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Revision 1.33 - (show annotations) (download)
Tue Jun 27 15:22:03 2006 UTC (17 years, 9 months ago) by cnh
Branch: MAIN
Changes since 1.32: +34 -0 lines
File MIME type: text/plain
Adding editors list

1 Editors
2
3 Overall - JM, AM, PH, CNH, EH3
4
5 Front content - EH3
6
7 Chapter 1 - CNH
8
9 Chapter 2 - JMC
10
11 Chapter 3 - AM
12
13 Chapter 4 - CNH
14
15 Chapter 5 - PH
16
17 Chapter 6 - AM
18
19 Chapter 7 - EH3
20
21 Chapter 8 - PH
22
23 Chapter 9 - CNH (Applications)
24
25 Chapter 10 - JMC (Under development chapter)
26
27 Biblio - EH3
28
29
30
31 Rebuild and set to do cron build - DONE on hugo
32
33 To do
34
35 - where to put under development links?
36 JMC would like to have some mention of unfinished things (checked in
37 but not that tested e.g. AB3)
38 Add an "Under development, chapter" - shortish description of what
39 is available (last chapter)
40
41 - add in example latex for formatting author names in different pieces.
42 this aknowledges peoples contributions and gives ref for who
43 to talk to.
44
45
46 o HTML, scripts and front content
47
48 - pick a URL
49 TBD
50
51 - mitgcm.org/r2_web_testing/latest
52 o add another short-cut for quick download
53
54 o add another short-cut
55 About
56 Installation
57 Contents
58 Overview
59 Tutorials (broken)
60 Browse Code
61
62 o words on http://mitgcm.org/r2_web_testing/latest
63 change to
64 "access on-line Auser manual/A and Atable of contents/A
65 and browse the Aoverview section/A"
66
67 o finite-volume doesn't leap to FV figure
68
69 o have another go at pnmcrop et al.
70
71 o Need an empty package as part of distribution. Check out atm_common
72
73 o Latex
74
75 Chapter 1 - CNH
76 o single kernel diagram -
77 add reference to MWR paper
78
79 o non-hydro
80 add reference to 1995 and 1999 papers
81 pdf of 1995 paper
82
83 o FV
84 add references to 1997 papers.
85
86 o Tangent linear/adjoint add reference to
87 Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc...
88
89 o platforms
90 Add reference to SC article and Scientific Programming article
91
92 o List of key papers needs to be updated and reformatted
93
94
95 o Global atmosphere: `Held Suarez',
96 update Adcroft reference
97 fix up ingrid link and frame (ingrid movies seem to be broken?)
98 Held and Suarez reference is not a link.
99
100 o Ocean Gyres
101 fix up frame link
102 make "lopped cell" a link to referenced paper.
103 add references (ask Steph/Mick)
104 online/offline paper
105
106 o Convection and mixing over topography
107 add in Legg references for convection and mixing over topography
108 and external link to CPT-GCE etc...
109
110 o Boundary forced internal waves
111 add in Legg references, obc's reference
112
113 o Parameter sensitivity
114 add in Bugnion references, Boyin references, Steph references
115
116 o State estimation
117 add in references from Patrick/Carl/Ichiro/Detlef etc...
118 update links to point to latest ECCO results
119 ECCO ingrid results have been moved
120 add forward links to "ECCO state estimation" chapter in manual
121
122 o Ocean biogeochemical cycles
123 add in references from Mick/Galen etc...
124 fix ingrid link ( date to date thing does not appear to work)
125 figure url does not have a "target=idontexist" entry
126
127 o Simulations of laboratory experiments
128 reference Wardle and Karsten papers
129 update links to include DDDAS "PIAB" page
130 cylindrical polar coordinates
131
132 o Continuos equations in ''r'' coordinates
133 add references to iso paper
134 no mention of z* and p* - forward reference to z*/p* in 2.
135 add that coupling also manifests through F, Q
136 add tracer transport
137
138 o Kinematic boundary conditions
139
140 o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
141 Non-hydrostatic forms
142 need to tidy up discussion of shallow-atmosphere to be
143 consistent with the code or change code to be consistent
144 with the discussion!
