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Revision 1.37 - (show annotations) (download)
Wed Jun 28 15:11:42 2006 UTC (17 years, 9 months ago) by cnh
Branch: MAIN
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One more thing to remember

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 Rebuild and set to do cron build - DONE on hugo
30
31 To do
32
33 - where to put under development links?
34 JMC would like to have some mention of unfinished things (checked in
35 but not that tested e.g. AB3)
36 Add an "Under development, chapter" - shortish description of what
37 is available (last chapter)
38
39 - add in example latex for formatting author names in different pieces.
40 this aknowledges peoples contributions and gives ref for who
41 to talk to.
42
43 o HTML, scripts and front content
44
45 - pick a URL
46 TBD
47
48 - mitgcm.org/r2_web_testing/latest
49 o add another short-cut for quick download
50
51 o add another short-cut
52 About
53 Installation
54 Contents
55 Overview
56 Tutorials (broken)
57 Browse Code
58
59 o words on http://mitgcm.org/r2_web_testing/latest
60 change to
61 "access on-line Auser manual/A and Atable of contents/A
62 and browse the Aoverview section/A"
63
64 o finite-volume doesn't leap to FV figure
65
66 o have another go at pnmcrop et al.
67
68 o Need an empty package as part of distribution. Check out atm_common
69
70 o Latex
71
72 Chapter 1 - CNH
73 o single kernel diagram -
74 add reference to MWR paper
75
76 o non-hydro
77 add reference to 1995 and 1999 papers
78 pdf of 1995 paper
79
80 o FV
81 add references to 1997 papers.
82
83 o Tangent linear/adjoint add reference to
84 Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc...
85
86 o platforms
87 Add reference to SC article and Scientific Programming article
88
89 o List of key papers needs to be updated and reformatted
90
91 o Global atmosphere: `Held Suarez',
92 update Adcroft reference
93 fix up ingrid link and frame (ingrid movies seem to be broken?)
94 Held and Suarez reference is not a link.
95
96 o Ocean Gyres
97 fix up frame link
98 make "lopped cell" a link to referenced paper.
99 add references (ask Steph/Mick)
100 online/offline paper
101
102 o Convection and mixing over topography
103 add in Legg references for convection and mixing over topography
104 and external link to CPT-GCE etc...
105
106 o Boundary forced internal waves
107 add in Legg references, obc's reference
108
109 o Parameter sensitivity
110 add in Bugnion references, Boyin references, Steph references
111
112 o State estimation
113 add in references from Patrick/Carl/Ichiro/Detlef etc...
114 update links to point to latest ECCO results
115 ECCO ingrid results have been moved
116 add forward links to "ECCO state estimation" chapter in manual
117
118 o Ocean biogeochemical cycles
119 add in references from Mick/Galen etc...
120 fix ingrid link ( date to date thing does not appear to work)
121 figure url does not have a "target=idontexist" entry
122
123 o Simulations of laboratory experiments
124 reference Wardle and Karsten papers
125 update links to include DDDAS "PIAB" page
126 cylindrical polar coordinates
127
128 o Continuos equations in ''r'' coordinates
129 add references to iso paper
130 no mention of z* and p* - forward reference to z*/p* in 2.
131 add that coupling also manifests through F, Q
132 add tracer transport
133
134 o Kinematic boundary conditions
135
136 o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
137 Non-hydrostatic forms
138 need to tidy up discussion of shallow-atmosphere to be
139 consistent with the code or change code to be consistent
140 with the discussion!
141 make references hyperlinks
142 add stuff too
143 JMC remove QNH atmosphere
144 need to sort out calc_gw for deep atmosphere
145
146 o Finding the pressure field
147 make references hyperlinks
148 add forward references to manual algorithm section
149 change Elliptic to "elliptic"
150
151 o Forcing and dissipation
152 make "physics packages" refer to chapter 6.
153 should we move "external forcing" et. al to a
154 generic_forcing_driver package?
155
156 viscosities
157 update to mention Smag/Leith (Ah and A4 not constant)
158 and to have forward references to numerical section
159 tracers
160 forward references to numerical section, reddy, GM etc...
