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Sun Jul 2 18:12:45 2006 UTC (17 years, 9 months ago) by edhill
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a "fix" for the artificial subscripting of in-line images has been found

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    
269     2.2 rigid-lid:
270    
271     - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
272     to stay closer to the code.
273 jmc 1.44 - mention section 2.5 implicit-Time-stepping (for vertical viscosity) <- DONE
274 cnh 1.10
275     2.3 linear free-surface:
276     - add ref(+link) to S/R names:
277 jmc 1.44 - add ref(+link) to Crank-Nickelson section 2.9.1 <- DONE
278 cnh 1.10
279     2.4 Adams-Bashforth
280 jmc 1.44 - add stability diagrams (I have some figures that I can put) <- DONE
281     - add link for var. forcing_In_AB and epsil_AB <- half DONE
282     - add S/R link for S/R ADAMS_BASHFORTH2 <-DONE
283 cnh 1.10
284     2.5 Implicit time-stepping
285     - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
286     SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
287     - update: also used for vertical advection
288    
289     2.6 Synchronous time-stepping:
290     - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
291     MOMENTUM_CORRECTION_STEP.
292    
293     2.7 Stagger baroclinic time-stepping
294     - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
295    
296     2.8 NH
297     - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
298    
299     2.9 Variants on Free-Surface
300 jmc 1.39 - Delta.t mis-written (eq.2.73) <- DONE
301     - Eq.Num missing <- DONE
302     - u* is stored in gU (and not in gUnm1) <- DONE
303     - Phi_nh in NH_VARS.h <- DONE
304 cnh 1.10 - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
305     INI_CG2D, INI_CG3D
306    
307     2.9.1 Crank-Nickelson
308     - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
309    
310     2.9.2 NLFS
311     - eq.Nb are wrong in html
312     - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
313 jmc 1.39 <- DONE
314 cnh 1.10
315     2.10.1 Notation
316     - Area definition is not really used like this
317    
318     >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
319    
320     Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
321     the model variables) are used (e.g., see section 2.10.5)
322 jmc 1.39 <- DONE
323 cnh 1.10
324     2.10.5 Horizontal grid:
325     - fig.2.8 : should use Aw,As consistently in this figure description,
326 jmc 1.39 in the figure itself, as it is in the text. <- DONE
327 cnh 1.10 - curvilinear:
328     to add: mention the angle of the grid direction relative to
329     Eastward, Northward direction.
330     + mention horizGridFile= in file "data" (PARM04)
331 cnh 1.13 - add cylindrical polar grid description
332 cnh 1.10 need to do a better job of relating model variables to this diagram
333    
334    
335     2.11 Continuity & Horizontal Pressure gradient terms
336     - mention that d.Phi/dr|s =g if using z coordinate
337     - eq. 2.90 not clear regarding \delta_k(P-E)
338     better to add the free surface eq: d.eta/dt = w_s + P-E
339    
340     2.12 Hydrostatic balance
341     - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
342     is hard to find
343     - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
344     and in section 1.3.4: remove the 1.3.4.3.2 subsection:
345     Quasi-nonhydrostatic Atmosphere
346    
347     2.13.2 Coriolis terms
348     - note: the discretization used when useEnergyConservingCoriolis=T
349     has no hFac and no Area and is still different from the form
350     described here (with Area & hFac);
351    
352     2.13.5 Lateral dissipation
353     - add description of how to use cosFactor & cosPower
354     - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
355     o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
356     in code need to explain why cos()3/2 turns out to be
357     scaling (not cos()2)
358 cnh 1.15 - need to reference the smag/leith section.
359 cnh 1.10
360     2.13.6 Vertical dissipation
361     - mention the implicit vertical viscosity option and ref to section 2.5
362     - add the parameter correspondence: Av <-> viscAr (and might change also
363     the notation to Ar)
364    
365     2.14 Vector invariant momentum equations
366     - indicate that the NH pieces (vertical momentum eq) are not yet coded
367     and that the NH code uses the flux form.
