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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 |
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o too many clicks to get to model manual. |
TBD |
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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 |
o add another short-cut for quick download |
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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 words on http://mitgcm.org/r2_web_testing/latest |
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John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen, |
change to |
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Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos, |
"access on-line Auser manual/A and Atable of contents/A |
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Gael - others? |
and browse the Aoverview section/A" |
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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 |
o finite-volume doesn't leap to FV figure |
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o date is 2002 |
o have another go at pnmcrop et al. |
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o fix search so it doesn't include advertisements |
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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 |
o Need an empty package as part of distribution. Check out atm_common |
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pnmcrop et al. |
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o Latex |
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Contents |
Chapter 1 - CNH |
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Intro - 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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186 |
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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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187 |
Change hydrodynamical to "dynamical" |
Change hydrodynamical to "dynamical" |
188 |
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189 |
Examples |
Examples |
221 |
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222 |
o Gas giant? |
o Gas giant? |
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Chapter 6 |
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224 |
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225 |
the master package diagram does not appear in the document |
>>>> from JM |
226 |
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pkg/ptracers doesn't seem to have any documentation (see packages list below) |
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228 |
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manual, section.2 : |
229 |
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230 |
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In general: |
231 |
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- add more refences/links to S/R & variable name |
232 |
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- would be nice to have an active link to the fortran-file |
233 |
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for all the S/R & eq.Number in the "calling-tree" boxes |
234 |
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- search for CALC_MOM_RHS and replace it by the appropriate S/R |
235 |
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(mom_flux_form, mom_vecinv, dynamics) |
236 |
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- Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h}) |
237 |
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was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}} |
238 |
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in section.2, \vec{\bf v} is used instead and 3.D velocity vector is |
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simply written \vec{v}. |
240 |
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I would suggest to keep the notation as they are (since they are consistent |
241 |
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inside each section) but may be to move the "notation.tex" piece |
242 |
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at the beginning of section.2 and to mention clearly the changes between |
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the 2 sections. |
244 |
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245 |
2.10.5 Horizontal grid |
in content: Horizontal Dissipation: 2 times in vector-invariant section |
246 |
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247 |
need to do a better job of relating model variables to this diagram |
2.1 time-stepping (part2/time_stepping.tex) |
248 |
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249 |
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- this is not clear to me: |
250 |
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Master list of packages |
>> In all the above configurations it is also possible to substitute the |
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>> Adams-Bashforth with an alternative time-stepping scheme for terms |