145 make references hyperlinks
146 add stuff too
147 JMC remove QNH atmosphere
148 need to sort out calc_gw for deep atmosphere
149
150 o Finding the pressure field
151 make references hyperlinks
152 add forward references to manual algorithm section
153 change Elliptic to "elliptic"
154
155 o Forcing and dissipation
156 make "physics packages" refer to chapter 6.
157 should we move "external forcing" et. al to a
158 generic_forcing_driver package?
159
160 viscosities
161 update to mention Smag/Leith (Ah and A4 not constant)
162 and to have forward references to numerical section
163 tracers
164 forward references to numerical section, reddy, GM etc...
165 add references to literature
166
167 o 1.3.8 Vector invariant form
168 forward references to numerical section
169
170 o 1.3.9 Adjoint
171 add a little more here + some hyperlink to chapter 5.
172
173 o 1.4 Appendix ATMOSPHERE
174
175 add some introductory words
176
177 o 1.6 Coordinate systems
178 o only has some words on spherical polar. add some brief words
179 to cover all of
180 - cartesian
181 - spherical
182 - cylindrical
183 - general orthogonal curvilinear (vector invariant)
184
185 o Equation of state options
186 add some discussion
187 can't remember what we said we were going to do here
188 PH to do something
189
190
191 Change hydrodynamical to "dynamical"
192
193 Examples
194
195 - extra "in action" cases
196
197 o high res ocean with diurnal atmospheric state forcing
198 - links to ingrid output
199 CNH/Dimitris
200
201 o realistic FIZHI from Andrea
202 - links to ingrid output
203 from AM
204
205 o with seaice on high res cube
206 - links to ingrid output
207 CNH/Dimitris
208
209 o coupled aqua, ridge world etc...
210 - links to ingrid output
211 get stuff from Daniel
212
213 o constrained lab simulation
214 - links to ingrid output for model and lab
215 fields
216 get stuff from Sai/Andrew
217
218 o sensitivity wrt to iron
219
220 o optimization
221 - update to link to latest ECCO sites and GF
222 related material
223
224 o eddy diffusivity transport application
225
226 o Gas giant?
227
228
229 >>>> from JM
230
231
232 manual, section.2 :
233
234 In general:
235 - add more refences/links to S/R & variable name
236 - would be nice to have an active link to the fortran-file
237 for all the S/R & eq.Number in the "calling-tree" boxes
238 - search for CALC_MOM_RHS and replace it by the appropriate S/R
239 (mom_flux_form, mom_vecinv, dynamics)
240 - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
241 was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
242 in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
243 simply written \vec{v}.
244 I would suggest to keep the notation as they are (since they are consistent
245 inside each section) but may be to move the "notation.tex" piece
246 at the beginning of section.2 and to mention clearly the changes between
247 the 2 sections.
248
249 in content: Horizontal Dissipation: 2 times in vector-invariant section
250
251 2.1 time-stepping (part2/time_stepping.tex)
252
253 - this is not clear to me:
254
255 >> In all the above configurations it is also possible to substitute the
256 >> Adams-Bashforth with an alternative time-stepping scheme for terms
257 >> evaluated explicitly in time
258
259
260 2.2 rigid-lid:
261
262 - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
263 to stay closer to the code.
264 - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
265
266 2.3 linear free-surface:
267 - add ref(+link) to S/R names:
268 - add ref(+link) to Crank-Nickelson section 2.9.1
269
270 2.4 Adams-Bashforth
271 - add stability diagrams (I have some figures that I can put)
272 - add link for var. forcing_In_AB
273 - add S/R link for S/R ADAMS_BASHFORTH2
274
275 2.5 Implicit time-stepping
276 - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
277 SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
278 - update: also used for vertical advection
279
280 2.6 Synchronous time-stepping:
281 - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
282 MOMENTUM_CORRECTION_STEP.
283
284 2.7 Stagger baroclinic time-stepping
285 - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
286
287 2.8 NH
288 - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
289
290 2.9 Variants on Free-Surface
291 - Delta.t mis-written (eq.2.73)
292 - Eq.Num missing (has been fixed since)
293 - u* is stored in gU (and not in gUnm1)
294 - Phi_nh in NH_VARS.h
295 - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
296 INI_CG2D, INI_CG3D
297
298 2.9.1 Crank-Nickelson
299 - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
300
301 2.9.2 NLFS
302 - eq.Nb are wrong in html
303 - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
304
305 2.10.1 Notation
306 - Area definition is not really used like this
307
308 >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
309
310 Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
311 the model variables) are used (e.g., see section 2.10.5)
312
313 2.10.5 Horizontal grid:
314 - fig.2.8 : should use Aw,As consistently in this figure description,
315 in the figure itself, as it is in the text.
