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root/OpenMD/branches/development/src/io/Globals.hpp
Revision: 1722
Committed: Thu May 24 14:23:40 2012 UTC (12 years, 11 months ago) by gezelter
File size: 8703 byte(s)
Log Message: 
Merging Shenyu's RNEMD changes from openmd-1 into the development branch.

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 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 chuckv 748 #include "utils/ParameterManager.hpp"
58 gezelter 2
59 gezelter 1390 namespace OpenMD {
60 gezelter 1291 class Globals : public DataHolder {
61 tim 665 public:
62 gezelter 1291 typedef std::pair<int, int> intPair;
63    
64 tim 665 Globals();
65 tim 770 virtual ~Globals();
66 tim 665
67 gezelter 1291 DeclareParameter(ForceField, std::string);
68     DeclareParameter(TargetTemp, RealType);
69     DeclareParameter(Ensemble, std::string);
70     DeclareParameter(Dt, RealType);
71     DeclareParameter(RunTime, RealType);
72     DeclareParameter(FinalConfig, std::string);
73     DeclareParameter(SampleTime, RealType);
74     DeclareParameter(ResetTime, RealType);
75     DeclareParameter(StatusTime, RealType);
76     DeclareParameter(CutoffRadius, RealType);
77     DeclareParameter(SwitchingRadius, RealType);
78     DeclareParameter(TempSet, bool);
79     DeclareParameter(ThermalTime, RealType);
80     DeclareParameter(UsePeriodicBoundaryConditions, bool);
81     DeclareParameter(TargetPressure, RealType);
82     DeclareParameter(UseAtomicVirial, bool);
83     DeclareParameter(TauThermostat, RealType);
84     DeclareParameter(TauBarostat, RealType);
85     DeclareParameter(ZconsTime, RealType);
86     DeclareParameter(ZconsTol, RealType);
87     DeclareParameter(ZconsForcePolicy, std::string);
88 gezelter 1313 DeclareParameter(Seed, unsigned long int);
89 gezelter 1291 DeclareParameter(UseInitalTime, bool);
90     DeclareParameter(UseIntialExtendedSystemState, bool);
91     DeclareParameter(OrthoBoxTolerance, RealType);
92     DeclareParameter(Minimizer, std::string);
93     DeclareParameter(MinimizerMaxIter, RealType);
94 gezelter 1423 DeclareParameter(MinimizerWriteFreq, int);
95 gezelter 1291 DeclareParameter(MinimizerStepSize, RealType);
96     DeclareParameter(MinimizerFTol, RealType);
97     DeclareParameter(MinimizerGTol, RealType);
98     DeclareParameter(MinimizerLSTol, RealType);
99     DeclareParameter(MinimizerLSMaxIter, int);
100     DeclareParameter(ZconsGap, RealType);
101     DeclareParameter(ZconsFixtime, RealType);
102     DeclareParameter(ZconsUsingSMD, bool);
103 cli2 1360 DeclareParameter(UseThermodynamicIntegration, bool);
104 gezelter 1291 DeclareParameter(ThermodynamicIntegrationLambda, RealType);
105     DeclareParameter(ThermodynamicIntegrationK, RealType);
106     DeclareParameter(ForceFieldVariant, std::string);
107     DeclareParameter(ForceFieldFileName, std::string);
108     DeclareParameter(SurfaceTension, RealType);
109     DeclareParameter(PrintPressureTensor, bool);
110     DeclareParameter(TaggedAtomPair, intPair);
111     DeclareParameter(PrintTaggedPairDistance, bool);
112     DeclareParameter(ElectrostaticSummationMethod, std::string);
113     DeclareParameter(ElectrostaticScreeningMethod, std::string);
114     DeclareParameter(DampingAlpha, RealType);
115     DeclareParameter(Dielectric, RealType);
116 gezelter 1528 DeclareParameter(CutoffMethod, std::string);
117 gezelter 1576 DeclareParameter(CutoffPolicy, std::string);
118 gezelter 1291 DeclareParameter(SwitchingFunctionType, std::string);
119     DeclareParameter(CompressDumpFile, bool);
120     DeclareParameter(OutputForceVector, bool);
121 gezelter 1629 DeclareParameter(OutputParticlePotential, bool);
122 gezelter 1714 DeclareParameter(OutputElectricField, bool);
123     DeclareParameter(OutputFluctuatingCharges, bool);
