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Revision 1.112 - (show annotations) (download)
Fri Dec 27 14:26:14 2002 UTC (21 years, 6 months ago) by cheisey
Branch: MAIN
CVS Tags: checkpoint47e_post, branch-exfmods-tag
Branch point for: branch-exfmods-curt
Changes since 1.111: +6 -1 lines
o created a tag prior to creating a branch

1 $Header: /u/u0/gcmpack/MITgcm/doc/tag-index,v 1.111 2002/12/16 21:51:50 mlosch Exp $
3 Notes on tags used in MITgcmUV
4 ==============================
6 checkpoint47e_post
7 o created a tag prior to creating a branch
11 checkpoint47d_post
12 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
13 at the bottom boundary had an erroneous half slip boundary condition
14 o added bottom drag and no slip boundary condition capabilities to
15 oceanic pressure coordinates code
16 o added new verification experiment global_ocean_pressure, this experiment is
17 also described in the tutorial section of the manual
18 checkpoint47d_pre
20 checkpoint47c_post
21 o Added a verification experiment for a global cubed-sphere ocean run
22 - verification/global_ocean.cubed32x32x30
23 - uses pkg/therm_seaice and pkg/bulk_forcing
26 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
27 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
28 when using P-coordinate; only implemented for atmospheric config.
29 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
30 NOTES: requires option NONLIN_FRSURF to be "#define".
31 o update advect_xz/results/output.txt (left from checkpoint44g_post)
33 checkpoint47b_post
34 Merging from release1_p9:
35 o pkg/seaice
36 - removed GOTO's and added taf directives
37 - double precision constants to reduce the g77 (Linux)
38 to F77 (SGI) differences reported in release1_p8
39 o tools/genmake
40 - added SGI options
41 o verification/testscript
42 - updated to that of checkpoint47a_post
43 o verification/global_ocean.90x40x15/input/eedata
44 - modified for SGI f77 compatibility
45 o verification/lab_sea
46 - added description of sea-ice model
47 - added missing matlab routines
48 - added test of thermodynamics parallelization
50 checkpoint47a_post
51 o new pkg: aim_v23
52 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
53 for now, keep the same surface forcing as before.
54 - Part-Cell implemented into AIM; check that Heat & Water are conserved
55 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
56 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
57 o add diagnostic of surface correction term in monitor output
59 o bulk_force and therm_seaice
60 - Two packages: bulk_force (Bulk forcing)
61 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
62 - Earlier integration from Stephaine Dutkiewicz
63 and Patrick Heimbach.
64 - Two ifdef statements for compile time,
67 checkpoint47
68 differentiable version of checkpoint46n_post
69 o bug fix in quasihydrostaticterms
70 o * "clean" adjoint code (in terms of extensive recomputations)
71 can now be obtained for all GMREDI options (i.e. for
76 * However, wrong gradient check problem remains unsolved.
77 * New CPP options have been introduced for different
78 tapering schemes
79 o external_fields_load now part of differentiation list
80 o pressure needs multiple storing;
81 would be nice to have store_pressure at beginning or
82 end of forward_step, e.g. by having phiHyd global (5-dim.)
83 (NB: pressure is needed for certain cases in find_rho,
84 which is also invoked through convective_adjustment).
85 o recomputations in find_rho for cases
86 'JMD95'/'UNESCO' or 'MDJWF' are OK.
87 o #define ATMOSPHERIC_LOADING should be differentiable
88 o ini_forcing shifted to begining of initialise_varia
89 o Incorporating QNVS line search routines into MITgcm
90 (this is separate code, and therefore not under pkg)
91 lsopt/, optim/
92 o Updated verification/carbon/
94 - GM_taper_scheme = 'ldd97'
96 checkpoint46n_post
97 Merging from release1_p8:
98 o verification/natl_box:
99 updating new external_fields_load routine
100 o New package: pkg/seaice
101 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
102 The sea-ice code is based on Hibler (1979-1980).
103 Two sea-ice dynamic solvers, ADI and LSR, are included.
104 In addition to computing prognostic sea-ice variables and diagnosing
105 the forcing/external data fields that drive the ocean model,
106 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
107 The implied surface heat flux is then stored in variable
108 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
109 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
110 non-local transport term. Because this call precedes model
111 thermodynamics, temperature under sea-ice may not be "exactly" at
112 the freezing point by the time theta is dumped or time-averaged.
