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Revision 1.202 - (show annotations) (download)
Mon Nov 3 03:51:35 2003 UTC (20 years, 6 months ago) by edhill
Branch: MAIN
CVS Tags: checkpoint51r_post
Branch point for: branch-nonh
Changes since 1.201: +6 -1 lines
 o created checkpoint51r_post

1 $Header: /u/u3/gcmpack/MITgcm/doc/tag-index,v 1.201 2003/10/30 19:21:04 heimbach Exp $
3 Notes on tags used in MITgcmUV
4 ==============================
6 checkpoint51r_post
7 o cleaned up or removed CPP_OPTIONS.h files
8 o updated results for some of the tests to reflect the new
9 optfiles (-ieee: -O0 instead of -O3)
11 checkpoint51q_post
12 o cd_code:
13 - moved cd_scheme.F -> cd_code_scheme.F
14 - separate read_checkpoint from cd_code_ini_vars.F
15 - separated cd_code part from write_checkpoint
16 - updated AD_SOURCE, generated .flow
17 - added CD_CODE_VARS.h to the_main_loop
18 - Moving cd_code specific store dir.s to pkg/cd_code
19 o ctrl package totally restructured
20 - pack/unpack now optional and decoupled from
21 xx_/adxx_ I/O
22 - ctrl_pack/unpack cleaned
23 (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
24 - confined inclusion of AD_CONFIG.h to where necessary.
25 o genmake2: changed AD dependencies from SRCFILES to AD_FILES
27 checkpoint51p_post
28 o create initial cd_code package
29 - WARNING: the initialization of fields within packages
30 is broken because INI_FIELDS (where READ_CHECKPOINT is
31 called) is called *before* PACKAGES_INIT_VARIABLES.
32 This seems to be backwards since
33 1) its important to initially zero the entire field including
34 the "halo" region
35 2) zeroing needs to be done *before* reading pickup info
36 and the pickup call might or might not happen in any
37 particular run
38 - this needs an overhaul for R2
39 o cleanup verification/*/code/GMREDI_OPTIONS.h
40 o cleanup testreport
42 checkpoint51o_post
43 o bringing AD-related verif's up to date with genmake2
44 - carbon/
45 - global_ocean.90x40x15/
46 - hs.94.1x64x5/
47 - (front_relax/ )
48 o (more) consistent directory structure for AD-related verif.'s
51 o bug fix in find_alpha.F for MDJWF:
52 - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
53 change rho -> rho-rhoConst
54 - replace call find_rho to find_rhonum
55 o initialisation of rFlx extended to full array (required by TAF)
56 and shifted to thermodynamics
57 o removed PTRACERS.h in ptracers routine
58 o added surfacetendencyPtr to S/R parameter list pracers_forcing
59 o Correcting initialisations for fVerU, fVerV.
60 o helping TAF to recognize dependency on kUp for
61 fVerU, fVerV
62 o Replacing delZ by delR in pkg/ctrl/
63 checkpoint51o_pre
65 o undid all of cp51 pending some cleanups and discussion
66 o added the [#include "AD_CONFIG.h"] statement to all files that need
67 it for adjoint/tl #defines
68 o re-worked the build logic in genmake2 to support AD_CONFIG.h
69 o removed tools/genmake since it no longer works
71 checkpoint51n_post
72 o modifications to make FREEZE flux visible to pkg/kpp
73 - moved surfaceTendencyTice from pkg/seaice to main code
75 - subroutine FREEZE now limits only surface temperature
76 (this means new output.txt for global_ocean.90x40x15,
77 global_ocean.cs32x15, and global_with_exf)
78 o added surface flux output variables to TIMEAVE_STATVARS
80 checkpoint51n_pre
81 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
82 o added [#include "AD_CONFIG.h"] to all files that use the following
83 defines:
88 checkpoint51m_post
89 o incorporating changes to get TAMC/TAF working in genmake2
90 - added new TAMC/TAF targets to the Makefile
91 - various cleanups related to package handling
92 - these changes should have no impact on the forward model
94 checkpoint51l_post
95 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
96 - faster algorithm for cal_addtime.F
97 - higher precision arithmetic, where needed
98 - pkg/exf *startdate variables changed from calendar date to
99 model integration time
101 checkpoint51l_pre
102 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
103 o enable to apply restoring on S & T only in a latitude band.
104 o update output (external_forcing_surf modif. change truncation errors)
105 global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
107 checkpoint51k_post
108 o change default to: useNHMTerms=.FALSE.
109 - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
110 adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
111 - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
112 exp1, ideal_2D_oce
113 - change data file of oceanic exp (leave the results unchanged for now)
114 exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
115 o set gravitySign automatically according to the vertical coordinate used
116 (and change sign: back to "logical" value: +1 when R increases downward)
117 o added an include barrier to the default CPP_OPTIONS.h and
118 removed the #include "PACKAGES_CONFIG.h" from it
119 o fix a bug in mom_fluxform (from chk51j_post)
121 checkpoint51j_post
122 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
123 o adjusted some flow directives (dynamics, thermodynamics)
124 o added cubed-sphere case to test cost function
125 o heckpoint_lev?_directives.h now include
126 pkg-specific directives, whenever those are enabled.
127 o Moving pkg-specific flow directives to corresponding pkg
128 Moving pkg-specific differentiation list to corresponding pkg
129 Moving pkg-specific checkpoint-lev storing to corresponding pkg
130 ---> conventions are
131 - pkg_ad.flow
132 - pkg_ad_diff.list
133 - pkg_ad_check_lev?_dir.h
135 checkpoint51i_post
136 o merge of the branch-genmake2
137 - knowingly breaks the older genmake
138 - automatic generation of all ALLOW_${PKG_NAME} defines
139 - new testreport supersedes older testscript
140 o large number of package inclusion and header cleanups
141 checkpoint51i_pre
143 o new output for adjoin of global ocean vector invariant
144 o fix for checkpoint of thermodynamic seaice and bulk_force
145 o Steph gchem various cleanups
147 checkpoint 51h_pre
148 o fixed some single quotes
149 o modify gchem pkg to be more versatile
150 o modifications to clean up dic pkg
151 o add pkg/cfc
153 checkpoint51g_post
154 o provide links for ARPACK and ADM*TLM
155 o start removing verification/vero/
156 o update AD-related stuff
157 (in particular some IF-statements in model/src/ routines)
158 o adding to verification/global_ocean.90x40x15/ adjoint of
159 vector invariant setup
161 checkpoint51f_post
162 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
163 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
164 of tracer Green's fucntions for ocean inversion project.
166 checkpoint51f_pre
167 o Added on-the-fly spatial interpolation capability
168 "USE_EXF_INTERPOLATION" to pkg/exf.
169 - This is a temporary Cartesian-grid hack until
170 the super-duper ESMF coupler becomes available.
