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root/OpenMD/branches/development/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.
branches/development/src/io/Globals.cpp (file contents), Revision 1744 by gezelter, Tue Jun 5 18:07:08 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	+
59		DefineParameter(ForceField, "forceField")
60
61		DefineOptionalParameter(TargetTemp, "targetTemp");
62		DefineOptionalParameter(Ensemble, "ensemble");
63		DefineOptionalParameter(Dt, "dt");
64		DefineOptionalParameter(RunTime, "runTime");
60	–	DefineOptionalParameter(InitialConfig, "initialConfig");
65		DefineOptionalParameter(FinalConfig, "finalConfig");
66		DefineOptionalParameter(SampleTime, "sampleTime");
67		DefineOptionalParameter(ResetTime, "resetTime");
68		DefineOptionalParameter(StatusTime, "statusTime");
69		DefineOptionalParameter(CutoffRadius, "cutoffRadius");
70		DefineOptionalParameter(SwitchingRadius, "switchingRadius");
67	–	DefineOptionalParameter(Dielectric, "dielectric");
71		DefineOptionalParameter(TempSet, "tempSet");
72		DefineOptionalParameter(ThermalTime, "thermalTime");
73	<	DefineOptionalParameter(TargetPressure, "targetPressure");
73	>	DefineOptionalParameter(TargetPressure, "targetPressure");
74		DefineOptionalParameter(TauThermostat, "tauThermostat");
75		DefineOptionalParameter(TauBarostat, "tauBarostat");
76		DefineOptionalParameter(ZconsTime, "zconsTime");
#	Line 76 | Line 79 | Globals::Globals() {
79		DefineOptionalParameter(Seed, "seed");
80		DefineOptionalParameter(Minimizer, "minimizer");
81		DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
82	<	DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
82	>	DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq");
83		DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
84		DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
85		DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
#	Line 89 | Line 92 | Globals::Globals() {
92		DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
93		DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
94		DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
95	<	DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
93	<	DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
94	<	DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
95	>	DefineOptionalParameter(DampingAlpha, "dampingAlpha");
96		DefineOptionalParameter(SurfaceTension, "surfaceTension");
97		DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
98	<	DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
99	<	DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
100	<	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
98	>	DefineOptionalParameter(PrintHeatFlux, "printHeatFlux");
99	>	DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
100	>	DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
101		DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
102	<	DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
102	>	DefineOptionalParameter(HydroPropFile, "HydroPropFile");
103	>	DefineOptionalParameter(Viscosity, "viscosity");
104	>	DefineOptionalParameter(BeadSize, "beadSize");
105	>	DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
106	>	DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
107	>	DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
108	>	DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
109	>	DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
110	>	DefineOptionalParameter(MTM_Ce, "MTM_Ce");
111	>	DefineOptionalParameter(MTM_G, "MTM_G");
112	>	DefineOptionalParameter(MTM_Io, "MTM_Io");
113	>	DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
114	>	DefineOptionalParameter(MTM_R, "MTM_R");
115	>	DefineOptionalParameter(Alpha, "alpha");
116	>
117	>
118		DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
119	+	DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
120		DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
121		DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
122		DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
123	<	DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
124	<	DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
125	<	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
126	<	DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
127	<	DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
128	<	DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
129	<	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
130	<	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
123	>	DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
124	>	DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
125	>	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
126	>	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false);
127	>	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false);
128	>	DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false);
129	>	DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false);
130	>	DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", false);
131		DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
132		DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
133	+	DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
134	+	DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
135
136	+	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
137	+	DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
138	+	DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
139	+	DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
140
141	<	deprecatedKeywords_.insert("nComponents");
142	<	deprecatedKeywords_.insert("nZconstraints");
141	>	deprecatedKeywords_.insert("nComponents");
142	>	deprecatedKeywords_.insert("nZconstraints");
