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Revision 1.1 - (show annotations) (download)
Wed Apr 5 14:30:29 2006 UTC (17 years, 11 months ago) by cnh
Branch: MAIN
File MIME type: text/plain
Adding todo list for the manual

1 Rebuild and set to do cron build
2
3 To do
4
5 - where to put under development links?
6
7 - mitgcm.org very front page.
8 o too many clicks to get to model manual.
9 make doc link go to mitgcm.org/r2_web_testing/latest
10 and add "HowTo" reference etc... to /latest page
11
12 - mitgcm.org/r2_web_testing/latest
13 o add another short-cut for quick download
14
15 o add another short-cut
16 About
17 Installation
18 Contents
19 Overview
20 Tutorials (broken)
21 Browse Code
22 Get Code (where does this go to?)
23
24 o authors
25 John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,
26 Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,
27 Gael - others?
28
29 o Tutorials side bar link is broken
30
31 o words
32 change to "access on-line Auser manual/A and Atable of contents/A
33 and browse the Aoverview section/A"
34
35 o finite-volume doesn't leap to FV figure
36
37 o date is 2002
38
39 o fix search so it doesn't include advertisements
40
41 o the src and equation links don't come through to
42 the html when they are in figures - see chapter 2 for some
43 examples.
44
45 o degree symbols keep getting "dropped down" - problem with
46 pnmcrop et al.
47
48
49 Contents
50
51 Intro - 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 Non-hydrostatic forms
117 need to tidy up discussion of shallow-atmosphere to be
118 consistent with the code or change code to be consistent
119 with the discussion!
120 make references hyperlinks
121 add stuff too
122
123 o Finding the pressure field
124 make references hyperlinks
125 add forward references to manual algorithm section
126 change Elliptic to "elliptic"
127
128 o Forcing and dissipation
129 make "physics packages" refer to chapter 6.
130 should we move "external forcing" et. al to a
131 generic_forcing_driver package?
132
133 viscosities
134 update to mention Smag/Leith (Ah and A4 not constant)
135 and to have forward references to numerical section
136 tracers
137 forward references to numerical section, reddy, GM etc...
138 add references to literature
139
140 o 1.3.8 Vector invariant form
141 forward references to numerical section
142
143 o 1.3.9 Adjoint
144 add a little more here + some hyperlink to chapter 5.
145
146 o 1.4 Appendix ATMOSPHERE
147
148 add some introductory words
149
150 o 1.6 Coordinate systems
151 o only has some words on spherical polar. add some brief words
152 to cover all of
153 - cartesian
154 - spherical
155 - cylindrical
156 - general orthogonal curvilinear (vector invariant)
157
158 o Equation of state options
159 add some discussion
160 can't remember what we said we were going to do here
161 PH to do something
162
163
164 Discretization and alg - JMC+CNH
165
166 Tutorials - AM
167 3.1 "Where to find"
168 o link to Pelican not needed
169 o mailman twice (why?)
170 o no htdig (gone? - I liked it)
171
172 intro part
173 individual experiments
174
175 offline - duplicate inputs, what is it, tidy up cfc v.
176 other offline.
177
178 Software - EH to review
179
180 some to be done on resource estimates at the end - needs sorting.
181
182 Automatic Diff - CE
183
184 Physical Packages - ???
185
186 Diags and tools - ???
187
188 Interface with ECCO - ???
189
190 Model uses - ???
191
192 Building document - ???
193 via cron
194 tweaking latex2html etc..
195
196 Src Code tree (rename
197 examples etc..) - ???
198
199 Documentation
200
201 1. Introduction
202
203 2. Discretization and Algorithm
204
205 2.13.5 Lateral dissipation
206 o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
207 in code need to explain why cos()3/2 turns out to be
208 scaling (not cos()2)
209
210 2.13.6 Vertical dissipation
211 o update to have reference to Baylors section
212 reference to implicit discussion in time-stepping part of manual
213
214
215
216 3. Tutorials
217 reorg'd into
218 intro part
219 individual experiments
220
221 4. Software Architecture
222
223 5. Automatic Differentiation
224
225 6. Physical Parameterization and Packages
226
227 7. Diagnostics and tools
228
229 8. Interface with ECCO
230
231 9. Model uses
232 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
233 (check in support for more names)
234
235 Need an empty package as part of distribution
236
237 latex2html equation formatting is still a bit weird in places. Need to have another go if we have a chance - especially the degree symbol seems to jump around somewhat!
