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revision 1.6 by cnh, Thu Apr 6 19:09:36 2006 UTC revision 1.40 by molod, Wed Jun 28 16:47:01 2006 UTC
# Line 1  Line 1 
1    Editors
2    
3     Overall       - JM, AM, PH, CNH, EH3
4    
5     Front content - EH3
6    
7     Chapter 1     - CNH
8    
9     Chapter 2     - JMC
10    
11     Chapter 3     -  AM
12    
13     Chapter 4     - CNH
14    
15     Chapter 5     -  PH
16    
17     Chapter 6     -  AM
18    
19     Chapter 7     - EH3
20    
21     Chapter 8     -  PH
22    
23     Chapter 9     - CNH (Applications)
24    
25     Chapter 10    - JMC (Under development chapter)
26    
27     Biblio        - EH3
28    
29  Rebuild and set to do cron build - DONE on hugo  Rebuild and set to do cron build - DONE on hugo
30    
31  To do  To do
# Line 5  To do Line 33  To do
33    - where to put under development links?    - where to put under development links?
34      JMC would like to have some mention of unfinished things (checked in      JMC would like to have some mention of unfinished things (checked in
35       but not that tested e.g. AB3)       but not that tested e.g. AB3)
36        Add an "Under development, chapter" - shortish description of what
37        is available (last chapter)
38    
39      - add in example latex for formatting author names in different pieces.
40        this aknowledges peoples contributions and gives ref for who
41        to talk to.
42    
43    - mitgcm.org very front page.  o HTML, scripts and front content
44      o too many clicks to get to model manual.  
45        make doc link go to mitgcm.org/r2_web_testing/latest    - pick a URL
46        and add "HowTo" reference etc... to /latest page      TBD
47    
48    - mitgcm.org/r2_web_testing/latest    - mitgcm.org/r2_web_testing/latest
49      o add another short-cut for quick download      o add another short-cut for quick download
# Line 21  To do Line 55  To do
55        Overview        Overview
56        Tutorials (broken)        Tutorials (broken)
57        Browse Code        Browse Code
       Get Code (where does this go to?)  
58    
59      o authors      o words on http://mitgcm.org/r2_web_testing/latest
60        John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,        change to
61        Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,         "access on-line Auser manual/A and Atable of contents/A
62        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"  
63    
64      o finite-volume doesn't leap to FV figure      o finite-volume doesn't leap to FV figure
65    
66      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.  
67    
68        o Need an empty package as part of distribution. Check out atm_common
69    
70  Contents  o Latex  
71    
72      Intro                  - CNH      Chapter 1                 - CNH
73        o single kernel diagram -        o single kernel diagram -
74            add reference to MWR paper            add reference to MWR paper
75    
# Line 65  Contents Line 88  Contents
88    
89        o List of key papers needs to be updated and reformatted        o List of key papers needs to be updated and reformatted
90    
   
91        o Global atmosphere: `Held Suarez',        o Global atmosphere: `Held Suarez',
92          update Adcroft reference          update Adcroft reference
93          fix up ingrid link and frame (ingrid movies seem to be broken?)          fix up ingrid link and frame (ingrid movies seem to be broken?)
# Line 111  Contents Line 133  Contents
133    
134        o Kinematic boundary conditions        o Kinematic boundary conditions
135    
136        o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms        o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
137          need to tidy up discussion of shallow-atmosphere to be          Non-hydrostatic forms
138          consistent with the code or change code to be consistent           need to tidy up discussion of shallow-atmosphere to be
139          with the discussion!           consistent with the code or change code to be consistent
140          make references hyperlinks           with the discussion!
141          add stuff too           make references hyperlinks
142             add stuff too
143             JMC remove QNH atmosphere
144             need to sort out calc_gw for deep atmosphere
145    
146        o Finding the pressure field        o Finding the pressure field
147          make references hyperlinks           make references hyperlinks
148          add forward references to manual algorithm section           add forward references to manual algorithm section
149          change Elliptic to "elliptic"           change Elliptic to "elliptic"
150    
151        o Forcing and dissipation        o Forcing and dissipation
152          make "physics packages" refer to chapter 6.           make "physics packages" refer to chapter 6.
153          should we move "external forcing" et. al to a           should we move "external forcing" et. al to a
154          generic_forcing_driver package?           generic_forcing_driver package?
155    
156          viscosities          viscosities
157          update to mention Smag/Leith (Ah and A4 not constant)           update to mention Smag/Leith (Ah and A4 not constant)
158          and to have forward references to numerical section           and to have forward references to numerical section
159          tracers           tracers
160          forward references to numerical section, reddy, GM etc...           forward references to numerical section, reddy, GM etc...
161          add references to literature           add references to literature
162    
163        o 1.3.8 Vector invariant form        o 1.3.8 Vector invariant form
164          forward references to numerical section          forward references to numerical section
# Line 159  Contents Line 184  Contents
184          PH to do something          PH to do something
185    
186    
     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  
   
