/[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 1.17 - (hide annotations) (download)
Thu Apr 6 20:38:43 2006 UTC (13 years, 4 months ago) by edhill
Branch: MAIN
Changes since 1.16: +0 -1 lines
File MIME type: text/plain
moved exch3 (was ex3) to contrib

1 cnh 1.4 Rebuild and set to do cron build - DONE on hugo
2 cnh 1.1
3     To do
4    
5     - where to put under development links?
6 cnh 1.6 JMC would like to have some mention of unfinished things (checked in
7     but not that tested e.g. AB3)
8 cnh 1.8 Add an "Under development, chapter" - shortish description of what
9     is available (last chapter)
10 cnh 1.7
11 cnh 1.9
12     o HTML, scripts and front content
13    
14 cnh 1.8 - pick a URL
15     TBD
16 cnh 1.1
17     - mitgcm.org/r2_web_testing/latest
18     o add another short-cut for quick download
19    
20     o add another short-cut
21     About
22     Installation
23     Contents
24     Overview
25     Tutorials (broken)
26     Browse Code
27 cnh 1.9
28     o mitgcm.org (front content) [DONE]
29 cnh 1.1 Get Code (where does this go to?)
30 cnh 1.9 get rid of * CVS current bullet
31     make HTML-enabled CVS code browser leap to MITgcm/MITgcm
32 cnh 1.1
33     o authors
34     John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,
35     Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,
36     Gael - others?
37    
38 cnh 1.9 o words on http://mitgcm.org/r2_web_testing/latest
39     change to
40     "access on-line Auser manual/A and Atable of contents/A
41     and browse the Aoverview section/A"
42 cnh 1.1
43     o finite-volume doesn't leap to FV figure
44    
45 cnh 1.9 o have another go at pnmcrop et al.
46 cnh 1.1
47 cnh 1.9 o Need an empty package as part of distribution. Check out atm_common
48 cnh 1.1
49 cnh 1.9 o Latex
50 cnh 1.1
51 cnh 1.9 Chapter 1 - CNH
52 cnh 1.1 o single kernel diagram -
53     add reference to MWR paper
54    
55     o non-hydro
56     add reference to 1995 and 1999 papers
57     pdf of 1995 paper
58    
59     o FV
60     add references to 1997 papers.
61    
62     o Tangent linear/adjoint add reference to
63     Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc...
64    
65     o platforms
66     Add reference to SC article and Scientific Programming article
67    
68     o List of key papers needs to be updated and reformatted
69    
70    
71     o Global atmosphere: `Held Suarez',
72     update Adcroft reference
73     fix up ingrid link and frame (ingrid movies seem to be broken?)
74     Held and Suarez reference is not a link.
75    
76     o Ocean Gyres
77     fix up frame link
78     make "lopped cell" a link to referenced paper.
79     add references (ask Steph/Mick)
80     online/offline paper
81    
82     o Convection and mixing over topography
83     add in Legg references for convection and mixing over topography
84     and external link to CPT-GCE etc...
85    
86     o Boundary forced internal waves
87     add in Legg references, obc's reference
88    
89     o Parameter sensitivity
90     add in Bugnion references, Boyin references, Steph references
91    
92     o State estimation
93     add in references from Patrick/Carl/Ichiro/Detlef etc...
94     update links to point to latest ECCO results
95     ECCO ingrid results have been moved
96     add forward links to "ECCO state estimation" chapter in manual
97    
98     o Ocean biogeochemical cycles
99     add in references from Mick/Galen etc...
100     fix ingrid link ( date to date thing does not appear to work)
101     figure url does not have a "target=idontexist" entry
102    
103     o Simulations of laboratory experiments
104     reference Wardle and Karsten papers
105     update links to include DDDAS "PIAB" page
106     cylindrical polar coordinates
107    
108     o Continuos equations in ''r'' coordinates
109     add references to iso paper
110     no mention of z* and p* - forward reference to z*/p* in 2.
111     add that coupling also manifests through F, Q
112     add tracer transport
113    
114     o Kinematic boundary conditions
115    
116 cnh 1.9 o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
117     Non-hydrostatic forms
118     need to tidy up discussion of shallow-atmosphere to be
119     consistent with the code or change code to be consistent
120     with the discussion!
