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root/OpenMD/branches/development/src/io/Globals.hpp
Revision: 1360
Committed: Mon Sep 7 16:31:51 2009 UTC (15 years, 7 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

File Contents

# User Rev Content
1 gezelter 507 /*
2 gezelter 246 * 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 gezelter 2
45     #include <iostream>
46    
47     #include <stdlib.h>
48     #include <vector>
49 tim 425 #include <string>
50     #include <map>
51 gezelter 2
52 tim 3 #include "types/Component.hpp"
53 tim 770 #include "types/ZconsStamp.hpp"
54 cli2 1360 #include "types/RestraintStamp.hpp"
55 tim 770 #include "types/MoleculeStamp.hpp"
56 chuckv 748 #include "utils/ParameterManager.hpp"
57 gezelter 2
58 tim 770 namespace oopse {
59 gezelter 1291 class Globals : public DataHolder {
60 tim 665 public:
61 gezelter 1291 typedef std::pair<int, int> intPair;
62    
63 tim 665 Globals();
64 tim 770 virtual ~Globals();
65 tim 665
66 gezelter 1291 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 gezelter 1313 DeclareParameter(Seed, unsigned long int);
88 gezelter 1291 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 cli2 1360 DeclareParameter(UseThermodynamicIntegration, bool);
103 gezelter 1291 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 gezelter 1355 DeclareParameter(ThermalConductivity, RealType);
125     DeclareParameter(ThermalLength, RealType);
126 gezelter 1291 DeclareParameter(UseSphericalBoundaryConditions, bool);
127     DeclareParameter(FrozenBufferRadius, RealType);
128     DeclareParameter(LangevinBufferRadius, RealType);
129     DeclareParameter(AccumulateBoxDipole, bool);
130     DeclareParameter(NeighborListNeighbors, int);
131 chuckv 1306 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 gezelter 1327 DeclareParameter(UseRNEMD, bool);
138     DeclareParameter(RNEMD_swapTime, RealType);
139     DeclareParameter(RNEMD_nBins, int);
140     DeclareParameter(RNEMD_swapType, std::string);
141 gezelter 1331 DeclareParameter(RNEMD_objectSelection, std::string);
142 gezelter 1354 DeclareParameter(UseRestraints, bool);
143     DeclareParameter(Restraint_file, std::string);
144 cli2 1360
145 gezelter 1291
146 tim 770 public:
147     bool addComponent(Component* comp);
148     bool addZConsStamp(ZConsStamp* zcons);
149 cli2 1360 bool addRestraintStamp(RestraintStamp* rest);
150 tim 770 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 gezelter 1291
155 tim 770 int getNZconsStamps() {return zconstraints_.size();}
156     std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;}
157     ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);}
158 cli2 1360
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 gezelter 1291
165 tim 770 virtual void validate();
166     private:
167 tim 895
168 tim 770 std::vector<Component*> components_;
169     std::vector<ZConsStamp*> zconstraints_;
170 cli2 1360 std::vector<RestraintStamp*> restraints_;
171 tim 770 std::map<std::string, MoleculeStamp*> moleculeStamps_;
172 gezelter 1291 std::pair<int, int> taggedAtomPair_;
173 gezelter 2 };
174 tim 770 }
175 tim 665 #endif
176 gezelter 2