MITgcm/manual/manual_todo.txt

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

   pkg/ptracers doesn't seem to have any documentation (see packages list below)
                martin volunteered - get martin to ask steph


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)
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

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. Model uses
   Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
   (check in support for more names)