238
239 Chapter 1
240
241 Change hydrodynamical to "dynamical"
242
243 Examples
244
245 - extra "in action" cases
246
247 o high res ocean with diurnal atmospheric state forcing
248 - links to ingrid output
249 CNH/Dimitris
250
251 o realistic FIZHI from Andrea
252 - links to ingrid output
253 from AM
254
255 o with seaice on high res cube
256 - links to ingrid output
257 CNH/Dimitris
258
259 o coupled aqua, ridge world etc...
260 - links to ingrid output
261 get stuff from Daniel
262
263 o constrained lab simulation
264 - links to ingrid output for model and lab
265 fields
266 get stuff from Sai/Andrew
267
268 o sensitivity wrt to iron
269
270 o optimization
271 - update to link to latest ECCO sites and GF
272 related material
273
274 o eddy diffusivity transport application
275
276 o Gas giant?
277
278 Chapter 6
279
280 the master package diagram does not appear in the document
281
282 pkg/ptracers doesn't seem to have any documentation (see packages list below)
283
284
285
286 2.10.5 Horizontal grid
287
288 need to do a better job of relating model variables to this diagram
289
290
291 Master list of packages
292
293 admtlm/ - autodiff (chapter 5)
294 aim/ - 6.4.1 (content needs fixing - JM to do)
295 aim_compon_interf/ - 6.6 (no content yet)
296 aim_ocn_coupler/ - 6.6 (no content yet)
297 aim_v23/ - retired
298 atm_common/ - 6.6 (no content yet)
299 autodiff/ - autodiff (chapter 5)
300 bulk_force/ - 6.3.3
301 cal/ - 6.3.5
302 cd_code/ - chapter 2 (JM check)
303 cfc/ - not sure
304 chronos/ - AM to check
305 compon_communic/ - 6.6 (no content yet)
306 cost/ - not sure, check with PH
307 ctrl/ - not sure, check with PH
308 debug/ - JM may do something in chapter 7 (utilities)
309 diagnostics/ - 7.1
310 dic/ - 6.7.2
311 ebm/ - not sure
312 ecco/ - chapter 8
313 embed_files/ - add something to chapter 7
314 ex3/ - rename to exch3
315 exch2/ - 6.2.2
316 exf/ - 6.3.4
317 fizhi/ - 6.4.3
318 flt/ - in chapter 2 (JM check)
319 gchem/ - 6.7.1
320 generic_advdiff/ - in chapter 2 (JM check)
321 ggl90/ - nothing, (Martin?)
322 gmredi/ - in chapter 2 (JM check). also need
323 Ferrari & Mc tapering
324 grdchk/ - grdchk (chapter 5 - check with PH)
325 gridalt/ - 6.2.4
326 kpp/ - 6.3.2
327 land/ - 6.4.2 (not connected to code - JM to fix)
328 matrix/ - Samar
329 mdsio/ - 7.3.1
330 mnc/ - 7.2.1
331 mom_common/ - in chapter 2 (JM check)
332 mom_fluxform/ - in chapter 2 (JM check)
333 mom_vecinv/ - in chapter 2 (JM check)
334 monitor/ - 7.4
335 my82/ - nothing, (martin?)
336 obcs/ - 6.3 (needs a check)
337 ocn_compon_interf/ - 6.6 (no content yet)
338 offline/ - nothing, tutorials that need work but no package section entry
339 opps/ - nothing, (martin?)
340 pp81/ - nothing, (martin?)
341 profiles/ - GAEL
342 ptracers/ - JM + SD to write something
343 rbcs/ - talk to steph
344 runclock/ - runclock
345 rw/ - not sure
346 sbo/ - text in sbo_descruption.tex but not linked into
347 part6
348 seaice/ - 6.5.2 - no equations, dimitris has promised some
349 shap_filt/ - chapter 2, JM to check
350 shelfice/ - nothing yet (martin?)
351 solver/ - empty
352 sphere/ - chapter 5 or 8 (PH to check)
353 therm_seaice/ - empty
354 thsice/ - 6.5.1 (JM to update?)
355 timeave/ - retiring......
356 zonal_filt/ - chapter 2 (JM to check)
357
358 Possible for chap 7 - Daniels grafix/ stuff
359
360 Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
361
362 Figure 6.8 is missing
363
364
365 >>>> From Ed
366
367 Here are the remaining bits for Chap 4 :
368
369 - The grammar/flow could still use some work. Boo was an English
370 major and has experience editing/proofing technical papers. I
371 could print out a copy and ask her to read it and suggest
372 improvements.