171 - See verification/global_with_exf/README for usage example.
172 - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
173 flags and modified pkg/seaice accordingly.
174 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
175 and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
176 non-local transport term.
178 checkpoint51e_post
179 o pkg/mom_vecinv:
180 - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
181 - add time-ave diagnostic of vorticity advection.
182 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
183 o atmospheric geopotential: - include water vapor effect;
184 - use p^kappa in p* scaling.
185 o land pkg: read initial state from files.
186 o AIM : add stratospheric drag in the upper level
188 checkpoint51d_post
189 o change function ILNBLNK (=> last non-blank char.) to return zero
190 (instead of the string length) when the string. char is empty
191 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
192 o modif's to restore TAMC compatibility
193 - avoid "_d" constructs in PARAMETER declarations
194 - avoid interrupting lines by comment lines
195 o Use cluster local disks for purely local I/O
196 vs. globally visible disks needed for ctrl stuff
197 (merged from ecco-branch)
198 - new active_file_loc... and mdsio_..._loc routines
199 - affected packages: autodiff, ctrl, grdchk, mdsio
201 checkpoint51c_post
202 o introducing integer flag debugLevel
203 - debLevZero: suppress all output
204 - debLevA: standard
205 - debLevB: equivalent to current debugMode=.TRUE.
206 o introducing pathname variable mdsioLocalDir for mdsio
207 that can be specified at runtime
208 (relevant for cluster I/O to local disk)
209 `
210 >>>checkpoint51b_post
211 adjoint of ptracers
212 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
213 o extended state in checkpoint_lev?, etc.
214 o alternative ctrl/cost with tr1 or ptracer
215 o new comlev1_bibj_ptracers
216 o new ptracers.flow
217 o made ptracers_forcing same as external_forcing_s
218 o added verification for adjoint with ptracers
219 - adm. grdchk fail so far
220 - tlm. grdchk OK
221 - checked tapelev/comlev recomputations: OK
222 <<<checkpoint51b_pre
224 checkpoint51a_post
225 o added code for biogeochemistry package
226 - new pkgs: dic, gchem
227 - new subroutine in ptracers
228 o modify code for biogeo packages
229 - in model/src and pkg/ptracers
231 checkpoint51
232 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
233 - autodiff, ctrl, exf, grdchk, seaice
234 kept separate packages
235 - cost, ecco, obcs
236 o updating verification/internal_wave, verification/lab_sea
237 (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
239 checkpoint50i_post
240 o Preparing next differentiable checkpoint and sync
241 of MAIN vs. ecco-branch
242 - 1st step: this one is differentiable
243 - 2nd step: next(! not this) checkpoint will have updated packages
244 from ecco-branch)
246 checkpoint50h_post
247 o new package "land": provide surface BC for AIM.
248 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
249 o AIM: use true log-P extrapolation for near surface temp (= as in
250 F.Molteni paper) ; update aim.5l_cs output.
251 o New variable in PARM03 for more flexible pickups
252 o somewhat cleaned package initialisation sequence for
253 ctrl/ cost/ ecco/ in packages_... routines
255 checkpoint50g_post
256 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
257 - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
258 - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
259 made the default because of faster convergence than ADI
261 checkpoint50f_post
262 o exf totally restructured
263 - replaced all exf_set_ routines by one generic exf_set_gen.F
264 and made sure it's still differentiable
265 - split exf_getffields.F into new exf_bulkformulae.F
266 - exf_inscal_/exf_outscal_ suffixes consistent with field names
267 - updated adjoint/makefile and relevant verif. accordingly
269 checkpoint50f_pre
270 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
271 + change Evap over land. (update aim.5l_cs output)
272 o added missing .cvsignores and made uniform across expts
273 o changed configuration of tidal_basin_2d expt
274 o added pkg/debug functions for tracing code in fatal crashes
275 o tidied pkg/monitor to use MONITOR_OPTIONS.h
276 o new fn in pkg/monitor to stop model if solution grows too big
277 o removed lots of single quotes from comments
279 checkpoint50e_post
280 o make KPP work with PTRACERS
281 - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
282 nearly a copy of kpp_transport_s
283 - there is no analogue to SurfaceTendencyS, so I have to use
284 gPtr(of the surface layer) instead
285 o add a new platform SunFire+mpi (SunFire 15000) to genmake
286 checkpoint50e_pre
288 checkpoint50d_post
289 o change kpp output from multiple-record state files to single-record state
290 files analogous to write_state.F
291 o reduce the output frequency of cg3d-related stuff to the monitor frequency,
292 analogous to the cg2d-related output.
293 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
294 so that writing to internal file fn (with length 512) fails.
295 checkpoint50d_pre
297 checkpoint50c_post
298 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
299 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
300 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
301 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
302 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
304 checkpoint50c_pre
305 Merging from release1_p13:
306 o bug fix for pkg/seaice dynamic solver
307 o Added SEAICE_initialHEFF to pkg/seaice
309 checkpoint50b_post
310 o store u*,v* in gU,V instead of in guNm1,gvNm1
311 o in order to put the momForcing out of the Adams-Bashforth:
312 move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
313 to timestep.F
314 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
315 o re-generate output for highly sensitive test-exp:
316 global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
318 checkpoint50b_pre
319 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
320 o corrected CPP option mismatch in exf_Bulk... functions for case
321 #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
323 checkpoint50a_post
324 o Bug fix for merging between c50 and KPP.
325 ikey was passed from thermodynamics to kpp_calc via
326 common block rather than being recomputed in kpp_calc,
327 in contradiction with new key itdkey.
328 New key ikppkey created, and tamc.h headers updated.
330 checkpoint50
331 - 2nd step of merge with ecco-branch:
332 merge changes in ecco-branch back into main trunk
333 - bug fix in find_alpha
334 - more storing in gmredi_calc_tensor.F, kpp_routines.F
335 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
336 - merged some sliced AD support routines
338 checkpoint49
339 merged from ecco-branch:
340 o exf:
341 - Enable initialisation of forcing fields to constant
342 (runtime) values.
343 - in exf_getffields.F
344 Reduce i-/j-loop to interior domain, discarding overlaps.
345 That also fixes wrong TAF-key computations for key_1, key_2
346 with bulf formulae.
347 - exf_init.F modify #ifdef for exf_init_evap
348 - exf_getffieldrec.F, ctrl_getrec.F
349 The following INT-usages are not safe:
350 fldsecs = int(fldsecs/fldperiod)*fldperiod
351 fldcount = int(fldsecs/fldperiod) + 1
352 and were modified.
353 o autodiff: checkpoint_lev...
354 - updated storing for bulk formulae (some arrays were missing)
355 - added state for seaice package
356 - synchronized with main branch
357 o DIVA:
358 Modif.s in
359 - the_main_loop.F
360 - the_model_main.F
361 and added cost_final_restore.F cost_final_store.F
362 o With these changes, it is possible to fully separate
363 the first forward run to compute the cost function (mdthe_main_loop)
364 and adjoint runs over individual DIVA intervals (adthe_main_loop)
365 into separate model executions.
