5 |
- where to put under development links? |
- where to put under development links? |
6 |
JMC would like to have some mention of unfinished things (checked in |
JMC would like to have some mention of unfinished things (checked in |
7 |
but not that tested e.g. AB3) |
but not that tested e.g. AB3) |
8 |
|
Add an "Under development, chapter" - shortish description of what |
9 |
|
is available (last chapter) |
10 |
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|
11 |
- mitgcm.org very front page. |
|
12 |
o too many clicks to get to model manual. |
o HTML, scripts and front content |
13 |
make doc link go to mitgcm.org/r2_web_testing/latest |
|
14 |
and add "HowTo" reference etc... to /latest page |
- pick a URL |
15 |
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TBD |
16 |
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|
17 |
- mitgcm.org/r2_web_testing/latest |
- mitgcm.org/r2_web_testing/latest |
18 |
o add another short-cut for quick download |
o add another short-cut for quick download |
24 |
Overview |
Overview |
25 |
Tutorials (broken) |
Tutorials (broken) |
26 |
Browse Code |
Browse Code |
|
Get Code (where does this go to?) |
|
27 |
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28 |
o authors |
o words on http://mitgcm.org/r2_web_testing/latest |
29 |
John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen, |
change to |
30 |
Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos, |
"access on-line Auser manual/A and Atable of contents/A |
31 |
Gael - others? |
and browse the Aoverview section/A" |
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o Tutorials side bar link is broken |
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o words |
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change to "access on-line Auser manual/A and Atable of contents/A |
|
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and browse the Aoverview section/A" |
|
32 |
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33 |
o finite-volume doesn't leap to FV figure |
o finite-volume doesn't leap to FV figure |
34 |
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35 |
o the src and equation links don't come through to |
o have another go at pnmcrop et al. |
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the html when they are in figures - see chapter 2 for some |
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examples. |
|
36 |
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37 |
o degree symbols keep getting "dropped down" - problem with |
o Need an empty package as part of distribution. Check out atm_common |
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pnmcrop et al. |
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38 |
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39 |
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o Latex |
40 |
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41 |
Contents |
Chapter 1 - CNH |
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Intro - CNH |
|
42 |
o single kernel diagram - |
o single kernel diagram - |
43 |
add reference to MWR paper |
add reference to MWR paper |
44 |
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103 |
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104 |
o Kinematic boundary conditions |
o Kinematic boundary conditions |
105 |
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106 |
o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms |
o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and |
107 |
need to tidy up discussion of shallow-atmosphere to be |
Non-hydrostatic forms |
108 |
consistent with the code or change code to be consistent |
need to tidy up discussion of shallow-atmosphere to be |
109 |
with the discussion! |
consistent with the code or change code to be consistent |
110 |
make references hyperlinks |
with the discussion! |
111 |
add stuff too |
make references hyperlinks |
112 |
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add stuff too |
113 |
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JMC remove QNH atmosphere |
114 |
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need to sort out calc_gw for deep atmosphere |
115 |
