| 3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 4 |
============================== |
============================== |
| 5 |
|
|
| 6 |
|
o incorporating changes to get TAMC/TAF working in genmake2 |
| 7 |
|
- added new TAMC/TAF targets to the Makefile |
| 8 |
|
- various cleanups related to package handling |
| 9 |
|
|
| 10 |
|
checkpoint51l_post |
| 11 |
|
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
| 12 |
|
- faster algorithm for cal_addtime.F |
| 13 |
|
- higher precision arithmetic, where needed |
| 14 |
|
- pkg/exf *startdate variables changed from calendar date to |
| 15 |
|
model integration time |
| 16 |
|
|
| 17 |
|
checkpoint51l_pre |
| 18 |
|
o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
| 19 |
|
o enable to apply restoring on S & T only in a latitude band. |
| 20 |
|
o update output (external_forcing_surf modif. change truncation errors) |
| 21 |
|
global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
| 22 |
|
|
| 23 |
|
checkpoint51k_post |
| 24 |
|
o change default to: useNHMTerms=.FALSE. |
| 25 |
|
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
| 26 |
|
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
| 27 |
|
- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
| 28 |
|
exp1, ideal_2D_oce |
| 29 |
|
- change data file of oceanic exp (leave the results unchanged for now) |
| 30 |
|
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
| 31 |
|
o set gravitySign automatically according to the vertical coordinate used |
| 32 |
|
(and change sign: back to "logical" value: +1 when R increases downward) |
| 33 |
|
o added an include barrier to the default CPP_OPTIONS.h and |
| 34 |
|
removed the #include "PACKAGES_CONFIG.h" from it |
| 35 |
|
o fix a bug in mom_fluxform (from chk51j_post) |
| 36 |
|
|
| 37 |
|
checkpoint51j_post |
| 38 |
|
o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
| 39 |
|
o adjusted some flow directives (dynamics, thermodynamics) |
| 40 |
|
o added cubed-sphere case to test cost function |
| 41 |
|
o heckpoint_lev?_directives.h now include |
| 42 |
|
pkg-specific directives, whenever those are enabled. |
| 43 |
|
o Moving pkg-specific flow directives to corresponding pkg |
| 44 |
|
Moving pkg-specific differentiation list to corresponding pkg |
| 45 |
|
Moving pkg-specific checkpoint-lev storing to corresponding pkg |
| 46 |
|
---> conventions are |
| 47 |
|
- pkg_ad.flow |
| 48 |
|
- pkg_ad_diff.list |
| 49 |
|
- pkg_ad_check_lev?_dir.h |
| 50 |
|
|
| 51 |
|
checkpoint51i_post |
| 52 |
|
o merge of the branch-genmake2 |
| 53 |
|
- knowingly breaks the older genmake |
| 54 |
|
- automatic generation of all ALLOW_${PKG_NAME} defines |
| 55 |
|
- new testreport supersedes older testscript |
| 56 |
|
o large number of package inclusion and header cleanups |
| 57 |
|
checkpoint51i_pre |
| 58 |
|
|
| 59 |
|
o new output for adjoin of global ocean vector invariant |
| 60 |
|
o fix for checkpoint of thermodynamic seaice and bulk_force |
| 61 |
|
o Steph gchem various cleanups |
| 62 |
|
|
| 63 |
|
checkpoint 51h_pre |
| 64 |
|
o fixed some single quotes |
| 65 |
|
o modify gchem pkg to be more versatile |
| 66 |
|
o modifications to clean up dic pkg |
| 67 |
|
o add pkg/cfc |
| 68 |
|
|
| 69 |
|
checkpoint51g_post |
| 70 |
|
o provide links for ARPACK and ADM*TLM |
| 71 |
|
o start removing verification/vero/ |
| 72 |
|
o update AD-related stuff |
| 73 |
|
(in particular some IF-statements in model/src/ routines) |
| 74 |
|
o adding to verification/global_ocean.90x40x15/ adjoint of |
| 75 |
|
vector invariant setup |
| 76 |
|
|
| 77 |
|
checkpoint51f_post |
| 78 |
|
o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
| 79 |
|
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
| 80 |
|
of tracer Green's fucntions for ocean inversion project. |
| 81 |
|