113 N.B.: fairly large differences in accuracy occur across
114 different platforms/compilers; comparison between
115 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
116 generated output gives:
117 T S U V
118 C D M c m s m s m s m s
119 n p a R g m m e . m m e . m m e . m m e .
120 f n k u 2 i a a d i a a d i a a d i a a d
121 g d e n d n x n . n x n . n x n . n x n .
123 Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
124 o GAD:
125 - generated new common blocks to account for call of
126 same gad routines with differing traceridentities
127 (needed to modify tracerIdentity indices in GAD.h)
128 - generated separate common blocks for case useCubedSphereExchange
129 (Department of Futurology)
130 - parameter lists to gmredi_?transport: added tracerIdentity
131 - added new key indices to tamc.h
132 o external_fields_load:
133 - added this routine to TAF list
134 - needed to make some common blocks global and additional storing
135 along the same lines as exf package (checkpoint_lev?_directives.h)
136 o exf:
137 updated external forcing package
138 - bug fixes carried over from ecco-branch
139 (missing OBCS_OPTIONS.h in two routines)
140 - enable easy to use "no forcing".
141 - added exf I/O for atmospheric loading
142 - added exf I/O for runoff data
143 - transfered scaling between exf <-> MITgcm to exf namelist
144 o Adding new verification experiment global_with_exf.
145 This verification experiment is almost identical to the
146 global_ocean.90x40x15 experiment, except that it uses
147 the exf (and cal) package instead of the
148 external_fields_load routine (cf README file).
150 checkpoint46m_post
151 o modified testscript to return -- when there are no lines of "%MON" output
152 o added new flag "quasiHydrostatic" for QH mode
153 and new routine quasihydrostaticterms()
154 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
155 New routine: mom_u_coriolis_nh()
156 o fixed sign of non-hydrostatic metric terms in u and v equations.
157 Depend on correct sign of gravitySign.
158 o added work.pc* to .cvsignore in aim directories using ifc
159 o introduced flag for controllin non-hydrostatic metric terms
160 o removed gravitySign from PARM04
161 o switched to g77/ifc from pgf77 in aim experiments
163 checkpoint46l_post
164 o made convective adjustment work with pressure coordinates:
165 - changed the direction of k-loop in convective_adjustment.F for the
166 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
167 - adjusted the reference pressure k-index in convective_adjustment.F
168 - adjusted the convection condition in convect.F (in analogy to
169 calc_ivdc.F)
170 - convective_adjustment no longer computes anything on the halos
171 - removed the warnings about negative salinity from find_rho.F and
172 find_alpha.F; instead the new routine look_for_neg_salinity, called
173 at the beginning of find_rho, find_alpha, and find_beta, does a
174 check of the entire slice, if CPP-option
176 checkpoint46l_pre
178 checkpoint46k_post
179 o fixed the verification/global_ocean.90x40x15 experiment:
180 - new bathymetry (the world according to A., JMC, and M.)
181 - new initial fields and forcing fields (*.bin files)
182 - new POLY3.COEFFS (for the next release one should switch to a full
183 equation of state: JMD95P or MDJWF)
184 - fixed several errors and redundancies in the data file
185 - experiment uses looped cells
186 - added matlab directory with diagnostic scripts for plotting of output
188 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
189 - read AIM physics parameters from a file (data.aimphys)
190 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
192 checkpoint46j_post
193 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
194 o move wVel computation at the end of the time step, in S/R integr_continuity
195 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
196 o update timeave pkg for wVel diagnostic.
197 checkpoint46j_pre
199 checkpoint46i_post
200 o Clean up AIM package (and keep the results unchanged):
201 include CPP_OPTION and use IMPLICT NONE in all routines ;
202 declare all the variables _RL ; use _d 0 for all numerical constants.
203 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
205 checkpoint46h_post
206 o cleaned up the use of rhoNil and rhoConst.
