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Revision 1.46 - (show annotations) (download)
Sun Jul 2 18:12:45 2006 UTC (17 years, 9 months ago) by edhill
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a "fix" for the artificial subscripting of in-line images has been found

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 Rebuild and set to do cron build - DONE on hugo
31
32 To do
33
34 - where to put under development links?
35 JMC would like to have some mention of unfinished things (checked in
36 but not that tested e.g. AB3)
37 Add an "Under development, chapter" - shortish description of what
38 is available (last chapter)
39
40 - add in example latex for formatting author names in different pieces.
41 this aknowledges peoples contributions and gives ref for who
42 to talk to.
43
44 o HTML, scripts and front content
45
46 - pick a URL: mitgcm.org/r2 <-- EH3's preferred base URL
47
48 - mitgcm.org/r2_web_testing/latest
49
50 o --DONE-- add another short-cut for quick download
51
52 o --DONE-- add another short-cut
53 About
54 Installation
55 Contents
56 Overview
57 Tutorials (broken)
58 Browse Code
59
60 o --DONE-- words on http://mitgcm.org/r2_web_testing/latest change to
61
62 o --DONE-- finite-volume doesn't leap to FV figure
63
64 o -- DONE ??? -- have another go at pnmcrop et al.
65
66 I've tried making a small change in latex2html which fixes
67 the oddball-lower-alignment issue that we were seeing with
68 most in-line expressions (that is, math embedded in text).
69 The fix results in some things being slightly raised but I
70 thin this is more asthetically pleasing than being somewhat
71 lowered as before. --EH3
72
73 To view the altered alignment, see:
74
75 http://eddy.csail.mit.edu/r2/latest/
76
77 o Need an empty package as part of distribution. Check out atm_common
78
79
80 o Latex
81
82 Chapter 1 - CNH
83 o single kernel diagram -
84 add reference to MWR paper
85
86 o non-hydro
87 add reference to 1995 and 1999 papers
88 pdf of 1995 paper
89
90 o FV
91 add references to 1997 papers.
92
93 o Tangent linear/adjoint add reference to
94 Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc...
95
96 o platforms
97 Add reference to SC article and Scientific Programming article
98
99 o List of key papers needs to be updated and reformatted
100
101 o Global atmosphere: `Held Suarez',
102 update Adcroft reference
103 fix up ingrid link and frame (ingrid movies seem to be broken?)
104 Held and Suarez reference is not a link.
105
106 o Ocean Gyres
107 fix up frame link
108 make "lopped cell" a link to referenced paper.
109 add references (ask Steph/Mick)
110 online/offline paper
111
112 o Convection and mixing over topography
113 add in Legg references for convection and mixing over topography
114 and external link to CPT-GCE etc...
115
116 o Boundary forced internal waves
117 add in Legg references, obc's reference
118
119 o Parameter sensitivity
120 add in Bugnion references, Boyin references, Steph references
121
122 o State estimation
123 add in references from Patrick/Carl/Ichiro/Detlef etc...
124 update links to point to latest ECCO results
125 ECCO ingrid results have been moved
126 add forward links to "ECCO state estimation" chapter in manual
127
128 o Ocean biogeochemical cycles
129 add in references from Mick/Galen etc...
130 fix ingrid link ( date to date thing does not appear to work)
131 figure url does not have a "target=idontexist" entry
132
133 o Simulations of laboratory experiments
134 reference Wardle and Karsten papers
135 update links to include DDDAS "PIAB" page
136 cylindrical polar coordinates
137
138 o Continuos equations in ''r'' coordinates
139 add references to iso paper
140 no mention of z* and p* - forward reference to z*/p* in 2.
141 add that coupling also manifests through F, Q
142 add tracer transport
143
144 o Kinematic boundary conditions
145
146 o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
147 Non-hydrostatic forms
148 need to tidy up discussion of shallow-atmosphere to be
149 consistent with the code or change code to be consistent
150 with the discussion!
151 make references hyperlinks
152 add stuff too
153 JMC remove QNH atmosphere
154 need to sort out calc_gw for deep atmosphere
155
156 o Finding the pressure field
157 make references hyperlinks
158 add forward references to manual algorithm section
159 change Elliptic to "elliptic"
160
161 o Forcing and dissipation
162 make "physics packages" refer to chapter 6.
