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Revision 1.188 - (show annotations) (download)
Fri Oct 17 00:44:32 2003 UTC (18 years, 9 months ago) by jmc
Branch: MAIN
CVS Tags: checkpoint51l_pre
Branch point for: tg2-branch
Changes since 1.187: +6 -1 lines
o add salt flux to forcing fields (used when salty sea-ice forms or melts)
o enable to apply restoring on S & T only in a latitude band.
o update output (external_forcing_surf modif. change truncation errors)
   global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.187 2003/10/16 17:14:34 jmc Exp $
2
3 Notes on tags used in MITgcmUV
4 ==============================
5 not yet tagged:
6 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
7 o enable to apply restoring on S & T only in a latitude band.
8 o update output (external_forcing_surf modif. change truncation errors)
9 global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
10
11 checkpoint51k_post
12 o change default to: useNHMTerms=.FALSE.
13 - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
14 adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
15 - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
16 exp1, ideal_2D_oce
17 - change data file of oceanic exp (leave the results unchanged for now)
18 exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
19 o set gravitySign automatically according to the vertical coordinate used
20 (and change sign: back to "logical" value: +1 when R increases downward)
21 o added an include barrier to the default CPP_OPTIONS.h and
22 removed the #include "PACKAGES_CONFIG.h" from it
23 o fix a bug in mom_fluxform (from chk51j_post)
24
25 checkpoint51j_post
26 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
27 o adjusted some flow directives (dynamics, thermodynamics)
28 o added cubed-sphere case to test cost function
29 o heckpoint_lev?_directives.h now include
30 pkg-specific directives, whenever those are enabled.
31 o Moving pkg-specific flow directives to corresponding pkg
32 Moving pkg-specific differentiation list to corresponding pkg
33 Moving pkg-specific checkpoint-lev storing to corresponding pkg
34 ---> conventions are
35 - pkg_ad.flow
36 - pkg_ad_diff.list
37 - pkg_ad_check_lev?_dir.h
38
39 checkpoint51i_post
40 o merge of the branch-genmake2
41 - knowingly breaks the older genmake
42 - automatic generation of all ALLOW_${PKG_NAME} defines
43 - new testreport supersedes older testscript
44 o large number of package inclusion and header cleanups
45 checkpoint51i_pre
46
47 o new output for adjoin of global ocean vector invariant
48 o fix for checkpoint of thermodynamic seaice and bulk_force
49 o Steph gchem various cleanups
50
51 checkpoint 51h_pre
52 o fixed some single quotes
53 o modify gchem pkg to be more versatile
54 o modifications to clean up dic pkg
55 o add pkg/cfc
56
57 checkpoint51g_post
58 o provide links for ARPACK and ADM*TLM
59 o start removing verification/vero/
60 o update AD-related stuff
61 (in particular some IF-statements in model/src/ routines)
62 o adding to verification/global_ocean.90x40x15/ adjoint of
63 vector invariant setup
64
65 checkpoint51f_post
66 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
67 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
68 of tracer Green's fucntions for ocean inversion project.
69
70 checkpoint51f_pre
71 o Added on-the-fly spatial interpolation capability
72 "USE_EXF_INTERPOLATION" to pkg/exf.
73 - This is a temporary Cartesian-grid hack until
74 the super-duper ESMF coupler becomes available.
75 - See verification/global_with_exf/README for usage example.
76 - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
77 flags and modified pkg/seaice accordingly.
78 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
79 and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
80 non-local transport term.
81
82 checkpoint51e_post
83 o pkg/mom_vecinv:
84 - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
85 - add time-ave diagnostic of vorticity advection.
86 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
87 o atmospheric geopotential: - include water vapor effect;
88 - use p^kappa in p* scaling.
89 o land pkg: read initial state from files.
90 o AIM : add stratospheric drag in the upper level
91
92 checkpoint51d_post
93 o change function ILNBLNK (=> last non-blank char.) to return zero
94 (instead of the string length) when the string. char is empty
95 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
96 o modif's to restore TAMC compatibility
97 - avoid "_d" constructs in PARAMETER declarations
98 - avoid interrupting lines by comment lines
99 o Use cluster local disks for purely local I/O
100 vs. globally visible disks needed for ctrl stuff
101 (merged from ecco-branch)
102 - new active_file_loc... and mdsio_..._loc routines
103 - affected packages: autodiff, ctrl, grdchk, mdsio
104
105 checkpoint51c_post
106 o introducing integer flag debugLevel
107 - debLevZero: suppress all output
108 - debLevA: standard
109 - debLevB: equivalent to current debugMode=.TRUE.
110 o introducing pathname variable mdsioLocalDir for mdsio
111 that can be specified at runtime
112 (relevant for cluster I/O to local disk)
113 `
114 >>>checkpoint51b_post
115 adjoint of ptracers
116 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
117 o extended state in checkpoint_lev?, etc.
118 o alternative ctrl/cost with tr1 or ptracer
119 o new comlev1_bibj_ptracers
120 o new ptracers.flow
121 o made ptracers_forcing same as external_forcing_s
122 o added verification for adjoint with ptracers
123 - adm. grdchk fail so far
124 - tlm. grdchk OK
125 - checked tapelev/comlev recomputations: OK
126 <<<checkpoint51b_pre
127
128 checkpoint51a_post
129 o added code for biogeochemistry package
130 - new pkgs: dic, gchem
131 - new subroutine in ptracers
132 o modify code for biogeo packages
133 - in model/src and pkg/ptracers
134
135 checkpoint51
136 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
137 - autodiff, ctrl, exf, grdchk, seaice
138 kept separate packages
139 - cost, ecco, obcs
140 o updating verification/internal_wave, verification/lab_sea
141 (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
142
143 checkpoint50i_post
144 o Preparing next differentiable checkpoint and sync
145 of MAIN vs. ecco-branch
146 - 1st step: this one is differentiable
147 - 2nd step: next(! not this) checkpoint will have updated packages
148 from ecco-branch)
149
150 checkpoint50h_post
151 o new package "land": provide surface BC for AIM.