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>> evaluated explicitly in time |
254 |
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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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256 |
Possible for chap 7 - Daniels grafix/ stuff |
2.2 rigid-lid: |
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258 |
Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started. |
- At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)" |
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to stay closer to the code. |
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- mention section 2.5 implicit-Time-stepping (for vertical viscosity) |
261 |
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Figure 6.8 is missing |
2.3 linear free-surface: |
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- add ref(+link) to S/R names: |
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- add ref(+link) to Crank-Nickelson section 2.9.1 |
265 |
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2.4 Adams-Bashforth |
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- add stability diagrams (I have some figures that I can put) |
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- add link for var. forcing_In_AB |
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- add S/R link for S/R ADAMS_BASHFORTH2 |
270 |
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271 |
>>>> From Ed |
2.5 Implicit time-stepping |
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- add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R |
273 |
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SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL |
274 |
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- update: also used for vertical advection |
275 |
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276 |
Here are the remaining bits for Chap 4 : |
2.6 Synchronous time-stepping: |
277 |
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- add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE, |
278 |
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MOMENTUM_CORRECTION_STEP. |
279 |
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280 |
- The grammar/flow could still use some work. Boo was an English |
2.7 Stagger baroclinic time-stepping |
281 |
major and has experience editing/proofing technical papers. I |
- mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end |
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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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282 |
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283 |
- missing references (if you point me towards URLs, I'll add them |
2.8 NH |
284 |
to the bibliography): |
- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D |
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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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285 |
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286 |
- There are a few empty sub-sections at the end of Chap 4 that |
2.9 Variants on Free-Surface |
287 |
should either be commented out or fleshed out. |
- Delta.t mis-written (eq.2.73) |
288 |
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- Eq.Num missing (has been fixed since) |
289 |
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- u* is stored in gU (and not in gUnm1) |
290 |
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- Phi_nh in NH_VARS.h |
291 |
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- add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D, |
292 |
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INI_CG2D, INI_CG3D |
293 |
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294 |
and thats about it for Chap 4. |
2.9.1 Crank-Nickelson |
295 |
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- link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater |
296 |
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297 |
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2.9.2 NLFS |
298 |
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- eq.Nb are wrong in html |
299 |
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- 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi) |
300 |
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301 |
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2.10.1 Notation |
302 |
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- Area definition is not really used like this |
303 |
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304 |
Add more to quick links on front page |
>> Ao : Area of the face orthogonal to "o" direction (o=u,v,w) |
305 |
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306 |
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Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to |
307 |
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the model variables) are used (e.g., see section 2.10.5) |
308 |
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309 |
