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root/OpenMD/trunk/src/io/Globals.hpp

Comparing trunk/src/io/Globals.hpp (file contents):
Revision 914 by tim, Thu Mar 23 15:02:02 2006 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 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, 234107 (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 {
63	<	class Globals : public DataHolder {
62	>	namespace OpenMD {
63	>	class Globals : public DataHolder {
64		public:
65	+	typedef std::pair<int, int> intPair;
66	+
67		Globals();
68		virtual ~Globals();
69
70	<	DeclareParameter(ForceField, std::string);
71	<	DeclareParameter(TargetTemp, double);
72	<	DeclareParameter(Ensemble, std::string);
73	<	DeclareParameter(Dt, double);
74	<	DeclareParameter(RunTime, double);
75	<	DeclareParameter(InitialConfig, std::string);
76	<	DeclareParameter(FinalConfig, std::string);
77	<	DeclareParameter(SampleTime, double);
78	<	DeclareParameter(ResetTime, double);
79	<	DeclareParameter(StatusTime, double);
80	<	DeclareParameter(CutoffRadius, double);
81	<	DeclareParameter(SwitchingRadius, double);
82	<	DeclareParameter(Dielectric, double);
83	<	DeclareParameter(TempSet, bool);
84	<	DeclareParameter(ThermalTime, double);
85	<	DeclareParameter(UsePeriodicBoundaryConditions, bool);
86	<	DeclareParameter(TargetPressure, double);
87	<	DeclareParameter(TauThermostat, double);
88	<	DeclareParameter(TauBarostat, double);
89	<	DeclareParameter(ZconsTime, double);
90	<	DeclareParameter(ZconsTol, double);
91	<	DeclareParameter(ZconsForcePolicy, std::string);
92	<	DeclareParameter(Seed, int);
93	<	DeclareParameter(UseInitalTime, bool);
94	<	DeclareParameter(UseIntialExtendedSystemState, bool);
95	<	DeclareParameter(OrthoBoxTolerance, double);
96	<	DeclareParameter(Minimizer, std::string);
97	<	DeclareParameter(MinimizerMaxIter, double);
98	<	DeclareParameter(MinimizerWriteFrq, int);
99	<	DeclareParameter(MinimizerStepSize, double);
100	<	DeclareParameter(MinimizerFTol, double);
101	<	DeclareParameter(MinimizerGTol, double);
102	<	DeclareParameter(MinimizerLSTol, double);
103	<	DeclareParameter(MinimizerLSMaxIter, int);
104	<	DeclareParameter(ZconsGap, double);
105	<	DeclareParameter(ZconsFixtime, double);
106	<	DeclareParameter(ZconsUsingSMD, bool);
107	<	DeclareParameter(UseSolidThermInt, bool);
108	<	DeclareParameter(UseLiquidThermInt, bool);
109	<	DeclareParameter(ThermodynamicIntegrationLambda, double);
110	<	DeclareParameter(ThermodynamicIntegrationK, double);
111	<	DeclareParameter(ForceFieldVariant, std::string);
112	<	DeclareParameter(ForceFieldFileName, std::string);
113	<	DeclareParameter(ThermIntDistSpringConst, double);
114	<	DeclareParameter(ThermIntThetaSpringConst, double);
115	<	DeclareParameter(ThermIntOmegaSpringConst, double);
116	<	DeclareParameter(SurfaceTension, double);
117	<	DeclareParameter(PrintPressureTensor, bool);
118	<	DeclareParameter(ElectrostaticSummationMethod, std::string);
119	<	DeclareParameter(ElectrostaticScreeningMethod, std::string);
120	<	DeclareParameter(DampingAlpha, double);
121	<	DeclareParameter(CutoffPolicy, std::string);
122	<	DeclareParameter(SwitchingFunctionType, std::string);
123	<	DeclareParameter(CompressDumpFile, bool);
124	<	DeclareParameter(OutputForceVector, bool);
125	<	DeclareParameter(SkinThickness, double);
126	<	DeclareParameter(StatFileFormat, std::string);
127	<	DeclareParameter(HydroPropFile, std::string);
128	<	DeclareParameter(Viscosity, double);
129	<	DeclareParameter(BeadSize, double);
130	<
70	>	DeclareParameter(ForceField, std::string);
71	>	DeclareParameter(TargetTemp, RealType);
72	>	DeclareParameter(Ensemble, std::string);
73	>	DeclareParameter(Dt, RealType);
74	>	DeclareParameter(RunTime, RealType);
75	>	DeclareParameter(FinalConfig, std::string);
76	>	DeclareParameter(SampleTime, RealType);
77	>	DeclareParameter(ResetTime, RealType);
78	>	DeclareParameter(StatusTime, RealType);
79	>	DeclareParameter(CutoffRadius, RealType);
80	>	DeclareParameter(SwitchingRadius, RealType);
81	>	DeclareParameter(TempSet, bool);
82	>	DeclareParameter(ThermalTime, RealType);
83	>	DeclareParameter(UsePeriodicBoundaryConditions, bool);
84	>	DeclareParameter(TargetPressure, RealType);
85	>	DeclareParameter(UseAtomicVirial, bool);
86	>	DeclareParameter(UseLongRangeCorrections, bool);
87	>	DeclareParameter(TauThermostat, RealType);
88	>	DeclareParameter(TauBarostat, RealType);
