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1 Rebuild and set to do cron build - DONE on hugo
2
3 To do
4
5 - where to put under development links?
6 JMC would like to have some mention of unfinished things (checked in
7 but not that tested e.g. AB3)
8 Add an "Under development, chapter" - shortish description of what
9 is available (last chapter)
10
11
12 o HTML, scripts and front content
13
14 - pick a URL
15 TBD
16
17 - mitgcm.org/r2_web_testing/latest
18 o add another short-cut for quick download
19
20 o add another short-cut
21 About
22 Installation
23 Contents
24 Overview
25 Tutorials (broken)
26 Browse Code
27
28 o mitgcm.org (front content) [DONE]
29 Get Code (where does this go to?)
30 get rid of * CVS current bullet
31 make HTML-enabled CVS code browser leap to MITgcm/MITgcm
32
33 o authors
34 John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,
35 Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,
36 Gael - others?
37
38 o words on http://mitgcm.org/r2_web_testing/latest
39 change to
40 "access on-line Auser manual/A and Atable of contents/A
41 and browse the Aoverview section/A"
42
43 o finite-volume doesn't leap to FV figure
44
45 o have another go at pnmcrop et al.
46
47 o Need an empty package as part of distribution. Check out atm_common
48
49 o Latex
50
51 Chapter 1 - CNH
52 o single kernel diagram -
53 add reference to MWR paper
54
55 o non-hydro
56 add reference to 1995 and 1999 papers
57 pdf of 1995 paper
58
59 o FV
60 add references to 1997 papers.
61
62 o Tangent linear/adjoint add reference to
63 Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc...
64
65 o platforms
66 Add reference to SC article and Scientific Programming article
67
68 o List of key papers needs to be updated and reformatted
69
70
71 o Global atmosphere: `Held Suarez',
72 update Adcroft reference
73 fix up ingrid link and frame (ingrid movies seem to be broken?)
74 Held and Suarez reference is not a link.
75
76 o Ocean Gyres
77 fix up frame link
78 make "lopped cell" a link to referenced paper.
79 add references (ask Steph/Mick)
80 online/offline paper
81
82 o Convection and mixing over topography
83 add in Legg references for convection and mixing over topography
84 and external link to CPT-GCE etc...
85
86 o Boundary forced internal waves
87 add in Legg references, obc's reference
88
89 o Parameter sensitivity
90 add in Bugnion references, Boyin references, Steph references
91
92 o State estimation
93 add in references from Patrick/Carl/Ichiro/Detlef etc...
94 update links to point to latest ECCO results
95 ECCO ingrid results have been moved
96 add forward links to "ECCO state estimation" chapter in manual
97
98 o Ocean biogeochemical cycles
99 add in references from Mick/Galen etc...
100 fix ingrid link ( date to date thing does not appear to work)
101 figure url does not have a "target=idontexist" entry
102
103 o Simulations of laboratory experiments
104 reference Wardle and Karsten papers
105 update links to include DDDAS "PIAB" page
106 cylindrical polar coordinates
107
108 o Continuos equations in ''r'' coordinates
109 add references to iso paper
110 no mention of z* and p* - forward reference to z*/p* in 2.
111 add that coupling also manifests through F, Q
112 add tracer transport
113
114 o Kinematic boundary conditions
115
116 o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
117 Non-hydrostatic forms
118 need to tidy up discussion of shallow-atmosphere to be
119 consistent with the code or change code to be consistent
120 with the discussion!
121 make references hyperlinks
122 add stuff too
123 JMC remove QNH atmosphere
124 need to sort out calc_gw for deep atmosphere
125
126 o Finding the pressure field
127 make references hyperlinks
128 add forward references to manual algorithm section
129 change Elliptic to "elliptic"
130
131 o Forcing and dissipation
132 make "physics packages" refer to chapter 6.
133 should we move "external forcing" et. al to a
134 generic_forcing_driver package?
135
136 viscosities
137 update to mention Smag/Leith (Ah and A4 not constant)
138 and to have forward references to numerical section
139 tracers
140 forward references to numerical section, reddy, GM etc...
141 add references to literature
142
143 o 1.3.8 Vector invariant form
144 forward references to numerical section
145
146 o 1.3.9 Adjoint
147 add a little more here + some hyperlink to chapter 5.
