| 1 |
Editors |
| 2 |
|
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Overall - JM, AM, PH, CNH, EH3 |
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|
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Front content - EH3 |
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|
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Chapter 1 - CNH |
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|
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Chapter 2 - JMC |
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|
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Chapter 3 - AM |
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|
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Chapter 4 - CNH |
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|
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Chapter 5 - PH |
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|
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Chapter 6 - AM |
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|
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Chapter 7 - EH3 |
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|
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Chapter 8 - PH |
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|
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Chapter 9 - CNH (Applications) |
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|
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Chapter 10 - JMC (Under development chapter) |
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|
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Biblio - EH3 |
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|
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|
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Rebuild and set to do cron build - DONE on hugo |
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|
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To do |
| 33 |
|
| 34 |
- 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. |
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|
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o HTML, scripts and front content |
| 45 |
|
| 46 |
- pick a URL: mitgcm.org/r2 <-- EH3's preferred base URL |
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|
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- mitgcm.org/r2_web_testing/latest |
| 49 |
|
| 50 |
o --DONE-- add another short-cut for quick download |
| 51 |
|
| 52 |
o --DONE-- add another short-cut |
| 53 |
About |
| 54 |
Installation |
| 55 |
Contents |
| 56 |
Overview |
| 57 |
Tutorials (broken) |
| 58 |
Browse Code |
| 59 |
|
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o --DONE-- words on http://mitgcm.org/r2_web_testing/latest change to |
| 61 |
|
| 62 |
o --DONE-- finite-volume doesn't leap to FV figure |
| 63 |
|
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o -- DONE ??? -- have another go at pnmcrop et al. |
| 65 |
|
| 66 |
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 |
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|
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To view the altered alignment, see: |
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|
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http://eddy.csail.mit.edu/r2/latest/ |
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|
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o Need an empty package as part of distribution. Check out atm_common |
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|
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|
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o Latex |
| 81 |
|
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Chapter 1 - CNH |
| 83 |
o single kernel diagram - |
| 84 |
add reference to MWR paper |
| 85 |
|
| 86 |
o non-hydro |
| 87 |
add reference to 1995 and 1999 papers |
| 88 |
pdf of 1995 paper |
| 89 |
|
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o FV |
| 91 |
add references to 1997 papers. |
| 92 |
|
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o Tangent linear/adjoint add reference to |
| 94 |
Heimbach papers, Marotzke, 1998 ECMWF, Bugi etc... |
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|
| 96 |
o platforms |
| 97 |
Add reference to SC article and Scientific Programming article |
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|
| 99 |
o List of key papers needs to be updated and reformatted |
| 100 |
|
| 101 |
o Global atmosphere: `Held Suarez', |
| 102 |
update Adcroft reference |
| 103 |
fix up ingrid link and frame (ingrid movies seem to be broken?) |
| 104 |
Held and Suarez reference is not a link. |
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|
| 106 |
o Ocean Gyres |
| 107 |
fix up frame link |
| 108 |
make "lopped cell" a link to referenced paper. |
| 109 |
add references (ask Steph/Mick) |
| 110 |
online/offline paper |
| 111 |
|
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o Convection and mixing over topography |
| 113 |
add in Legg references for convection and mixing over topography |
| 114 |
and external link to CPT-GCE etc... |
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|
| 116 |
o Boundary forced internal waves |
| 117 |
add in Legg references, obc's reference |
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|
| 119 |
o Parameter sensitivity |
| 120 |
add in Bugnion references, Boyin references, Steph references |
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|
| 122 |
o State estimation |
| 123 |
add in references from Patrick/Carl/Ichiro/Detlef etc... |
| 124 |
update links to point to latest ECCO results |
| 125 |
ECCO ingrid results have been moved |
| 126 |
add forward links to "ECCO state estimation" chapter in manual |
| 127 |
|
| 128 |
o Ocean biogeochemical cycles |
| 129 |
add in references from Mick/Galen etc... |
| 130 |
fix ingrid link ( date to date thing does not appear to work) |
| 131 |
figure url does not have a "target=idontexist" entry |
