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Revision 1.222 - (show annotations) (download)
Wed Dec 10 19:37:25 2003 UTC (20 years, 5 months ago) by dimitri
Branch: MAIN
Branch point for: netcdf-sm0
Changes since 1.221: +11 -2 lines
o changes to permit hi-res, cubed-sphere, configuration
  - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
  - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
  - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
    of surface winds for the cube
  (A verification experiment, based on global_ocean.cs32x15, but with
   pkg/seaice turned on and with on-the-fly interpolation from the NCEP
   Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
   complete with example surface forcing files and matlab scripts to look
   at the output and compare it with that of global_ocean.cs32x15.)

1 $Header: /usr/local/gcmpack/MITgcm/doc/tag-index,v 1.221 2003/12/08 02:13:59 dimitri Exp $
3 Notes on tags used in MITgcmUV
4 ==============================
6 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
7 o changes to permit hi-res, cubed-sphere, configuration
8 - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
9 - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
10 - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
11 of surface winds for the cube
12 (A verification experiment, based on global_ocean.cs32x15, but with
13 pkg/seaice turned on and with on-the-fly interpolation from the NCEP
14 Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
15 complete with example surface forcing files and matlab scripts to look
16 at the output and compare it with that of global_ocean.cs32x15.)
18 checkpoint52d_pre
19 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
20 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
22 checkpoint52c_post
23 o Fixing OPTIONS files for use of exf:
24 - ALLOW_ECCO not needed
25 - ECCO_CPPOPTIONS.h should not be included from
27 as has been the case in the past
28 - All cal/exf related options are currently set in
29 single header file. Should remain so until we
30 agree on a consistent new policy.
31 o Removed all CPP options for cal package.
32 cal has no more CPP options.
33 o modified STOREs in GAD_ADVECTION
34 o corrected key comp. for passkey
36 checkpoint52b_post
37 o new version: "thsice" of thermodynamic sea-ice pkg:
38 - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
39 - modify fluxes but do not change theta directly;
40 - light cleaning of bulk_force pkg (still needed with thsice).
41 - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
42 + output_thsice.txt to test thsice & bulk_force pkgs.
43 o put back grid & coriolis monitor output.
44 checkpoint52b_pre
46 o call "do_the_model_io" at the beginning (=> dump initial state)
47 o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
48 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
49 (need info on NUMBER_OF_PTRACERS)
50 o missing PTRACERS headers in some routines
51 o default tamc.h in pkg/autodiff supposed to crash
52 to ensure proper customization
54 checkpoint52a_post
55 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
56 - moved surfaceTendencyTice from pkg/seaice to main code
57 - subroutine FREEZE_SURFACE now limits only surface temperature
58 and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
59 => new output.txt for global_ocean.cs32x15 & global_with_exf
60 - keep the old version of FREEZE for backward compatibility;
61 global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
62 - corresponding modifs for TAF directives
63 o added surface flux output variables to TIMEAVE_STATVARS
64 o time-averaged output for pkg/ptracers
65 o fix problem with ECCO-related divided adjoint
66 snapshot file was missing some ad-variables,
67 but no warning issued by TAF
69 checkpoint52a_pre
70 o some bug fixes for #undef REAL4_IS_SLOW
72 checkpoint52 = ecco_c52_e35
73 o after testing adjoints of checkpoint51u_post
75 checkpoint51u_post
76 o this is the post-merge tag of the ecco-branch
77 (needs another clean checkout and re-testing)
78 o various natl_box_adjoint configs and results
79 but no input fields
80 o obcs adjoint not yet merged!
81 o adding ECCO global 1x1 and 2x2 degree configs
82 o updated/extended some store directives for seaice
83 o pkg/ecco now containes ecco-specific part of cost function
84 o top level routines the_main_loop, forward_step
85 supersede those in model/src/
86 previous input data.cost now in data.ecco
87 (new namelist ecco_cost_nml)
88 o in ctrl/ cleaned some cross-dependencies and updated CPP options
90 checkpoint51t_post
91 o this is the pre-merge tag of the ecco-branch
93 checkpoint51s_post
94 o cleanup: removed various obsolete #define-s
95 o pkg/grdchk
96 - renamed 'ph-grd 3' to 'grad-res'
97 - merged from ecco-branch
98 (remaining bug fixes for obcs gradient checks)
99 - additional high-precision output for testreport
100 (grep for 'precision_grdchk_result')
102 checkpoint51r_post
103 o cleaned up or removed CPP_OPTIONS.h files
104 o updated results for some of the tests to reflect the new
105 optfiles (-ieee: -O0 instead of -O3)
107 checkpoint51q_post
108 o cd_code:
109 - moved cd_scheme.F -> cd_code_scheme.F
110 - separate read_checkpoint from cd_code_ini_vars.F
111 - separated cd_code part from write_checkpoint
112 - updated AD_SOURCE, generated .flow
113 - added CD_CODE_VARS.h to the_main_loop
114 - Moving cd_code specific store dir.s to pkg/cd_code
115 o ctrl package totally restructured
116 - pack/unpack now optional and decoupled from
117 xx_/adxx_ I/O
118 - ctrl_pack/unpack cleaned
119 (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
120 - confined inclusion of AD_CONFIG.h to where necessary.
121 o genmake2: changed AD dependencies from SRCFILES to AD_FILES
123 checkpoint51p_post
124 o create initial cd_code package
125 - WARNING: the initialization of fields within packages
126 is broken because INI_FIELDS (where READ_CHECKPOINT is
127 called) is called *before* PACKAGES_INIT_VARIABLES.
128 This seems to be backwards since
129 1) its important to initially zero the entire field including
130 the "halo" region
131 2) zeroing needs to be done *before* reading pickup info
132 and the pickup call might or might not happen in any
133 particular run
134 - this needs an overhaul for R2
135 o cleanup verification/*/code/GMREDI_OPTIONS.h
136 o cleanup testreport
138 checkpoint51o_post
139 o bringing AD-related verif's up to date with genmake2
140 - carbon/
141 - global_ocean.90x40x15/
142 - hs.94.1x64x5/
143 - (front_relax/ )
144 o (more) consistent directory structure for AD-related verif.'s
147 o bug fix in find_alpha.F for MDJWF:
148 - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
149 change rho -> rho-rhoConst
150 - replace call find_rho to find_rhonum
151 o initialisation of rFlx extended to full array (required by TAF)
152 and shifted to thermodynamics
153 o removed PTRACERS.h in ptracers routine
154 o added surfacetendencyPtr to S/R parameter list pracers_forcing
155 o Correcting initialisations for fVerU, fVerV.
