/[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 1.37 by cnh, Wed Jun 28 15:11:42 2006 UTC revision 1.46 by edhill, Sun Jul 2 18:12:45 2006 UTC
# Line 26  Editors Line 26  Editors
26    
27   Biblio        - EH3   Biblio        - EH3
28    
29    
30  Rebuild and set to do cron build - DONE on hugo  Rebuild and set to do cron build - DONE on hugo
31    
32  To do  To do
# Line 42  To do Line 43  To do
43    
44  o HTML, scripts and front content  o HTML, scripts and front content
45    
46    - pick a URL    - pick a URL:  mitgcm.org/r2  <-- EH3's preferred base URL
     TBD  
47    
48    - mitgcm.org/r2_web_testing/latest    - mitgcm.org/r2_web_testing/latest
49      o add another short-cut for quick download      
50        o --DONE--  add another short-cut for quick download
51    
52        o --DONE--  add another short-cut
53                      About
54                      Installation
55                      Contents
56                      Overview
57                      Tutorials (broken)
58                      Browse Code
59    
60        o --DONE--  words on http://mitgcm.org/r2_web_testing/latest change to
61    
62        o --DONE--  finite-volume doesn't leap to FV figure
63    
64      o add another short-cut      o -- DONE ??? --  have another go at pnmcrop et al.
       About  
       Installation  
       Contents  
       Overview  
       Tutorials (broken)  
       Browse Code  
   
