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Revision 1.49 - (show annotations) (download)
Thu Jan 17 16:45:29 2008 UTC (11 years, 9 months ago) by jmc
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add little things

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 o Time-stepping outline
269 - what gets called when
270
271
272 2.2 rigid-lid:
273
274 - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
275 to stay closer to the code.
276 - mention section 2.5 implicit-Time-stepping (for vertical viscosity) <- DONE
277
278 2.3 linear free-surface:
279 - add ref(+link) to S/R names:
280 - add ref(+link) to Crank-Nickelson section 2.9.1 <- DONE
281
282 2.4 Adams-Bashforth
283 - add stability diagrams (I have some figures that I can put) <- DONE
284 - add link for var. forcing_In_AB and epsil_AB <- half DONE
285 - add S/R link for S/R ADAMS_BASHFORTH2 <-DONE
286
287 2.5 Implicit time-stepping
288 - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
289 SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
290 - update: also used for vertical advection
291
292 2.6 Synchronous time-stepping:
293 - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
294 MOMENTUM_CORRECTION_STEP.
295
296 2.7 Stagger baroclinic time-stepping
297 - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
298
299 2.8 NH
300 - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
301
302 2.9 Variants on Free-Surface
303 - Delta.t mis-written (eq.2.73) <- DONE
304 - Eq.Num missing <- DONE
305 - u* is stored in gU (and not in gUnm1) <- DONE
306 - Phi_nh in NH_VARS.h <- DONE
307 - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
308 INI_CG2D, INI_CG3D
309
310 2.9.1 Crank-Nickelson
311 - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
312
313 2.9.2 NLFS
314 - eq.Nb are wrong in html
315 - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
316 <- DONE
317
318 2.10.1 Notation
319 - Area definition is not really used like this
320
321 >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
322
323 Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
324 the model variables) are used (e.g., see section 2.10.5)
325 <- DONE
326
327 2.10.5 Horizontal grid:
328 - fig.2.8 : should use Aw,As consistently in this figure description,
329 in the figure itself, as it is in the text. <- DONE
330 - curvilinear:
331 to add: mention the angle of the grid direction relative to
332 Eastward, Northward direction.
333 + mention horizGridFile= in file "data" (PARM04)
334 - add cylindrical polar grid description
335 need to do a better job of relating model variables to this diagram
336
337
338 2.11 Continuity & Horizontal Pressure gradient terms
339 - mention that d.Phi/dr|s =g if using z coordinate
340 - eq. 2.90 not clear regarding \delta_k(P-E)
341 better to add the free surface eq: d.eta/dt = w_s + P-E
342
343 2.12 Hydrostatic balance
344 - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
345 is hard to find
346 - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
347 and in section 1.3.4: remove the 1.3.4.3.2 subsection:
348 Quasi-nonhydrostatic Atmosphere
349
350 2.13.2 Coriolis terms
351 - note: the discretization used when useEnergyConservingCoriolis=T
352 has no hFac and no Area and is still different from the form
353 described here (with Area & hFac);
354
355 2.13.5 Lateral dissipation
356 - add description of how to use cosFactor & cosPower
357 - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
358 o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
359 in code need to explain why cos()3/2 turns out to be
360 scaling (not cos()2)
361 - need to reference the smag/leith section.
362
363 2.13.6 Vertical dissipation
364 - mention the implicit vertical viscosity option and ref to section 2.5
365 - add the parameter correspondence: Av <-> viscAr (and might change also
366 the notation to Ar)
367
368 2.14 Vector invariant momentum equations
369 - indicate that the NH pieces (vertical momentum eq) are not yet coded
370 and that the NH code uses the flux form.
371
372 2.14.6 Horizontal dissipation -> Horizontal Divergence
373
374 2.14.7 Horizontal dissipation
375 - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
376 and A_D4,A_z4 <-> viscA4D,viscA4Z
377
378 2.16 & 2.17 & 2.18 :
379 - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
380 - fix equations 2.202 & 2.203 (thanks to Martin) <- DONE
381
382 2.20.2 mercator, non-dimensional Equations:
383 - does not use std notation
384 - would be better as an appendix of section 2.20:
385 (e.g changing the tile to:
386 - talk to Baylor
387 Appendix: non-dimensional Equations on Spherical-Polar grid.)
388 <- No (Chris said)
389
390
391 Diagrams of grid locations etc.... and what variables and output files
392 and/or netcdf variable names are not very easy to figure out and follow.
393 It would be good to redo and extend these diagrams and align with GRID.h
394 content.
395
396
397 JM
398
399
400 >>>> From Andrea
401
402 Chapter 3
403 --------
404
405 Almost all of the 'math mode' text is dropped down as subscripts
406
407 3.11.3.1 - refers to figures and equations, links are broken
408
409 3.12.3.2 - line 43: link to equation is broken
410 - line 51-53: link to equation is broken
411 - there is some mess of text hanging around the end of this section. remove? reformat?
412
413 3.13.4.1 - line 34 - link to equation is broken
414 - lines 60,61 - 1st (take out the 'r' in the superscript)
415
416 3.14.2 - link to theta-equation is broken
417 3.14.5.4 -- ALL of the bold links to variable names are broken
418 line 34: link to equation is broken
419
420 o Update basic intro with one and four layer gyres
421 - include advection options
422 - conservation analysis
423 - diagnostics
424
425 o Four degree adjoint
426 - both TAF and OpenAD based.