316 - curvilinear:
317 to add: mention the angle of the grid direction relative to
318 Eastward, Northward direction.
319 + mention horizGridFile= in file "data" (PARM04)
320 - add cylindrical polar grid description
321 need to do a better job of relating model variables to this diagram
322
323
324 2.11 Continuity & Horizontal Pressure gradient terms
325 - mention that d.Phi/dr|s =g if using z coordinate
326 - eq. 2.90 not clear regarding \delta_k(P-E)
327 better to add the free surface eq: d.eta/dt = w_s + P-E
328
329 2.12 Hydrostatic balance
330 - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
331 is hard to find
332 - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
333 and in section 1.3.4: remove the 1.3.4.3.2 subsection:
334 Quasi-nonhydrostatic Atmosphere
335
336 2.13.2 Coriolis terms
337 - note: the discretization used when useEnergyConservingCoriolis=T
338 has no hFac and no Area and is still different from the form
339 described here (with Area & hFac);
340
341 2.13.5 Lateral dissipation
342 - add description of how to use cosFactor & cosPower
343 - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
344 o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
345 in code need to explain why cos()3/2 turns out to be
346 scaling (not cos()2)
347 - need to reference the smag/leith section.
348
349 2.13.6 Vertical dissipation
350 - mention the implicit vertical viscosity option and ref to section 2.5
351 - add the parameter correspondence: Av <-> viscAr (and might change also
352 the notation to Ar)
353
354 2.14 Vector invariant momentum equations
355 - indicate that the NH pieces (vertical momentum eq) are not yet coded
356 and that the NH code uses the flux form.
357
358 2.14.6 Horizontal dissipation -> Horizontal Divergence
359
360 2.14.7 Horizontal dissipation
361 - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
362 and A_D4,A_z4 <-> viscA4D,viscA4Z
363
364 2.16 & 2.17 & 2.18 :
365 - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
366 - fix equations 2.202 & 2.203 (thanks to Martin)
367
368 2.20.2 mercator, non-dimensional Equations:
369 - does not use std notation
370 - would be better as an appendix of section 2.20:
371 (e.g changing the tile to:
372 - talk to Baylor
373 Appendix: non-dimensional Equations on Spherical-Polar grid.)
374
375
376 JM
377
378
379 >>>> From Andrea
380
381 Chapter 3
382 --------
383
384 Almost all of the 'math mode' text is dropped down as subscripts
385
386 3.1 - don't need a link to the outside of the document (remove it)
387 - link to htdig is broken
388
389 3.2.1 - link at bottom to source code points to section 3.2.1
390 (ie, to itself) - link should point to cvs code archive
391
392 3.2.2.1 - ('upgrading from an earlier version') belongs under
393 the cvs part, ie, should be 3.2.1.1
394
395 3.3 - remove reference to 'diags' section under MITgcm
396 - remove reference to 'exe' and 'bin' sections also
397 (remove the .cvsignore file under these directories in cvs)
398 - add a 'jobs' section, and a description as examples of run scripts
399 - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions
400 - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'
401 - under 'tools' the adjoint points to section 5 - this is now section 8
402 (but should be a floating reference)
403 - under 'utils' add a reference to exch2 - stuff for different resolutions
404 - the description of the pkg section refers directly to
405 section 3. should be section 6 (actually should be a floating reference)
406
407 3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
408 3.4.1 - links to the following experiments don't exist or are broken:
409 exp2 - should link to section 3.9
410 hs94.cs-32x32x5 - link to section 3.12
411 add 'convection' to the list, link to section 3.13
412 add 'plume on slope` to the list, link to section 3.14
413 add '??' link to section 3.15
414 add 'dic_example on slope` to the list, link to section 3.16
415 add '??' link to section 3.17
416 add 'offline' and link to section 3.18
417 clean up others and make links where they are needed
418 3.4.2 - text suggests to see section 2 for details about what is in the 'code'
419 and 'input' directories - should refer to the examples in this section
420 - add 'build' bullet - this is where the model is compiled and exectuable lives
421
422 3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
423 as the place where they live (add a link?)
