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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 2026 by gezelter, Wed Oct 22 12:23:59 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_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 <  DefineOptionalParameterWithDefaultValue(RNEMD_outputXyzTemperature, "RNEMD_outputXyzTemperature", false);
76 <  DefineOptionalParameterWithDefaultValue(RNEMD_outputRotTemperature, "RNEMD_outputRotTemperature", false);
77 <  DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
78 <  DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
79 <  DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
80 <  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 >    DefineOptionalParameter(UniformField, "uniformField");
95 >    DefineOptionalParameter(UniformGradient, "uniformGradient");
96 >    //DefineOptionalParameter(PeriodicField, "periodicField");
97 >    //DefineOptionalParameter(PeriodicFieldStrength, "periodicFieldStrength");
98 >    
99  
100 +    DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
101 +    DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
102 +    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
103 +    DefineOptionalParameter(HydroPropFile, "HydroPropFile");
104 +    DefineOptionalParameter(Viscosity, "viscosity");
105 +    DefineOptionalParameter(BeadSize, "beadSize");
106 +    DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
107 +    DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
108 +    DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
109 +    DefineOptionalParameter(UseMultipleTemperatureMethod,
110 +                            "useMultipleTemperatureMethod");
111 +    DefineOptionalParameter(ElectrostaticSummationMethod,
112 +                            "electrostaticSummationMethod");
113 +    DefineOptionalParameter(MTM_Ce, "MTM_Ce");
114 +    DefineOptionalParameter(MTM_G, "MTM_G");
115 +    DefineOptionalParameter(MTM_Io, "MTM_Io");
116 +    DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
117 +    DefineOptionalParameter(MTM_R, "MTM_R");
118 +    DefineOptionalParameter(Alpha, "alpha");
119 +    DefineOptionalParameter(ConstraintTime, "constraintTime");
120  
121 <  deprecatedKeywords_.insert("nComponents");
122 <  deprecatedKeywords_.insert("nZconstraints");
123 <  deprecatedKeywords_.insert("initialConfig");
124 <  deprecatedKeywords_.insert("thermIntDistSpringConst");
125 <  deprecatedKeywords_.insert("thermIntThetaSpringConst");
126 <  deprecatedKeywords_.insert("thermIntOmegaSpringConst");
127 <  deprecatedKeywords_.insert("useSolidThermInt");  
128 <  deprecatedKeywords_.insert("useLiquidThermInt");
129 <    
130 < }
121 >  
122 >    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions,
123 >                                            "usePeriodicBoundaryConditions",
124 >                                            true);
125 >    DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial",
126 >                                            true);
127 >    DefineOptionalParameterWithDefaultValue(UseLongRangeCorrections,
128 >                                            "useLongRangeCorrections", true);
129 >    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime",
130 >                                            false);
131 >    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState,
132 >                                            "useInitialExtendedSystemState",
133 >                                            false);
134 >    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance,
135 >                                            "orthoBoxTolerance", 1E-6);  
136 >    DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod",
137 >                                            "SHIFTED_FORCE");
138 >    DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod,
139 >                                            "electrostaticScreeningMethod",
140 >                                            "DAMPED");
141 >    DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
142 >    DefineOptionalParameterWithDefaultValue(CompressDumpFile,
143 >                                            "compressDumpFile", false);
144 >    DefineOptionalParameterWithDefaultValue(PrintHeatFlux, "printHeatFlux",
145 >                                            false);
146 >    DefineOptionalParameterWithDefaultValue(OutputForceVector,
147 >                                            "outputForceVector", false);
148 >    DefineOptionalParameterWithDefaultValue(OutputParticlePotential,
149 >                                            "outputParticlePotential", false);
150 >    DefineOptionalParameterWithDefaultValue(OutputElectricField,
151 >                                            "outputElectricField", false);
152 >    DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges,
153 >                                            "outputFluctuatingCharges", false);
154 >    DefineOptionalParameterWithDefaultValue(OutputSitePotential,
155 >                                            "outputSitePotential", false);
156 >    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness",
157 >                                            1.0);
158 >    DefineOptionalParameterWithDefaultValue(StatFileFormat,
159 >                                            "statFileFormat",
160 >                                            "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
161 >    DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions,
162 >                                            "useSphericalBoundaryConditions",
163 >                                            false);