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116 |
o Finding the pressure field |
o Finding the pressure field |
117 |
make references hyperlinks |
make references hyperlinks |
118 |
add forward references to manual algorithm section |
add forward references to manual algorithm section |
119 |
change Elliptic to "elliptic" |
change Elliptic to "elliptic" |
120 |
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|
121 |
o Forcing and dissipation |
o Forcing and dissipation |
122 |
make "physics packages" refer to chapter 6. |
make "physics packages" refer to chapter 6. |
123 |
should we move "external forcing" et. al to a |
should we move "external forcing" et. al to a |
124 |
generic_forcing_driver package? |
generic_forcing_driver package? |
125 |
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|
126 |
viscosities |
viscosities |
127 |
update to mention Smag/Leith (Ah and A4 not constant) |
update to mention Smag/Leith (Ah and A4 not constant) |
128 |
and to have forward references to numerical section |
and to have forward references to numerical section |
129 |
tracers |
tracers |
130 |
forward references to numerical section, reddy, GM etc... |
forward references to numerical section, reddy, GM etc... |
131 |
add references to literature |
add references to literature |
132 |
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|
133 |
o 1.3.8 Vector invariant form |
o 1.3.8 Vector invariant form |
134 |
forward references to numerical section |
forward references to numerical section |
154 |
PH to do something |
PH to do something |
155 |
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156 |
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Discretization and alg - JMC+CNH |
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Tutorials - AM |
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3.1 "Where to find" |
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o link to Pelican not needed |
|
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o mailman twice (why?) |
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o no htdig (gone? - I liked it) |
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intro part |
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individual experiments |
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offline - duplicate inputs, what is it, tidy up cfc v. |
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other offline. |
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Software - EH to review |
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some to be done on resource estimates at the end - needs sorting. |
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Automatic Diff - CE |
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Physical Packages - ??? |
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Diags and tools - ??? |
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Interface with ECCO - ??? |
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Model uses - ??? |
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Building document - ??? |
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via cron |
|
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tweaking latex2html etc.. |
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Src Code tree (rename |
|
|
examples etc..) - ??? |
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Documentation |
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1. Introduction |
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2. Discretization and Algorithm |
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|
2.13.5 Lateral dissipation |
|
|
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) |
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|
2.13.6 Vertical dissipation |
|
|
o update to have reference to Baylors section |
|
|
reference to implicit discussion in time-stepping part of manual |
|
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3. Tutorials |
|
|
reorg'd into |
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intro part |
|
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individual experiments |
