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root/OpenMD/branches/development/src/io/Globals.cpp

Comparing:
trunk/src/io/Globals.cpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/io/Globals.cpp (file contents), Revision 1780 by jmarr, Mon Aug 20 18:28:22 2012 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2	>	* Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
#	Line 36 | Line 36
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38		* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include <stdlib.h>
#	Line 51 | Line 52 | Globals::Globals() {
52
53		namespace OpenMD {
54		Globals::Globals() {
55	+
56	+	flucQpars_ = new FluctuatingChargeParameters();
57	+	rnemdPars_ = new RNEMDParameters();
58	+	minimizerPars_ = new MinimizerParameters();
59	+
60		DefineParameter(ForceField, "forceField")
61
62		DefineOptionalParameter(TargetTemp, "targetTemp");
#	Line 72 | Line 78 | Globals::Globals() {
78		DefineOptionalParameter(ZconsTol, "zconsTol");
79		DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
80		DefineOptionalParameter(Seed, "seed");
75	–	DefineOptionalParameter(Minimizer, "minimizer");
76	–	DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
77	–	DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
78	–	DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
79	–	DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
80	–	DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
81	–	DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
82	–	DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
81		DefineOptionalParameter(ZconsGap, "zconsGap");
82		DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
83		DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
#	Line 90 | Line 88 | Globals::Globals() {
88		DefineOptionalParameter(DampingAlpha, "dampingAlpha");
89		DefineOptionalParameter(SurfaceTension, "surfaceTension");
90		DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
91	+	DefineOptionalParameter(ElectricField, "electricField");
92	+
93		DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
94		DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
95	–	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
95		DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
96		DefineOptionalParameter(HydroPropFile, "HydroPropFile");
97		DefineOptionalParameter(Viscosity, "viscosity");
98		DefineOptionalParameter(BeadSize, "beadSize");
99		DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
100		DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
102	–	DefineOptionalParameter(ThermalConductivity, "thermalConductivity");
103	–	DefineOptionalParameter(ThermalLength, "thermalLength");
101		DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
102		DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
103	+	DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
104		DefineOptionalParameter(MTM_Ce, "MTM_Ce");
105		DefineOptionalParameter(MTM_G, "MTM_G");
106		DefineOptionalParameter(MTM_Io, "MTM_Io");
107		DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
108		DefineOptionalParameter(MTM_R, "MTM_R");
109	<
109	>	DefineOptionalParameter(Alpha, "alpha");
110
111
112		DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
#	Line 116 | Line 114 | Globals::Globals() {
114		DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
115		DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
116		DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
117	<	DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
117	>	DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
118		DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
119	<	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
120	<	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
121	<	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
119	>	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
120	>	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false);
121	>	DefineOptionalParameterWithDefaultValue(PrintHeatFlux, "printHeatFlux", false);
122	>	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false);
123	>	DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false);
124	>	DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false);
125	>	DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", false);
126		DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
127		DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
128		DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
129		DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
130
129	–	DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
130	–	DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
131	–	DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
132	–	DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
133	–	DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
134	–	DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
135	–	DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
131		DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
132		DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