|
| 82 |
|
checkpoint51f_pre |
| 83 |
|
o Added on-the-fly spatial interpolation capability |
| 84 |
|
"USE_EXF_INTERPOLATION" to pkg/exf. |
| 85 |
|
- This is a temporary Cartesian-grid hack until |
| 86 |
|
the super-duper ESMF coupler becomes available. |
| 87 |
|
- See verification/global_with_exf/README for usage example. |
| 88 |
|
- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
| 89 |
|
flags and modified pkg/seaice accordingly. |
| 90 |
|
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
| 91 |
|
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
| 92 |
|
non-local transport term. |
| 93 |
|
|
| 94 |
|
checkpoint51e_post |
| 95 |
|
o pkg/mom_vecinv: |
| 96 |
|
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
| 97 |
|
- add time-ave diagnostic of vorticity advection. |
| 98 |
|
o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. |
| 99 |
|
o atmospheric geopotential: - include water vapor effect; |
| 100 |
|
- use p^kappa in p* scaling. |
| 101 |
|
o land pkg: read initial state from files. |
| 102 |
|
o AIM : add stratospheric drag in the upper level |
| 103 |
|
|
| 104 |
|
checkpoint51d_post |
| 105 |
|
o change function ILNBLNK (=> last non-blank char.) to return zero |
| 106 |
|
(instead of the string length) when the string. char is empty |
| 107 |
|
o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) |
| 108 |
|
o modif's to restore TAMC compatibility |
| 109 |
|
- avoid "_d" constructs in PARAMETER declarations |
| 110 |
|
- avoid interrupting lines by comment lines |
| 111 |
|
o Use cluster local disks for purely local I/O |
| 112 |
|
vs. globally visible disks needed for ctrl stuff |
| 113 |
|
(merged from ecco-branch) |
| 114 |
|
- new active_file_loc... and mdsio_..._loc routines |
| 115 |
|
- affected packages: autodiff, ctrl, grdchk, mdsio |
| 116 |
|
|
| 117 |
|
checkpoint51c_post |
| 118 |
|
o introducing integer flag debugLevel |
| 119 |
|
- debLevZero: suppress all output |
| 120 |
|
- debLevA: standard |
| 121 |
|
- debLevB: equivalent to current debugMode=.TRUE. |
| 122 |
|
o introducing pathname variable mdsioLocalDir for mdsio |
| 123 |
|
that can be specified at runtime |
| 124 |
|
(relevant for cluster I/O to local disk) |
| 125 |
|
` |
| 126 |
|
>>>checkpoint51b_post |
| 127 |
|
adjoint of ptracers |
| 128 |
|
o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
| 129 |
|
o extended state in checkpoint_lev?, etc. |
| 130 |
|
o alternative ctrl/cost with tr1 or ptracer |
| 131 |
|
o new comlev1_bibj_ptracers |
| 132 |
|
o new ptracers.flow |
| 133 |
|
o made ptracers_forcing same as external_forcing_s |
| 134 |
|
o added verification for adjoint with ptracers |
| 135 |
|
- adm. grdchk fail so far |
| 136 |
|
- tlm. grdchk OK |
| 137 |
|
- checked tapelev/comlev recomputations: OK |
| 138 |
|
<<<checkpoint51b_pre |
| 139 |
|
|
| 140 |
|
checkpoint51a_post |
| 141 |
|
o added code for biogeochemistry package |
| 142 |
|
- new pkgs: dic, gchem |
| 143 |
|
- new subroutine in ptracers |
| 144 |
|
o modify code for biogeo packages |
| 145 |
|
- in model/src and pkg/ptracers |
| 146 |
|
|
| 147 |
|
checkpoint51 |
| 148 |
|
o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN |
| 149 |
|
- autodiff, ctrl, exf, grdchk, seaice |
| 150 |
|
kept separate packages |
| 151 |
|
- cost, ecco, obcs |
| 152 |
|
o updating verification/internal_wave, verification/lab_sea |
| 153 |
|
(all verif's pass on faulks.lcs.mit.edu RH7.3, g77) |
| 154 |
|
|
| 155 |
|
checkpoint50i_post |
| 156 |
|
o Preparing next differentiable checkpoint and sync |
| 157 |
|
of MAIN vs. ecco-branch |
| 158 |
|
- 1st step: this one is differentiable |
| 159 |
|
- 2nd step: next(! not this) checkpoint will have updated packages |
| 160 |
|
from ecco-branch) |
| 161 |
|
|
| 162 |
|
checkpoint50h_post |
| 163 |
|
