ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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 1744 by gezelter, Tue Jun 5 18:07:08 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	+
59		DefineParameter(ForceField, "forceField")
60
61		DefineOptionalParameter(TargetTemp, "targetTemp");
#	Line 74 | Line 79 | Globals::Globals() {
79		DefineOptionalParameter(Seed, "seed");
80		DefineOptionalParameter(Minimizer, "minimizer");
81		DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
82	<	DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
82	>	DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq");
83		DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
84		DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
85		DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
#	Line 90 | Line 95 | Globals::Globals() {
95		DefineOptionalParameter(DampingAlpha, "dampingAlpha");
96		DefineOptionalParameter(SurfaceTension, "surfaceTension");
97		DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
98	+	DefineOptionalParameter(PrintHeatFlux, "printHeatFlux");
99		DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
100		DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
95	–	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
101		DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
102		DefineOptionalParameter(HydroPropFile, "HydroPropFile");
103		DefineOptionalParameter(Viscosity, "viscosity");
104		DefineOptionalParameter(BeadSize, "beadSize");
105		DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
106		DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
102	–	DefineOptionalParameter(ThermalConductivity, "thermalConductivity");
103	–	DefineOptionalParameter(ThermalLength, "thermalLength");
107		DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
108		DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
109	+	DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
110		DefineOptionalParameter(MTM_Ce, "MTM_Ce");
111		DefineOptionalParameter(MTM_G, "MTM_G");
112		DefineOptionalParameter(MTM_Io, "MTM_Io");
113		DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
114		DefineOptionalParameter(MTM_R, "MTM_R");
115	<
115	>	DefineOptionalParameter(Alpha, "alpha");
116
117
118		DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
#	Line 116 | Line 120 | Globals::Globals() {
120		DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
121		DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
122		DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
123	<	DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
123	>	DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
124		DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
125	<	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
126	<	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
127	<	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
125	>	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
126	>	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false);
127	>	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false);
128	>	DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false);
129	>	DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false);
130	>	DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", false);
131		DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
132		DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
133		DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
134		DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
135
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");
136		DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
137		DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
138		DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
139	<
139	>	DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
140
141		deprecatedKeywords_.insert("nComponents");
142		deprecatedKeywords_.insert("nZconstraints");
#	Line 160 | Line 160 | void Globals::validate() {
160
161		CheckParameter(ForceField, isNotEmpty());
162		CheckParameter(TargetTemp, isPositive());
163	<	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"));
163	>	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"));
164		CheckParameter(Dt, isPositive());
165		CheckParameter(RunTime, isPositive());
166		CheckParameter(FinalConfig, isNotEmpty());
#	Line 178 | Line 178 | void Globals::validate() {
178		CheckParameter(Seed, isPositive());
179		CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
180		CheckParameter(MinimizerMaxIter, isPositive());
181	<	CheckParameter(MinimizerWriteFrq, isPositive());
181	>	CheckParameter(MinimizerWriteFreq, isPositive());
182		CheckParameter(MinimizerStepSize, isPositive());
183		CheckParameter(MinimizerFTol, isPositive());
184		CheckParameter(MinimizerGTol, isPositive());
#	Line 190 | Line 190 | void Globals::validate() {
190		CheckParameter(ThermodynamicIntegrationK, isPositive());
191		CheckParameter(ForceFieldVariant, isNotEmpty());
192		CheckParameter(ForceFieldFileName, isNotEmpty());
193	<	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
194	<	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
193	>	CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
194		CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
195	+	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
196	+	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
197		CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
197	–	//CheckParameter(StatFileFormat,);
198		CheckParameter(OrthoBoxTolerance, isPositive());
199		CheckParameter(DampingAlpha,isNonNegative());
200		CheckParameter(SkinThickness, isPositive());
201		CheckParameter(Viscosity, isNonNegative());
202	–	CheckParameter(ThermalConductivity, isNonNegative());
203	–	CheckParameter(ThermalLength, isNonNegative());
202		CheckParameter(BeadSize, isPositive());
203		CheckParameter(FrozenBufferRadius, isPositive());
204		CheckParameter(LangevinBufferRadius, isPositive());
205		CheckParameter(NeighborListNeighbors, isPositive());
206	<	CheckParameter(RNEMD_exchangeTime, isPositive());
207	<	CheckParameter(RNEMD_nBins, isPositive() && isEven());
208	<	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	<
206	>	CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
207	>	CheckParameter(Alpha, isPositive());
208	>
209		for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
210		if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
211		std::ostringstream oss;
#	Line 218 | Line 214 | void Globals::validate() {
214		}
215		}
216		}
217	<
217	>
218		bool Globals::addComponent(Component* comp) {
219		components_.push_back(comp);
220		return true;
#	Line 234 | Line 230 | bool Globals::addRestraintStamp(RestraintStamp* rest)
230		return true;
231		}
232
233	+	bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
234	+	if (flucQpars_ != NULL)
235	+	delete flucQpars_;
236	+
237	+	flucQpars_ = fqp;
238	+	return true;
239	+	}
240	+
241	+	bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
242	+	if (rnemdPars_ != NULL)
243	+	delete rnemdPars_;
244	+
245	+	rnemdPars_ = rnemdPars;
246	+	return true;
247	+	}
248	+
249		bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
250		std::string molStampName = molStamp->getName();
251		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 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines