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Revision 1.194.2.1 - (show annotations) (download)
Tue Oct 28 00:27:48 2003 UTC (18 years, 8 months ago) by dimitri
Branch: checkpoint51n_branch
Changes since 1.194: +30 -4 lines
No panic, this is not on main branch!

1 $Header: /usr/local/gcmpack/MITgcm/doc/tag-index,v 1.194 2003/10/23 07:14:48 dimitri Exp $
2
3 Notes on tags used in MITgcmUV
4 ==============================
5
6 M doc/tag-index
7 M model/src/forward_step.F
8 M model/src/initialise_varia.F
9 M model/src/the_model_main.F
10 M ocean_inversion_project/README
11 M ocean_inversion_project/code/PTRACERS.h
12 M ocean_inversion_project/code/PTRACERS_OPTIONS.h
13 M ocean_inversion_project/code/SIZE.h_mpi
14 R ocean_inversion_project/input/data
15 R ocean_inversion_project/input/data.1765-2005
16 A ocean_inversion_project/input/data.1765-2005.1
17 A ocean_inversion_project/input/data.1765-2005.2
18 M ocean_inversion_project/input/data.ptracers
19 A ocean_inversion_project/input/data.stationary.1
20 A ocean_inversion_project/input/data.stationary.2
21 A ocean_inversion_project/input/data.stationary.3
22 M ocean_inversion_project/input/data.test
23 M pkg/ptracers/PTRACERS.h
24 M pkg/ptracers/PTRACERS_STATV.h
25 M pkg/ptracers/ptracers_readparms.F
26 M pkg/ptracers/ptracers_statv_write.F
27 M pkg/ptracers/ptracers_statvars.F
28 A pkg/seaice/TODO.txt
29 M pkg/timeave/timeave_statv_write.F
30 M pkg/timeave/timeave_statvars.F
31
32 checkpoint51n_post
33 o modifications to make FREEZE flux visible to pkg/kpp
34 - moved surfaceTendencyTice from pkg/seaice to main code
35 - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
36 - subroutine FREEZE now limits only surface temperature
37 this means new output.txt for global_ocean.90x40x15,
38 global_ocean.cs32x15, and global_with_exf, but note
39 that results for these three experiments remain
40 bit-identical to before if allowFreezing=.FALSE.
41 o added surface flux output variables to TIMEAVE_STATVARS
42
43 checkpoint51n_pre
44 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
45 o added [#include "AD_CONFIG.h"] to all files that use the following
46 defines:
47 - ALLOW_ADJOINT_RUN
48 - ALLOW_TANGENTLINEAR_RUN
49 - ALLOW_ECCO_OPTIMIZATION
50
51 checkpoint51m_post
52 o incorporating changes to get TAMC/TAF working in genmake2
53 - added new TAMC/TAF targets to the Makefile
54 - various cleanups related to package handling
55 - these changes should have no impact on the forward model
56
57 checkpoint51l_post
58 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
59 - faster algorithm for cal_addtime.F
60 - higher precision arithmetic, where needed
61 - pkg/exf *startdate variables changed from calendar date to
62 model integration time
63
64 checkpoint51l_pre
65 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
66 o enable to apply restoring on S & T only in a latitude band.
67 o update output (external_forcing_surf modif. change truncation errors)
68 global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
69
70 checkpoint51k_post
71 o change default to: useNHMTerms=.FALSE.
72 - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
73 adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
74 - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
75 exp1, ideal_2D_oce
76 - change data file of oceanic exp (leave the results unchanged for now)
77 exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
78 o set gravitySign automatically according to the vertical coordinate used
79 (and change sign: back to "logical" value: +1 when R increases downward)
80 o added an include barrier to the default CPP_OPTIONS.h and
81 removed the #include "PACKAGES_CONFIG.h" from it
82 o fix a bug in mom_fluxform (from chk51j_post)
83
84 checkpoint51j_post
85 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
86 o adjusted some flow directives (dynamics, thermodynamics)
87 o added cubed-sphere case to test cost function
88 o heckpoint_lev?_directives.h now include
89 pkg-specific directives, whenever those are enabled.
90 o Moving pkg-specific flow directives to corresponding pkg
91 Moving pkg-specific differentiation list to corresponding pkg
92 Moving pkg-specific checkpoint-lev storing to corresponding pkg
93 ---> conventions are
94 - pkg_ad.flow
95 - pkg_ad_diff.list
96 - pkg_ad_check_lev?_dir.h
97
98 checkpoint51i_post
99 o merge of the branch-genmake2
100 - knowingly breaks the older genmake
101 - automatic generation of all ALLOW_${PKG_NAME} defines
102 - new testreport supersedes older testscript
103 o large number of package inclusion and header cleanups
104 checkpoint51i_pre
105
106 o new output for adjoin of global ocean vector invariant
107 o fix for checkpoint of thermodynamic seaice and bulk_force
108 o Steph gchem various cleanups
109
110 checkpoint 51h_pre
111 o fixed some single quotes
112 o modify gchem pkg to be more versatile
113 o modifications to clean up dic pkg
114 o add pkg/cfc
115
116 checkpoint51g_post
117 o provide links for ARPACK and ADM*TLM
118 o start removing verification/vero/
119 o update AD-related stuff
120 (in particular some IF-statements in model/src/ routines)
121 o adding to verification/global_ocean.90x40x15/ adjoint of
122 vector invariant setup
123
124 checkpoint51f_post
125 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
126 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
127 of tracer Green's fucntions for ocean inversion project.
128
129 checkpoint51f_pre
130 o Added on-the-fly spatial interpolation capability
131 "USE_EXF_INTERPOLATION" to pkg/exf.
132 - This is a temporary Cartesian-grid hack until
133 the super-duper ESMF coupler becomes available.
134 - See verification/global_with_exf/README for usage example.
135 - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
136 flags and modified pkg/seaice accordingly.
137 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
138 and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
139 non-local transport term.
140
141 checkpoint51e_post
142 o pkg/mom_vecinv:
143 - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
144 - add time-ave diagnostic of vorticity advection.
145 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
146 o atmospheric geopotential: - include water vapor effect;
147 - use p^kappa in p* scaling.
148 o land pkg: read initial state from files.
149 o AIM : add stratospheric drag in the upper level
150
151 checkpoint51d_post
152 o change function ILNBLNK (=> last non-blank char.) to return zero
153 (instead of the string length) when the string. char is empty
154 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
155 o modif's to restore TAMC compatibility
156 - avoid "_d" constructs in PARAMETER declarations
157 - avoid interrupting lines by comment lines
158 o Use cluster local disks for purely local I/O
159 vs. globally visible disks needed for ctrl stuff
160 (merged from ecco-branch)
161 - new active_file_loc... and mdsio_..._loc routines
162 - affected packages: autodiff, ctrl, grdchk, mdsio
163
164 checkpoint51c_post
165 o introducing integer flag debugLevel
166 - debLevZero: suppress all output
167 - debLevA: standard
168 - debLevB: equivalent to current debugMode=.TRUE.
