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root/OpenMD/trunk/src/io/Globals.hpp
Revision: 1559
Committed: Wed May 11 17:52:33 2011 UTC (14 years, 5 months ago) by skuang
File size: 7729 byte(s)
Log Message: 
added new variables for RNEMD
remove requirement of non-negative targetFlux for RNEMD

File Contents

# 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     * [4] Vardeman & Gezelter, in progress (2009).
40 gezelter 246 */
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 gezelter 1390 namespace OpenMD {
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 gezelter 1423 DeclareParameter(MinimizerWriteFreq, int);
94 gezelter 1291 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     DeclareParameter(UseSphericalBoundaryConditions, bool);
125     DeclareParameter(FrozenBufferRadius, RealType);
126     DeclareParameter(LangevinBufferRadius, RealType);
127     DeclareParameter(AccumulateBoxDipole, bool);
128     DeclareParameter(NeighborListNeighbors, int);
129 chuckv 1306 DeclareParameter(UseMultipleTemperatureMethod, bool);
130     DeclareParameter(MTM_Ce, RealType);
131     DeclareParameter(MTM_G, RealType);
132     DeclareParameter(MTM_Io, RealType);
133     DeclareParameter(MTM_Sigma, RealType);
134     DeclareParameter(MTM_R, RealType);
135 gezelter 1327 DeclareParameter(UseRNEMD, bool);
136 skuang 1367 DeclareParameter(RNEMD_exchangeTime, RealType);
137 gezelter 1327 DeclareParameter(RNEMD_nBins, int);
138 skuang 1367 DeclareParameter(RNEMD_logWidth, int);
139     DeclareParameter(RNEMD_exchangeType, std::string);
140 gezelter 1331 DeclareParameter(RNEMD_objectSelection, std::string);
141 skuang 1367 DeclareParameter(RNEMD_targetFlux, RealType);
142 skuang 1559 DeclareParameter(RNEMD_binShift, bool);
143     DeclareParameter(RNEMD_outputDimensionalTemperature, bool);
144 gezelter 1354 DeclareParameter(UseRestraints, bool);
145     DeclareParameter(Restraint_file, std::string);
146 chuckv 1402 DeclareParameter(HULL_Method, std::string);
147     DeclareParameter(Alpha, RealType);
148 gezelter 1291
149 tim 770 public:
150     bool addComponent(Component* comp);
151     bool addZConsStamp(ZConsStamp* zcons);
152 cli2 1360 bool addRestraintStamp(RestraintStamp* rest);
153 tim 770 bool addMoleculeStamp(MoleculeStamp* molStamp);
154     int getNComponents() {return components_.size();}
155     std::vector<Component*> getComponents() {return components_;}
156     Component* getComponentAt(int index) {return components_.at(index);}
157 gezelter 1291
158 tim 770 int getNZconsStamps() {return zconstraints_.size();}
159     std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;}
160     ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);}
161 cli2 1360
162     int getNRestraintStamps() {return restraints_.size();}
163     std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
164     RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}
165    
166     //std::string getRestraint_file(){
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 2 };
177 tim 770 }
178 tim 665 #endif

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