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Revision 1.8 - (show annotations) (download)
Thu Apr 6 19:14:57 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 - pick a URL
12 TBD
13
14 - mitgcm.org very front page.
15 o too many clicks to get to model manual.
16 make doc link go to mitgcm.org/r2_web_testing/latest
17 and add "HowTo" reference etc... to /latest page
18
19 - mitgcm.org/r2_web_testing/latest
20 o add another short-cut for quick download
21
22 o add another short-cut
23 About
24 Installation
25 Contents
26 Overview
27 Tutorials (broken)
28 Browse Code
29 Get Code (where does this go to?)
30
31 o authors
32 John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,
33 Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,
34 Gael - others?
35
36 o Tutorials side bar link is broken
37
38 o words
39 change to "access on-line Auser manual/A and Atable of contents/A
40 and browse the Aoverview section/A"
41
42 o finite-volume doesn't leap to FV figure
43
44 o the src and equation links don't come through to
45 the html when they are in figures - see chapter 2 for some
46 examples.
47
48 o degree symbols keep getting "dropped down" - problem with
49 pnmcrop et al.
50
51
52 Contents
53
54 Intro - CNH
55 o single kernel diagram -
56 add reference to MWR paper
57
58 o non-hydro
59 add reference to 1995 and 1999 papers
60 pdf of 1995 paper
61
62 o FV
63 add references to 1997 papers.
64
65 o Tangent linear/adjoint add reference to
66 Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc...
67
68 o platforms
69 Add reference to SC article and Scientific Programming article
70
71 o List of key papers needs to be updated and reformatted
72
73
74 o Global atmosphere: `Held Suarez',
75 update Adcroft reference
76 fix up ingrid link and frame (ingrid movies seem to be broken?)
77 Held and Suarez reference is not a link.
78
79 o Ocean Gyres
80 fix up frame link
81 make "lopped cell" a link to referenced paper.
82 add references (ask Steph/Mick)
83 online/offline paper
84
85 o Convection and mixing over topography
86 add in Legg references for convection and mixing over topography
87 and external link to CPT-GCE etc...
88
89 o Boundary forced internal waves
90 add in Legg references, obc's reference
91
92 o Parameter sensitivity
93 add in Bugnion references, Boyin references, Steph references
94
95 o State estimation
96 add in references from Patrick/Carl/Ichiro/Detlef etc...
97 update links to point to latest ECCO results
98 ECCO ingrid results have been moved
99 add forward links to "ECCO state estimation" chapter in manual
100
101 o Ocean biogeochemical cycles
102 add in references from Mick/Galen etc...
103 fix ingrid link ( date to date thing does not appear to work)
104 figure url does not have a "target=idontexist" entry
105
106 o Simulations of laboratory experiments
107 reference Wardle and Karsten papers
108 update links to include DDDAS "PIAB" page
109 cylindrical polar coordinates
110
111 o Continuos equations in ''r'' coordinates
112 add references to iso paper
113 no mention of z* and p* - forward reference to z*/p* in 2.
114 add that coupling also manifests through F, Q
115 add tracer transport
116
117 o Kinematic boundary conditions
118
119 o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms
120 need to tidy up discussion of shallow-atmosphere to be
121 consistent with the code or change code to be consistent
122 with the discussion!
123 make references hyperlinks
124 add stuff too
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 Discretization and alg - JMC+CNH
168
169 Tutorials - AM
170 3.1 "Where to find"
171 o link to Pelican not needed
172 o mailman twice (why?)
173 o no htdig (gone? - I liked it)
174
175 intro part
176 individual experiments
177
178 offline - duplicate inputs, what is it, tidy up cfc v.
179 other offline.
180
181 Software - EH to review
182
183 some to be done on resource estimates at the end - needs sorting.
184
185 Automatic Diff - CE
186
187 Physical Packages - ???
188
189 Diags and tools - ???
190
191 Interface with ECCO - ???
192
193 Model uses - ???
194
195 Building document - ???
196 via cron
197 tweaking latex2html etc..
198
199 Src Code tree (rename
200 examples etc..) - ???
201
202 Documentation
203
204 1. Introduction
205
206 2. Discretization and Algorithm
207
208 2.13.5 Lateral dissipation
209 o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
210 in code need to explain why cos()3/2 turns out to be
211 scaling (not cos()2)
212
213 2.13.6 Vertical dissipation
214 o update to have reference to Baylors section
215 reference to implicit discussion in time-stepping part of manual
216
217
218
219 3. Tutorials
220 reorg'd into
221 intro part
222 individual experiments
223
224 4. Software Architecture
225
226 5. Automatic Differentiation
227
228 6. Physical Parameterization and Packages
229
230 7. Diagnostics and tools
231
232 8. Interface with ECCO
233
234 9. Model uses
235 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
236 (check in support for more names)
237
238 Need an empty package as part of distribution
239
240 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!
