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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 1.1
9     - mitgcm.org very front page.
10     o too many clicks to get to model manual.
11     make doc link go to mitgcm.org/r2_web_testing/latest
12     and add "HowTo" reference etc... to /latest page
13    
14     - mitgcm.org/r2_web_testing/latest
15     o add another short-cut for quick download
16    
17     o add another short-cut
18     About
19     Installation
20     Contents
21     Overview
22     Tutorials (broken)
23     Browse Code
24     Get Code (where does this go to?)
25    
26     o authors
27     John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,
28     Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,
29     Gael - others?
30    
31     o Tutorials side bar link is broken
32    
33     o words
34     change to "access on-line Auser manual/A and Atable of contents/A
35     and browse the Aoverview section/A"
36    
37     o finite-volume doesn't leap to FV figure
38    
39     o the src and equation links don't come through to
40     the html when they are in figures - see chapter 2 for some
41     examples.
42    
43     o degree symbols keep getting "dropped down" - problem with
44     pnmcrop et al.
45    
46    
47     Contents
48    
49     Intro - CNH
50     o single kernel diagram -
51     add reference to MWR paper
52    
53     o non-hydro
54     add reference to 1995 and 1999 papers
55     pdf of 1995 paper
56    
57     o FV
58     add references to 1997 papers.
59    
60     o Tangent linear/adjoint add reference to
61     Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc...
62    
63     o platforms
64     Add reference to SC article and Scientific Programming article
65    
66     o List of key papers needs to be updated and reformatted
67    
68    
69     o Global atmosphere: `Held Suarez',
70     update Adcroft reference
71     fix up ingrid link and frame (ingrid movies seem to be broken?)
72     Held and Suarez reference is not a link.
73    
74     o Ocean Gyres
75     fix up frame link
76     make "lopped cell" a link to referenced paper.
77     add references (ask Steph/Mick)
78     online/offline paper
79    
80     o Convection and mixing over topography
81     add in Legg references for convection and mixing over topography
82     and external link to CPT-GCE etc...
83    
84     o Boundary forced internal waves
85     add in Legg references, obc's reference
86    
87     o Parameter sensitivity
88     add in Bugnion references, Boyin references, Steph references
89    
90     o State estimation
91     add in references from Patrick/Carl/Ichiro/Detlef etc...
92     update links to point to latest ECCO results
93     ECCO ingrid results have been moved
94     add forward links to "ECCO state estimation" chapter in manual
95    
96     o Ocean biogeochemical cycles
97     add in references from Mick/Galen etc...
98     fix ingrid link ( date to date thing does not appear to work)
99     figure url does not have a "target=idontexist" entry
100    
101     o Simulations of laboratory experiments
102     reference Wardle and Karsten papers
103     update links to include DDDAS "PIAB" page
104     cylindrical polar coordinates
105    
106     o Continuos equations in ''r'' coordinates
107     add references to iso paper
108     no mention of z* and p* - forward reference to z*/p* in 2.
109     add that coupling also manifests through F, Q
110     add tracer transport
111    
112     o Kinematic boundary conditions
113    
114     o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms
115     need to tidy up discussion of shallow-atmosphere to be
116     consistent with the code or change code to be consistent
117     with the discussion!
118     make references hyperlinks
119     add stuff too
120    
121     o Finding the pressure field
122     make references hyperlinks
123     add forward references to manual algorithm section
124     change Elliptic to "elliptic"
125    
126     o Forcing and dissipation
127     make "physics packages" refer to chapter 6.
128     should we move "external forcing" et. al to a
129     generic_forcing_driver package?
130    
131     viscosities
132     update to mention Smag/Leith (Ah and A4 not constant)
133     and to have forward references to numerical section
134     tracers
135     forward references to numerical section, reddy, GM etc...
136     add references to literature
137    
138     o 1.3.8 Vector invariant form
139     forward references to numerical section
140    
141     o 1.3.9 Adjoint
142     add a little more here + some hyperlink to chapter 5.
143    
144     o 1.4 Appendix ATMOSPHERE
145    
146     add some introductory words
147    
148     o 1.6 Coordinate systems
149     o only has some words on spherical polar. add some brief words
150     to cover all of
151     - cartesian
152     - spherical
153     - cylindrical
154     - general orthogonal curvilinear (vector invariant)
155    
156     o Equation of state options
157     add some discussion
158     can't remember what we said we were going to do here
159     PH to do something
160    
161    
162     Discretization and alg - JMC+CNH
163    
164     Tutorials - AM
165     3.1 "Where to find"
166     o link to Pelican not needed
167     o mailman twice (why?)
168     o no htdig (gone? - I liked it)
169    
170     intro part
171     individual experiments
172    
173     offline - duplicate inputs, what is it, tidy up cfc v.
174     other offline.
175    
176     Software - EH to review
177    
178     some to be done on resource estimates at the end - needs sorting.
179    
180     Automatic Diff - CE
181    
182     Physical Packages - ???
183    
184     Diags and tools - ???
185    
186     Interface with ECCO - ???
187    
188     Model uses - ???
189    
190     Building document - ???
191     via cron
192     tweaking latex2html etc..
193    
194     Src Code tree (rename
195     examples etc..) - ???
196    
197     Documentation
198    
199     1. Introduction
200    
201     2. Discretization and Algorithm
202    
203     2.13.5 Lateral dissipation
204     o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
205     in code need to explain why cos()3/2 turns out to be
206     scaling (not cos()2)
207    
208     2.13.6 Vertical dissipation
209     o update to have reference to Baylors section
210     reference to implicit discussion in time-stepping part of manual
211    
212    
213    
214     3. Tutorials
215     reorg'd into
216     intro part
217     individual experiments
218    
219     4. Software Architecture
220    
221     5. Automatic Differentiation
222    
223     6. Physical Parameterization and Packages
224    
225     7. Diagnostics and tools
226    
227     8. Interface with ECCO
228    
229     9. Model uses
230     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
231     (check in support for more names)
232    
233     Need an empty package as part of distribution
234    
235     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!
236    
237     Chapter 1
238    
239     Change hydrodynamical to "dynamical"
240    
241     Examples
242    
243     - extra "in action" cases
244    
245     o high res ocean with diurnal atmospheric state forcing
246     - links to ingrid output
247     CNH/Dimitris
248    
249     o realistic FIZHI from Andrea
250     - links to ingrid output
251     from AM
252    
253     o with seaice on high res cube
254     - links to ingrid output
255     CNH/Dimitris
256    
257     o coupled aqua, ridge world etc...
258     - links to ingrid output
259     get stuff from Daniel
260    
261     o constrained lab simulation
262     - links to ingrid output for model and lab
263     fields
264     get stuff from Sai/Andrew
265    
266     o sensitivity wrt to iron
267    
268     o optimization
269     - update to link to latest ECCO sites and GF
270     related material
271    
272     o eddy diffusivity transport application
273    
274     o Gas giant?
275    
276     Chapter 6
277    
278     the master package diagram does not appear in the document
279    
280     pkg/ptracers doesn't seem to have any documentation (see packages list below)
281    
282    
283    
284     2.10.5 Horizontal grid
285    
286     need to do a better job of relating model variables to this diagram
287    
288    
289     Master list of packages
290    
291     admtlm/ - autodiff (chapter 5)
292     aim/ - 6.4.1 (content needs fixing - JM to do)
293     aim_compon_interf/ - 6.6 (no content yet)
294     aim_ocn_coupler/ - 6.6 (no content yet)
295     aim_v23/ - retired
296     atm_common/ - 6.6 (no content yet)
297     autodiff/ - autodiff (chapter 5)
298     bulk_force/ - 6.3.3
299     cal/ - 6.3.5
300     cd_code/ - chapter 2 (JM check)
301     cfc/ - not sure
302     chronos/ - AM to check
303     compon_communic/ - 6.6 (no content yet)
304     cost/ - not sure, check with PH
305     ctrl/ - not sure, check with PH
306     debug/ - JM may do something in chapter 7 (utilities)
307     diagnostics/ - 7.1
308     dic/ - 6.7.2
309     ebm/ - not sure
310     ecco/ - chapter 8
311     embed_files/ - add something to chapter 7
312     ex3/ - rename to exch3
313     exch2/ - 6.2.2
314     exf/ - 6.3.4
315     fizhi/ - 6.4.3
316     flt/ - in chapter 2 (JM check)
317     gchem/ - 6.7.1
318     generic_advdiff/ - in chapter 2 (JM check)
319     ggl90/ - nothing, (Martin?)