366 This enables better tuning of DIVA to given queue sizes.
367 o Loss of cost function value in consecutive DIVA runs is
368 fixed by storing to 'costfinal' file.
369 o Appropriate call of ctrl_unpack/_pack,grdchk_main at
370 beginning/end of adjoint integration is accounted for.
371 The current changes apply to TAF-1.4.26.
372 TAF has one remaining bug, requiring one manual change
373 (see MITgcm manual).
374 o cal: synchronized between MAIN and ecco-branch
376 checkpoint48i_post
377 o Changes to restore differentiability of code w.r.t. previous tag
378 (mostly adding new routines to make list and replacing
379 pressure by totPhiHyd).
380 o Updated and merged grdchk package
381 - has both ADM and TLM checks
382 - works for single- and multi-proc.
383 - output cleaned
384 - worked successfully for parallel DIVA
385 o genmake:
386 - Adding -platform=SP4
387 - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
388 o Modif. for DIVA:
389 ctrl_unpack should not be called in intermediate DIVA interval.
390 (similar thing would apply for active files such as
391 tbar, sbar, psbar, which should not be reinitialised;
392 only relevant for ecco-branch)
394 checkpoint48h_post
395 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
396 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
397 o Added SEAICE_initialHEFF to pkg/seaice
398 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
400 checkpoint48g_post
401 --- EOS:
402 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
403 store total Potential in totPhyHyd for diagnostics & EOS.
404 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
405 --- Pressure/geopotential gradient:
406 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
407 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
408 ( changes results of global_ocean_pressure )
409 o NLFS + z-coord.: add eta*Rho' contribution.
410 o accurate phiHyd when using interface-W at the middle between 2 centers
411 ( changes results of ideal_2D_oce )
412 o includes r* 2nd term in potential gradient.
414 checkpoint48f_post
415 Merging from release1_p12:
416 o Modifications for using pkg/exf with pkg/seaice
417 - improved description of the various forcing configurations
418 - added basic radiation bulk formulae to pkg/exf
419 - units/sign fix for evap computation in exf_getffields.F
420 - updated verification/global_with_exf/results/output.txt
421 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
422 (SBO) core products, including oceanic mass, center-of-mass,
423 angular, and bottom pressure (see pkg/sbo/README.sbo).
424 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
425 to avoid negative values in shallow regions.
426 - updated verification/natl_box/results/output.txt
427 - updated verification/lab_sea/results/output.txt
428 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
429 o Added useSingleCpuIO option (see PARAMS.h).
430 o Updated useSingleCpuIO option in mdsio_writefield.F to
431 work with multi-field files, e.g., for single-file pickup.
432 o pkg/seaice:
433 - bug fix in growth.F: QNET for no shortwave case
434 - added HeffFile for specifying initial sea-ice thickness
435 - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
436 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
437 kpp_transport_t.F, forward_step.F, and the_main_loop.F
438 o pkg/seaice:
439 - adjoint-friendly modifications
440 - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
442 checkpoint48e_post
443 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
444 o dynamics: change definition of computational domain & adapt mom_fluxform
445 accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
446 o following exp works with Olx=Oly=2 (and pass through checkbounds option):
447 adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
448 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
449 global_ocean.90x40x15 global_with_exf global_ocean_pressure
450 inverted_barometer solid-body.cs-32x32x1
451 (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
453 checkpoint48d_post
454 o in preparation for r*:
455 a) use pre-computed gradient of hydrostatic potential:
456 changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
457 b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
458 => affects results of glob_oce_pressure (different truncation error)
459 update output.txt of ideal_2D_oce & global_ocean_pressure
461 checkpoint48d_pre
462 o in preparation for r*:
463 new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
464 pass the 2 comp. of the grad. as arguments to momentum S/R.
465 but for the moment, only used if it does not change the results.
466 o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
468 checkpoint48c_post
469 Modifications in treatment of initial flux forcing controls
470 to avoid extra storing of flux fields.
472 checkpoint48c_pre
473 o Added tidal_basin_2d experiment (currently 1D!)
474 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
476 checkpoint48b_post
477 o r* coordinate added in #ifdef NONLIN_FRSURF block.
478 (modification to pressure gradient not yet implemented)
479 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
480 (for U & V) that are used for vertical advection of momentum.
482 checkpoint48a_post
483 o In preparation for r*, use temp. array to compute vertical transport
484 in flux-form momentum pkg. => change results of few test-exp.
485 Update output of: exp4, exp5, front_relax, global_ocean_pressure,
486 lab_sea, natl_box & plume_on_slope
488 checkpoint48
489 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
491 checkpoint47j_post
492 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
493 o moved adexch from forward_step to addummy_in_stepping
494 o added exch in ctrl_map_...
495 o aveFreq.=0. at end of cost_final to avoid overwrite in
496 reverse checkpointing loop
497 o Yet more changes in gmredi:
498 * adgmredi_calc_tensor
499 avoiding all recomputation of gmredi_slope_limit
500 * adgmredi_x/y/rtransport
501 added flag for excessive storing to avoid recomp. of
502 u/v/rtans, dTdx/y/z
503 -> this is not really necessary and very memory-consuming
504 * adgmredi_slope_psi:
505 consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
506 * gmredi_slope_limit
507 re-activated full calculation of taperfct for case 'ac02'
508 o updating verification/ adjoints of carbon, global_ocean.90x40x15
510 checkpoint47i_post
511 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
512 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
513 default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
514 o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
515 o gmredi: fix few bugs.
517 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
518 This will be a good checkpoint to plug into the ecco-branch.
519 o few modif.'s to get latest version adjointed
520 (mainly kick out code in ini_linear_phisurf)
521 o modif's to run adjoint with exactConserv
522 o case GM_BOLUS_ADVEC should be cleaned
523 S/R gmredi_slope_psi should be cleaned
524 o verification/carbon now has exactConserv=.TRUE.
526 checkpoint47g_post
527 o time-average AIM output: becomes independent from statvars time-average
528 (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
529 o After TAF bug fix:
530 Tested adjoint of gmredi package.
531 Tests were done with checkpoint47 rather than with latest
532 checkpoint47f_post since the latter is broken for the adjoint
533 verification/carbon/ contains both ADM and TLM gradient checks.