152 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
153 o AIM: use true log-P extrapolation for near surface temp (= as in
154 F.Molteni paper) ; update aim.5l_cs output.
155 o New variable in PARM03 for more flexible pickups
156 o somewhat cleaned package initialisation sequence for
157 ctrl/ cost/ ecco/ in packages_... routines
158
159 checkpoint50g_post
160 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
161 - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
162 - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
163 made the default because of faster convergence than ADI
164
165 checkpoint50f_post
166 o exf totally restructured
167 - replaced all exf_set_ routines by one generic exf_set_gen.F
168 and made sure it's still differentiable
169 - split exf_getffields.F into new exf_bulkformulae.F
170 - exf_inscal_/exf_outscal_ suffixes consistent with field names
171 - updated adjoint/makefile and relevant verif. accordingly
172
173 checkpoint50f_pre
174 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
175 + change Evap over land. (update aim.5l_cs output)
176 o added missing .cvsignores and made uniform across expts
177 o changed configuration of tidal_basin_2d expt
178 o added pkg/debug functions for tracing code in fatal crashes
179 o tidied pkg/monitor to use MONITOR_OPTIONS.h
180 o new fn in pkg/monitor to stop model if solution grows too big
181 o removed lots of single quotes from comments
182
183 checkpoint50e_post
184 o make KPP work with PTRACERS
185 - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
186 nearly a copy of kpp_transport_s
187 - there is no analogue to SurfaceTendencyS, so I have to use
188 gPtr(of the surface layer) instead
189 o add a new platform SunFire+mpi (SunFire 15000) to genmake
190 checkpoint50e_pre
191
192 checkpoint50d_post
193 o change kpp output from multiple-record state files to single-record state
194 files analogous to write_state.F
195 o reduce the output frequency of cg3d-related stuff to the monitor frequency,
196 analogous to the cg2d-related output.
197 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
198 so that writing to internal file fn (with length 512) fails.
199 checkpoint50d_pre
200
201 checkpoint50c_post
202 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
203 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
204 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
205 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
206 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
207
208 checkpoint50c_pre
209 Merging from release1_p13:
210 o bug fix for pkg/seaice dynamic solver
211 o Added SEAICE_initialHEFF to pkg/seaice
212
213 checkpoint50b_post
214 o store u*,v* in gU,V instead of in guNm1,gvNm1
215 o in order to put the momForcing out of the Adams-Bashforth:
216 move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
217 to timestep.F
218 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
219 o re-generate output for highly sensitive test-exp:
220 global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
221
222 checkpoint50b_pre
223 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
224 o corrected CPP option mismatch in exf_Bulk... functions for case
225 #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
226
227 checkpoint50a_post
228 o Bug fix for merging between c50 and KPP.
229 ikey was passed from thermodynamics to kpp_calc via
230 common block rather than being recomputed in kpp_calc,
231 in contradiction with new key itdkey.
232 New key ikppkey created, and tamc.h headers updated.
233
234 checkpoint50
235 - 2nd step of merge with ecco-branch:
236 merge changes in ecco-branch back into main trunk
237 - bug fix in find_alpha
238 - more storing in gmredi_calc_tensor.F, kpp_routines.F
239 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
240 - merged some sliced AD support routines
241
242 checkpoint49
243 merged from ecco-branch:
244 o exf:
245 - Enable initialisation of forcing fields to constant
246 (runtime) values.
247 - in exf_getffields.F
248 Reduce i-/j-loop to interior domain, discarding overlaps.
249 That also fixes wrong TAF-key computations for key_1, key_2
250 with bulf formulae.
251 - exf_init.F modify #ifdef for exf_init_evap
252 - exf_getffieldrec.F, ctrl_getrec.F
253 The following INT-usages are not safe:
254 fldsecs = int(fldsecs/fldperiod)*fldperiod
255 fldcount = int(fldsecs/fldperiod) + 1
256 and were modified.
257 o autodiff: checkpoint_lev...
258 - updated storing for bulk formulae (some arrays were missing)
259 - added state for seaice package
260 - synchronized with main branch
261 o DIVA:
262 Modif.s in
263 - the_main_loop.F
264 - the_model_main.F
265 and added cost_final_restore.F cost_final_store.F
266 o With these changes, it is possible to fully separate
267 the first forward run to compute the cost function (mdthe_main_loop)
268 and adjoint runs over individual DIVA intervals (adthe_main_loop)
269 into separate model executions.
270 This enables better tuning of DIVA to given queue sizes.
271 o Loss of cost function value in consecutive DIVA runs is
272 fixed by storing to 'costfinal' file.
273 o Appropriate call of ctrl_unpack/_pack,grdchk_main at
274 beginning/end of adjoint integration is accounted for.
275 The current changes apply to TAF-1.4.26.
276 TAF has one remaining bug, requiring one manual change
277 (see MITgcm manual).
278 o cal: synchronized between MAIN and ecco-branch
279
280 checkpoint48i_post
281 o Changes to restore differentiability of code w.r.t. previous tag
282 (mostly adding new routines to make list and replacing
283 pressure by totPhiHyd).
284 o Updated and merged grdchk package
285 - has both ADM and TLM checks
286 - works for single- and multi-proc.
287 - output cleaned
288 - worked successfully for parallel DIVA
289 o genmake:
290 - Adding -platform=SP4
291 - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
292 o Modif. for DIVA:
293 ctrl_unpack should not be called in intermediate DIVA interval.
294 (similar thing would apply for active files such as
295 tbar, sbar, psbar, which should not be reinitialised;
296 only relevant for ecco-branch)
297
298 checkpoint48h_post
299 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
300 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
301 o Added SEAICE_initialHEFF to pkg/seaice
302 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
303
304 checkpoint48g_post
305 --- EOS:
306 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
307 store total Potential in totPhyHyd for diagnostics & EOS.
308 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
309 --- Pressure/geopotential gradient:
310 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
311 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
312 ( changes results of global_ocean_pressure )
313 o NLFS + z-coord.: add eta*Rho' contribution.
314 o accurate phiHyd when using interface-W at the middle between 2 centers
315 ( changes results of ideal_2D_oce )
316 o includes r* 2nd term in potential gradient.
317
318 checkpoint48f_post
319 Merging from release1_p12:
320 o Modifications for using pkg/exf with pkg/seaice
321 - improved description of the various forcing configurations
322 - added basic radiation bulk formulae to pkg/exf
323 - units/sign fix for evap computation in exf_getffields.F
324 - updated verification/global_with_exf/results/output.txt
325 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
326 (SBO) core products, including oceanic mass, center-of-mass,
327 angular, and bottom pressure (see pkg/sbo/README.sbo).
328 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
329 to avoid negative values in shallow regions.
330 - updated verification/natl_box/results/output.txt
331 - updated verification/lab_sea/results/output.txt
332 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
333 o Added useSingleCpuIO option (see PARAMS.h).
334 o Updated useSingleCpuIO option in mdsio_writefield.F to
335 work with multi-field files, e.g., for single-file pickup.
