| 2 |
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| 3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 4 |
============================== |
============================== |
| 5 |
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o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
| 6 |
|
configuration |
| 7 |
|
o give MNC the ability to create additional files rather than |
| 8 |
|
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
| 9 |
|
- the default is just less than 2GB which is a practical limit |
| 10 |
|
on many systems |
| 11 |
|
o Compute the non-local term using either KPP vertical diffusivity (=default) |
| 12 |
|
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
| 13 |
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|
| 14 |
|
checkpoint55h_post |
| 15 |
|
o add verification test "vermix" |
| 16 |
|
o remove all the *_ioinc flags and replace with the single global |
| 17 |
|
outputTypesInclusive flag |
| 18 |
|
o allow to set a vertical profile of vertical diffusivity for T & S |
| 19 |
|
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
| 20 |
|
o useMNC moved from data.mnc to data.pkg |
| 21 |
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|
| 22 |
|
checkpoint55g_post |
| 23 |
|
o Renaming carbon AD experiments to comply with testreport conventions |
| 24 |
|
o Updating adjoint of Held-Suarez hs94.1x64x5 |
| 25 |
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
| 26 |
|
have been fixed to avoid recomp. of do_oceanic_phys |
| 27 |
|
Works well for global_ocean.90x40x15, |
| 28 |
|
but recomp. issue remains for carbon |
| 29 |
|
o Updating adjoint output for natl_box_adjoint after |
| 30 |
|
pkg/ecco has been modified (see taga c55d_post) |
| 31 |
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|
| 32 |
|
checkpoint55f_post |
| 33 |
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o rename to timeave_init_fixed |
| 34 |
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|
| 35 |
|
checkpoint55e_post |
| 36 |
|
o some delicate re-shuffle of store directives to avoid one |
| 37 |
|
extra call of do_oceanic_physics |
| 38 |
|
affects ecco_the_main_loop.F, do_oceanic_physics.F |
| 39 |
|
checkpoint_lev1_directives.h |
| 40 |
|
o NB: this may break global_ocean adjoint temporarily, |
| 41 |
|
but it is clear how to fix it. Will do later, need this now. |
| 42 |
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|
| 43 |
|
checkpoint55d_post |
| 44 |
|
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
| 45 |
|
o ecco_cost_weights is modified to 1x1 runs |
| 46 |
|
o modifs to allow observations to be read in as |
| 47 |
|
single file or yearly files |
| 48 |
|
o enable to read exf forcing fields as either |
| 49 |
|
single file or yearly files (flag useExfYearlyFields) |
| 50 |
|
checkpoint55d_pre |
| 51 |
|
|
| 52 |
|
o switch between 2-level and 3-level checkpointing |
| 53 |
|
o add ability of MNC to write local and "partial" (eg. 2D slices where |
| 54 |
|
the full 3D field is never actually stored) arrays to NetCDF files |
| 55 |
|
with the correct (that is, the complete multi-dimensional) set of |
| 56 |
|
array indicies |
| 57 |
|
- used in mom_vecinv() to write the diagFreq output |
| 58 |
|
- tested (demonstrated) in verification/aim.5l_cs |
| 59 |
|
o further mnc-ification |
| 60 |
|
- add verification/lab_sea to the list with mnc setups |
| 61 |
|
- fix undefined mnc v-names in cd_code |
| 62 |
|
- add kpp to mnc output (both snapshot and timeave) |
| 63 |
|
o non-hydrostatic code |
| 64 |
|
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
| 65 |
|
in calc_gw.F |
| 66 |
|
- defaults to viscAh |
| 67 |
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
| 68 |
|
friction or Leith) in non-hydrostatic mode, as long as there is |
| 69 |
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
| 70 |
|
o pkg/cost |
| 71 |
|
extend simple cost functions to treat time mean quantities |
| 72 |
|
(T,U,V) via cost_accumulate_state from cost_tile |
| 73 |
|
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
| 74 |
|
be 2 times larger than the minimum size the advection scheme requires. |
| 75 |
|
now get a perfect conservation of salt in advect_cs test-exp (updated) |
| 76 |
|
o GGL90 (Gaspar's TKE mixed layer) |
| 77 |
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- add horizontal diffusion of TKE, requires exchanges in |
| 78 |
|
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
| 79 |
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default. In OPA there is no horizontal diffusion of TKE but the |
| 80 |
|
mixing coefficients are computed from a horizontal average of TKE of |
| 81 |
|
6 points or so. I think that diffusion has a little more physical |
| 82 |
|
justification. |
| 83 |
|