148
149 o 1.4 Appendix ATMOSPHERE
150
151 add some introductory words
152
153 o 1.6 Coordinate systems
154 o only has some words on spherical polar. add some brief words
155 to cover all of
156 - cartesian
157 - spherical
158 - cylindrical
159 - general orthogonal curvilinear (vector invariant)
160
161 o Equation of state options
162 add some discussion
163 can't remember what we said we were going to do here
164 PH to do something
165
166
167 Change hydrodynamical to "dynamical"
168
169 Examples
170
171 - extra "in action" cases
172
173 o high res ocean with diurnal atmospheric state forcing
174 - links to ingrid output
175 CNH/Dimitris
176
177 o realistic FIZHI from Andrea
178 - links to ingrid output
179 from AM
180
181 o with seaice on high res cube
182 - links to ingrid output
183 CNH/Dimitris
184
185 o coupled aqua, ridge world etc...
186 - links to ingrid output
187 get stuff from Daniel
188
189 o constrained lab simulation
190 - links to ingrid output for model and lab
191 fields
192 get stuff from Sai/Andrew
193
194 o sensitivity wrt to iron
195
196 o optimization
197 - update to link to latest ECCO sites and GF
198 related material
199
200 o eddy diffusivity transport application
201
202 o Gas giant?
203
204
205 >>>> from JM
206
207
208 manual, section.2 :
209
210 In general:
211 - add more refences/links to S/R & variable name
212 - would be nice to have an active link to the fortran-file
213 for all the S/R & eq.Number in the "calling-tree" boxes
214 - search for CALC_MOM_RHS and replace it by the appropriate S/R
215 (mom_flux_form, mom_vecinv, dynamics)
216 - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
217 was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
218 in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
219 simply written \vec{v}.
220 I would suggest to keep the notation as they are (since they are consistent
221 inside each section) but may be to move the "notation.tex" piece
222 at the beginning of section.2 and to mention clearly the changes between
223 the 2 sections.
224
225 in content: Horizontal Dissipation: 2 times in vector-invariant section
226
227 2.1 time-stepping (part2/time_stepping.tex)
228
229 - this is not clear to me:
230
231 >> In all the above configurations it is also possible to substitute the
232 >> Adams-Bashforth with an alternative time-stepping scheme for terms
233 >> evaluated explicitly in time
234
235
236 2.2 rigid-lid:
237
238 - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
239 to stay closer to the code.
240 - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
241
242 2.3 linear free-surface:
243 - add ref(+link) to S/R names:
244 - add ref(+link) to Crank-Nickelson section 2.9.1
245
246 2.4 Adams-Bashforth
247 - add stability diagrams (I have some figures that I can put)
248 - add link for var. forcing_In_AB
249 - add S/R link for S/R ADAMS_BASHFORTH2
250
251 2.5 Implicit time-stepping
252 - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
253 SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
254 - update: also used for vertical advection
255
256 2.6 Synchronous time-stepping:
257 - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
258 MOMENTUM_CORRECTION_STEP.
259
260 2.7 Stagger baroclinic time-stepping
261 - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
262
263 2.8 NH
264 - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
265
266 2.9 Variants on Free-Surface
267 - Delta.t mis-written (eq.2.73)
268 - Eq.Num missing (has been fixed since)
269 - u* is stored in gU (and not in gUnm1)
270 - Phi_nh in NH_VARS.h
271 - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
272 INI_CG2D, INI_CG3D
273
274 2.9.1 Crank-Nickelson
275 - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
276
277 2.9.2 NLFS
278 - eq.Nb are wrong in html
279 - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
280
281 2.10.1 Notation
282 - Area definition is not really used like this
283
284 >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
285
286 Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
287 the model variables) are used (e.g., see section 2.10.5)
288
289 2.10.5 Horizontal grid:
290 - fig.2.8 : should use Aw,As consistently in this figure description,
291 in the figure itself, as it is in the text.
292 - curvilinear:
293 to add: mention the angle of the grid direction relative to
294 Eastward, Northward direction.
295 + mention horizGridFile= in file "data" (PARM04)
296 - add cylindrical polar grid description
297 need to do a better job of relating model variables to this diagram
298
299
300 2.11 Continuity & Horizontal Pressure gradient terms
301 - mention that d.Phi/dr|s =g if using z coordinate
302 - eq. 2.90 not clear regarding \delta_k(P-E)
303 better to add the free surface eq: d.eta/dt = w_s + P-E
304
305 2.12 Hydrostatic balance
306 - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
307 is hard to find
308 - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
309 and in section 1.3.4: remove the 1.3.4.3.2 subsection:
310 Quasi-nonhydrostatic Atmosphere
311
312 2.13.2 Coriolis terms
313 - note: the discretization used when useEnergyConservingCoriolis=T
314 has no hFac and no Area and is still different from the form
315 described here (with Area & hFac);
316
317 2.13.5 Lateral dissipation
318 - add description of how to use cosFactor & cosPower
319 - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
320 o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
321 in code need to explain why cos()3/2 turns out to be
322 scaling (not cos()2)
323 - need to reference the smag/leith section.