534 Here they are, before they get changed/lost/stolen.
535 Mostly modif.'s to fix numerical sensitivities.
536 Gradient checks OK for
537 - GM_taper_scheme:
538 * clipping
539 * ac02
540 * linear
541 * glw91
542 * dm95
543 * ldd97
549 in conjunction with data.gmredi parameters to be checked in
550 in a few minutes under verification/carbon/code/
552 checkpoint47f_post
553 Merging from release1_p10:
554 o modifications for using pkg/exf with pkg/seaice
555 - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
557 - pkg/exf CPP options EXF_READ_EVAP and
559 - usage examples are Experiments 8 and 9 in
560 verification/lab_sea/README
561 - verification/lab_sea default experiment now uses
562 pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
564 checkpoint47e_post
565 o created a tag prior to creating a branch
567 checkpoint47d_post
568 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
569 at the bottom boundary had an erroneous half slip boundary condition
570 o added bottom drag and no slip boundary condition capabilities to
571 oceanic pressure coordinates code
572 o added new verification experiment global_ocean_pressure, this experiment is
573 also described in the tutorial section of the manual
574 checkpoint47d_pre
576 checkpoint47c_post
577 o Added a verification experiment for a global cubed-sphere ocean run
578 - verification/global_ocean.cubed32x32x30
579 - uses pkg/therm_seaice and pkg/bulk_forcing
581 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
582 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
583 when using P-coordinate; only implemented for atmospheric config.
584 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
585 NOTES: requires option NONLIN_FRSURF to be "#define".
586 o update advect_xz/results/output.txt (left from checkpoint44g_post)
588 checkpoint47b_post
589 Merging from release1_p9:
590 o pkg/seaice
591 - removed GOTO's and added taf directives
592 - double precision constants to reduce the g77 (Linux)
593 to F77 (SGI) differences reported in release1_p8
594 o tools/genmake
595 - added SGI options
596 o verification/testscript
597 - updated to that of checkpoint47a_post
598 o verification/global_ocean.90x40x15/input/eedata
599 - modified for SGI f77 compatibility
600 o verification/lab_sea
601 - added description of sea-ice model
602 - added missing matlab routines
603 - added test of thermodynamics parallelization
605 checkpoint47a_post
606 o new pkg: aim_v23
607 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
608 for now, keep the same surface forcing as before.
609 - Part-Cell implemented into AIM; check that Heat & Water are conserved
610 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
611 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
612 o add diagnostic of surface correction term in monitor output
614 o bulk_force and therm_seaice
615 - Two packages: bulk_force (Bulk forcing)
616 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
617 - Earlier integration from Stephaine Dutkiewicz
618 and Patrick Heimbach.
619 - Two ifdef statements for compile time,
622 checkpoint47
623 differentiable version of checkpoint46n_post
624 o bug fix in quasihydrostaticterms
625 o * "clean" adjoint code (in terms of extensive recomputations)
626 can now be obtained for all GMREDI options (i.e. for
631 * However, wrong gradient check problem remains unsolved.
632 * New CPP options have been introduced for different
633 tapering schemes
634 o external_fields_load now part of differentiation list
635 o pressure needs multiple storing;
636 would be nice to have store_pressure at beginning or
637 end of forward_step, e.g. by having phiHyd global (5-dim.)
638 (NB: pressure is needed for certain cases in find_rho,
639 which is also invoked through convective_adjustment).
640 o recomputations in find_rho for cases
641 'JMD95'/'UNESCO' or 'MDJWF' are OK.
642 o #define ATMOSPHERIC_LOADING should be differentiable
643 o ini_forcing shifted to begining of initialise_varia
644 o Incorporating QNVS line search routines into MITgcm
645 (this is separate code, and therefore not under pkg)
646 lsopt/, optim/
647 o Updated verification/carbon/
649 - GM_taper_scheme = 'ldd97'
651 checkpoint46n_post
652 Merging from release1_p8:
653 o verification/natl_box:
654 updating new external_fields_load routine
655 o New package: pkg/seaice
656 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
657 The sea-ice code is based on Hibler (1979-1980).
658 Two sea-ice dynamic solvers, ADI and LSR, are included.
659 In addition to computing prognostic sea-ice variables and diagnosing
660 the forcing/external data fields that drive the ocean model,
661 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
662 The implied surface heat flux is then stored in variable
663 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
664 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
665 non-local transport term. Because this call precedes model
666 thermodynamics, temperature under sea-ice may not be "exactly" at
667 the freezing point by the time theta is dumped or time-averaged.
668 N.B.: fairly large differences in accuracy occur across
669 different platforms/compilers; comparison between
670 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
671 generated output gives:
672 T S U V
673 C D M c m s m s m s m s
674 n p a R g m m e . m m e . m m e . m m e .
675 f n k u 2 i a a d i a a d i a a d i a a d
676 g d e n d n x n . n x n . n x n . n x n .
678 Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
679 o GAD:
680 - generated new common blocks to account for call of
681 same gad routines with differing traceridentities
682 (needed to modify tracerIdentity indices in GAD.h)
683 - generated separate common blocks for case useCubedSphereExchange
684 (Department of Futurology)
685 - parameter lists to gmredi_?transport: added tracerIdentity
686 - added new key indices to tamc.h
687 o external_fields_load:
688 - added this routine to TAF list
689 - needed to make some common blocks global and additional storing
690 along the same lines as exf package (checkpoint_lev?_directives.h)
691 o exf:
692 updated external forcing package
693 - bug fixes carried over from ecco-branch
694 (missing OBCS_OPTIONS.h in two routines)
695 - enable easy to use "no forcing".
696 - added exf I/O for atmospheric loading
697 - added exf I/O for runoff data
698 - transfered scaling between exf <-> MITgcm to exf namelist
699 o Adding new verification experiment global_with_exf.
700 This verification experiment is almost identical to the
701 global_ocean.90x40x15 experiment, except that it uses
702 the exf (and cal) package instead of the
703 external_fields_load routine (cf README file).
705 checkpoint46m_post
706 o modified testscript to return -- when there are no lines of "%MON" output
707 o added new flag "quasiHydrostatic" for QH mode
708 and new routine quasihydrostaticterms()
709 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
710 New routine: mom_u_coriolis_nh()
711 o fixed sign of non-hydrostatic metric terms in u and v equations.
712 Depend on correct sign of gravitySign.
713 o added work.pc* to .cvsignore in aim directories using ifc
714 o introduced flag for controllin non-hydrostatic metric terms
715 o removed gravitySign from PARM04
716 o switched to g77/ifc from pgf77 in aim experiments
718 checkpoint46l_post
719 o made convective adjustment work with pressure coordinates:
720 - changed the direction of k-loop in convective_adjustment.F for the
721 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
722 - adjusted the reference pressure k-index in convective_adjustment.F
723 - adjusted the convection condition in convect.F (in analogy to
724 calc_ivdc.F)
725 - convective_adjustment no longer computes anything on the halos
726 - removed the warnings about negative salinity from find_rho.F and
727 find_alpha.F; instead the new routine look_for_neg_salinity, called
728 at the beginning of find_rho, find_alpha, and find_beta, does a
729 check of the entire slice, if CPP-option
731 checkpoint46l_pre
733 checkpoint46k_post
734 o fixed the verification/global_ocean.90x40x15 experiment:
735 - new bathymetry (the world according to A., JMC, and M.)
