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revision 1.5 by edhill, Thu Apr 6 19:06:45 2006 UTC revision 1.14 by edhill, Thu Apr 6 20:14:48 2006 UTC
# Line 3  Rebuild and set to do cron build - DONE Line 3  Rebuild and set to do cron build - DONE
3  To do  To do
4    
5    - where to put under development links?    - where to put under development links?
6        JMC would like to have some mention of unfinished things (checked in
7         but not that tested e.g. AB3)
8        Add an "Under development, chapter" - shortish description of what
9        is available (last chapter)
10    
11    - mitgcm.org very front page.  
12      o too many clicks to get to model manual.  o HTML, scripts and front content
13        make doc link go to mitgcm.org/r2_web_testing/latest  
14        and add "HowTo" reference etc... to /latest page    - pick a URL
15        TBD
16    
17    - mitgcm.org/r2_web_testing/latest    - mitgcm.org/r2_web_testing/latest
18      o add another short-cut for quick download      o add another short-cut for quick download
# Line 19  To do Line 24  To do
24        Overview        Overview
25        Tutorials (broken)        Tutorials (broken)
26        Browse Code        Browse Code
27    
28        o mitgcm.org (front content) [DONE]
29        Get Code (where does this go to?)        Get Code (where does this go to?)
30          get rid of * CVS current bullet
31          make HTML-enabled CVS code browser leap to MITgcm/MITgcm
32    
33      o authors      o authors
34        John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,        John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,
35        Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,        Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,
36        Gael - others?        Gael - others?
37    
38      o Tutorials side bar link is broken      o words on http://mitgcm.org/r2_web_testing/latest
39          change to
40      o words         "access on-line Auser manual/A and Atable of contents/A
41        change to "access on-line Auser manual/A and Atable of contents/A          and browse the Aoverview section/A"
       and browse the Aoverview section/A"  
42    
43      o finite-volume doesn't leap to FV figure      o finite-volume doesn't leap to FV figure
44    
45      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.  
46    
47      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.  
48    
49    o Latex  
50    
51  Contents      Chapter 1                 - CNH
   
     Intro                  - CNH  
52        o single kernel diagram -        o single kernel diagram -
53            add reference to MWR paper            add reference to MWR paper
54    
# Line 109  Contents Line 113  Contents
113    
114        o Kinematic boundary conditions        o Kinematic boundary conditions
115    
116        o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms        o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
117          need to tidy up discussion of shallow-atmosphere to be          Non-hydrostatic forms
118          consistent with the code or change code to be consistent           need to tidy up discussion of shallow-atmosphere to be
119          with the discussion!           consistent with the code or change code to be consistent
120          make references hyperlinks           with the discussion!
121          add stuff too           make references hyperlinks
122             add stuff too
123             JMC remove QNH atmosphere
124             need to sort out calc_gw for deep atmosphere
125    
126        o Finding the pressure field        o Finding the pressure field
127          make references hyperlinks           make references hyperlinks
128          add forward references to manual algorithm section           add forward references to manual algorithm section
129          change Elliptic to "elliptic"           change Elliptic to "elliptic"
130    
131        o Forcing and dissipation        o Forcing and dissipation
132          make "physics packages" refer to chapter 6.           make "physics packages" refer to chapter 6.
133          should we move "external forcing" et. al to a           should we move "external forcing" et. al to a
134          generic_forcing_driver package?           generic_forcing_driver package?
135    
136          viscosities          viscosities
137          update to mention Smag/Leith (Ah and A4 not constant)           update to mention Smag/Leith (Ah and A4 not constant)
138          and to have forward references to numerical section           and to have forward references to numerical section
139          tracers           tracers
140          forward references to numerical section, reddy, GM etc...           forward references to numerical section, reddy, GM etc...
141          add references to literature           add references to literature
142    
143        o 1.3.8 Vector invariant form        o 1.3.8 Vector invariant form
144          forward references to numerical section          forward references to numerical section
# Line 157  Contents Line 164  Contents
164          PH to do something          PH to do something
165    
166    
     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  
   
