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

Comparing:
trunk/src/io/Globals.cpp (file contents), Revision 1293 by chuckv, Sun Sep 14 01:32:26 2008 UTC vs.
branches/development/src/io/Globals.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 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 74 | 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 88 | Line 88 | Globals::Globals() {
88		DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89		DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90		DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91	–	DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
92	–	DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
93	–	DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
91		DefineOptionalParameter(SurfaceTension, "surfaceTension");
92		DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
93		DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
#	Line 103 | Line 100 | Globals::Globals() {
100		DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
101		DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
102		DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
103	+	DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
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
107	–
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);
113	–	DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
114	–	DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
115	–	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
116	–	DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
117	–	DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
117		DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
118		DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
119		DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
#	Line 125 | Line 124 | Globals::Globals() {
124		DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
125		DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
126
127	+	DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
128	+	DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
129	+	DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
130	+	DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
131	+	DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
132	+	DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
133	+	DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
134	+	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
135	+	DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
136	+	DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
137	+	DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
138	+
139	+
140		deprecatedKeywords_.insert("nComponents");
141		deprecatedKeywords_.insert("nZconstraints");
142		deprecatedKeywords_.insert("initialConfig");
143	+	deprecatedKeywords_.insert("thermIntDistSpringConst");
144	+	deprecatedKeywords_.insert("thermIntThetaSpringConst");
145	+	deprecatedKeywords_.insert("thermIntOmegaSpringConst");
146	+	deprecatedKeywords_.insert("useSolidThermInt");
147	+	deprecatedKeywords_.insert("useLiquidThermInt");
148
149		}
150
151		Globals::~Globals() {
152		MemoryUtils::deletePointers(components_);
153		MemoryUtils::deletePointers(zconstraints_);
154	+	MemoryUtils::deletePointers(restraints_);
155		}
156
157		void Globals::validate() {
#	Line 159 | Line 177 | void Globals::validate() {
177		CheckParameter(Seed, isPositive());
178		CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
179		CheckParameter(MinimizerMaxIter, isPositive());
180	<	CheckParameter(MinimizerWriteFrq, isPositive());
180	>	CheckParameter(MinimizerWriteFreq, isPositive());
181		CheckParameter(MinimizerStepSize, isPositive());
182		CheckParameter(MinimizerFTol, isPositive());
183		CheckParameter(MinimizerGTol, isPositive());
#	Line 171 | Line 189 | void Globals::validate() {
189		CheckParameter(ThermodynamicIntegrationK, isPositive());
190		CheckParameter(ForceFieldVariant, isNotEmpty());
191		CheckParameter(ForceFieldFileName, isNotEmpty());
174	–	CheckParameter(ThermIntDistSpringConst, isPositive());
175	–	CheckParameter(ThermIntThetaSpringConst, isPositive());
176	–	CheckParameter(ThermIntOmegaSpringConst, isPositive());
192		CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
193		CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
194		CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
195		CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
196		//CheckParameter(StatFileFormat,);
197		CheckParameter(OrthoBoxTolerance, isPositive());
183	–	CheckParameter(ThermIntDistSpringConst, isPositive());
184	–	CheckParameter(ThermIntThetaSpringConst, isPositive());
185	–	CheckParameter(ThermIntOmegaSpringConst, isPositive());
198		CheckParameter(DampingAlpha,isNonNegative());
199		CheckParameter(SkinThickness, isPositive());
200		CheckParameter(Viscosity, isNonNegative());
#	Line 190 | Line 202 | void Globals::validate() {
202		CheckParameter(FrozenBufferRadius, isPositive());
203		CheckParameter(LangevinBufferRadius, isPositive());
204		CheckParameter(NeighborListNeighbors, isPositive());
205	+	CheckParameter(RNEMD_exchangeTime, isPositive());
206	+	CheckParameter(RNEMD_nBins, isPositive() && isEven());
207	+	CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
208	+	CheckParameter(RNEMD_targetFlux, isNonNegative());
209	+	CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
210	+	CheckParameter(Alpha, isPositive());
211
212	+
213		for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
214		if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
215		std::ostringstream oss;
216		oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
217	<	throw OOPSEException(oss.str());
217	>	throw OpenMDException(oss.str());
218		}
219		}
220		}
221	<
221	>
222		bool Globals::addComponent(Component* comp) {
223		components_.push_back(comp);
224		return true;
#	Line 210 | Line 229 | bool Globals::addZConsStamp(ZConsStamp* zcons) {
229		return true;
230		}
231
232	+	bool Globals::addRestraintStamp(RestraintStamp* rest) {
233	+	restraints_.push_back(rest);
234	+	return true;
235	+	}
236	+
237		bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
238		std::string molStampName = molStamp->getName();
239		std::map<std::string, MoleculeStamp*>::iterator i;
#	Line 221 | Line 245 | bool Globals::addMoleculeStamp(MoleculeStamp* molStamp
245		} else {
246		std::ostringstream oss;
247		oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
248	<	throw OOPSEException(oss.str());
248	>	throw OpenMDException(oss.str());
249		}
250		return ret;
251		}

Comparing:
trunk/src/io/Globals.cpp (property svn:keywords), Revision 1293 by chuckv, Sun Sep 14 01:32:26 2008 UTC vs.
branches/development/src/io/Globals.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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