427
428 o Coupled with biogeo setup
429 - based on CCGS setup
430
431
432 >>>> From Ed
433
434 Here are the remaining bits for Chap 4 :
435
436 - missing references (if you point me towards URLs, I'll add them
437 to the bibliography):
438 \ref{ref hoe and hill, ecmwf}
439 \ref{magicgarden}
440 \ref{IBMLAPI}
441 \ref{Memorychannel}
442 \ref{hoe-hill:99}
443
444 - There are a few empty sub-sections at the end of Chap 4 that
445 should either be commented out or fleshed out.
446
447 and thats about it for Chap 4.
448
449
450 Add more to quick links on front page
451
452 Chapter 6
453
454 the master package diagram does not appear in the document <- done
455 (<- needs an update: e.g. atm2d, salt_plume, shelfice ...)
456
457 Master list of packages (add this to beginning of chap 6)
458 (<- needs an update: e.g. atm2d, salt_plume, shelfice ...)
459
460 admtlm/ - autodiff (chapter 5)
461 aim/ - retired
462 aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM)
463 aim_ocn_coupler/ - 6.6 (no content yet)
464 aim_v23/ - 6.4.1 (content needs fixing - JM to do)
465 atm_common/ - nothing in this package (6.4.1 related)
466 autodiff/ - autodiff (chapter 5)
467 bulk_force/ - 6.3.3
468 cal/ - 6.3.5
469 cd_code/ - chapter 2 (JM check add a reference to paper,
470 mention parameter in data)
471 cfc/ - not sure (CNH to talk to Steph and Helen)
472 chronos/ - AM to check (not being used - Andrea to kill it)
473 compon_communic/ - 6.6 (no content yet)(Daniel + JM)
474 cost/ - not sure, check with PH
475 ctrl/ - not sure, check with PH
476 debug/ - JM may do something in chapter 7 (utilities)
477 diagnostics/ - 7.1
478 dic/ - 6.7.2
479 ebm/ - (check with PH)
480 ecco/ - chapter 8
481 embed_files/ - add something to chapter 7
482 exch2/ - 6.2.2
483 exf/ - 6.3.4
484 fizhi/ - 6.4.3
485 o Including FIZHI doc
486 - get things up to date
487 flt/ - (PH check)
488 gchem/ - 6.7.1
489 generic_advdiff/ - in chapter 2 (JM check)
490 ggl90/ - nothing, (Martin?)
491 gmredi/ - in chapter 2 (JM check). also need
492 Ferrari & Mc transition zone stuff (Samar doing this)
493 get dfer to read this
494 grdchk/ - grdchk (chapter 5 - check with PH)
495 gridalt/ - 6.2.4
496 kpp/ - 6.3.2
497 land/ - 6.4.2 (not connected to code Rong's notes - JM to fix)
498 matrix/ - Samar
499 mdsio/ - 7.3.1
500 mnc/ - 7.2.1
501 mom_common/ - in chapter 2 (JM check)
502 mom_fluxform/ - in chapter 2 (JM check)
503 mom_vecinv/ - in chapter 2 (JM check)
504 monitor/ - 7.4
505 my82/ - nothing, (martin?)
506 obcs/ - 6.3 (needs a check - ask PH to read)
507 ocn_compon_interf/ - 6.6 (no content yet)
508 offline/ - nothing, tutorials that need work but no package section entry
509 trivial to document (CNH to do)
510 opps/ - nothing, (martin?)
511 pp81/ - nothing, (martin?)
512 profiles/ - GAEL
513 ptracers/ - JM + SD + Martin to write something (nothing for this
514 at the moment)
515 AM has diagnostics table for this.
516 rbcs/ - CNH to talk to steph
517 runclock/ - runclock - CNH
518 rw/ - not sure - going to stay says JMC. quick IO calls
519 JMC to write a quick note for that.
520 sbo/ - text in sbo_descruption.tex but not linked into
521 part6 - CNH
522 seaice/ - 6.5.2 - no equations, dimitris has promised some
523 shap_filt/ - chapter 2, JM to check
524 shelfice/ - nothing yet (martin?)
525 solver/ - empty (go away?)
526 sphere/ - chapter 5 or 8 (PH to check)
527 therm_seaice/ - empty (go away?)
528 thsice/ - 6.5.1 (JM to update?)
529 timeave/ - retiring......
530 zonal_filt/ - chapter 2 (JM to check)
531
532 o Cost function packages
533 - floats, weights, profiles etc...
534
535
536 list an expeiment which uses package? CNH
537
538 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
539 Figure 6.8 is missing
540
541
542 ===== Chapter 7 ===== [EH3 editing] :
543
544 + JMC: please add description of:
545 - diagstat
546 - new temporal averaging feature
547
548 + update the RW / MDSIO description
549 -> new meta file
550 -> list all RW S/R that one should use instead of calling directly MDSIO
551
552 + add Graphix to the list of stuff in utils/matlab (Daniel)
553
554 + get bathymetry pre-processing stuff from Patrick and then describe it
555
556 + add something on spgrid mesh generator
557 o Grid generation
558 - more explanation and some step-by-step examples
559 - plotting grid examples
560
561
562 + add in gmaze PV calculation scripts plus write up on how it is calculated
563 http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/
564
565
566 andrea
567
568
569 9. Publications using MITgcm --> "Previous Applications of MITgcm"
570 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
571 (check in support for more names)
572
573 10. Under development
574
575 Constantinos LCML
576 o Legend/LCML examples and explanation
577 - examples and explanation!
578
579
580
581 Bibliography
582
583 tidy up from misc - .tex
584
585 Also
586
587 a link to the new manual
588 should appear on the front page (even if it's under construction).
589
590 updating:
591 http://mitgcm.org/r2_web_testing/latest/code_reference/callTree.html
592 which points to a 1.5 years old code. Would be good to generate a
593 new one, and even better, to try to keep it up-to-date.
594

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