736 - new initial fields and forcing fields (*.bin files)
737 - new POLY3.COEFFS (for the next release one should switch to a full
738 equation of state: JMD95P or MDJWF)
739 - fixed several errors and redundancies in the data file
740 - experiment uses looped cells
741 - added matlab directory with diagnostic scripts for plotting of output
743 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
744 - read AIM physics parameters from a file (data.aimphys)
745 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
747 checkpoint46j_post
748 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
749 o move wVel computation at the end of the time step, in S/R integr_continuity
750 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
751 o update timeave pkg for wVel diagnostic.
752 checkpoint46j_pre
754 checkpoint46i_post
755 o Clean up AIM package (and keep the results unchanged):
756 include CPP_OPTION and use IMPLICT NONE in all routines ;
757 declare all the variables _RL ; use _d 0 for all numerical constants.
758 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
760 checkpoint46h_post
761 o cleaned up the use of rhoNil and rhoConst.
762 - rhoNil should only appear in the LINEAR equation of state, everywhere
763 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
764 and the dynamical equations are all divided by rhoConst
765 o introduced new parameter rhoConstFresh, a reference density of fresh
766 water, to remove the fresh water flux's dependence on rhoNil. The default
767 value is 999.8 kg/m^3
768 o cleanup up external_forcing.F and external_forcing_surf.F
769 - can now be used by both OCEANIC and OCEANICP
770 checkpoint46h_pre
772 Added code to convert surface volume flux (fresh water) into
773 a mass flux when using P coordinates in the ocean (OCEANICP).
774 Note: It assumes you have set rho0=rhoConst=density of fresh water.
776 checkpoint46g_post
777 o Include a new diagnostic variable phiHydLow for the ocean model
778 - in z-coordinates, it is the bottom pressure anomaly
779 - in p-coordinates, it is the sea surface elevation
780 - in both cases, these variable have global drift, reflecting the mass
781 drift in z-coordinates and the volume drift in p-coordinates
782 - included time averaging for phiHydLow, be aware of the drift!
783 o depth-dependent computation of Bo_surf for pressure coordinates
784 in the ocean (buoyancyRelation='OCEANICP')
785 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
786 Theta, Salinity, and Pressure in the parameter list. This routine is
787 presently contained in find_rho.F. This routine does not give the
788 correct density for 'POLY3', which would be a z-dependent reference
789 density.
790 o cleaned up find_rho
791 - removed obsolete 'eqn' from the parameter list.
792 o added two new verification experiments: gop and goz
793 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
794 checkpoint46g_pre
796 checkpoint46f_post
797 o Enable tangent linear (forward mode) gradient checks:
798 - extended active file handling to g_... files
799 - added TANGENT_SIMULATION to theSimulationMode
800 - extended grdchk package accordingly
801 o added tangent linear setup in verification/carbon/code_ftl
802 o added adjoint setup in verification/front_relax/code_ad
804 checkpoint46e_post
805 o Added new equation of state -> MDJWF
806 - EOS of McDougall et al., 2002, JAOT, submitted
807 - caveat: the equation of state is only valid for a smaller (more
808 realistic?) range of values than JMD95P/Z and UNESCO
809 - added masks to the calculation of pressure in store_pressure
810 - added more check values for density in check_eos (ini_eos.F), some of
811 the old check values are out of the range of the MDJWF-eos, so don't
812 expect perfect matches for those
813 checkpoint46e_pre
815 checkpoint46d_post
816 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
817 'OCEANICP', also initialised field pressure correctly in ini_eos in the
818 case of pressure coordinates. eosType='JMD95Z' in
819 combination with buoyancyRelation='OCEANICP' now causes an error.
820 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
821 in find_alpha/beta.
822 checkpoint46d_pre
824 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
825 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
827 checkpoint46c_post
828 o Changes necessary for ocean in p-coordinates
829 - Added new buoyancy relation = 'OCEANICP'
830 - Added new parameters = gravitySign (this used to be contained inside
831 the factor dRdZ which I added when we first switched to R coordinates).
832 X GM/Redi is not compatible (yet)
833 X bottom drag and no-slip need to be debugged.
834 checkpoint46c_pre
836 checkpoint46b_post
837 o Added new equation of state -> JMD95Z and JMD95P
838 - EOS of Jackett and McDougall, 1995, JAOT
839 - moved all EOS parameters into EOS.h
840 - new routines ini_eos.F, store_pressure.F
841 o Added UNESCO EOS, but not recommended because it requires
842 in-situ temperature (see JMD95)
843 o Modified formatting for knudsen2.f in utils/knudsen2 and added
844 unesco.f to be used with POLY3
845 checkpoint46b_pre
847 checkpoint46a_post
848 o Added (atmospheric) pressure loading
849 - new field in FFIELDS.h, etc...
850 - new cpp flag ATMOSPHERIC_LOADING
851 o Changed hFacC to _hFacC in calc_phi_hyd.F
852 o Added SHORTWAVE_HEATING to some files for consistency
853 checkpoint46a_pre
855 checkpoint46
856 further merges from release1_p5
857 o new ctrl package
858 - adopted from ECCO environment to enable optimization
859 - added Eliassen Palm fluxes to controls
860 o added Eliassen Palm flux controls to gradient check package
861 o cost package
862 - Compatible with new ctrl package
863 - added Eliassen Palm cost hooks
864 - modif's of existing cost functions
865 o Adjoint-related bug fixes in kpp:
866 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
867 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
868 o autodiff package
869 - flow directives:
870 + new for S/R do_the_model_io
871 + enhanced for S/R checkpoint
872 + new gmredi.flow
873 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
874 disable adcommon.h/g_common.h by default.
875 - fixed problem for adjoint of global_max
876 o modified verification/carbon/
877 o New setup for adjoint of global_ocean
878 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
879 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
880 o incorporated hooks for sponge layer code (external_forcing.F)
882 checkpoint45d_post
883 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
884 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
885 (affects plume_on_slope "cg2d" output)
886 o add new parameter deltaTfreesurf for free-surface time stepping
887 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
888 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
889 o change phiMin in exp1 (to agree with documentation)
890 o add new flags:
891 - T,S forcing inside/outside Adams-Bashforth
892 - turn off temp,salt advection and/or forcing
893 - for each tracer, define internal flag for multiDimAdvection & A-B
894 o monitor: change definition of KE to check conservation of Energy
896 checkpoint45c_post
897 o Removed f90 comments ("!")
898 o Modified initialisations to enable exf package for MITgcm
899 (without invoking ECCO_PACKAGE).
