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revision 1.2 by molod, Thu Apr 6 00:48:34 2006 UTC revision 1.49 by jmc, Thu Jan 17 16:45:29 2008 UTC
# Line 1  Line 1 
1  Rebuild and set to do cron build  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    
30    Rebuild and set to do cron build - DONE on hugo
31    
32  To do  To do
33    
34    - where to put under development links?    - where to put under development links?
35        JMC would like to have some mention of unfinished things (checked in
36         but not that tested e.g. AB3)
37        Add an "Under development, chapter" - shortish description of what
38        is available (last chapter)
39    
40      - add in example latex for formatting author names in different pieces.
41        this aknowledges peoples contributions and gives ref for who
42        to talk to.
43    
44    - mitgcm.org very front page.  o HTML, scripts and front content
     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  
45    
46    - mitgcm.org/r2_web_testing/latest    - pick a URL:  mitgcm.org/r2  <-- EH3's preferred base URL
     o add another short-cut for quick download  
47    
48      o add another short-cut    - mitgcm.org/r2_web_testing/latest
49        About      
50        Installation      o --DONE--  add another short-cut for quick download
       Contents  
       Overview  
       Tutorials (broken)  
       Browse Code  
       Get Code (where does this go to?)  
51    
52      o authors      o --DONE--  add another short-cut
53        John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,                    About
54        Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,                    Installation
55        Gael - others?                    Contents
56                      Overview
57                      Tutorials (broken)
58                      Browse Code
59    
60      o Tutorials side bar link is broken      o --DONE--  words on http://mitgcm.org/r2_web_testing/latest change to
61    
62      o words      o --DONE--  finite-volume doesn't leap to FV figure
       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 -- DONE ??? --  have another go at pnmcrop et al.
65    
66      o date is 2002           I've tried making a small change in latex2html which fixes
67             the oddball-lower-alignment issue that we were seeing with
68             most in-line expressions (that is, math embedded in text).
69             The fix results in some things being slightly raised but I
70             thin this is more asthetically pleasing than being somewhat
71             lowered as before. --EH3
72    
73      o fix search so it doesn't include advertisements           To view the altered alignment, see:
74    
75      o the src and equation links don't come through to              http://eddy.csail.mit.edu/r2/latest/
       the html when they are in figures - see chapter 2 for some  
       examples.  
76    
77      o degree symbols keep getting "dropped down" - problem with      o Need an empty package as part of distribution. Check out atm_common
       pnmcrop et al.  
78    
79    
80  Contents  o Latex  
81    
82      Intro                  - CNH      Chapter 1                 - CNH
83        o single kernel diagram -        o single kernel diagram -
84            add reference to MWR paper            add reference to MWR paper
85    
# Line 67  Contents Line 98  Contents
98    
99        o List of key papers needs to be updated and reformatted        o List of key papers needs to be updated and reformatted
100    
   
101        o Global atmosphere: `Held Suarez',        o Global atmosphere: `Held Suarez',
102          update Adcroft reference          update Adcroft reference
103          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 113  Contents Line 143  Contents
143    
144        o Kinematic boundary conditions        o Kinematic boundary conditions
145    
146        o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms        o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
147          need to tidy up discussion of shallow-atmosphere to be          Non-hydrostatic forms
148          consistent with the code or change code to be consistent           need to tidy up discussion of shallow-atmosphere to be
149          with the discussion!           consistent with the code or change code to be consistent
150          make references hyperlinks           with the discussion!
151          add stuff too           make references hyperlinks
152             add stuff too
153             JMC remove QNH atmosphere
154             need to sort out calc_gw for deep atmosphere
155    
156        o Finding the pressure field        o Finding the pressure field
157          make references hyperlinks           make references hyperlinks
158          add forward references to manual algorithm section           add forward references to manual algorithm section
159          change Elliptic to "elliptic"           change Elliptic to "elliptic"
160    
161        o Forcing and dissipation        o Forcing and dissipation
162          make "physics packages" refer to chapter 6.           make "physics packages" refer to chapter 6.
