src/io/Globals.hpp

/*
 * Copyright (c) 2005 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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#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 "utils/ParameterManager.hpp"

namespace oopse {
  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(Minimizer, std::string);
    DeclareParameter(MinimizerMaxIter, RealType);
    DeclareParameter(MinimizerWriteFrq, int);
    DeclareParameter(MinimizerStepSize, RealType);
    DeclareParameter(MinimizerFTol, RealType);
    DeclareParameter(MinimizerGTol, RealType);
    DeclareParameter(MinimizerLSTol, RealType);
    DeclareParameter(MinimizerLSMaxIter, int);
    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(TaggedAtomPair, intPair);
    DeclareParameter(PrintTaggedPairDistance, bool);
    DeclareParameter(ElectrostaticSummationMethod, std::string);
    DeclareParameter(ElectrostaticScreeningMethod, std::string);
    DeclareParameter(DampingAlpha, RealType);
    DeclareParameter(Dielectric, RealType);
    DeclareParameter(CutoffPolicy, std::string);
    DeclareParameter(SwitchingFunctionType, std::string);
    DeclareParameter(CompressDumpFile, bool);
    DeclareParameter(OutputForceVector, bool);
    DeclareParameter(SkinThickness, RealType);
    DeclareParameter(StatFileFormat, std::string);    
    DeclareParameter(HydroPropFile, std::string);
    DeclareParameter(Viscosity, RealType);
    DeclareParameter(BeadSize, RealType);  
    DeclareParameter(ThermalConductivity, RealType);
    DeclareParameter(ThermalLength, 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(UseRNEMD, bool);
    DeclareParameter(RNEMD_swapTime, RealType);
    DeclareParameter(RNEMD_nBins, int);
    DeclareParameter(RNEMD_swapType, std::string);
    DeclareParameter(RNEMD_objectSelection, std::string);
    DeclareParameter(UseRestraints, bool);
    DeclareParameter(Restraint_file, std::string);