320     gmredi/ - in chapter 2 (JM check). also need
321     Ferrari & Mc tapering
322     grdchk/ - grdchk (chapter 5 - check with PH)
323     gridalt/ - 6.2.4
324     kpp/ - 6.3.2
325     land/ - 6.4.2 (not connected to code - JM to fix)
326     matrix/ - Samar
327     mdsio/ - 7.3.1
328     mnc/ - 7.2.1
329     mom_common/ - in chapter 2 (JM check)
330     mom_fluxform/ - in chapter 2 (JM check)
331     mom_vecinv/ - in chapter 2 (JM check)
332     monitor/ - 7.4
333     my82/ - nothing, (martin?)
334     obcs/ - 6.3 (needs a check)
335     ocn_compon_interf/ - 6.6 (no content yet)
336     offline/ - nothing, tutorials that need work but no package section entry
337     opps/ - nothing, (martin?)
338     pp81/ - nothing, (martin?)
339     profiles/ - GAEL
340     ptracers/ - JM + SD to write something
341     rbcs/ - talk to steph
342     runclock/ - runclock
343     rw/ - not sure
344     sbo/ - text in sbo_descruption.tex but not linked into
345     part6
346     seaice/ - 6.5.2 - no equations, dimitris has promised some
347     shap_filt/ - chapter 2, JM to check
348     shelfice/ - nothing yet (martin?)
349     solver/ - empty
350     sphere/ - chapter 5 or 8 (PH to check)
351     therm_seaice/ - empty
352     thsice/ - 6.5.1 (JM to update?)
353     timeave/ - retiring......
354     zonal_filt/ - chapter 2 (JM to check)
355    
356     Possible for chap 7 - Daniels grafix/ stuff
357    
358     Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
359    
360     Figure 6.8 is missing
361    
362    
363     >>>> From Ed
364    
365     Here are the remaining bits for Chap 4 :
366    
367     - The grammar/flow could still use some work. Boo was an English
368     major and has experience editing/proofing technical papers. I
369     could print out a copy and ask her to read it and suggest
370     improvements.
371    
372     - missing references (if you point me towards URLs, I'll add them
373     to the bibliography):
374     \ref{ref hoe and hill, ecmwf}
375     \ref{magicgarden}
376     \ref{IBMLAPI}
377     \ref{Memorychannel}
378     \ref{hoe-hill:99}
379    
380     - There are a few empty sub-sections at the end of Chap 4 that
381     should either be commented out or fleshed out.
382    
383     and thats about it for Chap 4.
384    
385    
386     Add more to quick links on front page
387    
388    
389     >>>> From Andrea
390    
391     to do list for chap 7:
392    
393    
394 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"
395 cnh 1.1 the links are pointing to the proper place
396    
397     7.5.1 - add Graphix to the list of stuff in utils/matlab
398     7.5.2 - empty
399    
400    
401     andrea
402    
403     >>>> From Andrea
404    
405     Chapter 3
406     --------
407    
408     Almost all of the 'math mode' text is dropped down as subscripts
409    
410     divide chapter 3 more clearly into 2 sections?
411     (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and
412     then 3.19 and 3.20 are informational again - rearrange subsections?)