169 o introducing pathname variable mdsioLocalDir for mdsio
170 that can be specified at runtime
171 (relevant for cluster I/O to local disk)
172 `
173 >>>checkpoint51b_post
174 adjoint of ptracers
175 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
176 o extended state in checkpoint_lev?, etc.
177 o alternative ctrl/cost with tr1 or ptracer
178 o new comlev1_bibj_ptracers
179 o new ptracers.flow
180 o made ptracers_forcing same as external_forcing_s
181 o added verification for adjoint with ptracers
182 - adm. grdchk fail so far
183 - tlm. grdchk OK
184 - checked tapelev/comlev recomputations: OK
185 <<<checkpoint51b_pre
186
187 checkpoint51a_post
188 o added code for biogeochemistry package
189 - new pkgs: dic, gchem
190 - new subroutine in ptracers
191 o modify code for biogeo packages
192 - in model/src and pkg/ptracers
193
194 checkpoint51
195 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
196 - autodiff, ctrl, exf, grdchk, seaice
197 kept separate packages
198 - cost, ecco, obcs
199 o updating verification/internal_wave, verification/lab_sea
200 (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
201
202 checkpoint50i_post
203 o Preparing next differentiable checkpoint and sync
204 of MAIN vs. ecco-branch
205 - 1st step: this one is differentiable
206 - 2nd step: next(! not this) checkpoint will have updated packages
207 from ecco-branch)
208
209 checkpoint50h_post
210 o new package "land": provide surface BC for AIM.
211 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
212 o AIM: use true log-P extrapolation for near surface temp (= as in
213 F.Molteni paper) ; update aim.5l_cs output.
214 o New variable in PARM03 for more flexible pickups
215 o somewhat cleaned package initialisation sequence for
216 ctrl/ cost/ ecco/ in packages_... routines
217
218 checkpoint50g_post
219 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
220 - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
221 - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
222 made the default because of faster convergence than ADI
223
224 checkpoint50f_post
225 o exf totally restructured
226 - replaced all exf_set_ routines by one generic exf_set_gen.F
227 and made sure it's still differentiable
228 - split exf_getffields.F into new exf_bulkformulae.F
229 - exf_inscal_/exf_outscal_ suffixes consistent with field names
230 - updated adjoint/makefile and relevant verif. accordingly
231
232 checkpoint50f_pre
233 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
234 + change Evap over land. (update aim.5l_cs output)
235 o added missing .cvsignores and made uniform across expts
236 o changed configuration of tidal_basin_2d expt
237 o added pkg/debug functions for tracing code in fatal crashes
238 o tidied pkg/monitor to use MONITOR_OPTIONS.h
239 o new fn in pkg/monitor to stop model if solution grows too big
240 o removed lots of single quotes from comments
241
242 checkpoint50e_post
243 o make KPP work with PTRACERS
244 - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
245 nearly a copy of kpp_transport_s
246 - there is no analogue to SurfaceTendencyS, so I have to use
247 gPtr(of the surface layer) instead
248 o add a new platform SunFire+mpi (SunFire 15000) to genmake
249 checkpoint50e_pre
250
251 checkpoint50d_post
252 o change kpp output from multiple-record state files to single-record state
253 files analogous to write_state.F
254 o reduce the output frequency of cg3d-related stuff to the monitor frequency,
255 analogous to the cg2d-related output.
256 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
257 so that writing to internal file fn (with length 512) fails.
258 checkpoint50d_pre
259
260 checkpoint50c_post
261 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
262 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
263 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
264 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
265 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
266
267 checkpoint50c_pre
268 Merging from release1_p13:
269 o bug fix for pkg/seaice dynamic solver
270 o Added SEAICE_initialHEFF to pkg/seaice
271
272 checkpoint50b_post
273 o store u*,v* in gU,V instead of in guNm1,gvNm1
274 o in order to put the momForcing out of the Adams-Bashforth:
275 move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
276 to timestep.F
277 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
278 o re-generate output for highly sensitive test-exp:
279 global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
280
281 checkpoint50b_pre
282 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
283 o corrected CPP option mismatch in exf_Bulk... functions for case
284 #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
285
286 checkpoint50a_post
287 o Bug fix for merging between c50 and KPP.
288 ikey was passed from thermodynamics to kpp_calc via
289 common block rather than being recomputed in kpp_calc,
290 in contradiction with new key itdkey.
291 New key ikppkey created, and tamc.h headers updated.
292
293 checkpoint50
294 - 2nd step of merge with ecco-branch:
295 merge changes in ecco-branch back into main trunk
296 - bug fix in find_alpha
297 - more storing in gmredi_calc_tensor.F, kpp_routines.F
298 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
299 - merged some sliced AD support routines
300
301 checkpoint49
302 merged from ecco-branch:
303 o exf:
304 - Enable initialisation of forcing fields to constant
305 (runtime) values.
306 - in exf_getffields.F
307 Reduce i-/j-loop to interior domain, discarding overlaps.
308 That also fixes wrong TAF-key computations for key_1, key_2
309 with bulf formulae.
310 - exf_init.F modify #ifdef for exf_init_evap
311 - exf_getffieldrec.F, ctrl_getrec.F
312 The following INT-usages are not safe:
313 fldsecs = int(fldsecs/fldperiod)*fldperiod
314 fldcount = int(fldsecs/fldperiod) + 1
315 and were modified.
316 o autodiff: checkpoint_lev...
317 - updated storing for bulk formulae (some arrays were missing)
318 - added state for seaice package
319 - synchronized with main branch
320 o DIVA:
321 Modif.s in
322 - the_main_loop.F
323 - the_model_main.F
324 and added cost_final_restore.F cost_final_store.F
325 o With these changes, it is possible to fully separate
326 the first forward run to compute the cost function (mdthe_main_loop)
327 and adjoint runs over individual DIVA intervals (adthe_main_loop)
328 into separate model executions.
329 This enables better tuning of DIVA to given queue sizes.
330 o Loss of cost function value in consecutive DIVA runs is
331 fixed by storing to 'costfinal' file.
332 o Appropriate call of ctrl_unpack/_pack,grdchk_main at
333 beginning/end of adjoint integration is accounted for.
334 The current changes apply to TAF-1.4.26.
335 TAF has one remaining bug, requiring one manual change
336 (see MITgcm manual).
337 o cal: synchronized between MAIN and ecco-branch
338
339 checkpoint48i_post
340 o Changes to restore differentiability of code w.r.t. previous tag
341 (mostly adding new routines to make list and replacing
342 pressure by totPhiHyd).
343 o Updated and merged grdchk package
344 - has both ADM and TLM checks
345 - works for single- and multi-proc.
