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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 edhill 1.46
30 cnh 1.4 Rebuild and set to do cron build - DONE on hugo
31 cnh 1.1
32     To do
33    
34     - where to put under development links?
35 cnh 1.6 JMC would like to have some mention of unfinished things (checked in
36     but not that tested e.g. AB3)
37 cnh 1.8 Add an "Under development, chapter" - shortish description of what
38     is available (last chapter)
39 cnh 1.7
40 cnh 1.33 - 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    
44 cnh 1.9 o HTML, scripts and front content
45    
46 edhill 1.46 - pick a URL: mitgcm.org/r2 <-- EH3's preferred base URL
47 cnh 1.1
48     - mitgcm.org/r2_web_testing/latest
49 edhill 1.46
50     o --DONE-- add another short-cut for quick download
51    
52     o --DONE-- add another short-cut
53     About
54     Installation
55     Contents
56     Overview
57     Tutorials (broken)
58     Browse Code
59    
60     o --DONE-- words on http://mitgcm.org/r2_web_testing/latest change to
61 cnh 1.1
62 edhill 1.46 o --DONE-- finite-volume doesn't leap to FV figure
63 cnh 1.1
64 edhill 1.46 o -- DONE ??? -- have another go at pnmcrop et al.
65 cnh 1.1
66 edhill 1.46 I've tried making a small change in latex2html which fixes
67     the oddball-lower-alignment issue that we were seeing with
68     most in-line expressions (that is, math embedded in text).
69     The fix results in some things being slightly raised but I
70     thin this is more asthetically pleasing than being somewhat
71     lowered as before. --EH3
72    
73     To view the altered alignment, see:
74    
75     http://eddy.csail.mit.edu/r2/latest/
76 cnh 1.1
77 cnh 1.9 o Need an empty package as part of distribution. Check out atm_common
78 cnh 1.1
79 edhill 1.46
80 cnh 1.9 o Latex
81 cnh 1.1
82 cnh 1.9 Chapter 1 - CNH
83 cnh 1.1 o single kernel diagram -
84     add reference to MWR paper
85    
86     o non-hydro
87     add reference to 1995 and 1999 papers
88     pdf of 1995 paper
89    
90     o FV
91     add references to 1997 papers.
92    
93     o Tangent linear/adjoint add reference to
94     Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc...
95    
96     o platforms
97     Add reference to SC article and Scientific Programming article
98    
99     o List of key papers needs to be updated and reformatted
100    
101     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    
106     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    
112     o Convection and mixing over topography
113     add in Legg references for convection and mixing over topography
114     and external link to CPT-GCE etc...
115    
116     o Boundary forced internal waves
117     add in Legg references, obc's reference
118    
119     o Parameter sensitivity
120     add in Bugnion references, Boyin references, Steph references
121    
122     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    
133     o Simulations of laboratory experiments
134     reference Wardle and Karsten papers
135     update links to include DDDAS "PIAB" page
136     cylindrical polar coordinates
137    
138     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    
144     o Kinematic boundary conditions
145    
146 cnh 1.9 o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
147     Non-hydrostatic forms
148     need to tidy up discussion of shallow-atmosphere to be
149     consistent with the code or change code to be consistent
150     with the discussion!
151     make references hyperlinks
152     add stuff too
153     JMC remove QNH atmosphere
154     need to sort out calc_gw for deep atmosphere
155 cnh 1.1
156     o Finding the pressure field
157 cnh 1.9 make references hyperlinks
158     add forward references to manual algorithm section
159     change Elliptic to "elliptic"
160 cnh 1.1
161     o Forcing and dissipation
162 cnh 1.9 make "physics packages" refer to chapter 6.
163     should we move "external forcing" et. al to a
164     generic_forcing_driver package?
165 cnh 1.1
166     viscosities
167 cnh 1.9 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...
171     add references to literature
172 cnh 1.1
173     o 1.3.8 Vector invariant form
174     forward references to numerical section
175    
176     o 1.3.9 Adjoint
177     add a little more here + some hyperlink to chapter 5.