     o words on http://mitgcm.org/r2_web_testing/latest  
       change to  
        "access on-line Auser manual/A and Atable of contents/A  
         and browse the Aoverview section/A"  
65    
66      o finite-volume doesn't leap to FV figure           I've tried making a small change in latex2html which fixes
67             the oddball-lower-alignment issue that we were seeing with
68             most in-line expressions (that is, math embedded in text).
69             The fix results in some things being slightly raised but I
70             thin this is more asthetically pleasing than being somewhat
71             lowered as before. --EH3
72    
73      o have another go at pnmcrop et al.           To view the altered alignment, see:
74    
75                http://eddy.csail.mit.edu/r2/latest/
76    
77      o Need an empty package as part of distribution. Check out atm_common      o Need an empty package as part of distribution. Check out atm_common
78    
79    
80  o Latex    o Latex  
81    
82      Chapter 1                 - CNH      Chapter 1                 - CNH
# Line 205  o Latex Line 215  o Latex
215            o coupled aqua, ridge world etc...            o coupled aqua, ridge world etc...
216              - links to ingrid output              - links to ingrid output
217                get stuff from Daniel                get stuff from Daniel
218                  Davids donut movie
219    
220            o constrained lab simulation            o constrained lab simulation
221              - links to ingrid output for model and lab              - links to ingrid output for model and lab
# Line 232  In general: Line 243  In general:
243  - would be nice to have an active link to the fortran-file  - would be nice to have an active link to the fortran-file
244    for all the S/R & eq.Number in the "calling-tree" boxes    for all the S/R & eq.Number in the "calling-tree" boxes
245  - search for CALC_MOM_RHS and replace it by the appropriate S/R  - search for CALC_MOM_RHS and replace it by the appropriate S/R
246    (mom_flux_form, mom_vecinv, dynamics)    (mom_flux_form, mom_vecinv, dynamics) <- DONE
247  - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})  - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
248  was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}  was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
249  in section.2, \vec{\bf v} is used instead and 3.D velocity vector is  in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
# Line 243  at the beginning of section.2 and to men Line 254  at the beginning of section.2 and to men
254  the 2 sections.  the 2 sections.
255    
256  in content: Horizontal Dissipation: 2 times in vector-invariant section  in content: Horizontal Dissipation: 2 times in vector-invariant section
257    <- DONE
258    
259  2.1 time-stepping (part2/time_stepping.tex)  2.1 time-stepping (part2/time_stepping.tex)
260    
# Line 251  in content: Horizontal Dissipation: 2 ti Line 263  in content: Horizontal Dissipation: 2 ti
263  >> In all the above configurations it is also possible to substitute the  >> In all the above configurations it is also possible to substitute the
264  >> Adams-Bashforth with an alternative time-stepping scheme for terms  >> Adams-Bashforth with an alternative time-stepping scheme for terms
265  >> evaluated explicitly in time  >> evaluated explicitly in time
266    <- Leave it general.
267    
268    
269  2.2 rigid-lid:  2.2 rigid-lid:
270    
271  - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"  - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
272    to stay closer to the code.    to stay closer to the code.
273  - mention section 2.5 implicit-Time-stepping (for vertical viscosity)  - mention section 2.5 implicit-Time-stepping (for vertical viscosity) <- DONE
274    
275  2.3 linear free-surface:  2.3 linear free-surface:
276  - add ref(+link) to S/R names:  - add ref(+link) to S/R names:
277  - add ref(+link) to Crank-Nickelson section 2.9.1  - add ref(+link) to Crank-Nickelson section 2.9.1 <- DONE
278    
279  2.4 Adams-Bashforth  2.4 Adams-Bashforth
280  - add stability diagrams (I have some figures that I can put)  - add stability diagrams (I have some figures that I can put) <- DONE
281  - add link for var. forcing_In_AB  - add link for var. forcing_In_AB and epsil_AB <- half DONE
282  - add S/R link for S/R ADAMS_BASHFORTH2  - add S/R link for S/R ADAMS_BASHFORTH2 <-DONE
283    
284  2.5 Implicit time-stepping  2.5 Implicit time-stepping
285  - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R  - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
# Line 284  in content: Horizontal Dissipation: 2 ti Line 297  in content: Horizontal Dissipation: 2 ti
297  - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D  - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
298    
299  2.9 Variants on Free-Surface  2.9 Variants on Free-Surface
300  - Delta.t mis-written (eq.2.73)  - Delta.t mis-written (eq.2.73) <- DONE
301  - Eq.Num missing (has been fixed since)  - Eq.Num missing <- DONE
302  - u* is stored in gU (and not in gUnm1)  - u* is stored in gU (and not in gUnm1) <- DONE
303  - Phi_nh in NH_VARS.h  - Phi_nh in NH_VARS.h <- DONE
304  - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,  - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
305    INI_CG2D, INI_CG3D    INI_CG2D, INI_CG3D
306    
# Line 297  in content: Horizontal Dissipation: 2 ti Line 310  in content: Horizontal Dissipation: 2 ti
310  2.9.2 NLFS  2.9.2 NLFS
311  - eq.Nb are wrong in html  - eq.Nb are wrong in html
312  - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)  - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
313     <- DONE
314    
315  2.10.1 Notation  2.10.1 Notation
316  - Area definition is not really used like this  - Area definition is not really used like this
# Line 305  in content: Horizontal Dissipation: 2 ti Line 319  in content: Horizontal Dissipation: 2 ti
319    
320    Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to    Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
321    the model variables) are used (e.g., see section 2.10.5)    the model variables) are used (e.g., see section 2.10.5)
322    <- DONE
323    
324  2.10.5 Horizontal grid:  2.10.5 Horizontal grid:
325  - fig.2.8 : should use Aw,As consistently in this figure description,  - fig.2.8 : should use Aw,As consistently in this figure description,
326    in the figure itself, as it is in the text.    in the figure itself, as it is in the text. <- DONE
327  - curvilinear:  - curvilinear:
328    to add: mention the angle of the grid direction relative to    to add: mention the angle of the grid direction relative to
329    Eastward, Northward direction.    Eastward, Northward direction.
# Line 359  in content: Horizontal Dissipation: 2 ti Line 374  in content: Horizontal Dissipation: 2 ti
374    
375  2.16 & 2.17 & 2.18 :  2.16 & 2.17 & 2.18 :
376   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
377   - fix equations 2.202 & 2.203 (thanks to Martin)   - fix equations 2.202 & 2.203 (thanks to Martin) <- DONE
378    
379  2.20.2 mercator, non-dimensional Equations:  2.20.2 mercator, non-dimensional Equations:
380  - does not use std notation  - does not use std notation
# Line 367  in content: Horizontal Dissipation: 2 ti Line 382  in content: Horizontal Dissipation: 2 ti
382  (e.g changing the tile to:  (e.g changing the tile to:
383  - talk to Baylor  - talk to Baylor
384   Appendix: non-dimensional Equations on Spherical-Polar grid.)   Appendix: non-dimensional Equations on Spherical-Polar grid.)
385     <- No (Chris said)
386    
387    
388  Diagrams of grid locations etc.... and what variables and output files  Diagrams of grid locations etc.... and what variables and output files
# Line 385  Chapter 3 Line 401  Chapter 3
401    
402  Almost all of the 'math mode' text is dropped down as subscripts  Almost all of the 'math mode' text is dropped down as subscripts
403    
404  3.1 - don't need a link to the outside of the document (remove it)  3.11.3.1 - refers to figures and equations, links are broken
     - link to htdig is broken  
   
 3.2.1 - link at bottom to source code points to section 3.2.1  
    (ie, to itself) - link should point to cvs code archive  
   
 3.2.2.1  - ('upgrading from an earlier version') belongs under  
       the cvs part, ie, should be 3.2.1.1  
405    
406  3.3 - remove reference to 'diags' section under MITgcm  3.12.3.2 - line 43: link to equation is broken
     - remove reference to 'exe' and 'bin' sections also  
       (remove the .cvsignore file under these directories in cvs)  
     - add a 'jobs' section, and a description as examples of run scripts  
     - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions  
     - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'  
     - under 'tools' the adjoint points to section 5 - this is now section 8  
       (but should be a floating reference)  
     - under 'utils' add a reference to exch2 - stuff for different resolutions  
     - the description of the pkg section refers directly to  
       section 3. should be section 6 (actually should be a floating reference)  
   
 3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)  
 3.4.1 - links to the following experiments don't exist or are broken:  
           exp2 - should link to section 3.9  
           hs94.cs-32x32x5 - link to section 3.12  
           add 'convection' to the list, link to section 3.13  
           add 'plume on slope` to the list, link to section 3.14  
           add '??' link to section 3.15  
           add 'dic_example on slope` to the list, link to section 3.16  
           add '??' link to section 3.17  
           add 'offline' and link to section 3.18  
           clean up others and make links where they are needed  
 3.4.2 - text suggests to see section 2 for details about what is in the 'code'  
         and 'input' directories - should refer to the examples in this section  
       - add 'build' bullet - this is where the model is compiled and exectuable lives  
   
 3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options  
       as the place where they live (add a link?)  
   
