeriodicBoundaryConditions",
119 >                                            true);
120 >    DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial",
121 >                                            true);
122 >    DefineOptionalParameterWithDefaultValue(UseLongRangeCorrections,
123 >                                            "useLongRangeCorrections", true);
124 >    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime",
125 >                                            false);
126 >    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState,
127 >                                            "useInitialExtendedSystemState",
128 >                                            false);
129 >    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance,
130 >                                            "orthoBoxTolerance", 1E-6);  
131 >    DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod",
132 >                                            "SHIFTED_FORCE");
133 >    DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod,
134 >                                            "electrostaticScreeningMethod",
135 >                                            "DAMPED");
136 >    DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
137 >    DefineOptionalParameterWithDefaultValue(CompressDumpFile,
138 >                                            "compressDumpFile", false);
139 >    DefineOptionalParameterWithDefaultValue(PrintHeatFlux, "printHeatFlux",
140 >                                            false);
141 >    DefineOptionalParameterWithDefaultValue(OutputForceVector,
142 >                                            "outputForceVector", false);
143 >    DefineOptionalParameterWithDefaultValue(OutputParticlePotential,
144 >                                            "outputParticlePotential", false);
145 >    DefineOptionalParameterWithDefaultValue(OutputElectricField,
146 >                                            "outputElectricField", false);
147 >    DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges,
148 >                                            "outputFluctuatingCharges", false);
149 >    DefineOptionalParameterWithDefaultValue(OutputSitePotential,
150 >                                            "outputSitePotential", false);
151 >    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness",
152 >                                            1.0);
153 >    DefineOptionalParameterWithDefaultValue(StatFileFormat,
154 >                                            "statFileFormat",
155 >                                            "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
156 >    DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions,
157 >                                            "useSphericalBoundaryConditions",
158 >                                            false);
159 >    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole,
160 >                                            "accumulateBoxDipole", false);
161 >    DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints",
162 >                                            false);
163 >    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file",
164 >                                            "idealCrystal.in");
165 >    DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration,
166 >                                            "useThermodynamicIntegration",
167 >                                            false);
168 >    DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
169  
170 < Globals::~Globals() {
170 >    deprecatedKeywords_.insert("nComponents");
171 >    deprecatedKeywords_.insert("nZconstraints");
172 >    deprecatedKeywords_.insert("initialConfig");
173 >    deprecatedKeywords_.insert("thermIntDistSpringConst");
174 >    deprecatedKeywords_.insert("thermIntThetaSpringConst");
175 >    deprecatedKeywords_.insert("thermIntOmegaSpringConst");
176 >    deprecatedKeywords_.insert("useSolidThermInt");  
177 >    deprecatedKeywords_.insert("useLiquidThermInt");
178 >    deprecatedKeywords_.insert("minimizerMaxIter");
179 >    deprecatedKeywords_.insert("minimizerWriteFreq");
180 >    deprecatedKeywords_.insert("minimizerStepSize");
181 >    deprecatedKeywords_.insert("minimizerFTol");
182 >    deprecatedKeywords_.insert("minimizerGTol");
183 >    deprecatedKeywords_.insert("minimizerLSTol");
184 >    deprecatedKeywords_.insert("minimizerLSMaxIter");
185 >
186 >    
187 >  }
188 >
189 >  Globals::~Globals() {
190      MemoryUtils::deletePointers(components_);
191      MemoryUtils::deletePointers(zconstraints_);
192      MemoryUtils::deletePointers(restraints_);
193 < }
193 >    delete flucQpars_;
194 >    delete rnemdPars_;
195 >    delete minimizerPars_;
196 >  }
197  
198 < void Globals::validate() {
199 <  DataHolder::validate();