413    
414     3.1 - don't need a link to the outside of the document (remove it)
415     - link to htdig is broken
416    
417     3.2.1 - link at bottom to source code points to section 3.2.1
418     (ie, to itself) - link should point to cvs code archive
419    
420     3.2.2.1 - ('upgrading from an earlier version') belongs under
421     the cvs part, ie, should be 3.2.1.1
422    
423     3.3 - remove reference to 'diags' section under MITgcm
424     - remove reference to 'exe' and 'bin' sections also
425     (remove the .cvsignore file under these directories in cvs)
426     - add a 'jobs' section, and a description as examples of run scripts
427     - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions
428     - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'
429     - under 'tools' the adjoint points to section 5 - this is now section 8
430     (but should be a floating reference)
431     - under 'utils' add a reference to exch2 - stuff for different resolutions
432     - the description of the pkg section refers directly to
433     section 3. should be section 6 (actually should be a floating reference)
434    
435     3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
436     3.4.1 - links to the following experiments don't exist or are broken:
437     exp2 - should link to section 3.9
438     hs94.cs-32x32x5 - link to section 3.12
439     add 'convection' to the list, link to section 3.13
440     add 'plume on slope` to the list, link to section 3.14
441     add '??' link to section 3.15
442     add 'dic_example on slope` to the list, link to section 3.16
443     add '??' link to section 3.17
444     add 'offline' and link to section 3.18
445     clean up others and make links where they are needed
446     3.4.2 - text suggests to see section 2 for details about what is in the 'code'
447     and 'input' directories - should refer to the examples in this section
448     - add 'build' bullet - this is where the model is compiled and exectuable lives
449    
450     3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
451     as the place where they live (add a link?)
452    
453     3.6.1 - Add some general 'approach' text - ie, output is controlled either by the
454     'data' file in the input directory or by the data.[pkg name] file for any
455     package running. And there is some default behavior when the 'state' dumps
456     are written.
457     3.6.1.2 - needs to be moved to inside section 3.6.2
458    
459     3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18)
460     underneath this one and leave the text for 3.7 in place
461    
462     All the 'overview' sections need some reference to the name of the experiment in
463     the verification directory
464    
465     3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
466     - is this experiment in the list from section 3.4???
467     3.10.3.1 - refers to figures and equations, links are broken
468    
469     3.11.3.2 - line 43: link to equation is broken
470     - line 51-53: link to equation is broken
471     - there is some mess of text hanging around the end of this section. remove? reformat?
472    
473     3.12.4.1 - line 34 - link to equation is broken
474     - lines 60,61 - 1st (take out the 'r' in the superscript)
475    
476     3.13.2 - link to theta-equation is broken
477     3.13.5.4 -- ALL of the bold links to variable names are broken
478     line 34: link to equation is broken
479    
480     3.15.1 - reference to 'fourth experiment' should be removed
481    
482     3.16.4 - strange formatting, presence of '>' symbols - remove them
483    
484     3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
485     3.17.3.1 - nothing filled in under file input/data - needs description
486    
487     3.18.2 - point to section 2 for details - need hyperlink
488    
489     3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
490     section 3.5 has the 'build' directory in the example
491    
492     3.20.1 - link to doc at end of section points to this section
493     3.20.2 - link to doc at end of section points to this section
494    
495     >>>> from JM
496    
497    
498    
499     manual, section.2 :
500    
501     In general:
502     - add more refences/links to S/R & variable name
503     - would be nice to have an active link to the fortran-file
504     for all the S/R & eq.Number in the "calling-tree" boxes
505     - search for CALC_MOM_RHS and replace it by the appropriate S/R
506     (mom_flux_form, mom_vecinv, dynamics)
507     - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
508     was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
509     in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
510     simply written \vec{v}.
511     I would suggest to keep the notation as they are (since they are consistent
512     inside each section) but may be to move the "notation.tex" piece
513     at the beginning of section.2 and to mention clearly the changes between
514     the 2 sections.
