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Wed Apr 5 14:30:29 2006 UTC (13 years, 3 months ago) by cnh
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Adding todo list for the manual

1 cnh 1.1 Rebuild and set to do cron build
2    
3     To do
4    
5     - where to put under development links?
6    
7     - mitgcm.org very front page.
8     o too many clicks to get to model manual.
9     make doc link go to mitgcm.org/r2_web_testing/latest
10     and add "HowTo" reference etc... to /latest page
11    
12     - mitgcm.org/r2_web_testing/latest
13     o add another short-cut for quick download
14    
15     o add another short-cut
16     About
17     Installation
18     Contents
19     Overview
20     Tutorials (broken)
21     Browse Code
22     Get Code (where does this go to?)
23    
24     o authors
25     John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,
26     Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,
27     Gael - others?
28    
29     o Tutorials side bar link is broken
30    
31     o words
32     change to "access on-line Auser manual/A and Atable of contents/A
33     and browse the Aoverview section/A"
34    
35     o finite-volume doesn't leap to FV figure
36    
37     o date is 2002
38    
39     o fix search so it doesn't include advertisements
40    
41     o the src and equation links don't come through to
42     the html when they are in figures - see chapter 2 for some
43     examples.
44    
45     o degree symbols keep getting "dropped down" - problem with
46     pnmcrop et al.
47    
48    
49     Contents
50    
51     Intro - CNH
52     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     o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms
117     need to tidy up discussion of shallow-atmosphere to be
118     consistent with the code or change code to be consistent
119     with the discussion!
120     make references hyperlinks
121     add stuff too
122    
123     o Finding the pressure field
124     make references hyperlinks
125     add forward references to manual algorithm section
126     change Elliptic to "elliptic"
127    
128     o Forcing and dissipation
129     make "physics packages" refer to chapter 6.
130     should we move "external forcing" et. al to a
131     generic_forcing_driver package?
132    
133     viscosities
134     update to mention Smag/Leith (Ah and A4 not constant)
135     and to have forward references to numerical section
136     tracers
137     forward references to numerical section, reddy, GM etc...
138     add references to literature
139    
140     o 1.3.8 Vector invariant form
141     forward references to numerical section
142    
143     o 1.3.9 Adjoint
144     add a little more here + some hyperlink to chapter 5.
145    
146     o 1.4 Appendix ATMOSPHERE
147    
148     add some introductory words
149    
150     o 1.6 Coordinate systems
151     o only has some words on spherical polar. add some brief words
152     to cover all of
153     - cartesian
154     - spherical
155     - cylindrical
156     - general orthogonal curvilinear (vector invariant)
157    
158     o Equation of state options
159     add some discussion
160     can't remember what we said we were going to do here
161     PH to do something
162    
163    
164     Discretization and alg - JMC+CNH
165    
166     Tutorials - AM
167     3.1 "Where to find"
168     o link to Pelican not needed
169     o mailman twice (why?)
170     o no htdig (gone? - I liked it)
171    
172     intro part
173     individual experiments
174    
175     offline - duplicate inputs, what is it, tidy up cfc v.
176     other offline.
177    
178     Software - EH to review
179    
180     some to be done on resource estimates at the end - needs sorting.
181    
182     Automatic Diff - CE
183    
184     Physical Packages - ???
185    
186     Diags and tools - ???
187    
188     Interface with ECCO - ???
189    
190     Model uses - ???
191    
192     Building document - ???
193     via cron
194     tweaking latex2html etc..
195    
196     Src Code tree (rename
197     examples etc..) - ???
198    
199     Documentation
200    
201     1. Introduction
202    
203     2. Discretization and Algorithm
204    
205     2.13.5 Lateral dissipation
206     o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
207     in code need to explain why cos()3/2 turns out to be
208     scaling (not cos()2)
209    
210     2.13.6 Vertical dissipation
211     o update to have reference to Baylors section
212     reference to implicit discussion in time-stepping part of manual
213    
214    
215    
216     3. Tutorials
217     reorg'd into
218     intro part
219     individual experiments
220    
221     4. Software Architecture
222    
223     5. Automatic Differentiation
224    
225     6. Physical Parameterization and Packages
226    
227     7. Diagnostics and tools
228    
229     8. Interface with ECCO
230    
231     9. Model uses
232     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
233     (check in support for more names)
234    
235     Need an empty package as part of distribution
236    
237     latex2html equation formatting is still a bit weird in places. Need to have another go if we have a chance - especially the degree symbol seems to jump around somewhat!
