| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
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|
| 7 |
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o script to test restart (for now, in MITgcm_contrib/jmc_script) |
| 8 |
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o pkg/seaice: new read/write pickup version. |
| 9 |
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read meta file and write only fields which are needed to restart. |
| 10 |
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( same logic as main pickup file ; also using pickupStrictlyMatch ) |
| 11 |
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o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) |
| 12 |
|
o lab_sea.hb87: modify the domain & update output.hb87.txt : |
| 13 |
|
lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 |
| 14 |
|
at j=1 & j=Ny+1 : this case is not treated correctly in the restart |
| 15 |
|
process. Fixed here by closing the domain at the Northern boundary. |
| 16 |
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o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. |
| 17 |
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o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing |
| 18 |
|
a set of consecutive levels in/from a 3-D array. |
| 19 |
|
o pkg/ptracers: |
| 20 |
|
use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). |
| 21 |
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to-do: fix pkg/diagnostics when large number of diagnostics are defined. |
| 22 |
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|
| 23 |
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checkpoint59j |
| 24 |
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o in pkgs: dic, obcs, offline, rbcs: |
| 25 |
|
standard way to compute coeff. for time interpolation between 2 time reccords |
| 26 |
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which retains full precision (& make results less dependent on compiler). |
| 27 |
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update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. |
| 28 |
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o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those |
| 29 |
|
packages instead of reading ice cover and wind speed separately |
| 30 |
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o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h |
| 31 |
|
(keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad |
| 32 |
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to allow to compile customized code before the update) |
| 33 |
|
o cleaning-up: |
| 34 |
|
- fix CPP instruction syntax in pkg/obcs |
| 35 |
|
- replace (some) call to MDSIO S/R with call to RW interface S/R ; and |
| 36 |
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add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio) |
| 37 |
|
- fix some threads issue in IO parts. |
| 38 |
|
o pkg/dic: |
| 39 |
|
- add tons of "_d 0" (--> much better testreports !) |
| 40 |
|
and then update outputs of tutorial_global_oce_biogeo |
| 41 |
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o pkg/mom_fluxform: |
| 42 |
|
add a special version of momentum advection intended to conserve momentum |
| 43 |
|
next to a bathymetry step or a coastline edge. (default = off = #undef) |
| 44 |
|
o new read/write pickup version: |
| 45 |
|
- for now, only implemented for main (mdsio) pickup file. |
| 46 |
|
- write out only what is needed to restart; merge pickup_nh , pickup_ph |
| 47 |
|
and main pickup together. |
| 48 |
|
- read meta file; read only what is needed to restart; stop if a field |
| 49 |
|
is missing (if pickupStrictlyMatch=T, = the default) or try to restart |
| 50 |
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if it make sense (even if the restart is not perfect). |
| 51 |
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- if no meta file, assume that pickup to read corresponds exactly to |
| 52 |
|
a pickup that would currently be written. |
| 53 |
|
- read pickup written in the old format (until checkpoint59i) if it |
| 54 |
|
recognizes an old meta file (no field-list). |
| 55 |
|
- add a meta file in exp. which starts from a pickup: 2 cases: |
| 56 |
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a) minimal meta file (with just file precision) + pickupStrictlyMatch=F |
| 57 |
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e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta |
| 58 |
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b) a meta file describing the content of the associated pickup file |
| 59 |
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e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta |
| 60 |
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o pkg/mdsio & pkg/rw: |
| 61 |
|
- new routine to read a meta file ; new set of routine to read |