178    
179     o 1.4 Appendix ATMOSPHERE
180    
181     add some introductory words
182    
183     o 1.6 Coordinate systems
184     o only has some words on spherical polar. add some brief words
185     to cover all of
186     - cartesian
187     - spherical
188     - cylindrical
189     - general orthogonal curvilinear (vector invariant)
190    
191     o Equation of state options
192     add some discussion
193     can't remember what we said we were going to do here
194     PH to do something
195    
196    
197     Change hydrodynamical to "dynamical"
198    
199     Examples
200    
201     - extra "in action" cases
202    
203     o high res ocean with diurnal atmospheric state forcing
204     - links to ingrid output
205     CNH/Dimitris
206    
207     o realistic FIZHI from Andrea
208     - links to ingrid output
209     from AM
210    
211     o with seaice on high res cube
212     - links to ingrid output
213     CNH/Dimitris
214    
215     o coupled aqua, ridge world etc...
216     - links to ingrid output
217     get stuff from Daniel
218 cnh 1.38 Davids donut movie
219 cnh 1.1
220     o constrained lab simulation
221     - links to ingrid output for model and lab
222     fields
223     get stuff from Sai/Andrew
224    
225     o sensitivity wrt to iron
226    
227     o optimization
228     - update to link to latest ECCO sites and GF
229     related material
230    
231     o eddy diffusivity transport application
232    
233     o Gas giant?
234    
235    
236 cnh 1.10 >>>> from JM
237    
238    
239     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 jmc 1.39 (mom_flux_form, mom_vecinv, dynamics) <- DONE
247 cnh 1.10 - 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 jmc 1.39 <- DONE
258 cnh 1.10
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 jmc 1.39 <- Leave it general.
267 cnh 1.10
268 cnh 1.47 o Time-stepping outline
269     - what gets called when
270    
271 cnh 1.10
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 jmc 1.44 - mention section 2.5 implicit-Time-stepping (for vertical viscosity) <- DONE
277 cnh 1.10
278     2.3 linear free-surface:
279     - add ref(+link) to S/R names:
280 jmc 1.44 - add ref(+link) to Crank-Nickelson section 2.9.1 <- DONE
281 cnh 1.10
282     2.4 Adams-Bashforth
283 jmc 1.44 - 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 cnh 1.10
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 jmc 1.39 - 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 cnh 1.10 - 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 jmc 1.39 <- DONE
317 cnh 1.10
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 jmc 1.39 <- DONE
326 cnh 1.10
327     2.10.5 Horizontal grid:
328     - fig.2.8 : should use Aw,As consistently in this figure description,
329 jmc 1.39 in the figure itself, as it is in the text. <- DONE
330 cnh 1.10 - 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 cnh 1.13 - add cylindrical polar grid description
335 cnh 1.10 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 cnh 1.15 - need to reference the smag/leith section.
362 cnh 1.10
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 jmc 1.39 - fix equations 2.202 & 2.203 (thanks to Martin) <- DONE
381 cnh 1.10
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 cnh 1.12 - talk to Baylor
387 cnh 1.10 Appendix: non-dimensional Equations on Spherical-Polar grid.)
388 jmc 1.39 <- No (Chris said)
389 cnh 1.34
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 cnh 1.12
396 cnh 1.10
397     JM
398    
399 cnh 1.11
400     >>>> From Andrea
401    
402     Chapter 3
403     --------
404    
405     Almost all of the 'math mode' text is dropped down as subscripts
406    
407 molod 1.43 3.11.3.1 - refers to figures and equations, links are broken
408 cnh 1.11
409 molod 1.43 3.12.3.2 - line 43: link to equation is broken
410 cnh 1.11 - 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 molod 1.43 3.13.4.1 - line 34 - link to equation is broken
414 cnh 1.11 - lines 60,61 - 1st (take out the 'r' in the superscript)
415    
416 molod 1.43 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 cnh 1.11 line 34: link to equation is broken
419    
420 cnh 1.47 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 cnh 1.10 >>>> 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 cnh 1.50 update organigramme
455     - include rbcs
456     (<- needs an update: e.g. atm2d, salt_plume, shelfice ...)
457 cnh 1.10
458     Master list of packages (add this to beginning of chap 6)
459 jmc 1.49 (<- needs an update: e.g. atm2d, salt_plume, shelfice ...)
