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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 1.8 - pick a URL
12     TBD
13 cnh 1.1
14     - mitgcm.org very front page.
15     o too many clicks to get to model manual.
16     make doc link go to mitgcm.org/r2_web_testing/latest
17     and add "HowTo" reference etc... to /latest page
18    
19     - mitgcm.org/r2_web_testing/latest
20     o add another short-cut for quick download
21    
22     o add another short-cut
23     About
24     Installation
25     Contents
26     Overview
27     Tutorials (broken)
28     Browse Code
29     Get Code (where does this go to?)
30    
31     o authors
32     John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,
33     Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,
34     Gael - others?
35    
36     o Tutorials side bar link is broken
37    
38     o words
39     change to "access on-line Auser manual/A and Atable of contents/A
40     and browse the Aoverview section/A"
41    
42     o finite-volume doesn't leap to FV figure
43    
44     o the src and equation links don't come through to
45     the html when they are in figures - see chapter 2 for some
46     examples.
47    
48     o degree symbols keep getting "dropped down" - problem with
49     pnmcrop et al.
50    
51    
52     Contents
53    
54     Intro - CNH
55     o single kernel diagram -
56     add reference to MWR paper
57    
58     o non-hydro
59     add reference to 1995 and 1999 papers
60     pdf of 1995 paper
61    
62     o FV
63     add references to 1997 papers.
64    
65     o Tangent linear/adjoint add reference to
66     Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc...
67    
68     o platforms
69     Add reference to SC article and Scientific Programming article
70    
71     o List of key papers needs to be updated and reformatted
72    
73    
74     o Global atmosphere: `Held Suarez',
75     update Adcroft reference
76     fix up ingrid link and frame (ingrid movies seem to be broken?)
77     Held and Suarez reference is not a link.
78    
79     o Ocean Gyres
80     fix up frame link
81     make "lopped cell" a link to referenced paper.
82     add references (ask Steph/Mick)
83     online/offline paper
84    
85     o Convection and mixing over topography
86     add in Legg references for convection and mixing over topography
87     and external link to CPT-GCE etc...
88    
89     o Boundary forced internal waves
90     add in Legg references, obc's reference
91    
92     o Parameter sensitivity
93     add in Bugnion references, Boyin references, Steph references
94    
95     o State estimation
96     add in references from Patrick/Carl/Ichiro/Detlef etc...
97     update links to point to latest ECCO results
98     ECCO ingrid results have been moved
99     add forward links to "ECCO state estimation" chapter in manual
100    
101     o Ocean biogeochemical cycles
102     add in references from Mick/Galen etc...
103     fix ingrid link ( date to date thing does not appear to work)
104     figure url does not have a "target=idontexist" entry
105    
106     o Simulations of laboratory experiments
107     reference Wardle and Karsten papers
108     update links to include DDDAS "PIAB" page
109     cylindrical polar coordinates
110    
111     o Continuos equations in ''r'' coordinates
112     add references to iso paper
113     no mention of z* and p* - forward reference to z*/p* in 2.
114     add that coupling also manifests through F, Q
115     add tracer transport
116    
117     o Kinematic boundary conditions
118    
119     o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms
120     need to tidy up discussion of shallow-atmosphere to be
121     consistent with the code or change code to be consistent
122     with the discussion!
123     make references hyperlinks
124     add stuff too
125    
126     o Finding the pressure field
127     make references hyperlinks
128     add forward references to manual algorithm section
129     change Elliptic to "elliptic"
130    
131     o Forcing and dissipation
132     make "physics packages" refer to chapter 6.
133     should we move "external forcing" et. al to a
134     generic_forcing_driver package?
135    
136     viscosities
137     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    
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     Discretization and alg - JMC+CNH
168    
169     Tutorials - AM
170     3.1 "Where to find"
171     o link to Pelican not needed
172     o mailman twice (why?)
173     o no htdig (gone? - I liked it)
174    
175     intro part
176     individual experiments
177    
178     offline - duplicate inputs, what is it, tidy up cfc v.
179     other offline.
180    
181     Software - EH to review
182    
183     some to be done on resource estimates at the end - needs sorting.
184    
185     Automatic Diff - CE
186    
187     Physical Packages - ???
188    
189     Diags and tools - ???
190    
191     Interface with ECCO - ???
192    
193     Model uses - ???
194    
195     Building document - ???
196     via cron
197     tweaking latex2html etc..
198    
199     Src Code tree (rename
200     examples etc..) - ???
201    
202     Documentation
203    
204     1. Introduction
205    
206     2. Discretization and Algorithm
207    
208     2.13.5 Lateral dissipation
209     o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
210     in code need to explain why cos()3/2 turns out to be
211     scaling (not cos()2)
212    
213     2.13.6 Vertical dissipation
214     o update to have reference to Baylors section
215     reference to implicit discussion in time-stepping part of manual
216    
217    
218    
219     3. Tutorials
220     reorg'd into
221     intro part
222     individual experiments
223    
224     4. Software Architecture
225    
226     5. Automatic Differentiation
227    
228     6. Physical Parameterization and Packages
229    
230     7. Diagnostics and tools
231    
232     8. Interface with ECCO
233    
234     9. Model uses
235     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
236     (check in support for more names)
237    
238     Need an empty package as part of distribution
239    
240     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!
