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Rebuild and set to do cron build |
Editors |
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Overall - JM, AM, PH, CNH, EH3 |
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Front content - EH3 |
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Chapter 1 - CNH |
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Chapter 2 - JMC |
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Chapter 3 - AM |
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Chapter 4 - CNH |
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Chapter 5 - PH |
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Chapter 6 - AM |
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Chapter 7 - EH3 |
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Chapter 8 - PH |
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Chapter 9 - CNH (Applications) |
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Chapter 10 - JMC (Under development chapter) |
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Biblio - EH3 |
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Rebuild and set to do cron build - DONE on hugo |
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To do |
To do |
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- where to put under development links? |
- where to put under development links? |
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JMC would like to have some mention of unfinished things (checked in |
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but not that tested e.g. AB3) |
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Add an "Under development, chapter" - shortish description of what |
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is available (last chapter) |
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- add in example latex for formatting author names in different pieces. |
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this aknowledges peoples contributions and gives ref for who |
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to talk to. |
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o HTML, scripts and front content |
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- mitgcm.org very front page. |
- pick a URL: mitgcm.org/r2 <-- EH3's preferred base URL |
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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 |
- mitgcm.org/r2_web_testing/latest |
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o add another short-cut for quick download |
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o --DONE-- add another short-cut for quick download |
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o add another short-cut |
o --DONE-- add another short-cut |
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About |
About |
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Installation |
Installation |
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Contents |
Contents |
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Overview |
Overview |
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Tutorials (broken) |
Tutorials (broken) |
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Browse Code |
Browse Code |
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Get Code (where does this go to?) |
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o authors |
o --DONE-- words on http://mitgcm.org/r2_web_testing/latest change to |
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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 |
o --DONE-- finite-volume doesn't leap to FV figure |
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o words |
o -- DONE ??? -- have another go at pnmcrop et al. |
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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 |
I've tried making a small change in latex2html which fixes |
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the oddball-lower-alignment issue that we were seeing with |
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most in-line expressions (that is, math embedded in text). |
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The fix results in some things being slightly raised but I |
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thin this is more asthetically pleasing than being somewhat |
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lowered as before. --EH3 |
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o date is 2002 |
To view the altered alignment, see: |
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o the src and equation links don't come through to |
http://eddy.csail.mit.edu/r2/latest/ |
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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 |
o Need an empty package as part of distribution. Check out atm_common |
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pnmcrop et al. |
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Contents |
o Latex |
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Intro - CNH |
Chapter 1 - CNH |
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o single kernel diagram - |
o single kernel diagram - |
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add reference to MWR paper |
add reference to MWR paper |
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o List of key papers needs to be updated and reformatted |
o List of key papers needs to be updated and reformatted |
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o Global atmosphere: `Held Suarez', |
o Global atmosphere: `Held Suarez', |
