| 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 pkg seaice |
| 8 |
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- re-introduce global field frWtrAtm for the case of |
| 9 |
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ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F) |
| 10 |
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- catch the case of an empty filename in seaice_cost_init_fixed.F |
| 11 |
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o pkg ecco: |
| 12 |
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- small bug fixes in the_main_loop |
| 13 |
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. fix order of monitor arguments |
| 14 |
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. change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY |
| 15 |
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. move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so |
| 16 |
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that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF |
| 17 |
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- replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the |
| 18 |
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imbalance diagnostics for wmean_h/sflux = 0 |
| 19 |
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- add actual values to f_obcsn/s/w/e in ecco_cost_final.F |
| 20 |
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- catch the case of empty filenames in ecco_cost_init_fixed.F |
| 21 |
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and ecco_readparms.F |
| 22 |
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- fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta) |
| 23 |
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to make this statement meaningfull |
| 24 |
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o pkg zonal_filt: |
| 25 |
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- change ZONAL_FILTER S/R interface (allows to filter 2-D fields) |
| 26 |
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- when using rStar, filter uVel*hFacW instead of uVel |
| 27 |
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(tested without topography: fix a Pb of growing instability with NLFS) |
| 28 |
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o pkg/aim/thsice: |
| 29 |
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-Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F |
| 30 |
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(works as SST restoring) |
| 31 |
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o pkg/thsice: |
| 32 |
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-add specific parameter for salt restoring in slab mixed-layer |
| 33 |
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(by default equal to the temperature restoring) |
| 34 |
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|
| 35 |
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checkpoint61v |
| 36 |
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o pkg/kpp: |
| 37 |
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-add double diffusive contributions as a hack, turned off by default |
| 38 |
|
for now, and the code can be excluded with a CPP-flag |
| 39 |
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EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX |
| 40 |
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-add a verification experiments to "vermix" to test this code |
| 41 |
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o pkg/mom_common: |
| 42 |
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Move computation of length scales to mom_init_fixed.F (avoid recomputation |
| 43 |
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at each time-steps*levels). |
| 44 |
|
o pkg/layers: |
| 45 |
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Created a new package for computing volume fluxes in temperature or |
| 46 |
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[not yet implemented] density layers, e.g. for calculating residual |
| 47 |
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overturning circulations. |
| 48 |
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o pkg/diagnostics: |
| 49 |
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implement a RS type version for the set of DIAGNOSTICS-FILL subroutines |
| 50 |
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o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option) |
| 51 |
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o pkg/mdsio (& pkg/rw): rework high level S/R interface: |
| 52 |
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To avoid mixing type (RS/RL) of input/output array argument, |
| 53 |
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replace single mixed-type array with a pair from each type (RS/RL). |
| 54 |
|
o setting pickupSuff force to start from a pickup (even if nIter0=0): this |
| 55 |
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is now implemented for all pkgs (previously only done for the main pickup) |
| 56 |
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|
| 57 |
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checkpoint61u |
| 58 |
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o pkg/obcs: |
| 59 |
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- change OB?eta from _RS to _RL and put them into a separate commen block |
| 60 |
|
- add code to read OB?eta from a file via obcs_prescribe_read: the code |
| 61 |
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compiles and does not destroy any other experiments, the data is read |
| 62 |
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properly, but the code is not tested in actual applications |
| 63 |
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o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to |
| 64 |
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create a meaningful unit attribute for the time coordinate variable |
| 65 |
|
o pkg/ebm: add plenty of missing "_d 0" ; |
| 66 |
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update results of experiment global_ocean_ebm (fwd + adjoint tests) |
| 67 |
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Notes: several pieces of code only works for (very) specific set up |
| 68 |
|
(domain size, lat range, etc ...); should be documented & stop if one |
| 69 |
|
of those assumptions is not meet. |
| 70 |
|
o pkg/seaice: add missing "_d 0" in HSNOW initialisation |
| 71 |
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update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests) |
| 72 |
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and offline_exf_seaice (seaicetd + adjoint). |
| 73 |
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o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC): |
| 74 |
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update results of experiments: lab_sea (4 fwd tests + 3 adjoint), |
| 75 |
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seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2). |
| 76 |
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o few changes to pass when compiling with strick checking of arguments |
| 77 |
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across S/R (allow to find few bugs in S/R calls). |
| 78 |
|
o pkg/seaice: |
| 79 |
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- seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new |
| 80 |
|
2d-fields, for slightly better performance |
| 81 |
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|
| 82 |
|
checkpoint61t |
| 83 |
|
o pkg/seaice: |
| 84 |
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- remove unused variables in seaice_evp |
| 85 |
|
- reduce number of SQRT in seaice_evp and seaice_calc_viscosities |
| 86 |
|
o eeset_parms.F, open_copy_data_file.F & ini_parms.F: |
| 87 |
|
named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT): |
| 88 |
|
each processor opens a different file (a fix from Matt). |
| 89 |
|
o cg2d: |
| 90 |
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use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F : |
| 91 |
|
this reduces number of EXCH calls by 2 when using exch2. |
| 92 |
|
For now, keep previous size array for gc2d_nsa.F to avoid Pb with store |
| 93 |
|
directives and missing simple EXCH (exch_s3d_rx) adjoint code. |
| 94 |
|
o pkg/thsice: |
| 95 |
|
add code for Near Infra-Red albedo (from Jeff) |
| 96 |
|
(turned on with run-time flag: thSIce_calc_albNIR, in data.ice). |
| 97 |
|
o ini_model_io: |
| 98 |
|
move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F |
| 99 |
|
MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F |
| 100 |
|
to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice. |
| 101 |
|
|
| 102 |
|
checkpoint61s |
| 103 |
|
o pkg/exch2 (exch2_rxN_cube*): |
| 104 |
|
remove last BARRIER (no need to synchronise after getting data from shared |
| 105 |
|
buffer (get) as long as any change to buffer (put,recv) is between BARRIER) |
| 106 |
|
o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH |
| 107 |
|
and generate new output (for the 2 tests) using default rotationPeriod. |
| 108 |
|
o pkg/exch2: |
| 109 |
|
- always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F |
| 110 |
|
(was already the case with AUTODIFF_EXCH2 defined) |
| 111 |
|
- add bj in exch2 arrays and S/R. |
| 112 |
|
- can now use pkg/exch2 for regular (non CS) set-up; switch test experiment |
| 113 |
|
MLAdjust to exch2 (identical results except with MPI -> truncation diff); |
| 114 |
|
o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep |
| 115 |
|
- adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY |
| 116 |
|
GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT |
| 117 |
|
- verification experiment natl_box.longstep |
| 118 |
|
o build_options: ifort+mpi_aces optfile (following Constantinos advise): |
| 119 |
|
