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Revision 1.39 - (show annotations) (download)
Wed Jun 28 16:27:02 2006 UTC (17 years, 9 months ago) by jmc
Branch: MAIN
Changes since 1.38: +12 -7 lines
File MIME type: text/plain
updated

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 3.1 - don't need a link to the outside of the document (remove it)
395 - link to htdig is broken
396
397 3.2.1 - link at bottom to source code points to section 3.2.1
398 (ie, to itself) - link should point to cvs code archive
399
400 3.2.2.1 - ('upgrading from an earlier version') belongs under
401 the cvs part, ie, should be 3.2.1.1
402
403 3.3 - remove reference to 'diags' section under MITgcm
404 - remove reference to 'exe' and 'bin' sections also
405 (remove the .cvsignore file under these directories in cvs)
406 - add a 'jobs' section, and a description as examples of run scripts
407 - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions
408 - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'
409 - under 'tools' the adjoint points to section 5 - this is now section 8
410 (but should be a floating reference)
411 - under 'utils' add a reference to exch2 - stuff for different resolutions
412 - the description of the pkg section refers directly to
413 section 3. should be section 6 (actually should be a floating reference)
414
415 3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
416 3.4.1 - links to the following experiments don't exist or are broken:
417 exp2 - should link to section 3.9
418 hs94.cs-32x32x5 - link to section 3.12
419 add 'convection' to the list, link to section 3.13
420 add 'plume on slope` to the list, link to section 3.14
421 add '??' link to section 3.15
422 add 'dic_example on slope` to the list, link to section 3.16
423 add '??' link to section 3.17
424 add 'offline' and link to section 3.18
425 clean up others and make links where they are needed
426 3.4.2 - text suggests to see section 2 for details about what is in the 'code'
427 and 'input' directories - should refer to the examples in this section
428 - add 'build' bullet - this is where the model is compiled and exectuable lives
429
430 3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
431 as the place where they live (add a link?)
432
433 3.6.1 - Add some general 'approach' text - ie, output is controlled either by the
434 'data' file in the input directory or by the data.[pkg name] file for any
435 package running. And there is some default behavior when the 'state' dumps
436 are written.
437 3.6.1.2 - needs to be moved to inside section 3.6.2
438
439 All the 'overview' sections need some reference to the name of the experiment in
440 the verification directory
441
442 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
443 - is this experiment in the list from section 3.4???
444 3.10.3.1 - refers to figures and equations, links are broken
445
446 3.11.3.2 - line 43: link to equation is broken
447 - line 51-53: link to equation is broken
448 - there is some mess of text hanging around the end of this section. remove? reformat?
449
450 3.12.4.1 - line 34 - link to equation is broken
451 - lines 60,61 - 1st (take out the 'r' in the superscript)
452
453 3.13.2 - link to theta-equation is broken
454 3.13.5.4 -- ALL of the bold links to variable names are broken
455 line 34: link to equation is broken
456
457 3.15.1 - reference to 'fourth experiment' should be removed
458
459 3.16.4 - strange formatting, presence of '>' symbols - remove them
460
461 3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
462 3.17.3.1 - nothing filled in under file input/data - needs description
463
464 3.18.2 - point to section 2 for details - need hyperlink
465
466 3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
467 section 3.5 has the 'build' directory in the example
468
469 3.20.1 - link to doc at end of section points to this section
470 3.20.2 - link to doc at end of section points to this section
471
472 offline - duplicate inputs, what is it, tidy up cfc v.
473 other offline. JM thinks these need tidying up.
474
475 Which of the following are which tutorial?
476 adjustment.128x64x1
477 adjustment.cs-32x32x1
478 advect_cs
479 advect_xy
480 advect_xz
481 aim.5l_cs
482 aim.5l_Equatorial_Channel
483 aim.5l_LatLon
484 biogeo
485 bottom_ctrl_5x5
486 cfc_example
487 cpl_aim+ocn
488 dome
489 exp2
490 exp4
491 exp5
492 fizhi-cs-32x32x10
493 fizhi-cs-aqualev20
494 fizhi-gridalt-hs
495 flt_example
496 front_relax
497 global1x1_tot
498 global2x2_tot
499 global_ocean.90x40x15
500 global_ocean.cs32x15
501 global_ocean.cubed32x32x30
502 global_ocean_ebm
503 global_with_exf
504 hs94.128x64x5
505 hs94.1x64x5
506 hs94.cs-32x32x5
507 ideal_2D_oce
508 internal_wave
509 inverted_barometer
510 lab_sea
511 matrix_example
512 MLAdjust
513 natl_box
514 natl_box_adjoint
515 OpenAD
516 rotating_tank
517 solid-body.cs-32x32x1
518 tidal_basin_2d
519 tutorial_baroclinic_gyre
520 tutorial_barotropic_gyre
521 tutorial_cfc_offline
522 tutorial_deep_convection
523 tutorial_global_oce_biogeo
524 tutorial_global_oce_in_p
525 tutorial_global_oce_latlon
526 tutorial_global_oce_optim
527 tutorial_held_suarez_cs
528 tutorial_offline
529 tutorial_plume_on_slope
530 tutorial_tracer_adjsens
531 vermix
532
533 >>>> From Ed
534
535 Here are the remaining bits for Chap 4 :
536
537 - missing references (if you point me towards URLs, I'll add them
538 to the bibliography):
539 \ref{ref hoe and hill, ecmwf}
540 \ref{magicgarden}
541 \ref{IBMLAPI}
542 \ref{Memorychannel}
543 \ref{hoe-hill:99}
544
545 - There are a few empty sub-sections at the end of Chap 4 that
546 should either be commented out or fleshed out.
