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root/OpenMD/trunk/src/io/Globals.cpp

Comparing trunk/src/io/Globals.cpp (file contents):
Revision 1398 by gezelter, Tue Dec 8 22:17:02 2009 UTC vs.
Revision 2011 by gezelter, Wed Aug 6 19:27:37 2014 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 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(MinimizerWriteFrq, "minimizerWriteFrq");
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");
54	>	Globals::Globals() {
55
56	+	flucQpars_ = new FluctuatingChargeParameters();
57	+	rnemdPars_ = new RNEMDParameters();
58	+	minimizerPars_ = new MinimizerParameters();
59
60	<
61	<	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
62	<	DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
63	<	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
64	<	DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
65	<	DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
66	<	DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
67	<	DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
68	<	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
69	<	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
70	<	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
71	<	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
72	<	DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
73	<	DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
74	<	DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", 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(UseRNEMD, "useRNEMD", false);
96	<	DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
97	<	DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
98	<	DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
99	<	DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
100	<	DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
101	<	DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
102	<	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
103	<	DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
104	<	DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
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	+
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	<	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	<
179	<	}
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	<	Globals::~Globals() {
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("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || 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(MinimizerWriteFrq, 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	<
251	<	for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
252	<	if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
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();
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		}
216	–	}
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		}
248	–
249	–
250	–	}

Comparing trunk/src/io/Globals.cpp (property svn:keywords):
Revision 1398 by gezelter, Tue Dec 8 22:17:02 2009 UTC vs.
Revision 2011 by gezelter, Wed Aug 6 19:27:37 2014 UTC

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