336 o pkg/seaice:
337 - bug fix in growth.F: QNET for no shortwave case
338 - added HeffFile for specifying initial sea-ice thickness
339 - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
340 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
341 kpp_transport_t.F, forward_step.F, and the_main_loop.F
342 o pkg/seaice:
343 - adjoint-friendly modifications
344 - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
345
346 checkpoint48e_post
347 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
348 o dynamics: change definition of computational domain & adapt mom_fluxform
349 accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
350 o following exp works with Olx=Oly=2 (and pass through checkbounds option):
351 adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
352 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
353 global_ocean.90x40x15 global_with_exf global_ocean_pressure
354 inverted_barometer solid-body.cs-32x32x1
355 (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
356
357 checkpoint48d_post
358 o in preparation for r*:
359 a) use pre-computed gradient of hydrostatic potential:
360 changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
361 b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
362 => affects results of glob_oce_pressure (different truncation error)
363 update output.txt of ideal_2D_oce & global_ocean_pressure
364
365 checkpoint48d_pre
366 o in preparation for r*:
367 new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
368 pass the 2 comp. of the grad. as arguments to momentum S/R.
369 but for the moment, only used if it does not change the results.
370 o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
371
372 checkpoint48c_post
373 Modifications in treatment of initial flux forcing controls
374 to avoid extra storing of flux fields.
375
376 checkpoint48c_pre
377 o Added tidal_basin_2d experiment (currently 1D!)
378 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
379
380 checkpoint48b_post
381 o r* coordinate added in #ifdef NONLIN_FRSURF block.
382 (modification to pressure gradient not yet implemented)
383 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
384 (for U & V) that are used for vertical advection of momentum.
385
386 checkpoint48a_post
387 o In preparation for r*, use temp. array to compute vertical transport
388 in flux-form momentum pkg. => change results of few test-exp.
389 Update output of: exp4, exp5, front_relax, global_ocean_pressure,
390 lab_sea, natl_box & plume_on_slope
391
392 checkpoint48
393 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
394
395 checkpoint47j_post
396 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
397 o moved adexch from forward_step to addummy_in_stepping
398 o added exch in ctrl_map_...
399 o aveFreq.=0. at end of cost_final to avoid overwrite in
400 reverse checkpointing loop
401 o Yet more changes in gmredi:
402 * adgmredi_calc_tensor
403 avoiding all recomputation of gmredi_slope_limit
404 * adgmredi_x/y/rtransport
405 added flag for excessive storing to avoid recomp. of
406 u/v/rtans, dTdx/y/z
407 -> this is not really necessary and very memory-consuming
408 * adgmredi_slope_psi:
409 consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
410 * gmredi_slope_limit
411 re-activated full calculation of taperfct for case 'ac02'
412 o updating verification/ adjoints of carbon, global_ocean.90x40x15
413
414 checkpoint47i_post
415 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
416 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
417 default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
418 o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
419 o gmredi: fix few bugs.
420
421 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
422 This will be a good checkpoint to plug into the ecco-branch.
423 o few modif.'s to get latest version adjointed
424 (mainly kick out code in ini_linear_phisurf)
425 o modif's to run adjoint with exactConserv
426 o case GM_BOLUS_ADVEC should be cleaned
427 S/R gmredi_slope_psi should be cleaned
428 o verification/carbon now has exactConserv=.TRUE.
429
430 checkpoint47g_post
431 o time-average AIM output: becomes independent from statvars time-average
432 (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
433 o After TAF bug fix:
434 Tested adjoint of gmredi package.
435 Tests were done with checkpoint47 rather than with latest
436 checkpoint47f_post since the latter is broken for the adjoint
437 verification/carbon/ contains both ADM and TLM gradient checks.
438 Here they are, before they get changed/lost/stolen.
439 Mostly modif.'s to fix numerical sensitivities.
440 Gradient checks OK for
441 - GM_taper_scheme:
442 * clipping
443 * ac02
444 * linear
445 * glw91
446 * dm95
447 * ldd97
448 - GMREDI_OPTIONS:
449 * GM_VISBECK_VARIABLE_K
450 * GM_NON_UNITY_DIAGONAL
451 * GM_EXTRA_DIAGONAL
452 * GM_BOLUS_ADVEC
453 in conjunction with data.gmredi parameters to be checked in
454 in a few minutes under verification/carbon/code/
455
456 checkpoint47f_post
457 Merging from release1_p10:
458 o modifications for using pkg/exf with pkg/seaice
459 - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
460 and SEAICE_EXTERNAL_FLUXES
461 - pkg/exf CPP options EXF_READ_EVAP and
462 EXF_NO_BULK_COMPUTATIONS
463 - usage examples are Experiments 8 and 9 in
464 verification/lab_sea/README
465 - verification/lab_sea default experiment now uses
466 pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
467
468 checkpoint47e_post
469 o created a tag prior to creating a branch
470
471 checkpoint47d_post
472 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
473 at the bottom boundary had an erroneous half slip boundary condition
474 o added bottom drag and no slip boundary condition capabilities to
475 oceanic pressure coordinates code
476 o added new verification experiment global_ocean_pressure, this experiment is
477 also described in the tutorial section of the manual
478 checkpoint47d_pre
479
480 checkpoint47c_post
481 o Added a verification experiment for a global cubed-sphere ocean run
482 - verification/global_ocean.cubed32x32x30
483 - uses pkg/therm_seaice and pkg/bulk_forcing
484
485 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
486 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
487 when using P-coordinate; only implemented for atmospheric config.
488 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
489 NOTES: requires option NONLIN_FRSURF to be "#define".
490 o update advect_xz/results/output.txt (left from checkpoint44g_post)
491
492 checkpoint47b_post
493 Merging from release1_p9:
494 o pkg/seaice
495 - removed GOTO's and added taf directives
496 - double precision constants to reduce the g77 (Linux)
497 to F77 (SGI) differences reported in release1_p8
498 o tools/genmake
499 - added SGI options
500 o verification/testscript
501 - updated to that of checkpoint47a_post
502 o verification/global_ocean.90x40x15/input/eedata
503 - modified for SGI f77 compatibility
504 o verification/lab_sea
505 - added description of sea-ice model
506 - added missing matlab routines
507 - added test of thermodynamics parallelization
508
509 checkpoint47a_post
510 o new pkg: aim_v23
511 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
512 for now, keep the same surface forcing as before.
513 - Part-Cell implemented into AIM; check that Heat & Water are conserved
514 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
515 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
516 o add diagnostic of surface correction term in monitor output
517
518 o bulk_force and therm_seaice
519 - Two packages: bulk_force (Bulk forcing)
520 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
521 - Earlier integration from Stephaine Dutkiewicz
522 and Patrick Heimbach.