164 >    DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole,
165 >                                            "accumulateBoxDipole", false);
166 >    DefineOptionalParameterWithDefaultValue(AccumulateBoxQuadrupole,
167 >                                            "accumulateBoxQuadrupole", false);
168 >    DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints",
169 >                                            false);
170 >    DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file",
171 >                                            "idealCrystal.in");
172 >    DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration,
173 >                                            "useThermodynamicIntegration",
174 >                                            false);
175 >    DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
176  
177 < Globals::~Globals() {
177 >    deprecatedKeywords_.insert("nComponents");
178 >    deprecatedKeywords_.insert("nZconstraints");
179 >    deprecatedKeywords_.insert("initialConfig");
180 >    deprecatedKeywords_.insert("thermIntDistSpringConst");
181 >    deprecatedKeywords_.insert("thermIntThetaSpringConst");
182 >    deprecatedKeywords_.insert("thermIntOmegaSpringConst");
183 >    deprecatedKeywords_.insert("useSolidThermInt");  
184 >    deprecatedKeywords_.insert("useLiquidThermInt");
185 >    deprecatedKeywords_.insert("minimizerMaxIter");
186 >    deprecatedKeywords_.insert("minimizerWriteFreq");
187 >    deprecatedKeywords_.insert("minimizerStepSize");
188 >    deprecatedKeywords_.insert("minimizerFTol");
189 >    deprecatedKeywords_.insert("minimizerGTol");
190 >    deprecatedKeywords_.insert("minimizerLSTol");
191 >    deprecatedKeywords_.insert("minimizerLSMaxIter");
192 >    deprecatedKeywords_.insert("electricField");
193 >
194 >    
195 >  }
196 >
197 >  Globals::~Globals() {
198      MemoryUtils::deletePointers(components_);
199      MemoryUtils::deletePointers(zconstraints_);
200      MemoryUtils::deletePointers(restraints_);
201 < }
201 >    delete flucQpars_;
202 >    delete rnemdPars_;
203 >    delete minimizerPars_;
204 >  }
205  
206 < void Globals::validate() {
207 <  DataHolder::validate();
206 >  void Globals::validate() {
207 >    DataHolder::validate();
208  
209 <  CheckParameter(ForceField, isNotEmpty());
210 <  CheckParameter(TargetTemp, isPositive());
211 <  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"));
212 <  CheckParameter(Dt, isPositive());
213 <  CheckParameter(RunTime, isPositive());
214 <  CheckParameter(FinalConfig, isNotEmpty());
215 <  CheckParameter(SampleTime, isNonNegative());
216 <  CheckParameter(ResetTime, isNonNegative());
217 <  CheckParameter(StatusTime, isNonNegative());
218 <  CheckParameter(CutoffRadius, isPositive());
219 <  CheckParameter(SwitchingRadius, isNonNegative());
220 <  CheckParameter(Dielectric, isPositive());
221 <  CheckParameter(ThermalTime,  isNonNegative());
222 <  CheckParameter(TauThermostat, isPositive());
223 <  CheckParameter(TauBarostat, isPositive());
224 <  CheckParameter(ZconsTime, isPositive());
225 <  CheckParameter(ZconsTol, isPositive());
226 <  CheckParameter(Seed, isPositive());
227 <  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
228 <  CheckParameter(MinimizerMaxIter, isPositive());
229 <  CheckParameter(MinimizerWriteFreq, isPositive());
230 <  CheckParameter(MinimizerStepSize, isPositive());
231 <  CheckParameter(MinimizerFTol, isPositive());
232 <  CheckParameter(MinimizerGTol, isPositive());
233 <  CheckParameter(MinimizerLSTol, isPositive());
234 <  CheckParameter(MinimizerLSMaxIter, isPositive());
235 <  CheckParameter(ZconsGap, isPositive());
236 <  CheckParameter(ZconsFixtime, isPositive());
237 <  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
238 <  CheckParameter(ThermodynamicIntegrationK, isPositive());
239 <  CheckParameter(ForceFieldVariant, isNotEmpty());
240 <  CheckParameter(ForceFieldFileName, isNotEmpty());
241 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
242 <  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
243 <  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
244 <  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
245 <  //CheckParameter(StatFileFormat,);    
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(RNEMD_exchangeTime, isPositive());
255 <  CheckParameter(RNEMD_nBins, isPositive() && isEven());
256 <  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"));
257 <  //CheckParameter(RNEMD_targetFlux, isNonNegative());
258 <  CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
259 <  CheckParameter(Alpha, isPositive());
260 <
209 >    CheckParameter(ForceField, isNotEmpty());
210 >    CheckParameter(TargetTemp, isPositive());
211 >    CheckParameter(Ensemble, isEqualIgnoreCase("NVE") ||
212 >                   isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") ||
213 >                   isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") ||
214 >                   isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT")  ||
215 >                   isEqualIgnoreCase("NPA") ||
216 >                   isEqualIgnoreCase("LANGEVINDYNAMICS") ||
217 >                   isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") ||
218 >                   isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") ||
219 >                   isEqualIgnoreCase("NGT") ||
220 >                   isEqualIgnoreCase("LANGEVINHULL") ||
221 >                   isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD"));
222 >    CheckParameter(Dt, isPositive());
223 >    CheckParameter(RunTime, isPositive());
224 >    CheckParameter(FinalConfig, isNotEmpty());
225 >    CheckParameter(SampleTime, isNonNegative());
