/[MITgcm]/manual/manual_todo.txt
ViewVC logotype

Annotation of /manual/manual_todo.txt

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph


Revision 1.41 - (hide annotations) (download)
Wed Jun 28 17:21:21 2006 UTC (17 years, 9 months ago) by molod
Branch: MAIN
Changes since 1.40: +0 -27 lines
File MIME type: text/plain
Remove some more stuff that is done

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     - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
264    
265     2.3 linear free-surface:
266     - add ref(+link) to S/R names:
267     - add ref(+link) to Crank-Nickelson section 2.9.1
268    
269     2.4 Adams-Bashforth
270     - add stability diagrams (I have some figures that I can put)
271     - add link for var. forcing_In_AB
272     - add S/R link for S/R ADAMS_BASHFORTH2
273    
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     3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
395     - is this experiment in the list from section 3.4???
396     3.10.3.1 - refers to figures and equations, links are broken
397    
398     3.11.3.2 - line 43: link to equation is broken
399     - line 51-53: link to equation is broken
400     - there is some mess of text hanging around the end of this section. remove? reformat?
401    
402     3.12.4.1 - line 34 - link to equation is broken
403     - lines 60,61 - 1st (take out the 'r' in the superscript)
404    
405     3.13.2 - link to theta-equation is broken
406     3.13.5.4 -- ALL of the bold links to variable names are broken
407     line 34: link to equation is broken
408    
409     3.15.1 - reference to 'fourth experiment' should be removed
410    
411     3.16.4 - strange formatting, presence of '>' symbols - remove them
412    
413     3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
414     3.17.3.1 - nothing filled in under file input/data - needs description
415    
416     3.18.2 - point to section 2 for details - need hyperlink
417    
418     3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
419     section 3.5 has the 'build' directory in the example
420    
421     3.20.1 - link to doc at end of section points to this section
422     3.20.2 - link to doc at end of section points to this section
423    
424     offline - duplicate inputs, what is it, tidy up cfc v.
425     other offline. JM thinks these need tidying up.
426 cnh 1.16
427     Which of the following are which tutorial?
428 jmc 1.31 adjustment.128x64x1
429     adjustment.cs-32x32x1
430 cnh 1.16 advect_cs
431 jmc 1.31 advect_xy
432 cnh 1.16 advect_xz
433 jmc 1.31 aim.5l_cs
434     aim.5l_Equatorial_Channel
435 cnh 1.16 aim.5l_LatLon
436 jmc 1.31 biogeo
437     bottom_ctrl_5x5
438     cfc_example
439     cpl_aim+ocn
440     dome
441 cnh 1.16 exp2
442 jmc 1.31 exp4
443     exp5
444 cnh 1.16 fizhi-cs-32x32x10
445 jmc 1.31 fizhi-cs-aqualev20
446     fizhi-gridalt-hs
447     flt_example
448     front_relax
449     global1x1_tot
450     global2x2_tot
451     global_ocean.90x40x15
452 cnh 1.16 global_ocean.cs32x15
453 jmc 1.31 global_ocean.cubed32x32x30
454     global_ocean_ebm
455     global_with_exf
456     hs94.128x64x5
457 cnh 1.16 hs94.1x64x5
458 jmc 1.31 hs94.cs-32x32x5
459     ideal_2D_oce
460     internal_wave
461     inverted_barometer
462     lab_sea
463     matrix_example
464     MLAdjust
465     natl_box
466 cnh 1.16 natl_box_adjoint
467 jmc 1.31 OpenAD
468     rotating_tank
469     solid-body.cs-32x32x1
470     tidal_basin_2d
471     tutorial_baroclinic_gyre
472     tutorial_barotropic_gyre
473     tutorial_cfc_offline
474     tutorial_deep_convection
475     tutorial_global_oce_biogeo
476     tutorial_global_oce_in_p
477     tutorial_global_oce_latlon
478     tutorial_global_oce_optim
479     tutorial_held_suarez_cs
480     tutorial_offline
481     tutorial_plume_on_slope
482     tutorial_tracer_adjsens
483 cnh 1.16 vermix
484    
485 cnh 1.10 >>>> From Ed
486    
487     Here are the remaining bits for Chap 4 :
488    
489     - missing references (if you point me towards URLs, I'll add them
490     to the bibliography):
491     \ref{ref hoe and hill, ecmwf}
492     \ref{magicgarden}
493     \ref{IBMLAPI}
494     \ref{Memorychannel}
495     \ref{hoe-hill:99}
496    
497     - There are a few empty sub-sections at the end of Chap 4 that
498     should either be commented out or fleshed out.
499    
500     and thats about it for Chap 4.
