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Revision 1.41 - (show annotations) (download)
Wed Jun 28 17:21:21 2006 UTC (17 years, 9 months ago) by molod
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Remove some more stuff that is done

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 Davids donut movie
209
210 o constrained lab simulation
211 - links to ingrid output for model and lab
212 fields
213 get stuff from Sai/Andrew
214
215 o sensitivity wrt to iron
216
217 o optimization
218 - update to link to latest ECCO sites and GF
219 related material
220
221 o eddy diffusivity transport application
222
223 o Gas giant?
224
225
226 >>>> from JM
227
228
229 manual, section.2 :
230
231 In general:
232 - add more refences/links to S/R & variable name
233 - would be nice to have an active link to the fortran-file
234 for all the S/R & eq.Number in the "calling-tree" boxes
235 - search for CALC_MOM_RHS and replace it by the appropriate S/R
236 (mom_flux_form, mom_vecinv, dynamics) <- DONE
237 - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
238 was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
239 in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
240 simply written \vec{v}.
241 I would suggest to keep the notation as they are (since they are consistent
242 inside each section) but may be to move the "notation.tex" piece
243 at the beginning of section.2 and to mention clearly the changes between
244 the 2 sections.
245
246 in content: Horizontal Dissipation: 2 times in vector-invariant section
247 <- DONE
248
249 2.1 time-stepping (part2/time_stepping.tex)
250
251 - this is not clear to me:
252
253 >> In all the above configurations it is also possible to substitute the
254 >> Adams-Bashforth with an alternative time-stepping scheme for terms
255 >> evaluated explicitly in time
256 <- Leave it general.
257
258
259 2.2 rigid-lid:
260
261 - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
262 to stay closer to the code.
263 - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
264
265 2.3 linear free-surface:
266 - add ref(+link) to S/R names:
267 - add ref(+link) to Crank-Nickelson section 2.9.1
268
269 2.4 Adams-Bashforth
270 - add stability diagrams (I have some figures that I can put)
271 - add link for var. forcing_In_AB
272 - add S/R link for S/R ADAMS_BASHFORTH2
273
274 2.5 Implicit time-stepping
275 - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
276 SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
277 - update: also used for vertical advection
278
279 2.6 Synchronous time-stepping:
280 - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
281 MOMENTUM_CORRECTION_STEP.
282
283 2.7 Stagger baroclinic time-stepping
284 - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
285
286 2.8 NH
287 - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
288
289 2.9 Variants on Free-Surface
290 - Delta.t mis-written (eq.2.73) <- DONE
291 - Eq.Num missing <- DONE
292 - u* is stored in gU (and not in gUnm1) <- DONE
293 - Phi_nh in NH_VARS.h <- DONE
294 - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
295 INI_CG2D, INI_CG3D
296
297 2.9.1 Crank-Nickelson
298 - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
299
300 2.9.2 NLFS
301 - eq.Nb are wrong in html
302 - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
303 <- DONE
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 <- DONE
313
314 2.10.5 Horizontal grid:
315 - fig.2.8 : should use Aw,As consistently in this figure description,
316 in the figure itself, as it is in the text. <- DONE
317 - curvilinear:
318 to add: mention the angle of the grid direction relative to
319 Eastward, Northward direction.
320 + mention horizGridFile= in file "data" (PARM04)
321 - add cylindrical polar grid description
322 need to do a better job of relating model variables to this diagram
323
324
325 2.11 Continuity & Horizontal Pressure gradient terms
326 - mention that d.Phi/dr|s =g if using z coordinate
327 - eq. 2.90 not clear regarding \delta_k(P-E)
328 better to add the free surface eq: d.eta/dt = w_s + P-E
329
330 2.12 Hydrostatic balance
331 - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
332 is hard to find
333 - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
334 and in section 1.3.4: remove the 1.3.4.3.2 subsection:
335 Quasi-nonhydrostatic Atmosphere
336
337 2.13.2 Coriolis terms
338 - note: the discretization used when useEnergyConservingCoriolis=T
339 has no hFac and no Area and is still different from the form
340 described here (with Area & hFac);
341
342 2.13.5 Lateral dissipation
343 - add description of how to use cosFactor & cosPower
344 - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
345 o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
346 in code need to explain why cos()3/2 turns out to be
347 scaling (not cos()2)
348 - need to reference the smag/leith section.