156 o helping TAF to recognize dependency on kUp for
157 fVerU, fVerV
158 o Replacing delZ by delR in pkg/ctrl/
159 checkpoint51o_pre
161 o undid all of cp51 pending some cleanups and discussion
162 o added the [#include "AD_CONFIG.h"] statement to all files that need
163 it for adjoint/tl #defines
164 o re-worked the build logic in genmake2 to support AD_CONFIG.h
165 o removed tools/genmake since it no longer works
167 checkpoint51n_post
168 o modifications to make FREEZE flux visible to pkg/kpp
169 - moved surfaceTendencyTice from pkg/seaice to main code
171 - subroutine FREEZE now limits only surface temperature
172 (this means new output.txt for global_ocean.90x40x15,
173 global_ocean.cs32x15, and global_with_exf)
174 o added surface flux output variables to TIMEAVE_STATVARS
176 checkpoint51n_pre
177 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
178 o added [#include "AD_CONFIG.h"] to all files that use the following
179 defines:
184 checkpoint51m_post
185 o incorporating changes to get TAMC/TAF working in genmake2
186 - added new TAMC/TAF targets to the Makefile
187 - various cleanups related to package handling
188 - these changes should have no impact on the forward model
190 checkpoint51l_post
191 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
192 - faster algorithm for cal_addtime.F
193 - higher precision arithmetic, where needed
194 - pkg/exf *startdate variables changed from calendar date to
195 model integration time
197 checkpoint51l_pre
198 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
199 o enable to apply restoring on S & T only in a latitude band.
200 o update output (external_forcing_surf modif. change truncation errors)
201 global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
203 checkpoint51k_post
204 o change default to: useNHMTerms=.FALSE.
205 - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
206 adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
207 - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
208 exp1, ideal_2D_oce
209 - change data file of oceanic exp (leave the results unchanged for now)
210 exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
211 o set gravitySign automatically according to the vertical coordinate used
212 (and change sign: back to "logical" value: +1 when R increases downward)
213 o added an include barrier to the default CPP_OPTIONS.h and
214 removed the #include "PACKAGES_CONFIG.h" from it
215 o fix a bug in mom_fluxform (from chk51j_post)
217 checkpoint51j_post
218 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
219 o adjusted some flow directives (dynamics, thermodynamics)
220 o added cubed-sphere case to test cost function
221 o heckpoint_lev?_directives.h now include
222 pkg-specific directives, whenever those are enabled.
223 o Moving pkg-specific flow directives to corresponding pkg
224 Moving pkg-specific differentiation list to corresponding pkg
225 Moving pkg-specific checkpoint-lev storing to corresponding pkg
226 ---> conventions are
227 - pkg_ad.flow
228 - pkg_ad_diff.list
229 - pkg_ad_check_lev?_dir.h
231 checkpoint51i_post
232 o merge of the branch-genmake2
233 - knowingly breaks the older genmake
234 - automatic generation of all ALLOW_${PKG_NAME} defines
235 - new testreport supersedes older testscript
236 o large number of package inclusion and header cleanups
237 checkpoint51i_pre
239 o new output for adjoin of global ocean vector invariant
240 o fix for checkpoint of thermodynamic seaice and bulk_force
241 o Steph gchem various cleanups
243 checkpoint 51h_pre
244 o fixed some single quotes
245 o modify gchem pkg to be more versatile
246 o modifications to clean up dic pkg
247 o add pkg/cfc
249 checkpoint51g_post
250 o provide links for ARPACK and ADM*TLM
251 o start removing verification/vero/
252 o update AD-related stuff
253 (in particular some IF-statements in model/src/ routines)
254 o adding to verification/global_ocean.90x40x15/ adjoint of
255 vector invariant setup
257 checkpoint51f_post
258 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
259 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
260 of tracer Green's fucntions for ocean inversion project.
262 checkpoint51f_pre
263 o Added on-the-fly spatial interpolation capability
264 "USE_EXF_INTERPOLATION" to pkg/exf.
265 - This is a temporary Cartesian-grid hack until
266 the super-duper ESMF coupler becomes available.
267 - See verification/global_with_exf/README for usage example.
268 - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
269 flags and modified pkg/seaice accordingly.
270 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
271 and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
272 non-local transport term.
274 checkpoint51e_post
275 o pkg/mom_vecinv:
276 - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
277 - add time-ave diagnostic of vorticity advection.
278 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
279 o atmospheric geopotential: - include water vapor effect;
280 - use p^kappa in p* scaling.
281 o land pkg: read initial state from files.
282 o AIM : add stratospheric drag in the upper level
284 checkpoint51d_post
285 o change function ILNBLNK (=> last non-blank char.) to return zero
286 (instead of the string length) when the string. char is empty
287 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
288 o modif's to restore TAMC compatibility
289 - avoid "_d" constructs in PARAMETER declarations
290 - avoid interrupting lines by comment lines
291 o Use cluster local disks for purely local I/O
292 vs. globally visible disks needed for ctrl stuff
293 (merged from ecco-branch)
294 - new active_file_loc... and mdsio_..._loc routines
295 - affected packages: autodiff, ctrl, grdchk, mdsio
297 checkpoint51c_post
298 o introducing integer flag debugLevel
299 - debLevZero: suppress all output
300 - debLevA: standard
301 - debLevB: equivalent to current debugMode=.TRUE.
302 o introducing pathname variable mdsioLocalDir for mdsio
303 that can be specified at runtime
304 (relevant for cluster I/O to local disk)
305 `
306 >>>checkpoint51b_post
307 adjoint of ptracers
308 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
309 o extended state in checkpoint_lev?, etc.
310 o alternative ctrl/cost with tr1 or ptracer
311 o new comlev1_bibj_ptracers
312 o new ptracers.flow
313 o made ptracers_forcing same as external_forcing_s
314 o added verification for adjoint with ptracers
315 - adm. grdchk fail so far
316 - tlm. grdchk OK
317 - checked tapelev/comlev recomputations: OK
318 <<<checkpoint51b_pre
320 checkpoint51a_post
321 o added code for biogeochemistry package
322 - new pkgs: dic, gchem
323 - new subroutine in ptracers
324 o modify code for biogeo packages
325 - in model/src and pkg/ptracers
327 checkpoint51
328 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
329 - autodiff, ctrl, exf, grdchk, seaice
330 kept separate packages
331 - cost, ecco, obcs
332 o updating verification/internal_wave, verification/lab_sea
333 (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
335 checkpoint50i_post
336 o Preparing next differentiable checkpoint and sync
337 of MAIN vs. ecco-branch
338 - 1st step: this one is differentiable
339 - 2nd step: next(! not this) checkpoint will have updated packages
340 from ecco-branch)
342 checkpoint50h_post
343 o new package "land": provide surface BC for AIM.
344 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
345 o AIM: use true log-P extrapolation for near surface temp (= as in
346 F.Molteni paper) ; update aim.5l_cs output.
347 o New variable in PARM03 for more flexible pickups
348 o somewhat cleaned package initialisation sequence for
349 ctrl/ cost/ ecco/ in packages_... routines
351 checkpoint50g_post
352 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
353 - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
354 - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
355 made the default because of faster convergence than ADI
357 checkpoint50f_post
358 o exf totally restructured
359 - replaced all exf_set_ routines by one generic exf_set_gen.F
360 and made sure it's still differentiable
361 - split exf_getffields.F into new exf_bulkformulae.F
362 - exf_inscal_/exf_outscal_ suffixes consistent with field names
363 - updated adjoint/makefile and relevant verif. accordingly
365 checkpoint50f_pre
366 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
367 + change Evap over land. (update aim.5l_cs output)
368 o added missing .cvsignores and made uniform across expts
369 o changed configuration of tidal_basin_2d expt
370 o added pkg/debug functions for tracing code in fatal crashes
371 o tidied pkg/monitor to use MONITOR_OPTIONS.h
372 o new fn in pkg/monitor to stop model if solution grows too big
373 o removed lots of single quotes from comments
375 checkpoint50e_post
376 o make KPP work with PTRACERS
377 - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
378 nearly a copy of kpp_transport_s
379 - there is no analogue to SurfaceTendencyS, so I have to use
380 gPtr(of the surface layer) instead
381 o add a new platform SunFire+mpi (SunFire 15000) to genmake
382 checkpoint50e_pre
384 checkpoint50d_post
385 o change kpp output from multiple-record state files to single-record state
386 files analogous to write_state.F
387 o reduce the output frequency of cg3d-related stuff to the monitor frequency,
388 analogous to the cg2d-related output.
