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Thu Apr 6 20:13:23 2006 UTC (13 years, 1 month 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 >>>> from JM
211
212
213 manual, section.2 :
214
215 In general:
216 - add more refences/links to S/R & variable name
217 - would be nice to have an active link to the fortran-file
218 for all the S/R & eq.Number in the "calling-tree" boxes
219 - search for CALC_MOM_RHS and replace it by the appropriate S/R
220 (mom_flux_form, mom_vecinv, dynamics)
221 - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
222 was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
223 in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
224 simply written \vec{v}.
225 I would suggest to keep the notation as they are (since they are consistent
226 inside each section) but may be to move the "notation.tex" piece
227 at the beginning of section.2 and to mention clearly the changes between
228 the 2 sections.
229
230 in content: Horizontal Dissipation: 2 times in vector-invariant section
231
232 2.1 time-stepping (part2/time_stepping.tex)
233
234 - this is not clear to me:
235
236 >> In all the above configurations it is also possible to substitute the
237 >> Adams-Bashforth with an alternative time-stepping scheme for terms
238 >> evaluated explicitly in time
239
240
241 2.2 rigid-lid:
242
243 - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
244 to stay closer to the code.
245 - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
246
247 2.3 linear free-surface:
248 - add ref(+link) to S/R names:
249 - add ref(+link) to Crank-Nickelson section 2.9.1
250
251 2.4 Adams-Bashforth
252 - add stability diagrams (I have some figures that I can put)
253 - add link for var. forcing_In_AB
254 - add S/R link for S/R ADAMS_BASHFORTH2
255
256 2.5 Implicit time-stepping
257 - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
258 SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
259 - update: also used for vertical advection
260
261 2.6 Synchronous time-stepping:
262 - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
263 MOMENTUM_CORRECTION_STEP.
264
265 2.7 Stagger baroclinic time-stepping
266 - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
267
268 2.8 NH
269 - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
270
271 2.9 Variants on Free-Surface
272 - Delta.t mis-written (eq.2.73)
273 - Eq.Num missing (has been fixed since)
274 - u* is stored in gU (and not in gUnm1)
275 - Phi_nh in NH_VARS.h
276 - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
277 INI_CG2D, INI_CG3D
278
279 2.9.1 Crank-Nickelson
280 - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
281
282 2.9.2 NLFS
283 - eq.Nb are wrong in html
284 - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
285
286 2.10.1 Notation
287 - Area definition is not really used like this
288
289 >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
290
291 Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
292 the model variables) are used (e.g., see section 2.10.5)
293
294 2.10.5 Horizontal grid:
295 - fig.2.8 : should use Aw,As consistently in this figure description,
296 in the figure itself, as it is in the text.
297 - curvilinear:
298 to add: mention the angle of the grid direction relative to
299 Eastward, Northward direction.
300 + mention horizGridFile= in file "data" (PARM04)
301 - add cylindrical polar grid description
302 need to do a better job of relating model variables to this diagram
303
304
305 2.11 Continuity & Horizontal Pressure gradient terms
306 - mention that d.Phi/dr|s =g if using z coordinate
307 - eq. 2.90 not clear regarding \delta_k(P-E)
308 better to add the free surface eq: d.eta/dt = w_s + P-E
309
310 2.12 Hydrostatic balance
311 - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
312 is hard to find
313 - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
314 and in section 1.3.4: remove the 1.3.4.3.2 subsection:
315 Quasi-nonhydrostatic Atmosphere
316
317 2.13.2 Coriolis terms
318 - note: the discretization used when useEnergyConservingCoriolis=T
319 has no hFac and no Area and is still different from the form
320 described here (with Area & hFac);
321
322 2.13.5 Lateral dissipation
323 - add description of how to use cosFactor & cosPower
324 - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
325 o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
326 in code need to explain why cos()3/2 turns out to be
327 scaling (not cos()2)
328
329 2.13.6 Vertical dissipation
330 - mention the implicit vertical viscosity option and ref to section 2.5
331 - add the parameter correspondence: Av <-> viscAr (and might change also
332 the notation to Ar)
333
334 2.14 Vector invariant momentum equations
335 - indicate that the NH pieces (vertical momentum eq) are not yet coded
336 and that the NH code uses the flux form.
