| 3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 4 |
============================== |
============================== |
| 5 |
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|
| 6 |
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checkpoint55 |
| 7 |
|
o up-to-date adjoint of previous breaks |
| 8 |
|
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
| 9 |
|
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
| 10 |
|
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
| 11 |
|
- carbon: * remove tr1-related adjoint verification |
| 12 |
|
* add ptracer as control variable |
| 13 |
|
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
| 14 |
|
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
| 15 |
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|
| 16 |
|
checkpoint54f_post |
| 17 |
|
o in verification/carbin/ remove experiment related to |
| 18 |
|
ALLOW_PASSIVE_TRACER (array tr1 etc) |
| 19 |
|
code_ad/ input_ad/ results_ad |
| 20 |
|
|
| 21 |
|
o add two new packages |
| 22 |
|
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
| 23 |
|
+ subject to optimization (memory) |
| 24 |
|
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
| 25 |
|
+ subject to reordering (many GOTOs in the original code) |
| 26 |
|
+ so far opps is called for every (i,j) point, and then operates in |
| 27 |
|
the vertical; one may want to reorder the scheme in order operate in |
| 28 |
|
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
| 29 |
|
fields) |
| 30 |
|
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
| 31 |
|
- all verification tests compile and run with linux_ia32_g77 |
| 32 |
|
- defaults are compatible with current input files--nothing |
| 33 |
|
should change if you were not previously using MNC |
| 34 |
|
- MNC output has been added in numerous places (eg. timeave) |
| 35 |
|
but there are still a few writes not yet do-able with MNC |
| 36 |
|
(this is in progress) |
| 37 |
|
- flags now allow for either/or/both use of MDSIO and MNC and |
| 38 |
|
documentation will soon follow |
| 39 |
|
- numerous small formatting cleanups for ProTeX |
| 40 |
|
o add version info (via BUILD_INFO.h) to MNC and stdout |
| 41 |
|
|
| 42 |
|
checkpoint54e_post |
| 43 |
|
o add two new packages |
| 44 |
|
- pp81 (Packanowski and Philander, 1981), Richardson number and |
| 45 |
|
stratification dependent mixing |
| 46 |
|
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
| 47 |
|
- these scheme operate in a similar manner as KPP (without ghat, of |
| 48 |
|
course), however there is only one diffusivity that is used for both |
| 49 |
|
temperature and salinity (and passive tracers)ç |
| 50 |
|
o add offline package |
| 51 |
|
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
| 52 |
|
provided by Stephanie Dutkiewicz |
| 53 |
|
o genmake2: add ability to search for C compilers and cleanup test output |
| 54 |
|
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
| 55 |
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|
| 56 |
|
checkpoint54d_post |
| 57 |
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o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
| 58 |
|
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
| 59 |
|
leading to additional shift by 5 days each year of integration |
| 60 |
|
(i.e. leading to considerable offset over the years) |
| 61 |
|
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
| 62 |
|
o start with no AB and no initial filtering (staggerTimeStep): |
| 63 |
|
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
| 64 |
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o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
| 65 |
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(external loading & cpl import/export stay in forward_step.F) |
| 66 |
|
o update coupling interface to work with new staggerTimeStep |
| 67 |
|
o change MDSIO ptracers_pickup. |
| 68 |
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o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
| 69 |
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o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
| 70 |
|
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
| 71 |
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|
| 72 |
|
checkpoint54c_post |
| 73 |
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o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
| 74 |
|
this affects (truncation error) output.txt of test-exp: |
| 75 |
|
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
| 76 |
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o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
| 77 |
|
o change Qnet to always be the net heat flux, (+upward). |
| 78 |
|
affects (truncation error) output of natl_box exp.: updated |
| 79 |
|
o define the max number of passive tracers in PTRACERS_SIZE.h |
| 80 |
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o start to test mnc routinely in exp0 |
| 81 |
