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

Comparing:
trunk/src/io/Globals.hpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/io/Globals.hpp (file contents), Revision 1729 by jmarr, Wed May 30 16:08:07 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 "utils/ParameterManager.hpp"
58
59	<	namespace oopse {
60	<	class Globals : public DataHolder {
59	>	namespace OpenMD {
60	>	class Globals : public DataHolder {
61		public:
62	+	typedef std::pair<int, int> intPair;
63	+
64		Globals();
65		virtual ~Globals();
66
67	<	DeclareParameter(ForceField, std::string);
68	<	DeclareParameter(TargetTemp, RealType);
69	<	DeclareParameter(Ensemble, std::string);
70	<	DeclareParameter(Dt, RealType);
71	<	DeclareParameter(RunTime, RealType);
72	<	DeclareParameter(InitialConfig, std::string);
73	<	DeclareParameter(FinalConfig, std::string);
74	<	DeclareParameter(SampleTime, RealType);
75	<	DeclareParameter(ResetTime, RealType);
76	<	DeclareParameter(StatusTime, RealType);
77	<	DeclareParameter(CutoffRadius, RealType);
78	<	DeclareParameter(SwitchingRadius, RealType);
79	<	DeclareParameter(Dielectric, RealType);
80	<	DeclareParameter(TempSet, bool);
81	<	DeclareParameter(ThermalTime, RealType);
82	<	DeclareParameter(UsePeriodicBoundaryConditions, bool);
83	<	DeclareParameter(TargetPressure, RealType);
84	<	DeclareParameter(TauThermostat, RealType);
85	<	DeclareParameter(TauBarostat, RealType);
86	<	DeclareParameter(ZconsTime, RealType);
87	<	DeclareParameter(ZconsTol, RealType);
88	<	DeclareParameter(ZconsForcePolicy, std::string);
89	<	DeclareParameter(Seed, int);
90	<	DeclareParameter(UseInitalTime, bool);
91	<	DeclareParameter(UseIntialExtendedSystemState, bool);
92	<	DeclareParameter(OrthoBoxTolerance, RealType);
93	<	DeclareParameter(Minimizer, std::string);
94	<	DeclareParameter(MinimizerMaxIter, RealType);
95	<	DeclareParameter(MinimizerWriteFrq, int);
96	<	DeclareParameter(MinimizerStepSize, RealType);
97	<	DeclareParameter(MinimizerFTol, RealType);
98	<	DeclareParameter(MinimizerGTol, RealType);
99	<	DeclareParameter(MinimizerLSTol, RealType);
100	<	DeclareParameter(MinimizerLSMaxIter, int);
101	<	DeclareParameter(ZconsGap, RealType);
102	<	DeclareParameter(ZconsFixtime, RealType);
103	<	DeclareParameter(ZconsUsingSMD, bool);
104	<	DeclareParameter(UseSolidThermInt, bool);
105	<	DeclareParameter(UseLiquidThermInt, bool);
106	<	DeclareParameter(ThermodynamicIntegrationLambda, RealType);
107	<	DeclareParameter(ThermodynamicIntegrationK, RealType);
108	<	DeclareParameter(ForceFieldVariant, std::string);
109	<	DeclareParameter(ForceFieldFileName, std::string);
110	<	DeclareParameter(ThermIntDistSpringConst, RealType);
111	<	DeclareParameter(ThermIntThetaSpringConst, RealType);
112	<	DeclareParameter(ThermIntOmegaSpringConst, RealType);
113	<	DeclareParameter(SurfaceTension, RealType);
114	<	DeclareParameter(PrintPressureTensor, bool);
115	<	DeclareParameter(ElectrostaticSummationMethod, std::string);
116	<	DeclareParameter(ElectrostaticScreeningMethod, std::string);
117	<	DeclareParameter(DampingAlpha, RealType);
118	<	DeclareParameter(CutoffPolicy, std::string);
119	<	DeclareParameter(SwitchingFunctionType, std::string);
120	<	DeclareParameter(CompressDumpFile, bool);
121	<	DeclareParameter(OutputForceVector, bool);
122	<	DeclareParameter(SkinThickness, RealType);
123	<	DeclareParameter(StatFileFormat, std::string);
124	<	DeclareParameter(HydroPropFile, std::string);
