src/io/Globals.hpp

/*
 * Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#ifndef IO_GLOBALS_HPP
#define IO_GLOBALS_HPP

#include <iostream>

#include <stdlib.h>
#include <vector>
#include <string>
#include <map>

#include "types/Component.hpp"
#include "types/ZconsStamp.hpp"
#include "types/RestraintStamp.hpp"
#include "types/MoleculeStamp.hpp"
#include "flucq/FluctuatingChargeParameters.hpp"
#include "rnemd/RNEMDParameters.hpp"
#include "optimization/MinimizerParameters.hpp"
#include "utils/ParameterManager.hpp"

namespace OpenMD {
  class Globals : public DataHolder {
  public:
    typedef std::pair<int, int> intPair;

    Globals();
    virtual ~Globals();
    
    DeclareParameter(ForceField, std::string);
    DeclareParameter(TargetTemp, RealType);
    DeclareParameter(Ensemble, std::string);
    DeclareParameter(Dt, RealType);
    DeclareParameter(RunTime, RealType);
    DeclareParameter(FinalConfig, std::string);
    DeclareParameter(SampleTime, RealType);
    DeclareParameter(ResetTime, RealType);
    DeclareParameter(StatusTime, RealType);
    DeclareParameter(CutoffRadius, RealType);
    DeclareParameter(SwitchingRadius, RealType);
    DeclareParameter(TempSet, bool);
    DeclareParameter(ThermalTime, RealType);
    DeclareParameter(UsePeriodicBoundaryConditions, bool);
    DeclareParameter(TargetPressure, RealType);
    DeclareParameter(UseAtomicVirial, bool);
    DeclareParameter(TauThermostat, RealType);
    DeclareParameter(TauBarostat, RealType);
    DeclareParameter(ZconsTime, RealType);
    DeclareParameter(ZconsTol, RealType);
    DeclareParameter(ZconsForcePolicy, std::string);
    DeclareParameter(Seed, unsigned long int);
    DeclareParameter(UseInitalTime, bool);
    DeclareParameter(UseIntialExtendedSystemState, bool);
    DeclareParameter(OrthoBoxTolerance, RealType);
    DeclareParameter(ZconsGap, RealType);
    DeclareParameter(ZconsFixtime, RealType);
    DeclareParameter(ZconsUsingSMD, bool);
    DeclareParameter(UseThermodynamicIntegration, bool);
    DeclareParameter(ThermodynamicIntegrationLambda, RealType);
    DeclareParameter(ThermodynamicIntegrationK, RealType);
    DeclareParameter(ForceFieldVariant, std::string);
    DeclareParameter(ForceFieldFileName, std::string);
    DeclareParameter(SurfaceTension, RealType);
    DeclareParameter(PrintPressureTensor, bool);
    DeclareParameter(PrintHeatFlux, bool);
    DeclareParameter(TaggedAtomPair, intPair);
    DeclareParameter(PrintTaggedPairDistance, bool);
    DeclareParameter(ElectrostaticSummationMethod, std::string);
    DeclareParameter(ElectrostaticScreeningMethod, std::string);
    DeclareParameter(DampingAlpha, RealType);
    DeclareParameter(Dielectric, RealType);
    DeclareParameter(CutoffMethod, std::string);
    DeclareParameter(CutoffPolicy, std::string);
    DeclareParameter(SwitchingFunctionType, std::string);
    DeclareParameter(CompressDumpFile, bool);
    DeclareParameter(OutputForceVector, bool);
    DeclareParameter(OutputParticlePotential, bool);
    DeclareParameter(OutputElectricField, bool);
    DeclareParameter(OutputFluctuatingCharges, bool);
    DeclareParameter(SkinThickness, RealType);
    DeclareParameter(StatFileFormat, std::string);    
    DeclareParameter(HydroPropFile, std::string);
    DeclareParameter(Viscosity, RealType);
    DeclareParameter(BeadSize, RealType);  
    DeclareParameter(UseSphericalBoundaryConditions, bool);
    DeclareParameter(FrozenBufferRadius, RealType);
    DeclareParameter(LangevinBufferRadius, RealType);
    DeclareParameter(AccumulateBoxDipole, bool);
    DeclareParameter(NeighborListNeighbors, int);
    DeclareParameter(UseMultipleTemperatureMethod, bool);
    DeclareParameter(MTM_Ce, RealType);
    DeclareParameter(MTM_G, RealType);
    DeclareParameter(MTM_Io, RealType);
    DeclareParameter(MTM_Sigma, RealType);    
    DeclareParameter(MTM_R, RealType);    
    DeclareParameter(UseRestraints, bool);
    DeclareParameter(Restraint_file, std::string);
    DeclareParameter(HULL_Method, std::string);
    DeclareParameter(Alpha, RealType);
    DeclareAlterableParameter(MDfileVersion, int);

