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 |