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4. Software Architecture |
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5. Automatic Differentiation |
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6. Physical Parameterization and Packages |
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7. Diagnostics and tools |
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8. Interface with ECCO |
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9. Model uses |
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Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
|
|
(check in support for more names) |
|
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Need an empty package as part of distribution |
|
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|
|
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! |
|
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Chapter 1 |
|
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|
157 |
Change hydrodynamical to "dynamical" |
Change hydrodynamical to "dynamical" |
158 |
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|
159 |
Examples |
Examples |
191 |
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192 |
o Gas giant? |
o Gas giant? |
193 |
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Chapter 6 |
|
194 |
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|
195 |
the master package diagram does not appear in the document |
>>>> from JM |
196 |
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pkg/ptracers doesn't seem to have any documentation (see packages list below) |
|
197 |
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198 |
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manual, section.2 : |
199 |
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|
200 |
|
In general: |
201 |
|
- add more refences/links to S/R & variable name |
202 |
|
- would be nice to have an active link to the fortran-file |
203 |
|
for all the S/R & eq.Number in the "calling-tree" boxes |
204 |
|
- search for CALC_MOM_RHS and replace it by the appropriate S/R |
205 |
|
(mom_flux_form, mom_vecinv, dynamics) |
206 |
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- Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h}) |
207 |
|
was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}} |
208 |
|
in section.2, \vec{\bf v} is used instead and 3.D velocity vector is |
209 |
|
simply written \vec{v}. |
210 |
|
I would suggest to keep the notation as they are (since they are consistent |
211 |
|
inside each section) but may be to move the "notation.tex" piece |
212 |
|
at the beginning of section.2 and to mention clearly the changes between |
213 |
|
the 2 sections. |
214 |
|
|
215 |
2.10.5 Horizontal grid |
in content: Horizontal Dissipation: 2 times in vector-invariant section |
216 |
|
|
217 |
need to do a better job of relating model variables to this diagram |
2.1 time-stepping (part2/time_stepping.tex) |
218 |
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|
219 |
|
- this is not clear to me: |
220 |
|
|
221 |
Master list of packages |
>> In all the above configurations it is also possible to substitute the |
222 |
|
>> Adams-Bashforth with an alternative time-stepping scheme for terms |
223 |
|
>> evaluated explicitly in time |
224 |
|
|
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admtlm/ - autodiff (chapter 5) |
|
|
aim/ - 6.4.1 (content needs fixing - JM to do) |
|
|
aim_compon_interf/ - 6.6 (no content yet) |
|
|
aim_ocn_coupler/ - 6.6 (no content yet) |
|
|
aim_v23/ - retired |
|
|
atm_common/ - 6.6 (no content yet) |
|
|
autodiff/ - autodiff (chapter 5) |
|
|
bulk_force/ - 6.3.3 |
|
|
cal/ - 6.3.5 |
|
|
cd_code/ - chapter 2 (JM check) |
|
|
cfc/ - not sure |
|
|
chronos/ - AM to check |
|
|
compon_communic/ - 6.6 (no content yet) |
|
|
cost/ - not sure, check with PH |
|
|
ctrl/ - not sure, check with PH |
|
|
debug/ - JM may do something in chapter 7 (utilities) |
|
|
diagnostics/ - 7.1 |
|
|
dic/ - 6.7.2 |
|
|
ebm/ - not sure |
|
|
ecco/ - chapter 8 |
|
|
embed_files/ - add something to chapter 7 |
|
|
ex3/ - rename to exch3 |
|
|
exch2/ - 6.2.2 |
|
|
exf/ - 6.3.4 |
|
|
fizhi/ - 6.4.3 |
|
|
flt/ - in chapter 2 (JM check) |
|
|
gchem/ - 6.7.1 |