125	<	DeclareParameter(Viscosity, RealType);
126	<	DeclareParameter(BeadSize, RealType);
127	<	DeclareParameter(UseSphericalBoundaryConditions, bool);
128	<	DeclareParameter(FrozenBufferRadius, RealType);
129	<	DeclareParameter(LangevinBufferRadius, RealType);
130	<
67	>	DeclareParameter(ForceField, std::string);
68	>	DeclareParameter(TargetTemp, RealType);
69	>	DeclareParameter(Ensemble, std::string);
70	>	DeclareParameter(Dt, RealType);
71	>	DeclareParameter(RunTime, RealType);
72	>	DeclareParameter(FinalConfig, std::string);
73	>	DeclareParameter(SampleTime, RealType);
74	>	DeclareParameter(ResetTime, RealType);
75	>	DeclareParameter(StatusTime, RealType);
76	>	DeclareParameter(CutoffRadius, RealType);
77	>	DeclareParameter(SwitchingRadius, RealType);
78	>	DeclareParameter(TempSet, bool);
79	>	DeclareParameter(ThermalTime, RealType);
80	>	DeclareParameter(UsePeriodicBoundaryConditions, bool);
81	>	DeclareParameter(TargetPressure, RealType);
82	>	DeclareParameter(UseAtomicVirial, bool);
83	>	DeclareParameter(TauThermostat, RealType);
84	>	DeclareParameter(TauBarostat, RealType);
85	>	DeclareParameter(ZconsTime, RealType);
86	>	DeclareParameter(ZconsTol, RealType);
87	>	DeclareParameter(ZconsForcePolicy, std::string);
88	>	DeclareParameter(Seed, unsigned long int);
89	>	DeclareParameter(UseInitalTime, bool);
90	>	DeclareParameter(UseIntialExtendedSystemState, bool);
91	>	DeclareParameter(OrthoBoxTolerance, RealType);
92	>	DeclareParameter(Minimizer, std::string);
93	>	DeclareParameter(MinimizerMaxIter, RealType);
94	>	DeclareParameter(MinimizerWriteFreq, int);
95	>	DeclareParameter(MinimizerStepSize, RealType);
96	>	DeclareParameter(MinimizerFTol, RealType);
97	>	DeclareParameter(MinimizerGTol, RealType);
98	>	DeclareParameter(MinimizerLSTol, RealType);
99	>	DeclareParameter(MinimizerLSMaxIter, int);
100	>	DeclareParameter(ZconsGap, RealType);
101	>	DeclareParameter(ZconsFixtime, RealType);
102	>	DeclareParameter(ZconsUsingSMD, bool);
103	>	DeclareParameter(UseThermodynamicIntegration, bool);
104	>	DeclareParameter(ThermodynamicIntegrationLambda, RealType);
105	>	DeclareParameter(ThermodynamicIntegrationK, RealType);
106	>	DeclareParameter(ForceFieldVariant, std::string);
107	>	DeclareParameter(ForceFieldFileName, std::string);
108	>	DeclareParameter(SurfaceTension, RealType);
109	>	DeclareParameter(PrintPressureTensor, bool);
110	>	DeclareParameter(PrintHeatFlux, bool);
111	>	DeclareParameter(TaggedAtomPair, intPair);
112	>	DeclareParameter(PrintTaggedPairDistance, bool);
113	>	DeclareParameter(ElectrostaticSummationMethod, std::string);
114	>	DeclareParameter(ElectrostaticScreeningMethod, std::string);
115	>	DeclareParameter(DampingAlpha, RealType);
116	>	DeclareParameter(Dielectric, RealType);
117	>	DeclareParameter(CutoffMethod, std::string);
118	>	DeclareParameter(CutoffPolicy, std::string);
119	>	DeclareParameter(SwitchingFunctionType, std::string);
120	>	DeclareParameter(CompressDumpFile, bool);
121	>	DeclareParameter(OutputForceVector, bool);
122	>	DeclareParameter(OutputParticlePotential, bool);
123	>	DeclareParameter(OutputElectricField, bool);
124	>	DeclareParameter(OutputFluctuatingCharges, bool);
125	>	DeclareParameter(SkinThickness, RealType);
126	>	DeclareParameter(StatFileFormat, std::string);
127	>	DeclareParameter(HydroPropFile, std::string);
128	>	DeclareParameter(Viscosity, RealType);
129	>	DeclareParameter(BeadSize, RealType);
130	>	DeclareParameter(UseSphericalBoundaryConditions, bool);