  public:
    bool addComponent(Component* comp);
    bool addZConsStamp(ZConsStamp* zcons);
    bool addRestraintStamp(RestraintStamp* rest);
    bool addMoleculeStamp(MoleculeStamp* molStamp);
    int getNComponents() {return components_.size();}
    std::vector<Component*> getComponents() {return components_;}
    Component* getComponentAt(int index) {return components_.at(index);}    
    
    int getNZconsStamps() {return zconstraints_.size();}
    std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;}
    ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);}    

    int getNRestraintStamps() {return restraints_.size();}
    std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
    RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}    

    bool addFluctuatingChargeParameters(FluctuatingChargeParameters* flucqPars);
    FluctuatingChargeParameters* getFluctuatingChargeParameters() {return flucQpars_;}

    bool addRNEMDParameters(RNEMDParameters* rnemdPars);
    RNEMDParameters* getRNEMDParameters() {return rnemdPars_;}

    bool addMinimizerParameters(MinimizerParameters* miniPars);
    MinimizerParameters* getMinimizerParameters() {return minimizerPars_;}
    
    virtual void validate();
  private:
    
    std::vector<Component*> components_;
    std::vector<ZConsStamp*> zconstraints_;    
    std::vector<RestraintStamp*> restraints_;    
    std::map<std::string, MoleculeStamp*> moleculeStamps_;
    std::pair<int, int> taggedAtomPair_;
    FluctuatingChargeParameters* flucQpars_;
    RNEMDParameters* rnemdPars_;
    MinimizerParameters* minimizerPars_;
};
}
#endif
Revision:	1746
Committed:	Wed Jun 6 02:18:54 2012 UTC (12 years, 10 months ago) by gezelter
File size:	7906 byte(s)
Log Message:	added a minimizer parsing block
#	User	Rev	Content
1	gezelter	507	/*
2	chuckv	1402	* Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved.
3	gezelter	246	*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43			#ifndef IO_GLOBALS_HPP
44			#define IO_GLOBALS_HPP
45	gezelter	2
46			#include <iostream>
47
48			#include <stdlib.h>
49			#include <vector>
50	tim	425	#include <string>
51			#include <map>
52	gezelter	2
53	tim	3	#include "types/Component.hpp"
54	tim	770	#include "types/ZconsStamp.hpp"
55	cli2	1360	#include "types/RestraintStamp.hpp"
56	tim	770	#include "types/MoleculeStamp.hpp"
57	gezelter	1731	#include "flucq/FluctuatingChargeParameters.hpp"
58			#include "rnemd/RNEMDParameters.hpp"
59	gezelter	1746	#include "optimization/MinimizerParameters.hpp"
60	chuckv	748	#include "utils/ParameterManager.hpp"
61	gezelter	2
62	gezelter	1390	namespace OpenMD {
63	gezelter	1291	class Globals : public DataHolder {
64	tim	665	public:
65	gezelter	1291	typedef std::pair<int, int> intPair;
66
67	tim	665	Globals();
68	tim	770	virtual ~Globals();
69	tim	665
70	gezelter	1291	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(TauThermostat, RealType);
87			DeclareParameter(TauBarostat, RealType);
88			DeclareParameter(ZconsTime, RealType);
89			DeclareParameter(ZconsTol, RealType);
90			DeclareParameter(ZconsForcePolicy, std::string);
91	gezelter	1313	DeclareParameter(Seed, unsigned long int);
92	gezelter	1291	DeclareParameter(UseInitalTime, bool);
93			DeclareParameter(UseIntialExtendedSystemState, bool);
94			DeclareParameter(OrthoBoxTolerance, RealType);
95			DeclareParameter(ZconsGap, RealType);
96			DeclareParameter(ZconsFixtime, RealType);
97			DeclareParameter(ZconsUsingSMD, bool);
98	cli2	1360	DeclareParameter(UseThermodynamicIntegration, bool);
99	gezelter	1291	DeclareParameter(ThermodynamicIntegrationLambda, RealType);
100			DeclareParameter(ThermodynamicIntegrationK, RealType);
101			DeclareParameter(ForceFieldVariant, std::string);