143	>	deprecatedKeywords_.insert("initialConfig");
144	>	deprecatedKeywords_.insert("thermIntDistSpringConst");
145	>	deprecatedKeywords_.insert("thermIntThetaSpringConst");
146	>	deprecatedKeywords_.insert("thermIntOmegaSpringConst");
147	>	deprecatedKeywords_.insert("useSolidThermInt");
148	>	deprecatedKeywords_.insert("useLiquidThermInt");
149
150		}
151
152		Globals::~Globals() {
153		MemoryUtils::deletePointers(components_);
154		MemoryUtils::deletePointers(zconstraints_);
155	+	MemoryUtils::deletePointers(restraints_);
156		}
157
158		void Globals::validate() {
#	Line 130 | Line 160 | void Globals::validate() {
160
161		CheckParameter(ForceField, isNotEmpty());
162		CheckParameter(TargetTemp, isPositive());
163	<	CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT")  );
163	>	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"));
164		CheckParameter(Dt, isPositive());
165		CheckParameter(RunTime, isPositive());
136	–	CheckParameter(InitialConfig, isNotEmpty());
166		CheckParameter(FinalConfig, isNotEmpty());
167		CheckParameter(SampleTime, isNonNegative());
168		CheckParameter(ResetTime, isNonNegative());
#	Line 142 | Line 171 | void Globals::validate() {
171		CheckParameter(SwitchingRadius, isNonNegative());
172		CheckParameter(Dielectric, isPositive());
173		CheckParameter(ThermalTime,  isNonNegative());
145	–	CheckParameter(TargetPressure,  isPositive());
174		CheckParameter(TauThermostat, isPositive());
175		CheckParameter(TauBarostat, isPositive());
176		CheckParameter(ZconsTime, isPositive());
#	Line 150 | Line 178 | void Globals::validate() {
178		CheckParameter(Seed, isPositive());
179		CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
180		CheckParameter(MinimizerMaxIter, isPositive());
181	<	CheckParameter(MinimizerWriteFrq, isPositive());
181	>	CheckParameter(MinimizerWriteFreq, isPositive());
182		CheckParameter(MinimizerStepSize, isPositive());
183		CheckParameter(MinimizerFTol, isPositive());
184		CheckParameter(MinimizerGTol, isPositive());
#	Line 158 | Line 186 | void Globals::validate() {
186		CheckParameter(MinimizerLSMaxIter, isPositive());
187		CheckParameter(ZconsGap, isPositive());
188		CheckParameter(ZconsFixtime, isPositive());
189	<	CheckParameter(ThermodynamicIntegrationLambda, isPositive());
189	>	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
190		CheckParameter(ThermodynamicIntegrationK, isPositive());
191		CheckParameter(ForceFieldVariant, isNotEmpty());
192		CheckParameter(ForceFieldFileName, isNotEmpty());
193	<	CheckParameter(ThermIntDistSpringConst, isPositive());
166	<	CheckParameter(ThermIntThetaSpringConst, isPositive());
167	<	CheckParameter(ThermIntOmegaSpringConst, isPositive());
168	<	CheckParameter(SurfaceTension, isPositive());
169	<	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
170	<	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
193	>	CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
194		CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
195	+	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
196	+	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
197		CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
173	–	//CheckParameter(StatFileFormat,);
174	–	//CheckParameter(MixingRule,);
198		CheckParameter(OrthoBoxTolerance, isPositive());
176	–	CheckParameter(ThermIntDistSpringConst, isPositive());
177	–	CheckParameter(ThermIntThetaSpringConst, isPositive());
178	–	CheckParameter(ThermIntOmegaSpringConst, isPositive());
199		CheckParameter(DampingAlpha,isNonNegative());
200		CheckParameter(SkinThickness, isPositive());
201	<
201	>	CheckParameter(Viscosity, isNonNegative());
202	>	CheckParameter(BeadSize, isPositive());
203	>	CheckParameter(FrozenBufferRadius, isPositive());
204	>	CheckParameter(LangevinBufferRadius, isPositive());
205	>	CheckParameter(NeighborListNeighbors, isPositive());
206	>	CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
207	>	CheckParameter(Alpha, isPositive());
208	>
209		for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
210		if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
211		std::ostringstream oss;
212		oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
213	<	throw OOPSEException(oss.str());
213	>	throw OpenMDException(oss.str());
214		}
215		}
216		}
217	<
217	>
218		bool Globals::addComponent(Component* comp) {
219		components_.push_back(comp);
220		return true;
#	Line 198 | Line 225 | bool Globals::addZConsStamp(ZConsStamp* zcons) {
225		return true;
226		}
227
228	+	bool Globals::addRestraintStamp(RestraintStamp* rest) {
229	+	restraints_.push_back(rest);
230	+	return true;
231	+	}
232	+
233	+	bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
234	+	if (flucQpars_ != NULL)
235	+	delete flucQpars_;
236	+
237	+	flucQpars_ = fqp;
238	+	return true;
239	+	}
240	+
241	+	bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
242	+	if (rnemdPars_ != NULL)
243	+	delete rnemdPars_;
244	+
245	+	rnemdPars_ = rnemdPars;
246	+	return true;
247	+	}
248	+
249		bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
250		std::string molStampName = molStamp->getName();
251		std::map<std::string, MoleculeStamp*>::iterator i;
#	Line 209 | Line 257 | bool Globals::addMoleculeStamp(MoleculeStamp* molStamp
257		} else {
258		std::ostringstream oss;
259		oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
260	<	throw OOPSEException(oss.str());
260	>	throw OpenMDException(oss.str());
261		}
262		return ret;
263		}

Comparing:
trunk/src/io/Globals.cpp (property svn:keywords), Revision 866 by chuckv, Fri Jan 13 19:17:34 2006 UTC vs.
branches/development/src/io/Globals.cpp (property svn:keywords), Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC

#	Line 0 | Line 1
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