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update Adcroft reference |
update Adcroft reference |
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fix up ingrid link and frame (ingrid movies seem to be broken?) |
fix up ingrid link and frame (ingrid movies seem to be broken?) |
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o Kinematic boundary conditions |
o Kinematic boundary conditions |
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o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms |
o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and |
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need to tidy up discussion of shallow-atmosphere to be |
Non-hydrostatic forms |
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consistent with the code or change code to be consistent |
need to tidy up discussion of shallow-atmosphere to be |
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with the discussion! |
consistent with the code or change code to be consistent |
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make references hyperlinks |
with the discussion! |
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add stuff too |
make references hyperlinks |
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add stuff too |
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JMC remove QNH atmosphere |
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need to sort out calc_gw for deep atmosphere |
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o Finding the pressure field |
o Finding the pressure field |
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make references hyperlinks |
make references hyperlinks |
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add forward references to manual algorithm section |
add forward references to manual algorithm section |
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change Elliptic to "elliptic" |
change Elliptic to "elliptic" |
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o Forcing and dissipation |
o Forcing and dissipation |
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make "physics packages" refer to chapter 6. |
make "physics packages" refer to chapter 6. |
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should we move "external forcing" et. al to a |
should we move "external forcing" et. al to a |
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generic_forcing_driver package? |
generic_forcing_driver package? |
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viscosities |
viscosities |
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update to mention Smag/Leith (Ah and A4 not constant) |
update to mention Smag/Leith (Ah and A4 not constant) |
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and to have forward references to numerical section |
and to have forward references to numerical section |
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tracers |
tracers |
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forward references to numerical section, reddy, GM etc... |
forward references to numerical section, reddy, GM etc... |
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add references to literature |
add references to literature |
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o 1.3.8 Vector invariant form |
o 1.3.8 Vector invariant form |
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forward references to numerical section |
forward references to numerical section |
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PH to do something |
PH to do something |
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196 |
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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" |
Change hydrodynamical to "dynamical" |
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Examples |
Examples |
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o coupled aqua, ridge world etc... |
o coupled aqua, ridge world etc... |
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- links to ingrid output |
- links to ingrid output |
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get stuff from Daniel |
get stuff from Daniel |
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Davids donut movie |
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o constrained lab simulation |
o constrained lab simulation |
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- links to ingrid output for model and lab |
- links to ingrid output for model and lab |
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o Gas giant? |
o Gas giant? |
234 |
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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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7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu" |
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the links are pointing to the proper place |
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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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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 |
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- under 'tools' add a reference to 'build_options'. refer to the 'optfiles' |
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- under 'tools' the adjoint points to section 5 - this is now section 8 |
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(but should be a floating reference) |
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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 |
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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' |
