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Revision 1.32 - (hide annotations) (download)
Tue Jun 27 15:13:26 2006 UTC (13 years, 3 months ago) by edhill
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explain ch7 todo

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 words on http://mitgcm.org/r2_web_testing/latest
29     change to
30     "access on-line Auser manual/A and Atable of contents/A
31     and browse the Aoverview section/A"
32 cnh 1.1
33     o finite-volume doesn't leap to FV figure
34    
35 cnh 1.9 o have another go at pnmcrop et al.
36 cnh 1.1
37 cnh 1.9 o Need an empty package as part of distribution. Check out atm_common
38 cnh 1.1
39 cnh 1.9 o Latex
40 cnh 1.1
41 cnh 1.9 Chapter 1 - CNH
42 cnh 1.1 o single kernel diagram -
43     add reference to MWR paper
44    
45     o non-hydro
46     add reference to 1995 and 1999 papers
47     pdf of 1995 paper
48    
49     o FV
50     add references to 1997 papers.
51    
52     o Tangent linear/adjoint add reference to
53     Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc...
54    
55     o platforms
56     Add reference to SC article and Scientific Programming article
57    
58     o List of key papers needs to be updated and reformatted
59    
60    
61     o Global atmosphere: `Held Suarez',
62     update Adcroft reference
63     fix up ingrid link and frame (ingrid movies seem to be broken?)
64     Held and Suarez reference is not a link.
65    
66     o Ocean Gyres
67     fix up frame link
68     make "lopped cell" a link to referenced paper.
69     add references (ask Steph/Mick)
70     online/offline paper
71    
72     o Convection and mixing over topography
73     add in Legg references for convection and mixing over topography
74     and external link to CPT-GCE etc...
75    
76     o Boundary forced internal waves
77     add in Legg references, obc's reference
78    
79     o Parameter sensitivity
80     add in Bugnion references, Boyin references, Steph references
81    
82     o State estimation
83     add in references from Patrick/Carl/Ichiro/Detlef etc...
84     update links to point to latest ECCO results
85     ECCO ingrid results have been moved
86     add forward links to "ECCO state estimation" chapter in manual
87    
88     o Ocean biogeochemical cycles
89     add in references from Mick/Galen etc...
90     fix ingrid link ( date to date thing does not appear to work)
91     figure url does not have a "target=idontexist" entry
92    
93     o Simulations of laboratory experiments
94     reference Wardle and Karsten papers
95     update links to include DDDAS "PIAB" page
96     cylindrical polar coordinates
97    
98     o Continuos equations in ''r'' coordinates
99     add references to iso paper
100     no mention of z* and p* - forward reference to z*/p* in 2.
101     add that coupling also manifests through F, Q
102     add tracer transport
103    
104     o Kinematic boundary conditions
105    
106 cnh 1.9 o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
107     Non-hydrostatic forms
108     need to tidy up discussion of shallow-atmosphere to be
109     consistent with the code or change code to be consistent
110     with the discussion!
111     make references hyperlinks
112     add stuff too
113     JMC remove QNH atmosphere
114     need to sort out calc_gw for deep atmosphere
115 cnh 1.1
116     o Finding the pressure field
117 cnh 1.9 make references hyperlinks
118     add forward references to manual algorithm section
119     change Elliptic to "elliptic"
120 cnh 1.1
121     o Forcing and dissipation
122 cnh 1.9 make "physics packages" refer to chapter 6.
123     should we move "external forcing" et. al to a
124     generic_forcing_driver package?
125 cnh 1.1
126     viscosities
127 cnh 1.9 update to mention Smag/Leith (Ah and A4 not constant)
128     and to have forward references to numerical section
129     tracers
130     forward references to numerical section, reddy, GM etc...
131     add references to literature
132 cnh 1.1
133     o 1.3.8 Vector invariant form
134     forward references to numerical section
135    
136     o 1.3.9 Adjoint
137     add a little more here + some hyperlink to chapter 5.