133		DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
134	+	DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
135
140	–
136		deprecatedKeywords_.insert("nComponents");
137		deprecatedKeywords_.insert("nZconstraints");
138		deprecatedKeywords_.insert("initialConfig");
#	Line 146 | Line 141 | Globals::Globals() {
141		deprecatedKeywords_.insert("thermIntOmegaSpringConst");
142		deprecatedKeywords_.insert("useSolidThermInt");
143		deprecatedKeywords_.insert("useLiquidThermInt");
144	+	deprecatedKeywords_.insert("minimizerMaxIter");
145	+	deprecatedKeywords_.insert("minimizerWriteFreq");
146	+	deprecatedKeywords_.insert("minimizerStepSize");
147	+	deprecatedKeywords_.insert("minimizerFTol");
148	+	deprecatedKeywords_.insert("minimizerGTol");
149	+	deprecatedKeywords_.insert("minimizerLSTol");
150	+	deprecatedKeywords_.insert("minimizerLSMaxIter");
151	+
152
153		}
154
#	Line 160 | Line 163 | void Globals::validate() {
163
164		CheckParameter(ForceField, isNotEmpty());
165		CheckParameter(TargetTemp, isPositive());
166	<	CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || isEqualIgnoreCase("SMIPD"));
166	>	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"));
167		CheckParameter(Dt, isPositive());
168		CheckParameter(RunTime, isPositive());
169		CheckParameter(FinalConfig, isNotEmpty());
#	Line 176 | Line 179 | void Globals::validate() {
179		CheckParameter(ZconsTime, isPositive());
180		CheckParameter(ZconsTol, isPositive());
181		CheckParameter(Seed, isPositive());
179	–	CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
180	–	CheckParameter(MinimizerMaxIter, isPositive());
181	–	CheckParameter(MinimizerWriteFrq, isPositive());
182	–	CheckParameter(MinimizerStepSize, isPositive());
183	–	CheckParameter(MinimizerFTol, isPositive());
184	–	CheckParameter(MinimizerGTol, isPositive());
185	–	CheckParameter(MinimizerLSTol, isPositive());
186	–	CheckParameter(MinimizerLSMaxIter, isPositive());
182		CheckParameter(ZconsGap, isPositive());
183		CheckParameter(ZconsFixtime, isPositive());
184		CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
185		CheckParameter(ThermodynamicIntegrationK, isPositive());
186		CheckParameter(ForceFieldVariant, isNotEmpty());
187		CheckParameter(ForceFieldFileName, isNotEmpty());
188	<	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
194	<	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
188	>	CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
189		CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
190	+	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
191	+	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
192		CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
197	–	//CheckParameter(StatFileFormat,);
193		CheckParameter(OrthoBoxTolerance, isPositive());
194		CheckParameter(DampingAlpha,isNonNegative());
195		CheckParameter(SkinThickness, isPositive());
196		CheckParameter(Viscosity, isNonNegative());
202	–	CheckParameter(ThermalConductivity, isNonNegative());
203	–	CheckParameter(ThermalLength, isNonNegative());
197		CheckParameter(BeadSize, isPositive());
198		CheckParameter(FrozenBufferRadius, isPositive());
199		CheckParameter(LangevinBufferRadius, isPositive());
200		CheckParameter(NeighborListNeighbors, isPositive());
201	<	CheckParameter(RNEMD_exchangeTime, isPositive());
202	<	CheckParameter(RNEMD_nBins, isPositive() && isEven());
203	<	CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
211	<	CheckParameter(RNEMD_targetFlux, isNonNegative());
212	<
201	>	CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
202	>	CheckParameter(Alpha, isPositive());
203	>
204		for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
205		if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
206		std::ostringstream oss;
#	Line 218 | Line 209 | void Globals::validate() {
209		}
210		}
211		}
212	<
212	>
213		bool Globals::addComponent(Component* comp) {
214		components_.push_back(comp);
215		return true;
#	Line 234 | Line 225 | bool Globals::addRestraintStamp(RestraintStamp* rest)
225		return true;
226		}
227
228	+	bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
229	+	if (flucQpars_ != NULL)
230	+	delete flucQpars_;
231	+
232	+	flucQpars_ = fqp;
233	+	return true;
234	+	}
235	+
236	+	bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
237	+	if (rnemdPars_ != NULL)
238	+	delete rnemdPars_;
239	+
240	+	rnemdPars_ = rnemdPars;
241	+	return true;
242	+	}
243	+
244	+	bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
245	+	if (minimizerPars_ != NULL)
246	+	delete minimizerPars_;
247	+
248	+	minimizerPars_ = miniPars;
249	+	return true;
250	+	}
251	+
252		bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
253		std::string molStampName = molStamp->getName();
254		std::map<std::string, MoleculeStamp*>::iterator i;

Comparing:
trunk/src/io/Globals.cpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/io/Globals.cpp (property svn:keywords), Revision 1780 by jmarr, Mon Aug 20 18:28:22 2012 UTC

#	Line 0 | Line 1
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