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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 1629 by gezelter, Wed Sep 14 21:15:17 2011 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include <stdlib.h>
#	Line 49 | Line 49
49		#include "utils/MemoryUtils.hpp"
50		#include "utils/simError.h"
51
52	<	namespace oopse {
52	>	namespace OpenMD {
53		Globals::Globals() {
54		DefineParameter(ForceField, "forceField")
55
#	Line 57 | Line 57 | Globals::Globals() {
57		DefineOptionalParameter(Ensemble, "ensemble");
58		DefineOptionalParameter(Dt, "dt");
59		DefineOptionalParameter(RunTime, "runTime");
60	–	//DefineOptionalParameter(InitialConfig, "initialConfig");
60		DefineOptionalParameter(FinalConfig, "finalConfig");
61		DefineOptionalParameter(SampleTime, "sampleTime");
62		DefineOptionalParameter(ResetTime, "resetTime");
63		DefineOptionalParameter(StatusTime, "statusTime");
64		DefineOptionalParameter(CutoffRadius, "cutoffRadius");
65		DefineOptionalParameter(SwitchingRadius, "switchingRadius");
67	–	DefineOptionalParameter(Dielectric, "dielectric");
66		DefineOptionalParameter(TempSet, "tempSet");
67		DefineOptionalParameter(ThermalTime, "thermalTime");
68	<	DefineOptionalParameter(TargetPressure, "targetPressure");
68	>	DefineOptionalParameter(TargetPressure, "targetPressure");
69		DefineOptionalParameter(TauThermostat, "tauThermostat");
70		DefineOptionalParameter(TauBarostat, "tauBarostat");
71		DefineOptionalParameter(ZconsTime, "zconsTime");
#	Line 76 | Line 74 | Globals::Globals() {
74		DefineOptionalParameter(Seed, "seed");
75		DefineOptionalParameter(Minimizer, "minimizer");
76		DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
77	<	DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
77	>	DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq");
78		DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
79		DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
80		DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
#	Line 89 | Line 87 | Globals::Globals() {
87		DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
88		DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89		DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90	<	DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
93	<	DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
94	<	DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
90	>	DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91		DefineOptionalParameter(SurfaceTension, "surfaceTension");
92		DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
93	<	DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
94	<	DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
99	<	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
93	>	DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
94	>	DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
95		DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
96		DefineOptionalParameter(HydroPropFile, "HydroPropFile");
97		DefineOptionalParameter(Viscosity, "viscosity");
98		DefineOptionalParameter(BeadSize, "beadSize");
99		DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
100		DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
101	+	DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
102	+	DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
103	+	DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
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");
109	+	DefineOptionalParameter(Alpha, "alpha");
110	+
111
112		DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
113	+	DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
114		DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
115		DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
116		DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
117	<	DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
118	<	DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
119	<	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(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
118	>	DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
119	>	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
120		DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
121		DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
122	+	DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", 0);
123		DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
124		DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
125		DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
126		DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
127
128	+	DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
129	+	DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
130	+	DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
131	+	DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
132	+	DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
133	+	DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
134	+	DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
135	+	DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false);
136	+	DefineOptionalParameterWithDefaultValue(RNEMD_outputDimensionalTemperature, "RNEMD_outputDimensionalTemperature", false);
137	+	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
