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Comparing branches/development/src/io/Globals.cpp (file contents):
Revision 1729 by jmarr, Wed May 30 16:08:07 2012 UTC vs.
Revision 1877 by gezelter, Thu Jun 6 15:43:35 2013 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() {
55 <  DefineParameter(ForceField, "forceField")
56 <
57 <  DefineOptionalParameter(TargetTemp, "targetTemp");
58 <  DefineOptionalParameter(Ensemble, "ensemble");
59 <  DefineOptionalParameter(Dt, "dt");
60 <  DefineOptionalParameter(RunTime, "runTime");
61 <  DefineOptionalParameter(FinalConfig, "finalConfig");
62 <  DefineOptionalParameter(SampleTime, "sampleTime");
63 <  DefineOptionalParameter(ResetTime, "resetTime");
64 <  DefineOptionalParameter(StatusTime, "statusTime");
65 <  DefineOptionalParameter(CutoffRadius, "cutoffRadius");
66 <  DefineOptionalParameter(SwitchingRadius, "switchingRadius");
67 <  DefineOptionalParameter(TempSet, "tempSet");
68 <  DefineOptionalParameter(ThermalTime, "thermalTime");
69 <  DefineOptionalParameter(TargetPressure, "targetPressure");  
70 <  DefineOptionalParameter(TauThermostat, "tauThermostat");
71 <  DefineOptionalParameter(TauBarostat, "tauBarostat");
72 <  DefineOptionalParameter(ZconsTime, "zconsTime");
73 <  DefineOptionalParameter(ZconsTol, "zconsTol");
74 <  DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
75 <  DefineOptionalParameter(Seed, "seed");
76 <  DefineOptionalParameter(Minimizer, "minimizer");
77 <  DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
78 <  DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq");
79 <  DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
80 <  DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
81 <  DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
82 <  DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
83 <  DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
84 <  DefineOptionalParameter(ZconsGap, "zconsGap");
85 <  DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
86 <  DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
87 <  DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
88 <  DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
89 <  DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
90 <  DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
91 <  DefineOptionalParameter(DampingAlpha, "dampingAlpha");
92 <  DefineOptionalParameter(SurfaceTension, "surfaceTension");
93 <  DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
94 <  DefineOptionalParameter(PrintHeatFlux, "printHeatFlux");
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, "useMultipleTemperatureMethod");
105 <  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
106 <  DefineOptionalParameter(MTM_Ce, "MTM_Ce");
107 <  DefineOptionalParameter(MTM_G, "MTM_G");
108 <  DefineOptionalParameter(MTM_Io, "MTM_Io");
109 <  DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
110 <  DefineOptionalParameter(MTM_R, "MTM_R");
111 <  DefineOptionalParameter(Alpha, "alpha");
112 <
54 >  Globals::Globals() {
55    
56 <  DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
57 <  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
58 <  DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
117 <  DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
118 <  DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
119 <  DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
120 <  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
121 <  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
122 <  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false);
123 <  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false);
124 <  DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false);
125 <  DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false);
126 <  DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", false);
127 <  DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
128 <  DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
129 <  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
130 <  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_targetJzKE, "RNEMD_targetJzKE", 0.0);
67 <  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpx, "RNEMD_targetJzpx", 0.0);
68 <  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpy, "RNEMD_targetJzpy", 0.0);
69 <  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpz, "RNEMD_targetJzpz", 0.0);
70 <  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
71 <  DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false);
72 <  DefineOptionalParameterWithDefaultValue(RNEMD_outputTemperature, "RNEMD_outputTemperature", false);
73 <  DefineOptionalParameterWithDefaultValue(RNEMD_outputVx, "RNEMD_outputVx", false);
74 <  DefineOptionalParameterWithDefaultValue(RNEMD_outputVy, "RNEMD_outputVy", false);
75 <  // James put this in.
