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Thu Apr 6 19:54:06 2006 UTC (17 years, 11 months ago) by cnh
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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 very front page.
18 o too many clicks to get to model manual.
19 make doc link go to mitgcm.org/r2_web_testing/latest
20 and add "HowTo" reference etc... to /latest page
21
22 - mitgcm.org/r2_web_testing/latest
23 o add another short-cut for quick download
24
25 o add another short-cut
26 About
27 Installation
28 Contents
29 Overview
30 Tutorials (broken)
31 Browse Code
32
33 o mitgcm.org (front content) [DONE]
34 Get Code (where does this go to?)
35 get rid of * CVS current bullet
36 make HTML-enabled CVS code browser leap to MITgcm/MITgcm
37
38 o authors
39 John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,
40 Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,
41 Gael - others?
42
43 o words on http://mitgcm.org/r2_web_testing/latest
44 change to
45 "access on-line Auser manual/A and Atable of contents/A
46 and browse the Aoverview section/A"
47
48 o finite-volume doesn't leap to FV figure
49
50 o have another go at pnmcrop et al.
51
52 o Need an empty package as part of distribution. Check out atm_common
53
54 o Latex
55
56 Chapter 1 - CNH
57 o single kernel diagram -
58 add reference to MWR paper
59
60 o non-hydro
61 add reference to 1995 and 1999 papers
62 pdf of 1995 paper
63
64 o FV
65 add references to 1997 papers.
66
67 o Tangent linear/adjoint add reference to
68 Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc...
69
70 o platforms
71 Add reference to SC article and Scientific Programming article
72
73 o List of key papers needs to be updated and reformatted
74
75
76 o Global atmosphere: `Held Suarez',
77 update Adcroft reference
78 fix up ingrid link and frame (ingrid movies seem to be broken?)
79 Held and Suarez reference is not a link.
80
81 o Ocean Gyres
82 fix up frame link
83 make "lopped cell" a link to referenced paper.
84 add references (ask Steph/Mick)
85 online/offline paper
86
87 o Convection and mixing over topography
88 add in Legg references for convection and mixing over topography
89 and external link to CPT-GCE etc...
90
91 o Boundary forced internal waves
92 add in Legg references, obc's reference
93
94 o Parameter sensitivity
95 add in Bugnion references, Boyin references, Steph references
96
97 o State estimation
98 add in references from Patrick/Carl/Ichiro/Detlef etc...
99 update links to point to latest ECCO results
100 ECCO ingrid results have been moved
101 add forward links to "ECCO state estimation" chapter in manual
102
103 o Ocean biogeochemical cycles
104 add in references from Mick/Galen etc...
105 fix ingrid link ( date to date thing does not appear to work)
106 figure url does not have a "target=idontexist" entry
107
108 o Simulations of laboratory experiments
109 reference Wardle and Karsten papers
110 update links to include DDDAS "PIAB" page
111 cylindrical polar coordinates
112
113 o Continuos equations in ''r'' coordinates
114 add references to iso paper
115 no mention of z* and p* - forward reference to z*/p* in 2.
116 add that coupling also manifests through F, Q
117 add tracer transport
118
119 o Kinematic boundary conditions
120
121 o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
122 Non-hydrostatic forms
123 need to tidy up discussion of shallow-atmosphere to be
124 consistent with the code or change code to be consistent
125 with the discussion!
126 make references hyperlinks
127 add stuff too
128 JMC remove QNH atmosphere
129 need to sort out calc_gw for deep atmosphere
130
131 o Finding the pressure field
132 make references hyperlinks
133 add forward references to manual algorithm section
134 change Elliptic to "elliptic"
135
136 o Forcing and dissipation
137 make "physics packages" refer to chapter 6.
138 should we move "external forcing" et. al to a
139 generic_forcing_driver package?
140
141 viscosities
142 update to mention Smag/Leith (Ah and A4 not constant)
143 and to have forward references to numerical section
144 tracers
145 forward references to numerical section, reddy, GM etc...
146 add references to literature
147
148 o 1.3.8 Vector invariant form
149 forward references to numerical section
150
151 o 1.3.9 Adjoint
152 add a little more here + some hyperlink to chapter 5.