424
425 3.6.1 - Add some general 'approach' text - ie, output is controlled either by the
426 'data' file in the input directory or by the data.[pkg name] file for any
427 package running. And there is some default behavior when the 'state' dumps
428 are written.
429 3.6.1.2 - needs to be moved to inside section 3.6.2
430
431 All the 'overview' sections need some reference to the name of the experiment in
432 the verification directory
433
434 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
435 - is this experiment in the list from section 3.4???
436 3.10.3.1 - refers to figures and equations, links are broken
437
438 3.11.3.2 - line 43: link to equation is broken
439 - line 51-53: link to equation is broken
440 - there is some mess of text hanging around the end of this section. remove? reformat?
441
442 3.12.4.1 - line 34 - link to equation is broken
443 - lines 60,61 - 1st (take out the 'r' in the superscript)
444
445 3.13.2 - link to theta-equation is broken
446 3.13.5.4 -- ALL of the bold links to variable names are broken
447 line 34: link to equation is broken
448
449 3.15.1 - reference to 'fourth experiment' should be removed
450
451 3.16.4 - strange formatting, presence of '>' symbols - remove them
452
453 3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
454 3.17.3.1 - nothing filled in under file input/data - needs description
455
456 3.18.2 - point to section 2 for details - need hyperlink
457
458 3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
459 section 3.5 has the 'build' directory in the example
460
461 3.20.1 - link to doc at end of section points to this section
462 3.20.2 - link to doc at end of section points to this section
463
464 offline - duplicate inputs, what is it, tidy up cfc v.
465 other offline. JM thinks these need tidying up.
466
467 Which of the following are which tutorial?
468 adjustment.128x64x1
469 adjustment.cs-32x32x1
470 advect_cs
471 advect_xy
472 advect_xz
473 aim.5l_cs
474 aim.5l_Equatorial_Channel
475 aim.5l_LatLon
476 biogeo
477 bottom_ctrl_5x5
478 cfc_example
479 cpl_aim+ocn
480 dome
481 exp2
482 exp4
483 exp5
484 fizhi-cs-32x32x10
485 fizhi-cs-aqualev20
486 fizhi-gridalt-hs
487 flt_example
488 front_relax
489 global1x1_tot
490 global2x2_tot
491 global_ocean.90x40x15
492 global_ocean.cs32x15
493 global_ocean.cubed32x32x30
494 global_ocean_ebm
495 global_with_exf
496 hs94.128x64x5
497 hs94.1x64x5
498 hs94.cs-32x32x5
499 ideal_2D_oce
500 internal_wave
501 inverted_barometer
502 lab_sea
503 matrix_example
504 MLAdjust
505 natl_box
506 natl_box_adjoint
507 OpenAD
508 rotating_tank
509 solid-body.cs-32x32x1
510 tidal_basin_2d
511 tutorial_baroclinic_gyre
512 tutorial_barotropic_gyre
513 tutorial_cfc_offline
514 tutorial_deep_convection
515 tutorial_global_oce_biogeo
516 tutorial_global_oce_in_p
517 tutorial_global_oce_latlon
518 tutorial_global_oce_optim
519 tutorial_held_suarez_cs
520 tutorial_offline
521 tutorial_plume_on_slope
522 tutorial_tracer_adjsens
523 vermix
524
525 >>>> From Ed
526
527 Here are the remaining bits for Chap 4 :
528
529 - missing references (if you point me towards URLs, I'll add them
530 to the bibliography):
531 \ref{ref hoe and hill, ecmwf}
532 \ref{magicgarden}
533 \ref{IBMLAPI}
534 \ref{Memorychannel}
535 \ref{hoe-hill:99}
536
537 - There are a few empty sub-sections at the end of Chap 4 that
538 should either be commented out or fleshed out.
539
540 and thats about it for Chap 4.