76 <  DefineOptionalParameterWithDefaultValue(RNEMD_outputDen, "RNEMD_outputDen", false);
77 <  DefineOptionalParameterWithDefaultValue(RNEMD_outputAh, "RNEMD_outputAh", false);
78 <  DefineOptionalParameterWithDefaultValue(RNEMD_outputVz, "RNEMD_outputVz", false);  
79 <  DefineOptionalParameterWithDefaultValue(RNEMD_outputXyzTemperature, "RNEMD_outputXyzTemperature", false);
80 <  DefineOptionalParameterWithDefaultValue(RNEMD_outputRotTemperature, "RNEMD_outputRotTemperature", false);
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 <  DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
96 <  DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
97 <  DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
98 <  DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
99 <  DefineOptionalParameterWithDefaultValue(FlucQPropagator, "flucQ.propagator", "NVT");
100 <  DefineOptionalParameterWithDefaultValue(FlucQFriction, "flucQ.friction", 1600.0);    
101 <  DefineOptionalParameterWithDefaultValue(FlucQTolerance, "flucQ.tolerance", 1.0e-6);    
102 <  DefineOptionalParameterWithDefaultValue(FlucQMaxIterations, "flucQ.maxIterations", 100);    
103 <  DefineOptionalParameterWithDefaultValue(FlucQTargetTemp, "flucQ.targetTemp", 1.0e-6);
104 <  DefineOptionalParameterWithDefaultValue(FlucQtauThermostat, "flucQ.tauThermostat", 10.0);
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  
115 <  deprecatedKeywords_.insert("nComponents");
116 <  deprecatedKeywords_.insert("nZconstraints");
117 <  deprecatedKeywords_.insert("initialConfig");
118 <  deprecatedKeywords_.insert("thermIntDistSpringConst");
119 <  deprecatedKeywords_.insert("thermIntThetaSpringConst");
120 <  deprecatedKeywords_.insert("thermIntOmegaSpringConst");
121 <  deprecatedKeywords_.insert("useSolidThermInt");  
122 <  deprecatedKeywords_.insert("useLiquidThermInt");
123 <    
124 < }
115 >  
116 >    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions,
117 >                                            "usePeriodicBoundaryConditions",
118 >                                            true);
119 >    DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial",
120 >                                            true);
121 >    DefineOptionalParameterWithDefaultValue(UseLongRangeCorrections,
122 >                                            "useLongRangeCorrections", true);
123 >    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime",
124 >                                            false);
125 >    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState,
126 >                                            "useInitialExtendedSystemState",
127 >                                            false);
128 >    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance,
129 >                                            "orthoBoxTolerance", 1E-6);  
130 >    DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod",
131 >                                            "SHIFTED_FORCE");
132 >    DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod,
133 >                                            "electrostaticScreeningMethod",
134 >                                            "DAMPED");
135 >    DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
136 >    DefineOptionalParameterWithDefaultValue(CompressDumpFile,
137 >                                            "compressDumpFile", false);
138 >    DefineOptionalParameterWithDefaultValue(PrintHeatFlux, "printHeatFlux",
139 >                                            false);
140 >    DefineOptionalParameterWithDefaultValue(OutputForceVector,
141 >                                            "outputForceVector", false);
142 >    DefineOptionalParameterWithDefaultValue(OutputParticlePotential,
143 >                                            "outputParticlePotential", false);
144 >    DefineOptionalParameterWithDefaultValue(OutputElectricField,
145 >                                            "outputElectricField", false);
146 >    DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges,
147 >                                            "outputFluctuatingCharges", false);
148 >    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness",
149 >                                            1.0);
150 >    DefineOptionalParameterWithDefaultValue(StatFileFormat,
151 >                                            "statFileFormat",
152 >                                            "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
153 >    DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions,
154 >                                            "useSphericalBoundaryConditions",
155 >                                            false);
156 >    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole,
157 >                                            "accumulateBoxDipole", false);
158 >    DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints",
159 >                                            false);
160 >    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file",
161 >                                            "idealCrystal.in");
162 >    DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration,
163 >                                            "useThermodynamicIntegration",
164 >                                            false);
165 >    DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
166  
167 < Globals::~Globals() {
167 >    deprecatedKeywords_.insert("nComponents");
168 >    deprecatedKeywords_.insert("nZconstraints");
