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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 very front page.
18     o too many clicks to get to model manual.
19     make doc link go to mitgcm.org/r2_web_testing/latest
20     and add "HowTo" reference etc... to /latest page
21    
22     - mitgcm.org/r2_web_testing/latest
23     o add another short-cut for quick download
24    
25     o add another short-cut
26     About
27     Installation
28     Contents
29     Overview
30     Tutorials (broken)
31     Browse Code
32 cnh 1.9
33     o mitgcm.org (front content) [DONE]
34 cnh 1.1 Get Code (where does this go to?)
35 cnh 1.9 get rid of * CVS current bullet
36     make HTML-enabled CVS code browser leap to MITgcm/MITgcm
37 cnh 1.1
38     o authors
39     John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,
40     Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,
41     Gael - others?
42    
43 cnh 1.9 o words on http://mitgcm.org/r2_web_testing/latest
44     change to
45     "access on-line Auser manual/A and Atable of contents/A
46     and browse the Aoverview section/A"
47 cnh 1.1
48     o finite-volume doesn't leap to FV figure
49    
50 cnh 1.9 o have another go at pnmcrop et al.
51 cnh 1.1
52 cnh 1.9 o Need an empty package as part of distribution. Check out atm_common
53 cnh 1.1
54 cnh 1.9 o Latex
55 cnh 1.1
56 cnh 1.9 Chapter 1 - CNH
57 cnh 1.1 o single kernel diagram -
58     add reference to MWR paper
59    
60     o non-hydro
61     add reference to 1995 and 1999 papers
62     pdf of 1995 paper
63    
64     o FV
65     add references to 1997 papers.
66    
67     o Tangent linear/adjoint add reference to
68     Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc...
69    
70     o platforms
71     Add reference to SC article and Scientific Programming article
72    
73     o List of key papers needs to be updated and reformatted
74    
75    
76     o Global atmosphere: `Held Suarez',
77     update Adcroft reference
78     fix up ingrid link and frame (ingrid movies seem to be broken?)
79     Held and Suarez reference is not a link.
80    
81     o Ocean Gyres
82     fix up frame link
83     make "lopped cell" a link to referenced paper.
84     add references (ask Steph/Mick)
85     online/offline paper
86    
87     o Convection and mixing over topography
88     add in Legg references for convection and mixing over topography
89     and external link to CPT-GCE etc...
90    
91     o Boundary forced internal waves
92     add in Legg references, obc's reference
93    
94     o Parameter sensitivity
95     add in Bugnion references, Boyin references, Steph references
96    
97     o State estimation
98     add in references from Patrick/Carl/Ichiro/Detlef etc...
99     update links to point to latest ECCO results
100     ECCO ingrid results have been moved
101     add forward links to "ECCO state estimation" chapter in manual
102    
103     o Ocean biogeochemical cycles
104     add in references from Mick/Galen etc...
105     fix ingrid link ( date to date thing does not appear to work)
106     figure url does not have a "target=idontexist" entry
107    
108     o Simulations of laboratory experiments
109     reference Wardle and Karsten papers
110     update links to include DDDAS "PIAB" page
111     cylindrical polar coordinates
112    
113     o Continuos equations in ''r'' coordinates
114     add references to iso paper
115     no mention of z* and p* - forward reference to z*/p* in 2.
116     add that coupling also manifests through F, Q
117     add tracer transport
118    
119     o Kinematic boundary conditions
120    
121 cnh 1.9 o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
122     Non-hydrostatic forms
123     need to tidy up discussion of shallow-atmosphere to be
124     consistent with the code or change code to be consistent
125     with the discussion!
126     make references hyperlinks
127     add stuff too
128     JMC remove QNH atmosphere
129     need to sort out calc_gw for deep atmosphere
130 cnh 1.1
131     o Finding the pressure field
132 cnh 1.9 make references hyperlinks
133     add forward references to manual algorithm section
134     change Elliptic to "elliptic"
135 cnh 1.1
136     o Forcing and dissipation
137 cnh 1.9 make "physics packages" refer to chapter 6.
138     should we move "external forcing" et. al to a
139     generic_forcing_driver package?
140 cnh 1.1
141     viscosities
142 cnh 1.9 update to mention Smag/Leith (Ah and A4 not constant)
143     and to have forward references to numerical section
144     tracers
145     forward references to numerical section, reddy, GM etc...
146     add references to literature
147 cnh 1.1
148     o 1.3.8 Vector invariant form
149     forward references to numerical section
150    
151     o 1.3.9 Adjoint
152     add a little more here + some hyperlink to chapter 5.
153    
154     o 1.4 Appendix ATMOSPHERE
155    
156     add some introductory words
157    
158     o 1.6 Coordinate systems
159     o only has some words on spherical polar. add some brief words
160     to cover all of
161     - cartesian
162     - spherical
163     - cylindrical
164     - general orthogonal curvilinear (vector invariant)
165    
166     o Equation of state options
167     add some discussion
168     can't remember what we said we were going to do here
169     PH to do something
170    
171    
172     Change hydrodynamical to "dynamical"
173    
174     Examples
175    
176     - extra "in action" cases
177    
178     o high res ocean with diurnal atmospheric state forcing
179     - links to ingrid output
180     CNH/Dimitris
181    
182     o realistic FIZHI from Andrea
183     - links to ingrid output
184     from AM
185    
186     o with seaice on high res cube
187     - links to ingrid output
188     CNH/Dimitris
189    
190     o coupled aqua, ridge world etc...
191     - links to ingrid output
192     get stuff from Daniel
193    
194     o constrained lab simulation
195     - links to ingrid output for model and lab
196     fields
197     get stuff from Sai/Andrew
198    
199     o sensitivity wrt to iron
200    
201     o optimization
202     - update to link to latest ECCO sites and GF
203     related material
204    
205     o eddy diffusivity transport application
206    
207     o Gas giant?
208    
209    
210 cnh 1.10 >>>> from JM
211    
212    
213     manual, section.2 :
214    
215     In general:
216     - add more refences/links to S/R & variable name
217     - would be nice to have an active link to the fortran-file
218     for all the S/R & eq.Number in the "calling-tree" boxes
219     - search for CALC_MOM_RHS and replace it by the appropriate S/R
220     (mom_flux_form, mom_vecinv, dynamics)
221     - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
222     was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
223     in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
224     simply written \vec{v}.
225     I would suggest to keep the notation as they are (since they are consistent
226     inside each section) but may be to move the "notation.tex" piece
227     at the beginning of section.2 and to mention clearly the changes between
228     the 2 sections.
229    
230     in content: Horizontal Dissipation: 2 times in vector-invariant section
231    
232     2.1 time-stepping (part2/time_stepping.tex)
233    
234     - this is not clear to me:
235    
236     >> In all the above configurations it is also possible to substitute the
237     >> Adams-Bashforth with an alternative time-stepping scheme for terms
238     >> evaluated explicitly in time
239    
240    
241     2.2 rigid-lid:
242    
243     - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
244     to stay closer to the code.
245     - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
246    
247     2.3 linear free-surface:
248     - add ref(+link) to S/R names:
249     - add ref(+link) to Crank-Nickelson section 2.9.1
250    
251     2.4 Adams-Bashforth
252     - add stability diagrams (I have some figures that I can put)
253     - add link for var. forcing_In_AB
254     - add S/R link for S/R ADAMS_BASHFORTH2
255    
256     2.5 Implicit time-stepping
257     - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
258     SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
259     - update: also used for vertical advection
260    
261     2.6 Synchronous time-stepping:
262     - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
263     MOMENTUM_CORRECTION_STEP.
264    
265     2.7 Stagger baroclinic time-stepping
266     - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
267    
268     2.8 NH
269     - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
270    
271     2.9 Variants on Free-Surface
272     - Delta.t mis-written (eq.2.73)
273     - Eq.Num missing (has been fixed since)
274     - u* is stored in gU (and not in gUnm1)
275     - Phi_nh in NH_VARS.h
276     - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
277     INI_CG2D, INI_CG3D
278    
279     2.9.1 Crank-Nickelson
280     - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
281    
282     2.9.2 NLFS
283     - eq.Nb are wrong in html
284     - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
285    
286     2.10.1 Notation
287     - Area definition is not really used like this
288    
289     >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
290    
291     Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
292     the model variables) are used (e.g., see section 2.10.5)
293    
294     2.10.5 Horizontal grid:
295     - fig.2.8 : should use Aw,As consistently in this figure description,
296     in the figure itself, as it is in the text.
297     - curvilinear:
298     to add: mention the angle of the grid direction relative to
299     Eastward, Northward direction.
300     + mention horizGridFile= in file "data" (PARM04)
301     - add cylindrical grid description
302     need to do a better job of relating model variables to this diagram
303    
304    
305     2.11 Continuity & Horizontal Pressure gradient terms
306     - mention that d.Phi/dr|s =g if using z coordinate
307     - eq. 2.90 not clear regarding \delta_k(P-E)
308     better to add the free surface eq: d.eta/dt = w_s + P-E
309    
310     2.12 Hydrostatic balance
311     - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
312     is hard to find
313     - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
314     and in section 1.3.4: remove the 1.3.4.3.2 subsection:
315     Quasi-nonhydrostatic Atmosphere
316    
317     2.13.2 Coriolis terms
318     - note: the discretization used when useEnergyConservingCoriolis=T
319     has no hFac and no Area and is still different from the form
320     described here (with Area & hFac);
321    
322     2.13.5 Lateral dissipation
323     - add description of how to use cosFactor & cosPower
324     - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
325     o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
326     in code need to explain why cos()3/2 turns out to be
327     scaling (not cos()2)
328    
329     2.13.6 Vertical dissipation
330     - mention the implicit vertical viscosity option and ref to section 2.5
331     - add the parameter correspondence: Av <-> viscAr (and might change also
332     the notation to Ar)
333    
334     2.14 Vector invariant momentum equations
335     - indicate that the NH pieces (vertical momentum eq) are not yet coded
336     and that the NH code uses the flux form.