allow different versions of ifort (8 or 9) and different versions |
| 120 |
|
of mpi (mpich or mpich2) to be used with the same optfile. |
| 121 |
|
requires to load a netcdf module and set MPI_INC_DIR (see comments inside |
| 122 |
|
optfile). Change testing scripts (example_scripts/ACESgrid) accordingly. |
| 123 |
|
o pkg/seaice: |
| 124 |
|
fix previous modif (3-level field removed) for old-pickup reading |
| 125 |
|
|
| 126 |
|
checkpoint61r |
| 127 |
|
o pkg/seaice: |
| 128 |
|
- clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps: |
| 129 |
|
1. introduce fields for time step (N-1) |
| 130 |
|
2. do not use levels 2 and 3 anymore (but keep them) |
| 131 |
|
3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This |
| 132 |
|
includes changes to pkg/thsice/thsice_get_velocity.F, |
| 133 |
|
model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and |
| 134 |
|
pkg/obcs/obcs_apply_uvice.F. |
| 135 |
|
- completely remove code for leap-frog time stepping for second order |
| 136 |
|
advection |
| 137 |
|
- adjusted adjoint accordingly; |
| 138 |
|
gradient checks have improved by an order of magnitude! |
| 139 |
|
|
| 140 |
|
checkpoint61q |
| 141 |
|
o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver |
| 142 |
|
- the boundary conditions along open boundaries are unclear, because the |
| 143 |
|
associated masks are set to zero and are thus treated as closed when |
| 144 |
|
applying the slip-boundary conditions. |
| 145 |
|
- move initialisation of grid variables from seaice_init_varia to _fixed |
| 146 |
|
o adding doc/diags_changes.txt |
| 147 |
|
o model/src: |
| 148 |
|
do_the_model_io: rename few pkg S/R which are called from do_the_model_io, |
| 149 |
|
to avoid "_diags" naming if no relation to pkg/diagnostics. |
| 150 |
|
ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF |
| 151 |
|
file and only call PLOT_FIELD_XYZ if debugMode=T. |
| 152 |
|
remove few PLOT_FIELD_XY calls outside initialisation. |
| 153 |
|
remove few unnecessary BARRIER. |
| 154 |
|
o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling |
| 155 |
|
of salt_plume package in Southern Ocean |
| 156 |
|
o pkg/thsice: |
| 157 |
|
- fix hOceMxL in overlap (needed for sea-ice advection); |
| 158 |
|
update output of experiment global_ocean.cs32x15.icedyn. |
| 159 |
|
o pkg/seaice: |
| 160 |
|
- make the (placeholder-)tracer IceAge a little more meaningful |
| 161 |
|
by avoiding ridging of age due to convergent ice flow |
| 162 |
|
- add diagnostics for surface temperature, atmospheric and oceanic |
| 163 |
|
heat flux, and atmospheric and oceanic ice growth |
| 164 |
|
|
| 165 |
|
checkpoint61p |
| 166 |
|
o eesupp (global_max & global_sum): |
| 167 |
|
- add one more element to buffer (start at index 0) for GL_MAX/SUM output; |
| 168 |
|
- remove starting & endding barrier (no longer needed) |
| 169 |
|
o pkg/mdsio, writelocal: |
| 170 |
|
works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined |
| 171 |
|
(remove the STOP): uses shared buffer IO to store data from all threads |
| 172 |
|
and then let master-thread write nThreads tiles. |
| 173 |
|
o pkg/mdsio (read/write field): |
| 174 |
|
- tiled IO done in 1 piece (all levels at a time); |
| 175 |
|
- new header file "MDSIO_BUFF_3D.h" with 3-D buffers. |
| 176 |
|
- multi-threaded: allow to read/write local (non-shared) array |
| 177 |
|
(was already working with singleCpuIO ; now works also without); |
| 178 |
|
=> no longer needs barrier call after reading a file (added inside |
| 179 |
|
mds_read/write field). |
| 180 |
|
- move barrier calls outside gather/scatter_2d to mds_read/write_field |
| 181 |
|
o pkg/obcs/exf |
| 182 |
|
- exf_getffieldrec.F: add a few ". _d 0" and |
| 183 |
|
add code to catch the case fldperiod = 0. |
| 184 |
|
- obcs_precribe_read.F: change if statements so that they match |
| 185 |
|
the variable type (_RL) |
| 186 |
|
- add a separate exf_iprec_obcs to exf_set_obcs (by default equal to |
| 187 |
|
exf_iprec) as part of namelist EXF_NML_01 |
| 188 |
|
o pkg/mdsio: |
| 189 |
|
- read/write tiled (local) files: read/write 1-level tile chunk at a time |
| 190 |
|
(instead of segment of length sNx); expected to speed up tiled IO. |
| 191 |
|
o pkg/exch2: |
| 192 |
|
- take buffer copy from/to array out of S/R exch2_send/recv into new |
| 193 |
|
S/R exch2_put/get ; Exch of local variable now works with MPI+MTH |
| 194 |
|
(tested by removing commom block statement in SOLVE_FOR_PRESSURE.h). |
| 195 |
|
- ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get) |
| 196 |
|
- simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds |
| 197 |
|
(which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by |
| 198 |
|
including Topology header file (and common blocks). |
| 199 |
|
- implement EXCH_IGNORE_CORNERS in scalar exchange (rx1); |
| 200 |
|
remove 2nd exch call in exch2_s3d_rx (no longer needed). |
| 201 |
|
- document S/R arg. list (+ update some comments) |
| 202 |
|
o pkg/seaice: |
| 203 |
|
- added SEAICE_CLIM_AIR code, which permits modulation of surface air |
| 204 |
|
temperature and humidity over sea ice based on climatological values. |
| 205 |
|
- clean up computation of Hibler+Bryan (1987) stress coupling for the case |
| 206 |
|
of LSR (this change is expected to change the results slightly because now |
| 207 |
|
it uses slightly difference moduli from the second last LSR solution, but |
| 208 |
|
that is more consistent with the stress computations; this part of the code |
| 209 |
|
is not tested in the verification experiments) |
| 210 |
|
- fix diagnostics for flux of ice in case of B-grid |
| 211 |
|
- turn strain rates eij and press into global fields within global |
| 212 |
|
common block in SEAICE.h for more straighforward diagnostics |
| 213 |
|
- fix diagnostics for principal stress components, press, zeta, eta |
| 214 |
|
to give something meaning full |
| 215 |
|
o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate |
| 216 |
|
new output (all 4 tests) using default rotationPeriod. |
| 217 |
|
o pkg KPP: |
| 218 |
|
- add flag (LimitHblStable) to avoid limiting BL depth under stable conditions |
| 219 |
|
- fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1 |
| 220 |
|
and normal grid from 1 to Nr) |
| 221 |
|
o Fix computations of L4rdt in mom_calc_visc.F |
| 222 |
|
o eesupp: |
| 223 |
|
new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg): |
| 224 |
|
should be called before a "stop" if we know that all process are going |
| 225 |
|
to stop; if one Proc does call this S/R, will hang in MPI_FINALISE. |
| 226 |
|
|
| 227 |
|
checkpoint61o |
| 228 |
|
o pkg/exch2: change check_depths to issue just a warning (instead of error+stop) |
| 229 |
|
o model/src/ini_curvilinear_grid.F: |
| 230 |
|
compute angleSin/CosC when they are not read from a file |
| 231 |
|
o pkg/seaice: |
| 232 |
|
add pseudo time stepping for LSOR |
| 233 |
|
o pkg/exch2: |
| 234 |
|
temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW |
| 235 |
|
o pkg/seaice: |
| 236 |
|
Adding separate sea ice albedo, drag coefficients, and HO in Southern |
| 237 |
|
Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h |
| 238 |
|
o SingleCpuIO: |
| 239 |
|
fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used. |
| 240 |
|
o pkg/seaice: |
| 241 |
|
put exchanged variable in (local) common block for MPI+Multi-Threads |
| 242 |
|
to work (necessary with exch1, and for now with exch2 too). |
| 243 |
|
o verification: to get more experiments tested with mpi, mth and mpi+mth, |
| 244 |
|
change tiling of: |
| 245 |
|
aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15, |
| 246 |
|
hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope |
| 247 |
|
update output of exp: |
| 248 |
|
exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5), |
| 249 |
|
tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod) |
| 250 |
|
+ ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU |
| 251 |
|
(note: output.txt generated on faulks using only 1 tile) |
| 252 |
|
o eesupp & mdsio (SingleCpuIO): |
| 253 |
|
- remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time |
| 254 |
|
parameter "W2_useE2ioLayOut" (read from file "data.exch2"). |
| 255 |
|
Note: was not effective for globalFile & useSingleCpuIO=F; now fixed. |
| 256 |
|
- move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc). |
| 257 |
|
- fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same |
| 258 |
|
gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array). |
| 259 |
|
o pkg/exch2: |
| 260 |
|
- new code to set-up W2-Exch2 topology (replace matlab-topology-generator): |
| 261 |
|
read parameter file "data.exch2" if it exists; otherwise try default regular |
| 262 |
|
cube without blank-tile; new header file "W2_EXCH2_SIZE.h"; |
| 263 |
|
- update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible |
| 264 |
|
with new code (not to be used, just as a backup solution). |
| 265 |
|
- add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2" |
| 266 |
|
in utils/exch2/input. |
| 267 |
|
|
| 268 |
|
checkpoint61n |
| 269 |
|
o eesupp & mdsio (SingleCpuIO): |
| 270 |
|
- move mapping to global io-buffer inside gather_2d/scater_2d: this save |
| 271 |
|
memory (1 less 2D global RL array); skip 1 buffer copy; and only send/ |
| 272 |
|
receive real*4 array (instead of real*8) to read/write 32.bit files. |
| 273 |
|
(new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S |
| 274 |
|
and remove new mapping S/R) |
| 275 |
|
o pkg/mdsio: in preparation for topology-generator within pkg/exch2: |
| 276 |
|
- Change declaration of SingleCpuIO buffer, reduced to only 1 dim.: |
| 277 |
|
xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h |
| 278 |
|
when using exch2. Add S/R to map global io-buffer to global model array. |
| 279 |
|
- uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt. |
| 280 |
|
|
| 281 |
|
checkpoint61m |
| 282 |
|
o write_utils : change WRITE_1D_R8 to WRITE_1D_RL |
| 283 |
|
and add 3 other S/R for other types (R4,R8,RS). |
| 284 |
|
Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument. |
| 285 |
|
