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root/OpenMD/branches/development/src/io/Globals.cpp

Comparing:
trunk/src/io/Globals.cpp (file contents), Revision 1032 by gezelter, Fri Sep 1 19:16:02 2006 UTC vs.
branches/development/src/io/Globals.cpp (file contents), Revision 1749 by gezelter, Thu Jun 7 02:47:21 2012 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2	>	* Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
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, 24107 (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 {
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");
60	–	//DefineOptionalParameter(InitialConfig, "initialConfig");
66		DefineOptionalParameter(FinalConfig, "finalConfig");
67		DefineOptionalParameter(SampleTime, "sampleTime");
68		DefineOptionalParameter(ResetTime, "resetTime");
69		DefineOptionalParameter(StatusTime, "statusTime");
70		DefineOptionalParameter(CutoffRadius, "cutoffRadius");
71		DefineOptionalParameter(SwitchingRadius, "switchingRadius");
67	–	DefineOptionalParameter(Dielectric, "dielectric");
72		DefineOptionalParameter(TempSet, "tempSet");
73		DefineOptionalParameter(ThermalTime, "thermalTime");
74	<	DefineOptionalParameter(TargetPressure, "targetPressure");
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");
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");
81		DefineOptionalParameter(ZconsGap, "zconsGap");
82		DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
83		DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
#	Line 89 | Line 85 | Globals::Globals() {
85		DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
86		DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
87		DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
88	<	DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
93	<	DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
94	<	DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
88	>	DefineOptionalParameter(DampingAlpha, "dampingAlpha");
89		DefineOptionalParameter(SurfaceTension, "surfaceTension");
90		DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
91	<	DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
92	<	DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
93	<	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
91	>
92	>	DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
93	>	DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
94		DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
95		DefineOptionalParameter(HydroPropFile, "HydroPropFile");
96		DefineOptionalParameter(Viscosity, "viscosity");
97		DefineOptionalParameter(BeadSize, "beadSize");
98		DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
99		DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
100	+	DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
101	+	DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
102	+	DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
103	+	DefineOptionalParameter(MTM_Ce, "MTM_Ce");
104	+	DefineOptionalParameter(MTM_G, "MTM_G");
105	+	DefineOptionalParameter(MTM_Io, "MTM_Io");
106	+	DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
107	+	DefineOptionalParameter(MTM_R, "MTM_R");
108	+	DefineOptionalParameter(Alpha, "alpha");
109	+
110
111		DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
112	+	DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
113		DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
114		DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
115		DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
116	<	DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
117	<	DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
118	<	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
119	<	DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
120	<	DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
121	<	DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
122	<	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
123	<	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
116	>	DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
117	>	DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
118	>	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
119	>	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false);
120	>	DefineOptionalParameterWithDefaultValue(PrintHeatFlux, "printHeatFlux", false);
121	>	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false);
122	>	DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false);
123	>	DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false);
124	>	DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", false);
125		DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
126		DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
127		DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
128		DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
129
130	+	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
131	+	DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
132	+	DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
133	+	DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
134
135	<	deprecatedKeywords_.insert("nComponents");
136	<	deprecatedKeywords_.insert("nZconstraints");
137	<	deprecatedKeywords_.insert("initialConfig");
135	>	deprecatedKeywords_.insert("nComponents");
136	>	deprecatedKeywords_.insert("nZconstraints");
137	>	deprecatedKeywords_.insert("initialConfig");
138	>	deprecatedKeywords_.insert("thermIntDistSpringConst");
139	>	deprecatedKeywords_.insert("thermIntThetaSpringConst");
140	>	deprecatedKeywords_.insert("thermIntOmegaSpringConst");
141	>	deprecatedKeywords_.insert("useSolidThermInt");
142	>	deprecatedKeywords_.insert("useLiquidThermInt");
143	>	deprecatedKeywords_.insert("minimizerMaxIter");
144	>	deprecatedKeywords_.insert("minimizerWriteFreq");