523 - Two ifdef statements for compile time,
524 ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
525
526 checkpoint47
527 differentiable version of checkpoint46n_post
528 o bug fix in quasihydrostaticterms
529 o * "clean" adjoint code (in terms of extensive recomputations)
530 can now be obtained for all GMREDI options (i.e. for
531 - GM_VISBECK_VARIABLE_K
532 - GM_NON_UNITY_DIAGONAL
533 - GM_EXTRA_DIAGONAL
534 - GM_BOLUS_ADVEC )
535 * However, wrong gradient check problem remains unsolved.
536 * New CPP options have been introduced for different
537 tapering schemes
538 o external_fields_load now part of differentiation list
539 o pressure needs multiple storing;
540 would be nice to have store_pressure at beginning or
541 end of forward_step, e.g. by having phiHyd global (5-dim.)
542 (NB: pressure is needed for certain cases in find_rho,
543 which is also invoked through convective_adjustment).
544 o recomputations in find_rho for cases
545 'JMD95'/'UNESCO' or 'MDJWF' are OK.
546 o #define ATMOSPHERIC_LOADING should be differentiable
547 o ini_forcing shifted to begining of initialise_varia
548 o Incorporating QNVS line search routines into MITgcm
549 (this is separate code, and therefore not under pkg)
550 lsopt/, optim/
551 o Updated verification/carbon/
552 - #define GM_VISBECK_VARIABLE_K
553 - GM_taper_scheme = 'ldd97'
554
555 checkpoint46n_post
556 Merging from release1_p8:
557 o verification/natl_box:
558 updating new external_fields_load routine
559 o New package: pkg/seaice
560 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
561 The sea-ice code is based on Hibler (1979-1980).
562 Two sea-ice dynamic solvers, ADI and LSR, are included.
563 In addition to computing prognostic sea-ice variables and diagnosing
564 the forcing/external data fields that drive the ocean model,
565 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
566 The implied surface heat flux is then stored in variable
567 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
568 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
569 non-local transport term. Because this call precedes model
570 thermodynamics, temperature under sea-ice may not be "exactly" at
571 the freezing point by the time theta is dumped or time-averaged.
572 N.B.: fairly large differences in accuracy occur across
573 different platforms/compilers; comparison between
574 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
575 generated output gives:
576 T S U V
577 C D M c m s m s m s m s
578 n p a R g m m e . m m e . m m e . m m e .
579 f n k u 2 i a a d i a a d i a a d i a a d
580 g d e n d n x n . n x n . n x n . n x n .
581
582 Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
583 o GAD:
584 - generated new common blocks to account for call of
585 same gad routines with differing traceridentities
586 (needed to modify tracerIdentity indices in GAD.h)
587 - generated separate common blocks for case useCubedSphereExchange
588 (Department of Futurology)
589 - parameter lists to gmredi_?transport: added tracerIdentity
590 - added new key indices to tamc.h
591 o external_fields_load:
592 - added this routine to TAF list
593 - needed to make some common blocks global and additional storing
594 along the same lines as exf package (checkpoint_lev?_directives.h)
595 o exf:
596 updated external forcing package
597 - bug fixes carried over from ecco-branch
598 (missing OBCS_OPTIONS.h in two routines)
599 - enable easy to use "no forcing".
600 - added exf I/O for atmospheric loading
601 - added exf I/O for runoff data
602 - transfered scaling between exf <-> MITgcm to exf namelist
603 o Adding new verification experiment global_with_exf.
604 This verification experiment is almost identical to the
605 global_ocean.90x40x15 experiment, except that it uses
606 the exf (and cal) package instead of the
607 external_fields_load routine (cf README file).
608
609 checkpoint46m_post
610 o modified testscript to return -- when there are no lines of "%MON" output
611 o added new flag "quasiHydrostatic" for QH mode
612 and new routine quasihydrostaticterms()
613 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
614 New routine: mom_u_coriolis_nh()
615 o fixed sign of non-hydrostatic metric terms in u and v equations.
616 Depend on correct sign of gravitySign.
617 o added work.pc* to .cvsignore in aim directories using ifc
618 o introduced flag for controllin non-hydrostatic metric terms
619 o removed gravitySign from PARM04
620 o switched to g77/ifc from pgf77 in aim experiments
621
622 checkpoint46l_post
623 o made convective adjustment work with pressure coordinates:
624 - changed the direction of k-loop in convective_adjustment.F for the
625 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
626 - adjusted the reference pressure k-index in convective_adjustment.F
627 - adjusted the convection condition in convect.F (in analogy to
628 calc_ivdc.F)
629 - convective_adjustment no longer computes anything on the halos
630 - removed the warnings about negative salinity from find_rho.F and
631 find_alpha.F; instead the new routine look_for_neg_salinity, called
632 at the beginning of find_rho, find_alpha, and find_beta, does a
633 check of the entire slice, if CPP-option
634 CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
635 checkpoint46l_pre
636
637 checkpoint46k_post
638 o fixed the verification/global_ocean.90x40x15 experiment:
639 - new bathymetry (the world according to A., JMC, and M.)
640 - new initial fields and forcing fields (*.bin files)
641 - new POLY3.COEFFS (for the next release one should switch to a full
642 equation of state: JMD95P or MDJWF)
643 - fixed several errors and redundancies in the data file
644 - experiment uses looped cells
645 - added matlab directory with diagnostic scripts for plotting of output
646
647 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
648 - read AIM physics parameters from a file (data.aimphys)
649 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
650
651 checkpoint46j_post
652 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
653 o move wVel computation at the end of the time step, in S/R integr_continuity
654 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
655 o update timeave pkg for wVel diagnostic.
656 checkpoint46j_pre
657
658 checkpoint46i_post
659 o Clean up AIM package (and keep the results unchanged):
660 include CPP_OPTION and use IMPLICT NONE in all routines ;
661 declare all the variables _RL ; use _d 0 for all numerical constants.
662 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
663
664 checkpoint46h_post
665 o cleaned up the use of rhoNil and rhoConst.
666 - rhoNil should only appear in the LINEAR equation of state, everywhere
667 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
668 and the dynamical equations are all divided by rhoConst
669 o introduced new parameter rhoConstFresh, a reference density of fresh
670 water, to remove the fresh water flux's dependence on rhoNil. The default
671 value is 999.8 kg/m^3
672 o cleanup up external_forcing.F and external_forcing_surf.F
673 - can now be used by both OCEANIC and OCEANICP
674 checkpoint46h_pre
675
676 Added code to convert surface volume flux (fresh water) into
677 a mass flux when using P coordinates in the ocean (OCEANICP).