187      Change hydrodynamical to "dynamical"      Change hydrodynamical to "dynamical"
188    
189      Examples      Examples
# Line 257  Chapter 1 Line 205  Chapter 1
205            o coupled aqua, ridge world etc...            o coupled aqua, ridge world etc...
206              - links to ingrid output              - links to ingrid output
207                get stuff from Daniel                get stuff from Daniel
208                  Davids donut movie
209    
210            o constrained lab simulation            o constrained lab simulation
211              - links to ingrid output for model and lab              - links to ingrid output for model and lab
# Line 273  Chapter 1 Line 222  Chapter 1
222    
223            o Gas giant?            o Gas giant?
224    
 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)  
   
   
   
 2.10.5 Horizontal grid  
   
    need to do a better job of relating model variables to this diagram  
   
   
 Master list of packages  
   
 admtlm/               - autodiff (chapter 5)  
 aim/                  - 6.4.1 (content needs fixing - JM to do)  
 aim_compon_interf/    - 6.6 (no content yet)  
 aim_ocn_coupler/      - 6.6 (no content yet)  
 aim_v23/              - retired  
 atm_common/           - 6.6 (no content yet)  
 autodiff/             - autodiff (chapter 5)  
 bulk_force/           - 6.3.3  
 cal/                  - 6.3.5  
 cd_code/              - chapter 2 (JM check)  
 cfc/                  - not sure  
 chronos/              - AM to check  
 compon_communic/      - 6.6 (no content yet)  
 cost/                 - not sure, check with PH  
 ctrl/                 - not sure, check with PH  
 debug/                - JM may do something in chapter 7 (utilities)  
 diagnostics/          - 7.1  
 dic/                  - 6.7.2  
 ebm/                  - not sure  
 ecco/                 - chapter 8  
 embed_files/          - add something to chapter 7  
 ex3/                  - rename to exch3  
 exch2/                - 6.2.2  
 exf/                  - 6.3.4  
 fizhi/                - 6.4.3  
 flt/                  - in chapter 2 (JM check)  
 gchem/                - 6.7.1  
 generic_advdiff/      - in chapter 2 (JM check)  
 ggl90/                - nothing, (Martin?)  
 gmredi/               - in chapter 2 (JM check). also need  
                         Ferrari & Mc tapering  
 grdchk/               - grdchk (chapter 5 - check with PH)  
 gridalt/              - 6.2.4  
 kpp/                  - 6.3.2  
 land/                 - 6.4.2 (not connected to code - JM to fix)  
 matrix/               - Samar  
 mdsio/                - 7.3.1  
 mnc/                  - 7.2.1  
 mom_common/           - in chapter 2 (JM check)  
 mom_fluxform/         - in chapter 2 (JM check)  
 mom_vecinv/           - in chapter 2 (JM check)  
 monitor/              - 7.4  
 my82/                 - nothing, (martin?)  
 obcs/                 - 6.3 (needs a check)  
 ocn_compon_interf/    - 6.6 (no content yet)  
 offline/              - nothing, tutorials that need work but no package   section entry  
 opps/                 - nothing, (martin?)  
 pp81/                 - nothing, (martin?)  
 profiles/             - GAEL  
 ptracers/             - JM + SD to write something  
 rbcs/                 - talk to steph  
 runclock/             - runclock  
 rw/                   - not sure  
 sbo/                  - text in sbo_descruption.tex but not linked into  
                         part6  
 seaice/               - 6.5.2 - no equations, dimitris has promised some  
 shap_filt/            - chapter 2, JM to check  
 shelfice/             - nothing yet (martin?)  
 solver/               - empty  
 sphere/               - chapter 5 or 8 (PH to check)  
 therm_seaice/         - empty  
 thsice/               - 6.5.1 (JM to update?)  
 timeave/              - retiring......  
 zonal_filt/           - chapter 2 (JM to check)  
   