207 - rhoNil should only appear in the LINEAR equation of state, everywhere
208 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
209 and the dynamical equations are all divided by rhoConst
210 o introduced new parameter rhoConstFresh, a reference density of fresh
211 water, to remove the fresh water flux's dependence on rhoNil. The default
212 value is 999.8 kg/m^3
213 o cleanup up external_forcing.F and external_forcing_surf.F
214 - can now be used by both OCEANIC and OCEANICP
215 checkpoint46h_pre
217 Added code to convert surface volume flux (fresh water) into
218 a mass flux when using P coordinates in the ocean (OCEANICP).
219 Note: It assumes you have set rho0=rhoConst=density of fresh water.
221 checkpoint46g_post
222 o Include a new diagnostic variable phiHydLow for the ocean model
223 - in z-coordinates, it is the bottom pressure anomaly
224 - in p-coordinates, it is the sea surface elevation
225 - in both cases, these variable have global drift, reflecting the mass
226 drift in z-coordinates and the volume drift in p-coordinates
227 - included time averaging for phiHydLow, be aware of the drift!
228 o depth-dependent computation of Bo_surf for pressure coordinates
229 in the ocean (buoyancyRelation='OCEANICP')
230 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
231 Theta, Salinity, and Pressure in the parameter list. This routine is
232 presently contained in find_rho.F. This routine does not give the
233 correct density for 'POLY3', which would be a z-dependent reference
234 density.
235 o cleaned up find_rho
236 - removed obsolete 'eqn' from the parameter list.
237 o added two new verification experiments: gop and goz
238 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
239 checkpoint46g_pre
241 checkpoint46f_post
242 o Enable tangent linear (forward mode) gradient checks:
243 - extended active file handling to g_... files
244 - added TANGENT_SIMULATION to theSimulationMode
245 - extended grdchk package accordingly
246 o added tangent linear setup in verification/carbon/code_ftl
247 o added adjoint setup in verification/front_relax/code_ad
249 checkpoint46e_post
250 o Added new equation of state -> MDJWF
251 - EOS of McDougall et al., 2002, JAOT, submitted
252 - caveat: the equation of state is only valid for a smaller (more
253 realistic?) range of values than JMD95P/Z and UNESCO
254 - added masks to the calculation of pressure in store_pressure
255 - added more check values for density in check_eos (ini_eos.F), some of
256 the old check values are out of the range of the MDJWF-eos, so don't
257 expect perfect matches for those
258 checkpoint46e_pre
260 checkpoint46d_post
261 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
262 'OCEANICP', also initialised field pressure correctly in ini_eos in the
263 case of pressure coordinates. eosType='JMD95Z' in
264 combination with buoyancyRelation='OCEANICP' now causes an error.
265 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
266 in find_alpha/beta.
267 checkpoint46d_pre
269 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
270 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
272 checkpoint46c_post
273 o Changes necessary for ocean in p-coordinates
274 - Added new buoyancy relation = 'OCEANICP'
275 - Added new parameters = gravitySign (this used to be contained inside
276 the factor dRdZ which I added when we first switched to R coordinates).
277 X GM/Redi is not compatible (yet)
278 X bottom drag and no-slip need to be debugged.
279 checkpoint46c_pre
281 checkpoint46b_post
282 o Added new equation of state -> JMD95Z and JMD95P
283 - EOS of Jackett and McDougall, 1995, JAOT
284 - moved all EOS parameters into EOS.h
285 - new routines ini_eos.F, store_pressure.F
286 o Added UNESCO EOS, but not recommended because it requires
287 in-situ temperature (see JMD95)
288 o Modified formatting for knudsen2.f in utils/knudsen2 and added
289 unesco.f to be used with POLY3
290 checkpoint46b_pre
292 checkpoint46a_post
293 o Added (atmospheric) pressure loading
294 - new field in FFIELDS.h, etc...
295 - new cpp flag ATMOSPHERIC_LOADING
296 o Changed hFacC to _hFacC in calc_phi_hyd.F
297 o Added SHORTWAVE_HEATING to some files for consistency
298 checkpoint46a_pre
300 checkpoint46
301 further merges from release1_p5
302 o new ctrl package
303 - adopted from ECCO environment to enable optimization
304 - added Eliassen Palm fluxes to controls
305 o added Eliassen Palm flux controls to gradient check package
306 o cost package
307 - Compatible with new ctrl package
308 - added Eliassen Palm cost hooks
309 - modif's of existing cost functions
310 o Adjoint-related bug fixes in kpp:
311 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
312 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
313 o autodiff package
314 - flow directives:
315 + new for S/R do_the_model_io
316 + enhanced for S/R checkpoint
317 + new gmredi.flow
318 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
319 disable adcommon.h/g_common.h by default.
