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

Comparing trunk/src/io/Globals.cpp (file contents):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 2057 by gezelter, Tue Mar 3 15:22:26 2015 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
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
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, 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 45 | Line 46
46		#include <string>
47
48		#include "io/Globals.hpp"
49	+	#include "io/ParamConstraint.hpp"
50	+	#include "utils/MemoryUtils.hpp"
51		#include "utils/simError.h"
52
53	<	#include "io/ParamConstraint.hpp"
53	>	namespace OpenMD {
54	>	Globals::Globals() {
55	>
56	>	flucQpars_ = new FluctuatingChargeParameters();
57	>	rnemdPars_ = new RNEMDParameters();
58	>	minimizerPars_ = new MinimizerParameters();
59
60	<	namespace oopse {
53	<	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(InitialConfig, "initialConfig");
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(Dielectric, "dielectric");
68	<	DefineOptionalParameter(TempSet, "tempSet");
69	<	DefineOptionalParameter(ThermalTime, "thermalTime");
70	<	DefineOptionalParameter(TargetPressure, "targetPressure");
71	<	DefineOptionalParameter(TauThermostat, "tauThermostat");
72	<	DefineOptionalParameter(TauBarostat, "tauBarostat");
73	<	DefineOptionalParameter(ZconsTime, "zconsTime");
74	<	DefineOptionalParameter(ZconsTol, "zconsTol");
75	<	DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
76	<	DefineOptionalParameter(Seed, "seed");
77	<	DefineOptionalParameter(Minimizer, "minimizer");
78	<	DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
79	<	DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
80	<	DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
81	<	DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
82	<	DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
83	<	DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
84	<	DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
85	<	DefineOptionalParameter(ZconsGap, "zconsGap");
86	<	DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
87	<	DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
88	<	DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
89	<	DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
90	<	DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
91	<	DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
92	<	DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
93	<	DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
94	<	DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
95	<	DefineOptionalParameter(SurfaceTension, "surfaceTension");
96	<	DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
97	<	DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
98	<	DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
99	<	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
100	<	DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
101	<	DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
102	<	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
103	<	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
104	<	DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
105	<	DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
106	<	DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
107	<	DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
108	<	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
109	<	DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
110	<	DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
111	<	DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
112	<	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
113	<	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
114	<	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
115	<	DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
116	<
117	<
118	<	deprecatedKeywords_.insert("nComponents");
119	<	deprecatedKeywords_.insert("nZconstraints");
60	>	DefineParameter(ForceField, "forceField");
61
62	<	}
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(UniformGradientStrength, "uniformGradientStrength");
96	>	DefineOptionalParameter(UniformGradientDirection1, "uniformGradientDirection1");
97	>	DefineOptionalParameter(UniformGradientDirection2, "uniformGradientDirection2");
98	>	//DefineOptionalParameter(PeriodicField, "periodicField");
99	>	//DefineOptionalParameter(PeriodicFieldStrength, "periodicFieldStrength");
100	>
101
102	<	Globals::~Globals() {
102	>	DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
103	>	DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
104	>	DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
105	>	DefineOptionalParameter(HydroPropFile, "HydroPropFile");
106	>	DefineOptionalParameter(Viscosity, "viscosity");
107	>	DefineOptionalParameter(BeadSize, "beadSize");
108	>	DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
109	>	DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
110	>	DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
111	>	DefineOptionalParameter(UseMultipleTemperatureMethod,
112	>	"useMultipleTemperatureMethod");
113	>	DefineOptionalParameter(ElectrostaticSummationMethod,
114	>	"electrostaticSummationMethod");
115	>	DefineOptionalParameter(MTM_Ce, "MTM_Ce");
116	>	DefineOptionalParameter(MTM_G, "MTM_G");
