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Revision 1.7 - (show annotations) (download)
Thu Apr 6 19:10:53 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"
9
10 - pick a URL (whine whine whine whine whine whine
11 whine whine whine whine whine whine ...........)
12
13 - mitgcm.org very front page.
14 o too many clicks to get to model manual.
15 make doc link go to mitgcm.org/r2_web_testing/latest
16 and add "HowTo" reference etc... to /latest page
17
18 - mitgcm.org/r2_web_testing/latest
19 o add another short-cut for quick download
20
21 o add another short-cut
22 About
23 Installation
24 Contents
25 Overview
26 Tutorials (broken)
27 Browse Code
28 Get Code (where does this go to?)
29
30 o authors
31 John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,
32 Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,
33 Gael - others?
34
35 o Tutorials side bar link is broken
36
37 o words
38 change to "access on-line Auser manual/A and Atable of contents/A
39 and browse the Aoverview section/A"
40
41 o finite-volume doesn't leap to FV figure
42
43 o the src and equation links don't come through to
44 the html when they are in figures - see chapter 2 for some
45 examples.
46
47 o degree symbols keep getting "dropped down" - problem with
48 pnmcrop et al.
49
50
51 Contents
52
53 Intro - CNH
54 o single kernel diagram -
55 add reference to MWR paper
56
57 o non-hydro
58 add reference to 1995 and 1999 papers
59 pdf of 1995 paper
60
61 o FV
62 add references to 1997 papers.
63
64 o Tangent linear/adjoint add reference to
65 Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc...
66
67 o platforms
68 Add reference to SC article and Scientific Programming article
69
70 o List of key papers needs to be updated and reformatted
71
72
73 o Global atmosphere: `Held Suarez',
74 update Adcroft reference
75 fix up ingrid link and frame (ingrid movies seem to be broken?)
76 Held and Suarez reference is not a link.
77
78 o Ocean Gyres
79 fix up frame link
80 make "lopped cell" a link to referenced paper.
81 add references (ask Steph/Mick)
82 online/offline paper
83
84 o Convection and mixing over topography
85 add in Legg references for convection and mixing over topography
86 and external link to CPT-GCE etc...
87
88 o Boundary forced internal waves
89 add in Legg references, obc's reference
90
91 o Parameter sensitivity
92 add in Bugnion references, Boyin references, Steph references
93
94 o State estimation
95 add in references from Patrick/Carl/Ichiro/Detlef etc...
96 update links to point to latest ECCO results
97 ECCO ingrid results have been moved
98 add forward links to "ECCO state estimation" chapter in manual
99
100 o Ocean biogeochemical cycles
101 add in references from Mick/Galen etc...
102 fix ingrid link ( date to date thing does not appear to work)
103 figure url does not have a "target=idontexist" entry
104
105 o Simulations of laboratory experiments
106 reference Wardle and Karsten papers
107 update links to include DDDAS "PIAB" page
108 cylindrical polar coordinates
109
110 o Continuos equations in ''r'' coordinates
111 add references to iso paper
112 no mention of z* and p* - forward reference to z*/p* in 2.
113 add that coupling also manifests through F, Q
114 add tracer transport
115
116 o Kinematic boundary conditions
117
118 o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms
119 need to tidy up discussion of shallow-atmosphere to be
120 consistent with the code or change code to be consistent
121 with the discussion!
122 make references hyperlinks
123 add stuff too
124
125 o Finding the pressure field
126 make references hyperlinks
127 add forward references to manual algorithm section
128 change Elliptic to "elliptic"
129
130 o Forcing and dissipation
131 make "physics packages" refer to chapter 6.
132 should we move "external forcing" et. al to a
133 generic_forcing_driver package?
134
135 viscosities
136 update to mention Smag/Leith (Ah and A4 not constant)
137 and to have forward references to numerical section
138 tracers
139 forward references to numerical section, reddy, GM etc...