161 add references to literature
162
163 o 1.3.8 Vector invariant form
164 forward references to numerical section
165
166 o 1.3.9 Adjoint
167 add a little more here + some hyperlink to chapter 5.
168
169 o 1.4 Appendix ATMOSPHERE
170
171 add some introductory words
172
173 o 1.6 Coordinate systems
174 o only has some words on spherical polar. add some brief words
175 to cover all of
176 - cartesian
177 - spherical
178 - cylindrical
179 - general orthogonal curvilinear (vector invariant)
180
181 o Equation of state options
182 add some discussion
183 can't remember what we said we were going to do here
184 PH to do something
185
186
187 Change hydrodynamical to "dynamical"
188
189 Examples
190
191 - extra "in action" cases
192
193 o high res ocean with diurnal atmospheric state forcing
194 - links to ingrid output
195 CNH/Dimitris
196
197 o realistic FIZHI from Andrea
198 - links to ingrid output
199 from AM
200
201 o with seaice on high res cube
202 - links to ingrid output
203 CNH/Dimitris
204
205 o coupled aqua, ridge world etc...
206 - links to ingrid output
207 get stuff from Daniel
208
209 o constrained lab simulation
210 - links to ingrid output for model and lab
211 fields
212 get stuff from Sai/Andrew
213
214 o sensitivity wrt to iron
215
216 o optimization
217 - update to link to latest ECCO sites and GF
218 related material
219
220 o eddy diffusivity transport application
221
222 o Gas giant?
223
224
225 >>>> from JM
226
227
228 manual, section.2 :
229
230 In general:
231 - add more refences/links to S/R & variable name
232 - would be nice to have an active link to the fortran-file
233 for all the S/R & eq.Number in the "calling-tree" boxes
234 - search for CALC_MOM_RHS and replace it by the appropriate S/R
235 (mom_flux_form, mom_vecinv, dynamics)
236 - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
237 was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
238 in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
239 simply written \vec{v}.
240 I would suggest to keep the notation as they are (since they are consistent
241 inside each section) but may be to move the "notation.tex" piece
242 at the beginning of section.2 and to mention clearly the changes between
243 the 2 sections.
244
245 in content: Horizontal Dissipation: 2 times in vector-invariant section
246
247 2.1 time-stepping (part2/time_stepping.tex)
248
249 - this is not clear to me:
250
251 >> In all the above configurations it is also possible to substitute the
252 >> Adams-Bashforth with an alternative time-stepping scheme for terms
253 >> evaluated explicitly in time
254
255
256 2.2 rigid-lid:
257
258 - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
259 to stay closer to the code.
260 - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
261
262 2.3 linear free-surface:
263 - add ref(+link) to S/R names:
264 - add ref(+link) to Crank-Nickelson section 2.9.1
265
266 2.4 Adams-Bashforth
267 - add stability diagrams (I have some figures that I can put)
268 - add link for var. forcing_In_AB
269 - add S/R link for S/R ADAMS_BASHFORTH2
270
271 2.5 Implicit time-stepping
272 - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
273 SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
274 - update: also used for vertical advection
275
276 2.6 Synchronous time-stepping:
277 - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
278 MOMENTUM_CORRECTION_STEP.
279
280 2.7 Stagger baroclinic time-stepping
281 - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
282
283 2.8 NH
284 - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
285
286 2.9 Variants on Free-Surface
287 - Delta.t mis-written (eq.2.73)
288 - Eq.Num missing (has been fixed since)
289 - u* is stored in gU (and not in gUnm1)
290 - Phi_nh in NH_VARS.h
291 - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
292 INI_CG2D, INI_CG3D
293
294 2.9.1 Crank-Nickelson
295 - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
296
297 2.9.2 NLFS
298 - eq.Nb are wrong in html
299 - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
300
301 2.10.1 Notation
302 - Area definition is not really used like this
303
304 >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
305
306 Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
307 the model variables) are used (e.g., see section 2.10.5)
308
309 2.10.5 Horizontal grid:
310 - fig.2.8 : should use Aw,As consistently in this figure description,
311 in the figure itself, as it is in the text.
