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gmaze PV needs to be in post-proc

1 cnh 1.33 Editors
2    
3     Overall - JM, AM, PH, CNH, EH3
4    
5     Front content - EH3
6    
7     Chapter 1 - CNH
8    
9     Chapter 2 - JMC
10    
11     Chapter 3 - AM
12    
13     Chapter 4 - CNH
14    
15     Chapter 5 - PH
16    
17     Chapter 6 - AM
18    
19     Chapter 7 - EH3
20    
21     Chapter 8 - PH
22    
23     Chapter 9 - CNH (Applications)
24    
25     Chapter 10 - JMC (Under development chapter)
26    
27     Biblio - EH3
28    
29 cnh 1.4 Rebuild and set to do cron build - DONE on hugo
30 cnh 1.1
31     To do
32    
33     - where to put under development links?
34 cnh 1.6 JMC would like to have some mention of unfinished things (checked in
35     but not that tested e.g. AB3)
36 cnh 1.8 Add an "Under development, chapter" - shortish description of what
37     is available (last chapter)
38 cnh 1.7
39 cnh 1.33 - add in example latex for formatting author names in different pieces.
40     this aknowledges peoples contributions and gives ref for who
41     to talk to.
42    
43 cnh 1.9 o HTML, scripts and front content
44    
45 cnh 1.8 - pick a URL
46     TBD
47 cnh 1.1
48     - mitgcm.org/r2_web_testing/latest
49     o add another short-cut for quick download
50    
51     o add another short-cut
52     About
53     Installation
54     Contents
55     Overview
56     Tutorials (broken)
57     Browse Code
58 cnh 1.9
59     o words on http://mitgcm.org/r2_web_testing/latest
60     change to
61     "access on-line Auser manual/A and Atable of contents/A
62     and browse the Aoverview section/A"
63 cnh 1.1
64     o finite-volume doesn't leap to FV figure
65    
66 cnh 1.9 o have another go at pnmcrop et al.
67 cnh 1.1
68 cnh 1.9 o Need an empty package as part of distribution. Check out atm_common
69 cnh 1.1
70 cnh 1.9 o Latex
71 cnh 1.1
72 cnh 1.9 Chapter 1 - CNH
73 cnh 1.1 o single kernel diagram -
74     add reference to MWR paper
75    
76     o non-hydro
77     add reference to 1995 and 1999 papers
78     pdf of 1995 paper
79    
80     o FV
81     add references to 1997 papers.
82    
83     o Tangent linear/adjoint add reference to
84     Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc...
85    
86     o platforms
87     Add reference to SC article and Scientific Programming article
88    
89     o List of key papers needs to be updated and reformatted
90    
91     o Global atmosphere: `Held Suarez',
92     update Adcroft reference
93     fix up ingrid link and frame (ingrid movies seem to be broken?)
94     Held and Suarez reference is not a link.
95    
96     o Ocean Gyres
97     fix up frame link
98     make "lopped cell" a link to referenced paper.
99     add references (ask Steph/Mick)
100     online/offline paper
101    
102     o Convection and mixing over topography
103     add in Legg references for convection and mixing over topography
104     and external link to CPT-GCE etc...
105    
106     o Boundary forced internal waves
107     add in Legg references, obc's reference
108    
109     o Parameter sensitivity
110     add in Bugnion references, Boyin references, Steph references
111    
112     o State estimation
113     add in references from Patrick/Carl/Ichiro/Detlef etc...
114     update links to point to latest ECCO results
115     ECCO ingrid results have been moved
116     add forward links to "ECCO state estimation" chapter in manual
117    
118     o Ocean biogeochemical cycles
119     add in references from Mick/Galen etc...
120     fix ingrid link ( date to date thing does not appear to work)
121     figure url does not have a "target=idontexist" entry
122    
123     o Simulations of laboratory experiments
124     reference Wardle and Karsten papers
125     update links to include DDDAS "PIAB" page
126     cylindrical polar coordinates
127    
128     o Continuos equations in ''r'' coordinates
129     add references to iso paper
130     no mention of z* and p* - forward reference to z*/p* in 2.
