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cnh |
1.4 |
Rebuild and set to do cron build - DONE on hugo |
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cnh |
1.1 |
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To do |
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- where to put under development links? |
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- mitgcm.org very front page. |
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o too many clicks to get to model manual. |
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make doc link go to mitgcm.org/r2_web_testing/latest |
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and add "HowTo" reference etc... to /latest page |
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- mitgcm.org/r2_web_testing/latest |
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o add another short-cut for quick download |
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o add another short-cut |
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About |
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Installation |
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Contents |
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Overview |
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Tutorials (broken) |
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Browse Code |
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Get Code (where does this go to?) |
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o authors |
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John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen, |
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Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos, |
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Gael - others? |
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o Tutorials side bar link is broken |
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o words |
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change to "access on-line Auser manual/A and Atable of contents/A |
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and browse the Aoverview section/A" |
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o finite-volume doesn't leap to FV figure |
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o the src and equation links don't come through to |
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the html when they are in figures - see chapter 2 for some |
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examples. |
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o degree symbols keep getting "dropped down" - problem with |
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pnmcrop et al. |
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Contents |
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Intro - CNH |
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o single kernel diagram - |
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add reference to MWR paper |
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o non-hydro |
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add reference to 1995 and 1999 papers |
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pdf of 1995 paper |
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o FV |
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add references to 1997 papers. |
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o Tangent linear/adjoint add reference to |
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Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc... |
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o platforms |
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Add reference to SC article and Scientific Programming article |
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o List of key papers needs to be updated and reformatted |
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o Global atmosphere: `Held Suarez', |
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update Adcroft reference |
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fix up ingrid link and frame (ingrid movies seem to be broken?) |
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Held and Suarez reference is not a link. |
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o Ocean Gyres |
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fix up frame link |
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make "lopped cell" a link to referenced paper. |
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add references (ask Steph/Mick) |
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online/offline paper |
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o Convection and mixing over topography |
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add in Legg references for convection and mixing over topography |
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and external link to CPT-GCE etc... |
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o Boundary forced internal waves |
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add in Legg references, obc's reference |
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o Parameter sensitivity |
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add in Bugnion references, Boyin references, Steph references |
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o State estimation |
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add in references from Patrick/Carl/Ichiro/Detlef etc... |
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update links to point to latest ECCO results |
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ECCO ingrid results have been moved |
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add forward links to "ECCO state estimation" chapter in manual |
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o Ocean biogeochemical cycles |
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add in references from Mick/Galen etc... |
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fix ingrid link ( date to date thing does not appear to work) |
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figure url does not have a "target=idontexist" entry |
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o Simulations of laboratory experiments |
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reference Wardle and Karsten papers |
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update links to include DDDAS "PIAB" page |
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cylindrical polar coordinates |
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o Continuos equations in ''r'' coordinates |
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add references to iso paper |
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no mention of z* and p* - forward reference to z*/p* in 2. |
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add that coupling also manifests through F, Q |
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add tracer transport |
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o Kinematic boundary conditions |
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o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms |
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need to tidy up discussion of shallow-atmosphere to be |
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consistent with the code or change code to be consistent |
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with the discussion! |
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make references hyperlinks |
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add stuff too |
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o Finding the pressure field |
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make references hyperlinks |
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add forward references to manual algorithm section |
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change Elliptic to "elliptic" |
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o Forcing and dissipation |
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make "physics packages" refer to chapter 6. |
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should we move "external forcing" et. al to a |
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generic_forcing_driver package? |
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viscosities |
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update to mention Smag/Leith (Ah and A4 not constant) |
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and to have forward references to numerical section |
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tracers |
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forward references to numerical section, reddy, GM etc... |
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add references to literature |
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o 1.3.8 Vector invariant form |
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forward references to numerical section |
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o 1.3.9 Adjoint |
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add a little more here + some hyperlink to chapter 5. |