547
548 and thats about it for Chap 4.
549
550
551 Add more to quick links on front page
552
553 Chapter 6
554
555 the master package diagram does not appear in the document
556
557 Master list of packages (add this to beginning of chap 6)
558
559 admtlm/ - autodiff (chapter 5)
560 aim/ - retired
561 aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM)
562 aim_ocn_coupler/ - 6.6 (no content yet)
563 aim_v23/ - 6.4.1 (content needs fixing - JM to do)
564 atm_common/ - nothing in this package (6.4.1 related)
565 autodiff/ - autodiff (chapter 5)
566 bulk_force/ - 6.3.3
567 cal/ - 6.3.5
568 cd_code/ - chapter 2 (JM check add a reference to paper,
569 mention parameter in data)
570 cfc/ - not sure (CNH to talk to Steph and Helen)
571 chronos/ - AM to check (not being used - Andrea to kill it)
572 compon_communic/ - 6.6 (no content yet)(Daniel + JM)
573 cost/ - not sure, check with PH
574 ctrl/ - not sure, check with PH
575 debug/ - JM may do something in chapter 7 (utilities)
576 diagnostics/ - 7.1
577 dic/ - 6.7.2
578 ebm/ - (check with PH)
579 ecco/ - chapter 8
580 embed_files/ - add something to chapter 7
581 exch2/ - 6.2.2
582 exf/ - 6.3.4
583 fizhi/ - 6.4.3
584 flt/ - (PH check)
585 gchem/ - 6.7.1
586 generic_advdiff/ - in chapter 2 (JM check)
587 ggl90/ - nothing, (Martin?)
588 gmredi/ - in chapter 2 (JM check). also need
589 Ferrari & Mc transition zone stuff (Samar doing this)
590 get dfer to read this
591 grdchk/ - grdchk (chapter 5 - check with PH)
592 gridalt/ - 6.2.4
593 kpp/ - 6.3.2
594 land/ - 6.4.2 (not connected to code Rong's notes - JM to fix)
595 matrix/ - Samar
596 mdsio/ - 7.3.1
597 mnc/ - 7.2.1
598 mom_common/ - in chapter 2 (JM check)
599 mom_fluxform/ - in chapter 2 (JM check)
600 mom_vecinv/ - in chapter 2 (JM check)
601 monitor/ - 7.4
602 my82/ - nothing, (martin?)
603 obcs/ - 6.3 (needs a check - ask PH to read)
604 ocn_compon_interf/ - 6.6 (no content yet)
605 offline/ - nothing, tutorials that need work but no package section entry
606 trivial to document (CNH to do)
607 opps/ - nothing, (martin?)
608 pp81/ - nothing, (martin?)
609 profiles/ - GAEL
610 ptracers/ - JM + SD + Martin to write something (nothing for this
611 at the moment)
612 AM has diagnostics table for this.
613 rbcs/ - CNH to talk to steph
614 runclock/ - runclock - CNH
615 rw/ - not sure - going to stay says JMC. quick IO calls
616 JMC to write a quick note for that.
617 sbo/ - text in sbo_descruption.tex but not linked into
618 part6 - CNH
619 seaice/ - 6.5.2 - no equations, dimitris has promised some
620 shap_filt/ - chapter 2, JM to check
621 shelfice/ - nothing yet (martin?)
622 solver/ - empty (go away?)
623 sphere/ - chapter 5 or 8 (PH to check)
624 therm_seaice/ - empty (go away?)
625 thsice/ - 6.5.1 (JM to update?)
626 timeave/ - retiring......
627 zonal_filt/ - chapter 2 (JM to check)
628
629 list an expeiment which uses package? CNH
630
631 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
632 Figure 6.8 is missing
633
634
635 ===== Chapter 7 ===== [EH3 editing] :
636
637 7.1.x - JMC: please add description of:
638 - diagstat
639 - new temporal averaging feature
640
641 7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
642
643 7.5.2 - get bathymetry pre-processing stuff from Patrick
644 and then describe it
645
646 add something on spgrid mesh generator (maybe)?
647
648
649 andrea
650
651
652 9. Publications using MITgcm --> "Previous Applications of MITgcm"
653 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
654 (check in support for more names)
655
656 10. Under development
657
658 Constantinos LCML
659
660
661 Bibliography
662
663 tidy up from misc - .tex

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