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Revision 1.178 - (show annotations) (download)
Wed Sep 24 06:50:26 2003 UTC (18 years, 10 months ago) by dimitri
Branch: MAIN
CVS Tags: branchpoint-genmake2
Branch point for: branch-genmake2
Changes since 1.177: +2 -2 lines
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
  of tracer Green's fucntions for ocean inversion project.

1 $Header: /usr/local/gcmpack/MITgcm/doc/tag-index,v 1.177 2003/09/23 04:34:23 dimitri Exp $
2
3 Notes on tags used in MITgcmUV
4 ==============================
5
6 untagged
7 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
8 of tracer Green's fucntions for ocean inversion project.
9
10 checkpoint51f_pre
11 o Added on-the-fly spatial interpolation capability
12 "USE_EXF_INTERPOLATION" to pkg/exf.
13 - This is a temporary Cartesian-grid hack until
14 the super-duper ESMF coupler becomes available.
15 - See verification/global_with_exf/README for usage example.
16 - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
17 flags and modified pkg/seaice accordingly.
18 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
19 and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
20 non-local transport term.
21
22 checkpoint51e_post
23 o pkg/mom_vecinv:
24 - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
25 - add time-ave diagnostic of vorticity advection.
26 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
27 o atmospheric geopotential: - include water vapor effect;
28 - use p^kappa in p* scaling.
29 o land pkg: read initial state from files.
30 o AIM : add stratospheric drag in the upper level
31
32 checkpoint51d_post
33 o change function ILNBLNK (=> last non-blank char.) to return zero
34 (instead of the string length) when the string. char is empty
35 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
36 o modif's to restore TAMC compatibility
37 - avoid "_d" constructs in PARAMETER declarations
38 - avoid interrupting lines by comment lines
39 o Use cluster local disks for purely local I/O
40 vs. globally visible disks needed for ctrl stuff
41 (merged from ecco-branch)
42 - new active_file_loc... and mdsio_..._loc routines
43 - affected packages: autodiff, ctrl, grdchk, mdsio
44
45 checkpoint51c_post
46 o introducing integer flag debugLevel
47 - debLevZero: suppress all output
48 - debLevA: standard
49 - debLevB: equivalent to current debugMode=.TRUE.
50 o introducing pathname variable mdsioLocalDir for mdsio
51 that can be specified at runtime
52 (relevant for cluster I/O to local disk)
53 `
54 >>>checkpoint51b_post
55 adjoint of ptracers
56 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
57 o extended state in checkpoint_lev?, etc.
58 o alternative ctrl/cost with tr1 or ptracer
59 o new comlev1_bibj_ptracers
60 o new ptracers.flow
61 o made ptracers_forcing same as external_forcing_s
62 o added verification for adjoint with ptracers
63 - adm. grdchk fail so far
64 - tlm. grdchk OK
65 - checked tapelev/comlev recomputations: OK
66 <<<checkpoint51b_pre
67
68 checkpoint51a_post
69 o added code for biogeochemistry package
70 - new pkgs: dic, gchem
71 - new subroutine in ptracers
72 o modify code for biogeo packages
73 - in model/src and pkg/ptracers
74
75 checkpoint51
76 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
77 - autodiff, ctrl, exf, grdchk, seaice
78 kept separate packages
79 - cost, ecco, obcs
80 o updating verification/internal_wave, verification/lab_sea
81 (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
82
83 checkpoint50i_post
84 o Preparing next differentiable checkpoint and sync
85 of MAIN vs. ecco-branch
86 - 1st step: this one is differentiable
87 - 2nd step: next(! not this) checkpoint will have updated packages
88 from ecco-branch)
89
90 checkpoint50h_post
91 o new package "land": provide surface BC for AIM.
92 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
93 o AIM: use true log-P extrapolation for near surface temp (= as in
94 F.Molteni paper) ; update aim.5l_cs output.
95 o New variable in PARM03 for more flexible pickups
96 o somewhat cleaned package initialisation sequence for
97 ctrl/ cost/ ecco/ in packages_... routines
98
99 checkpoint50g_post
100 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
101 - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
102 - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
103 made the default because of faster convergence than ADI
104
105 checkpoint50f_post
106 o exf totally restructured
107 - replaced all exf_set_ routines by one generic exf_set_gen.F
108 and made sure it's still differentiable
109 - split exf_getffields.F into new exf_bulkformulae.F
110 - exf_inscal_/exf_outscal_ suffixes consistent with field names
111 - updated adjoint/makefile and relevant verif. accordingly
112
113 checkpoint50f_pre
114 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
115 + change Evap over land. (update aim.5l_cs output)
116 o added missing .cvsignores and made uniform across expts
117 o changed configuration of tidal_basin_2d expt
118 o added pkg/debug functions for tracing code in fatal crashes
119 o tidied pkg/monitor to use MONITOR_OPTIONS.h
120 o new fn in pkg/monitor to stop model if solution grows too big
121 o removed lots of single quotes from comments
122
123 checkpoint50e_post
124 o make KPP work with PTRACERS
125 - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
126 nearly a copy of kpp_transport_s
127 - there is no analogue to SurfaceTendencyS, so I have to use
128 gPtr(of the surface layer) instead
129 o add a new platform SunFire+mpi (SunFire 15000) to genmake
130 checkpoint50e_pre
131
132 checkpoint50d_post
133 o change kpp output from multiple-record state files to single-record state
134 files analogous to write_state.F
135 o reduce the output frequency of cg3d-related stuff to the monitor frequency,
136 analogous to the cg2d-related output.
137 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
138 so that writing to internal file fn (with length 512) fails.
139 checkpoint50d_pre
140
141 checkpoint50c_post
142 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
143 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
144 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
145 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
146 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
147
148 checkpoint50c_pre
149 Merging from release1_p13:
150 o bug fix for pkg/seaice dynamic solver
151 o Added SEAICE_initialHEFF to pkg/seaice
152
153 checkpoint50b_post
154 o store u*,v* in gU,V instead of in guNm1,gvNm1
155 o in order to put the momForcing out of the Adams-Bashforth:
156 move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
157 to timestep.F
158 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
159 o re-generate output for highly sensitive test-exp:
160 global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
161
162 checkpoint50b_pre
163 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
164 o corrected CPP option mismatch in exf_Bulk... functions for case
165 #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
166
167 checkpoint50a_post
168 o Bug fix for merging between c50 and KPP.
