205 |
o coupled aqua, ridge world etc... |
o coupled aqua, ridge world etc... |
206 |
- links to ingrid output |
- links to ingrid output |
207 |
get stuff from Daniel |
get stuff from Daniel |
208 |
|
Davids donut movie |
209 |
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|
210 |
o constrained lab simulation |
o constrained lab simulation |
211 |
- links to ingrid output for model and lab |
- links to ingrid output for model and lab |
233 |
- would be nice to have an active link to the fortran-file |
- would be nice to have an active link to the fortran-file |
234 |
for all the S/R & eq.Number in the "calling-tree" boxes |
for all the S/R & eq.Number in the "calling-tree" boxes |
235 |
- 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 |
236 |
(mom_flux_form, mom_vecinv, dynamics) |
(mom_flux_form, mom_vecinv, dynamics) <- DONE |
237 |
- 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}) |
238 |
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}} |
239 |
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 |
244 |
the 2 sections. |
the 2 sections. |
245 |
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|
246 |
in content: Horizontal Dissipation: 2 times in vector-invariant section |
in content: Horizontal Dissipation: 2 times in vector-invariant section |
247 |
|
<- DONE |
248 |
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|
249 |
2.1 time-stepping (part2/time_stepping.tex) |
2.1 time-stepping (part2/time_stepping.tex) |
250 |
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|
253 |
>> In all the above configurations it is also possible to substitute the |
>> In all the above configurations it is also possible to substitute the |
254 |
>> Adams-Bashforth with an alternative time-stepping scheme for terms |
>> Adams-Bashforth with an alternative time-stepping scheme for terms |
255 |
>> evaluated explicitly in time |
>> evaluated explicitly in time |
256 |
|
<- Leave it general. |
257 |
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258 |
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|
259 |
2.2 rigid-lid: |
2.2 rigid-lid: |
287 |
- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D |
- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D |
288 |
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|
289 |
2.9 Variants on Free-Surface |
2.9 Variants on Free-Surface |
290 |
- Delta.t mis-written (eq.2.73) |
- Delta.t mis-written (eq.2.73) <- DONE |
291 |
- Eq.Num missing (has been fixed since) |
- Eq.Num missing <- DONE |
292 |
- u* is stored in gU (and not in gUnm1) |
- u* is stored in gU (and not in gUnm1) <- DONE |
293 |
- Phi_nh in NH_VARS.h |
- Phi_nh in NH_VARS.h <- DONE |
294 |
- 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, |
295 |
INI_CG2D, INI_CG3D |
INI_CG2D, INI_CG3D |
296 |
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|
300 |
2.9.2 NLFS |
2.9.2 NLFS |
301 |
- eq.Nb are wrong in html |
- eq.Nb are wrong in html |
302 |
- 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) |
303 |
|
<- DONE |
304 |
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|
305 |
2.10.1 Notation |
2.10.1 Notation |
306 |
- Area definition is not really used like this |
- Area definition is not really used like this |
309 |
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|
310 |
Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to |
Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to |
311 |
the model variables) are used (e.g., see section 2.10.5) |
the model variables) are used (e.g., see section 2.10.5) |
312 |
|
<- DONE |
313 |
|
|
314 |
2.10.5 Horizontal grid: |
2.10.5 Horizontal grid: |
315 |
- fig.2.8 : should use Aw,As consistently in this figure description, |
- fig.2.8 : should use Aw,As consistently in this figure description, |
316 |
in the figure itself, as it is in the text. |
in the figure itself, as it is in the text. <- DONE |
317 |
- curvilinear: |
- curvilinear: |
318 |
to add: mention the angle of the grid direction relative to |
to add: mention the angle of the grid direction relative to |
319 |
Eastward, Northward direction. |
Eastward, Northward direction. |
364 |
|
|
365 |
2.16 & 2.17 & 2.18 : |
2.16 & 2.17 & 2.18 : |
366 |
- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
367 |
- fix equations 2.202 & 2.203 (thanks to Martin) |
- fix equations 2.202 & 2.203 (thanks to Martin) <- DONE |
368 |
|
|
369 |
2.20.2 mercator, non-dimensional Equations: |
2.20.2 mercator, non-dimensional Equations: |
370 |
- does not use std notation |
- does not use std notation |
372 |
(e.g changing the tile to: |
(e.g changing the tile to: |
373 |
- talk to Baylor |
- talk to Baylor |
374 |
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
375 |
|
<- No (Chris said) |
376 |
|
|
377 |
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|
378 |
Diagrams of grid locations etc.... and what variables and output files |
Diagrams of grid locations etc.... and what variables and output files |
391 |
|
|
392 |
Almost all of the 'math mode' text is dropped down as subscripts |
Almost all of the 'math mode' text is dropped down as subscripts |
393 |
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3.1 - don't need a link to the outside of the document (remove it) |
|
|
- link to htdig is broken |
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|
3.2.1 - link at bottom to source code points to section 3.2.1 |
|
|
(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 |
|
|