373
374 - missing references (if you point me towards URLs, I'll add them
375 to the bibliography):
376 \ref{ref hoe and hill, ecmwf}
377 \ref{magicgarden}
378 \ref{IBMLAPI}
379 \ref{Memorychannel}
380 \ref{hoe-hill:99}
381
382 - There are a few empty sub-sections at the end of Chap 4 that
383 should either be commented out or fleshed out.
384
385 and thats about it for Chap 4.
386
387
388 Add more to quick links on front page
389
390
391 >>>> From Andrea
392
393 to do list for chap 7:
394
395
396 7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernal Diagnostics Menu"
397 the links are pointing to the proper place
398
399 7.1.4.0.1 - the link at the bottom to the fizhi diagnostic menu is broken
400 - there should be links here to the diagnostic menus from other packages
401
402 7.5.1 - add Graphix to the list of stuff in utils/matlab
403 7.5.2 - empty
404
405
406 andrea
407
408 >>>> From Andrea
409
410 Chapter 3
411 --------
412
413 Almost all of the 'math mode' text is dropped down as subscripts
414
415 divide chapter 3 more clearly into 2 sections?
416 (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and
417 then 3.19 and 3.20 are informational again - rearrange subsections?)
418
419 3.1 - don't need a link to the outside of the document (remove it)
420 - link to htdig is broken
421
422 3.2.1 - link at bottom to source code points to section 3.2.1
423 (ie, to itself) - link should point to cvs code archive
424
425 3.2.2.1 - ('upgrading from an earlier version') belongs under
426 the cvs part, ie, should be 3.2.1.1
427
428 3.3 - remove reference to 'diags' section under MITgcm
429 - remove reference to 'exe' and 'bin' sections also
430 (remove the .cvsignore file under these directories in cvs)
431 - add a 'jobs' section, and a description as examples of run scripts
432 - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions
433 - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'
434 - under 'tools' the adjoint points to section 5 - this is now section 8
435 (but should be a floating reference)
436 - under 'utils' add a reference to exch2 - stuff for different resolutions
437 - the description of the pkg section refers directly to
438 section 3. should be section 6 (actually should be a floating reference)
439
440 3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
441 3.4.1 - links to the following experiments don't exist or are broken:
442 exp2 - should link to section 3.9
443 hs94.cs-32x32x5 - link to section 3.12
444 add 'convection' to the list, link to section 3.13
445 add 'plume on slope` to the list, link to section 3.14
446 add '??' link to section 3.15
447 add 'dic_example on slope` to the list, link to section 3.16
448 add '??' link to section 3.17
449 add 'offline' and link to section 3.18
450 clean up others and make links where they are needed
451 3.4.2 - text suggests to see section 2 for details about what is in the 'code'
452 and 'input' directories - should refer to the examples in this section
453 - add 'build' bullet - this is where the model is compiled and exectuable lives
454
455 3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
456 as the place where they live (add a link?)
457
458 3.6.1 - Add some general 'approach' text - ie, output is controlled either by the
459 'data' file in the input directory or by the data.[pkg name] file for any
460 package running. And there is some default behavior when the 'state' dumps
461 are written.
462 3.6.1.2 - needs to be moved to inside section 3.6.2
463
464 3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18)
465 underneath this one and leave the text for 3.7 in place
466
467 All the 'overview' sections need some reference to the name of the experiment in
468 the verification directory
469
470 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
471 - is this experiment in the list from section 3.4???
472 3.10.3.1 - refers to figures and equations, links are broken
473
474 3.11.3.2 - line 43: link to equation is broken
475 - line 51-53: link to equation is broken
476 - there is some mess of text hanging around the end of this section. remove? reformat?
477
478 3.12.4.1 - line 34 - link to equation is broken
479 - lines 60,61 - 1st (take out the 'r' in the superscript)
480
481 3.13.2 - link to theta-equation is broken
482 3.13.5.4 -- ALL of the bold links to variable names are broken
483 line 34: link to equation is broken
484
485 3.15.1 - reference to 'fourth experiment' should be removed
486
487 3.16.4 - strange formatting, presence of '>' symbols - remove them
488
489 3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
490 3.17.3.1 - nothing filled in under file input/data - needs description
491
492 3.18.2 - point to section 2 for details - need hyperlink
493
494 3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
495 section 3.5 has the 'build' directory in the example
496
497 3.20.1 - link to doc at end of section points to this section
498 3.20.2 - link to doc at end of section points to this section
499
500 >>>> from JM
501
502
503
504 manual, section.2 :
505
506 In general:
507 - add more refences/links to S/R & variable name
508 - would be nice to have an active link to the fortran-file
509 for all the S/R & eq.Number in the "calling-tree" boxes
510 - search for CALC_MOM_RHS and replace it by the appropriate S/R
511 (mom_flux_form, mom_vecinv, dynamics)
512 - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
513 was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
514 in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
515 simply written \vec{v}.
