--- manual/manual_todo.txt 2006/06/28 18:59:04 1.42 +++ manual/manual_todo.txt 2008/01/17 17:35:59 1.50 @@ -26,6 +26,7 @@ Biblio - EH3 + Rebuild and set to do cron build - DONE on hugo To do @@ -42,31 +43,40 @@ 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 add another short-cut - 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" + o --DONE-- finite-volume doesn't leap to FV figure - o finite-volume doesn't leap to FV figure + o -- DONE ??? -- have another go at pnmcrop et al. - o have another go at pnmcrop et al. + 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 + + To view the altered alignment, see: + + 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 @@ -255,21 +265,24 @@ >> evaluated explicitly in time <- Leave it general. + o Time-stepping outline + - what gets called when + 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 @@ -391,19 +404,31 @@ Almost all of the 'math mode' text is dropped down as subscripts -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 + o Update basic intro with one and four layer gyres + - include advection options + - conservation analysis + - diagnostics + + o Four degree adjoint + - both TAF and OpenAD based. + + o Coupled with biogeo setup + - based on CCGS setup + + >>>> From Ed Here are the remaining bits for Chap 4 : @@ -426,9 +451,12 @@ Chapter 6 - the master package diagram does not appear in the document + update organigramme + - include rbcs + (<- needs an update: e.g. atm2d, salt_plume, shelfice ...) Master list of packages (add this to beginning of chap 6) + (<- needs an update: e.g. atm2d, salt_plume, shelfice ...) admtlm/ - autodiff (chapter 5) aim/ - retired @@ -455,6 +483,8 @@ exch2/ - 6.2.2 exf/ - 6.3.4 fizhi/ - 6.4.3 + o Including FIZHI doc + - get things up to date flt/ - (PH check) gchem/ - 6.7.1 generic_advdiff/ - in chapter 2 (JM check) @@ -500,6 +530,10 @@ timeave/ - retiring...... zonal_filt/ - chapter 2 (JM to check) + o Cost function packages + - floats, weights, profiles etc... + + list an expeiment which uses package? CNH 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 @@ -508,16 +542,26 @@ ===== Chapter 7 ===== [EH3 editing] : -7.1.x - JMC: please add description of: + + JMC: please add description of: - diagstat - new temporal averaging feature -7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel) + + update the RW / MDSIO description + -> new meta file + -> list all RW S/R that one should use instead of calling directly MDSIO + + + add Graphix to the list of stuff in utils/matlab (Daniel) + + + get bathymetry pre-processing stuff from Patrick and then describe it + + + add something on spgrid mesh generator + o Grid generation + - more explanation and some step-by-step examples + - plotting grid examples -7.5.2 - get bathymetry pre-processing stuff from Patrick - and then describe it -add something on spgrid mesh generator (maybe)? + + 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 @@ -530,8 +574,22 @@ 10. Under development Constantinos LCML + o Legend/LCML examples and explanation + - examples and explanation! + Bibliography tidy up from misc - .tex + +Also + +a link to the new manual +should appear on the front page (even if it's under construction). + +updating: +http://mitgcm.org/r2_web_testing/latest/code_reference/callTree.html +which points to a 1.5 years old code. Would be good to generate a +new one, and even better, to try to keep it up-to-date. +