| 1 |
Rebuild and set to do cron build |
| 2 |
|
| 3 |
To do |
| 4 |
|
| 5 |
- where to put under development links? |
| 6 |
|
| 7 |
- mitgcm.org very front page. |
| 8 |
o too many clicks to get to model manual. |
| 9 |
make doc link go to mitgcm.org/r2_web_testing/latest |
| 10 |
and add "HowTo" reference etc... to /latest page |
| 11 |
|
| 12 |
- mitgcm.org/r2_web_testing/latest |
| 13 |
o add another short-cut for quick download |
| 14 |
|
| 15 |
o add another short-cut |
| 16 |
About |
| 17 |
Installation |
| 18 |
Contents |
| 19 |
Overview |
| 20 |
Tutorials (broken) |
| 21 |
Browse Code |
| 22 |
Get Code (where does this go to?) |
| 23 |
|
| 24 |
o authors |
| 25 |
John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen, |
| 26 |
Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos, |
| 27 |
Gael - others? |
| 28 |
|
| 29 |
o Tutorials side bar link is broken |
| 30 |
|
| 31 |
o words |
| 32 |
change to "access on-line Auser manual/A and Atable of contents/A |
| 33 |
and browse the Aoverview section/A" |
| 34 |
|
| 35 |
o finite-volume doesn't leap to FV figure |
| 36 |
|
| 37 |
o date is 2002 |
| 38 |
|
| 39 |
o fix search so it doesn't include advertisements |
| 40 |
|
| 41 |
o the src and equation links don't come through to |
| 42 |
the html when they are in figures - see chapter 2 for some |
| 43 |
examples. |
| 44 |
|
| 45 |
o degree symbols keep getting "dropped down" - problem with |
| 46 |
pnmcrop et al. |
| 47 |
|
| 48 |
|
| 49 |
Contents |
| 50 |
|
| 51 |
Intro - CNH |
| 52 |
o single kernel diagram - |
| 53 |
add reference to MWR paper |
| 54 |
|
| 55 |
o non-hydro |
| 56 |
add reference to 1995 and 1999 papers |
| 57 |
pdf of 1995 paper |
| 58 |
|
| 59 |
o FV |
| 60 |
add references to 1997 papers. |
| 61 |
|
| 62 |
o Tangent linear/adjoint add reference to |
| 63 |
Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc... |
| 64 |
|
| 65 |
o platforms |
| 66 |
Add reference to SC article and Scientific Programming article |
| 67 |
|
| 68 |
o List of key papers needs to be updated and reformatted |
| 69 |
|
| 70 |
|
| 71 |
o Global atmosphere: `Held Suarez', |
| 72 |
update Adcroft reference |
| 73 |
fix up ingrid link and frame (ingrid movies seem to be broken?) |
| 74 |
Held and Suarez reference is not a link. |
| 75 |
|
| 76 |
o Ocean Gyres |
| 77 |
fix up frame link |
| 78 |
make "lopped cell" a link to referenced paper. |
| 79 |
add references (ask Steph/Mick) |
| 80 |
online/offline paper |
| 81 |
|
| 82 |
o Convection and mixing over topography |
| 83 |
add in Legg references for convection and mixing over topography |
| 84 |
and external link to CPT-GCE etc... |
| 85 |
|
| 86 |
o Boundary forced internal waves |
| 87 |
add in Legg references, obc's reference |
| 88 |
|
| 89 |
o Parameter sensitivity |
| 90 |
add in Bugnion references, Boyin references, Steph references |
| 91 |
|
| 92 |
o State estimation |
| 93 |
add in references from Patrick/Carl/Ichiro/Detlef etc... |
| 94 |
update links to point to latest ECCO results |
| 95 |
ECCO ingrid results have been moved |
| 96 |
add forward links to "ECCO state estimation" chapter in manual |
| 97 |
|
| 98 |
o Ocean biogeochemical cycles |
| 99 |
add in references from Mick/Galen etc... |
| 100 |
fix ingrid link ( date to date thing does not appear to work) |
| 101 |
figure url does not have a "target=idontexist" entry |
| 102 |
|
| 103 |
o Simulations of laboratory experiments |
