| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
|
|
| 7 |
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o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep |
| 8 |
|
- adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY |
| 9 |
|
GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT |
| 10 |
|
- verification experiment natl_box.longstep |
| 11 |
|
o build_options: ifort+mpi_aces optfile (following Constantinos advise): |
| 12 |
|
allow different versions of ifort (8 or 9) and different versions |
| 13 |
|
of mpi (mpich or mpich2) to be used with the same optfile. |
| 14 |
|
requires to load a netcdf module and set MPI_INC_DIR (see comments inside |
| 15 |
|
optfile). Change testing scripts (example_scripts/ACESgrid) accordingly. |
| 16 |
|
|
| 17 |
|
checkpoint61r |
| 18 |
|
o pkg/seaice: |
| 19 |
|
- clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps: |
| 20 |
|
1. introduce fields for time step (N-1) |
| 21 |
|
2. do not use levels 2 and 3 anymore (but keep them) |
| 22 |
|
3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This |
| 23 |
|
includes changes to pkg/thsice/thsice_get_velocity.F, |
| 24 |
|
model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and |
| 25 |
|
pkg/obcs/obcs_apply_uvice.F. |
| 26 |
|
- completely remove code for leap-frog time stepping for second order |
| 27 |
|
advection |
| 28 |
|
- adjusted adjoint accordingly; |
| 29 |
|
gradient checks have improved by an order of magnitude! |
| 30 |
|
|
| 31 |
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checkpoint61q |
| 32 |
|
o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver |
| 33 |
|
- the boundary conditions along open boundaries are unclear, because the |
| 34 |
|
associated masks are set to zero and are thus treated as closed when |
| 35 |
|
applying the slip-boundary conditions. |
| 36 |
|
- move initialisation of grid variables from seaice_init_varia to _fixed |
| 37 |
|
o adding doc/diags_changes.txt |
| 38 |
|
o model/src: |
| 39 |
|
do_the_model_io: rename few pkg S/R which are called from do_the_model_io, |
| 40 |
|
to avoid "_diags" naming if no relation to pkg/diagnostics. |
| 41 |
|
ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF |
| 42 |
|
file and only call PLOT_FIELD_XYZ if debugMode=T. |
| 43 |
|
remove few PLOT_FIELD_XY calls outside initialisation. |
| 44 |
|
remove few unnecessary BARRIER. |
| 45 |
|
o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling |
| 46 |
|
of salt_plume package in Southern Ocean |
| 47 |
|
o pkg/thsice: |
| 48 |
|
- fix hOceMxL in overlap (needed for sea-ice advection); |
| 49 |
|
update output of experiment global_ocean.cs32x15.icedyn. |
| 50 |
|
o pkg/seaice: |
| 51 |
|
- make the (placeholder-)tracer IceAge a little more meaningful |
| 52 |
|
by avoiding ridging of age due to convergent ice flow |
| 53 |
|
- add diagnostics for surface temperature, atmospheric and oceanic |
| 54 |
|
heat flux, and atmospheric and oceanic ice growth |
| 55 |
|
|
| 56 |
|
checkpoint61p |
| 57 |
|
o eesupp (global_max & global_sum): |
| 58 |
|
- add one more element to buffer (start at index 0) for GL_MAX/SUM output; |
| 59 |
|
- remove starting & endding barrier (no longer needed) |
| 60 |
|
o pkg/mdsio, writelocal: |
| 61 |
|
works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined |
| 62 |
|
(remove the STOP): uses shared buffer IO to store data from all threads |
| 63 |
|
and then let master-thread write nThreads tiles. |
| 64 |
|
o pkg/mdsio (read/write field): |
| 65 |
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- tiled IO done in 1 piece (all levels at a time); |
| 66 |
|
- new header file "MDSIO_BUFF_3D.h" with 3-D buffers. |
| 67 |
|
- multi-threaded: allow to read/write local (non-shared) array |
| 68 |
|
(was already working with singleCpuIO ; now works also without); |
| 69 |
|
=> no longer needs barrier call after reading a file (added inside |
| 70 |
|
mds_read/write field). |
| 71 |
|
- move barrier calls outside gather/scatter_2d to mds_read/write_field |
| 72 |
|
o pkg/obcs/exf |
| 73 |
|
- exf_getffieldrec.F: add a few ". _d 0" and |