678 Note: It assumes you have set rho0=rhoConst=density of fresh water.
679
680 checkpoint46g_post
681 o Include a new diagnostic variable phiHydLow for the ocean model
682 - in z-coordinates, it is the bottom pressure anomaly
683 - in p-coordinates, it is the sea surface elevation
684 - in both cases, these variable have global drift, reflecting the mass
685 drift in z-coordinates and the volume drift in p-coordinates
686 - included time averaging for phiHydLow, be aware of the drift!
687 o depth-dependent computation of Bo_surf for pressure coordinates
688 in the ocean (buoyancyRelation='OCEANICP')
689 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
690 Theta, Salinity, and Pressure in the parameter list. This routine is
691 presently contained in find_rho.F. This routine does not give the
692 correct density for 'POLY3', which would be a z-dependent reference
693 density.
694 o cleaned up find_rho
695 - removed obsolete 'eqn' from the parameter list.
696 o added two new verification experiments: gop and goz
697 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
698 checkpoint46g_pre
699
700 checkpoint46f_post
701 o Enable tangent linear (forward mode) gradient checks:
702 - extended active file handling to g_... files
703 - added TANGENT_SIMULATION to theSimulationMode
704 - extended grdchk package accordingly
705 o added tangent linear setup in verification/carbon/code_ftl
706 o added adjoint setup in verification/front_relax/code_ad
707
708 checkpoint46e_post
709 o Added new equation of state -> MDJWF
710 - EOS of McDougall et al., 2002, JAOT, submitted
711 - caveat: the equation of state is only valid for a smaller (more
712 realistic?) range of values than JMD95P/Z and UNESCO
713 - added masks to the calculation of pressure in store_pressure
714 - added more check values for density in check_eos (ini_eos.F), some of
715 the old check values are out of the range of the MDJWF-eos, so don't
716 expect perfect matches for those
717 checkpoint46e_pre
718
719 checkpoint46d_post
720 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
721 'OCEANICP', also initialised field pressure correctly in ini_eos in the
722 case of pressure coordinates. eosType='JMD95Z' in
723 combination with buoyancyRelation='OCEANICP' now causes an error.
724 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
725 in find_alpha/beta.
726 checkpoint46d_pre
727
728 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
729 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
730
731 checkpoint46c_post
732 o Changes necessary for ocean in p-coordinates
733 - Added new buoyancy relation = 'OCEANICP'
734 - Added new parameters = gravitySign (this used to be contained inside
735 the factor dRdZ which I added when we first switched to R coordinates).
736 X GM/Redi is not compatible (yet)
737 X bottom drag and no-slip need to be debugged.
738 checkpoint46c_pre
739
740 checkpoint46b_post
741 o Added new equation of state -> JMD95Z and JMD95P
742 - EOS of Jackett and McDougall, 1995, JAOT
743 - moved all EOS parameters into EOS.h
744 - new routines ini_eos.F, store_pressure.F
745 o Added UNESCO EOS, but not recommended because it requires
746 in-situ temperature (see JMD95)
747 o Modified formatting for knudsen2.f in utils/knudsen2 and added
748 unesco.f to be used with POLY3
749 checkpoint46b_pre
750
751 checkpoint46a_post
752 o Added (atmospheric) pressure loading
753 - new field in FFIELDS.h, etc...
754 - new cpp flag ATMOSPHERIC_LOADING
755 o Changed hFacC to _hFacC in calc_phi_hyd.F
756 o Added SHORTWAVE_HEATING to some files for consistency
757 checkpoint46a_pre
758
759 checkpoint46
760 further merges from release1_p5
761 o new ctrl package
762 - adopted from ECCO environment to enable optimization
763 - added Eliassen Palm fluxes to controls
764 o added Eliassen Palm flux controls to gradient check package
765 o cost package
766 - Compatible with new ctrl package
767 - added Eliassen Palm cost hooks
768 - modif's of existing cost functions
769 o Adjoint-related bug fixes in kpp:
770 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
771 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
772 o autodiff package
773 - flow directives:
774 + new for S/R do_the_model_io
775 + enhanced for S/R checkpoint
776 + new gmredi.flow
777 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
778 disable adcommon.h/g_common.h by default.
779 - fixed problem for adjoint of global_max
780 o modified verification/carbon/
781 o New setup for adjoint of global_ocean
782 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
783 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
784 o incorporated hooks for sponge layer code (external_forcing.F)
785
786 checkpoint45d_post
787 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
788 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
789 (affects plume_on_slope "cg2d" output)
790 o add new parameter deltaTfreesurf for free-surface time stepping
791 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
792 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
793 o change phiMin in exp1 (to agree with documentation)
794 o add new flags:
795 - T,S forcing inside/outside Adams-Bashforth
796 - turn off temp,salt advection and/or forcing
797 - for each tracer, define internal flag for multiDimAdvection & A-B
798 o monitor: change definition of KE to check conservation of Energy
799
800 checkpoint45c_post
801 o Removed f90 comments ("!")
802 o Modified initialisations to enable exf package for MITgcm
803 (without invoking ECCO_PACKAGE).
804 o modifications to gradient check package (Martin Losch)
805 - enable centered differences
806 - modified format of standard output
807
808 checkpoint45b_post
809 o cleaned exchange calls in cg2d
810 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
811 o included CPP option SINGLE_LAYER_MODE in thermodynamics
812 to configure barotropic setup (Martin Losch)
813 o moved some initialisations within bi,bj loop in dynamics
814 (TAF flow dependency)
815 o in initialise_varia, moved call packages_init_variables
816 before convective_adjustment_init
817 (corresponding adjustment of TAF tape initialisation).
818 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
819
820 checkpoint45a_post
821 o compute Rho over the whole domain (extend iMin,jMin indices)
822 o specific exchange for X-slice domain (case Ny=1)
823 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
824 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
825
826 checkpoint44h_post = checkpoint45
827 o Fix to restore differentiability:
828 place at which packages_init_variables is called in
829 initialise_varia is crucial for reverse control flow.
830 o modifications in GMRedi to enable stable adjoint
831 (corresponding modif's in thermodynamics, dynamics)
832 o added missing hook for sponge layer code in external_forcing
833 o modified test cost functions
834 o storing in gad_advection (plus removal of write(0,*)!
835 o missing headers TR1.h added in convective_adjustment routines
836 o errorMessageUnit set non-equal zero in eeboot
837 (conflict on some platforms, e.g. IBM SP3)
838 o modified carbon verif.