169 ikey was passed from thermodynamics to kpp_calc via
170 common block rather than being recomputed in kpp_calc,
171 in contradiction with new key itdkey.
172 New key ikppkey created, and tamc.h headers updated.
173
174 checkpoint50
175 - 2nd step of merge with ecco-branch:
176 merge changes in ecco-branch back into main trunk
177 - bug fix in find_alpha
178 - more storing in gmredi_calc_tensor.F, kpp_routines.F
179 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
180 - merged some sliced AD support routines
181
182 checkpoint49
183 merged from ecco-branch:
184 o exf:
185 - Enable initialisation of forcing fields to constant
186 (runtime) values.
187 - in exf_getffields.F
188 Reduce i-/j-loop to interior domain, discarding overlaps.
189 That also fixes wrong TAF-key computations for key_1, key_2
190 with bulf formulae.
191 - exf_init.F modify #ifdef for exf_init_evap
192 - exf_getffieldrec.F, ctrl_getrec.F
193 The following INT-usages are not safe:
194 fldsecs = int(fldsecs/fldperiod)*fldperiod
195 fldcount = int(fldsecs/fldperiod) + 1
196 and were modified.
197 o autodiff: checkpoint_lev...
198 - updated storing for bulk formulae (some arrays were missing)
199 - added state for seaice package
200 - synchronized with main branch
201 o DIVA:
202 Modif.s in
203 - the_main_loop.F
204 - the_model_main.F
205 and added cost_final_restore.F cost_final_store.F
206 o With these changes, it is possible to fully separate
207 the first forward run to compute the cost function (mdthe_main_loop)
208 and adjoint runs over individual DIVA intervals (adthe_main_loop)
209 into separate model executions.
210 This enables better tuning of DIVA to given queue sizes.
211 o Loss of cost function value in consecutive DIVA runs is
212 fixed by storing to 'costfinal' file.
213 o Appropriate call of ctrl_unpack/_pack,grdchk_main at
214 beginning/end of adjoint integration is accounted for.
215 The current changes apply to TAF-1.4.26.
216 TAF has one remaining bug, requiring one manual change
217 (see MITgcm manual).
218 o cal: synchronized between MAIN and ecco-branch
219
220 checkpoint48i_post
221 o Changes to restore differentiability of code w.r.t. previous tag
222 (mostly adding new routines to make list and replacing
223 pressure by totPhiHyd).
224 o Updated and merged grdchk package
225 - has both ADM and TLM checks
226 - works for single- and multi-proc.
227 - output cleaned
228 - worked successfully for parallel DIVA
229 o genmake:
230 - Adding -platform=SP4
231 - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
232 o Modif. for DIVA:
233 ctrl_unpack should not be called in intermediate DIVA interval.
234 (similar thing would apply for active files such as
235 tbar, sbar, psbar, which should not be reinitialised;
236 only relevant for ecco-branch)
237
238 checkpoint48h_post
239 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
240 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
241 o Added SEAICE_initialHEFF to pkg/seaice
242 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
243
244 checkpoint48g_post
245 --- EOS:
246 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
247 store total Potential in totPhyHyd for diagnostics & EOS.
248 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
249 --- Pressure/geopotential gradient:
250 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
251 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
252 ( changes results of global_ocean_pressure )
253 o NLFS + z-coord.: add eta*Rho' contribution.
254 o accurate phiHyd when using interface-W at the middle between 2 centers
255 ( changes results of ideal_2D_oce )
256 o includes r* 2nd term in potential gradient.
257
258 checkpoint48f_post
259 Merging from release1_p12:
260 o Modifications for using pkg/exf with pkg/seaice
261 - improved description of the various forcing configurations
262 - added basic radiation bulk formulae to pkg/exf
263 - units/sign fix for evap computation in exf_getffields.F
264 - updated verification/global_with_exf/results/output.txt
265 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
266 (SBO) core products, including oceanic mass, center-of-mass,
267 angular, and bottom pressure (see pkg/sbo/README.sbo).
268 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
269 to avoid negative values in shallow regions.
270 - updated verification/natl_box/results/output.txt
271 - updated verification/lab_sea/results/output.txt
272 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
273 o Added useSingleCpuIO option (see PARAMS.h).
274 o Updated useSingleCpuIO option in mdsio_writefield.F to
275 work with multi-field files, e.g., for single-file pickup.
276 o pkg/seaice:
277 - bug fix in growth.F: QNET for no shortwave case
278 - added HeffFile for specifying initial sea-ice thickness
279 - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
280 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
281 kpp_transport_t.F, forward_step.F, and the_main_loop.F
282 o pkg/seaice:
283 - adjoint-friendly modifications
284 - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
285
286 checkpoint48e_post
287 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
288 o dynamics: change definition of computational domain & adapt mom_fluxform
289 accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
290 o following exp works with Olx=Oly=2 (and pass through checkbounds option):
291 adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
292 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
293 global_ocean.90x40x15 global_with_exf global_ocean_pressure
294 inverted_barometer solid-body.cs-32x32x1
295 (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
296
297 checkpoint48d_post
298 o in preparation for r*:
299 a) use pre-computed gradient of hydrostatic potential:
300 changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
301 b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
302 => affects results of glob_oce_pressure (different truncation error)
303 update output.txt of ideal_2D_oce & global_ocean_pressure
304
305 checkpoint48d_pre
306 o in preparation for r*:
307 new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
308 pass the 2 comp. of the grad. as arguments to momentum S/R.
309 but for the moment, only used if it does not change the results.
310 o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
311
312 checkpoint48c_post
313 Modifications in treatment of initial flux forcing controls
314 to avoid extra storing of flux fields.
315
316 checkpoint48c_pre
317 o Added tidal_basin_2d experiment (currently 1D!)
318 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
319
320 checkpoint48b_post
321 o r* coordinate added in #ifdef NONLIN_FRSURF block.
322 (modification to pressure gradient not yet implemented)
323 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
324 (for U & V) that are used for vertical advection of momentum.
325
326 checkpoint48a_post
327 o In preparation for r*, use temp. array to compute vertical transport
328 in flux-form momentum pkg. => change results of few test-exp.