|
o add sea-ice loading (sIceLoad) as a new forcing field. |
| 82 |
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|
| 83 |
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checkpoint54b_post |
| 84 |
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o add testreport "-j JOBS" option for parallel builds (tested and pretty |
| 85 |
|
impressive on Altix and Opteron systems) |
| 86 |
|
o diagnostics can now write NetCDF files through the mnc package |
| 87 |
|
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
| 88 |
|
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
| 89 |
|
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
| 90 |
|
affects (truncation error) output of lab_sea & natl_box exp.: updated |
| 91 |
|
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
| 92 |
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|
| 93 |
|
checkpoint54a_post |
| 94 |
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o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
| 95 |
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o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
| 96 |
|
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
| 97 |
|
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
| 98 |
|
+ internal_wave (shift in writing cg2d_ini_res) |
| 99 |
|
checkpoint54a_pre |
| 100 |
|
|
| 101 |
|
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
| 102 |
|
- modified verification/lab_sea and natl_box_adjoint accordingly |
| 103 |
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|
| 104 |
|
checkpoint54 |
| 105 |
|
checkpoint53g_post |
| 106 |
|
o prepare splitting of thermodynamics: store convect.counter in common block |
| 107 |
|
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
| 108 |
|
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
| 109 |
|
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
| 110 |
|
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
| 111 |
|
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
| 112 |
|
o restore adjointability |
| 113 |
|
|
| 114 |
|
checkpoint53f_post |
| 115 |
|
o modifications that affect AIM experiment results (update output.txt): |
| 116 |
|
- no advection of S at top interface Nr (pkg/generic_advdiff) |
| 117 |
|
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
| 118 |
|
o AIM pkg: |
| 119 |
|
- include stability function into surf.Flux derivative relative to Tsurf |
| 120 |
|
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
| 121 |
|
|
| 122 |
|
checkpoint53e_post |
| 123 |
|
o merged cylindrical coord configuration |
| 124 |
|
o added rotating_tank experiment |
| 125 |
|
checkpoint53e_pre |
| 126 |
|
|
| 127 |
|
checkpoint53d_post |
| 128 |
|
o faulks upgraded: re-generate output.txt that have changed: |
| 129 |
|
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
| 130 |
|
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
| 131 |
|
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
| 132 |
|
o added Sadourny discretization of Coriolis |
| 133 |
|
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
| 134 |
|
- re-enabled use of omega3 (useAbsVorticity) |
| 135 |
|
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
| 136 |
|
vector-invariant equations |
| 137 |
|
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
| 138 |
|
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
| 139 |
|
hopefully without new bugs |
| 140 |
|
- still to do: biharmonic friction for non-hydrostatic w |
| 141 |
|
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
| 142 |
|
o regenerated output for global_ocean_ebm (using -ieee) |
| 143 |
|
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
| 144 |
|
of mom_common/ |
| 145 |
|
- simple re-arrangement of instructions within computing loop |
| 146 |
|
checkpoint53d_pre |
| 147 |
|
|
| 148 |
|
checkpoint53c_post |
| 149 |
|
o new version of coupler for AIM+thSIce and Ocean models |
| 150 |
|
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
| 151 |
|
- land: change Evaporation of snow |
| 152 |
|
- aim with thSIce: fix bug in snow-precip. |
| 153 |
|
o changes to calc_gw.F |
| 154 |
|
- bug fix for w^2 term near the bottom boundary |
| 155 |
|
- (hopefully) improve the lateral slip boundary condtions for use with |
| 156 |
|
partial/looped cells |
| 157 |
|
- because the bug fix changes two verification experiments anyway (exp5 |
| 158 |
|
and plume on slope), change the lateral boundary condition from half slip |
| 159 |
|
to the value of no_slip_sides |
| 160 |
|
o ebm package wasnt quite up to the parallel task. Fixed that. |
| 161 |
|
o Adjoint of EBM package + verification |
| 162 |
|
* TLM OK |
| 163 |
|
* ADM not sufficient accuracy yet (needs further testing) |
| 164 |
|
|
| 165 |
|
checkpoint53b_post |
| 166 |
|
o Commiting new energy balance model to repository |
| 167 |
|
* package is pkg/ebm |
| 168 |
|
* verif. is verification/global_ocean_ebm |
| 169 |
|
* references are in ebm_driver.F |