349
350 2.13.6 Vertical dissipation
351 - mention the implicit vertical viscosity option and ref to section 2.5
352 - add the parameter correspondence: Av <-> viscAr (and might change also
353 the notation to Ar)
354
355 2.14 Vector invariant momentum equations
356 - indicate that the NH pieces (vertical momentum eq) are not yet coded
357 and that the NH code uses the flux form.
358
359 2.14.6 Horizontal dissipation -> Horizontal Divergence
360
361 2.14.7 Horizontal dissipation
362 - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
363 and A_D4,A_z4 <-> viscA4D,viscA4Z
364
365 2.16 & 2.17 & 2.18 :
366 - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
367 - fix equations 2.202 & 2.203 (thanks to Martin) <- DONE
368
369 2.20.2 mercator, non-dimensional Equations:
370 - does not use std notation
371 - would be better as an appendix of section 2.20:
372 (e.g changing the tile to:
373 - talk to Baylor
374 Appendix: non-dimensional Equations on Spherical-Polar grid.)
375 <- No (Chris said)
376
377
378 Diagrams of grid locations etc.... and what variables and output files
379 and/or netcdf variable names are not very easy to figure out and follow.
380 It would be good to redo and extend these diagrams and align with GRID.h
381 content.
382
383
384 JM
385
386
387 >>>> From Andrea
388
389 Chapter 3
390 --------
391
392 Almost all of the 'math mode' text is dropped down as subscripts
393
394 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
395 - is this experiment in the list from section 3.4???
396 3.10.3.1 - refers to figures and equations, links are broken
397
398 3.11.3.2 - line 43: link to equation is broken
399 - line 51-53: link to equation is broken
400 - there is some mess of text hanging around the end of this section. remove? reformat?
401
402 3.12.4.1 - line 34 - link to equation is broken
403 - lines 60,61 - 1st (take out the 'r' in the superscript)
404
405 3.13.2 - link to theta-equation is broken
406 3.13.5.4 -- ALL of the bold links to variable names are broken
407 line 34: link to equation is broken
408
409 3.15.1 - reference to 'fourth experiment' should be removed
410
411 3.16.4 - strange formatting, presence of '>' symbols - remove them
412
413 3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
414 3.17.3.1 - nothing filled in under file input/data - needs description
415
416 3.18.2 - point to section 2 for details - need hyperlink
417
418 3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
419 section 3.5 has the 'build' directory in the example
420
421 3.20.1 - link to doc at end of section points to this section
422 3.20.2 - link to doc at end of section points to this section
423
424 offline - duplicate inputs, what is it, tidy up cfc v.
425 other offline. JM thinks these need tidying up.
426
427 Which of the following are which tutorial?
428 adjustment.128x64x1
429 adjustment.cs-32x32x1
430 advect_cs
431 advect_xy
432 advect_xz
433 aim.5l_cs
434 aim.5l_Equatorial_Channel
435 aim.5l_LatLon
436 biogeo
437 bottom_ctrl_5x5
438 cfc_example
439 cpl_aim+ocn
440 dome
441 exp2
442 exp4
443 exp5
444 fizhi-cs-32x32x10
445 fizhi-cs-aqualev20
446 fizhi-gridalt-hs
447 flt_example
448 front_relax
449 global1x1_tot
450 global2x2_tot
451 global_ocean.90x40x15
452 global_ocean.cs32x15
453 global_ocean.cubed32x32x30
454 global_ocean_ebm
455 global_with_exf
456 hs94.128x64x5
457 hs94.1x64x5
458 hs94.cs-32x32x5
459 ideal_2D_oce
460 internal_wave
461 inverted_barometer
462 lab_sea
463 matrix_example
464 MLAdjust
465 natl_box
466 natl_box_adjoint
467 OpenAD
468 rotating_tank
469 solid-body.cs-32x32x1
470 tidal_basin_2d
471 tutorial_baroclinic_gyre
472 tutorial_barotropic_gyre
473 tutorial_cfc_offline
474 tutorial_deep_convection
475 tutorial_global_oce_biogeo
476 tutorial_global_oce_in_p
477 tutorial_global_oce_latlon
478 tutorial_global_oce_optim
479 tutorial_held_suarez_cs
480 tutorial_offline
481 tutorial_plume_on_slope
482 tutorial_tracer_adjsens
483 vermix
484
485 >>>> From Ed
486
487 Here are the remaining bits for Chap 4 :
488
489 - missing references (if you point me towards URLs, I'll add them
490 to the bibliography):
491 \ref{ref hoe and hill, ecmwf}
492 \ref{magicgarden}
493 \ref{IBMLAPI}
494 \ref{Memorychannel}
495 \ref{hoe-hill:99}
496
497 - There are a few empty sub-sections at the end of Chap 4 that
498 should either be commented out or fleshed out.