o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros): |
| 286 |
|
- ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ; |
| 287 |
|
- reduce number of macro definitions (keep only those which are used); |
| 288 |
|
can always call directly the corrresponding S/R if needed. |
| 289 |
|
- everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix |
| 290 |
|
_R4/_R8 to _RS/_RL when applied to _RS/_RL variable. |
| 291 |
|
Fixed wrong type of arg in: |
| 292 |
|
atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F |
| 293 |
|
ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F |
| 294 |
|
To fix: global_sum of var in common block is wrong (multi-threaded) in: |
| 295 |
|
dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F |
| 296 |
|
To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops) |
| 297 |
|
o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd |
| 298 |
|
"nlfs" mpi test is going to stop when checking for unconnected tile egdes. |
| 299 |
|
o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error |
| 300 |
|
o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile |
| 301 |
|
edges are closed (zero depth); might happen with "blank tiles"; |
| 302 |
|
for now, disabled if using OBCS. |
| 303 |
|
o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi": |
| 304 |
|
link *_mpi files from "MODS" dir) to return to a strait-forward behavior. |
| 305 |
|
o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D) |
| 306 |
|
to reduce length of 1.D array print in STDOUT. |
| 307 |
|
o adjustment.cs-32x32x1: changed to oceanic test with 1 continent |
| 308 |
|
+ use 48 tiles (16x8): this will allow to test "blank tiles". |
| 309 |
|
o start to test MPI + multi-threaded (change testreport to skip tests |
| 310 |
|
where number of tiles do not match). |
| 311 |
|
o genmake2: add option "-omp" to turn on Open-MP ; |
| 312 |
|
passed to testreport (if using -mth) ; merge few (*+mth) optfiles. |
| 313 |
|
o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them) |
| 314 |
|
and keep the original tile numbering. Note: compatible with old |
| 315 |
|
W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files. |
| 316 |
|
|
| 317 |
|
checkpoint61l |
| 318 |
|
o Overlaps had been forgotten in calculating ijk keys : fixed |
| 319 |
|
o fix cyrus makedepend for gcc 4.4 |
| 320 |
|
o experiment fizhi-cs-aqualev20: |
| 321 |
|
switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE) |
| 322 |
|
and generate new output. Note: new output is much closer to the old |
| 323 |
|
one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from |
| 324 |
|
the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007. |
| 325 |
|
o pkg/fizhi: |
| 326 |
|
- change to avoid indices going deliberately over array-bounds |
| 327 |
|
- remove unnecessary MPI stuff |
| 328 |
|
- perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY" |
| 329 |
|
- new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE: |
| 330 |
|
does not go over array-bounds and therefore returns reliable output. |
| 331 |
|
- in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls: |
| 332 |
|
this S/R has 4 output arguments, which are used inside "get_alarm"; |
| 333 |
|
when it is called with the same variable "ndum" in place of several |
| 334 |
|
output arguments, this produces weird side effect inside "get_alarm" |
| 335 |
|
(e.g., datein=dates(n) is overwritten by timein=times(n) since both |
| 336 |
|
datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum" |
| 337 |
|
address) and produces error. |
| 338 |
|
o tools/gemake2: (March 27-29 2009) |
| 339 |
|
with option "-mpi": link *_mpi files from "MODS" dir (this is what |
| 340 |
|
testreport does). |
| 341 |
|
o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output |
| 342 |
|
o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F: |
| 343 |
|
update lab_sea.lsr & lab_sea.salt_plume results |
| 344 |
|
o pkg/seaice: |
| 345 |
|
Major overhaul of the LSOR solver: change discretization from original |
| 346 |
|
finite differences to finite volume. The old routine is still in the |
| 347 |
|
file seaice_lsr.F and can be turned on with the CPP-flag |
| 348 |
|
SEAICE_OLD_AND_BAD_DISCRETIZATION |
| 349 |
|
Along with this change, the discretization of the strain rates is changed. |
| 350 |
|
The same flag turns on the old discretization in seaice_calc_strainrates.F |
| 351 |
|
All verification experiments with seaice are affected (except for |
| 352 |
|
seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old |
| 353 |
|
results by setting the above flag. |
| 354 |
|
Further changes involve changes in defaults: |
| 355 |
|
- ALLOW_FLOODING is defined and turned on by default |
| 356 |
|
- SEAICEadvSnow = .true. is now the default |
| 357 |
|
- SEAICEadvSalt = .true. is now the default |
| 358 |
|
- SEAICEadvAge = .true. is now the default |
| 359 |
|
- SEAICE_clipVelocities = .false. is now the default |
| 360 |
|
(as per J. Zhang's recommendation) |
| 361 |
|
- B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE |
| 362 |
|
is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS |
| 363 |
|
- seaice_growth: replace computation of UG by a simple copy from wspeed |
| 364 |
|
|
| 365 |
|
checkpoint61k |
| 366 |
|
o pkg/seaice: a few bug fixes mostly concerning the metric terms: |
| 367 |
|
seaice_lsr: fixed a few metric terms, |
| 368 |
|
affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs |
| 369 |
|
add more debugging diagnostics |
| 370 |
|
seaice_evp: removed superfluous many metric terms of FV discretization |
| 371 |
|
of stress divergence |
| 372 |
|
affects lab_sea, lab_sea.hb87 |
| 373 |
|
seaice_ocean_stress: removed superfluous many metric terms of FV discretization |
| 374 |
|
of stress divergence for non-evp solver |
| 375 |
|
(this part is not tested anywhere) |
| 376 |
|
seaice_calc_strainrates: fixed a bug in no-slip boundary conditions, |
| 377 |
|
they were effectively only half slip |
| 378 |
|
affects lab_sea.hb87 |
| 379 |
|
updated all relevant verification experiments (except lab_sea//output_adm.txt |
| 380 |
|
which was left over, but fails at level 7 & 6) |
| 381 |
|
|
| 382 |
|
checkpoint61j |
| 383 |
|
o pkg/seaice: turn a few hard wired parameters into run time parameters |
| 384 |
|
o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model |
| 385 |
|
time in seconds as promised by the usints in seaice_monitor and exf_monitor |
| 386 |
|
o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids |
| 387 |
|
that are not cubed-sphere grids |
| 388 |
|
o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR |
| 389 |
|
o pkg/ctrl: |
| 390 |
|
fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low) |
| 391 |
|
o non-hydrostatic (calc_gw.F): |
| 392 |
|
fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec |
| 393 |
|
update output of exp. global_ocean.cs32x15.viscA4 |
| 394 |
|
o remove backward compatibility for thetaMin,phiMin |
| 395 |
|
(replaced by xgOrigin,ygOrigin on Jan 27, 2009) |
| 396 |
|
o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the |
| 397 |
|
interpolated wind field not only for curvilineargrid=.true., but also |
| 398 |
|
for a rotated grid (rotateGrid=.true.) |
| 399 |
|
o pkg/exf: add capability to bypass interpolation for runoff |
| 400 |
|
by setting yet another CPP-flag |
| 401 |
|
o eesupp/src, B-grid exchange: |
| 402 |
|
add simple (6 tiles, non MPI) CS exch + standard interface S/R. |
| 403 |
|
o autodiff |
| 404 |
|
new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV |
| 405 |
|
allows to switch to single-prec common blocks; |
| 406 |
|
corresponding switch occurs in tamc.h, integer isbyte |
| 407 |
|
TAF store directivs "byte" and "kind" seem equivalent; |
| 408 |
|
Most tamc.h have been updated correspondingly. |
| 409 |
|
|
| 410 |
|
checkpoint61i |
| 411 |
|
o autodiff: |
| 412 |
|
fix autodiff_sore/_restore indices for obcs |
| 413 |
|
(spotted by I. Hoteit, M. Mazloff) |
| 414 |
|
o pkg/autodiff, pkg/ctrl: |
| 415 |
|
Add flag to reduce all tapelev I/O to single-prec. |
| 416 |
|
In data.ctrl set |
| 417 |
|
doSinglePrecTapelev = .TRUE. |
| 418 |
|
o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2: |
| 419 |
|
check in hack for SX8 compiler (for dxV, dyU); remove it afterwards. |
| 420 |
|
o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for |
| 421 |
|
real fresh water flux (not yet) |
| 422 |
|
o pkg/mdsio & rw: |
| 423 |
|
- add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta) |
| 424 |
|
- add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX. |
| 425 |
|
o pkg/flt: |
| 426 |
|
- replace FLT_INIT by 3-steps standard initialization S/R: readparms, |
| 427 |
|
init_fixed & ini_varia. |
| 428 |
|
- clean-up & simplify linear interpolation S/R: |
| 429 |
|
move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid. |
| 430 |
|
- fix some indices (mainly vertical index) ; add IMPLICIT NONE. |
| 431 |
|
- more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R. |
| 432 |
|
- add vert. coordinate & horiz. indices to output files. |
| 433 |
|
- change vertical position in initial condition, from index to depth [m]. |
| 434 |
|
- store horizontal (decimal) indices i,j in common block (instead of coord. x,y) |
| 435 |
|
(easier to get to a curvilinear grid) ; delX,delY no longer used. |
| 436 |
|
o pkg/ggl90: a few modifications: |
| 437 |
|
- fix bottom boundary condition, and interpolation of KappaE |
| 438 |
|
near top and bottom |
| 439 |
|
- use same set of viscosity/diffusivity for TKE/momnetum/tracer |
| 440 |
|
- add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH) |
| 441 |
|
- add a few options for mixing-length upper limit (--> mxlMaxFlag) |
| 442 |
|
o rename thetaMin,phiMin -> xgOrigin,ygOrigin |
| 443 |
|
(maintain temporary backward compatibility, until next checkpoint) |
| 444 |
|
|
| 445 |
|
checkpoint61h |
| 446 |
|
o pkg/diagnostics with "periodic averaging diagnostics": |
| 447 |
|
fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. |
| 448 |
|
o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82 |
| 449 |
|