|
|
generic_advdiff/ - in chapter 2 (JM check) |
|
|
ggl90/ - nothing, (Martin?) |
|
|
gmredi/ - in chapter 2 (JM check). also need |
|
|
Ferrari & Mc tapering |
|
|
grdchk/ - grdchk (chapter 5 - check with PH) |
|
|
gridalt/ - 6.2.4 |
|
|
kpp/ - 6.3.2 |
|
|
land/ - 6.4.2 (not connected to code - JM to fix) |
|
|
matrix/ - Samar |
|
|
mdsio/ - 7.3.1 |
|
|
mnc/ - 7.2.1 |
|
|
mom_common/ - in chapter 2 (JM check) |
|
|
mom_fluxform/ - in chapter 2 (JM check) |
|
|
mom_vecinv/ - in chapter 2 (JM check) |
|
|
monitor/ - 7.4 |
|
|
my82/ - nothing, (martin?) |
|
|
obcs/ - 6.3 (needs a check) |
|
|
ocn_compon_interf/ - 6.6 (no content yet) |
|
|
offline/ - nothing, tutorials that need work but no package section entry |
|
|
opps/ - nothing, (martin?) |
|
|
pp81/ - nothing, (martin?) |
|
|
profiles/ - GAEL |
|
|
ptracers/ - JM + SD to write something |
|
|
rbcs/ - talk to steph |
|
|
runclock/ - runclock |
|
|
rw/ - not sure |
|
|
sbo/ - text in sbo_descruption.tex but not linked into |
|
|
part6 |
|
|
seaice/ - 6.5.2 - no equations, dimitris has promised some |
|
|
shap_filt/ - chapter 2, JM to check |
|
|
shelfice/ - nothing yet (martin?) |
|
|
solver/ - empty |
|
|
sphere/ - chapter 5 or 8 (PH to check) |
|
|
therm_seaice/ - empty |
|
|
thsice/ - 6.5.1 (JM to update?) |
|
|
timeave/ - retiring...... |
|
|
zonal_filt/ - chapter 2 (JM to check) |
|
225 |
|
|
226 |
Possible for chap 7 - Daniels grafix/ stuff |
2.2 rigid-lid: |
227 |
|
|
228 |
Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started. |
- At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)" |
229 |
|
to stay closer to the code. |
230 |
|
- mention section 2.5 implicit-Time-stepping (for vertical viscosity) |
231 |
|
|
232 |
Figure 6.8 is missing |
2.3 linear free-surface: |
233 |
|
- add ref(+link) to S/R names: |
234 |
|
- add ref(+link) to Crank-Nickelson section 2.9.1 |
235 |
|
|
236 |
|
2.4 Adams-Bashforth |
237 |
|
- add stability diagrams (I have some figures that I can put) |
238 |
|
- add link for var. forcing_In_AB |
239 |
|
- add S/R link for S/R ADAMS_BASHFORTH2 |
240 |
|
|
241 |
>>>> From Ed |
2.5 Implicit time-stepping |
242 |
|
- add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R |
243 |
|
SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL |
244 |
|
- update: also used for vertical advection |
245 |
|
|
246 |
Here are the remaining bits for Chap 4 : |
2.6 Synchronous time-stepping: |
247 |
|
- add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE, |
248 |
|
MOMENTUM_CORRECTION_STEP. |
249 |
|
|
250 |
- The grammar/flow could still use some work. Boo was an English |
2.7 Stagger baroclinic time-stepping |
251 |
major and has experience editing/proofing technical papers. I |
- mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end |
|
could print out a copy and ask her to read it and suggest |
|
|
improvements. |
|
252 |
|
|
253 |
- missing references (if you point me towards URLs, I'll add them |
2.8 NH |
254 |
to the bibliography): |
- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D |
|
\ref{ref hoe and hill, ecmwf} |
|
|
\ref{magicgarden} |
|
|
\ref{IBMLAPI} |
|
|
\ref{Memorychannel} |
|
|
\ref{hoe-hill:99} |
|
255 |
|
|
256 |
- There are a few empty sub-sections at the end of Chap 4 that |
2.9 Variants on Free-Surface |
257 |
should either be commented out or fleshed out. |
- Delta.t mis-written (eq.2.73) |
258 |
|
- Eq.Num missing (has been fixed since) |
259 |
|
- u* is stored in gU (and not in gUnm1) |
260 |
|
- Phi_nh in NH_VARS.h |
261 |
|
- add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D, |
262 |
|
INI_CG2D, INI_CG3D |
263 |
|
|
264 |
and thats about it for Chap 4. |
2.9.1 Crank-Nickelson |
265 |
|
- link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater |
266 |
|
|
267 |
|
2.9.2 NLFS |
268 |
|
- eq.Nb are wrong in html |
269 |
|
- 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi) |
270 |
|
|
271 |
|
2.10.1 Notation |
272 |
|
- Area definition is not really used like this |
273 |
|
|
274 |
Add more to quick links on front page |
>> Ao : Area of the face orthogonal to "o" direction (o=u,v,w) |
275 |
|
|
276 |
|
Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to |
277 |
|