117	>	DefineOptionalParameter(MTM_Io, "MTM_Io");
118	>	DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
119	>	DefineOptionalParameter(MTM_R, "MTM_R");
120	>	DefineOptionalParameter(Alpha, "alpha");
121	>	DefineOptionalParameter(ConstraintTime, "constraintTime");
122
123	<
124	<	}
125	<
126	<	void Globals::validate() {
127	<	DataHolder::validate();
128	<
129	<	CheckParameter(ForceField, isNotEmpty());
130	<	CheckParameter(TargetTemp, isPositive());
131	<	CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) || isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf")) || isEqualIgnoreCase(std::string("NPTxyz")) );
132	<	CheckParameter(Dt, isPositive());
133	<	CheckParameter(RunTime, isPositive());
134	<	CheckParameter(InitialConfig, isNotEmpty());
135	<	CheckParameter(FinalConfig, isNotEmpty());
136	<	CheckParameter(SampleTime, isNonNegative());
137	<	CheckParameter(ResetTime, isNonNegative());
138	<	CheckParameter(StatusTime, isNonNegative());
139	<	CheckParameter(CutoffRadius, isPositive());
140	<	CheckParameter(SwitchingRadius, isNonNegative());
141	<	CheckParameter(Dielectric, isPositive());
142	<	CheckParameter(ThermalTime,  isNonNegative());
143	<	CheckParameter(TargetPressure,  isPositive());
144	<	CheckParameter(TauThermostat, isPositive());
145	<	CheckParameter(TauBarostat, isPositive());
146	<	CheckParameter(ZconsTime, isPositive());
147	<	CheckParameter(ZconsTol, isPositive());
148	<	CheckParameter(Seed, isPositive());
149	<	CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
150	<	CheckParameter(MinimizerMaxIter, isPositive());
151	<	CheckParameter(MinimizerWriteFrq, isPositive());
152	<	CheckParameter(MinimizerStepSize, isPositive());
153	<	CheckParameter(MinimizerFTol, isPositive());
154	<	CheckParameter(MinimizerGTol, isPositive());
155	<	CheckParameter(MinimizerLSTol, isPositive());
156	<	CheckParameter(MinimizerLSMaxIter, isPositive());
157	<	CheckParameter(ZconsGap, isPositive());
158	<	CheckParameter(ZconsFixtime, isPositive());
159	<	CheckParameter(ThermodynamicIntegrationLambda, isPositive());
160	<	CheckParameter(ThermodynamicIntegrationK, isPositive());
161	<	CheckParameter(ForceFieldVariant, isNotEmpty());
162	<	CheckParameter(ForceFieldFileName, isNotEmpty());
163	<	CheckParameter(ThermIntDistSpringConst, isPositive());
164	<	CheckParameter(ThermIntThetaSpringConst, isPositive());
165	<	CheckParameter(ThermIntOmegaSpringConst, isPositive());
166	<	CheckParameter(SurfaceTension, isPositive());
167	<	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE")) || isEqualIgnoreCase(std::string("REACTION_FIELD")));
168	<	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED")));
169	<	CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
170	<	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase(std::string("CUBIC")) || isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
171	<	//CheckParameter(StatFileFormat,);
172	<	//CheckParameter(MixingRule,);
173	<	CheckParameter(OrthoBoxTolerance, isPositive());
174	<	CheckParameter(ThermIntDistSpringConst, isPositive());
175	<	CheckParameter(ThermIntThetaSpringConst, isPositive());
176	<	CheckParameter(ThermIntOmegaSpringConst, isPositive());
177	<	CheckParameter(DampingAlpha,isNonNegative());
180	<	CheckParameter(SkinThickness, isPositive());
123	>
124	>	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions,
125	>	"usePeriodicBoundaryConditions",
126	>	true);
127	>	DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial",
128	>	true);
129	>	DefineOptionalParameterWithDefaultValue(UseLongRangeCorrections,
130	>	"useLongRangeCorrections", true);
131	>	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime",
132	>	false);
133	>	DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState,
134	>	"useInitialExtendedSystemState",
135	>	false);
136	>	DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance,
137	>	"orthoBoxTolerance", 1E-6);
138	>	DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod",
139	>	"SHIFTED_FORCE");
140	>	DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod,
141	>	"electrostaticScreeningMethod",
142	>	"DAMPED");
143	>	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
144	>	DefineOptionalParameterWithDefaultValue(CompressDumpFile,
145	>	"compressDumpFile", false);
146	>	DefineOptionalParameterWithDefaultValue(PrintHeatFlux, "printHeatFlux",
147	>	false);
148	>	DefineOptionalParameterWithDefaultValue(OutputForceVector,
149	>	"outputForceVector", false);
150	>	DefineOptionalParameterWithDefaultValue(OutputParticlePotential,
151	>	"outputParticlePotential", false);
152	>	DefineOptionalParameterWithDefaultValue(OutputElectricField,
153	>	"outputElectricField", false);
154	>	DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges,
155	>	"outputFluctuatingCharges", false);
156	>	DefineOptionalParameterWithDefaultValue(OutputSitePotential,
157	>	"outputSitePotential", false);
158	>	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness",
159	>	1.0);
160	>	DefineOptionalParameterWithDefaultValue(StatFileFormat,
161	>	"statFileFormat",
162	>	"TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
163	>	DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions,
164	>	"useSphericalBoundaryConditions",
165	>	false);
166	>	DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole,
167	>	"accumulateBoxDipole", false);
