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revision 1.8 by cnh, Thu Apr 6 19:14:57 2006 UTC revision 1.46 by edhill, Sun Jul 2 18:12:45 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    
30  Rebuild and set to do cron build - DONE on hugo  Rebuild and set to do cron build - DONE on hugo
31    
32  To do  To do
# Line 8  To do Line 37  To do
37      Add an "Under development, chapter" - shortish description of what      Add an "Under development, chapter" - shortish description of what
38      is available (last chapter)      is available (last chapter)
39    
40    - pick a URL    - add in example latex for formatting author names in different pieces.
41      TBD      this aknowledges peoples contributions and gives ref for who
42        to talk to.
43    
44    o HTML, scripts and front content
45    
46    - mitgcm.org very front page.    - pick a URL:  mitgcm.org/r2  <-- EH3's preferred base URL
     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  
47    
48    - mitgcm.org/r2_web_testing/latest    - mitgcm.org/r2_web_testing/latest
49      o add another short-cut for quick download      
50        o --DONE--  add another short-cut for quick download
51    
52      o add another short-cut      o --DONE--  add another short-cut
53        About                    About
54        Installation                    Installation
55        Contents                    Contents
56        Overview                    Overview
57        Tutorials (broken)                    Tutorials (broken)
58        Browse Code                    Browse Code
       Get Code (where does this go to?)  
59    
60      o authors      o --DONE--  words on http://mitgcm.org/r2_web_testing/latest change to
       John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen,  
       Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos,  
       Gael - others?  
61    
62      o Tutorials side bar link is broken      o --DONE--  finite-volume doesn't leap to FV figure
63    
64      o words      o -- DONE ??? --  have another go at pnmcrop et al.
       change to "access on-line Auser manual/A and Atable of contents/A  
       and browse the Aoverview section/A"  
65    
66      o finite-volume doesn't leap to FV figure           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 the src and equation links don't come through to           To view the altered alignment, see:
       the html when they are in figures - see chapter 2 for some  
       examples.  
74    
75      o degree symbols keep getting "dropped down" - problem with              http://eddy.csail.mit.edu/r2/latest/
       pnmcrop et al.  
76    
77        o Need an empty package as part of distribution. Check out atm_common
78    
 Contents  
79    
80      Intro                  - CNH  o Latex  
81    
82        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 70  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 116  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 164  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 262  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 278  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 508  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 519  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 527  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    
269  2.2 rigid-lid:  2.2 rigid-lid:
270    
271  - 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)"
272    to stay closer to the code.    to stay closer to the code.
273  - mention section 2.5 implicit-Time-stepping (for vertical viscosity)  - mention section 2.5 implicit-Time-stepping (for vertical viscosity) <- DONE
274    
275  2.3 linear free-surface:  2.3 linear free-surface:
276  - add ref(+link) to S/R names:  - add ref(+link) to S/R names:
277  - add ref(+link) to Crank-Nickelson section 2.9.1  - add ref(+link) to Crank-Nickelson section 2.9.1 <- DONE
278    
279  2.4 Adams-Bashforth  2.4 Adams-Bashforth
280  - add stability diagrams (I have some figures that I can put)  - add stability diagrams (I have some figures that I can put) <- DONE
281  - add link for var. forcing_In_AB  - add link for var. forcing_In_AB and epsil_AB <- half DONE
282  - add S/R link for S/R ADAMS_BASHFORTH2  - add S/R link for S/R ADAMS_BASHFORTH2 <-DONE
283    
284  2.5 Implicit time-stepping  2.5 Implicit time-stepping
285  - 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 560  in content: Horizontal Dissipation: 2 ti Line 297  in content: Horizontal Dissipation: 2 ti
297  - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D  - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
298    
299  2.9 Variants on Free-Surface  2.9 Variants on Free-Surface
300  - Delta.t mis-written (eq.2.73)  - Delta.t mis-written (eq.2.73) <- DONE
301  - Eq.Num missing (has been fixed since)  - Eq.Num missing <- DONE
302  - u* is stored in gU (and not in gUnm1)  - u* is stored in gU (and not in gUnm1) <- DONE
303  - Phi_nh in NH_VARS.h  - Phi_nh in NH_VARS.h <- DONE
304  - 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,
305    INI_CG2D, INI_CG3D    INI_CG2D, INI_CG3D
306    
# Line 573  in content: Horizontal Dissipation: 2 ti Line 310  in content: Horizontal Dissipation: 2 ti
310  2.9.2 NLFS  2.9.2 NLFS
311  - eq.Nb are wrong in html  - eq.Nb are wrong in html
312  - 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)
313     <- DONE
314    
315  2.10.1 Notation  2.10.1 Notation
316  - Area definition is not really used like this  - Area definition is not really used like this
# Line 581  in content: Horizontal Dissipation: 2 ti Line 319  in content: Horizontal Dissipation: 2 ti
319    
320    Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to    Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
321    the model variables) are used (e.g., see section 2.10.5)    the model variables) are used (e.g., see section 2.10.5)
322    <- DONE
323    
324  2.10.5 Horizontal grid:  2.10.5 Horizontal grid:
325  - fig.2.8 : should use Aw,As consistently in this figure description,  - fig.2.8 : should use Aw,As consistently in this figure description,
326    in the figure itself, as it is in the text.    in the figure itself, as it is in the text. <- DONE
327  - curvilinear:  - curvilinear:
328    to add: mention the angle of the grid direction relative to    to add: mention the angle of the grid direction relative to