140 add references to literature
141
142 o 1.3.8 Vector invariant form
143 forward references to numerical section
144
145 o 1.3.9 Adjoint
146 add a little more here + some hyperlink to chapter 5.
147
148 o 1.4 Appendix ATMOSPHERE
149
150 add some introductory words
151
152 o 1.6 Coordinate systems
153 o only has some words on spherical polar. add some brief words
154 to cover all of
155 - cartesian
156 - spherical
157 - cylindrical
158 - general orthogonal curvilinear (vector invariant)
159
160 o Equation of state options
161 add some discussion
162 can't remember what we said we were going to do here
163 PH to do something
164
165
166 Discretization and alg - JMC+CNH
167
168 Tutorials - AM
169 3.1 "Where to find"
170 o link to Pelican not needed
171 o mailman twice (why?)
172 o no htdig (gone? - I liked it)
173
174 intro part
175 individual experiments
176
177 offline - duplicate inputs, what is it, tidy up cfc v.
178 other offline.
179
180 Software - EH to review
181
182 some to be done on resource estimates at the end - needs sorting.
183
184 Automatic Diff - CE
185
186 Physical Packages - ???
187
188 Diags and tools - ???
189
190 Interface with ECCO - ???
191
192 Model uses - ???
193
194 Building document - ???
195 via cron
196 tweaking latex2html etc..
197
198 Src Code tree (rename
199 examples etc..) - ???
200
201 Documentation
202
203 1. Introduction
204
205 2. Discretization and Algorithm
206
207 2.13.5 Lateral dissipation
208 o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
209 in code need to explain why cos()3/2 turns out to be
210 scaling (not cos()2)
211
212 2.13.6 Vertical dissipation
213 o update to have reference to Baylors section
214 reference to implicit discussion in time-stepping part of manual
215
216
217
218 3. Tutorials
219 reorg'd into
220 intro part
221 individual experiments
222
223 4. Software Architecture
224
225 5. Automatic Differentiation
226
227 6. Physical Parameterization and Packages
228
229 7. Diagnostics and tools
230
231 8. Interface with ECCO
232
233 9. Model uses
234 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
235 (check in support for more names)
236
237 Need an empty package as part of distribution
238
239 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!
240
241 Chapter 1
242
243 Change hydrodynamical to "dynamical"
244
245 Examples
246
247 - extra "in action" cases
248
249 o high res ocean with diurnal atmospheric state forcing
250 - links to ingrid output
251 CNH/Dimitris
252
253 o realistic FIZHI from Andrea
254 - links to ingrid output
255 from AM
256
257 o with seaice on high res cube
258 - links to ingrid output
259 CNH/Dimitris
260
261 o coupled aqua, ridge world etc...
262 - links to ingrid output
263 get stuff from Daniel
264
265 o constrained lab simulation
266 - links to ingrid output for model and lab
267 fields
268 get stuff from Sai/Andrew
269
270 o sensitivity wrt to iron
271
272 o optimization
273 - update to link to latest ECCO sites and GF
274 related material
275
276 o eddy diffusivity transport application
277
278 o Gas giant?
279
280 Chapter 6
281
282 the master package diagram does not appear in the document
283
284 pkg/ptracers doesn't seem to have any documentation (see packages list below)
285
286
287
288 2.10.5 Horizontal grid
289
290 need to do a better job of relating model variables to this diagram
291
292
293 Master list of packages
294
295 admtlm/ - autodiff (chapter 5)
296 aim/ - 6.4.1 (content needs fixing - JM to do)
297 aim_compon_interf/ - 6.6 (no content yet)
298 aim_ocn_coupler/ - 6.6 (no content yet)
299 aim_v23/ - retired
300 atm_common/ - 6.6 (no content yet)
301 autodiff/ - autodiff (chapter 5)
302 bulk_force/ - 6.3.3
303 cal/ - 6.3.5
304 cd_code/ - chapter 2 (JM check)
305 cfc/ - not sure
306 chronos/ - AM to check
307 compon_communic/ - 6.6 (no content yet)
308 cost/ - not sure, check with PH
309 ctrl/ - not sure, check with PH
310 debug/ - JM may do something in chapter 7 (utilities)
311 diagnostics/ - 7.1
312 dic/ - 6.7.2
313 ebm/ - not sure
314 ecco/ - chapter 8
315 embed_files/ - add something to chapter 7
316 ex3/ - rename to exch3
317 exch2/ - 6.2.2
318 exf/ - 6.3.4
319 fizhi/ - 6.4.3
320 flt/ - in chapter 2 (JM check)
321 gchem/ - 6.7.1
322 generic_advdiff/ - in chapter 2 (JM check)
323 ggl90/ - nothing, (Martin?)