153
154 o 1.4 Appendix ATMOSPHERE
155
156 add some introductory words
157
158 o 1.6 Coordinate systems
159 o only has some words on spherical polar. add some brief words
160 to cover all of
161 - cartesian
162 - spherical
163 - cylindrical
164 - general orthogonal curvilinear (vector invariant)
165
166 o Equation of state options
167 add some discussion
168 can't remember what we said we were going to do here
169 PH to do something
170
171
172 Change hydrodynamical to "dynamical"
173
174 Examples
175
176 - extra "in action" cases
177
178 o high res ocean with diurnal atmospheric state forcing
179 - links to ingrid output
180 CNH/Dimitris
181
182 o realistic FIZHI from Andrea
183 - links to ingrid output
184 from AM
185
186 o with seaice on high res cube
187 - links to ingrid output
188 CNH/Dimitris
189
190 o coupled aqua, ridge world etc...
191 - links to ingrid output
192 get stuff from Daniel
193
194 o constrained lab simulation
195 - links to ingrid output for model and lab
196 fields
197 get stuff from Sai/Andrew
198
199 o sensitivity wrt to iron
200
201 o optimization
202 - update to link to latest ECCO sites and GF
203 related material
204
205 o eddy diffusivity transport application
206
207 o Gas giant?
208
209
210 Master list of packages
211
212 admtlm/ - autodiff (chapter 5)
213 aim/ - 6.4.1 (content needs fixing - JM to do)
214 aim_compon_interf/ - 6.6 (no content yet)
215 aim_ocn_coupler/ - 6.6 (no content yet)
216 aim_v23/ - retired
217 atm_common/ - 6.6 (no content yet)
218 autodiff/ - autodiff (chapter 5)
219 bulk_force/ - 6.3.3
220 cal/ - 6.3.5
221 cd_code/ - chapter 2 (JM check)
222 cfc/ - not sure
223 chronos/ - AM to check
224 compon_communic/ - 6.6 (no content yet)
225 cost/ - not sure, check with PH
226 ctrl/ - not sure, check with PH
227 debug/ - JM may do something in chapter 7 (utilities)
228 diagnostics/ - 7.1
229 dic/ - 6.7.2
230 ebm/ - not sure
231 ecco/ - chapter 8
232 embed_files/ - add something to chapter 7
233 ex3/ - rename to exch3
234 exch2/ - 6.2.2
235 exf/ - 6.3.4
236 fizhi/ - 6.4.3
237 flt/ - in chapter 2 (JM check)
238 gchem/ - 6.7.1
239 generic_advdiff/ - in chapter 2 (JM check)
240 ggl90/ - nothing, (Martin?)
241 gmredi/ - in chapter 2 (JM check). also need
242 Ferrari & Mc tapering
243 grdchk/ - grdchk (chapter 5 - check with PH)
244 gridalt/ - 6.2.4
245 kpp/ - 6.3.2
246 land/ - 6.4.2 (not connected to code - JM to fix)
247 matrix/ - Samar
248 mdsio/ - 7.3.1
249 mnc/ - 7.2.1
250 mom_common/ - in chapter 2 (JM check)
251 mom_fluxform/ - in chapter 2 (JM check)
252 mom_vecinv/ - in chapter 2 (JM check)
253 monitor/ - 7.4
254 my82/ - nothing, (martin?)
255 obcs/ - 6.3 (needs a check)
256 ocn_compon_interf/ - 6.6 (no content yet)
257 offline/ - nothing, tutorials that need work but no package section entry
258 opps/ - nothing, (martin?)
259 pp81/ - nothing, (martin?)
260 profiles/ - GAEL
261 ptracers/ - JM + SD to write something
262 rbcs/ - talk to steph
263 runclock/ - runclock
264 rw/ - not sure
265 sbo/ - text in sbo_descruption.tex but not linked into
266 part6
267 seaice/ - 6.5.2 - no equations, dimitris has promised some
268 shap_filt/ - chapter 2, JM to check
269 shelfice/ - nothing yet (martin?)
270 solver/ - empty
271 sphere/ - chapter 5 or 8 (PH to check)
272 therm_seaice/ - empty
273 thsice/ - 6.5.1 (JM to update?)
274 timeave/ - retiring......
275 zonal_filt/ - chapter 2 (JM to check)
276
277 Possible for chap 7 - Daniels grafix/ stuff
278
279 Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
280
281 Figure 6.8 is missing
282
283
284 >>>> From Ed
285
286 Here are the remaining bits for Chap 4 :
287
288 - The grammar/flow could still use some work. Boo was an English
289 major and has experience editing/proofing technical papers. I
290 could print out a copy and ask her to read it and suggest
291 improvements.