| 62 |
|
Multiple-fields file (with meta file). |
| 63 |
|
o added open boundary conditions capability for seaice |
| 64 |
|
HSNOW, HSALT, UICE, and VICE |
| 65 |
|
|
| 66 |
|
checkpoint59i |
| 67 |
|
o adjoint: |
| 68 |
|
* fix multiDimAdvection adjoint |
| 69 |
|
(partial recomputation problem by TAF for fVerT(:,:,kDown) |
| 70 |
|
and comlev1 size definition (maxpass vs. max. number of tracers) |
| 71 |
|
* verification/global_ocean.90x45x15 adjoint now tests |
| 72 |
|
NLFS and multiDimAdvection using DST3 (=30) |
| 73 |
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* verification/lab_sea now tests multiDimAdvection using DST3 (=30) |
| 74 |
|
o pkg/kpp: add "_d 0" to real constant (if missing); |
| 75 |
|
update output of exp: natl_box (10.digits); vermix (std, 7.digits) |
| 76 |
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and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). |
| 77 |
|
o prepare for "clever pickup" implementation: add new header file "RESTART.h" |
| 78 |
|
for internal parameters related to restart process (formerly from PARAMS.h) |
| 79 |
|
and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. |
| 80 |
|
o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed |
| 81 |
|
as argument. (only atm2d & obcs write_pickup have not yet been updated) |
| 82 |
|
o pkg/monitor: |
| 83 |
|
- use GLOBAL_SUM_TILE instead of _GLOBAL_SUM |
| 84 |
|
- fix mon_stats_rs (statistics over the full domain, even where field is zero) |
| 85 |
|
- account for deep Atmosphere factor and density factor (anelastic) |
| 86 |
|
o added open boundary conditions capability for seaice HEFF and AREA |
| 87 |
|
o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) |
| 88 |
|
thermodynamics |
| 89 |
|
- requires a little reorganization, which affects the testreport results |
| 90 |
|
of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, |
| 91 |
|
so that now the conservative form is tested |
| 92 |
|
- add a few comments |
| 93 |
|
o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* |
| 94 |
|
o add a little bit of code to gad_os7mp_adv_?.F to help vectorization |
| 95 |
|
o add new diagnostics to seaice: advective, diffusive fluxes (only for |
| 96 |
|
multidim-advection, for scheme 2 they are not filled) and transports, |
| 97 |
|
thermodynamic growth rates |
| 98 |
|
o change units of EmPmR (inside the code, + within coupling interface) |
| 99 |
|
from m/s to kg/m2/s (mass flux) but leave input file unchanged. |
| 100 |
|
Affects results @ truncation level (cg2d match) and update output of |
| 101 |
|
experiments: lab_sea(6), global_ocean.90x40x15(10), |
| 102 |
|
global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) |
| 103 |
|
+ adjoint results: global_ocean_ebm(11) and lab_sea (12). |
| 104 |
|
Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). |
| 105 |
|
Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). |
| 106 |
|
|
| 107 |
|
checkpoint59h |
| 108 |
|
o pkg/exf: |
| 109 |
|
- improve vectorization by moving if-statement out of loops in |
| 110 |
|
exf_mapfields, exf_radiation |
| 111 |
|
- exf_bulkformulae.F: introduce 2D fields and vectorize code |
| 112 |
|
o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package |
| 113 |
|
o testreport: |
| 114 |
|
- allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE |
| 115 |
|
monitor & update offline_exf_seaice exp. output. |
| 116 |
|
- AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) |
| 117 |
|
o pkg/seaice: |
| 118 |
|
- bug fix in the evp solver: boundary conditions were affected be |
| 119 |
|
masking of zMax/zMin (changes results) |
| 120 |
|
- minor bug fix in boundary conditions in seaice_calc_strainrates |
| 121 |
|
(changes results for no_slip) |
| 122 |
|
- seaice_lsr.F: make interpolation of eta dependent on boundaries |
| 123 |
|
- replace hardcoded lower limit for zeta (zMin) by runtime parameter |
| 124 |
|
- add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean |
| 125 |
|
stress formulation and no-slip boundary conditions |
| 126 |
|
o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP |
| 127 |
|
in gad_calc_rhs.F ; add few safety stops in initialisation phase. |
| 128 |
|
o pkg/seaice: a first HSALT time stepping equation has been checked in |
| 129 |
|
o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV |
| 130 |
|
in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem |
| 131 |
|
without requiring DO-IF statements |
| 132 |
|
o pkg/thsice: |
| 133 |
|
use continuous power-law function for partition of energy between lateral |
| 134 |
|
melting/freezing and thinning/thickening ; old code using step function |
| 135 |
|
still available with #undef THSICE_FRACEN_POWERLAW |
| 136 |
|
update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice |
| 137 |
|
o testreport: change AD testing : check against results/output_adm.txt |
| 138 |
|
using same scripts as for forward test. |