o new package "land": provide surface BC for AIM. |
| 164 |
|
o pkg/ptracers: apply exchange to all tracers after reading a pickup. |
| 165 |
|
o AIM: use true log-P extrapolation for near surface temp (= as in |
| 166 |
|
F.Molteni paper) ; update aim.5l_cs output. |
| 167 |
|
o New variable in PARM03 for more flexible pickups |
| 168 |
|
o somewhat cleaned package initialisation sequence for |
| 169 |
|
ctrl/ cost/ ecco/ in packages_... routines |
| 170 |
|
|
| 171 |
|
checkpoint50g_post |
| 172 |
|
o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
| 173 |
|
- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
| 174 |
|
- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
| 175 |
|
made the default because of faster convergence than ADI |
| 176 |
|
|
| 177 |
|
checkpoint50f_post |
| 178 |
|
o exf totally restructured |
| 179 |
|
- replaced all exf_set_ routines by one generic exf_set_gen.F |
| 180 |
|
and made sure it's still differentiable |
| 181 |
|
- split exf_getffields.F into new exf_bulkformulae.F |
| 182 |
|
- exf_inscal_/exf_outscal_ suffixes consistent with field names |
| 183 |
|
- updated adjoint/makefile and relevant verif. accordingly |
| 184 |
|
|
| 185 |
|
checkpoint50f_pre |
| 186 |
|
o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; |
| 187 |
|
+ change Evap over land. (update aim.5l_cs output) |
| 188 |
|
o added missing .cvsignores and made uniform across expts |
| 189 |
|
o changed configuration of tidal_basin_2d expt |
| 190 |
|
o added pkg/debug functions for tracing code in fatal crashes |
| 191 |
|
o tidied pkg/monitor to use MONITOR_OPTIONS.h |
| 192 |
|
o new fn in pkg/monitor to stop model if solution grows too big |
| 193 |
|
o removed lots of single quotes from comments |
| 194 |
|
|
| 195 |
|
checkpoint50e_post |
| 196 |
|
o make KPP work with PTRACERS |
| 197 |
|
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
| 198 |
|
nearly a copy of kpp_transport_s |
| 199 |
|
- there is no analogue to SurfaceTendencyS, so I have to use |
| 200 |
|
gPtr(of the surface layer) instead |
| 201 |
|
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
| 202 |
|
checkpoint50e_pre |
| 203 |
|
|
| 204 |
|
checkpoint50d_post |
| 205 |
|
o change kpp output from multiple-record state files to single-record state |
| 206 |
|
files analogous to write_state.F |
| 207 |
|
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
| 208 |
|
analogous to the cg2d-related output. |
| 209 |
|
o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
| 210 |
|
so that writing to internal file fn (with length 512) fails. |
| 211 |
|
checkpoint50d_pre |
| 212 |
|
|
| 213 |
|
checkpoint50c_post |
| 214 |
|
o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) |
| 215 |
|
o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. |
| 216 |
|
o add time-average diagnostic of U*V and vertical diffusive flux for theta. |
| 217 |
|
o bug fixed in convective adjustment diagnostic (multi-tile set-up). |
| 218 |
|
o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. |
| 219 |
|
|
| 220 |
|
checkpoint50c_pre |
| 221 |
|
Merging from release1_p13: |
| 222 |
|
o bug fix for pkg/seaice dynamic solver |
| 223 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
| 224 |
|
|
| 225 |
|
checkpoint50b_post |
| 226 |
|
o store u*,v* in gU,V instead of in guNm1,gvNm1 |
| 227 |
|
o in order to put the momForcing out of the Adams-Bashforth: |
| 228 |
|
move forcing & CD-scheme calls from mom_fluxform & mom_vecinv |
| 229 |
|
to timestep.F |
| 230 |
|
o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays |
| 231 |
|
o re-generate output for highly sensitive test-exp: |
| 232 |
|
global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box |
| 233 |
|
|
| 234 |
|
checkpoint50b_pre |
| 235 |
|
o restore the use of momAdvection & useCoriolis flags (mom_vecinv) |