515    
516     in content: Horizontal Dissipation: 2 times in vector-invariant section
517    
518     2.1 time-stepping (part2/time_stepping.tex)
519    
520     - this is not clear to me:
521    
522     >> In all the above configurations it is also possible to substitute the
523     >> Adams-Bashforth with an alternative time-stepping scheme for terms
524     >> evaluated explicitly in time
525    
526    
527     2.2 rigid-lid:
528    
529     - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
530     to stay closer to the code.
531     - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
532    
533     2.3 linear free-surface:
534     - add ref(+link) to S/R names:
535     - add ref(+link) to Crank-Nickelson section 2.9.1
536    
537     2.4 Adams-Bashforth
538     - add stability diagrams (I have some figures that I can put)
539     - add link for var. forcing_In_AB
540     - add S/R link for S/R ADAMS_BASHFORTH2
541    
542     2.5 Implicit time-stepping
543     - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
544     SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
545     - update: also used for vertical advection
546    
547     2.6 Synchronous time-stepping:
548     - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
549     MOMENTUM_CORRECTION_STEP.
550    
551     2.7 Stagger baroclinic time-stepping
552     - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
553    
554     2.8 NH
555     - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
556    
557     2.9 Variants on Free-Surface
558     - Delta.t mis-written (eq.2.73)
559     - Eq.Num missing (has been fixed since)
560     - u* is stored in gU (and not in gUnm1)
561     - Phi_nh in NH_VARS.h
562     - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
563     INI_CG2D, INI_CG3D
564    
565     2.9.1 Crank-Nickelson
566     - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
567    
568     2.9.2 NLFS
569     - eq.Nb are wrong in html
570     - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
571    
572     2.10.1 Notation
573     - Area definition is not really used like this
574    
575     >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
576    
577     Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
578     the model variables) are used (e.g., see section 2.10.5)
579    
580     2.10.5 Horizontal grid:
581     - fig.2.8 : should use Aw,As consistently in this figure description,
582     in the figure itself, as it is in the text.
583     - curvilinear:
584     to add: mention the angle of the grid direction relative to
585     Eastward, Northward direction.
586     + mention horizGridFile= in file "data" (PARM04)
587     - add cylindrical grid description
588    
589     2.11 Continuity & Horizontal Pressure gradient terms
590     - mention that d.Phi/dr|s =g if using z coordinate
591     - eq. 2.90 not clear regarding \delta_k(P-E)
592     better to add the free surface eq: d.eta/dt = w_s + P-E
593    
594     2.12 Hydrostatic balance
595     - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
596     is hard to find
597     - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
598     and in section 1.3.4: remove the 1.3.4.3.2 subsection:
599     Quasi-nonhydrostatic Atmosphere
600    
601     2.13.2 Coriolis terms
602     - note: the discretization used when useEnergyConservingCoriolis=T
603     has no hFac and no Area and is still different from the form
604     described here (with Area & hFac);
605    
606     2.13.5 Lateral dissipation
607     - add description of how to use cosFactor & cosPower
608     - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
609    
610     2.13.6 Vertical dissipation
611     - mention the implicit vertical viscosity option and ref to section 2.5
612     - add the parameter correspondence: Av <-> viscAr (and might change also
613     the notation to Ar)
614    
615     2.14 Vector invariant momentum equations
616     - indicate that the NH pieces (vertical momentum eq) are not yet coded
617     and that the NH code uses the flux form.
618    
619     2.14.6 Horizontal dissipation -> Horizontal Divergence
620    
621     2.14.7 Horizontal dissipation
622     - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
623     and A_D4,A_z4 <-> viscA4D,viscA4Z
624    
625     2.16 & 2.17 & 2.18 :
626     - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
627    
628     2.20.2 mercator, non-dimensional Equations:
629     - does not use std notation
630     - would be better as an appendix of section 2.20:
631     (e.g changing the tile to:
632     Appendix: non-dimensional Equations on Spherical-Polar grid.)
633    
634     JM
635    

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