312 - curvilinear:
313 to add: mention the angle of the grid direction relative to
314 Eastward, Northward direction.
315 + mention horizGridFile= in file "data" (PARM04)
316 - add cylindrical polar grid description
317 need to do a better job of relating model variables to this diagram
318
319
320 2.11 Continuity & Horizontal Pressure gradient terms
321 - mention that d.Phi/dr|s =g if using z coordinate
322 - eq. 2.90 not clear regarding \delta_k(P-E)
323 better to add the free surface eq: d.eta/dt = w_s + P-E
324
325 2.12 Hydrostatic balance
326 - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
327 is hard to find
328 - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
329 and in section 1.3.4: remove the 1.3.4.3.2 subsection:
330 Quasi-nonhydrostatic Atmosphere
331
332 2.13.2 Coriolis terms
333 - note: the discretization used when useEnergyConservingCoriolis=T
334 has no hFac and no Area and is still different from the form
335 described here (with Area & hFac);
336
337 2.13.5 Lateral dissipation
338 - add description of how to use cosFactor & cosPower
339 - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
340 o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
341 in code need to explain why cos()3/2 turns out to be
342 scaling (not cos()2)
343 - need to reference the smag/leith section.
344
345 2.13.6 Vertical dissipation
346 - mention the implicit vertical viscosity option and ref to section 2.5
347 - add the parameter correspondence: Av <-> viscAr (and might change also
348 the notation to Ar)
349
350 2.14 Vector invariant momentum equations
351 - indicate that the NH pieces (vertical momentum eq) are not yet coded
352 and that the NH code uses the flux form.
353
354 2.14.6 Horizontal dissipation -> Horizontal Divergence
355
356 2.14.7 Horizontal dissipation
357 - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
358 and A_D4,A_z4 <-> viscA4D,viscA4Z
359
360 2.16 & 2.17 & 2.18 :
361 - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
362 - fix equations 2.202 & 2.203 (thanks to Martin)
363
364 2.20.2 mercator, non-dimensional Equations:
365 - does not use std notation
366 - would be better as an appendix of section 2.20:
367 (e.g changing the tile to:
368 - talk to Baylor
369 Appendix: non-dimensional Equations on Spherical-Polar grid.)
370
371
372 Diagrams of grid locations etc.... and what variables and output files
373 and/or netcdf variable names are not very easy to figure out and follow.
374 It would be good to redo and extend these diagrams and align with GRID.h
375 content.
376
377
378 JM
379
380
381 >>>> From Andrea
382
383 Chapter 3
384 --------
385
386 Almost all of the 'math mode' text is dropped down as subscripts
387
388 3.1 - don't need a link to the outside of the document (remove it)
389 - link to htdig is broken
390
391 3.2.1 - link at bottom to source code points to section 3.2.1
392 (ie, to itself) - link should point to cvs code archive
393
394 3.2.2.1 - ('upgrading from an earlier version') belongs under
395 the cvs part, ie, should be 3.2.1.1
396
397 3.3 - remove reference to 'diags' section under MITgcm
398 - remove reference to 'exe' and 'bin' sections also
399 (remove the .cvsignore file under these directories in cvs)
400 - add a 'jobs' section, and a description as examples of run scripts
401 - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions
402 - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'
403 - under 'tools' the adjoint points to section 5 - this is now section 8
404 (but should be a floating reference)
405 - under 'utils' add a reference to exch2 - stuff for different resolutions
406 - the description of the pkg section refers directly to
407 section 3. should be section 6 (actually should be a floating reference)
408
409 3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
410 3.4.1 - links to the following experiments don't exist or are broken:
411 exp2 - should link to section 3.9
412 hs94.cs-32x32x5 - link to section 3.12
413 add 'convection' to the list, link to section 3.13
414 add 'plume on slope` to the list, link to section 3.14
415 add '??' link to section 3.15
416 add 'dic_example on slope` to the list, link to section 3.16
417 add '??' link to section 3.17
418 add 'offline' and link to section 3.18
419 clean up others and make links where they are needed
420 3.4.2 - text suggests to see section 2 for details about what is in the 'code'
421 and 'input' directories - should refer to the examples in this section
422 - add 'build' bullet - this is where the model is compiled and exectuable lives
423
424 3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
425 as the place where they live (add a link?)