346 - output cleaned
347 - worked successfully for parallel DIVA
348 o genmake:
349 - Adding -platform=SP4
350 - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
351 o Modif. for DIVA:
352 ctrl_unpack should not be called in intermediate DIVA interval.
353 (similar thing would apply for active files such as
354 tbar, sbar, psbar, which should not be reinitialised;
355 only relevant for ecco-branch)
356
357 checkpoint48h_post
358 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
359 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
360 o Added SEAICE_initialHEFF to pkg/seaice
361 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
362
363 checkpoint48g_post
364 --- EOS:
365 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
366 store total Potential in totPhyHyd for diagnostics & EOS.
367 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
368 --- Pressure/geopotential gradient:
369 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
370 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
371 ( changes results of global_ocean_pressure )
372 o NLFS + z-coord.: add eta*Rho' contribution.
373 o accurate phiHyd when using interface-W at the middle between 2 centers
374 ( changes results of ideal_2D_oce )
375 o includes r* 2nd term in potential gradient.
376
377 checkpoint48f_post
378 Merging from release1_p12:
379 o Modifications for using pkg/exf with pkg/seaice
380 - improved description of the various forcing configurations
381 - added basic radiation bulk formulae to pkg/exf
382 - units/sign fix for evap computation in exf_getffields.F
383 - updated verification/global_with_exf/results/output.txt
384 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
385 (SBO) core products, including oceanic mass, center-of-mass,
386 angular, and bottom pressure (see pkg/sbo/README.sbo).
387 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
388 to avoid negative values in shallow regions.
389 - updated verification/natl_box/results/output.txt
390 - updated verification/lab_sea/results/output.txt
391 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
392 o Added useSingleCpuIO option (see PARAMS.h).
393 o Updated useSingleCpuIO option in mdsio_writefield.F to
394 work with multi-field files, e.g., for single-file pickup.
395 o pkg/seaice:
396 - bug fix in growth.F: QNET for no shortwave case
397 - added HeffFile for specifying initial sea-ice thickness
398 - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
399 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
400 kpp_transport_t.F, forward_step.F, and the_main_loop.F
401 o pkg/seaice:
402 - adjoint-friendly modifications
403 - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
404
405 checkpoint48e_post
406 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
407 o dynamics: change definition of computational domain & adapt mom_fluxform
408 accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
409 o following exp works with Olx=Oly=2 (and pass through checkbounds option):
410 adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
411 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
412 global_ocean.90x40x15 global_with_exf global_ocean_pressure
413 inverted_barometer solid-body.cs-32x32x1
414 (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
415
416 checkpoint48d_post
417 o in preparation for r*:
418 a) use pre-computed gradient of hydrostatic potential:
419 changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
420 b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
421 => affects results of glob_oce_pressure (different truncation error)
422 update output.txt of ideal_2D_oce & global_ocean_pressure
423
424 checkpoint48d_pre
425 o in preparation for r*:
426 new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
427 pass the 2 comp. of the grad. as arguments to momentum S/R.
428 but for the moment, only used if it does not change the results.
429 o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
430
431 checkpoint48c_post
432 Modifications in treatment of initial flux forcing controls
433 to avoid extra storing of flux fields.
434
435 checkpoint48c_pre
436 o Added tidal_basin_2d experiment (currently 1D!)
437 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
438
439 checkpoint48b_post
440 o r* coordinate added in #ifdef NONLIN_FRSURF block.
441 (modification to pressure gradient not yet implemented)
442 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
443 (for U & V) that are used for vertical advection of momentum.
444
445 checkpoint48a_post
446 o In preparation for r*, use temp. array to compute vertical transport
447 in flux-form momentum pkg. => change results of few test-exp.
448 Update output of: exp4, exp5, front_relax, global_ocean_pressure,
449 lab_sea, natl_box & plume_on_slope
450
451 checkpoint48
452 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
453
454 checkpoint47j_post
455 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
456 o moved adexch from forward_step to addummy_in_stepping
457 o added exch in ctrl_map_...
458 o aveFreq.=0. at end of cost_final to avoid overwrite in
459 reverse checkpointing loop
460 o Yet more changes in gmredi:
461 * adgmredi_calc_tensor
462 avoiding all recomputation of gmredi_slope_limit
463 * adgmredi_x/y/rtransport
464 added flag for excessive storing to avoid recomp. of
465 u/v/rtans, dTdx/y/z
466 -> this is not really necessary and very memory-consuming
467 * adgmredi_slope_psi:
468 consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
469 * gmredi_slope_limit
470 re-activated full calculation of taperfct for case 'ac02'
471 o updating verification/ adjoints of carbon, global_ocean.90x40x15
472
473 checkpoint47i_post
474 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
475 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
476 default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
477 o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
478 o gmredi: fix few bugs.
479
480 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
481 This will be a good checkpoint to plug into the ecco-branch.
482 o few modif.'s to get latest version adjointed
483 (mainly kick out code in ini_linear_phisurf)
484 o modif's to run adjoint with exactConserv
485 o case GM_BOLUS_ADVEC should be cleaned
486 S/R gmredi_slope_psi should be cleaned
487 o verification/carbon now has exactConserv=.TRUE.
488
489 checkpoint47g_post
490 o time-average AIM output: becomes independent from statvars time-average
491 (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
492 o After TAF bug fix:
493 Tested adjoint of gmredi package.
494 Tests were done with checkpoint47 rather than with latest
495 checkpoint47f_post since the latter is broken for the adjoint
496 verification/carbon/ contains both ADM and TLM gradient checks.
497 Here they are, before they get changed/lost/stolen.
498 Mostly modif.'s to fix numerical sensitivities.
499 Gradient checks OK for
500 - GM_taper_scheme:
501 * clipping
502 * ac02
503 * linear
504 * glw91
505 * dm95
506 * ldd97
507 - GMREDI_OPTIONS:
508 * GM_VISBECK_VARIABLE_K
509 * GM_NON_UNITY_DIAGONAL
510 * GM_EXTRA_DIAGONAL
511 * GM_BOLUS_ADVEC
512 in conjunction with data.gmredi parameters to be checked in
513 in a few minutes under verification/carbon/code/
514
515 checkpoint47f_post
516 Merging from release1_p10:
517 o modifications for using pkg/exf with pkg/seaice
518 - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
519 and SEAICE_EXTERNAL_FLUXES
520 - pkg/exf CPP options EXF_READ_EVAP and
521 EXF_NO_BULK_COMPUTATIONS
522 - usage examples are Experiments 8 and 9 in
523 verification/lab_sea/README
524 - verification/lab_sea default experiment now uses
525 pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
526
527 checkpoint47e_post
528 o created a tag prior to creating a branch
529
530 checkpoint47d_post
531 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
532 at the bottom boundary had an erroneous half slip boundary condition
533 o added bottom drag and no slip boundary condition capabilities to
534 oceanic pressure coordinates code
535 o added new verification experiment global_ocean_pressure, this experiment is
536 also described in the tutorial section of the manual
537 checkpoint47d_pre
538
539 checkpoint47c_post
540 o Added a verification experiment for a global cubed-sphere ocean run
541 - verification/global_ocean.cubed32x32x30
542 - uses pkg/therm_seaice and pkg/bulk_forcing
543
544 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
545 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
546 when using P-coordinate; only implemented for atmospheric config.