the model variables) are used (e.g., see section 2.10.5) |
278 |
|
|
279 |
>>>> From Andrea |
2.10.5 Horizontal grid: |
280 |
|
- fig.2.8 : should use Aw,As consistently in this figure description, |
281 |
|
in the figure itself, as it is in the text. |
282 |
|
- curvilinear: |
283 |
|
to add: mention the angle of the grid direction relative to |
284 |
|
Eastward, Northward direction. |
285 |
|
+ mention horizGridFile= in file "data" (PARM04) |
286 |
|
- add cylindrical polar grid description |
287 |
|
need to do a better job of relating model variables to this diagram |
288 |
|
|
|
to do list for chap 7: |
|
289 |
|
|
290 |
|
2.11 Continuity & Horizontal Pressure gradient terms |
291 |
|
- mention that d.Phi/dr|s =g if using z coordinate |
292 |
|
- eq. 2.90 not clear regarding \delta_k(P-E) |
293 |
|
better to add the free surface eq: d.eta/dt = w_s + P-E |
294 |
|
|
295 |
7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu" |
2.12 Hydrostatic balance |
296 |
the links are pointing to the proper place |
- add ref to Atmosphere Appendix section (1.4) since Adcroft 2002 |
297 |
|
is hard to find |
298 |
|
- add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H) |
299 |
|
and in section 1.3.4: remove the 1.3.4.3.2 subsection: |
300 |
|
Quasi-nonhydrostatic Atmosphere |
301 |
|
|
302 |
7.5.1 - add Graphix to the list of stuff in utils/matlab |
2.13.2 Coriolis terms |
303 |
7.5.2 - empty |
- note: the discretization used when useEnergyConservingCoriolis=T |
304 |
|
has no hFac and no Area and is still different from the form |
305 |
|
described here (with Area & hFac); |
306 |
|
|
307 |
|
2.13.5 Lateral dissipation |
308 |
|
- add description of how to use cosFactor & cosPower |
309 |
|
- add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4 |
310 |
|
o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags |
311 |
|
in code need to explain why cos()3/2 turns out to be |
312 |
|
scaling (not cos()2) |
313 |
|
- need to reference the smag/leith section. |
314 |
|
|
315 |
|
2.13.6 Vertical dissipation |
316 |
|
- mention the implicit vertical viscosity option and ref to section 2.5 |
317 |
|
- add the parameter correspondence: Av <-> viscAr (and might change also |
318 |
|
the notation to Ar) |
319 |
|
|
320 |
|
2.14 Vector invariant momentum equations |
321 |
|
- indicate that the NH pieces (vertical momentum eq) are not yet coded |
322 |
|
and that the NH code uses the flux form. |
323 |
|
|
324 |
|
2.14.6 Horizontal dissipation -> Horizontal Divergence |
325 |
|
|
326 |
|
2.14.7 Horizontal dissipation |
327 |
|
- add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ |
328 |
|
and A_D4,A_z4 <-> viscA4D,viscA4Z |
329 |
|
|
330 |
|
2.16 & 2.17 & 2.18 : |
331 |
|
- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
332 |
|
- fix equations 2.202 & 2.203 (thanks to Martin) |
333 |
|
|
334 |
|
2.20.2 mercator, non-dimensional Equations: |
335 |
|
- does not use std notation |
336 |
|
- would be better as an appendix of section 2.20: |
337 |
|
(e.g changing the tile to: |
338 |
|
- talk to Baylor |
339 |
|
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
340 |
|
|
341 |
|
|
342 |
|
JM |
343 |
|
|
|
andrea |
|
344 |
|
|
345 |
>>>> From Andrea |
>>>> From Andrea |
346 |
|
|
349 |
|
|
350 |
Almost all of the 'math mode' text is dropped down as subscripts |
Almost all of the 'math mode' text is dropped down as subscripts |
351 |
|
|
|
divide chapter 3 more clearly into 2 sections? |
|
|
(ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and |
|
|
then 3.19 and 3.20 are informational again - rearrange subsections?) |
|
|
|
|
352 |
3.1 - don't need a link to the outside of the document (remove it) |
3.1 - don't need a link to the outside of the document (remove it) |
353 |
- link to htdig is broken |
- link to htdig is broken |
354 |
|
|
394 |
are written. |
are written. |
395 |
3.6.1.2 - needs to be moved to inside section 3.6.2 |
3.6.1.2 - needs to be moved to inside section 3.6.2 |
396 |
|
|
|
3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18) |
|
|
underneath this one and leave the text for 3.7 in place |
|
|
|
|
397 |
All the 'overview' sections need some reference to the name of the experiment in |