131     add that coupling also manifests through F, Q
132     add tracer transport
133    
134     o Kinematic boundary conditions
135    
136 cnh 1.9 o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
137     Non-hydrostatic forms
138     need to tidy up discussion of shallow-atmosphere to be
139     consistent with the code or change code to be consistent
140     with the discussion!
141     make references hyperlinks
142     add stuff too
143     JMC remove QNH atmosphere
144     need to sort out calc_gw for deep atmosphere
145 cnh 1.1
146     o Finding the pressure field
147 cnh 1.9 make references hyperlinks
148     add forward references to manual algorithm section
149     change Elliptic to "elliptic"
150 cnh 1.1
151     o Forcing and dissipation
152 cnh 1.9 make "physics packages" refer to chapter 6.
153     should we move "external forcing" et. al to a
154     generic_forcing_driver package?
155 cnh 1.1
156     viscosities
157 cnh 1.9 update to mention Smag/Leith (Ah and A4 not constant)
158     and to have forward references to numerical section
159     tracers
160     forward references to numerical section, reddy, GM etc...
161     add references to literature
162 cnh 1.1
163     o 1.3.8 Vector invariant form
164     forward references to numerical section
165    
166     o 1.3.9 Adjoint
167     add a little more here + some hyperlink to chapter 5.
168    
169     o 1.4 Appendix ATMOSPHERE
170    
171     add some introductory words
172    
173     o 1.6 Coordinate systems
174     o only has some words on spherical polar. add some brief words
175     to cover all of
176     - cartesian
177     - spherical
178     - cylindrical
179     - general orthogonal curvilinear (vector invariant)
180    
181     o Equation of state options
182     add some discussion
183     can't remember what we said we were going to do here
184     PH to do something
185    
186    
187     Change hydrodynamical to "dynamical"
188    
189     Examples
190    
191     - extra "in action" cases
192    
193     o high res ocean with diurnal atmospheric state forcing
194     - links to ingrid output
195     CNH/Dimitris
196    
197     o realistic FIZHI from Andrea
198     - links to ingrid output
199     from AM
200    
201     o with seaice on high res cube
202     - links to ingrid output
203     CNH/Dimitris
204    
205     o coupled aqua, ridge world etc...
206     - links to ingrid output
207     get stuff from Daniel
208 cnh 1.38 Davids donut movie
209 cnh 1.1
210     o constrained lab simulation
211     - links to ingrid output for model and lab
212     fields
213     get stuff from Sai/Andrew
214    
215     o sensitivity wrt to iron
216    
217     o optimization
218     - update to link to latest ECCO sites and GF
219     related material
220    
221     o eddy diffusivity transport application
222    
223     o Gas giant?
224    
225    
226 cnh 1.10 >>>> from JM
227    
228    
229     manual, section.2 :
230    
231     In general:
232     - add more refences/links to S/R & variable name
233     - would be nice to have an active link to the fortran-file
234     for all the S/R & eq.Number in the "calling-tree" boxes
235     - search for CALC_MOM_RHS and replace it by the appropriate S/R
236 jmc 1.39 (mom_flux_form, mom_vecinv, dynamics) <- DONE
237 cnh 1.10 - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
238     was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
239     in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
240     simply written \vec{v}.
241     I would suggest to keep the notation as they are (since they are consistent
242     inside each section) but may be to move the "notation.tex" piece
243     at the beginning of section.2 and to mention clearly the changes between
244     the 2 sections.
245    
246     in content: Horizontal Dissipation: 2 times in vector-invariant section
247 jmc 1.39 <- DONE
248 cnh 1.10
249     2.1 time-stepping (part2/time_stepping.tex)
250    
251     - this is not clear to me:
252    
253     >> In all the above configurations it is also possible to substitute the
254     >> Adams-Bashforth with an alternative time-stepping scheme for terms
255     >> evaluated explicitly in time
256 jmc 1.39 <- Leave it general.