460 cnh 1.1
461     admtlm/ - autodiff (chapter 5)
462 cnh 1.10 aim/ - retired
463 cnh 1.16 aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM)
464 cnh 1.1 aim_ocn_coupler/ - 6.6 (no content yet)
465 cnh 1.10 aim_v23/ - 6.4.1 (content needs fixing - JM to do)
466 cnh 1.16 atm_common/ - nothing in this package (6.4.1 related)
467 cnh 1.1 autodiff/ - autodiff (chapter 5)
468     bulk_force/ - 6.3.3
469     cal/ - 6.3.5
470 cnh 1.16 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 cnh 1.1 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 cnh 1.16 ebm/ - (check with PH)
481 cnh 1.1 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 cnh 1.47 o Including FIZHI doc
487     - get things up to date
488 cnh 1.18 flt/ - (PH check)
489 cnh 1.1 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 cnh 1.18 Ferrari & Mc transition zone stuff (Samar doing this)
494     get dfer to read this
495 cnh 1.1 grdchk/ - grdchk (chapter 5 - check with PH)
496     gridalt/ - 6.2.4
497     kpp/ - 6.3.2
498 cnh 1.18 land/ - 6.4.2 (not connected to code Rong's notes - JM to fix)
499 cnh 1.1 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 cnh 1.19 obcs/ - 6.3 (needs a check - ask PH to read)
508 cnh 1.1 ocn_compon_interf/ - 6.6 (no content yet)
509     offline/ - nothing, tutorials that need work but no package section entry
510 cnh 1.19 trivial to document (CNH to do)
511 cnh 1.1 opps/ - nothing, (martin?)
512     pp81/ - nothing, (martin?)
513     profiles/ - GAEL
514 cnh 1.19 ptracers/ - JM + SD + Martin to write something (nothing for this
515     at the moment)
516     AM has diagnostics table for this.
517 cnh 1.20 rbcs/ - CNH to talk to steph
518     runclock/ - runclock - CNH
519 cnh 1.21 rw/ - not sure - going to stay says JMC. quick IO calls
520 cnh 1.22 JMC to write a quick note for that.
521 cnh 1.1 sbo/ - text in sbo_descruption.tex but not linked into
522 cnh 1.22 part6 - CNH
523 cnh 1.1 seaice/ - 6.5.2 - no equations, dimitris has promised some
524     shap_filt/ - chapter 2, JM to check
525     shelfice/ - nothing yet (martin?)
526 cnh 1.22 solver/ - empty (go away?)
527 cnh 1.1 sphere/ - chapter 5 or 8 (PH to check)
528 cnh 1.22 therm_seaice/ - empty (go away?)
529 cnh 1.1 thsice/ - 6.5.1 (JM to update?)
530     timeave/ - retiring......
531     zonal_filt/ - chapter 2 (JM to check)
532    
533 cnh 1.47 o Cost function packages
534     - floats, weights, profiles etc...
535    
536    
537 cnh 1.20 list an expeiment which uses package? CNH
538    
539 cnh 1.10 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
540     Figure 6.8 is missing
541 cnh 1.9
542 cnh 1.1
543 edhill 1.32 ===== Chapter 7 ===== [EH3 editing] :
544 cnh 1.1
545 edhill 1.46 + JMC: please add description of:
546 edhill 1.36 - diagstat
547     - new temporal averaging feature
548 cnh 1.1
549 jmc 1.49 + 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 edhill 1.46 + add Graphix to the list of stuff in utils/matlab (Daniel)
554 cnh 1.1
555 edhill 1.46 + get bathymetry pre-processing stuff from Patrick and then describe it
556 cnh 1.1
557 edhill 1.46 + add something on spgrid mesh generator
558 cnh 1.47 o Grid generation
559     - more explanation and some step-by-step examples
560     - plotting grid examples
561    
562 cnh 1.37
563 edhill 1.46 + 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 cnh 1.45
566 cnh 1.1
567     andrea
568    
569 cnh 1.9
570 edhill 1.28 9. Publications using MITgcm --> "Previous Applications of MITgcm"
571 cnh 1.9 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
572     (check in support for more names)
573 cnh 1.24
574     10. Under development
575 cnh 1.26
576 cnh 1.35 Constantinos LCML
577 cnh 1.47 o Legend/LCML examples and explanation
578     - examples and explanation!
579    
580 cnh 1.35
581 cnh 1.26
582     Bibliography
583 cnh 1.27
584     tidy up from misc - .tex
585 cnh 1.47
586 cnh 1.48 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    

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