324 gmredi/ - in chapter 2 (JM check). also need
325 Ferrari & Mc tapering
326 grdchk/ - grdchk (chapter 5 - check with PH)
327 gridalt/ - 6.2.4
328 kpp/ - 6.3.2
329 land/ - 6.4.2 (not connected to code - JM to fix)
330 matrix/ - Samar
331 mdsio/ - 7.3.1
332 mnc/ - 7.2.1
333 mom_common/ - in chapter 2 (JM check)
334 mom_fluxform/ - in chapter 2 (JM check)
335 mom_vecinv/ - in chapter 2 (JM check)
336 monitor/ - 7.4
337 my82/ - nothing, (martin?)
338 obcs/ - 6.3 (needs a check)
339 ocn_compon_interf/ - 6.6 (no content yet)
340 offline/ - nothing, tutorials that need work but no package section entry
341 opps/ - nothing, (martin?)
342 pp81/ - nothing, (martin?)
343 profiles/ - GAEL
344 ptracers/ - JM + SD to write something
345 rbcs/ - talk to steph
346 runclock/ - runclock
347 rw/ - not sure
348 sbo/ - text in sbo_descruption.tex but not linked into
349 part6
350 seaice/ - 6.5.2 - no equations, dimitris has promised some
351 shap_filt/ - chapter 2, JM to check
352 shelfice/ - nothing yet (martin?)
353 solver/ - empty
354 sphere/ - chapter 5 or 8 (PH to check)
355 therm_seaice/ - empty
356 thsice/ - 6.5.1 (JM to update?)
357 timeave/ - retiring......
358 zonal_filt/ - chapter 2 (JM to check)
359
360 Possible for chap 7 - Daniels grafix/ stuff
361
362 Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
363
364 Figure 6.8 is missing
365
366
367 >>>> From Ed
368
369 Here are the remaining bits for Chap 4 :
370
371 - The grammar/flow could still use some work. Boo was an English
372 major and has experience editing/proofing technical papers. I
373 could print out a copy and ask her to read it and suggest
374 improvements.
375
376 - missing references (if you point me towards URLs, I'll add them
377 to the bibliography):
378 \ref{ref hoe and hill, ecmwf}
379 \ref{magicgarden}
380 \ref{IBMLAPI}
381 \ref{Memorychannel}
382 \ref{hoe-hill:99}
383
384 - There are a few empty sub-sections at the end of Chap 4 that
385 should either be commented out or fleshed out.
386
387 and thats about it for Chap 4.
388
389
390 Add more to quick links on front page
391
392
393 >>>> From Andrea
394
395 to do list for chap 7:
396
397
398 7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"
399 the links are pointing to the proper place
400
401 7.5.1 - add Graphix to the list of stuff in utils/matlab
402 7.5.2 - empty
403
404
405 andrea
406
407 >>>> From Andrea
408
409 Chapter 3
410 --------
411
412 Almost all of the 'math mode' text is dropped down as subscripts
413
414 divide chapter 3 more clearly into 2 sections?
415 (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and
416 then 3.19 and 3.20 are informational again - rearrange subsections?)