| 104 |
reference Wardle and Karsten papers |
| 105 |
update links to include DDDAS "PIAB" page |
| 106 |
cylindrical polar coordinates |
| 107 |
|
| 108 |
o Continuos equations in ''r'' coordinates |
| 109 |
add references to iso paper |
| 110 |
no mention of z* and p* - forward reference to z*/p* in 2. |
| 111 |
add that coupling also manifests through F, Q |
| 112 |
add tracer transport |
| 113 |
|
| 114 |
o Kinematic boundary conditions |
| 115 |
|
| 116 |
o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms |
| 117 |
need to tidy up discussion of shallow-atmosphere to be |
| 118 |
consistent with the code or change code to be consistent |
| 119 |
with the discussion! |
| 120 |
make references hyperlinks |
| 121 |
add stuff too |
| 122 |
|
| 123 |
o Finding the pressure field |
| 124 |
make references hyperlinks |
| 125 |
add forward references to manual algorithm section |
| 126 |
change Elliptic to "elliptic" |
| 127 |
|
| 128 |
o Forcing and dissipation |
| 129 |
make "physics packages" refer to chapter 6. |
| 130 |
should we move "external forcing" et. al to a |
| 131 |
generic_forcing_driver package? |
| 132 |
|
| 133 |
viscosities |
| 134 |
update to mention Smag/Leith (Ah and A4 not constant) |
| 135 |
and to have forward references to numerical section |
| 136 |
tracers |
| 137 |
forward references to numerical section, reddy, GM etc... |
| 138 |
add references to literature |
| 139 |
|
| 140 |
o 1.3.8 Vector invariant form |
| 141 |
forward references to numerical section |
| 142 |
|
| 143 |
o 1.3.9 Adjoint |
| 144 |
add a little more here + some hyperlink to chapter 5. |
| 145 |
|
| 146 |
o 1.4 Appendix ATMOSPHERE |
| 147 |
|
| 148 |
add some introductory words |
| 149 |
|
| 150 |
o 1.6 Coordinate systems |
| 151 |
o only has some words on spherical polar. add some brief words |
| 152 |
to cover all of |
| 153 |
- cartesian |
| 154 |
- spherical |
| 155 |
- cylindrical |
| 156 |
- general orthogonal curvilinear (vector invariant) |
| 157 |
|
| 158 |
o Equation of state options |
| 159 |
add some discussion |
| 160 |
can't remember what we said we were going to do here |
| 161 |
PH to do something |
| 162 |
|
| 163 |
|
| 164 |
Discretization and alg - JMC+CNH |
| 165 |
|
| 166 |
Tutorials - AM |
| 167 |
3.1 "Where to find" |
| 168 |
o link to Pelican not needed |
| 169 |
o mailman twice (why?) |
| 170 |
o no htdig (gone? - I liked it) |
| 171 |
|
| 172 |
intro part |
| 173 |
individual experiments |
| 174 |
|
| 175 |
offline - duplicate inputs, what is it, tidy up cfc v. |
| 176 |
other offline. |
| 177 |
|
| 178 |
Software - EH to review |
| 179 |
|
| 180 |
some to be done on resource estimates at the end - needs sorting. |
| 181 |
|
| 182 |
Automatic Diff - CE |
| 183 |
|
| 184 |
Physical Packages - ??? |
| 185 |
|
| 186 |
Diags and tools - ??? |
| 187 |
|
| 188 |
Interface with ECCO - ??? |
| 189 |
|
| 190 |
Model uses - ??? |
| 191 |
|
| 192 |
Building document - ??? |
| 193 |
via cron |
| 194 |
tweaking latex2html etc.. |
| 195 |
|
| 196 |
Src Code tree (rename |
| 197 |
examples etc..) - ??? |
| 198 |
|
| 199 |
Documentation |
| 200 |
|
| 201 |
1. Introduction |
| 202 |
|
| 203 |
2. Discretization and Algorithm |
| 204 |
|
| 205 |
2.13.5 Lateral dissipation |
| 206 |
o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags |
| 207 |
in code need to explain why cos()3/2 turns out to be |
| 208 |
scaling (not cos()2) |
| 209 |
