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

Comparing trunk/src/io/Globals.cpp (file contents):
Revision 1024 by tim, Wed Aug 30 18:42:29 2006 UTC vs.
Revision 2034 by gezelter, Mon Nov 3 16:49:03 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() {
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	<	DefineOptionalParameter(HydroPropFile, "HydroPropFile");
102	<	DefineOptionalParameter(Viscosity, "viscosity");
103	<	DefineOptionalParameter(BeadSize, "beadSize");
104	<	DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
105	<	DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
53	>	namespace OpenMD {
54	>	Globals::Globals() {
55
56	<	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
57	<	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
58	<	DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
110	<	DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
111	<	DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
112	<	DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
113	<	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
114	<	DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
115	<	DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
116	<	DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
117	<	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
118	<	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
119	<	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
120	<	DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
121	<	DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
122	<	DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
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	+	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	+	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	+	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		deprecatedKeywords_.insert("nComponents");
180		deprecatedKeywords_.insert("nZconstraints");
181		deprecatedKeywords_.insert("initialConfig");
182	<
183	<	}
184	<
185	<	Globals::~Globals() {
186	<	MemoryUtils::deletePointers(components_);
187	<	MemoryUtils::deletePointers(zconstraints_);
188	<	}
189	<
190	<	void Globals::validate() {
191	<	DataHolder::validate();
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
196	<	CheckParameter(ForceField, isNotEmpty());
197	<	CheckParameter(TargetTemp, isPositive());
198	<	CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT"));
199	<	CheckParameter(Dt, isPositive());
200	<	CheckParameter(RunTime, isPositive());
201	<	//CheckParameter(InitialConfig, isNotEmpty());
202	<	CheckParameter(FinalConfig, isNotEmpty());
203	<	CheckParameter(SampleTime, isNonNegative());
204	<	CheckParameter(ResetTime, isNonNegative());
205	<	CheckParameter(StatusTime, isNonNegative());
206	<	CheckParameter(CutoffRadius, isPositive());
207	<	CheckParameter(SwitchingRadius, isNonNegative());
208	<	CheckParameter(Dielectric, isPositive());
209	<	CheckParameter(ThermalTime,  isNonNegative());
210	<	//  CheckParameter(TargetPressure,  isPositive());
211	<	CheckParameter(TauThermostat, isPositive());
212	<	CheckParameter(TauBarostat, isPositive());
213	<	CheckParameter(ZconsTime, isPositive());
214	<	CheckParameter(ZconsTol, isPositive());
215	<	CheckParameter(Seed, isPositive());
216	<	CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
217	<	CheckParameter(MinimizerMaxIter, isPositive());
218	<	CheckParameter(MinimizerWriteFrq, isPositive());
219	<	CheckParameter(MinimizerStepSize, isPositive());
220	<	CheckParameter(MinimizerFTol, isPositive());
221	<	CheckParameter(MinimizerGTol, isPositive());
222	<	CheckParameter(MinimizerLSTol, isPositive());
223	<	CheckParameter(MinimizerLSMaxIter, isPositive());
224	<	CheckParameter(ZconsGap, isPositive());
225	<	CheckParameter(ZconsFixtime, isPositive());
226	<	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
227	<	CheckParameter(ThermodynamicIntegrationK, isPositive());
228	<	CheckParameter(ForceFieldVariant, isNotEmpty());
229	<	CheckParameter(ForceFieldFileName, isNotEmpty());
230	<	CheckParameter(ThermIntDistSpringConst, isPositive());
231	<	CheckParameter(ThermIntThetaSpringConst, isPositive());
232	<	CheckParameter(ThermIntOmegaSpringConst, isPositive());
233	<	//  CheckParameter(SurfaceTension, isNonNegative());
234	<	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
235	<	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
236	<	CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
237	<	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
238	<	//CheckParameter(StatFileFormat,);
239	<	CheckParameter(OrthoBoxTolerance, isPositive());
240	<	CheckParameter(ThermIntDistSpringConst, isPositive());
241	<	CheckParameter(ThermIntThetaSpringConst, isPositive());
242	<	CheckParameter(ThermIntOmegaSpringConst, isPositive());
243	<	CheckParameter(DampingAlpha,isNonNegative());
244	<	CheckParameter(SkinThickness, isPositive());
245	<	CheckParameter(Viscosity, isNonNegative());
246	<	CheckParameter(BeadSize, isPositive());
247	<	CheckParameter(FrozenBufferRadius, isPositive());
248	<	CheckParameter(LangevinBufferRadius, isPositive());
249	<	for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
250	<	if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
196	>
197	>	}
198	>
199	>	Globals::~Globals() {
200	>	MemoryUtils::deletePointers(components_);
201	>	MemoryUtils::deletePointers(zconstraints_);
202	>	MemoryUtils::deletePointers(restraints_);
203	>	delete flucQpars_;
204	>	delete rnemdPars_;
205	>	delete minimizerPars_;
206	>	}
207	>
208	>	void Globals::validate() {
209	>	DataHolder::validate();
210	>
211	>	CheckParameter(ForceField, isNotEmpty());
212	>	CheckParameter(TargetTemp, isPositive());
213	>	CheckParameter(Ensemble, isEqualIgnoreCase("NVE") ||
214	>	isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") ||