226 >    CheckParameter(ResetTime, isNonNegative());
227 >    CheckParameter(StatusTime, isNonNegative());
228 >    CheckParameter(CutoffRadius, isPositive());
229 >    CheckParameter(SwitchingRadius, isNonNegative());
230 >    CheckParameter(Dielectric, isPositive());
231 >    CheckParameter(ThermalTime,  isNonNegative());
232 >    CheckParameter(TauThermostat, isPositive());
233 >    CheckParameter(TauBarostat, isPositive());
234 >    CheckParameter(ZconsTime, isPositive());
235 >    CheckParameter(ZconsTol, isPositive());
236 >    CheckParameter(Seed, isPositive());
237 >    CheckParameter(ZconsGap, isPositive());
238 >    CheckParameter(ZconsFixtime, isPositive());
239 >    CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
240 >    CheckParameter(ThermodynamicIntegrationK, isPositive());
241 >    CheckParameter(ForceFieldVariant, isNotEmpty());
242 >    CheckParameter(ForceFieldFileName, isNotEmpty());
243 >    CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") ||
244 >                   isEqualIgnoreCase("SWITCHED") ||
245 >                   isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
246 >                   isEqualIgnoreCase("SHIFTED_FORCE") ||
247 >                   isEqualIgnoreCase("TAYLOR_SHIFTED") ||
248 >                   isEqualIgnoreCase("EWALD_FULL"));
249 >    CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") ||
250 >                   isEqualIgnoreCase("MAX") ||
251 >                   isEqualIgnoreCase("TRADITIONAL"));
252 >    CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") ||
253 >                   isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") ||
254 >                   isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
255 >                   isEqualIgnoreCase("SHIFTED_FORCE") ||
256 >                   isEqualIgnoreCase("REACTION_FIELD") ||
257 >                   isEqualIgnoreCase("TAYLOR_SHIFTED"));
258 >    CheckParameter(ElectrostaticScreeningMethod,
259 >                   isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
260 >    CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") ||
261 >                   isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
262 >    CheckParameter(OrthoBoxTolerance, isPositive());  
263 >    CheckParameter(DampingAlpha,isNonNegative());
264 >    CheckParameter(SkinThickness, isPositive());
265 >    CheckParameter(Viscosity, isNonNegative());
266 >    CheckParameter(BeadSize, isPositive());
267 >    CheckParameter(FrozenBufferRadius, isPositive());
268 >    CheckParameter(LangevinBufferRadius, isPositive());
269 >    CheckParameter(NeighborListNeighbors, isPositive());
270 >    CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") ||
271 >                   isEqualIgnoreCase("AlphaShape"));
272 >    CheckParameter(Alpha, isPositive());
273    
274 <  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
275 <    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
274 >    for(std::vector<Component*>::iterator i = components_.begin();
275 >        i != components_.end(); ++i) {
276 >      if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
277          std::ostringstream oss;
278 <        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
278 >        oss << "Globals Error: can not find molecule stamp for component "
279 >            << (*i)->getType() << std::endl;
280          throw OpenMDException(oss.str());          
281 +      }
282      }
283    }
231 – }
284    
285 < bool Globals::addComponent(Component* comp) {
285 >  bool Globals::addComponent(Component* comp) {
286      components_.push_back(comp);
287      return true;
288 < }
288 >  }
289  
290 < bool Globals::addZConsStamp(ZConsStamp* zcons) {
290 >  bool Globals::addZConsStamp(ZConsStamp* zcons) {
291      zconstraints_.push_back(zcons);
292      return true;
293 < }
293 >  }
294  
295 < bool Globals::addRestraintStamp(RestraintStamp* rest) {
295 >  bool Globals::addRestraintStamp(RestraintStamp* rest) {
296      restraints_.push_back(rest);
297      return true;
298 < }
298 >  }
299  
300 < bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
300 >  bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
301 >    if (flucQpars_ != NULL)
302 >      delete flucQpars_;
303 >    
304 >    flucQpars_ = fqp;
305 >    return true;
306 >  }
307 >
308 >  bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
309 >    if (rnemdPars_ != NULL)
310 >      delete rnemdPars_;
311 >    
312 >    rnemdPars_ = rnemdPars;
313 >    return true;
314 >  }
315 >
316 >  bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
317 >    if (minimizerPars_ != NULL)
318 >      delete minimizerPars_;
319 >    
320 >    minimizerPars_ = miniPars;
321 >    return true;
322 >  }
323 >
324 >  bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
325      std::string molStampName = molStamp->getName();
326      std::map<std::string, MoleculeStamp*>::iterator i;
327      bool ret = false;
328      i = moleculeStamps_.find(molStampName);
329      if (i == moleculeStamps_.end()) {
330 <        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
331 <        ret = true;
330 >      moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
331 >      ret = true;
332      } else {
333 <        std::ostringstream oss;
334 <        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
335 <        throw OpenMDException(oss.str());  
333 >      std::ostringstream oss;
334 >      oss << "Globals Error: Molecule Stamp " << molStamp->getName()
335 >          << "appears multiple times\n";
336 >      throw OpenMDException(oss.str());  
337      }
338      return ret;
339 +  }
340   }
263 –
264 –
265 – }

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