|
| 210 |
2.13.6 Vertical dissipation |
| 211 |
o update to have reference to Baylors section |
| 212 |
reference to implicit discussion in time-stepping part of manual |
| 213 |
|
| 214 |
|
| 215 |
|
| 216 |
3. Tutorials |
| 217 |
reorg'd into |
| 218 |
intro part |
| 219 |
individual experiments |
| 220 |
|
| 221 |
4. Software Architecture |
| 222 |
|
| 223 |
5. Automatic Differentiation |
| 224 |
|
| 225 |
6. Physical Parameterization and Packages |
| 226 |
|
| 227 |
7. Diagnostics and tools |
| 228 |
|
| 229 |
8. Interface with ECCO |
| 230 |
|
| 231 |
9. Model uses |
| 232 |
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
| 233 |
(check in support for more names) |
| 234 |
|
| 235 |
Need an empty package as part of distribution |
| 236 |
|
| 237 |
latex2html equation formatting is still a bit weird in places. Need to have another go if we have a chance - especially the degree symbol seems to jump around somewhat! |
| 238 |
|
| 239 |
Chapter 1 |
| 240 |
|
| 241 |
Change hydrodynamical to "dynamical" |
| 242 |
|
| 243 |
Examples |
| 244 |
|
| 245 |
- extra "in action" cases |
| 246 |
|
| 247 |
o high res ocean with diurnal atmospheric state forcing |
| 248 |
- links to ingrid output |
| 249 |
CNH/Dimitris |
| 250 |
|
| 251 |
o realistic FIZHI from Andrea |
| 252 |
- links to ingrid output |
| 253 |
from AM |
| 254 |
|
| 255 |
o with seaice on high res cube |
| 256 |
- links to ingrid output |
| 257 |
CNH/Dimitris |
| 258 |
|
| 259 |
o coupled aqua, ridge world etc... |
| 260 |
- links to ingrid output |
| 261 |
get stuff from Daniel |
| 262 |
|
| 263 |
o constrained lab simulation |
| 264 |
- links to ingrid output for model and lab |
| 265 |
fields |
| 266 |
get stuff from Sai/Andrew |
| 267 |
|
| 268 |
o sensitivity wrt to iron |
| 269 |
|
| 270 |
o optimization |
| 271 |
- update to link to latest ECCO sites and GF |
| 272 |
related material |
| 273 |
|
| 274 |
o eddy diffusivity transport application |
| 275 |
|
| 276 |
o Gas giant? |
| 277 |
|
| 278 |
Chapter 6 |
| 279 |
|
| 280 |
the master package diagram does not appear in the document |
| 281 |
|
| 282 |
pkg/ptracers doesn't seem to have any documentation (see packages list below) |
| 283 |
|
| 284 |
|
| 285 |
|
| 286 |
2.10.5 Horizontal grid |
| 287 |
|
| 288 |
need to do a better job of relating model variables to this diagram |
| 289 |
|
| 290 |
|
| 291 |
Master list of packages |
| 292 |
|
| 293 |
admtlm/ - autodiff (chapter 5) |
| 294 |
aim/ - 6.4.1 (content needs fixing - JM to do) |
| 295 |
aim_compon_interf/ - 6.6 (no content yet) |
| 296 |
aim_ocn_coupler/ - 6.6 (no content yet) |
| 297 |
aim_v23/ - retired |
| 298 |
atm_common/ - 6.6 (no content yet) |
| 299 |
autodiff/ - autodiff (chapter 5) |
| 300 |
bulk_force/ - 6.3.3 |
| 301 |
cal/ - 6.3.5 |
| 302 |
cd_code/ - chapter 2 (JM check) |
| 303 |
cfc/ - not sure |
| 304 |
chronos/ - AM to check |
| 305 |
compon_communic/ - 6.6 (no content yet) |
| 306 |
cost/ - not sure, check with PH |
| 307 |
ctrl/ - not sure, check with PH |
| 308 |
debug/ - JM may do something in chapter 7 (utilities) |
| 309 |
diagnostics/ - 7.1 |
| 310 |
dic/ - 6.7.2 |
| 311 |
ebm/ - not sure |
| 312 |
ecco/ - chapter 8 |
| 313 |
embed_files/ - add something to chapter 7 |
| 314 |
ex3/ - rename to exch3 |
| 315 |
exch2/ - 6.2.2 |
| 316 |
exf/ - 6.3.4 |
| 317 |
fizhi/ - 6.4.3 |
| 318 |
flt/ - in chapter 2 (JM check) |
| 319 |
gchem/ - 6.7.1 |
| 320 |