 3.6.1 - Add some general 'approach' text - ie, output is controlled either by the  
         'data' file in the input directory or by the data.[pkg name] file for any  
         package running. And there is some default behavior when the 'state' dumps  
         are written.  
 3.6.1.2 - needs to be moved to inside section 3.6.2  
   
 All the 'overview' sections need some reference to the name of the experiment in  
 the verification directory  
   
 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript  
      - is this experiment in the list from section 3.4???  
 3.10.3.1 - refers to figures and equations, links are broken  
   
 3.11.3.2 - line 43: link to equation is broken  
407           - line 51-53: link to equation is broken           - line 51-53: link to equation is broken
408           - there is some mess of text hanging around the end of this section. remove? reformat?           - there is some mess of text hanging around the end of this section. remove? reformat?
409    
410  3.12.4.1 - line 34 - link to equation is broken  3.13.4.1 - line 34 - link to equation is broken
411           - lines 60,61 - 1st (take out the 'r' in the superscript)           - lines 60,61 - 1st (take out the 'r' in the superscript)
412    
413  3.13.2 - link to theta-equation is broken  3.14.2 - link to theta-equation is broken
414  3.13.5.4 -- ALL of the bold links to variable names are broken  3.14.5.4 -- ALL of the bold links to variable names are broken
415              line 34: link to equation is broken              line 34: link to equation is broken
416    
 3.15.1 - reference to 'fourth experiment' should be removed  
   
 3.16.4 - strange formatting, presence of '>' symbols - remove them  
   
 3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4  
 3.17.3.1 - nothing filled in under file input/data - needs description  
   
 3.18.2 - point to section 2 for details - need hyperlink  
   
 3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!  
          section 3.5 has the 'build' directory in the example  
   
 3.20.1 - 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  
   
      offline - duplicate inputs, what is it, tidy up cfc v.  
                other offline. JM thinks these need tidying up.  
   
 Which of the following are which tutorial?  
 adjustment.128x64x1  
 adjustment.cs-32x32x1  
 advect_cs  
 advect_xy  
 advect_xz  
 aim.5l_cs  
 aim.5l_Equatorial_Channel  
 aim.5l_LatLon  
 biogeo  
 bottom_ctrl_5x5  
 cfc_example  
 cpl_aim+ocn  
 dome  
 exp2  
 exp4  
 exp5  
 fizhi-cs-32x32x10  
 fizhi-cs-aqualev20  
 fizhi-gridalt-hs  
 flt_example  
 front_relax  
 global1x1_tot  
 global2x2_tot  
 global_ocean.90x40x15  
 global_ocean.cs32x15  
 global_ocean.cubed32x32x30  
 global_ocean_ebm  
 global_with_exf  
 hs94.128x64x5  
 hs94.1x64x5  
 hs94.cs-32x32x5  
 ideal_2D_oce  
 internal_wave  
 inverted_barometer  
 lab_sea  
 matrix_example  
 MLAdjust  
 natl_box  
 natl_box_adjoint  
 OpenAD  
 rotating_tank  
 solid-body.cs-32x32x1  
 tidal_basin_2d  
 tutorial_baroclinic_gyre  
 tutorial_barotropic_gyre  
 tutorial_cfc_offline  
 tutorial_deep_convection  
 tutorial_global_oce_biogeo  
 tutorial_global_oce_in_p  
 tutorial_global_oce_latlon  
 tutorial_global_oce_optim  
 tutorial_held_suarez_cs  
 tutorial_offline  
 tutorial_plume_on_slope  
 tutorial_tracer_adjsens  
 vermix  
   
417  >>>> From Ed  >>>> From Ed
418    
419  Here are the remaining bits for Chap 4 :  Here are the remaining bits for Chap 4 :
# Line 628  list an expeiment which uses package? CN Line 518  list an expeiment which uses package? CN
518    
519  =====  Chapter 7  =====  [EH3 editing] :  =====  Chapter 7  =====  [EH3 editing] :
520    
521  7.1.x - JMC: please add description of:   + JMC: please add description of:
522          - diagstat          - diagstat
523          - new temporal averaging feature          - new temporal averaging feature
524    
525  7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)   + add Graphix to the list of stuff in utils/matlab (Daniel)
526    
527     + get bathymetry pre-processing stuff from Patrick and then describe it
528    
529  7.5.2 - get bathymetry pre-processing stuff from Patrick   + add something on spgrid mesh generator
         and then describe it  
530    
531  add something on spgrid mesh generator (maybe)?   + add in gmaze PV calculation scripts plus write up on how it is calculated
532         http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/
533    
534    
535  andrea  andrea
Legend:
Removed from v.1.37  
changed lines
  Added in v.1.46
  ViewVC Help
Powered by ViewVC 1.1.22