1 |
Editors |
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|
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Overall - JM, AM, PH, CNH, EH3 |
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|
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Front content - EH3 |
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|
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Chapter 1 - CNH |
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|
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Chapter 2 - JMC |
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|
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Chapter 3 - AM |
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|
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Chapter 4 - CNH |
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|
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Chapter 5 - PH |
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|
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Chapter 6 - AM |
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|
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Chapter 7 - EH3 |
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|
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Chapter 8 - PH |
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|
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Chapter 9 - CNH (Applications) |
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|
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Chapter 10 - JMC (Under development chapter) |
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|
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Biblio - EH3 |
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|
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|
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Rebuild and set to do cron build - DONE on hugo |
31 |
|
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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 |
|
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- 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 |
|
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o HTML, scripts and front content |
45 |
|
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- pick a URL: mitgcm.org/r2 <-- EH3's preferred base URL |
47 |
|
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- mitgcm.org/r2_web_testing/latest |
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|
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o --DONE-- add another short-cut for quick download |
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|
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o --DONE-- add another short-cut |
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About |
54 |
Installation |
55 |
Contents |
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Overview |
57 |
Tutorials (broken) |
58 |
Browse Code |
59 |
|
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o --DONE-- words on http://mitgcm.org/r2_web_testing/latest change to |
61 |
|
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o --DONE-- finite-volume doesn't leap to FV figure |
63 |
|
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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 |
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most in-line expressions (that is, math embedded in text). |
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The fix results in some things being slightly raised but I |
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thin this is more asthetically pleasing than being somewhat |
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lowered as before. --EH3 |
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|
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To view the altered alignment, see: |
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|
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http://eddy.csail.mit.edu/r2/latest/ |
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|
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o Need an empty package as part of distribution. Check out atm_common |
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|
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|
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o Latex |
81 |
|
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Chapter 1 - CNH |
83 |
o single kernel diagram - |
84 |
add reference to MWR paper |
85 |
|
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o non-hydro |
87 |
add reference to 1995 and 1999 papers |
88 |
pdf of 1995 paper |
89 |
|
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o FV |
91 |
add references to 1997 papers. |
92 |
|
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o Tangent linear/adjoint add reference to |
94 |
Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc... |
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|
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o platforms |
97 |
Add reference to SC article and Scientific Programming article |
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|
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o List of key papers needs to be updated and reformatted |
100 |
|
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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 |
|
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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 |
|