168	>	DefineOptionalParameterWithDefaultValue(AccumulateBoxQuadrupole,
169	>	"accumulateBoxQuadrupole", false);
170	>	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints",
171	>	false);
172	>	DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file",
173	>	"idealCrystal.in");
174	>	DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration,
175	>	"useThermodynamicIntegration",
176	>	false);
177	>	DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
178
179	<	for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
180	<	if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
181	<	std::cout << "Globals Error: can not find molecule stamp for component" << std::endl;
179	>	deprecatedKeywords_.insert("nComponents");
180	>	deprecatedKeywords_.insert("nZconstraints");
181	>	deprecatedKeywords_.insert("initialConfig");
182	>	deprecatedKeywords_.insert("thermIntDistSpringConst");
183	>	deprecatedKeywords_.insert("thermIntThetaSpringConst");
184	>	deprecatedKeywords_.insert("thermIntOmegaSpringConst");
185	>	deprecatedKeywords_.insert("useSolidThermInt");
186	>	deprecatedKeywords_.insert("useLiquidThermInt");
187	>	deprecatedKeywords_.insert("minimizerMaxIter");
188	>	deprecatedKeywords_.insert("minimizerWriteFreq");
189	>	deprecatedKeywords_.insert("minimizerStepSize");
190	>	deprecatedKeywords_.insert("minimizerFTol");
191	>	deprecatedKeywords_.insert("minimizerGTol");
192	>	deprecatedKeywords_.insert("minimizerLSTol");
193	>	deprecatedKeywords_.insert("minimizerLSMaxIter");
194	>	deprecatedKeywords_.insert("electricField");
195	>	deprecatedKeywords_.insert("cutoffPolicy");
196	>	}
197	>
198	>	Globals::~Globals() {
199	>	MemoryUtils::deletePointers(components_);
200	>	MemoryUtils::deletePointers(zconstraints_);
201	>	MemoryUtils::deletePointers(restraints_);
202	>	delete flucQpars_;
203	>	delete rnemdPars_;
204	>	delete minimizerPars_;
205	>	}
206	>
207	>	void Globals::validate() {
208	>	DataHolder::validate();
209	>
210	>	CheckParameter(ForceField, isNotEmpty());
211	>	CheckParameter(TargetTemp, isPositive());
212	>	CheckParameter(Ensemble, isEqualIgnoreCase("NVE") ||
213	>	isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") ||
214	>	isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") ||
215	>	isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT")  ||
216	>	isEqualIgnoreCase("NPA") ||
217	>	isEqualIgnoreCase("LANGEVINDYNAMICS") ||
218	>	isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") ||
219	>	isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") ||
220	>	isEqualIgnoreCase("NGT") ||
221	>	isEqualIgnoreCase("LANGEVINHULL") ||
222	>	isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD"));
223	>	CheckParameter(Dt, isPositive());
224	>	CheckParameter(RunTime, isPositive());
225	>	CheckParameter(FinalConfig, isNotEmpty());
226	>	CheckParameter(SampleTime, isNonNegative());
227	>	CheckParameter(ResetTime, isNonNegative());
228	>	CheckParameter(StatusTime, isNonNegative());
229	>	CheckParameter(CutoffRadius, isPositive());
230	>	CheckParameter(SwitchingRadius, isNonNegative());
231	>	CheckParameter(Dielectric, isPositive());
232	>	CheckParameter(ThermalTime,  isNonNegative());
233	>	CheckParameter(TauThermostat, isPositive());
234	>	CheckParameter(TauBarostat, isPositive());
235	>	CheckParameter(ZconsTime, isPositive());
236	>	CheckParameter(ZconsTol, isPositive());
237	>	CheckParameter(Seed, isPositive());
238	>	CheckParameter(ZconsGap, isPositive());
239	>	CheckParameter(ZconsFixtime, isPositive());
240	>	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
241	>	CheckParameter(ThermodynamicIntegrationK, isPositive());
242	>	CheckParameter(ForceFieldVariant, isNotEmpty());
243	>	CheckParameter(ForceFieldFileName, isNotEmpty());
244	>	CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") ||
245	>	isEqualIgnoreCase("SWITCHED") ||
246	>	isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
247	>	isEqualIgnoreCase("SHIFTED_FORCE") ||
248	>	isEqualIgnoreCase("TAYLOR_SHIFTED") ||
249	>	isEqualIgnoreCase("EWALD_FULL"));
250	>	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") ||
251	>	isEqualIgnoreCase("HARD") ||
252	>	isEqualIgnoreCase("SWITCHED") ||
253	>	isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
254	>	isEqualIgnoreCase("SHIFTED_FORCE") ||
255	>	isEqualIgnoreCase("REACTION_FIELD") ||
256	>	isEqualIgnoreCase("TAYLOR_SHIFTED"));
257	>	CheckParameter(ElectrostaticScreeningMethod,
258	>	isEqualIgnoreCase("UNDAMPED") ||
259	>	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();
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 "
279	>	<< (*i)->getType() << std::endl;
280	>	throw OpenMDException(oss.str());
281	>	}
282		}
283		}
284	<	}
285	<
189	<	bool Globals::addComponent(Component* comp) {
284	>
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::addMoleculeStamp(MoleculeStamp* molStamp) {
295	>	bool Globals::addRestraintStamp(RestraintStamp* rest) {
296	>	restraints_.push_back(rest);
297	>	return true;
298	>	}
299	>
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	<
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		}
212	–
213	–
214	–	}

Comparing trunk/src/io/Globals.cpp (property svn:keywords):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 2057 by gezelter, Tue Mar 3 15:22:26 2015 UTC

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