>>>> From Andrea |
2.10.5 Horizontal grid: |
310 |
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- fig.2.8 : should use Aw,As consistently in this figure description, |
311 |
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in the figure itself, as it is in the text. |
312 |
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- curvilinear: |
313 |
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to add: mention the angle of the grid direction relative to |
314 |
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Eastward, Northward direction. |
315 |
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+ mention horizGridFile= in file "data" (PARM04) |
316 |
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- add cylindrical polar grid description |
317 |
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need to do a better job of relating model variables to this diagram |
318 |
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to do list for chap 7: |
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319 |
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320 |
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2.11 Continuity & Horizontal Pressure gradient terms |
321 |
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- mention that d.Phi/dr|s =g if using z coordinate |
322 |
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- eq. 2.90 not clear regarding \delta_k(P-E) |
323 |
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better to add the free surface eq: d.eta/dt = w_s + P-E |
324 |
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325 |
7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu" |
2.12 Hydrostatic balance |
326 |
the links are pointing to the proper place |
- add ref to Atmosphere Appendix section (1.4) since Adcroft 2002 |
327 |
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is hard to find |
328 |
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- add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H) |
329 |
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and in section 1.3.4: remove the 1.3.4.3.2 subsection: |
330 |
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Quasi-nonhydrostatic Atmosphere |
331 |
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332 |
7.5.1 - add Graphix to the list of stuff in utils/matlab |
2.13.2 Coriolis terms |
333 |
7.5.2 - empty |
- note: the discretization used when useEnergyConservingCoriolis=T |
334 |
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has no hFac and no Area and is still different from the form |
335 |
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described here (with Area & hFac); |
336 |
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337 |
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2.13.5 Lateral dissipation |
338 |
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- add description of how to use cosFactor & cosPower |
339 |
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- add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4 |
340 |
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o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags |
341 |
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in code need to explain why cos()3/2 turns out to be |
342 |
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scaling (not cos()2) |
343 |
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- need to reference the smag/leith section. |
344 |
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345 |
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2.13.6 Vertical dissipation |
346 |
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- mention the implicit vertical viscosity option and ref to section 2.5 |
347 |
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- add the parameter correspondence: Av <-> viscAr (and might change also |
348 |
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the notation to Ar) |
349 |
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350 |
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2.14 Vector invariant momentum equations |
351 |
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- indicate that the NH pieces (vertical momentum eq) are not yet coded |
352 |
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and that the NH code uses the flux form. |
353 |
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354 |
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2.14.6 Horizontal dissipation -> Horizontal Divergence |
355 |
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356 |
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2.14.7 Horizontal dissipation |
357 |
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- add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ |
358 |
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and A_D4,A_z4 <-> viscA4D,viscA4Z |
359 |
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360 |
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2.16 & 2.17 & 2.18 : |
361 |
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- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