167      Change hydrodynamical to "dynamical"      Change hydrodynamical to "dynamical"
168    
169      Examples      Examples
# Line 271  Chapter 1 Line 201  Chapter 1
201    
202            o Gas giant?            o Gas giant?
203    
 Chapter 6  
204    
205     the master package diagram does not appear in the document  >>>> from JM
206    
    pkg/ptracers doesn't seem to have any documentation (see packages list below)  
207    
208    manual, section.2 :
209    
210    In general:
211    - add more refences/links to S/R & variable name
212    - would be nice to have an active link to the fortran-file
213      for all the S/R & eq.Number in the "calling-tree" boxes
214    - search for CALC_MOM_RHS and replace it by the appropriate S/R
215      (mom_flux_form, mom_vecinv, dynamics)
216    - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
217    was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
218    in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
219    simply written \vec{v}.
220    I would suggest to keep the notation as they are (since they are consistent
221    inside each section) but may be to move the "notation.tex" piece
222    at the beginning of section.2 and to mention clearly the changes between
223    the 2 sections.
224    
225  2.10.5 Horizontal grid  in content: Horizontal Dissipation: 2 times in vector-invariant section
226    
227     need to do a better job of relating model variables to this diagram  2.1 time-stepping (part2/time_stepping.tex)
228    
229    - this is not clear to me:
230    
231  Master list of packages  >> In all the above configurations it is also possible to substitute the
232    >> Adams-Bashforth with an alternative time-stepping scheme for terms
233    >> evaluated explicitly in time
234    
 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)  
235    
236  Possible for chap 7 - Daniels grafix/ stuff  2.2 rigid-lid:
237    
238  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)"
239      to stay closer to the code.
240    - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
241    
242  Figure 6.8 is missing  2.3 linear free-surface:
243    - add ref(+link) to S/R names:
244    - add ref(+link) to Crank-Nickelson section 2.9.1
245    
246    2.4 Adams-Bashforth
247    - add stability diagrams (I have some figures that I can put)
248    - add link for var. forcing_In_AB
249    - add S/R link for S/R ADAMS_BASHFORTH2
250    
251  >>>> From Ed  2.5 Implicit time-stepping
252    - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
253            SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
254    - update: also used for vertical advection
255    
256  Here are the remaining bits for Chap 4 :  2.6 Synchronous time-stepping:
257    - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,  
258                       MOMENTUM_CORRECTION_STEP.
259    
260   - The grammar/flow could still use some work.  Boo was an English  2.7 Stagger baroclinic time-stepping
261     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.  
262    
263   - missing references (if you point me towards URLs, I'll add them  2.8 NH
264     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}  
265    
266   - There are a few empty sub-sections at the end of Chap 4 that  2.9 Variants on Free-Surface
267     should either be commented out or fleshed out.  - Delta.t mis-written (eq.2.73)
268    - Eq.Num missing (has been fixed since)
269    - u* is stored in gU (and not in gUnm1)
270    - Phi_nh in NH_VARS.h
271    - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
272      INI_CG2D, INI_CG3D
273    
274  and thats about it for Chap 4.  2.9.1 Crank-Nickelson
275    - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
276    
277    2.9.2 NLFS
278    - eq.Nb are wrong in html
279    - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
280    
281    2.10.1 Notation
282    - Area definition is not really used like this
283    
284  Add more to quick links on front page  >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
285    
286      Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
287      the model variables) are used (e.g., see section 2.10.5)
288    
289  >>>> From Andrea  2.10.5 Horizontal grid:
290    - fig.2.8 : should use Aw,As consistently in this figure description,
291      in the figure itself, as it is in the text.
292    - curvilinear:
293      to add: mention the angle of the grid direction relative to
294      Eastward, Northward direction.
295      + mention horizGridFile= in file "data" (PARM04)
296    - add cylindrical polar grid description
297       need to do a better job of relating model variables to this diagram
298    
 to do list for chap 7:  
299    
300    2.11 Continuity & Horizontal Pressure gradient terms
301     - mention that d.Phi/dr|s =g if using z coordinate
302     - eq. 2.90 not clear regarding \delta_k(P-E)
303     better to add the free surface eq: d.eta/dt = w_s + P-E
304    
305  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
306          the links are pointing to the proper place   - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
307       is hard to find
308     - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
309        and in section 1.3.4: remove the 1.3.4.3.2 subsection:
310                           Quasi-nonhydrostatic Atmosphere
311    
312  7.5.1 - add Graphix to the list of stuff in utils/matlab  2.13.2 Coriolis terms
313  7.5.2 - empty   - note: the discretization used when useEnergyConservingCoriolis=T  
314       has no hFac and no Area and is still different from the form
315       described here (with Area & hFac);
316    
317    2.13.5 Lateral dissipation
318     - add description of how to use cosFactor & cosPower
319     - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
320        o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
321          in code need to explain why cos()3/2 turns out to be
322          scaling (not cos()2)
323    
324    2.13.6 Vertical dissipation
325     - mention the implicit vertical viscosity option and ref to section 2.5
326     - add the parameter correspondence: Av <-> viscAr (and might change also
327       the notation to Ar)
328    
329    2.14 Vector invariant momentum equations
330     - indicate that the NH pieces (vertical momentum eq) are not yet coded
331       and that the NH code uses the flux form.
332    
333    2.14.6 Horizontal dissipation -> Horizontal Divergence
334    
335    2.14.7 Horizontal dissipation
336     - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ  
337       and A_D4,A_z4 <-> viscA4D,viscA4Z
338    
339    2.16 & 2.17 & 2.18 :
340     - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
341    
342    2.20.2 mercator, non-dimensional Equations:
343    - does not use std notation
344    - would be better as an appendix of section 2.20:
345    (e.g changing the tile to:
346    - talk to Baylor
347     Appendix: non-dimensional Equations on Spherical-Polar grid.)
348    
349    
350    JM
351    
 andrea  
352    
353  >>>> From Andrea  >>>> From Andrea
354    
# Line 490  the verification directory Line 442  the verification directory
442  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
443  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
444    
445  >>>> from JM       offline - duplicate inputs, what is it, tidy up cfc v.
446                   other offline. JM thinks these need tidying up.
447    >>>> From Ed
   
 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  
   
 2.1 time-stepping (part2/time_stepping.tex)  
   
 - this is not clear to me:  
   
 >> In all the above configurations it is also possible to substitute the  
 >> Adams-Bashforth with an alternative time-stepping scheme for terms  
 >> evaluated explicitly in time  
448    
449    Here are the remaining bits for Chap 4 :
450    
451  2.2 rigid-lid:   - The grammar/flow could still use some work.  Boo was an English
452       major and has experience editing/proofing technical papers.  I
453       could print out a copy and ask her to read it and suggest
454       improvements.
455    
456  - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"   - missing references (if you point me towards URLs, I'll add them
457    to stay closer to the code.     to the bibliography):
458  - mention section 2.5 implicit-Time-stepping (for vertical viscosity)       \ref{ref hoe and hill, ecmwf}
459         \ref{magicgarden}
460         \ref{IBMLAPI}
461         \ref{Memorychannel}
462         \ref{hoe-hill:99}
463    
464  2.3 linear free-surface:   - There are a few empty sub-sections at the end of Chap 4 that
465  - add ref(+link) to S/R names:     should either be commented out or fleshed out.
 - add ref(+link) to Crank-Nickelson section 2.9.1  
466    
467  2.4 Adams-Bashforth  and thats about it for Chap 4.
 - 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  
468    
 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  
469    
470  2.6 Synchronous time-stepping:  Add more to quick links on front page
 - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,    
                    MOMENTUM_CORRECTION_STEP.  
471    
472  2.7 Stagger baroclinic time-stepping  Chapter 6
 - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end  
473    
474  2.8 NH     the master package diagram does not appear in the document
 - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D  
475    
476  2.9 Variants on Free-Surface     pkg/ptracers doesn't seem to have any documentation (see packages list below)
 - Delta.t mis-written (eq.2.73)  
 - Eq.Num missing (has been fixed since)  
 - u* is stored in gU (and not in gUnm1)  
 - Phi_nh in NH_VARS.h  
 - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,  
   INI_CG2D, INI_CG3D  
477    
 2.9.1 Crank-Nickelson  
 - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater  
   
 2.9.2 NLFS  
 - eq.Nb are wrong in html  
 - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)  
478    
479  2.10.1 Notation  Master list of packages (add this to beginning of chap 6)
 - Area definition is not really used like this  
480    
481  >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)  admtlm/               - autodiff (chapter 5)
482    aim/                  - retired
483    aim_compon_interf/    - 6.6 (no content yet)
484    aim_ocn_coupler/      - 6.6 (no content yet)
485    aim_v23/              - 6.4.1 (content needs fixing - JM to do)
486    atm_common/           - 6.6 (no content yet)
487    autodiff/             - autodiff (chapter 5)
488    bulk_force/           - 6.3.3
489    cal/                  - 6.3.5
490    cd_code/              - chapter 2 (JM check)
491    cfc/                  - not sure
492    chronos/              - AM to check
493    compon_communic/      - 6.6 (no content yet)
494    cost/                 - not sure, check with PH
495    ctrl/                 - not sure, check with PH
496    debug/                - JM may do something in chapter 7 (utilities)
497    diagnostics/          - 7.1
498    dic/                  - 6.7.2
499    ebm/                  - not sure
500    ecco/                 - chapter 8
501    embed_files/          - add something to chapter 7
502    ex3/                  - rename to exch3
503    exch2/                - 6.2.2
504    exf/                  - 6.3.4
505    fizhi/                - 6.4.3
506    flt/                  - in chapter 2 (JM check)
507    gchem/                - 6.7.1
508    generic_advdiff/      - in chapter 2 (JM check)
509    ggl90/                - nothing, (Martin?)
510    gmredi/               - in chapter 2 (JM check). also need
511                            Ferrari & Mc tapering
512    grdchk/               - grdchk (chapter 5 - check with PH)
513    gridalt/              - 6.2.4
514    kpp/                  - 6.3.2
515    land/                 - 6.4.2 (not connected to code - JM to fix)
516    matrix/               - Samar
517    mdsio/                - 7.3.1
518    mnc/                  - 7.2.1
519    mom_common/           - in chapter 2 (JM check)
520    mom_fluxform/         - in chapter 2 (JM check)
521    mom_vecinv/           - in chapter 2 (JM check)
522    monitor/              - 7.4
523    my82/                 - nothing, (martin?)
524    obcs/                 - 6.3 (needs a check)
525    ocn_compon_interf/    - 6.6 (no content yet)
526    offline/              - nothing, tutorials that need work but no package   section entry
527    opps/                 - nothing, (martin?)
528    pp81/                 - nothing, (martin?)
529    profiles/             - GAEL
530    ptracers/             - JM + SD to write something
531    rbcs/                 - talk to steph
532    runclock/             - runclock
533    rw/                   - not sure
534    sbo/                  - text in sbo_descruption.tex but not linked into
535                            part6
536    seaice/               - 6.5.2 - no equations, dimitris has promised some
537    shap_filt/            - chapter 2, JM to check
538    shelfice/             - nothing yet (martin?)
539    solver/               - empty
540    sphere/               - chapter 5 or 8 (PH to check)
541    therm_seaice/         - empty
542    thsice/               - 6.5.1 (JM to update?)
543    timeave/              - retiring......
544    zonal_filt/           - chapter 2 (JM to check)
545    
546    Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to  Possible for chap 7 - Daniels grafix/ stuff
   the model variables) are used (e.g., see section 2.10.5)  
547    
548  2.10.5 Horizontal grid:  Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
 - 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  
549    
550  2.11 Continuity & Horizontal Pressure gradient terms  Figure 6.8 is missing
  - mention that d.Phi/dr|s =g if using z coordinate  
  - eq. 2.90 not clear regarding \delta_k(P-E)  
  better to add the free surface eq: d.eta/dt = w_s + P-E  
551    
552  2.12 Hydrostatic balance  6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
553   - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002   Figure 6.8 is missing
    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  
554    
 2.13.2 Coriolis terms  
  - note: the discretization used when useEnergyConservingCoriolis=T    
    has no hFac and no Area and is still different from the form  
    described here (with Area & hFac);  
555    
556  2.13.5 Lateral dissipation  >>>> From Andrea
  - add description of how to use cosFactor & cosPower  
  - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4  
557    
558  2.13.6 Vertical dissipation  to do list for chap 7:
  - 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)  
559    
 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.  
560    
561  2.14.6 Horizontal dissipation -> Horizontal Divergence  7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"
562            the links are pointing to the proper place
563    
564  2.14.7 Horizontal dissipation  7.5.1 - add Graphix to the list of stuff in utils/matlab
565   - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ    7.5.2 - empty
    and A_D4,A_z4 <-> viscA4D,viscA4Z  
566    
 2.16 & 2.17 & 2.18 :  
  - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options  
567    
568  2.20.2 mercator, non-dimensional Equations:  andrea
 - 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.)  
569    
 JM  
570    
571    9. Model uses
572       Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
573       (check in support for more names)
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