329 Update output of: exp4, exp5, front_relax, global_ocean_pressure,
330 lab_sea, natl_box & plume_on_slope
331
332 checkpoint48
333 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
334
335 checkpoint47j_post
336 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
337 o moved adexch from forward_step to addummy_in_stepping
338 o added exch in ctrl_map_...
339 o aveFreq.=0. at end of cost_final to avoid overwrite in
340 reverse checkpointing loop
341 o Yet more changes in gmredi:
342 * adgmredi_calc_tensor
343 avoiding all recomputation of gmredi_slope_limit
344 * adgmredi_x/y/rtransport
345 added flag for excessive storing to avoid recomp. of
346 u/v/rtans, dTdx/y/z
347 -> this is not really necessary and very memory-consuming
348 * adgmredi_slope_psi:
349 consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
350 * gmredi_slope_limit
351 re-activated full calculation of taperfct for case 'ac02'
352 o updating verification/ adjoints of carbon, global_ocean.90x40x15
353
354 checkpoint47i_post
355 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
356 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
357 default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
358 o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
359 o gmredi: fix few bugs.
360
361 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
362 This will be a good checkpoint to plug into the ecco-branch.
363 o few modif.'s to get latest version adjointed
364 (mainly kick out code in ini_linear_phisurf)
365 o modif's to run adjoint with exactConserv
366 o case GM_BOLUS_ADVEC should be cleaned
367 S/R gmredi_slope_psi should be cleaned
368 o verification/carbon now has exactConserv=.TRUE.
369
370 checkpoint47g_post
371 o time-average AIM output: becomes independent from statvars time-average
372 (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
373 o After TAF bug fix:
374 Tested adjoint of gmredi package.
375 Tests were done with checkpoint47 rather than with latest
376 checkpoint47f_post since the latter is broken for the adjoint
377 verification/carbon/ contains both ADM and TLM gradient checks.
378 Here they are, before they get changed/lost/stolen.
379 Mostly modif.'s to fix numerical sensitivities.
380 Gradient checks OK for
381 - GM_taper_scheme:
382 * clipping
383 * ac02
384 * linear
385 * glw91
386 * dm95
387 * ldd97
388 - GMREDI_OPTIONS:
389 * GM_VISBECK_VARIABLE_K
390 * GM_NON_UNITY_DIAGONAL
391 * GM_EXTRA_DIAGONAL
392 * GM_BOLUS_ADVEC
393 in conjunction with data.gmredi parameters to be checked in
394 in a few minutes under verification/carbon/code/
395
396 checkpoint47f_post
397 Merging from release1_p10:
398 o modifications for using pkg/exf with pkg/seaice
399 - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
400 and SEAICE_EXTERNAL_FLUXES
401 - pkg/exf CPP options EXF_READ_EVAP and
402 EXF_NO_BULK_COMPUTATIONS
403 - usage examples are Experiments 8 and 9 in
404 verification/lab_sea/README
405 - verification/lab_sea default experiment now uses
406 pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
407
408 checkpoint47e_post
409 o created a tag prior to creating a branch
410
411 checkpoint47d_post
412 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
413 at the bottom boundary had an erroneous half slip boundary condition
414 o added bottom drag and no slip boundary condition capabilities to
415 oceanic pressure coordinates code
416 o added new verification experiment global_ocean_pressure, this experiment is
417 also described in the tutorial section of the manual
418 checkpoint47d_pre
419
420 checkpoint47c_post
421 o Added a verification experiment for a global cubed-sphere ocean run
422 - verification/global_ocean.cubed32x32x30
423 - uses pkg/therm_seaice and pkg/bulk_forcing
424
425 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
426 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
427 when using P-coordinate; only implemented for atmospheric config.
428 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
429 NOTES: requires option NONLIN_FRSURF to be "#define".
430 o update advect_xz/results/output.txt (left from checkpoint44g_post)
431
432 checkpoint47b_post
433 Merging from release1_p9:
434 o pkg/seaice
435 - removed GOTO's and added taf directives
436 - double precision constants to reduce the g77 (Linux)
437 to F77 (SGI) differences reported in release1_p8
438 o tools/genmake
439 - added SGI options
440 o verification/testscript
441 - updated to that of checkpoint47a_post
442 o verification/global_ocean.90x40x15/input/eedata
443 - modified for SGI f77 compatibility
444 o verification/lab_sea
445 - added description of sea-ice model
446 - added missing matlab routines
447 - added test of thermodynamics parallelization
448
449 checkpoint47a_post
450 o new pkg: aim_v23
451 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
452 for now, keep the same surface forcing as before.
453 - Part-Cell implemented into AIM; check that Heat & Water are conserved
454 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
455 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
456 o add diagnostic of surface correction term in monitor output
457
458 o bulk_force and therm_seaice
459 - Two packages: bulk_force (Bulk forcing)
460 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
461 - Earlier integration from Stephaine Dutkiewicz
462 and Patrick Heimbach.
463 - Two ifdef statements for compile time,
464 ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
465
466 checkpoint47
467 differentiable version of checkpoint46n_post
468 o bug fix in quasihydrostaticterms
469 o * "clean" adjoint code (in terms of extensive recomputations)
470 can now be obtained for all GMREDI options (i.e. for
471 - GM_VISBECK_VARIABLE_K
472 - GM_NON_UNITY_DIAGONAL
473 - GM_EXTRA_DIAGONAL
474 - GM_BOLUS_ADVEC )
475 * However, wrong gradient check problem remains unsolved.
476 * New CPP options have been introduced for different
477 tapering schemes
478 o external_fields_load now part of differentiation list
479 o pressure needs multiple storing;
480 would be nice to have store_pressure at beginning or
481 end of forward_step, e.g. by having phiHyd global (5-dim.)
482 (NB: pressure is needed for certain cases in find_rho,
483 which is also invoked through convective_adjustment).
484 o recomputations in find_rho for cases
485 'JMD95'/'UNESCO' or 'MDJWF' are OK.