generic_advdiff/ - in chapter 2 (JM check) |
| 321 |
ggl90/ - nothing, (Martin?) |
| 322 |
gmredi/ - in chapter 2 (JM check). also need |
| 323 |
Ferrari & Mc tapering |
| 324 |
grdchk/ - grdchk (chapter 5 - check with PH) |
| 325 |
gridalt/ - 6.2.4 |
| 326 |
kpp/ - 6.3.2 |
| 327 |
land/ - 6.4.2 (not connected to code - JM to fix) |
| 328 |
matrix/ - Samar |
| 329 |
mdsio/ - 7.3.1 |
| 330 |
mnc/ - 7.2.1 |
| 331 |
mom_common/ - in chapter 2 (JM check) |
| 332 |
mom_fluxform/ - in chapter 2 (JM check) |
| 333 |
mom_vecinv/ - in chapter 2 (JM check) |
| 334 |
monitor/ - 7.4 |
| 335 |
my82/ - nothing, (martin?) |
| 336 |
obcs/ - 6.3 (needs a check) |
| 337 |
ocn_compon_interf/ - 6.6 (no content yet) |
| 338 |
offline/ - nothing, tutorials that need work but no package section entry |
| 339 |
opps/ - nothing, (martin?) |
| 340 |
pp81/ - nothing, (martin?) |
| 341 |
profiles/ - GAEL |
| 342 |
ptracers/ - JM + SD to write something |
| 343 |
rbcs/ - talk to steph |
| 344 |
runclock/ - runclock |
| 345 |
rw/ - not sure |
| 346 |
sbo/ - text in sbo_descruption.tex but not linked into |
| 347 |
part6 |
| 348 |
seaice/ - 6.5.2 - no equations, dimitris has promised some |
| 349 |
shap_filt/ - chapter 2, JM to check |
| 350 |
shelfice/ - nothing yet (martin?) |
| 351 |
solver/ - empty |
| 352 |
sphere/ - chapter 5 or 8 (PH to check) |
| 353 |
therm_seaice/ - empty |
| 354 |
thsice/ - 6.5.1 (JM to update?) |
| 355 |
timeave/ - retiring...... |
| 356 |
zonal_filt/ - chapter 2 (JM to check) |
| 357 |
|
| 358 |
Possible for chap 7 - Daniels grafix/ stuff |
| 359 |
|
| 360 |
Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started. |
| 361 |
|
| 362 |
Figure 6.8 is missing |
| 363 |
|
| 364 |
|
| 365 |
>>>> From Ed |
| 366 |
|
| 367 |
Here are the remaining bits for Chap 4 : |
| 368 |
|
| 369 |
- The grammar/flow could still use some work. Boo was an English |
| 370 |
major and has experience editing/proofing technical papers. I |
| 371 |
could print out a copy and ask her to read it and suggest |
| 372 |
improvements. |
| 373 |
|
| 374 |
- missing references (if you point me towards URLs, I'll add them |
| 375 |
to the bibliography): |
| 376 |
\ref{ref hoe and hill, ecmwf} |
| 377 |
\ref{magicgarden} |
| 378 |
\ref{IBMLAPI} |
| 379 |
\ref{Memorychannel} |
| 380 |
\ref{hoe-hill:99} |
| 381 |
|
| 382 |
- There are a few empty sub-sections at the end of Chap 4 that |
| 383 |
should either be commented out or fleshed out. |
| 384 |
|
| 385 |
and thats about it for Chap 4. |
| 386 |
|
| 387 |
|
| 388 |
Add more to quick links on front page |
| 389 |
|
| 390 |
|
| 391 |
>>>> From Andrea |
| 392 |
|
| 393 |
to do list for chap 7: |
| 394 |
|
| 395 |
|
| 396 |
7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu" |
| 397 |
the links are pointing to the proper place |
| 398 |
|
| 399 |
7.5.1 - add Graphix to the list of stuff in utils/matlab |
| 400 |
7.5.2 - empty |
| 401 |
|
| 402 |
|
| 403 |
andrea |
| 404 |
|
| 405 |
>>>> From Andrea |
| 406 |
|
| 407 |
Chapter 3 |
| 408 |
-------- |
| 409 |
|
| 410 |
Almost all of the 'math mode' text is dropped down as subscripts |
| 411 |
|
| 412 |
divide chapter 3 more clearly into 2 sections? |
| 413 |
(ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and |
| 414 |
then 3.19 and 3.20 are informational again - rearrange subsections?) |
| 415 |
|
| 416 |
3.1 - don't need a link to the outside of the document (remove it) |
| 417 |