292
293 - missing references (if you point me towards URLs, I'll add them
294 to the bibliography):
295 \ref{ref hoe and hill, ecmwf}
296 \ref{magicgarden}
297 \ref{IBMLAPI}
298 \ref{Memorychannel}
299 \ref{hoe-hill:99}
300
301 - There are a few empty sub-sections at the end of Chap 4 that
302 should either be commented out or fleshed out.
303
304 and thats about it for Chap 4.
305
306
307 Add more to quick links on front page
308
309 Chapter 6
310
311 the master package diagram does not appear in the document
312
313 pkg/ptracers doesn't seem to have any documentation (see packages list below)
314
315
316 >>>> From Andrea
317
318 to do list for chap 7:
319
320
321 7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"
322 the links are pointing to the proper place
323
324 7.5.1 - add Graphix to the list of stuff in utils/matlab
325 7.5.2 - empty
326
327
328 andrea
329
330 >>>> From Andrea
331
332 Chapter 3
333 --------
334
335 Almost all of the 'math mode' text is dropped down as subscripts
336
337 divide chapter 3 more clearly into 2 sections?
338 (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and
339 then 3.19 and 3.20 are informational again - rearrange subsections?)
340
341 3.1 - don't need a link to the outside of the document (remove it)
342 - link to htdig is broken
343
344 3.2.1 - link at bottom to source code points to section 3.2.1
345 (ie, to itself) - link should point to cvs code archive
346
347 3.2.2.1 - ('upgrading from an earlier version') belongs under
348 the cvs part, ie, should be 3.2.1.1
349
350 3.3 - remove reference to 'diags' section under MITgcm
351 - remove reference to 'exe' and 'bin' sections also
352 (remove the .cvsignore file under these directories in cvs)
353 - add a 'jobs' section, and a description as examples of run scripts
354 - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions
355 - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'
356 - under 'tools' the adjoint points to section 5 - this is now section 8
357 (but should be a floating reference)
358 - under 'utils' add a reference to exch2 - stuff for different resolutions
359 - the description of the pkg section refers directly to
360 section 3. should be section 6 (actually should be a floating reference)
361
362 3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
363 3.4.1 - links to the following experiments don't exist or are broken:
364 exp2 - should link to section 3.9
365 hs94.cs-32x32x5 - link to section 3.12
366 add 'convection' to the list, link to section 3.13
367 add 'plume on slope` to the list, link to section 3.14
368 add '??' link to section 3.15
369 add 'dic_example on slope` to the list, link to section 3.16
370 add '??' link to section 3.17
371 add 'offline' and link to section 3.18
372 clean up others and make links where they are needed
373 3.4.2 - text suggests to see section 2 for details about what is in the 'code'
374 and 'input' directories - should refer to the examples in this section
375 - add 'build' bullet - this is where the model is compiled and exectuable lives
376
377 3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
378 as the place where they live (add a link?)
379
380 3.6.1 - Add some general 'approach' text - ie, output is controlled either by the
381 'data' file in the input directory or by the data.[pkg name] file for any
382 package running. And there is some default behavior when the 'state' dumps
383 are written.
384 3.6.1.2 - needs to be moved to inside section 3.6.2
385
386 3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18)
387 underneath this one and leave the text for 3.7 in place
388
389 All the 'overview' sections need some reference to the name of the experiment in
390 the verification directory
391
392 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
393 - is this experiment in the list from section 3.4???
394 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
397 - line 51-53: link to equation is broken
398 - there is some mess of text hanging around the end of this section. remove? reformat?
399
400 3.12.4.1 - line 34 - link to equation is broken
401 - lines 60,61 - 1st (take out the 'r' in the superscript)
402
403 3.13.2 - link to theta-equation is broken
404 3.13.5.4 -- ALL of the bold links to variable names are broken
405 line 34: link to equation is broken
406
407 3.15.1 - reference to 'fourth experiment' should be removed
408
409 3.16.4 - strange formatting, presence of '>' symbols - remove them
410
411 3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
412 3.17.3.1 - nothing filled in under file input/data - needs description
413
414 3.18.2 - point to section 2 for details - need hyperlink
415
416 3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
417 section 3.5 has the 'build' directory in the example
418
419 3.20.1 - link to doc at end of section points to this section
420 3.20.2 - link to doc at end of section points to this section
421
422 offline - duplicate inputs, what is it, tidy up cfc v.
423 other offline. JM thinks these need tidying up.
424
425 >>>> from JM
426
427
428
429 manual, section.2 :
430
431 In general:
432 - add more refences/links to S/R & variable name
433 - would be nice to have an active link to the fortran-file
434 for all the S/R & eq.Number in the "calling-tree" boxes
435 - search for CALC_MOM_RHS and replace it by the appropriate S/R
436 (mom_flux_form, mom_vecinv, dynamics)
437 - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
438 was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
439 in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
440 simply written \vec{v}.