| 74 |
|
add code to catch the case fldperiod = 0. |
| 75 |
|
- obcs_precribe_read.F: change if statements so that they match |
| 76 |
|
the variable type (_RL) |
| 77 |
|
- add a separate exf_iprec_obcs to exf_set_obcs (by default equal to |
| 78 |
|
exf_iprec) as part of namelist EXF_NML_01 |
| 79 |
|
o pkg/mdsio: |
| 80 |
|
- read/write tiled (local) files: read/write 1-level tile chunk at a time |
| 81 |
|
(instead of segment of length sNx); expected to speed up tiled IO. |
| 82 |
|
o pkg/exch2: |
| 83 |
|
- take buffer copy from/to array out of S/R exch2_send/recv into new |
| 84 |
|
S/R exch2_put/get ; Exch of local variable now works with MPI+MTH |
| 85 |
|
(tested by removing commom block statement in SOLVE_FOR_PRESSURE.h). |
| 86 |
|
- ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get) |
| 87 |
|
- simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds |
| 88 |
|
(which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by |
| 89 |
|
including Topology header file (and common blocks). |
| 90 |
|
- implement EXCH_IGNORE_CORNERS in scalar exchange (rx1); |
| 91 |
|
remove 2nd exch call in exch2_s3d_rx (no longer needed). |
| 92 |
|
- document S/R arg. list (+ update some comments) |
| 93 |
|
o pkg/seaice: |
| 94 |
|
- added SEAICE_CLIM_AIR code, which permits modulation of surface air |
| 95 |
|
temperature and humidity over sea ice based on climatological values. |
| 96 |
|
- clean up computation of Hibler+Bryan (1987) stress coupling for the case |
| 97 |
|
of LSR (this change is expected to change the results slightly because now |
| 98 |
|
it uses slightly difference moduli from the second last LSR solution, but |
| 99 |
|
that is more consistent with the stress computations; this part of the code |
| 100 |
|
is not tested in the verification experiments) |
| 101 |
|
- fix diagnostics for flux of ice in case of B-grid |
| 102 |
|
- turn strain rates eij and press into global fields within global |
| 103 |
|
common block in SEAICE.h for more straighforward diagnostics |
| 104 |
|
- fix diagnostics for principal stress components, press, zeta, eta |
| 105 |
|
to give something meaning full |
| 106 |
|
o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate |
| 107 |
|
new output (all 4 tests) using default rotationPeriod. |
| 108 |
|
o pkg KPP: |
| 109 |
|
- add flag (LimitHblStable) to avoid limiting BL depth under stable conditions |
| 110 |
|
- fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1 |
| 111 |
|
and normal grid from 1 to Nr) |
| 112 |
|
o Fix computations of L4rdt in mom_calc_visc.F |
| 113 |
|
o eesupp: |
| 114 |
|
new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg): |
| 115 |
|
should be called before a "stop" if we know that all process are going |
| 116 |
|
to stop; if one Proc does call this S/R, will hang in MPI_FINALISE. |
| 117 |
|
|
| 118 |
|
checkpoint61o |
| 119 |
|
o pkg/exch2: change check_depths to issue just a warning (instead of error+stop) |
| 120 |
|
o model/src/ini_curvilinear_grid.F: |
| 121 |
|
compute angleSin/CosC when they are not read from a file |
| 122 |
|
o pkg/seaice: |
| 123 |
|
add pseudo time stepping for LSOR |
| 124 |
|
o pkg/exch2: |
| 125 |
|
temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW |
| 126 |
|
o pkg/seaice: |
| 127 |
|
Adding separate sea ice albedo, drag coefficients, and HO in Southern |
| 128 |
|
Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h |
| 129 |
|
o SingleCpuIO: |
| 130 |
|
fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used. |
| 131 |
|
o pkg/seaice: |
| 132 |
|
put exchanged variable in (local) common block for MPI+Multi-Threads |
| 133 |
|
to work (necessary with exch1, and for now with exch2 too). |
| 134 |
|
o verification: to get more experiments tested with mpi, mth and mpi+mth, |
| 135 |
|
change tiling of: |
| 136 |
|
aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15, |
| 137 |
|
hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope |
| 138 |
|
update output of exp: |
| 139 |
|
exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5), |
| 140 |
|
tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod) |
| 141 |
|
+ ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU |
| 142 |
|
(note: output.txt generated on faulks using only 1 tile) |
| 143 |
|
o eesupp & mdsio (SingleCpuIO): |
| 144 |
|
- remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time |
| 145 |
|
parameter "W2_useE2ioLayOut" (read from file "data.exch2"). |
| 146 |
|
Note: was not effective for globalFile & useSingleCpuIO=F; now fixed. |
| 147 |
|
- move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc). |
| 148 |
|
- fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same |
| 149 |
|
gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array). |
| 150 |
|
o pkg/exch2: |
| 151 |
|
- new code to set-up W2-Exch2 topology (replace matlab-topology-generator): |
| 152 |
|
read parameter file "data.exch2" if it exists; otherwise try default regular |
| 153 |
|
cube without blank-tile; new header file "W2_EXCH2_SIZE.h"; |
| 154 |
|
- update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible |
| 155 |
|
with new code (not to be used, just as a backup solution). |
| 156 |
|
- add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2" |
| 157 |
|
in utils/exch2/input. |
| 158 |
|
|
| 159 |
|
checkpoint61n |
| 160 |
|
o eesupp & mdsio (SingleCpuIO): |
| 161 |
|
- move mapping to global io-buffer inside gather_2d/scater_2d: this save |
| 162 |
|
memory (1 less 2D global RL array); skip 1 buffer copy; and only send/ |
| 163 |
|
receive real*4 array (instead of real*8) to read/write 32.bit files. |
| 164 |
|
(new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S |
| 165 |
|
and remove new mapping S/R) |
| 166 |
|
o pkg/mdsio: in preparation for topology-generator within pkg/exch2: |
| 167 |
|
- Change declaration of SingleCpuIO buffer, reduced to only 1 dim.: |
| 168 |
|
xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h |
| 169 |
|
when using exch2. Add S/R to map global io-buffer to global model array. |
| 170 |
|
- uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt. |
| 171 |
|
|
| 172 |
|
checkpoint61m |
| 173 |
|
o write_utils : change WRITE_1D_R8 to WRITE_1D_RL |
| 174 |
|
and add 3 other S/R for other types (R4,R8,RS). |
| 175 |
|
Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument. |
| 176 |
|
o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros): |
| 177 |
|
- ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ; |
| 178 |
|
- reduce number of macro definitions (keep only those which are used); |
| 179 |
|
can always call directly the corrresponding S/R if needed. |
| 180 |
|
- everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix |
| 181 |
|
_R4/_R8 to _RS/_RL when applied to _RS/_RL variable. |
| 182 |
|
Fixed wrong type of arg in: |
| 183 |
|
atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F |
| 184 |
|
ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F |
| 185 |
|
To fix: global_sum of var in common block is wrong (multi-threaded) in: |
| 186 |
|
dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F |
| 187 |
|
To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops) |
| 188 |
|
o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd |
| 189 |
|
"nlfs" mpi test is going to stop when checking for unconnected tile egdes. |
| 190 |
|
o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error |
| 191 |
|
o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile |
| 192 |
|
edges are closed (zero depth); might happen with "blank tiles"; |
| 193 |
|
for now, disabled if using OBCS. |
| 194 |
|
o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi": |
| 195 |
|
link *_mpi files from "MODS" dir) to return to a strait-forward behavior. |
| 196 |
|
o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D) |
| 197 |
|
to reduce length of 1.D array print in STDOUT. |
| 198 |
|
o adjustment.cs-32x32x1: changed to oceanic test with 1 continent |
| 199 |
|
+ use 48 tiles (16x8): this will allow to test "blank tiles". |
| 200 |
|
o start to test MPI + multi-threaded (change testreport to skip tests |
| 201 |
|
where number of tiles do not match). |
| 202 |
