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Revision 1.5 - (show annotations) (download)
Thu Apr 6 19:06:45 2006 UTC (13 years, 4 months ago) by edhill
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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
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 the src and equation links don't come through to
38 the html when they are in figures - see chapter 2 for some
39 examples.
40
41 o degree symbols keep getting "dropped down" - problem with
42 pnmcrop et al.
43
44
45 Contents
46
47 Intro - CNH
48 o single kernel diagram -
49 add reference to MWR paper
50
51 o non-hydro
52 add reference to 1995 and 1999 papers
53 pdf of 1995 paper
54
55 o FV
56 add references to 1997 papers.
57
58 o Tangent linear/adjoint add reference to
59 Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc...
60
61 o platforms
62 Add reference to SC article and Scientific Programming article
63
64 o List of key papers needs to be updated and reformatted
65
66
67 o Global atmosphere: `Held Suarez',
68 update Adcroft reference
69 fix up ingrid link and frame (ingrid movies seem to be broken?)
70 Held and Suarez reference is not a link.
71
72 o Ocean Gyres
73 fix up frame link
74 make "lopped cell" a link to referenced paper.
75 add references (ask Steph/Mick)
76 online/offline paper
77
78 o Convection and mixing over topography
79 add in Legg references for convection and mixing over topography
80 and external link to CPT-GCE etc...
81
82 o Boundary forced internal waves
83 add in Legg references, obc's reference
84
85 o Parameter sensitivity
86 add in Bugnion references, Boyin references, Steph references
87
88 o State estimation
89 add in references from Patrick/Carl/Ichiro/Detlef etc...
90 update links to point to latest ECCO results
91 ECCO ingrid results have been moved
92 add forward links to "ECCO state estimation" chapter in manual
93
94 o Ocean biogeochemical cycles
95 add in references from Mick/Galen etc...
96 fix ingrid link ( date to date thing does not appear to work)
97 figure url does not have a "target=idontexist" entry
98
99 o Simulations of laboratory experiments
100 reference Wardle and Karsten papers
101 update links to include DDDAS "PIAB" page
102 cylindrical polar coordinates
103
104 o Continuos equations in ''r'' coordinates
105 add references to iso paper
106 no mention of z* and p* - forward reference to z*/p* in 2.
107 add that coupling also manifests through F, Q
108 add tracer transport
109
110 o Kinematic boundary conditions
111
112 o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms
113 need to tidy up discussion of shallow-atmosphere to be
114 consistent with the code or change code to be consistent
115 with the discussion!
116 make references hyperlinks
117 add stuff too
118
119 o Finding the pressure field
120 make references hyperlinks
121 add forward references to manual algorithm section
122 change Elliptic to "elliptic"
123
124 o Forcing and dissipation
125 make "physics packages" refer to chapter 6.
126 should we move "external forcing" et. al to a
127 generic_forcing_driver package?
128
129 viscosities
130 update to mention Smag/Leith (Ah and A4 not constant)
131 and to have forward references to numerical section
132 tracers
133 forward references to numerical section, reddy, GM etc...
134 add references to literature
135
136 o 1.3.8 Vector invariant form
137 forward references to numerical section
138
139 o 1.3.9 Adjoint
140 add a little more here + some hyperlink to chapter 5.
141
142 o 1.4 Appendix ATMOSPHERE
143
144 add some introductory words
145
146 o 1.6 Coordinate systems
147 o only has some words on spherical polar. add some brief words
148 to cover all of
149 - cartesian
150 - spherical
151 - cylindrical
152 - general orthogonal curvilinear (vector invariant)
153
154 o Equation of state options
155 add some discussion
156 can't remember what we said we were going to do here
157 PH to do something
158
159
160 Discretization and alg - JMC+CNH
161
162 Tutorials - AM
163 3.1 "Where to find"
164 o link to Pelican not needed
165 o mailman twice (why?)
166 o no htdig (gone? - I liked it)
167
168 intro part
169 individual experiments
170
171 offline - duplicate inputs, what is it, tidy up cfc v.
172 other offline.
173
174 Software - EH to review
175
176 some to be done on resource estimates at the end - needs sorting.
177
178 Automatic Diff - CE
179
180 Physical Packages - ???
181
182 Diags and tools - ???
183
184 Interface with ECCO - ???
185
186 Model uses - ???
187
188 Building document - ???
189 via cron
190 tweaking latex2html etc..
191
192 Src Code tree (rename
193 examples etc..) - ???