89	>	DeclareParameter(ZconsTime, RealType);
90	>	DeclareParameter(ZconsTol, RealType);
91	>	DeclareParameter(ZconsForcePolicy, std::string);
92	>	DeclareParameter(Seed, unsigned long int);
93	>	DeclareParameter(UseInitalTime, bool);
94	>	DeclareParameter(UseIntialExtendedSystemState, bool);
95	>	DeclareParameter(OrthoBoxTolerance, RealType);
96	>	DeclareParameter(ZconsGap, RealType);
97	>	DeclareParameter(ZconsFixtime, RealType);
98	>	DeclareParameter(ZconsUsingSMD, bool);
99	>	DeclareParameter(UseThermodynamicIntegration, bool);
100	>	DeclareParameter(ThermodynamicIntegrationLambda, RealType);
101	>	DeclareParameter(ThermodynamicIntegrationK, RealType);
102	>	DeclareParameter(ForceFieldVariant, std::string);
103	>	DeclareParameter(ForceFieldFileName, std::string);
104	>	DeclareParameter(SurfaceTension, RealType);
105	>	DeclareParameter(PrintPressureTensor, bool);
106	>	DeclareParameter(PrintHeatFlux, bool);
107	>	DeclareParameter(TaggedAtomPair, intPair);
108	>	DeclareParameter(PrintTaggedPairDistance, bool);
109	>	DeclareParameter(ElectrostaticSummationMethod, std::string);
110	>	DeclareParameter(ElectrostaticScreeningMethod, std::string);
111	>	DeclareParameter(DampingAlpha, RealType);
112	>	DeclareParameter(Dielectric, RealType);
113	>	DeclareParameter(CutoffMethod, std::string);
114	>	DeclareParameter(CutoffPolicy, std::string);
115	>	DeclareParameter(SwitchingFunctionType, std::string);
116	>	DeclareParameter(CompressDumpFile, bool);
117	>	DeclareParameter(OutputForceVector, bool);
118	>	DeclareParameter(OutputParticlePotential, bool);
119	>	DeclareParameter(OutputElectricField, bool);
120	>	DeclareParameter(OutputFluctuatingCharges, bool);
121	>	DeclareParameter(OutputSitePotential, 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	>	DeclareParameter(AccumulateBoxDipole, bool);
131	>	DeclareParameter(NeighborListNeighbors, int);
132	>	DeclareParameter(UseMultipleTemperatureMethod, bool);
133	>	DeclareParameter(MTM_Ce, RealType);
134	>	DeclareParameter(MTM_G, RealType);
135	>	DeclareParameter(MTM_Io, RealType);
136	>	DeclareParameter(MTM_Sigma, RealType);
137	>	DeclareParameter(MTM_R, RealType);
138	>	DeclareParameter(UseRestraints, bool);
139	>	DeclareParameter(Restraint_file, std::string);
140	>	DeclareParameter(HULL_Method, std::string);
141	>	DeclareParameter(Alpha, RealType);
142	>	DeclareAlterableParameter(MDfileVersion, int);
143	>	DeclareParameter(ElectricField, OpenMD::Vector3d);
144	>	DeclareParameter(ConstraintTime, RealType);
145	>
146		public:
147		bool addComponent(Component* comp);
148		bool addZConsStamp(ZConsStamp* zcons);
149	+	bool addRestraintStamp(RestraintStamp* rest);
150		bool addMoleculeStamp(MoleculeStamp* molStamp);
151		int getNComponents() {return components_.size();}
152		std::vector<Component*> getComponents() {return components_;}
153		Component* getComponentAt(int index) {return components_.at(index);}
154	<
154	>
155		int getNZconsStamps() {return zconstraints_.size();}
156		std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;}
157		ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);}
158
159	+	int getNRestraintStamps() {return restraints_.size();}
160	+	std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
161	+	RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}
162	+
163	+	bool addFluctuatingChargeParameters(FluctuatingChargeParameters* flucqPars);
164	+	FluctuatingChargeParameters* getFluctuatingChargeParameters() {return flucQpars_;}
165	+
166	+	bool addRNEMDParameters(RNEMDParameters* rnemdPars);
167	+	RNEMDParameters* getRNEMDParameters() {return rnemdPars_;}
168	+
169	+	bool addMinimizerParameters(MinimizerParameters* miniPars);
170	+	MinimizerParameters* getMinimizerParameters() {return minimizerPars_;}
171	+
172		virtual void validate();
173		private:
174
175		std::vector<Component*> components_;
176		std::vector<ZConsStamp*> zconstraints_;
177	+	std::vector<RestraintStamp*> restraints_;
178		std::map<std::string, MoleculeStamp*> moleculeStamps_;
179	<
179	>	std::pair<int, int> taggedAtomPair_;
180	>	FluctuatingChargeParameters* flucQpars_;
181	>	RNEMDParameters* rnemdPars_;
182	>	MinimizerParameters* minimizerPars_;
183		};
184		}
185		#endif
146	–

Comparing trunk/src/io/Globals.hpp (property svn:keywords):
Revision 914 by tim, Thu Mar 23 15:02:02 2006 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

#	Line 0 | Line 1
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