207 |
o Gas giant? |
o Gas giant? |
208 |
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209 |
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|
210 |
Master list of packages |
>>>> from JM |
211 |
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|
212 |
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|
213 |
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manual, section.2 : |
214 |
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|
215 |
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In general: |
216 |
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- add more refences/links to S/R & variable name |
217 |
|
- would be nice to have an active link to the fortran-file |
218 |
|
for all the S/R & eq.Number in the "calling-tree" boxes |
219 |
|
- search for CALC_MOM_RHS and replace it by the appropriate S/R |
220 |
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(mom_flux_form, mom_vecinv, dynamics) |
221 |
|
- Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h}) |
222 |
|
was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}} |
223 |
|
in section.2, \vec{\bf v} is used instead and 3.D velocity vector is |
224 |
|
simply written \vec{v}. |
225 |
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I would suggest to keep the notation as they are (since they are consistent |
226 |
|
inside each section) but may be to move the "notation.tex" piece |
227 |
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at the beginning of section.2 and to mention clearly the changes between |
228 |
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the 2 sections. |
229 |
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|
230 |
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in content: Horizontal Dissipation: 2 times in vector-invariant section |
231 |
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|
232 |
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2.1 time-stepping (part2/time_stepping.tex) |
233 |
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|
234 |
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- this is not clear to me: |
235 |
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|
236 |
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>> In all the above configurations it is also possible to substitute the |
237 |
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>> Adams-Bashforth with an alternative time-stepping scheme for terms |
238 |
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>> evaluated explicitly in time |
239 |
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|
240 |
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|
241 |
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2.2 rigid-lid: |
242 |
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|
243 |
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- At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)" |
244 |
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to stay closer to the code. |
245 |
|
- mention section 2.5 implicit-Time-stepping (for vertical viscosity) |
246 |
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|
247 |
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2.3 linear free-surface: |
248 |
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- add ref(+link) to S/R names: |
249 |
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- add ref(+link) to Crank-Nickelson section 2.9.1 |
250 |
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|
251 |
|
2.4 Adams-Bashforth |
252 |
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- add stability diagrams (I have some figures that I can put) |
253 |
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- add link for var. forcing_In_AB |
254 |
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- add S/R link for S/R ADAMS_BASHFORTH2 |
255 |
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|
256 |
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2.5 Implicit time-stepping |
257 |
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- add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R |
258 |
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SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL |
259 |
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- update: also used for vertical advection |
260 |
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|
261 |