163          should we move "external forcing" et. al to a           should we move "external forcing" et. al to a
164          generic_forcing_driver package?           generic_forcing_driver package?
165    
166          viscosities          viscosities
167          update to mention Smag/Leith (Ah and A4 not constant)           update to mention Smag/Leith (Ah and A4 not constant)
168          and to have forward references to numerical section           and to have forward references to numerical section
169          tracers           tracers
170          forward references to numerical section, reddy, GM etc...           forward references to numerical section, reddy, GM etc...
171          add references to literature           add references to literature
172    
173        o 1.3.8 Vector invariant form        o 1.3.8 Vector invariant form
174          forward references to numerical section          forward references to numerical section
# Line 161  Contents Line 194  Contents
194          PH to do something          PH to do something
195    
196    
     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  
   
197      Change hydrodynamical to "dynamical"      Change hydrodynamical to "dynamical"
198    
199      Examples      Examples
# Line 259  Chapter 1 Line 215  Chapter 1
215            o coupled aqua, ridge world etc...            o coupled aqua, ridge world etc...
216              - links to ingrid output              - links to ingrid output
217                get stuff from Daniel                get stuff from Daniel
218                  Davids donut movie
219    
220            o constrained lab simulation            o constrained lab simulation
221              - links to ingrid output for model and lab              - links to ingrid output for model and lab
# Line 275  Chapter 1 Line 232  Chapter 1
232    
233            o Gas giant?            o Gas giant?
234    
 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  
235    
236  >>>> from JM  >>>> from JM
237    
238    
   
239  manual, section.2 :  manual, section.2 :
240    
241  In general:  In general:
# Line 505  In general: Line 243  In general:
243  - would be nice to have an active link to the fortran-file  - would be nice to have an active link to the fortran-file
244    for all the S/R & eq.Number in the "calling-tree" boxes    for all the S/R & eq.Number in the "calling-tree" boxes
245  - 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
246    (mom_flux_form, mom_vecinv, dynamics)    (mom_flux_form, mom_vecinv, dynamics) <- DONE
247  - 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})
248  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}}
249  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 516  at the beginning of section.2 and to men Line 254  at the beginning of section.2 and to men
254  the 2 sections.  the 2 sections.
255    
256  in content: Horizontal Dissipation: 2 times in vector-invariant section  in content: Horizontal Dissipation: 2 times in vector-invariant section
257    <- DONE
258    
259  2.1 time-stepping (part2/time_stepping.tex)  2.1 time-stepping (part2/time_stepping.tex)
260    
# Line 524  in content: Horizontal Dissipation: 2 ti Line 263  in content: Horizontal Dissipation: 2 ti
263  >> In all the above configurations it is also possible to substitute the  >> In all the above configurations it is also possible to substitute the
264  >> Adams-Bashforth with an alternative time-stepping scheme for terms  >> Adams-Bashforth with an alternative time-stepping scheme for terms
265  >> evaluated explicitly in time  >> evaluated explicitly in time
266    <- Leave it general.
267    
268     o Time-stepping outline
269       - what gets called when
270    
271    
272  2.2 rigid-lid:  2.2 rigid-lid:
273    
274  - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"  - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
275    to stay closer to the code.    to stay closer to the code.