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
| 84 |
|
was in vain) |
| 85 |
|
- mask tke-variable in ggl90_init |
| 86 |
|
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
| 87 |
|
o fix biharmonic diffusion on CS-grid. |
| 88 |
|
o more obcs stuff |
| 89 |
|
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
| 90 |
|
for reading boundary values. This routine is called from |
| 91 |
|
obcs_prescribe_read |
| 92 |
|
- updated obcs_check |
| 93 |
|
- changed sponge layer relaxation parameter units for days to seconds |
| 94 |
|
- turned off sponge layer by default |
| 95 |
|
- changed argument list of OBCS_CALC to myTime+deltaTclock |
| 96 |
|
- fixed about 35 bugs in obcs_external_fields_load |
| 97 |
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|
| 98 |
|
checkpoint55c_post |
| 99 |
|
o obcs stuff |
| 100 |
|
- new runtime flags useOBCSprescribe, useOBCSbalance |
| 101 |
|
- re-arranged obcs_calc |
| 102 |
|
- moved exf_getobcs to obcs_prescibe_read |
| 103 |
|
obcs_prescibe_read is called after ORLANSKI stuff |
| 104 |
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and independent of it (executable can contain all). |
| 105 |
|
- updated obcs_check |
| 106 |
|
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
| 107 |
|
These may be necessary only if tangential velocities are |
| 108 |
|
prescribed at OB, not sure, needs testing. |
| 109 |
|
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
| 110 |
|
which simplifies the calls and passes the ifc check-bounds test |
| 111 |
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|
| 112 |
|
checkpoint55b_post |
| 113 |
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o add a 2D scalar, Z location, exchange_2 routine. |
| 114 |
|
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
| 115 |
|
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
| 116 |
|
affects advect_cs results (for the wrong reason): update output.txt |
| 117 |
|
o use a more standard discretization for biharmonic viscosity ; |
| 118 |
|
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
| 119 |
|
affects results of dome set-up: update output.txt |
| 120 |
|
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
| 121 |
|
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
| 122 |
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|
| 123 |
|
checkpoint55a_post |
| 124 |
|
o merged code to |
| 125 |
|
* prescribe/read time-dependent open boundaries |
| 126 |
|
(works in conjunction with exf, cal) |
| 127 |
|
* sponge layer code for open boundaries |
| 128 |
|
* each boundary N/S/E/W now has its own CPP option |
| 129 |
|
(healthy for the adjoint) |
| 130 |
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|
| 131 |
|
checkpoint55 |
| 132 |
|
o up-to-date adjoint of previous breaks |
| 133 |
|
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
| 134 |
|
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
| 135 |
|
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
| 136 |
|
- carbon: * remove tr1-related adjoint verification |
| 137 |
|
* add ptracer as control variable |
| 138 |
|
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
| 139 |
|
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
| 140 |
|
|
| 141 |
|
checkpoint54f_post |
| 142 |
|
o in verification/carbin/ remove experiment related to |
| 143 |
|
ALLOW_PASSIVE_TRACER (array tr1 etc) |
| 144 |
|
code_ad/ input_ad/ results_ad |
| 145 |
|
|
| 146 |
|
o add two new packages |
| 147 |
|
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
| 148 |
|
+ subject to optimization (memory) |
| 149 |
|
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
| 150 |
|
+ subject to reordering (many GOTOs in the original code) |
| 151 |
|
+ so far opps is called for every (i,j) point, and then operates in |
| 152 |
|
the vertical; one may want to reorder the scheme in order operate in |
| 153 |
|
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
| 154 |
|
fields) |
| 155 |
|
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
| 156 |
|
- all verification tests compile and run with linux_ia32_g77 |
| 157 |
|
- defaults are compatible with current input files--nothing |
| 158 |
|
should change if you were not previously using MNC |
| 159 |
|
- MNC output has been added in numerous places (eg. timeave) |
| 160 |
|
but there are still a few writes not yet do-able with MNC |
| 161 |
|
(this is in progress) |
| 162 |
|
- flags now allow for either/or/both use of MDSIO and MNC and |
| 163 |
|
documentation will soon follow |
| 164 |
|
- numerous small formatting cleanups for ProTeX |
| 165 |
|
o add version info (via BUILD_INFO.h) to MNC and stdout |
| 166 |
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|
| 167 |
|
checkpoint54e_post |
| 168 |
|
o add two new packages |
| 169 |
|