337
338 2.14.6 Horizontal dissipation -> Horizontal Divergence
339
340 2.14.7 Horizontal dissipation
341 - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
342 and A_D4,A_z4 <-> viscA4D,viscA4Z
343
344 2.16 & 2.17 & 2.18 :
345 - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
346
347 2.20.2 mercator, non-dimensional Equations:
348 - does not use std notation
349 - would be better as an appendix of section 2.20:
350 (e.g changing the tile to:
351 - talk to Baylor
352 Appendix: non-dimensional Equations on Spherical-Polar grid.)
353
354
355 JM
356
357
358 >>>> From Andrea
359
360 Chapter 3
361 --------
362
363 Almost all of the 'math mode' text is dropped down as subscripts
364
365 divide chapter 3 more clearly into 2 sections?
366 (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and
367 then 3.19 and 3.20 are informational again - rearrange subsections?)
368
369 3.1 - don't need a link to the outside of the document (remove it)
370 - link to htdig is broken
371
372 3.2.1 - link at bottom to source code points to section 3.2.1
373 (ie, to itself) - link should point to cvs code archive
374
375 3.2.2.1 - ('upgrading from an earlier version') belongs under
376 the cvs part, ie, should be 3.2.1.1
377
378 3.3 - remove reference to 'diags' section under MITgcm
379 - remove reference to 'exe' and 'bin' sections also
380 (remove the .cvsignore file under these directories in cvs)
381 - add a 'jobs' section, and a description as examples of run scripts
382 - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions
383 - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'
384 - under 'tools' the adjoint points to section 5 - this is now section 8
385 (but should be a floating reference)
386 - under 'utils' add a reference to exch2 - stuff for different resolutions
387 - the description of the pkg section refers directly to
388 section 3. should be section 6 (actually should be a floating reference)
389
390 3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
391 3.4.1 - links to the following experiments don't exist or are broken:
392 exp2 - should link to section 3.9
393 hs94.cs-32x32x5 - link to section 3.12
394 add 'convection' to the list, link to section 3.13
395 add 'plume on slope` to the list, link to section 3.14
396 add '??' link to section 3.15
397 add 'dic_example on slope` to the list, link to section 3.16
398 add '??' link to section 3.17
399 add 'offline' and link to section 3.18
400 clean up others and make links where they are needed
401 3.4.2 - text suggests to see section 2 for details about what is in the 'code'
402 and 'input' directories - should refer to the examples in this section
403 - add 'build' bullet - this is where the model is compiled and exectuable lives
404
405 3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
406 as the place where they live (add a link?)
407
408 3.6.1 - Add some general 'approach' text - ie, output is controlled either by the
409 'data' file in the input directory or by the data.[pkg name] file for any
410 package running. And there is some default behavior when the 'state' dumps
411 are written.
412 3.6.1.2 - needs to be moved to inside section 3.6.2
413
414 3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18)
415 underneath this one and leave the text for 3.7 in place
416
417 All the 'overview' sections need some reference to the name of the experiment in
418 the verification directory
419
420 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
421 - is this experiment in the list from section 3.4???
422 3.10.3.1 - refers to figures and equations, links are broken
423
424 3.11.3.2 - line 43: link to equation is broken
425 - line 51-53: link to equation is broken
426 - there is some mess of text hanging around the end of this section. remove? reformat?
427
428 3.12.4.1 - line 34 - link to equation is broken
429 - lines 60,61 - 1st (take out the 'r' in the superscript)
430
431 3.13.2 - link to theta-equation is broken
432 3.13.5.4 -- ALL of the bold links to variable names are broken
433 line 34: link to equation is broken
434
435 3.15.1 - reference to 'fourth experiment' should be removed
436
437 3.16.4 - strange formatting, presence of '>' symbols - remove them
438
439 3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
440 3.17.3.1 - nothing filled in under file input/data - needs description
441
442 3.18.2 - point to section 2 for details - need hyperlink
443
444 3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
445 section 3.5 has the 'build' directory in the example
446
447 3.20.1 - link to doc at end of section points to this section
448 3.20.2 - link to doc at end of section points to this section
449
450 offline - duplicate inputs, what is it, tidy up cfc v.
451 other offline. JM thinks these need tidying up.
452 >>>> From Ed
453
454 Here are the remaining bits for Chap 4 :
455
456 - The grammar/flow could still use some work. Boo was an English
457 major and has experience editing/proofing technical papers. I
458 could print out a copy and ask her to read it and suggest
459 improvements.