| 139 |
|
|
| 140 |
|
checkpoint59g |
| 141 |
|
o adjoint testing: in preparation for changing testreport: |
| 142 |
|
- output format: cost and grad written on separated lines |
| 143 |
|
- ad output results in directory "results" (instead of "results_ad") |
| 144 |
|
o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
| 145 |
|
o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
| 146 |
|
o pkg/ecco: allow user defined cost function contributions |
| 147 |
|
o testreport: |
| 148 |
|
Allow to choose (per experiment) the list of tested output variables |
| 149 |
|
and the main variable (used to issue a pass/FAIL ) ; |
| 150 |
|
- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
| 151 |
|
- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
| 152 |
|
Also modify printing of summary: |
| 153 |
|
a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
| 154 |
|
b) echo the list of tested variables in the individual summary.txt of |
| 155 |
|
each experiment. |
| 156 |
|
o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
| 157 |
|
threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
| 158 |
|
(but still depend on the tile decompostion of the domain). |
| 159 |
|
o pkg/seaice: change a discretization detail to make the B-grid code |
| 160 |
|
"more symmetric". This change is likely to remove all "ridges/leads" that |
| 161 |
|
where quasi-aligned with the grid in B-grid solutions. It may also be |
| 162 |
|
the solution to the stress coupling issues with the B-grid. |
| 163 |
|
o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
| 164 |
|
remove .cvsignore from input dir. (since testreport no longer run here). |
| 165 |
|
o pkg/thsice: |
| 166 |
|
- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
| 167 |
|
- fix reshaping of sea-ice just after advection: |
| 168 |
|
melt all the ice only if ice-volume is too small. |
| 169 |
|
- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
| 170 |
|
prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
| 171 |
|
and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
| 172 |
|
o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
| 173 |
|
tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
| 174 |
|
o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
| 175 |
|
forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
| 176 |
|
(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
| 177 |
|
and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
| 178 |
|
of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
| 179 |
|
-> update output.txt |
| 180 |
|
o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
| 181 |
|
this affects truncation error: -> update output.txt of exp: |
| 182 |
|
global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
| 183 |
|
ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
| 184 |
|
|
| 185 |
|
checkpoint59f |
| 186 |
|
o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
| 187 |
|
o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
| 188 |
|
a bounded range (in forward mode) |
| 189 |
|
o pkg/ecco, ctrl, autodiff and mom_common: |
| 190 |
|
internal parameter controls, completements of implementations |
| 191 |
|
o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
| 192 |
|
o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
| 193 |
|
(not seem any difference in testing results). |
| 194 |
|
o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
| 195 |
|
at face corners. |
| 196 |
|
o pkg/generic_advdiff: |
| 197 |
|
- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
| 198 |
|
loop range indices for computing vertical advection tendency |
| 199 |
|
and do the calculation in the interior only (no overlap) ; |
| 200 |
|
for now, only implemented for SOM advection (to save CPU time). |
| 201 |
|
- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
| 202 |
|
o exch2 adjoint |
| 203 |
|
First set of changes: |
| 204 |
|
- add exch2 hand-written adjoint templates |
| 205 |
|
- exch2 hand-written no longer use TAF-flag 'nownew_arg' |
| 206 |
|
This will require cleanup in pkg/autodiff/*.F |
| 207 |
|
(changed routines currently kept separate in verif. code/) |
| 208 |
|
- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
| 209 |
|
that used to hide exch2 or cubed-sphere specific code |
| 210 |
|
(commented via 'cph-exch2') |
| 211 |
|
o pkg/seaice |
| 212 |
|
- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
| 213 |
|
o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
| 214 |
|
output of global_ocean.cs32x15.thsice . |
| 215 |
|
|
| 216 |
|
checkpoint59e |
| 217 |
|
o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
| 218 |
|
for B-grid vector (not yet tested) and C-grid vector (<- only used |
| 219 |
|
when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). |
| 220 |
|
o starting implementation of Duffy et al. (GRL 1999) salt plume scheme |
| 221 |
|
(#ifdef ALLOW_SALT_PLUME) |
| 222 |
|