547 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
548 NOTES: requires option NONLIN_FRSURF to be "#define".
549 o update advect_xz/results/output.txt (left from checkpoint44g_post)
550
551 checkpoint47b_post
552 Merging from release1_p9:
553 o pkg/seaice
554 - removed GOTO's and added taf directives
555 - double precision constants to reduce the g77 (Linux)
556 to F77 (SGI) differences reported in release1_p8
557 o tools/genmake
558 - added SGI options
559 o verification/testscript
560 - updated to that of checkpoint47a_post
561 o verification/global_ocean.90x40x15/input/eedata
562 - modified for SGI f77 compatibility
563 o verification/lab_sea
564 - added description of sea-ice model
565 - added missing matlab routines
566 - added test of thermodynamics parallelization
567
568 checkpoint47a_post
569 o new pkg: aim_v23
570 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
571 for now, keep the same surface forcing as before.
572 - Part-Cell implemented into AIM; check that Heat & Water are conserved
573 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
574 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
575 o add diagnostic of surface correction term in monitor output
576
577 o bulk_force and therm_seaice
578 - Two packages: bulk_force (Bulk forcing)
579 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
580 - Earlier integration from Stephaine Dutkiewicz
581 and Patrick Heimbach.
582 - Two ifdef statements for compile time,
583 ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
584
585 checkpoint47
586 differentiable version of checkpoint46n_post
587 o bug fix in quasihydrostaticterms
588 o * "clean" adjoint code (in terms of extensive recomputations)
589 can now be obtained for all GMREDI options (i.e. for
590 - GM_VISBECK_VARIABLE_K
591 - GM_NON_UNITY_DIAGONAL
592 - GM_EXTRA_DIAGONAL
593 - GM_BOLUS_ADVEC )
594 * However, wrong gradient check problem remains unsolved.
595 * New CPP options have been introduced for different
596 tapering schemes
597 o external_fields_load now part of differentiation list
598 o pressure needs multiple storing;
599 would be nice to have store_pressure at beginning or
600 end of forward_step, e.g. by having phiHyd global (5-dim.)
601 (NB: pressure is needed for certain cases in find_rho,
602 which is also invoked through convective_adjustment).
603 o recomputations in find_rho for cases
604 'JMD95'/'UNESCO' or 'MDJWF' are OK.
605 o #define ATMOSPHERIC_LOADING should be differentiable
606 o ini_forcing shifted to begining of initialise_varia
607 o Incorporating QNVS line search routines into MITgcm
608 (this is separate code, and therefore not under pkg)
609 lsopt/, optim/
610 o Updated verification/carbon/
611 - #define GM_VISBECK_VARIABLE_K
612 - GM_taper_scheme = 'ldd97'
613
614 checkpoint46n_post
615 Merging from release1_p8:
616 o verification/natl_box:
617 updating new external_fields_load routine
618 o New package: pkg/seaice
619 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
620 The sea-ice code is based on Hibler (1979-1980).
621 Two sea-ice dynamic solvers, ADI and LSR, are included.
622 In addition to computing prognostic sea-ice variables and diagnosing
623 the forcing/external data fields that drive the ocean model,
624 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
625 The implied surface heat flux is then stored in variable
626 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
627 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
628 non-local transport term. Because this call precedes model
629 thermodynamics, temperature under sea-ice may not be "exactly" at
630 the freezing point by the time theta is dumped or time-averaged.
631 N.B.: fairly large differences in accuracy occur across
632 different platforms/compilers; comparison between
633 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
634 generated output gives:
635 T S U V
636 C D M c m s m s m s m s
637 n p a R g m m e . m m e . m m e . m m e .
638 f n k u 2 i a a d i a a d i a a d i a a d
639 g d e n d n x n . n x n . n x n . n x n .
640
641 Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
642 o GAD:
643 - generated new common blocks to account for call of
644 same gad routines with differing traceridentities
645 (needed to modify tracerIdentity indices in GAD.h)
646 - generated separate common blocks for case useCubedSphereExchange
647 (Department of Futurology)
648 - parameter lists to gmredi_?transport: added tracerIdentity
649 - added new key indices to tamc.h
650 o external_fields_load:
651 - added this routine to TAF list
652 - needed to make some common blocks global and additional storing
653 along the same lines as exf package (checkpoint_lev?_directives.h)
654 o exf:
655 updated external forcing package
656 - bug fixes carried over from ecco-branch
657 (missing OBCS_OPTIONS.h in two routines)
658 - enable easy to use "no forcing".
659 - added exf I/O for atmospheric loading
660 - added exf I/O for runoff data
661 - transfered scaling between exf <-> MITgcm to exf namelist
662 o Adding new verification experiment global_with_exf.
663 This verification experiment is almost identical to the
664 global_ocean.90x40x15 experiment, except that it uses
665 the exf (and cal) package instead of the
666 external_fields_load routine (cf README file).
667
668 checkpoint46m_post
669 o modified testscript to return -- when there are no lines of "%MON" output
670 o added new flag "quasiHydrostatic" for QH mode
671 and new routine quasihydrostaticterms()
672 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
673 New routine: mom_u_coriolis_nh()
674 o fixed sign of non-hydrostatic metric terms in u and v equations.
675 Depend on correct sign of gravitySign.
676 o added work.pc* to .cvsignore in aim directories using ifc
677 o introduced flag for controllin non-hydrostatic metric terms
678 o removed gravitySign from PARM04
679 o switched to g77/ifc from pgf77 in aim experiments
680
681 checkpoint46l_post
682 o made convective adjustment work with pressure coordinates:
683 - changed the direction of k-loop in convective_adjustment.F for the
684 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
685 - adjusted the reference pressure k-index in convective_adjustment.F
686 - adjusted the convection condition in convect.F (in analogy to
687 calc_ivdc.F)
688 - convective_adjustment no longer computes anything on the halos
689 - removed the warnings about negative salinity from find_rho.F and
690 find_alpha.F; instead the new routine look_for_neg_salinity, called
691 at the beginning of find_rho, find_alpha, and find_beta, does a
692 check of the entire slice, if CPP-option
693 CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
694 checkpoint46l_pre
695
696 checkpoint46k_post
697 o fixed the verification/global_ocean.90x40x15 experiment:
698 - new bathymetry (the world according to A., JMC, and M.)