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o 1.4 Appendix ATMOSPHERE |
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add some introductory words |
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o 1.6 Coordinate systems |
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o only has some words on spherical polar. add some brief words |
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to cover all of |
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- cartesian |
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- spherical |
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- cylindrical |
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- general orthogonal curvilinear (vector invariant) |
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o Equation of state options |
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add some discussion |
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can't remember what we said we were going to do here |
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PH to do something |
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Discretization and alg - JMC+CNH |
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Tutorials - AM |
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3.1 "Where to find" |
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o link to Pelican not needed |
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o mailman twice (why?) |
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o no htdig (gone? - I liked it) |
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intro part |
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individual experiments |
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offline - duplicate inputs, what is it, tidy up cfc v. |
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other offline. |
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Software - EH to review |
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some to be done on resource estimates at the end - needs sorting. |
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Automatic Diff - CE |
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Physical Packages - ??? |
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Diags and tools - ??? |
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Interface with ECCO - ??? |
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Model uses - ??? |
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Building document - ??? |
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via cron |
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tweaking latex2html etc.. |
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Src Code tree (rename |
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examples etc..) - ??? |
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Documentation |
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1. Introduction |
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2. Discretization and Algorithm |
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2.13.5 Lateral dissipation |
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o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags |
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in code need to explain why cos()3/2 turns out to be |
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scaling (not cos()2) |
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2.13.6 Vertical dissipation |
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o update to have reference to Baylors section |
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reference to implicit discussion in time-stepping part of manual |
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3. Tutorials |
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reorg'd into |
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intro part |
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individual experiments |
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4. Software Architecture |
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5. Automatic Differentiation |
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6. Physical Parameterization and Packages |
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7. Diagnostics and tools |
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8. Interface with ECCO |
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9. Model uses |
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Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
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(check in support for more names) |
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Need an empty package as part of distribution |
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latex2html equation formatting is still a bit weird in places. Need to have another go if we have a chance - especially the degree symbol seems to jump around somewhat! |
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Chapter 1 |
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Change hydrodynamical to "dynamical" |
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Examples |
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- extra "in action" cases |
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o high res ocean with diurnal atmospheric state forcing |
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- links to ingrid output |
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CNH/Dimitris |
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o realistic FIZHI from Andrea |
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- links to ingrid output |
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from AM |
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o with seaice on high res cube |
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- links to ingrid output |
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CNH/Dimitris |
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o coupled aqua, ridge world etc... |
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- links to ingrid output |
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get stuff from Daniel |
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o constrained lab simulation |
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- links to ingrid output for model and lab |
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fields |
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get stuff from Sai/Andrew |
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o sensitivity wrt to iron |
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o optimization |
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- update to link to latest ECCO sites and GF |
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related material |
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o eddy diffusivity transport application |
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o Gas giant? |
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Chapter 6 |
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the master package diagram does not appear in the document |
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pkg/ptracers doesn't seem to have any documentation (see packages list below) |
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2.10.5 Horizontal grid |
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need to do a better job of relating model variables to this diagram |
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Master list of packages |
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admtlm/ - autodiff (chapter 5) |
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aim/ - 6.4.1 (content needs fixing - JM to do) |
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aim_compon_interf/ - 6.6 (no content yet) |
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aim_ocn_coupler/ - 6.6 (no content yet) |
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aim_v23/ - retired |
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atm_common/ - 6.6 (no content yet) |
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autodiff/ - autodiff (chapter 5) |
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bulk_force/ - 6.3.3 |
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cal/ - 6.3.5 |
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cd_code/ - chapter 2 (JM check) |
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cfc/ - not sure |
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chronos/ - AM to check |
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compon_communic/ - 6.6 (no content yet) |
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cost/ - not sure, check with PH |
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ctrl/ - not sure, check with PH |
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debug/ - JM may do something in chapter 7 (utilities) |
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diagnostics/ - 7.1 |
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dic/ - 6.7.2 |
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ebm/ - not sure |
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ecco/ - chapter 8 |