|
o genmake2: add option "-omp" to turn on Open-MP ; |
| 203 |
|
passed to testreport (if using -mth) ; merge few (*+mth) optfiles. |
| 204 |
|
o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them) |
| 205 |
|
and keep the original tile numbering. Note: compatible with old |
| 206 |
|
W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files. |
| 207 |
|
|
| 208 |
|
checkpoint61l |
| 209 |
|
o Overlaps had been forgotten in calculating ijk keys : fixed |
| 210 |
|
o fix cyrus makedepend for gcc 4.4 |
| 211 |
|
o experiment fizhi-cs-aqualev20: |
| 212 |
|
switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE) |
| 213 |
|
and generate new output. Note: new output is much closer to the old |
| 214 |
|
one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from |
| 215 |
|
the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007. |
| 216 |
|
o pkg/fizhi: |
| 217 |
|
- change to avoid indices going deliberately over array-bounds |
| 218 |
|
- remove unnecessary MPI stuff |
| 219 |
|
- perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY" |
| 220 |
|
- new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE: |
| 221 |
|
does not go over array-bounds and therefore returns reliable output. |
| 222 |
|
- in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls: |
| 223 |
|
this S/R has 4 output arguments, which are used inside "get_alarm"; |
| 224 |
|
when it is called with the same variable "ndum" in place of several |
| 225 |
|
output arguments, this produces weird side effect inside "get_alarm" |
| 226 |
|
(e.g., datein=dates(n) is overwritten by timein=times(n) since both |
| 227 |
|
datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum" |
| 228 |
|
address) and produces error. |
| 229 |
|
o tools/gemake2: (March 27-29 2009) |
| 230 |
|
with option "-mpi": link *_mpi files from "MODS" dir (this is what |
| 231 |
|
testreport does). |
| 232 |
|
o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output |
| 233 |
|
o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F: |
| 234 |
|
update lab_sea.lsr & lab_sea.salt_plume results |
| 235 |
|
o pkg/seaice: |
| 236 |
|
Major overhaul of the LSOR solver: change discretization from original |
| 237 |
|
finite differences to finite volume. The old routine is still in the |
| 238 |
|
file seaice_lsr.F and can be turned on with the CPP-flag |
| 239 |
|
SEAICE_OLD_AND_BAD_DISCRETIZATION |
| 240 |
|
Along with this change, the discretization of the strain rates is changed. |
| 241 |
|
The same flag turns on the old discretization in seaice_calc_strainrates.F |
| 242 |
|
All verification experiments with seaice are affected (except for |
| 243 |
|
seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old |
| 244 |
|
results by setting the above flag. |
| 245 |
|
Further changes involve changes in defaults: |
| 246 |
|
- ALLOW_FLOODING is defined and turned on by default |
| 247 |
|
- SEAICEadvSnow = .true. is now the default |
| 248 |
|
- SEAICEadvSalt = .true. is now the default |
| 249 |
|
- SEAICEadvAge = .true. is now the default |
| 250 |
|
- SEAICE_clipVelocities = .false. is now the default |
| 251 |
|
(as per J. Zhang's recommendation) |
| 252 |
|
- B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE |
| 253 |
|
is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS |
| 254 |
|
- seaice_growth: replace computation of UG by a simple copy from wspeed |
| 255 |
|
|
| 256 |
|
checkpoint61k |
| 257 |
|
o pkg/seaice: a few bug fixes mostly concerning the metric terms: |
| 258 |
|
seaice_lsr: fixed a few metric terms, |
| 259 |
|
affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs |
| 260 |
|
add more debugging diagnostics |
| 261 |
|
seaice_evp: removed superfluous many metric terms of FV discretization |
| 262 |
|
of stress divergence |
| 263 |
|
affects lab_sea, lab_sea.hb87 |
| 264 |
|
seaice_ocean_stress: removed superfluous many metric terms of FV discretization |
| 265 |
|
of stress divergence for non-evp solver |
| 266 |
|
(this part is not tested anywhere) |
| 267 |
|
seaice_calc_strainrates: fixed a bug in no-slip boundary conditions, |