486 o #define ATMOSPHERIC_LOADING should be differentiable
487 o ini_forcing shifted to begining of initialise_varia
488 o Incorporating QNVS line search routines into MITgcm
489 (this is separate code, and therefore not under pkg)
490 lsopt/, optim/
491 o Updated verification/carbon/
492 - #define GM_VISBECK_VARIABLE_K
493 - GM_taper_scheme = 'ldd97'
494
495 checkpoint46n_post
496 Merging from release1_p8:
497 o verification/natl_box:
498 updating new external_fields_load routine
499 o New package: pkg/seaice
500 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
501 The sea-ice code is based on Hibler (1979-1980).
502 Two sea-ice dynamic solvers, ADI and LSR, are included.
503 In addition to computing prognostic sea-ice variables and diagnosing
504 the forcing/external data fields that drive the ocean model,
505 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
506 The implied surface heat flux is then stored in variable
507 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
508 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
509 non-local transport term. Because this call precedes model
510 thermodynamics, temperature under sea-ice may not be "exactly" at
511 the freezing point by the time theta is dumped or time-averaged.
512 N.B.: fairly large differences in accuracy occur across
513 different platforms/compilers; comparison between
514 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
515 generated output gives:
516 T S U V
517 C D M c m s m s m s m s
518 n p a R g m m e . m m e . m m e . m m e .
519 f n k u 2 i a a d i a a d i a a d i a a d
520 g d e n d n x n . n x n . n x n . n x n .
521
522 Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
523 o GAD:
524 - generated new common blocks to account for call of
525 same gad routines with differing traceridentities
526 (needed to modify tracerIdentity indices in GAD.h)
527 - generated separate common blocks for case useCubedSphereExchange
528 (Department of Futurology)
529 - parameter lists to gmredi_?transport: added tracerIdentity
530 - added new key indices to tamc.h
531 o external_fields_load:
532 - added this routine to TAF list
533 - needed to make some common blocks global and additional storing
534 along the same lines as exf package (checkpoint_lev?_directives.h)
535 o exf:
536 updated external forcing package
537 - bug fixes carried over from ecco-branch
538 (missing OBCS_OPTIONS.h in two routines)
539 - enable easy to use "no forcing".
540 - added exf I/O for atmospheric loading
541 - added exf I/O for runoff data
542 - transfered scaling between exf <-> MITgcm to exf namelist
543 o Adding new verification experiment global_with_exf.
544 This verification experiment is almost identical to the
545 global_ocean.90x40x15 experiment, except that it uses
546 the exf (and cal) package instead of the
547 external_fields_load routine (cf README file).
548
549 checkpoint46m_post
550 o modified testscript to return -- when there are no lines of "%MON" output
551 o added new flag "quasiHydrostatic" for QH mode
552 and new routine quasihydrostaticterms()
553 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
554 New routine: mom_u_coriolis_nh()
555 o fixed sign of non-hydrostatic metric terms in u and v equations.
556 Depend on correct sign of gravitySign.
557 o added work.pc* to .cvsignore in aim directories using ifc
558 o introduced flag for controllin non-hydrostatic metric terms
559 o removed gravitySign from PARM04
560 o switched to g77/ifc from pgf77 in aim experiments
561
562 checkpoint46l_post
563 o made convective adjustment work with pressure coordinates:
564 - changed the direction of k-loop in convective_adjustment.F for the
565 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
566 - adjusted the reference pressure k-index in convective_adjustment.F
567 - adjusted the convection condition in convect.F (in analogy to
568 calc_ivdc.F)
569 - convective_adjustment no longer computes anything on the halos
570 - removed the warnings about negative salinity from find_rho.F and
571 find_alpha.F; instead the new routine look_for_neg_salinity, called
572 at the beginning of find_rho, find_alpha, and find_beta, does a
573 check of the entire slice, if CPP-option
574 CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
575 checkpoint46l_pre
576
577 checkpoint46k_post
578 o fixed the verification/global_ocean.90x40x15 experiment:
579 - new bathymetry (the world according to A., JMC, and M.)
580 - new initial fields and forcing fields (*.bin files)
581 - new POLY3.COEFFS (for the next release one should switch to a full
582 equation of state: JMD95P or MDJWF)
583 - fixed several errors and redundancies in the data file
584 - experiment uses looped cells
585 - added matlab directory with diagnostic scripts for plotting of output
586
587 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
588 - read AIM physics parameters from a file (data.aimphys)
589 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
590
591 checkpoint46j_post
592 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
593 o move wVel computation at the end of the time step, in S/R integr_continuity
594 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
595 o update timeave pkg for wVel diagnostic.
596 checkpoint46j_pre
597
598 checkpoint46i_post
599 o Clean up AIM package (and keep the results unchanged):
600 include CPP_OPTION and use IMPLICT NONE in all routines ;
601 declare all the variables _RL ; use _d 0 for all numerical constants.
602 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
603
604 checkpoint46h_post
605 o cleaned up the use of rhoNil and rhoConst.
606 - rhoNil should only appear in the LINEAR equation of state, everywhere
607 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
608 and the dynamical equations are all divided by rhoConst
609 o introduced new parameter rhoConstFresh, a reference density of fresh
610 water, to remove the fresh water flux's dependence on rhoNil. The default
611 value is 999.8 kg/m^3
612 o cleanup up external_forcing.F and external_forcing_surf.F
613 - can now be used by both OCEANIC and OCEANICP
614 checkpoint46h_pre
615
616 Added code to convert surface volume flux (fresh water) into
617 a mass flux when using P coordinates in the ocean (OCEANICP).
618 Note: It assumes you have set rho0=rhoConst=density of fresh water.
619
620 checkpoint46g_post
621 o Include a new diagnostic variable phiHydLow for the ocean model
622 - in z-coordinates, it is the bottom pressure anomaly
623 - in p-coordinates, it is the sea surface elevation
624 - in both cases, these variable have global drift, reflecting the mass
625 drift in z-coordinates and the volume drift in p-coordinates
626 - included time averaging for phiHydLow, be aware of the drift!
627 o depth-dependent computation of Bo_surf for pressure coordinates
628 in the ocean (buoyancyRelation='OCEANICP')
629 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
630 Theta, Salinity, and Pressure in the parameter list. This routine is
631 presently contained in find_rho.F. This routine does not give the
632 correct density for 'POLY3', which would be a z-dependent reference
633 density.
634 o cleaned up find_rho
635 - removed obsolete 'eqn' from the parameter list.