389 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
390 so that writing to internal file fn (with length 512) fails.
391 checkpoint50d_pre
393 checkpoint50c_post
394 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
395 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
396 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
397 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
398 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
400 checkpoint50c_pre
401 Merging from release1_p13:
402 o bug fix for pkg/seaice dynamic solver
403 o Added SEAICE_initialHEFF to pkg/seaice
405 checkpoint50b_post
406 o store u*,v* in gU,V instead of in guNm1,gvNm1
407 o in order to put the momForcing out of the Adams-Bashforth:
408 move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
409 to timestep.F
410 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
411 o re-generate output for highly sensitive test-exp:
412 global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
414 checkpoint50b_pre
415 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
416 o corrected CPP option mismatch in exf_Bulk... functions for case
417 #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
419 checkpoint50a_post
420 o Bug fix for merging between c50 and KPP.
421 ikey was passed from thermodynamics to kpp_calc via
422 common block rather than being recomputed in kpp_calc,
423 in contradiction with new key itdkey.
424 New key ikppkey created, and tamc.h headers updated.
426 checkpoint50
427 - 2nd step of merge with ecco-branch:
428 merge changes in ecco-branch back into main trunk
429 - bug fix in find_alpha
430 - more storing in gmredi_calc_tensor.F, kpp_routines.F
431 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
432 - merged some sliced AD support routines
434 checkpoint49
435 merged from ecco-branch:
436 o exf:
437 - Enable initialisation of forcing fields to constant
438 (runtime) values.
439 - in exf_getffields.F
440 Reduce i-/j-loop to interior domain, discarding overlaps.
441 That also fixes wrong TAF-key computations for key_1, key_2
442 with bulf formulae.
443 - exf_init.F modify #ifdef for exf_init_evap
444 - exf_getffieldrec.F, ctrl_getrec.F
445 The following INT-usages are not safe:
446 fldsecs = int(fldsecs/fldperiod)*fldperiod
447 fldcount = int(fldsecs/fldperiod) + 1
448 and were modified.
449 o autodiff: checkpoint_lev...
450 - updated storing for bulk formulae (some arrays were missing)
451 - added state for seaice package
452 - synchronized with main branch
453 o DIVA:
454 Modif.s in
455 - the_main_loop.F
456 - the_model_main.F
457 and added cost_final_restore.F cost_final_store.F
458 o With these changes, it is possible to fully separate
459 the first forward run to compute the cost function (mdthe_main_loop)
460 and adjoint runs over individual DIVA intervals (adthe_main_loop)
461 into separate model executions.
462 This enables better tuning of DIVA to given queue sizes.
463 o Loss of cost function value in consecutive DIVA runs is
464 fixed by storing to 'costfinal' file.
465 o Appropriate call of ctrl_unpack/_pack,grdchk_main at
466 beginning/end of adjoint integration is accounted for.
467 The current changes apply to TAF-1.4.26.
468 TAF has one remaining bug, requiring one manual change
469 (see MITgcm manual).
470 o cal: synchronized between MAIN and ecco-branch
472 checkpoint48i_post
473 o Changes to restore differentiability of code w.r.t. previous tag
474 (mostly adding new routines to make list and replacing
475 pressure by totPhiHyd).
476 o Updated and merged grdchk package
477 - has both ADM and TLM checks
478 - works for single- and multi-proc.
479 - output cleaned
480 - worked successfully for parallel DIVA
481 o genmake:
482 - Adding -platform=SP4
483 - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
484 o Modif. for DIVA:
485 ctrl_unpack should not be called in intermediate DIVA interval.
486 (similar thing would apply for active files such as
487 tbar, sbar, psbar, which should not be reinitialised;
488 only relevant for ecco-branch)
490 checkpoint48h_post
491 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
492 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
493 o Added SEAICE_initialHEFF to pkg/seaice
494 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
496 checkpoint48g_post
497 --- EOS:
498 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
499 store total Potential in totPhyHyd for diagnostics & EOS.
500 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
501 --- Pressure/geopotential gradient:
502 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
503 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
504 ( changes results of global_ocean_pressure )
505 o NLFS + z-coord.: add eta*Rho' contribution.
506 o accurate phiHyd when using interface-W at the middle between 2 centers
507 ( changes results of ideal_2D_oce )
508 o includes r* 2nd term in potential gradient.
510 checkpoint48f_post
511 Merging from release1_p12:
512 o Modifications for using pkg/exf with pkg/seaice
513 - improved description of the various forcing configurations
514 - added basic radiation bulk formulae to pkg/exf
515 - units/sign fix for evap computation in exf_getffields.F
516 - updated verification/global_with_exf/results/output.txt
517 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
518 (SBO) core products, including oceanic mass, center-of-mass,
519 angular, and bottom pressure (see pkg/sbo/README.sbo).
520 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
521 to avoid negative values in shallow regions.
522 - updated verification/natl_box/results/output.txt
523 - updated verification/lab_sea/results/output.txt
524 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
525 o Added useSingleCpuIO option (see PARAMS.h).
526 o Updated useSingleCpuIO option in mdsio_writefield.F to
527 work with multi-field files, e.g., for single-file pickup.
528 o pkg/seaice:
529 - bug fix in growth.F: QNET for no shortwave case
530 - added HeffFile for specifying initial sea-ice thickness
531 - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
532 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
533 kpp_transport_t.F, forward_step.F, and the_main_loop.F
534 o pkg/seaice:
535 - adjoint-friendly modifications
536 - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
538 checkpoint48e_post
539 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
540 o dynamics: change definition of computational domain & adapt mom_fluxform
541 accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
542 o following exp works with Olx=Oly=2 (and pass through checkbounds option):
543 adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
544 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
545 global_ocean.90x40x15 global_with_exf global_ocean_pressure
546 inverted_barometer solid-body.cs-32x32x1
547 (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
549 checkpoint48d_post
550 o in preparation for r*:
551 a) use pre-computed gradient of hydrostatic potential:
552 changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
553 b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
554 => affects results of glob_oce_pressure (different truncation error)
555 update output.txt of ideal_2D_oce & global_ocean_pressure
557 checkpoint48d_pre
558 o in preparation for r*:
559 new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
560 pass the 2 comp. of the grad. as arguments to momentum S/R.
561 but for the moment, only used if it does not change the results.
562 o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
564 checkpoint48c_post
565 Modifications in treatment of initial flux forcing controls
566 to avoid extra storing of flux fields.
568 checkpoint48c_pre
569 o Added tidal_basin_2d experiment (currently 1D!)
570 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
572 checkpoint48b_post
573 o r* coordinate added in #ifdef NONLIN_FRSURF block.
574 (modification to pressure gradient not yet implemented)
575 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
576 (for U & V) that are used for vertical advection of momentum.
578 checkpoint48a_post
579 o In preparation for r*, use temp. array to compute vertical transport
580 in flux-form momentum pkg. => change results of few test-exp.