324
325 2.13.6 Vertical dissipation
326 - mention the implicit vertical viscosity option and ref to section 2.5
327 - add the parameter correspondence: Av <-> viscAr (and might change also
328 the notation to Ar)
329
330 2.14 Vector invariant momentum equations
331 - indicate that the NH pieces (vertical momentum eq) are not yet coded
332 and that the NH code uses the flux form.
333
334 2.14.6 Horizontal dissipation -> Horizontal Divergence
335
336 2.14.7 Horizontal dissipation
337 - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
338 and A_D4,A_z4 <-> viscA4D,viscA4Z
339
340 2.16 & 2.17 & 2.18 :
341 - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
342
343 2.20.2 mercator, non-dimensional Equations:
344 - does not use std notation
345 - would be better as an appendix of section 2.20:
346 (e.g changing the tile to:
347 - talk to Baylor
348 Appendix: non-dimensional Equations on Spherical-Polar grid.)
349
350
351 JM
352
353
354 >>>> From Andrea
355
356 Chapter 3
357 --------
358
359 Almost all of the 'math mode' text is dropped down as subscripts
360
361 divide chapter 3 more clearly into 2 sections?
362 (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and
363 then 3.19 and 3.20 are informational again - rearrange subsections?)
364 [DONE]
365
366 3.1 - don't need a link to the outside of the document (remove it)
367 - link to htdig is broken
368
369 3.2.1 - link at bottom to source code points to section 3.2.1
370 (ie, to itself) - link should point to cvs code archive
371
372 3.2.2.1 - ('upgrading from an earlier version') belongs under
373 the cvs part, ie, should be 3.2.1.1
374
375 3.3 - remove reference to 'diags' section under MITgcm
376 - remove reference to 'exe' and 'bin' sections also
377 (remove the .cvsignore file under these directories in cvs)
378 - add a 'jobs' section, and a description as examples of run scripts
379 - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions
380 - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'
381 - under 'tools' the adjoint points to section 5 - this is now section 8
382 (but should be a floating reference)
383 - under 'utils' add a reference to exch2 - stuff for different resolutions
384 - the description of the pkg section refers directly to
385 section 3. should be section 6 (actually should be a floating reference)
386
387 3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
388 3.4.1 - links to the following experiments don't exist or are broken:
389 exp2 - should link to section 3.9
390 hs94.cs-32x32x5 - link to section 3.12
391 add 'convection' to the list, link to section 3.13
392 add 'plume on slope` to the list, link to section 3.14
393 add '??' link to section 3.15
394 add 'dic_example on slope` to the list, link to section 3.16
395 add '??' link to section 3.17
396 add 'offline' and link to section 3.18
397 clean up others and make links where they are needed
398 3.4.2 - text suggests to see section 2 for details about what is in the 'code'
399 and 'input' directories - should refer to the examples in this section
400 - add 'build' bullet - this is where the model is compiled and exectuable lives
401
402 3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
403 as the place where they live (add a link?)
404
405 3.6.1 - Add some general 'approach' text - ie, output is controlled either by the
406 'data' file in the input directory or by the data.[pkg name] file for any
407 package running. And there is some default behavior when the 'state' dumps
408 are written.
409 3.6.1.2 - needs to be moved to inside section 3.6.2
410
411 3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18)
412 underneath this one and leave the text for 3.7 in place
413
414 All the 'overview' sections need some reference to the name of the experiment in
415 the verification directory
416
417 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
418 - is this experiment in the list from section 3.4???
419 3.10.3.1 - refers to figures and equations, links are broken
420
421 3.11.3.2 - line 43: link to equation is broken
422 - line 51-53: link to equation is broken
423 - there is some mess of text hanging around the end of this section. remove? reformat?
424
425 3.12.4.1 - line 34 - link to equation is broken
426 - lines 60,61 - 1st (take out the 'r' in the superscript)
427
428 3.13.2 - link to theta-equation is broken
429 3.13.5.4 -- ALL of the bold links to variable names are broken
430 line 34: link to equation is broken
431
432 3.15.1 - reference to 'fourth experiment' should be removed
433
434 3.16.4 - strange formatting, presence of '>' symbols - remove them
435
436 3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
437 3.17.3.1 - nothing filled in under file input/data - needs description
438
439 3.18.2 - point to section 2 for details - need hyperlink
440
441 3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
442 section 3.5 has the 'build' directory in the example
443
444 3.20.1 - link to doc at end of section points to this section
445 3.20.2 - link to doc at end of section points to this section
446
447 offline - duplicate inputs, what is it, tidy up cfc v.