121     make references hyperlinks
122     add stuff too
123     JMC remove QNH atmosphere
124     need to sort out calc_gw for deep atmosphere
125 cnh 1.1
126     o Finding the pressure field
127 cnh 1.9 make references hyperlinks
128     add forward references to manual algorithm section
129     change Elliptic to "elliptic"
130 cnh 1.1
131     o Forcing and dissipation
132 cnh 1.9 make "physics packages" refer to chapter 6.
133     should we move "external forcing" et. al to a
134     generic_forcing_driver package?
135 cnh 1.1
136     viscosities
137 cnh 1.9 update to mention Smag/Leith (Ah and A4 not constant)
138     and to have forward references to numerical section
139     tracers
140     forward references to numerical section, reddy, GM etc...
141     add references to literature
142 cnh 1.1
143     o 1.3.8 Vector invariant form
144     forward references to numerical section
145    
146     o 1.3.9 Adjoint
147     add a little more here + some hyperlink to chapter 5.
148    
149     o 1.4 Appendix ATMOSPHERE
150    
151     add some introductory words
152    
153     o 1.6 Coordinate systems
154     o only has some words on spherical polar. add some brief words
155     to cover all of
156     - cartesian
157     - spherical
158     - cylindrical
159     - general orthogonal curvilinear (vector invariant)
160    
161     o Equation of state options
162     add some discussion
163     can't remember what we said we were going to do here
164     PH to do something
165    
166    
167     Change hydrodynamical to "dynamical"
168    
169     Examples
170    
171     - extra "in action" cases
172    
173     o high res ocean with diurnal atmospheric state forcing
174     - links to ingrid output
175     CNH/Dimitris
176    
177     o realistic FIZHI from Andrea
178     - links to ingrid output
179     from AM
180    
181     o with seaice on high res cube
182     - links to ingrid output
183     CNH/Dimitris
184    
185     o coupled aqua, ridge world etc...
186     - links to ingrid output
187     get stuff from Daniel
188    
189     o constrained lab simulation
190     - links to ingrid output for model and lab
191     fields
192     get stuff from Sai/Andrew
193    
194     o sensitivity wrt to iron
195    
196     o optimization
197     - update to link to latest ECCO sites and GF
198     related material
199    
200     o eddy diffusivity transport application
201    
202     o Gas giant?
203    
204    
205 cnh 1.10 >>>> from JM
206    
207    
208     manual, section.2 :
209    
210     In general:
211     - add more refences/links to S/R & variable name
212     - would be nice to have an active link to the fortran-file
213     for all the S/R & eq.Number in the "calling-tree" boxes
214     - search for CALC_MOM_RHS and replace it by the appropriate S/R
215     (mom_flux_form, mom_vecinv, dynamics)
216     - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
217     was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
218     in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
219     simply written \vec{v}.
220     I would suggest to keep the notation as they are (since they are consistent
221     inside each section) but may be to move the "notation.tex" piece
222     at the beginning of section.2 and to mention clearly the changes between
223     the 2 sections.
224    
225     in content: Horizontal Dissipation: 2 times in vector-invariant section
226    
227     2.1 time-stepping (part2/time_stepping.tex)
228    
229     - this is not clear to me:
230    
231     >> In all the above configurations it is also possible to substitute the
232     >> Adams-Bashforth with an alternative time-stepping scheme for terms
233     >> evaluated explicitly in time
234    
235    
236     2.2 rigid-lid:
237    
238     - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
239     to stay closer to the code.
240     - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
241    
242     2.3 linear free-surface:
243     - add ref(+link) to S/R names:
244     - add ref(+link) to Crank-Nickelson section 2.9.1
245    
246     2.4 Adams-Bashforth
247     - add stability diagrams (I have some figures that I can put)
248     - add link for var. forcing_In_AB
249     - add S/R link for S/R ADAMS_BASHFORTH2
250    
251     2.5 Implicit time-stepping
252     - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
253     SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
254     - update: also used for vertical advection
255    
256     2.6 Synchronous time-stepping:
257     - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
258     MOMENTUM_CORRECTION_STEP.
259    
260     2.7 Stagger baroclinic time-stepping
261     - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
262    
263     2.8 NH
264     - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
265    
266     2.9 Variants on Free-Surface
267     - Delta.t mis-written (eq.2.73)
268     - Eq.Num missing (has been fixed since)
269     - u* is stored in gU (and not in gUnm1)
270     - Phi_nh in NH_VARS.h
271     - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
272     INI_CG2D, INI_CG3D
273    
274     2.9.1 Crank-Nickelson
275     - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
276    
277     2.9.2 NLFS
278     - eq.Nb are wrong in html
279     - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
280    
281     2.10.1 Notation
282     - Area definition is not really used like this
283    
284     >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
285    
286     Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
287     the model variables) are used (e.g., see section 2.10.5)
288    
289     2.10.5 Horizontal grid:
290     - fig.2.8 : should use Aw,As consistently in this figure description,
291     in the figure itself, as it is in the text.