276  - mention section 2.5 implicit-Time-stepping (for vertical viscosity)  - mention section 2.5 implicit-Time-stepping (for vertical viscosity) <- DONE
277    
278  2.3 linear free-surface:  2.3 linear free-surface:
279  - add ref(+link) to S/R names:  - add ref(+link) to S/R names:
280  - add ref(+link) to Crank-Nickelson section 2.9.1  - add ref(+link) to Crank-Nickelson section 2.9.1 <- DONE
281    
282  2.4 Adams-Bashforth  2.4 Adams-Bashforth
283  - add stability diagrams (I have some figures that I can put)  - add stability diagrams (I have some figures that I can put) <- DONE
284  - add link for var. forcing_In_AB  - add link for var. forcing_In_AB and epsil_AB <- half DONE
285  - add S/R link for S/R ADAMS_BASHFORTH2  - add S/R link for S/R ADAMS_BASHFORTH2 <-DONE
286    
287  2.5 Implicit time-stepping  2.5 Implicit time-stepping
288  - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R  - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
# Line 557  in content: Horizontal Dissipation: 2 ti Line 300  in content: Horizontal Dissipation: 2 ti
300  - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D  - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
301    
302  2.9 Variants on Free-Surface  2.9 Variants on Free-Surface
303  - Delta.t mis-written (eq.2.73)  - Delta.t mis-written (eq.2.73) <- DONE
304  - Eq.Num missing (has been fixed since)  - Eq.Num missing <- DONE
305  - u* is stored in gU (and not in gUnm1)  - u* is stored in gU (and not in gUnm1) <- DONE
306  - Phi_nh in NH_VARS.h  - Phi_nh in NH_VARS.h <- DONE
307  - 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,
308    INI_CG2D, INI_CG3D    INI_CG2D, INI_CG3D
309    
# Line 570  in content: Horizontal Dissipation: 2 ti Line 313  in content: Horizontal Dissipation: 2 ti
313  2.9.2 NLFS  2.9.2 NLFS
314  - eq.Nb are wrong in html  - eq.Nb are wrong in html
315  - 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)
316     <- DONE
317    
318  2.10.1 Notation  2.10.1 Notation
319  - Area definition is not really used like this  - Area definition is not really used like this
# Line 578  in content: Horizontal Dissipation: 2 ti Line 322  in content: Horizontal Dissipation: 2 ti
322    
323    Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to    Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
324    the model variables) are used (e.g., see section 2.10.5)    the model variables) are used (e.g., see section 2.10.5)
325    <- DONE
326    
327  2.10.5 Horizontal grid:  2.10.5 Horizontal grid:
328  - fig.2.8 : should use Aw,As consistently in this figure description,  - fig.2.8 : should use Aw,As consistently in this figure description,
329    in the figure itself, as it is in the text.    in the figure itself, as it is in the text. <- DONE
330  - curvilinear:  - curvilinear:
331    to add: mention the angle of the grid direction relative to    to add: mention the angle of the grid direction relative to
332    Eastward, Northward direction.    Eastward, Northward direction.
333    + mention horizGridFile= in file "data" (PARM04)    + mention horizGridFile= in file "data" (PARM04)
334  - add cylindrical grid description  - add cylindrical polar grid description
335       need to do a better job of relating model variables to this diagram
336    
337    
338  2.11 Continuity & Horizontal Pressure gradient terms  2.11 Continuity & Horizontal Pressure gradient terms
339   - mention that d.Phi/dr|s =g if using z coordinate   - mention that d.Phi/dr|s =g if using z coordinate
# Line 608  in content: Horizontal Dissipation: 2 ti Line 355  in content: Horizontal Dissipation: 2 ti
355  2.13.5 Lateral dissipation  2.13.5 Lateral dissipation
356   - add description of how to use cosFactor & cosPower   - add description of how to use cosFactor & cosPower
357   - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4   - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
358        o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
359          in code need to explain why cos()3/2 turns out to be
360          scaling (not cos()2)
361     - need to reference the smag/leith section.
362    
363  2.13.6 Vertical dissipation  2.13.6 Vertical dissipation
364   - 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 626  in content: Horizontal Dissipation: 2 ti Line 377  in content: Horizontal Dissipation: 2 ti
377    
378  2.16 & 2.17 & 2.18 :  2.16 & 2.17 & 2.18 :
379   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
380     - fix equations 2.202 & 2.203 (thanks to Martin) <- DONE
381    
382  2.20.2 mercator, non-dimensional Equations:  2.20.2 mercator, non-dimensional Equations:
383  - does not use std notation  - does not use std notation
384  - would be better as an appendix of section 2.20:  - would be better as an appendix of section 2.20:
385  (e.g changing the tile to:  (e.g changing the tile to:
386    - talk to Baylor
387   Appendix: non-dimensional Equations on Spherical-Polar grid.)   Appendix: non-dimensional Equations on Spherical-Polar grid.)