the cvs part, ie, should be 3.2.1.1 |
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3.3 - remove reference to 'diags' section under MITgcm |
|
|
- remove reference to 'exe' and 'bin' sections also |
|
|
(remove the .cvsignore file under these directories in cvs) |
|
|
- add a 'jobs' section, and a description as examples of run scripts |
|
|
- add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions |
|
|
- under 'tools' add a reference to 'build_options'. refer to the 'optfiles' |
|
|
- under 'tools' the adjoint points to section 5 - this is now section 8 |
|
|
(but should be a floating reference) |
|
|
- under 'utils' add a reference to exch2 - stuff for different resolutions |
|
|
- the description of the pkg section refers directly to |
|
|
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) |
|
|
3.4.1 - links to the following experiments don't exist or are broken: |
|
|
exp2 - should link to section 3.9 |
|
|
hs94.cs-32x32x5 - link to section 3.12 |
|
|
add 'convection' to the list, link to section 3.13 |
|
|
add 'plume on slope` to the list, link to section 3.14 |
|
|
add '??' link to section 3.15 |
|
|
add 'dic_example on slope` to the list, link to section 3.16 |
|
|
add '??' link to section 3.17 |
|
|
add 'offline' and link to section 3.18 |
|
|
clean up others and make links where they are needed |
|
|
3.4.2 - text suggests to see section 2 for details about what is in the 'code' |
|
|
and 'input' directories - should refer to the examples in this section |
|
|
- 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 |
|
|
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 |
|
|
'data' file in the input directory or by the data.[pkg name] file for any |
|
|
package running. And there is some default behavior when the 'state' dumps |
|
|
are written. |
|
|
3.6.1.2 - needs to be moved to inside section 3.6.2 |
|
|
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|
|
All the 'overview' sections need some reference to the name of the experiment in |
|
|
the verification directory |
|
|
|
|
|
3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript |
|
|
- is this experiment in the list from section 3.4??? |
|
394 |
3.10.3.1 - refers to figures and equations, links are broken |
3.10.3.1 - refers to figures and equations, links are broken |
395 |
|
|
396 |
3.11.3.2 - line 43: link to equation is broken |
3.11.3.2 - line 43: link to equation is broken |
404 |
3.13.5.4 -- ALL of the bold links to variable names are broken |
3.13.5.4 -- ALL of the bold links to variable names are broken |
405 |
line 34: link to equation is broken |
line 34: link to equation is broken |
406 |
|
|
|
3.15.1 - reference to 'fourth experiment' should be removed |
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|
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|
|
3.16.4 - strange formatting, presence of '>' symbols - remove them |
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|
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|
|
3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4 |
|
|
3.17.3.1 - nothing filled in under file input/data - needs description |
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|
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|
|
3.18.2 - point to section 2 for details - need hyperlink |
|
|
|
|
|
3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true! |
|
|
section 3.5 has the 'build' directory in the example |
|
|
|
|
|
3.20.1 - 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 |
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|
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|
|
offline - duplicate inputs, what is it, tidy up cfc v. |
|
|
other offline. JM thinks these need tidying up. |
|
|
|
|
|
Which of the following are which tutorial? |
|
|
adjustment.128x64x1 |
|
|
adjustment.cs-32x32x1 |
|
|
advect_cs |
|
|
advect_xy |
|
|
advect_xz |
|
|
aim.5l_cs |
|
|
aim.5l_Equatorial_Channel |
|
|
aim.5l_LatLon |
|
|
biogeo |
|
|
bottom_ctrl_5x5 |
|
|
cfc_example |
|
|
cpl_aim+ocn |
|
|
dome |
|
|
exp2 |
|
|
exp4 |
|
|
exp5 |
|
|
fizhi-cs-32x32x10 |
|
|
fizhi-cs-aqualev20 |
|
|
fizhi-gridalt-hs |
|
|
flt_example |
|
|
front_relax |
|
|
global1x1_tot |
|
|
global2x2_tot |
|
|
global_ocean.90x40x15 |
|
|
global_ocean.cs32x15 |
|
|
global_ocean.cubed32x32x30 |
|
|
global_ocean_ebm |
|
|
global_with_exf |
|
|
hs94.128x64x5 |
|
|
hs94.1x64x5 |
|
|
hs94.cs-32x32x5 |
|
|
ideal_2D_oce |
|
|
internal_wave |
|
|
inverted_barometer |
|
|
lab_sea |
|
|
matrix_example |
|
|
MLAdjust |
|
|
natl_box |
|
|
natl_box_adjoint |
|
|
OpenAD |
|
|
rotating_tank |
|
|
solid-body.cs-32x32x1 |
|
|
tidal_basin_2d |
|
|
tutorial_baroclinic_gyre |
|
|
tutorial_barotropic_gyre |
|
|
tutorial_cfc_offline |
|
|
tutorial_deep_convection |
|
|
tutorial_global_oce_biogeo |
|
|
tutorial_global_oce_in_p |
|
|
tutorial_global_oce_latlon |
|
|
tutorial_global_oce_optim |
|
|
tutorial_held_suarez_cs |
|
|
tutorial_offline |
|
|
tutorial_plume_on_slope |
|
|
tutorial_tracer_adjsens |
|
|
vermix |
|
|
|
|
407 |
>>>> From Ed |
>>>> From Ed |
408 |
|
|
409 |
Here are the remaining bits for Chap 4 : |
Here are the remaining bits for Chap 4 : |
517 |
7.5.2 - get bathymetry pre-processing stuff from Patrick |
7.5.2 - get bathymetry pre-processing stuff from Patrick |
518 |
and then describe it |
and then describe it |
519 |
|
|
520 |
|
add something on spgrid mesh generator (maybe)? |
521 |
|
|
522 |
|
|
523 |
andrea |
andrea |
524 |
|
|