o pkg/obcs: fix loop ranges for balancing code |
| 450 |
|
o pkg/flt: |
| 451 |
|
- improve criteria for finding which tile owns a float. |
| 452 |
|
- fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case. |
| 453 |
|
o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg |
| 454 |
|
aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling |
| 455 |
|
with ocean biogeo) |
| 456 |
|
o pkg/flt: |
| 457 |
|
- do some cleaning and fix the restart ; |
| 458 |
|
- add output.txt in flt_example/results to get this pkg tested. |
| 459 |
|
o genmake2: add an EXTENDED_SRC option and flag. |
| 460 |
|
for now, cannot be turned on on command line (only through genmake_local) |
| 461 |
|
o pkg/mdsio: read/write vector: |
| 462 |
|
- singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS |
| 463 |
|
- singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR |
| 464 |
|
& MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. |
| 465 |
|
- affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) |
| 466 |
|
(drop to 4 digits matching for grad). But this test does not look very |
| 467 |
|
reliable (was already failling on eddy, fc5, at 6.digits). Update output. |
| 468 |
|
|
| 469 |
|
checkpoint61g |
| 470 |
|
o pkg/flt: |
| 471 |
|
- move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) |
| 472 |
|
+ make OPTIONS file more standard. |
| 473 |
|
- rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) |
| 474 |
|
- fix _BYTESWAPIO CPP-Flag |
| 475 |
|
- standard reading of file-parameter "data.flt" |
| 476 |
|
- fix argument list of S/R FLT_RESTART |
| 477 |
|
still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F |
| 478 |
|
o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell |
| 479 |
|
o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to |
| 480 |
|
a still unfixed compiler/optimization bug |
| 481 |
|
|
| 482 |
|
checkpoint61f |
| 483 |
|
o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; |
| 484 |
|
update results of global_ocean.cs32x15.icedyn test. |
| 485 |
|
o move getcon.F from model/src to pkg/fizhi. |
| 486 |
|
o pkg/exf: add parameter for extrapolation of temp up to the surface |
| 487 |
|
and option to prevent negative evap (in bulk_largeyeager04 only). |
| 488 |
|
o Prather Advection scheme: fix tracer conservation for divergent flow |
| 489 |
|
(e.g., when using NonLin Free-Surface). |
| 490 |
|
o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead |
| 491 |
|
o gmredi (Visbeck-variable-K): |
| 492 |
|
- add more parameters to Visbeck-variable-K. |
| 493 |
|
- use a 5 points average for dSigmaR in Visbeck-K calculation |
| 494 |
|
(more "homogenous": same stencil and same weights as in dSigmaH) |
| 495 |
|
- update output of ideal_2D_oce experiment. |
| 496 |
|
o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 |
| 497 |
|
(#undef REAL4_IS_SLOW) |
| 498 |
|
- pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 |
| 499 |
|
coordinate variable |
| 500 |
|
- pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables |
| 501 |
|
(surface forcing fields), removes some of the functionality |
| 502 |
|
- model/src/write_grid.F: write _RS variables as RS-netcdf variables |
| 503 |
|
- model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but |
| 504 |
|
probably not all: copy _RS surface flux fields to RL field before |
| 505 |
|
calling DIAGNOSTICS_FILL |
| 506 |
|
- model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into |
| 507 |
|
real*4 (CALL EXCH_*_RS) versions. |
| 508 |
|
- tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 |
| 509 |
|
(generate new output). |
| 510 |
|
|
| 511 |
|
checkpoint61e |
| 512 |
|
o gmredi (Visbeck-variable-K): |
| 513 |
|
- fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h |
| 514 |
|
- change computation of Visbeck-K where Slope > Smax : |
| 515 |
|
now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct) |
| 516 |
|
previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output. |
| 517 |
|
o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic |
| 518 |
|
to be the same as with Z-coord. (i.e., m/s & no-units respectively). |
| 519 |
|
o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc) |
| 520 |
|
o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz |
| 521 |
|
does not become too large (to avoid precision problems in implicit-diffusion |
| 522 |
|
solver); update ideal_2D_oce output. |
| 523 |
|
o pkg ggl90: |
| 524 |
|
- in ggl90_cal.F: compute only one set of visc/diff, used to |
| 525 |
|
step forward TKE/T/S/momentum |
| 526 |
|
- default value of GGL90viscMax/GGL90diffMax larger and equal (to |
| 527 |
|
have Prandlt =1) |
| 528 |
|
o gmredi (fm07): |
| 529 |
|
- add lower limit on Transition layer thickness + lower limit on 1/lambda |
| 530 |
|
- allow to set few more params from data.gmredi |
| 531 |
|
o pkg ggl90: |
| 532 |
|
- add missing sqrt(2) factor in computation of mixing length |
| 533 |
|
scale in ggl90_calc.F |
| 534 |
|
(see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) |
| 535 |
|
|
| 536 |
|
checkpoint61d |
| 537 |
|
o adjoint modifs |
| 538 |
|
- adapt to new field rhoInSitu |
| 539 |
|
- allow to revert from StoreDynVars2D, StoreDynVars3D |
| 540 |
|
to individual fields |
| 541 |
|
(switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) |
| 542 |
|
o store 3-D (in-situ) density in commom block (DYNVARS.h) |
| 543 |
|
- save 1 rho computation. |
| 544 |
|
- no longer modify T & S inland when using down_slope pkg. |
| 545 |
|
o gad_som : allow to switch to SOM advection for T & S without corresponding |
| 546 |
|
pickup files (using new S/R: MDS_CHECK4FILE). |
| 547 |
|
o keep removing _BEGIN/_END_MASTER between MDSIO S/R call |
| 548 |
|
(for useSingleCpuIO to work in multi-threaded) |
| 549 |
|
o pkg/shelfice: |
| 550 |
|
- disentangle parameters: retire shelfIceFile in data/PARM05 and substitute |
| 551 |
|
with SHELFICEtopoFile in data.shelfice |
| 552 |
|
- move code for reading ice shelf topography and modifying hFacC into separate |
| 553 |
|
subroutines of the shelfice package |
| 554 |
|
- separate initialisation of "fixed" and "variable" variables |
| 555 |
|
- kTopC is not (yet) replaced by kSurfC, although this is possible |
| 556 |
|
o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
| 557 |
|
o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
| 558 |
|
and rename: |
| 559 |
|
ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
| 560 |
|
ini_reference_state.F --> load_ref_files.F (- set anelastic factors) |
| 561 |
|
o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) |
| 562 |
|
|
| 563 |
|
checkpoint61c |
| 564 |
|
o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" |
| 565 |
|
to add mass source/sink of fluid in the interior (3-D generalisation |
| 566 |
|
of oceanic real-fresh water flux). |
| 567 |
|
o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) |
| 568 |
|
o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) |
| 569 |
|
o new pkg: down_slope |
| 570 |
|
density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). |
| 571 |
|
- presently, modify T & S inland (dwnslp_calc_rho.F). |
| 572 |
|
can be avoided if rho was stored in common bloc and used in calc_phi_hyd. |
| 573 |
|
- implementation for ocean in P-coords not tested. |
| 574 |
|
- add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. |
| 575 |
|
o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) |
| 576 |
|
(to facilitate conversion of oceanic pkg to p-coordinate). |
| 577 |
|
o change FIND_RHO to FIND_RHO_2D : |
| 578 |
|
pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. |
| 579 |
|
o new pkg: cheapaml |
| 580 |
|
|
| 581 |
|
checkpoint61b |
| 582 |
|
o exch2: |
| 583 |
|
change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) |
| 584 |
|
- no longer depend on the order sequence (N,S,E,W). |
| 585 |
|
- 3rd exchange no longer needed (tested with 24 tiles). |
| 586 |
|
- same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) |
| 587 |
|
- exch_UV_A-grid readily available (but not yet tested). |
| 588 |
|
comment out 3rd exch call and remove copy of V to U at SE & NE face-corners |
| 589 |
|
(both are no longer needed) in exch_uv: no effect in forward run; but |
| 590 |
|
get truncation error differences with adjoint exch. |
| 591 |
|
o exch2: |
| 592 |
|
- change index-bounds storage (moved from target to local tile, |
| 593 |
|
more intuitive this way) ; rename/remove some variables. |
| 594 |
|
- change utils/exch2/matlab-topology-generator & code_mods accordingly. |
| 595 |
|
|
| 596 |
|
checkpoint61a |
| 597 |
|
o exch2/matlab-topology-generator: |
| 598 |
|
fix bug in index bounds for N-S internal exchange (hard to tell if this |
| 599 |
|
had any effect on the solution). |
| 600 |
|
o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf |
| 601 |
|
is exceeded |
| 602 |
|
o testreport: modify syntax of awk, so that it works also with |
| 603 |
|
awk, and not only with nawk and gawk |
| 604 |
|
|
| 605 |
|
checkpoint61 |
| 606 |
|
o autodiff |
| 607 |
|
Change default for TAF usage by removing argument '-nonew_arg' |
| 608 |
|
This changes TAF subroutine argument list (ordering of active var.) |
| 609 |
|
Omission of this flag leads to incompatibility w.r.t. TAMC |
| 610 |
|
To restore TAMC-compatibility, need following modifs: |
| 611 |
|
* use adoptfile tools/adjoint_options/adjoint_tamc_compatibility |
| 612 |
|
* use CPP option #define AUTODIFF_TAMC_COMPATIBILITY |
| 613 |
|
Tested TAF version is 1.9.22 |
| 614 |
|
N.B.: exch2 hand-written adjoint code currently not TAMC compatible |
| 615 |
|
|
| 616 |
|
checkpoint60 |
| 617 |
|
--->>> This is the last checkpoint for which generating the adjoint |
| 618 |
|
--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" |
| 619 |
|
--->>> by default. |
| 620 |
|
--->>> Future checkpoints will ommit this flag by default. |
| 621 |
|
o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. |
| 622 |
|
o pkg/grdchk: Add gradient check to etan0 perturbations. |
| 623 |
|
o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). |
| 624 |
|