417
418 3.1 - don't need a link to the outside of the document (remove it)
419 - link to htdig is broken
420
421 3.2.1 - link at bottom to source code points to section 3.2.1
422 (ie, to itself) - link should point to cvs code archive
423
424 3.2.2.1 - ('upgrading from an earlier version') belongs under
425 the cvs part, ie, should be 3.2.1.1
426
427 3.3 - remove reference to 'diags' section under MITgcm
428 - remove reference to 'exe' and 'bin' sections also
429 (remove the .cvsignore file under these directories in cvs)
430 - add a 'jobs' section, and a description as examples of run scripts
431 - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions
432 - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'
433 - under 'tools' the adjoint points to section 5 - this is now section 8
434 (but should be a floating reference)
435 - under 'utils' add a reference to exch2 - stuff for different resolutions
436 - the description of the pkg section refers directly to
437 section 3. should be section 6 (actually should be a floating reference)
438
439 3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
440 3.4.1 - links to the following experiments don't exist or are broken:
441 exp2 - should link to section 3.9
442 hs94.cs-32x32x5 - link to section 3.12
443 add 'convection' to the list, link to section 3.13
444 add 'plume on slope` to the list, link to section 3.14
445 add '??' link to section 3.15
446 add 'dic_example on slope` to the list, link to section 3.16
447 add '??' link to section 3.17
448 add 'offline' and link to section 3.18
449 clean up others and make links where they are needed
450 3.4.2 - text suggests to see section 2 for details about what is in the 'code'
451 and 'input' directories - should refer to the examples in this section
452 - add 'build' bullet - this is where the model is compiled and exectuable lives
453
454 3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
455 as the place where they live (add a link?)
456
457 3.6.1 - Add some general 'approach' text - ie, output is controlled either by the
458 'data' file in the input directory or by the data.[pkg name] file for any
459 package running. And there is some default behavior when the 'state' dumps
460 are written.
461 3.6.1.2 - needs to be moved to inside section 3.6.2
462
463 3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18)
464 underneath this one and leave the text for 3.7 in place
465
466 All the 'overview' sections need some reference to the name of the experiment in
467 the verification directory
468
469 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
470 - is this experiment in the list from section 3.4???
471 3.10.3.1 - refers to figures and equations, links are broken
472
473 3.11.3.2 - line 43: link to equation is broken
474 - line 51-53: link to equation is broken
475 - there is some mess of text hanging around the end of this section. remove? reformat?
476
477 3.12.4.1 - line 34 - link to equation is broken
478 - lines 60,61 - 1st (take out the 'r' in the superscript)
479
480 3.13.2 - link to theta-equation is broken
481 3.13.5.4 -- ALL of the bold links to variable names are broken
482 line 34: link to equation is broken
483
484 3.15.1 - reference to 'fourth experiment' should be removed
485
486 3.16.4 - strange formatting, presence of '>' symbols - remove them
487
488 3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
489 3.17.3.1 - nothing filled in under file input/data - needs description
490
491 3.18.2 - point to section 2 for details - need hyperlink
492
493 3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
494 section 3.5 has the 'build' directory in the example
495
496 3.20.1 - link to doc at end of section points to this section
497 3.20.2 - link to doc at end of section points to this section
498
499 >>>> from JM
500
501
502
503 manual, section.2 :
504
505 In general:
506 - add more refences/links to S/R & variable name
507 - would be nice to have an active link to the fortran-file
508 for all the S/R & eq.Number in the "calling-tree" boxes
509 - search for CALC_MOM_RHS and replace it by the appropriate S/R
510 (mom_flux_form, mom_vecinv, dynamics)
511 - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
512 was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
513 in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
514 simply written \vec{v}.
515 I would suggest to keep the notation as they are (since they are consistent
516 inside each section) but may be to move the "notation.tex" piece
517 at the beginning of section.2 and to mention clearly the changes between
518 the 2 sections.