102			DeclareParameter(ForceFieldFileName, std::string);
103			DeclareParameter(SurfaceTension, RealType);
104			DeclareParameter(PrintPressureTensor, bool);
105	gezelter	1723	DeclareParameter(PrintHeatFlux, bool);
106	gezelter	1291	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	gezelter	1528	DeclareParameter(CutoffMethod, std::string);
113	gezelter	1576	DeclareParameter(CutoffPolicy, std::string);
114	gezelter	1291	DeclareParameter(SwitchingFunctionType, std::string);
115			DeclareParameter(CompressDumpFile, bool);
116			DeclareParameter(OutputForceVector, bool);
117	gezelter	1629	DeclareParameter(OutputParticlePotential, bool);
118	gezelter	1714	DeclareParameter(OutputElectricField, bool);
119			DeclareParameter(OutputFluctuatingCharges, bool);
120	gezelter	1291	DeclareParameter(SkinThickness, RealType);
121			DeclareParameter(StatFileFormat, std::string);
122			DeclareParameter(HydroPropFile, std::string);
123			DeclareParameter(Viscosity, RealType);
124			DeclareParameter(BeadSize, RealType);
125			DeclareParameter(UseSphericalBoundaryConditions, bool);
126			DeclareParameter(FrozenBufferRadius, RealType);
127			DeclareParameter(LangevinBufferRadius, RealType);
128			DeclareParameter(AccumulateBoxDipole, bool);
129			DeclareParameter(NeighborListNeighbors, int);
130	chuckv	1306	DeclareParameter(UseMultipleTemperatureMethod, bool);
131			DeclareParameter(MTM_Ce, RealType);
132			DeclareParameter(MTM_G, RealType);
133			DeclareParameter(MTM_Io, RealType);
134			DeclareParameter(MTM_Sigma, RealType);
135			DeclareParameter(MTM_R, RealType);
136	gezelter	1354	DeclareParameter(UseRestraints, bool);
137			DeclareParameter(Restraint_file, std::string);
138	chuckv	1402	DeclareParameter(HULL_Method, std::string);
139			DeclareParameter(Alpha, RealType);
140	gezelter	1613	DeclareAlterableParameter(MDfileVersion, int);
141	gezelter	1715
142	tim	770	public:
143			bool addComponent(Component* comp);
144			bool addZConsStamp(ZConsStamp* zcons);
145	cli2	1360	bool addRestraintStamp(RestraintStamp* rest);
146	tim	770	bool addMoleculeStamp(MoleculeStamp* molStamp);
147			int getNComponents() {return components_.size();}
148			std::vector<Component*> getComponents() {return components_;}
149			Component* getComponentAt(int index) {return components_.at(index);}
150	gezelter	1291
151	tim	770	int getNZconsStamps() {return zconstraints_.size();}
152			std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;}
153			ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);}
154	cli2	1360
155			int getNRestraintStamps() {return restraints_.size();}
156			std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
157			RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}
158	gezelter	1731
159			bool addFluctuatingChargeParameters(FluctuatingChargeParameters* flucqPars);
160			FluctuatingChargeParameters* getFluctuatingChargeParameters() {return flucQpars_;}
161
162			bool addRNEMDParameters(RNEMDParameters* rnemdPars);
163			RNEMDParameters* getRNEMDParameters() {return rnemdPars_;}
164	gezelter	1746
165			bool addMinimizerParameters(MinimizerParameters* miniPars);
166			MinimizerParameters* getMinimizerParameters() {return minimizerPars_;}
167	gezelter	1291
168	tim	770	virtual void validate();
169			private:
170	tim	895
171	tim	770	std::vector<Component*> components_;
172			std::vector<ZConsStamp*> zconstraints_;
173	cli2	1360	std::vector<RestraintStamp*> restraints_;
174	tim	770	std::map<std::string, MoleculeStamp*> moleculeStamps_;
175	gezelter	1291	std::pair<int, int> taggedAtomPair_;
176	gezelter	1731	FluctuatingChargeParameters* flucQpars_;
177			RNEMDParameters* rnemdPars_;
178	gezelter	1746	MinimizerParameters* minimizerPars_;
179	gezelter	2	};
180	tim	770	}
181	tim	665	#endif