426
427 3.6.1 - Add some general 'approach' text - ie, output is controlled either by the
428 'data' file in the input directory or by the data.[pkg name] file for any
429 package running. And there is some default behavior when the 'state' dumps
430 are written.
431 3.6.1.2 - needs to be moved to inside section 3.6.2
432
433 All the 'overview' sections need some reference to the name of the experiment in
434 the verification directory
435
436 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
437 - is this experiment in the list from section 3.4???
438 3.10.3.1 - refers to figures and equations, links are broken
439
440 3.11.3.2 - line 43: link to equation is broken
441 - line 51-53: link to equation is broken
442 - there is some mess of text hanging around the end of this section. remove? reformat?
443
444 3.12.4.1 - line 34 - link to equation is broken
445 - lines 60,61 - 1st (take out the 'r' in the superscript)
446
447 3.13.2 - link to theta-equation is broken
448 3.13.5.4 -- ALL of the bold links to variable names are broken
449 line 34: link to equation is broken
450
451 3.15.1 - reference to 'fourth experiment' should be removed
452
453 3.16.4 - strange formatting, presence of '>' symbols - remove them
454
455 3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
456 3.17.3.1 - nothing filled in under file input/data - needs description
457
458 3.18.2 - point to section 2 for details - need hyperlink
459
460 3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
461 section 3.5 has the 'build' directory in the example
462
463 3.20.1 - link to doc at end of section points to this section
464 3.20.2 - link to doc at end of section points to this section
465
466 offline - duplicate inputs, what is it, tidy up cfc v.
467 other offline. JM thinks these need tidying up.
468
469 Which of the following are which tutorial?
470 adjustment.128x64x1
471 adjustment.cs-32x32x1
472 advect_cs
473 advect_xy
474 advect_xz
475 aim.5l_cs
476 aim.5l_Equatorial_Channel
477 aim.5l_LatLon
478 biogeo
479 bottom_ctrl_5x5
480 cfc_example
481 cpl_aim+ocn
482 dome
483 exp2
484 exp4
485 exp5
486 fizhi-cs-32x32x10
487 fizhi-cs-aqualev20
488 fizhi-gridalt-hs
489 flt_example
490 front_relax
491 global1x1_tot
492 global2x2_tot
493 global_ocean.90x40x15
494 global_ocean.cs32x15
495 global_ocean.cubed32x32x30
496 global_ocean_ebm
497 global_with_exf
498 hs94.128x64x5
499 hs94.1x64x5
500 hs94.cs-32x32x5
501 ideal_2D_oce
502 internal_wave
503 inverted_barometer
504 lab_sea
505 matrix_example
506 MLAdjust
507 natl_box
508 natl_box_adjoint
509 OpenAD
510 rotating_tank
511 solid-body.cs-32x32x1
512 tidal_basin_2d
513 tutorial_baroclinic_gyre
514 tutorial_barotropic_gyre
515 tutorial_cfc_offline
516 tutorial_deep_convection
517 tutorial_global_oce_biogeo
518 tutorial_global_oce_in_p
519 tutorial_global_oce_latlon
520 tutorial_global_oce_optim
521 tutorial_held_suarez_cs
522 tutorial_offline
523 tutorial_plume_on_slope
524 tutorial_tracer_adjsens
525 vermix
526
527 >>>> From Ed
528
529 Here are the remaining bits for Chap 4 :
530
531 - missing references (if you point me towards URLs, I'll add them
532 to the bibliography):
533 \ref{ref hoe and hill, ecmwf}
534 \ref{magicgarden}
535 \ref{IBMLAPI}
536 \ref{Memorychannel}
537 \ref{hoe-hill:99}
538
539 - There are a few empty sub-sections at the end of Chap 4 that
540 should either be commented out or fleshed out.
541
542 and thats about it for Chap 4.