581 Update output of: exp4, exp5, front_relax, global_ocean_pressure,
582 lab_sea, natl_box & plume_on_slope
584 checkpoint48
585 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
587 checkpoint47j_post
588 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
589 o moved adexch from forward_step to addummy_in_stepping
590 o added exch in ctrl_map_...
591 o aveFreq.=0. at end of cost_final to avoid overwrite in
592 reverse checkpointing loop
593 o Yet more changes in gmredi:
594 * adgmredi_calc_tensor
595 avoiding all recomputation of gmredi_slope_limit
596 * adgmredi_x/y/rtransport
597 added flag for excessive storing to avoid recomp. of
598 u/v/rtans, dTdx/y/z
599 -> this is not really necessary and very memory-consuming
600 * adgmredi_slope_psi:
601 consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
602 * gmredi_slope_limit
603 re-activated full calculation of taperfct for case 'ac02'
604 o updating verification/ adjoints of carbon, global_ocean.90x40x15
606 checkpoint47i_post
607 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
608 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
609 default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
610 o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
611 o gmredi: fix few bugs.
613 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
614 This will be a good checkpoint to plug into the ecco-branch.
615 o few modif.'s to get latest version adjointed
616 (mainly kick out code in ini_linear_phisurf)
617 o modif's to run adjoint with exactConserv
618 o case GM_BOLUS_ADVEC should be cleaned
619 S/R gmredi_slope_psi should be cleaned
620 o verification/carbon now has exactConserv=.TRUE.
622 checkpoint47g_post
623 o time-average AIM output: becomes independent from statvars time-average
624 (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
625 o After TAF bug fix:
626 Tested adjoint of gmredi package.
627 Tests were done with checkpoint47 rather than with latest
628 checkpoint47f_post since the latter is broken for the adjoint
629 verification/carbon/ contains both ADM and TLM gradient checks.
630 Here they are, before they get changed/lost/stolen.
631 Mostly modif.'s to fix numerical sensitivities.
632 Gradient checks OK for
633 - GM_taper_scheme:
634 * clipping
635 * ac02
636 * linear
637 * glw91
638 * dm95
639 * ldd97
645 in conjunction with data.gmredi parameters to be checked in
646 in a few minutes under verification/carbon/code/
648 checkpoint47f_post
649 Merging from release1_p10:
650 o modifications for using pkg/exf with pkg/seaice
651 - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
653 - pkg/exf CPP options EXF_READ_EVAP and
655 - usage examples are Experiments 8 and 9 in
656 verification/lab_sea/README
657 - verification/lab_sea default experiment now uses
658 pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
660 checkpoint47e_post
661 o created a tag prior to creating a branch
663 checkpoint47d_post
664 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
665 at the bottom boundary had an erroneous half slip boundary condition
666 o added bottom drag and no slip boundary condition capabilities to
667 oceanic pressure coordinates code
668 o added new verification experiment global_ocean_pressure, this experiment is
669 also described in the tutorial section of the manual
670 checkpoint47d_pre
672 checkpoint47c_post
673 o Added a verification experiment for a global cubed-sphere ocean run
674 - verification/global_ocean.cubed32x32x30
675 - uses pkg/therm_seaice and pkg/bulk_forcing
677 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
678 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
679 when using P-coordinate; only implemented for atmospheric config.
680 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
681 NOTES: requires option NONLIN_FRSURF to be "#define".
682 o update advect_xz/results/output.txt (left from checkpoint44g_post)
684 checkpoint47b_post
685 Merging from release1_p9:
686 o pkg/seaice
687 - removed GOTO's and added taf directives
688 - double precision constants to reduce the g77 (Linux)
689 to F77 (SGI) differences reported in release1_p8
690 o tools/genmake
691 - added SGI options
692 o verification/testscript
693 - updated to that of checkpoint47a_post
694 o verification/global_ocean.90x40x15/input/eedata
695 - modified for SGI f77 compatibility
696 o verification/lab_sea
697 - added description of sea-ice model
698 - added missing matlab routines
699 - added test of thermodynamics parallelization
701 checkpoint47a_post
702 o new pkg: aim_v23
703 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
704 for now, keep the same surface forcing as before.
705 - Part-Cell implemented into AIM; check that Heat & Water are conserved
706 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
707 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
708 o add diagnostic of surface correction term in monitor output
710 o bulk_force and therm_seaice
711 - Two packages: bulk_force (Bulk forcing)
712 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
713 - Earlier integration from Stephaine Dutkiewicz
714 and Patrick Heimbach.
715 - Two ifdef statements for compile time,
718 checkpoint47
719 differentiable version of checkpoint46n_post
720 o bug fix in quasihydrostaticterms
721 o * "clean" adjoint code (in terms of extensive recomputations)
722 can now be obtained for all GMREDI options (i.e. for
727 * However, wrong gradient check problem remains unsolved.
728 * New CPP options have been introduced for different
729 tapering schemes
730 o external_fields_load now part of differentiation list
731 o pressure needs multiple storing;
732 would be nice to have store_pressure at beginning or
733 end of forward_step, e.g. by having phiHyd global (5-dim.)
734 (NB: pressure is needed for certain cases in find_rho,
735 which is also invoked through convective_adjustment).
736 o recomputations in find_rho for cases
737 'JMD95'/'UNESCO' or 'MDJWF' are OK.
738 o #define ATMOSPHERIC_LOADING should be differentiable
739 o ini_forcing shifted to begining of initialise_varia
740 o Incorporating QNVS line search routines into MITgcm
741 (this is separate code, and therefore not under pkg)
742 lsopt/, optim/
743 o Updated verification/carbon/
745 - GM_taper_scheme = 'ldd97'
747 checkpoint46n_post
748 Merging from release1_p8:
749 o verification/natl_box:
750 updating new external_fields_load routine
751 o New package: pkg/seaice
752 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
753 The sea-ice code is based on Hibler (1979-1980).
754 Two sea-ice dynamic solvers, ADI and LSR, are included.
755 In addition to computing prognostic sea-ice variables and diagnosing
756 the forcing/external data fields that drive the ocean model,
757 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
758 The implied surface heat flux is then stored in variable
759 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
760 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
761 non-local transport term. Because this call precedes model
762 thermodynamics, temperature under sea-ice may not be "exactly" at
763 the freezing point by the time theta is dumped or time-averaged.
764 N.B.: fairly large differences in accuracy occur across
765 different platforms/compilers; comparison between
766 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
767 generated output gives:
768 T S U V
769 C D M c m s m s m s m s
770 n p a R g m m e . m m e . m m e . m m e .
771 f n k u 2 i a a d i a a d i a a d i a a d
772 g d e n d n x n . n x n . n x n . n x n .
774 Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
775 o GAD:
776 - generated new common blocks to account for call of
777 same gad routines with differing traceridentities
778 (needed to modify tracerIdentity indices in GAD.h)
779 - generated separate common blocks for case useCubedSphereExchange
780 (Department of Futurology)
781 - parameter lists to gmredi_?transport: added tracerIdentity
782 - added new key indices to tamc.h
783 o external_fields_load:
784 - added this routine to TAF list
785 - needed to make some common blocks global and additional storing
786 along the same lines as exf package (checkpoint_lev?_directives.h)
787 o exf:
788 updated external forcing package
789 - bug fixes carried over from ecco-branch
790 (missing OBCS_OPTIONS.h in two routines)
791 - enable easy to use "no forcing".