292     - curvilinear:
293     to add: mention the angle of the grid direction relative to
294     Eastward, Northward direction.
295     + mention horizGridFile= in file "data" (PARM04)
296 cnh 1.13 - add cylindrical polar grid description
297 cnh 1.10 need to do a better job of relating model variables to this diagram
298    
299    
300     2.11 Continuity & Horizontal Pressure gradient terms
301     - mention that d.Phi/dr|s =g if using z coordinate
302     - eq. 2.90 not clear regarding \delta_k(P-E)
303     better to add the free surface eq: d.eta/dt = w_s + P-E
304    
305     2.12 Hydrostatic balance
306     - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
307     is hard to find
308     - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
309     and in section 1.3.4: remove the 1.3.4.3.2 subsection:
310     Quasi-nonhydrostatic Atmosphere
311    
312     2.13.2 Coriolis terms
313     - note: the discretization used when useEnergyConservingCoriolis=T
314     has no hFac and no Area and is still different from the form
315     described here (with Area & hFac);
316    
317     2.13.5 Lateral dissipation
318     - add description of how to use cosFactor & cosPower
319     - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
320     o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
321     in code need to explain why cos()3/2 turns out to be
322     scaling (not cos()2)
323 cnh 1.15 - need to reference the smag/leith section.
324 cnh 1.10
325     2.13.6 Vertical dissipation
326     - mention the implicit vertical viscosity option and ref to section 2.5
327     - add the parameter correspondence: Av <-> viscAr (and might change also
328     the notation to Ar)
329    
330     2.14 Vector invariant momentum equations
331     - indicate that the NH pieces (vertical momentum eq) are not yet coded
332     and that the NH code uses the flux form.
333    
334     2.14.6 Horizontal dissipation -> Horizontal Divergence
335    
336     2.14.7 Horizontal dissipation
337     - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
338     and A_D4,A_z4 <-> viscA4D,viscA4Z
339    
340     2.16 & 2.17 & 2.18 :
341     - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
342    
343     2.20.2 mercator, non-dimensional Equations:
344     - does not use std notation
345     - would be better as an appendix of section 2.20:
346     (e.g changing the tile to:
347 cnh 1.12 - talk to Baylor
348 cnh 1.10 Appendix: non-dimensional Equations on Spherical-Polar grid.)
349 cnh 1.12
350 cnh 1.10
351     JM
352    
353 cnh 1.11
354     >>>> From Andrea
355    
356     Chapter 3
357     --------
358    
359     Almost all of the 'math mode' text is dropped down as subscripts
360    
361     divide chapter 3 more clearly into 2 sections?
362     (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and
363     then 3.19 and 3.20 are informational again - rearrange subsections?)
364 cnh 1.15 [DONE]
365 cnh 1.11
366     3.1 - don't need a link to the outside of the document (remove it)
367     - link to htdig is broken
368    
369     3.2.1 - link at bottom to source code points to section 3.2.1
370     (ie, to itself) - link should point to cvs code archive
371    
372     3.2.2.1 - ('upgrading from an earlier version') belongs under
373     the cvs part, ie, should be 3.2.1.1
374    
375     3.3 - remove reference to 'diags' section under MITgcm
376     - remove reference to 'exe' and 'bin' sections also
377     (remove the .cvsignore file under these directories in cvs)
378     - add a 'jobs' section, and a description as examples of run scripts
379     - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions
380     - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'
381     - under 'tools' the adjoint points to section 5 - this is now section 8
382     (but should be a floating reference)
383     - under 'utils' add a reference to exch2 - stuff for different resolutions
384     - the description of the pkg section refers directly to
385     section 3. should be section 6 (actually should be a floating reference)
386    
387     3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
388     3.4.1 - links to the following experiments don't exist or are broken:
389     exp2 - should link to section 3.9
390     hs94.cs-32x32x5 - link to section 3.12
391     add 'convection' to the list, link to section 3.13
392     add 'plume on slope` to the list, link to section 3.14
393     add '??' link to section 3.15
394     add 'dic_example on slope` to the list, link to section 3.16
395     add '??' link to section 3.17
396     add 'offline' and link to section 3.18
397     clean up others and make links where they are needed
398     3.4.2 - text suggests to see section 2 for details about what is in the 'code'
399     and 'input' directories - should refer to the examples in this section
400     - add 'build' bullet - this is where the model is compiled and exectuable lives
401    
402     3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
403     as the place where they live (add a link?)
