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root/OpenMD/branches/development/src/io/Globals.hpp
Revision: 1402
Committed: Fri Jan 8 17:15:27 2010 UTC (15 years, 3 months ago) by chuckv
Original Path: trunk/src/io/Globals.hpp
File size: 7620 byte(s)
Log Message: 
Added preliminary code for Alpha Hull calculation using qhull.
Added preliminary support to SMIPD to support Alpha Hull.
Alpha Hull does not yet add the correct things to triangle to be returned to SMPID. 
Preliminary changes for shadow hamiltonian integrator.
Chages to md files so they will work in openMD.

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     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     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 gezelter 1354 DeclareParameter(UseRestraints, bool);
143     DeclareParameter(Restraint_file, std::string);
144 chuckv 1402 DeclareParameter(HULL_Method, std::string);
145     DeclareParameter(Alpha, RealType);
146 gezelter 1291
147 tim 770 public:
148     bool addComponent(Component* comp);
149     bool addZConsStamp(ZConsStamp* zcons);
150 cli2 1360 bool addRestraintStamp(RestraintStamp* rest);
151 tim 770 bool addMoleculeStamp(MoleculeStamp* molStamp);
152     int getNComponents() {return components_.size();}
153     std::vector<Component*> getComponents() {return components_;}
154     Component* getComponentAt(int index) {return components_.at(index);}
155 gezelter 1291
156 tim 770 int getNZconsStamps() {return zconstraints_.size();}
157     std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;}
158     ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);}
159 cli2 1360
160     int getNRestraintStamps() {return restraints_.size();}
161     std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
162     RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}
163    
164     //std::string getRestraint_file(){
165 gezelter 1291
166 tim 770 virtual void validate();
167     private:
168 tim 895
169 tim 770 std::vector<Component*> components_;
170     std::vector<ZConsStamp*> zconstraints_;
171 cli2 1360 std::vector<RestraintStamp*> restraints_;
172 tim 770 std::map<std::string, MoleculeStamp*> moleculeStamps_;
173 gezelter 1291 std::pair<int, int> taggedAtomPair_;
174 gezelter 2 };
175 tim 770 }
176 tim 665 #endif