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embed_files/ - add something to chapter 7 |
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ex3/ - rename to exch3 |
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exch2/ - 6.2.2 |
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exf/ - 6.3.4 |
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fizhi/ - 6.4.3 |
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flt/ - in chapter 2 (JM check) |
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gchem/ - 6.7.1 |
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generic_advdiff/ - in chapter 2 (JM check) |
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ggl90/ - nothing, (Martin?) |
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gmredi/ - in chapter 2 (JM check). also need |
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Ferrari & Mc tapering |
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grdchk/ - grdchk (chapter 5 - check with PH) |
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gridalt/ - 6.2.4 |
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kpp/ - 6.3.2 |
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land/ - 6.4.2 (not connected to code - JM to fix) |
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matrix/ - Samar |
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mdsio/ - 7.3.1 |
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mnc/ - 7.2.1 |
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mom_common/ - in chapter 2 (JM check) |
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mom_fluxform/ - in chapter 2 (JM check) |
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mom_vecinv/ - in chapter 2 (JM check) |
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monitor/ - 7.4 |
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my82/ - nothing, (martin?) |
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obcs/ - 6.3 (needs a check) |
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ocn_compon_interf/ - 6.6 (no content yet) |
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offline/ - nothing, tutorials that need work but no package section entry |
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opps/ - nothing, (martin?) |
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pp81/ - nothing, (martin?) |
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profiles/ - GAEL |
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ptracers/ - JM + SD to write something |
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rbcs/ - talk to steph |
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runclock/ - runclock |
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rw/ - not sure |
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sbo/ - text in sbo_descruption.tex but not linked into |
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part6 |
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seaice/ - 6.5.2 - no equations, dimitris has promised some |
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shap_filt/ - chapter 2, JM to check |
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shelfice/ - nothing yet (martin?) |
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solver/ - empty |
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sphere/ - chapter 5 or 8 (PH to check) |
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therm_seaice/ - empty |
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thsice/ - 6.5.1 (JM to update?) |
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timeave/ - retiring...... |
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zonal_filt/ - chapter 2 (JM to check) |
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Possible for chap 7 - Daniels grafix/ stuff |
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Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started. |
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Figure 6.8 is missing |
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>>>> From Ed |
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Here are the remaining bits for Chap 4 : |
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- The grammar/flow could still use some work. Boo was an English |
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major and has experience editing/proofing technical papers. I |
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could print out a copy and ask her to read it and suggest |
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improvements. |
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- missing references (if you point me towards URLs, I'll add them |
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to the bibliography): |
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\ref{ref hoe and hill, ecmwf} |
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\ref{magicgarden} |
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\ref{IBMLAPI} |
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\ref{Memorychannel} |
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\ref{hoe-hill:99} |
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- There are a few empty sub-sections at the end of Chap 4 that |
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should either be commented out or fleshed out. |
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and thats about it for Chap 4. |
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Add more to quick links on front page |
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>>>> From Andrea |
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to do list for chap 7: |
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molod |
1.2 |
7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu" |
| 393 |
cnh |
1.1 |
the links are pointing to the proper place |
| 394 |
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7.5.1 - add Graphix to the list of stuff in utils/matlab |
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7.5.2 - empty |
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andrea |
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>>>> From Andrea |
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Chapter 3 |
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-------- |
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Almost all of the 'math mode' text is dropped down as subscripts |
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| 408 |
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divide chapter 3 more clearly into 2 sections? |
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(ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and |
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then 3.19 and 3.20 are informational again - rearrange subsections?) |
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3.1 - don't need a link to the outside of the document (remove it) |
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- link to htdig is broken |
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3.2.1 - link at bottom to source code points to section 3.2.1 |
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(ie, to itself) - link should point to cvs code archive |
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3.2.2.1 - ('upgrading from an earlier version') belongs under |
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the cvs part, ie, should be 3.2.1.1 |
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3.3 - remove reference to 'diags' section under MITgcm |
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- remove reference to 'exe' and 'bin' sections also |
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(remove the .cvsignore file under these directories in cvs) |
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- add a 'jobs' section, and a description as examples of run scripts |
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- add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions |
| 426 |
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- under 'tools' add a reference to 'build_options'. refer to the 'optfiles' |
| 427 |
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- under 'tools' the adjoint points to section 5 - this is now section 8 |
| 428 |
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(but should be a floating reference) |
| 429 |
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- under 'utils' add a reference to exch2 - stuff for different resolutions |
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- the description of the pkg section refers directly to |
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section 3. should be section 6 (actually should be a floating reference) |
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3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10) |
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3.4.1 - links to the following experiments don't exist or are broken: |
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exp2 - should link to section 3.9 |
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hs94.cs-32x32x5 - link to section 3.12 |
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add 'convection' to the list, link to section 3.13 |