- link to htdig is broken |
| 418 |
|
| 419 |
3.2.1 - link at bottom to source code points to section 3.2.1 |
| 420 |
(ie, to itself) - link should point to cvs code archive |
| 421 |
|
| 422 |
3.2.2.1 - ('upgrading from an earlier version') belongs under |
| 423 |
the cvs part, ie, should be 3.2.1.1 |
| 424 |
|
| 425 |
3.3 - remove reference to 'diags' section under MITgcm |
| 426 |
- remove reference to 'exe' and 'bin' sections also |
| 427 |
(remove the .cvsignore file under these directories in cvs) |
| 428 |
- add a 'jobs' section, and a description as examples of run scripts |
| 429 |
- add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions |
| 430 |
- under 'tools' add a reference to 'build_options'. refer to the 'optfiles' |
| 431 |
- under 'tools' the adjoint points to section 5 - this is now section 8 |
| 432 |
(but should be a floating reference) |
| 433 |
- under 'utils' add a reference to exch2 - stuff for different resolutions |
| 434 |
- the description of the pkg section refers directly to |
| 435 |
section 3. should be section 6 (actually should be a floating reference) |
| 436 |
|
| 437 |
3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10) |
| 438 |
3.4.1 - links to the following experiments don't exist or are broken: |
| 439 |
exp2 - should link to section 3.9 |
| 440 |
hs94.cs-32x32x5 - link to section 3.12 |
| 441 |
add 'convection' to the list, link to section 3.13 |
| 442 |
add 'plume on slope` to the list, link to section 3.14 |
| 443 |
add '??' link to section 3.15 |
| 444 |
add 'dic_example on slope` to the list, link to section 3.16 |
| 445 |
add '??' link to section 3.17 |
| 446 |
add 'offline' and link to section 3.18 |
| 447 |
clean up others and make links where they are needed |
| 448 |
3.4.2 - text suggests to see section 2 for details about what is in the 'code' |
| 449 |
and 'input' directories - should refer to the examples in this section |
| 450 |
- add 'build' bullet - this is where the model is compiled and exectuable lives |
| 451 |
|
| 452 |
3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options |
| 453 |
as the place where they live (add a link?) |
| 454 |
|
| 455 |
3.6.1 - Add some general 'approach' text - ie, output is controlled either by the |
| 456 |
'data' file in the input directory or by the data.[pkg name] file for any |
| 457 |
package running. And there is some default behavior when the 'state' dumps |
| 458 |
are written. |
| 459 |
3.6.1.2 - needs to be moved to inside section 3.6.2 |
| 460 |
|
| 461 |
3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18) |
| 462 |
underneath this one and leave the text for 3.7 in place |
| 463 |
|
| 464 |
All the 'overview' sections need some reference to the name of the experiment in |
| 465 |
the verification directory |
| 466 |
|
| 467 |
3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript |
| 468 |
- is this experiment in the list from section 3.4??? |
| 469 |
3.10.3.1 - refers to figures and equations, links are broken |
| 470 |
|
| 471 |
3.11.3.2 - line 43: link to equation is broken |
| 472 |
- line 51-53: link to equation is broken |
| 473 |
- there is some mess of text hanging around the end of this section. remove? reformat? |
| 474 |
|
| 475 |
3.12.4.1 - line 34 - link to equation is broken |
| 476 |
- lines 60,61 - 1st (take out the 'r' in the superscript) |
| 477 |
|
| 478 |
3.13.2 - link to theta-equation is broken |
| 479 |