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and 'input' directories - should refer to the examples in this section |
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- add 'build' bullet - this is where the model is compiled and exectuable lives |
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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?) |
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3.6.1 - Add some general 'approach' text - ie, output is controlled either by the |
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'data' file in the input directory or by the data.[pkg name] file for any |
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package running. And there is some default behavior when the 'state' dumps |
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are written. |
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3.6.1.2 - needs to be moved to inside section 3.6.2 |
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3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18) |
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underneath this one and leave the text for 3.7 in place |
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All the 'overview' sections need some reference to the name of the experiment in |
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the verification directory |
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3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript |
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- is this experiment in the list from section 3.4??? |
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3.10.3.1 - refers to figures and equations, links are broken |
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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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3.12.4.1 - line 34 - link to equation is broken |
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- lines 60,61 - 1st (take out the 'r' in the superscript) |
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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 |
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3.15.1 - reference to 'fourth experiment' should be removed |
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3.16.4 - strange formatting, presence of '>' symbols - remove them |
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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 |
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3.18.2 - point to section 2 for details - need hyperlink |
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3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true! |
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section 3.5 has the 'build' directory in the example |
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3.20.1 - link to doc at end of section points to this section |
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3.20.2 - link to doc at end of section points to this section |
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236 |
>>>> from JM |
>>>> from JM |
237 |
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238 |
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239 |
manual, section.2 : |
manual, section.2 : |
240 |
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241 |
In general: |
In general: |
243 |
- would be nice to have an active link to the fortran-file |
- would be nice to have an active link to the fortran-file |
244 |
for all the S/R & eq.Number in the "calling-tree" boxes |
for all the S/R & eq.Number in the "calling-tree" boxes |
245 |
- search for CALC_MOM_RHS and replace it by the appropriate S/R |
- search for CALC_MOM_RHS and replace it by the appropriate S/R |
246 |
(mom_flux_form, mom_vecinv, dynamics) |
(mom_flux_form, mom_vecinv, dynamics) <- DONE |
247 |
- Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h}) |
- Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h}) |
248 |
was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}} |
was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}} |
249 |
in section.2, \vec{\bf v} is used instead and 3.D velocity vector is |
in section.2, \vec{\bf v} is used instead and 3.D velocity vector is |
254 |
the 2 sections. |
the 2 sections. |
255 |
|
|
256 |
in content: Horizontal Dissipation: 2 times in vector-invariant section |
in content: Horizontal Dissipation: 2 times in vector-invariant section |
257 |
|
<- DONE |
258 |
|
|
259 |
2.1 time-stepping (part2/time_stepping.tex) |
2.1 time-stepping (part2/time_stepping.tex) |
260 |
|
|
263 |
>> In all the above configurations it is also possible to substitute the |
>> In all the above configurations it is also possible to substitute the |
264 |
>> Adams-Bashforth with an alternative time-stepping scheme for terms |
>> Adams-Bashforth with an alternative time-stepping scheme for terms |
265 |
>> evaluated explicitly in time |
>> evaluated explicitly in time |
266 |
|
<- Leave it general. |
267 |
|
|
268 |
|
o Time-stepping outline |
269 |
|
- what gets called when |
270 |
|
|
271 |
|
|
272 |
2.2 rigid-lid: |
2.2 rigid-lid: |
273 |
|
|
274 |
- At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)" |
- At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)" |
275 |
to stay closer to the code. |
to stay closer to the code. |
276 |
- mention section 2.5 implicit-Time-stepping (for vertical viscosity) |
- mention section 2.5 implicit-Time-stepping (for vertical viscosity) <- DONE |
277 |
|
|
278 |
2.3 linear free-surface: |
2.3 linear free-surface: |
279 |
- add ref(+link) to S/R names: |
- add ref(+link) to S/R names: |
280 |