238    
239     Chapter 1
240    
241     Change hydrodynamical to "dynamical"
242    
243     Examples
244    
245     - extra "in action" cases
246    
247     o high res ocean with diurnal atmospheric state forcing
248     - links to ingrid output
249     CNH/Dimitris
250    
251     o realistic FIZHI from Andrea
252     - links to ingrid output
253     from AM
254    
255     o with seaice on high res cube
256     - links to ingrid output
257     CNH/Dimitris
258    
259     o coupled aqua, ridge world etc...
260     - links to ingrid output
261     get stuff from Daniel
262    
263     o constrained lab simulation
264     - links to ingrid output for model and lab
265     fields
266     get stuff from Sai/Andrew
267    
268     o sensitivity wrt to iron
269    
270     o optimization
271     - update to link to latest ECCO sites and GF
272     related material
273    
274     o eddy diffusivity transport application
275    
276     o Gas giant?
277    
278     Chapter 6
279    
280     the master package diagram does not appear in the document
281    
282     pkg/ptracers doesn't seem to have any documentation (see packages list below)
283    
284    
285    
286     2.10.5 Horizontal grid
287    
288     need to do a better job of relating model variables to this diagram
289    
290    
291     Master list of packages
292    
293     admtlm/ - autodiff (chapter 5)
294     aim/ - 6.4.1 (content needs fixing - JM to do)
295     aim_compon_interf/ - 6.6 (no content yet)
296     aim_ocn_coupler/ - 6.6 (no content yet)
297     aim_v23/ - retired
298     atm_common/ - 6.6 (no content yet)
299     autodiff/ - autodiff (chapter 5)
300     bulk_force/ - 6.3.3
301     cal/ - 6.3.5
302     cd_code/ - chapter 2 (JM check)
303     cfc/ - not sure
304     chronos/ - AM to check
305     compon_communic/ - 6.6 (no content yet)
306     cost/ - not sure, check with PH
307     ctrl/ - not sure, check with PH
308     debug/ - JM may do something in chapter 7 (utilities)
309     diagnostics/ - 7.1
310     dic/ - 6.7.2
311     ebm/ - not sure
312     ecco/ - chapter 8
313     embed_files/ - add something to chapter 7
314     ex3/ - rename to exch3
315     exch2/ - 6.2.2
316     exf/ - 6.3.4
317     fizhi/ - 6.4.3
318     flt/ - in chapter 2 (JM check)
319     gchem/ - 6.7.1
320     generic_advdiff/ - in chapter 2 (JM check)
321     ggl90/ - nothing, (Martin?)
322     gmredi/ - in chapter 2 (JM check). also need
323     Ferrari & Mc tapering
324     grdchk/ - grdchk (chapter 5 - check with PH)
325     gridalt/ - 6.2.4
326     kpp/ - 6.3.2
327     land/ - 6.4.2 (not connected to code - JM to fix)
328     matrix/ - Samar
329     mdsio/ - 7.3.1
330     mnc/ - 7.2.1
331     mom_common/ - in chapter 2 (JM check)
332     mom_fluxform/ - in chapter 2 (JM check)
333     mom_vecinv/ - in chapter 2 (JM check)
334     monitor/ - 7.4
335     my82/ - nothing, (martin?)
336     obcs/ - 6.3 (needs a check)
337     ocn_compon_interf/ - 6.6 (no content yet)
338     offline/ - nothing, tutorials that need work but no package section entry
339     opps/ - nothing, (martin?)
340     pp81/ - nothing, (martin?)
341     profiles/ - GAEL
342     ptracers/ - JM + SD to write something
343     rbcs/ - talk to steph
344     runclock/ - runclock
345     rw/ - not sure
346     sbo/ - text in sbo_descruption.tex but not linked into
347     part6
348     seaice/ - 6.5.2 - no equations, dimitris has promised some
349     shap_filt/ - chapter 2, JM to check
350     shelfice/ - nothing yet (martin?)
351     solver/ - empty
352     sphere/ - chapter 5 or 8 (PH to check)
353     therm_seaice/ - empty
354     thsice/ - 6.5.1 (JM to update?)
355     timeave/ - retiring......
356     zonal_filt/ - chapter 2 (JM to check)
357    
358     Possible for chap 7 - Daniels grafix/ stuff
359    
360     Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
361    
362     Figure 6.8 is missing
363    
364    
365     >>>> From Ed
366    
367     Here are the remaining bits for Chap 4 :
368    
369     - The grammar/flow could still use some work. Boo was an English
370     major and has experience editing/proofing technical papers. I
371     could print out a copy and ask her to read it and suggest
372     improvements.