o pkg/autodiff: more flexibility in zeroadj. |
| 625 |
|
model/src: modifying do_oceanic_phys.F accordingly. |
| 626 |
|
o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. |
| 627 |
|
o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option |
| 628 |
|
special setup of gmredi for which the adjoint is stable |
| 629 |
|
enough for parameter optimization. |
| 630 |
|
o bridging the gap between eddy stress and GM. |
| 631 |
|
-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) |
| 632 |
|
along with a change in CPP option (now ALLOW_EDDYPSI). |
| 633 |
|
-> when using GM w/ GM_AdvForm: |
| 634 |
|
The total eddy streamfunction (Psi = eddyPsi + K x Slope) |
| 635 |
|
is applied either in the tracer Eq. or in momentum Eq. |
| 636 |
|
depending on data.gmredi (intro. GM_InMomAsStress). |
| 637 |
|
-> ALLOW_EDDYPSI_CONTROL for estimation purpose. |
| 638 |
|
The key modifications are in model/src/taueddy_external_forcing.F |
| 639 |
|
pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F |
| 640 |
|
|
| 641 |
|
checkpoint59r |
| 642 |
|
o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array |
| 643 |
|
from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); |
| 644 |
|
fix option to read coriolis(@ cell-corner) from files with CS-grid. |
| 645 |
|
o pkg/mnc: add some attributes to standard 1D-coordinate variables |
| 646 |
|
o pkg/diagnostics: enforce missing_value attribute for scalar variables at |
| 647 |
|
mass points, when using mnc for output |
| 648 |
|
- add runtime parameter (missing_value, missing_value_int) to override |
| 649 |
|
default (which is the value of getcon('UNDEF')) |
| 650 |
|
o pkg/mnc: prepare mnc for the actual use of missing values with the |
| 651 |
|
diagnostics package: small fix in mnc_cw_readwrite.template and more |
| 652 |
|
initialisation of never used fields |
| 653 |
|
- replace mnc_common.h and mnc_id_header.h with corresponding upper case |
| 654 |
|
versions |
| 655 |
|
o pkg/thsice/thsice_ini_vars.F added default initial values so that |
| 656 |
|
thermodynamics sea ice solver does not blow up when some initial fields |
| 657 |
|
are missing. |
| 658 |
|
o move from external_forcing_surf.F to ini_forcing.F |
| 659 |
|
the p-coord. hack consisting in using pLoad to set phi0surf ; |
| 660 |
|
update output of tutorial_global_oce_in_p (affected @ truncation level). |
| 661 |
|
o Freshen up a bit hs94.1x64x5, notably: |
| 662 |
|
remove rotationPeriod and tRef=5*0. (adjoint only), and add |
| 663 |
|
exactConserv=.TRUE. |
| 664 |
|
o pkg/generic_advdiff: |
| 665 |
|
change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
| 666 |
|
applies to files where Temperature & Salinity 2nd Order moments are used. |
| 667 |
|
o pkg/ptracers: add second-order moment advection schemes (80 and 81); |
| 668 |
|
this uses a dynamically allocated internal state data structure |
| 669 |
|
(#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) |
| 670 |
|
and requires a fortran 90 compiler |
| 671 |
|
|
| 672 |
|
checkpoint59q |
| 673 |
|
o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) |
| 674 |
|
(from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) |
| 675 |
|
o Refresh tutorial_global_oce_biogeo, notably: |
| 676 |
|
- change bathymetry (put back seamounts in ACC, use hFacs) |
| 677 |
|
- change EOS (POLY3 --> JMD95Z) |
| 678 |
|
- use Bryan-Lewis vertical diffusivity |
| 679 |
|
- use multidimensional advection |
| 680 |
|
- remove old virtual virtual in dic pkg, now done through ptracer pkg |
| 681 |
|
- change a couple of parameters in dic pkg |
| 682 |
|
o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F |
| 683 |
|
o pkg/obcs: change default to OBCSfixTopo = .true., |
| 684 |
|
- set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result |
| 685 |
|
- replace "debugMode" with "debugLevel .GE. debLevB" |
| 686 |
|
o implementation of TAF directives for gchem,cfc,dic |
| 687 |
|
o remove "exp5" (replaced by tutorial_deep_convection). |
| 688 |
|
o pkg/obcs: add code to fix topography gradients normal to open boundaries; |
| 689 |
|
this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; |
| 690 |
|
the code can be turned on by setting OBCSfixTopo = .true. in data.obcs |
| 691 |
|
--> changes results in exp4, seaice_obcs |
| 692 |
|
o tutorial_deep_convection : |
| 693 |
|
update the set-up and increase resolution and domain size ; start |
| 694 |
|
from pseudo initial conditions = output at t=120mn in order to see |
| 695 |
|
something happening when running testreport. |
| 696 |
|
o pkg/seaice: add os7mp as an advection scheme |
| 697 |
|
add check for advection schemes |
| 698 |
|
add a flag for restoring T and S underneath sea ice |
| 699 |
|
o pkg/my82: add netcdf-support and diagnostics |
| 700 |
|
o thsice pkg: |
| 701 |
|
- Now hsMax limits snow height by turning it into ice following |
| 702 |
|
flooding scheme (and now conserving energy) |
| 703 |
|
- Slight rewriting of the formula in thsice_calc_thick.F |
| 704 |
|
- Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos |
| 705 |
|
--> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice |
| 706 |
|
|
| 707 |
|
checkpoint59p |
| 708 |
|
o gchem / dic / cfc : |
| 709 |
|
- add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); |
| 710 |
|
- add new parameter files: "data.dic" & "data.cfc" ; |
| 711 |
|
- various re-arrangement in initialisation & header file ; |
| 712 |
|
- fix tutorial_global_oce_biogeo for multi-threaded test. |
| 713 |
|
o pkg/dic: test for "pickup_dic" file when restarting ; |
| 714 |
|
if no pickup-file, can restart with a re-initialised pH (same as it did |
| 715 |
|
before) providing pickupStrictlyMatch is set to False. |
| 716 |
|
o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP |
| 717 |
|
+ fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP |
| 718 |
|
o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2 |
| 719 |
|
and staggerTimeStep is off (needed for stability of Internal-wave dynamics). |
| 720 |
|
o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax, |
| 721 |
|
& lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers |
| 722 |
|
(note: not clear to me what lambdaTr1ClimRelax is still used for ...) |
| 723 |
|
o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which |
| 724 |
|
scheme to use for vorticty-term ; |
| 725 |
|
- compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F |
| 726 |
|
(with default selectVortScheme, return to original discretisation) |
| 727 |
|
- remove weird combination (e.g.: upwindVorticity & highOrderVorticity) |
| 728 |
|
o pkg/seaice: add a line to the summary to indicate grid type (B/C) |
| 729 |
|
o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the |
| 730 |
|
bottom ; only used with variable horizontal viscosity and non-hydrostatic. |
| 731 |
|
also fix diagnostics VISCAHW & VISCA4W. |
| 732 |
|
|
| 733 |
|
checkpoint59o |
| 734 |
|
o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). |
| 735 |
|
o change the loop ordering in most gad_*_adv_x.F to improve vectorization: |
| 736 |
|
move a few statemens out the main loop into separate loops |
| 737 |
|
o pkg/shelfice: |
| 738 |
|
- sort out freshwater flux; convert freshwater fluxes to mass fluxes |
| 739 |
|
(kg/m^2/s), does not break tests, because in verification/isomip, |
| 740 |
|
rhoConstFresh=rhoConst (by accident) |
| 741 |
|
- rearrange computation of tLoc, sLoc, pLoc to make code more efficient |
| 742 |
|
- move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into |
| 743 |
|
new file model/src/seawater.F, so that they are available for all pkgs. |
| 744 |
|
- convert potential temperature into in-situ temperature. This changes the |
| 745 |
|
isomip tests => update tests |
| 746 |
|
o add a flag writePickupAtEnd (default=true) to be able to suppress |
| 747 |
|
writing a pickup at the last timestep |
| 748 |
|
o tools/mpack-1.6 : |
| 749 |
|
- disable automake (not working) and autoconf (not needed). |
| 750 |
|
- update to version 1.6.4 which fix MD5 code on some 64 bits platforms |
| 751 |
|
also cleaner with much less compilation warnings. |
| 752 |
|
o pkg/profiles: |
| 753 |
|
rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg |
| 754 |
|
(for "less than 32 characters name" compiler requirement) |
| 755 |
|
o pkg/obcs and pkg/exf: added capability to specify seaice open boundary |
| 756 |
|
conditions that have a different sampling frequency than S/T/U/V obcs |
| 757 |
|
o pkg/diagnostics (stats-diags): |
| 758 |
|
- fix global Min/Max in case 1 processor get only empty tiles |
| 759 |
|
o genmake2: replace (4 times) |
| 760 |
|
make genmake_tc_1.o >> genmake_warnings 2>&1 |
| 761 |
|
with |
| 762 |
|
COMM="$CC $CFLAGS -c genmake_tc_1.c" |
| 763 |
|
echo $COMM >> genmake_warnings |
| 764 |
|
$COMM >> genmake_warnings 2>&1 |
| 765 |
|
to make genmake2 always see the value of CC as specified in the optfile. |
| 766 |
|
o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid. |
| 767 |
|
- add diagnostics for 1srt & 2nd Order moments and sub-grid variance. |
| 768 |
|
- modify verification advect_cs test to test SOM-advection on CS-grid. |
| 769 |
|
o pkg/ctrl: |
| 770 |
|
- Rewrite of ctrl_map_ini_ecco.F, |
| 771 |
|
introducing a generic routine (ctrl_map_ini_gen.F). |
| 772 |
|
- Modification of ctrl_bound/adctrl_bound handling control vector bounds. |
| 773 |
|
|
| 774 |
|
checkpoint59n |
| 775 |
|
o pkg/diagnostics: for large number of diagnostics, store diagnostic mate |
| 776 |
|
number in dedicate array "hdiag": |
| 777 |
|
- new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST |
| 778 |
|
with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST. |
| 779 |
|
- many small changes (integer format) for large number of diagnostics |
| 780 |
|
- start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with |
| 781 |
|
a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23. |
| 782 |
|
o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For |
| 783 |
|
usingSphericalGrid, this allows to define the rotated grid coordinates |
| 784 |
|
via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the |