320 - fixed problem for adjoint of global_max
321 o modified verification/carbon/
322 o New setup for adjoint of global_ocean
323 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
324 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
325 o incorporated hooks for sponge layer code (external_forcing.F)
327 checkpoint45d_post
328 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
329 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
330 (affects plume_on_slope "cg2d" output)
331 o add new parameter deltaTfreesurf for free-surface time stepping
332 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
333 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
334 o change phiMin in exp1 (to agree with documentation)
335 o add new flags:
336 - T,S forcing inside/outside Adams-Bashforth
337 - turn off temp,salt advection and/or forcing
338 - for each tracer, define internal flag for multiDimAdvection & A-B
339 o monitor: change definition of KE to check conservation of Energy
341 checkpoint45c_post
342 o Removed f90 comments ("!")
343 o Modified initialisations to enable exf package for MITgcm
344 (without invoking ECCO_PACKAGE).
345 o modifications to gradient check package (Martin Losch)
346 - enable centered differences
347 - modified format of standard output
349 checkpoint45b_post
350 o cleaned exchange calls in cg2d
351 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
352 o included CPP option SINGLE_LAYER_MODE in thermodynamics
353 to configure barotropic setup (Martin Losch)
354 o moved some initialisations within bi,bj loop in dynamics
355 (TAF flow dependency)
356 o in initialise_varia, moved call packages_init_variables
357 before convective_adjustment_init
358 (corresponding adjustment of TAF tape initialisation).
359 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
361 checkpoint45a_post
362 o compute Rho over the whole domain (extend iMin,jMin indices)
363 o specific exchange for X-slice domain (case Ny=1)
364 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
365 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
367 checkpoint44h_post = checkpoint45
368 o Fix to restore differentiability:
369 place at which packages_init_variables is called in
370 initialise_varia is crucial for reverse control flow.
371 o modifications in GMRedi to enable stable adjoint
372 (corresponding modif's in thermodynamics, dynamics)
373 o added missing hook for sponge layer code in external_forcing
374 o modified test cost functions
375 o storing in gad_advection (plus removal of write(0,*)!
376 o missing headers TR1.h added in convective_adjustment routines
377 o errorMessageUnit set non-equal zero in eeboot
378 (conflict on some platforms, e.g. IBM SP3)
379 o modified carbon verif.
381 checkpoint44h_pre
382 o vertical grid option: allow to put the Interface at the middle between
383 2 cell-centers ; replace delZ in pkg/kpp by drF.
384 o GM Advective form: Tracers are advected using the residual transport (=
385 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
387 checkpoint44g_post
388 o fix surface correction term in multiDimAdvection (affects plume_on_slope
389 results) ; ifdef missing in thermodynamics.F
391 checkpoint44f_pre,checkpoint44f_post
392 o added PTRACERS package
393 This allows an arbitrary number of passive tracers to be integrated
394 forward simultaneously with the dynamicaly model.
395 + Implemented so far:
396 - basic forward algorithm (time-stepping, advection, diffusion, convection)
397 - I/O and checkpointing
398 - GM/Redi *but* using the GM/Redi coefficient of Salt
399 + Not implemented so far:
400 - KPP
401 - OBCS
402 + No specific example supplied (yet) but global_ocean.90x40x15 has the
403 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
404 line in data.pkg.
405 + This package is disabled by default since it increases storage.
408 o testscript: added -cleanup option
409 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
410 b) enable to filter 2D fields.