337    
338     2.14.6 Horizontal dissipation -> Horizontal Divergence
339    
340     2.14.7 Horizontal dissipation
341     - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
342     and A_D4,A_z4 <-> viscA4D,viscA4Z
343    
344     2.16 & 2.17 & 2.18 :
345     - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
346    
347     2.20.2 mercator, non-dimensional Equations:
348     - does not use std notation
349     - would be better as an appendix of section 2.20:
350     (e.g changing the tile to:
351     Appendix: non-dimensional Equations on Spherical-Polar grid.)
352    
353     JM
354    
355     >>>> From Ed
356    
357     Here are the remaining bits for Chap 4 :
358    
359     - The grammar/flow could still use some work. Boo was an English
360     major and has experience editing/proofing technical papers. I
361     could print out a copy and ask her to read it and suggest
362     improvements.
363    
364     - missing references (if you point me towards URLs, I'll add them
365     to the bibliography):
366     \ref{ref hoe and hill, ecmwf}
367     \ref{magicgarden}
368     \ref{IBMLAPI}
369     \ref{Memorychannel}
370     \ref{hoe-hill:99}
371    
372     - There are a few empty sub-sections at the end of Chap 4 that
373     should either be commented out or fleshed out.
374    
375     and thats about it for Chap 4.
376    
377    
378     Add more to quick links on front page
379    
380     Chapter 6
381    
382     the master package diagram does not appear in the document
383    
384     pkg/ptracers doesn't seem to have any documentation (see packages list below)
385    
386    
387     Master list of packages (add this to beginning of chap 6)
388 cnh 1.1
389     admtlm/ - autodiff (chapter 5)
390 cnh 1.10 aim/ - retired
391 cnh 1.1 aim_compon_interf/ - 6.6 (no content yet)
392     aim_ocn_coupler/ - 6.6 (no content yet)
393 cnh 1.10 aim_v23/ - 6.4.1 (content needs fixing - JM to do)
394 cnh 1.1 atm_common/ - 6.6 (no content yet)
395     autodiff/ - autodiff (chapter 5)
396     bulk_force/ - 6.3.3
397     cal/ - 6.3.5
398     cd_code/ - chapter 2 (JM check)
399     cfc/ - not sure
400     chronos/ - AM to check
401     compon_communic/ - 6.6 (no content yet)
402     cost/ - not sure, check with PH
403     ctrl/ - not sure, check with PH
404     debug/ - JM may do something in chapter 7 (utilities)
405     diagnostics/ - 7.1
406     dic/ - 6.7.2
407     ebm/ - not sure
408     ecco/ - chapter 8
409     embed_files/ - add something to chapter 7
410     ex3/ - rename to exch3
411     exch2/ - 6.2.2
412     exf/ - 6.3.4
413     fizhi/ - 6.4.3
414     flt/ - in chapter 2 (JM check)
415     gchem/ - 6.7.1
416     generic_advdiff/ - in chapter 2 (JM check)
417     ggl90/ - nothing, (Martin?)
418     gmredi/ - in chapter 2 (JM check). also need
419     Ferrari & Mc tapering
420     grdchk/ - grdchk (chapter 5 - check with PH)
421     gridalt/ - 6.2.4
422     kpp/ - 6.3.2
423     land/ - 6.4.2 (not connected to code - JM to fix)
424     matrix/ - Samar
425     mdsio/ - 7.3.1
426     mnc/ - 7.2.1
427     mom_common/ - in chapter 2 (JM check)
428     mom_fluxform/ - in chapter 2 (JM check)
429     mom_vecinv/ - in chapter 2 (JM check)
430     monitor/ - 7.4
431     my82/ - nothing, (martin?)
432     obcs/ - 6.3 (needs a check)
433     ocn_compon_interf/ - 6.6 (no content yet)
434     offline/ - nothing, tutorials that need work but no package section entry
435     opps/ - nothing, (martin?)
436     pp81/ - nothing, (martin?)
437     profiles/ - GAEL
438     ptracers/ - JM + SD to write something
439     rbcs/ - talk to steph
440     runclock/ - runclock
441     rw/ - not sure
442     sbo/ - text in sbo_descruption.tex but not linked into
443     part6
444     seaice/ - 6.5.2 - no equations, dimitris has promised some
445     shap_filt/ - chapter 2, JM to check
446     shelfice/ - nothing yet (martin?)