373    
374     - missing references (if you point me towards URLs, I'll add them
375     to the bibliography):
376     \ref{ref hoe and hill, ecmwf}
377     \ref{magicgarden}
378     \ref{IBMLAPI}
379     \ref{Memorychannel}
380     \ref{hoe-hill:99}
381    
382     - There are a few empty sub-sections at the end of Chap 4 that
383     should either be commented out or fleshed out.
384    
385     and thats about it for Chap 4.
386    
387    
388     Add more to quick links on front page
389    
390    
391     >>>> From Andrea
392    
393     to do list for chap 7:
394    
395    
396     7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernal Diagnostics Menu"
397     the links are pointing to the proper place
398    
399     7.1.4.0.1 - the link at the bottom to the fizhi diagnostic menu is broken
400     - there should be links here to the diagnostic menus from other packages
401    
402     7.5.1 - add Graphix to the list of stuff in utils/matlab
403     7.5.2 - empty
404    
405    
406     andrea
407    
408     >>>> From Andrea
409    
410     Chapter 3
411     --------
412    
413     Almost all of the 'math mode' text is dropped down as subscripts
414    
415     divide chapter 3 more clearly into 2 sections?
416     (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and
417     then 3.19 and 3.20 are informational again - rearrange subsections?)
418    
419     3.1 - don't need a link to the outside of the document (remove it)
420     - link to htdig is broken
421    
422     3.2.1 - link at bottom to source code points to section 3.2.1
423     (ie, to itself) - link should point to cvs code archive
424    
425     3.2.2.1 - ('upgrading from an earlier version') belongs under
426     the cvs part, ie, should be 3.2.1.1
427    
428     3.3 - remove reference to 'diags' section under MITgcm
429     - remove reference to 'exe' and 'bin' sections also
430     (remove the .cvsignore file under these directories in cvs)
431     - add a 'jobs' section, and a description as examples of run scripts
432     - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions
433     - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'
434     - under 'tools' the adjoint points to section 5 - this is now section 8
435     (but should be a floating reference)
436     - under 'utils' add a reference to exch2 - stuff for different resolutions
437     - the description of the pkg section refers directly to
438     section 3. should be section 6 (actually should be a floating reference)
439    
440     3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
441     3.4.1 - links to the following experiments don't exist or are broken:
442     exp2 - should link to section 3.9
443     hs94.cs-32x32x5 - link to section 3.12
444     add 'convection' to the list, link to section 3.13
445     add 'plume on slope` to the list, link to section 3.14
446     add '??' link to section 3.15
447     add 'dic_example on slope` to the list, link to section 3.16
448     add '??' link to section 3.17
449     add 'offline' and link to section 3.18
450     clean up others and make links where they are needed
451     3.4.2 - text suggests to see section 2 for details about what is in the 'code'
452     and 'input' directories - should refer to the examples in this section
453     - add 'build' bullet - this is where the model is compiled and exectuable lives
454    
455     3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
456     as the place where they live (add a link?)
457    
458     3.6.1 - Add some general 'approach' text - ie, output is controlled either by the
459     'data' file in the input directory or by the data.[pkg name] file for any
460     package running. And there is some default behavior when the 'state' dumps
461     are written.
462     3.6.1.2 - needs to be moved to inside section 3.6.2
463    
464     3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18)
465     underneath this one and leave the text for 3.7 in place
466    
467     All the 'overview' sections need some reference to the name of the experiment in
468     the verification directory
469    
470     3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
471     - is this experiment in the list from section 3.4???
472     3.10.3.1 - refers to figures and equations, links are broken
473    
474     3.11.3.2 - line 43: link to equation is broken
475     - line 51-53: link to equation is broken
476     - there is some mess of text hanging around the end of this section. remove? reformat?
477    
478     3.12.4.1 - line 34 - link to equation is broken
479     - lines 60,61 - 1st (take out the 'r' in the superscript)
480    
481     3.13.2 - link to theta-equation is broken
482     3.13.5.4 -- ALL of the bold links to variable names are broken
483     line 34: link to equation is broken
484    
485     3.15.1 - reference to 'fourth experiment' should be removed
486    
487     3.16.4 - strange formatting, presence of '>' symbols - remove them
488    
489     3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
490     3.17.3.1 - nothing filled in under file input/data - needs description
491    
492     3.18.2 - point to section 2 for details - need hyperlink
493    
494     3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
495     section 3.5 has the 'build' directory in the example
496    
497     3.20.1 - link to doc at end of section points to this section
498     3.20.2 - link to doc at end of section points to this section
499    
500     >>>> from JM
501    
502    
503    
504     manual, section.2 :
505    
506     In general:
507     - add more refences/links to S/R & variable name
508     - would be nice to have an active link to the fortran-file
509     for all the S/R & eq.Number in the "calling-tree" boxes
510     - search for CALC_MOM_RHS and replace it by the appropriate S/R
511     (mom_flux_form, mom_vecinv, dynamics)
512     - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
513     was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
514     in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
515     simply written \vec{v}.