All the 'overview' sections need some reference to the name of the experiment in |
398 |
the verification directory |
the verification directory |
399 |
|
|
427 |
3.20.1 - link to doc at end of section points to this section |
3.20.1 - link to doc at end of section points to this section |
428 |
3.20.2 - link to doc at end of section points to this section |
3.20.2 - link to doc at end of section points to this section |
429 |
|
|
430 |
>>>> from JM |
offline - duplicate inputs, what is it, tidy up cfc v. |
431 |
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other offline. JM thinks these need tidying up. |
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manual, section.2 : |
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In general: |
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- add more refences/links to S/R & variable name |
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- would be nice to have an active link to the fortran-file |
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for all the S/R & eq.Number in the "calling-tree" boxes |
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- search for CALC_MOM_RHS and replace it by the appropriate S/R |
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(mom_flux_form, mom_vecinv, dynamics) |
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- Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h}) |
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was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}} |
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in section.2, \vec{\bf v} is used instead and 3.D velocity vector is |
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simply written \vec{v}. |
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I would suggest to keep the notation as they are (since they are consistent |
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inside each section) but may be to move the "notation.tex" piece |
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at the beginning of section.2 and to mention clearly the changes between |
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the 2 sections. |
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in content: Horizontal Dissipation: 2 times in vector-invariant section |
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2.1 time-stepping (part2/time_stepping.tex) |
|
432 |
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433 |
- this is not clear to me: |
Which of the following are which tutorial? |
434 |
|
adjustment.128x64x1 |
435 |
>> In all the above configurations it is also possible to substitute the |
adjustment.cs-32x32x1 |
436 |
>> Adams-Bashforth with an alternative time-stepping scheme for terms |
advect_cs |
437 |
>> evaluated explicitly in time |
advect_xy |
438 |
|
advect_xz |
439 |
|
aim.5l_cs |
440 |
|
aim.5l_Equatorial_Channel |
441 |
|
aim.5l_LatLon |
442 |
|
biogeo |
443 |
|
bottom_ctrl_5x5 |
444 |
|
cfc_example |
445 |
|
cpl_aim+ocn |
446 |
|
dome |
447 |
|
exp2 |
448 |
|
exp4 |
449 |
|
exp5 |
450 |
|
fizhi-cs-32x32x10 |
451 |
|
fizhi-cs-aqualev20 |
452 |
|
fizhi-gridalt-hs |
453 |
|
flt_example |
454 |
|
front_relax |
455 |
|
global1x1_tot |
456 |
|
global2x2_tot |
457 |
|
global_ocean.90x40x15 |
458 |
|
global_ocean.cs32x15 |
459 |
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global_ocean.cubed32x32x30 |
460 |
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global_ocean_ebm |
461 |
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global_with_exf |
462 |
|
hs94.128x64x5 |
463 |
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hs94.1x64x5 |
464 |
|
hs94.cs-32x32x5 |
465 |
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ideal_2D_oce |
466 |
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internal_wave |
467 |
|
inverted_barometer |
468 |
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lab_sea |
469 |
|
matrix_example |
470 |
|
MLAdjust |
471 |
|
natl_box |
472 |
|
natl_box_adjoint |
473 |
|
OpenAD |
474 |
|
rotating_tank |
475 |
|
solid-body.cs-32x32x1 |
476 |
|
tidal_basin_2d |
477 |
|
tutorial_baroclinic_gyre |
478 |
|
tutorial_barotropic_gyre |
479 |
|
tutorial_cfc_offline |
480 |
|
tutorial_deep_convection |
