ViewVC Help

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

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

Comparing trunk/src/io/Globals.cpp (file contents):
Revision 866 by chuckv, Fri Jan 13 19:17:34 2006 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
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 49 | Line 50
50		#include "utils/MemoryUtils.hpp"
51		#include "utils/simError.h"
52
53	<	namespace oopse {
54	<	Globals::Globals() {
55	<	DefineParameter(ForceField, "forceField")
56	<
57	<	DefineOptionalParameter(TargetTemp, "targetTemp");
58	<	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");
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");
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	+	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	+	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
187	<	}
187	>	}
188
189	<	Globals::~Globals() {
189	>	Globals::~Globals() {
190		MemoryUtils::deletePointers(components_);
191		MemoryUtils::deletePointers(zconstraints_);
192	<	}
192	>	MemoryUtils::deletePointers(restraints_);
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")  );
204	<	CheckParameter(Dt, isPositive());
205	<	CheckParameter(RunTime, isPositive());
206	<	CheckParameter(InitialConfig, isNotEmpty());
207	<	CheckParameter(FinalConfig, isNotEmpty());
208	<	CheckParameter(SampleTime, isNonNegative());
209	<	CheckParameter(ResetTime, isNonNegative());
210	<	CheckParameter(StatusTime, isNonNegative());
211	<	CheckParameter(CutoffRadius, isPositive());
212	<	CheckParameter(SwitchingRadius, isNonNegative());
213	<	CheckParameter(Dielectric, isPositive());
214	<	CheckParameter(ThermalTime,  isNonNegative());
215	<	CheckParameter(TargetPressure,  isPositive());
216	<	CheckParameter(TauThermostat, isPositive());
217	<	CheckParameter(TauBarostat, isPositive());
218	<	CheckParameter(ZconsTime, isPositive());
219	<	CheckParameter(ZconsTol, isPositive());
220	<	CheckParameter(Seed, isPositive());
221	<	CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
222	<	CheckParameter(MinimizerMaxIter, isPositive());
223	<	CheckParameter(MinimizerWriteFrq, isPositive());
224	<	CheckParameter(MinimizerStepSize, isPositive());
225	<	CheckParameter(MinimizerFTol, isPositive());
226	<	CheckParameter(MinimizerGTol, isPositive());
227	<	CheckParameter(MinimizerLSTol, isPositive());
228	<	CheckParameter(MinimizerLSMaxIter, isPositive());
229	<	CheckParameter(ZconsGap, isPositive());
230	<	CheckParameter(ZconsFixtime, isPositive());
231	<	CheckParameter(ThermodynamicIntegrationLambda, isPositive());
232	<	CheckParameter(ThermodynamicIntegrationK, isPositive());
233	<	CheckParameter(ForceFieldVariant, isNotEmpty());
234	<	CheckParameter(ForceFieldFileName, isNotEmpty());
235	<	CheckParameter(ThermIntDistSpringConst, isPositive());
236	<	CheckParameter(ThermIntThetaSpringConst, isPositive());
237	<	CheckParameter(ThermIntOmegaSpringConst, isPositive());
238	<	CheckParameter(SurfaceTension, isPositive());
239	<	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
240	<	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
241	<	CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
242	<	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
243	<	//CheckParameter(StatFileFormat,);
244	<	//CheckParameter(MixingRule,);
245	<	CheckParameter(OrthoBoxTolerance, isPositive());
246	<	CheckParameter(ThermIntDistSpringConst, isPositive());
247	<	CheckParameter(ThermIntThetaSpringConst, isPositive());
248	<	CheckParameter(ThermIntOmegaSpringConst, isPositive());
249	<	CheckParameter(DampingAlpha,isNonNegative());
250	<	CheckParameter(SkinThickness, isPositive());
251	<
252	<	for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
253	<	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;
271	<	throw OOPSEException(oss.str());
270	>	oss << "Globals Error: can not find molecule stamp for component "
271	>	<< (*i)->getType() << std::endl;
272	>	throw OpenMDException(oss.str());
273	>	}
274		}
275		}
276	<	}
277	<
191	<	bool Globals::addComponent(Component* comp) {
276	>
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::addMoleculeStamp(MoleculeStamp* molStamp) {
287	>	bool Globals::addRestraintStamp(RestraintStamp* rest) {
288	>	restraints_.push_back(rest);
289	>	return true;
290	>	}
291	>
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 OOPSEException(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		}
216	–
217	–
218	–	}

Comparing trunk/src/io/Globals.cpp (property svn:keywords):
Revision 866 by chuckv, Fri Jan 13 19:17:34 2006 UTC vs.
Revision 2011 by gezelter, Wed Aug 6 19:27:37 2014 UTC

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

Diff Legend

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