792 - added exf I/O for atmospheric loading
793 - added exf I/O for runoff data
794 - transfered scaling between exf <-> MITgcm to exf namelist
795 o Adding new verification experiment global_with_exf.
796 This verification experiment is almost identical to the
797 global_ocean.90x40x15 experiment, except that it uses
798 the exf (and cal) package instead of the
799 external_fields_load routine (cf README file).
801 checkpoint46m_post
802 o modified testscript to return -- when there are no lines of "%MON" output
803 o added new flag "quasiHydrostatic" for QH mode
804 and new routine quasihydrostaticterms()
805 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
806 New routine: mom_u_coriolis_nh()
807 o fixed sign of non-hydrostatic metric terms in u and v equations.
808 Depend on correct sign of gravitySign.
809 o added work.pc* to .cvsignore in aim directories using ifc
810 o introduced flag for controllin non-hydrostatic metric terms
811 o removed gravitySign from PARM04
812 o switched to g77/ifc from pgf77 in aim experiments
814 checkpoint46l_post
815 o made convective adjustment work with pressure coordinates:
816 - changed the direction of k-loop in convective_adjustment.F for the
817 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
818 - adjusted the reference pressure k-index in convective_adjustment.F
819 - adjusted the convection condition in convect.F (in analogy to
820 calc_ivdc.F)
821 - convective_adjustment no longer computes anything on the halos
822 - removed the warnings about negative salinity from find_rho.F and
823 find_alpha.F; instead the new routine look_for_neg_salinity, called
824 at the beginning of find_rho, find_alpha, and find_beta, does a
825 check of the entire slice, if CPP-option
827 checkpoint46l_pre
829 checkpoint46k_post
830 o fixed the verification/global_ocean.90x40x15 experiment:
831 - new bathymetry (the world according to A., JMC, and M.)
832 - new initial fields and forcing fields (*.bin files)
833 - new POLY3.COEFFS (for the next release one should switch to a full
834 equation of state: JMD95P or MDJWF)
835 - fixed several errors and redundancies in the data file
836 - experiment uses looped cells
837 - added matlab directory with diagnostic scripts for plotting of output
839 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
840 - read AIM physics parameters from a file (data.aimphys)
841 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
843 checkpoint46j_post
844 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
845 o move wVel computation at the end of the time step, in S/R integr_continuity
846 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
847 o update timeave pkg for wVel diagnostic.
848 checkpoint46j_pre
850 checkpoint46i_post
851 o Clean up AIM package (and keep the results unchanged):
852 include CPP_OPTION and use IMPLICT NONE in all routines ;
853 declare all the variables _RL ; use _d 0 for all numerical constants.
854 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
856 checkpoint46h_post
857 o cleaned up the use of rhoNil and rhoConst.
858 - rhoNil should only appear in the LINEAR equation of state, everywhere
859 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
860 and the dynamical equations are all divided by rhoConst
861 o introduced new parameter rhoConstFresh, a reference density of fresh
862 water, to remove the fresh water flux's dependence on rhoNil. The default
863 value is 999.8 kg/m^3
864 o cleanup up external_forcing.F and external_forcing_surf.F
865 - can now be used by both OCEANIC and OCEANICP
866 checkpoint46h_pre
868 Added code to convert surface volume flux (fresh water) into
869 a mass flux when using P coordinates in the ocean (OCEANICP).
870 Note: It assumes you have set rho0=rhoConst=density of fresh water.
872 checkpoint46g_post
873 o Include a new diagnostic variable phiHydLow for the ocean model
874 - in z-coordinates, it is the bottom pressure anomaly
875 - in p-coordinates, it is the sea surface elevation
876 - in both cases, these variable have global drift, reflecting the mass
877 drift in z-coordinates and the volume drift in p-coordinates
878 - included time averaging for phiHydLow, be aware of the drift!
879 o depth-dependent computation of Bo_surf for pressure coordinates
880 in the ocean (buoyancyRelation='OCEANICP')
881 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
882 Theta, Salinity, and Pressure in the parameter list. This routine is
883 presently contained in find_rho.F. This routine does not give the
884 correct density for 'POLY3', which would be a z-dependent reference
885 density.
886 o cleaned up find_rho
887 - removed obsolete 'eqn' from the parameter list.
888 o added two new verification experiments: gop and goz
889 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
890 checkpoint46g_pre
892 checkpoint46f_post
893 o Enable tangent linear (forward mode) gradient checks:
894 - extended active file handling to g_... files
895 - added TANGENT_SIMULATION to theSimulationMode
896 - extended grdchk package accordingly
897 o added tangent linear setup in verification/carbon/code_ftl
898 o added adjoint setup in verification/front_relax/code_ad
900 checkpoint46e_post
901 o Added new equation of state -> MDJWF
902 - EOS of McDougall et al., 2002, JAOT, submitted
903 - caveat: the equation of state is only valid for a smaller (more
904 realistic?) range of values than JMD95P/Z and UNESCO
905 - added masks to the calculation of pressure in store_pressure
906 - added more check values for density in check_eos (ini_eos.F), some of
907 the old check values are out of the range of the MDJWF-eos, so don't
908 expect perfect matches for those
909 checkpoint46e_pre
911 checkpoint46d_post
912 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
913 'OCEANICP', also initialised field pressure correctly in ini_eos in the
914 case of pressure coordinates. eosType='JMD95Z' in
915 combination with buoyancyRelation='OCEANICP' now causes an error.
916 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
917 in find_alpha/beta.
918 checkpoint46d_pre
920 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
921 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
923 checkpoint46c_post
924 o Changes necessary for ocean in p-coordinates
925 - Added new buoyancy relation = 'OCEANICP'
926 - Added new parameters = gravitySign (this used to be contained inside
927 the factor dRdZ which I added when we first switched to R coordinates).
928 X GM/Redi is not compatible (yet)
929 X bottom drag and no-slip need to be debugged.
930 checkpoint46c_pre
932 checkpoint46b_post
933 o Added new equation of state -> JMD95Z and JMD95P
934 - EOS of Jackett and McDougall, 1995, JAOT
935 - moved all EOS parameters into EOS.h
936 - new routines ini_eos.F, store_pressure.F
937 o Added UNESCO EOS, but not recommended because it requires
938 in-situ temperature (see JMD95)
939 o Modified formatting for knudsen2.f in utils/knudsen2 and added
940 unesco.f to be used with POLY3
941 checkpoint46b_pre
943 checkpoint46a_post
944 o Added (atmospheric) pressure loading
945 - new field in FFIELDS.h, etc...
946 - new cpp flag ATMOSPHERIC_LOADING
947 o Changed hFacC to _hFacC in calc_phi_hyd.F
948 o Added SHORTWAVE_HEATING to some files for consistency
949 checkpoint46a_pre
951 checkpoint46
952 further merges from release1_p5
953 o new ctrl package
954 - adopted from ECCO environment to enable optimization
955 - added Eliassen Palm fluxes to controls
956 o added Eliassen Palm flux controls to gradient check package
957 o cost package
958 - Compatible with new ctrl package
959 - added Eliassen Palm cost hooks
960 - modif's of existing cost functions
961 o Adjoint-related bug fixes in kpp:
962 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
963 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
964 o autodiff package
965 - flow directives:
966 + new for S/R do_the_model_io
967 + enhanced for S/R checkpoint
968 + new gmredi.flow
969 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
970 disable adcommon.h/g_common.h by default.