519
520 in content: Horizontal Dissipation: 2 times in vector-invariant section
521
522 2.1 time-stepping (part2/time_stepping.tex)
523
524 - this is not clear to me:
525
526 >> In all the above configurations it is also possible to substitute the
527 >> Adams-Bashforth with an alternative time-stepping scheme for terms
528 >> evaluated explicitly in time
529
530
531 2.2 rigid-lid:
532
533 - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
534 to stay closer to the code.
535 - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
536
537 2.3 linear free-surface:
538 - add ref(+link) to S/R names:
539 - add ref(+link) to Crank-Nickelson section 2.9.1
540
541 2.4 Adams-Bashforth
542 - add stability diagrams (I have some figures that I can put)
543 - add link for var. forcing_In_AB
544 - add S/R link for S/R ADAMS_BASHFORTH2
545
546 2.5 Implicit time-stepping
547 - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
548 SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
549 - update: also used for vertical advection
550
551 2.6 Synchronous time-stepping:
552 - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
553 MOMENTUM_CORRECTION_STEP.
554
555 2.7 Stagger baroclinic time-stepping
556 - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
557
558 2.8 NH
559 - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
560
561 2.9 Variants on Free-Surface
562 - Delta.t mis-written (eq.2.73)
563 - Eq.Num missing (has been fixed since)
564 - u* is stored in gU (and not in gUnm1)
565 - Phi_nh in NH_VARS.h
566 - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
567 INI_CG2D, INI_CG3D
568
569 2.9.1 Crank-Nickelson
570 - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
571
572 2.9.2 NLFS
573 - eq.Nb are wrong in html
574 - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
575
576 2.10.1 Notation
577 - Area definition is not really used like this
578
579 >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
580
581 Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
582 the model variables) are used (e.g., see section 2.10.5)
583
584 2.10.5 Horizontal grid:
585 - fig.2.8 : should use Aw,As consistently in this figure description,
586 in the figure itself, as it is in the text.
587 - curvilinear:
588 to add: mention the angle of the grid direction relative to
589 Eastward, Northward direction.
590 + mention horizGridFile= in file "data" (PARM04)
591 - add cylindrical grid description
592
593 2.11 Continuity & Horizontal Pressure gradient terms
594 - mention that d.Phi/dr|s =g if using z coordinate
595 - eq. 2.90 not clear regarding \delta_k(P-E)
596 better to add the free surface eq: d.eta/dt = w_s + P-E
597
598 2.12 Hydrostatic balance
599 - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
600 is hard to find
601 - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
602 and in section 1.3.4: remove the 1.3.4.3.2 subsection:
603 Quasi-nonhydrostatic Atmosphere
604
605 2.13.2 Coriolis terms
606 - note: the discretization used when useEnergyConservingCoriolis=T
607 has no hFac and no Area and is still different from the form
608 described here (with Area & hFac);
609
610 2.13.5 Lateral dissipation
611 - add description of how to use cosFactor & cosPower
612 - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
613
614 2.13.6 Vertical dissipation
615 - mention the implicit vertical viscosity option and ref to section 2.5
616 - add the parameter correspondence: Av <-> viscAr (and might change also
617 the notation to Ar)
618
619 2.14 Vector invariant momentum equations
620 - indicate that the NH pieces (vertical momentum eq) are not yet coded
621 and that the NH code uses the flux form.
622
623 2.14.6 Horizontal dissipation -> Horizontal Divergence
624
625 2.14.7 Horizontal dissipation
626 - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
627 and A_D4,A_z4 <-> viscA4D,viscA4Z
628
629 2.16 & 2.17 & 2.18 :
630 - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
631
632 2.20.2 mercator, non-dimensional Equations:
633 - does not use std notation
634 - would be better as an appendix of section 2.20:
635 (e.g changing the tile to:
636 Appendix: non-dimensional Equations on Spherical-Polar grid.)
637
638 JM
639

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