499
500 and thats about it for Chap 4.
501
502
503 Add more to quick links on front page
504
505 Chapter 6
506
507 the master package diagram does not appear in the document
508
509 Master list of packages (add this to beginning of chap 6)
510
511 admtlm/ - autodiff (chapter 5)
512 aim/ - retired
513 aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM)
514 aim_ocn_coupler/ - 6.6 (no content yet)
515 aim_v23/ - 6.4.1 (content needs fixing - JM to do)
516 atm_common/ - nothing in this package (6.4.1 related)
517 autodiff/ - autodiff (chapter 5)
518 bulk_force/ - 6.3.3
519 cal/ - 6.3.5
520 cd_code/ - chapter 2 (JM check add a reference to paper,
521 mention parameter in data)
522 cfc/ - not sure (CNH to talk to Steph and Helen)
523 chronos/ - AM to check (not being used - Andrea to kill it)
524 compon_communic/ - 6.6 (no content yet)(Daniel + JM)
525 cost/ - not sure, check with PH
526 ctrl/ - not sure, check with PH
527 debug/ - JM may do something in chapter 7 (utilities)
528 diagnostics/ - 7.1
529 dic/ - 6.7.2
530 ebm/ - (check with PH)
531 ecco/ - chapter 8
532 embed_files/ - add something to chapter 7
533 exch2/ - 6.2.2
534 exf/ - 6.3.4
535 fizhi/ - 6.4.3
536 flt/ - (PH check)
537 gchem/ - 6.7.1
538 generic_advdiff/ - in chapter 2 (JM check)
539 ggl90/ - nothing, (Martin?)
540 gmredi/ - in chapter 2 (JM check). also need
541 Ferrari & Mc transition zone stuff (Samar doing this)
542 get dfer to read this
543 grdchk/ - grdchk (chapter 5 - check with PH)
544 gridalt/ - 6.2.4
545 kpp/ - 6.3.2
546 land/ - 6.4.2 (not connected to code Rong's notes - JM to fix)
547 matrix/ - Samar
548 mdsio/ - 7.3.1
549 mnc/ - 7.2.1
550 mom_common/ - in chapter 2 (JM check)
551 mom_fluxform/ - in chapter 2 (JM check)
552 mom_vecinv/ - in chapter 2 (JM check)
553 monitor/ - 7.4
554 my82/ - nothing, (martin?)
555 obcs/ - 6.3 (needs a check - ask PH to read)
556 ocn_compon_interf/ - 6.6 (no content yet)
557 offline/ - nothing, tutorials that need work but no package section entry
558 trivial to document (CNH to do)
559 opps/ - nothing, (martin?)
560 pp81/ - nothing, (martin?)
561 profiles/ - GAEL
562 ptracers/ - JM + SD + Martin to write something (nothing for this
563 at the moment)
564 AM has diagnostics table for this.
565 rbcs/ - CNH to talk to steph
566 runclock/ - runclock - CNH
567 rw/ - not sure - going to stay says JMC. quick IO calls
568 JMC to write a quick note for that.
569 sbo/ - text in sbo_descruption.tex but not linked into
570 part6 - CNH
571 seaice/ - 6.5.2 - no equations, dimitris has promised some
572 shap_filt/ - chapter 2, JM to check
573 shelfice/ - nothing yet (martin?)
574 solver/ - empty (go away?)
575 sphere/ - chapter 5 or 8 (PH to check)
576 therm_seaice/ - empty (go away?)
577 thsice/ - 6.5.1 (JM to update?)
578 timeave/ - retiring......
579 zonal_filt/ - chapter 2 (JM to check)
580
581 list an expeiment which uses package? CNH
582
583 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
584 Figure 6.8 is missing
585
586
587 ===== Chapter 7 ===== [EH3 editing] :
588
589 7.1.x - JMC: please add description of:
590 - diagstat
591 - new temporal averaging feature
592
593 7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
594
595 7.5.2 - get bathymetry pre-processing stuff from Patrick
596 and then describe it
597
598 add something on spgrid mesh generator (maybe)?
599
600
601 andrea
602
603
604 9. Publications using MITgcm --> "Previous Applications of MITgcm"
605 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
606 (check in support for more names)
607
608 10. Under development
609
610 Constantinos LCML
611
612
613 Bibliography
614
615 tidy up from misc - .tex

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