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

Comparing:
trunk/src/io/Globals.hpp (file contents), Revision 1331 by gezelter, Thu Apr 2 16:04:52 2009 UTC vs.
branches/development/src/io/Globals.hpp (file contents), Revision 1780 by jmarr, Mon Aug 20 18:28:22 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		#ifndef IO_GLOBALS_HPP
#	Line 51 | Line 52
52
53		#include "types/Component.hpp"
54		#include "types/ZconsStamp.hpp"
55	+	#include "types/RestraintStamp.hpp"
56		#include "types/MoleculeStamp.hpp"
57	+	#include "flucq/FluctuatingChargeParameters.hpp"
58	+	#include "rnemd/RNEMDParameters.hpp"
59	+	#include "optimization/MinimizerParameters.hpp"
60		#include "utils/ParameterManager.hpp"
61
62	<	namespace oopse {
62	>	namespace OpenMD {
63		class Globals : public DataHolder {
64		public:
65		typedef std::pair<int, int> intPair;
#	Line 87 | Line 92 | namespace oopse {
92		DeclareParameter(UseInitalTime, bool);
93		DeclareParameter(UseIntialExtendedSystemState, bool);
94		DeclareParameter(OrthoBoxTolerance, RealType);
90	–	DeclareParameter(Minimizer, std::string);
91	–	DeclareParameter(MinimizerMaxIter, RealType);
92	–	DeclareParameter(MinimizerWriteFrq, int);
93	–	DeclareParameter(MinimizerStepSize, RealType);
94	–	DeclareParameter(MinimizerFTol, RealType);
95	–	DeclareParameter(MinimizerGTol, RealType);
96	–	DeclareParameter(MinimizerLSTol, RealType);
97	–	DeclareParameter(MinimizerLSMaxIter, int);
95		DeclareParameter(ZconsGap, RealType);
96		DeclareParameter(ZconsFixtime, RealType);
97		DeclareParameter(ZconsUsingSMD, bool);
98	<	DeclareParameter(UseSolidThermInt, bool);
102	<	DeclareParameter(UseLiquidThermInt, bool);
98	>	DeclareParameter(UseThermodynamicIntegration, bool);
99		DeclareParameter(ThermodynamicIntegrationLambda, RealType);
100		DeclareParameter(ThermodynamicIntegrationK, RealType);
101		DeclareParameter(ForceFieldVariant, std::string);
102		DeclareParameter(ForceFieldFileName, std::string);
107	–	DeclareParameter(ThermIntDistSpringConst, RealType);
108	–	DeclareParameter(ThermIntThetaSpringConst, RealType);
109	–	DeclareParameter(ThermIntOmegaSpringConst, RealType);
103		DeclareParameter(SurfaceTension, RealType);
104		DeclareParameter(PrintPressureTensor, bool);
105	+	DeclareParameter(PrintHeatFlux, bool);
106		DeclareParameter(TaggedAtomPair, intPair);
107		DeclareParameter(PrintTaggedPairDistance, bool);
108		DeclareParameter(ElectrostaticSummationMethod, std::string);
109		DeclareParameter(ElectrostaticScreeningMethod, std::string);
110		DeclareParameter(DampingAlpha, RealType);
111		DeclareParameter(Dielectric, RealType);
112	+	DeclareParameter(CutoffMethod, std::string);
113		DeclareParameter(CutoffPolicy, std::string);
114		DeclareParameter(SwitchingFunctionType, std::string);
115		DeclareParameter(CompressDumpFile, bool);
116		DeclareParameter(OutputForceVector, bool);
117	+	DeclareParameter(OutputParticlePotential, bool);
118	+	DeclareParameter(OutputElectricField, bool);
119	+	DeclareParameter(OutputFluctuatingCharges, bool);
120		DeclareParameter(SkinThickness, RealType);
121		DeclareParameter(StatFileFormat, std::string);
122		DeclareParameter(HydroPropFile, std::string);
#	Line 135 | Line 133 | namespace oopse {
133		DeclareParameter(MTM_Io, RealType);
134		DeclareParameter(MTM_Sigma, RealType);
135		DeclareParameter(MTM_R, RealType);
136	<	DeclareParameter(UseRNEMD, bool);
137	<	DeclareParameter(RNEMD_swapTime, RealType);
138	<	DeclareParameter(RNEMD_nBins, int);
139	<	DeclareParameter(RNEMD_swapType, std::string);
140	<	DeclareParameter(RNEMD_objectSelection, std::string);
141	<
136	>	DeclareParameter(UseRestraints, bool);
137	>	DeclareParameter(Restraint_file, std::string);
138	>	DeclareParameter(HULL_Method, std::string);
139	>	DeclareParameter(Alpha, RealType);
140	>	DeclareAlterableParameter(MDfileVersion, int);
141	>	DeclareParameter(ElectricField, OpenMD::Vector3d);
142	>
143		public:
144		bool addComponent(Component* comp);
145		bool addZConsStamp(ZConsStamp* zcons);
146	+	bool addRestraintStamp(RestraintStamp* rest);
147		bool addMoleculeStamp(MoleculeStamp* molStamp);
148		int getNComponents() {return components_.size();}
149		std::vector<Component*> getComponents() {return components_;}
#	Line 152 | Line 152 | namespace oopse {
152		int getNZconsStamps() {return zconstraints_.size();}
153		std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;}
154		ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);}
155	+
156	+	int getNRestraintStamps() {return restraints_.size();}
157	+	std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
158	+	RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}
159	+
160	+	bool addFluctuatingChargeParameters(FluctuatingChargeParameters* flucqPars);
161	+	FluctuatingChargeParameters* getFluctuatingChargeParameters() {return flucQpars_;}
162	+
163	+	bool addRNEMDParameters(RNEMDParameters* rnemdPars);
164	+	RNEMDParameters* getRNEMDParameters() {return rnemdPars_;}
165	+
166	+	bool addMinimizerParameters(MinimizerParameters* miniPars);
167	+	MinimizerParameters* getMinimizerParameters() {return minimizerPars_;}
168
169		virtual void validate();
170		private:
171
172		std::vector<Component*> components_;
173		std::vector<ZConsStamp*> zconstraints_;
174	+	std::vector<RestraintStamp*> restraints_;
175		std::map<std::string, MoleculeStamp*> moleculeStamps_;
176		std::pair<int, int> taggedAtomPair_;
177	+	FluctuatingChargeParameters* flucQpars_;
178	+	RNEMDParameters* rnemdPars_;
179	+	MinimizerParameters* minimizerPars_;
180		};
181		}
182		#endif
166	–

Comparing:
trunk/src/io/Globals.hpp (property svn:keywords), Revision 1331 by gezelter, Thu Apr 2 16:04:52 2009 UTC vs.
branches/development/src/io/Globals.hpp (property svn:keywords), Revision 1780 by jmarr, Mon Aug 20 18:28:22 2012 UTC

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