388     <- No (Chris said)
389    
390    
391    Diagrams of grid locations etc.... and what variables and output files
392    and/or netcdf variable names are not very easy to figure out and follow.
393    It would be good to redo and extend these diagrams and align with GRID.h
394    content.
395    
396    
397  JM  JM
398    
399    
400    >>>> From Andrea
401    
402    Chapter 3
403    --------
404    
405    Almost all of the 'math mode' text is dropped down as subscripts
406    
407    3.11.3.1 - refers to figures and equations, links are broken
408    
409    3.12.3.2 - line 43: link to equation is broken
410             - line 51-53: link to equation is broken
411             - there is some mess of text hanging around the end of this section. remove? reformat?
412    
413    3.13.4.1 - line 34 - link to equation is broken
414             - lines 60,61 - 1st (take out the 'r' in the superscript)
415    
416    3.14.2 - link to theta-equation is broken
417    3.14.5.4 -- ALL of the bold links to variable names are broken
418                line 34: link to equation is broken
419    
420     o Update basic intro with one and four layer gyres
421       - include advection options
422       - conservation analysis
423       - diagnostics
424    
425     o Four degree adjoint
426       - both TAF and OpenAD based.
427    
428     o Coupled with biogeo setup
429       - based on CCGS setup
430    
431    
432    >>>> From Ed
433    
434    Here are the remaining bits for Chap 4 :
435    
436     - missing references (if you point me towards URLs, I'll add them
437       to the bibliography):
438         \ref{ref hoe and hill, ecmwf}
439         \ref{magicgarden}
440         \ref{IBMLAPI}
441         \ref{Memorychannel}
442         \ref{hoe-hill:99}
443    
444     - There are a few empty sub-sections at the end of Chap 4 that
445       should either be commented out or fleshed out.
446    
447    and thats about it for Chap 4.
448    
449    
450    Add more to quick links on front page
451    
452    Chapter 6
453    
454       the master package diagram does not appear in the document <- done
455     (<- needs an update: e.g. atm2d, salt_plume, shelfice ...)
456    
457    Master list of packages (add this to beginning of chap 6)
458     (<- needs an update: e.g. atm2d, salt_plume, shelfice ...)
459    
460    admtlm/               - autodiff (chapter 5)
461    aim/                  - retired
462    aim_compon_interf/    - 6.6 (no content yet)(Daniel + JM)
463    aim_ocn_coupler/      - 6.6 (no content yet)
464    aim_v23/              - 6.4.1 (content needs fixing - JM to do)
465    atm_common/           - nothing in this package (6.4.1 related)
466    autodiff/             - autodiff (chapter 5)
467    bulk_force/           - 6.3.3
468    cal/                  - 6.3.5
469    cd_code/              - chapter 2 (JM check add a reference to paper,
470                              mention parameter in data)
471    cfc/                  - not sure  (CNH to talk to Steph and Helen)
472    chronos/              - AM to check (not being used - Andrea to kill it)
473    compon_communic/      - 6.6 (no content yet)(Daniel + JM)
474    cost/                 - not sure, check with PH
475    ctrl/                 - not sure, check with PH
476    debug/                - JM may do something in chapter 7 (utilities)
477    diagnostics/          - 7.1
478    dic/                  - 6.7.2
479    ebm/                  - (check with PH)
480    ecco/                 - chapter 8
481    embed_files/          - add something to chapter 7
482    exch2/                - 6.2.2
483    exf/                  - 6.3.4
484    fizhi/                - 6.4.3
485     o Including FIZHI doc
486       - get things up to date
487    flt/                  - (PH check)
488    gchem/                - 6.7.1
489    generic_advdiff/      - in chapter 2 (JM check)
490    ggl90/                - nothing, (Martin?)