362 |
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- fix equations 2.202 & 2.203 (thanks to Martin) |
363 |
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364 |
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2.20.2 mercator, non-dimensional Equations: |
365 |
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- does not use std notation |
366 |
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- would be better as an appendix of section 2.20: |
367 |
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(e.g changing the tile to: |
368 |
|
- talk to Baylor |
369 |
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Appendix: non-dimensional Equations on Spherical-Polar grid.) |
370 |
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|
371 |
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|
372 |
|
Diagrams of grid locations etc.... and what variables and output files |
373 |
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and/or netcdf variable names are not very easy to figure out and follow. |
374 |
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It would be good to redo and extend these diagrams and align with GRID.h |
375 |
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content. |
376 |
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|
377 |
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378 |
|
JM |
379 |
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andrea |
|
380 |
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|
381 |
>>>> From Andrea |
>>>> From Andrea |
382 |
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|
385 |
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|
386 |
Almost all of the 'math mode' text is dropped down as subscripts |
Almost all of the 'math mode' text is dropped down as subscripts |
387 |
|
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|
divide chapter 3 more clearly into 2 sections? |
|
|
(ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and |
|
|
then 3.19 and 3.20 are informational again - rearrange subsections?) |
|
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|
388 |
3.1 - don't need a link to the outside of the document (remove it) |
3.1 - don't need a link to the outside of the document (remove it) |
389 |
- link to htdig is broken |
- link to htdig is broken |
390 |
|
|
430 |
are written. |
are written. |
431 |
3.6.1.2 - needs to be moved to inside section 3.6.2 |
3.6.1.2 - needs to be moved to inside section 3.6.2 |
432 |
|
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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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|
433 |
All the 'overview' sections need some reference to the name of the experiment in |
All the 'overview' sections need some reference to the name of the experiment in |
434 |
the verification directory |
the verification directory |
435 |
|
|
463 |
3.20.1 - link to doc at end of section points to this section |
3.20.1 - link to doc at end of section points to this section |
464 |
3.20.2 - link to doc at end of section points to this section |
3.20.2 - link to doc at end of section points to this section |
465 |
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|
466 |
>>>> from JM |
offline - duplicate inputs, what is it, tidy up cfc v. |
467 |
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other offline. JM thinks these need tidying up. |
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manual, section.2 : |
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In general: |
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- add more refences/links to S/R & variable name |
|
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- would be nice to have an active link to the fortran-file |
|
|
for all the S/R & eq.Number in the "calling-tree" boxes |
|
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- search for CALC_MOM_RHS and replace it by the appropriate S/R |
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|
(mom_flux_form, mom_vecinv, dynamics) |
|
|
- Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h}) |
|
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was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}} |
|
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in section.2, \vec{\bf v} is used instead and 3.D velocity vector is |
|
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simply written \vec{v}. |
|
|
I would suggest to keep the notation as they are (since they are consistent |
|
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inside each section) but may be to move the "notation.tex" piece |
|
|
at the beginning of section.2 and to mention clearly the changes between |
|
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the 2 sections. |
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|
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in content: Horizontal Dissipation: 2 times in vector-invariant section |
|
468 |
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|
469 |
2.1 time-stepping (part2/time_stepping.tex) |
Which of the following are which tutorial? |