636 o added two new verification experiments: gop and goz
637 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
638 checkpoint46g_pre
639
640 checkpoint46f_post
641 o Enable tangent linear (forward mode) gradient checks:
642 - extended active file handling to g_... files
643 - added TANGENT_SIMULATION to theSimulationMode
644 - extended grdchk package accordingly
645 o added tangent linear setup in verification/carbon/code_ftl
646 o added adjoint setup in verification/front_relax/code_ad
647
648 checkpoint46e_post
649 o Added new equation of state -> MDJWF
650 - EOS of McDougall et al., 2002, JAOT, submitted
651 - caveat: the equation of state is only valid for a smaller (more
652 realistic?) range of values than JMD95P/Z and UNESCO
653 - added masks to the calculation of pressure in store_pressure
654 - added more check values for density in check_eos (ini_eos.F), some of
655 the old check values are out of the range of the MDJWF-eos, so don't
656 expect perfect matches for those
657 checkpoint46e_pre
658
659 checkpoint46d_post
660 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
661 'OCEANICP', also initialised field pressure correctly in ini_eos in the
662 case of pressure coordinates. eosType='JMD95Z' in
663 combination with buoyancyRelation='OCEANICP' now causes an error.
664 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
665 in find_alpha/beta.
666 checkpoint46d_pre
667
668 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
669 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
670
671 checkpoint46c_post
672 o Changes necessary for ocean in p-coordinates
673 - Added new buoyancy relation = 'OCEANICP'
674 - Added new parameters = gravitySign (this used to be contained inside
675 the factor dRdZ which I added when we first switched to R coordinates).
676 X GM/Redi is not compatible (yet)
677 X bottom drag and no-slip need to be debugged.
678 checkpoint46c_pre
679
680 checkpoint46b_post
681 o Added new equation of state -> JMD95Z and JMD95P
682 - EOS of Jackett and McDougall, 1995, JAOT
683 - moved all EOS parameters into EOS.h
684 - new routines ini_eos.F, store_pressure.F
685 o Added UNESCO EOS, but not recommended because it requires
686 in-situ temperature (see JMD95)
687 o Modified formatting for knudsen2.f in utils/knudsen2 and added
688 unesco.f to be used with POLY3
689 checkpoint46b_pre
690
691 checkpoint46a_post
692 o Added (atmospheric) pressure loading
693 - new field in FFIELDS.h, etc...
694 - new cpp flag ATMOSPHERIC_LOADING
695 o Changed hFacC to _hFacC in calc_phi_hyd.F
696 o Added SHORTWAVE_HEATING to some files for consistency
697 checkpoint46a_pre
698
699 checkpoint46
700 further merges from release1_p5
701 o new ctrl package
702 - adopted from ECCO environment to enable optimization
703 - added Eliassen Palm fluxes to controls
704 o added Eliassen Palm flux controls to gradient check package
705 o cost package
706 - Compatible with new ctrl package
707 - added Eliassen Palm cost hooks
708 - modif's of existing cost functions
709 o Adjoint-related bug fixes in kpp:
710 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
711 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
712 o autodiff package
713 - flow directives:
714 + new for S/R do_the_model_io
715 + enhanced for S/R checkpoint
716 + new gmredi.flow
717 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
718 disable adcommon.h/g_common.h by default.
719 - fixed problem for adjoint of global_max
720 o modified verification/carbon/
721 o New setup for adjoint of global_ocean
722 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
723 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
724 o incorporated hooks for sponge layer code (external_forcing.F)
725
726 checkpoint45d_post
727 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
728 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
729 (affects plume_on_slope "cg2d" output)
730 o add new parameter deltaTfreesurf for free-surface time stepping
731 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
732 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
733 o change phiMin in exp1 (to agree with documentation)
734 o add new flags:
735 - T,S forcing inside/outside Adams-Bashforth
736 - turn off temp,salt advection and/or forcing
737 - for each tracer, define internal flag for multiDimAdvection & A-B
738 o monitor: change definition of KE to check conservation of Energy
739
740 checkpoint45c_post
741 o Removed f90 comments ("!")
742 o Modified initialisations to enable exf package for MITgcm
743 (without invoking ECCO_PACKAGE).
744 o modifications to gradient check package (Martin Losch)
745 - enable centered differences
746 - modified format of standard output
747
748 checkpoint45b_post
749 o cleaned exchange calls in cg2d
750 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
751 o included CPP option SINGLE_LAYER_MODE in thermodynamics
752 to configure barotropic setup (Martin Losch)
753 o moved some initialisations within bi,bj loop in dynamics
754 (TAF flow dependency)
755 o in initialise_varia, moved call packages_init_variables
756 before convective_adjustment_init
757 (corresponding adjustment of TAF tape initialisation).
758 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
759
760 checkpoint45a_post
761 o compute Rho over the whole domain (extend iMin,jMin indices)
762 o specific exchange for X-slice domain (case Ny=1)
763 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
764 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
765
766 checkpoint44h_post = checkpoint45
767 o Fix to restore differentiability:
768 place at which packages_init_variables is called in
769 initialise_varia is crucial for reverse control flow.
770 o modifications in GMRedi to enable stable adjoint
771 (corresponding modif's in thermodynamics, dynamics)
772 o added missing hook for sponge layer code in external_forcing
773 o modified test cost functions
774 o storing in gad_advection (plus removal of write(0,*)!
775 o missing headers TR1.h added in convective_adjustment routines
776 o errorMessageUnit set non-equal zero in eeboot
777 (conflict on some platforms, e.g. IBM SP3)
778 o modified carbon verif.
779
780 checkpoint44h_pre
781 o vertical grid option: allow to put the Interface at the middle between
782 2 cell-centers ; replace delZ in pkg/kpp by drF.
783 o GM Advective form: Tracers are advected using the residual transport (=
784 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
785
786 checkpoint44g_post
787 o fix surface correction term in multiDimAdvection (affects plume_on_slope
788 results) ; ifdef missing in thermodynamics.F
789
790 checkpoint44f_pre,checkpoint44f_post
791 o added PTRACERS package
792 This allows an arbitrary number of passive tracers to be integrated
793 forward simultaneously with the dynamicaly model.