| 785 |
|
geographical coordinates according to the inverse of the rotation defined |
| 786 |
|
by the Euler angles, so that Coriolis parameter and online-interpolation by |
| 787 |
|
exf works with the geographical coordinates on XC/YC/XG/YG. |
| 788 |
|
Naturally, this feature does not work with all packages, so some |
| 789 |
|
combinations are prohibited in config_summary (flt, flt_zonal, ecco, |
| 790 |
|
profiles), because there the coordinates are assumed to be regular |
| 791 |
|
spherical grid coordinates. |
| 792 |
|
o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc: |
| 793 |
|
- introduce isopycnal diffusion coefficient control. |
| 794 |
|
o tools/adjoint_options: |
| 795 |
|
- additional control vector components. |
| 796 |
|
o pkg/mnc: have mnc create marginally meaning full coordinate variables |
| 797 |
|
(that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 |
| 798 |
|
o pkg/mypackage: |
| 799 |
|
- add example of read/write pickup for state-var ; |
| 800 |
|
- add entry points to the main code for state-vars diags & write-pickup. |
| 801 |
|
o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year |
| 802 |
|
transitions for useExfYearlyFields |
| 803 |
|
- add new subroutine that determines the file to read from for |
| 804 |
|
use*YearlyFields = .TRUE. and .FALSE. |
| 805 |
|
- add a verification experiment to global_with_exf that tests |
| 806 |
|
useExfYearlyFields with USE_EXF_INTERPOLATION defined |
| 807 |
|
o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in |
| 808 |
|
analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new |
| 809 |
|
subroutines (which could be generated from a template, because they are |
| 810 |
|
almost identical), for now they are included in obcs_prescribe_read.F for |
| 811 |
|
simplicity |
| 812 |
|
o pkg/exf: |
| 813 |
|
- add a little more diagnostic to exf_interp_read (in analogy to |
| 814 |
|
mds_read_field, can be turned off with debugLevel < debugLevA=1) |
| 815 |
|
- improve vectorizability of exf_interp for TARGET_NEC_SX, makes code |
| 816 |
|
ugly but fast by unrolling short inner loops, inserting a unroll=8 |
| 817 |
|
directive in routine lagran, and splitting a loop and making do while the |
| 818 |
|
outermost loop (the latter requires the intoduction of index arrays) |
| 819 |
|
o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice |
| 820 |
|
o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver |
| 821 |
|
http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html |
| 822 |
|
o verification/seaice_obcs: updated for restart test and latest options |
| 823 |
|
o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different |
| 824 |
|
ice rheology (so-called truncated ellipse, that gets rid of tensile stress); |
| 825 |
|
for now this is only available for the C-grid code and also within |
| 826 |
|
#ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code |
| 827 |
|
|
| 828 |
|
checkpoint59m |
| 829 |
|
o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) |
| 830 |
|
and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature |
| 831 |
|
o gad_som : fix flux output (& diagnostics) to have same units as other |
| 832 |
|
advection scheme fluxes (was previously multiplied by deltaT). |
| 833 |
|
o added verification/seaice_obcs both to test seaice open boundaries |
| 834 |
|
and to provide an example matlab scrpt for generating them |
| 835 |
|
o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume |
| 836 |
|
o pkg/salt_plume: clean up salt_plume_frac.F to |
| 837 |
|
remove redundancy in PlumeMethod 1 and 4 |
| 838 |
|
o pkg/kpp: added saltplume diagnostics |
| 839 |
|
o pkg/obcs and pkg/seaice: |
| 840 |
|
- do not set uice and vice to zero when OB*icefile are unspecified |
| 841 |
|
- OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default |
| 842 |
|
- moved seaice tracer obcs after call to seaice_growth |
| 843 |
|
o pkg/salt_plume: added various options for salt plume depth |
| 844 |
|
criterion and for vertical distribution of the salt |
| 845 |
|
|
| 846 |
|
checkpoint59l |
| 847 |
|
o pkg/ptracers: new version of ptracers pickup: |
| 848 |
|
read meta file and write only fields which are needed to restart. |
| 849 |
|
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
| 850 |
|
o pkg/seaice: |
| 851 |
|
- add timescale for melting due to warm mixed layer as a means of |
| 852 |
|
setting SEAICE_availHeatFrac more conveniently |
| 853 |
|
- add a CPP-flag/runtime parameter check for flooding algorithm |
| 854 |
|
- reformulated availHeat in seaice_growth.F to be independent of AREA |
| 855 |
|
o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent |
| 856 |
|
unit changes |
| 857 |
|
o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint |
| 858 |
|
o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC |
| 859 |
|
SX vector computer. |
| 860 |
|
o pkg/seaice: |
| 861 |
|
- removed SEAICE_FFIELDS.h and seaice_get_forcing.F |
| 862 |
|
seaice forcing fields can now be read only through pkg/exf |
| 863 |
|
- removed some unused halos |
| 864 |
|
o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP |
| 865 |
|
o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL |
| 866 |
|
or U/VICE from U/VWIND before computing U/VSTRESS |
| 867 |
|
|
| 868 |
|
checkpoint59k |
| 869 |
|
o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between |
| 870 |
|
dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. |
| 871 |
|
o fix un-initialised variable problem (in mom_vecinv & shap_filt): |
| 872 |
|
all experiments pass when compile with un-initialised var. checking option. |
| 873 |
|
o added pkg/salt_plume |
| 874 |
|
o script to test restart (for now, in MITgcm_contrib/jmc_script) |
| 875 |
|
o pkg/seaice: new read/write pickup version. |
| 876 |
|
read meta file and write only fields which are needed to restart. |
| 877 |
|
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
| 878 |
|
o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) |
| 879 |
|
o lab_sea.hb87: modify the domain & update output.hb87.txt : |
| 880 |
|
lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 |
| 881 |
|
at j=1 & j=Ny+1 : this case is not treated correctly in the restart |
| 882 |
|
process. Fixed here by closing the domain at the Northern boundary. |
| 883 |
|
o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. |
| 884 |
|
o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing |
| 885 |
|
a set of consecutive levels in/from a 3-D array. |
| 886 |
|
o pkg/ptracers: |
| 887 |
|
use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). |
| 888 |
|
to-do: fix pkg/diagnostics when large number of diagnostics are defined. |
| 889 |
|
|
| 890 |
|
checkpoint59j |
| 891 |
|
o in pkgs: dic, obcs, offline, rbcs: |
| 892 |
|
standard way to compute coeff. for time interpolation between 2 time reccords |
| 893 |
|
which retains full precision (& make results less dependent on compiler). |
| 894 |
|
update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. |
| 895 |
|
o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those |
| 896 |
|
packages instead of reading ice cover and wind speed separately |
| 897 |
|
o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h |
| 898 |
|
(keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad |
| 899 |
|
to allow to compile customized code before the update) |
| 900 |
|
o cleaning-up: |
| 901 |
|
- fix CPP instruction syntax in pkg/obcs |
| 902 |
|
- replace (some) call to MDSIO S/R with call to RW interface S/R ; and |
| 903 |
|
add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio) |
| 904 |
|
- fix some threads issue in IO parts. |
| 905 |
|
o pkg/dic: |
| 906 |
|
- add tons of "_d 0" (--> much better testreports !) |
| 907 |
|
and then update outputs of tutorial_global_oce_biogeo |
| 908 |
|
o pkg/mom_fluxform: |
| 909 |
|
add a special version of momentum advection intended to conserve momentum |
| 910 |
|
next to a bathymetry step or a coastline edge. (default = off = #undef) |
| 911 |
|
o new read/write pickup version: |
| 912 |
|
- for now, only implemented for main (mdsio) pickup file. |
| 913 |
|
- write out only what is needed to restart; merge pickup_nh , pickup_ph |
| 914 |
|
and main pickup together. |
| 915 |
|
- read meta file; read only what is needed to restart; stop if a field |
| 916 |
|
is missing (if pickupStrictlyMatch=T, = the default) or try to restart |
| 917 |
|
if it make sense (even if the restart is not perfect). |
| 918 |
|
- if no meta file, assume that pickup to read corresponds exactly to |
| 919 |
|
a pickup that would currently be written. |
| 920 |
|
- read pickup written in the old format (until checkpoint59i) if it |
| 921 |
|
recognizes an old meta file (no field-list). |
| 922 |
|
- add a meta file in exp. which starts from a pickup: 2 cases: |
| 923 |
|
a) minimal meta file (with just file precision) + pickupStrictlyMatch=F |
| 924 |
|
e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta |
| 925 |
|
b) a meta file describing the content of the associated pickup file |
| 926 |
|
e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta |
| 927 |
|
o pkg/mdsio & pkg/rw: |
| 928 |
|
- new routine to read a meta file ; new set of routine to read |
| 929 |
|
Multiple-fields file (with meta file). |
| 930 |
|
o added open boundary conditions capability for seaice |
| 931 |
|
HSNOW, HSALT, UICE, and VICE |
| 932 |
|
|
| 933 |
|
checkpoint59i |
| 934 |
|
o adjoint: |
| 935 |
|
* fix multiDimAdvection adjoint |
| 936 |
|
(partial recomputation problem by TAF for fVerT(:,:,kDown) |
| 937 |
|
and comlev1 size definition (maxpass vs. max. number of tracers) |
| 938 |
|
* verification/global_ocean.90x45x15 adjoint now tests |
| 939 |
|
NLFS and multiDimAdvection using DST3 (=30) |
| 940 |
|
* verification/lab_sea now tests multiDimAdvection using DST3 (=30) |
| 941 |
|
o pkg/kpp: add "_d 0" to real constant (if missing); |
| 942 |
|
update output of exp: natl_box (10.digits); vermix (std, 7.digits) |
| 943 |
|
and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). |
