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Revision 1.32 - (show annotations) (download)
Tue Jun 27 15:13:26 2006 UTC (13 years, 3 months ago) by edhill
Branch: MAIN
Changes since 1.31: +7 -7 lines
File MIME type: text/plain
explain ch7 todo

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

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