329    Eastward, Northward direction.    Eastward, Northward direction.
330    + mention horizGridFile= in file "data" (PARM04)    + mention horizGridFile= in file "data" (PARM04)
331  - add cylindrical grid description  - add cylindrical polar grid description
332       need to do a better job of relating model variables to this diagram
333    
334    
335  2.11 Continuity & Horizontal Pressure gradient terms  2.11 Continuity & Horizontal Pressure gradient terms
336   - mention that d.Phi/dr|s =g if using z coordinate   - mention that d.Phi/dr|s =g if using z coordinate
# Line 611  in content: Horizontal Dissipation: 2 ti Line 352  in content: Horizontal Dissipation: 2 ti
352  2.13.5 Lateral dissipation  2.13.5 Lateral dissipation
353   - add description of how to use cosFactor & cosPower   - add description of how to use cosFactor & cosPower
354   - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4   - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4
355        o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
356          in code need to explain why cos()3/2 turns out to be
357          scaling (not cos()2)
358     - need to reference the smag/leith section.
359    
360  2.13.6 Vertical dissipation  2.13.6 Vertical dissipation
361   - 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 629  in content: Horizontal Dissipation: 2 ti Line 374  in content: Horizontal Dissipation: 2 ti
374    
375  2.16 & 2.17 & 2.18 :  2.16 & 2.17 & 2.18 :
376   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
377     - fix equations 2.202 & 2.203 (thanks to Martin) <- DONE
378    
379  2.20.2 mercator, non-dimensional Equations:  2.20.2 mercator, non-dimensional Equations:
380  - does not use std notation  - does not use std notation
381  - would be better as an appendix of section 2.20:  - would be better as an appendix of section 2.20:
382  (e.g changing the tile to:  (e.g changing the tile to:
383    - talk to Baylor
384   Appendix: non-dimensional Equations on Spherical-Polar grid.)   Appendix: non-dimensional Equations on Spherical-Polar grid.)
385     <- No (Chris said)
386    
387    
388    Diagrams of grid locations etc.... and what variables and output files
389    and/or netcdf variable names are not very easy to figure out and follow.
390    It would be good to redo and extend these diagrams and align with GRID.h
391    content.
392    
393    
394  JM  JM
395    
396    
397    >>>> From Andrea
398    
399    Chapter 3
400    --------
401    
402    Almost all of the 'math mode' text is dropped down as subscripts
403    
404    3.11.3.1 - refers to figures and equations, links are broken
405    
406    3.12.3.2 - line 43: link to equation is broken
407             - line 51-53: link to equation is broken
408             - there is some mess of text hanging around the end of this section. remove? reformat?
409    
410    3.13.4.1 - line 34 - link to equation is broken
411             - lines 60,61 - 1st (take out the 'r' in the superscript)
412    
413    3.14.2 - link to theta-equation is broken
414    3.14.5.4 -- ALL of the bold links to variable names are broken
415                line 34: link to equation is broken
416    
417    >>>> From Ed
418    
419    Here are the remaining bits for Chap 4 :
420    
421     - missing references (if you point me towards URLs, I'll add them
422       to the bibliography):
423         \ref{ref hoe and hill, ecmwf}
424         \ref{magicgarden}
425         \ref{IBMLAPI}
426         \ref{Memorychannel}
427         \ref{hoe-hill:99}
428    
429     - There are a few empty sub-sections at the end of Chap 4 that
430       should either be commented out or fleshed out.
431    
432    and thats about it for Chap 4.
