--- manual/manual_todo.txt 2006/06/27 22:34:55 1.36 +++ manual/manual_todo.txt 2006/07/02 18:12:45 1.46 @@ -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 --DONE-- finite-volume doesn't leap to FV figure - 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 ??? -- have another go at pnmcrop et al. - o finite-volume doesn't leap to FV figure + 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 have another go at pnmcrop et al. + 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 @@ -205,6 +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 @@ -232,7 +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 @@ -243,6 +254,7 @@ the 2 sections. in content: Horizontal Dissipation: 2 times in vector-invariant section +<- DONE 2.1 time-stepping (part2/time_stepping.tex) @@ -251,22 +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 @@ -284,10 +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 @@ -297,6 +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 @@ -305,10 +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. @@ -359,7 +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) + - fix equations 2.202 & 2.203 (thanks to Martin) <- DONE 2.20.2 mercator, non-dimensional Equations: - does not use std notation @@ -367,6 +382,7 @@ (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 @@ -385,145 +401,19 @@ Almost all of the 'math mode' text is dropped down as subscripts -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 +3.11.3.1 - refers to figures and equations, links are broken -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 - -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 +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? -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 - >>>> From Ed Here are the remaining bits for Chap 4 : @@ -628,14 +518,18 @@ ===== 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) + + 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 -7.5.2 - get bathymetry pre-processing stuff from Patrick - and then describe it + + 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