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revision 1.5 by edhill, Thu Apr 6 19:06:45 2006 UTC revision 1.35 by cnh, Tue Jun 27 16:32:14 2006 UTC
# Line 1  Line 1 
1    Editors
2    
3     Overall       - JM, AM, PH, CNH, EH3
4    
5     Front content - EH3
6    
7     Chapter 1     - CNH
8    
9     Chapter 2     - JMC
10    
11     Chapter 3     -  AM
12    
13     Chapter 4     - CNH
14    
15     Chapter 5     -  PH
16    
17     Chapter 6     -  AM
18    
19     Chapter 7     - EH3
20    
21     Chapter 8     -  PH
22    
23     Chapter 9     - CNH (Applications)
24    
25     Chapter 10    - JMC (Under development chapter)
26    
27     Biblio        - EH3
28    
29  Rebuild and set to do cron build - DONE on hugo  Rebuild and set to do cron build - DONE on hugo
30    
31  To do  To do
32    
33    - where to put under development links?    - where to put under development links?
34        JMC would like to have some mention of unfinished things (checked in
35         but not that tested e.g. AB3)
36        Add an "Under development, chapter" - shortish description of what
37        is available (last chapter)
38    
39      - add in example latex for formatting author names in different pieces.
40        this aknowledges peoples contributions and gives ref for who
41        to talk to.
42    
43    o HTML, scripts and front content
44    
45    - mitgcm.org very front page.    - pick a URL
46      o too many clicks to get to model manual.      TBD
       make doc link go to mitgcm.org/r2_web_testing/latest  
       and add "HowTo" reference etc... to /latest page  
47    
48    - mitgcm.org/r2_web_testing/latest    - mitgcm.org/r2_web_testing/latest
49      o add another short-cut for quick download      o add another short-cut for quick download
# Line 19  To do Line 55  To do
55        Overview        Overview
56        Tutorials (broken)        Tutorials (broken)
57        Browse Code        Browse Code
       Get Code (where does this go to?)  
58    
59      o authors      o words on http://mitgcm.org/r2_web_testing/latest
60        John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,        change to
61        Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,         "access on-line Auser manual/A and Atable of contents/A
62        Gael - others?          and browse the Aoverview section/A"
   
     o Tutorials side bar link is broken  
   
     o words  
       change to "access on-line Auser manual/A and Atable of contents/A  
       and browse the Aoverview section/A"  
63    
64      o finite-volume doesn't leap to FV figure      o finite-volume doesn't leap to FV figure
65    
66      o the src and equation links don't come through to      o have another go at pnmcrop et al.
       the html when they are in figures - see chapter 2 for some  
       examples.  
67    
68      o degree symbols keep getting "dropped down" - problem with      o Need an empty package as part of distribution. Check out atm_common
       pnmcrop et al.  
69    
70    o Latex  
71    
72  Contents      Chapter 1                 - CNH
   
     Intro                  - CNH  
73        o single kernel diagram -        o single kernel diagram -
74            add reference to MWR paper            add reference to MWR paper
75    
# Line 63  Contents Line 88  Contents
88    
89        o List of key papers needs to be updated and reformatted        o List of key papers needs to be updated and reformatted
90    
   