198 >  void Globals::validate() {
199 >    DataHolder::validate();
200  
201 <  CheckParameter(ForceField, isNotEmpty());
202 <  CheckParameter(TargetTemp, isPositive());
203 <  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"));
204 <  CheckParameter(Dt, isPositive());
205 <  CheckParameter(RunTime, isPositive());
206 <  CheckParameter(FinalConfig, isNotEmpty());
207 <  CheckParameter(SampleTime, isNonNegative());
208 <  CheckParameter(ResetTime, isNonNegative());
209 <  CheckParameter(StatusTime, isNonNegative());
210 <  CheckParameter(CutoffRadius, isPositive());
211 <  CheckParameter(SwitchingRadius, isNonNegative());
212 <  CheckParameter(Dielectric, isPositive());
213 <  CheckParameter(ThermalTime,  isNonNegative());
214 <  CheckParameter(TauThermostat, isPositive());
215 <  CheckParameter(TauBarostat, isPositive());
216 <  CheckParameter(ZconsTime, isPositive());
217 <  CheckParameter(ZconsTol, isPositive());
218 <  CheckParameter(Seed, isPositive());
219 <  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
220 <  CheckParameter(MinimizerMaxIter, isPositive());
221 <  CheckParameter(MinimizerWriteFreq, isPositive());
222 <  CheckParameter(MinimizerStepSize, isPositive());
223 <  CheckParameter(MinimizerFTol, isPositive());
224 <  CheckParameter(MinimizerGTol, isPositive());
225 <  CheckParameter(MinimizerLSTol, isPositive());
226 <  CheckParameter(MinimizerLSMaxIter, isPositive());
227 <  CheckParameter(ZconsGap, isPositive());
228 <  CheckParameter(ZconsFixtime, isPositive());
229 <  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
230 <  CheckParameter(ThermodynamicIntegrationK, isPositive());
231 <  CheckParameter(ForceFieldVariant, isNotEmpty());
232 <  CheckParameter(ForceFieldFileName, isNotEmpty());
233 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
234 <  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
235 <  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
236 <  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
237 <  //CheckParameter(StatFileFormat,);    
238 <  CheckParameter(OrthoBoxTolerance, isPositive());  
239 <  CheckParameter(DampingAlpha,isNonNegative());
240 <  CheckParameter(SkinThickness, isPositive());
241 <  CheckParameter(Viscosity, isNonNegative());
242 <  CheckParameter(BeadSize, isPositive());
243 <  CheckParameter(FrozenBufferRadius, isPositive());
244 <  CheckParameter(LangevinBufferRadius, isPositive());
245 <  CheckParameter(NeighborListNeighbors, isPositive());
246 <  CheckParameter(RNEMD_exchangeTime, isPositive());
247 <  CheckParameter(RNEMD_nBins, isPositive() && isEven());
248 <  CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
249 <  //CheckParameter(RNEMD_targetFlux, isNonNegative());
250 <  CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
251 <  CheckParameter(Alpha, isPositive());
252 <
201 >    CheckParameter(ForceField, isNotEmpty());
202 >    CheckParameter(TargetTemp, isPositive());
203 >    CheckParameter(Ensemble, isEqualIgnoreCase("NVE") ||
204 >                   isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") ||
205 >                   isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") ||
206 >                   isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT")  ||
207 >                   isEqualIgnoreCase("NPA") ||
208 >                   isEqualIgnoreCase("LANGEVINDYNAMICS") ||
209 >                   isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") ||
210 >                   isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") ||
211 >                   isEqualIgnoreCase("NGT") ||
212 >                   isEqualIgnoreCase("LANGEVINHULL") ||
213 >                   isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD"));
214 >    CheckParameter(Dt, isPositive());
215 >    CheckParameter(RunTime, isPositive());
216 >    CheckParameter(FinalConfig, isNotEmpty());
217 >    CheckParameter(SampleTime, isNonNegative());
218 >    CheckParameter(ResetTime, isNonNegative());
219 >    CheckParameter(StatusTime, isNonNegative());
220 >    CheckParameter(CutoffRadius, isPositive());
221 >    CheckParameter(SwitchingRadius, isNonNegative());
222 >    CheckParameter(Dielectric, isPositive());
223 >    CheckParameter(ThermalTime,  isNonNegative());
224 >    CheckParameter(TauThermostat, isPositive());
225 >    CheckParameter(TauBarostat, isPositive());
226 >    CheckParameter(ZconsTime, isPositive());
227 >    CheckParameter(ZconsTol, isPositive());
228 >    CheckParameter(Seed, isPositive());
229 >    CheckParameter(ZconsGap, isPositive());
230 >    CheckParameter(ZconsFixtime, isPositive());
231 >    CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
232 >    CheckParameter(ThermodynamicIntegrationK, isPositive());
233 >    CheckParameter(ForceFieldVariant, isNotEmpty());