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2.6 Synchronous time-stepping: |
262 |
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- add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE, |
263 |
|
MOMENTUM_CORRECTION_STEP. |
264 |
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|
265 |
|
2.7 Stagger baroclinic time-stepping |
266 |
|
- mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end |
267 |
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|
268 |
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2.8 NH |
269 |
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- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D |
270 |
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|
271 |
|
2.9 Variants on Free-Surface |
272 |
|
- Delta.t mis-written (eq.2.73) |
273 |
|
- Eq.Num missing (has been fixed since) |
274 |
|
- u* is stored in gU (and not in gUnm1) |
275 |
|
- Phi_nh in NH_VARS.h |
276 |
|
- add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D, |
277 |
|
INI_CG2D, INI_CG3D |
278 |
|
|
279 |
|
2.9.1 Crank-Nickelson |
280 |
|
- link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater |
281 |
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|
282 |
|
2.9.2 NLFS |
283 |
|
- eq.Nb are wrong in html |
284 |
|
- 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi) |
285 |
|
|
286 |
|
2.10.1 Notation |
287 |
|
- Area definition is not really used like this |
288 |
|
|
289 |
|
>> Ao : Area of the face orthogonal to "o" direction (o=u,v,w) |
290 |
|
|
291 |
|
Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to |
292 |
|
the model variables) are used (e.g., see section 2.10.5) |
293 |
|
|
294 |
|
2.10.5 Horizontal grid: |
295 |
|
- fig.2.8 : should use Aw,As consistently in this figure description, |
296 |
|
in the figure itself, as it is in the text. |
297 |
|
- curvilinear: |
298 |
|
to add: mention the angle of the grid direction relative to |
299 |
|
Eastward, Northward direction. |
300 |
|
+ mention horizGridFile= in file "data" (PARM04) |
301 |
|
- add cylindrical grid description |
302 |
|
need to do a better job of relating model variables to this diagram |
303 |
|
|
304 |
|
|
305 |
|
2.11 Continuity & Horizontal Pressure gradient terms |
306 |
|
- mention that d.Phi/dr|s =g if using z coordinate |
307 |
|
- eq. 2.90 not clear regarding \delta_k(P-E) |
308 |
|
better to add the free surface eq: d.eta/dt = w_s + P-E |
309 |
|
|
310 |
|
2.12 Hydrostatic balance |
311 |
|
- add ref to Atmosphere Appendix section (1.4) since Adcroft 2002 |
312 |
|
is hard to find |
313 |
|
- add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H) |
314 |
|
and in section 1.3.4: remove the 1.3.4.3.2 subsection: |
315 |
|
Quasi-nonhydrostatic Atmosphere |
316 |
|
|
317 |
|
2.13.2 Coriolis terms |
318 |
|
- note: the discretization used when useEnergyConservingCoriolis=T |
319 |
|
has no hFac and no Area and is still different from the form |
320 |
|
described here (with Area & hFac); |
321 |
|
|
322 |
|
2.13.5 Lateral dissipation |
323 |
|
- add description of how to use cosFactor & cosPower |
324 |
|
- add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4 |
325 |
|
o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags |
326 |
|
in code need to explain why cos()3/2 turns out to be |
327 |
|
scaling (not cos()2) |
328 |
|
|
329 |
|
2.13.6 Vertical dissipation |
330 |
|
- mention the implicit vertical viscosity option and ref to section 2.5 |
331 |
|
- add the parameter correspondence: Av <-> viscAr (and might change also |
332 |
|
the notation to Ar) |
333 |
|
|
334 |
|
2.14 Vector invariant momentum equations |
335 |
|
- indicate that the NH pieces (vertical momentum eq) are not yet coded |
336 |
|
and that the NH code uses the flux form. |
337 |
|
|
338 |
|
2.14.6 Horizontal dissipation -> Horizontal Divergence |
339 |
|
|
340 |
|
2.14.7 Horizontal dissipation |
341 |
|
- add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ |
342 |
|
and A_D4,A_z4 <-> viscA4D,viscA4Z |
343 |
|
|
344 |
|
2.16 & 2.17 & 2.18 : |
345 |
|
- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
346 |
|
|
347 |
|
2.20.2 mercator, non-dimensional Equations: |
348 |
|
- does not use std notation |
349 |
|
- would be better as an appendix of section 2.20: |
350 |
|
(e.g changing the tile to: |
351 |
|
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
352 |
|
|
353 |
|
JM |
354 |
|
|
355 |
|
>>>> From Ed |
356 |
|
|
357 |
|