971 - fixed problem for adjoint of global_max
972 o modified verification/carbon/
973 o New setup for adjoint of global_ocean
974 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
975 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
976 o incorporated hooks for sponge layer code (external_forcing.F)
978 checkpoint45d_post
979 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
980 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
981 (affects plume_on_slope "cg2d" output)
982 o add new parameter deltaTfreesurf for free-surface time stepping
983 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
984 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
985 o change phiMin in exp1 (to agree with documentation)
986 o add new flags:
987 - T,S forcing inside/outside Adams-Bashforth
988 - turn off temp,salt advection and/or forcing
989 - for each tracer, define internal flag for multiDimAdvection & A-B
990 o monitor: change definition of KE to check conservation of Energy
992 checkpoint45c_post
993 o Removed f90 comments ("!")
994 o Modified initialisations to enable exf package for MITgcm
995 (without invoking ECCO_PACKAGE).
996 o modifications to gradient check package (Martin Losch)
997 - enable centered differences
998 - modified format of standard output
1000 checkpoint45b_post
1001 o cleaned exchange calls in cg2d
1002 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
1003 o included CPP option SINGLE_LAYER_MODE in thermodynamics
1004 to configure barotropic setup (Martin Losch)
1005 o moved some initialisations within bi,bj loop in dynamics
1006 (TAF flow dependency)
1007 o in initialise_varia, moved call packages_init_variables
1008 before convective_adjustment_init
1009 (corresponding adjustment of TAF tape initialisation).
1010 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
1012 checkpoint45a_post
1013 o compute Rho over the whole domain (extend iMin,jMin indices)
1014 o specific exchange for X-slice domain (case Ny=1)
1015 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
1016 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
1018 checkpoint44h_post = checkpoint45
1019 o Fix to restore differentiability:
1020 place at which packages_init_variables is called in
1021 initialise_varia is crucial for reverse control flow.
1022 o modifications in GMRedi to enable stable adjoint
1023 (corresponding modif's in thermodynamics, dynamics)
1024 o added missing hook for sponge layer code in external_forcing
1025 o modified test cost functions
1026 o storing in gad_advection (plus removal of write(0,*)!
1027 o missing headers TR1.h added in convective_adjustment routines
1028 o errorMessageUnit set non-equal zero in eeboot
1029 (conflict on some platforms, e.g. IBM SP3)
1030 o modified carbon verif.
1032 checkpoint44h_pre
1033 o vertical grid option: allow to put the Interface at the middle between
1034 2 cell-centers ; replace delZ in pkg/kpp by drF.
1035 o GM Advective form: Tracers are advected using the residual transport (=
1036 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
1038 checkpoint44g_post
1039 o fix surface correction term in multiDimAdvection (affects plume_on_slope
1040 results) ; ifdef missing in thermodynamics.F
1042 checkpoint44f_pre,checkpoint44f_post
1043 o added PTRACERS package
1044 This allows an arbitrary number of passive tracers to be integrated
1045 forward simultaneously with the dynamicaly model.
1046 + Implemented so far:
1047 - basic forward algorithm (time-stepping, advection, diffusion, convection)
1048 - I/O and checkpointing
1049 - GM/Redi *but* using the GM/Redi coefficient of Salt
1050 + Not implemented so far:
1051 - KPP
1052 - OBCS
1053 + No specific example supplied (yet) but global_ocean.90x40x15 has the
1054 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
1055 line in data.pkg.
1056 + This package is disabled by default since it increases storage.
1059 o testscript: added -cleanup option
1060 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
1061 b) enable to filter 2D fields.
1063 checkpoint44e_pre,post
1064 o re-wrote convective adjustment to use pre-calculated weights
1065 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
1066 Adds: model/src/convective_weights.F, convectively_mixtracer.F
1067 Original calls to convect() still in place.
1069 chkpt44d_pre,post
1070 o added missing EXCLUDE_MONITOR flags
1071 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
1072 (incompatible typ in MIN/MAX expressions caused problems
1073 on IBM SP3)
1074 o in genmake added variable MAKEDEPEND
1075 plus resetting for case SunOS
1076 o added timer_stats.c routine for IBM SP3
1077 o removed variables in dynamics
1078 !!! I forgot to create tag chkpt44d_pre !!!
1079 !!! But chkpt44d_pre = chkpt44c_post !!!
1081 o real fresh water flux implemented with non-linear free-surface.
1083 chkpt44c_pre,post
1084 o few fix (mask in shap_s2, EmPmR in external_field_load,
1085 USE_NATURAL_BCS in solve_for_P);
1086 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
1088 checkpoint44b_pre/_post
1089 o merge of relevant stuff from the ecco-branch:
1090 - genmake: removed $S64 overwrite for case SunOS
1091 - pkg/exf: update and corrections for field swapping and obcs
1092 - pkg/ecco: parameter lists for the_model_main, the_main_loop
1093 harmonized between ECCO and MITgcm
1094 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
1095 updated checkpointing_lev... lists for obcs
1096 - model/src: minor changes in forward_step, plot_field
1097 added directive for divided adjoint in the_main_loop
1098 - pkg/mdsio: added mdsio_gl_slice
1100 o check parameters & config (chkpt44a_pre,post)
1101 o OBC and NonLin_FrSurf.
1103 checkpoint44
1104 o fix bug in mom_vi_del2uv
1105 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
1106 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
1107 o update AIM experiments (NCEP input files)
1108 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
1109 o added some stuff for AD
1111 checkpoint43
1112 o added two new advection tests
1113 o added global 4x4 degree ocean test
1114 o added test of H&S94 with free surface on cube
1115 o some final mods for gradient check, adjoint,...
1117 checkpoint42
1118 Fixed AD-related problems:
1119 o Store directives up-to-date with re-arranged Adams-Bashforth
1120 (mainly thermodynamics.F)
1121 o New store directives for multi-dim. advection schemes
1123 * new common block and key passkey
1124 (mainly gad_advection.F)
1125 o Modified store directives for split of dynamics/thermodynamics
1126 for the case ALLOW_KPP
1127 o Cleaned argument list for timestep_tracer.F
1129 checkpoint41
1130 o re-formatted/added comments in prologues of key subroutines
1131 to work with protex
1133 checkpoint40
1134 o moved calc_gs, calc_gt and calc_tr1 back to model/src
1135 o added FLT (floats) package from Arne along with demo. experiment
1136 o re-arranged Adams-Bashforth scheme for tracers to allow easier
1137 implementation of forward-in-time forcing terms
1138 o more mods for non-linear free-surface including new variable
1139 o modified multi-dim method to work on cube
1140 o bug fix in KPP (from DM)
1142 checkpoint40pre9
1143 o added DST advection schemes
1144 o fix MPI bug on SGI's
1145 o modifications for non-linear free-surface
1146 o fixed conditionals for fixed flow/passive tracer only mode
1147 o added tension/strain form of stress tensor
1148 o changes to commenting of arguments for TAF/TAMC
1149 o added/updated many matlab scripts
1150 o added multi-dimensional advection method for tracers
1152 checkpoint40pre8
1153 o new package rw/
1154 Added method for dumping intermediate local arrays:
1155 mdsio_writetile - same as mdsio_writefield except works from inside
1156 bi,bj loop
1157 mdsio_writelocal - same as mdsio_writetile except works for local
1158 arrays
1159 write_local_r? - higher-level wrapper for mdsio_writelocal
1160 Controlled by diagFreq. Defaults to zero (ie. no dumps)
1161 Example given at end of mom_vecinv.F that dumps some local arrays.
1162 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
1163 control flux-form versus vector invariant code.
