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revision 1.5 by edhill, Thu Apr 6 19:06:45 2006 UTC revision 1.27 by cnh, Thu Apr 6 20:57:57 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     - need to reference the smag/leith section.
324    
325    2.13.6 Vertical dissipation
326     - mention the implicit vertical viscosity option and ref to section 2.5
327     - add the parameter correspondence: Av <-> viscAr (and might change also
328       the notation to Ar)
329    
330    2.14 Vector invariant momentum equations
331     - indicate that the NH pieces (vertical momentum eq) are not yet coded
332       and that the NH code uses the flux form.
333    
334    2.14.6 Horizontal dissipation -> Horizontal Divergence
335    
336    2.14.7 Horizontal dissipation
337     - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ  
338       and A_D4,A_z4 <-> viscA4D,viscA4Z
339    
340    2.16 & 2.17 & 2.18 :
341     - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
342    
343    2.20.2 mercator, non-dimensional Equations:
344    - does not use std notation
345    - would be better as an appendix of section 2.20:
346    (e.g changing the tile to:
347    - talk to Baylor
348     Appendix: non-dimensional Equations on Spherical-Polar grid.)
349    
350    
351    JM
352    
 andrea  
353    
354  >>>> From Andrea  >>>> From Andrea
355    
# Line 408  Almost all of the 'math mode' text is dr Line 361  Almost all of the 'math mode' text is dr
361  divide chapter 3 more clearly into 2 sections?  divide chapter 3 more clearly into 2 sections?
362     (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and     (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and
363      then 3.19 and 3.20 are informational again - rearrange subsections?)      then 3.19 and 3.20 are informational again - rearrange subsections?)
364    [DONE]
365    
366  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)
367      - link to htdig is broken      - link to htdig is broken
# Line 490  the verification directory Line 444  the verification directory
444  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
445  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
446    
447  >>>> from JM       offline - duplicate inputs, what is it, tidy up cfc v.
448                   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  
   
 2.1 time-stepping (part2/time_stepping.tex)  
449    
450  - this is not clear to me:  Which of the following are which tutorial?
451    ! MLAdjust
452    adjust_nlfs.cs-32x32x1
453    aim.5l_XZ_Equatorial_Slice
454    biogeo
455    aim.5l_zon-ave
456    coupled_ucla
457    cfc_offline
458    exp3
459    global2x2_tot
460    global1x1_tot
461    global_ocean.cubed_wEXF
462    global_with_CFC11
463    goz
464    gop
465    natl_box_obcs
466    natl_box_forward
467    spinup_optim
468    tutorial_held_suarez_cs
469    vero
470    inverted_barometer
471    global_ocean.cubed32x32x30
472    exp1
473    advect_cs
474    dic_example
475    fizhi-gridalt-hs
476    global_ocean_pressure
477    matrix_example
478    exp4
479    solid-body.cs-32x32x1
480    cfc_example
481    flt_example
482    adjustment.cs-32x32x1
483    advect_xz
484    rotating_tank
485    ideal_2D_oce
486    global_ocean.90x40x15
487    front_relax
488    aim.5l_LatLon
489    lab_sea
490    hs94.cs-32x32x5
491    global_with_exf
492    exp2
493    tidal_basin_2d
494    fizhi-cs-32x32x10
495    exp5
496    global_ocean.cs32x15
497    OpenAD
498    hs94.1x64x5
499    fizhi-cs-aqualev10
500    exp0
501    dome
502    aim.5l_Equatorial_Channel
503    aim.5l_cs
504    hs94.128x64x5
505    prm
506    carbon
507    plume_on_slope
508    natl_box_adjoint
509    vermix
510    cpl_aim+ocn
511    global_ocean_ebm
512    internal_wave
513    advect_xy
514    natl_box
515    adjustment.128x64x1
516    
517  >> In all the above configurations it is also possible to substitute the  >>>> From Ed
 >> Adams-Bashforth with an alternative time-stepping scheme for terms  
 >> evaluated explicitly in time  
518    
519    Here are the remaining bits for Chap 4 :
520    
521  2.2 rigid-lid:   - missing references (if you point me towards URLs, I'll add them
522       to the bibliography):
523         \ref{ref hoe and hill, ecmwf}
524         \ref{magicgarden}
525         \ref{IBMLAPI}
526         \ref{Memorychannel}
527         \ref{hoe-hill:99}
528    
529  - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"   - There are a few empty sub-sections at the end of Chap 4 that
530    to stay closer to the code.     should either be commented out or fleshed out.
 - mention section 2.5 implicit-Time-stepping (for vertical viscosity)  
531    
532  2.3 linear free-surface:  and thats about it for Chap 4.
 - add ref(+link) to S/R names:  
 - add ref(+link) to Crank-Nickelson section 2.9.1  
533    
 2.4 Adams-Bashforth  
 - 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  
534    
535  2.5 Implicit time-stepping  Add more to quick links on front page
 - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R  
         SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL  
 - update: also used for vertical advection  
536    
537  2.6 Synchronous time-stepping:  Chapter 6
 - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,    
                    MOMENTUM_CORRECTION_STEP.  
538    
539  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  
540    
541  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  
542    
543  2.9 Variants on Free-Surface  admtlm/               - autodiff (chapter 5)
544  - Delta.t mis-written (eq.2.73)  aim/                  - retired
545  - Eq.Num missing (has been fixed since)  aim_compon_interf/    - 6.6 (no content yet)(Daniel + JM)
546  - u* is stored in gU (and not in gUnm1)  aim_ocn_coupler/      - 6.6 (no content yet)
547  - Phi_nh in NH_VARS.h  aim_v23/              - 6.4.1 (content needs fixing - JM to do)
548  - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,  atm_common/           - nothing in this package (6.4.1 related)
549    INI_CG2D, INI_CG3D  autodiff/             - autodiff (chapter 5)
550    bulk_force/           - 6.3.3
551    cal/                  - 6.3.5
552    cd_code/              - chapter 2 (JM check add a reference to paper,
553                              mention parameter in data)
554    cfc/                  - not sure  (CNH to talk to Steph and Helen)
555    chronos/              - AM to check (not being used - Andrea to kill it)
556    compon_communic/      - 6.6 (no content yet)(Daniel + JM)
557    cost/                 - not sure, check with PH
558    ctrl/                 - not sure, check with PH
559    debug/                - JM may do something in chapter 7 (utilities)
560    diagnostics/          - 7.1
561    dic/                  - 6.7.2
562    ebm/                  - (check with PH)
563    ecco/                 - chapter 8
564    embed_files/          - add something to chapter 7
565    exch2/                - 6.2.2
566    exf/                  - 6.3.4
567    fizhi/                - 6.4.3
568    flt/                  - (PH check)
569    gchem/                - 6.7.1
570    generic_advdiff/      - in chapter 2 (JM check)
571    ggl90/                - nothing, (Martin?)
572    gmredi/               - in chapter 2 (JM check). also need
573                            Ferrari & Mc transition zone stuff (Samar doing this)
574                            get dfer to read this
575    grdchk/               - grdchk (chapter 5 - check with PH)
576    gridalt/              - 6.2.4
577    kpp/                  - 6.3.2
578    land/                 - 6.4.2 (not connected to code Rong's notes - JM to fix)
579    matrix/               - Samar
580    mdsio/                - 7.3.1
581    mnc/                  - 7.2.1
582    mom_common/           - in chapter 2 (JM check)
583    mom_fluxform/         - in chapter 2 (JM check)
584    mom_vecinv/           - in chapter 2 (JM check)
585    monitor/              - 7.4
586    my82/                 - nothing, (martin?)
587    obcs/                 - 6.3 (needs a check - ask PH to read)
588    ocn_compon_interf/    - 6.6 (no content yet)
589    offline/              - nothing, tutorials that need work but no package   section entry
590                            trivial to document (CNH to do)
591    opps/                 - nothing, (martin?)
592    pp81/                 - nothing, (martin?)
593    profiles/             - GAEL
594    ptracers/             - JM + SD + Martin to write something (nothing for this
595                              at the moment)
596                            AM has diagnostics table for this.
597    rbcs/                 - CNH to talk to steph
598    runclock/             - runclock - CNH
599    rw/                   - not sure - going to stay says JMC. quick IO calls
600                            JMC to write a quick note for that.
601    sbo/                  - text in sbo_descruption.tex but not linked into
602                            part6 - CNH
603    seaice/               - 6.5.2 - no equations, dimitris has promised some
604    shap_filt/            - chapter 2, JM to check
605    shelfice/             - nothing yet (martin?)
606    solver/               - empty (go away?)
607    sphere/               - chapter 5 or 8 (PH to check)
608    therm_seaice/         - empty (go away?)
609    thsice/               - 6.5.1 (JM to update?)
610    timeave/              - retiring......
611    zonal_filt/           - chapter 2 (JM to check)
612    
613  2.9.1 Crank-Nickelson  list an expeiment which uses package? CNH
 - 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)  
614    
615  2.10.1 Notation  [DONE]Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
 - Area definition is not really used like this  
616    
617  >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)  6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
618     Figure 6.8 is missing
619    
   Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to  
   the model variables) are used (e.g., see section 2.10.5)  
620    
621  2.10.5 Horizontal grid:  >>>> From Andrea
 - 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  
622    
623  2.11 Continuity & Horizontal Pressure gradient terms  to do list for chap 7:
  - 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  
624    
 2.12 Hydrostatic balance  
  - 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  
625    
626  2.13.2 Coriolis terms  7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"
627   - note: the discretization used when useEnergyConservingCoriolis=T            the links are pointing to the proper place
    has no hFac and no Area and is still different from the form  
    described here (with Area & hFac);  
628    
629  2.13.5 Lateral dissipation  7.5.1 - add Graphix to the list of stuff in utils/matlab
630   - add description of how to use cosFactor & cosPower  7.5.2 - empty
  - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4  
631    
 2.13.6 Vertical dissipation  
  - 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)  
632    
633  2.14 Vector invariant momentum equations  andrea
  - indicate that the NH pieces (vertical momentum eq) are not yet coded  
    and that the NH code uses the flux form.  
634    
 2.14.6 Horizontal dissipation -> Horizontal Divergence  
635    
636  2.14.7 Horizontal dissipation  9. Publications using MITgcm
637   - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ       Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
638     and A_D4,A_z4 <-> viscA4D,viscA4Z     (check in support for more names)
639    
640  2.16 & 2.17 & 2.18 :  10. Under development
  - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options  
641    
 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.)  
642    
643  JM  Bibliography
644    
645     tidy up from misc - .tex

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