839
840 checkpoint44h_pre
841 o vertical grid option: allow to put the Interface at the middle between
842 2 cell-centers ; replace delZ in pkg/kpp by drF.
843 o GM Advective form: Tracers are advected using the residual transport (=
844 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
845
846 checkpoint44g_post
847 o fix surface correction term in multiDimAdvection (affects plume_on_slope
848 results) ; ifdef missing in thermodynamics.F
849
850 checkpoint44f_pre,checkpoint44f_post
851 o added PTRACERS package
852 This allows an arbitrary number of passive tracers to be integrated
853 forward simultaneously with the dynamicaly model.
854 + Implemented so far:
855 - basic forward algorithm (time-stepping, advection, diffusion, convection)
856 - I/O and checkpointing
857 - GM/Redi *but* using the GM/Redi coefficient of Salt
858 + Not implemented so far:
859 - KPP
860 - OBCS
861 + No specific example supplied (yet) but global_ocean.90x40x15 has the
862 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
863 line in data.pkg.
864 + This package is disabled by default since it increases storage.
865
866
867 o testscript: added -cleanup option
868 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
869 b) enable to filter 2D fields.
870
871 checkpoint44e_pre,post
872 o re-wrote convective adjustment to use pre-calculated weights
873 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
874 Adds: model/src/convective_weights.F, convectively_mixtracer.F
875 Original calls to convect() still in place.
876
877 chkpt44d_pre,post
878 o added missing EXCLUDE_MONITOR flags
879 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
880 (incompatible typ in MIN/MAX expressions caused problems
881 on IBM SP3)
882 o in genmake added variable MAKEDEPEND
883 plus resetting for case SunOS
884 o added timer_stats.c routine for IBM SP3
885 o removed variables in dynamics
886 !!! I forgot to create tag chkpt44d_pre !!!
887 !!! But chkpt44d_pre = chkpt44c_post !!!
888
889 o real fresh water flux implemented with non-linear free-surface.
890
891 chkpt44c_pre,post
892 o few fix (mask in shap_s2, EmPmR in external_field_load,
893 USE_NATURAL_BCS in solve_for_P);
894 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
895
896 checkpoint44b_pre/_post
897 o merge of relevant stuff from the ecco-branch:
898 - genmake: removed $S64 overwrite for case SunOS
899 - pkg/exf: update and corrections for field swapping and obcs
900 - pkg/ecco: parameter lists for the_model_main, the_main_loop
901 harmonized between ECCO and MITgcm
902 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
903 updated checkpointing_lev... lists for obcs
904 - model/src: minor changes in forward_step, plot_field
905 added directive for divided adjoint in the_main_loop
906 - pkg/mdsio: added mdsio_gl_slice
907
908 o check parameters & config (chkpt44a_pre,post)
909 o OBC and NonLin_FrSurf.
910
911 checkpoint44
912 o fix bug in mom_vi_del2uv
913 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
914 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
915 o update AIM experiments (NCEP input files)
916 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
917 o added some stuff for AD
918
919 checkpoint43
920 o added two new advection tests
921 o added global 4x4 degree ocean test
922 o added test of H&S94 with free surface on cube
923 o some final mods for gradient check, adjoint,...
924
925 checkpoint42
926 Fixed AD-related problems:
927 o Store directives up-to-date with re-arranged Adams-Bashforth
928 (mainly thermodynamics.F)
929 o New store directives for multi-dim. advection schemes
930 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
931 * new common block and key passkey
932 (mainly gad_advection.F)
933 o Modified store directives for split of dynamics/thermodynamics
934 for the case ALLOW_KPP
935 o Cleaned argument list for timestep_tracer.F
936
937 checkpoint41
938 o re-formatted/added comments in prologues of key subroutines
939 to work with protex
940
941 checkpoint40
942 o moved calc_gs, calc_gt and calc_tr1 back to model/src
943 o added FLT (floats) package from Arne along with demo. experiment
944 o re-arranged Adams-Bashforth scheme for tracers to allow easier
945 implementation of forward-in-time forcing terms
946 o more mods for non-linear free-surface including new variable
947 o modified multi-dim method to work on cube
948 o bug fix in KPP (from DM)
949
950 checkpoint40pre9
951 o added DST advection schemes
952 o fix MPI bug on SGI's
953 o modifications for non-linear free-surface
954 o fixed conditionals for fixed flow/passive tracer only mode
955 o added tension/strain form of stress tensor
956 o changes to commenting of arguments for TAF/TAMC
957 o added/updated many matlab scripts
958 o added multi-dimensional advection method for tracers
959
960 checkpoint40pre8
961 o new package rw/
962 Added method for dumping intermediate local arrays:
963 mdsio_writetile - same as mdsio_writefield except works from inside
964 bi,bj loop
965 mdsio_writelocal - same as mdsio_writetile except works for local
966 arrays
967 write_local_r? - higher-level wrapper for mdsio_writelocal
968 Controlled by diagFreq. Defaults to zero (ie. no dumps)
969 Example given at end of mom_vecinv.F that dumps some local arrays.
970 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
971 control flux-form versus vector invariant code.
972 Switch is runtime flag vectorInvariantMomentum (defaults to false)
973 or genmake -DISABLE ...
974 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
975 (additional storing is now needed for case vecinv;
976 currently nothing implemented to switch this storing off
977 in case fluxform is used since no CPP flag available).
978
979 checkpoint40pre7
980 o bug fix in dynamics.F
981 calc_viscosity called before k=1,Nr loop.
982 o added some #ifdef's ALLOW_PASSIVE_TRACER
983 o cleaned initialisations in ctrl_map_ini
984 related to TAF
985
986 checkpoint40pre6
987 o split dynamics into thermodynamics & dynamics
988 o corresponding split of calc_diffusivity into
989 calc_diffusivity, calc_viscosity
990 (kpp_calc_diff, kpp_calc_visc).
991 o Added diffkr, kapgm to control variables
992 o bug fix in gmredi_slope_limit for ldd97
993
994 checkpoint40pre5
995 o proper initialization of Adams-Bashforth time stepping
996 + uses forward step for very first step of model (iter=0)
997 o re-generated *all* output since almost all output is modified by this
998 change (sorry but we've been putting this one off for about 2 years)
999 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
1000 *not* regenerated since they are already out of date and I don't
1001 want to create the impression that they are suddenly working.