138    
139     o 1.4 Appendix ATMOSPHERE
140    
141     add some introductory words
142    
143     o 1.6 Coordinate systems
144     o only has some words on spherical polar. add some brief words
145     to cover all of
146     - cartesian
147     - spherical
148     - cylindrical
149     - general orthogonal curvilinear (vector invariant)
150    
151     o Equation of state options
152     add some discussion
153     can't remember what we said we were going to do here
154     PH to do something
155    
156    
157     Change hydrodynamical to "dynamical"
158    
159     Examples
160    
161     - extra "in action" cases
162    
163     o high res ocean with diurnal atmospheric state forcing
164     - links to ingrid output
165     CNH/Dimitris
166    
167     o realistic FIZHI from Andrea
168     - links to ingrid output
169     from AM
170    
171     o with seaice on high res cube
172     - links to ingrid output
173     CNH/Dimitris
174    
175     o coupled aqua, ridge world etc...
176     - links to ingrid output
177     get stuff from Daniel
178    
179     o constrained lab simulation
180     - links to ingrid output for model and lab
181     fields
182     get stuff from Sai/Andrew
183    
184     o sensitivity wrt to iron
185    
186     o optimization
187     - update to link to latest ECCO sites and GF
188     related material
189    
190     o eddy diffusivity transport application
191    
192     o Gas giant?
193    
194    
195 cnh 1.10 >>>> from JM
196    
197    
198     manual, section.2 :
199    
200     In general:
201     - add more refences/links to S/R & variable name
202     - would be nice to have an active link to the fortran-file
203     for all the S/R & eq.Number in the "calling-tree" boxes
204     - search for CALC_MOM_RHS and replace it by the appropriate S/R
205     (mom_flux_form, mom_vecinv, dynamics)
206     - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
207     was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
208     in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
209     simply written \vec{v}.
210     I would suggest to keep the notation as they are (since they are consistent
211     inside each section) but may be to move the "notation.tex" piece
212     at the beginning of section.2 and to mention clearly the changes between
213     the 2 sections.
214    
215     in content: Horizontal Dissipation: 2 times in vector-invariant section
216    
217     2.1 time-stepping (part2/time_stepping.tex)
218    
219     - this is not clear to me:
220    
221     >> In all the above configurations it is also possible to substitute the
222     >> Adams-Bashforth with an alternative time-stepping scheme for terms
223     >> evaluated explicitly in time
224    
225    
226     2.2 rigid-lid:
227    
228     - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
229     to stay closer to the code.
230     - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
231    
232     2.3 linear free-surface:
233     - add ref(+link) to S/R names:
234     - add ref(+link) to Crank-Nickelson section 2.9.1
235    
236     2.4 Adams-Bashforth
237     - add stability diagrams (I have some figures that I can put)
238     - add link for var. forcing_In_AB
239     - add S/R link for S/R ADAMS_BASHFORTH2
240    
241     2.5 Implicit time-stepping
242     - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
243     SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
244     - update: also used for vertical advection
245    
246     2.6 Synchronous time-stepping:
247     - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
248     MOMENTUM_CORRECTION_STEP.
249    
250     2.7 Stagger baroclinic time-stepping
251     - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
252    
253     2.8 NH
254     - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
255    
256     2.9 Variants on Free-Surface
257     - Delta.t mis-written (eq.2.73)
258     - Eq.Num missing (has been fixed since)
259     - u* is stored in gU (and not in gUnm1)
260     - Phi_nh in NH_VARS.h
261     - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
262     INI_CG2D, INI_CG3D
263    
264     2.9.1 Crank-Nickelson
265     - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
266    
267     2.9.2 NLFS
268     - eq.Nb are wrong in html
269     - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
270    
271     2.10.1 Notation
272     - Area definition is not really used like this
273    
274     >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
275    
276     Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
277     the model variables) are used (e.g., see section 2.10.5)
278    
279     2.10.5 Horizontal grid:
280     - fig.2.8 : should use Aw,As consistently in this figure description,
281     in the figure itself, as it is in the text.
282     - curvilinear:
283     to add: mention the angle of the grid direction relative to
284     Eastward, Northward direction.
285     + mention horizGridFile= in file "data" (PARM04)
286 cnh 1.13 - add cylindrical polar grid description
287 cnh 1.10 need to do a better job of relating model variables to this diagram
288    
289    
290     2.11 Continuity & Horizontal Pressure gradient terms
291     - mention that d.Phi/dr|s =g if using z coordinate
292     - eq. 2.90 not clear regarding \delta_k(P-E)
293     better to add the free surface eq: d.eta/dt = w_s + P-E
294    
295     2.12 Hydrostatic balance
296     - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
297     is hard to find
298     - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
299     and in section 1.3.4: remove the 1.3.4.3.2 subsection:
300     Quasi-nonhydrostatic Atmosphere
301    
302     2.13.2 Coriolis terms
303     - note: the discretization used when useEnergyConservingCoriolis=T
304     has no hFac and no Area and is still different from the form
305     described here (with Area & hFac);
306    
307     2.13.5 Lateral dissipation
308     - add description of how to use cosFactor & cosPower
309     - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
310     o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
311     in code need to explain why cos()3/2 turns out to be
312     scaling (not cos()2)
313 cnh 1.15 - need to reference the smag/leith section.