501    
502    
503     Add more to quick links on front page
504    
505     Chapter 6
506    
507     the master package diagram does not appear in the document
508    
509     Master list of packages (add this to beginning of chap 6)
510 cnh 1.1
511     admtlm/ - autodiff (chapter 5)
512 cnh 1.10 aim/ - retired
513 cnh 1.16 aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM)
514 cnh 1.1 aim_ocn_coupler/ - 6.6 (no content yet)
515 cnh 1.10 aim_v23/ - 6.4.1 (content needs fixing - JM to do)
516 cnh 1.16 atm_common/ - nothing in this package (6.4.1 related)
517 cnh 1.1 autodiff/ - autodiff (chapter 5)
518     bulk_force/ - 6.3.3
519     cal/ - 6.3.5
520 cnh 1.16 cd_code/ - chapter 2 (JM check add a reference to paper,
521     mention parameter in data)
522     cfc/ - not sure (CNH to talk to Steph and Helen)
523     chronos/ - AM to check (not being used - Andrea to kill it)
524     compon_communic/ - 6.6 (no content yet)(Daniel + JM)
525 cnh 1.1 cost/ - not sure, check with PH
526     ctrl/ - not sure, check with PH
527     debug/ - JM may do something in chapter 7 (utilities)
528     diagnostics/ - 7.1
529     dic/ - 6.7.2
530 cnh 1.16 ebm/ - (check with PH)
531 cnh 1.1 ecco/ - chapter 8
532     embed_files/ - add something to chapter 7
533     exch2/ - 6.2.2
534     exf/ - 6.3.4
535     fizhi/ - 6.4.3
536 cnh 1.18 flt/ - (PH check)
537 cnh 1.1 gchem/ - 6.7.1
538     generic_advdiff/ - in chapter 2 (JM check)
539     ggl90/ - nothing, (Martin?)
540     gmredi/ - in chapter 2 (JM check). also need
541 cnh 1.18 Ferrari & Mc transition zone stuff (Samar doing this)
542     get dfer to read this
543 cnh 1.1 grdchk/ - grdchk (chapter 5 - check with PH)
544     gridalt/ - 6.2.4
545     kpp/ - 6.3.2
546 cnh 1.18 land/ - 6.4.2 (not connected to code Rong's notes - JM to fix)
547 cnh 1.1 matrix/ - Samar
548     mdsio/ - 7.3.1
549     mnc/ - 7.2.1
550     mom_common/ - in chapter 2 (JM check)
551     mom_fluxform/ - in chapter 2 (JM check)
552     mom_vecinv/ - in chapter 2 (JM check)
553     monitor/ - 7.4
554     my82/ - nothing, (martin?)
555 cnh 1.19 obcs/ - 6.3 (needs a check - ask PH to read)
556 cnh 1.1 ocn_compon_interf/ - 6.6 (no content yet)
557     offline/ - nothing, tutorials that need work but no package section entry
558 cnh 1.19 trivial to document (CNH to do)
559 cnh 1.1 opps/ - nothing, (martin?)
560     pp81/ - nothing, (martin?)
561     profiles/ - GAEL
562 cnh 1.19 ptracers/ - JM + SD + Martin to write something (nothing for this
563     at the moment)
564     AM has diagnostics table for this.
565 cnh 1.20 rbcs/ - CNH to talk to steph
566     runclock/ - runclock - CNH
567 cnh 1.21 rw/ - not sure - going to stay says JMC. quick IO calls
568 cnh 1.22 JMC to write a quick note for that.
569 cnh 1.1 sbo/ - text in sbo_descruption.tex but not linked into
570 cnh 1.22 part6 - CNH
571 cnh 1.1 seaice/ - 6.5.2 - no equations, dimitris has promised some
572     shap_filt/ - chapter 2, JM to check
573     shelfice/ - nothing yet (martin?)
574 cnh 1.22 solver/ - empty (go away?)
575 cnh 1.1 sphere/ - chapter 5 or 8 (PH to check)
576 cnh 1.22 therm_seaice/ - empty (go away?)
577 cnh 1.1 thsice/ - 6.5.1 (JM to update?)
578     timeave/ - retiring......
579     zonal_filt/ - chapter 2 (JM to check)
580    
581 cnh 1.20 list an expeiment which uses package? CNH
582    
583 cnh 1.10 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
584     Figure 6.8 is missing
585 cnh 1.9
586 cnh 1.1
587 edhill 1.32 ===== Chapter 7 ===== [EH3 editing] :
588 cnh 1.1
589 edhill 1.36 7.1.x - JMC: please add description of:
590     - diagstat
591     - new temporal averaging feature
592 cnh 1.1
593 edhill 1.32 7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
594 cnh 1.1
595 edhill 1.32 7.5.2 - get bathymetry pre-processing stuff from Patrick
596     and then describe it
597 cnh 1.1
598 cnh 1.37 add something on spgrid mesh generator (maybe)?
599    
600 cnh 1.1
601     andrea
602    
603 cnh 1.9
604 edhill 1.28 9. Publications using MITgcm --> "Previous Applications of MITgcm"
605 cnh 1.9 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
606     (check in support for more names)
607 cnh 1.24
608     10. Under development
609 cnh 1.26
610 cnh 1.35 Constantinos LCML
611    
612 cnh 1.26
613     Bibliography
614 cnh 1.27
615     tidy up from misc - .tex

  ViewVC Help
Powered by ViewVC 1.1.22