368    
369     2.14.6 Horizontal dissipation -> Horizontal Divergence
370    
371     2.14.7 Horizontal dissipation
372     - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
373     and A_D4,A_z4 <-> viscA4D,viscA4Z
374    
375     2.16 & 2.17 & 2.18 :
376     - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
377 jmc 1.39 - fix equations 2.202 & 2.203 (thanks to Martin) <- DONE
378 cnh 1.10
379     2.20.2 mercator, non-dimensional Equations:
380     - does not use std notation
381     - would be better as an appendix of section 2.20:
382     (e.g changing the tile to:
383 cnh 1.12 - talk to Baylor
384 cnh 1.10 Appendix: non-dimensional Equations on Spherical-Polar grid.)
385 jmc 1.39 <- No (Chris said)
386 cnh 1.34
387    
388     Diagrams of grid locations etc.... and what variables and output files
389     and/or netcdf variable names are not very easy to figure out and follow.
390     It would be good to redo and extend these diagrams and align with GRID.h
391     content.
392 cnh 1.12
393 cnh 1.10
394     JM
395    
396 cnh 1.11
397     >>>> From Andrea
398    
399     Chapter 3
400     --------
401    
402     Almost all of the 'math mode' text is dropped down as subscripts
403    
404 molod 1.43 3.11.3.1 - refers to figures and equations, links are broken
405 cnh 1.11
406 molod 1.43 3.12.3.2 - line 43: link to equation is broken
407 cnh 1.11 - line 51-53: link to equation is broken
408     - there is some mess of text hanging around the end of this section. remove? reformat?
409    
410 molod 1.43 3.13.4.1 - line 34 - link to equation is broken
411 cnh 1.11 - lines 60,61 - 1st (take out the 'r' in the superscript)
412    
413 molod 1.43 3.14.2 - link to theta-equation is broken
414     3.14.5.4 -- ALL of the bold links to variable names are broken
415 cnh 1.11 line 34: link to equation is broken
416    
417 cnh 1.10 >>>> From Ed
418    
419     Here are the remaining bits for Chap 4 :
420    
421     - missing references (if you point me towards URLs, I'll add them
422     to the bibliography):
423     \ref{ref hoe and hill, ecmwf}
424     \ref{magicgarden}
425     \ref{IBMLAPI}
426     \ref{Memorychannel}
427     \ref{hoe-hill:99}
428    
429     - There are a few empty sub-sections at the end of Chap 4 that
430     should either be commented out or fleshed out.
431    
432     and thats about it for Chap 4.
433    
434    
435     Add more to quick links on front page
436    
437     Chapter 6
438    
439     the master package diagram does not appear in the document
440    
441     Master list of packages (add this to beginning of chap 6)
442 cnh 1.1
443     admtlm/ - autodiff (chapter 5)
444 cnh 1.10 aim/ - retired
445 cnh 1.16 aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM)
446 cnh 1.1 aim_ocn_coupler/ - 6.6 (no content yet)
447 cnh 1.10 aim_v23/ - 6.4.1 (content needs fixing - JM to do)
448 cnh 1.16 atm_common/ - nothing in this package (6.4.1 related)
449 cnh 1.1 autodiff/ - autodiff (chapter 5)
450     bulk_force/ - 6.3.3
451     cal/ - 6.3.5
452 cnh 1.16 cd_code/ - chapter 2 (JM check add a reference to paper,
453     mention parameter in data)
454     cfc/ - not sure (CNH to talk to Steph and Helen)
455     chronos/ - AM to check (not being used - Andrea to kill it)
456     compon_communic/ - 6.6 (no content yet)(Daniel + JM)
457 cnh 1.1 cost/ - not sure, check with PH
458     ctrl/ - not sure, check with PH
459     debug/ - JM may do something in chapter 7 (utilities)
460     diagnostics/ - 7.1
461     dic/ - 6.7.2
462 cnh 1.16 ebm/ - (check with PH)
463 cnh 1.1 ecco/ - chapter 8
464     embed_files/ - add something to chapter 7
465     exch2/ - 6.2.2
466     exf/ - 6.3.4
467     fizhi/ - 6.4.3
468 cnh 1.18 flt/ - (PH check)
469 cnh 1.1 gchem/ - 6.7.1
470     generic_advdiff/ - in chapter 2 (JM check)
471     ggl90/ - nothing, (Martin?)