314 cnh 1.10
315     2.13.6 Vertical dissipation
316     - mention the implicit vertical viscosity option and ref to section 2.5
317     - add the parameter correspondence: Av <-> viscAr (and might change also
318     the notation to Ar)
319    
320     2.14 Vector invariant momentum equations
321     - indicate that the NH pieces (vertical momentum eq) are not yet coded
322     and that the NH code uses the flux form.
323    
324     2.14.6 Horizontal dissipation -> Horizontal Divergence
325    
326     2.14.7 Horizontal dissipation
327     - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
328     and A_D4,A_z4 <-> viscA4D,viscA4Z
329    
330     2.16 & 2.17 & 2.18 :
331     - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
332 jmc 1.30 - fix equations 2.202 & 2.203 (thanks to Martin)
333 cnh 1.10
334     2.20.2 mercator, non-dimensional Equations:
335     - does not use std notation
336     - would be better as an appendix of section 2.20:
337     (e.g changing the tile to:
338 cnh 1.12 - talk to Baylor
339 cnh 1.10 Appendix: non-dimensional Equations on Spherical-Polar grid.)
340 cnh 1.12
341 cnh 1.10
342     JM
343    
344 cnh 1.11
345     >>>> From Andrea
346    
347     Chapter 3
348     --------
349    
350     Almost all of the 'math mode' text is dropped down as subscripts
351    
352     3.1 - don't need a link to the outside of the document (remove it)
353     - link to htdig is broken
354    
355     3.2.1 - link at bottom to source code points to section 3.2.1
356     (ie, to itself) - link should point to cvs code archive
357    
358     3.2.2.1 - ('upgrading from an earlier version') belongs under
359     the cvs part, ie, should be 3.2.1.1
360    
361     3.3 - remove reference to 'diags' section under MITgcm
362     - remove reference to 'exe' and 'bin' sections also
363     (remove the .cvsignore file under these directories in cvs)
364     - add a 'jobs' section, and a description as examples of run scripts
365     - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions
366     - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'
367     - under 'tools' the adjoint points to section 5 - this is now section 8
368     (but should be a floating reference)
369     - under 'utils' add a reference to exch2 - stuff for different resolutions
370     - the description of the pkg section refers directly to
371     section 3. should be section 6 (actually should be a floating reference)
372    
373     3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
374     3.4.1 - links to the following experiments don't exist or are broken:
375     exp2 - should link to section 3.9
376     hs94.cs-32x32x5 - link to section 3.12
377     add 'convection' to the list, link to section 3.13
378     add 'plume on slope` to the list, link to section 3.14
379     add '??' link to section 3.15
380     add 'dic_example on slope` to the list, link to section 3.16
381     add '??' link to section 3.17
382     add 'offline' and link to section 3.18
383     clean up others and make links where they are needed
384     3.4.2 - text suggests to see section 2 for details about what is in the 'code'
385     and 'input' directories - should refer to the examples in this section
386     - add 'build' bullet - this is where the model is compiled and exectuable lives
387    
388     3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
389     as the place where they live (add a link?)
390    
391     3.6.1 - Add some general 'approach' text - ie, output is controlled either by the
392     'data' file in the input directory or by the data.[pkg name] file for any
393     package running. And there is some default behavior when the 'state' dumps
394     are written.
395     3.6.1.2 - needs to be moved to inside section 3.6.2
396    
397     All the 'overview' sections need some reference to the name of the experiment in
398     the verification directory
399    
400     3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
401     - is this experiment in the list from section 3.4???
402     3.10.3.1 - refers to figures and equations, links are broken
403    
404     3.11.3.2 - line 43: link to equation is broken
405     - line 51-53: link to equation is broken
406     - there is some mess of text hanging around the end of this section. remove? reformat?