1002 o removed KAP stuff for DEC's
1003 o modified/added many .cvsignore files in */code and */input
1004 o added new expt "solid-body.cs-32x32x1"
1005 + this uses an alternative form of ini_curvilinear_grid.F which
1006 is not necessarily any better than the current one...
1007
1008 checkpoint40pre4
1009 o added re-initialisations of utrans,vtrans,rtrans in
1010 calc_common_factors which are crucial for TAF.
1011 o extended iMin,jMin range for calc_common_factors,
1012 calc_diffusivity
1013 o added option ALLOW_PASSIVE_TRACER
1014 o a few minor updates and fixes
1015
1016 checkpoint40pre3
1017 o created calc_gtr1.F for gad package
1018 o split the_main_loop and re-introduced forward_step
1019 o some recomputations of nIter0 for TAMC
1020
1021 checkpoint40pre2
1022 o Updated to latest branch of AJA, JMC
1023 o Added gradient check package
1024 o Added routines for passive tracer handling
1025 o Added carbon sequestration sensitivity experiment
1026
1027 checkpoint39
1028 o Modifications and fixes to support TAMC
1029 (mainly missing or wrong directives)
1030 o Corrected common blocks when fooling TAMC to produce adjoint I/O
1031 in addummy_in_stepping
1032 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
1033 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
1034 o Included following packages:
1035 cal: calendar
1036 exf: external forcing
1037 ecco: essential routines to control use of cal, exf
1038 (NB: this is not the full ECCO environment)
1039 o disabled some packages by default in genmake
1040
1041 checkpoint38
1042 o see notes_c37_adj.txt
1043 o corrected wrong layer index in external_forcing_t
1044 o replaced the_main_loop/forward_step by the_main_loop
1045 o removed forceoutput from write_state
1046 (replaced criteria for initial/final state)
1047 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
1048
1049 checkpoint37
1050 o mdsio.F routine split and packaged in pkg/mdsio
1051 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
1052 used unless genmake -disable=mdsio)
1053 o allow a more precise surface-geopotential gradient for the atmosphere
1054 taking into account the change in space of Alpha (=1/rho) at the surface.
1055 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
1056 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
1057 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
1058 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
1059 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
1060 o Time-Average diagnostics defined as a pseudo package "timeave".
1061 o pickup files : old pickup (before c35) did not work with new code (c35
1062 and after) unless activating 2 commented lines in initialise-varia.
1063 o Non-Hydrostatic pickup file Pb fixed.
1064 o bug with Rigid-lid version (since c35) fixed.
1065
1066 checkpoint36
1067 o implement Crank-Nickelson barotropic time-stepping
1068 o recover Time-Average diagnostics
1069 o fix Pb in checkpoint (PR#19)
1070 o AIM become a standard package ; clean unused CPP_kees
1071
1072 checkpoint35
1073 o subtantial rewrite of dynamics.f
1074 o allows staggered time-stepping
1075 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
1076 o added bottom drag (linear + quadratic)
1077
1078 checkpoint34
1079 o Modified exchange routines for correct reverse simulation.
1080 o Added verification output to comply with bug fix in impldiff.F
1081 as of c33 (exp2, natl_box).
1082 o Corrected store directives in dynamics.F
1083 o Corrected array boundaries in impldiff.F
1084 o Corrected array dimensions in gmredi.
1085 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
1086 o Added routine GLOBAL_SUM_INT to global_sum.F
1087 o Added mdsio_gl.F for ECCO purposes.
1088
1089 checkpoint33
1090 o Fixed bug in lower BC in impldiff.F
1091 o Fixed confusion about units of forcing arrays in FFIELDS.h
1092 namely Fu,Fv,Qnet,Qsw,EmPmR:
1093 - Removed verification/natl_box/code/external_fields_scale.F
1094 (did not differ from that in model/src)
1095 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
1096 (see FFIELDS.h for description)
1097 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
1098 kpp_calc.F and kpp_transport_t.F
1099 - Removed model/src/external_fields_scale.F and calls to it
1100 - verification/natl_box uses flux data with "atmospheric" sign so
1101 a special version of external_fields_load.F is used to
1102 change the data as it's read in. This way, the arrays
1103 have the right units and signs at all times tha a user could
1104 possibly use them.
1105 o Corrected genmake to delete a temporary file during configuration
1106
1107 checkpoint32
1108 o Scaling of forcing fields moved from external_forcing.F to
1109 external_fields_scale.F, called directly after loading fields.
1110 o Surface relaxation terms added to surface tendency fields in
1111 extra subroutine.
1112 o impldiff.F changed to avoid storing by TAMC of huge intermediate
1113 fields.
1114 o Changes in GMRedi to comply with packaging structure.
1115 o Modifications and bug fixes in KPP package.
1116 o Verification experiment for KPP added (verification/nat_box/)
1117
1118 checkpoint31
1119 o Packages interface brought in line with defined standard
1120 -> new routines packages_...F
1121 -> changes in initialise_fixed.F, initialise_varia.F
1122 -> enables initialisation interface for ECCO package
1123 o Rescaling of external forcing fields immediately after read
1124 (removed from external_forcing.F)
1125 -> new: surface_fields_scale.F
1126 -> affects ini_foorcing.F, external_fields_load.F
1127 o Computation of surface tendencies before tendency updates.
1128 -> new: external_forcing_surf.F
1129 o Change of variable names useGMRedi, useKPP, useECCO
1130 o Further changes in dynamics.F, impldiff.F for TAMC
1131 o Tested for experiments 0, 2, 4.
1132 - not yet tested for GMRedi.
1133 - not yet tested for KPP.
1134
1135 checkpoint30
1136 o Updates for OBCs
1137 o New experiment for test OBCs (internal_wave)
1138 o New output.txt in verification/exp4/results/
1139 o Updates for KPP: calculation of viscosity corrected, new variables
1140 kpp_dumpFreq and kpp_taveFreq
1141 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
1142 and entry for T90 in genmake
1143
1144 checkpoint29
1145 o packaged KPP and GM/Redi
1146
1147 checkpoint28
1148 o Corrected initialization of hFacMin for difference vertical coordinates
1149 o Modified calculation of partial cell thickness to more robust algorithm
1150 o config_summary.F: replaced write_1D_... by write_0D_...
1151 read_write.F: added subroutines write_0D_...
1152 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
1153 included some initialisations required for TAMC.
1154 o routine calc_isoslopes: modified sqrt computation to make it
1155 differentiable for zero argument.
1156 o routines dynamics, impldiff:
1157 included store directives and tape key computations required for TAMC.
1158 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
1159
1160 checkpoint27
1161 o fixed calc_isoslopes() to so that cancellation of terms in tensor
1162 formulation works properly with variable resolution.