- pp81 (Packanowski and Philander, 1981), Richardson number and |
| 170 |
|
stratification dependent mixing |
| 171 |
|
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
| 172 |
|
- these scheme operate in a similar manner as KPP (without ghat, of |
| 173 |
|
course), however there is only one diffusivity that is used for both |
| 174 |
|
temperature and salinity (and passive tracers)ç |
| 175 |
|
o add offline package |
| 176 |
|
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
| 177 |
|
provided by Stephanie Dutkiewicz |
| 178 |
|
o genmake2: add ability to search for C compilers and cleanup test output |
| 179 |
|
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
| 180 |
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|
| 181 |
|
checkpoint54d_post |
| 182 |
|
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
| 183 |
|
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
| 184 |
|
leading to additional shift by 5 days each year of integration |
| 185 |
|
(i.e. leading to considerable offset over the years) |
| 186 |
|
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
| 187 |
|
o start with no AB and no initial filtering (staggerTimeStep): |
| 188 |
|
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
| 189 |
|
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
| 190 |
|
(external loading & cpl import/export stay in forward_step.F) |
| 191 |
|
o update coupling interface to work with new staggerTimeStep |
| 192 |
|
o change MDSIO ptracers_pickup. |
| 193 |
|
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
| 194 |
|
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
| 195 |
|
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
| 196 |
|
|
| 197 |
|
checkpoint54c_post |
| 198 |
|
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
| 199 |
|
this affects (truncation error) output.txt of test-exp: |
| 200 |
|
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
| 201 |
|
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
| 202 |
|
o change Qnet to always be the net heat flux, (+upward). |
| 203 |
|
affects (truncation error) output of natl_box exp.: updated |
| 204 |
|
o define the max number of passive tracers in PTRACERS_SIZE.h |
| 205 |
|
o start to test mnc routinely in exp0 |
| 206 |
|
o add sea-ice loading (sIceLoad) as a new forcing field. |
| 207 |
|
|
| 208 |
|
checkpoint54b_post |
| 209 |
|
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
| 210 |
|
impressive on Altix and Opteron systems) |
| 211 |
|
o diagnostics can now write NetCDF files through the mnc package |
| 212 |
|
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
| 213 |
|
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
| 214 |
|
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
| 215 |
|
affects (truncation error) output of lab_sea & natl_box exp.: updated |
| 216 |
|
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
| 217 |
|
|
| 218 |
|
checkpoint54a_post |
| 219 |
|
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
| 220 |
|
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
| 221 |
|
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
| 222 |
|
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
| 223 |
|
+ internal_wave (shift in writing cg2d_ini_res) |
| 224 |
|
checkpoint54a_pre |
| 225 |
|
|
| 226 |
|
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
| 227 |
|
- modified verification/lab_sea and natl_box_adjoint accordingly |
| 228 |
|
|
| 229 |
|
checkpoint54 |
| 230 |
|
checkpoint53g_post |
| 231 |
|
o prepare splitting of thermodynamics: store convect.counter in common block |
| 232 |
|
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
| 233 |
|
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
| 234 |
|
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
| 235 |
|
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
| 236 |
|
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
| 237 |
|
o restore adjointability |
| 238 |
|
|
| 239 |
|
checkpoint53f_post |
| 240 |
|
o modifications that affect AIM experiment results (update output.txt): |
| 241 |
|
- no advection of S at top interface Nr (pkg/generic_advdiff) |
| 242 |
|
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
| 243 |
|
o AIM pkg: |
| 244 |
|
- include stability function into surf.Flux derivative relative to Tsurf |
| 245 |
|
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
| 246 |
|
|
| 247 |
|
checkpoint53e_post |
| 248 |
|
o merged cylindrical coord configuration |
| 249 |
|
o added rotating_tank experiment |
| 250 |
|
checkpoint53e_pre |
| 251 |
|
|
| 252 |
|
checkpoint53d_post |
| 253 |
|
o faulks upgraded: re-generate output.txt that have changed: |
| 254 |
|
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
| 255 |
|
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