145	>	deprecatedKeywords_.insert("minimizerStepSize");
146	>	deprecatedKeywords_.insert("minimizerFTol");
147	>	deprecatedKeywords_.insert("minimizerGTol");
148	>	deprecatedKeywords_.insert("minimizerLSTol");
149	>	deprecatedKeywords_.insert("minimizerLSMaxIter");
150	>
151
152		}
153
154		Globals::~Globals() {
155		MemoryUtils::deletePointers(components_);
156		MemoryUtils::deletePointers(zconstraints_);
157	+	MemoryUtils::deletePointers(restraints_);
158		}
159
160		void Globals::validate() {
#	Line 138 | Line 162 | void Globals::validate() {
162
163		CheckParameter(ForceField, isNotEmpty());
164		CheckParameter(TargetTemp, isPositive());
165	<	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"));
165	>	CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || isEqualIgnoreCase("LANGEVINHULL") || isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD"));
166		CheckParameter(Dt, isPositive());
167		CheckParameter(RunTime, isPositive());
144	–	//CheckParameter(InitialConfig, isNotEmpty());
168		CheckParameter(FinalConfig, isNotEmpty());
169		CheckParameter(SampleTime, isNonNegative());
170		CheckParameter(ResetTime, isNonNegative());
#	Line 150 | Line 173 | void Globals::validate() {
173		CheckParameter(SwitchingRadius, isNonNegative());
174		CheckParameter(Dielectric, isPositive());
175		CheckParameter(ThermalTime,  isNonNegative());
153	–	//  CheckParameter(TargetPressure,  isPositive());
176		CheckParameter(TauThermostat, isPositive());
177		CheckParameter(TauBarostat, isPositive());
178		CheckParameter(ZconsTime, isPositive());
179		CheckParameter(ZconsTol, isPositive());
180		CheckParameter(Seed, isPositive());
159	–	CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
160	–	CheckParameter(MinimizerMaxIter, isPositive());
161	–	CheckParameter(MinimizerWriteFrq, isPositive());
162	–	CheckParameter(MinimizerStepSize, isPositive());
163	–	CheckParameter(MinimizerFTol, isPositive());
164	–	CheckParameter(MinimizerGTol, isPositive());
165	–	CheckParameter(MinimizerLSTol, isPositive());
166	–	CheckParameter(MinimizerLSMaxIter, isPositive());
181		CheckParameter(ZconsGap, isPositive());
182		CheckParameter(ZconsFixtime, isPositive());
183		CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
184		CheckParameter(ThermodynamicIntegrationK, isPositive());
185		CheckParameter(ForceFieldVariant, isNotEmpty());
186		CheckParameter(ForceFieldFileName, isNotEmpty());
187	<	CheckParameter(ThermIntDistSpringConst, isPositive());
174	<	CheckParameter(ThermIntThetaSpringConst, isPositive());
175	<	CheckParameter(ThermIntOmegaSpringConst, isPositive());
176	<	//  CheckParameter(SurfaceTension, isNonNegative());
177	<	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
178	<	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
187	>	CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
188		CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
189	+	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
190	+	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
191		CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
181	–	//CheckParameter(StatFileFormat,);
192		CheckParameter(OrthoBoxTolerance, isPositive());
183	–	CheckParameter(ThermIntDistSpringConst, isPositive());
184	–	CheckParameter(ThermIntThetaSpringConst, isPositive());
185	–	CheckParameter(ThermIntOmegaSpringConst, isPositive());
193		CheckParameter(DampingAlpha,isNonNegative());
194		CheckParameter(SkinThickness, isPositive());
195		CheckParameter(Viscosity, isNonNegative());
196		CheckParameter(BeadSize, isPositive());
197		CheckParameter(FrozenBufferRadius, isPositive());
198		CheckParameter(LangevinBufferRadius, isPositive());
199	+	CheckParameter(NeighborListNeighbors, isPositive());
200	+	CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
201	+	CheckParameter(Alpha, isPositive());
202	+
203		for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
204		if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
205		std::ostringstream oss;
206		oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
207	<	throw OOPSEException(oss.str());
207	>	throw OpenMDException(oss.str());
208		}
209		}
210		}
211	<
211	>
212		bool Globals::addComponent(Component* comp) {
213		components_.push_back(comp);
214		return true;
#	Line 208 | Line 219 | bool Globals::addZConsStamp(ZConsStamp* zcons) {
219		return true;
220		}
221
222	+	bool Globals::addRestraintStamp(RestraintStamp* rest) {
223	+	restraints_.push_back(rest);
224	+	return true;
225	+	}
226	+
227	+	bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
228	+	if (flucQpars_ != NULL)
229	+	delete flucQpars_;
230	+
231	+	flucQpars_ = fqp;
232	+	return true;
233	+	}
234	+
235	+	bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
236	+	if (rnemdPars_ != NULL)
237	+	delete rnemdPars_;
238	+
239	+	rnemdPars_ = rnemdPars;
240	+	return true;
241	+	}
242	+
243	+	bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
244	+	if (minimizerPars_ != NULL)
245	+	delete minimizerPars_;
246	+
247	+	minimizerPars_ = miniPars;
248	+	return true;
249	+	}
250	+
251		bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
252		std::string molStampName = molStamp->getName();
253		std::map<std::string, MoleculeStamp*>::iterator i;
#	Line 219 | Line 259 | bool Globals::addMoleculeStamp(MoleculeStamp* molStamp
259		} else {
260		std::ostringstream oss;
261		oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
262	<	throw OOPSEException(oss.str());
262	>	throw OpenMDException(oss.str());
263		}
264		return ret;
265		}

Comparing:
trunk/src/io/Globals.cpp (property svn:keywords), Revision 1032 by gezelter, Fri Sep 1 19:16:02 2006 UTC vs.
branches/development/src/io/Globals.cpp (property svn:keywords), Revision 1749 by gezelter, Thu Jun 7 02:47:21 2012 UTC

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