3.13.5.4 -- ALL of the bold links to variable names are broken |
| 480 |
line 34: link to equation is broken |
| 481 |
|
| 482 |
3.15.1 - reference to 'fourth experiment' should be removed |
| 483 |
|
| 484 |
3.16.4 - strange formatting, presence of '>' symbols - remove them |
| 485 |
|
| 486 |
3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4 |
| 487 |
3.17.3.1 - nothing filled in under file input/data - needs description |
| 488 |
|
| 489 |
3.18.2 - point to section 2 for details - need hyperlink |
| 490 |
|
| 491 |
3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true! |
| 492 |
section 3.5 has the 'build' directory in the example |
| 493 |
|
| 494 |
3.20.1 - link to doc at end of section points to this section |
| 495 |
3.20.2 - link to doc at end of section points to this section |
| 496 |
|
| 497 |
>>>> from JM |
| 498 |
|
| 499 |
|
| 500 |
|
| 501 |
manual, section.2 : |
| 502 |
|
| 503 |
In general: |
| 504 |
- add more refences/links to S/R & variable name |
| 505 |
- would be nice to have an active link to the fortran-file |
| 506 |
for all the S/R & eq.Number in the "calling-tree" boxes |
| 507 |
- search for CALC_MOM_RHS and replace it by the appropriate S/R |
| 508 |
(mom_flux_form, mom_vecinv, dynamics) |
| 509 |
- Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h}) |
| 510 |
was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}} |
| 511 |
in section.2, \vec{\bf v} is used instead and 3.D velocity vector is |
| 512 |
simply written \vec{v}. |
| 513 |
I would suggest to keep the notation as they are (since they are consistent |
| 514 |
inside each section) but may be to move the "notation.tex" piece |
| 515 |
at the beginning of section.2 and to mention clearly the changes between |
| 516 |
the 2 sections. |
| 517 |
|
| 518 |
in content: Horizontal Dissipation: 2 times in vector-invariant section |
| 519 |
|
| 520 |
2.1 time-stepping (part2/time_stepping.tex) |
| 521 |
|
| 522 |
- this is not clear to me: |
| 523 |
|
| 524 |
>> In all the above configurations it is also possible to substitute the |
| 525 |
>> Adams-Bashforth with an alternative time-stepping scheme for terms |
| 526 |
>> evaluated explicitly in time |
| 527 |
|
| 528 |
|
| 529 |
2.2 rigid-lid: |
| 530 |
|
| 531 |
- At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)" |
| 532 |
to stay closer to the code. |
| 533 |
- mention section 2.5 implicit-Time-stepping (for vertical viscosity) |
| 534 |
|
| 535 |
2.3 linear free-surface: |
| 536 |
- add ref(+link) to S/R names: |
| 537 |
- add ref(+link) to Crank-Nickelson section 2.9.1 |
| 538 |
|
| 539 |
2.4 Adams-Bashforth |
| 540 |
- add stability diagrams (I have some figures that I can put) |
| 541 |
- add link for var. forcing_In_AB |
| 542 |
- add S/R link for S/R ADAMS_BASHFORTH2 |
| 543 |
|
| 544 |
2.5 Implicit time-stepping |
| 545 |
- add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R |
| 546 |
SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL |
| 547 |
- update: also used for vertical advection |
| 548 |
|
| 549 |
2.6 Synchronous time-stepping: |
| 550 |
- add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE, |
| 551 |
MOMENTUM_CORRECTION_STEP. |
| 552 |
|
| 553 |
2.7 Stagger baroclinic time-stepping |
| 554 |
- mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end |
| 555 |
|
| 556 |
2.8 NH |
| 557 |
- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D |
| 558 |
|
| 559 |