900 o modifications to gradient check package (Martin Losch)
901 - enable centered differences
902 - modified format of standard output
904 checkpoint45b_post
905 o cleaned exchange calls in cg2d
906 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
907 o included CPP option SINGLE_LAYER_MODE in thermodynamics
908 to configure barotropic setup (Martin Losch)
909 o moved some initialisations within bi,bj loop in dynamics
910 (TAF flow dependency)
911 o in initialise_varia, moved call packages_init_variables
912 before convective_adjustment_init
913 (corresponding adjustment of TAF tape initialisation).
914 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
916 checkpoint45a_post
917 o compute Rho over the whole domain (extend iMin,jMin indices)
918 o specific exchange for X-slice domain (case Ny=1)
919 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
920 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
922 checkpoint44h_post = checkpoint45
923 o Fix to restore differentiability:
924 place at which packages_init_variables is called in
925 initialise_varia is crucial for reverse control flow.
926 o modifications in GMRedi to enable stable adjoint
927 (corresponding modif's in thermodynamics, dynamics)
928 o added missing hook for sponge layer code in external_forcing
929 o modified test cost functions
930 o storing in gad_advection (plus removal of write(0,*)!
931 o missing headers TR1.h added in convective_adjustment routines
932 o errorMessageUnit set non-equal zero in eeboot
933 (conflict on some platforms, e.g. IBM SP3)
934 o modified carbon verif.
936 checkpoint44h_pre
937 o vertical grid option: allow to put the Interface at the middle between
938 2 cell-centers ; replace delZ in pkg/kpp by drF.
939 o GM Advective form: Tracers are advected using the residual transport (=
940 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
942 checkpoint44g_post
943 o fix surface correction term in multiDimAdvection (affects plume_on_slope
944 results) ; ifdef missing in thermodynamics.F
946 checkpoint44f_pre,checkpoint44f_post
947 o added PTRACERS package
948 This allows an arbitrary number of passive tracers to be integrated
949 forward simultaneously with the dynamicaly model.
950 + Implemented so far:
951 - basic forward algorithm (time-stepping, advection, diffusion, convection)
952 - I/O and checkpointing
953 - GM/Redi *but* using the GM/Redi coefficient of Salt
954 + Not implemented so far:
955 - KPP
956 - OBCS
957 + No specific example supplied (yet) but global_ocean.90x40x15 has the
958 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
959 line in data.pkg.
960 + This package is disabled by default since it increases storage.
963 o testscript: added -cleanup option
964 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
965 b) enable to filter 2D fields.
967 checkpoint44e_pre,post
968 o re-wrote convective adjustment to use pre-calculated weights
969 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
970 Adds: model/src/convective_weights.F, convectively_mixtracer.F
971 Original calls to convect() still in place.
973 chkpt44d_pre,post
974 o added missing EXCLUDE_MONITOR flags
975 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
976 (incompatible typ in MIN/MAX expressions caused problems
977 on IBM SP3)
978 o in genmake added variable MAKEDEPEND
979 plus resetting for case SunOS
980 o added timer_stats.c routine for IBM SP3
981 o removed variables in dynamics
982 !!! I forgot to create tag chkpt44d_pre !!!
983 !!! But chkpt44d_pre = chkpt44c_post !!!
985 o real fresh water flux implemented with non-linear free-surface.
987 chkpt44c_pre,post
988 o few fix (mask in shap_s2, EmPmR in external_field_load,
989 USE_NATURAL_BCS in solve_for_P);
990 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
992 checkpoint44b_pre/_post
993 o merge of relevant stuff from the ecco-branch:
994 - genmake: removed $S64 overwrite for case SunOS
995 - pkg/exf: update and corrections for field swapping and obcs
996 - pkg/ecco: parameter lists for the_model_main, the_main_loop
997 harmonized between ECCO and MITgcm
998 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
999 updated checkpointing_lev... lists for obcs
1000 - model/src: minor changes in forward_step, plot_field
1001 added directive for divided adjoint in the_main_loop
1002 - pkg/mdsio: added mdsio_gl_slice
1004 o check parameters & config (chkpt44a_pre,post)
1005 o OBC and NonLin_FrSurf.
1007 checkpoint44
1008 o fix bug in mom_vi_del2uv
1009 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
1010 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
1011 o update AIM experiments (NCEP input files)
1012 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
1013 o added some stuff for AD
1015 checkpoint43
1016 o added two new advection tests
1017 o added global 4x4 degree ocean test
1018 o added test of H&S94 with free surface on cube
1019 o some final mods for gradient check, adjoint,...
1021 checkpoint42
1022 Fixed AD-related problems:
1023 o Store directives up-to-date with re-arranged Adams-Bashforth
1024 (mainly thermodynamics.F)
1025 o New store directives for multi-dim. advection schemes
1027 * new common block and key passkey
1028 (mainly gad_advection.F)
1029 o Modified store directives for split of dynamics/thermodynamics
1030 for the case ALLOW_KPP
1031 o Cleaned argument list for timestep_tracer.F
1033 checkpoint41
1034 o re-formatted/added comments in prologues of key subroutines
1035 to work with protex
1037 checkpoint40
1038 o moved calc_gs, calc_gt and calc_tr1 back to model/src
1039 o added FLT (floats) package from Arne along with demo. experiment
1040 o re-arranged Adams-Bashforth scheme for tracers to allow easier
1041 implementation of forward-in-time forcing terms
1042 o more mods for non-linear free-surface including new variable
1043 o modified multi-dim method to work on cube
1044 o bug fix in KPP (from DM)
1046 checkpoint40pre9
1047 o added DST advection schemes
1048 o fix MPI bug on SGI's
1049 o modifications for non-linear free-surface
1050 o fixed conditionals for fixed flow/passive tracer only mode
1051 o added tension/strain form of stress tensor
1052 o changes to commenting of arguments for TAF/TAMC
1053 o added/updated many matlab scripts
1054 o added multi-dimensional advection method for tracers
1056 checkpoint40pre8
1057 o new package rw/
1058 Added method for dumping intermediate local arrays:
1059 mdsio_writetile - same as mdsio_writefield except works from inside
1060 bi,bj loop
1061 mdsio_writelocal - same as mdsio_writetile except works for local
1062 arrays
1063 write_local_r? - higher-level wrapper for mdsio_writelocal
1064 Controlled by diagFreq. Defaults to zero (ie. no dumps)
1065 Example given at end of mom_vecinv.F that dumps some local arrays.
1066 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
1067 control flux-form versus vector invariant code.
1068 Switch is runtime flag vectorInvariantMomentum (defaults to false)
1069 or genmake -DISABLE ...
1070 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
1071 (additional storing is now needed for case vecinv;
1072 currently nothing implemented to switch this storing off
1073 in case fluxform is used since no CPP flag available).
1075 checkpoint40pre7
1076 o bug fix in dynamics.F
1077 calc_viscosity called before k=1,Nr loop.