- add ref(+link) to Crank-Nickelson section 2.9.1 |
- add ref(+link) to Crank-Nickelson section 2.9.1 <- DONE |
281 |
|
|
282 |
2.4 Adams-Bashforth |
2.4 Adams-Bashforth |
283 |
- add stability diagrams (I have some figures that I can put) |
- add stability diagrams (I have some figures that I can put) <- DONE |
284 |
- add link for var. forcing_In_AB |
- add link for var. forcing_In_AB and epsil_AB <- half DONE |
285 |
- add S/R link for S/R ADAMS_BASHFORTH2 |
- add S/R link for S/R ADAMS_BASHFORTH2 <-DONE |
286 |
|
|
287 |
2.5 Implicit time-stepping |
2.5 Implicit time-stepping |
288 |
- add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R |
- add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R |
300 |
- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D |
- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D |
301 |
|
|
302 |
2.9 Variants on Free-Surface |
2.9 Variants on Free-Surface |
303 |
- Delta.t mis-written (eq.2.73) |
- Delta.t mis-written (eq.2.73) <- DONE |
304 |
- Eq.Num missing (has been fixed since) |
- Eq.Num missing <- DONE |
305 |
- u* is stored in gU (and not in gUnm1) |
- u* is stored in gU (and not in gUnm1) <- DONE |
306 |
- Phi_nh in NH_VARS.h |
- Phi_nh in NH_VARS.h <- DONE |
307 |
- add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D, |
- add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D, |
308 |
INI_CG2D, INI_CG3D |
INI_CG2D, INI_CG3D |
309 |
|
|
313 |
2.9.2 NLFS |
2.9.2 NLFS |
314 |
- eq.Nb are wrong in html |
- eq.Nb are wrong in html |
315 |
- 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi) |
- 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi) |
316 |
|
<- DONE |
317 |
|
|
318 |
2.10.1 Notation |
2.10.1 Notation |
319 |
- Area definition is not really used like this |
- Area definition is not really used like this |
322 |
|
|
323 |
Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to |
Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to |
324 |
the model variables) are used (e.g., see section 2.10.5) |
the model variables) are used (e.g., see section 2.10.5) |
325 |
|
<- DONE |
326 |
|
|
327 |
2.10.5 Horizontal grid: |
2.10.5 Horizontal grid: |
328 |
- fig.2.8 : should use Aw,As consistently in this figure description, |
- fig.2.8 : should use Aw,As consistently in this figure description, |
329 |
in the figure itself, as it is in the text. |
in the figure itself, as it is in the text. <- DONE |
330 |
- curvilinear: |
- curvilinear: |
331 |
to add: mention the angle of the grid direction relative to |
to add: mention the angle of the grid direction relative to |
332 |
Eastward, Northward direction. |
Eastward, Northward direction. |
333 |
+ mention horizGridFile= in file "data" (PARM04) |
+ mention horizGridFile= in file "data" (PARM04) |
334 |
- add cylindrical grid description |
- add cylindrical polar grid description |
335 |
|
need to do a better job of relating model variables to this diagram |
336 |
|
|
337 |
|
|
338 |
2.11 Continuity & Horizontal Pressure gradient terms |
2.11 Continuity & Horizontal Pressure gradient terms |
339 |
- mention that d.Phi/dr|s =g if using z coordinate |
- mention that d.Phi/dr|s =g if using z coordinate |
355 |
2.13.5 Lateral dissipation |
2.13.5 Lateral dissipation |
356 |
- add description of how to use cosFactor & cosPower |
- add description of how to use cosFactor & cosPower |
357 |
- add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4 |
- add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4 |
358 |
|
o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags |
359 |
|
in code need to explain why cos()3/2 turns out to be |
360 |
|
scaling (not cos()2) |
361 |
|
- need to reference the smag/leith section. |
362 |
|
|
363 |
2.13.6 Vertical dissipation |
2.13.6 Vertical dissipation |
364 |
- mention the implicit vertical viscosity option and ref to section 2.5 |
- mention the implicit vertical viscosity option and ref to section 2.5 |
377 |
|
|
378 |
2.16 & 2.17 & 2.18 : |
2.16 & 2.17 & 2.18 : |
379 |
- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
380 |
|
- fix equations 2.202 & 2.203 (thanks to Martin) <- DONE |
381 |
|
|
382 |
2.20.2 mercator, non-dimensional Equations: |
2.20.2 mercator, non-dimensional Equations: |
383 |
- does not use std notation |
- does not use std notation |
384 |
- would be better as an appendix of section 2.20: |
- would be better as an appendix of section 2.20: |
385 |
(e.g changing the tile to: |
(e.g changing the tile to: |
386 |
|
- talk to Baylor |
387 |
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
388 |
|
<- No (Chris said) |
389 |
|
|
390 |
|
|
391 |
|
Diagrams of grid locations etc.... and what variables and output files |
392 |
|
and/or netcdf variable names are not very easy to figure out and follow. |
393 |
|
It would be good to redo and extend these diagrams and align with GRID.h |
394 |
|
content. |
395 |
|
|
396 |
|
|
397 |
JM |
JM |
398 |
|
|
399 |
|
|
400 |
|
>>>> From Andrea |
401 |
|
|
402 |
|
Chapter 3 |
403 |
|
-------- |
404 |
|
|
405 |
|
Almost all of the 'math mode' text is dropped down as subscripts |
406 |
|
|
407 |
|
3.11.3.1 - refers to figures and equations, links are broken |
408 |
|
|
409 |
|
3.12.3.2 - line 43: link to equation is broken |
410 |
|
- line 51-53: link to equation is broken |
411 |
|
- there is some mess of text hanging around the end of this section. remove? reformat? |
412 |
|
|
413 |
|
3.13.4.1 - line 34 - link to equation is broken |
414 |
|
- lines 60,61 - 1st (take out the 'r' in the superscript) |
415 |
|
|
416 |
|
3.14.2 - link to theta-equation is broken |
417 |
|
3.14.5.4 -- ALL of the bold links to variable names are broken |
418 |
|
line 34: link to equation is broken |
419 |
|
|
420 |