2.9 Variants on Free-Surface |
| 560 |
- Delta.t mis-written (eq.2.73) |
| 561 |
- Eq.Num missing (has been fixed since) |
| 562 |
- u* is stored in gU (and not in gUnm1) |
| 563 |
- Phi_nh in NH_VARS.h |
| 564 |
- add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D, |
| 565 |
INI_CG2D, INI_CG3D |
| 566 |
|
| 567 |
2.9.1 Crank-Nickelson |
| 568 |
- link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater |
| 569 |
|
| 570 |
2.9.2 NLFS |
| 571 |
- eq.Nb are wrong in html |
| 572 |
- 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi) |
| 573 |
|
| 574 |
2.10.1 Notation |
| 575 |
- Area definition is not really used like this |
| 576 |
|
| 577 |
>> Ao : Area of the face orthogonal to "o" direction (o=u,v,w) |
| 578 |
|
| 579 |
Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to |
| 580 |
the model variables) are used (e.g., see section 2.10.5) |
| 581 |
|
| 582 |
2.10.5 Horizontal grid: |
| 583 |
- fig.2.8 : should use Aw,As consistently in this figure description, |
| 584 |
in the figure itself, as it is in the text. |
| 585 |
- curvilinear: |
| 586 |
to add: mention the angle of the grid direction relative to |
| 587 |
Eastward, Northward direction. |
| 588 |
+ mention horizGridFile= in file "data" (PARM04) |
| 589 |
- add cylindrical grid description |
| 590 |
|
| 591 |
2.11 Continuity & Horizontal Pressure gradient terms |
| 592 |
- mention that d.Phi/dr|s =g if using z coordinate |
| 593 |
- eq. 2.90 not clear regarding \delta_k(P-E) |
| 594 |
better to add the free surface eq: d.eta/dt = w_s + P-E |
| 595 |
|
| 596 |
2.12 Hydrostatic balance |
| 597 |
- add ref to Atmosphere Appendix section (1.4) since Adcroft 2002 |
| 598 |
is hard to find |
| 599 |
- add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H) |
| 600 |
and in section 1.3.4: remove the 1.3.4.3.2 subsection: |
| 601 |
Quasi-nonhydrostatic Atmosphere |
| 602 |
|
| 603 |
2.13.2 Coriolis terms |
| 604 |
- note: the discretization used when useEnergyConservingCoriolis=T |
| 605 |
has no hFac and no Area and is still different from the form |
| 606 |
described here (with Area & hFac); |
| 607 |
|
| 608 |
2.13.5 Lateral dissipation |
| 609 |
- add description of how to use cosFactor & cosPower |
| 610 |
- add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4 |
| 611 |
|
| 612 |
2.13.6 Vertical dissipation |
| 613 |
- mention the implicit vertical viscosity option and ref to section 2.5 |
| 614 |
- add the parameter correspondence: Av <-> viscAr (and might change also |
| 615 |
the notation to Ar) |
| 616 |
|
| 617 |
2.14 Vector invariant momentum equations |
| 618 |
- indicate that the NH pieces (vertical momentum eq) are not yet coded |
| 619 |
and that the NH code uses the flux form. |
| 620 |
|
| 621 |
2.14.6 Horizontal dissipation -> Horizontal Divergence |
| 622 |
|
| 623 |
2.14.7 Horizontal dissipation |
| 624 |
- add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ |
| 625 |
and A_D4,A_z4 <-> viscA4D,viscA4Z |
| 626 |
|
| 627 |
2.16 & 2.17 & 2.18 : |
| 628 |
- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
| 629 |
|
| 630 |
2.20.2 mercator, non-dimensional Equations: |
| 631 |
- does not use std notation |
| 632 |
- would be better as an appendix of section 2.20: |
| 633 |
(e.g changing the tile to: |
| 634 |
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
| 635 |
|
| 636 |
JM |
| 637 |
|
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