1078 o added some #ifdef's ALLOW_PASSIVE_TRACER
1079 o cleaned initialisations in ctrl_map_ini
1080 related to TAF
1082 checkpoint40pre6
1083 o split dynamics into thermodynamics & dynamics
1084 o corresponding split of calc_diffusivity into
1085 calc_diffusivity, calc_viscosity
1086 (kpp_calc_diff, kpp_calc_visc).
1087 o Added diffkr, kapgm to control variables
1088 o bug fix in gmredi_slope_limit for ldd97
1090 checkpoint40pre5
1091 o proper initialization of Adams-Bashforth time stepping
1092 + uses forward step for very first step of model (iter=0)
1093 o re-generated *all* output since almost all output is modified by this
1094 change (sorry but we've been putting this one off for about 2 years)
1095 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
1096 *not* regenerated since they are already out of date and I don't
1097 want to create the impression that they are suddenly working.
1098 o removed KAP stuff for DEC's
1099 o modified/added many .cvsignore files in */code and */input
1100 o added new expt "solid-body.cs-32x32x1"
1101 + this uses an alternative form of ini_curvilinear_grid.F which
1102 is not necessarily any better than the current one...
1104 checkpoint40pre4
1105 o added re-initialisations of utrans,vtrans,rtrans in
1106 calc_common_factors which are crucial for TAF.
1107 o extended iMin,jMin range for calc_common_factors,
1108 calc_diffusivity
1109 o added option ALLOW_PASSIVE_TRACER
1110 o a few minor updates and fixes
1112 checkpoint40pre3
1113 o created calc_gtr1.F for gad package
1114 o split the_main_loop and re-introduced forward_step
1115 o some recomputations of nIter0 for TAMC
1117 checkpoint40pre2
1118 o Updated to latest branch of AJA, JMC
1119 o Added gradient check package
1120 o Added routines for passive tracer handling
1121 o Added carbon sequestration sensitivity experiment
1123 checkpoint39
1124 o Modifications and fixes to support TAMC
1125 (mainly missing or wrong directives)
1126 o Corrected common blocks when fooling TAMC to produce adjoint I/O
1127 in addummy_in_stepping
1128 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
1129 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
1130 o Included following packages:
1131 cal: calendar
1132 exf: external forcing
1133 ecco: essential routines to control use of cal, exf
1134 (NB: this is not the full ECCO environment)
1135 o disabled some packages by default in genmake
1137 checkpoint38
1138 o see notes_c37_adj.txt
1139 o corrected wrong layer index in external_forcing_t
1140 o replaced the_main_loop/forward_step by the_main_loop
1141 o removed forceoutput from write_state
1142 (replaced criteria for initial/final state)
1143 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
1145 checkpoint37
1146 o mdsio.F routine split and packaged in pkg/mdsio
1147 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
1148 used unless genmake -disable=mdsio)
1149 o allow a more precise surface-geopotential gradient for the atmosphere
1150 taking into account the change in space of Alpha (=1/rho) at the surface.
1151 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
1152 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
1153 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
1154 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
1155 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
1156 o Time-Average diagnostics defined as a pseudo package "timeave".
1157 o pickup files : old pickup (before c35) did not work with new code (c35
1158 and after) unless activating 2 commented lines in initialise-varia.
1159 o Non-Hydrostatic pickup file Pb fixed.
1160 o bug with Rigid-lid version (since c35) fixed.
1162 checkpoint36
1163 o implement Crank-Nickelson barotropic time-stepping
1164 o recover Time-Average diagnostics
1165 o fix Pb in checkpoint (PR#19)
1166 o AIM become a standard package ; clean unused CPP_kees
1168 checkpoint35
1169 o subtantial rewrite of dynamics.f
1170 o allows staggered time-stepping
1171 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
1172 o added bottom drag (linear + quadratic)
1174 checkpoint34
1175 o Modified exchange routines for correct reverse simulation.
1176 o Added verification output to comply with bug fix in impldiff.F
1177 as of c33 (exp2, natl_box).
1178 o Corrected store directives in dynamics.F
1179 o Corrected array boundaries in impldiff.F
1180 o Corrected array dimensions in gmredi.
1181 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
1182 o Added routine GLOBAL_SUM_INT to global_sum.F
1183 o Added mdsio_gl.F for ECCO purposes.
1185 checkpoint33
1186 o Fixed bug in lower BC in impldiff.F
1187 o Fixed confusion about units of forcing arrays in FFIELDS.h
1188 namely Fu,Fv,Qnet,Qsw,EmPmR:
1189 - Removed verification/natl_box/code/external_fields_scale.F
1190 (did not differ from that in model/src)
1191 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
1192 (see FFIELDS.h for description)
1193 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
1194 kpp_calc.F and kpp_transport_t.F
1195 - Removed model/src/external_fields_scale.F and calls to it
1196 - verification/natl_box uses flux data with "atmospheric" sign so
1197 a special version of external_fields_load.F is used to
1198 change the data as it's read in. This way, the arrays
1199 have the right units and signs at all times tha a user could
1200 possibly use them.
1201 o Corrected genmake to delete a temporary file during configuration
1203 checkpoint32
1204 o Scaling of forcing fields moved from external_forcing.F to
1205 external_fields_scale.F, called directly after loading fields.
1206 o Surface relaxation terms added to surface tendency fields in
1207 extra subroutine.
1208 o impldiff.F changed to avoid storing by TAMC of huge intermediate
1209 fields.
1210 o Changes in GMRedi to comply with packaging structure.
1211 o Modifications and bug fixes in KPP package.
1212 o Verification experiment for KPP added (verification/nat_box/)
1214 checkpoint31
1215 o Packages interface brought in line with defined standard
1216 -> new routines packages_...F
1217 -> changes in initialise_fixed.F, initialise_varia.F
1218 -> enables initialisation interface for ECCO package
1219 o Rescaling of external forcing fields immediately after read
1220 (removed from external_forcing.F)
1221 -> new: surface_fields_scale.F
1222 -> affects ini_foorcing.F, external_fields_load.F
1223 o Computation of surface tendencies before tendency updates.
1224 -> new: external_forcing_surf.F
1225 o Change of variable names useGMRedi, useKPP, useECCO
1226 o Further changes in dynamics.F, impldiff.F for TAMC
1227 o Tested for experiments 0, 2, 4.
1228 - not yet tested for GMRedi.
1229 - not yet tested for KPP.
1231 checkpoint30
1232 o Updates for OBCs
1233 o New experiment for test OBCs (internal_wave)
1234 o New output.txt in verification/exp4/results/
1235 o Updates for KPP: calculation of viscosity corrected, new variables
1236 kpp_dumpFreq and kpp_taveFreq
1237 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
1238 and entry for T90 in genmake
1240 checkpoint29
1241 o packaged KPP and GM/Redi
1243 checkpoint28
1244 o Corrected initialization of hFacMin for difference vertical coordinates
1245 o Modified calculation of partial cell thickness to more robust algorithm
1246 o config_summary.F: replaced write_1D_... by write_0D_...