| 268 |
|
they were effectively only half slip |
| 269 |
|
affects lab_sea.hb87 |
| 270 |
|
updated all relevant verification experiments (except lab_sea//output_adm.txt |
| 271 |
|
which was left over, but fails at level 7 & 6) |
| 272 |
|
|
| 273 |
|
checkpoint61j |
| 274 |
|
o pkg/seaice: turn a few hard wired parameters into run time parameters |
| 275 |
|
o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model |
| 276 |
|
time in seconds as promised by the usints in seaice_monitor and exf_monitor |
| 277 |
|
o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids |
| 278 |
|
that are not cubed-sphere grids |
| 279 |
|
o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR |
| 280 |
|
o pkg/ctrl: |
| 281 |
|
fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low) |
| 282 |
|
o non-hydrostatic (calc_gw.F): |
| 283 |
|
fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec |
| 284 |
|
update output of exp. global_ocean.cs32x15.viscA4 |
| 285 |
|
o remove backward compatibility for thetaMin,phiMin |
| 286 |
|
(replaced by xgOrigin,ygOrigin on Jan 27, 2009) |
| 287 |
|
o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the |
| 288 |
|
interpolated wind field not only for curvilineargrid=.true., but also |
| 289 |
|
for a rotated grid (rotateGrid=.true.) |
| 290 |
|
o pkg/exf: add capability to bypass interpolation for runoff |
| 291 |
|
by setting yet another CPP-flag |
| 292 |
|
o eesupp/src, B-grid exchange: |
| 293 |
|
add simple (6 tiles, non MPI) CS exch + standard interface S/R. |
| 294 |
|
o autodiff |
| 295 |
|
new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV |
| 296 |
|
allows to switch to single-prec common blocks; |
| 297 |
|
corresponding switch occurs in tamc.h, integer isbyte |
| 298 |
|
TAF store directivs "byte" and "kind" seem equivalent; |
| 299 |
|
Most tamc.h have been updated correspondingly. |
| 300 |
|
|
| 301 |
|
checkpoint61i |
| 302 |
|
o autodiff: |
| 303 |
|
fix autodiff_sore/_restore indices for obcs |
| 304 |
|
(spotted by I. Hoteit, M. Mazloff) |
| 305 |
|
o pkg/autodiff, pkg/ctrl: |
| 306 |
|
Add flag to reduce all tapelev I/O to single-prec. |
| 307 |
|
In data.ctrl set |
| 308 |
|
doSinglePrecTapelev = .TRUE. |
| 309 |
|
o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2: |
| 310 |
|
check in hack for SX8 compiler (for dxV, dyU); remove it afterwards. |
| 311 |
|
o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for |
| 312 |
|
real fresh water flux (not yet) |
| 313 |
|
o pkg/mdsio & rw: |
| 314 |
|
- add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta) |
| 315 |
|
- add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX. |
| 316 |
|
o pkg/flt: |
| 317 |
|
- replace FLT_INIT by 3-steps standard initialization S/R: readparms, |
| 318 |
|
init_fixed & ini_varia. |
| 319 |
|
- clean-up & simplify linear interpolation S/R: |
| 320 |
|
move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid. |
| 321 |
|
- fix some indices (mainly vertical index) ; add IMPLICIT NONE. |
| 322 |
|
- more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R. |
| 323 |
|
- add vert. coordinate & horiz. indices to output files. |
| 324 |
|
- change vertical position in initial condition, from index to depth [m]. |
| 325 |
|
- store horizontal (decimal) indices i,j in common block (instead of coord. x,y) |
| 326 |
|
(easier to get to a curvilinear grid) ; delX,delY no longer used. |
| 327 |
|
o pkg/ggl90: a few modifications: |
| 328 |
|
- fix bottom boundary condition, and interpolation of KappaE |
| 329 |
|
near top and bottom |
| 330 |
|
- use same set of viscosity/diffusivity for TKE/momnetum/tracer |
| 331 |
|
- add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH) |
| 332 |
|
- add a few options for mixing-length upper limit (--> mxlMaxFlag) |
| 333 |
|
o rename thetaMin,phiMin -> xgOrigin,ygOrigin |
| 334 |
|
(maintain temporary backward compatibility, until next checkpoint) |
| 335 |
|
|
| 336 |
|
checkpoint61h |
| 337 |
|
o pkg/diagnostics with "periodic averaging diagnostics": |
| 338 |
|
fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. |