481 |
|
tutorial_global_oce_biogeo |
482 |
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tutorial_global_oce_in_p |
483 |
|
tutorial_global_oce_latlon |
484 |
|
tutorial_global_oce_optim |
485 |
|
tutorial_held_suarez_cs |
486 |
|
tutorial_offline |
487 |
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tutorial_plume_on_slope |
488 |
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tutorial_tracer_adjsens |
489 |
|
vermix |
490 |
|
|
491 |
|
>>>> From Ed |
492 |
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|
493 |
2.2 rigid-lid: |
Here are the remaining bits for Chap 4 : |
494 |
|
|
495 |
- At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)" |
- missing references (if you point me towards URLs, I'll add them |
496 |
to stay closer to the code. |
to the bibliography): |
497 |
- mention section 2.5 implicit-Time-stepping (for vertical viscosity) |
\ref{ref hoe and hill, ecmwf} |
498 |
|
\ref{magicgarden} |
499 |
|
\ref{IBMLAPI} |
500 |
|
\ref{Memorychannel} |
501 |
|
\ref{hoe-hill:99} |
502 |
|
|
503 |
2.3 linear free-surface: |
- There are a few empty sub-sections at the end of Chap 4 that |
504 |
- add ref(+link) to S/R names: |
should either be commented out or fleshed out. |
|
- add ref(+link) to Crank-Nickelson section 2.9.1 |
|
505 |
|
|
506 |
2.4 Adams-Bashforth |
and thats about it for Chap 4. |
|
- 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 |
|
507 |
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2.5 Implicit time-stepping |
|
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- add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R |
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SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL |
|
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- update: also used for vertical advection |
|
508 |
|
|
509 |
2.6 Synchronous time-stepping: |
Add more to quick links on front page |
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- add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE, |
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|
MOMENTUM_CORRECTION_STEP. |
|
510 |
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|
511 |
2.7 Stagger baroclinic time-stepping |
Chapter 6 |
|
- mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end |
|
512 |
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|
513 |
2.8 NH |
the master package diagram does not appear in the document |
|
- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D |
|
514 |
|
|
515 |
2.9 Variants on Free-Surface |
Master list of packages (add this to beginning of chap 6) |
|
- 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 |
|
516 |
|
|
517 |
2.9.1 Crank-Nickelson |
admtlm/ - autodiff (chapter 5) |
518 |
- link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater |
aim/ - retired |
519 |
|
aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM) |
520 |
2.9.2 NLFS |
aim_ocn_coupler/ - 6.6 (no content yet) |
521 |
- eq.Nb are wrong in html |
aim_v23/ - 6.4.1 (content needs fixing - JM to do) |
522 |
- 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi) |
atm_common/ - nothing in this package (6.4.1 related) |
523 |
|
autodiff/ - autodiff (chapter 5) |
524 |
|
bulk_force/ - 6.3.3 |
525 |
|
cal/ - 6.3.5 |
526 |
|
cd_code/ - chapter 2 (JM check add a reference to paper, |
527 |
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mention parameter in data) |
528 |
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cfc/ - not sure (CNH to talk to Steph and Helen) |
529 |
|
chronos/ - AM to check (not being used - Andrea to kill it) |
530 |
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compon_communic/ - 6.6 (no content yet)(Daniel + JM) |
531 |
|
cost/ - not sure, check with PH |
532 |
|
ctrl/ - not sure, check with PH |
533 |
|
debug/ - JM may do something in chapter 7 (utilities) |
534 |
|
diagnostics/ - 7.1 |
535 |
|
dic/ - 6.7.2 |
536 |
|
ebm/ - (check with PH) |
537 |
|
ecco/ - chapter 8 |
538 |
|
embed_files/ - add something to chapter 7 |
539 |
|
exch2/ - 6.2.2 |
540 |
|
exf/ - 6.3.4 |
541 |
|
fizhi/ - 6.4.3 |
542 |
|
flt/ - (PH check) |
543 |
|
gchem/ - 6.7.1 |
544 |
|
generic_advdiff/ - in chapter 2 (JM check) |
