--- manual/manual_todo.txt 2006/04/06 20:49:14 1.20 +++ manual/manual_todo.txt 2006/07/02 18:12:45 1.46 @@ -1,3 +1,32 @@ +Editors + + Overall - JM, AM, PH, CNH, EH3 + + Front content - EH3 + + Chapter 1 - CNH + + Chapter 2 - JMC + + Chapter 3 - AM + + Chapter 4 - CNH + + Chapter 5 - PH + + Chapter 6 - AM + + Chapter 7 - EH3 + + Chapter 8 - PH + + Chapter 9 - CNH (Applications) + + Chapter 10 - JMC (Under development chapter) + + Biblio - EH3 + + Rebuild and set to do cron build - DONE on hugo To do @@ -8,44 +37,46 @@ Add an "Under development, chapter" - shortish description of what is available (last chapter) + - add in example latex for formatting author names in different pieces. + this aknowledges peoples contributions and gives ref for who + to talk to. o HTML, scripts and front content - - pick a URL - TBD + - pick a URL: mitgcm.org/r2 <-- EH3's preferred base URL - mitgcm.org/r2_web_testing/latest - o add another short-cut for quick download + + o --DONE-- add another short-cut for quick download + + o --DONE-- add another short-cut + About + Installation + Contents + Overview + Tutorials (broken) + Browse Code + + o --DONE-- words on http://mitgcm.org/r2_web_testing/latest change to + + o --DONE-- finite-volume doesn't leap to FV figure + + o -- DONE ??? -- have another go at pnmcrop et al. - o add another short-cut - About - Installation - Contents - Overview - Tutorials (broken) - Browse Code - - o mitgcm.org (front content) [DONE] - Get Code (where does this go to?) - get rid of * CVS current bullet - make HTML-enabled CVS code browser leap to MITgcm/MITgcm - - o authors - John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen, - Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos, - Gael - others? - - 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" + I've tried making a small change in latex2html which fixes + the oddball-lower-alignment issue that we were seeing with + most in-line expressions (that is, math embedded in text). + The fix results in some things being slightly raised but I + thin this is more asthetically pleasing than being somewhat + lowered as before. --EH3 - o finite-volume doesn't leap to FV figure + To view the altered alignment, see: - o have another go at pnmcrop et al. + http://eddy.csail.mit.edu/r2/latest/ o Need an empty package as part of distribution. Check out atm_common + o Latex Chapter 1 - CNH @@ -67,7 +98,6 @@ o List of key papers needs to be updated and reformatted - o Global atmosphere: `Held Suarez', update Adcroft reference fix up ingrid link and frame (ingrid movies seem to be broken?) @@ -185,6 +215,7 @@ o coupled aqua, ridge world etc... - links to ingrid output get stuff from Daniel + Davids donut movie o constrained lab simulation - links to ingrid output for model and lab @@ -212,7 +243,7 @@ - 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) + (mom_flux_form, mom_vecinv, dynamics) <- DONE - 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 @@ -223,6 +254,7 @@ the 2 sections. in content: Horizontal Dissipation: 2 times in vector-invariant section +<- DONE 2.1 time-stepping (part2/time_stepping.tex) @@ -231,22 +263,23 @@ >> 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 +<- Leave it general. 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) +- mention section 2.5 implicit-Time-stepping (for vertical viscosity) <- DONE 2.3 linear free-surface: - add ref(+link) to S/R names: -- add ref(+link) to Crank-Nickelson section 2.9.1 +- add ref(+link) to Crank-Nickelson section 2.9.1 <- DONE 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 +- add stability diagrams (I have some figures that I can put) <- DONE +- add link for var. forcing_In_AB and epsil_AB <- half DONE +- add S/R link for S/R ADAMS_BASHFORTH2 <-DONE 2.5 Implicit time-stepping - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R @@ -264,10 +297,10 @@ - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D 2.9 Variants on Free-Surface -- 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 +- Delta.t mis-written (eq.2.73) <- DONE +- Eq.Num missing <- DONE +- u* is stored in gU (and not in gUnm1) <- DONE +- Phi_nh in NH_VARS.h <- DONE - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D, INI_CG2D, INI_CG3D @@ -277,6 +310,7 @@ 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) + <- DONE 2.10.1 Notation - Area definition is not really used like this @@ -285,10 +319,11 @@ Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to the model variables) are used (e.g., see section 2.10.5) +<- DONE 2.10.5 Horizontal grid: - fig.2.8 : should use Aw,As consistently in this figure description, - in the figure itself, as it is in the text. + in the figure itself, as it is in the text. <- DONE - curvilinear: to add: mention the angle of the grid direction relative to Eastward, Northward direction. @@ -339,6 +374,7 @@ 2.16 & 2.17 & 2.18 : - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options + - fix equations 2.202 & 2.203 (thanks to Martin) <- DONE 2.20.2 mercator, non-dimensional Equations: - does not use std notation @@ -346,6 +382,13 @@ (e.g changing the tile to: - talk to Baylor Appendix: non-dimensional Equations on Spherical-Polar grid.) + <- No (Chris said) + + +Diagrams of grid locations etc.... and what variables and output files +and/or netcdf variable names are not very easy to figure out and follow. +It would be good to redo and extend these diagrams and align with GRID.h +content. JM @@ -358,162 +401,19 @@ Almost all of the 'math mode' text is dropped down as subscripts -divide chapter 3 more clearly into 2 sections? - (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and - then 3.19 and 3.20 are informational again - rearrange subsections?) -[DONE] - -3.1 - don't need a link to the outside of the document (remove it) - - 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 - -3.3 - remove reference to 'diags' section under MITgcm - - 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 - -3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18) - underneath this one and leave the text for 3.7 in place - -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 +3.11.3.1 - refers to figures and equations, links are broken -3.11.3.2 - line 43: link to equation is broken +3.12.3.2 - line 43: link to equation is broken - line 51-53: link to equation is broken - there is some mess of text hanging around the end of this section. remove? reformat? -3.12.4.1 - line 34 - link to equation is broken +3.13.4.1 - line 34 - link to equation is broken - lines 60,61 - 1st (take out the 'r' in the superscript) -3.13.2 - link to theta-equation is broken -3.13.5.4 -- ALL of the bold links to variable names are broken +3.14.2 - link to theta-equation is broken +3.14.5.4 -- ALL of the bold links to variable names are broken line 34: link to equation is broken -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? -! MLAdjust -adjust_nlfs.cs-32x32x1 -aim.5l_XZ_Equatorial_Slice -biogeo -aim.5l_zon-ave -coupled_ucla -cfc_offline -exp3 -global2x2_tot -global1x1_tot -global_ocean.cubed_wEXF -global_with_CFC11 -goz -gop -natl_box_obcs -natl_box_forward -spinup_optim -tutorial_held_suarez_cs -vero -inverted_barometer -global_ocean.cubed32x32x30 -exp1 -advect_cs -dic_example -fizhi-gridalt-hs -global_ocean_pressure -matrix_example -exp4 -solid-body.cs-32x32x1 -cfc_example -flt_example -adjustment.cs-32x32x1 -advect_xz -rotating_tank -ideal_2D_oce -global_ocean.90x40x15 -front_relax -aim.5l_LatLon -lab_sea -hs94.cs-32x32x5 -global_with_exf -exp2 -tidal_basin_2d -fizhi-cs-32x32x10 -exp5 -global_ocean.cs32x15 -OpenAD -hs94.1x64x5 -fizhi-cs-aqualev10 -exp0 -dome -aim.5l_Equatorial_Channel -aim.5l_cs -hs94.128x64x5 -prm -carbon -plume_on_slope -natl_box_adjoint -vermix -cpl_aim+ocn -global_ocean_ebm -internal_wave -advect_xy -natl_box -adjustment.128x64x1 - >>>> From Ed Here are the remaining bits for Chap 4 : @@ -596,46 +496,54 @@ AM has diagnostics table for this. rbcs/ - CNH to talk to steph runclock/ - runclock - CNH -rw/ - not sure - going to stay says JMC +rw/ - not sure - going to stay says JMC. quick IO calls + JMC to write a quick note for that. sbo/ - text in sbo_descruption.tex but not linked into - part6 + part6 - CNH seaice/ - 6.5.2 - no equations, dimitris has promised some shap_filt/ - chapter 2, JM to check shelfice/ - nothing yet (martin?) -solver/ - empty +solver/ - empty (go away?) sphere/ - chapter 5 or 8 (PH to check) -therm_seaice/ - empty +therm_seaice/ - empty (go away?) thsice/ - 6.5.1 (JM to update?) timeave/ - retiring...... zonal_filt/ - chapter 2 (JM to check) list an expeiment which uses package? CNH -Possible for chap 7 - Daniels grafix/ stuff - -Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started. - -Figure 6.8 is missing - 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 Figure 6.8 is missing ->>>> From Andrea +===== Chapter 7 ===== [EH3 editing] : -to do list for chap 7: + + JMC: please add description of: + - diagstat + - new temporal averaging feature + + add Graphix to the list of stuff in utils/matlab (Daniel) -7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu" - the links are pointing to the proper place + + get bathymetry pre-processing stuff from Patrick and then describe it -7.5.1 - add Graphix to the list of stuff in utils/matlab -7.5.2 - empty + + add something on spgrid mesh generator + + + add in gmaze PV calculation scripts plus write up on how it is calculated + http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/ andrea -9. Model uses +9. Publications using MITgcm --> "Previous Applications of MITgcm" Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... (check in support for more names) + +10. Under development + +Constantinos LCML + + +Bibliography + + tidy up from misc - .tex