| 256 |
|
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
| 257 |
|
o added Sadourny discretization of Coriolis |
| 258 |
|
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
| 259 |
|
- re-enabled use of omega3 (useAbsVorticity) |
| 260 |
|
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
| 261 |
|
vector-invariant equations |
| 262 |
|
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
| 263 |
|
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
| 264 |
|
hopefully without new bugs |
| 265 |
|
- still to do: biharmonic friction for non-hydrostatic w |
| 266 |
|
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
| 267 |
|
o regenerated output for global_ocean_ebm (using -ieee) |
| 268 |
|
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
| 269 |
|
of mom_common/ |
| 270 |
|
- simple re-arrangement of instructions within computing loop |
| 271 |
|
checkpoint53d_pre |
| 272 |
|
|
| 273 |
|
checkpoint53c_post |
| 274 |
|
o new version of coupler for AIM+thSIce and Ocean models |
| 275 |
|
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
| 276 |
|
- land: change Evaporation of snow |
| 277 |
|
- aim with thSIce: fix bug in snow-precip. |
| 278 |
|
o changes to calc_gw.F |
| 279 |
|
- bug fix for w^2 term near the bottom boundary |
| 280 |
|
- (hopefully) improve the lateral slip boundary condtions for use with |
| 281 |
|
partial/looped cells |
| 282 |
|
- because the bug fix changes two verification experiments anyway (exp5 |
| 283 |
|
and plume on slope), change the lateral boundary condition from half slip |
| 284 |
|
to the value of no_slip_sides |
| 285 |
|
o ebm package wasnt quite up to the parallel task. Fixed that. |
| 286 |
|
o Adjoint of EBM package + verification |
| 287 |
|
* TLM OK |
| 288 |
|
* ADM not sufficient accuracy yet (needs further testing) |
| 289 |
|
|
| 290 |
|
checkpoint53b_post |
| 291 |
|
o Commiting new energy balance model to repository |
| 292 |
|
* package is pkg/ebm |
| 293 |
|
* verif. is verification/global_ocean_ebm |
| 294 |
|
* references are in ebm_driver.F |
| 295 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
| 296 |
|
C Global thermohaline circulation. Part I: |
| 297 |
|
C Sensitivity to atmospheric moisture transport. |
| 298 |
|
C J. Climate 12(1), 71-82 |
| 299 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
| 300 |
|
C Global thermohaline circulation. Part II: |
| 301 |
|
C Sensitivity with interactive transport. |
| 302 |
|
C J. Climate 12(1), 83-91 |
| 303 |
|
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
| 304 |
|
C Destabilization of the thermohaline circulation |
| 305 |
|
C by atmospheric eddy transports. |
| 306 |
|
C J. Climate 7(12), 1870-1882 |
| 307 |
|
o Will need long integration testing. |
| 308 |
|
checkpoint53b_pre |
| 309 |
|
|
| 310 |
|
o created pkg/mom_common in preparation for variable viscosity code |
| 311 |
|
o renamed and split ini_mnc_io |
| 312 |
|
o pkg/land: only liquid water can diffuse or run-off |
| 313 |
|
o AIM using land: soil wetness availability account for snow |
| 314 |
|
o added printMapIncludesZeros to EEPARMS namelist |
| 315 |
|
|
| 316 |
|
checkpoint53a_post |
| 317 |
|
o restore TAMC compatiility for exf_constants.h |
| 318 |
|
(no usage of _d in .h) |
| 319 |
|
o Additional storing in KPP in an attempt to fix |
| 320 |
|
TAMC problem with adjoint of KPP code. |
| 321 |
|
(no success...) |
| 322 |
|
Identical code works fine with TAF. |
| 323 |
|
o Fixed verification/natl_box_adjoint experiments. |
| 324 |
|
Initial conditions for Experiments 4 and 5 are now |
| 325 |
|
set to "SEAICE_initialHEFF=0", which is more reasonable, |
| 326 |
|
and hence gives results closer to that of Experiment 2. |
| 327 |
|
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
| 328 |
|
|
| 329 |
|
checkpoint53 |
| 330 |
|
o stable checkpoint with up to date adjoint |
| 331 |
|
TLM tests only run for 1st grdchk at the moment. Its unclear if |
| 332 |
|
this is a code problem or a problem with resetting code for g_ |
| 333 |
|
variables that is being autogenerated wrong. |
| 334 |
|
Otherwise: |
| 335 |
|
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
| 336 |
|
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
| 337 |
|
are both still in chaos following their security messes. |
| 338 |
|
|
| 339 |
|
checkpoint52n_post |
| 340 |
|
o various build (mostly genmake2) changes including: |
| 341 |
|
- ability to build/run more easily within Cygwin and MacOS X |
| 342 |
|
- more complicated Makefiles with a stronger dependence on Gnu Make |
| 343 |
o pkg/seaice modifications |
o pkg/seaice modifications |
| 344 |
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
| 345 |
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
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