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revision 1.5 by edhill, Thu Apr 6 19:06:45 2006 UTC revision 1.12 by cnh, Thu Apr 6 20:12:55 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    
12    o HTML, scripts and front content
13    
14      - pick a URL
15        TBD
16    
17    - mitgcm.org very front page.    - mitgcm.org very front page.
18      o too many clicks to get to model manual.      o too many clicks to get to model manual.
# Line 19  To do Line 29  To do
29        Overview        Overview
30        Tutorials (broken)        Tutorials (broken)
31        Browse Code        Browse Code
32    
33        o mitgcm.org (front content) [DONE]
34        Get Code (where does this go to?)        Get Code (where does this go to?)
35          get rid of * CVS current bullet
36          make HTML-enabled CVS code browser leap to MITgcm/MITgcm
37    
38      o authors      o authors
39        John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,        John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,
40        Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,        Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,
41        Gael - others?        Gael - others?
42    
43      o Tutorials side bar link is broken      o words on http://mitgcm.org/r2_web_testing/latest
44          change to
45      o words         "access on-line Auser manual/A and Atable of contents/A
46        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"  
47    
48      o finite-volume doesn't leap to FV figure      o finite-volume doesn't leap to FV figure
49    
50      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.  
   
     o degree symbols keep getting "dropped down" - problem with  
       pnmcrop et al.  
51    
52        o Need an empty package as part of distribution. Check out atm_common
53    
54  Contents  o Latex  
55    
56      Intro                  - CNH      Chapter 1                 - CNH
57        o single kernel diagram -        o single kernel diagram -
58            add reference to MWR paper            add reference to MWR paper
59    
# Line 109  Contents Line 118  Contents
118    
119        o Kinematic boundary conditions        o Kinematic boundary conditions
120    
121        o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms        o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
122          need to tidy up discussion of shallow-atmosphere to be          Non-hydrostatic forms
123          consistent with the code or change code to be consistent           need to tidy up discussion of shallow-atmosphere to be
124          with the discussion!           consistent with the code or change code to be consistent
125          make references hyperlinks           with the discussion!
126          add stuff too           make references hyperlinks
127             add stuff too
128             JMC remove QNH atmosphere
129             need to sort out calc_gw for deep atmosphere
130    
131        o Finding the pressure field        o Finding the pressure field
132          make references hyperlinks           make references hyperlinks
133          add forward references to manual algorithm section           add forward references to manual algorithm section
134          change Elliptic to "elliptic"           change Elliptic to "elliptic"
135    
136        o Forcing and dissipation        o Forcing and dissipation
137          make "physics packages" refer to chapter 6.           make "physics packages" refer to chapter 6.
138          should we move "external forcing" et. al to a           should we move "external forcing" et. al to a
139          generic_forcing_driver package?           generic_forcing_driver package?
140    
141          viscosities          viscosities
142          update to mention Smag/Leith (Ah and A4 not constant)           update to mention Smag/Leith (Ah and A4 not constant)
143          and to have forward references to numerical section           and to have forward references to numerical section
144          tracers           tracers
145          forward references to numerical section, reddy, GM etc...           forward references to numerical section, reddy, GM etc...
146          add references to literature           add references to literature
147    
148        o 1.3.8 Vector invariant form        o 1.3.8 Vector invariant form
149          forward references to numerical section          forward references to numerical section
# Line 157  Contents Line 169  Contents
169          PH to do something          PH to do something
170    
171    
     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  
   
172      Change hydrodynamical to "dynamical"      Change hydrodynamical to "dynamical"
173    
174      Examples      Examples
# Line 271  Chapter 1 Line 206  Chapter 1
206    
207            o Gas giant?            o Gas giant?
208    
 Chapter 6  
209    
210     the master package diagram does not appear in the document  >>>> from JM
211    
    pkg/ptracers doesn't seem to have any documentation (see packages list below)  
212    
213    manual, section.2 :
214    
215    In general:
216    - add more refences/links to S/R & variable name
217    - would be nice to have an active link to the fortran-file
218      for all the S/R & eq.Number in the "calling-tree" boxes
219    - search for CALC_MOM_RHS and replace it by the appropriate S/R
220      (mom_flux_form, mom_vecinv, dynamics)
221    - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
222    was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
223    in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
224    simply written \vec{v}.
225    I would suggest to keep the notation as they are (since they are consistent
226    inside each section) but may be to move the "notation.tex" piece
227    at the beginning of section.2 and to mention clearly the changes between
228    the 2 sections.
229    
230  2.10.5 Horizontal grid  in content: Horizontal Dissipation: 2 times in vector-invariant section
231    
232     need to do a better job of relating model variables to this diagram  2.1 time-stepping (part2/time_stepping.tex)
233    
234    - this is not clear to me:
235    
236  Master list of packages  >> In all the above configurations it is also possible to substitute the
237    >> Adams-Bashforth with an alternative time-stepping scheme for terms
238    >> evaluated explicitly in time
239    
 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)  
240    
241  Possible for chap 7 - Daniels grafix/ stuff  2.2 rigid-lid:
242    
243  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)"
244      to stay closer to the code.
245    - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
246    
247  Figure 6.8 is missing  2.3 linear free-surface:
248    - add ref(+link) to S/R names:
249    - add ref(+link) to Crank-Nickelson section 2.9.1
250    
251    2.4 Adams-Bashforth
252    - add stability diagrams (I have some figures that I can put)
253    - add link for var. forcing_In_AB
254    - add S/R link for S/R ADAMS_BASHFORTH2
255    
256  >>>> From Ed  2.5 Implicit time-stepping
257    - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
258            SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
259    - update: also used for vertical advection
260    
261  Here are the remaining bits for Chap 4 :  2.6 Synchronous time-stepping:
262    - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,  
263                       MOMENTUM_CORRECTION_STEP.
264    
265   - The grammar/flow could still use some work.  Boo was an English  2.7 Stagger baroclinic time-stepping
266     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.  
267    
268   - missing references (if you point me towards URLs, I'll add them  2.8 NH
269     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}  
270    
271   - There are a few empty sub-sections at the end of Chap 4 that  2.9 Variants on Free-Surface
272     should either be commented out or fleshed out.  - Delta.t mis-written (eq.2.73)
273    - Eq.Num missing (has been fixed since)
274    - u* is stored in gU (and not in gUnm1)
275    - Phi_nh in NH_VARS.h
276    - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
277      INI_CG2D, INI_CG3D
278    
279  and thats about it for Chap 4.  2.9.1 Crank-Nickelson
280    - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
281    
282    2.9.2 NLFS
283    - eq.Nb are wrong in html
284    - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
285    
286    2.10.1 Notation
287    - Area definition is not really used like this
288    
289  Add more to quick links on front page  >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
290    
291      Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
292      the model variables) are used (e.g., see section 2.10.5)
293    
294  >>>> From Andrea  2.10.5 Horizontal grid:
295    - fig.2.8 : should use Aw,As consistently in this figure description,
296      in the figure itself, as it is in the text.
297    - curvilinear:
298      to add: mention the angle of the grid direction relative to
299      Eastward, Northward direction.
300      + mention horizGridFile= in file "data" (PARM04)
301    - add cylindrical grid description
302       need to do a better job of relating model variables to this diagram
303    
 to do list for chap 7:  
304    
305    2.11 Continuity & Horizontal Pressure gradient terms
306     - mention that d.Phi/dr|s =g if using z coordinate
307     - eq. 2.90 not clear regarding \delta_k(P-E)
308     better to add the free surface eq: d.eta/dt = w_s + P-E
309    
310    2.12 Hydrostatic balance
311     - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
312       is hard to find
313     - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
314        and in section 1.3.4: remove the 1.3.4.3.2 subsection:
315                           Quasi-nonhydrostatic Atmosphere
316    
317  7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"  2.13.2 Coriolis terms
318          the links are pointing to the proper place   - note: the discretization used when useEnergyConservingCoriolis=T  
319       has no hFac and no Area and is still different from the form
320       described here (with Area & hFac);
321    
322  7.5.1 - add Graphix to the list of stuff in utils/matlab  2.13.5 Lateral dissipation
323  7.5.2 - empty   - add description of how to use cosFactor & cosPower
324     - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
325        o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
326          in code need to explain why cos()3/2 turns out to be
327          scaling (not cos()2)
328    
329    2.13.6 Vertical dissipation
330     - mention the implicit vertical viscosity option and ref to section 2.5
331     - add the parameter correspondence: Av <-> viscAr (and might change also
332       the notation to Ar)
333    
334    2.14 Vector invariant momentum equations
335     - indicate that the NH pieces (vertical momentum eq) are not yet coded
336       and that the NH code uses the flux form.
337    
338    2.14.6 Horizontal dissipation -> Horizontal Divergence
339    
340    2.14.7 Horizontal dissipation
341     - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ  
342       and A_D4,A_z4 <-> viscA4D,viscA4Z
343    
344    2.16 & 2.17 & 2.18 :
345     - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
346    
347    2.20.2 mercator, non-dimensional Equations:
348    - does not use std notation
349    - would be better as an appendix of section 2.20:
350    (e.g changing the tile to:
351    - talk to Baylor
352     Appendix: non-dimensional Equations on Spherical-Polar grid.)
353    
354    
355    JM
356    
 andrea  
357    
358  >>>> From Andrea  >>>> From Andrea
359    
# Line 490  the verification directory Line 447  the verification directory
447  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
448  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
449    
450  >>>> from JM       offline - duplicate inputs, what is it, tidy up cfc v.
451                   other offline. JM thinks these need tidying up.
452    >>>> 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  
453    
454    Here are the remaining bits for Chap 4 :
455    
456  2.2 rigid-lid:   - The grammar/flow could still use some work.  Boo was an English
457       major and has experience editing/proofing technical papers.  I
458       could print out a copy and ask her to read it and suggest
459       improvements.
460    
461  - 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
462    to stay closer to the code.     to the bibliography):
463  - mention section 2.5 implicit-Time-stepping (for vertical viscosity)       \ref{ref hoe and hill, ecmwf}
464         \ref{magicgarden}
465         \ref{IBMLAPI}
466         \ref{Memorychannel}
467         \ref{hoe-hill:99}
468    
469  2.3 linear free-surface:   - There are a few empty sub-sections at the end of Chap 4 that
470  - 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  
471    
472  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  
473    
 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  
474    
475  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.  
476    
477  2.7 Stagger baroclinic time-stepping  Chapter 6
 - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end  
478    
479  2.8 NH     the master package diagram does not appear in the document
 - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D  
480    
481  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  
482    
 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)  
483    
484  2.10.1 Notation  Master list of packages (add this to beginning of chap 6)
 - Area definition is not really used like this  
485    
486  >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)  admtlm/               - autodiff (chapter 5)
487    aim/                  - retired
488    aim_compon_interf/    - 6.6 (no content yet)
489    aim_ocn_coupler/      - 6.6 (no content yet)
490    aim_v23/              - 6.4.1 (content needs fixing - JM to do)
491    atm_common/           - 6.6 (no content yet)
492    autodiff/             - autodiff (chapter 5)
493    bulk_force/           - 6.3.3
494    cal/                  - 6.3.5
495    cd_code/              - chapter 2 (JM check)
496    cfc/                  - not sure
497    chronos/              - AM to check
498    compon_communic/      - 6.6 (no content yet)
499    cost/                 - not sure, check with PH
500    ctrl/                 - not sure, check with PH
501    debug/                - JM may do something in chapter 7 (utilities)
502    diagnostics/          - 7.1
503    dic/                  - 6.7.2
504    ebm/                  - not sure
505    ecco/                 - chapter 8
506    embed_files/          - add something to chapter 7
507    ex3/                  - rename to exch3
508    exch2/                - 6.2.2
509    exf/                  - 6.3.4
510    fizhi/                - 6.4.3
511    flt/                  - in chapter 2 (JM check)
512    gchem/                - 6.7.1
513    generic_advdiff/      - in chapter 2 (JM check)
514    ggl90/                - nothing, (Martin?)
515    gmredi/               - in chapter 2 (JM check). also need
516                            Ferrari & Mc tapering
517    grdchk/               - grdchk (chapter 5 - check with PH)
518    gridalt/              - 6.2.4
519    kpp/                  - 6.3.2
520    land/                 - 6.4.2 (not connected to code - JM to fix)
521    matrix/               - Samar
522    mdsio/                - 7.3.1
523    mnc/                  - 7.2.1
524    mom_common/           - in chapter 2 (JM check)
525    mom_fluxform/         - in chapter 2 (JM check)
526    mom_vecinv/           - in chapter 2 (JM check)
527    monitor/              - 7.4
528    my82/                 - nothing, (martin?)
529    obcs/                 - 6.3 (needs a check)
530    ocn_compon_interf/    - 6.6 (no content yet)
531    offline/              - nothing, tutorials that need work but no package   section entry
532    opps/                 - nothing, (martin?)
533    pp81/                 - nothing, (martin?)
534    profiles/             - GAEL
535    ptracers/             - JM + SD to write something
536    rbcs/                 - talk to steph
537    runclock/             - runclock
538    rw/                   - not sure
539    sbo/                  - text in sbo_descruption.tex but not linked into
540                            part6
541    seaice/               - 6.5.2 - no equations, dimitris has promised some
542    shap_filt/            - chapter 2, JM to check
543    shelfice/             - nothing yet (martin?)
544    solver/               - empty
545    sphere/               - chapter 5 or 8 (PH to check)
546    therm_seaice/         - empty
547    thsice/               - 6.5.1 (JM to update?)
548    timeave/              - retiring......
549    zonal_filt/           - chapter 2 (JM to check)
550    
551    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)  
552    
553  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  
554    
555  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  
556    
557  2.12 Hydrostatic balance  6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
558   - 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  
559    
 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);  
560    
561  2.13.5 Lateral dissipation  >>>> From Andrea
  - add description of how to use cosFactor & cosPower  
  - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4  
562    
563  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)  
564    
 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.  
565    
566  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"
567            the links are pointing to the proper place
568    
569  2.14.7 Horizontal dissipation  7.5.1 - add Graphix to the list of stuff in utils/matlab
570   - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ    7.5.2 - empty
    and A_D4,A_z4 <-> viscA4D,viscA4Z  
571    
 2.16 & 2.17 & 2.18 :  
  - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options  
572    
573  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.)  
574    
 JM  
575    
576    9. Model uses
577       Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
578       (check in support for more names)
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