1164 Switch is runtime flag vectorInvariantMomentum (defaults to false)
1165 or genmake -DISABLE ...
1166 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
1167 (additional storing is now needed for case vecinv;
1168 currently nothing implemented to switch this storing off
1169 in case fluxform is used since no CPP flag available).
1171 checkpoint40pre7
1172 o bug fix in dynamics.F
1173 calc_viscosity called before k=1,Nr loop.
1174 o added some #ifdef's ALLOW_PASSIVE_TRACER
1175 o cleaned initialisations in ctrl_map_ini
1176 related to TAF
1178 checkpoint40pre6
1179 o split dynamics into thermodynamics & dynamics
1180 o corresponding split of calc_diffusivity into
1181 calc_diffusivity, calc_viscosity
1182 (kpp_calc_diff, kpp_calc_visc).
1183 o Added diffkr, kapgm to control variables
1184 o bug fix in gmredi_slope_limit for ldd97
1186 checkpoint40pre5
1187 o proper initialization of Adams-Bashforth time stepping
1188 + uses forward step for very first step of model (iter=0)
1189 o re-generated *all* output since almost all output is modified by this
1190 change (sorry but we've been putting this one off for about 2 years)
1191 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
1192 *not* regenerated since they are already out of date and I don't
1193 want to create the impression that they are suddenly working.
1194 o removed KAP stuff for DEC's
1195 o modified/added many .cvsignore files in */code and */input
1196 o added new expt "solid-body.cs-32x32x1"
1197 + this uses an alternative form of ini_curvilinear_grid.F which
1198 is not necessarily any better than the current one...
1200 checkpoint40pre4
1201 o added re-initialisations of utrans,vtrans,rtrans in
1202 calc_common_factors which are crucial for TAF.
1203 o extended iMin,jMin range for calc_common_factors,
1204 calc_diffusivity
1205 o added option ALLOW_PASSIVE_TRACER
1206 o a few minor updates and fixes
1208 checkpoint40pre3
1209 o created calc_gtr1.F for gad package
1210 o split the_main_loop and re-introduced forward_step
1211 o some recomputations of nIter0 for TAMC
1213 checkpoint40pre2
1214 o Updated to latest branch of AJA, JMC
1215 o Added gradient check package
1216 o Added routines for passive tracer handling
1217 o Added carbon sequestration sensitivity experiment
1219 checkpoint39
1220 o Modifications and fixes to support TAMC
1221 (mainly missing or wrong directives)
1222 o Corrected common blocks when fooling TAMC to produce adjoint I/O
1223 in addummy_in_stepping
1224 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
1225 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
1226 o Included following packages:
1227 cal: calendar
1228 exf: external forcing
1229 ecco: essential routines to control use of cal, exf
1230 (NB: this is not the full ECCO environment)
1231 o disabled some packages by default in genmake
1233 checkpoint38
1234 o see notes_c37_adj.txt
1235 o corrected wrong layer index in external_forcing_t
1236 o replaced the_main_loop/forward_step by the_main_loop
1237 o removed forceoutput from write_state
1238 (replaced criteria for initial/final state)
1239 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
1241 checkpoint37
1242 o mdsio.F routine split and packaged in pkg/mdsio
1243 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
1244 used unless genmake -disable=mdsio)
1245 o allow a more precise surface-geopotential gradient for the atmosphere
1246 taking into account the change in space of Alpha (=1/rho) at the surface.
1247 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
1248 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
1249 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
1250 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
1251 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
1252 o Time-Average diagnostics defined as a pseudo package "timeave".
1253 o pickup files : old pickup (before c35) did not work with new code (c35
1254 and after) unless activating 2 commented lines in initialise-varia.
1255 o Non-Hydrostatic pickup file Pb fixed.
1256 o bug with Rigid-lid version (since c35) fixed.
1258 checkpoint36
1259 o implement Crank-Nickelson barotropic time-stepping
1260 o recover Time-Average diagnostics
1261 o fix Pb in checkpoint (PR#19)
1262 o AIM become a standard package ; clean unused CPP_kees
1264 checkpoint35
1265 o subtantial rewrite of dynamics.f
1266 o allows staggered time-stepping
1267 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
1268 o added bottom drag (linear + quadratic)
1270 checkpoint34
1271 o Modified exchange routines for correct reverse simulation.
1272 o Added verification output to comply with bug fix in impldiff.F
1273 as of c33 (exp2, natl_box).
1274 o Corrected store directives in dynamics.F
1275 o Corrected array boundaries in impldiff.F
1276 o Corrected array dimensions in gmredi.
1277 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
1278 o Added routine GLOBAL_SUM_INT to global_sum.F
1279 o Added mdsio_gl.F for ECCO purposes.
1281 checkpoint33
1282 o Fixed bug in lower BC in impldiff.F
1283 o Fixed confusion about units of forcing arrays in FFIELDS.h
1284 namely Fu,Fv,Qnet,Qsw,EmPmR:
1285 - Removed verification/natl_box/code/external_fields_scale.F
1286 (did not differ from that in model/src)
1287 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
1288 (see FFIELDS.h for description)
1289 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
1290 kpp_calc.F and kpp_transport_t.F
1291 - Removed model/src/external_fields_scale.F and calls to it
1292 - verification/natl_box uses flux data with "atmospheric" sign so
1293 a special version of external_fields_load.F is used to
1294 change the data as it's read in. This way, the arrays
1295 have the right units and signs at all times tha a user could
1296 possibly use them.
1297 o Corrected genmake to delete a temporary file during configuration
1299 checkpoint32
1300 o Scaling of forcing fields moved from external_forcing.F to
1301 external_fields_scale.F, called directly after loading fields.
1302 o Surface relaxation terms added to surface tendency fields in
1303 extra subroutine.
1304 o impldiff.F changed to avoid storing by TAMC of huge intermediate
1305 fields.
1306 o Changes in GMRedi to comply with packaging structure.
1307 o Modifications and bug fixes in KPP package.
1308 o Verification experiment for KPP added (verification/nat_box/)
1310 checkpoint31
1311 o Packages interface brought in line with defined standard
1312 -> new routines packages_...F
1313 -> changes in initialise_fixed.F, initialise_varia.F
1314 -> enables initialisation interface for ECCO package
1315 o Rescaling of external forcing fields immediately after read
1316 (removed from external_forcing.F)
1317 -> new: surface_fields_scale.F
1318 -> affects ini_foorcing.F, external_fields_load.F
1319 o Computation of surface tendencies before tendency updates.
1320 -> new: external_forcing_surf.F
1321 o Change of variable names useGMRedi, useKPP, useECCO
1322 o Further changes in dynamics.F, impldiff.F for TAMC
1323 o Tested for experiments 0, 2, 4.
1324 - not yet tested for GMRedi.
1325 - not yet tested for KPP.
