Chapter 8 Configuring Fluidity - The Applied Modelling and ...

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xiv LIST OF FIGURES 10.27Plots of the tidal harmonic phases in the Mediterranean Sea from ICOM and the high resolution model of Tsimplis et al. [1995]. . . . . . . . . . . . . . . . . . . . . . . . . . . 198 10.28Locations of 62 tide gauges in the Mediterranean Sea. Modified from Wells [2008] with data originally taken from Tsimplis et al. [1995]. . . . . . . . . . . . . . . . . . . . . . . 199 10.29Scatter diagrams plotting harmonic amplitudes from ICOM at each gauge location against tide gauge data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
Chapter 1 Getting started 1.1 Introduction This first chapter gives a brief guide to setting-up, running and visualising simulations. It is assumed that you have access to a system running Linux or UNIX with all the Fluidity supporting libraries installed; if not, you may wish to reference appendix F which contains detailed information for your systems administrator to help setting up a Linux workstation. 1.2 Obtaining Fluidity 1.2.1 Overview Fluidity is primarily distributed as source code, which takes the form of instructions that are passed through a compiler to generate binary files that your operating system can run. If you come from a UNIX background you will probably be used to this form of distribution; if however you come from a Windows or Mac background you may be used to programs being distributed as pre-compiled packages which you need do nothing more than put in place and run. There are obvious benefits to the ready-to-run approach, namely that they do not generally require you to install any more software other than the specific program you want, and they have a very short lead-time before you are up and running. However, there are a number of obvious disadvantages, particularly that making any changes to the program you have just received is extremely difficult, and there is an underlying assumption that the computer you run the program on will be substantially the same as the computer the program was compiled on. For the majority of Fluidity users the disadvantages of pre-compiled binaries will outweigh the benefits, and distribution of source code is the best solution. Indeed, even if you receive a copy of Fluidity as a pre-compiled binary, the licence (LGPL) under which Fluidity is distributed requires that the original source code is also made available. Fluidity is a very actively developed code. The code is distributed both via released source archives (gzipped tarballs) and through Subversion (SVN). If you are not familiar with subversion you may be familiar with CVS (Concurrent Versions System) and in that case transitioning to using subversion should be a painless process as the syntax is virtually identical. 1.2.2 Fluidity source packages Fluidity is released as compressed source archives which can be downloaded from links on the Fluidity homepage, http://amcg.ese.ic.ac.uk/Fluidity . 1
Page 1: Fluidity�Manual Applied Modelling
Page 5 and 6: Contents 1 Getting started 1 1.1 In
Page 7 and 8: CONTENTS vii 7.3 The Gmsh format .
Page 9 and 10: CONTENTS ix 9.4.3 Stat file diagnos
Page 11 and 12: List of Figures 2.1 Schematic of co
Page 13: LIST OF FIGURES xiii 10.8 Schematic
Page 17 and 18: 1.2 Obtaining Fluidity 3 The third,
Page 19 and 20: 1.3 Building Fluidity 5 1.2.3.4 Oth
Page 21 and 22: 1.3 Building Fluidity 7 1.3.2.2 Spe
Page 23 and 24: 1.5 Running diamond 9 Signal handli
Page 25 and 26: Chapter 2 Model equations 2.1 How t
Page 27 and 28: 2.3 Fluid equations 13 2.2.2.2 Neum
Page 29 and 30: 2.3 Fluid equations 15 2.3.2.2 Comp
Page 31 and 32: 2.3 Fluid equations 17 2.3.4 Moment
Page 33 and 34: 2.4 Extensions, assumptions and der
Page 39 and 40: Chapter 3 Numerical discretisation
Page 41 and 42: 3.2 Spatial discretisation of the a
Page 63 and 64: 3.3 The time loop 49 The coupled li
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3.4 Time discretisation of the adve
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3.6 Pressure equation for incompres
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3.7 Velocity and pressure element p
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3.8 Balance pressure 57 3.8 Balance
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3.10 Linear solvers 59 When reachin
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3.11 Algorithm for detectors (Lagra
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Chapter 4 Parameterisations Althoug
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4.1 Generic length scale turbulence
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4.3 Large-Eddy Simulation (LES) 67
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4.3 Large-Eddy Simulation (LES) 69
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Chapter 5 Embedded models The param
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5.1 Biology 73 where kN is the half
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Chapter 6 Adaptive remeshing 6.1 Mo
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6.4 Metric formation 77 By contrast
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6.6 Related topics 79 There are two
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Chapter 7 Mesh generation This chap
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7.2 The triangle format 83 1 Rema
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7.3 The Gmsh format 85 three parts:
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7.6 Decomposing meshes for parallel
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7.9 Non-Fluidity tools 89 7.7 Pseud
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7.9 Non-Fluidity tools 91 7.9.3 Imp
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Chapter 8 Configuring Fluidity 8.1
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8.3 The options tree 95 Figure 8.2:
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8.3 The options tree 97 8.3.4 IO Th