407    
408     3.12.4.1 - line 34 - link to equation is broken
409     - lines 60,61 - 1st (take out the 'r' in the superscript)
410    
411     3.13.2 - link to theta-equation is broken
412     3.13.5.4 -- ALL of the bold links to variable names are broken
413     line 34: link to equation is broken
414    
415     3.15.1 - reference to 'fourth experiment' should be removed
416    
417     3.16.4 - strange formatting, presence of '>' symbols - remove them
418    
419     3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
420     3.17.3.1 - nothing filled in under file input/data - needs description
421    
422     3.18.2 - point to section 2 for details - need hyperlink
423    
424     3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
425     section 3.5 has the 'build' directory in the example
426    
427     3.20.1 - link to doc at end of section points to this section
428     3.20.2 - link to doc at end of section points to this section
429    
430     offline - duplicate inputs, what is it, tidy up cfc v.
431     other offline. JM thinks these need tidying up.
432 cnh 1.16
433     Which of the following are which tutorial?
434 jmc 1.31 adjustment.128x64x1
435     adjustment.cs-32x32x1
436 cnh 1.16 advect_cs
437 jmc 1.31 advect_xy
438 cnh 1.16 advect_xz
439 jmc 1.31 aim.5l_cs
440     aim.5l_Equatorial_Channel
441 cnh 1.16 aim.5l_LatLon
442 jmc 1.31 biogeo
443     bottom_ctrl_5x5
444     cfc_example
445     cpl_aim+ocn
446     dome
447 cnh 1.16 exp2
448 jmc 1.31 exp4
449     exp5
450 cnh 1.16 fizhi-cs-32x32x10
451 jmc 1.31 fizhi-cs-aqualev20
452     fizhi-gridalt-hs
453     flt_example
454     front_relax
455     global1x1_tot
456     global2x2_tot
457     global_ocean.90x40x15
458 cnh 1.16 global_ocean.cs32x15
459 jmc 1.31 global_ocean.cubed32x32x30
460     global_ocean_ebm
461     global_with_exf
462     hs94.128x64x5
463 cnh 1.16 hs94.1x64x5
464 jmc 1.31 hs94.cs-32x32x5
465     ideal_2D_oce
466     internal_wave
467     inverted_barometer
468     lab_sea
469     matrix_example
470     MLAdjust
471     natl_box
472 cnh 1.16 natl_box_adjoint
473 jmc 1.31 OpenAD
474     rotating_tank
475     solid-body.cs-32x32x1
476     tidal_basin_2d
477     tutorial_baroclinic_gyre
478     tutorial_barotropic_gyre
479     tutorial_cfc_offline
480     tutorial_deep_convection
481     tutorial_global_oce_biogeo
482     tutorial_global_oce_in_p
483     tutorial_global_oce_latlon
484     tutorial_global_oce_optim
485     tutorial_held_suarez_cs
486     tutorial_offline
487     tutorial_plume_on_slope
488     tutorial_tracer_adjsens
489 cnh 1.16 vermix
490    
491 cnh 1.10 >>>> From Ed
492    
493     Here are the remaining bits for Chap 4 :
494    
495     - missing references (if you point me towards URLs, I'll add them
496     to the bibliography):
497     \ref{ref hoe and hill, ecmwf}
498     \ref{magicgarden}
499     \ref{IBMLAPI}
500     \ref{Memorychannel}
501     \ref{hoe-hill:99}
502    
503     - There are a few empty sub-sections at the end of Chap 4 that
504     should either be commented out or fleshed out.
505    
506     and thats about it for Chap 4.