404    
405     3.6.1 - Add some general 'approach' text - ie, output is controlled either by the
406     'data' file in the input directory or by the data.[pkg name] file for any
407     package running. And there is some default behavior when the 'state' dumps
408     are written.
409     3.6.1.2 - needs to be moved to inside section 3.6.2
410    
411     3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18)
412     underneath this one and leave the text for 3.7 in place
413    
414     All the 'overview' sections need some reference to the name of the experiment in
415     the verification directory
416    
417     3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
418     - is this experiment in the list from section 3.4???
419     3.10.3.1 - refers to figures and equations, links are broken
420    
421     3.11.3.2 - line 43: link to equation is broken
422     - line 51-53: link to equation is broken
423     - there is some mess of text hanging around the end of this section. remove? reformat?
424    
425     3.12.4.1 - line 34 - link to equation is broken
426     - lines 60,61 - 1st (take out the 'r' in the superscript)
427    
428     3.13.2 - link to theta-equation is broken
429     3.13.5.4 -- ALL of the bold links to variable names are broken
430     line 34: link to equation is broken
431    
432     3.15.1 - reference to 'fourth experiment' should be removed
433    
434     3.16.4 - strange formatting, presence of '>' symbols - remove them
435    
436     3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
437     3.17.3.1 - nothing filled in under file input/data - needs description
438    
439     3.18.2 - point to section 2 for details - need hyperlink
440    
441     3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
442     section 3.5 has the 'build' directory in the example
443    
444     3.20.1 - link to doc at end of section points to this section
445     3.20.2 - link to doc at end of section points to this section
446    
447     offline - duplicate inputs, what is it, tidy up cfc v.
448     other offline. JM thinks these need tidying up.
449 cnh 1.16
450     Which of the following are which tutorial?
451     ! MLAdjust
452     adjust_nlfs.cs-32x32x1
453     aim.5l_XZ_Equatorial_Slice
454     biogeo
455     aim.5l_zon-ave
456     coupled_ucla
457     cfc_offline
458     exp3
459     global2x2_tot
460     global1x1_tot
461     global_ocean.cubed_wEXF
462     global_with_CFC11
463     goz
464     gop
465     natl_box_obcs
466     natl_box_forward
467     spinup_optim
468     tutorial_held_suarez_cs
469     vero
470     inverted_barometer
471     global_ocean.cubed32x32x30
472     exp1
473     advect_cs
474     dic_example
475     fizhi-gridalt-hs
476     global_ocean_pressure
477     matrix_example
478     exp4
479     solid-body.cs-32x32x1
480     cfc_example
481     flt_example
482     adjustment.cs-32x32x1
483     advect_xz
484     rotating_tank
485     ideal_2D_oce
486     global_ocean.90x40x15
487     front_relax
488     aim.5l_LatLon
489     lab_sea
490     hs94.cs-32x32x5
491     global_with_exf
492     exp2
493     tidal_basin_2d
494     fizhi-cs-32x32x10
495     exp5
496     global_ocean.cs32x15
497     OpenAD
498     hs94.1x64x5
499     fizhi-cs-aqualev10
500     exp0
501     dome
502     aim.5l_Equatorial_Channel
503     aim.5l_cs
504     hs94.128x64x5
505     prm
506     carbon
507     plume_on_slope
508     natl_box_adjoint
509     vermix
510     cpl_aim+ocn
511     global_ocean_ebm
512     internal_wave
513     advect_xy
514     natl_box
515     adjustment.128x64x1
516    
517 cnh 1.10 >>>> From Ed
518    
519     Here are the remaining bits for Chap 4 :
520    
521     - missing references (if you point me towards URLs, I'll add them
522     to the bibliography):
523     \ref{ref hoe and hill, ecmwf}
524     \ref{magicgarden}
525     \ref{IBMLAPI}
526     \ref{Memorychannel}
527     \ref{hoe-hill:99}
528    
529     - There are a few empty sub-sections at the end of Chap 4 that
530     should either be commented out or fleshed out.