Here are the remaining bits for Chap 4 : |
358 |
|
|
359 |
|
- The grammar/flow could still use some work. Boo was an English |
360 |
|
major and has experience editing/proofing technical papers. I |
361 |
|
could print out a copy and ask her to read it and suggest |
362 |
|
improvements. |
363 |
|
|
364 |
|
- missing references (if you point me towards URLs, I'll add them |
365 |
|
to the bibliography): |
366 |
|
\ref{ref hoe and hill, ecmwf} |
367 |
|
\ref{magicgarden} |
368 |
|
\ref{IBMLAPI} |
369 |
|
\ref{Memorychannel} |
370 |
|
\ref{hoe-hill:99} |
371 |
|
|
372 |
|
- There are a few empty sub-sections at the end of Chap 4 that |
373 |
|
should either be commented out or fleshed out. |
374 |
|
|
375 |
|
and thats about it for Chap 4. |
376 |
|
|
377 |
|
|
378 |
|
Add more to quick links on front page |
379 |
|
|
380 |
|
Chapter 6 |
381 |
|
|
382 |
|
the master package diagram does not appear in the document |
383 |
|
|
384 |
|
pkg/ptracers doesn't seem to have any documentation (see packages list below) |
385 |
|
|
386 |
|
|
387 |
|
Master list of packages (add this to beginning of chap 6) |
388 |
|
|
389 |
admtlm/ - autodiff (chapter 5) |
admtlm/ - autodiff (chapter 5) |
390 |
aim/ - 6.4.1 (content needs fixing - JM to do) |
aim/ - retired |
391 |
aim_compon_interf/ - 6.6 (no content yet) |
aim_compon_interf/ - 6.6 (no content yet) |
392 |
aim_ocn_coupler/ - 6.6 (no content yet) |
aim_ocn_coupler/ - 6.6 (no content yet) |
393 |
aim_v23/ - retired |
aim_v23/ - 6.4.1 (content needs fixing - JM to do) |
394 |
atm_common/ - 6.6 (no content yet) |
atm_common/ - 6.6 (no content yet) |
395 |
autodiff/ - autodiff (chapter 5) |
autodiff/ - autodiff (chapter 5) |
396 |
bulk_force/ - 6.3.3 |
bulk_force/ - 6.3.3 |
457 |
|
|
458 |
Figure 6.8 is missing |
Figure 6.8 is missing |
459 |
|
|
460 |
|
6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
461 |
>>>> From Ed |
Figure 6.8 is missing |
|
|
|
|
Here are the remaining bits for Chap 4 : |
|
|
|
|
|
- The grammar/flow could still use some work. Boo was an English |
|
|
major and has experience editing/proofing technical papers. I |
|
|
could print out a copy and ask her to read it and suggest |
|
|
improvements. |
|
|
|
|
|
- missing references (if you point me towards URLs, I'll add them |
|
|
to the bibliography): |
|
|
\ref{ref hoe and hill, ecmwf} |
|
|
\ref{magicgarden} |
|
|
\ref{IBMLAPI} |
|
|
\ref{Memorychannel} |
|
|
\ref{hoe-hill:99} |
|
|
|
|
|
- There are a few empty sub-sections at the end of Chap 4 that |
|
|
should either be commented out or fleshed out. |
|
|
|
|
|
and thats about it for Chap 4. |
|
|
|
|
|
|
|
|
Add more to quick links on front page |
|
|
|
|
|
Chapter 6 |
|
|
|
|
|
the master package diagram does not appear in the document |
|
|
|
|
|
pkg/ptracers doesn't seem to have any documentation (see packages list below) |
|
462 |
|
|
463 |
|
|
464 |
>>>> From Andrea |
>>>> From Andrea |
570 |
offline - duplicate inputs, what is it, tidy up cfc v. |
offline - duplicate inputs, what is it, tidy up cfc v. |
571 |
other offline. JM thinks these need tidying up. |
other offline. JM thinks these need tidying up. |
572 |
|
|
|
>>>> from JM |
|
|
|
|
|
|
|
|
|
|
|
manual, section.2 : |
|
|
|
|
|
In general: |
|
|
- add more refences/links to S/R & variable name |
|
|
- would be nice to have an active link to the fortran-file |
|
|
for all the S/R & eq.Number in the "calling-tree" boxes |
|
|
- search for CALC_MOM_RHS and replace it by the appropriate S/R |
|
|
(mom_flux_form, mom_vecinv, dynamics) |
|
|
- Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h}) |
|
|
was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}} |
|
|
in section.2, \vec{\bf v} is used instead and 3.D velocity vector is |
|
|
simply written \vec{v}. |
|
|
I would suggest to keep the notation as they are (since they are consistent |
|
|
inside each section) but may be to move the "notation.tex" piece |
|
|
at the beginning of section.2 and to mention clearly the changes between |
|
|
the 2 sections. |
|
|
|
|
|
in content: Horizontal Dissipation: 2 times in vector-invariant section |
|
|
|
|
|
2.1 time-stepping (part2/time_stepping.tex) |
|
|
|
|
|
- this is not clear to me: |
|
|
|
|
|
>> In all the above configurations it is also possible to substitute the |
|
|
>> Adams-Bashforth with an alternative time-stepping scheme for terms |
|
|
>> evaluated explicitly in time |
|
|
|
|
|
|
|
|
2.2 rigid-lid: |
|
|
|
|
|