169 >    deprecatedKeywords_.insert("initialConfig");
170 >    deprecatedKeywords_.insert("thermIntDistSpringConst");
171 >    deprecatedKeywords_.insert("thermIntThetaSpringConst");
172 >    deprecatedKeywords_.insert("thermIntOmegaSpringConst");
173 >    deprecatedKeywords_.insert("useSolidThermInt");  
174 >    deprecatedKeywords_.insert("useLiquidThermInt");
175 >    deprecatedKeywords_.insert("minimizerMaxIter");
176 >    deprecatedKeywords_.insert("minimizerWriteFreq");
177 >    deprecatedKeywords_.insert("minimizerStepSize");
178 >    deprecatedKeywords_.insert("minimizerFTol");
179 >    deprecatedKeywords_.insert("minimizerGTol");
180 >    deprecatedKeywords_.insert("minimizerLSTol");
181 >    deprecatedKeywords_.insert("minimizerLSMaxIter");
182 >
183 >    
184 >  }
185 >
186 >  Globals::~Globals() {
187      MemoryUtils::deletePointers(components_);
188      MemoryUtils::deletePointers(zconstraints_);
189      MemoryUtils::deletePointers(restraints_);
190 < }
190 >  }
191  
192 < void Globals::validate() {
193 <  DataHolder::validate();
192 >  void Globals::validate() {
193 >    DataHolder::validate();
194  
195 <  CheckParameter(ForceField, isNotEmpty());
196 <  CheckParameter(TargetTemp, isPositive());
197 <  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"));
198 <  CheckParameter(Dt, isPositive());
199 <  CheckParameter(RunTime, isPositive());
200 <  CheckParameter(FinalConfig, isNotEmpty());
201 <  CheckParameter(SampleTime, isNonNegative());
202 <  CheckParameter(ResetTime, isNonNegative());
203 <  CheckParameter(StatusTime, isNonNegative());
204 <  CheckParameter(CutoffRadius, isPositive());
205 <  CheckParameter(SwitchingRadius, isNonNegative());
206 <  CheckParameter(Dielectric, isPositive());
207 <  CheckParameter(ThermalTime,  isNonNegative());
208 <  CheckParameter(TauThermostat, isPositive());
209 <  CheckParameter(TauBarostat, isPositive());
210 <  CheckParameter(ZconsTime, isPositive());
211 <  CheckParameter(ZconsTol, isPositive());
212 <  CheckParameter(Seed, isPositive());
213 <  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
214 <  CheckParameter(MinimizerMaxIter, isPositive());
215 <  CheckParameter(MinimizerWriteFreq, isPositive());
216 <  CheckParameter(MinimizerStepSize, isPositive());
217 <  CheckParameter(MinimizerFTol, isPositive());
218 <  CheckParameter(MinimizerGTol, isPositive());
219 <  CheckParameter(MinimizerLSTol, isPositive());
220 <  CheckParameter(MinimizerLSMaxIter, isPositive());
221 <  CheckParameter(ZconsGap, isPositive());
222 <  CheckParameter(ZconsFixtime, isPositive());
223 <  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
224 <  CheckParameter(ThermodynamicIntegrationK, isPositive());
225 <  CheckParameter(ForceFieldVariant, isNotEmpty());
226 <  CheckParameter(ForceFieldFileName, isNotEmpty());
227 <  CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
228 <  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
229 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
230 <  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
231 <  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
232 <  CheckParameter(OrthoBoxTolerance, isPositive());  
233 <  CheckParameter(DampingAlpha,isNonNegative());
234 <  CheckParameter(SkinThickness, isPositive());
235 <  CheckParameter(Viscosity, isNonNegative());
236 <  CheckParameter(BeadSize, isPositive());
237 <  CheckParameter(FrozenBufferRadius, isPositive());
238 <  CheckParameter(LangevinBufferRadius, isPositive());
239 <  CheckParameter(NeighborListNeighbors, isPositive());
240 <  CheckParameter(RNEMD_exchangeTime, isPositive());
241 <  CheckParameter(RNEMD_nBins, isPositive() && isEven());
242 <  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"));
243 <  CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
244 <  CheckParameter(Alpha, isPositive());
245 <  CheckParameter(FlucQPropagator, isEqualIgnoreCase("NVT") || isEqualIgnoreCase("Langevin") || isEqualIgnoreCase("Minimizer") || isEqualIgnoreCase("Exact") );
246 <  CheckParameter(FlucQFriction, isNonNegative());    
247 <  CheckParameter(FlucQTolerance, isPositive());    
248 <  CheckParameter(FlucQMaxIterations, isPositive());    
249 <  CheckParameter(FlucQTargetTemp,  isNonNegative());
250 <  CheckParameter(FlucQtauThermostat, isPositive());
195 >    CheckParameter(ForceField, isNotEmpty());
196 >    CheckParameter(TargetTemp, isPositive());
197 >    CheckParameter(Ensemble, isEqualIgnoreCase("NVE") ||
198 >                   isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") ||
199 >                   isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") ||
200 >                   isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT")  ||
201 >                   isEqualIgnoreCase("LANGEVINDYNAMICS") ||
202 >                   isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") ||
203 >                   isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") ||
204 >                   isEqualIgnoreCase("NGT") ||
205 >                   isEqualIgnoreCase("LANGEVINHULL") ||
206 >                   isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD"));
207 >    CheckParameter(Dt, isPositive());
208 >    CheckParameter(RunTime, isPositive());
209 >    CheckParameter(FinalConfig, isNotEmpty());
210 >    CheckParameter(SampleTime, isNonNegative());
211 >    CheckParameter(ResetTime, isNonNegative());
212 >    CheckParameter(StatusTime, isNonNegative());
213 >    CheckParameter(CutoffRadius, isPositive());