412 checkpoint44e_pre,post
413 o re-wrote convective adjustment to use pre-calculated weights
414 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
415 Adds: model/src/convective_weights.F, convectively_mixtracer.F
416 Original calls to convect() still in place.
418 chkpt44d_pre,post
419 o added missing EXCLUDE_MONITOR flags
420 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
421 (incompatible typ in MIN/MAX expressions caused problems
422 on IBM SP3)
423 o in genmake added variable MAKEDEPEND
424 plus resetting for case SunOS
425 o added timer_stats.c routine for IBM SP3
426 o removed variables in dynamics
427 !!! I forgot to create tag chkpt44d_pre !!!
428 !!! But chkpt44d_pre = chkpt44c_post !!!
430 o real fresh water flux implemented with non-linear free-surface.
432 chkpt44c_pre,post
433 o few fix (mask in shap_s2, EmPmR in external_field_load,
434 USE_NATURAL_BCS in solve_for_P);
435 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
437 checkpoint44b_pre/_post
438 o merge of relevant stuff from the ecco-branch:
439 - genmake: removed $S64 overwrite for case SunOS
440 - pkg/exf: update and corrections for field swapping and obcs
441 - pkg/ecco: parameter lists for the_model_main, the_main_loop
442 harmonized between ECCO and MITgcm
443 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
444 updated checkpointing_lev... lists for obcs
445 - model/src: minor changes in forward_step, plot_field
446 added directive for divided adjoint in the_main_loop
447 - pkg/mdsio: added mdsio_gl_slice
449 o check parameters & config (chkpt44a_pre,post)
450 o OBC and NonLin_FrSurf.
452 checkpoint44
453 o fix bug in mom_vi_del2uv
454 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
455 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
456 o update AIM experiments (NCEP input files)
457 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
458 o added some stuff for AD
460 checkpoint43
461 o added two new advection tests
462 o added global 4x4 degree ocean test
463 o added test of H&S94 with free surface on cube
464 o some final mods for gradient check, adjoint,...
466 checkpoint42
467 Fixed AD-related problems:
468 o Store directives up-to-date with re-arranged Adams-Bashforth
469 (mainly thermodynamics.F)
470 o New store directives for multi-dim. advection schemes
472 * new common block and key passkey
473 (mainly gad_advection.F)
474 o Modified store directives for split of dynamics/thermodynamics
475 for the case ALLOW_KPP
476 o Cleaned argument list for timestep_tracer.F
478 checkpoint41
479 o re-formatted/added comments in prologues of key subroutines
480 to work with protex
482 checkpoint40
483 o moved calc_gs, calc_gt and calc_tr1 back to model/src
484 o added FLT (floats) package from Arne along with demo. experiment
485 o re-arranged Adams-Bashforth scheme for tracers to allow easier
486 implementation of forward-in-time forcing terms
487 o more mods for non-linear free-surface including new variable
488 o modified multi-dim method to work on cube
489 o bug fix in KPP (from DM)
491 checkpoint40pre9
492 o added DST advection schemes
493 o fix MPI bug on SGI's
494 o modifications for non-linear free-surface
495 o fixed conditionals for fixed flow/passive tracer only mode
496 o added tension/strain form of stress tensor
497 o changes to commenting of arguments for TAF/TAMC
498 o added/updated many matlab scripts
499 o added multi-dimensional advection method for tracers
501 checkpoint40pre8
502 o new package rw/
503 Added method for dumping intermediate local arrays:
504 mdsio_writetile - same as mdsio_writefield except works from inside
505 bi,bj loop
506 mdsio_writelocal - same as mdsio_writetile except works for local
507 arrays
508 write_local_r? - higher-level wrapper for mdsio_writelocal
509 Controlled by diagFreq. Defaults to zero (ie. no dumps)
510 Example given at end of mom_vecinv.F that dumps some local arrays.
511 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
512 control flux-form versus vector invariant code.
513 Switch is runtime flag vectorInvariantMomentum (defaults to false)
514 or genmake -DISABLE ...
515 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
516 (additional storing is now needed for case vecinv;
517 currently nothing implemented to switch this storing off
518 in case fluxform is used since no CPP flag available).
520 checkpoint40pre7
521 o bug fix in dynamics.F
522 calc_viscosity called before k=1,Nr loop.
523 o added some #ifdef's ALLOW_PASSIVE_TRACER
524 o cleaned initialisations in ctrl_map_ini
525 related to TAF
527 checkpoint40pre6
528 o split dynamics into thermodynamics & dynamics
529 o corresponding split of calc_diffusivity into
530 calc_diffusivity, calc_viscosity
531 (kpp_calc_diff, kpp_calc_visc).