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8.3 The options tree 99 Checkpoint
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8.3 The options tree 101 8.3.5.3 Fi
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8.4 Meshes 103 if t < 4000.0: omega
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8.5 Material/Phase 105 8.4.2.4 Extr
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8.6 Fields 107 dent field). This is
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8.7 Advected quantities: momentum a
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8.7 Advected quantities: momentum a
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8.9 Solution of linear systems 113
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8.10 Equation of State (EoS) 115 8.
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8.11 Subgridscale Parameterisations
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8.12 Boundary conditions 119 8.12.3
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8.12 Boundary conditions 121 • ..
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8.16 Large scale low aspect ratio o
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8.16 Large scale low aspect ratio o
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8.17 Geophysical fluid dynamics pro
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8.18 Mesh adaptivity 129 An Element
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8.19 Multiple material/phase models
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8.19 Multiple material/phase models
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8.20 Compressible fluid model 135 t
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Chapter 9 Visualisation and Diagnos
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9.2 Online diagnostics 139 Gravitat
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9.2 Online diagnostics 141 Absolute
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9.2 Online diagnostics 143 Figure 9
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9.3 Offline diagnostics 145 Program
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9.3 Offline diagnostics 147 Additio
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9.3 Offline diagnostics 149 9.3.3.1
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9.3 Offline diagnostics 151 Script
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9.3 Offline diagnostics 153 TARGET
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9.3 Offline diagnostics 155 Figure
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9.4 The stat file 157 It is also po
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9.4 The stat file 159 9.4.3 Stat fi
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Temperature min fluid .../stat/incl
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9.4 The stat file 163 9.4.3.1 Surfa
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9.4 The stat file 165 ...
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Chapter 10 Examples 10.1 Introducti
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10.2 One dimensional advection 169
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10.3 The lock-exchange 171 10.2.4 E
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10.3 The lock-exchange 173 basic se
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10.4 Lid-driven cavity 175 domain f
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10.5 Backward facing step 177 Figur
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10.5 Backward facing step 179 No-no
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10.5 Backward facing step 181 Evolu
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10.6 Flow past a sphere: drag calcu
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10.7 Rotating periodic channel 185
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10.8 Water column collapse 187 Exam
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10.8 Water column collapse 189 (a)
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10.8 Water column collapse 191 (a)
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10.9 The restratification following
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10.10 Tides in the Mediterranean Se
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Bibliography M. T. Ainsworth and J.
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C. J. Cotter, D. A. Ham, and C. C.
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A. Birol Kara, Harley E. Hurlburt,
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J. R. Shewchuk. An introduction to
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Appendix A About this manual A.1 In
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A.3 Style guide 211 The options pro
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A.3 Style guide 213 A.3.8.3 Derivat
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Appendix B Mathematical notation Th
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Appendix C Useful numbers The table
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Appendix D Dimensional analysis D.1
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D.2 Dimensionless parameters 221 Na
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Appendix E The Fluidity Python stat
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E.6 Debugging with an interactive P
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Appendix F External libraries F.1 I
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F.4 Manual install of external libr
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Appendix G Troubleshooting G.1 Back
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Index absorption term . . . . . . .
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geostrophic balance . . . . . . . .
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