| 944 |
|
o prepare for "clever pickup" implementation: add new header file "RESTART.h" |
| 945 |
|
for internal parameters related to restart process (formerly from PARAMS.h) |
| 946 |
|
and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. |
| 947 |
|
o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed |
| 948 |
|
as argument. (only atm2d & obcs write_pickup have not yet been updated) |
| 949 |
|
o pkg/monitor: |
| 950 |
|
- use GLOBAL_SUM_TILE instead of _GLOBAL_SUM |
| 951 |
|
- fix mon_stats_rs (statistics over the full domain, even where field is zero) |
| 952 |
|
- account for deep Atmosphere factor and density factor (anelastic) |
| 953 |
|
o added open boundary conditions capability for seaice HEFF and AREA |
| 954 |
|
o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) |
| 955 |
|
thermodynamics |
| 956 |
|
- requires a little reorganization, which affects the testreport results |
| 957 |
|
of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, |
| 958 |
|
so that now the conservative form is tested |
| 959 |
|
- add a few comments |
| 960 |
|
o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* |
| 961 |
|
o add a little bit of code to gad_os7mp_adv_?.F to help vectorization |
| 962 |
|
o add new diagnostics to seaice: advective, diffusive fluxes (only for |
| 963 |
|
multidim-advection, for scheme 2 they are not filled) and transports, |
| 964 |
|
thermodynamic growth rates |
| 965 |
|
o change units of EmPmR (inside the code, + within coupling interface) |
| 966 |
|
from m/s to kg/m2/s (mass flux) but leave input file unchanged. |
| 967 |
|
Affects results @ truncation level (cg2d match) and update output of |
| 968 |
|
experiments: lab_sea(6), global_ocean.90x40x15(10), |
| 969 |
|
global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) |
| 970 |
|
+ adjoint results: global_ocean_ebm(11) and lab_sea (12). |
| 971 |
|
Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). |
| 972 |
|
Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). |
| 973 |
|
|
| 974 |
|
checkpoint59h |
| 975 |
|
o pkg/exf: |
| 976 |
|
- improve vectorization by moving if-statement out of loops in |
| 977 |
|
exf_mapfields, exf_radiation |
| 978 |
|
- exf_bulkformulae.F: introduce 2D fields and vectorize code |
| 979 |
|
o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package |
| 980 |
|
o testreport: |
| 981 |
|
- allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE |
| 982 |
|
monitor & update offline_exf_seaice exp. output. |
| 983 |
|
- AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) |
| 984 |
|
o pkg/seaice: |
| 985 |
|
- bug fix in the evp solver: boundary conditions were affected be |
| 986 |
|
masking of zMax/zMin (changes results) |
| 987 |
|
- minor bug fix in boundary conditions in seaice_calc_strainrates |
| 988 |
|
(changes results for no_slip) |
| 989 |
|
- seaice_lsr.F: make interpolation of eta dependent on boundaries |
| 990 |
|
- replace hardcoded lower limit for zeta (zMin) by runtime parameter |
| 991 |
|
- add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean |
| 992 |
|
stress formulation and no-slip boundary conditions |
| 993 |
|
o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP |
| 994 |
|
in gad_calc_rhs.F ; add few safety stops in initialisation phase. |
| 995 |
|
o pkg/seaice: a first HSALT time stepping equation has been checked in |
| 996 |
|
o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV |
| 997 |
|
in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem |
| 998 |
|
without requiring DO-IF statements |
| 999 |
|
o pkg/thsice: |
| 1000 |
|
use continuous power-law function for partition of energy between lateral |
| 1001 |
|
melting/freezing and thinning/thickening ; old code using step function |
| 1002 |
|
still available with #undef THSICE_FRACEN_POWERLAW |
| 1003 |
|
update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice |
| 1004 |
|
o testreport: change AD testing : check against results/output_adm.txt |
| 1005 |
|
using same scripts as for forward test. |
| 1006 |
|
|
| 1007 |
|
checkpoint59g |
| 1008 |
|
o adjoint testing: in preparation for changing testreport: |
| 1009 |
|
- output format: cost and grad written on separated lines |
| 1010 |
|
- ad output results in directory "results" (instead of "results_ad") |
| 1011 |
|
o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
| 1012 |
|
o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
| 1013 |
|
o pkg/ecco: allow user defined cost function contributions |
| 1014 |
|
o testreport: |
| 1015 |
|
Allow to choose (per experiment) the list of tested output variables |
| 1016 |
|
and the main variable (used to issue a pass/FAIL ) ; |
| 1017 |
|
- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
| 1018 |
|
- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
| 1019 |
|
Also modify printing of summary: |
| 1020 |
|
a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
| 1021 |
|
b) echo the list of tested variables in the individual summary.txt of |
| 1022 |
|
each experiment. |
| 1023 |
|
o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
| 1024 |
|
threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
| 1025 |
|
(but still depend on the tile decompostion of the domain). |
| 1026 |
|
o pkg/seaice: change a discretization detail to make the B-grid code |
| 1027 |
|
"more symmetric". This change is likely to remove all "ridges/leads" that |
| 1028 |
|
where quasi-aligned with the grid in B-grid solutions. It may also be |
| 1029 |
|
the solution to the stress coupling issues with the B-grid. |
| 1030 |
|
o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
| 1031 |
|
remove .cvsignore from input dir. (since testreport no longer run here). |
| 1032 |
|
o pkg/thsice: |
| 1033 |
|
- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
| 1034 |
|
- fix reshaping of sea-ice just after advection: |
| 1035 |
|
melt all the ice only if ice-volume is too small. |
| 1036 |
|
- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
| 1037 |
|
prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
| 1038 |
|
and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
| 1039 |
|
o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
| 1040 |
|
tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
| 1041 |
|
o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
| 1042 |
|
forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
| 1043 |
|
(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
| 1044 |
|
and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
| 1045 |
|
of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
| 1046 |
|
-> update output.txt |
| 1047 |
|
o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
| 1048 |
|
this affects truncation error: -> update output.txt of exp: |
| 1049 |
|
global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
| 1050 |
|
ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
| 1051 |
|
|
| 1052 |
|
checkpoint59f |
| 1053 |
|
o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
| 1054 |
|
o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
| 1055 |
|
a bounded range (in forward mode) |
| 1056 |
|
o pkg/ecco, ctrl, autodiff and mom_common: |
| 1057 |
|
internal parameter controls, completements of implementations |
| 1058 |
|
o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
| 1059 |
|
o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
| 1060 |
|
(not seem any difference in testing results). |
| 1061 |
|
o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
| 1062 |
|
at face corners. |
| 1063 |
|
o pkg/generic_advdiff: |
| 1064 |
|
- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
| 1065 |
|
loop range indices for computing vertical advection tendency |
| 1066 |
|
and do the calculation in the interior only (no overlap) ; |
| 1067 |
|
for now, only implemented for SOM advection (to save CPU time). |
| 1068 |
|
- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
| 1069 |
|
o exch2 adjoint |
| 1070 |
|
First set of changes: |
| 1071 |
|
- add exch2 hand-written adjoint templates |
| 1072 |
|
- exch2 hand-written no longer use TAF-flag 'nownew_arg' |
| 1073 |
|
This will require cleanup in pkg/autodiff/*.F |
| 1074 |
|
(changed routines currently kept separate in verif. code/) |
| 1075 |
|
- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
| 1076 |
|
that used to hide exch2 or cubed-sphere specific code |
| 1077 |
|
(commented via 'cph-exch2') |
| 1078 |
|
o pkg/seaice |
| 1079 |
|
- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
| 1080 |
|
o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
| 1081 |
|
output of global_ocean.cs32x15.thsice . |
| 1082 |
|
|
| 1083 |
|
checkpoint59e |
| 1084 |
|
o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
| 1085 |
|
for B-grid vector (not yet tested) and C-grid vector (<- only used |
| 1086 |
|
when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). |
| 1087 |
|
o starting implementation of Duffy et al. (GRL 1999) salt plume scheme |
| 1088 |
|
(#ifdef ALLOW_SALT_PLUME) |
| 1089 |
|
o gather_2d/scatter_2d: removed halo regions |
| 1090 |
|
o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
| 1091 |
|
scheme and the corresponding test case (under front_relax dir). For now, |
| 1092 |
|
only available with Skew-flux form and not yet tested in realistic set-up. |
| 1093 |
|
adjoint: store directives updated, but gradient checks deteriorated, |
| 1094 |
|
so maybe GM/Redi adjoint is now broken. |
| 1095 |
|
o seaice adjoint |
| 1096 |
|
* add AREA, HEFF, HSNOW as control variable |
| 1097 |
|
(should not change lab_sea results) |
| 1098 |
|
* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
| 1099 |
|
o pkg/seaice: |
| 1100 |
|
* added computation of saltFlux in seaice_growth; |
| 1101 |
|
For time being, sea ice salinity is assumed constant |
| 1102 |
|
contribution of snow flooding to freshening of sea ice is neglected. |
| 1103 |
|
SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
| 1104 |
|
defaults to 0.0 in order to maintain backward compatibility. |
| 1105 |
|
Typical values for SEAICE_salinity are 4 to 10 g/kg. |
