/[MITgcm]/manual/manual_todo.txt

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-revision 1.5 by edhill,
Thu Apr  6 19:06:45 2006 UTC
+revision 1.34 by cnh,
Tue Jun 27 15:28:10 2006 UTC
 Line 1
+ Editors
+  Overall       - JM, AM, PH, CNH, EH3
+  Front content - EH3
+  Chapter 1     - CNH
+  Chapter 2     - JMC
+  Chapter 3     -  AM
+  Chapter 4     - CNH
+  Chapter 5     -  PH
+  Chapter 6     -  AM
+  Chapter 7     - EH3
+  Chapter 8     -  PH
+  Chapter 9     - CNH (Applications)
+  Chapter 10    - JMC (Under development chapter)
+  Biblio        - EH3
  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)
+   - add in example latex for formatting author names in different pieces.
+     this aknowledges peoples contributions and gives ref for who
+     to talk to.
-   - mitgcm.org very front page.
-     o too many clicks to get to model manual.
+ o HTML, scripts and front content
-       make doc link go to mitgcm.org/r2_web_testing/latest
-       and add "HowTo" reference etc... to /latest page
+   - pick a URL
+     TBD
    - mitgcm.org/r2_web_testing/latest
      o add another short-cut for quick download
-Line 19 
 To do
+Line 58 
 To do
        Overview
        Tutorials (broken)
        Browse Code
-       Get Code (where does this go to?)
-     o authors
+     o words on http://mitgcm.org/r2_web_testing/latest
-       John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,
+       change to
-       Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,
+        "access on-line Auser manual/A and Atable of contents/A
-       Gael - others?
+         and browse the Aoverview section/A"
-     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 finite-volume doesn't leap to FV figure
-     o the src and equation links don't come through to
+     o have another go at pnmcrop et al.
-       the html when they are in figures - see chapter 2 for some
-       examples.
-     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
- Contents
+ o Latex
-     Intro                  - CNH
+     Chapter 1                 - CNH
        o single kernel diagram -
            add reference to MWR paper
-Line 109 
 Contents
+Line 137 
 Contents
        o Kinematic boundary conditions
-       o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms
+       o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
-         need to tidy up discussion of shallow-atmosphere to be
+         Non-hydrostatic forms
-         consistent with the code or change code to be consistent
+          need to tidy up discussion of shallow-atmosphere to be
-         with the discussion!
+          consistent with the code or change code to be consistent
-         make references hyperlinks
+          with the discussion!
-         add stuff too
+          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
+          make references hyperlinks
-         add forward references to manual algorithm section
+          add forward references to manual algorithm section
-         change Elliptic to "elliptic"
+          change Elliptic to "elliptic"
        o Forcing and dissipation
-         make "physics packages" refer to chapter 6.
+          make "physics packages" refer to chapter 6.
-         should we move "external forcing" et. al to a
+          should we move "external forcing" et. al to a
-         generic_forcing_driver package?
+          generic_forcing_driver package?
          viscosities
-         update to mention Smag/Leith (Ah and A4 not constant)
+          update to mention Smag/Leith (Ah and A4 not constant)
-         and to have forward references to numerical section
+          and to have forward references to numerical section
-         tracers
+          tracers
-         forward references to numerical section, reddy, GM etc...
+          forward references to numerical section, reddy, GM etc...
-         add references to literature
+          add references to literature
        o 1.3.8 Vector invariant form
          forward references to numerical section
-Line 157 
 Contents
+Line 188 
 Contents
          PH to do something
-     Discretization and alg - JMC+CNH
-     Tutorials              - AM
-.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
-. Introduction
-. Discretization and Algorithm
-.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)
-.13.6 Vertical dissipation
-     o update to have reference to Baylors section
-       reference to implicit discussion in time-stepping part of manual
-. Tutorials
-    reorg'd into
-    intro part
-    individual experiments
-. Software Architecture
-. Automatic Differentiation
-. Physical Parameterization and Packages
-. Diagnostics and tools
-. Interface with ECCO
-. 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
-Line 271 
 Chapter 1
+Line 225 
 Chapter 1
            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.
-.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
+.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 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
+.3 linear free-surface:
+ - add ref(+link) to S/R names:
+ - add ref(+link) to Crank-Nickelson section 2.9.1
+.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
+.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 :
+.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
+.7 Stagger baroclinic time-stepping
-    major and has experience editing/proofing technical papers.  I
+ - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
-    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
+.8 NH
-    to the bibliography):
+ - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
-      \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
+.9 Variants on Free-Surface
-    should either be commented out or fleshed out.
+ - 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.