470 |
|
adjustment.128x64x1 |
471 |
|
adjustment.cs-32x32x1 |
472 |
|
advect_cs |
473 |
|
advect_xy |
474 |
|
advect_xz |
475 |
|
aim.5l_cs |
476 |
|
aim.5l_Equatorial_Channel |
477 |
|
aim.5l_LatLon |
478 |
|
biogeo |
479 |
|
bottom_ctrl_5x5 |
480 |
|
cfc_example |
481 |
|
cpl_aim+ocn |
482 |
|
dome |
483 |
|
exp2 |
484 |
|
exp4 |
485 |
|
exp5 |
486 |
|
fizhi-cs-32x32x10 |
487 |
|
fizhi-cs-aqualev20 |
488 |
|
fizhi-gridalt-hs |
489 |
|
flt_example |
490 |
|
front_relax |
491 |
|
global1x1_tot |
492 |
|
global2x2_tot |
493 |
|
global_ocean.90x40x15 |
494 |
|
global_ocean.cs32x15 |
495 |
|
global_ocean.cubed32x32x30 |
496 |
|
global_ocean_ebm |
497 |
|
global_with_exf |
498 |
|
hs94.128x64x5 |
499 |
|
hs94.1x64x5 |
500 |
|
hs94.cs-32x32x5 |
501 |
|
ideal_2D_oce |
502 |
|
internal_wave |
503 |
|
inverted_barometer |
504 |
|
lab_sea |
505 |
|
matrix_example |
506 |
|
MLAdjust |
507 |
|
natl_box |
508 |
|
natl_box_adjoint |
509 |
|
OpenAD |
510 |
|
rotating_tank |
511 |
|
solid-body.cs-32x32x1 |
512 |
|
tidal_basin_2d |
513 |
|
tutorial_baroclinic_gyre |
514 |
|
tutorial_barotropic_gyre |
515 |
|
tutorial_cfc_offline |
516 |
|
tutorial_deep_convection |
517 |
|
tutorial_global_oce_biogeo |
518 |
|
tutorial_global_oce_in_p |
519 |
|
tutorial_global_oce_latlon |
520 |
|
tutorial_global_oce_optim |
521 |
|
tutorial_held_suarez_cs |
522 |
|
tutorial_offline |
523 |
|
tutorial_plume_on_slope |
524 |
|
tutorial_tracer_adjsens |
525 |
|
vermix |
526 |
|
|
527 |
- this is not clear to me: |
>>>> From Ed |
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|
>> In all the above configurations it is also possible to substitute the |
|
|
>> Adams-Bashforth with an alternative time-stepping scheme for terms |
|
|
>> evaluated explicitly in time |
|
528 |
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|
529 |
|
Here are the remaining bits for Chap 4 : |
530 |
|
|
531 |
2.2 rigid-lid: |
- missing references (if you point me towards URLs, I'll add them |
532 |
|
to the bibliography): |
533 |
|
\ref{ref hoe and hill, ecmwf} |
534 |
|
\ref{magicgarden} |
535 |
|
\ref{IBMLAPI} |
536 |
|
\ref{Memorychannel} |
537 |
|
\ref{hoe-hill:99} |
538 |
|
|
539 |
- At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)" |
- There are a few empty sub-sections at the end of Chap 4 that |
540 |
to stay closer to the code. |
should either be commented out or fleshed out. |
|
- mention section 2.5 implicit-Time-stepping (for vertical viscosity) |
|
541 |
|
|
542 |
2.3 linear free-surface: |
and thats about it for Chap 4. |
|
- add ref(+link) to S/R names: |
|
|
- add ref(+link) to Crank-Nickelson section 2.9.1 |
|
543 |
|
|
|
2.4 Adams-Bashforth |
|
|
- add stability diagrams (I have some figures that I can put) |
|
|
- add link for var. forcing_In_AB |
|
|
- add S/R link for S/R ADAMS_BASHFORTH2 |
|
544 |
|
|
545 |
2.5 Implicit time-stepping |
Add more to quick links on front page |
|
- add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R |
|
|
SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL |
|
|
- update: also used for vertical advection |
|
546 |
|
|
547 |
2.6 Synchronous time-stepping: |
Chapter 6 |
|
- add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE, |
|
|
MOMENTUM_CORRECTION_STEP. |
|
548 |
|
|
549 |
2.7 Stagger baroclinic time-stepping |
the master package diagram does not appear in the document |
|
- mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end |
|
550 |
|
|
551 |
2.8 NH |
Master list of packages (add this to beginning of chap 6) |
|
- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D |
|
552 |
|
|
553 |
2.9 Variants on Free-Surface |
admtlm/ - autodiff (chapter 5) |
554 |
- Delta.t mis-written (eq.2.73) |
aim/ - retired |
555 |
- Eq.Num missing (has been fixed since) |
aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM) |
556 |
- u* is stored in gU (and not in gUnm1) |
aim_ocn_coupler/ - 6.6 (no content yet) |
557 |
- Phi_nh in NH_VARS.h |
aim_v23/ - 6.4.1 (content needs fixing - JM to do) |
558 |
- add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D, |
atm_common/ - nothing in this package (6.4.1 related) |
559 |
INI_CG2D, INI_CG3D |
autodiff/ - autodiff (chapter 5) |
560 |
|
bulk_force/ - 6.3.3 |
561 |
2.9.1 Crank-Nickelson |
cal/ - 6.3.5 |
562 |
- link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater |
cd_code/ - chapter 2 (JM check add a reference to paper, |
563 |
|
mention parameter in data) |
564 |
2.9.2 NLFS |
cfc/ - not sure (CNH to talk to Steph and Helen) |
565 |
- eq.Nb are wrong in html |
chronos/ - AM to check (not being used - Andrea to kill it) |
566 |
- 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi) |
compon_communic/ - 6.6 (no content yet)(Daniel + JM) |
567 |
|
cost/ - not sure, check with PH |
568 |
|
ctrl/ - not sure, check with PH |
569 |
|
debug/ - JM may do something in chapter 7 (utilities) |
570 |
|
diagnostics/ - 7.1 |
571 |
|
dic/ - 6.7.2 |
572 |
|
ebm/ - (check with PH) |
573 |
|
ecco/ - chapter 8 |
574 |
|
embed_files/ - add something to chapter 7 |
575 |
|
exch2/ - 6.2.2 |
576 |
|
exf/ - 6.3.4 |
577 |
|
fizhi/ - 6.4.3 |
578 |
|
flt/ - (PH check) |
579 |
|
gchem/ - 6.7.1 |
580 |
|