91        o Global atmosphere: `Held Suarez',        o Global atmosphere: `Held Suarez',
92          update Adcroft reference          update Adcroft reference
93          fix up ingrid link and frame (ingrid movies seem to be broken?)          fix up ingrid link and frame (ingrid movies seem to be broken?)
# Line 109  Contents Line 133  Contents
133    
134        o Kinematic boundary conditions        o Kinematic boundary conditions
135    
136        o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms        o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
137          need to tidy up discussion of shallow-atmosphere to be          Non-hydrostatic forms
138          consistent with the code or change code to be consistent           need to tidy up discussion of shallow-atmosphere to be
139          with the discussion!           consistent with the code or change code to be consistent
140          make references hyperlinks           with the discussion!
141          add stuff too           make references hyperlinks
142             add stuff too
143             JMC remove QNH atmosphere
144             need to sort out calc_gw for deep atmosphere
145    
146        o Finding the pressure field        o Finding the pressure field
147          make references hyperlinks           make references hyperlinks
148          add forward references to manual algorithm section           add forward references to manual algorithm section
149          change Elliptic to "elliptic"           change Elliptic to "elliptic"
150    
151        o Forcing and dissipation        o Forcing and dissipation
152          make "physics packages" refer to chapter 6.           make "physics packages" refer to chapter 6.
153          should we move "external forcing" et. al to a           should we move "external forcing" et. al to a
154          generic_forcing_driver package?           generic_forcing_driver package?
155    
156          viscosities          viscosities
157          update to mention Smag/Leith (Ah and A4 not constant)           update to mention Smag/Leith (Ah and A4 not constant)
158          and to have forward references to numerical section           and to have forward references to numerical section
159          tracers           tracers
160          forward references to numerical section, reddy, GM etc...           forward references to numerical section, reddy, GM etc...
161          add references to literature           add references to literature
162    
163        o 1.3.8 Vector invariant form        o 1.3.8 Vector invariant form
164          forward references to numerical section          forward references to numerical section
# Line 157  Contents Line 184  Contents
184          PH to do something          PH to do something
185    
186    
     Discretization and alg - JMC+CNH  
   
     Tutorials              - AM  
      3.1 "Where to find"  
        o link to Pelican not needed  
        o mailman twice (why?)  
        o no htdig (gone? - I liked it)  
   
      intro part  
      individual experiments  
   
      offline - duplicate inputs, what is it, tidy up cfc v.  
                other offline.  
   
     Software               - EH to review  
   
     some to be done on resource estimates at the end - needs sorting.  
   
     Automatic Diff         - CE  
   
     Physical Packages      - ???  
   
     Diags and tools        - ???  
   
     Interface with ECCO    - ???  
   
     Model uses             - ???  
   
     Building document      - ???  
     via cron  
     tweaking latex2html etc..  
   
     Src Code tree (rename  
     examples etc..)        - ???  
   
 Documentation  
   
 1. Introduction  
   
 2. Discretization and Algorithm  
   
    2.13.5 Lateral dissipation  
     o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags  
       in code need to explain why cos()3/2 turns out to be  
       scaling (not cos()2)  
   
    2.13.6 Vertical dissipation  
     o update to have reference to Baylors section  
       reference to implicit discussion in time-stepping part of manual  
   
   
   
 3. Tutorials  
    reorg'd into  
    intro part  
    individual experiments  
   
 4. Software Architecture  
   
 5. Automatic Differentiation  
   
 6. Physical Parameterization and Packages  
   
 7. Diagnostics and tools  
   
 8. Interface with ECCO  
   
 9. Model uses  
    Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...  
    (check in support for more names)  
   
  Need an empty package as part of distribution  
   
  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!  
   
