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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 |
Rebuild and set to do cron build - DONE on hugo |
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To do |
To do |
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Add an "Under development, chapter" - shortish description of what |
Add an "Under development, chapter" - shortish description of what |
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is available (last chapter) |
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 |
o HTML, scripts and front content |
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Tutorials (broken) |
Tutorials (broken) |
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Browse Code |
Browse Code |
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o mitgcm.org (front content) [DONE] |
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Get Code (where does this go to?) |
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get rid of * CVS current bullet |
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make HTML-enabled CVS code browser leap to MITgcm/MITgcm |
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o authors |
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John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen, |
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Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos, |
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Gael - others? |
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o words on http://mitgcm.org/r2_web_testing/latest |
o words on http://mitgcm.org/r2_web_testing/latest |
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change to |
change to |
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"access on-line Auser manual/A and Atable of contents/A |
"access on-line Auser manual/A and Atable of contents/A |
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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 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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- would be nice to have an active link to the fortran-file |
- would be nice to have an active link to the fortran-file |
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for all the S/R & eq.Number in the "calling-tree" boxes |
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 |
- search for CALC_MOM_RHS and replace it by the appropriate S/R |
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(mom_flux_form, mom_vecinv, dynamics) |
(mom_flux_form, mom_vecinv, dynamics) <- DONE |
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- 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}) |
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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}} |
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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 |
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the 2 sections. |
the 2 sections. |
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in content: Horizontal Dissipation: 2 times in vector-invariant section |
in content: Horizontal Dissipation: 2 times in vector-invariant section |
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<- DONE |
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2.1 time-stepping (part2/time_stepping.tex) |
2.1 time-stepping (part2/time_stepping.tex) |
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>> In all the above configurations it is also possible to substitute the |
>> 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 |
>> Adams-Bashforth with an alternative time-stepping scheme for terms |
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>> evaluated explicitly in time |
>> evaluated explicitly in time |
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<- Leave it general. |
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2.2 rigid-lid: |
2.2 rigid-lid: |
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- 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)" |
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to stay closer to the code. |
to stay closer to the code. |
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- mention section 2.5 implicit-Time-stepping (for vertical viscosity) |
- mention section 2.5 implicit-Time-stepping (for vertical viscosity) <- DONE |
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2.3 linear free-surface: |
2.3 linear free-surface: |
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- add ref(+link) to S/R names: |
- add ref(+link) to S/R names: |
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- add ref(+link) to Crank-Nickelson section 2.9.1 |
- add ref(+link) to Crank-Nickelson section 2.9.1 <- DONE |
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2.4 Adams-Bashforth |
2.4 Adams-Bashforth |
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- add stability diagrams (I have some figures that I can put) |
- add stability diagrams (I have some figures that I can put) <- DONE |
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- add link for var. forcing_In_AB |
- add link for var. forcing_In_AB and epsil_AB <- half DONE |
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- add S/R link for S/R ADAMS_BASHFORTH2 |
- add S/R link for S/R ADAMS_BASHFORTH2 <-DONE |
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2.5 Implicit time-stepping |
2.5 Implicit time-stepping |
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- 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 |
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- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D |
- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D |
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2.9 Variants on Free-Surface |
2.9 Variants on Free-Surface |
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- Delta.t mis-written (eq.2.73) |
- Delta.t mis-written (eq.2.73) <- DONE |
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- Eq.Num missing (has been fixed since) |
- Eq.Num missing <- DONE |
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- u* is stored in gU (and not in gUnm1) |
- u* is stored in gU (and not in gUnm1) <- DONE |
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- Phi_nh in NH_VARS.h |
- Phi_nh in NH_VARS.h <- DONE |
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- 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, |
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INI_CG2D, INI_CG3D |
INI_CG2D, INI_CG3D |
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2.9.2 NLFS |
2.9.2 NLFS |
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- eq.Nb are wrong in html |
- eq.Nb are wrong in html |
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- 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) |
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<- DONE |
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2.10.1 Notation |
2.10.1 Notation |
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- Area definition is not really used like this |
- Area definition is not really used like this |
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Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to |
Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to |
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the model variables) are used (e.g., see section 2.10.5) |
the model variables) are used (e.g., see section 2.10.5) |
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<- DONE |
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2.10.5 Horizontal grid: |
2.10.5 Horizontal grid: |
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- fig.2.8 : should use Aw,As consistently in this figure description, |
- fig.2.8 : should use Aw,As consistently in this figure description, |
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in the figure itself, as it is in the text. |
in the figure itself, as it is in the text. <- DONE |
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- curvilinear: |
- curvilinear: |
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to add: mention the angle of the grid direction relative to |
to add: mention the angle of the grid direction relative to |
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Eastward, Northward direction. |
Eastward, Northward direction. |
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2.16 & 2.17 & 2.18 : |
2.16 & 2.17 & 2.18 : |
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- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
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- fix equations 2.202 & 2.203 (thanks to Martin) <- DONE |
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2.20.2 mercator, non-dimensional Equations: |
2.20.2 mercator, non-dimensional Equations: |
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- does not use std notation |
- does not use std notation |
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(e.g changing the tile to: |
(e.g changing the tile to: |
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- talk to Baylor |
- talk to Baylor |
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Appendix: non-dimensional Equations on Spherical-Polar grid.) |
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
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<- No (Chris said) |
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Diagrams of grid locations etc.... and what variables and output files |