1327 checkpoint30
1328 o Updates for OBCs
1329 o New experiment for test OBCs (internal_wave)
1330 o New output.txt in verification/exp4/results/
1331 o Updates for KPP: calculation of viscosity corrected, new variables
1332 kpp_dumpFreq and kpp_taveFreq
1333 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
1334 and entry for T90 in genmake
1336 checkpoint29
1337 o packaged KPP and GM/Redi
1339 checkpoint28
1340 o Corrected initialization of hFacMin for difference vertical coordinates
1341 o Modified calculation of partial cell thickness to more robust algorithm
1342 o config_summary.F: replaced write_1D_... by write_0D_...
1343 read_write.F: added subroutines write_0D_...
1344 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
1345 included some initialisations required for TAMC.
1346 o routine calc_isoslopes: modified sqrt computation to make it
1347 differentiable for zero argument.
1348 o routines dynamics, impldiff:
1349 included store directives and tape key computations required for TAMC.
1350 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
1352 checkpoint27
1353 o fixed calc_isoslopes() to so that cancellation of terms in tensor
1354 formulation works properly with variable resolution.
1355 o restructured the calling tree between the_model_main() and dynamics()
1356 o split initialise() into initialise_fixed() and initialise_varia()
1357 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
1358 in new routine ini_psurf()
1360 checkpoint26
1361 o moved some #ifdef in optional routines to encompass everything
1362 except the argument declarations. This was using up some memory.
1363 o fixed macros like _ADT to work with both versions of Linux cpp
1364 o cleaned up some unused and uninitialized variables
1365 (helps when debugging with strict compile options)
1366 o split up CPP_EEOPTIONS.h into options and macros
1367 (macros are now in eesupp/inc/CPP_EEMACROS.h)
1368 o patch for 2 processor JAM mode
1370 checkpoint25
1371 o updates for OBCs and NH
1372 o dramatically reduced memory usage
1373 o added "JAM" routines for use on Artic network
1374 o parameterization of convection by implicit vertical diffusion
1375 o added a diagnostic of convective index
1376 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
1377 (this is was partly for OBCs and NH but also in anticipation of
1378 an explicit free-surface option)
1379 o initial state input files for U and V
1381 checkpoint24
1382 o Removed some spurious "REAL"s
1383 o Updated KPP to latest version from JPL
1384 o Added a COS(latitude) in horizontal viscosity
1386 checkpoint23
1387 o Added del^4 diffusion for salt and temperature
1388 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
1390 checkpoint22
1391 o Made many small changes: implicit none, format(i5), etc...
1392 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
1394 checkpoint21
1395 o Introduced new I/O package that supports direct-access records (mdsio.F)
1396 o Split-up mid-level I/O routines
1397 o Updated input data for experiments 0,1,2,4 and 5
1398 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
1400 checkpoint20
1401 o Tidied up open-boundaries some more
1402 o Added non-hydrostatic code
1403 o Fixed some input data
1404 o Modified MPI start-up to work in "coupled" context.
1406 checkpoint19
1407 o Tidied up directory structure for verification experiments.
1408 o Added new code for open boundaries.
1409 o Corrected advective terms near boundaries.
1410 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
1411 o Implemented free-slip/no-slip BCs and del^4 dissipation.
1412 o Split default parameters out of ini_parms.F into set_defaults.F.
1414 checkpoint18
1415 o Further changes for optional code generation with
1416 CPP - ugh!
1418 checkpoint17
1419 o Beginning to incorporating modularity
1420 for supporting atmos. and ocean configs.
1421 o Small changes for TAMC complinace
1422 o New ultra simple test case. Barotropic box
1423 configuration "exp0".
1425 checkpoint16
1426 o Minor changes to exchange routines to support
1427 accumulation in reverse mode. Adjoint of an
1428 assignment is an addition.
1429 o Changes to support compilation by TAMC (LR(1)
1430 syntax) and by g77 under Linux ( 72 character
1431 limit ).
1433 checkpoint15
1434 Rewrote exchange routines to allow
1435 o General tile <-> tile connectivity.
1436 o TAMC reverse mode flag ( is this really needed? )
1437 o Variable width overlap and exchange region widths.
1438 o Hooks for sharing data via DMA, Arctic, Memory Channel,
1439 shmput/shmget, VIA, SYSV shmem and every other cool
1440 communication method.
1442 checkpoint14
1443 Consistent isomorphism chages made. These allow dynamical core
1444 to support both pressure and meters as a vertical coordinate.
1446 checkpoint13
1447 Release which corrects global_max problem and a couple
1448 of KGM time-averaging diagnostic errors. Also contains
1449 a double-gyre experiment setup as well as the baseline
1450 4 degree global template. The double gyre template is
1451 organised to allow it to be applied automatically to
1452 the baseline configuration.
1454 branch-point-rdot
1455 A few tidy-ups have been made bt the real point of this
1456 check-point (excuse the pun) is to allow a branch to be
1457 made for the purposes of adding the rDot alterations.
1458 I don't want to commit the rDot to the main-trunk until
1459 we've actually tested it...
1461 checkpoint12
1462 Tidy up and added generic genmake script (formerly
1463 configure script).
1464 Released to testers.
1466 checkpoint11
1467 Re-arranged initialise() and introduced ini_vertical_grid()
1468 and ini_masks_etc().
1470 checkpoint10
1471 Introduced the configure script.
1472 Separated out the diags package.
1473 Added template for writing time-averages of tile/intermediate quantities.
1474 Updated SIZE.h in exp2 and made the data big-endian.
1476 checkpoint9
1477 MPI fix. Filename changes (meta/data). salbin*y stuff.
1478 General tidy-up.
1479 SST.bin SSS.bin added to verification/exp2
1481 checkpoint8
1482 Inludes time-dependant forcing and time-averaging.
1483 Works at 4x4 and 2.8125x2.8125 global
1485 checkpoint7-4degree-ref
1486 Branch from checkpoint7. Released for application to
1487 global modeling and general modeling - process studies, regional
1488 model etc..
1489 Configured for verification/exp2 - 4 degree global, two process.
1491 checkpoint7
1492 Created by cnh
1493 Simple 4 degree global simulation
1494 configuration.
1495 Includes climatological wind,
1496 hydrography, bathymetry etc
1497 Does not include Heat Flux and E-P
1499 checkpoint6
1500 Created by cnh
1501 merged checkpoint5 with CD and
1502 spherical polar code.
1503 Still some problems with GM Redi
1504 abd full topography.
1506 checkpoint5
1507 Created by AJA
1508 contains updates to GM Redi
1509 and reordered timestepping loop
1510 for Implicit Diffusion.
1512 checkpoint4
1513 Created by cnh
1514 Contains memory saving macros ( _rdxc etc..) for when
1515 grid variations are limited.
1516 Contains polynomial coeffs for EOS and knudsen program
1517 for generation.
1519 checkpoint3
1520 Created by cnh
1521 Added extra flags for runtime options
1522 Added this file
1523 Added implicit free-surface
1524 Added pre-conditioner
1525 Put compare01 into repository ( compare01/... )
1526 Put data and eedata into repository ( verification/exp1 )
1528 checkpoint2
1529 Created by AJA
1530 Added GM/Redi
1532 checkpoint1
1533 Created by AJA
1534 Restructured kloop in dynamics.F
1535 Added non-linear EOS
1537 baseline
1538 Original checked in code

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