131	>	DeclareParameter(FrozenBufferRadius, RealType);
132	>	DeclareParameter(LangevinBufferRadius, RealType);
133	>	DeclareParameter(AccumulateBoxDipole, bool);
134	>	DeclareParameter(NeighborListNeighbors, int);
135	>	DeclareParameter(UseMultipleTemperatureMethod, bool);
136	>	DeclareParameter(MTM_Ce, RealType);
137	>	DeclareParameter(MTM_G, RealType);
138	>	DeclareParameter(MTM_Io, RealType);
139	>	DeclareParameter(MTM_Sigma, RealType);
140	>	DeclareParameter(MTM_R, RealType);
141	>	DeclareParameter(UseRNEMD, bool);
142	>	DeclareParameter(RNEMD_exchangeTime, RealType);
143	>	DeclareParameter(RNEMD_nBins, int);
144	>	DeclareParameter(RNEMD_logWidth, int);
145	>	DeclareParameter(RNEMD_exchangeType, std::string);
146	>	DeclareParameter(RNEMD_objectSelection, std::string);
147	>	DeclareParameter(RNEMD_targetFlux, RealType);
148	>	DeclareParameter(RNEMD_targetJzKE, RealType);
149	>	DeclareParameter(RNEMD_targetJzpx, RealType);
150	>	DeclareParameter(RNEMD_targetJzpy, RealType);
151	>	DeclareParameter(RNEMD_targetJzpz, RealType);
152	>	DeclareParameter(RNEMD_binShift, bool);
153	>	DeclareParameter(RNEMD_outputTemperature, bool);
154	>	DeclareParameter(RNEMD_outputVx, bool);
155	>	DeclareParameter(RNEMD_outputVy, bool);
156	>	// James put this in.
157	>	DeclareParameter(RNEMD_outputDen, bool);
158	>	DeclareParameter(RNEMD_outputVz, bool);
159	>	DeclareParameter(RNEMD_outputAh, bool);
160	>	DeclareParameter(RNEMD_outputXyzTemperature, bool);
161	>	DeclareParameter(RNEMD_outputRotTemperature, bool);
162	>	DeclareParameter(UseRestraints, bool);
163	>	DeclareParameter(Restraint_file, std::string);
164	>	DeclareParameter(HULL_Method, std::string);
165	>	DeclareParameter(Alpha, RealType);
166	>	DeclareParameter(FlucQPropagator, std::string);
167	>	DeclareParameter(FlucQFriction, RealType);
168	>	DeclareParameter(FlucQTolerance, RealType);
169	>	DeclareParameter(FlucQMaxIterations, int);
170	>	DeclareParameter(FlucQTargetTemp, RealType);
171	>	DeclareParameter(FlucQtauThermostat, RealType);
172	>	DeclareAlterableParameter(MDfileVersion, int);
173	>
174		public:
175		bool addComponent(Component* comp);
176		bool addZConsStamp(ZConsStamp* zcons);
177	+	bool addRestraintStamp(RestraintStamp* rest);
178		bool addMoleculeStamp(MoleculeStamp* molStamp);
179		int getNComponents() {return components_.size();}
180		std::vector<Component*> getComponents() {return components_;}
181		Component* getComponentAt(int index) {return components_.at(index);}
182	<
182	>
183		int getNZconsStamps() {return zconstraints_.size();}
184		std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;}
185		ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);}
186
187	+	int getNRestraintStamps() {return restraints_.size();}
188	+	std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
189	+	RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}
190	+
191		virtual void validate();
192		private:
193
194		std::vector<Component*> components_;
195		std::vector<ZConsStamp*> zconstraints_;
196	+	std::vector<RestraintStamp*> restraints_;
197		std::map<std::string, MoleculeStamp*> moleculeStamps_;
198	<
198	>	std::pair<int, int> taggedAtomPair_;
199		};
200		}
201		#endif
149	–

Comparing:
trunk/src/io/Globals.hpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/io/Globals.hpp (property svn:keywords), Revision 1729 by jmarr, Wed May 30 16:08:07 2012 UTC

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