    
  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);}    

    //std::string getRestraint_file(){
    
    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_;
};
}
#endif

Revision:	1360
Committed:	Mon Sep 7 16:31:51 2009 UTC (15 years, 8 months ago) by cli2
Original Path:	*trunk/src/io/Globals.hpp*
File size:	7486 byte(s)
Log Message:	Added new restraint infrastructure Added MolecularRestraints Added ObjectRestraints Added RestraintStamp Updated thermodynamic integration to use ObjectRestraints Added Quaternion mathematics for twist swing decompositions Significantly updated RestWriter and RestReader to use dump-like files Added selections for x, y, and z coordinates of atoms Removed monolithic Restraints class Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody Added some rotational capabilities to prinicpalAxisCalculator
#	Content
1	/*
2	* Copyright (c) 2005 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
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41
42	#ifndef IO_GLOBALS_HPP
43	#define IO_GLOBALS_HPP
44
45	#include <iostream>
46
47	#include <stdlib.h>
48	#include <vector>
49	#include <string>
50	#include <map>
51
52	#include "types/Component.hpp"
53	#include "types/ZconsStamp.hpp"
54	#include "types/RestraintStamp.hpp"
55	#include "types/MoleculeStamp.hpp"
56	#include "utils/ParameterManager.hpp"
57
58	namespace oopse {
59	class Globals : public DataHolder {
60	public:
61	typedef std::pair<int, int> intPair;
62
63	Globals();
64	virtual ~Globals();
65
66	DeclareParameter(ForceField, std::string);
67	DeclareParameter(TargetTemp, RealType);
68	DeclareParameter(Ensemble, std::string);
69	DeclareParameter(Dt, RealType);
70	DeclareParameter(RunTime, RealType);
71	DeclareParameter(FinalConfig, std::string);
72	DeclareParameter(SampleTime, RealType);
73	DeclareParameter(ResetTime, RealType);
74	DeclareParameter(StatusTime, RealType);
75	DeclareParameter(CutoffRadius, RealType);
76	DeclareParameter(SwitchingRadius, RealType);
77	DeclareParameter(TempSet, bool);
78	DeclareParameter(ThermalTime, RealType);
79	DeclareParameter(UsePeriodicBoundaryConditions, bool);
80	DeclareParameter(TargetPressure, RealType);
81	DeclareParameter(UseAtomicVirial, bool);
82	DeclareParameter(TauThermostat, RealType);
83	DeclareParameter(TauBarostat, RealType);
84	DeclareParameter(ZconsTime, RealType);
85	DeclareParameter(ZconsTol, RealType);
86	DeclareParameter(ZconsForcePolicy, std::string);
87	DeclareParameter(Seed, unsigned long int);
88	DeclareParameter(UseInitalTime, bool);
89	DeclareParameter(UseIntialExtendedSystemState, bool);
90	DeclareParameter(OrthoBoxTolerance, RealType);
91	DeclareParameter(Minimizer, std::string);
92	DeclareParameter(MinimizerMaxIter, RealType);
93	DeclareParameter(MinimizerWriteFrq, int);
94	DeclareParameter(MinimizerStepSize, RealType);
95	DeclareParameter(MinimizerFTol, RealType);
96	DeclareParameter(MinimizerGTol, RealType);
97	DeclareParameter(MinimizerLSTol, RealType);
98	DeclareParameter(MinimizerLSMaxIter, int);
99	DeclareParameter(ZconsGap, RealType);
100	DeclareParameter(ZconsFixtime, RealType);
101	DeclareParameter(ZconsUsingSMD, bool);
102	DeclareParameter(UseThermodynamicIntegration, bool);
103	DeclareParameter(ThermodynamicIntegrationLambda, RealType);
104	DeclareParameter(ThermodynamicIntegrationK, RealType);
105	DeclareParameter(ForceFieldVariant, std::string);
106	DeclareParameter(ForceFieldFileName, std::string);
107	DeclareParameter(SurfaceTension, RealType);
108	DeclareParameter(PrintPressureTensor, bool);
109	DeclareParameter(TaggedAtomPair, intPair);
110	DeclareParameter(PrintTaggedPairDistance, bool);
111	DeclareParameter(ElectrostaticSummationMethod, std::string);
112	DeclareParameter(ElectrostaticScreeningMethod, std::string);
113	DeclareParameter(DampingAlpha, RealType);
114	DeclareParameter(Dielectric, RealType);
115	DeclareParameter(CutoffPolicy, std::string);
116	DeclareParameter(SwitchingFunctionType, std::string);
117	DeclareParameter(CompressDumpFile, bool);
118	DeclareParameter(OutputForceVector, bool);
119	DeclareParameter(SkinThickness, RealType);
120	DeclareParameter(StatFileFormat, std::string);
121	DeclareParameter(HydroPropFile, std::string);
122	DeclareParameter(Viscosity, RealType);
123	DeclareParameter(BeadSize, RealType);
124	DeclareParameter(ThermalConductivity, RealType);
125	DeclareParameter(ThermalLength, RealType);
126	DeclareParameter(UseSphericalBoundaryConditions, bool);
127	DeclareParameter(FrozenBufferRadius, RealType);
128	DeclareParameter(LangevinBufferRadius, RealType);
129	DeclareParameter(AccumulateBoxDipole, bool);
130	DeclareParameter(NeighborListNeighbors, int);
131	DeclareParameter(UseMultipleTemperatureMethod, bool);
132	DeclareParameter(MTM_Ce, RealType);
133	DeclareParameter(MTM_G, RealType);
134	DeclareParameter(MTM_Io, RealType);
135	DeclareParameter(MTM_Sigma, RealType);
136	DeclareParameter(MTM_R, RealType);
137	DeclareParameter(UseRNEMD, bool);
138	DeclareParameter(RNEMD_swapTime, RealType);
139	DeclareParameter(RNEMD_nBins, int);
140	DeclareParameter(RNEMD_swapType, std::string);
141	DeclareParameter(RNEMD_objectSelection, std::string);
142	DeclareParameter(UseRestraints, bool);
143	DeclareParameter(Restraint_file, std::string);
144
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
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	//std::string getRestraint_file(){
164
165	virtual void validate();
166	private:
167
168	std::vector<Component*> components_;
169	std::vector<ZConsStamp*> zconstraints_;
170	std::vector<RestraintStamp*> restraints_;
171	std::map<std::string, MoleculeStamp*> moleculeStamps_;
172	std::pair<int, int> taggedAtomPair_;
173	};
174	}
175	#endif
176