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and/or netcdf variable names are not very easy to figure out and follow. |
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It would be good to redo and extend these diagrams and align with GRID.h |
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content. |
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JM |
JM |
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Almost all of the 'math mode' text is dropped down as subscripts |
Almost all of the 'math mode' text is dropped down as subscripts |
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divide chapter 3 more clearly into 2 sections? |
3.11.3.1 - refers to figures and equations, links are broken |
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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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[DONE] |
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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 |
3.12.3.2 - line 43: link to equation is broken |
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- line 51-53: link to equation is broken |
- 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? |
- 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 |
3.13.4.1 - line 34 - link to equation is broken |
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- lines 60,61 - 1st (take out the 'r' in the superscript) |
- lines 60,61 - 1st (take out the 'r' in the superscript) |
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3.13.2 - link to theta-equation is broken |
3.14.2 - link to theta-equation is broken |
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3.13.5.4 -- ALL of the bold links to variable names are broken |
3.14.5.4 -- ALL of the bold links to variable names are broken |
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line 34: link to equation is broken |
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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offline - duplicate inputs, what is it, tidy up cfc v. |
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other offline. JM thinks these need tidying up. |
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Which of the following are which tutorial? |
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! MLAdjust |
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adjust_nlfs.cs-32x32x1 |
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aim.5l_XZ_Equatorial_Slice |
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biogeo |
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aim.5l_zon-ave |
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coupled_ucla |
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cfc_offline |
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exp3 |
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global2x2_tot |
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global1x1_tot |
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global_ocean.cubed_wEXF |
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global_with_CFC11 |
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goz |
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gop |
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natl_box_obcs |
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natl_box_forward |
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spinup_optim |
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tutorial_held_suarez_cs |
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vero |
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inverted_barometer |
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global_ocean.cubed32x32x30 |
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exp1 |
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advect_cs |
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dic_example |
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fizhi-gridalt-hs |
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global_ocean_pressure |
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matrix_example |
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exp4 |
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solid-body.cs-32x32x1 |
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cfc_example |
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flt_example |
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adjustment.cs-32x32x1 |
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advect_xz |
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rotating_tank |
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ideal_2D_oce |
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global_ocean.90x40x15 |
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front_relax |
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aim.5l_LatLon |
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lab_sea |
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hs94.cs-32x32x5 |
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global_with_exf |
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exp2 |
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tidal_basin_2d |
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fizhi-cs-32x32x10 |
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exp5 |
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global_ocean.cs32x15 |
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OpenAD |
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hs94.1x64x5 |
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fizhi-cs-aqualev10 |
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exp0 |
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dome |
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aim.5l_Equatorial_Channel |
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aim.5l_cs |
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hs94.128x64x5 |
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prm |
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carbon |
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plume_on_slope |
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natl_box_adjoint |
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vermix |
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cpl_aim+ocn |
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global_ocean_ebm |
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internal_wave |
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advect_xy |
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natl_box |
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adjustment.128x64x1 |
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| 407 |
>>>> From Ed |
>>>> From Ed |
| 408 |
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| 409 |
Here are the remaining bits for Chap 4 : |
Here are the remaining bits for Chap 4 : |
| 502 |
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| 503 |
list an expeiment which uses package? CNH |
list an expeiment which uses package? CNH |
| 504 |
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[DONE]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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| 505 |
6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
| 506 |
Figure 6.8 is missing |
Figure 6.8 is missing |
| 507 |
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| 508 |
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| 509 |
>>>> From Andrea |
===== Chapter 7 ===== [EH3 editing] : |
| 510 |
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| 511 |
to do list for chap 7: |
7.1.x - JMC: please add description of: |
| 512 |
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- diagstat |
| 513 |
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- new temporal averaging feature |
| 514 |
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| 515 |
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7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel) |
| 516 |
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| 517 |
7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu" |
7.5.2 - get bathymetry pre-processing stuff from Patrick |
| 518 |
the links are pointing to the proper place |
and then describe it |
| 519 |
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| 520 |
7.5.1 - add Graphix to the list of stuff in utils/matlab |
add something on spgrid mesh generator (maybe)? |
| 521 |
7.5.2 - empty |
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add in gmaze PV calculation scripts plus write up on how it is calculated |
| 523 |
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http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/ |
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| 526 |
andrea |
andrea |
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| 529 |
9. Publications using MITgcm |
9. Publications using MITgcm --> "Previous Applications of MITgcm" |
| 530 |
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
| 531 |
(check in support for more names) |
(check in support for more names) |
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| 533 |
10. Under development |
10. Under development |
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Constantinos LCML |
| 536 |
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| 537 |
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| 538 |
Bibliography |
Bibliography |
| 539 |
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tidy up from misc - .tex |
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