257 cnh 1.10
258    
259     2.2 rigid-lid:
260    
261     - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
262     to stay closer to the code.
263 jmc 1.44 - mention section 2.5 implicit-Time-stepping (for vertical viscosity) <- DONE
264 cnh 1.10
265     2.3 linear free-surface:
266     - add ref(+link) to S/R names:
267 jmc 1.44 - add ref(+link) to Crank-Nickelson section 2.9.1 <- DONE
268 cnh 1.10
269     2.4 Adams-Bashforth
270 jmc 1.44 - add stability diagrams (I have some figures that I can put) <- DONE
271     - add link for var. forcing_In_AB and epsil_AB <- half DONE
272     - add S/R link for S/R ADAMS_BASHFORTH2 <-DONE
273 cnh 1.10
274     2.5 Implicit time-stepping
275     - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
276     SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
277     - update: also used for vertical advection
278    
279     2.6 Synchronous time-stepping:
280     - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
281     MOMENTUM_CORRECTION_STEP.
282    
283     2.7 Stagger baroclinic time-stepping
284     - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
285    
286     2.8 NH
287     - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
288    
289     2.9 Variants on Free-Surface
290 jmc 1.39 - Delta.t mis-written (eq.2.73) <- DONE
291     - Eq.Num missing <- DONE
292     - u* is stored in gU (and not in gUnm1) <- DONE
293     - Phi_nh in NH_VARS.h <- DONE
294 cnh 1.10 - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
295     INI_CG2D, INI_CG3D
296    
297     2.9.1 Crank-Nickelson
298     - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
299    
300     2.9.2 NLFS
301     - eq.Nb are wrong in html
302     - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
303 jmc 1.39 <- DONE
304 cnh 1.10
305     2.10.1 Notation
306     - Area definition is not really used like this
307    
308     >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
309    
310     Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
311     the model variables) are used (e.g., see section 2.10.5)
312 jmc 1.39 <- DONE
313 cnh 1.10
314     2.10.5 Horizontal grid:
315     - fig.2.8 : should use Aw,As consistently in this figure description,
316 jmc 1.39 in the figure itself, as it is in the text. <- DONE
317 cnh 1.10 - curvilinear:
318     to add: mention the angle of the grid direction relative to
319     Eastward, Northward direction.
320     + mention horizGridFile= in file "data" (PARM04)
321 cnh 1.13 - add cylindrical polar grid description
322 cnh 1.10 need to do a better job of relating model variables to this diagram
323    
324    
325     2.11 Continuity & Horizontal Pressure gradient terms
326     - mention that d.Phi/dr|s =g if using z coordinate
327     - eq. 2.90 not clear regarding \delta_k(P-E)
328     better to add the free surface eq: d.eta/dt = w_s + P-E
329    
330     2.12 Hydrostatic balance
331     - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
332     is hard to find
333     - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
334     and in section 1.3.4: remove the 1.3.4.3.2 subsection:
335     Quasi-nonhydrostatic Atmosphere
336    
337     2.13.2 Coriolis terms
338     - note: the discretization used when useEnergyConservingCoriolis=T
339     has no hFac and no Area and is still different from the form
340     described here (with Area & hFac);
341    
342     2.13.5 Lateral dissipation
343     - add description of how to use cosFactor & cosPower
344     - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
345     o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
346     in code need to explain why cos()3/2 turns out to be
347     scaling (not cos()2)
348 cnh 1.15 - need to reference the smag/leith section.
349 cnh 1.10
350     2.13.6 Vertical dissipation
351     - mention the implicit vertical viscosity option and ref to section 2.5
352     - add the parameter correspondence: Av <-> viscAr (and might change also
353     the notation to Ar)
354    
355     2.14 Vector invariant momentum equations
356     - indicate that the NH pieces (vertical momentum eq) are not yet coded
357     and that the NH code uses the flux form.