794 + Implemented so far:
795 - basic forward algorithm (time-stepping, advection, diffusion, convection)
796 - I/O and checkpointing
797 - GM/Redi *but* using the GM/Redi coefficient of Salt
798 + Not implemented so far:
799 - KPP
800 - OBCS
801 + No specific example supplied (yet) but global_ocean.90x40x15 has the
802 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
803 line in data.pkg.
804 + This package is disabled by default since it increases storage.
805
806
807 o testscript: added -cleanup option
808 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
809 b) enable to filter 2D fields.
810
811 checkpoint44e_pre,post
812 o re-wrote convective adjustment to use pre-calculated weights
813 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
814 Adds: model/src/convective_weights.F, convectively_mixtracer.F
815 Original calls to convect() still in place.
816
817 chkpt44d_pre,post
818 o added missing EXCLUDE_MONITOR flags
819 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
820 (incompatible typ in MIN/MAX expressions caused problems
821 on IBM SP3)
822 o in genmake added variable MAKEDEPEND
823 plus resetting for case SunOS
824 o added timer_stats.c routine for IBM SP3
825 o removed variables in dynamics
826 !!! I forgot to create tag chkpt44d_pre !!!
827 !!! But chkpt44d_pre = chkpt44c_post !!!
828
829 o real fresh water flux implemented with non-linear free-surface.
830
831 chkpt44c_pre,post
832 o few fix (mask in shap_s2, EmPmR in external_field_load,
833 USE_NATURAL_BCS in solve_for_P);
834 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
835
836 checkpoint44b_pre/_post
837 o merge of relevant stuff from the ecco-branch:
838 - genmake: removed $S64 overwrite for case SunOS
839 - pkg/exf: update and corrections for field swapping and obcs
840 - pkg/ecco: parameter lists for the_model_main, the_main_loop
841 harmonized between ECCO and MITgcm
842 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
843 updated checkpointing_lev... lists for obcs
844 - model/src: minor changes in forward_step, plot_field
845 added directive for divided adjoint in the_main_loop
846 - pkg/mdsio: added mdsio_gl_slice
847
848 o check parameters & config (chkpt44a_pre,post)
849 o OBC and NonLin_FrSurf.
850
851 checkpoint44
852 o fix bug in mom_vi_del2uv
853 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
854 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
855 o update AIM experiments (NCEP input files)
856 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
857 o added some stuff for AD
858
859 checkpoint43
860 o added two new advection tests
861 o added global 4x4 degree ocean test
862 o added test of H&S94 with free surface on cube
863 o some final mods for gradient check, adjoint,...
864
865 checkpoint42
866 Fixed AD-related problems:
867 o Store directives up-to-date with re-arranged Adams-Bashforth
868 (mainly thermodynamics.F)
869 o New store directives for multi-dim. advection schemes
870 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
871 * new common block and key passkey
872 (mainly gad_advection.F)
873 o Modified store directives for split of dynamics/thermodynamics
874 for the case ALLOW_KPP
875 o Cleaned argument list for timestep_tracer.F
876
877 checkpoint41
878 o re-formatted/added comments in prologues of key subroutines
879 to work with protex
880
881 checkpoint40
882 o moved calc_gs, calc_gt and calc_tr1 back to model/src
883 o added FLT (floats) package from Arne along with demo. experiment
884 o re-arranged Adams-Bashforth scheme for tracers to allow easier
885 implementation of forward-in-time forcing terms
886 o more mods for non-linear free-surface including new variable
887 o modified multi-dim method to work on cube
888 o bug fix in KPP (from DM)
889
890 checkpoint40pre9
891 o added DST advection schemes
892 o fix MPI bug on SGI's
893 o modifications for non-linear free-surface
894 o fixed conditionals for fixed flow/passive tracer only mode
895 o added tension/strain form of stress tensor
896 o changes to commenting of arguments for TAF/TAMC
897 o added/updated many matlab scripts
898 o added multi-dimensional advection method for tracers
899
900 checkpoint40pre8
901 o new package rw/
902 Added method for dumping intermediate local arrays:
903 mdsio_writetile - same as mdsio_writefield except works from inside
904 bi,bj loop
905 mdsio_writelocal - same as mdsio_writetile except works for local
906 arrays
907 write_local_r? - higher-level wrapper for mdsio_writelocal
908 Controlled by diagFreq. Defaults to zero (ie. no dumps)
909 Example given at end of mom_vecinv.F that dumps some local arrays.
910 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
911 control flux-form versus vector invariant code.
912 Switch is runtime flag vectorInvariantMomentum (defaults to false)
913 or genmake -DISABLE ...
914 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
915 (additional storing is now needed for case vecinv;
916 currently nothing implemented to switch this storing off
917 in case fluxform is used since no CPP flag available).
918
919 checkpoint40pre7
920 o bug fix in dynamics.F
921 calc_viscosity called before k=1,Nr loop.
922 o added some #ifdef's ALLOW_PASSIVE_TRACER
923 o cleaned initialisations in ctrl_map_ini
924 related to TAF
925
926 checkpoint40pre6
927 o split dynamics into thermodynamics & dynamics
928 o corresponding split of calc_diffusivity into
929 calc_diffusivity, calc_viscosity
930 (kpp_calc_diff, kpp_calc_visc).
931 o Added diffkr, kapgm to control variables
932 o bug fix in gmredi_slope_limit for ldd97
933
934 checkpoint40pre5
935 o proper initialization of Adams-Bashforth time stepping
936 + uses forward step for very first step of model (iter=0)
937 o re-generated *all* output since almost all output is modified by this
938 change (sorry but we've been putting this one off for about 2 years)
939 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
940 *not* regenerated since they are already out of date and I don't
941 want to create the impression that they are suddenly working.
942 o removed KAP stuff for DEC's
943 o modified/added many .cvsignore files in */code and */input
944 o added new expt "solid-body.cs-32x32x1"
945 + this uses an alternative form of ini_curvilinear_grid.F which
946 is not necessarily any better than the current one...
947
948 checkpoint40pre4
949 o added re-initialisations of utrans,vtrans,rtrans in
950 calc_common_factors which are crucial for TAF.