 Chapter 1  
   
187      Change hydrodynamical to "dynamical"      Change hydrodynamical to "dynamical"
188    
189      Examples      Examples
# Line 271  Chapter 1 Line 221  Chapter 1
221    
222            o Gas giant?            o Gas giant?
223    
 Chapter 6  
224    
225     the master package diagram does not appear in the document  >>>> from JM
226    
    pkg/ptracers doesn't seem to have any documentation (see packages list below)  
227    
228    manual, section.2 :
229    
230    In general:
231    - add more refences/links to S/R & variable name
232    - would be nice to have an active link to the fortran-file
233      for all the S/R & eq.Number in the "calling-tree" boxes
234    - search for CALC_MOM_RHS and replace it by the appropriate S/R
235      (mom_flux_form, mom_vecinv, dynamics)
236    - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
237    was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
238    in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
239    simply written \vec{v}.
240    I would suggest to keep the notation as they are (since they are consistent
241    inside each section) but may be to move the "notation.tex" piece
242    at the beginning of section.2 and to mention clearly the changes between
243    the 2 sections.
244    
245  2.10.5 Horizontal grid  in content: Horizontal Dissipation: 2 times in vector-invariant section
246    
247     need to do a better job of relating model variables to this diagram  2.1 time-stepping (part2/time_stepping.tex)
248    
249    - this is not clear to me:
250    
251  Master list of packages  >> In all the above configurations it is also possible to substitute the
252    >> Adams-Bashforth with an alternative time-stepping scheme for terms
253    >> evaluated explicitly in time
254    
 admtlm/               - autodiff (chapter 5)  
 aim/                  - 6.4.1 (content needs fixing - JM to do)  
 aim_compon_interf/    - 6.6 (no content yet)  
 aim_ocn_coupler/      - 6.6 (no content yet)  
 aim_v23/              - retired  
 atm_common/           - 6.6 (no content yet)  
 autodiff/             - autodiff (chapter 5)  
 bulk_force/           - 6.3.3  
 cal/                  - 6.3.5  
 cd_code/              - chapter 2 (JM check)  
 cfc/                  - not sure  
 chronos/              - AM to check  
 compon_communic/      - 6.6 (no content yet)  
 cost/                 - not sure, check with PH  
 ctrl/                 - not sure, check with PH  
 debug/                - JM may do something in chapter 7 (utilities)  
 diagnostics/          - 7.1  
 dic/                  - 6.7.2  
 ebm/                  - not sure  
 ecco/                 - chapter 8  
 embed_files/          - add something to chapter 7  
 ex3/                  - rename to exch3  
 exch2/                - 6.2.2  
 exf/                  - 6.3.4  
 fizhi/                - 6.4.3  
 flt/                  - in chapter 2 (JM check)  
 gchem/                - 6.7.1  
 generic_advdiff/      - in chapter 2 (JM check)  
 ggl90/                - nothing, (Martin?)  
 gmredi/               - in chapter 2 (JM check). also need  
                         Ferrari & Mc tapering  
 grdchk/               - grdchk (chapter 5 - check with PH)  
 gridalt/              - 6.2.4  
 kpp/                  - 6.3.2  
 land/                 - 6.4.2 (not connected to code - JM to fix)  
 matrix/               - Samar  
 mdsio/                - 7.3.1  
 mnc/                  - 7.2.1  
 mom_common/           - in chapter 2 (JM check)  
 mom_fluxform/         - in chapter 2 (JM check)  
 mom_vecinv/           - in chapter 2 (JM check)  
 monitor/              - 7.4  
 my82/                 - nothing, (martin?)  
 obcs/                 - 6.3 (needs a check)  
 ocn_compon_interf/    - 6.6 (no content yet)  
 offline/              - nothing, tutorials that need work but no package   section entry  
 opps/                 - nothing, (martin?)  
 pp81/                 - nothing, (martin?)  
 profiles/             - GAEL  
 ptracers/             - JM + SD to write something  
 rbcs/                 - talk to steph  
 runclock/             - runclock  
 rw/                   - not sure  
 sbo/                  - text in sbo_descruption.tex but not linked into  
                         part6  
 seaice/               - 6.5.2 - no equations, dimitris has promised some  
 shap_filt/            - chapter 2, JM to check  
 shelfice/             - nothing yet (martin?)  
 solver/               - empty  
 sphere/               - chapter 5 or 8 (PH to check)  
 therm_seaice/         - empty  
 thsice/               - 6.5.1 (JM to update?)  
 timeave/              - retiring......  
 zonal_filt/           - chapter 2 (JM to check)  
255    
256  Possible for chap 7 - Daniels grafix/ stuff  2.2 rigid-lid:
257    
258  Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.  - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
259      to stay closer to the code.
260    - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
261    
262  Figure 6.8 is missing  2.3 linear free-surface:
263    - add ref(+link) to S/R names:
264    - add ref(+link) to Crank-Nickelson section 2.9.1
265    
266    2.4 Adams-Bashforth
267    - add stability diagrams (I have some figures that I can put)
268    - add link for var. forcing_In_AB
269    - add S/R link for S/R ADAMS_BASHFORTH2
270    
271  >>>> From Ed  2.5 Implicit time-stepping
272    - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
273            SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