545 |
|
ggl90/ - nothing, (Martin?) |
546 |
|
gmredi/ - in chapter 2 (JM check). also need |
547 |
|
Ferrari & Mc transition zone stuff (Samar doing this) |
548 |
|
get dfer to read this |
549 |
|
grdchk/ - grdchk (chapter 5 - check with PH) |
550 |
|
gridalt/ - 6.2.4 |
551 |
|
kpp/ - 6.3.2 |
552 |
|
land/ - 6.4.2 (not connected to code Rong's notes - JM to fix) |
553 |
|
matrix/ - Samar |
554 |
|
mdsio/ - 7.3.1 |
555 |
|
mnc/ - 7.2.1 |
556 |
|
mom_common/ - in chapter 2 (JM check) |
557 |
|
mom_fluxform/ - in chapter 2 (JM check) |
558 |
|
mom_vecinv/ - in chapter 2 (JM check) |
559 |
|
monitor/ - 7.4 |
560 |
|
my82/ - nothing, (martin?) |
561 |
|
obcs/ - 6.3 (needs a check - ask PH to read) |
562 |
|
ocn_compon_interf/ - 6.6 (no content yet) |
563 |
|
offline/ - nothing, tutorials that need work but no package section entry |
564 |
|
trivial to document (CNH to do) |
565 |
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opps/ - nothing, (martin?) |
566 |
|
pp81/ - nothing, (martin?) |
567 |
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profiles/ - GAEL |
568 |
|
ptracers/ - JM + SD + Martin to write something (nothing for this |
569 |
|
at the moment) |
570 |
|
AM has diagnostics table for this. |
571 |
|
rbcs/ - CNH to talk to steph |
572 |
|
runclock/ - runclock - CNH |
573 |
|
rw/ - not sure - going to stay says JMC. quick IO calls |
574 |
|
JMC to write a quick note for that. |
575 |
|
sbo/ - text in sbo_descruption.tex but not linked into |
576 |
|
part6 - CNH |
577 |
|
seaice/ - 6.5.2 - no equations, dimitris has promised some |
578 |
|
shap_filt/ - chapter 2, JM to check |
579 |
|
shelfice/ - nothing yet (martin?) |
580 |
|
solver/ - empty (go away?) |
581 |
|
sphere/ - chapter 5 or 8 (PH to check) |
582 |
|
therm_seaice/ - empty (go away?) |
583 |
|
thsice/ - 6.5.1 (JM to update?) |
584 |
|
timeave/ - retiring...... |
585 |
|
zonal_filt/ - chapter 2 (JM to check) |
586 |
|
|
587 |
2.10.1 Notation |
list an expeiment which uses package? CNH |
|
- Area definition is not really used like this |
|
588 |
|
|
589 |
>> Ao : Area of the face orthogonal to "o" direction (o=u,v,w) |
6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
590 |
|
Figure 6.8 is missing |
591 |
|
|
|
Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to |
|
|
the model variables) are used (e.g., see section 2.10.5) |
|
592 |
|
|
593 |
2.10.5 Horizontal grid: |
>>>> From Andrea |
|
- 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 |
|
594 |
|
|
595 |
2.11 Continuity & Horizontal Pressure gradient terms |
to do list for chap 7: |
|
- 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 |
|
596 |
|
|
|
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 |
|
597 |
|
|
598 |
2.13.2 Coriolis terms |
7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu" |
599 |
- note: the discretization used when useEnergyConservingCoriolis=T |
the links are pointing to the proper place |
|
has no hFac and no Area and is still different from the form |
|
|
described here (with Area & hFac); |
|
600 |
|
|
601 |
2.13.5 Lateral dissipation |
7.5.1 - add Graphix to the list of stuff in utils/matlab |
602 |
- add description of how to use cosFactor & cosPower |
7.5.2 - empty |
|
- add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4 |
|
603 |
|
|
|
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) |
|
604 |
|
|
605 |
2.14 Vector invariant momentum equations |
andrea |
|
- indicate that the NH pieces (vertical momentum eq) are not yet coded |
|
|
and that the NH code uses the flux form. |
|
606 |
|
|
|
2.14.6 Horizontal dissipation -> Horizontal Divergence |
|
607 |
|
|
608 |
2.14.7 Horizontal dissipation |
9. Publications using MITgcm --> "Previous Applications of MITgcm" |
609 |
- add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ |
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
610 |
and A_D4,A_z4 <-> viscA4D,viscA4Z |
(check in support for more names) |
611 |
|
|
612 |
2.16 & 2.17 & 2.18 : |
10. Under development |
|
- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
|
613 |
|
|
|
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.) |
|
614 |
|
|
615 |
JM |
Bibliography |
616 |
|
|
617 |
|
tidy up from misc - .tex |