| 339 |
|
o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82 |
| 340 |
|
o pkg/obcs: fix loop ranges for balancing code |
| 341 |
|
o pkg/flt: |
| 342 |
|
- improve criteria for finding which tile owns a float. |
| 343 |
|
- fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case. |
| 344 |
|
o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg |
| 345 |
|
aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling |
| 346 |
|
with ocean biogeo) |
| 347 |
|
o pkg/flt: |
| 348 |
|
- do some cleaning and fix the restart ; |
| 349 |
|
- add output.txt in flt_example/results to get this pkg tested. |
| 350 |
|
o genmake2: add an EXTENDED_SRC option and flag. |
| 351 |
|
for now, cannot be turned on on command line (only through genmake_local) |
| 352 |
|
o pkg/mdsio: read/write vector: |
| 353 |
|
- singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS |
| 354 |
|
- singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR |
| 355 |
|
& MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. |
| 356 |
|
- affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) |
| 357 |
|
(drop to 4 digits matching for grad). But this test does not look very |
| 358 |
|
reliable (was already failling on eddy, fc5, at 6.digits). Update output. |
| 359 |
|
|
| 360 |
|
checkpoint61g |
| 361 |
|
o pkg/flt: |
| 362 |
|
- move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) |
| 363 |
|
+ make OPTIONS file more standard. |
| 364 |
|
- rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) |
| 365 |
|
- fix _BYTESWAPIO CPP-Flag |
| 366 |
|
- standard reading of file-parameter "data.flt" |
| 367 |
|
- fix argument list of S/R FLT_RESTART |
| 368 |
|
still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F |
| 369 |
|
o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell |
| 370 |
|
o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to |
| 371 |
|
a still unfixed compiler/optimization bug |
| 372 |
|
|
| 373 |
|
checkpoint61f |
| 374 |
|
o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; |
| 375 |
|
update results of global_ocean.cs32x15.icedyn test. |
| 376 |
|
o move getcon.F from model/src to pkg/fizhi. |
| 377 |
|
o pkg/exf: add parameter for extrapolation of temp up to the surface |
| 378 |
|
and option to prevent negative evap (in bulk_largeyeager04 only). |
| 379 |
|
o Prather Advection scheme: fix tracer conservation for divergent flow |
| 380 |
|
(e.g., when using NonLin Free-Surface). |
| 381 |
|
o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead |
| 382 |
|
o gmredi (Visbeck-variable-K): |
| 383 |
|
- add more parameters to Visbeck-variable-K. |
| 384 |
|
- use a 5 points average for dSigmaR in Visbeck-K calculation |
| 385 |
|
(more "homogenous": same stencil and same weights as in dSigmaH) |
| 386 |
|
- update output of ideal_2D_oce experiment. |
| 387 |
|
o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 |
| 388 |
|
(#undef REAL4_IS_SLOW) |
| 389 |
|
- pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 |
| 390 |
|
coordinate variable |
| 391 |
|
- pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables |
| 392 |
|
(surface forcing fields), removes some of the functionality |
| 393 |
|
- model/src/write_grid.F: write _RS variables as RS-netcdf variables |
| 394 |
|
- model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but |
| 395 |
|
probably not all: copy _RS surface flux fields to RL field before |
| 396 |
|
calling DIAGNOSTICS_FILL |
| 397 |
|
- model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into |
| 398 |
|
real*4 (CALL EXCH_*_RS) versions. |
| 399 |
|
- tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 |
| 400 |
|
(generate new output). |
| 401 |
|
|
| 402 |
|
checkpoint61e |
| 403 |
|
o gmredi (Visbeck-variable-K): |
| 404 |
|
- fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h |
| 405 |
|
- change computation of Visbeck-K where Slope > Smax : |
| 406 |
|
now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct) |
| 407 |
|
previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output. |
| 408 |
|
o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic |
| 409 |
|
to be the same as with Z-coord. (i.e., m/s & no-units respectively). |
| 410 |
|
o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc) |
| 411 |
|
o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz |
| 412 |
|
does not become too large (to avoid precision problems in implicit-diffusion |
| 413 |
|
solver); update ideal_2D_oce output. |
| 414 |
|
o pkg ggl90: |
| 415 |
|
- in ggl90_cal.F: compute only one set of visc/diff, used to |
| 416 |
|
step forward TKE/T/S/momentum |
| 417 |
|
- default value of GGL90viscMax/GGL90diffMax larger and equal (to |
| 418 |
|
have Prandlt =1) |
| 419 |
|
o gmredi (fm07): |
| 420 |
|
- add lower limit on Transition layer thickness + lower limit on 1/lambda |
| 421 |
|
- allow to set few more params from data.gmredi |
| 422 |
|
o pkg ggl90: |
| 423 |
|
- add missing sqrt(2) factor in computation of mixing length |
| 424 |
|
scale in ggl90_calc.F |
| 425 |
|
(see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) |
| 426 |
|
|
| 427 |
|
checkpoint61d |
| 428 |
|
o adjoint modifs |
| 429 |
|
- adapt to new field rhoInSitu |
| 430 |
|
- allow to revert from StoreDynVars2D, StoreDynVars3D |
| 431 |
|
to individual fields |
| 432 |
|
(switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) |
| 433 |
|
o store 3-D (in-situ) density in commom block (DYNVARS.h) |
| 434 |
|
- save 1 rho computation. |
| 435 |
|
- no longer modify T & S inland when using down_slope pkg. |
| 436 |
|
o gad_som : allow to switch to SOM advection for T & S without corresponding |
| 437 |
|
pickup files (using new S/R: MDS_CHECK4FILE). |
| 438 |
|
o keep removing _BEGIN/_END_MASTER between MDSIO S/R call |
| 439 |
|
(for useSingleCpuIO to work in multi-threaded) |
| 440 |
|
o pkg/shelfice: |
| 441 |
|
- disentangle parameters: retire shelfIceFile in data/PARM05 and substitute |
| 442 |
|
with SHELFICEtopoFile in data.shelfice |
| 443 |
|
- move code for reading ice shelf topography and modifying hFacC into separate |
| 444 |
|
subroutines of the shelfice package |
| 445 |
|
- separate initialisation of "fixed" and "variable" variables |
| 446 |
|
- kTopC is not (yet) replaced by kSurfC, although this is possible |
| 447 |
|
o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
| 448 |
|
o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
| 449 |
|
and rename: |
| 450 |
|
ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
| 451 |
|
ini_reference_state.F --> load_ref_files.F (- set anelastic factors) |
| 452 |
|
o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) |
| 453 |
|
|
| 454 |
|
checkpoint61c |
| 455 |
|
o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" |
| 456 |
|
to add mass source/sink of fluid in the interior (3-D generalisation |
| 457 |
|
of oceanic real-fresh water flux). |
| 458 |
|
o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) |
| 459 |
|
o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) |
| 460 |
|
o new pkg: down_slope |
| 461 |
|
density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). |
| 462 |
|
- presently, modify T & S inland (dwnslp_calc_rho.F). |
| 463 |
|
can be avoided if rho was stored in common bloc and used in calc_phi_hyd. |
| 464 |
|
- implementation for ocean in P-coords not tested. |
| 465 |
|
- add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. |
| 466 |
|
o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) |
| 467 |
|
(to facilitate conversion of oceanic pkg to p-coordinate). |
| 468 |
|
o change FIND_RHO to FIND_RHO_2D : |
| 469 |
|
pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. |
| 470 |
|
o new pkg: cheapaml |
| 471 |
|
|
| 472 |
|
checkpoint61b |
| 473 |
|
o exch2: |
| 474 |
|
change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) |
| 475 |
|
- no longer depend on the order sequence (N,S,E,W). |
| 476 |
|
- 3rd exchange no longer needed (tested with 24 tiles). |
| 477 |
|
- same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) |
| 478 |
|
- exch_UV_A-grid readily available (but not yet tested). |
| 479 |
|
comment out 3rd exch call and remove copy of V to U at SE & NE face-corners |