274    - update: also used for vertical advection
275    
276  Here are the remaining bits for Chap 4 :  2.6 Synchronous time-stepping:
277    - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,  
278                       MOMENTUM_CORRECTION_STEP.
279    
280   - The grammar/flow could still use some work.  Boo was an English  2.7 Stagger baroclinic time-stepping
281     major and has experience editing/proofing technical papers.  I  - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
    could print out a copy and ask her to read it and suggest  
    improvements.  
282    
283   - missing references (if you point me towards URLs, I'll add them  2.8 NH
284     to the bibliography):  - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
      \ref{ref hoe and hill, ecmwf}  
      \ref{magicgarden}  
      \ref{IBMLAPI}  
      \ref{Memorychannel}  
      \ref{hoe-hill:99}  
285    
286   - There are a few empty sub-sections at the end of Chap 4 that  2.9 Variants on Free-Surface
287     should either be commented out or fleshed out.  - Delta.t mis-written (eq.2.73)
288    - Eq.Num missing (has been fixed since)
289    - u* is stored in gU (and not in gUnm1)
290    - Phi_nh in NH_VARS.h
291    - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
292      INI_CG2D, INI_CG3D
293    
294  and thats about it for Chap 4.  2.9.1 Crank-Nickelson
295    - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
296    
297    2.9.2 NLFS
298    - eq.Nb are wrong in html
299    - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
300    
301    2.10.1 Notation
302    - Area definition is not really used like this
303    
304  Add more to quick links on front page  >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
305    
306      Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
307      the model variables) are used (e.g., see section 2.10.5)
308    
309  >>>> From Andrea  2.10.5 Horizontal grid:
310    - fig.2.8 : should use Aw,As consistently in this figure description,
311      in the figure itself, as it is in the text.
312    - curvilinear:
313      to add: mention the angle of the grid direction relative to
314      Eastward, Northward direction.
315      + mention horizGridFile= in file "data" (PARM04)
316    - add cylindrical polar grid description
317       need to do a better job of relating model variables to this diagram
318    
 to do list for chap 7:  
319    
320    2.11 Continuity & Horizontal Pressure gradient terms
321     - mention that d.Phi/dr|s =g if using z coordinate
322     - eq. 2.90 not clear regarding \delta_k(P-E)
323     better to add the free surface eq: d.eta/dt = w_s + P-E
324    
325  7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"  2.12 Hydrostatic balance
326          the links are pointing to the proper place   - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
327       is hard to find
328     - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
329        and in section 1.3.4: remove the 1.3.4.3.2 subsection:
330                           Quasi-nonhydrostatic Atmosphere
331    
332  7.5.1 - add Graphix to the list of stuff in utils/matlab  2.13.2 Coriolis terms
333  7.5.2 - empty   - note: the discretization used when useEnergyConservingCoriolis=T  
334       has no hFac and no Area and is still different from the form
335       described here (with Area & hFac);
336    
337    2.13.5 Lateral dissipation
338     - add description of how to use cosFactor & cosPower
339     - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
340        o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
341          in code need to explain why cos()3/2 turns out to be
342          scaling (not cos()2)
343     - need to reference the smag/leith section.
344    
345    2.13.6 Vertical dissipation
346     - mention the implicit vertical viscosity option and ref to section 2.5
347     - add the parameter correspondence: Av <-> viscAr (and might change also
348       the notation to Ar)
349    
350    2.14 Vector invariant momentum equations
351     - indicate that the NH pieces (vertical momentum eq) are not yet coded
352       and that the NH code uses the flux form.
353    
354    2.14.6 Horizontal dissipation -> Horizontal Divergence
355    
356    2.14.7 Horizontal dissipation
357     - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ  
358       and A_D4,A_z4 <-> viscA4D,viscA4Z
359    
360    2.16 & 2.17 & 2.18 :
361     - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
362     - fix equations 2.202 & 2.203 (thanks to Martin)
363    
364    2.20.2 mercator, non-dimensional Equations:
365    - does not use std notation
366    - would be better as an appendix of section 2.20:
367    (e.g changing the tile to:
368    - talk to Baylor
369     Appendix: non-dimensional Equations on Spherical-Polar grid.)
370    
371    
372    Diagrams of grid locations etc.... and what variables and output files
373    and/or netcdf variable names are not very easy to figure out and follow.
374    It would be good to redo and extend these diagrams and align with GRID.h
375    content.
376    
377    
378    JM
379    
 andrea  
380    
381  >>>> From Andrea  >>>> From Andrea
382    
# Line 405  Chapter 3 Line 385  Chapter 3
385    
386  Almost all of the 'math mode' text is dropped down as subscripts  Almost all of the 'math mode' text is dropped down as subscripts
387    
 divide chapter 3 more clearly into 2 sections?  
    (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and  
     then 3.19 and 3.20 are informational again - rearrange subsections?)  
   
