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

Comparing:
trunk/src/io/Globals.cpp (file contents), Revision 1341 by skuang, Fri May 8 19:47:05 2009 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");
#	Line 72 | Line 78 | Globals::Globals() {
78		DefineOptionalParameter(ZconsTol, "zconsTol");
79		DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
80		DefineOptionalParameter(Seed, "seed");
75	–	DefineOptionalParameter(Minimizer, "minimizer");
76	–	DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
77	–	DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
78	–	DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
79	–	DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
80	–	DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
81	–	DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
82	–	DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
81		DefineOptionalParameter(ZconsGap, "zconsGap");
82		DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
83		DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
#	Line 88 | Line 86 | Globals::Globals() {
86		DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
87		DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
88		DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91	–	DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
92	–	DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
93	–	DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
89		DefineOptionalParameter(SurfaceTension, "surfaceTension");
90		DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
91	+
92		DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
93		DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
98	–	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
94		DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
95		DefineOptionalParameter(HydroPropFile, "HydroPropFile");
96		DefineOptionalParameter(Viscosity, "viscosity");
#	Line 104 | Line 99 | Globals::Globals() {
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	<
108	>	DefineOptionalParameter(Alpha, "alpha");
109
110
111		DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
#	Line 117 | Line 113 | Globals::Globals() {
113		DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
114		DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
115		DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
116	<	DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
121	<	DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
122	<	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
123	<	DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
124	<	DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
125	<	DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
116	>	DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
117		DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
118	<	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
119	<	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
120	<	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
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(UseRNEMD, "useRNEMD", false);
131	<	DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
132	<	DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
133	<	DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
139	<	DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
140	<
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");
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 155 | 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") || isEqualIgnoreCase("SMIPD"));
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());
168		CheckParameter(FinalConfig, isNotEmpty());
#	Line 171 | Line 178 | void Globals::validate() {
178		CheckParameter(ZconsTime, isPositive());
179		CheckParameter(ZconsTol, isPositive());
180		CheckParameter(Seed, isPositive());
174	–	CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
175	–	CheckParameter(MinimizerMaxIter, isPositive());
176	–	CheckParameter(MinimizerWriteFrq, isPositive());
177	–	CheckParameter(MinimizerStepSize, isPositive());
178	–	CheckParameter(MinimizerFTol, isPositive());
179	–	CheckParameter(MinimizerGTol, isPositive());
180	–	CheckParameter(MinimizerLSTol, isPositive());
181	–	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());
189	<	CheckParameter(ThermIntThetaSpringConst, isPositive());
190	<	CheckParameter(ThermIntOmegaSpringConst, isPositive());
191	<	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
192	<	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"));
195	–	//CheckParameter(StatFileFormat,);
192		CheckParameter(OrthoBoxTolerance, isPositive());
197	–	CheckParameter(ThermIntDistSpringConst, isPositive());
198	–	CheckParameter(ThermIntThetaSpringConst, isPositive());
199	–	CheckParameter(ThermIntOmegaSpringConst, isPositive());
193		CheckParameter(DampingAlpha,isNonNegative());
194		CheckParameter(SkinThickness, isPositive());
195		CheckParameter(Viscosity, isNonNegative());
#	Line 204 | Line 197 | void Globals::validate() {
197		CheckParameter(FrozenBufferRadius, isPositive());
198		CheckParameter(LangevinBufferRadius, isPositive());
199		CheckParameter(NeighborListNeighbors, isPositive());
200	<	CheckParameter(RNEMD_swapTime, isPositive());
201	<	CheckParameter(RNEMD_nBins, isPositive() && isEven());
202	<	CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
210	<
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 227 | 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 238 | 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 1341 by skuang, Fri May 8 19:47:05 2009 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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