1163 o restructured the calling tree between the_model_main() and dynamics()
1164 o split initialise() into initialise_fixed() and initialise_varia()
1165 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
1166 in new routine ini_psurf()
1167
1168 checkpoint26
1169 o moved some #ifdef in optional routines to encompass everything
1170 except the argument declarations. This was using up some memory.
1171 o fixed macros like _ADT to work with both versions of Linux cpp
1172 o cleaned up some unused and uninitialized variables
1173 (helps when debugging with strict compile options)
1174 o split up CPP_EEOPTIONS.h into options and macros
1175 (macros are now in eesupp/inc/CPP_EEMACROS.h)
1176 o patch for 2 processor JAM mode
1177
1178 checkpoint25
1179 o updates for OBCs and NH
1180 o dramatically reduced memory usage
1181 o added "JAM" routines for use on Artic network
1182 o parameterization of convection by implicit vertical diffusion
1183 o added a diagnostic of convective index
1184 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
1185 (this is was partly for OBCs and NH but also in anticipation of
1186 an explicit free-surface option)
1187 o initial state input files for U and V
1188
1189 checkpoint24
1190 o Removed some spurious "REAL"s
1191 o Updated KPP to latest version from JPL
1192 o Added a COS(latitude) in horizontal viscosity
1193
1194 checkpoint23
1195 o Added del^4 diffusion for salt and temperature
1196 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
1197
1198 checkpoint22
1199 o Made many small changes: implicit none, format(i5), etc...
1200 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
1201
1202 checkpoint21
1203 o Introduced new I/O package that supports direct-access records (mdsio.F)
1204 o Split-up mid-level I/O routines
1205 o Updated input data for experiments 0,1,2,4 and 5
1206 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
1207
1208 checkpoint20
1209 o Tidied up open-boundaries some more
1210 o Added non-hydrostatic code
1211 o Fixed some input data
1212 o Modified MPI start-up to work in "coupled" context.
1213
1214 checkpoint19
1215 o Tidied up directory structure for verification experiments.
1216 o Added new code for open boundaries.
1217 o Corrected advective terms near boundaries.
1218 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
1219 o Implemented free-slip/no-slip BCs and del^4 dissipation.
1220 o Split default parameters out of ini_parms.F into set_defaults.F.
1221
1222 checkpoint18
1223 o Further changes for optional code generation with
1224 CPP - ugh!
1225
1226 checkpoint17
1227 o Beginning to incorporating modularity
1228 for supporting atmos. and ocean configs.
1229 o Small changes for TAMC complinace
1230 o New ultra simple test case. Barotropic box
1231 configuration "exp0".
1232
1233 checkpoint16
1234 o Minor changes to exchange routines to support
1235 accumulation in reverse mode. Adjoint of an
1236 assignment is an addition.
1237 o Changes to support compilation by TAMC (LR(1)
1238 syntax) and by g77 under Linux ( 72 character
1239 limit ).
1240
1241 checkpoint15
1242 Rewrote exchange routines to allow
1243 o General tile <-> tile connectivity.
1244 o TAMC reverse mode flag ( is this really needed? )
1245 o Variable width overlap and exchange region widths.
1246 o Hooks for sharing data via DMA, Arctic, Memory Channel,
1247 shmput/shmget, VIA, SYSV shmem and every other cool
1248 communication method.
1249
1250 checkpoint14
1251 Consistent isomorphism chages made. These allow dynamical core
1252 to support both pressure and meters as a vertical coordinate.
1253
1254 checkpoint13
1255 Release which corrects global_max problem and a couple
1256 of KGM time-averaging diagnostic errors. Also contains
1257 a double-gyre experiment setup as well as the baseline
1258 4 degree global template. The double gyre template is
1259 organised to allow it to be applied automatically to
1260 the baseline configuration.
1261
1262 branch-point-rdot
1263 A few tidy-ups have been made bt the real point of this
1264 check-point (excuse the pun) is to allow a branch to be
1265 made for the purposes of adding the rDot alterations.
1266 I don't want to commit the rDot to the main-trunk until
1267 we've actually tested it...
1268
1269 checkpoint12
1270 Tidy up and added generic genmake script (formerly
1271 configure script).
1272 Released to testers.
1273
1274 checkpoint11
1275 Re-arranged initialise() and introduced ini_vertical_grid()
1276 and ini_masks_etc().
1277
1278 checkpoint10
1279 Introduced the configure script.
1280 Separated out the diags package.
1281 Added template for writing time-averages of tile/intermediate quantities.
1282 Updated SIZE.h in exp2 and made the data big-endian.
1283
1284 checkpoint9
1285 MPI fix. Filename changes (meta/data). salbin*y stuff.
1286 General tidy-up.
1287 SST.bin SSS.bin added to verification/exp2
1288
1289 checkpoint8
1290 Inludes time-dependant forcing and time-averaging.
1291 Works at 4x4 and 2.8125x2.8125 global
1292
1293 checkpoint7-4degree-ref
1294 Branch from checkpoint7. Released for application to
1295 global modeling and general modeling - process studies, regional
1296 model etc..
1297 Configured for verification/exp2 - 4 degree global, two process.
1298
1299 checkpoint7
1300 Created by cnh
1301 Simple 4 degree global simulation
1302 configuration.
1303 Includes climatological wind,
1304 hydrography, bathymetry etc
1305 Does not include Heat Flux and E-P
1306
1307 checkpoint6
1308 Created by cnh
1309 merged checkpoint5 with CD and
1310 spherical polar code.
1311 Still some problems with GM Redi
1312 abd full topography.
1313
1314 checkpoint5
1315 Created by AJA
1316 contains updates to GM Redi
1317 and reordered timestepping loop
1318 for Implicit Diffusion.
1319
1320 checkpoint4
1321 Created by cnh
1322 Contains memory saving macros ( _rdxc etc..) for when
1323 grid variations are limited.
1324 Contains polynomial coeffs for EOS and knudsen program
1325 for generation.
1326
1327 checkpoint3
1328 Created by cnh
1329 Added extra flags for runtime options
1330 Added this file
1331 Added implicit free-surface
1332 Added pre-conditioner
1333 Put compare01 into repository ( compare01/... )
1334 Put data and eedata into repository ( verification/exp1 )
1335
1336 checkpoint2
1337 Created by AJA
1338 Added GM/Redi
1339
1340 checkpoint1
1341 Created by AJA
1342 Restructured kloop in dynamics.F
1343 Added non-linear EOS
1344
1345 baseline
1346 Original checked in code

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