388  3.1 - don't need a link to the outside of the document (remove it)  3.1 - don't need a link to the outside of the document (remove it)
389      - link to htdig is broken      - link to htdig is broken
390    
# Line 454  divide chapter 3 more clearly into 2 sec Line 430  divide chapter 3 more clearly into 2 sec
430          are written.          are written.
431  3.6.1.2 - needs to be moved to inside section 3.6.2  3.6.1.2 - needs to be moved to inside section 3.6.2
432    
 3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18)  
       underneath this one and leave the text for 3.7 in place  
   
433  All the 'overview' sections need some reference to the name of the experiment in  All the 'overview' sections need some reference to the name of the experiment in
434  the verification directory  the verification directory
435    
# Line 490  the verification directory Line 463  the verification directory
463  3.20.1 - link to doc at end of section points to this section  3.20.1 - link to doc at end of section points to this section
464  3.20.2 - link to doc at end of section points to this section  3.20.2 - link to doc at end of section points to this section
465    
466  >>>> from JM       offline - duplicate inputs, what is it, tidy up cfc v.
467                   other offline. JM thinks these need tidying up.
   
   
 manual, section.2 :  
   
 In general:  
 - add more refences/links to S/R & variable name  
 - would be nice to have an active link to the fortran-file  
   for all the S/R & eq.Number in the "calling-tree" boxes  
 - search for CALC_MOM_RHS and replace it by the appropriate S/R  
   (mom_flux_form, mom_vecinv, dynamics)  
 - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})  
 was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}  
 in section.2, \vec{\bf v} is used instead and 3.D velocity vector is  
 simply written \vec{v}.  
 I would suggest to keep the notation as they are (since they are consistent  
 inside each section) but may be to move the "notation.tex" piece  
 at the beginning of section.2 and to mention clearly the changes between  
 the 2 sections.  
   
 in content: Horizontal Dissipation: 2 times in vector-invariant section  
468    
469  2.1 time-stepping (part2/time_stepping.tex)  Which of the following are which tutorial?
470    adjustment.128x64x1
471    adjustment.cs-32x32x1
472    advect_cs
473    advect_xy
474    advect_xz
475    aim.5l_cs
476    aim.5l_Equatorial_Channel
477    aim.5l_LatLon
478    biogeo
479    bottom_ctrl_5x5
480    cfc_example
481    cpl_aim+ocn
482    dome
483    exp2
484    exp4
485    exp5
486    fizhi-cs-32x32x10
487    fizhi-cs-aqualev20
488    fizhi-gridalt-hs
489    flt_example
490    front_relax
491    global1x1_tot
492    global2x2_tot
493    global_ocean.90x40x15
494    global_ocean.cs32x15
495    global_ocean.cubed32x32x30
496    global_ocean_ebm
497    global_with_exf
498    hs94.128x64x5
499    hs94.1x64x5
500    hs94.cs-32x32x5
501    ideal_2D_oce
502    internal_wave
503    inverted_barometer
504    lab_sea
505    matrix_example
506    MLAdjust
507    natl_box
508    natl_box_adjoint
509    OpenAD
510    rotating_tank
511    solid-body.cs-32x32x1
512    tidal_basin_2d
513    tutorial_baroclinic_gyre
514    tutorial_barotropic_gyre
515    tutorial_cfc_offline
516    tutorial_deep_convection
517    tutorial_global_oce_biogeo
518    tutorial_global_oce_in_p
519    tutorial_global_oce_latlon
520    tutorial_global_oce_optim
521    tutorial_held_suarez_cs
522    tutorial_offline
523    tutorial_plume_on_slope
524    tutorial_tracer_adjsens
525    vermix
526    
527  - this is not clear to me:  >>>> From Ed
528    
529  >> In all the above configurations it is also possible to substitute the  Here are the remaining bits for Chap 4 :
 >> Adams-Bashforth with an alternative time-stepping scheme for terms  
 >> evaluated explicitly in time  
530    
531     - missing references (if you point me towards URLs, I'll add them
532       to the bibliography):
533         \ref{ref hoe and hill, ecmwf}
534         \ref{magicgarden}
535         \ref{IBMLAPI}
536         \ref{Memorychannel}
537         \ref{hoe-hill:99}
538    
539  2.2 rigid-lid:   - There are a few empty sub-sections at the end of Chap 4 that
540       should either be commented out or fleshed out.
541    
542  - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"  and thats about it for Chap 4.
   to stay closer to the code.  
 - mention section 2.5 implicit-Time-stepping (for vertical viscosity)  
543    
 2.3 linear free-surface:  
 - add ref(+link) to S/R names:  
 - add ref(+link) to Crank-Nickelson section 2.9.1  
544    
545  2.4 Adams-Bashforth  Add more to quick links on front page
 - add stability diagrams (I have some figures that I can put)  
 - add link for var. forcing_In_AB  
 - add S/R link for S/R ADAMS_BASHFORTH2  
   