532 o Added diffkr, kapgm to control variables
533 o bug fix in gmredi_slope_limit for ldd97
535 checkpoint40pre5
536 o proper initialization of Adams-Bashforth time stepping
537 + uses forward step for very first step of model (iter=0)
538 o re-generated *all* output since almost all output is modified by this
539 change (sorry but we've been putting this one off for about 2 years)
540 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
541 *not* regenerated since they are already out of date and I don't
542 want to create the impression that they are suddenly working.
543 o removed KAP stuff for DEC's
544 o modified/added many .cvsignore files in */code and */input
545 o added new expt "solid-body.cs-32x32x1"
546 + this uses an alternative form of ini_curvilinear_grid.F which
547 is not necessarily any better than the current one...
549 checkpoint40pre4
550 o added re-initialisations of utrans,vtrans,rtrans in
551 calc_common_factors which are crucial for TAF.
552 o extended iMin,jMin range for calc_common_factors,
553 calc_diffusivity
554 o added option ALLOW_PASSIVE_TRACER
555 o a few minor updates and fixes
557 checkpoint40pre3
558 o created calc_gtr1.F for gad package
559 o split the_main_loop and re-introduced forward_step
560 o some recomputations of nIter0 for TAMC
562 checkpoint40pre2
563 o Updated to latest branch of AJA, JMC
564 o Added gradient check package
565 o Added routines for passive tracer handling
566 o Added carbon sequestration sensitivity experiment
568 checkpoint39
569 o Modifications and fixes to support TAMC
570 (mainly missing or wrong directives)
571 o Corrected common blocks when fooling TAMC to produce adjoint I/O
572 in addummy_in_stepping
573 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
574 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
575 o Included following packages:
576 cal: calendar
577 exf: external forcing
578 ecco: essential routines to control use of cal, exf
579 (NB: this is not the full ECCO environment)
580 o disabled some packages by default in genmake
582 checkpoint38
583 o see notes_c37_adj.txt
584 o corrected wrong layer index in external_forcing_t
585 o replaced the_main_loop/forward_step by the_main_loop
586 o removed forceoutput from write_state
587 (replaced criteria for initial/final state)
588 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
590 checkpoint37
591 o mdsio.F routine split and packaged in pkg/mdsio
592 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
593 used unless genmake -disable=mdsio)
594 o allow a more precise surface-geopotential gradient for the atmosphere
595 taking into account the change in space of Alpha (=1/rho) at the surface.
596 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
597 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
598 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
599 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
600 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
601 o Time-Average diagnostics defined as a pseudo package "timeave".
602 o pickup files : old pickup (before c35) did not work with new code (c35
603 and after) unless activating 2 commented lines in initialise-varia.
604 o Non-Hydrostatic pickup file Pb fixed.
605 o bug with Rigid-lid version (since c35) fixed.
607 checkpoint36
608 o implement Crank-Nickelson barotropic time-stepping
609 o recover Time-Average diagnostics
610 o fix Pb in checkpoint (PR#19)
611 o AIM become a standard package ; clean unused CPP_kees
613 checkpoint35
614 o subtantial rewrite of dynamics.f
615 o allows staggered time-stepping
616 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
617 o added bottom drag (linear + quadratic)
619 checkpoint34
620 o Modified exchange routines for correct reverse simulation.
621 o Added verification output to comply with bug fix in impldiff.F
622 as of c33 (exp2, natl_box).
623 o Corrected store directives in dynamics.F
624 o Corrected array boundaries in impldiff.F
625 o Corrected array dimensions in gmredi.
626 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
627 o Added routine GLOBAL_SUM_INT to global_sum.F
628 o Added mdsio_gl.F for ECCO purposes.