| 170 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
| 171 |
|
C Global thermohaline circulation. Part I: |
| 172 |
|
C Sensitivity to atmospheric moisture transport. |
| 173 |
|
C J. Climate 12(1), 71-82 |
| 174 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
| 175 |
|
C Global thermohaline circulation. Part II: |
| 176 |
|
C Sensitivity with interactive transport. |
| 177 |
|
C J. Climate 12(1), 83-91 |
| 178 |
|
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
| 179 |
|
C Destabilization of the thermohaline circulation |
| 180 |
|
C by atmospheric eddy transports. |
| 181 |
|
C J. Climate 7(12), 1870-1882 |
| 182 |
|
o Will need long integration testing. |
| 183 |
|
checkpoint53b_pre |
| 184 |
|
|
| 185 |
|
o created pkg/mom_common in preparation for variable viscosity code |
| 186 |
|
o renamed and split ini_mnc_io |
| 187 |
|
o pkg/land: only liquid water can diffuse or run-off |
| 188 |
|
o AIM using land: soil wetness availability account for snow |
| 189 |
|
o added printMapIncludesZeros to EEPARMS namelist |
| 190 |
|
|
| 191 |
|
checkpoint53a_post |
| 192 |
|
o restore TAMC compatiility for exf_constants.h |
| 193 |
|
(no usage of _d in .h) |
| 194 |
|
o Additional storing in KPP in an attempt to fix |
| 195 |
|
TAMC problem with adjoint of KPP code. |
| 196 |
|
(no success...) |
| 197 |
|
Identical code works fine with TAF. |
| 198 |
|
o Fixed verification/natl_box_adjoint experiments. |
| 199 |
|
Initial conditions for Experiments 4 and 5 are now |
| 200 |
|
set to "SEAICE_initialHEFF=0", which is more reasonable, |
| 201 |
|
and hence gives results closer to that of Experiment 2. |
| 202 |
|
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
| 203 |
|
|
| 204 |
|
checkpoint53 |
| 205 |
|
o stable checkpoint with up to date adjoint |
| 206 |
|
TLM tests only run for 1st grdchk at the moment. Its unclear if |
| 207 |
|
this is a code problem or a problem with resetting code for g_ |
| 208 |
|
variables that is being autogenerated wrong. |
| 209 |
|
Otherwise: |
| 210 |
|
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
| 211 |
|
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
| 212 |
|
are both still in chaos following their security messes. |
| 213 |
|
|
| 214 |
|
checkpoint52n_post |
| 215 |
|
o various build (mostly genmake2) changes including: |
| 216 |
|
- ability to build/run more easily within Cygwin and MacOS X |
| 217 |
|
- more complicated Makefiles with a stronger dependence on Gnu Make |
| 218 |
|
o pkg/seaice modifications |
| 219 |
|
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
| 220 |
|
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
| 221 |
|
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
| 222 |
|
- changed proxy for geostrophic velocity and updated |
| 223 |
|
verification/lab_sea/results/* accordingly |
| 224 |
|
- removed ADI dynamic solver from pkg/seaice |
| 225 |
|
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
| 226 |
|
they caused a segmentation fault under certain circumstances |
| 227 |
|
- removed unused field WATR |
| 228 |
|
o bug fix in exf-package: |
| 229 |
|
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
| 230 |
|
now reflect that. |
| 231 |
|
o small fixes in the cal-package: |
| 232 |
|
- set reference date to first of January for the 'model'-calendar |
| 233 |
|
- failing of cal_CheckDate in cal_FullDate now actually results in a |
| 234 |
|
warning |
| 235 |
|
o small modifications in exf-package to increase flexibility: |
| 236 |
|
- change climtempfreeze from a constant to a runtime parameter that |
| 237 |
|
is specified in data.exf_clim (default = -1.9) |
| 238 |
|
- introduce runtime parameter windstressmax (default = 2.0) that is |
| 239 |
|
specified in data.exf |
| 240 |
|
o fix in pkg/thsice: |
| 241 |
|
- update Evap (Tsf changes) to be consistent with Latent heat flux |
| 242 |
|
- maintain snow precipitation unchanged (even if Tsf >=0). |
| 243 |
|
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
| 244 |
|
|
| 245 |
|
checkpoint52m_post |
| 246 |
|
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
| 247 |
|
this does not change any of the results, because myIter=0 in swfrac always |
| 248 |
|
lead to jwtype=2 (the default anyway), but the call makes little sense |
| 249 |
|
as a default |
| 250 |
|
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
| 251 |
|
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
| 252 |
|
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
| 253 |
|
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
| 254 |
|
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
| 255 |
|
o extending useSingleCpuIO option to work with new exch2 I/O format |
| 256 |
|
- old-style, missing-tile I/O is still accessible by defining CPP |
| 257 |
|
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
| 258 |
|
o monitor package can write to NetCDF files and/or STDOUT |
| 259 |
|
o fix re-definition bug in MNC_GRID_INIT_ALL() |