 Possible for chap 7 - Daniels grafix/ stuff  
   
 Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.  
   
 Figure 6.8 is missing  
   
   
 >>>> From Ed  
   
 Here are the remaining bits for Chap 4 :  
   
  - The grammar/flow could still use some work.  Boo was an English  
    major and has experience editing/proofing technical papers.  I  
    could print out a copy and ask her to read it and suggest  
    improvements.  
   
  - missing references (if you point me towards URLs, I'll add them  
    to the bibliography):  
      \ref{ref hoe and hill, ecmwf}  
      \ref{magicgarden}  
      \ref{IBMLAPI}  
      \ref{Memorychannel}  
      \ref{hoe-hill:99}  
   
  - There are a few empty sub-sections at the end of Chap 4 that  
    should either be commented out or fleshed out.  
   
 and thats about it for Chap 4.  
   
   
 Add more to quick links on front page  
   
   
 >>>> From Andrea  
   
 to do list for chap 7:  
   
   
 7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"  
         the links are pointing to the proper place  
   
 7.5.1 - add Graphix to the list of stuff in utils/matlab  
 7.5.2 - empty  
   
   
 andrea  
   
 >>>> From Andrea  
   
 Chapter 3  
 --------  
   
 Almost all of the 'math mode' text is dropped down as subscripts  
   
 divide chapter 3 more clearly into 2 sections?  
    (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and  
     then 3.19 and 3.20 are informational again - rearrange subsections?)  
   
 3.1 - don't need a link to the outside of the document (remove it)  
     - link to htdig is broken  
   
 3.2.1 - link at bottom to source code points to section 3.2.1  
    (ie, to itself) - link should point to cvs code archive  
   
 3.2.2.1  - ('upgrading from an earlier version') belongs under  
       the cvs part, ie, should be 3.2.1.1  
   
 3.3 - remove reference to 'diags' section under MITgcm  
     - remove reference to 'exe' and 'bin' sections also  
       (remove the .cvsignore file under these directories in cvs)  
     - add a 'jobs' section, and a description as examples of run scripts  
     - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions  
     - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'  
     - under 'tools' the adjoint points to section 5 - this is now section 8  
       (but should be a floating reference)  
     - under 'utils' add a reference to exch2 - stuff for different resolutions  
     - the description of the pkg section refers directly to  
       section 3. should be section 6 (actually should be a floating reference)  
   
 3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)  
 3.4.1 - links to the following experiments don't exist or are broken:  
           exp2 - should link to section 3.9  
           hs94.cs-32x32x5 - link to section 3.12  
           add 'convection' to the list, link to section 3.13  
           add 'plume on slope` to the list, link to section 3.14  
           add '??' link to section 3.15  
           add 'dic_example on slope` to the list, link to section 3.16  
           add '??' link to section 3.17  
           add 'offline' and link to section 3.18  
           clean up others and make links where they are needed  
 3.4.2 - text suggests to see section 2 for details about what is in the 'code'  
         and 'input' directories - should refer to the examples in this section  
       - add 'build' bullet - this is where the model is compiled and exectuable lives  
   
 3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options  
       as the place where they live (add a link?)  
   
 3.6.1 - Add some general 'approach' text - ie, output is controlled either by the  
         'data' file in the input directory or by the data.[pkg name] file for any  
         package running. And there is some default behavior when the 'state' dumps  
         are written.  
 3.6.1.2 - needs to be moved to inside section 3.6.2  
   
 3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18)  
       underneath this one and leave the text for 3.7 in place  
   
 All the 'overview' sections need some reference to the name of the experiment in  
 the verification directory  
   
 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript  
      - is this experiment in the list from section 3.4???  
 3.10.3.1 - refers to figures and equations, links are broken  
   
 3.11.3.2 - line 43: link to equation is broken  
          - line 51-53: link to equation is broken  
          - there is some mess of text hanging around the end of this section. remove? reformat?  
   