472     gmredi/ - in chapter 2 (JM check). also need
473 cnh 1.18 Ferrari & Mc transition zone stuff (Samar doing this)
474     get dfer to read this
475 cnh 1.1 grdchk/ - grdchk (chapter 5 - check with PH)
476     gridalt/ - 6.2.4
477     kpp/ - 6.3.2
478 cnh 1.18 land/ - 6.4.2 (not connected to code Rong's notes - JM to fix)
479 cnh 1.1 matrix/ - Samar
480     mdsio/ - 7.3.1
481     mnc/ - 7.2.1
482     mom_common/ - in chapter 2 (JM check)
483     mom_fluxform/ - in chapter 2 (JM check)
484     mom_vecinv/ - in chapter 2 (JM check)
485     monitor/ - 7.4
486     my82/ - nothing, (martin?)
487 cnh 1.19 obcs/ - 6.3 (needs a check - ask PH to read)
488 cnh 1.1 ocn_compon_interf/ - 6.6 (no content yet)
489     offline/ - nothing, tutorials that need work but no package section entry
490 cnh 1.19 trivial to document (CNH to do)
491 cnh 1.1 opps/ - nothing, (martin?)
492     pp81/ - nothing, (martin?)
493     profiles/ - GAEL
494 cnh 1.19 ptracers/ - JM + SD + Martin to write something (nothing for this
495     at the moment)
496     AM has diagnostics table for this.
497 cnh 1.20 rbcs/ - CNH to talk to steph
498     runclock/ - runclock - CNH
499 cnh 1.21 rw/ - not sure - going to stay says JMC. quick IO calls
500 cnh 1.22 JMC to write a quick note for that.
501 cnh 1.1 sbo/ - text in sbo_descruption.tex but not linked into
502 cnh 1.22 part6 - CNH
503 cnh 1.1 seaice/ - 6.5.2 - no equations, dimitris has promised some
504     shap_filt/ - chapter 2, JM to check
505     shelfice/ - nothing yet (martin?)
506 cnh 1.22 solver/ - empty (go away?)
507 cnh 1.1 sphere/ - chapter 5 or 8 (PH to check)
508 cnh 1.22 therm_seaice/ - empty (go away?)
509 cnh 1.1 thsice/ - 6.5.1 (JM to update?)
510     timeave/ - retiring......
511     zonal_filt/ - chapter 2 (JM to check)
512    
513 cnh 1.20 list an expeiment which uses package? CNH
514    
515 cnh 1.10 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
516     Figure 6.8 is missing
517 cnh 1.9
518 cnh 1.1
519 edhill 1.32 ===== Chapter 7 ===== [EH3 editing] :
520 cnh 1.1
521 edhill 1.46 + JMC: please add description of:
522 edhill 1.36 - diagstat
523     - new temporal averaging feature
524 cnh 1.1
525 edhill 1.46 + add Graphix to the list of stuff in utils/matlab (Daniel)
526 cnh 1.1
527 edhill 1.46 + get bathymetry pre-processing stuff from Patrick and then describe it
528 cnh 1.1
529 edhill 1.46 + add something on spgrid mesh generator
530 cnh 1.37
531 edhill 1.46 + add in gmaze PV calculation scripts plus write up on how it is calculated
532     http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/
533 cnh 1.45
534 cnh 1.1
535     andrea
536    
537 cnh 1.9
538 edhill 1.28 9. Publications using MITgcm --> "Previous Applications of MITgcm"
539 cnh 1.9 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
540     (check in support for more names)
541 cnh 1.24
542     10. Under development
543 cnh 1.26
544 cnh 1.35 Constantinos LCML
545    
546 cnh 1.26
547     Bibliography
548 cnh 1.27
549     tidy up from misc - .tex

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