516 I would suggest to keep the notation as they are (since they are consistent
517 inside each section) but may be to move the "notation.tex" piece
518 at the beginning of section.2 and to mention clearly the changes between
519 the 2 sections.
520
521 in content: Horizontal Dissipation: 2 times in vector-invariant section
522
523 2.1 time-stepping (part2/time_stepping.tex)
524
525 - this is not clear to me:
526
527 >> In all the above configurations it is also possible to substitute the
528 >> Adams-Bashforth with an alternative time-stepping scheme for terms
529 >> evaluated explicitly in time
530
531
532 2.2 rigid-lid:
533
534 - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
535 to stay closer to the code.
536 - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
537
538 2.3 linear free-surface:
539 - add ref(+link) to S/R names:
540 - add ref(+link) to Crank-Nickelson section 2.9.1
541
542 2.4 Adams-Bashforth
543 - add stability diagrams (I have some figures that I can put)
544 - add link for var. forcing_In_AB
545 - add S/R link for S/R ADAMS_BASHFORTH2
546
547 2.5 Implicit time-stepping
548 - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
549 SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
550 - update: also used for vertical advection
551
552 2.6 Synchronous time-stepping:
553 - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
554 MOMENTUM_CORRECTION_STEP.
555
556 2.7 Stagger baroclinic time-stepping
557 - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
558
559 2.8 NH
560 - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
561
562 2.9 Variants on Free-Surface
563 - Delta.t mis-written (eq.2.73)
564 - Eq.Num missing (has been fixed since)
565 - u* is stored in gU (and not in gUnm1)
566 - Phi_nh in NH_VARS.h
567 - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
568 INI_CG2D, INI_CG3D
569
570 2.9.1 Crank-Nickelson
571 - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
572
573 2.9.2 NLFS
574 - eq.Nb are wrong in html
575 - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
576
577 2.10.1 Notation
578 - Area definition is not really used like this
579
580 >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
581
582 Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
583 the model variables) are used (e.g., see section 2.10.5)
584
585 2.10.5 Horizontal grid:
586 - fig.2.8 : should use Aw,As consistently in this figure description,
587 in the figure itself, as it is in the text.
588 - curvilinear:
589 to add: mention the angle of the grid direction relative to
590 Eastward, Northward direction.
591 + mention horizGridFile= in file "data" (PARM04)
592 - add cylindrical grid description
593
594 2.11 Continuity & Horizontal Pressure gradient terms
595 - mention that d.Phi/dr|s =g if using z coordinate
596 - eq. 2.90 not clear regarding \delta_k(P-E)
597 better to add the free surface eq: d.eta/dt = w_s + P-E
598
599 2.12 Hydrostatic balance
600 - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
601 is hard to find
602 - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
603 and in section 1.3.4: remove the 1.3.4.3.2 subsection:
604 Quasi-nonhydrostatic Atmosphere
605
606 2.13.2 Coriolis terms
607 - note: the discretization used when useEnergyConservingCoriolis=T
608 has no hFac and no Area and is still different from the form
609 described here (with Area & hFac);
610
611 2.13.5 Lateral dissipation
612 - add description of how to use cosFactor & cosPower
613 - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
614
615 2.13.6 Vertical dissipation
616 - mention the implicit vertical viscosity option and ref to section 2.5
617 - add the parameter correspondence: Av <-> viscAr (and might change also
618 the notation to Ar)
619
620 2.14 Vector invariant momentum equations
621 - indicate that the NH pieces (vertical momentum eq) are not yet coded
622 and that the NH code uses the flux form.
623
624 2.14.6 Horizontal dissipation -> Horizontal Divergence
625
626 2.14.7 Horizontal dissipation
627 - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
628 and A_D4,A_z4 <-> viscA4D,viscA4Z
629
630 2.16 & 2.17 & 2.18 :
631 - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
632
633 2.20.2 mercator, non-dimensional Equations:
634 - does not use std notation
635 - would be better as an appendix of section 2.20:
636 (e.g changing the tile to:
637 Appendix: non-dimensional Equations on Spherical-Polar grid.)
638
639 JM
640

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