| 260 |
|
o doc/api_reference added |
| 261 |
|
- a framework for building an API Reference Manual using all |
| 262 |
|
the "protex" comments embedded in the code |
| 263 |
|
- see pkg/generic_advdiff, pkg/mnc for examples |
| 264 |
|
o MNC: |
| 265 |
|
- make myThid the last argument for all subroutines |
| 266 |
|
- new default for the grid files: NO halos |
| 267 |
|
- add useMNC and other run-time flags |
| 268 |
|
- separate per-file-group handling of the unlimited dimension |
| 269 |
|
- early initialization of MNC w/ flags read at the eeboot stage |
| 270 |
|
and lookup tables set in initialize_fixed |
| 271 |
|
- write all MNC output to a freshly-created directory |
| 272 |
|
o thermodynamics sea-ice (thsice) is now tested with testreport. |
| 273 |
|
o test exp. advect_cs: use the standard cs32 grid ; update output. |
| 274 |
|
o Added functionality to grdchk: |
| 275 |
|
pick global i,j,k position (or nearest wet) where to perform check. |
| 276 |
|
|
| 277 |
|
checkpoint52l_post |
| 278 |
|
o new land formulation: |
| 279 |
|
a) use ground enthalpy as prognostic variable to ensure exact |
| 280 |
|
energy conservation. |
| 281 |
|
b) account for water temperature and for latent heat of freezing |
| 282 |
|
in all processes (rain, run-off, ground storage) |
| 283 |
|
c) compute surface and ground temperature implicitly. |
| 284 |
|
o aim_v23 modification for new land model: |
| 285 |
|
a) Treat separately land / ocean / sea-ice surface fluxes |
| 286 |
|
to allow implicit computation of land & sea-ice surface temp. |
| 287 |
|
b) add snow precipitation. |
| 288 |
|
checkpoint52l_pre |
| 289 |
|
|
| 290 |
|
o fix problem (when 1 tile is empty) in min/max monitor. |
| 291 |
|
o fix bug in timeAve (u,vZetatave in common block) |
| 292 |
|
o no restoring terms under ice for pkg/seaice |
| 293 |
|
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
| 294 |
|
o bug fix for pkg/seaice pickups |
| 295 |
|
o change MNC call locations and add coordinate attributes |
| 296 |
|
o mask vorticity at the corner ; affects global_ocean.cs output |
| 297 |
|
o fix ini_curvilinear_grid ; test CS experiments with mpi |
| 298 |
|
o aim.5l_cs: modify sea-ice fraction input file ; update output |
| 299 |
|
o exf: Adding simple range check routine for exf fields after read |
| 300 |
|
|
| 301 |
|
checkpoint52k_post |
| 302 |
|
o removed top-level directory "diags" |
| 303 |
|
- we migrated these functions to pkg/timeave a long time ago |
| 304 |
|
o fixed bug introduced in pkg/monitor |
| 305 |
|
o accuracy ctrlprec = 32 insuffient for gradient checks using |
| 306 |
|
averaged fields (I/O via cost_averages) |
| 307 |
|
-> use ctrl.h in active_file*.F to control I/O precision. |
| 308 |
|
o paramter list of CALL ADTHE_MAIN_LOOP |
| 309 |
|
o added initial do_the_model_io to ecco |
| 310 |
|
o set all ...Freq to zero after cost_final |
| 311 |
|
taveFreq, dumpFreq, pChkptFreq |
| 312 |
|
o MAIN and ECCO differentiability restored |
| 313 |
|
|
| 314 |
|
checkpoint52j_post |
| 315 |
|
o fix nchklev in tamc.h for global_ocean... |
| 316 |
|
o Bringing flow and store directives up-to-date |
| 317 |
|
o Really weird thing! |
| 318 |
|
call do_the_model_io from the_main_loop with parameters |
| 319 |
|
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
| 320 |
|
TAF places a faulty re-call of initialise_varia |
| 321 |
|
after cost_final call which should not be there! |
| 322 |
|
checkpoint52j_pre |
| 323 |
|
|
| 324 |
|
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
| 325 |
|
error messages |
| 326 |
|
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
| 327 |
|
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
| 328 |
|
debug output |
| 329 |
|
o modfied mdsio_writefield.F to handle non-global files under exch2 |
| 330 |
|
o update AIM Cubed-Sphere exp (aim.5l_cs): |
| 331 |
|
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
| 332 |
|
o update AIM Equatorial Channel exp: |
| 333 |
|
use standard aim_v23 pkg and change the SST fields to be more realistic. |
| 334 |
|
o globalFile now works with exch2 |
| 335 |
|
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
| 336 |
|
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
| 337 |
|
o limit timeave output for hi-res integrations |
| 338 |
|
|
| 339 |
|
checkpoint52i_post |
| 340 |
|
o removed CPP_EEOPTIONS.h from verification/*/code |
| 341 |
|
o updated the tiling for global_ocean_pressure |
| 342 |
|
checkpoint52i_pre |
| 343 |
|
|
| 344 |
|
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
| 345 |
|
the old pkg/aim). |
| 346 |
|
|
| 347 |
|
checkpoint52h_pre |
| 348 |
|
o shortened offending lines in exch2_send_rx?.template |
| 349 |
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
| 350 |
o genmake2: add build & execute test for NetCDF code |
o genmake2: add build & execute test for NetCDF code |
| 351 |
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
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