447     solver/ - empty
448     sphere/ - chapter 5 or 8 (PH to check)
449     therm_seaice/ - empty
450     thsice/ - 6.5.1 (JM to update?)
451     timeave/ - retiring......
452     zonal_filt/ - chapter 2 (JM to check)
453    
454     Possible for chap 7 - Daniels grafix/ stuff
455    
456     Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
457    
458     Figure 6.8 is missing
459    
460 cnh 1.10 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
461     Figure 6.8 is missing
462 cnh 1.9
463 cnh 1.1
464     >>>> From Andrea
465    
466     to do list for chap 7:
467    
468    
469 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"
470 cnh 1.1 the links are pointing to the proper place
471    
472     7.5.1 - add Graphix to the list of stuff in utils/matlab
473     7.5.2 - empty
474    
475    
476     andrea
477    
478     >>>> From Andrea
479    
480     Chapter 3
481     --------
482    
483     Almost all of the 'math mode' text is dropped down as subscripts
484    
485     divide chapter 3 more clearly into 2 sections?
486     (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and
487     then 3.19 and 3.20 are informational again - rearrange subsections?)
488    
489     3.1 - don't need a link to the outside of the document (remove it)
490     - link to htdig is broken
491    
492     3.2.1 - link at bottom to source code points to section 3.2.1
493     (ie, to itself) - link should point to cvs code archive
494    
495     3.2.2.1 - ('upgrading from an earlier version') belongs under
496     the cvs part, ie, should be 3.2.1.1
497    
498     3.3 - remove reference to 'diags' section under MITgcm
499     - remove reference to 'exe' and 'bin' sections also
500     (remove the .cvsignore file under these directories in cvs)
501     - add a 'jobs' section, and a description as examples of run scripts
502     - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions
503     - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'
504     - under 'tools' the adjoint points to section 5 - this is now section 8
505     (but should be a floating reference)
506     - under 'utils' add a reference to exch2 - stuff for different resolutions
507     - the description of the pkg section refers directly to
508     section 3. should be section 6 (actually should be a floating reference)
509    
510     3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
511     3.4.1 - links to the following experiments don't exist or are broken:
512     exp2 - should link to section 3.9
513     hs94.cs-32x32x5 - link to section 3.12
514     add 'convection' to the list, link to section 3.13
515     add 'plume on slope` to the list, link to section 3.14
516     add '??' link to section 3.15
517     add 'dic_example on slope` to the list, link to section 3.16
518     add '??' link to section 3.17
519     add 'offline' and link to section 3.18
520     clean up others and make links where they are needed
521     3.4.2 - text suggests to see section 2 for details about what is in the 'code'
522     and 'input' directories - should refer to the examples in this section
523     - add 'build' bullet - this is where the model is compiled and exectuable lives
524    
525     3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
526     as the place where they live (add a link?)
527    
528     3.6.1 - Add some general 'approach' text - ie, output is controlled either by the
529     'data' file in the input directory or by the data.[pkg name] file for any
530     package running. And there is some default behavior when the 'state' dumps
531     are written.
532     3.6.1.2 - needs to be moved to inside section 3.6.2
533    
534     3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18)
535     underneath this one and leave the text for 3.7 in place
536    
537     All the 'overview' sections need some reference to the name of the experiment in
538     the verification directory
539    
540     3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
541     - is this experiment in the list from section 3.4???
542     3.10.3.1 - refers to figures and equations, links are broken
543    
544     3.11.3.2 - line 43: link to equation is broken
545     - line 51-53: link to equation is broken
546     - there is some mess of text hanging around the end of this section. remove? reformat?
547    
548     3.12.4.1 - line 34 - link to equation is broken
549     - lines 60,61 - 1st (take out the 'r' in the superscript)
550    
551     3.13.2 - link to theta-equation is broken
552     3.13.5.4 -- ALL of the bold links to variable names are broken
553     line 34: link to equation is broken
554    
555     3.15.1 - reference to 'fourth experiment' should be removed
556    
557     3.16.4 - strange formatting, presence of '>' symbols - remove them
558    
559     3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
560     3.17.3.1 - nothing filled in under file input/data - needs description
561    
562     3.18.2 - point to section 2 for details - need hyperlink
563    
564     3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
565     section 3.5 has the 'build' directory in the example
566    
567     3.20.1 - link to doc at end of section points to this section
568     3.20.2 - link to doc at end of section points to this section
569    
570 cnh 1.9 offline - duplicate inputs, what is it, tidy up cfc v.
571     other offline. JM thinks these need tidying up.
572    
573    
574     9. Model uses
575     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
576     (check in support for more names)

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