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|
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o Simulations of laboratory experiments |
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reference Wardle and Karsten papers |
| 135 |
update links to include DDDAS "PIAB" page |
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cylindrical polar coordinates |
| 137 |
|
| 138 |
o Continuos equations in ''r'' coordinates |
| 139 |
add references to iso paper |
| 140 |
no mention of z* and p* - forward reference to z*/p* in 2. |
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add that coupling also manifests through F, Q |
| 142 |
add tracer transport |
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|
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o Kinematic boundary conditions |
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|
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o Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and |
| 147 |
Non-hydrostatic forms |
| 148 |
need to tidy up discussion of shallow-atmosphere to be |
| 149 |
consistent with the code or change code to be consistent |
| 150 |
with the discussion! |
| 151 |
make references hyperlinks |
| 152 |
add stuff too |
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JMC remove QNH atmosphere |
| 154 |
need to sort out calc_gw for deep atmosphere |
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|
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o Finding the pressure field |
| 157 |
make references hyperlinks |
| 158 |
add forward references to manual algorithm section |
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change Elliptic to "elliptic" |
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|
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o Forcing and dissipation |
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make "physics packages" refer to chapter 6. |
| 163 |
should we move "external forcing" et. al to a |
| 164 |
generic_forcing_driver package? |
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|
| 166 |
viscosities |
| 167 |
update to mention Smag/Leith (Ah and A4 not constant) |
| 168 |
and to have forward references to numerical section |
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tracers |
| 170 |
forward references to numerical section, reddy, GM etc... |
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add references to literature |
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|
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o 1.3.8 Vector invariant form |
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forward references to numerical section |
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|
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o 1.3.9 Adjoint |
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add a little more here + some hyperlink to chapter 5. |
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|
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o 1.4 Appendix ATMOSPHERE |
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|
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add some introductory words |
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|
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o 1.6 Coordinate systems |
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o only has some words on spherical polar. add some brief words |
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to cover all of |
| 186 |
- cartesian |
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- spherical |
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- cylindrical |
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- general orthogonal curvilinear (vector invariant) |
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|
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o Equation of state options |
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add some discussion |
| 193 |
can't remember what we said we were going to do here |
| 194 |
PH to do something |
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|
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|
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Change hydrodynamical to "dynamical" |
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|
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Examples |
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|
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- extra "in action" cases |
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|
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o high res ocean with diurnal atmospheric state forcing |
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- links to ingrid output |
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CNH/Dimitris |
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|
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o realistic FIZHI from Andrea |
| 208 |
- links to ingrid output |
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from AM |
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|
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o with seaice on high res cube |
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- links to ingrid output |
| 213 |
CNH/Dimitris |
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|
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o coupled aqua, ridge world etc... |
| 216 |
- links to ingrid output |
| 217 |
get stuff from Daniel |
| 218 |
Davids donut movie |
| 219 |
|
| 220 |
o constrained lab simulation |
| 221 |
- links to ingrid output for model and lab |
| 222 |
fields |
| 223 |
get stuff from Sai/Andrew |
| 224 |
|
| 225 |
o sensitivity wrt to iron |
| 226 |
|
| 227 |
o optimization |
| 228 |
- update to link to latest ECCO sites and GF |
| 229 |
related material |
| 230 |
|
| 231 |
o eddy diffusivity transport application |
| 232 |
|
| 233 |
o Gas giant? |
| 234 |
|
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|