124 gezelter 1291 DeclareParameter(SkinThickness, RealType);
125     DeclareParameter(StatFileFormat, std::string);
126     DeclareParameter(HydroPropFile, std::string);
127     DeclareParameter(Viscosity, RealType);
128     DeclareParameter(BeadSize, RealType);
129     DeclareParameter(UseSphericalBoundaryConditions, bool);
130     DeclareParameter(FrozenBufferRadius, RealType);
131     DeclareParameter(LangevinBufferRadius, RealType);
132     DeclareParameter(AccumulateBoxDipole, bool);
133     DeclareParameter(NeighborListNeighbors, int);
134 chuckv 1306 DeclareParameter(UseMultipleTemperatureMethod, bool);
135     DeclareParameter(MTM_Ce, RealType);
136     DeclareParameter(MTM_G, RealType);
137     DeclareParameter(MTM_Io, RealType);
138     DeclareParameter(MTM_Sigma, RealType);
139     DeclareParameter(MTM_R, RealType);
140 gezelter 1327 DeclareParameter(UseRNEMD, bool);
141 skuang 1367 DeclareParameter(RNEMD_exchangeTime, RealType);
142 gezelter 1327 DeclareParameter(RNEMD_nBins, int);
143 skuang 1367 DeclareParameter(RNEMD_logWidth, int);
144     DeclareParameter(RNEMD_exchangeType, std::string);
145 gezelter 1331 DeclareParameter(RNEMD_objectSelection, std::string);
146 skuang 1367 DeclareParameter(RNEMD_targetFlux, RealType);
147 gezelter 1722 DeclareParameter(RNEMD_targetJzKE, RealType);
148     DeclareParameter(RNEMD_targetJzpx, RealType);
149     DeclareParameter(RNEMD_targetJzpy, RealType);
150     DeclareParameter(RNEMD_targetJzpz, RealType);
151 gezelter 1629 DeclareParameter(RNEMD_binShift, bool);
152 gezelter 1722 DeclareParameter(RNEMD_outputTemperature, bool);
153     DeclareParameter(RNEMD_outputVx, bool);
154     DeclareParameter(RNEMD_outputVy, bool);
155     DeclareParameter(RNEMD_outputXyzTemperature, bool);
156     DeclareParameter(RNEMD_outputRotTemperature, bool);
157 gezelter 1354 DeclareParameter(UseRestraints, bool);
158     DeclareParameter(Restraint_file, std::string);
159 chuckv 1402 DeclareParameter(HULL_Method, std::string);
160     DeclareParameter(Alpha, RealType);
161 gezelter 1715 DeclareParameter(FlucQPropagator, std::string);
162     DeclareParameter(FlucQFriction, RealType);
163     DeclareParameter(FlucQTolerance, RealType);
164     DeclareParameter(FlucQMaxIterations, int);
165     DeclareParameter(FlucQTargetTemp, RealType);
166     DeclareParameter(FlucQtauThermostat, RealType);
167 gezelter 1613 DeclareAlterableParameter(MDfileVersion, int);
168 gezelter 1715
169 tim 770 public:
170     bool addComponent(Component* comp);
171     bool addZConsStamp(ZConsStamp* zcons);
172 cli2 1360 bool addRestraintStamp(RestraintStamp* rest);
173 tim 770 bool addMoleculeStamp(MoleculeStamp* molStamp);
174     int getNComponents() {return components_.size();}
175     std::vector<Component*> getComponents() {return components_;}
176     Component* getComponentAt(int index) {return components_.at(index);}
177 gezelter 1291
178 tim 770 int getNZconsStamps() {return zconstraints_.size();}
179     std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;}
180     ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);}
181 cli2 1360
182     int getNRestraintStamps() {return restraints_.size();}
183     std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
184     RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}
185 gezelter 1291
186 tim 770 virtual void validate();
187     private:
188 tim 895
189 tim 770 std::vector<Component*> components_;
190     std::vector<ZConsStamp*> zconstraints_;
191 cli2 1360 std::vector<RestraintStamp*> restraints_;
192 tim 770 std::map<std::string, MoleculeStamp*> moleculeStamps_;
193 gezelter 1291 std::pair<int, int> taggedAtomPair_;
194 gezelter 2 };
195 tim 770 }
196 tim 665 #endif

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