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root/group/trunk/OOPSE-4/src/io/Globals.hpp
Revision: 3448
Committed: Thu Sep 11 19:40:59 2008 UTC (17 years, 1 month ago) by gezelter
File size: 6591 byte(s)
Log Message: 
Added some logic to print out a special pair distance as a column in
the stat file.  To use this feature, use taggedAtomPair = "0, 10" and
printTaggedPairDistance = "true" in the md file.  Then, the distance
between integrableObjects 0 and 10 will be computed and printed in
the stat file on each statWrite.

File Contents

# User Rev Content
1 gezelter 2204 /*
2 gezelter 1930 * 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 1490
45     #include <iostream>
46    
47     #include <stdlib.h>
48     #include <vector>
49 tim 2109 #include <string>
50     #include <map>
51 gezelter 1490
52 tim 1492 #include "types/Component.hpp"
53 tim 2469 #include "types/ZconsStamp.hpp"
54     #include "types/MoleculeStamp.hpp"
55 chuckv 2447 #include "utils/ParameterManager.hpp"
56 gezelter 1490
57 tim 2469 namespace oopse {
58 gezelter 3448 class Globals : public DataHolder {
59 tim 2364 public:
60 gezelter 3448 typedef std::pair<int, int> intPair;
61    
62 tim 2364 Globals();
63 tim 2469 virtual ~Globals();
64 tim 2364
65 gezelter 3448 DeclareParameter(ForceField, std::string);
66     DeclareParameter(TargetTemp, RealType);
67     DeclareParameter(Ensemble, std::string);
68     DeclareParameter(Dt, RealType);
69     DeclareParameter(RunTime, RealType);
70     DeclareParameter(FinalConfig, std::string);
71     DeclareParameter(SampleTime, RealType);
72     DeclareParameter(ResetTime, RealType);
73     DeclareParameter(StatusTime, RealType);
74     DeclareParameter(CutoffRadius, RealType);
75     DeclareParameter(SwitchingRadius, RealType);
76     DeclareParameter(TempSet, bool);
77     DeclareParameter(ThermalTime, RealType);
78     DeclareParameter(UsePeriodicBoundaryConditions, bool);
79     DeclareParameter(TargetPressure, RealType);
80     DeclareParameter(UseAtomicVirial, bool);
81     DeclareParameter(TauThermostat, RealType);
82     DeclareParameter(TauBarostat, RealType);
83     DeclareParameter(ZconsTime, RealType);
84     DeclareParameter(ZconsTol, RealType);
85     DeclareParameter(ZconsForcePolicy, std::string);
86     DeclareParameter(Seed, int);
87     DeclareParameter(UseInitalTime, bool);
88     DeclareParameter(UseIntialExtendedSystemState, bool);
89     DeclareParameter(OrthoBoxTolerance, RealType);
90     DeclareParameter(Minimizer, std::string);
91     DeclareParameter(MinimizerMaxIter, RealType);
92     DeclareParameter(MinimizerWriteFrq, int);
93     DeclareParameter(MinimizerStepSize, RealType);
94     DeclareParameter(MinimizerFTol, RealType);
95     DeclareParameter(MinimizerGTol, RealType);
96     DeclareParameter(MinimizerLSTol, RealType);
97     DeclareParameter(MinimizerLSMaxIter, int);
98     DeclareParameter(ZconsGap, RealType);
99     DeclareParameter(ZconsFixtime, RealType);
100     DeclareParameter(ZconsUsingSMD, bool);
101     DeclareParameter(UseSolidThermInt, bool);
102     DeclareParameter(UseLiquidThermInt, bool);
103     DeclareParameter(ThermodynamicIntegrationLambda, RealType);
104     DeclareParameter(ThermodynamicIntegrationK, RealType);
105     DeclareParameter(ForceFieldVariant, std::string);
106     DeclareParameter(ForceFieldFileName, std::string);
107     DeclareParameter(ThermIntDistSpringConst, RealType);
108     DeclareParameter(ThermIntThetaSpringConst, RealType);
109     DeclareParameter(ThermIntOmegaSpringConst, RealType);
110     DeclareParameter(SurfaceTension, RealType);
111     DeclareParameter(PrintPressureTensor, bool);
112     DeclareParameter(TaggedAtomPair, intPair);
113     DeclareParameter(PrintTaggedPairDistance, bool);
114     DeclareParameter(ElectrostaticSummationMethod, std::string);
115     DeclareParameter(ElectrostaticScreeningMethod, std::string);
116     DeclareParameter(DampingAlpha, RealType);
117     DeclareParameter(Dielectric, 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     DeclareParameter(AccumulateBoxDipole, bool);
131     DeclareParameter(NeighborListNeighbors, int);
132    
133    
134 tim 2469 public:
135     bool addComponent(Component* comp);
136     bool addZConsStamp(ZConsStamp* zcons);
137     bool addMoleculeStamp(MoleculeStamp* molStamp);
138     int getNComponents() {return components_.size();}
139     std::vector<Component*> getComponents() {return components_;}
140     Component* getComponentAt(int index) {return components_.at(index);}
141 gezelter 3448
142 tim 2469 int getNZconsStamps() {return zconstraints_.size();}
143     std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;}
144     ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);}
145 gezelter 3448
146 tim 2469 virtual void validate();
147     private:
148 tim 2611
149 tim 2469 std::vector<Component*> components_;
150     std::vector<ZConsStamp*> zconstraints_;
151     std::map<std::string, MoleculeStamp*> moleculeStamps_;
152 gezelter 3448 std::pair<int, int> taggedAtomPair_;
153 tim 2364
154 gezelter 1490 };
155 tim 2469 }
156 tim 2364 #endif
157 gezelter 1490