194
195 Documentation
196
197 1. Introduction
198
199 2. Discretization and Algorithm
200
201 2.13.5 Lateral dissipation
202 o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
203 in code need to explain why cos()3/2 turns out to be
204 scaling (not cos()2)
205
206 2.13.6 Vertical dissipation
207 o update to have reference to Baylors section
208 reference to implicit discussion in time-stepping part of manual
209
210
211
212 3. Tutorials
213 reorg'd into
214 intro part
215 individual experiments
216
217 4. Software Architecture
218
219 5. Automatic Differentiation
220
221 6. Physical Parameterization and Packages
222
223 7. Diagnostics and tools
224
225 8. Interface with ECCO
226
227 9. Model uses
228 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
229 (check in support for more names)
230
231 Need an empty package as part of distribution
232
233 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!
234
235 Chapter 1
236
237 Change hydrodynamical to "dynamical"
238
239 Examples
240
241 - extra "in action" cases
242
243 o high res ocean with diurnal atmospheric state forcing
244 - links to ingrid output
245 CNH/Dimitris
246
247 o realistic FIZHI from Andrea
248 - links to ingrid output
249 from AM
250
251 o with seaice on high res cube
252 - links to ingrid output
253 CNH/Dimitris
254
255 o coupled aqua, ridge world etc...
256 - links to ingrid output
257 get stuff from Daniel
258
259 o constrained lab simulation
260 - links to ingrid output for model and lab
261 fields
262 get stuff from Sai/Andrew
263
264 o sensitivity wrt to iron
265
266 o optimization
267 - update to link to latest ECCO sites and GF
268 related material
269
270 o eddy diffusivity transport application
271
272 o Gas giant?
273
274 Chapter 6
275
276 the master package diagram does not appear in the document
277
278 pkg/ptracers doesn't seem to have any documentation (see packages list below)
279
280
281
282 2.10.5 Horizontal grid
283
284 need to do a better job of relating model variables to this diagram
285
286
287 Master list of packages
288
289 admtlm/ - autodiff (chapter 5)
290 aim/ - 6.4.1 (content needs fixing - JM to do)
291 aim_compon_interf/ - 6.6 (no content yet)
292 aim_ocn_coupler/ - 6.6 (no content yet)
293 aim_v23/ - retired
294 atm_common/ - 6.6 (no content yet)
295 autodiff/ - autodiff (chapter 5)
296 bulk_force/ - 6.3.3
297 cal/ - 6.3.5
298 cd_code/ - chapter 2 (JM check)
299 cfc/ - not sure
300 chronos/ - AM to check
301 compon_communic/ - 6.6 (no content yet)
302 cost/ - not sure, check with PH
303 ctrl/ - not sure, check with PH
304 debug/ - JM may do something in chapter 7 (utilities)
305 diagnostics/ - 7.1
306 dic/ - 6.7.2
307 ebm/ - not sure
308 ecco/ - chapter 8
309 embed_files/ - add something to chapter 7
310 ex3/ - rename to exch3
311 exch2/ - 6.2.2
312 exf/ - 6.3.4
313 fizhi/ - 6.4.3
314 flt/ - in chapter 2 (JM check)
315 gchem/ - 6.7.1
316 generic_advdiff/ - in chapter 2 (JM check)
317 ggl90/ - nothing, (Martin?)
318 gmredi/ - in chapter 2 (JM check). also need
319 Ferrari & Mc tapering
320 grdchk/ - grdchk (chapter 5 - check with PH)
321 gridalt/ - 6.2.4
322 kpp/ - 6.3.2
323 land/ - 6.4.2 (not connected to code - JM to fix)
324 matrix/ - Samar
325 mdsio/ - 7.3.1
326 mnc/ - 7.2.1
327 mom_common/ - in chapter 2 (JM check)
328 mom_fluxform/ - in chapter 2 (JM check)
329 mom_vecinv/ - in chapter 2 (JM check)
330 monitor/ - 7.4
331 my82/ - nothing, (martin?)
332 obcs/ - 6.3 (needs a check)
333 ocn_compon_interf/ - 6.6 (no content yet)
334 offline/ - nothing, tutorials that need work but no package section entry
335 opps/ - nothing, (martin?)
336 pp81/ - nothing, (martin?)
337 profiles/ - GAEL
338 ptracers/ - JM + SD to write something
339 rbcs/ - talk to steph
340 runclock/ - runclock
341 rw/ - not sure
342 sbo/ - text in sbo_descruption.tex but not linked into
343 part6
344 seaice/ - 6.5.2 - no equations, dimitris has promised some
345 shap_filt/ - chapter 2, JM to check
346 shelfice/ - nothing yet (martin?)
347 solver/ - empty
348 sphere/ - chapter 5 or 8 (PH to check)
349 therm_seaice/ - empty
350 thsice/ - 6.5.1 (JM to update?)