 3.12.4.1 - line 34 - link to equation is broken  
          - lines 60,61 - 1st (take out the 'r' in the superscript)  
   
 3.13.2 - link to theta-equation is broken  
 3.13.5.4 -- ALL of the bold links to variable names are broken  
             line 34: link to equation is broken  
   
 3.15.1 - reference to 'fourth experiment' should be removed  
   
 3.16.4 - strange formatting, presence of '>' symbols - remove them  
   
 3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4  
 3.17.3.1 - nothing filled in under file input/data - needs description  
   
 3.18.2 - point to section 2 for details - need hyperlink  
   
 3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!  
          section 3.5 has the 'build' directory in the example  
   
 3.20.1 - link to doc at end of section points to this section  
 3.20.2 - link to doc at end of section points to this section  
225    
226  >>>> from JM  >>>> from JM
227    
228    
   
229  manual, section.2 :  manual, section.2 :
230    
231  In general:  In general:
# Line 503  In general: Line 233  In general:
233  - would be nice to have an active link to the fortran-file  - would be nice to have an active link to the fortran-file
234    for all the S/R & eq.Number in the "calling-tree" boxes    for all the S/R & eq.Number in the "calling-tree" boxes
235  - search for CALC_MOM_RHS and replace it by the appropriate S/R  - search for CALC_MOM_RHS and replace it by the appropriate S/R
236    (mom_flux_form, mom_vecinv, dynamics)    (mom_flux_form, mom_vecinv, dynamics) <- DONE
237  - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})  - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
238  was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}  was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
239  in section.2, \vec{\bf v} is used instead and 3.D velocity vector is  in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
# Line 514  at the beginning of section.2 and to men Line 244  at the beginning of section.2 and to men
244  the 2 sections.  the 2 sections.
245    
246  in content: Horizontal Dissipation: 2 times in vector-invariant section  in content: Horizontal Dissipation: 2 times in vector-invariant section
247    <- DONE
248    
249  2.1 time-stepping (part2/time_stepping.tex)  2.1 time-stepping (part2/time_stepping.tex)
250    
# Line 522  in content: Horizontal Dissipation: 2 ti Line 253  in content: Horizontal Dissipation: 2 ti
253  >> In all the above configurations it is also possible to substitute the  >> In all the above configurations it is also possible to substitute the
254  >> Adams-Bashforth with an alternative time-stepping scheme for terms  >> Adams-Bashforth with an alternative time-stepping scheme for terms
255  >> evaluated explicitly in time  >> evaluated explicitly in time
256    <- Leave it general.
257    
258    
259  2.2 rigid-lid:  2.2 rigid-lid:
# Line 555  in content: Horizontal Dissipation: 2 ti Line 287  in content: Horizontal Dissipation: 2 ti
287  - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D  - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
288    
289  2.9 Variants on Free-Surface  2.9 Variants on Free-Surface
290  - Delta.t mis-written (eq.2.73)  - Delta.t mis-written (eq.2.73) <- DONE
291  - Eq.Num missing (has been fixed since)  - Eq.Num missing <- DONE
292  - u* is stored in gU (and not in gUnm1)  - u* is stored in gU (and not in gUnm1) <- DONE
293  - Phi_nh in NH_VARS.h  - Phi_nh in NH_VARS.h <- DONE
294  - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,  - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
295    INI_CG2D, INI_CG3D    INI_CG2D, INI_CG3D
296    
# Line 568  in content: Horizontal Dissipation: 2 ti Line 300  in content: Horizontal Dissipation: 2 ti
300  2.9.2 NLFS  2.9.2 NLFS
301  - eq.Nb are wrong in html  - eq.Nb are wrong in html
302  - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)  - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
303     <- DONE
304    
305  2.10.1 Notation  2.10.1 Notation
306  - Area definition is not really used like this  - Area definition is not really used like this
# Line 576  in content: Horizontal Dissipation: 2 ti Line 309  in content: Horizontal Dissipation: 2 ti
309    
310    Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to    Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
311    the model variables) are used (e.g., see section 2.10.5)    the model variables) are used (e.g., see section 2.10.5)
