Rebuild and set to do cron build - DONE on hugo To do - where to put under development links? JMC would like to have some mention of unfinished things (checked in but not that tested e.g. AB3) Add an "Under development, chapter" - shortish description of what is available (last chapter) o HTML, scripts and front content - pick a URL TBD - mitgcm.org/r2_web_testing/latest o add another short-cut for quick download 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" o finite-volume doesn't leap to FV figure o have another go at pnmcrop et al. o Need an empty package as part of distribution. Check out atm_common o Latex Chapter 1 - CNH o single kernel diagram - add reference to MWR paper o non-hydro add reference to 1995 and 1999 papers pdf of 1995 paper o FV add references to 1997 papers. o Tangent linear/adjoint add reference to Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc... o platforms Add reference to SC article and Scientific Programming article 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?) Held and Suarez reference is not a link. o Ocean Gyres fix up frame link make "lopped cell" a link to referenced paper. add references (ask Steph/Mick) online/offline paper o Convection and mixing over topography add in Legg references for convection and mixing over topography and external link to CPT-GCE etc... o Boundary forced internal waves add in Legg references, obc's reference o Parameter sensitivity add in Bugnion references, Boyin references, Steph references o State estimation add in references from Patrick/Carl/Ichiro/Detlef etc... update links to point to latest ECCO results ECCO ingrid results have been moved add forward links to "ECCO state estimation" chapter in manual o Ocean biogeochemical cycles add in references from Mick/Galen etc... fix ingrid link ( date to date thing does not appear to work) figure url does not have a "target=idontexist" entry o Simulations of laboratory experiments reference Wardle and Karsten papers update links to include DDDAS "PIAB" page cylindrical polar coordinates o Continuos equations in ''r'' coordinates add references to iso paper no mention of z* and p* - forward reference to z*/p* in 2. add that coupling also manifests through F, Q add tracer transport o Kinematic boundary conditions o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms need to tidy up discussion of shallow-atmosphere to be consistent with the code or change code to be consistent with the discussion! make references hyperlinks add stuff too JMC remove QNH atmosphere need to sort out calc_gw for deep atmosphere o Finding the pressure field make references hyperlinks add forward references to manual algorithm section change Elliptic to "elliptic" o Forcing and dissipation make "physics packages" refer to chapter 6. should we move "external forcing" et. al to a generic_forcing_driver package? viscosities update to mention Smag/Leith (Ah and A4 not constant) and to have forward references to numerical section tracers forward references to numerical section, reddy, GM etc... add references to literature o 1.3.8 Vector invariant form forward references to numerical section o 1.3.9 Adjoint add a little more here + some hyperlink to chapter 5. o 1.4 Appendix ATMOSPHERE add some introductory words o 1.6 Coordinate systems o only has some words on spherical polar. add some brief words to cover all of - cartesian - spherical - cylindrical - general orthogonal curvilinear (vector invariant) o Equation of state options add some discussion can't remember what we said we were going to do here PH to do something Change hydrodynamical to "dynamical" Examples - extra "in action" cases o high res ocean with diurnal atmospheric state forcing - links to ingrid output CNH/Dimitris o realistic FIZHI from Andrea - links to ingrid output from AM o with seaice on high res cube - links to ingrid output CNH/Dimitris o coupled aqua, ridge world etc... - links to ingrid output get stuff from Daniel o constrained lab simulation - links to ingrid output for model and lab fields get stuff from Sai/Andrew o sensitivity wrt to iron o optimization - update to link to latest ECCO sites and GF related material o eddy diffusivity transport application o Gas giant? >>>> from JM manual, section.2 : In general: - add more refences/links to S/R & variable name - 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) - 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 simply written \vec{v}. I would suggest to keep the notation as they are (since they are consistent inside each section) but may be to move the "notation.tex" piece at the beginning of section.2 and to mention clearly the changes between the 2 sections. in content: Horizontal Dissipation: 2 times in vector-invariant section 2.1 time-stepping (part2/time_stepping.tex) - this is not clear to me: >> 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 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) 2.3 linear free-surface: - add ref(+link) to S/R names: - add ref(+link) to Crank-Nickelson section 2.9.1 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 2.5 Implicit time-stepping - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL - update: also used for vertical advection 2.6 Synchronous time-stepping: - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE, MOMENTUM_CORRECTION_STEP. 2.7 Stagger baroclinic time-stepping - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end 2.8 NH - 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 - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D, INI_CG2D, INI_CG3D 2.9.1 Crank-Nickelson - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater 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) 2.10.1 Notation - Area definition is not really used like this >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w) Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to the model variables) are used (e.g., see section 2.10.5) 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. - curvilinear: to add: mention the angle of the grid direction relative to Eastward, Northward direction. + mention horizGridFile= in file "data" (PARM04) - add cylindrical polar grid description need to do a better job of relating model variables to this diagram 2.11 Continuity & Horizontal Pressure gradient terms - mention that d.Phi/dr|s =g if using z coordinate - eq. 2.90 not clear regarding \delta_k(P-E) better to add the free surface eq: d.eta/dt = w_s + P-E 2.12 Hydrostatic balance - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002 is hard to find - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H) and in section 1.3.4: remove the 1.3.4.3.2 subsection: Quasi-nonhydrostatic Atmosphere 2.13.2 Coriolis terms - note: the discretization used when useEnergyConservingCoriolis=T has no hFac and no Area and is still different from the form described here (with Area & hFac); 2.13.5 Lateral dissipation - add description of how to use cosFactor & cosPower - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4 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 - add the parameter correspondence: Av <-> viscAr (and might change also the notation to Ar) 2.14 Vector invariant momentum equations - indicate that the NH pieces (vertical momentum eq) are not yet coded and that the NH code uses the flux form. 2.14.6 Horizontal dissipation -> Horizontal Divergence 2.14.7 Horizontal dissipation - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ and A_D4,A_z4 <-> viscA4D,viscA4Z 2.16 & 2.17 & 2.18 : - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options 2.20.2 mercator, non-dimensional Equations: - 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 >>>> 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 tidy up from misc - .tex