1247 read_write.F: added subroutines write_0D_...
1248 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
1249 included some initialisations required for TAMC.
1250 o routine calc_isoslopes: modified sqrt computation to make it
1251 differentiable for zero argument.
1252 o routines dynamics, impldiff:
1253 included store directives and tape key computations required for TAMC.
1254 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
1256 checkpoint27
1257 o fixed calc_isoslopes() to so that cancellation of terms in tensor
1258 formulation works properly with variable resolution.
1259 o restructured the calling tree between the_model_main() and dynamics()
1260 o split initialise() into initialise_fixed() and initialise_varia()
1261 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
1262 in new routine ini_psurf()
1264 checkpoint26
1265 o moved some #ifdef in optional routines to encompass everything
1266 except the argument declarations. This was using up some memory.
1267 o fixed macros like _ADT to work with both versions of Linux cpp
1268 o cleaned up some unused and uninitialized variables
1269 (helps when debugging with strict compile options)
1270 o split up CPP_EEOPTIONS.h into options and macros
1271 (macros are now in eesupp/inc/CPP_EEMACROS.h)
1272 o patch for 2 processor JAM mode
1274 checkpoint25
1275 o updates for OBCs and NH
1276 o dramatically reduced memory usage
1277 o added "JAM" routines for use on Artic network
1278 o parameterization of convection by implicit vertical diffusion
1279 o added a diagnostic of convective index
1280 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
1281 (this is was partly for OBCs and NH but also in anticipation of
1282 an explicit free-surface option)
1283 o initial state input files for U and V
1285 checkpoint24
1286 o Removed some spurious "REAL"s
1287 o Updated KPP to latest version from JPL
1288 o Added a COS(latitude) in horizontal viscosity
1290 checkpoint23
1291 o Added del^4 diffusion for salt and temperature
1292 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
1294 checkpoint22
1295 o Made many small changes: implicit none, format(i5), etc...
1296 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
1298 checkpoint21
1299 o Introduced new I/O package that supports direct-access records (mdsio.F)
1300 o Split-up mid-level I/O routines
1301 o Updated input data for experiments 0,1,2,4 and 5
1302 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
1304 checkpoint20
1305 o Tidied up open-boundaries some more
1306 o Added non-hydrostatic code
1307 o Fixed some input data
1308 o Modified MPI start-up to work in "coupled" context.
1310 checkpoint19
1311 o Tidied up directory structure for verification experiments.
1312 o Added new code for open boundaries.
1313 o Corrected advective terms near boundaries.
1314 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
1315 o Implemented free-slip/no-slip BCs and del^4 dissipation.
1316 o Split default parameters out of ini_parms.F into set_defaults.F.
1318 checkpoint18
1319 o Further changes for optional code generation with
1320 CPP - ugh!
1322 checkpoint17
1323 o Beginning to incorporating modularity
1324 for supporting atmos. and ocean configs.
1325 o Small changes for TAMC complinace
1326 o New ultra simple test case. Barotropic box
1327 configuration "exp0".
1329 checkpoint16
1330 o Minor changes to exchange routines to support
1331 accumulation in reverse mode. Adjoint of an
1332 assignment is an addition.
1333 o Changes to support compilation by TAMC (LR(1)
1334 syntax) and by g77 under Linux ( 72 character
1335 limit ).
1337 checkpoint15
1338 Rewrote exchange routines to allow
1339 o General tile <-> tile connectivity.
1340 o TAMC reverse mode flag ( is this really needed? )
1341 o Variable width overlap and exchange region widths.
1342 o Hooks for sharing data via DMA, Arctic, Memory Channel,
1343 shmput/shmget, VIA, SYSV shmem and every other cool
1344 communication method.
1346 checkpoint14
1347 Consistent isomorphism chages made. These allow dynamical core
1348 to support both pressure and meters as a vertical coordinate.
1350 checkpoint13
1351 Release which corrects global_max problem and a couple
1352 of KGM time-averaging diagnostic errors. Also contains
1353 a double-gyre experiment setup as well as the baseline
1354 4 degree global template. The double gyre template is
1355 organised to allow it to be applied automatically to
1356 the baseline configuration.
1358 branch-point-rdot
1359 A few tidy-ups have been made bt the real point of this
1360 check-point (excuse the pun) is to allow a branch to be
1361 made for the purposes of adding the rDot alterations.
1362 I don't want to commit the rDot to the main-trunk until
1363 we've actually tested it...
1365 checkpoint12
1366 Tidy up and added generic genmake script (formerly
1367 configure script).
1368 Released to testers.
1370 checkpoint11
1371 Re-arranged initialise() and introduced ini_vertical_grid()
1372 and ini_masks_etc().
1374 checkpoint10
1375 Introduced the configure script.
1376 Separated out the diags package.
1377 Added template for writing time-averages of tile/intermediate quantities.
1378 Updated SIZE.h in exp2 and made the data big-endian.
1380 checkpoint9
1381 MPI fix. Filename changes (meta/data). salbin*y stuff.
1382 General tidy-up.
1383 SST.bin SSS.bin added to verification/exp2
1385 checkpoint8
1386 Inludes time-dependant forcing and time-averaging.
1387 Works at 4x4 and 2.8125x2.8125 global
1389 checkpoint7-4degree-ref
1390 Branch from checkpoint7. Released for application to
1391 global modeling and general modeling - process studies, regional
1392 model etc..
1393 Configured for verification/exp2 - 4 degree global, two process.
1395 checkpoint7
1396 Created by cnh
1397 Simple 4 degree global simulation
1398 configuration.
1399 Includes climatological wind,
1400 hydrography, bathymetry etc
1401 Does not include Heat Flux and E-P
1403 checkpoint6
1404 Created by cnh
1405 merged checkpoint5 with CD and
1406 spherical polar code.
1407 Still some problems with GM Redi
1408 abd full topography.
1410 checkpoint5
1411 Created by AJA
1412 contains updates to GM Redi
1413 and reordered timestepping loop
1414 for Implicit Diffusion.
1416 checkpoint4
1417 Created by cnh
1418 Contains memory saving macros ( _rdxc etc..) for when
1419 grid variations are limited.
1420 Contains polynomial coeffs for EOS and knudsen program
1421 for generation.
1423 checkpoint3
1424 Created by cnh
1425 Added extra flags for runtime options
1426 Added this file
1427 Added implicit free-surface
1428 Added pre-conditioner
1429 Put compare01 into repository ( compare01/... )
1430 Put data and eedata into repository ( verification/exp1 )
1432 checkpoint2
1433 Created by AJA
1434 Added GM/Redi
1436 checkpoint1
1437 Created by AJA
1438 Restructured kloop in dynamics.F
1439 Added non-linear EOS
1441 baseline
1442 Original checked in code

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