| 236 |
>>>> from JM |
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|
| 238 |
|
| 239 |
manual, section.2 : |
| 240 |
|
| 241 |
In general: |
| 242 |
- add more refences/links to S/R & variable name |
| 243 |
- 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 |
| 245 |
- search for CALC_MOM_RHS and replace it by the appropriate S/R |
| 246 |
(mom_flux_form, mom_vecinv, dynamics) <- DONE |
| 247 |
- 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}} |
| 249 |
in section.2, \vec{\bf v} is used instead and 3.D velocity vector is |
| 250 |
simply written \vec{v}. |
| 251 |
I would suggest to keep the notation as they are (since they are consistent |
| 252 |
inside each section) but may be to move the "notation.tex" piece |
| 253 |
at the beginning of section.2 and to mention clearly the changes between |
| 254 |
the 2 sections. |
| 255 |
|
| 256 |
in content: Horizontal Dissipation: 2 times in vector-invariant section |
| 257 |
<- DONE |
| 258 |
|
| 259 |
2.1 time-stepping (part2/time_stepping.tex) |
| 260 |
|
| 261 |
- this is not clear to me: |
| 262 |
|
| 263 |
>> In all the above configurations it is also possible to substitute the |
| 264 |
>> Adams-Bashforth with an alternative time-stepping scheme for terms |
| 265 |
>> evaluated explicitly in time |
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<- Leave it general. |
| 267 |
|
| 268 |
|
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2.2 rigid-lid: |
| 270 |
|
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- At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)" |
| 272 |
to stay closer to the code. |
| 273 |
- mention section 2.5 implicit-Time-stepping (for vertical viscosity) <- DONE |
| 274 |
|
| 275 |
2.3 linear free-surface: |
| 276 |
- add ref(+link) to S/R names: |
| 277 |
- add ref(+link) to Crank-Nickelson section 2.9.1 <- DONE |
| 278 |
|
| 279 |
2.4 Adams-Bashforth |
| 280 |
- add stability diagrams (I have some figures that I can put) <- DONE |
| 281 |
- add link for var. forcing_In_AB and epsil_AB <- half DONE |
| 282 |
- add S/R link for S/R ADAMS_BASHFORTH2 <-DONE |
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|
| 284 |
2.5 Implicit time-stepping |
| 285 |
- add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R |
| 286 |
SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL |
| 287 |
- update: also used for vertical advection |
| 288 |
|
| 289 |
2.6 Synchronous time-stepping: |
| 290 |
- add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE, |
| 291 |
MOMENTUM_CORRECTION_STEP. |
| 292 |
|
| 293 |
2.7 Stagger baroclinic time-stepping |
| 294 |
- mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end |
| 295 |
|
| 296 |
2.8 NH |
| 297 |
- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D |
| 298 |
|
| 299 |
2.9 Variants on Free-Surface |
| 300 |
- Delta.t mis-written (eq.2.73) <- DONE |
| 301 |
- Eq.Num missing <- DONE |
| 302 |
- u* is stored in gU (and not in gUnm1) <- DONE |
| 303 |
- Phi_nh in NH_VARS.h <- DONE |
| 304 |
- add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D, |
| 305 |
INI_CG2D, INI_CG3D |
| 306 |
|
| 307 |
2.9.1 Crank-Nickelson |
| 308 |
- link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater |
| 309 |
|
| 310 |
2.9.2 NLFS |
| 311 |
- eq.Nb are wrong in html |
| 312 |
- 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi) |
| 313 |
<- DONE |
| 314 |
|
| 315 |
2.10.1 Notation |
| 316 |
- Area definition is not really used like this |
| 317 |
|
| 318 |
>> Ao : Area of the face orthogonal to "o" direction (o=u,v,w) |
| 319 |
|
| 320 |
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) |
| 322 |
<- DONE |
| 323 |
|
| 324 |
2.10.5 Horizontal grid: |
| 325 |
- fig.2.8 : should use Aw,As consistently in this figure description, |
| 326 |
in the figure itself, as it is in the text. <- DONE |
| 327 |
- curvilinear: |
| 328 |
to add: mention the angle of the grid direction relative to |
| 329 |
Eastward, Northward direction. |
| 330 |
+ mention horizGridFile= in file "data" (PARM04) |
| 331 |
- 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 |
| 336 |
- mention that d.Phi/dr|s =g if using z coordinate |
| 337 |
- eq. 2.90 not clear regarding \delta_k(P-E) |
| 338 |
better to add the free surface eq: d.eta/dt = w_s + P-E |
| 339 |
|
| 340 |
2.12 Hydrostatic balance |
| 341 |
- add ref to Atmosphere Appendix section (1.4) since Adcroft 2002 |
| 342 |
is hard to find |
| 343 |
- add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H) |
| 344 |
and in section 1.3.4: remove the 1.3.4.3.2 subsection: |
| 345 |
Quasi-nonhydrostatic Atmosphere |
| 346 |
|
| 347 |
2.13.2 Coriolis terms |
| 348 |
- note: the discretization used when useEnergyConservingCoriolis=T |
| 349 |
has no hFac and no Area and is still different from the form |
| 350 |
described here (with Area & hFac); |
| 351 |
|
| 352 |
2.13.5 Lateral dissipation |
| 353 |
- add description of how to use cosFactor & cosPower |
| 354 |
- 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 |
| 361 |
- mention the implicit vertical viscosity option and ref to section 2.5 |
| 362 |
- add the parameter correspondence: Av <-> viscAr (and might change also |
| 363 |
the notation to Ar) |
| 364 |
|
| 365 |
2.14 Vector invariant momentum equations |
| 366 |
- indicate that the NH pieces (vertical momentum eq) are not yet coded |
| 367 |
and that the NH code uses the flux form. |
| 368 |
|
| 369 |
2.14.6 Horizontal dissipation -> Horizontal Divergence |
| 370 |
|
| 371 |
2.14.7 Horizontal dissipation |
| 372 |
- add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ |
| 373 |
and A_D4,A_z4 <-> viscA4D,viscA4Z |
| 374 |
|
| 375 |
2.16 & 2.17 & 2.18 : |
| 376 |
- 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: |
| 380 |
- does not use std notation |
| 381 |
- would be better as an appendix of section 2.20: |
| 382 |
(e.g changing the tile to: |
| 383 |
- talk to Baylor |
| 384 |
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 |
| 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 |