699 - new initial fields and forcing fields (*.bin files)
700 - new POLY3.COEFFS (for the next release one should switch to a full
701 equation of state: JMD95P or MDJWF)
702 - fixed several errors and redundancies in the data file
703 - experiment uses looped cells
704 - added matlab directory with diagnostic scripts for plotting of output
705
706 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
707 - read AIM physics parameters from a file (data.aimphys)
708 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
709
710 checkpoint46j_post
711 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
712 o move wVel computation at the end of the time step, in S/R integr_continuity
713 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
714 o update timeave pkg for wVel diagnostic.
715 checkpoint46j_pre
716
717 checkpoint46i_post
718 o Clean up AIM package (and keep the results unchanged):
719 include CPP_OPTION and use IMPLICT NONE in all routines ;
720 declare all the variables _RL ; use _d 0 for all numerical constants.
721 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
722
723 checkpoint46h_post
724 o cleaned up the use of rhoNil and rhoConst.
725 - rhoNil should only appear in the LINEAR equation of state, everywhere
726 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
727 and the dynamical equations are all divided by rhoConst
728 o introduced new parameter rhoConstFresh, a reference density of fresh
729 water, to remove the fresh water flux's dependence on rhoNil. The default
730 value is 999.8 kg/m^3
731 o cleanup up external_forcing.F and external_forcing_surf.F
732 - can now be used by both OCEANIC and OCEANICP
733 checkpoint46h_pre
734
735 Added code to convert surface volume flux (fresh water) into
736 a mass flux when using P coordinates in the ocean (OCEANICP).
737 Note: It assumes you have set rho0=rhoConst=density of fresh water.
738
739 checkpoint46g_post
740 o Include a new diagnostic variable phiHydLow for the ocean model
741 - in z-coordinates, it is the bottom pressure anomaly
742 - in p-coordinates, it is the sea surface elevation
743 - in both cases, these variable have global drift, reflecting the mass
744 drift in z-coordinates and the volume drift in p-coordinates
745 - included time averaging for phiHydLow, be aware of the drift!
746 o depth-dependent computation of Bo_surf for pressure coordinates
747 in the ocean (buoyancyRelation='OCEANICP')
748 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
749 Theta, Salinity, and Pressure in the parameter list. This routine is
750 presently contained in find_rho.F. This routine does not give the
751 correct density for 'POLY3', which would be a z-dependent reference
752 density.
753 o cleaned up find_rho
754 - removed obsolete 'eqn' from the parameter list.
755 o added two new verification experiments: gop and goz
756 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
757 checkpoint46g_pre
758
759 checkpoint46f_post
760 o Enable tangent linear (forward mode) gradient checks:
761 - extended active file handling to g_... files
762 - added TANGENT_SIMULATION to theSimulationMode
763 - extended grdchk package accordingly
764 o added tangent linear setup in verification/carbon/code_ftl
765 o added adjoint setup in verification/front_relax/code_ad
766
767 checkpoint46e_post
768 o Added new equation of state -> MDJWF
769 - EOS of McDougall et al., 2002, JAOT, submitted
770 - caveat: the equation of state is only valid for a smaller (more
771 realistic?) range of values than JMD95P/Z and UNESCO
772 - added masks to the calculation of pressure in store_pressure
773 - added more check values for density in check_eos (ini_eos.F), some of
774 the old check values are out of the range of the MDJWF-eos, so don't
775 expect perfect matches for those
776 checkpoint46e_pre
777
778 checkpoint46d_post
779 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
780 'OCEANICP', also initialised field pressure correctly in ini_eos in the
781 case of pressure coordinates. eosType='JMD95Z' in
782 combination with buoyancyRelation='OCEANICP' now causes an error.
783 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
784 in find_alpha/beta.
785 checkpoint46d_pre
786
787 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
788 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
789
790 checkpoint46c_post
791 o Changes necessary for ocean in p-coordinates
792 - Added new buoyancy relation = 'OCEANICP'
793 - Added new parameters = gravitySign (this used to be contained inside
794 the factor dRdZ which I added when we first switched to R coordinates).
795 X GM/Redi is not compatible (yet)
796 X bottom drag and no-slip need to be debugged.
797 checkpoint46c_pre
798
799 checkpoint46b_post
800 o Added new equation of state -> JMD95Z and JMD95P
801 - EOS of Jackett and McDougall, 1995, JAOT
802 - moved all EOS parameters into EOS.h
803 - new routines ini_eos.F, store_pressure.F
804 o Added UNESCO EOS, but not recommended because it requires
805 in-situ temperature (see JMD95)
806 o Modified formatting for knudsen2.f in utils/knudsen2 and added
807 unesco.f to be used with POLY3
808 checkpoint46b_pre
809
810 checkpoint46a_post
811 o Added (atmospheric) pressure loading
812 - new field in FFIELDS.h, etc...
813 - new cpp flag ATMOSPHERIC_LOADING
814 o Changed hFacC to _hFacC in calc_phi_hyd.F
815 o Added SHORTWAVE_HEATING to some files for consistency
816 checkpoint46a_pre
817
818 checkpoint46
819 further merges from release1_p5
820 o new ctrl package
821 - adopted from ECCO environment to enable optimization
822 - added Eliassen Palm fluxes to controls
823 o added Eliassen Palm flux controls to gradient check package
824 o cost package
825 - Compatible with new ctrl package
826 - added Eliassen Palm cost hooks
827 - modif's of existing cost functions
828 o Adjoint-related bug fixes in kpp:
829 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
830 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
831 o autodiff package
832 - flow directives:
833 + new for S/R do_the_model_io
834 + enhanced for S/R checkpoint
835 + new gmredi.flow
836 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
837 disable adcommon.h/g_common.h by default.
838 - fixed problem for adjoint of global_max
839 o modified verification/carbon/
840 o New setup for adjoint of global_ocean
841 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
842 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
843 o incorporated hooks for sponge layer code (external_forcing.F)
844
845 checkpoint45d_post
846 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
847 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
848 (affects plume_on_slope "cg2d" output)
849 o add new parameter deltaTfreesurf for free-surface time stepping
850 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
851 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
852 o change phiMin in exp1 (to agree with documentation)
853 o add new flags:
854 - T,S forcing inside/outside Adams-Bashforth
855 - turn off temp,salt advection and/or forcing
856 - for each tracer, define internal flag for multiDimAdvection & A-B
857 o monitor: change definition of KE to check conservation of Energy
858
859 checkpoint45c_post
860 o Removed f90 comments ("!")
861 o Modified initialisations to enable exf package for MITgcm
862 (without invoking ECCO_PACKAGE).
863 o modifications to gradient check package (Martin Losch)
864 - enable centered differences
865 - modified format of standard output
866
867 checkpoint45b_post
868 o cleaned exchange calls in cg2d
869 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
870 o included CPP option SINGLE_LAYER_MODE in thermodynamics
871 to configure barotropic setup (Martin Losch)
872 o moved some initialisations within bi,bj loop in dynamics
873 (TAF flow dependency)
874 o in initialise_varia, moved call packages_init_variables
875 before convective_adjustment_init
876 (corresponding adjustment of TAF tape initialisation).