312    <- DONE
313    
314  2.10.5 Horizontal grid:  2.10.5 Horizontal grid:
315  - fig.2.8 : should use Aw,As consistently in this figure description,  - fig.2.8 : should use Aw,As consistently in this figure description,
316    in the figure itself, as it is in the text.    in the figure itself, as it is in the text. <- DONE
317  - curvilinear:  - curvilinear:
318    to add: mention the angle of the grid direction relative to    to add: mention the angle of the grid direction relative to
319    Eastward, Northward direction.    Eastward, Northward direction.
320    + mention horizGridFile= in file "data" (PARM04)    + mention horizGridFile= in file "data" (PARM04)
321  - add cylindrical grid description  - add cylindrical polar grid description
322       need to do a better job of relating model variables to this diagram
323    
324    
325  2.11 Continuity & Horizontal Pressure gradient terms  2.11 Continuity & Horizontal Pressure gradient terms
326   - mention that d.Phi/dr|s =g if using z coordinate   - mention that d.Phi/dr|s =g if using z coordinate
# Line 606  in content: Horizontal Dissipation: 2 ti Line 342  in content: Horizontal Dissipation: 2 ti
342  2.13.5 Lateral dissipation  2.13.5 Lateral dissipation
343   - add description of how to use cosFactor & cosPower   - add description of how to use cosFactor & cosPower
344   - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4   - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
345        o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
346          in code need to explain why cos()3/2 turns out to be
347          scaling (not cos()2)
348     - need to reference the smag/leith section.
349    
350  2.13.6 Vertical dissipation  2.13.6 Vertical dissipation
351   - mention the implicit vertical viscosity option and ref to section 2.5   - mention the implicit vertical viscosity option and ref to section 2.5
# Line 624  in content: Horizontal Dissipation: 2 ti Line 364  in content: Horizontal Dissipation: 2 ti
364    
365  2.16 & 2.17 & 2.18 :  2.16 & 2.17 & 2.18 :
366   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
367     - fix equations 2.202 & 2.203 (thanks to Martin) <- DONE
368    
369  2.20.2 mercator, non-dimensional Equations:  2.20.2 mercator, non-dimensional Equations:
370  - does not use std notation  - does not use std notation
371  - would be better as an appendix of section 2.20:  - would be better as an appendix of section 2.20:
372  (e.g changing the tile to:  (e.g changing the tile to:
373    - talk to Baylor
374   Appendix: non-dimensional Equations on Spherical-Polar grid.)   Appendix: non-dimensional Equations on Spherical-Polar grid.)
375     <- No (Chris said)
376    
377    
378    Diagrams of grid locations etc.... and what variables and output files
379    and/or netcdf variable names are not very easy to figure out and follow.
380    It would be good to redo and extend these diagrams and align with GRID.h
381    content.
382    
383    
384  JM  JM
385    
386    
387    >>>> From Andrea
388    
389    Chapter 3
390    --------
391    
392    Almost all of the 'math mode' text is dropped down as subscripts
393    
394    3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
395    3.4.1 - links to the following experiments don't exist or are broken:
396              exp2 - should link to section 3.9
397              hs94.cs-32x32x5 - link to section 3.12
398              add 'convection' to the list, link to section 3.13
399              add 'plume on slope` to the list, link to section 3.14
400              add '??' link to section 3.15
401              add 'dic_example on slope` to the list, link to section 3.16
402              add '??' link to section 3.17
403              add 'offline' and link to section 3.18
404              clean up others and make links where they are needed
405    3.4.2 - text suggests to see section 2 for details about what is in the 'code'
406            and 'input' directories - should refer to the examples in this section
407          - add 'build' bullet - this is where the model is compiled and exectuable lives
408    
409    3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
410          as the place where they live (add a link?)
411    
412    3.6.1 - Add some general 'approach' text - ie, output is controlled either by the