|
o Update basic intro with one and four layer gyres |
421 |
|
- include advection options |
422 |
|
- conservation analysis |
423 |
|
- diagnostics |
424 |
|
|
425 |
|
o Four degree adjoint |
426 |
|
- both TAF and OpenAD based. |
427 |
|
|
428 |
|
o Coupled with biogeo setup |
429 |
|
- based on CCGS setup |
430 |
|
|
431 |
|
|
432 |
|
>>>> From Ed |
433 |
|
|
434 |
|
Here are the remaining bits for Chap 4 : |
435 |
|
|
436 |
|
- missing references (if you point me towards URLs, I'll add them |
437 |
|
to the bibliography): |
438 |
|
\ref{ref hoe and hill, ecmwf} |
439 |
|
\ref{magicgarden} |
440 |
|
\ref{IBMLAPI} |
441 |
|
\ref{Memorychannel} |
442 |
|
\ref{hoe-hill:99} |
443 |
|
|
444 |
|
- There are a few empty sub-sections at the end of Chap 4 that |
445 |
|
should either be commented out or fleshed out. |
446 |
|
|
447 |
|
and thats about it for Chap 4. |
448 |
|
|
449 |
|
|
450 |
|
Add more to quick links on front page |
451 |
|
|
452 |
|
Chapter 6 |
453 |
|
|
454 |
|
the master package diagram does not appear in the document |
455 |
|
|
456 |
|
Master list of packages (add this to beginning of chap 6) |
457 |
|
|
458 |
|
admtlm/ - autodiff (chapter 5) |
459 |
|
aim/ - retired |
460 |
|
aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM) |
461 |
|
aim_ocn_coupler/ - 6.6 (no content yet) |
462 |
|
aim_v23/ - 6.4.1 (content needs fixing - JM to do) |
463 |
|
atm_common/ - nothing in this package (6.4.1 related) |
464 |
|
autodiff/ - autodiff (chapter 5) |
465 |
|
bulk_force/ - 6.3.3 |
466 |
|
cal/ - 6.3.5 |
467 |
|
cd_code/ - chapter 2 (JM check add a reference to paper, |
468 |
|
mention parameter in data) |
469 |
|
cfc/ - not sure (CNH to talk to Steph and Helen) |
470 |
|
chronos/ - AM to check (not being used - Andrea to kill it) |
471 |
|
compon_communic/ - 6.6 (no content yet)(Daniel + JM) |
472 |
|
cost/ - not sure, check with PH |
473 |
|
ctrl/ - not sure, check with PH |
474 |
|
debug/ - JM may do something in chapter 7 (utilities) |
475 |
|
diagnostics/ - 7.1 |
476 |
|
dic/ - 6.7.2 |
477 |
|
ebm/ - (check with PH) |
478 |
|
ecco/ - chapter 8 |
479 |
|
embed_files/ - add something to chapter 7 |
480 |
|
exch2/ - 6.2.2 |
481 |
|
exf/ - 6.3.4 |
482 |
|
fizhi/ - 6.4.3 |
483 |
|
o Including FIZHI doc |
484 |
|
- get things up to date |
485 |
|
flt/ - (PH check) |
486 |
|
gchem/ - 6.7.1 |
487 |
|
generic_advdiff/ - in chapter 2 (JM check) |
488 |
|
ggl90/ - nothing, (Martin?) |
489 |
|
gmredi/ - in chapter 2 (JM check). also need |
490 |
|
Ferrari & Mc transition zone stuff (Samar doing this) |
491 |
|
get dfer to read this |
492 |
|
grdchk/ - grdchk (chapter 5 - check with PH) |
493 |
|
gridalt/ - 6.2.4 |
494 |
|
kpp/ - 6.3.2 |
495 |
|
land/ - 6.4.2 (not connected to code Rong's notes - JM to fix) |
496 |
|
matrix/ - Samar |
497 |
|
mdsio/ - 7.3.1 |
498 |
|
mnc/ - 7.2.1 |
499 |
|
mom_common/ - in chapter 2 (JM check) |
500 |
|
mom_fluxform/ - in chapter 2 (JM check) |
501 |
|
mom_vecinv/ - in chapter 2 (JM check) |
502 |
|
monitor/ - 7.4 |
503 |
|
my82/ - nothing, (martin?) |
504 |
|
obcs/ - 6.3 (needs a check - ask PH to read) |
505 |
|
ocn_compon_interf/ - 6.6 (no content yet) |
506 |
|
offline/ - nothing, tutorials that need work but no package section entry |
507 |
|
trivial to document (CNH to do) |
508 |
|
opps/ - nothing, (martin?) |
509 |
|
pp81/ - nothing, (martin?) |
510 |
|
profiles/ - GAEL |
511 |
|
ptracers/ - JM + SD + Martin to write something (nothing for this |
512 |
|
at the moment) |
513 |
|
AM has diagnostics table for this. |
514 |
|
rbcs/ - CNH to talk to steph |
515 |
|
runclock/ - runclock - CNH |
516 |
|
rw/ - not sure - going to stay says JMC. quick IO calls |
517 |
|
JMC to write a quick note for that. |
518 |
|
sbo/ - text in sbo_descruption.tex but not linked into |
519 |
|
part6 - CNH |
520 |
|
seaice/ - 6.5.2 - no equations, dimitris has promised some |
521 |
|
shap_filt/ - chapter 2, JM to check |
522 |
|
shelfice/ - nothing yet (martin?) |
523 |
|
solver/ - empty (go away?) |
524 |
|
sphere/ - chapter 5 or 8 (PH to check) |
525 |
|
therm_seaice/ - empty (go away?) |
526 |
|
thsice/ - 6.5.1 (JM to update?) |
527 |
|
timeave/ - retiring...... |
528 |
|
zonal_filt/ - chapter 2 (JM to check) |
529 |
|
|
530 |
|
o Cost function packages |
531 |
|
- floats, weights, profiles etc... |
532 |
|
|
533 |
|
|
534 |
|
list an expeiment which uses package? CNH |
535 |
|
|
536 |
|
6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
537 |
|
Figure 6.8 is missing |
538 |
|
|
539 |
|
|
540 |
|
===== Chapter 7 ===== [EH3 editing] : |
541 |
|
|
542 |
|
+ JMC: please add description of: |
543 |
|
- diagstat |
544 |
|
- new temporal averaging feature |
545 |
|
|
546 |
|
+ add Graphix to the list of stuff in utils/matlab (Daniel) |
547 |
|
|
548 |
|
+ get bathymetry pre-processing stuff from Patrick and then describe it |
549 |
|
|
550 |
|
+ add something on spgrid mesh generator |
551 |
|
o Grid generation |
552 |
|
- more explanation and some step-by-step examples |
553 |
|
- plotting grid examples |
554 |
|
|
555 |
|
|
556 |
|
+ add in gmaze PV calculation scripts plus write up on how it is calculated |
557 |
|
http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/ |
558 |
|
|
559 |
|
|
560 |
|
andrea |
561 |
|
|
562 |
|
|
563 |
|
9. Publications using MITgcm --> "Previous Applications of MITgcm" |
564 |
|
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
565 |
|
(check in support for more names) |
566 |
|
|
567 |
|
10. Under development |
568 |
|
|
569 |
|
Constantinos LCML |
570 |
|
o Legend/LCML examples and explanation |
571 |
|
- examples and explanation! |
572 |
|
|
573 |
|
|
574 |
|
|
575 |
|
Bibliography |
576 |
|
|
577 |
|
tidy up from misc - .tex |
578 |
|
|