| 236 |
|
o corrected CPP option mismatch in exf_Bulk... functions for case |
| 237 |
|
#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
| 238 |
|
|
| 239 |
|
checkpoint50a_post |
| 240 |
|
o Bug fix for merging between c50 and KPP. |
| 241 |
|
ikey was passed from thermodynamics to kpp_calc via |
| 242 |
|
common block rather than being recomputed in kpp_calc, |
| 243 |
|
in contradiction with new key itdkey. |
| 244 |
|
New key ikppkey created, and tamc.h headers updated. |
| 245 |
|
|
| 246 |
|
checkpoint50 |
| 247 |
|
- 2nd step of merge with ecco-branch: |
| 248 |
|
merge changes in ecco-branch back into main trunk |
| 249 |
|
- bug fix in find_alpha |
| 250 |
|
- more storing in gmredi_calc_tensor.F, kpp_routines.F |
| 251 |
|
- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
| 252 |
|
- merged some sliced AD support routines |
| 253 |
|
|
| 254 |
|
checkpoint49 |
| 255 |
|
merged from ecco-branch: |
| 256 |
|
o exf: |
| 257 |
|
- Enable initialisation of forcing fields to constant |
| 258 |
|
(runtime) values. |
| 259 |
|
- in exf_getffields.F |
| 260 |
|
Reduce i-/j-loop to interior domain, discarding overlaps. |
| 261 |
|
That also fixes wrong TAF-key computations for key_1, key_2 |
| 262 |
|
with bulf formulae. |
| 263 |
|
- exf_init.F modify #ifdef for exf_init_evap |
| 264 |
|
- exf_getffieldrec.F, ctrl_getrec.F |
| 265 |
|
The following INT-usages are not safe: |
| 266 |
|
fldsecs = int(fldsecs/fldperiod)*fldperiod |
| 267 |
|
fldcount = int(fldsecs/fldperiod) + 1 |
| 268 |
|
and were modified. |
| 269 |
|
o autodiff: checkpoint_lev... |
| 270 |
|
- updated storing for bulk formulae (some arrays were missing) |
| 271 |
|
- added state for seaice package |
| 272 |
|
- synchronized with main branch |
| 273 |
|
o DIVA: |
| 274 |
|
Modif.s in |
| 275 |
|
- the_main_loop.F |
| 276 |
|
- the_model_main.F |
| 277 |
|
and added cost_final_restore.F cost_final_store.F |
| 278 |
|
o With these changes, it is possible to fully separate |
| 279 |
|
the first forward run to compute the cost function (mdthe_main_loop) |
| 280 |
|
and adjoint runs over individual DIVA intervals (adthe_main_loop) |
| 281 |
|
into separate model executions. |
| 282 |
|
This enables better tuning of DIVA to given queue sizes. |
| 283 |
|
o Loss of cost function value in consecutive DIVA runs is |
| 284 |
|
fixed by storing to 'costfinal' file. |
| 285 |
|
o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
| 286 |
|
beginning/end of adjoint integration is accounted for. |
| 287 |
|
The current changes apply to TAF-1.4.26. |
| 288 |
|
TAF has one remaining bug, requiring one manual change |
| 289 |
|
(see MITgcm manual). |
| 290 |
|
o cal: synchronized between MAIN and ecco-branch |
| 291 |
|
|
| 292 |
|
checkpoint48i_post |
| 293 |
|
o Changes to restore differentiability of code w.r.t. previous tag |
| 294 |
|
(mostly adding new routines to make list and replacing |
| 295 |
|
pressure by totPhiHyd). |
| 296 |
|
o Updated and merged grdchk package |
| 297 |
|
- has both ADM and TLM checks |
| 298 |
|
- works for single- and multi-proc. |
| 299 |
|
- output cleaned |
| 300 |
|
- worked successfully for parallel DIVA |
| 301 |
|
o genmake: |
| 302 |
|
- Adding -platform=SP4 |
| 303 |
|
- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
| 304 |
|
o Modif. for DIVA: |
| 305 |
|
ctrl_unpack should not be called in intermediate DIVA interval. |
| 306 |
|
(similar thing would apply for active files such as |
| 307 |
|
tbar, sbar, psbar, which should not be reinitialised; |
| 308 |
|
only relevant for ecco-branch) |
| 309 |
|
|
| 310 |
|
checkpoint48h_post |
| 311 |
|
o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
| 312 |
|
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
| 313 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