441 I would suggest to keep the notation as they are (since they are consistent
442 inside each section) but may be to move the "notation.tex" piece
443 at the beginning of section.2 and to mention clearly the changes between
444 the 2 sections.
445
446 in content: Horizontal Dissipation: 2 times in vector-invariant section
447
448 2.1 time-stepping (part2/time_stepping.tex)
449
450 - this is not clear to me:
451
452 >> In all the above configurations it is also possible to substitute the
453 >> Adams-Bashforth with an alternative time-stepping scheme for terms
454 >> evaluated explicitly in time
455
456
457 2.2 rigid-lid:
458
459 - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
460 to stay closer to the code.
461 - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
462
463 2.3 linear free-surface:
464 - add ref(+link) to S/R names:
465 - add ref(+link) to Crank-Nickelson section 2.9.1
466
467 2.4 Adams-Bashforth
468 - add stability diagrams (I have some figures that I can put)
469 - add link for var. forcing_In_AB
470 - add S/R link for S/R ADAMS_BASHFORTH2
471
472 2.5 Implicit time-stepping
473 - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
474 SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
475 - update: also used for vertical advection
476
477 2.6 Synchronous time-stepping:
478 - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
479 MOMENTUM_CORRECTION_STEP.
480
481 2.7 Stagger baroclinic time-stepping
482 - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
483
484 2.8 NH
485 - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
486
487 2.9 Variants on Free-Surface
488 - Delta.t mis-written (eq.2.73)
489 - Eq.Num missing (has been fixed since)
490 - u* is stored in gU (and not in gUnm1)
491 - Phi_nh in NH_VARS.h
492 - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
493 INI_CG2D, INI_CG3D
494
495 2.9.1 Crank-Nickelson
496 - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
497
498 2.9.2 NLFS
499 - eq.Nb are wrong in html
500 - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
501
502 2.10.1 Notation
503 - Area definition is not really used like this
504
505 >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
506
507 Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
508 the model variables) are used (e.g., see section 2.10.5)
509
510 2.10.5 Horizontal grid:
511 - fig.2.8 : should use Aw,As consistently in this figure description,
512 in the figure itself, as it is in the text.
513 - curvilinear:
514 to add: mention the angle of the grid direction relative to
515 Eastward, Northward direction.
516 + mention horizGridFile= in file "data" (PARM04)
517 - add cylindrical grid description
518 need to do a better job of relating model variables to this diagram
519
520
521 2.11 Continuity & Horizontal Pressure gradient terms
522 - mention that d.Phi/dr|s =g if using z coordinate
523 - eq. 2.90 not clear regarding \delta_k(P-E)
524 better to add the free surface eq: d.eta/dt = w_s + P-E
525
526 2.12 Hydrostatic balance
527 - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
528 is hard to find
529 - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
530 and in section 1.3.4: remove the 1.3.4.3.2 subsection:
531 Quasi-nonhydrostatic Atmosphere
532
533 2.13.2 Coriolis terms
534 - note: the discretization used when useEnergyConservingCoriolis=T
535 has no hFac and no Area and is still different from the form
536 described here (with Area & hFac);
537
538 2.13.5 Lateral dissipation
539 - add description of how to use cosFactor & cosPower
540 - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
541 o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
542 in code need to explain why cos()3/2 turns out to be
543 scaling (not cos()2)
544
545 2.13.6 Vertical dissipation
546 - mention the implicit vertical viscosity option and ref to section 2.5
547 - add the parameter correspondence: Av <-> viscAr (and might change also
548 the notation to Ar)
549
550 2.14 Vector invariant momentum equations
551 - indicate that the NH pieces (vertical momentum eq) are not yet coded
552 and that the NH code uses the flux form.
553
554 2.14.6 Horizontal dissipation -> Horizontal Divergence
555
556 2.14.7 Horizontal dissipation
557 - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
558 and A_D4,A_z4 <-> viscA4D,viscA4Z
559
560 2.16 & 2.17 & 2.18 :
561 - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
562
563 2.20.2 mercator, non-dimensional Equations:
564 - does not use std notation
565 - would be better as an appendix of section 2.20:
566 (e.g changing the tile to:
567 Appendix: non-dimensional Equations on Spherical-Polar grid.)
568
569 JM
570
571
572 9. Model uses
573 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
574 (check in support for more names)

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