+.9.1 Crank-Nickelson
+ - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
+.9.2 NLFS
+ - eq.Nb are wrong in html
+ - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
+.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
+.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:
+.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
-.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"
+.12 Hydrostatic balance
-         the links are pointing to the proper place
+  - 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
-.5.1 - add Graphix to the list of stuff in utils/matlab
+.13.2 Coriolis terms
-.5.2 - empty
+  - 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);
+.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.
+.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)
+.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.
+.14.6 Horizontal dissipation -> Horizontal Divergence
+.14.7 Horizontal dissipation
+  - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
+    and A_D4,A_z4 <-> viscA4D,viscA4Z
+.16 & 2.17 & 2.18 :
+  - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
+  - fix equations 2.202 & 2.203 (thanks to Martin)
+.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.)
+ Diagrams of grid locations etc.... and what variables and output files
+ and/or netcdf variable names are not very easy to figure out and follow.
+ It would be good to redo and extend these diagrams and align with GRID.h
+ content.
+ JM
- andrea
  >>>> From Andrea
-Line 405 
 Chapter 3
+Line 389 
 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?)
 .1 - don't need a link to the outside of the document (remove it)
      - link to htdig is broken
-Line 454 
 divide chapter 3 more clearly into 2 sec
+Line 434 
 divide chapter 3 more clearly into 2 sec
          are written.
 .6.1.2 - needs to be moved to inside section 3.6.2
-.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
-Line 490 
 the verification directory
+Line 467 
 the verification directory
 .20.1 - link to doc at end of section points to this section
 .20.2 - link to doc at end of section points to this section
- >>>> from JM
+      offline - duplicate inputs, what is it, tidy up cfc v.
+                other offline. JM thinks these need tidying up.
- 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
-.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
+ 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
-.2 rigid-lid:
+ >>>> From Ed
- - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
+ Here are the remaining bits for Chap 4 :
-   to stay closer to the code.
- - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
-.3 linear free-surface:
+  - missing references (if you point me towards URLs, I'll add them
- - add ref(+link) to S/R names:
+    to the bibliography):
- - add ref(+link) to Crank-Nickelson section 2.9.1
+      \ref{ref hoe and hill, ecmwf}
+      \ref{magicgarden}
+      \ref{IBMLAPI}
+      \ref{Memorychannel}
+      \ref{hoe-hill:99}
-.4 Adams-Bashforth
+  - There are a few empty sub-sections at the end of Chap 4 that
- - add stability diagrams (I have some figures that I can put)
+    should either be commented out or fleshed out.
- - add link for var. forcing_In_AB
- - add S/R link for S/R ADAMS_BASHFORTH2
-.5 Implicit time-stepping
+ and thats about it for Chap 4.
- - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
-         SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
- - update: also used for vertical advection
-.6 Synchronous time-stepping:
- - add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,
-                    MOMENTUM_CORRECTION_STEP.
-.7 Stagger baroclinic time-stepping
+ Add more to quick links on front page
- - mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
-.8 NH
+ Chapter 6
- - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
-.9 Variants on Free-Surface
+    the master package diagram does not appear in the document
- - 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
-.9.1 Crank-Nickelson
+ Master list of packages (add this to beginning of chap 6)
- - link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
-.9.2 NLFS
- - eq.Nb are wrong in html
- - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
-.10.1 Notation
+ admtlm/               - autodiff (chapter 5)
- - Area definition is not really used like this
+ 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)
- >> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
+ list an expeiment which uses package? CNH
-   Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
+.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
-   the model variables) are used (e.g., see section 2.10.5)
+  Figure 6.8 is missing
-.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
-.11 Continuity & Horizontal Pressure gradient terms
+ =====  Chapter 7  =====  [EH3 editing] :
-  - 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
-.12 Hydrostatic balance
+.1.1 - links to section 7.1.4: the text of the first
-  - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
+         one should read "see MITgcm Kernel Diagnostics Menu"
-    is hard to find
+         the links are pointing to the proper place
-  - 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
-.13.2 Coriolis terms
+.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
-  - 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);
-.13.5 Lateral dissipation
+.5.2 - get bathymetry pre-processing stuff from Patrick
-  - add description of how to use cosFactor & cosPower
+         and then describe it
-  - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
-.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)
-.14 Vector invariant momentum equations
+ andrea
-  - indicate that the NH pieces (vertical momentum eq) are not yet coded
-    and that the NH code uses the flux form.
-.14.6 Horizontal dissipation -> Horizontal Divergence
-.14.7 Horizontal dissipation
+. Publications using MITgcm --> "Previous Applications of MITgcm"
-  - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ
+    Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
-    and A_D4,A_z4 <-> viscA4D,viscA4Z
+    (check in support for more names)
-.16 & 2.17 & 2.18 :
+. Under development
-  - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
-.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

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