358    
359     2.14.6 Horizontal dissipation -> Horizontal Divergence
360    
361     2.14.7 Horizontal dissipation
362     - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
363     and A_D4,A_z4 <-> viscA4D,viscA4Z
364    
365     2.16 & 2.17 & 2.18 :
366     - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
367 jmc 1.39 - fix equations 2.202 & 2.203 (thanks to Martin) <- DONE
368 cnh 1.10
369     2.20.2 mercator, non-dimensional Equations:
370     - does not use std notation
371     - would be better as an appendix of section 2.20:
372     (e.g changing the tile to:
373 cnh 1.12 - talk to Baylor
374 cnh 1.10 Appendix: non-dimensional Equations on Spherical-Polar grid.)
375 jmc 1.39 <- No (Chris said)
376 cnh 1.34
377    
378     Diagrams of grid locations etc.... and what variables and output files
379     and/or netcdf variable names are not very easy to figure out and follow.
380     It would be good to redo and extend these diagrams and align with GRID.h
381     content.
382 cnh 1.12
383 cnh 1.10
384     JM
385    
386 cnh 1.11
387     >>>> From Andrea
388    
389     Chapter 3
390     --------
391    
392     Almost all of the 'math mode' text is dropped down as subscripts
393    
394 molod 1.43 3.11.3.1 - refers to figures and equations, links are broken
395 cnh 1.11
396 molod 1.43 3.12.3.2 - line 43: link to equation is broken
397 cnh 1.11 - line 51-53: link to equation is broken
398     - there is some mess of text hanging around the end of this section. remove? reformat?
399    
400 molod 1.43 3.13.4.1 - line 34 - link to equation is broken
401 cnh 1.11 - lines 60,61 - 1st (take out the 'r' in the superscript)
402    
403 molod 1.43 3.14.2 - link to theta-equation is broken
404     3.14.5.4 -- ALL of the bold links to variable names are broken
405 cnh 1.11 line 34: link to equation is broken
406    
407 cnh 1.10 >>>> From Ed
408    
409     Here are the remaining bits for Chap 4 :
410    
411     - missing references (if you point me towards URLs, I'll add them
412     to the bibliography):
413     \ref{ref hoe and hill, ecmwf}
414     \ref{magicgarden}
415     \ref{IBMLAPI}
416     \ref{Memorychannel}
417     \ref{hoe-hill:99}
418    
419     - There are a few empty sub-sections at the end of Chap 4 that
420     should either be commented out or fleshed out.
421    
422     and thats about it for Chap 4.
423    
424    
425     Add more to quick links on front page
426    
427     Chapter 6
428    
429     the master package diagram does not appear in the document
430    
431     Master list of packages (add this to beginning of chap 6)
432 cnh 1.1
433     admtlm/ - autodiff (chapter 5)
434 cnh 1.10 aim/ - retired
435 cnh 1.16 aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM)
436 cnh 1.1 aim_ocn_coupler/ - 6.6 (no content yet)
437 cnh 1.10 aim_v23/ - 6.4.1 (content needs fixing - JM to do)
438 cnh 1.16 atm_common/ - nothing in this package (6.4.1 related)
439 cnh 1.1 autodiff/ - autodiff (chapter 5)
440     bulk_force/ - 6.3.3
441     cal/ - 6.3.5
442 cnh 1.16 cd_code/ - chapter 2 (JM check add a reference to paper,
443     mention parameter in data)
444     cfc/ - not sure (CNH to talk to Steph and Helen)
445     chronos/ - AM to check (not being used - Andrea to kill it)
446     compon_communic/ - 6.6 (no content yet)(Daniel + JM)
447 cnh 1.1 cost/ - not sure, check with PH
448     ctrl/ - not sure, check with PH
449     debug/ - JM may do something in chapter 7 (utilities)
450     diagnostics/ - 7.1
451     dic/ - 6.7.2
452 cnh 1.16 ebm/ - (check with PH)
453 cnh 1.1 ecco/ - chapter 8
454     embed_files/ - add something to chapter 7
455     exch2/ - 6.2.2
456     exf/ - 6.3.4
457     fizhi/ - 6.4.3
458 cnh 1.18 flt/ - (PH check)
459 cnh 1.1 gchem/ - 6.7.1
460     generic_advdiff/ - in chapter 2 (JM check)
461     ggl90/ - nothing, (Martin?)