541
542
543 Add more to quick links on front page
544
545 Chapter 6
546
547 the master package diagram does not appear in the document
548
549 Master list of packages (add this to beginning of chap 6)
550
551 admtlm/ - autodiff (chapter 5)
552 aim/ - retired
553 aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM)
554 aim_ocn_coupler/ - 6.6 (no content yet)
555 aim_v23/ - 6.4.1 (content needs fixing - JM to do)
556 atm_common/ - nothing in this package (6.4.1 related)
557 autodiff/ - autodiff (chapter 5)
558 bulk_force/ - 6.3.3
559 cal/ - 6.3.5
560 cd_code/ - chapter 2 (JM check add a reference to paper,
561 mention parameter in data)
562 cfc/ - not sure (CNH to talk to Steph and Helen)
563 chronos/ - AM to check (not being used - Andrea to kill it)
564 compon_communic/ - 6.6 (no content yet)(Daniel + JM)
565 cost/ - not sure, check with PH
566 ctrl/ - not sure, check with PH
567 debug/ - JM may do something in chapter 7 (utilities)
568 diagnostics/ - 7.1
569 dic/ - 6.7.2
570 ebm/ - (check with PH)
571 ecco/ - chapter 8
572 embed_files/ - add something to chapter 7
573 exch2/ - 6.2.2
574 exf/ - 6.3.4
575 fizhi/ - 6.4.3
576 flt/ - (PH check)
577 gchem/ - 6.7.1
578 generic_advdiff/ - in chapter 2 (JM check)
579 ggl90/ - nothing, (Martin?)
580 gmredi/ - in chapter 2 (JM check). also need
581 Ferrari & Mc transition zone stuff (Samar doing this)
582 get dfer to read this
583 grdchk/ - grdchk (chapter 5 - check with PH)
584 gridalt/ - 6.2.4
585 kpp/ - 6.3.2
586 land/ - 6.4.2 (not connected to code Rong's notes - JM to fix)
587 matrix/ - Samar
588 mdsio/ - 7.3.1
589 mnc/ - 7.2.1
590 mom_common/ - in chapter 2 (JM check)
591 mom_fluxform/ - in chapter 2 (JM check)
592 mom_vecinv/ - in chapter 2 (JM check)
593 monitor/ - 7.4
594 my82/ - nothing, (martin?)
595 obcs/ - 6.3 (needs a check - ask PH to read)
596 ocn_compon_interf/ - 6.6 (no content yet)
597 offline/ - nothing, tutorials that need work but no package section entry
598 trivial to document (CNH to do)
599 opps/ - nothing, (martin?)
600 pp81/ - nothing, (martin?)
601 profiles/ - GAEL
602 ptracers/ - JM + SD + Martin to write something (nothing for this
603 at the moment)
604 AM has diagnostics table for this.
605 rbcs/ - CNH to talk to steph
606 runclock/ - runclock - CNH
607 rw/ - not sure - going to stay says JMC. quick IO calls
608 JMC to write a quick note for that.
609 sbo/ - text in sbo_descruption.tex but not linked into
610 part6 - CNH
611 seaice/ - 6.5.2 - no equations, dimitris has promised some
612 shap_filt/ - chapter 2, JM to check
613 shelfice/ - nothing yet (martin?)
614 solver/ - empty (go away?)
615 sphere/ - chapter 5 or 8 (PH to check)
616 therm_seaice/ - empty (go away?)
617 thsice/ - 6.5.1 (JM to update?)
618 timeave/ - retiring......
619 zonal_filt/ - chapter 2 (JM to check)
620
621 list an expeiment which uses package? CNH
622
623 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
624 Figure 6.8 is missing
625
626
627 ===== Chapter 7 ===== [EH3 editing] :
628
629 7.1.1 - links to section 7.1.4: the text of the first
630 one should read "see MITgcm Kernel Diagnostics Menu"
631 the links are pointing to the proper place
632
633 7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
634
635 7.5.2 - get bathymetry pre-processing stuff from Patrick
636 and then describe it
637
638
639 andrea
640
641
642 9. Publications using MITgcm --> "Previous Applications of MITgcm"
643 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
644 (check in support for more names)
645
646 10. Under development
647
648
649 Bibliography
650
651 tidy up from misc - .tex

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