951 o extended iMin,jMin range for calc_common_factors,
952 calc_diffusivity
953 o added option ALLOW_PASSIVE_TRACER
954 o a few minor updates and fixes
955
956 checkpoint40pre3
957 o created calc_gtr1.F for gad package
958 o split the_main_loop and re-introduced forward_step
959 o some recomputations of nIter0 for TAMC
960
961 checkpoint40pre2
962 o Updated to latest branch of AJA, JMC
963 o Added gradient check package
964 o Added routines for passive tracer handling
965 o Added carbon sequestration sensitivity experiment
966
967 checkpoint39
968 o Modifications and fixes to support TAMC
969 (mainly missing or wrong directives)
970 o Corrected common blocks when fooling TAMC to produce adjoint I/O
971 in addummy_in_stepping
972 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
973 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
974 o Included following packages:
975 cal: calendar
976 exf: external forcing
977 ecco: essential routines to control use of cal, exf
978 (NB: this is not the full ECCO environment)
979 o disabled some packages by default in genmake
980
981 checkpoint38
982 o see notes_c37_adj.txt
983 o corrected wrong layer index in external_forcing_t
984 o replaced the_main_loop/forward_step by the_main_loop
985 o removed forceoutput from write_state
986 (replaced criteria for initial/final state)
987 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
988
989 checkpoint37
990 o mdsio.F routine split and packaged in pkg/mdsio
991 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
992 used unless genmake -disable=mdsio)
993 o allow a more precise surface-geopotential gradient for the atmosphere
994 taking into account the change in space of Alpha (=1/rho) at the surface.
995 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
996 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
997 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
998 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
999 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
1000 o Time-Average diagnostics defined as a pseudo package "timeave".
1001 o pickup files : old pickup (before c35) did not work with new code (c35
1002 and after) unless activating 2 commented lines in initialise-varia.
1003 o Non-Hydrostatic pickup file Pb fixed.
1004 o bug with Rigid-lid version (since c35) fixed.
1005
1006 checkpoint36
1007 o implement Crank-Nickelson barotropic time-stepping
1008 o recover Time-Average diagnostics
1009 o fix Pb in checkpoint (PR#19)
1010 o AIM become a standard package ; clean unused CPP_kees
1011
1012 checkpoint35
1013 o subtantial rewrite of dynamics.f
1014 o allows staggered time-stepping
1015 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
1016 o added bottom drag (linear + quadratic)
1017
1018 checkpoint34
1019 o Modified exchange routines for correct reverse simulation.
1020 o Added verification output to comply with bug fix in impldiff.F
1021 as of c33 (exp2, natl_box).
1022 o Corrected store directives in dynamics.F
1023 o Corrected array boundaries in impldiff.F
1024 o Corrected array dimensions in gmredi.
1025 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
1026 o Added routine GLOBAL_SUM_INT to global_sum.F
1027 o Added mdsio_gl.F for ECCO purposes.
1028
1029 checkpoint33
1030 o Fixed bug in lower BC in impldiff.F
1031 o Fixed confusion about units of forcing arrays in FFIELDS.h
1032 namely Fu,Fv,Qnet,Qsw,EmPmR:
1033 - Removed verification/natl_box/code/external_fields_scale.F
1034 (did not differ from that in model/src)
1035 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
1036 (see FFIELDS.h for description)
1037 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
1038 kpp_calc.F and kpp_transport_t.F
1039 - Removed model/src/external_fields_scale.F and calls to it
1040 - verification/natl_box uses flux data with "atmospheric" sign so
1041 a special version of external_fields_load.F is used to
1042 change the data as it's read in. This way, the arrays
1043 have the right units and signs at all times tha a user could
1044 possibly use them.
1045 o Corrected genmake to delete a temporary file during configuration
1046
1047 checkpoint32
1048 o Scaling of forcing fields moved from external_forcing.F to
1049 external_fields_scale.F, called directly after loading fields.
1050 o Surface relaxation terms added to surface tendency fields in
1051 extra subroutine.
1052 o impldiff.F changed to avoid storing by TAMC of huge intermediate
1053 fields.
1054 o Changes in GMRedi to comply with packaging structure.
1055 o Modifications and bug fixes in KPP package.
1056 o Verification experiment for KPP added (verification/nat_box/)
1057
1058 checkpoint31
1059 o Packages interface brought in line with defined standard
1060 -> new routines packages_...F
1061 -> changes in initialise_fixed.F, initialise_varia.F
1062 -> enables initialisation interface for ECCO package
1063 o Rescaling of external forcing fields immediately after read
1064 (removed from external_forcing.F)
1065 -> new: surface_fields_scale.F
1066 -> affects ini_foorcing.F, external_fields_load.F
1067 o Computation of surface tendencies before tendency updates.
1068 -> new: external_forcing_surf.F
1069 o Change of variable names useGMRedi, useKPP, useECCO
1070 o Further changes in dynamics.F, impldiff.F for TAMC
1071 o Tested for experiments 0, 2, 4.
1072 - not yet tested for GMRedi.
1073 - not yet tested for KPP.
1074
1075 checkpoint30
1076 o Updates for OBCs
1077 o New experiment for test OBCs (internal_wave)
1078 o New output.txt in verification/exp4/results/
1079 o Updates for KPP: calculation of viscosity corrected, new variables
1080 kpp_dumpFreq and kpp_taveFreq
1081 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
1082 and entry for T90 in genmake
1083
1084 checkpoint29
1085 o packaged KPP and GM/Redi
1086
1087 checkpoint28
1088 o Corrected initialization of hFacMin for difference vertical coordinates
1089 o Modified calculation of partial cell thickness to more robust algorithm
1090 o config_summary.F: replaced write_1D_... by write_0D_...
1091 read_write.F: added subroutines write_0D_...
1092 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
1093 included some initialisations required for TAMC.
1094 o routine calc_isoslopes: modified sqrt computation to make it
1095 differentiable for zero argument.
1096 o routines dynamics, impldiff:
1097 included store directives and tape key computations required for TAMC.
1098 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
1099
1100 checkpoint27
1101 o fixed calc_isoslopes() to so that cancellation of terms in tensor
1102 formulation works properly with variable resolution.
1103 o restructured the calling tree between the_model_main() and dynamics()
1104 o split initialise() into initialise_fixed() and initialise_varia()
1105 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
1106 in new routine ini_psurf()
1107
1108 checkpoint26
1109 o moved some #ifdef in optional routines to encompass everything
1110 except the argument declarations. This was using up some memory.