413            'data' file in the input directory or by the data.[pkg name] file for any
414            package running. And there is some default behavior when the 'state' dumps
415            are written.
416    3.6.1.2 - needs to be moved to inside section 3.6.2
417    
418    All the 'overview' sections need some reference to the name of the experiment in
419    the verification directory
420    
421    3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
422         - is this experiment in the list from section 3.4???
423    3.10.3.1 - refers to figures and equations, links are broken
424    
425    3.11.3.2 - line 43: link to equation is broken
426             - line 51-53: link to equation is broken
427             - there is some mess of text hanging around the end of this section. remove? reformat?
428    
429    3.12.4.1 - line 34 - link to equation is broken
430             - lines 60,61 - 1st (take out the 'r' in the superscript)
431    
432    3.13.2 - link to theta-equation is broken
433    3.13.5.4 -- ALL of the bold links to variable names are broken
434                line 34: link to equation is broken
435    
436    3.15.1 - reference to 'fourth experiment' should be removed
437    
438    3.16.4 - strange formatting, presence of '>' symbols - remove them
439    
440    3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
441    3.17.3.1 - nothing filled in under file input/data - needs description
442    
443    3.18.2 - point to section 2 for details - need hyperlink
444    
445    3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
446             section 3.5 has the 'build' directory in the example
447    
448    3.20.1 - link to doc at end of section points to this section
449    3.20.2 - link to doc at end of section points to this section
450    
451         offline - duplicate inputs, what is it, tidy up cfc v.
452                   other offline. JM thinks these need tidying up.
453    
454    Which of the following are which tutorial?
455    adjustment.128x64x1
456    adjustment.cs-32x32x1
457    advect_cs
458    advect_xy
459    advect_xz
460    aim.5l_cs
461    aim.5l_Equatorial_Channel
462    aim.5l_LatLon
463    biogeo
464    bottom_ctrl_5x5
465    cfc_example
466    cpl_aim+ocn
467    dome
468    exp2
469    exp4
470    exp5
471    fizhi-cs-32x32x10
472    fizhi-cs-aqualev20
473    fizhi-gridalt-hs
474    flt_example
475    front_relax
476    global1x1_tot
477    global2x2_tot
478    global_ocean.90x40x15
479    global_ocean.cs32x15
480    global_ocean.cubed32x32x30
481    global_ocean_ebm
482    global_with_exf
483    hs94.128x64x5
484    hs94.1x64x5
485    hs94.cs-32x32x5
486    ideal_2D_oce
487    internal_wave
488    inverted_barometer
489    lab_sea
490    matrix_example
491    MLAdjust
492    natl_box
493    natl_box_adjoint
494    OpenAD
495    rotating_tank
496    solid-body.cs-32x32x1
497    tidal_basin_2d
498    tutorial_baroclinic_gyre
499    tutorial_barotropic_gyre
500    tutorial_cfc_offline
501    tutorial_deep_convection
502    tutorial_global_oce_biogeo
503    tutorial_global_oce_in_p
504    tutorial_global_oce_latlon
505    tutorial_global_oce_optim
506    tutorial_held_suarez_cs
507    tutorial_offline
508    tutorial_plume_on_slope
509    tutorial_tracer_adjsens
510    vermix
511    
512    >>>> From Ed
513    
514    Here are the remaining bits for Chap 4 :
515    
516     - missing references (if you point me towards URLs, I'll add them
517       to the bibliography):
518         \ref{ref hoe and hill, ecmwf}
519         \ref{magicgarden}
520         \ref{IBMLAPI}
521         \ref{Memorychannel}
522         \ref{hoe-hill:99}
523    
524     - There are a few empty sub-sections at the end of Chap 4 that
525       should either be commented out or fleshed out.
526    
527    and thats about it for Chap 4.
528    
529    
530    Add more to quick links on front page
531    
532    Chapter 6
533    
534       the master package diagram does not appear in the document
535    
536    Master list of packages (add this to beginning of chap 6)
537    
538    admtlm/               - autodiff (chapter 5)
539    aim/                  - retired
540    aim_compon_interf/    - 6.6 (no content yet)(Daniel + JM)
541    aim_ocn_coupler/      - 6.6 (no content yet)
542    aim_v23/              - 6.4.1 (content needs fixing - JM to do)
543    atm_common/           - nothing in this package (6.4.1 related)
544    autodiff/             - autodiff (chapter 5)