234 >    CheckParameter(ForceFieldFileName, isNotEmpty());
235 >    CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") ||
236 >                   isEqualIgnoreCase("SWITCHED") ||
237 >                   isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
238 >                   isEqualIgnoreCase("SHIFTED_FORCE") ||
239 >                   isEqualIgnoreCase("TAYLOR_SHIFTED") ||
240 >                   isEqualIgnoreCase("EWALD_FULL"));
241 >    CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") ||
242 >                   isEqualIgnoreCase("MAX") ||
243 >                   isEqualIgnoreCase("TRADITIONAL"));
244 >    CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") ||
245 >                   isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") ||
246 >                   isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
247 >                   isEqualIgnoreCase("SHIFTED_FORCE") ||
248 >                   isEqualIgnoreCase("REACTION_FIELD") ||
249 >                   isEqualIgnoreCase("TAYLOR_SHIFTED"));
250 >    CheckParameter(ElectrostaticScreeningMethod,
251 >                   isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
252 >    CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") ||
253 >                   isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
254 >    CheckParameter(OrthoBoxTolerance, isPositive());  
255 >    CheckParameter(DampingAlpha,isNonNegative());
256 >    CheckParameter(SkinThickness, isPositive());
257 >    CheckParameter(Viscosity, isNonNegative());
258 >    CheckParameter(BeadSize, isPositive());
259 >    CheckParameter(FrozenBufferRadius, isPositive());
260 >    CheckParameter(LangevinBufferRadius, isPositive());
261 >    CheckParameter(NeighborListNeighbors, isPositive());
262 >    CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") ||
263 >                   isEqualIgnoreCase("AlphaShape"));
264 >    CheckParameter(Alpha, isPositive());
265    
266 <  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
267 <    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
266 >    for(std::vector<Component*>::iterator i = components_.begin();
267 >        i != components_.end(); ++i) {
268 >      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
269          std::ostringstream oss;
270 <        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
270 >        oss << "Globals Error: can not find molecule stamp for component "
271 >            << (*i)->getType() << std::endl;
272          throw OpenMDException(oss.str());          
273 +      }
274      }
275    }
223 – }
276    
277 < bool Globals::addComponent(Component* comp) {
277 >  bool Globals::addComponent(Component* comp) {
278      components_.push_back(comp);
279      return true;
280 < }
280 >  }
281  
282 < bool Globals::addZConsStamp(ZConsStamp* zcons) {
282 >  bool Globals::addZConsStamp(ZConsStamp* zcons) {
283      zconstraints_.push_back(zcons);
284      return true;
285 < }
285 >  }
286  
287 < bool Globals::addRestraintStamp(RestraintStamp* rest) {
287 >  bool Globals::addRestraintStamp(RestraintStamp* rest) {
288      restraints_.push_back(rest);
289      return true;
290 < }
290 >  }
291  
292 < bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
292 >  bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
293 >    if (flucQpars_ != NULL)
294 >      delete flucQpars_;
295 >    
296 >    flucQpars_ = fqp;
297 >    return true;
298 >  }
299 >
300 >  bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
301 >    if (rnemdPars_ != NULL)
302 >      delete rnemdPars_;
303 >    
304 >    rnemdPars_ = rnemdPars;
305 >    return true;
306 >  }
307 >
308 >  bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
309 >    if (minimizerPars_ != NULL)
310 >      delete minimizerPars_;
311 >    
312 >    minimizerPars_ = miniPars;
313 >    return true;
314 >  }
315 >
316 >  bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
317      std::string molStampName = molStamp->getName();
318      std::map<std::string, MoleculeStamp*>::iterator i;
319      bool ret = false;
320      i = moleculeStamps_.find(molStampName);
321      if (i == moleculeStamps_.end()) {
322 <        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
323 <        ret = true;
322 >      moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
323 >      ret = true;
324      } else {
325 <        std::ostringstream oss;
326 <        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
327 <        throw OpenMDException(oss.str());  
325 >      std::ostringstream oss;
326 >      oss << "Globals Error: Molecule Stamp " << molStamp->getName()
327 >          << "appears multiple times\n";
328 >      throw OpenMDException(oss.str());  
329      }
330      return ret;
331 +  }
332   }
255 –
256 –
257 – }

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