877 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
878
879 checkpoint45a_post
880 o compute Rho over the whole domain (extend iMin,jMin indices)
881 o specific exchange for X-slice domain (case Ny=1)
882 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
883 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
884
885 checkpoint44h_post = checkpoint45
886 o Fix to restore differentiability:
887 place at which packages_init_variables is called in
888 initialise_varia is crucial for reverse control flow.
889 o modifications in GMRedi to enable stable adjoint
890 (corresponding modif's in thermodynamics, dynamics)
891 o added missing hook for sponge layer code in external_forcing
892 o modified test cost functions
893 o storing in gad_advection (plus removal of write(0,*)!
894 o missing headers TR1.h added in convective_adjustment routines
895 o errorMessageUnit set non-equal zero in eeboot
896 (conflict on some platforms, e.g. IBM SP3)
897 o modified carbon verif.
898
899 checkpoint44h_pre
900 o vertical grid option: allow to put the Interface at the middle between
901 2 cell-centers ; replace delZ in pkg/kpp by drF.
902 o GM Advective form: Tracers are advected using the residual transport (=
903 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
904
905 checkpoint44g_post
906 o fix surface correction term in multiDimAdvection (affects plume_on_slope
907 results) ; ifdef missing in thermodynamics.F
908
909 checkpoint44f_pre,checkpoint44f_post
910 o added PTRACERS package
911 This allows an arbitrary number of passive tracers to be integrated
912 forward simultaneously with the dynamicaly model.
913 + Implemented so far:
914 - basic forward algorithm (time-stepping, advection, diffusion, convection)
915 - I/O and checkpointing
916 - GM/Redi *but* using the GM/Redi coefficient of Salt
917 + Not implemented so far:
918 - KPP
919 - OBCS
920 + No specific example supplied (yet) but global_ocean.90x40x15 has the
921 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
922 line in data.pkg.
923 + This package is disabled by default since it increases storage.
924
925
926 o testscript: added -cleanup option
927 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
928 b) enable to filter 2D fields.
929
930 checkpoint44e_pre,post
931 o re-wrote convective adjustment to use pre-calculated weights
932 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
933 Adds: model/src/convective_weights.F, convectively_mixtracer.F
934 Original calls to convect() still in place.
935
936 chkpt44d_pre,post
937 o added missing EXCLUDE_MONITOR flags
938 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
939 (incompatible typ in MIN/MAX expressions caused problems
940 on IBM SP3)
941 o in genmake added variable MAKEDEPEND
942 plus resetting for case SunOS
943 o added timer_stats.c routine for IBM SP3
944 o removed variables in dynamics
945 !!! I forgot to create tag chkpt44d_pre !!!
946 !!! But chkpt44d_pre = chkpt44c_post !!!
947
948 o real fresh water flux implemented with non-linear free-surface.
949
950 chkpt44c_pre,post
951 o few fix (mask in shap_s2, EmPmR in external_field_load,
952 USE_NATURAL_BCS in solve_for_P);
953 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
954
955 checkpoint44b_pre/_post
956 o merge of relevant stuff from the ecco-branch:
957 - genmake: removed $S64 overwrite for case SunOS
958 - pkg/exf: update and corrections for field swapping and obcs
959 - pkg/ecco: parameter lists for the_model_main, the_main_loop
960 harmonized between ECCO and MITgcm
961 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
962 updated checkpointing_lev... lists for obcs
963 - model/src: minor changes in forward_step, plot_field
964 added directive for divided adjoint in the_main_loop
965 - pkg/mdsio: added mdsio_gl_slice
966
967 o check parameters & config (chkpt44a_pre,post)
968 o OBC and NonLin_FrSurf.
969
970 checkpoint44
971 o fix bug in mom_vi_del2uv
972 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
973 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
974 o update AIM experiments (NCEP input files)
975 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
976 o added some stuff for AD
977
978 checkpoint43
979 o added two new advection tests
980 o added global 4x4 degree ocean test
981 o added test of H&S94 with free surface on cube
982 o some final mods for gradient check, adjoint,...
983
984 checkpoint42
985 Fixed AD-related problems:
986 o Store directives up-to-date with re-arranged Adams-Bashforth
987 (mainly thermodynamics.F)
988 o New store directives for multi-dim. advection schemes
989 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
990 * new common block and key passkey
991 (mainly gad_advection.F)
992 o Modified store directives for split of dynamics/thermodynamics
993 for the case ALLOW_KPP
994 o Cleaned argument list for timestep_tracer.F
995
996 checkpoint41
997 o re-formatted/added comments in prologues of key subroutines
998 to work with protex
999
1000 checkpoint40
1001 o moved calc_gs, calc_gt and calc_tr1 back to model/src
1002 o added FLT (floats) package from Arne along with demo. experiment
1003 o re-arranged Adams-Bashforth scheme for tracers to allow easier
1004 implementation of forward-in-time forcing terms
1005 o more mods for non-linear free-surface including new variable
1006 o modified multi-dim method to work on cube
1007 o bug fix in KPP (from DM)
1008
1009 checkpoint40pre9
1010 o added DST advection schemes
1011 o fix MPI bug on SGI's
1012 o modifications for non-linear free-surface
1013 o fixed conditionals for fixed flow/passive tracer only mode
1014 o added tension/strain form of stress tensor
1015 o changes to commenting of arguments for TAF/TAMC
1016 o added/updated many matlab scripts
1017 o added multi-dimensional advection method for tracers
1018
1019 checkpoint40pre8
1020 o new package rw/
1021 Added method for dumping intermediate local arrays:
1022 mdsio_writetile - same as mdsio_writefield except works from inside
1023 bi,bj loop
1024 mdsio_writelocal - same as mdsio_writetile except works for local
1025 arrays
1026 write_local_r? - higher-level wrapper for mdsio_writelocal
1027 Controlled by diagFreq. Defaults to zero (ie. no dumps)
1028 Example given at end of mom_vecinv.F that dumps some local arrays.
1029 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
1030 control flux-form versus vector invariant code.
1031 Switch is runtime flag vectorInvariantMomentum (defaults to false)
1032 or genmake -DISABLE ...
1033 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
1034 (additional storing is now needed for case vecinv;
1035 currently nothing implemented to switch this storing off
1036 in case fluxform is used since no CPP flag available).
1037
1038 checkpoint40pre7
1039 o bug fix in dynamics.F
1040 calc_viscosity called before k=1,Nr loop.
1041 o added some #ifdef's ALLOW_PASSIVE_TRACER
1042 o cleaned initialisations in ctrl_map_ini
1043 related to TAF
1044
1045 checkpoint40pre6
1046 o split dynamics into thermodynamics & dynamics
1047 o corresponding split of calc_diffusivity into
1048 calc_diffusivity, calc_viscosity
1049 (kpp_calc_diff, kpp_calc_visc).