138	+	DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
139	+	DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
140	+	DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
141
142	<	deprecatedKeywords_.insert("nComponents");
143	<	deprecatedKeywords_.insert("nZconstraints");
144	<	deprecatedKeywords_.insert("initialConfig");
142	>
143	>
144	>	deprecatedKeywords_.insert("nComponents");
145	>	deprecatedKeywords_.insert("nZconstraints");
146	>	deprecatedKeywords_.insert("initialConfig");
147	>	deprecatedKeywords_.insert("thermIntDistSpringConst");
148	>	deprecatedKeywords_.insert("thermIntThetaSpringConst");
149	>	deprecatedKeywords_.insert("thermIntOmegaSpringConst");
150	>	deprecatedKeywords_.insert("useSolidThermInt");
151	>	deprecatedKeywords_.insert("useLiquidThermInt");
152
153		}
154
155		Globals::~Globals() {
156		MemoryUtils::deletePointers(components_);
157		MemoryUtils::deletePointers(zconstraints_);
158	+	MemoryUtils::deletePointers(restraints_);
159		}
160
161		void Globals::validate() {
#	Line 138 | Line 163 | void Globals::validate() {
163
164		CheckParameter(ForceField, isNotEmpty());
165		CheckParameter(TargetTemp, isPositive());
166	<	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"));
166	>	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"));
167		CheckParameter(Dt, isPositive());
168		CheckParameter(RunTime, isPositive());
144	–	//CheckParameter(InitialConfig, isNotEmpty());
169		CheckParameter(FinalConfig, isNotEmpty());
170		CheckParameter(SampleTime, isNonNegative());
171		CheckParameter(ResetTime, isNonNegative());
#	Line 150 | Line 174 | void Globals::validate() {
174		CheckParameter(SwitchingRadius, isNonNegative());
175		CheckParameter(Dielectric, isPositive());
176		CheckParameter(ThermalTime,  isNonNegative());
153	–	//  CheckParameter(TargetPressure,  isPositive());
177		CheckParameter(TauThermostat, isPositive());
178		CheckParameter(TauBarostat, isPositive());
179		CheckParameter(ZconsTime, isPositive());
#	Line 158 | Line 181 | void Globals::validate() {
181		CheckParameter(Seed, isPositive());
182		CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
183		CheckParameter(MinimizerMaxIter, isPositive());
184	<	CheckParameter(MinimizerWriteFrq, isPositive());
184	>	CheckParameter(MinimizerWriteFreq, isPositive());
185		CheckParameter(MinimizerStepSize, isPositive());
186		CheckParameter(MinimizerFTol, isPositive());
187		CheckParameter(MinimizerGTol, isPositive());
#	Line 170 | Line 193 | void Globals::validate() {
193		CheckParameter(ThermodynamicIntegrationK, isPositive());
194		CheckParameter(ForceFieldVariant, isNotEmpty());
195		CheckParameter(ForceFieldFileName, isNotEmpty());
196	<	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"));
196	>	CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
197		CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
198	+	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
199	+	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
200		CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
181	–	//CheckParameter(StatFileFormat,);
201		CheckParameter(OrthoBoxTolerance, isPositive());
183	–	CheckParameter(ThermIntDistSpringConst, isPositive());
184	–	CheckParameter(ThermIntThetaSpringConst, isPositive());
185	–	CheckParameter(ThermIntOmegaSpringConst, isPositive());
202		CheckParameter(DampingAlpha,isNonNegative());
203		CheckParameter(SkinThickness, isPositive());
204		CheckParameter(Viscosity, isNonNegative());
205		CheckParameter(BeadSize, isPositive());
206		CheckParameter(FrozenBufferRadius, isPositive());
207		CheckParameter(LangevinBufferRadius, isPositive());
208	+	CheckParameter(NeighborListNeighbors, isPositive());
209	+	CheckParameter(RNEMD_exchangeTime, isPositive());
210	+	CheckParameter(RNEMD_nBins, isPositive() && isEven());
211	+	CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
212	+	CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
213	+	CheckParameter(Alpha, isPositive());
214	+
215	+
216		for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
217		if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
218		std::ostringstream oss;
219		oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
220	<	throw OOPSEException(oss.str());
220	>	throw OpenMDException(oss.str());
221		}
222		}
223		}
224	<
224	>
225		bool Globals::addComponent(Component* comp) {
226		components_.push_back(comp);
227		return true;
#	Line 208 | Line 232 | bool Globals::addZConsStamp(ZConsStamp* zcons) {
232		return true;
233		}
234
235	+	bool Globals::addRestraintStamp(RestraintStamp* rest) {
236	+	restraints_.push_back(rest);
237	+	return true;
238	+	}
239	+
240		bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
241		std::string molStampName = molStamp->getName();
242		std::map<std::string, MoleculeStamp*>::iterator i;
#	Line 219 | Line 248 | bool Globals::addMoleculeStamp(MoleculeStamp* molStamp
248		} else {
249		std::ostringstream oss;
250		oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
251	<	throw OOPSEException(oss.str());
251	>	throw OpenMDException(oss.str());
252		}
253		return ret;
254		}

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 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC

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