 2.5 Implicit time-stepping  
 - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R  
         SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL  
 - update: also used for vertical advection  
546    
547  2.6 Synchronous time-stepping:  Chapter 6
 - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,    
                    MOMENTUM_CORRECTION_STEP.  
548    
549  2.7 Stagger baroclinic time-stepping     the master package diagram does not appear in the document
 - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end  
550    
551  2.8 NH  Master list of packages (add this to beginning of chap 6)
 - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D  
552    
553  2.9 Variants on Free-Surface  admtlm/               - autodiff (chapter 5)
554  - Delta.t mis-written (eq.2.73)  aim/                  - retired
555  - Eq.Num missing (has been fixed since)  aim_compon_interf/    - 6.6 (no content yet)(Daniel + JM)
556  - u* is stored in gU (and not in gUnm1)  aim_ocn_coupler/      - 6.6 (no content yet)
557  - Phi_nh in NH_VARS.h  aim_v23/              - 6.4.1 (content needs fixing - JM to do)
558  - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,  atm_common/           - nothing in this package (6.4.1 related)
559    INI_CG2D, INI_CG3D  autodiff/             - autodiff (chapter 5)
560    bulk_force/           - 6.3.3
561  2.9.1 Crank-Nickelson  cal/                  - 6.3.5
562  - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater  cd_code/              - chapter 2 (JM check add a reference to paper,
563                              mention parameter in data)
564  2.9.2 NLFS  cfc/                  - not sure  (CNH to talk to Steph and Helen)
565  - eq.Nb are wrong in html  chronos/              - AM to check (not being used - Andrea to kill it)
566  - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)  compon_communic/      - 6.6 (no content yet)(Daniel + JM)
567    cost/                 - not sure, check with PH
568    ctrl/                 - not sure, check with PH
569    debug/                - JM may do something in chapter 7 (utilities)
570    diagnostics/          - 7.1
571    dic/                  - 6.7.2
572    ebm/                  - (check with PH)
573    ecco/                 - chapter 8
574    embed_files/          - add something to chapter 7
575    exch2/                - 6.2.2
576    exf/                  - 6.3.4
577    fizhi/                - 6.4.3
578    flt/                  - (PH check)
579    gchem/                - 6.7.1
580    generic_advdiff/      - in chapter 2 (JM check)
581    ggl90/                - nothing, (Martin?)
582    gmredi/               - in chapter 2 (JM check). also need
583                            Ferrari & Mc transition zone stuff (Samar doing this)
584                            get dfer to read this
585    grdchk/               - grdchk (chapter 5 - check with PH)
586    gridalt/              - 6.2.4
587    kpp/                  - 6.3.2
588    land/                 - 6.4.2 (not connected to code Rong's notes - JM to fix)
589    matrix/               - Samar
590    mdsio/                - 7.3.1
591    mnc/                  - 7.2.1
592    mom_common/           - in chapter 2 (JM check)
593    mom_fluxform/         - in chapter 2 (JM check)
594    mom_vecinv/           - in chapter 2 (JM check)
595    monitor/              - 7.4
596    my82/                 - nothing, (martin?)
597    obcs/                 - 6.3 (needs a check - ask PH to read)
598    ocn_compon_interf/    - 6.6 (no content yet)
599    offline/              - nothing, tutorials that need work but no package   section entry
600                            trivial to document (CNH to do)
601    opps/                 - nothing, (martin?)
602    pp81/                 - nothing, (martin?)
603    profiles/             - GAEL
604    ptracers/             - JM + SD + Martin to write something (nothing for this
605                              at the moment)
606                            AM has diagnostics table for this.
607    rbcs/                 - CNH to talk to steph
608    runclock/             - runclock - CNH
