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Thu Apr 6 20:14:48 2006 UTC (17 years, 11 months ago) by edhill
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make Documentation link more direct

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    
324     2.13.6 Vertical dissipation
325     - mention the implicit vertical viscosity option and ref to section 2.5
326     - add the parameter correspondence: Av <-> viscAr (and might change also
327     the notation to Ar)
328    
329     2.14 Vector invariant momentum equations
330     - indicate that the NH pieces (vertical momentum eq) are not yet coded
331     and that the NH code uses the flux form.
332    
333     2.14.6 Horizontal dissipation -> Horizontal Divergence
334    
335     2.14.7 Horizontal dissipation
336     - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
337     and A_D4,A_z4 <-> viscA4D,viscA4Z
338    
339     2.16 & 2.17 & 2.18 :
340     - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
341    
342     2.20.2 mercator, non-dimensional Equations:
343     - does not use std notation
344     - would be better as an appendix of section 2.20:
345     (e.g changing the tile to:
346 cnh 1.12 - talk to Baylor
347 cnh 1.10 Appendix: non-dimensional Equations on Spherical-Polar grid.)
348 cnh 1.12
349 cnh 1.10
350     JM
351    
352 cnh 1.11
353     >>>> From Andrea
354    
355     Chapter 3
356     --------
357    
358     Almost all of the 'math mode' text is dropped down as subscripts
359    
360     divide chapter 3 more clearly into 2 sections?
361     (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and
362     then 3.19 and 3.20 are informational again - rearrange subsections?)
363    
364     3.1 - don't need a link to the outside of the document (remove it)
365     - link to htdig is broken
366    
367     3.2.1 - link at bottom to source code points to section 3.2.1
368     (ie, to itself) - link should point to cvs code archive
369    
370     3.2.2.1 - ('upgrading from an earlier version') belongs under
371     the cvs part, ie, should be 3.2.1.1
372    
373     3.3 - remove reference to 'diags' section under MITgcm
374     - remove reference to 'exe' and 'bin' sections also
375     (remove the .cvsignore file under these directories in cvs)
376     - add a 'jobs' section, and a description as examples of run scripts
377     - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions
378     - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'
379     - under 'tools' the adjoint points to section 5 - this is now section 8
380     (but should be a floating reference)
381     - under 'utils' add a reference to exch2 - stuff for different resolutions
382     - the description of the pkg section refers directly to
383     section 3. should be section 6 (actually should be a floating reference)
384    
385     3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
386     3.4.1 - links to the following experiments don't exist or are broken:
387     exp2 - should link to section 3.9
388     hs94.cs-32x32x5 - link to section 3.12
389     add 'convection' to the list, link to section 3.13
390     add 'plume on slope` to the list, link to section 3.14
391     add '??' link to section 3.15
392     add 'dic_example on slope` to the list, link to section 3.16
393     add '??' link to section 3.17
394     add 'offline' and link to section 3.18
395     clean up others and make links where they are needed
396     3.4.2 - text suggests to see section 2 for details about what is in the 'code'
397     and 'input' directories - should refer to the examples in this section
398     - add 'build' bullet - this is where the model is compiled and exectuable lives
399    
400     3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
401     as the place where they live (add a link?)
402    
403     3.6.1 - Add some general 'approach' text - ie, output is controlled either by the
404     'data' file in the input directory or by the data.[pkg name] file for any
405     package running. And there is some default behavior when the 'state' dumps
406     are written.
407     3.6.1.2 - needs to be moved to inside section 3.6.2
408    
409     3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18)
410     underneath this one and leave the text for 3.7 in place
411    
412     All the 'overview' sections need some reference to the name of the experiment in
413     the verification directory
414    
415     3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
416     - is this experiment in the list from section 3.4???
417     3.10.3.1 - refers to figures and equations, links are broken
418    
419     3.11.3.2 - line 43: link to equation is broken
420     - line 51-53: link to equation is broken
421     - there is some mess of text hanging around the end of this section. remove? reformat?
422    
423     3.12.4.1 - line 34 - link to equation is broken
424     - lines 60,61 - 1st (take out the 'r' in the superscript)
425    
426     3.13.2 - link to theta-equation is broken
427     3.13.5.4 -- ALL of the bold links to variable names are broken
428     line 34: link to equation is broken
429    
430     3.15.1 - reference to 'fourth experiment' should be removed
431    
432     3.16.4 - strange formatting, presence of '>' symbols - remove them
433    
434     3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
435     3.17.3.1 - nothing filled in under file input/data - needs description
436    
437     3.18.2 - point to section 2 for details - need hyperlink
438    
439     3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
440     section 3.5 has the 'build' directory in the example
441    
442     3.20.1 - link to doc at end of section points to this section
443     3.20.2 - link to doc at end of section points to this section
444    
445     offline - duplicate inputs, what is it, tidy up cfc v.