163 should we move "external forcing" et. al to a
164 generic_forcing_driver package?
165
166 viscosities
167 update to mention Smag/Leith (Ah and A4 not constant)
168 and to have forward references to numerical section
169 tracers
170 forward references to numerical section, reddy, GM etc...
171 add references to literature
172
173 o 1.3.8 Vector invariant form
174 forward references to numerical section
175
176 o 1.3.9 Adjoint
177 add a little more here + some hyperlink to chapter 5.
178
179 o 1.4 Appendix ATMOSPHERE
180
181 add some introductory words
182
183 o 1.6 Coordinate systems
184 o only has some words on spherical polar. add some brief words
185 to cover all of
186 - cartesian
187 - spherical
188 - cylindrical
189 - general orthogonal curvilinear (vector invariant)
190
191 o Equation of state options
192 add some discussion
193 can't remember what we said we were going to do here
194 PH to do something
195
196
197 Change hydrodynamical to "dynamical"
198
199 Examples
200
201 - extra "in action" cases
202
203 o high res ocean with diurnal atmospheric state forcing
204 - links to ingrid output
205 CNH/Dimitris
206
207 o realistic FIZHI from Andrea
208 - links to ingrid output
209 from AM
210
211 o with seaice on high res cube
212 - links to ingrid output
213 CNH/Dimitris
214
215 o coupled aqua, ridge world etc...
216 - links to ingrid output
217 get stuff from Daniel
218 Davids donut movie
219
220 o constrained lab simulation
221 - links to ingrid output for model and lab
222 fields
223 get stuff from Sai/Andrew
224
225 o sensitivity wrt to iron
226
227 o optimization
228 - update to link to latest ECCO sites and GF
229 related material
230
231 o eddy diffusivity transport application
232
233 o Gas giant?
234
235
236 >>>> from JM
237
238
239 manual, section.2 :
240
241 In general:
242 - add more refences/links to S/R & variable name
243 - would be nice to have an active link to the fortran-file
244 for all the S/R & eq.Number in the "calling-tree" boxes
245 - search for CALC_MOM_RHS and replace it by the appropriate S/R
246 (mom_flux_form, mom_vecinv, dynamics) <- DONE
247 - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
248 was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
249 in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
250 simply written \vec{v}.
251 I would suggest to keep the notation as they are (since they are consistent
252 inside each section) but may be to move the "notation.tex" piece
253 at the beginning of section.2 and to mention clearly the changes between
254 the 2 sections.
255
256 in content: Horizontal Dissipation: 2 times in vector-invariant section
257 <- DONE
258
259 2.1 time-stepping (part2/time_stepping.tex)
260
261 - this is not clear to me:
262
263 >> In all the above configurations it is also possible to substitute the
264 >> Adams-Bashforth with an alternative time-stepping scheme for terms
265 >> evaluated explicitly in time
266 <- Leave it general.
267
268
269 2.2 rigid-lid:
270
271 - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
272 to stay closer to the code.
273 - mention section 2.5 implicit-Time-stepping (for vertical viscosity) <- DONE
274
275 2.3 linear free-surface:
276 - add ref(+link) to S/R names:
277 - add ref(+link) to Crank-Nickelson section 2.9.1 <- DONE
278
279 2.4 Adams-Bashforth
280 - add stability diagrams (I have some figures that I can put) <- DONE
281 - add link for var. forcing_In_AB and epsil_AB <- half DONE
282 - add S/R link for S/R ADAMS_BASHFORTH2 <-DONE
283
284 2.5 Implicit time-stepping
285 - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
286 SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
287 - update: also used for vertical advection
288
289 2.6 Synchronous time-stepping:
290 - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
291 MOMENTUM_CORRECTION_STEP.
292
293 2.7 Stagger baroclinic time-stepping
294 - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
295
296 2.8 NH
297 - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
298
299 2.9 Variants on Free-Surface
300 - Delta.t mis-written (eq.2.73) <- DONE
301 - Eq.Num missing <- DONE
302 - u* is stored in gU (and not in gUnm1) <- DONE
303 - Phi_nh in NH_VARS.h <- DONE
304 - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
305 INI_CG2D, INI_CG3D
306
307 2.9.1 Crank-Nickelson
308 - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
309
310 2.9.2 NLFS
311 - eq.Nb are wrong in html
312 - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
313 <- DONE
314
315 2.10.1 Notation
316 - Area definition is not really used like this
317
318 >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
319
320 Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
321 the model variables) are used (e.g., see section 2.10.5)
322 <- DONE
323
324 2.10.5 Horizontal grid:
325 - fig.2.8 : should use Aw,As consistently in this figure description,
326 in the figure itself, as it is in the text. <- DONE
327 - curvilinear:
328 to add: mention the angle of the grid direction relative to
329 Eastward, Northward direction.
330 + mention horizGridFile= in file "data" (PARM04)
331 - add cylindrical polar grid description
332 need to do a better job of relating model variables to this diagram
333
334
335 2.11 Continuity & Horizontal Pressure gradient terms
336 - mention that d.Phi/dr|s =g if using z coordinate
337 - eq. 2.90 not clear regarding \delta_k(P-E)
338 better to add the free surface eq: d.eta/dt = w_s + P-E
339
340 2.12 Hydrostatic balance
341 - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
342 is hard to find
343 - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
344 and in section 1.3.4: remove the 1.3.4.3.2 subsection:
345 Quasi-nonhydrostatic Atmosphere
346
347 2.13.2 Coriolis terms
348 - note: the discretization used when useEnergyConservingCoriolis=T
349 has no hFac and no Area and is still different from the form
350 described here (with Area & hFac);
351
352 2.13.5 Lateral dissipation
353 - add description of how to use cosFactor & cosPower
354 - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
355 o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
356 in code need to explain why cos()3/2 turns out to be
357 scaling (not cos()2)
358 - need to reference the smag/leith section.
359
360 2.13.6 Vertical dissipation
361 - mention the implicit vertical viscosity option and ref to section 2.5
362 - add the parameter correspondence: Av <-> viscAr (and might change also
363 the notation to Ar)
364
365 2.14 Vector invariant momentum equations
366 - indicate that the NH pieces (vertical momentum eq) are not yet coded
367 and that the NH code uses the flux form.
368
369 2.14.6 Horizontal dissipation -> Horizontal Divergence
370
371 2.14.7 Horizontal dissipation
372 - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
373 and A_D4,A_z4 <-> viscA4D,viscA4Z
374
375 2.16 & 2.17 & 2.18 :
376 - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
377 - fix equations 2.202 & 2.203 (thanks to Martin) <- DONE
378
379 2.20.2 mercator, non-dimensional Equations:
380 - does not use std notation
381 - would be better as an appendix of section 2.20:
382 (e.g changing the tile to:
383 - talk to Baylor
384 Appendix: non-dimensional Equations on Spherical-Polar grid.)
385 <- No (Chris said)
386
387
388 Diagrams of grid locations etc.... and what variables and output files
389 and/or netcdf variable names are not very easy to figure out and follow.
390 It would be good to redo and extend these diagrams and align with GRID.h
391 content.
392
393
394 JM
395
396
397 >>>> From Andrea
398
399 Chapter 3
400 --------
401
402 Almost all of the 'math mode' text is dropped down as subscripts
403
404 3.11.3.1 - refers to figures and equations, links are broken
405
406 3.12.3.2 - line 43: link to equation is broken
407 - line 51-53: link to equation is broken
408 - there is some mess of text hanging around the end of this section. remove? reformat?
409
410 3.13.4.1 - line 34 - link to equation is broken
411 - lines 60,61 - 1st (take out the 'r' in the superscript)
412
413 3.14.2 - link to theta-equation is broken
414 3.14.5.4 -- ALL of the bold links to variable names are broken
415 line 34: link to equation is broken
416
417 >>>> From Ed
418
419 Here are the remaining bits for Chap 4 :
420
421 - missing references (if you point me towards URLs, I'll add them
422 to the bibliography):
423 \ref{ref hoe and hill, ecmwf}
424 \ref{magicgarden}
425 \ref{IBMLAPI}
426 \ref{Memorychannel}
427 \ref{hoe-hill:99}
428
429 - There are a few empty sub-sections at the end of Chap 4 that
430 should either be commented out or fleshed out.
431
432 and thats about it for Chap 4.