433    
434    
435    Add more to quick links on front page
436    
437    Chapter 6
438    
439       the master package diagram does not appear in the document
440    
441    Master list of packages (add this to beginning of chap 6)
442    
443    admtlm/               - autodiff (chapter 5)
444    aim/                  - retired
445    aim_compon_interf/    - 6.6 (no content yet)(Daniel + JM)
446    aim_ocn_coupler/      - 6.6 (no content yet)
447    aim_v23/              - 6.4.1 (content needs fixing - JM to do)
448    atm_common/           - nothing in this package (6.4.1 related)
449    autodiff/             - autodiff (chapter 5)
450    bulk_force/           - 6.3.3
451    cal/                  - 6.3.5
452    cd_code/              - chapter 2 (JM check add a reference to paper,
453                              mention parameter in data)
454    cfc/                  - not sure  (CNH to talk to Steph and Helen)
455    chronos/              - AM to check (not being used - Andrea to kill it)
456    compon_communic/      - 6.6 (no content yet)(Daniel + JM)
457    cost/                 - not sure, check with PH
458    ctrl/                 - not sure, check with PH
459    debug/                - JM may do something in chapter 7 (utilities)
460    diagnostics/          - 7.1
461    dic/                  - 6.7.2
462    ebm/                  - (check with PH)
463    ecco/                 - chapter 8
464    embed_files/          - add something to chapter 7
465    exch2/                - 6.2.2
466    exf/                  - 6.3.4
467    fizhi/                - 6.4.3
468    flt/                  - (PH check)
469    gchem/                - 6.7.1
470    generic_advdiff/      - in chapter 2 (JM check)
471    ggl90/                - nothing, (Martin?)
472    gmredi/               - in chapter 2 (JM check). also need
473                            Ferrari & Mc transition zone stuff (Samar doing this)
474                            get dfer to read this
475    grdchk/               - grdchk (chapter 5 - check with PH)
476    gridalt/              - 6.2.4
477    kpp/                  - 6.3.2
478    land/                 - 6.4.2 (not connected to code Rong's notes - JM to fix)
479    matrix/               - Samar
480    mdsio/                - 7.3.1
481    mnc/                  - 7.2.1
482    mom_common/           - in chapter 2 (JM check)
483    mom_fluxform/         - in chapter 2 (JM check)
484    mom_vecinv/           - in chapter 2 (JM check)
485    monitor/              - 7.4
486    my82/                 - nothing, (martin?)
487    obcs/                 - 6.3 (needs a check - ask PH to read)
488    ocn_compon_interf/    - 6.6 (no content yet)
489    offline/              - nothing, tutorials that need work but no package   section entry
490                            trivial to document (CNH to do)
491    opps/                 - nothing, (martin?)
492    pp81/                 - nothing, (martin?)
493    profiles/             - GAEL
494    ptracers/             - JM + SD + Martin to write something (nothing for this
495                              at the moment)
496                            AM has diagnostics table for this.
497    rbcs/                 - CNH to talk to steph
498    runclock/             - runclock - CNH
499    rw/                   - not sure - going to stay says JMC. quick IO calls
500                            JMC to write a quick note for that.
501    sbo/                  - text in sbo_descruption.tex but not linked into
502                            part6 - CNH
503    seaice/               - 6.5.2 - no equations, dimitris has promised some
504    shap_filt/            - chapter 2, JM to check
505    shelfice/             - nothing yet (martin?)
506    solver/               - empty (go away?)
507    sphere/               - chapter 5 or 8 (PH to check)
508    therm_seaice/         - empty (go away?)
509    thsice/               - 6.5.1 (JM to update?)
510    timeave/              - retiring......
511    zonal_filt/           - chapter 2 (JM to check)
512    
513    list an expeiment which uses package? CNH
514    
515    6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
516     Figure 6.8 is missing
517    
518    
519    =====  Chapter 7  =====  [EH3 editing] :
520    
521     + JMC: please add description of:
522            - diagstat
523            - new temporal averaging feature
524    
525     + add Graphix to the list of stuff in utils/matlab (Daniel)
526    
527     + get bathymetry pre-processing stuff from Patrick and then describe it
528    
529     + add something on spgrid mesh generator
530    
531     + add in gmaze PV calculation scripts plus write up on how it is calculated
532         http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/
533    
534    
535    andrea
536    
537    
538    9. Publications using MITgcm --> "Previous Applications of MITgcm"
539       Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
540       (check in support for more names)
541    
542    10. Under development
543    
544    Constantinos LCML
545    
546    
547    Bibliography
548    
549     tidy up from misc - .tex

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