446     other offline. JM thinks these need tidying up.
447 cnh 1.10 >>>> From Ed
448    
449     Here are the remaining bits for Chap 4 :
450    
451     - The grammar/flow could still use some work. Boo was an English
452     major and has experience editing/proofing technical papers. I
453     could print out a copy and ask her to read it and suggest
454     improvements.
455    
456     - missing references (if you point me towards URLs, I'll add them
457     to the bibliography):
458     \ref{ref hoe and hill, ecmwf}
459     \ref{magicgarden}
460     \ref{IBMLAPI}
461     \ref{Memorychannel}
462     \ref{hoe-hill:99}
463    
464     - There are a few empty sub-sections at the end of Chap 4 that
465     should either be commented out or fleshed out.
466    
467     and thats about it for Chap 4.
468    
469    
470     Add more to quick links on front page
471    
472     Chapter 6
473    
474     the master package diagram does not appear in the document
475    
476     pkg/ptracers doesn't seem to have any documentation (see packages list below)
477    
478    
479     Master list of packages (add this to beginning of chap 6)
480 cnh 1.1
481     admtlm/ - autodiff (chapter 5)
482 cnh 1.10 aim/ - retired
483 cnh 1.1 aim_compon_interf/ - 6.6 (no content yet)
484     aim_ocn_coupler/ - 6.6 (no content yet)
485 cnh 1.10 aim_v23/ - 6.4.1 (content needs fixing - JM to do)
486 cnh 1.1 atm_common/ - 6.6 (no content yet)
487     autodiff/ - autodiff (chapter 5)
488     bulk_force/ - 6.3.3
489     cal/ - 6.3.5
490     cd_code/ - chapter 2 (JM check)
491     cfc/ - not sure
492     chronos/ - AM to check
493     compon_communic/ - 6.6 (no content yet)
494     cost/ - not sure, check with PH
495     ctrl/ - not sure, check with PH
496     debug/ - JM may do something in chapter 7 (utilities)
497     diagnostics/ - 7.1
498     dic/ - 6.7.2
499     ebm/ - not sure
500     ecco/ - chapter 8
501     embed_files/ - add something to chapter 7
502     ex3/ - rename to exch3
503     exch2/ - 6.2.2
504     exf/ - 6.3.4
505     fizhi/ - 6.4.3
506     flt/ - in chapter 2 (JM check)
507     gchem/ - 6.7.1
508     generic_advdiff/ - in chapter 2 (JM check)
509     ggl90/ - nothing, (Martin?)
510     gmredi/ - in chapter 2 (JM check). also need
511     Ferrari & Mc tapering
512     grdchk/ - grdchk (chapter 5 - check with PH)
513     gridalt/ - 6.2.4
514     kpp/ - 6.3.2
515     land/ - 6.4.2 (not connected to code - JM to fix)
516     matrix/ - Samar
517     mdsio/ - 7.3.1
518     mnc/ - 7.2.1
519     mom_common/ - in chapter 2 (JM check)
520     mom_fluxform/ - in chapter 2 (JM check)
521     mom_vecinv/ - in chapter 2 (JM check)
522     monitor/ - 7.4
523     my82/ - nothing, (martin?)
524     obcs/ - 6.3 (needs a check)
525     ocn_compon_interf/ - 6.6 (no content yet)
526     offline/ - nothing, tutorials that need work but no package section entry
527     opps/ - nothing, (martin?)
528     pp81/ - nothing, (martin?)
529     profiles/ - GAEL
530     ptracers/ - JM + SD to write something
531     rbcs/ - talk to steph
532     runclock/ - runclock
533     rw/ - not sure
534     sbo/ - text in sbo_descruption.tex but not linked into
535     part6
536     seaice/ - 6.5.2 - no equations, dimitris has promised some
537     shap_filt/ - chapter 2, JM to check
538     shelfice/ - nothing yet (martin?)
539     solver/ - empty
540     sphere/ - chapter 5 or 8 (PH to check)
541     therm_seaice/ - empty
542     thsice/ - 6.5.1 (JM to update?)
543     timeave/ - retiring......
544     zonal_filt/ - chapter 2 (JM to check)
545    
546     Possible for chap 7 - Daniels grafix/ stuff
547    
548     Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
549    
550     Figure 6.8 is missing
551    
552 cnh 1.10 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
553     Figure 6.8 is missing
554 cnh 1.9
555 cnh 1.1
556     >>>> From Andrea
557    
558     to do list for chap 7:
559    
560    
561 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"
562 cnh 1.1 the links are pointing to the proper place
563    
564     7.5.1 - add Graphix to the list of stuff in utils/matlab
565     7.5.2 - empty
566    
567    
568     andrea
569    
570 cnh 1.9
571     9. Model uses
572     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
573     (check in support for more names)

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