--- manual/manual_todo.txt 2006/04/06 19:06:45 1.5 +++ manual/manual_todo.txt 2006/06/26 00:41:02 1.31 @@ -3,11 +3,16 @@ 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) - - 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 + +o HTML, scripts and front content + + - pick a URL + TBD - mitgcm.org/r2_web_testing/latest o add another short-cut for quick download @@ -19,32 +24,21 @@ Overview Tutorials (broken) Browse Code - Get Code (where does this go to?) - o authors - John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen, - Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos, - Gael - others? - - o Tutorials side bar link is broken - - o words - change to "access on-line Auser manual/A and Atable of contents/A - and browse the Aoverview section/A" + 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 the src and equation links don't come through to - the html when they are in figures - see chapter 2 for some - examples. + o have another go at pnmcrop et al. - o degree symbols keep getting "dropped down" - problem with - pnmcrop et al. + o Need an empty package as part of distribution. Check out atm_common +o Latex -Contents - - Intro - CNH + Chapter 1 - CNH o single kernel diagram - add reference to MWR paper @@ -109,29 +103,32 @@ 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 + 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" + 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? + 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 + 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 @@ -157,83 +154,6 @@ PH to do something - Discretization and alg - JMC+CNH - - Tutorials - AM - 3.1 "Where to find" - o link to Pelican not needed - o mailman twice (why?) - o no htdig (gone? - I liked it) - - intro part - individual experiments - - offline - duplicate inputs, what is it, tidy up cfc v. - other offline. - - Software - EH to review - - some to be done on resource estimates at the end - needs sorting. - - Automatic Diff - CE - - Physical Packages - ??? - - Diags and tools - ??? - - Interface with ECCO - ??? - - Model uses - ??? - - Building document - ??? - via cron - tweaking latex2html etc.. - - Src Code tree (rename - examples etc..) - ??? - -Documentation - -1. Introduction - -2. Discretization and Algorithm - - 2.13.5 Lateral dissipation - 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) - - 2.13.6 Vertical dissipation - o update to have reference to Baylors section - reference to implicit discussion in time-stepping part of manual - - - -3. Tutorials - reorg'd into - intro part - individual experiments - -4. Software Architecture - -5. Automatic Differentiation - -6. Physical Parameterization and Packages - -7. Diagnostics and tools - -8. Interface with ECCO - -9. Model uses - Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... - (check in support for more names) - - Need an empty package as part of distribution - - latex2html equation formatting is still a bit weird in places. Need to have another go if we have a chance - especially the degree symbol seems to jump around somewhat! - -Chapter 1 - Change hydrodynamical to "dynamical" Examples @@ -271,132 +191,156 @@ o Gas giant? -Chapter 6 - the master package diagram does not appear in the document +>>>> from JM - pkg/ptracers doesn't seem to have any documentation (see packages list below) +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. -2.10.5 Horizontal grid +in content: Horizontal Dissipation: 2 times in vector-invariant section - need to do a better job of relating model variables to this diagram +2.1 time-stepping (part2/time_stepping.tex) +- this is not clear to me: -Master list of packages +>> 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 -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 +2.2 rigid-lid: -Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started. +- 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) -Figure 6.8 is missing +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 ->>>> From Ed +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 -Here are the remaining bits for Chap 4 : +2.6 Synchronous time-stepping: +- add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE, + MOMENTUM_CORRECTION_STEP. - - 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. +2.7 Stagger baroclinic time-stepping +- mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end - - 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} +2.8 NH +- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D - - There are a few empty sub-sections at the end of Chap 4 that - should either be commented out or fleshed out. +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 -and thats about it for Chap 4. +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 -Add more to quick links on front page +>> 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) ->>>> From Andrea +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 -to do list for chap 7: +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 -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 +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 -7.5.1 - add Graphix to the list of stuff in utils/matlab -7.5.2 - empty +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 + - fix equations 2.202 & 2.203 (thanks to Martin) + +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 -andrea >>>> From Andrea @@ -405,10 +349,6 @@ 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 @@ -454,9 +394,6 @@ 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 @@ -490,144 +427,191 @@ 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 ->>>> 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) + offline - duplicate inputs, what is it, tidy up cfc v. + other offline. JM thinks these need tidying up. -- 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 +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 -2.2 rigid-lid: +Here are the remaining bits for Chap 4 : -- 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) + - 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} -2.3 linear free-surface: -- add ref(+link) to S/R names: -- add ref(+link) to Crank-Nickelson section 2.9.1 + - There are a few empty sub-sections at the end of Chap 4 that + should either be commented out or fleshed out. -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 +and thats about it for Chap 4. -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. +Add more to quick links on front page -2.7 Stagger baroclinic time-stepping -- mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end +Chapter 6 -2.8 NH -- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D + the master package diagram does not appear in the document -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 +Master list of packages (add this to beginning of chap 6) -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) +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) -2.10.1 Notation -- Area definition is not really used like this +list an expeiment which uses package? CNH ->> Ao : Area of the face orthogonal to "o" direction (o=u,v,w) +6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 + Figure 6.8 is missing - 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 grid description +>>>> From Andrea -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 +to do list for chap 7: -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); +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 -2.13.5 Lateral dissipation - - add description of how to use cosFactor & cosPower - - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4 +7.5.1 - add Graphix to the list of stuff in utils/matlab +7.5.2 - empty -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. +andrea -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 +9. Publications using MITgcm --> "Previous Applications of MITgcm" + Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... + (check in support for more names) -2.16 & 2.17 & 2.18 : - - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options +10. Under development -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: - Appendix: non-dimensional Equations on Spherical-Polar grid.) -JM +Bibliography + tidy up from misc - .tex