- At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)" |
|
|
to stay closer to the code. |
|
|
- mention section 2.5 implicit-Time-stepping (for vertical viscosity) |
|
|
|
|
|
2.3 linear free-surface: |
|
|
- add ref(+link) to S/R names: |
|
|
- add ref(+link) to Crank-Nickelson section 2.9.1 |
|
|
|
|
|
2.4 Adams-Bashforth |
|
|
- add stability diagrams (I have some figures that I can put) |
|
|
- add link for var. forcing_In_AB |
|
|
- add S/R link for S/R ADAMS_BASHFORTH2 |
|
|
|
|
|
2.5 Implicit time-stepping |
|
|
- add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R |
|
|
SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL |
|
|
- update: also used for vertical advection |
|
|
|
|
|
2.6 Synchronous time-stepping: |
|
|
- add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE, |
|
|
MOMENTUM_CORRECTION_STEP. |
|
|
|
|
|
2.7 Stagger baroclinic time-stepping |
|
|
- mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end |
|
|
|
|
|
2.8 NH |
|
|
- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D |
|
|
|
|
|
2.9 Variants on Free-Surface |
|
|
- Delta.t mis-written (eq.2.73) |
|
|
- Eq.Num missing (has been fixed since) |
|
|
- u* is stored in gU (and not in gUnm1) |
|
|
- Phi_nh in NH_VARS.h |
|
|
- add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D, |
|
|
INI_CG2D, INI_CG3D |
|
|
|
|
|
2.9.1 Crank-Nickelson |
|
|
- link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater |
|
|
|
|
|
2.9.2 NLFS |
|
|
- eq.Nb are wrong in html |
|
|
- 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi) |
|
|
|
|
|
2.10.1 Notation |
|
|
- Area definition is not really used like this |
|
|
|
|
|
>> Ao : Area of the face orthogonal to "o" direction (o=u,v,w) |
|
|
|
|
|
Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to |
|
|
the model variables) are used (e.g., see section 2.10.5) |
|
|
|
|
|
2.10.5 Horizontal grid: |
|
|
- fig.2.8 : should use Aw,As consistently in this figure description, |
|
|
in the figure itself, as it is in the text. |
|
|
- curvilinear: |
|
|
to add: mention the angle of the grid direction relative to |
|
|
Eastward, Northward direction. |
|
|
+ mention horizGridFile= in file "data" (PARM04) |
|
|
- add cylindrical grid description |
|
|
need to do a better job of relating model variables to this diagram |
|
|
|
|
|
|
|
|
2.11 Continuity & Horizontal Pressure gradient terms |
|
|
- mention that d.Phi/dr|s =g if using z coordinate |
|
|
- eq. 2.90 not clear regarding \delta_k(P-E) |
|
|
better to add the free surface eq: d.eta/dt = w_s + P-E |
|
|
|
|
|
2.12 Hydrostatic balance |
|
|
- add ref to Atmosphere Appendix section (1.4) since Adcroft 2002 |
|
|
is hard to find |
|
|
- add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H) |
|
|
and in section 1.3.4: remove the 1.3.4.3.2 subsection: |
|
|
Quasi-nonhydrostatic Atmosphere |
|
|
|
|
|
2.13.2 Coriolis terms |
|
|
- note: the discretization used when useEnergyConservingCoriolis=T |
|
|
has no hFac and no Area and is still different from the form |
|
|
described here (with Area & hFac); |
|
|
|
|
|
2.13.5 Lateral dissipation |
|
|
- add description of how to use cosFactor & cosPower |
|
|
- add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4 |
|
|
o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags |
|
|
in code need to explain why cos()3/2 turns out to be |
|
|
scaling (not cos()2) |
|
|
|
|
|
2.13.6 Vertical dissipation |
|
|
- mention the implicit vertical viscosity option and ref to section 2.5 |
|
|
- add the parameter correspondence: Av <-> viscAr (and might change also |
|
|
the notation to Ar) |
|
|
|
|
|
2.14 Vector invariant momentum equations |
|
|
- indicate that the NH pieces (vertical momentum eq) are not yet coded |
|
|
and that the NH code uses the flux form. |
|
|
|
|
|
2.14.6 Horizontal dissipation -> Horizontal Divergence |
|
|
|
|
|
2.14.7 Horizontal dissipation |
|
|
- add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ |
|
|
and A_D4,A_z4 <-> viscA4D,viscA4Z |
|
|
|
|
|
2.16 & 2.17 & 2.18 : |
|
|
- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
|
|
|
|
|
2.20.2 mercator, non-dimensional Equations: |
|
|
- does not use std notation |
|
|
- would be better as an appendix of section 2.20: |
|
|
(e.g changing the tile to: |
|
|
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
|
|
|
|
|
JM |
|
|
|
|
573 |
|
|
574 |
9. Model uses |
9. Model uses |
575 |
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |