/[MITgcm]/manual/manual_todo.txt
ViewVC logotype

Diff of /manual/manual_todo.txt

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.9 by cnh, Thu Apr 6 19:54:06 2006 UTC revision 1.14 by edhill, Thu Apr 6 20:14:48 2006 UTC
# Line 14  o HTML, scripts and front content Line 14  o HTML, scripts and front content
14    - pick a URL    - pick a URL
15      TBD      TBD
16    
   - mitgcm.org very front page.  
     o too many clicks to get to model manual.  
       make doc link go to mitgcm.org/r2_web_testing/latest  
       and add "HowTo" reference etc... to /latest page  
   
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
19    
# Line 207  o Latex Line 202  o Latex
202            o Gas giant?            o Gas giant?
203    
204    
205  Master list of packages  >>>> from JM
206    
 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)  
207    
208  Possible for chap 7 - Daniels grafix/ stuff  manual, section.2 :
209    
210  Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.  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  Figure 6.8 is missing  in content: Horizontal Dissipation: 2 times in vector-invariant section
226    
227    2.1 time-stepping (part2/time_stepping.tex)
228    
229  >>>> From Ed  - this is not clear to me:
230    
231  Here are the remaining bits for Chap 4 :  >> 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    
  - The grammar/flow could still use some work.  Boo was an English  
    major and has experience editing/proofing technical papers.  I  
    could print out a copy and ask her to read it and suggest  
    improvements.  
235    
236   - missing references (if you point me towards URLs, I'll add them  2.2 rigid-lid:
    to the bibliography):  
      \ref{ref hoe and hill, ecmwf}  
      \ref{magicgarden}  
      \ref{IBMLAPI}  
      \ref{Memorychannel}  
      \ref{hoe-hill:99}  
237    
238   - There are a few empty sub-sections at the end of Chap 4 that  - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
239     should either be commented out or fleshed out.    to stay closer to the code.
240    - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
241    
242  and thats about it for Chap 4.  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  Add more to quick links on front page  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  Chapter 6  2.6 Synchronous time-stepping:
257    - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,  
258                       MOMENTUM_CORRECTION_STEP.
259    
260     the master package diagram does not appear in the document  2.7 Stagger baroclinic time-stepping
261    - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
262    
263     pkg/ptracers doesn't seem to have any documentation (see packages list below)  2.8 NH
264    - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
265    
266    2.9 Variants on Free-Surface
267    - 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  >>>> From Andrea  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  to do list for chap 7:  2.10.1 Notation
282    - Area definition is not really used like this
283    
284    >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
285    
286  7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"    Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
287          the links are pointing to the proper place    the model variables) are used (e.g., see section 2.10.5)
288    
289  7.5.1 - add Graphix to the list of stuff in utils/matlab  2.10.5 Horizontal grid:
290  7.5.2 - empty  - 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    
299    
300  andrea  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    2.12 Hydrostatic balance
306     - 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    2.13.2 Coriolis terms
313     - 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    
352    
353  >>>> From Andrea  >>>> From Andrea
354    
# Line 421  the verification directory Line 444  the verification directory
444    
445       offline - duplicate inputs, what is it, tidy up cfc v.       offline - duplicate inputs, what is it, tidy up cfc v.
446                 other offline. JM thinks these need tidying up.                 other offline. JM thinks these need tidying up.
447    >>>> From Ed
448    
449  >>>> from JM  Here are the remaining bits for Chap 4 :
   
   
   
 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  
   
   
 2.2 rigid-lid:  
   
 - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"  
   to stay closer to the code.  
 - mention section 2.5 implicit-Time-stepping (for vertical viscosity)  
450    
451  2.3 linear free-surface:   - The grammar/flow could still use some work.  Boo was an English
452  - add ref(+link) to S/R names:     major and has experience editing/proofing technical papers.  I
453  - add ref(+link) to Crank-Nickelson section 2.9.1     could print out a copy and ask her to read it and suggest
454       improvements.
455    
456  2.4 Adams-Bashforth   - missing references (if you point me towards URLs, I'll add them
457  - add stability diagrams (I have some figures that I can put)     to the bibliography):
458  - add link for var. forcing_In_AB       \ref{ref hoe and hill, ecmwf}
459  - add S/R link for S/R ADAMS_BASHFORTH2       \ref{magicgarden}
460         \ref{IBMLAPI}
461         \ref{Memorychannel}
462         \ref{hoe-hill:99}
463    
464  2.5 Implicit time-stepping   - There are a few empty sub-sections at the end of Chap 4 that
465  - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R     should either be commented out or fleshed out.
         SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL  
 - update: also used for vertical advection  
466    
467  2.6 Synchronous time-stepping:  and thats about it for Chap 4.
 - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,    
                    MOMENTUM_CORRECTION_STEP.  
468    
 2.7 Stagger baroclinic time-stepping  
 - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end  
469    
470  2.8 NH  Add more to quick links on front page
 - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D  
471    
472  2.9 Variants on Free-Surface  Chapter 6
 - 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  
473    
474  2.9.1 Crank-Nickelson     the master package diagram does not appear in the document
 - 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)  
475    
476  2.10.1 Notation     pkg/ptracers doesn't seem to have any documentation (see packages list below)
 - Area definition is not really used like this  
477    
 >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)  
478    
479    Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to  Master list of packages (add this to beginning of chap 6)
   the model variables) are used (e.g., see section 2.10.5)  
480    
481  2.10.5 Horizontal grid:  admtlm/               - autodiff (chapter 5)
482  - fig.2.8 : should use Aw,As consistently in this figure description,  aim/                  - retired
483    in the figure itself, as it is in the text.  aim_compon_interf/    - 6.6 (no content yet)
484  - curvilinear:  aim_ocn_coupler/      - 6.6 (no content yet)
485    to add: mention the angle of the grid direction relative to  aim_v23/              - 6.4.1 (content needs fixing - JM to do)
486    Eastward, Northward direction.  atm_common/           - 6.6 (no content yet)
487    + mention horizGridFile= in file "data" (PARM04)  autodiff/             - autodiff (chapter 5)
488  - add cylindrical grid description  bulk_force/           - 6.3.3
489     need to do a better job of relating model variables to this diagram  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    Possible for chap 7 - Daniels grafix/ stuff
547    
548  2.11 Continuity & Horizontal Pressure gradient terms  Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
  - 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  
549    
550  2.12 Hydrostatic balance  Figure 6.8 is missing
  - 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  
551    
552  2.13.2 Coriolis terms  6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
553   - note: the discretization used when useEnergyConservingCoriolis=T     Figure 6.8 is missing
    has no hFac and no Area and is still different from the form  
    described here (with Area & hFac);  
554    
 2.13.5 Lateral dissipation  
  - add description of how to use cosFactor & cosPower  
  - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4  
     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)  
555    
556  2.13.6 Vertical dissipation  >>>> From 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)  
557    
558  2.14 Vector invariant momentum equations  to do list for chap 7:
  - indicate that the NH pieces (vertical momentum eq) are not yet coded  
    and that the NH code uses the flux form.  
559    
 2.14.6 Horizontal dissipation -> Horizontal Divergence  
560    
561  2.14.7 Horizontal dissipation  7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"
562   - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ            the links are pointing to the proper place
    and A_D4,A_z4 <-> viscA4D,viscA4Z  
563    
564  2.16 & 2.17 & 2.18 :  7.5.1 - add Graphix to the list of stuff in utils/matlab
565   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options  7.5.2 - empty
566    
 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.)  
567    
568  JM  andrea
569    
570    
571  9. Model uses  9. Model uses

Legend:
Removed from v.1.9  
changed lines
  Added in v.1.14

  ViewVC Help
Powered by ViewVC 1.1.22