| 1106 |
|
* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
| 1107 |
|
* added SEAICE_availHeatFrac, which specifies fraction of surface level |
| 1108 |
|
heat content used to melt or grow ice |
| 1109 |
|
* commented out cap of HICE: it helps keep ice thinner |
| 1110 |
|
* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
| 1111 |
|
* applied OBCS T/S mask to HEFFM sea ice mask |
| 1112 |
|
|
| 1113 |
|
checkpoint59d |
| 1114 |
|
o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
| 1115 |
|
for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
| 1116 |
|
(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
| 1117 |
|
o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
| 1118 |
|
and change default value of parameter "GM_Small_Number"; |
| 1119 |
|
update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
| 1120 |
|
global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
| 1121 |
|
tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
| 1122 |
|
o pkg/ecco: cost function when applying pkg/smooth to controls |
| 1123 |
|
o pkg/ctrl: add forcingPrecond run time parameter |
| 1124 |
|
o pkg/seaice: |
| 1125 |
|
- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
| 1126 |
|
- fix bug in metric terms of u-equation in LSR solver (implicit part), |
| 1127 |
|
changes verification/lab_sea |
| 1128 |
|
- rearrange implicit part of u-equation in LSR solver to make it easier to |
| 1129 |
|
read, understand, and debug. This causes changes at the truncation level. |
| 1130 |
|
- fix (serious) bug in the boundary conditions (sign error in the implicit |
| 1131 |
|
part) of the LSR solver. Changes all LSR results. |
| 1132 |
|
- fixed problem with HSNOW initialization to avoid thick snow when AREA |
| 1133 |
|
is initilized with small values - does not change lab_sea results. |
| 1134 |
|
- added HsnowFile initialization capability |
| 1135 |
|
o pkg/smooth: addition to model/src and pkg/ctrl so allow |
| 1136 |
|
initialization of pkg/smooth and application to control vector |
| 1137 |
|
o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
| 1138 |
|
o dependencies: pkg/profiles requires pkg/cal |
| 1139 |
|
o pkg/profiles: |
| 1140 |
|
- added option ALLOW_PROFILES_GENERICGRID |
| 1141 |
|
-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
| 1142 |
|
that interpolation information (grid points and coefficients) is provided |
| 1143 |
|
within the netcdf input files. |
| 1144 |
|
-> sample matlab scripts can be found in MITgcm_contrib/gael |
| 1145 |
|
that allow you to prepare netcdf input files. |
| 1146 |
|
- also modified: cleaner include statements, cleaner error print statements, |
| 1147 |
|
cleaner stops when error, and more tests of the netcdf input files consistency. |
| 1148 |
|
o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
| 1149 |
|
o pkg/seaice: |
| 1150 |
|
- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
| 1151 |
|
requires a new routine: seaice_diagnostics_fill.F |
| 1152 |
|
- make sure that seaice does not move if not forced (pressure replacement |
| 1153 |
|
method, Hibler and Ip, 1995), changes results |
| 1154 |
|
- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
| 1155 |
|
- SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). |
| 1156 |
|
It is turned off by default (=-1.), because it changes the results. |
| 1157 |
|
- make it possible to read AREA from a file, too. |
| 1158 |
|
|
| 1159 |
|
checkpoint59c |
| 1160 |
|
o add S/R and diagnostics for oceanic mixed-layer depth |
| 1161 |
|
o move GMRedi call after all vertical mixing schemes (including KPP) |
| 1162 |
|
o pkg/thsice: |
| 1163 |
|
- ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs |
| 1164 |
|
(melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice |
| 1165 |
|
o pkg/obcs: |
| 1166 |
|
- bug fix for balance code |
| 1167 |
|
o pkg/seaice: |
| 1168 |
|
- allow values of SEAICE_elasticParm > 1 |
| 1169 |
|
- add new parameter SEAICE_evpTauRelax as an alternative |
| 1170 |
|
to SEAICE_elasticParm |
| 1171 |
|
- make lsr boundary conditions free slip (by default), changes result |
| 1172 |
|
- add code for no slip boundary conditions for lsr |
| 1173 |
|
- set minimum of zeta to zero (and not 4e8) (changes results) |
| 1174 |
|
- add a cap on AREA after advecting AREA if seaice_growth is not called |
| 1175 |
|
o change calculation of Visbeck K: |
| 1176 |
|
- no longer depend on tapering scheme; instead, compute slope (limited |
| 1177 |
|
by GM_maxSlope). this is equivalent to what was comuted before with |
| 1178 |
|
clipping or linear tappering. |
| 1179 |
|
- fix vertical averaging (wrong by 1/2 level) |
| 1180 |
|
- leave the old version (but will not be maintained) within |
| 1181 |
|
#ifdef OLD_VISBECK_CALC / #endif |
| 1182 |
|
- update output of exp. ideal_2D_oce |
| 1183 |
|
o change error catch in calc_r_star to improve vectorization |
| 1184 |
|
o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
| 1185 |
|
add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
| 1186 |
|
o adjoint: |
| 1187 |
|
Re-organized adjoint checkpointing according to Matt Mazloff |
| 1188 |
|
(but with modifs/completions/cleanups) |
| 1189 |
|
Storing is now bundled into large arrays to optimized I/O |
| 1190 |
|
(and second step in cleanup of the_main_loop) |
| 1191 |
|
|
| 1192 |
|
checkpoint59b |
| 1193 |
|
o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
| 1194 |
|
- export/import (between ocean & coupler) fields needed for ocean DIC. |
| 1195 |
|
o pkg/seaice: |
| 1196 |
|
- get rid of three more exchanges seaice_calc_viscosities (required |
| 1197 |
|
different loop boundaries in seaice_lsr and seaice_ocean_stress) |
| 1198 |
|
- bug fix in seaice_ocean_stress (update of lab_sea required) |
| 1199 |
|
- reduce loop boundaries to necessary minimum also in seaice_evp |
| 1200 |
|
- go back to the old way of computing deltaC/Z as the adjoint likes that |
| 1201 |
|
better |
| 1202 |
|
o Refresh of tutorial_global_oce_latlon (includes changing salinity-like |
| 1203 |
|
passive tracer to an Age Tracer) + update output.txt |
| 1204 |
|
o pkg/exf: |
| 1205 |
|
- implement A-grid / C-grid selection for wind-stress input files. |
| 1206 |
|
- clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) |
| 1207 |
|
for now, in exf_bulk_largeyeager04.F only : |
| 1208 |
|
- change implementation for case where windspeed + 2. components wind-stress |
| 1209 |
|
are read-in. AND use rhoConstFresh to convert evap. |
| 1210 |
|
o pkg/seaice: |
| 1211 |
|
- use correct EXCH_UV for wind-forcing (on A-grid). |
| 1212 |
|
- change SEAICE_OPTIONS.h to limit the number of option combinations (regarding |
| 1213 |
|
SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops. |
| 1214 |
|
o pkg/exf: |
| 1215 |
|
- default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC) |
| 1216 |
|
EXF_INTERPOLATION: |
| 1217 |
|
- merge global_with_exf/code version of exf_interp_read.F |
| 1218 |
|
to the main code ; |
| 1219 |
|
- Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when |
| 1220 |
|
reading the file ; Important: This options needs to be defined to recover |
| 1221 |
|
previous code. |
| 1222 |
|
otherwise, use fixed size array to read in (size=exf_interp_bufferSize). |
| 1223 |
|
- no longer loose real*8 precision along the way when using exf_iprec=64. |
| 1224 |
o pkg/seaice: rearrangement of common blocks (really needs more cleaning up) |
o pkg/seaice: rearrangement of common blocks (really needs more cleaning up) |
| 1225 |
- change discretisation of evp-solver in order to avoid another exchange |
- change discretisation of evp-solver in order to avoid another exchange |
| 1226 |
(changes lab_sea) and clean up a little |
(changes lab_sea) and clean up a little |
| 1241 |
o pkg/thsice: |
o pkg/thsice: |
| 1242 |
fix few little problems, in thsice_calc_thickn.F: |
fix few little problems, in thsice_calc_thickn.F: |
| 1243 |
- growth vertically (and not laterally) if iceFrac == iceMaskMax |
- growth vertically (and not laterally) if iceFrac == iceMaskMax |
| 1244 |
- melt laterally only if hIce < hThinIce (as the comments say) |
- melt only laterally if hIce < hThinIce (as the comments say) |
| 1245 |
and in thsice_extend.F: |
and in thsice_extend.F: |
| 1246 |
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
| 1247 |
- start to form ice as soon as the minimum ice-volume is reachable. |
- start to form ice as soon as the minimum ice-volume is reachable. |
| 1278 |
ATMOSPHERIC_LOADING is #define). |
ATMOSPHERIC_LOADING is #define). |
| 1279 |
o pkg/kpp: replaced _KPP_RL with _RL |
o pkg/kpp: replaced _KPP_RL with _RL |
| 1280 |
o bug fixes for vertical diffusivity computations when both KPP and |
o bug fixes for vertical diffusivity computations when both KPP and |
| 1281 |
3D diffusivity arrays are used. |
3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F |
| 1282 |
|
are no longer updating the vertical diffusivity array |
| 1283 |
|
(passed as argument) but are (re-) setting those arrays. |
| 1284 |
o pkg/seaice: fix bug in evp solver, while doing that |
o pkg/seaice: fix bug in evp solver, while doing that |
| 1285 |
- change (improve?) discretization of stress computations for both |
- change (improve?) discretization of stress computations for both |
| 1286 |
cgrid-lsr and evp solver |
cgrid-lsr and evp solver |
| 2762 |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
| 2763 |
- these scheme operate in a similar manner as KPP (without ghat, of |
- these scheme operate in a similar manner as KPP (without ghat, of |
| 2764 |
course), however there is only one diffusivity that is used for both |
course), however there is only one diffusivity that is used for both |
| 2765 |
temperature and salinity (and passive tracers)ç |
temperature and salinity (and passive tracers) |
| 2766 |
o add offline package |
o add offline package |
| 2767 |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
| 2768 |
provided by Stephanie Dutkiewicz |
provided by Stephanie Dutkiewicz |
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