448 other offline. JM thinks these need tidying up.
449 >>>> From Ed
450
451 Here are the remaining bits for Chap 4 :
452
453 - The grammar/flow could still use some work. Boo was an English
454 major and has experience editing/proofing technical papers. I
455 could print out a copy and ask her to read it and suggest
456 improvements.
457
458 - missing references (if you point me towards URLs, I'll add them
459 to the bibliography):
460 \ref{ref hoe and hill, ecmwf}
461 \ref{magicgarden}
462 \ref{IBMLAPI}
463 \ref{Memorychannel}
464 \ref{hoe-hill:99}
465
466 - There are a few empty sub-sections at the end of Chap 4 that
467 should either be commented out or fleshed out.
468
469 and thats about it for Chap 4.
470
471
472 Add more to quick links on front page
473
474 Chapter 6
475
476 the master package diagram does not appear in the document
477
478 pkg/ptracers doesn't seem to have any documentation (see packages list below)
479
480
481 Master list of packages (add this to beginning of chap 6)
482
483 admtlm/ - autodiff (chapter 5)
484 aim/ - retired
485 aim_compon_interf/ - 6.6 (no content yet)
486 aim_ocn_coupler/ - 6.6 (no content yet)
487 aim_v23/ - 6.4.1 (content needs fixing - JM to do)
488 atm_common/ - 6.6 (no content yet)
489 autodiff/ - autodiff (chapter 5)
490 bulk_force/ - 6.3.3
491 cal/ - 6.3.5
492 cd_code/ - chapter 2 (JM check)
493 cfc/ - not sure
494 chronos/ - AM to check
495 compon_communic/ - 6.6 (no content yet)
496 cost/ - not sure, check with PH
497 ctrl/ - not sure, check with PH
498 debug/ - JM may do something in chapter 7 (utilities)
499 diagnostics/ - 7.1
500 dic/ - 6.7.2
501 ebm/ - not sure
502 ecco/ - chapter 8
503 embed_files/ - add something to chapter 7
504 ex3/ - rename to exch3
505 exch2/ - 6.2.2
506 exf/ - 6.3.4
507 fizhi/ - 6.4.3
508 flt/ - in chapter 2 (JM check)
509 gchem/ - 6.7.1
510 generic_advdiff/ - in chapter 2 (JM check)
511 ggl90/ - nothing, (Martin?)
512 gmredi/ - in chapter 2 (JM check). also need
513 Ferrari & Mc tapering
514 grdchk/ - grdchk (chapter 5 - check with PH)
515 gridalt/ - 6.2.4
516 kpp/ - 6.3.2
517 land/ - 6.4.2 (not connected to code - JM to fix)
518 matrix/ - Samar
519 mdsio/ - 7.3.1
520 mnc/ - 7.2.1
521 mom_common/ - in chapter 2 (JM check)
522 mom_fluxform/ - in chapter 2 (JM check)
523 mom_vecinv/ - in chapter 2 (JM check)
524 monitor/ - 7.4
525 my82/ - nothing, (martin?)
526 obcs/ - 6.3 (needs a check)
527 ocn_compon_interf/ - 6.6 (no content yet)
528 offline/ - nothing, tutorials that need work but no package section entry
529 opps/ - nothing, (martin?)
530 pp81/ - nothing, (martin?)
531 profiles/ - GAEL
532 ptracers/ - JM + SD to write something
533 rbcs/ - talk to steph
534 runclock/ - runclock
535 rw/ - not sure
536 sbo/ - text in sbo_descruption.tex but not linked into
537 part6
538 seaice/ - 6.5.2 - no equations, dimitris has promised some
539 shap_filt/ - chapter 2, JM to check
540 shelfice/ - nothing yet (martin?)
541 solver/ - empty
542 sphere/ - chapter 5 or 8 (PH to check)
543 therm_seaice/ - empty
544 thsice/ - 6.5.1 (JM to update?)
545 timeave/ - retiring......
546 zonal_filt/ - chapter 2 (JM to check)
547
548 Possible for chap 7 - Daniels grafix/ stuff
549
550 Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
551
552 Figure 6.8 is missing
553
554 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
555 Figure 6.8 is missing
556
557
558 >>>> From Andrea
559
560 to do list for chap 7:
561
562
563 7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"
564 the links are pointing to the proper place
565
566 7.5.1 - add Graphix to the list of stuff in utils/matlab
567 7.5.2 - empty
568
569
570 andrea
571
572
573 9. Model uses
574 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
575 (check in support for more names)

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