531    
532     and thats about it for Chap 4.
533    
534    
535     Add more to quick links on front page
536    
537     Chapter 6
538    
539     the master package diagram does not appear in the document
540    
541     pkg/ptracers doesn't seem to have any documentation (see packages list below)
542 cnh 1.16 martin volunteered - get martin to ask steph
543 cnh 1.10
544    
545     Master list of packages (add this to beginning of chap 6)
546 cnh 1.1
547     admtlm/ - autodiff (chapter 5)
548 cnh 1.10 aim/ - retired
549 cnh 1.16 aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM)
550 cnh 1.1 aim_ocn_coupler/ - 6.6 (no content yet)
551 cnh 1.10 aim_v23/ - 6.4.1 (content needs fixing - JM to do)
552 cnh 1.16 atm_common/ - nothing in this package (6.4.1 related)
553 cnh 1.1 autodiff/ - autodiff (chapter 5)
554     bulk_force/ - 6.3.3
555     cal/ - 6.3.5
556 cnh 1.16 cd_code/ - chapter 2 (JM check add a reference to paper,
557     mention parameter in data)
558     cfc/ - not sure (CNH to talk to Steph and Helen)
559     chronos/ - AM to check (not being used - Andrea to kill it)
560     compon_communic/ - 6.6 (no content yet)(Daniel + JM)
561 cnh 1.1 cost/ - not sure, check with PH
562     ctrl/ - not sure, check with PH
563     debug/ - JM may do something in chapter 7 (utilities)
564     diagnostics/ - 7.1
565     dic/ - 6.7.2
566 cnh 1.16 ebm/ - (check with PH)
567 cnh 1.1 ecco/ - chapter 8
568     embed_files/ - add something to chapter 7
569     exch2/ - 6.2.2
570     exf/ - 6.3.4
571     fizhi/ - 6.4.3
572     flt/ - in chapter 2 (JM check)
573     gchem/ - 6.7.1
574     generic_advdiff/ - in chapter 2 (JM check)
575     ggl90/ - nothing, (Martin?)
576     gmredi/ - in chapter 2 (JM check). also need
577     Ferrari & Mc tapering
578     grdchk/ - grdchk (chapter 5 - check with PH)
579     gridalt/ - 6.2.4
580     kpp/ - 6.3.2
581     land/ - 6.4.2 (not connected to code - JM to fix)
582     matrix/ - Samar
583     mdsio/ - 7.3.1
584     mnc/ - 7.2.1
585     mom_common/ - in chapter 2 (JM check)
586     mom_fluxform/ - in chapter 2 (JM check)
587     mom_vecinv/ - in chapter 2 (JM check)
588     monitor/ - 7.4
589     my82/ - nothing, (martin?)
590     obcs/ - 6.3 (needs a check)
591     ocn_compon_interf/ - 6.6 (no content yet)
592     offline/ - nothing, tutorials that need work but no package section entry
593     opps/ - nothing, (martin?)
594     pp81/ - nothing, (martin?)
595     profiles/ - GAEL
596     ptracers/ - JM + SD to write something
597     rbcs/ - talk to steph
598     runclock/ - runclock
599     rw/ - not sure
600     sbo/ - text in sbo_descruption.tex but not linked into
601     part6
602     seaice/ - 6.5.2 - no equations, dimitris has promised some
603     shap_filt/ - chapter 2, JM to check
604     shelfice/ - nothing yet (martin?)
605     solver/ - empty
606     sphere/ - chapter 5 or 8 (PH to check)
607     therm_seaice/ - empty
608     thsice/ - 6.5.1 (JM to update?)
609     timeave/ - retiring......
610     zonal_filt/ - chapter 2 (JM to check)
611    
612     Possible for chap 7 - Daniels grafix/ stuff
613    
614     Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
615    
616     Figure 6.8 is missing
617    
618 cnh 1.10 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
619     Figure 6.8 is missing
620 cnh 1.9
621 cnh 1.1
622     >>>> From Andrea
623    
624     to do list for chap 7:
625    
626    
627 molod 1.2 7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"
628 cnh 1.1 the links are pointing to the proper place
629    
630     7.5.1 - add Graphix to the list of stuff in utils/matlab
631     7.5.2 - empty
632    
633    
634     andrea
635    
636 cnh 1.9
637     9. Model uses
638     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
639     (check in support for more names)

  ViewVC Help
Powered by ViewVC 1.1.22