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Revision 1.45 - (show annotations) (download)
Thu Jun 29 17:45:14 2006 UTC (17 years, 9 months ago) by cnh
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gmaze PV needs to be in post-proc

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) <- DONE
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 <- DONE
268
269 2.4 Adams-Bashforth
270 - add stability diagrams (I have some figures that I can put) <- DONE
271 - add link for var. forcing_In_AB and epsil_AB <- half DONE
272 - add S/R link for S/R ADAMS_BASHFORTH2 <-DONE
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 3.11.3.1 - refers to figures and equations, links are broken
395
396 3.12.3.2 - line 43: link to equation is broken
397 - line 51-53: link to equation is broken
398 - there is some mess of text hanging around the end of this section. remove? reformat?
399
400 3.13.4.1 - line 34 - link to equation is broken
401 - lines 60,61 - 1st (take out the 'r' in the superscript)
402
403 3.14.2 - link to theta-equation is broken
404 3.14.5.4 -- ALL of the bold links to variable names are broken
405 line 34: link to equation is broken
406
407 >>>> From Ed
408
409 Here are the remaining bits for Chap 4 :
410
411 - missing references (if you point me towards URLs, I'll add them
412 to the bibliography):
413 \ref{ref hoe and hill, ecmwf}
414 \ref{magicgarden}
415 \ref{IBMLAPI}
416 \ref{Memorychannel}
417 \ref{hoe-hill:99}
418
419 - There are a few empty sub-sections at the end of Chap 4 that
420 should either be commented out or fleshed out.
421
422 and thats about it for Chap 4.
423
424
425 Add more to quick links on front page
426
427 Chapter 6
428
429 the master package diagram does not appear in the document
430
431 Master list of packages (add this to beginning of chap 6)
432
433 admtlm/ - autodiff (chapter 5)
434 aim/ - retired
435 aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM)
436 aim_ocn_coupler/ - 6.6 (no content yet)
437 aim_v23/ - 6.4.1 (content needs fixing - JM to do)
438 atm_common/ - nothing in this package (6.4.1 related)
439 autodiff/ - autodiff (chapter 5)
440 bulk_force/ - 6.3.3
441 cal/ - 6.3.5
442 cd_code/ - chapter 2 (JM check add a reference to paper,
443 mention parameter in data)
444 cfc/ - not sure (CNH to talk to Steph and Helen)
445 chronos/ - AM to check (not being used - Andrea to kill it)
446 compon_communic/ - 6.6 (no content yet)(Daniel + JM)
447 cost/ - not sure, check with PH
448 ctrl/ - not sure, check with PH
449 debug/ - JM may do something in chapter 7 (utilities)
450 diagnostics/ - 7.1
451 dic/ - 6.7.2
452 ebm/ - (check with PH)
453 ecco/ - chapter 8
454 embed_files/ - add something to chapter 7
455 exch2/ - 6.2.2
456 exf/ - 6.3.4
457 fizhi/ - 6.4.3
458 flt/ - (PH check)
459 gchem/ - 6.7.1
460 generic_advdiff/ - in chapter 2 (JM check)
461 ggl90/ - nothing, (Martin?)
462 gmredi/ - in chapter 2 (JM check). also need
463 Ferrari & Mc transition zone stuff (Samar doing this)
464 get dfer to read this
465 grdchk/ - grdchk (chapter 5 - check with PH)
466 gridalt/ - 6.2.4
467 kpp/ - 6.3.2
468 land/ - 6.4.2 (not connected to code Rong's notes - JM to fix)
469 matrix/ - Samar
470 mdsio/ - 7.3.1
471 mnc/ - 7.2.1
472 mom_common/ - in chapter 2 (JM check)
473 mom_fluxform/ - in chapter 2 (JM check)
474 mom_vecinv/ - in chapter 2 (JM check)
475 monitor/ - 7.4
476 my82/ - nothing, (martin?)
477 obcs/ - 6.3 (needs a check - ask PH to read)
478 ocn_compon_interf/ - 6.6 (no content yet)
479 offline/ - nothing, tutorials that need work but no package section entry
480 trivial to document (CNH to do)
481 opps/ - nothing, (martin?)
482 pp81/ - nothing, (martin?)
483 profiles/ - GAEL
484 ptracers/ - JM + SD + Martin to write something (nothing for this
485 at the moment)
486 AM has diagnostics table for this.
487 rbcs/ - CNH to talk to steph
488 runclock/ - runclock - CNH
489 rw/ - not sure - going to stay says JMC. quick IO calls
490 JMC to write a quick note for that.
491 sbo/ - text in sbo_descruption.tex but not linked into
492 part6 - CNH
493 seaice/ - 6.5.2 - no equations, dimitris has promised some
494 shap_filt/ - chapter 2, JM to check
495 shelfice/ - nothing yet (martin?)
496 solver/ - empty (go away?)
497 sphere/ - chapter 5 or 8 (PH to check)
498 therm_seaice/ - empty (go away?)
499 thsice/ - 6.5.1 (JM to update?)
500 timeave/ - retiring......
501 zonal_filt/ - chapter 2 (JM to check)
502
503 list an expeiment which uses package? CNH
504
505 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
506 Figure 6.8 is missing
507
508
509 ===== Chapter 7 ===== [EH3 editing] :
510
511 7.1.x - JMC: please add description of:
512 - diagstat
513 - new temporal averaging feature
514
515 7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
516
517 7.5.2 - get bathymetry pre-processing stuff from Patrick
518 and then describe it
519
520 add something on spgrid mesh generator (maybe)?
521
522 add in gmaze PV calculation scripts plus write up on how it is calculated
523 http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/
524
525
526 andrea
527
528
529 9. Publications using MITgcm --> "Previous Applications of MITgcm"
530 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
531 (check in support for more names)
532
533 10. Under development
534
535 Constantinos LCML
536
537
538 Bibliography
539
540 tidy up from misc - .tex

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