--- manual/manual_todo.txt 2006/04/06 19:54:06 1.9 +++ manual/manual_todo.txt 2006/04/06 20:57:41 1.26 @@ -14,11 +14,6 @@ - pick a URL TBD - - 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 - - mitgcm.org/r2_web_testing/latest o add another short-cut for quick download @@ -207,225 +202,9 @@ o Gas giant? -Master list of packages - -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) - -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 - - ->>>> From Ed - -Here are the remaining bits for Chap 4 : - - - 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. - - - missing references (if you point me towards URLs, I'll add them - to the bibliography): - \ref{ref hoe and hill, ecmwf} - \ref{magicgarden} - \ref{IBMLAPI} - \ref{Memorychannel} - \ref{hoe-hill:99} - - - There are a few empty sub-sections at the end of Chap 4 that - should either be commented out or fleshed out. - -and thats about it for Chap 4. - - -Add more to quick links on front page - -Chapter 6 - - the master package diagram does not appear in the document - - pkg/ptracers doesn't seem to have any documentation (see packages list below) - - ->>>> From Andrea - -to do list for chap 7: - - -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 - -7.5.1 - add Graphix to the list of stuff in utils/matlab -7.5.2 - empty - - -andrea - ->>>> From Andrea - -Chapter 3 --------- - -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?) - -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 - -3.11.3.2 - 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 - - 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 - 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. - >>>> from JM - manual, section.2 : In general: @@ -514,7 +293,7 @@ to add: mention the angle of the grid direction relative to Eastward, Northward direction. + mention horizGridFile= in file "data" (PARM04) -- add cylindrical grid description +- add cylindrical polar grid description need to do a better job of relating model variables to this diagram @@ -541,6 +320,7 @@ 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) + - need to reference the smag/leith section. 2.13.6 Vertical dissipation - mention the implicit vertical viscosity option and ref to section 2.5 @@ -564,11 +344,300 @@ - does not use std notation - would be better as an appendix of section 2.20: (e.g changing the tile to: +- talk to Baylor Appendix: non-dimensional Equations on Spherical-Polar grid.) + JM -9. Model uses +>>>> From Andrea + +Chapter 3 +-------- + +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 + +3.11.3.2 - 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 + - 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 + 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 : + + - missing references (if you point me towards URLs, I'll add them + to the bibliography): + \ref{ref hoe and hill, ecmwf} + \ref{magicgarden} + \ref{IBMLAPI} + \ref{Memorychannel} + \ref{hoe-hill:99} + + - There are a few empty sub-sections at the end of Chap 4 that + should either be commented out or fleshed out. + +and thats about it for Chap 4. + + +Add more to quick links on front page + +Chapter 6 + + the master package diagram does not appear in the document + +Master list of packages (add this to beginning of chap 6) + +admtlm/ - autodiff (chapter 5) +aim/ - retired +aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM) +aim_ocn_coupler/ - 6.6 (no content yet) +aim_v23/ - 6.4.1 (content needs fixing - JM to do) +atm_common/ - nothing in this package (6.4.1 related) +autodiff/ - autodiff (chapter 5) +bulk_force/ - 6.3.3 +cal/ - 6.3.5 +cd_code/ - chapter 2 (JM check add a reference to paper, + mention parameter in data) +cfc/ - not sure (CNH to talk to Steph and Helen) +chronos/ - AM to check (not being used - Andrea to kill it) +compon_communic/ - 6.6 (no content yet)(Daniel + JM) +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/ - (check with PH) +ecco/ - chapter 8 +embed_files/ - add something to chapter 7 +exch2/ - 6.2.2 +exf/ - 6.3.4 +fizhi/ - 6.4.3 +flt/ - (PH 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 transition zone stuff (Samar doing this) + get dfer to read this +grdchk/ - grdchk (chapter 5 - check with PH) +gridalt/ - 6.2.4 +kpp/ - 6.3.2 +land/ - 6.4.2 (not connected to code Rong's notes - 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 - ask PH to read) +ocn_compon_interf/ - 6.6 (no content yet) +offline/ - nothing, tutorials that need work but no package section entry + trivial to document (CNH to do) +opps/ - nothing, (martin?) +pp81/ - nothing, (martin?) +profiles/ - GAEL +ptracers/ - JM + SD + Martin to write something (nothing for this + at the moment) + AM has diagnostics table for this. +rbcs/ - CNH to talk to steph +runclock/ - runclock - CNH +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 - CNH +seaice/ - 6.5.2 - no equations, dimitris has promised some +shap_filt/ - chapter 2, JM to check +shelfice/ - nothing yet (martin?) +solver/ - empty (go away?) +sphere/ - chapter 5 or 8 (PH to check) +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 + +[DONE]Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started. + +6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 + Figure 6.8 is missing + + +>>>> From Andrea + +to do list for chap 7: + + +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 + +7.5.1 - add Graphix to the list of stuff in utils/matlab +7.5.2 - empty + + +andrea + + +9. Publications using MITgcm Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... (check in support for more names) + +10. Under development + + +Bibliography