351 timeave/ - retiring......
352 zonal_filt/ - chapter 2 (JM to check)
353
354 Possible for chap 7 - Daniels grafix/ stuff
355
356 Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
357
358 Figure 6.8 is missing
359
360
361 >>>> From Ed
362
363 Here are the remaining bits for Chap 4 :
364
365 - The grammar/flow could still use some work. Boo was an English
366 major and has experience editing/proofing technical papers. I
367 could print out a copy and ask her to read it and suggest
368 improvements.
369
370 - missing references (if you point me towards URLs, I'll add them
371 to the bibliography):
372 \ref{ref hoe and hill, ecmwf}
373 \ref{magicgarden}
374 \ref{IBMLAPI}
375 \ref{Memorychannel}
376 \ref{hoe-hill:99}
377
378 - There are a few empty sub-sections at the end of Chap 4 that
379 should either be commented out or fleshed out.
380
381 and thats about it for Chap 4.
382
383
384 Add more to quick links on front page
385
386
387 >>>> From Andrea
388
389 to do list for chap 7:
390
391
392 7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"
393 the links are pointing to the proper place
394
395 7.5.1 - add Graphix to the list of stuff in utils/matlab
396 7.5.2 - empty
397
398
399 andrea
400
401 >>>> From Andrea
402
403 Chapter 3
404 --------
405
406 Almost all of the 'math mode' text is dropped down as subscripts
407
408 divide chapter 3 more clearly into 2 sections?
409 (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and
410 then 3.19 and 3.20 are informational again - rearrange subsections?)
411
412 3.1 - don't need a link to the outside of the document (remove it)
413 - link to htdig is broken
414
415 3.2.1 - link at bottom to source code points to section 3.2.1
416 (ie, to itself) - link should point to cvs code archive
417
418 3.2.2.1 - ('upgrading from an earlier version') belongs under
419 the cvs part, ie, should be 3.2.1.1
420
421 3.3 - remove reference to 'diags' section under MITgcm
422 - remove reference to 'exe' and 'bin' sections also
423 (remove the .cvsignore file under these directories in cvs)
424 - add a 'jobs' section, and a description as examples of run scripts
425 - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions
426 - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'
427 - under 'tools' the adjoint points to section 5 - this is now section 8
428 (but should be a floating reference)
429 - under 'utils' add a reference to exch2 - stuff for different resolutions
430 - the description of the pkg section refers directly to
431 section 3. should be section 6 (actually should be a floating reference)
432
433 3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
434 3.4.1 - links to the following experiments don't exist or are broken:
435 exp2 - should link to section 3.9
436 hs94.cs-32x32x5 - link to section 3.12
437 add 'convection' to the list, link to section 3.13
438 add 'plume on slope` to the list, link to section 3.14
439 add '??' link to section 3.15
440 add 'dic_example on slope` to the list, link to section 3.16
441 add '??' link to section 3.17
442 add 'offline' and link to section 3.18
443 clean up others and make links where they are needed
444 3.4.2 - text suggests to see section 2 for details about what is in the 'code'
445 and 'input' directories - should refer to the examples in this section
446 - add 'build' bullet - this is where the model is compiled and exectuable lives
447
448 3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
449 as the place where they live (add a link?)
450
451 3.6.1 - Add some general 'approach' text - ie, output is controlled either by the
452 'data' file in the input directory or by the data.[pkg name] file for any
453 package running. And there is some default behavior when the 'state' dumps
454 are written.
455 3.6.1.2 - needs to be moved to inside section 3.6.2
456
457 3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18)
458 underneath this one and leave the text for 3.7 in place
459
460 All the 'overview' sections need some reference to the name of the experiment in
461 the verification directory
462
463 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
464 - is this experiment in the list from section 3.4???
465 3.10.3.1 - refers to figures and equations, links are broken
466
467 3.11.3.2 - line 43: link to equation is broken
468 - line 51-53: link to equation is broken
469 - there is some mess of text hanging around the end of this section. remove? reformat?
470
471 3.12.4.1 - line 34 - link to equation is broken
472 - lines 60,61 - 1st (take out the 'r' in the superscript)
473
474 3.13.2 - link to theta-equation is broken
475 3.13.5.4 -- ALL of the bold links to variable names are broken
476 line 34: link to equation is broken
477
478 3.15.1 - reference to 'fourth experiment' should be removed
479
480 3.16.4 - strange formatting, presence of '>' symbols - remove them
481
482 3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
483 3.17.3.1 - nothing filled in under file input/data - needs description
484
485 3.18.2 - point to section 2 for details - need hyperlink
486
487 3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
488 section 3.5 has the 'build' directory in the example
489
490 3.20.1 - link to doc at end of section points to this section
491 3.20.2 - link to doc at end of section points to this section
492
493 >>>> from JM
494
495
496
497 manual, section.2 :
498
499 In general:
500 - add more refences/links to S/R & variable name
501 - would be nice to have an active link to the fortran-file
502 for all the S/R & eq.Number in the "calling-tree" boxes
503 - search for CALC_MOM_RHS and replace it by the appropriate S/R
504 (mom_flux_form, mom_vecinv, dynamics)
505 - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
506 was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
507 in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
508 simply written \vec{v}.