516     I would suggest to keep the notation as they are (since they are consistent
517     inside each section) but may be to move the "notation.tex" piece
518     at the beginning of section.2 and to mention clearly the changes between
519     the 2 sections.
520    
521     in content: Horizontal Dissipation: 2 times in vector-invariant section
522    
523     2.1 time-stepping (part2/time_stepping.tex)
524    
525     - this is not clear to me:
526    
527     >> In all the above configurations it is also possible to substitute the
528     >> Adams-Bashforth with an alternative time-stepping scheme for terms
529     >> evaluated explicitly in time
530    
531    
532     2.2 rigid-lid:
533    
534     - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
535     to stay closer to the code.
536     - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
537    
538     2.3 linear free-surface:
539     - add ref(+link) to S/R names:
540     - add ref(+link) to Crank-Nickelson section 2.9.1
541    
542     2.4 Adams-Bashforth
543     - add stability diagrams (I have some figures that I can put)
544     - add link for var. forcing_In_AB
545     - add S/R link for S/R ADAMS_BASHFORTH2
546    
547     2.5 Implicit time-stepping
548     - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
549     SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
550     - update: also used for vertical advection
551    
552     2.6 Synchronous time-stepping:
553     - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
554     MOMENTUM_CORRECTION_STEP.
555    
556     2.7 Stagger baroclinic time-stepping
557     - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
558    
559     2.8 NH
560     - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
561    
562     2.9 Variants on Free-Surface
563     - Delta.t mis-written (eq.2.73)
564     - Eq.Num missing (has been fixed since)
565     - u* is stored in gU (and not in gUnm1)
566     - Phi_nh in NH_VARS.h
567     - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
568     INI_CG2D, INI_CG3D
569    
570     2.9.1 Crank-Nickelson
571     - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
572    
573     2.9.2 NLFS
574     - eq.Nb are wrong in html
575     - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
576    
577     2.10.1 Notation
578     - Area definition is not really used like this
579    
580     >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
581    
582     Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
583     the model variables) are used (e.g., see section 2.10.5)
584    
585     2.10.5 Horizontal grid:
586     - fig.2.8 : should use Aw,As consistently in this figure description,
587     in the figure itself, as it is in the text.
588     - curvilinear:
589     to add: mention the angle of the grid direction relative to
590     Eastward, Northward direction.
591     + mention horizGridFile= in file "data" (PARM04)
592     - add cylindrical grid description
593    
594     2.11 Continuity & Horizontal Pressure gradient terms
595     - mention that d.Phi/dr|s =g if using z coordinate
596     - eq. 2.90 not clear regarding \delta_k(P-E)
597     better to add the free surface eq: d.eta/dt = w_s + P-E
598    
599     2.12 Hydrostatic balance
600     - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
601     is hard to find
602     - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
603     and in section 1.3.4: remove the 1.3.4.3.2 subsection:
604     Quasi-nonhydrostatic Atmosphere
605    
606     2.13.2 Coriolis terms
607     - note: the discretization used when useEnergyConservingCoriolis=T
608     has no hFac and no Area and is still different from the form
609     described here (with Area & hFac);
610    
611     2.13.5 Lateral dissipation
612     - add description of how to use cosFactor & cosPower
613     - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
614    
615     2.13.6 Vertical dissipation
616     - mention the implicit vertical viscosity option and ref to section 2.5
617     - add the parameter correspondence: Av <-> viscAr (and might change also
618     the notation to Ar)
619    
620     2.14 Vector invariant momentum equations
621     - indicate that the NH pieces (vertical momentum eq) are not yet coded
622     and that the NH code uses the flux form.
623    
624     2.14.6 Horizontal dissipation -> Horizontal Divergence
625    
626     2.14.7 Horizontal dissipation
627     - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
628     and A_D4,A_z4 <-> viscA4D,viscA4Z
629    
630     2.16 & 2.17 & 2.18 :
631     - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
632    
633     2.20.2 mercator, non-dimensional Equations:
634     - does not use std notation
635     - would be better as an appendix of section 2.20:
636     (e.g changing the tile to:
637     Appendix: non-dimensional Equations on Spherical-Polar grid.)
638    
639     JM
640    

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