462     gmredi/ - in chapter 2 (JM check). also need
463 cnh 1.18 Ferrari & Mc transition zone stuff (Samar doing this)
464     get dfer to read this
465 cnh 1.1 grdchk/ - grdchk (chapter 5 - check with PH)
466     gridalt/ - 6.2.4
467     kpp/ - 6.3.2
468 cnh 1.18 land/ - 6.4.2 (not connected to code Rong's notes - JM to fix)
469 cnh 1.1 matrix/ - Samar
470     mdsio/ - 7.3.1
471     mnc/ - 7.2.1
472     mom_common/ - in chapter 2 (JM check)
473     mom_fluxform/ - in chapter 2 (JM check)
474     mom_vecinv/ - in chapter 2 (JM check)
475     monitor/ - 7.4
476     my82/ - nothing, (martin?)
477 cnh 1.19 obcs/ - 6.3 (needs a check - ask PH to read)
478 cnh 1.1 ocn_compon_interf/ - 6.6 (no content yet)
479     offline/ - nothing, tutorials that need work but no package section entry
480 cnh 1.19 trivial to document (CNH to do)
481 cnh 1.1 opps/ - nothing, (martin?)
482     pp81/ - nothing, (martin?)
483     profiles/ - GAEL
484 cnh 1.19 ptracers/ - JM + SD + Martin to write something (nothing for this
485     at the moment)
486     AM has diagnostics table for this.
487 cnh 1.20 rbcs/ - CNH to talk to steph
488     runclock/ - runclock - CNH
489 cnh 1.21 rw/ - not sure - going to stay says JMC. quick IO calls
490 cnh 1.22 JMC to write a quick note for that.
491 cnh 1.1 sbo/ - text in sbo_descruption.tex but not linked into
492 cnh 1.22 part6 - CNH
493 cnh 1.1 seaice/ - 6.5.2 - no equations, dimitris has promised some
494     shap_filt/ - chapter 2, JM to check
495     shelfice/ - nothing yet (martin?)
496 cnh 1.22 solver/ - empty (go away?)
497 cnh 1.1 sphere/ - chapter 5 or 8 (PH to check)
498 cnh 1.22 therm_seaice/ - empty (go away?)
499 cnh 1.1 thsice/ - 6.5.1 (JM to update?)
500     timeave/ - retiring......
501     zonal_filt/ - chapter 2 (JM to check)
502    
503 cnh 1.20 list an expeiment which uses package? CNH
504    
505 cnh 1.10 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
506     Figure 6.8 is missing
507 cnh 1.9
508 cnh 1.1
509 edhill 1.32 ===== Chapter 7 ===== [EH3 editing] :
510 cnh 1.1
511 edhill 1.36 7.1.x - JMC: please add description of:
512     - diagstat
513     - new temporal averaging feature
514 cnh 1.1
515 edhill 1.32 7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
516 cnh 1.1
517 edhill 1.32 7.5.2 - get bathymetry pre-processing stuff from Patrick
518     and then describe it
519 cnh 1.1
520 cnh 1.37 add something on spgrid mesh generator (maybe)?
521    
522 cnh 1.45 add in gmaze PV calculation scripts plus write up on how it is calculated
523     http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/
524    
525 cnh 1.1
526     andrea
527    
528 cnh 1.9
529 edhill 1.28 9. Publications using MITgcm --> "Previous Applications of MITgcm"
530 cnh 1.9 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
531     (check in support for more names)
532 cnh 1.24
533     10. Under development
534 cnh 1.26
535 cnh 1.35 Constantinos LCML
536    
537 cnh 1.26
538     Bibliography
539 cnh 1.27
540     tidy up from misc - .tex

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