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o Convection and mixing over topography |
113 |
add in Legg references for convection and mixing over topography |
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and external link to CPT-GCE etc... |
115 |
|
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o Boundary forced internal waves |
117 |
add in Legg references, obc's reference |
118 |
|
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o Parameter sensitivity |
120 |
add in Bugnion references, Boyin references, Steph references |
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|
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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 |
|
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o Simulations of laboratory experiments |
134 |
reference Wardle and Karsten papers |
135 |
update links to include DDDAS "PIAB" page |
136 |
cylindrical polar coordinates |
137 |
|
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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 |
|
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o Kinematic boundary conditions |
145 |
|
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o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and |
147 |
Non-hydrostatic forms |
148 |
need to tidy up discussion of shallow-atmosphere to be |
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consistent with the code or change code to be consistent |
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with the discussion! |
151 |
make references hyperlinks |
152 |
add stuff too |
153 |
JMC remove QNH atmosphere |
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need to sort out calc_gw for deep atmosphere |
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|
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o Finding the pressure field |
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make references hyperlinks |
158 |
add forward references to manual algorithm section |
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change Elliptic to "elliptic" |
160 |
|
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o Forcing and dissipation |
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make "physics packages" refer to chapter 6. |
163 |
should we move "external forcing" et. al to a |
164 |
generic_forcing_driver package? |
165 |
|
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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... |
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add references to literature |
172 |
|
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o 1.3.8 Vector invariant form |
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forward references to numerical section |
175 |
|
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o 1.3.9 Adjoint |
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add a little more here + some hyperlink to chapter 5. |
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|
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o 1.4 Appendix ATMOSPHERE |
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|
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add some introductory words |
182 |
|
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o 1.6 Coordinate systems |
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o only has some words on spherical polar. add some brief words |
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to cover all of |
186 |
- cartesian |
187 |
- spherical |
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- cylindrical |
189 |
- general orthogonal curvilinear (vector invariant) |
190 |
|
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o Equation of state options |
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add some discussion |
193 |
can't remember what we said we were going to do here |
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PH to do something |
195 |
|
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|
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Change hydrodynamical to "dynamical" |
198 |
|
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Examples |
200 |
|
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- extra "in action" cases |
202 |
|
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o high res ocean with diurnal atmospheric state forcing |
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- links to ingrid output |
205 |
CNH/Dimitris |
206 |
|
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o realistic FIZHI from Andrea |
208 |
- links to ingrid output |
209 |
from AM |
210 |
|
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o with seaice on high res cube |
212 |
- links to ingrid output |
213 |
CNH/Dimitris |
214 |
|
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o coupled aqua, ridge world etc... |
216 |
- links to ingrid output |
217 |
get stuff from Daniel |
218 |
Davids donut movie |
219 |
|
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o constrained lab simulation |
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- links to ingrid output for model and lab |
222 |
fields |
223 |
get stuff from Sai/Andrew |
224 |
|
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o sensitivity wrt to iron |
226 |
|
227 |
o optimization |
228 |
- update to link to latest ECCO sites and GF |
229 |
related material |
230 |
|
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o eddy diffusivity transport application |
232 |
|
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o Gas giant? |
