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

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