| 480 |
|
(both are no longer needed) in exch_uv: no effect in forward run; but |
| 481 |
|
get truncation error differences with adjoint exch. |
| 482 |
|
o exch2: |
| 483 |
|
- change index-bounds storage (moved from target to local tile, |
| 484 |
|
more intuitive this way) ; rename/remove some variables. |
| 485 |
|
- change utils/exch2/matlab-topology-generator & code_mods accordingly. |
| 486 |
|
|
| 487 |
|
checkpoint61a |
| 488 |
|
o exch2/matlab-topology-generator: |
| 489 |
|
fix bug in index bounds for N-S internal exchange (hard to tell if this |
| 490 |
|
had any effect on the solution). |
| 491 |
|
o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf |
| 492 |
|
is exceeded |
| 493 |
|
o testreport: modify syntax of awk, so that it works also with |
| 494 |
|
awk, and not only with nawk and gawk |
| 495 |
|
|
| 496 |
|
checkpoint61 |
| 497 |
|
o autodiff |
| 498 |
|
Change default for TAF usage by removing argument '-nonew_arg' |
| 499 |
|
This changes TAF subroutine argument list (ordering of active var.) |
| 500 |
|
Omission of this flag leads to incompatibility w.r.t. TAMC |
| 501 |
|
To restore TAMC-compatibility, need following modifs: |
| 502 |
|
* use adoptfile tools/adjoint_options/adjoint_tamc_compatibility |
| 503 |
|
* use CPP option #define AUTODIFF_TAMC_COMPATIBILITY |
| 504 |
|
Tested TAF version is 1.9.22 |
| 505 |
|
N.B.: exch2 hand-written adjoint code currently not TAMC compatible |
| 506 |
|
|
| 507 |
|
checkpoint60 |
| 508 |
|
--->>> This is the last checkpoint for which generating the adjoint |
| 509 |
|
--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" |
| 510 |
|
--->>> by default. |
| 511 |
|
--->>> Future checkpoints will ommit this flag by default. |
| 512 |
|
o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. |
| 513 |
|
o pkg/grdchk: Add gradient check to etan0 perturbations. |
| 514 |
|
o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). |
| 515 |
|
o pkg/autodiff: more flexibility in zeroadj. |
| 516 |
|
model/src: modifying do_oceanic_phys.F accordingly. |
| 517 |
|
o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. |
| 518 |
|
o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option |
| 519 |
|
special setup of gmredi for which the adjoint is stable |
| 520 |
|
enough for parameter optimization. |
| 521 |
o bridging the gap between eddy stress and GM. |
o bridging the gap between eddy stress and GM. |
| 522 |
-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) |
-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) |
| 523 |
along with a change in CPP option (now ALLOW_EDDYPSI). |
along with a change in CPP option (now ALLOW_EDDYPSI). |
| 528 |
-> ALLOW_EDDYPSI_CONTROL for estimation purpose. |
-> ALLOW_EDDYPSI_CONTROL for estimation purpose. |
| 529 |
The key modifications are in model/src/taueddy_external_forcing.F |
The key modifications are in model/src/taueddy_external_forcing.F |
| 530 |
pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F |
pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F |
| 531 |
|
|
| 532 |
checkpoint59r |
checkpoint59r |
| 533 |
o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array |
o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array |
| 534 |
from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); |
from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); |
| 2653 |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
| 2654 |
- these scheme operate in a similar manner as KPP (without ghat, of |
- these scheme operate in a similar manner as KPP (without ghat, of |
| 2655 |
course), however there is only one diffusivity that is used for both |
course), however there is only one diffusivity that is used for both |
| 2656 |
temperature and salinity (and passive tracers)ç |
temperature and salinity (and passive tracers) |
| 2657 |
o add offline package |
o add offline package |
| 2658 |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
| 2659 |
provided by Stephanie Dutkiewicz |
provided by Stephanie Dutkiewicz |
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