1111 o fixed macros like _ADT to work with both versions of Linux cpp
1112 o cleaned up some unused and uninitialized variables
1113 (helps when debugging with strict compile options)
1114 o split up CPP_EEOPTIONS.h into options and macros
1115 (macros are now in eesupp/inc/CPP_EEMACROS.h)
1116 o patch for 2 processor JAM mode
1117
1118 checkpoint25
1119 o updates for OBCs and NH
1120 o dramatically reduced memory usage
1121 o added "JAM" routines for use on Artic network
1122 o parameterization of convection by implicit vertical diffusion
1123 o added a diagnostic of convective index
1124 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
1125 (this is was partly for OBCs and NH but also in anticipation of
1126 an explicit free-surface option)
1127 o initial state input files for U and V
1128
1129 checkpoint24
1130 o Removed some spurious "REAL"s
1131 o Updated KPP to latest version from JPL
1132 o Added a COS(latitude) in horizontal viscosity
1133
1134 checkpoint23
1135 o Added del^4 diffusion for salt and temperature
1136 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
1137
1138 checkpoint22
1139 o Made many small changes: implicit none, format(i5), etc...
1140 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
1141
1142 checkpoint21
1143 o Introduced new I/O package that supports direct-access records (mdsio.F)
1144 o Split-up mid-level I/O routines
1145 o Updated input data for experiments 0,1,2,4 and 5
1146 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
1147
1148 checkpoint20
1149 o Tidied up open-boundaries some more
1150 o Added non-hydrostatic code
1151 o Fixed some input data
1152 o Modified MPI start-up to work in "coupled" context.
1153
1154 checkpoint19
1155 o Tidied up directory structure for verification experiments.
1156 o Added new code for open boundaries.
1157 o Corrected advective terms near boundaries.
1158 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
1159 o Implemented free-slip/no-slip BCs and del^4 dissipation.
1160 o Split default parameters out of ini_parms.F into set_defaults.F.
1161
1162 checkpoint18
1163 o Further changes for optional code generation with
1164 CPP - ugh!
1165
1166 checkpoint17
1167 o Beginning to incorporating modularity
1168 for supporting atmos. and ocean configs.
1169 o Small changes for TAMC complinace
1170 o New ultra simple test case. Barotropic box
1171 configuration "exp0".
1172
1173 checkpoint16
1174 o Minor changes to exchange routines to support
1175 accumulation in reverse mode. Adjoint of an
1176 assignment is an addition.
1177 o Changes to support compilation by TAMC (LR(1)
1178 syntax) and by g77 under Linux ( 72 character
1179 limit ).
1180
1181 checkpoint15
1182 Rewrote exchange routines to allow
1183 o General tile <-> tile connectivity.
1184 o TAMC reverse mode flag ( is this really needed? )
1185 o Variable width overlap and exchange region widths.
1186 o Hooks for sharing data via DMA, Arctic, Memory Channel,
1187 shmput/shmget, VIA, SYSV shmem and every other cool
1188 communication method.
1189
1190 checkpoint14
1191 Consistent isomorphism chages made. These allow dynamical core
1192 to support both pressure and meters as a vertical coordinate.
1193
1194 checkpoint13
1195 Release which corrects global_max problem and a couple
1196 of KGM time-averaging diagnostic errors. Also contains
1197 a double-gyre experiment setup as well as the baseline
1198 4 degree global template. The double gyre template is
1199 organised to allow it to be applied automatically to
1200 the baseline configuration.
1201
1202 branch-point-rdot
1203 A few tidy-ups have been made bt the real point of this
1204 check-point (excuse the pun) is to allow a branch to be
1205 made for the purposes of adding the rDot alterations.
1206 I don't want to commit the rDot to the main-trunk until
1207 we've actually tested it...
1208
1209 checkpoint12
1210 Tidy up and added generic genmake script (formerly
1211 configure script).
1212 Released to testers.
1213
1214 checkpoint11
1215 Re-arranged initialise() and introduced ini_vertical_grid()
1216 and ini_masks_etc().
1217
1218 checkpoint10
1219 Introduced the configure script.
1220 Separated out the diags package.
1221 Added template for writing time-averages of tile/intermediate quantities.
1222 Updated SIZE.h in exp2 and made the data big-endian.
1223
1224 checkpoint9
1225 MPI fix. Filename changes (meta/data). salbin*y stuff.
1226 General tidy-up.
1227 SST.bin SSS.bin added to verification/exp2
1228
1229 checkpoint8
1230 Inludes time-dependant forcing and time-averaging.
1231 Works at 4x4 and 2.8125x2.8125 global
1232
1233 checkpoint7-4degree-ref
1234 Branch from checkpoint7. Released for application to
1235 global modeling and general modeling - process studies, regional
1236 model etc..
1237 Configured for verification/exp2 - 4 degree global, two process.
1238
1239 checkpoint7
1240 Created by cnh
1241 Simple 4 degree global simulation
1242 configuration.
1243 Includes climatological wind,
1244 hydrography, bathymetry etc
1245 Does not include Heat Flux and E-P
1246
1247 checkpoint6
1248 Created by cnh
1249 merged checkpoint5 with CD and
1250 spherical polar code.
1251 Still some problems with GM Redi
1252 abd full topography.
1253
1254 checkpoint5
1255 Created by AJA
1256 contains updates to GM Redi
1257 and reordered timestepping loop
1258 for Implicit Diffusion.
1259
1260 checkpoint4
1261 Created by cnh
1262 Contains memory saving macros ( _rdxc etc..) for when
1263 grid variations are limited.
1264 Contains polynomial coeffs for EOS and knudsen program
1265 for generation.
1266
1267 checkpoint3
1268 Created by cnh
1269 Added extra flags for runtime options
1270 Added this file
1271 Added implicit free-surface
1272 Added pre-conditioner
1273 Put compare01 into repository ( compare01/... )
1274 Put data and eedata into repository ( verification/exp1 )
1275
1276 checkpoint2
1277 Created by AJA
1278 Added GM/Redi
1279
1280 checkpoint1
1281 Created by AJA
1282 Restructured kloop in dynamics.F
1283 Added non-linear EOS
1284
1285 baseline
1286 Original checked in code

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