1050 o Added diffkr, kapgm to control variables
1051 o bug fix in gmredi_slope_limit for ldd97
1052
1053 checkpoint40pre5
1054 o proper initialization of Adams-Bashforth time stepping
1055 + uses forward step for very first step of model (iter=0)
1056 o re-generated *all* output since almost all output is modified by this
1057 change (sorry but we've been putting this one off for about 2 years)
1058 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
1059 *not* regenerated since they are already out of date and I don't
1060 want to create the impression that they are suddenly working.
1061 o removed KAP stuff for DEC's
1062 o modified/added many .cvsignore files in */code and */input
1063 o added new expt "solid-body.cs-32x32x1"
1064 + this uses an alternative form of ini_curvilinear_grid.F which
1065 is not necessarily any better than the current one...
1066
1067 checkpoint40pre4
1068 o added re-initialisations of utrans,vtrans,rtrans in
1069 calc_common_factors which are crucial for TAF.
1070 o extended iMin,jMin range for calc_common_factors,
1071 calc_diffusivity
1072 o added option ALLOW_PASSIVE_TRACER
1073 o a few minor updates and fixes
1074
1075 checkpoint40pre3
1076 o created calc_gtr1.F for gad package
1077 o split the_main_loop and re-introduced forward_step
1078 o some recomputations of nIter0 for TAMC
1079
1080 checkpoint40pre2
1081 o Updated to latest branch of AJA, JMC
1082 o Added gradient check package
1083 o Added routines for passive tracer handling
1084 o Added carbon sequestration sensitivity experiment
1085
1086 checkpoint39
1087 o Modifications and fixes to support TAMC
1088 (mainly missing or wrong directives)
1089 o Corrected common blocks when fooling TAMC to produce adjoint I/O
1090 in addummy_in_stepping
1091 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
1092 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
1093 o Included following packages:
1094 cal: calendar
1095 exf: external forcing
1096 ecco: essential routines to control use of cal, exf
1097 (NB: this is not the full ECCO environment)
1098 o disabled some packages by default in genmake
1099
1100 checkpoint38
1101 o see notes_c37_adj.txt
1102 o corrected wrong layer index in external_forcing_t
1103 o replaced the_main_loop/forward_step by the_main_loop
1104 o removed forceoutput from write_state
1105 (replaced criteria for initial/final state)
1106 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
1107
1108 checkpoint37
1109 o mdsio.F routine split and packaged in pkg/mdsio
1110 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
1111 used unless genmake -disable=mdsio)
1112 o allow a more precise surface-geopotential gradient for the atmosphere
1113 taking into account the change in space of Alpha (=1/rho) at the surface.
1114 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
1115 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
1116 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
1117 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
1118 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
1119 o Time-Average diagnostics defined as a pseudo package "timeave".
1120 o pickup files : old pickup (before c35) did not work with new code (c35
1121 and after) unless activating 2 commented lines in initialise-varia.
1122 o Non-Hydrostatic pickup file Pb fixed.
1123 o bug with Rigid-lid version (since c35) fixed.
1124
1125 checkpoint36
1126 o implement Crank-Nickelson barotropic time-stepping
1127 o recover Time-Average diagnostics
1128 o fix Pb in checkpoint (PR#19)
1129 o AIM become a standard package ; clean unused CPP_kees
1130
1131 checkpoint35
1132 o subtantial rewrite of dynamics.f
1133 o allows staggered time-stepping
1134 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
1135 o added bottom drag (linear + quadratic)
1136
1137 checkpoint34
1138 o Modified exchange routines for correct reverse simulation.
1139 o Added verification output to comply with bug fix in impldiff.F
1140 as of c33 (exp2, natl_box).
1141 o Corrected store directives in dynamics.F
1142 o Corrected array boundaries in impldiff.F
1143 o Corrected array dimensions in gmredi.
1144 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
1145 o Added routine GLOBAL_SUM_INT to global_sum.F
1146 o Added mdsio_gl.F for ECCO purposes.
1147
1148 checkpoint33
1149 o Fixed bug in lower BC in impldiff.F
1150 o Fixed confusion about units of forcing arrays in FFIELDS.h
1151 namely Fu,Fv,Qnet,Qsw,EmPmR:
1152 - Removed verification/natl_box/code/external_fields_scale.F
1153 (did not differ from that in model/src)
1154 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
1155 (see FFIELDS.h for description)
1156 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
1157 kpp_calc.F and kpp_transport_t.F
1158 - Removed model/src/external_fields_scale.F and calls to it
1159 - verification/natl_box uses flux data with "atmospheric" sign so
1160 a special version of external_fields_load.F is used to
1161 change the data as it's read in. This way, the arrays
1162 have the right units and signs at all times tha a user could
1163 possibly use them.
1164 o Corrected genmake to delete a temporary file during configuration
1165
1166 checkpoint32
1167 o Scaling of forcing fields moved from external_forcing.F to
1168 external_fields_scale.F, called directly after loading fields.
1169 o Surface relaxation terms added to surface tendency fields in
1170 extra subroutine.
1171 o impldiff.F changed to avoid storing by TAMC of huge intermediate
1172 fields.
1173 o Changes in GMRedi to comply with packaging structure.
1174 o Modifications and bug fixes in KPP package.
1175 o Verification experiment for KPP added (verification/nat_box/)
1176
1177 checkpoint31
1178 o Packages interface brought in line with defined standard
1179 -> new routines packages_...F
1180 -> changes in initialise_fixed.F, initialise_varia.F
1181 -> enables initialisation interface for ECCO package
1182 o Rescaling of external forcing fields immediately after read
1183 (removed from external_forcing.F)
1184 -> new: surface_fields_scale.F
1185 -> affects ini_foorcing.F, external_fields_load.F
1186 o Computation of surface tendencies before tendency updates.
1187 -> new: external_forcing_surf.F
1188 o Change of variable names useGMRedi, useKPP, useECCO
1189 o Further changes in dynamics.F, impldiff.F for TAMC
1190 o Tested for experiments 0, 2, 4.
1191 - not yet tested for GMRedi.
1192 - not yet tested for KPP.
1193
1194 checkpoint30
1195 o Updates for OBCs
1196 o New experiment for test OBCs (internal_wave)
1197 o New output.txt in verification/exp4/results/
1198 o Updates for KPP: calculation of viscosity corrected, new variables
1199 kpp_dumpFreq and kpp_taveFreq
1200 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
1201 and entry for T90 in genmake
1202
1203 checkpoint29
1204 o packaged KPP and GM/Redi
1205
1206 checkpoint28
1207 o Corrected initialization of hFacMin for difference vertical coordinates
1208 o Modified calculation of partial cell thickness to more robust algorithm
1209 o config_summary.F: replaced write_1D_... by write_0D_...
1210 read_write.F: added subroutines write_0D_...
1211 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
1212 included some initialisations required for TAMC.