214 >    CheckParameter(SwitchingRadius, isNonNegative());
215 >    CheckParameter(Dielectric, isPositive());
216 >    CheckParameter(ThermalTime,  isNonNegative());
217 >    CheckParameter(TauThermostat, isPositive());
218 >    CheckParameter(TauBarostat, isPositive());
219 >    CheckParameter(ZconsTime, isPositive());
220 >    CheckParameter(ZconsTol, isPositive());
221 >    CheckParameter(Seed, isPositive());
222 >    CheckParameter(ZconsGap, isPositive());
223 >    CheckParameter(ZconsFixtime, isPositive());
224 >    CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
225 >    CheckParameter(ThermodynamicIntegrationK, isPositive());
226 >    CheckParameter(ForceFieldVariant, isNotEmpty());
227 >    CheckParameter(ForceFieldFileName, isNotEmpty());
228 >    CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") ||
229 >                   isEqualIgnoreCase("SWITCHED") ||
230 >                   isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
231 >                   isEqualIgnoreCase("SHIFTED_FORCE") ||
232 >                   isEqualIgnoreCase("TAYLOR_SHIFTED"));
233 >    CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") ||
234 >                   isEqualIgnoreCase("MAX") ||
235 >                   isEqualIgnoreCase("TRADITIONAL"));
236 >    CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") ||
237 >                   isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") ||
238 >                   isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
239 >                   isEqualIgnoreCase("SHIFTED_FORCE") ||
240 >                   isEqualIgnoreCase("REACTION_FIELD") ||
241 >                   isEqualIgnoreCase("TAYLOR_SHIFTED"));
242 >    CheckParameter(ElectrostaticScreeningMethod,
243 >                   isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
244 >    CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") ||
245 >                   isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
246 >    CheckParameter(OrthoBoxTolerance, isPositive());  
247 >    CheckParameter(DampingAlpha,isNonNegative());
248 >    CheckParameter(SkinThickness, isPositive());
249 >    CheckParameter(Viscosity, isNonNegative());
250 >    CheckParameter(BeadSize, isPositive());
251 >    CheckParameter(FrozenBufferRadius, isPositive());
252 >    CheckParameter(LangevinBufferRadius, isPositive());
253 >    CheckParameter(NeighborListNeighbors, isPositive());
254 >    CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") ||
255 >                   isEqualIgnoreCase("AlphaShape"));
256 >    CheckParameter(Alpha, isPositive());
257    
258 <  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
259 <    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
258 >    for(std::vector<Component*>::iterator i = components_.begin();
259 >        i != components_.end(); ++i) {
260 >      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
261          std::ostringstream oss;
262 <        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
262 >        oss << "Globals Error: can not find molecule stamp for component "
263 >            << (*i)->getType() << std::endl;
264          throw OpenMDException(oss.str());          
265 +      }
266      }
267    }
268 < }
269 <
251 < bool Globals::addComponent(Component* comp) {
268 >  
269 >  bool Globals::addComponent(Component* comp) {
270      components_.push_back(comp);
271      return true;
272 < }
272 >  }
273  
274 < bool Globals::addZConsStamp(ZConsStamp* zcons) {
274 >  bool Globals::addZConsStamp(ZConsStamp* zcons) {
275      zconstraints_.push_back(zcons);
276      return true;
277 < }
277 >  }
278  
279 < bool Globals::addRestraintStamp(RestraintStamp* rest) {
279 >  bool Globals::addRestraintStamp(RestraintStamp* rest) {
280      restraints_.push_back(rest);
281      return true;
282 < }
282 >  }
283  
284 < bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
284 >  bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
285 >    if (flucQpars_ != NULL)
286 >      delete flucQpars_;
287 >    
288 >    flucQpars_ = fqp;
289 >    return true;
290 >  }
291 >
292 >  bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
293 >    if (rnemdPars_ != NULL)
294 >      delete rnemdPars_;
295 >    
296 >    rnemdPars_ = rnemdPars;
297 >    return true;
298 >  }
299 >
300 >  bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
301 >    if (minimizerPars_ != NULL)
302 >      delete minimizerPars_;
303 >    
304 >    minimizerPars_ = miniPars;
305 >    return true;
306 >  }
307 >
308 >  bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
309      std::string molStampName = molStamp->getName();
310      std::map<std::string, MoleculeStamp*>::iterator i;
311      bool ret = false;
312      i = moleculeStamps_.find(molStampName);
313      if (i == moleculeStamps_.end()) {
314 <        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
315 <        ret = true;
314 >      moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
315 >      ret = true;
316      } else {
317 <        std::ostringstream oss;
318 <        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
319 <        throw OpenMDException(oss.str());  
317 >      std::ostringstream oss;
318 >      oss << "Globals Error: Molecule Stamp " << molStamp->getName()
319 >          << "appears multiple times\n";
320 >      throw OpenMDException(oss.str());  
321      }
322      return ret;
323 +  }
324   }
281 –
282 –
283 – }

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