509 I would suggest to keep the notation as they are (since they are consistent
510 inside each section) but may be to move the "notation.tex" piece
511 at the beginning of section.2 and to mention clearly the changes between
512 the 2 sections.
513
514 in content: Horizontal Dissipation: 2 times in vector-invariant section
515
516 2.1 time-stepping (part2/time_stepping.tex)
517
518 - this is not clear to me:
519
520 >> In all the above configurations it is also possible to substitute the
521 >> Adams-Bashforth with an alternative time-stepping scheme for terms
522 >> evaluated explicitly in time
523
524
525 2.2 rigid-lid:
526
527 - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
528 to stay closer to the code.
529 - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
530
531 2.3 linear free-surface:
532 - add ref(+link) to S/R names:
533 - add ref(+link) to Crank-Nickelson section 2.9.1
534
535 2.4 Adams-Bashforth
536 - add stability diagrams (I have some figures that I can put)
537 - add link for var. forcing_In_AB
538 - add S/R link for S/R ADAMS_BASHFORTH2
539
540 2.5 Implicit time-stepping
541 - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
542 SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
543 - update: also used for vertical advection
544
545 2.6 Synchronous time-stepping:
546 - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
547 MOMENTUM_CORRECTION_STEP.
548
549 2.7 Stagger baroclinic time-stepping
550 - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
551
552 2.8 NH
553 - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
554
555 2.9 Variants on Free-Surface
556 - Delta.t mis-written (eq.2.73)
557 - Eq.Num missing (has been fixed since)
558 - u* is stored in gU (and not in gUnm1)
559 - Phi_nh in NH_VARS.h
560 - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
561 INI_CG2D, INI_CG3D
562
563 2.9.1 Crank-Nickelson
564 - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
565
566 2.9.2 NLFS
567 - eq.Nb are wrong in html
568 - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
569
570 2.10.1 Notation
571 - Area definition is not really used like this
572
573 >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
574
575 Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
576 the model variables) are used (e.g., see section 2.10.5)
577
578 2.10.5 Horizontal grid:
579 - fig.2.8 : should use Aw,As consistently in this figure description,
580 in the figure itself, as it is in the text.
581 - curvilinear:
582 to add: mention the angle of the grid direction relative to
583 Eastward, Northward direction.
584 + mention horizGridFile= in file "data" (PARM04)
585 - add cylindrical grid description
586
587 2.11 Continuity & Horizontal Pressure gradient terms
588 - mention that d.Phi/dr|s =g if using z coordinate
589 - eq. 2.90 not clear regarding \delta_k(P-E)
590 better to add the free surface eq: d.eta/dt = w_s + P-E
591
592 2.12 Hydrostatic balance
593 - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
594 is hard to find
595 - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
596 and in section 1.3.4: remove the 1.3.4.3.2 subsection:
597 Quasi-nonhydrostatic Atmosphere
598
599 2.13.2 Coriolis terms
600 - note: the discretization used when useEnergyConservingCoriolis=T
601 has no hFac and no Area and is still different from the form
602 described here (with Area & hFac);
603
604 2.13.5 Lateral dissipation
605 - add description of how to use cosFactor & cosPower
606 - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
607
608 2.13.6 Vertical dissipation
609 - mention the implicit vertical viscosity option and ref to section 2.5
610 - add the parameter correspondence: Av <-> viscAr (and might change also
611 the notation to Ar)
612
613 2.14 Vector invariant momentum equations
614 - indicate that the NH pieces (vertical momentum eq) are not yet coded
615 and that the NH code uses the flux form.
616
617 2.14.6 Horizontal dissipation -> Horizontal Divergence
618
619 2.14.7 Horizontal dissipation
620 - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
621 and A_D4,A_z4 <-> viscA4D,viscA4Z
622
623 2.16 & 2.17 & 2.18 :
624 - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
625
626 2.20.2 mercator, non-dimensional Equations:
627 - does not use std notation
628 - would be better as an appendix of section 2.20:
629 (e.g changing the tile to:
630 Appendix: non-dimensional Equations on Spherical-Polar grid.)
631
632 JM
633

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