241
242 Chapter 1
243
244 Change hydrodynamical to "dynamical"
245
246 Examples
247
248 - extra "in action" cases
249
250 o high res ocean with diurnal atmospheric state forcing
251 - links to ingrid output
252 CNH/Dimitris
253
254 o realistic FIZHI from Andrea
255 - links to ingrid output
256 from AM
257
258 o with seaice on high res cube
259 - links to ingrid output
260 CNH/Dimitris
261
262 o coupled aqua, ridge world etc...
263 - links to ingrid output
264 get stuff from Daniel
265
266 o constrained lab simulation
267 - links to ingrid output for model and lab
268 fields
269 get stuff from Sai/Andrew
270
271 o sensitivity wrt to iron
272
273 o optimization
274 - update to link to latest ECCO sites and GF
275 related material
276
277 o eddy diffusivity transport application
278
279 o Gas giant?
280
281 Chapter 6
282
283 the master package diagram does not appear in the document
284
285 pkg/ptracers doesn't seem to have any documentation (see packages list below)
286
287
288
289 2.10.5 Horizontal grid
290
291 need to do a better job of relating model variables to this diagram
292
293
294 Master list of packages
295
296 admtlm/ - autodiff (chapter 5)
297 aim/ - 6.4.1 (content needs fixing - JM to do)
298 aim_compon_interf/ - 6.6 (no content yet)
299 aim_ocn_coupler/ - 6.6 (no content yet)
300 aim_v23/ - retired
301 atm_common/ - 6.6 (no content yet)
302 autodiff/ - autodiff (chapter 5)
303 bulk_force/ - 6.3.3
304 cal/ - 6.3.5
305 cd_code/ - chapter 2 (JM check)
306 cfc/ - not sure
307 chronos/ - AM to check
308 compon_communic/ - 6.6 (no content yet)
309 cost/ - not sure, check with PH
310 ctrl/ - not sure, check with PH
311 debug/ - JM may do something in chapter 7 (utilities)
312 diagnostics/ - 7.1
313 dic/ - 6.7.2
314 ebm/ - not sure
315 ecco/ - chapter 8
316 embed_files/ - add something to chapter 7
317 ex3/ - rename to exch3
318 exch2/ - 6.2.2
319 exf/ - 6.3.4
320 fizhi/ - 6.4.3
321 flt/ - in chapter 2 (JM check)
322 gchem/ - 6.7.1
323 generic_advdiff/ - in chapter 2 (JM check)
324 ggl90/ - nothing, (Martin?)
325 gmredi/ - in chapter 2 (JM check). also need
326 Ferrari & Mc tapering
327 grdchk/ - grdchk (chapter 5 - check with PH)
328 gridalt/ - 6.2.4
329 kpp/ - 6.3.2
330 land/ - 6.4.2 (not connected to code - JM to fix)
331 matrix/ - Samar
332 mdsio/ - 7.3.1
333 mnc/ - 7.2.1
334 mom_common/ - in chapter 2 (JM check)
335 mom_fluxform/ - in chapter 2 (JM check)
336 mom_vecinv/ - in chapter 2 (JM check)
337 monitor/ - 7.4
338 my82/ - nothing, (martin?)
339 obcs/ - 6.3 (needs a check)
340 ocn_compon_interf/ - 6.6 (no content yet)
341 offline/ - nothing, tutorials that need work but no package section entry
342 opps/ - nothing, (martin?)
343 pp81/ - nothing, (martin?)
344 profiles/ - GAEL
345 ptracers/ - JM + SD to write something
346 rbcs/ - talk to steph
347 runclock/ - runclock
348 rw/ - not sure
349 sbo/ - text in sbo_descruption.tex but not linked into
350 part6
351 seaice/ - 6.5.2 - no equations, dimitris has promised some
352 shap_filt/ - chapter 2, JM to check
353 shelfice/ - nothing yet (martin?)
354 solver/ - empty
355 sphere/ - chapter 5 or 8 (PH to check)
356 therm_seaice/ - empty
357 thsice/ - 6.5.1 (JM to update?)
358 timeave/ - retiring......
359 zonal_filt/ - chapter 2 (JM to check)
360
361 Possible for chap 7 - Daniels grafix/ stuff
362
363 Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
364
365 Figure 6.8 is missing
366
367
368 >>>> From Ed
369
370 Here are the remaining bits for Chap 4 :
371
372 - The grammar/flow could still use some work. Boo was an English
373 major and has experience editing/proofing technical papers. I
374 could print out a copy and ask her to read it and suggest
375 improvements.
376
377 - missing references (if you point me towards URLs, I'll add them
378 to the bibliography):
379 \ref{ref hoe and hill, ecmwf}
380 \ref{magicgarden}
381 \ref{IBMLAPI}
382 \ref{Memorychannel}
383 \ref{hoe-hill:99}
384
385 - There are a few empty sub-sections at the end of Chap 4 that
386 should either be commented out or fleshed out.
387
388 and thats about it for Chap 4.
389
390
391 Add more to quick links on front page
392
393
394 >>>> From Andrea
395
396 to do list for chap 7:
397
398
399 7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"
400 the links are pointing to the proper place
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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