433
434
435 Add more to quick links on front page
436
437 Chapter 6
438
439 the master package diagram does not appear in the document
440
441 Master list of packages (add this to beginning of chap 6)
442
443 admtlm/ - autodiff (chapter 5)
444 aim/ - retired
445 aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM)
446 aim_ocn_coupler/ - 6.6 (no content yet)
447 aim_v23/ - 6.4.1 (content needs fixing - JM to do)
448 atm_common/ - nothing in this package (6.4.1 related)
449 autodiff/ - autodiff (chapter 5)
450 bulk_force/ - 6.3.3
451 cal/ - 6.3.5
452 cd_code/ - chapter 2 (JM check add a reference to paper,
453 mention parameter in data)
454 cfc/ - not sure (CNH to talk to Steph and Helen)
455 chronos/ - AM to check (not being used - Andrea to kill it)
456 compon_communic/ - 6.6 (no content yet)(Daniel + JM)
457 cost/ - not sure, check with PH
458 ctrl/ - not sure, check with PH
459 debug/ - JM may do something in chapter 7 (utilities)
460 diagnostics/ - 7.1
461 dic/ - 6.7.2
462 ebm/ - (check with PH)
463 ecco/ - chapter 8
464 embed_files/ - add something to chapter 7
465 exch2/ - 6.2.2
466 exf/ - 6.3.4
467 fizhi/ - 6.4.3
468 flt/ - (PH check)
469 gchem/ - 6.7.1
470 generic_advdiff/ - in chapter 2 (JM check)
471 ggl90/ - nothing, (Martin?)
472 gmredi/ - in chapter 2 (JM check). also need
473 Ferrari & Mc transition zone stuff (Samar doing this)
474 get dfer to read this
475 grdchk/ - grdchk (chapter 5 - check with PH)
476 gridalt/ - 6.2.4
477 kpp/ - 6.3.2
478 land/ - 6.4.2 (not connected to code Rong's notes - JM to fix)
479 matrix/ - Samar
480 mdsio/ - 7.3.1
481 mnc/ - 7.2.1
482 mom_common/ - in chapter 2 (JM check)
483 mom_fluxform/ - in chapter 2 (JM check)
484 mom_vecinv/ - in chapter 2 (JM check)
485 monitor/ - 7.4
486 my82/ - nothing, (martin?)
487 obcs/ - 6.3 (needs a check - ask PH to read)
488 ocn_compon_interf/ - 6.6 (no content yet)
489 offline/ - nothing, tutorials that need work but no package section entry
490 trivial to document (CNH to do)
491 opps/ - nothing, (martin?)
492 pp81/ - nothing, (martin?)
493 profiles/ - GAEL
494 ptracers/ - JM + SD + Martin to write something (nothing for this
495 at the moment)
496 AM has diagnostics table for this.
497 rbcs/ - CNH to talk to steph
498 runclock/ - runclock - CNH
499 rw/ - not sure - going to stay says JMC. quick IO calls
500 JMC to write a quick note for that.
501 sbo/ - text in sbo_descruption.tex but not linked into
502 part6 - CNH
503 seaice/ - 6.5.2 - no equations, dimitris has promised some
504 shap_filt/ - chapter 2, JM to check
505 shelfice/ - nothing yet (martin?)
506 solver/ - empty (go away?)
507 sphere/ - chapter 5 or 8 (PH to check)
508 therm_seaice/ - empty (go away?)
509 thsice/ - 6.5.1 (JM to update?)
510 timeave/ - retiring......
511 zonal_filt/ - chapter 2 (JM to check)
512
513 list an expeiment which uses package? CNH
514
515 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
516 Figure 6.8 is missing
517
518
519 ===== Chapter 7 ===== [EH3 editing] :
520
521 + JMC: please add description of:
522 - diagstat
523 - new temporal averaging feature
524
525 + add Graphix to the list of stuff in utils/matlab (Daniel)
526
527 + get bathymetry pre-processing stuff from Patrick and then describe it
528
529 + add something on spgrid mesh generator
530
531 + add in gmaze PV calculation scripts plus write up on how it is calculated
532 http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/
533
534
535 andrea
536
537
538 9. Publications using MITgcm --> "Previous Applications of MITgcm"
539 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
540 (check in support for more names)
541
542 10. Under development
543
544 Constantinos LCML
545
546
547 Bibliography
548
549 tidy up from misc - .tex

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