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add 'plume on slope` to the list, link to section 3.14 |
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add '??' link to section 3.15 |
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add 'dic_example on slope` to the list, link to section 3.16 |
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add '??' link to section 3.17 |
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add 'offline' and link to section 3.18 |
| 443 |
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clean up others and make links where they are needed |
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3.4.2 - text suggests to see section 2 for details about what is in the 'code' |
| 445 |
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and 'input' directories - should refer to the examples in this section |
| 446 |
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- add 'build' bullet - this is where the model is compiled and exectuable lives |
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| 448 |
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3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options |
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as the place where they live (add a link?) |
| 450 |
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3.6.1 - Add some general 'approach' text - ie, output is controlled either by the |
| 452 |
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'data' file in the input directory or by the data.[pkg name] file for any |
| 453 |
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package running. And there is some default behavior when the 'state' dumps |
| 454 |
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are written. |
| 455 |
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3.6.1.2 - needs to be moved to inside section 3.6.2 |
| 456 |
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| 457 |
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3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18) |
| 458 |
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underneath this one and leave the text for 3.7 in place |
| 459 |
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| 460 |
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All the 'overview' sections need some reference to the name of the experiment in |
| 461 |
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the verification directory |
| 462 |
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| 463 |
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3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript |
| 464 |
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- is this experiment in the list from section 3.4??? |
| 465 |
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3.10.3.1 - refers to figures and equations, links are broken |
| 466 |
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| 467 |
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3.11.3.2 - line 43: link to equation is broken |
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- line 51-53: link to equation is broken |
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- there is some mess of text hanging around the end of this section. remove? reformat? |
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| 471 |
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3.12.4.1 - line 34 - link to equation is broken |
| 472 |
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- lines 60,61 - 1st (take out the 'r' in the superscript) |
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| 474 |
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3.13.2 - link to theta-equation is broken |
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3.13.5.4 -- ALL of the bold links to variable names are broken |
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line 34: link to equation is broken |
| 477 |
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| 478 |
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3.15.1 - reference to 'fourth experiment' should be removed |
| 479 |
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| 480 |
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3.16.4 - strange formatting, presence of '>' symbols - remove them |
| 481 |
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| 482 |
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3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4 |
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3.17.3.1 - nothing filled in under file input/data - needs description |
| 484 |
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| 485 |
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3.18.2 - point to section 2 for details - need hyperlink |
| 486 |
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| 487 |
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3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true! |
| 488 |
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section 3.5 has the 'build' directory in the example |
| 489 |
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| 490 |
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3.20.1 - link to doc at end of section points to this section |
| 491 |
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3.20.2 - link to doc at end of section points to this section |
| 492 |
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| 493 |
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>>>> from JM |
| 494 |
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| 495 |
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| 496 |
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| 497 |
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manual, section.2 : |
| 498 |
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| 499 |
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In general: |
| 500 |
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- add more refences/links to S/R & variable name |
| 501 |
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- would be nice to have an active link to the fortran-file |
| 502 |
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for all the S/R & eq.Number in the "calling-tree" boxes |
| 503 |
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- search for CALC_MOM_RHS and replace it by the appropriate S/R |
| 504 |
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(mom_flux_form, mom_vecinv, dynamics) |
| 505 |
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- Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h}) |
| 506 |
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was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}} |
| 507 |
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in section.2, \vec{\bf v} is used instead and 3.D velocity vector is |
| 508 |
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simply written \vec{v}. |
| 509 |
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I would suggest to keep the notation as they are (since they are consistent |
| 510 |
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inside each section) but may be to move the "notation.tex" piece |
| 511 |
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at the beginning of section.2 and to mention clearly the changes between |
| 512 |
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the 2 sections. |
| 513 |
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| 514 |
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in content: Horizontal Dissipation: 2 times in vector-invariant section |
| 515 |
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| 516 |
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2.1 time-stepping (part2/time_stepping.tex) |
| 517 |
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| 518 |
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- this is not clear to me: |
| 519 |
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| 520 |
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>> In all the above configurations it is also possible to substitute the |
| 521 |
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>> Adams-Bashforth with an alternative time-stepping scheme for terms |
| 522 |
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>> evaluated explicitly in time |
| 523 |
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| 524 |
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| 525 |
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2.2 rigid-lid: |
| 526 |
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| 527 |
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- At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)" |
| 528 |
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to stay closer to the code. |
| 529 |
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- mention section 2.5 implicit-Time-stepping (for vertical viscosity) |
| 530 |
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| 531 |
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2.3 linear free-surface: |
| 532 |
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- add ref(+link) to S/R names: |
| 533 |
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- add ref(+link) to Crank-Nickelson section 2.9.1 |
| 534 |
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| 535 |