o gather_2d/scatter_2d: removed halo regions |
| 223 |
|
o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
| 224 |
|
scheme and the corresponding test case (under front_relax dir). For now, |
| 225 |
|
only available with Skew-flux form and not yet tested in realistic set-up. |
| 226 |
|
adjoint: store directives updated, but gradient checks deteriorated, |
| 227 |
|
so maybe GM/Redi adjoint is now broken. |
| 228 |
|
o seaice adjoint |
| 229 |
|
* add AREA, HEFF, HSNOW as control variable |
| 230 |
|
(should not change lab_sea results) |
| 231 |
|
* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
| 232 |
|
o pkg/seaice: |
| 233 |
|
* added computation of saltFlux in seaice_growth; |
| 234 |
|
For time being, sea ice salinity is assumed constant |
| 235 |
|
contribution of snow flooding to freshening of sea ice is neglected. |
| 236 |
|
SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
| 237 |
|
defaults to 0.0 in order to maintain backward compatibility. |
| 238 |
|
Typical values for SEAICE_salinity are 4 to 10 g/kg. |
| 239 |
|
* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
| 240 |
|
* added SEAICE_availHeatFrac, which specifies fraction of surface level |
| 241 |
|
heat content used to melt or grow ice |
| 242 |
|
* commented out cap of HICE: it helps keep ice thinner |
| 243 |
|
* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
| 244 |
|
* applied OBCS T/S mask to HEFFM sea ice mask |
| 245 |
|
|
| 246 |
|
checkpoint59d |
| 247 |
|
o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
| 248 |
|
for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
| 249 |
|
(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
| 250 |
|
o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
| 251 |
|
and change default value of parameter "GM_Small_Number"; |
| 252 |
|
update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
| 253 |
|
global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
| 254 |
|
tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
| 255 |
|
o pkg/ecco: cost function when applying pkg/smooth to controls |
| 256 |
|
o pkg/ctrl: add forcingPrecond run time parameter |
| 257 |
|
o pkg/seaice: |
| 258 |
|
- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
| 259 |
|
- fix bug in metric terms of u-equation in LSR solver (implicit part), |
| 260 |
|
changes verification/lab_sea |
| 261 |
|
- rearrange implicit part of u-equation in LSR solver to make it easier to |
| 262 |
|
read, understand, and debug. This causes changes at the truncation level. |
| 263 |
|
- fix (serious) bug in the boundary conditions (sign error in the implicit |
| 264 |
|
part) of the LSR solver. Changes all LSR results. |
| 265 |
|
- fixed problem with HSNOW initialization to avoid thick snow when AREA |
| 266 |
|
is initilized with small values - does not change lab_sea results. |
| 267 |
|
- added HsnowFile initialization capability |
| 268 |
|
o pkg/smooth: addition to model/src and pkg/ctrl so allow |
| 269 |
|
initialization of pkg/smooth and application to control vector |
| 270 |
|
o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
| 271 |
|
o dependencies: pkg/profiles requires pkg/cal |
| 272 |
o pkg/profiles: |
o pkg/profiles: |
| 273 |
- added option ALLOW_PROFILES_GENERICGRID |
- added option ALLOW_PROFILES_GENERICGRID |
| 274 |
-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
| 278 |
that allow you to prepare netcdf input files. |
that allow you to prepare netcdf input files. |
| 279 |
- also modified: cleaner include statements, cleaner error print statements, |
- also modified: cleaner include statements, cleaner error print statements, |
| 280 |
cleaner stops when error, and more tests of the netcdf input files consistency. |
cleaner stops when error, and more tests of the netcdf input files consistency. |
|
|
|
| 281 |
o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
| 282 |
o pkg/seaice: |
o pkg/seaice: |
| 283 |
- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
| 411 |
ATMOSPHERIC_LOADING is #define). |
ATMOSPHERIC_LOADING is #define). |
| 412 |
o pkg/kpp: replaced _KPP_RL with _RL |
o pkg/kpp: replaced _KPP_RL with _RL |
| 413 |
o bug fixes for vertical diffusivity computations when both KPP and |
o bug fixes for vertical diffusivity computations when both KPP and |
| 414 |
3D diffusivity arrays are used. |
3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F |
| 415 |
|
are no longer updating the vertical diffusivity array |
| 416 |
|
(passed as argument) but are (re-) setting those arrays. |
| 417 |
o pkg/seaice: fix bug in evp solver, while doing that |
o pkg/seaice: fix bug in evp solver, while doing that |
| 418 |
- change (improve?) discretization of stress computations for both |
- change (improve?) discretization of stress computations for both |
| 419 |
cgrid-lsr and evp solver |
cgrid-lsr and evp solver |
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