234 |
|
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|
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>>>> from JM |
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|
238 |
|
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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 |
|
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|
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 |
update organigramme |
455 |
- include rbcs |
456 |
(<- needs an update: e.g. atm2d, salt_plume, shelfice ...) |
457 |
|
458 |
Master list of packages (add this to beginning of chap 6) |
459 |
(<- needs an update: e.g. atm2d, salt_plume, shelfice ...) |
460 |
|
461 |
admtlm/ - autodiff (chapter 5) |
462 |
aim/ - retired |
463 |
aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM) |
464 |
aim_ocn_coupler/ - 6.6 (no content yet) |
465 |
aim_v23/ - 6.4.1 (content needs fixing - JM to do) |
466 |
atm_common/ - nothing in this package (6.4.1 related) |
467 |
autodiff/ - autodiff (chapter 5) |
468 |
bulk_force/ - 6.3.3 |
469 |
cal/ - 6.3.5 |
470 |
cd_code/ - chapter 2 (JM check add a reference to paper, |
471 |
mention parameter in data) |
472 |
cfc/ - not sure (CNH to talk to Steph and Helen) |
473 |
chronos/ - AM to check (not being used - Andrea to kill it) |
474 |
compon_communic/ - 6.6 (no content yet)(Daniel + JM) |
475 |
cost/ - not sure, check with PH |
476 |
ctrl/ - not sure, check with PH |
477 |
debug/ - JM may do something in chapter 7 (utilities) |
478 |
diagnostics/ - 7.1 |
479 |
dic/ - 6.7.2 |
480 |
ebm/ - (check with PH) |
481 |
ecco/ - chapter 8 |
482 |
embed_files/ - add something to chapter 7 |
483 |
exch2/ - 6.2.2 |
484 |
exf/ - 6.3.4 |
485 |
fizhi/ - 6.4.3 |
486 |
o Including FIZHI doc |
487 |
- get things up to date |
488 |
flt/ - (PH check) |
489 |
gchem/ - 6.7.1 |
490 |
generic_advdiff/ - in chapter 2 (JM check) |
491 |
ggl90/ - nothing, (Martin?) |
492 |
gmredi/ - in chapter 2 (JM check). also need |
493 |
Ferrari & Mc transition zone stuff (Samar doing this) |
494 |
get dfer to read this |
495 |
grdchk/ - grdchk (chapter 5 - check with PH) |
496 |
gridalt/ - 6.2.4 |
497 |
kpp/ - 6.3.2 |
498 |
land/ - 6.4.2 (not connected to code Rong's notes - JM to fix) |
499 |
matrix/ - Samar |
500 |
mdsio/ - 7.3.1 |
501 |
mnc/ - 7.2.1 |
502 |
mom_common/ - in chapter 2 (JM check) |
503 |
mom_fluxform/ - in chapter 2 (JM check) |
504 |
mom_vecinv/ - in chapter 2 (JM check) |
505 |
monitor/ - 7.4 |
506 |
my82/ - nothing, (martin?) |
507 |
obcs/ - 6.3 (needs a check - ask PH to read) |
508 |
ocn_compon_interf/ - 6.6 (no content yet) |
509 |
offline/ - nothing, tutorials that need work but no package section entry |
510 |
trivial to document (CNH to do) |
511 |
opps/ - nothing, (martin?) |
512 |
pp81/ - nothing, (martin?) |
513 |
profiles/ - GAEL |
514 |
ptracers/ - JM + SD + Martin to write something (nothing for this |
515 |
at the moment) |
516 |
AM has diagnostics table for this. |
517 |
rbcs/ - CNH to talk to steph |
518 |
runclock/ - runclock - CNH |
519 |
rw/ - not sure - going to stay says JMC. quick IO calls |
520 |
JMC to write a quick note for that. |
521 |
sbo/ - text in sbo_descruption.tex but not linked into |
522 |
part6 - CNH |
523 |
seaice/ - 6.5.2 - no equations, dimitris has promised some |
524 |
shap_filt/ - chapter 2, JM to check |
525 |
shelfice/ - nothing yet (martin?) |
526 |
solver/ - empty (go away?) |
527 |
sphere/ - chapter 5 or 8 (PH to check) |
528 |
therm_seaice/ - empty (go away?) |
529 |
thsice/ - 6.5.1 (JM to update?) |
530 |
timeave/ - retiring...... |
531 |
zonal_filt/ - chapter 2 (JM to check) |
532 |
|
533 |
o Cost function packages |
534 |
- floats, weights, profiles etc... |
535 |
|
536 |
|
537 |
list an expeiment which uses package? CNH |
538 |
|
539 |
6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
540 |
Figure 6.8 is missing |
541 |
|
542 |
|
543 |
===== Chapter 7 ===== [EH3 editing] : |
544 |
|
545 |
+ JMC: please add description of: |
546 |
- diagstat |
547 |
- new temporal averaging feature |
548 |
|
549 |
+ update the RW / MDSIO description |
550 |
-> new meta file |
551 |
-> list all RW S/R that one should use instead of calling directly MDSIO |
552 |
|
553 |
+ add Graphix to the list of stuff in utils/matlab (Daniel) |
554 |
|
555 |
+ get bathymetry pre-processing stuff from Patrick and then describe it |
556 |
|
557 |
+ add something on spgrid mesh generator |
558 |
o Grid generation |
559 |
- more explanation and some step-by-step examples |
560 |
- plotting grid examples |
561 |
|
562 |
|
563 |
+ add in gmaze PV calculation scripts plus write up on how it is calculated |
564 |
http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/ |
565 |
|
566 |
|
567 |
andrea |
568 |
|
569 |
|
570 |
9. Publications using MITgcm --> "Previous Applications of MITgcm" |
571 |
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
572 |
(check in support for more names) |
573 |
|
574 |
10. Under development |
575 |
|
576 |
Constantinos LCML |
577 |
o Legend/LCML examples and explanation |
578 |
- examples and explanation! |
579 |
|
580 |
|
581 |
|
582 |
Bibliography |
583 |
|
584 |
tidy up from misc - .tex |
585 |
|
586 |
Also |
587 |
|
588 |
a link to the new manual |
589 |
should appear on the front page (even if it's under construction). |
590 |
|
591 |
updating: |
592 |
http://mitgcm.org/r2_web_testing/latest/code_reference/callTree.html |
593 |
which points to a 1.5 years old code. Would be good to generate a |
594 |
new one, and even better, to try to keep it up-to-date. |
595 |
|