543
544
545 Add more to quick links on front page
546
547 Chapter 6
548
549 the master package diagram does not appear in the document
550
551 Master list of packages (add this to beginning of chap 6)
552
553 admtlm/ - autodiff (chapter 5)
554 aim/ - retired
555 aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM)
556 aim_ocn_coupler/ - 6.6 (no content yet)
557 aim_v23/ - 6.4.1 (content needs fixing - JM to do)
558 atm_common/ - nothing in this package (6.4.1 related)
559 autodiff/ - autodiff (chapter 5)
560 bulk_force/ - 6.3.3
561 cal/ - 6.3.5
562 cd_code/ - chapter 2 (JM check add a reference to paper,
563 mention parameter in data)
564 cfc/ - not sure (CNH to talk to Steph and Helen)
565 chronos/ - AM to check (not being used - Andrea to kill it)
566 compon_communic/ - 6.6 (no content yet)(Daniel + JM)
567 cost/ - not sure, check with PH
568 ctrl/ - not sure, check with PH
569 debug/ - JM may do something in chapter 7 (utilities)
570 diagnostics/ - 7.1
571 dic/ - 6.7.2
572 ebm/ - (check with PH)
573 ecco/ - chapter 8
574 embed_files/ - add something to chapter 7
575 exch2/ - 6.2.2
576 exf/ - 6.3.4
577 fizhi/ - 6.4.3
578 flt/ - (PH check)
579 gchem/ - 6.7.1
580 generic_advdiff/ - in chapter 2 (JM check)
581 ggl90/ - nothing, (Martin?)
582 gmredi/ - in chapter 2 (JM check). also need
583 Ferrari & Mc transition zone stuff (Samar doing this)
584 get dfer to read this
585 grdchk/ - grdchk (chapter 5 - check with PH)
586 gridalt/ - 6.2.4
587 kpp/ - 6.3.2
588 land/ - 6.4.2 (not connected to code Rong's notes - JM to fix)
589 matrix/ - Samar
590 mdsio/ - 7.3.1
591 mnc/ - 7.2.1
592 mom_common/ - in chapter 2 (JM check)
593 mom_fluxform/ - in chapter 2 (JM check)
594 mom_vecinv/ - in chapter 2 (JM check)
595 monitor/ - 7.4
596 my82/ - nothing, (martin?)
597 obcs/ - 6.3 (needs a check - ask PH to read)
598 ocn_compon_interf/ - 6.6 (no content yet)
599 offline/ - nothing, tutorials that need work but no package section entry
600 trivial to document (CNH to do)
601 opps/ - nothing, (martin?)
602 pp81/ - nothing, (martin?)
603 profiles/ - GAEL
604 ptracers/ - JM + SD + Martin to write something (nothing for this
605 at the moment)
606 AM has diagnostics table for this.
607 rbcs/ - CNH to talk to steph
608 runclock/ - runclock - CNH
609 rw/ - not sure - going to stay says JMC. quick IO calls
610 JMC to write a quick note for that.
611 sbo/ - text in sbo_descruption.tex but not linked into
612 part6 - CNH
613 seaice/ - 6.5.2 - no equations, dimitris has promised some
614 shap_filt/ - chapter 2, JM to check
615 shelfice/ - nothing yet (martin?)
616 solver/ - empty (go away?)
617 sphere/ - chapter 5 or 8 (PH to check)
618 therm_seaice/ - empty (go away?)
619 thsice/ - 6.5.1 (JM to update?)
620 timeave/ - retiring......
621 zonal_filt/ - chapter 2 (JM to check)
622
623 list an expeiment which uses package? CNH
624
625 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
626 Figure 6.8 is missing
627
628
629 ===== Chapter 7 ===== [EH3 editing] :
630
631 7.1.x - JMC: please add description of:
632 - diagstat
633 - new temporal averaging feature
634
635 7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
636
637 7.5.2 - get bathymetry pre-processing stuff from Patrick
638 and then describe it
639
640 add something on spgrid mesh generator (maybe)?
641
642
643 andrea
644
645
646 9. Publications using MITgcm --> "Previous Applications of MITgcm"
647 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
648 (check in support for more names)
649
650 10. Under development
651
652 Constantinos LCML
653
654
655 Bibliography
656
657 tidy up from misc - .tex

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