| 314 |
|
o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
| 315 |
|
|
| 316 |
|
checkpoint48g_post |
| 317 |
|
--- EOS: |
| 318 |
|
o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
| 319 |
|
store total Potential in totPhyHyd for diagnostics & EOS. |
| 320 |
|
o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
| 321 |
|
--- Pressure/geopotential gradient: |
| 322 |
|
o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
| 323 |
|
o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
| 324 |
|
( changes results of global_ocean_pressure ) |
| 325 |
|
o NLFS + z-coord.: add eta*Rho' contribution. |
| 326 |
|
o accurate phiHyd when using interface-W at the middle between 2 centers |
| 327 |
|
( changes results of ideal_2D_oce ) |
| 328 |
|
o includes r* 2nd term in potential gradient. |
| 329 |
|
|
| 330 |
|
checkpoint48f_post |
| 331 |
|
Merging from release1_p12: |
| 332 |
|
o Modifications for using pkg/exf with pkg/seaice |
| 333 |
|
- improved description of the various forcing configurations |
| 334 |
|
- added basic radiation bulk formulae to pkg/exf |
| 335 |
|
- units/sign fix for evap computation in exf_getffields.F |
| 336 |
|
- updated verification/global_with_exf/results/output.txt |
| 337 |
|
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
| 338 |
|
(SBO) core products, including oceanic mass, center-of-mass, |
| 339 |
|
angular, and bottom pressure (see pkg/sbo/README.sbo). |
| 340 |
|
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
| 341 |
|
to avoid negative values in shallow regions. |
| 342 |
|
- updated verification/natl_box/results/output.txt |
| 343 |
|
- updated verification/lab_sea/results/output.txt |
| 344 |
|
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
| 345 |
|
o Added useSingleCpuIO option (see PARAMS.h). |
| 346 |
|
o Updated useSingleCpuIO option in mdsio_writefield.F to |
| 347 |
|
work with multi-field files, e.g., for single-file pickup. |
| 348 |
|
o pkg/seaice: |
| 349 |
|
- bug fix in growth.F: QNET for no shortwave case |
| 350 |
|
- added HeffFile for specifying initial sea-ice thickness |
| 351 |
|
- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
| 352 |
|
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
| 353 |
|
kpp_transport_t.F, forward_step.F, and the_main_loop.F |
| 354 |
|
o pkg/seaice: |
| 355 |
|
- adjoint-friendly modifications |
| 356 |
|
- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
| 357 |
|
|
| 358 |
|
checkpoint48e_post |
| 359 |
|
o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) |
| 360 |
|
o dynamics: change definition of computational domain & adapt mom_fluxform |
| 361 |
|
accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. |
| 362 |
|
o following exp works with Olx=Oly=2 (and pass through checkbounds option): |
| 363 |
|
adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 |
| 364 |
|
exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 |
| 365 |
|
global_ocean.90x40x15 global_with_exf global_ocean_pressure |
| 366 |
|
inverted_barometer solid-body.cs-32x32x1 |
| 367 |
|
(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) |
| 368 |
|
|
| 369 |
|
checkpoint48d_post |
| 370 |
|
o in preparation for r*: |
| 371 |
|
a) use pre-computed gradient of hydrostatic potential: |
| 372 |
|
changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce |
| 373 |
|
b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: |
| 374 |
|
=> affects results of glob_oce_pressure (different truncation error) |
| 375 |
|
update output.txt of ideal_2D_oce & global_ocean_pressure |
| 376 |
|
|
| 377 |
checkpoint48d_pre |
checkpoint48d_pre |
| 378 |
o in preparation for r*: |
o in preparation for r*: |
| 379 |
new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
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