609    rw/                   - not sure - going to stay says JMC. quick IO calls
610                            JMC to write a quick note for that.
611    sbo/                  - text in sbo_descruption.tex but not linked into
612                            part6 - CNH
613    seaice/               - 6.5.2 - no equations, dimitris has promised some
614    shap_filt/            - chapter 2, JM to check
615    shelfice/             - nothing yet (martin?)
616    solver/               - empty (go away?)
617    sphere/               - chapter 5 or 8 (PH to check)
618    therm_seaice/         - empty (go away?)
619    thsice/               - 6.5.1 (JM to update?)
620    timeave/              - retiring......
621    zonal_filt/           - chapter 2 (JM to check)
622    
623  2.10.1 Notation  list an expeiment which uses package? CNH
 - Area definition is not really used like this  
624    
625  >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)  6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
626     Figure 6.8 is missing
627    
   Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to  
   the model variables) are used (e.g., see section 2.10.5)  
628    
629  2.10.5 Horizontal grid:  =====  Chapter 7  =====  [EH3 editing] :
 - fig.2.8 : should use Aw,As consistently in this figure description,  
   in the figure itself, as it is in the text.  
 - curvilinear:  
   to add: mention the angle of the grid direction relative to  
   Eastward, Northward direction.  
   + mention horizGridFile= in file "data" (PARM04)  
 - add cylindrical grid description  
630    
631  2.11 Continuity & Horizontal Pressure gradient terms  7.1.1 - links to section 7.1.4: the text of the first
632   - mention that d.Phi/dr|s =g if using z coordinate          one should read "see MITgcm Kernel Diagnostics Menu"
633   - eq. 2.90 not clear regarding \delta_k(P-E)          the links are pointing to the proper place
  better to add the free surface eq: d.eta/dt = w_s + P-E  
634    
635  2.12 Hydrostatic balance  7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
  - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002  
    is hard to find  
  - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)  
     and in section 1.3.4: remove the 1.3.4.3.2 subsection:  
                        Quasi-nonhydrostatic Atmosphere  
636    
637  2.13.2 Coriolis terms  7.5.2 - get bathymetry pre-processing stuff from Patrick
638   - note: the discretization used when useEnergyConservingCoriolis=T            and then describe it
    has no hFac and no Area and is still different from the form  
    described here (with Area & hFac);  
639    
 2.13.5 Lateral dissipation  
  - add description of how to use cosFactor & cosPower  
  - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4  
640    
641  2.13.6 Vertical dissipation  andrea
  - mention the implicit vertical viscosity option and ref to section 2.5  
  - add the parameter correspondence: Av <-> viscAr (and might change also  
    the notation to Ar)  
642    
 2.14 Vector invariant momentum equations  
  - indicate that the NH pieces (vertical momentum eq) are not yet coded  
    and that the NH code uses the flux form.  
643    
644  2.14.6 Horizontal dissipation -> Horizontal Divergence  9. Publications using MITgcm --> "Previous Applications of MITgcm"
645       Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
646       (check in support for more names)
647    
648  2.14.7 Horizontal dissipation  10. Under development
  - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ    
    and A_D4,A_z4 <-> viscA4D,viscA4Z  
649    
650  2.16 & 2.17 & 2.18 :  Constantinos LCML
  - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options  
651    
 2.20.2 mercator, non-dimensional Equations:  
 - does not use std notation  
 - would be better as an appendix of section 2.20:  
 (e.g changing the tile to:  
  Appendix: non-dimensional Equations on Spherical-Polar grid.)  
652    
653  JM  Bibliography
654    
655     tidy up from misc - .tex

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