generic_advdiff/ - in chapter 2 (JM check) |
581 |
|
ggl90/ - nothing, (Martin?) |
582 |
|
gmredi/ - in chapter 2 (JM check). also need |
583 |
|
Ferrari & Mc transition zone stuff (Samar doing this) |
584 |
|
get dfer to read this |
585 |
|
grdchk/ - grdchk (chapter 5 - check with PH) |
586 |
|
gridalt/ - 6.2.4 |
587 |
|
kpp/ - 6.3.2 |
588 |
|
land/ - 6.4.2 (not connected to code Rong's notes - JM to fix) |
589 |
|
matrix/ - Samar |
590 |
|
mdsio/ - 7.3.1 |
591 |
|
mnc/ - 7.2.1 |
592 |
|
mom_common/ - in chapter 2 (JM check) |
593 |
|
mom_fluxform/ - in chapter 2 (JM check) |
594 |
|
mom_vecinv/ - in chapter 2 (JM check) |
595 |
|
monitor/ - 7.4 |
596 |
|
my82/ - nothing, (martin?) |
597 |
|
obcs/ - 6.3 (needs a check - ask PH to read) |
598 |
|
ocn_compon_interf/ - 6.6 (no content yet) |
599 |
|
offline/ - nothing, tutorials that need work but no package section entry |
600 |
|
trivial to document (CNH to do) |
601 |
|
opps/ - nothing, (martin?) |
602 |
|
pp81/ - nothing, (martin?) |
603 |
|
profiles/ - GAEL |
604 |
|
ptracers/ - JM + SD + Martin to write something (nothing for this |
605 |
|
at the moment) |
606 |
|
AM has diagnostics table for this. |
607 |
|
rbcs/ - CNH to talk to steph |
608 |
|
runclock/ - runclock - CNH |
609 |
|
rw/ - not sure - going to stay says JMC. quick IO calls |
610 |
|
JMC to write a quick note for that. |
611 |
|
sbo/ - text in sbo_descruption.tex but not linked into |
612 |
|
part6 - CNH |
613 |
|
seaice/ - 6.5.2 - no equations, dimitris has promised some |
614 |
|
shap_filt/ - chapter 2, JM to check |
615 |
|
shelfice/ - nothing yet (martin?) |
616 |
|
solver/ - empty (go away?) |
617 |
|
sphere/ - chapter 5 or 8 (PH to check) |
618 |
|
therm_seaice/ - empty (go away?) |
619 |
|
thsice/ - 6.5.1 (JM to update?) |
620 |
|
timeave/ - retiring...... |
621 |
|
zonal_filt/ - chapter 2 (JM to check) |
622 |
|
|
623 |
2.10.1 Notation |
list an expeiment which uses package? CNH |
|
- Area definition is not really used like this |
|
624 |
|
|
625 |
>> Ao : Area of the face orthogonal to "o" direction (o=u,v,w) |
6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
626 |
|
Figure 6.8 is missing |
627 |
|
|
|
Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to |
|
|
the model variables) are used (e.g., see section 2.10.5) |
|
628 |
|
|
629 |
2.10.5 Horizontal grid: |
===== Chapter 7 ===== [EH3 editing] : |
|
- fig.2.8 : should use Aw,As consistently in this figure description, |
|
|
in the figure itself, as it is in the text. |
|
|
- curvilinear: |
|
|
to add: mention the angle of the grid direction relative to |
|
|
Eastward, Northward direction. |
|
|
+ mention horizGridFile= in file "data" (PARM04) |
|
|
- add cylindrical grid description |
|
630 |
|
|
631 |
2.11 Continuity & Horizontal Pressure gradient terms |
7.1.x - JMC: please add description of: |
632 |
- mention that d.Phi/dr|s =g if using z coordinate |
- diagstat |
633 |
- eq. 2.90 not clear regarding \delta_k(P-E) |
- new temporal averaging feature |
|
better to add the free surface eq: d.eta/dt = w_s + P-E |
|
634 |
|
|
635 |
2.12 Hydrostatic balance |
7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel) |
|
- add ref to Atmosphere Appendix section (1.4) since Adcroft 2002 |
|
|
is hard to find |
|
|
- add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H) |
|
|
and in section 1.3.4: remove the 1.3.4.3.2 subsection: |
|
|
Quasi-nonhydrostatic Atmosphere |
|
636 |
|
|
637 |
2.13.2 Coriolis terms |
7.5.2 - get bathymetry pre-processing stuff from Patrick |
638 |
- note: the discretization used when useEnergyConservingCoriolis=T |
and then describe it |
|
has no hFac and no Area and is still different from the form |
|
|
described here (with Area & hFac); |
|
639 |
|
|
|
2.13.5 Lateral dissipation |
|
|
- add description of how to use cosFactor & cosPower |
|
|
- add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4 |
|
640 |
|
|
641 |
2.13.6 Vertical dissipation |
andrea |
|
- mention the implicit vertical viscosity option and ref to section 2.5 |
|
|
- add the parameter correspondence: Av <-> viscAr (and might change also |
|
|
the notation to Ar) |
|
642 |
|
|
|
2.14 Vector invariant momentum equations |
|
|
- indicate that the NH pieces (vertical momentum eq) are not yet coded |
|
|
and that the NH code uses the flux form. |
|
643 |
|
|
644 |
2.14.6 Horizontal dissipation -> Horizontal Divergence |
9. Publications using MITgcm --> "Previous Applications of MITgcm" |
645 |
|
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
646 |
|
(check in support for more names) |
647 |
|
|
648 |
2.14.7 Horizontal dissipation |
10. Under development |
|
- add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ |
|
|
and A_D4,A_z4 <-> viscA4D,viscA4Z |
|
649 |
|
|
650 |
2.16 & 2.17 & 2.18 : |
Constantinos LCML |
|
- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
|
651 |
|
|
|
2.20.2 mercator, non-dimensional Equations: |
|
|
- does not use std notation |
|
|
- would be better as an appendix of section 2.20: |
|
|
(e.g changing the tile to: |
|
|
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
|
652 |
|
|
653 |
JM |
Bibliography |
654 |
|
|
655 |
|
tidy up from misc - .tex |