1213 o routine calc_isoslopes: modified sqrt computation to make it
1214 differentiable for zero argument.
1215 o routines dynamics, impldiff:
1216 included store directives and tape key computations required for TAMC.
1217 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
1218
1219 checkpoint27
1220 o fixed calc_isoslopes() to so that cancellation of terms in tensor
1221 formulation works properly with variable resolution.
1222 o restructured the calling tree between the_model_main() and dynamics()
1223 o split initialise() into initialise_fixed() and initialise_varia()
1224 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
1225 in new routine ini_psurf()
1226
1227 checkpoint26
1228 o moved some #ifdef in optional routines to encompass everything
1229 except the argument declarations. This was using up some memory.
1230 o fixed macros like _ADT to work with both versions of Linux cpp
1231 o cleaned up some unused and uninitialized variables
1232 (helps when debugging with strict compile options)
1233 o split up CPP_EEOPTIONS.h into options and macros
1234 (macros are now in eesupp/inc/CPP_EEMACROS.h)
1235 o patch for 2 processor JAM mode
1236
1237 checkpoint25
1238 o updates for OBCs and NH
1239 o dramatically reduced memory usage
1240 o added "JAM" routines for use on Artic network
1241 o parameterization of convection by implicit vertical diffusion
1242 o added a diagnostic of convective index
1243 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
1244 (this is was partly for OBCs and NH but also in anticipation of
1245 an explicit free-surface option)
1246 o initial state input files for U and V
1247
1248 checkpoint24
1249 o Removed some spurious "REAL"s
1250 o Updated KPP to latest version from JPL
1251 o Added a COS(latitude) in horizontal viscosity
1252
1253 checkpoint23
1254 o Added del^4 diffusion for salt and temperature
1255 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
1256
1257 checkpoint22
1258 o Made many small changes: implicit none, format(i5), etc...
1259 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
1260
1261 checkpoint21
1262 o Introduced new I/O package that supports direct-access records (mdsio.F)
1263 o Split-up mid-level I/O routines
1264 o Updated input data for experiments 0,1,2,4 and 5
1265 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
1266
1267 checkpoint20
1268 o Tidied up open-boundaries some more
1269 o Added non-hydrostatic code
1270 o Fixed some input data
1271 o Modified MPI start-up to work in "coupled" context.
1272
1273 checkpoint19
1274 o Tidied up directory structure for verification experiments.
1275 o Added new code for open boundaries.
1276 o Corrected advective terms near boundaries.
1277 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
1278 o Implemented free-slip/no-slip BCs and del^4 dissipation.
1279 o Split default parameters out of ini_parms.F into set_defaults.F.
1280
1281 checkpoint18
1282 o Further changes for optional code generation with
1283 CPP - ugh!
1284
1285 checkpoint17
1286 o Beginning to incorporating modularity
1287 for supporting atmos. and ocean configs.
1288 o Small changes for TAMC complinace
1289 o New ultra simple test case. Barotropic box
1290 configuration "exp0".
1291
1292 checkpoint16
1293 o Minor changes to exchange routines to support
1294 accumulation in reverse mode. Adjoint of an
1295 assignment is an addition.
1296 o Changes to support compilation by TAMC (LR(1)
1297 syntax) and by g77 under Linux ( 72 character
1298 limit ).
1299
1300 checkpoint15
1301 Rewrote exchange routines to allow
1302 o General tile <-> tile connectivity.
1303 o TAMC reverse mode flag ( is this really needed? )
1304 o Variable width overlap and exchange region widths.
1305 o Hooks for sharing data via DMA, Arctic, Memory Channel,
1306 shmput/shmget, VIA, SYSV shmem and every other cool
1307 communication method.
1308
1309 checkpoint14
1310 Consistent isomorphism chages made. These allow dynamical core
1311 to support both pressure and meters as a vertical coordinate.
1312
1313 checkpoint13
1314 Release which corrects global_max problem and a couple
1315 of KGM time-averaging diagnostic errors. Also contains
1316 a double-gyre experiment setup as well as the baseline
1317 4 degree global template. The double gyre template is
1318 organised to allow it to be applied automatically to
1319 the baseline configuration.
1320
1321 branch-point-rdot
1322 A few tidy-ups have been made bt the real point of this
1323 check-point (excuse the pun) is to allow a branch to be
1324 made for the purposes of adding the rDot alterations.
1325 I don't want to commit the rDot to the main-trunk until
1326 we've actually tested it...
1327
1328 checkpoint12
1329 Tidy up and added generic genmake script (formerly
1330 configure script).
1331 Released to testers.
1332
1333 checkpoint11
1334 Re-arranged initialise() and introduced ini_vertical_grid()
1335 and ini_masks_etc().
1336
1337 checkpoint10
1338 Introduced the configure script.
1339 Separated out the diags package.
1340 Added template for writing time-averages of tile/intermediate quantities.
1341 Updated SIZE.h in exp2 and made the data big-endian.
1342
1343 checkpoint9
1344 MPI fix. Filename changes (meta/data). salbin*y stuff.
1345 General tidy-up.
1346 SST.bin SSS.bin added to verification/exp2
1347
1348 checkpoint8
1349 Inludes time-dependant forcing and time-averaging.
1350 Works at 4x4 and 2.8125x2.8125 global
1351
1352 checkpoint7-4degree-ref
1353 Branch from checkpoint7. Released for application to
1354 global modeling and general modeling - process studies, regional
1355 model etc..
1356 Configured for verification/exp2 - 4 degree global, two process.
1357
1358 checkpoint7
1359 Created by cnh
1360 Simple 4 degree global simulation
1361 configuration.
1362 Includes climatological wind,
1363 hydrography, bathymetry etc
1364 Does not include Heat Flux and E-P
1365
1366 checkpoint6
1367 Created by cnh
1368 merged checkpoint5 with CD and
1369 spherical polar code.
1370 Still some problems with GM Redi
1371 abd full topography.
1372
1373 checkpoint5
1374 Created by AJA
1375 contains updates to GM Redi
1376 and reordered timestepping loop
1377 for Implicit Diffusion.
1378
1379 checkpoint4
1380 Created by cnh
1381 Contains memory saving macros ( _rdxc etc..) for when
1382 grid variations are limited.
1383 Contains polynomial coeffs for EOS and knudsen program
1384 for generation.
1385
1386 checkpoint3
1387 Created by cnh
1388 Added extra flags for runtime options
1389 Added this file
1390 Added implicit free-surface
1391 Added pre-conditioner
1392 Put compare01 into repository ( compare01/... )
1393 Put data and eedata into repository ( verification/exp1 )
1394
1395 checkpoint2
1396 Created by AJA
1397 Added GM/Redi
1398
1399 checkpoint1
1400 Created by AJA
1401 Restructured kloop in dynamics.F
1402 Added non-linear EOS
1403
1404 baseline
1405 Original checked in code

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