545    bulk_force/           - 6.3.3
546    cal/                  - 6.3.5
547    cd_code/              - chapter 2 (JM check add a reference to paper,
548                              mention parameter in data)
549    cfc/                  - not sure  (CNH to talk to Steph and Helen)
550    chronos/              - AM to check (not being used - Andrea to kill it)
551    compon_communic/      - 6.6 (no content yet)(Daniel + JM)
552    cost/                 - not sure, check with PH
553    ctrl/                 - not sure, check with PH
554    debug/                - JM may do something in chapter 7 (utilities)
555    diagnostics/          - 7.1
556    dic/                  - 6.7.2
557    ebm/                  - (check with PH)
558    ecco/                 - chapter 8
559    embed_files/          - add something to chapter 7
560    exch2/                - 6.2.2
561    exf/                  - 6.3.4
562    fizhi/                - 6.4.3
563    flt/                  - (PH check)
564    gchem/                - 6.7.1
565    generic_advdiff/      - in chapter 2 (JM check)
566    ggl90/                - nothing, (Martin?)
567    gmredi/               - in chapter 2 (JM check). also need
568                            Ferrari & Mc transition zone stuff (Samar doing this)
569                            get dfer to read this
570    grdchk/               - grdchk (chapter 5 - check with PH)
571    gridalt/              - 6.2.4
572    kpp/                  - 6.3.2
573    land/                 - 6.4.2 (not connected to code Rong's notes - JM to fix)
574    matrix/               - Samar
575    mdsio/                - 7.3.1
576    mnc/                  - 7.2.1
577    mom_common/           - in chapter 2 (JM check)
578    mom_fluxform/         - in chapter 2 (JM check)
579    mom_vecinv/           - in chapter 2 (JM check)
580    monitor/              - 7.4
581    my82/                 - nothing, (martin?)
582    obcs/                 - 6.3 (needs a check - ask PH to read)
583    ocn_compon_interf/    - 6.6 (no content yet)
584    offline/              - nothing, tutorials that need work but no package   section entry
585                            trivial to document (CNH to do)
586    opps/                 - nothing, (martin?)
587    pp81/                 - nothing, (martin?)
588    profiles/             - GAEL
589    ptracers/             - JM + SD + Martin to write something (nothing for this
590                              at the moment)
591                            AM has diagnostics table for this.
592    rbcs/                 - CNH to talk to steph
593    runclock/             - runclock - CNH
594    rw/                   - not sure - going to stay says JMC. quick IO calls
595                            JMC to write a quick note for that.
596    sbo/                  - text in sbo_descruption.tex but not linked into
597                            part6 - CNH
598    seaice/               - 6.5.2 - no equations, dimitris has promised some
599    shap_filt/            - chapter 2, JM to check
600    shelfice/             - nothing yet (martin?)
601    solver/               - empty (go away?)
602    sphere/               - chapter 5 or 8 (PH to check)
603    therm_seaice/         - empty (go away?)
604    thsice/               - 6.5.1 (JM to update?)
605    timeave/              - retiring......
606    zonal_filt/           - chapter 2 (JM to check)
607    
608    list an expeiment which uses package? CNH
609    
610    6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
611     Figure 6.8 is missing
612    
613    
614    =====  Chapter 7  =====  [EH3 editing] :
615    
616    7.1.x - JMC: please add description of:
617            - diagstat
618            - new temporal averaging feature
619    
620    7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
621    
622    7.5.2 - get bathymetry pre-processing stuff from Patrick
623            and then describe it
624    
625    add something on spgrid mesh generator (maybe)?
626    
627    
628    andrea
629    
630    
631    9. Publications using MITgcm --> "Previous Applications of MITgcm"
632       Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
633       (check in support for more names)
634    
635    10. Under development
636    
637    Constantinos LCML
638    
639    
640    Bibliography
641    
642     tidy up from misc - .tex
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