507    
508    
509     Add more to quick links on front page
510    
511     Chapter 6
512    
513     the master package diagram does not appear in the document
514    
515     Master list of packages (add this to beginning of chap 6)
516 cnh 1.1
517     admtlm/ - autodiff (chapter 5)
518 cnh 1.10 aim/ - retired
519 cnh 1.16 aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM)
520 cnh 1.1 aim_ocn_coupler/ - 6.6 (no content yet)
521 cnh 1.10 aim_v23/ - 6.4.1 (content needs fixing - JM to do)
522 cnh 1.16 atm_common/ - nothing in this package (6.4.1 related)
523 cnh 1.1 autodiff/ - autodiff (chapter 5)
524     bulk_force/ - 6.3.3
525     cal/ - 6.3.5
526 cnh 1.16 cd_code/ - chapter 2 (JM check add a reference to paper,
527     mention parameter in data)
528     cfc/ - not sure (CNH to talk to Steph and Helen)
529     chronos/ - AM to check (not being used - Andrea to kill it)
530     compon_communic/ - 6.6 (no content yet)(Daniel + JM)
531 cnh 1.1 cost/ - not sure, check with PH
532     ctrl/ - not sure, check with PH
533     debug/ - JM may do something in chapter 7 (utilities)
534     diagnostics/ - 7.1
535     dic/ - 6.7.2
536 cnh 1.16 ebm/ - (check with PH)
537 cnh 1.1 ecco/ - chapter 8
538     embed_files/ - add something to chapter 7
539     exch2/ - 6.2.2
540     exf/ - 6.3.4
541     fizhi/ - 6.4.3
542 cnh 1.18 flt/ - (PH check)
543 cnh 1.1 gchem/ - 6.7.1
544     generic_advdiff/ - in chapter 2 (JM check)
545     ggl90/ - nothing, (Martin?)
546     gmredi/ - in chapter 2 (JM check). also need
547 cnh 1.18 Ferrari & Mc transition zone stuff (Samar doing this)
548     get dfer to read this
549 cnh 1.1 grdchk/ - grdchk (chapter 5 - check with PH)
550     gridalt/ - 6.2.4
551     kpp/ - 6.3.2
552 cnh 1.18 land/ - 6.4.2 (not connected to code Rong's notes - JM to fix)
553 cnh 1.1 matrix/ - Samar
554     mdsio/ - 7.3.1
555     mnc/ - 7.2.1
556     mom_common/ - in chapter 2 (JM check)
557     mom_fluxform/ - in chapter 2 (JM check)
558     mom_vecinv/ - in chapter 2 (JM check)
559     monitor/ - 7.4
560     my82/ - nothing, (martin?)
561 cnh 1.19 obcs/ - 6.3 (needs a check - ask PH to read)
562 cnh 1.1 ocn_compon_interf/ - 6.6 (no content yet)
563     offline/ - nothing, tutorials that need work but no package section entry
564 cnh 1.19 trivial to document (CNH to do)
565 cnh 1.1 opps/ - nothing, (martin?)
566     pp81/ - nothing, (martin?)
567     profiles/ - GAEL
568 cnh 1.19 ptracers/ - JM + SD + Martin to write something (nothing for this
569     at the moment)
570     AM has diagnostics table for this.
571 cnh 1.20 rbcs/ - CNH to talk to steph
572     runclock/ - runclock - CNH
573 cnh 1.21 rw/ - not sure - going to stay says JMC. quick IO calls
574 cnh 1.22 JMC to write a quick note for that.
575 cnh 1.1 sbo/ - text in sbo_descruption.tex but not linked into
576 cnh 1.22 part6 - CNH
577 cnh 1.1 seaice/ - 6.5.2 - no equations, dimitris has promised some
578     shap_filt/ - chapter 2, JM to check
579     shelfice/ - nothing yet (martin?)
580 cnh 1.22 solver/ - empty (go away?)
581 cnh 1.1 sphere/ - chapter 5 or 8 (PH to check)
582 cnh 1.22 therm_seaice/ - empty (go away?)
583 cnh 1.1 thsice/ - 6.5.1 (JM to update?)
584     timeave/ - retiring......
585     zonal_filt/ - chapter 2 (JM to check)
586    
587 cnh 1.20 list an expeiment which uses package? CNH
588    
589 cnh 1.10 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
590     Figure 6.8 is missing
591 cnh 1.9
592 cnh 1.1
593 edhill 1.32 ===== Chapter 7 ===== [EH3 editing] :
594 cnh 1.1
595 edhill 1.32 7.1.1 - links to section 7.1.4: the text of the first
596     one should read "see MITgcm Kernel Diagnostics Menu"
597     the links are pointing to the proper place
598 cnh 1.1
599 edhill 1.32 7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
600 cnh 1.1
601 edhill 1.32 7.5.2 - get bathymetry pre-processing stuff from Patrick
602     and then describe it
603 cnh 1.1
604    
605     andrea
606    
607 cnh 1.9
608 edhill 1.28 9. Publications using MITgcm --> "Previous Applications of MITgcm"
609 cnh 1.9 Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
610     (check in support for more names)
611 cnh 1.24
612     10. Under development
613 cnh 1.26
614    
615     Bibliography
616 cnh 1.27
617     tidy up from misc - .tex

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