215	>	isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") ||
216	>	isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT")  ||
217	>	isEqualIgnoreCase("NPA") ||
218	>	isEqualIgnoreCase("LANGEVINDYNAMICS") ||
219	>	isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") ||
220	>	isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") ||
221	>	isEqualIgnoreCase("NGT") ||
222	>	isEqualIgnoreCase("LANGEVINHULL") ||
223	>	isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD"));
224	>	CheckParameter(Dt, isPositive());
225	>	CheckParameter(RunTime, isPositive());
226	>	CheckParameter(FinalConfig, isNotEmpty());
227	>	CheckParameter(SampleTime, isNonNegative());
228	>	CheckParameter(ResetTime, isNonNegative());
229	>	CheckParameter(StatusTime, isNonNegative());
230	>	CheckParameter(CutoffRadius, isPositive());
231	>	CheckParameter(SwitchingRadius, isNonNegative());
232	>	CheckParameter(Dielectric, isPositive());
233	>	CheckParameter(ThermalTime,  isNonNegative());
234	>	CheckParameter(TauThermostat, isPositive());
235	>	CheckParameter(TauBarostat, isPositive());
236	>	CheckParameter(ZconsTime, isPositive());
237	>	CheckParameter(ZconsTol, isPositive());
238	>	CheckParameter(Seed, isPositive());
239	>	CheckParameter(ZconsGap, isPositive());
240	>	CheckParameter(ZconsFixtime, isPositive());
241	>	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
242	>	CheckParameter(ThermodynamicIntegrationK, isPositive());
243	>	CheckParameter(ForceFieldVariant, isNotEmpty());
244	>	CheckParameter(ForceFieldFileName, isNotEmpty());
245	>	CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") ||
246	>	isEqualIgnoreCase("SWITCHED") ||
247	>	isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
248	>	isEqualIgnoreCase("SHIFTED_FORCE") ||
249	>	isEqualIgnoreCase("TAYLOR_SHIFTED") ||
250	>	isEqualIgnoreCase("EWALD_FULL"));
251	>	CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") ||
252	>	isEqualIgnoreCase("MAX") ||
253	>	isEqualIgnoreCase("TRADITIONAL"));
254	>	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") ||
255	>	isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") ||
256	>	isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
257	>	isEqualIgnoreCase("SHIFTED_FORCE") ||
258	>	isEqualIgnoreCase("REACTION_FIELD") ||
259	>	isEqualIgnoreCase("TAYLOR_SHIFTED"));
260	>	CheckParameter(ElectrostaticScreeningMethod,
261	>	isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
262	>	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") ||
263	>	isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
264	>	CheckParameter(OrthoBoxTolerance, isPositive());
265	>	CheckParameter(DampingAlpha,isNonNegative());
266	>	CheckParameter(SkinThickness, isPositive());
267	>	CheckParameter(Viscosity, isNonNegative());
268	>	CheckParameter(BeadSize, isPositive());
269	>	CheckParameter(FrozenBufferRadius, isPositive());
270	>	CheckParameter(LangevinBufferRadius, isPositive());
271	>	CheckParameter(NeighborListNeighbors, isPositive());
272	>	CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") ||
273	>	isEqualIgnoreCase("AlphaShape"));
274	>	CheckParameter(Alpha, isPositive());
275	>
276	>	for(std::vector<Component*>::iterator i = components_.begin();
277	>	i != components_.end(); ++i) {
278	>	if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
279		std::ostringstream oss;
280	<	oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
281	<	throw OOPSEException(oss.str());
280	>	oss << "Globals Error: can not find molecule stamp for component "
281	>	<< (*i)->getType() << std::endl;
282	>	throw OpenMDException(oss.str());
283	>	}
284		}
285		}
286	<	}
287	<
201	<	bool Globals::addComponent(Component* comp) {
286	>
287	>	bool Globals::addComponent(Component* comp) {
288		components_.push_back(comp);
289		return true;
290	<	}
290	>	}
291
292	<	bool Globals::addZConsStamp(ZConsStamp* zcons) {
292	>	bool Globals::addZConsStamp(ZConsStamp* zcons) {
293		zconstraints_.push_back(zcons);
294		return true;
295	<	}
295	>	}
296
297	<	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
297	>	bool Globals::addRestraintStamp(RestraintStamp* rest) {
298	>	restraints_.push_back(rest);
299	>	return true;
300	>	}
301	>
302	>	bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
303	>	if (flucQpars_ != NULL)
304	>	delete flucQpars_;
305	>
306	>	flucQpars_ = fqp;
307	>	return true;
308	>	}
309	>
310	>	bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
311	>	if (rnemdPars_ != NULL)
312	>	delete rnemdPars_;
313	>
314	>	rnemdPars_ = rnemdPars;
315	>	return true;
316	>	}
317	>
318	>	bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
319	>	if (minimizerPars_ != NULL)
320	>	delete minimizerPars_;
321	>
322	>	minimizerPars_ = miniPars;
323	>	return true;
324	>	}
325	>
326	>	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
327		std::string molStampName = molStamp->getName();
328		std::map<std::string, MoleculeStamp*>::iterator i;
329		bool ret = false;
330		i = moleculeStamps_.find(molStampName);
331		if (i == moleculeStamps_.end()) {
332	<	moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
333	<	ret = true;
332	>	moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
333	>	ret = true;
334		} else {
335	<	std::ostringstream oss;
336	<	oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
337	<	throw OOPSEException(oss.str());
335	>	std::ostringstream oss;
336	>	oss << "Globals Error: Molecule Stamp " << molStamp->getName()
337	>	<< "appears multiple times\n";
338	>	throw OpenMDException(oss.str());
339		}
340		return ret;
341	+	}
342		}
226	–
227	–
228	–	}

Comparing trunk/src/io/Globals.cpp (property svn:keywords):
Revision 1024 by tim, Wed Aug 30 18:42:29 2006 UTC vs.
Revision 2034 by gezelter, Mon Nov 3 16:49:03 2014 UTC

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