241    
242     Chapter 1
243    
244     Change hydrodynamical to "dynamical"
245    
246     Examples
247    
248     - extra "in action" cases
249    
250     o high res ocean with diurnal atmospheric state forcing
251     - links to ingrid output
252     CNH/Dimitris
253    
254     o realistic FIZHI from Andrea
255     - links to ingrid output
256     from AM
257    
258     o with seaice on high res cube
259     - links to ingrid output
260     CNH/Dimitris
261    
262     o coupled aqua, ridge world etc...
263     - links to ingrid output
264     get stuff from Daniel
265    
266     o constrained lab simulation
267     - links to ingrid output for model and lab
268     fields
269     get stuff from Sai/Andrew
270    
271     o sensitivity wrt to iron
272    
273     o optimization
274     - update to link to latest ECCO sites and GF
275     related material
276    
277     o eddy diffusivity transport application
278    
279     o Gas giant?
280    
281     Chapter 6
282    
283     the master package diagram does not appear in the document
284    
285     pkg/ptracers doesn't seem to have any documentation (see packages list below)
286    
287    
288    
289     2.10.5 Horizontal grid
290    
291     need to do a better job of relating model variables to this diagram
292    
293    
294     Master list of packages
295    
296     admtlm/ - autodiff (chapter 5)
297     aim/ - 6.4.1 (content needs fixing - JM to do)
298     aim_compon_interf/ - 6.6 (no content yet)
299     aim_ocn_coupler/ - 6.6 (no content yet)
300     aim_v23/ - retired
301     atm_common/ - 6.6 (no content yet)
302     autodiff/ - autodiff (chapter 5)
303     bulk_force/ - 6.3.3
304     cal/ - 6.3.5
305     cd_code/ - chapter 2 (JM check)
306     cfc/ - not sure
307     chronos/ - AM to check
308     compon_communic/ - 6.6 (no content yet)
309     cost/ - not sure, check with PH
310     ctrl/ - not sure, check with PH
311     debug/ - JM may do something in chapter 7 (utilities)
312     diagnostics/ - 7.1
313     dic/ - 6.7.2
314     ebm/ - not sure
315     ecco/ - chapter 8
316     embed_files/ - add something to chapter 7
317     ex3/ - rename to exch3
318     exch2/ - 6.2.2
319     exf/ - 6.3.4
320     fizhi/ - 6.4.3
321     flt/ - in chapter 2 (JM check)
322     gchem/ - 6.7.1
323     generic_advdiff/ - in chapter 2 (JM check)
324     ggl90/ - nothing, (Martin?)
325     gmredi/ - in chapter 2 (JM check). also need
326     Ferrari & Mc tapering
327     grdchk/ - grdchk (chapter 5 - check with PH)
328     gridalt/ - 6.2.4
329     kpp/ - 6.3.2
330     land/ - 6.4.2 (not connected to code - JM to fix)
331     matrix/ - Samar
332     mdsio/ - 7.3.1
333     mnc/ - 7.2.1
334     mom_common/ - in chapter 2 (JM check)
335     mom_fluxform/ - in chapter 2 (JM check)
336     mom_vecinv/ - in chapter 2 (JM check)
337     monitor/ - 7.4
338     my82/ - nothing, (martin?)
339     obcs/ - 6.3 (needs a check)
340     ocn_compon_interf/ - 6.6 (no content yet)
341     offline/ - nothing, tutorials that need work but no package section entry
342     opps/ - nothing, (martin?)
343     pp81/ - nothing, (martin?)
344     profiles/ - GAEL
345     ptracers/ - JM + SD to write something
346     rbcs/ - talk to steph
347     runclock/ - runclock
348     rw/ - not sure
349     sbo/ - text in sbo_descruption.tex but not linked into
350     part6
351     seaice/ - 6.5.2 - no equations, dimitris has promised some
352     shap_filt/ - chapter 2, JM to check
353     shelfice/ - nothing yet (martin?)
354     solver/ - empty
355     sphere/ - chapter 5 or 8 (PH to check)
356     therm_seaice/ - empty
357     thsice/ - 6.5.1 (JM to update?)
358     timeave/ - retiring......
359     zonal_filt/ - chapter 2 (JM to check)
360    
361     Possible for chap 7 - Daniels grafix/ stuff
362    
363     Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
364    
365     Figure 6.8 is missing
366    
367    
368     >>>> From Ed
369    
370     Here are the remaining bits for Chap 4 :
371    
372     - The grammar/flow could still use some work. Boo was an English
373     major and has experience editing/proofing technical papers. I
374     could print out a copy and ask her to read it and suggest
375     improvements.
376    
377     - missing references (if you point me towards URLs, I'll add them
378     to the bibliography):
379     \ref{ref hoe and hill, ecmwf}
380     \ref{magicgarden}
381     \ref{IBMLAPI}
382     \ref{Memorychannel}
383     \ref{hoe-hill:99}
384    
385     - There are a few empty sub-sections at the end of Chap 4 that
386     should either be commented out or fleshed out.
387    
388     and thats about it for Chap 4.
389    
390    
391     Add more to quick links on front page
392    
393    
394     >>>> From Andrea
395    
396     to do list for chap 7:
397    
398    
399 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"
400 cnh 1.1 the links are pointing to the proper place
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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