460
461 - missing references (if you point me towards URLs, I'll add them
462 to the bibliography):
463 \ref{ref hoe and hill, ecmwf}
464 \ref{magicgarden}
465 \ref{IBMLAPI}
466 \ref{Memorychannel}
467 \ref{hoe-hill:99}
468
469 - There are a few empty sub-sections at the end of Chap 4 that
470 should either be commented out or fleshed out.
471
472 and thats about it for Chap 4.
473
474
475 Add more to quick links on front page
476
477 Chapter 6
478
479 the master package diagram does not appear in the document
480
481 pkg/ptracers doesn't seem to have any documentation (see packages list below)
482
483
484 Master list of packages (add this to beginning of chap 6)
485
486 admtlm/ - autodiff (chapter 5)
487 aim/ - retired
488 aim_compon_interf/ - 6.6 (no content yet)
489 aim_ocn_coupler/ - 6.6 (no content yet)
490 aim_v23/ - 6.4.1 (content needs fixing - JM to do)
491 atm_common/ - 6.6 (no content yet)
492 autodiff/ - autodiff (chapter 5)
493 bulk_force/ - 6.3.3
494 cal/ - 6.3.5
495 cd_code/ - chapter 2 (JM check)
496 cfc/ - not sure
497 chronos/ - AM to check
498 compon_communic/ - 6.6 (no content yet)
499 cost/ - not sure, check with PH
500 ctrl/ - not sure, check with PH
501 debug/ - JM may do something in chapter 7 (utilities)
502 diagnostics/ - 7.1
503 dic/ - 6.7.2
504 ebm/ - not sure
505 ecco/ - chapter 8
506 embed_files/ - add something to chapter 7
507 ex3/ - rename to exch3
508 exch2/ - 6.2.2
509 exf/ - 6.3.4
510 fizhi/ - 6.4.3
511 flt/ - in chapter 2 (JM check)
512 gchem/ - 6.7.1
513 generic_advdiff/ - in chapter 2 (JM check)
514 ggl90/ - nothing, (Martin?)
515 gmredi/ - in chapter 2 (JM check). also need
516 Ferrari & Mc tapering
517 grdchk/ - grdchk (chapter 5 - check with PH)
518 gridalt/ - 6.2.4
519 kpp/ - 6.3.2
520 land/ - 6.4.2 (not connected to code - JM to fix)
521 matrix/ - Samar
522 mdsio/ - 7.3.1
523 mnc/ - 7.2.1
524 mom_common/ - in chapter 2 (JM check)
525 mom_fluxform/ - in chapter 2 (JM check)
526 mom_vecinv/ - in chapter 2 (JM check)
527 monitor/ - 7.4
528 my82/ - nothing, (martin?)
529 obcs/ - 6.3 (needs a check)
530 ocn_compon_interf/ - 6.6 (no content yet)
531 offline/ - nothing, tutorials that need work but no package section entry
532 opps/ - nothing, (martin?)
533 pp81/ - nothing, (martin?)
534 profiles/ - GAEL
535 ptracers/ - JM + SD to write something
536 rbcs/ - talk to steph
537 runclock/ - runclock
538 rw/ - not sure
539 sbo/ - text in sbo_descruption.tex but not linked into
540 part6
541 seaice/ - 6.5.2 - no equations, dimitris has promised some
542 shap_filt/ - chapter 2, JM to check
543 shelfice/ - nothing yet (martin?)
544 solver/ - empty
545 sphere/ - chapter 5 or 8 (PH to check)
546 therm_seaice/ - empty
547 thsice/ - 6.5.1 (JM to update?)
548 timeave/ - retiring......
549 zonal_filt/ - chapter 2 (JM to check)
550
551 Possible for chap 7 - Daniels grafix/ stuff
552
553 Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
554
555 Figure 6.8 is missing
556
557 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
558 Figure 6.8 is missing
559
560
561 >>>> From Andrea
562
563 to do list for chap 7:
564
565
566 7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"
567 the links are pointing to the proper place
568
569 7.5.1 - add Graphix to the list of stuff in utils/matlab
570 7.5.2 - empty
571
572
573 andrea
574
575
576 9. Model uses
577 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
578 (check in support for more names)

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