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2.4 Adams-Bashforth |
| 536 |
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- add stability diagrams (I have some figures that I can put) |
| 537 |
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- add link for var. forcing_In_AB |
| 538 |
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- add S/R link for S/R ADAMS_BASHFORTH2 |
| 539 |
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| 540 |
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2.5 Implicit time-stepping |
| 541 |
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- add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R |
| 542 |
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SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL |
| 543 |
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- update: also used for vertical advection |
| 544 |
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| 545 |
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2.6 Synchronous time-stepping: |
| 546 |
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- add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE, |
| 547 |
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MOMENTUM_CORRECTION_STEP. |
| 548 |
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| 549 |
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2.7 Stagger baroclinic time-stepping |
| 550 |
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- mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end |
| 551 |
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| 552 |
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2.8 NH |
| 553 |
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- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D |
| 554 |
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| 555 |
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2.9 Variants on Free-Surface |
| 556 |
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- Delta.t mis-written (eq.2.73) |
| 557 |
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- Eq.Num missing (has been fixed since) |
| 558 |
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- u* is stored in gU (and not in gUnm1) |
| 559 |
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- Phi_nh in NH_VARS.h |
| 560 |
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- add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D, |
| 561 |
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INI_CG2D, INI_CG3D |
| 562 |
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| 563 |
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2.9.1 Crank-Nickelson |
| 564 |
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- link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater |
| 565 |
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| 566 |
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2.9.2 NLFS |
| 567 |
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- eq.Nb are wrong in html |
| 568 |
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- 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi) |
| 569 |
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| 570 |
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2.10.1 Notation |
| 571 |
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- Area definition is not really used like this |
| 572 |
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|
| 573 |
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>> Ao : Area of the face orthogonal to "o" direction (o=u,v,w) |
| 574 |
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| 575 |
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Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to |
| 576 |
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the model variables) are used (e.g., see section 2.10.5) |
| 577 |
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| 578 |
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2.10.5 Horizontal grid: |
| 579 |
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- fig.2.8 : should use Aw,As consistently in this figure description, |
| 580 |
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in the figure itself, as it is in the text. |
| 581 |
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- curvilinear: |
| 582 |
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to add: mention the angle of the grid direction relative to |
| 583 |
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Eastward, Northward direction. |
| 584 |
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+ mention horizGridFile= in file "data" (PARM04) |
| 585 |
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- add cylindrical grid description |
| 586 |
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| 587 |
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2.11 Continuity & Horizontal Pressure gradient terms |
| 588 |
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- mention that d.Phi/dr|s =g if using z coordinate |
| 589 |
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- eq. 2.90 not clear regarding \delta_k(P-E) |
| 590 |
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better to add the free surface eq: d.eta/dt = w_s + P-E |
| 591 |
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| 592 |
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2.12 Hydrostatic balance |
| 593 |
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- add ref to Atmosphere Appendix section (1.4) since Adcroft 2002 |
| 594 |
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is hard to find |
| 595 |
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- add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H) |
| 596 |
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and in section 1.3.4: remove the 1.3.4.3.2 subsection: |
| 597 |
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Quasi-nonhydrostatic Atmosphere |
| 598 |
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| 599 |
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2.13.2 Coriolis terms |
| 600 |
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- note: the discretization used when useEnergyConservingCoriolis=T |
| 601 |
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has no hFac and no Area and is still different from the form |
| 602 |
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described here (with Area & hFac); |
| 603 |
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| 604 |
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2.13.5 Lateral dissipation |
| 605 |
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- add description of how to use cosFactor & cosPower |
| 606 |
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- add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4 |
| 607 |
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| 608 |
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2.13.6 Vertical dissipation |
| 609 |
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- mention the implicit vertical viscosity option and ref to section 2.5 |
| 610 |
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- add the parameter correspondence: Av <-> viscAr (and might change also |
| 611 |
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the notation to Ar) |
| 612 |
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| 613 |
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2.14 Vector invariant momentum equations |
| 614 |
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- indicate that the NH pieces (vertical momentum eq) are not yet coded |
| 615 |
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and that the NH code uses the flux form. |
| 616 |
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| 617 |
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2.14.6 Horizontal dissipation -> Horizontal Divergence |
| 618 |
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| 619 |
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2.14.7 Horizontal dissipation |
| 620 |
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- add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ |
| 621 |
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and A_D4,A_z4 <-> viscA4D,viscA4Z |
| 622 |
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| 623 |
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2.16 & 2.17 & 2.18 : |
| 624 |
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- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
| 625 |
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| 626 |
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2.20.2 mercator, non-dimensional Equations: |
| 627 |
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- does not use std notation |
| 628 |
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- would be better as an appendix of section 2.20: |
| 629 |
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(e.g changing the tile to: |
| 630 |
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Appendix: non-dimensional Equations on Spherical-Polar grid.) |
| 631 |
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| 632 |
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JM |
| 633 |
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