491    gmredi/               - in chapter 2 (JM check). also need
492                            Ferrari & Mc transition zone stuff (Samar doing this)
493                            get dfer to read this
494    grdchk/               - grdchk (chapter 5 - check with PH)
495    gridalt/              - 6.2.4
496    kpp/                  - 6.3.2
497    land/                 - 6.4.2 (not connected to code Rong's notes - JM to fix)
498    matrix/               - Samar
499    mdsio/                - 7.3.1
500    mnc/                  - 7.2.1
501    mom_common/           - in chapter 2 (JM check)
502    mom_fluxform/         - in chapter 2 (JM check)
503    mom_vecinv/           - in chapter 2 (JM check)
504    monitor/              - 7.4
505    my82/                 - nothing, (martin?)
506    obcs/                 - 6.3 (needs a check - ask PH to read)
507    ocn_compon_interf/    - 6.6 (no content yet)
508    offline/              - nothing, tutorials that need work but no package   section entry
509                            trivial to document (CNH to do)
510    opps/                 - nothing, (martin?)
511    pp81/                 - nothing, (martin?)
512    profiles/             - GAEL
513    ptracers/             - JM + SD + Martin to write something (nothing for this
514                              at the moment)
515                            AM has diagnostics table for this.
516    rbcs/                 - CNH to talk to steph
517    runclock/             - runclock - CNH
518    rw/                   - not sure - going to stay says JMC. quick IO calls
519                            JMC to write a quick note for that.
520    sbo/                  - text in sbo_descruption.tex but not linked into
521                            part6 - CNH
522    seaice/               - 6.5.2 - no equations, dimitris has promised some
523    shap_filt/            - chapter 2, JM to check
524    shelfice/             - nothing yet (martin?)
525    solver/               - empty (go away?)
526    sphere/               - chapter 5 or 8 (PH to check)
527    therm_seaice/         - empty (go away?)
528    thsice/               - 6.5.1 (JM to update?)
529    timeave/              - retiring......
530    zonal_filt/           - chapter 2 (JM to check)
531    
532     o Cost function packages
533       - floats, weights, profiles etc...
534    
535    
536    list an expeiment which uses package? CNH
537    
538    6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
539     Figure 6.8 is missing
540    
541    
542    =====  Chapter 7  =====  [EH3 editing] :
543    
544     + JMC: please add description of:
545            - diagstat
546            - new temporal averaging feature
547    
548     + update the RW / MDSIO description
549       -> new meta file
550       -> list all RW S/R that one should use instead of calling directly MDSIO
551    
552     + add Graphix to the list of stuff in utils/matlab (Daniel)
553    
554     + get bathymetry pre-processing stuff from Patrick and then describe it
555    
556     + add something on spgrid mesh generator
557     o Grid generation
558       - more explanation and some step-by-step examples
559       - plotting grid examples
560    
561    
562     + add in gmaze PV calculation scripts plus write up on how it is calculated
563         http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/
564    
565    
566    andrea
567    
568    
569    9. Publications using MITgcm --> "Previous Applications of MITgcm"
570       Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
571       (check in support for more names)
572    
573    10. Under development
574    
575    Constantinos LCML
576     o Legend/LCML examples and explanation
577       - examples and explanation!
578    
579    
580    
581    Bibliography
582    
583     tidy up from misc - .tex
584    
585    Also
586    
587    a link to the new manual
588    should appear on the front page (even if it's under construction).
589    
590    updating:
591    http://mitgcm.org/r2_web_testing/latest/code_reference/callTree.html
592    which points to a 1.5 years old code. Would be good to generate a
593    new one, and even better, to try to keep it up-to-date.
594    
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