630 checkpoint33
631 o Fixed bug in lower BC in impldiff.F
632 o Fixed confusion about units of forcing arrays in FFIELDS.h
633 namely Fu,Fv,Qnet,Qsw,EmPmR:
634 - Removed verification/natl_box/code/external_fields_scale.F
635 (did not differ from that in model/src)
636 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
637 (see FFIELDS.h for description)
638 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
639 kpp_calc.F and kpp_transport_t.F
640 - Removed model/src/external_fields_scale.F and calls to it
641 - verification/natl_box uses flux data with "atmospheric" sign so
642 a special version of external_fields_load.F is used to
643 change the data as it's read in. This way, the arrays
644 have the right units and signs at all times tha a user could
645 possibly use them.
646 o Corrected genmake to delete a temporary file during configuration
648 checkpoint32
649 o Scaling of forcing fields moved from external_forcing.F to
650 external_fields_scale.F, called directly after loading fields.
651 o Surface relaxation terms added to surface tendency fields in
652 extra subroutine.
653 o impldiff.F changed to avoid storing by TAMC of huge intermediate
654 fields.
655 o Changes in GMRedi to comply with packaging structure.
656 o Modifications and bug fixes in KPP package.
657 o Verification experiment for KPP added (verification/nat_box/)
659 checkpoint31
660 o Packages interface brought in line with defined standard
661 -> new routines packages_...F
662 -> changes in initialise_fixed.F, initialise_varia.F
663 -> enables initialisation interface for ECCO package
664 o Rescaling of external forcing fields immediately after read
665 (removed from external_forcing.F)
666 -> new: surface_fields_scale.F
667 -> affects ini_foorcing.F, external_fields_load.F
668 o Computation of surface tendencies before tendency updates.
669 -> new: external_forcing_surf.F
670 o Change of variable names useGMRedi, useKPP, useECCO
671 o Further changes in dynamics.F, impldiff.F for TAMC
672 o Tested for experiments 0, 2, 4.
673 - not yet tested for GMRedi.
674 - not yet tested for KPP.
676 checkpoint30
677 o Updates for OBCs
678 o New experiment for test OBCs (internal_wave)
679 o New output.txt in verification/exp4/results/
680 o Updates for KPP: calculation of viscosity corrected, new variables
681 kpp_dumpFreq and kpp_taveFreq
682 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
683 and entry for T90 in genmake
685 checkpoint29
686 o packaged KPP and GM/Redi
688 checkpoint28
689 o Corrected initialization of hFacMin for difference vertical coordinates
690 o Modified calculation of partial cell thickness to more robust algorithm
691 o config_summary.F: replaced write_1D_... by write_0D_...
692 read_write.F: added subroutines write_0D_...
693 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
694 included some initialisations required for TAMC.
695 o routine calc_isoslopes: modified sqrt computation to make it
696 differentiable for zero argument.
697 o routines dynamics, impldiff:
698 included store directives and tape key computations required for TAMC.
699 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
701 checkpoint27
702 o fixed calc_isoslopes() to so that cancellation of terms in tensor
703 formulation works properly with variable resolution.
704 o restructured the calling tree between the_model_main() and dynamics()
705 o split initialise() into initialise_fixed() and initialise_varia()
706 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
707 in new routine ini_psurf()
709 checkpoint26
710 o moved some #ifdef in optional routines to encompass everything
711 except the argument declarations. This was using up some memory.
712 o fixed macros like _ADT to work with both versions of Linux cpp
713 o cleaned up some unused and uninitialized variables
714 (helps when debugging with strict compile options)
715 o split up CPP_EEOPTIONS.h into options and macros
716 (macros are now in eesupp/inc/CPP_EEMACROS.h)
717 o patch for 2 processor JAM mode
719 checkpoint25
720 o updates for OBCs and NH
721 o dramatically reduced memory usage
722 o added "JAM" routines for use on Artic network
723 o parameterization of convection by implicit vertical diffusion
724 o added a diagnostic of convective index
725 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
726 (this is was partly for OBCs and NH but also in anticipation of
727 an explicit free-surface option)
728 o initial state input files for U and V
730 checkpoint24
731 o Removed some spurious "REAL"s
732 o Updated KPP to latest version from JPL
733 o Added a COS(latitude) in horizontal viscosity
735 checkpoint23
736 o Added del^4 diffusion for salt and temperature
737 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
739 checkpoint22
740 o Made many small changes: implicit none, format(i5), etc...
741 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
743 checkpoint21
744 o Introduced new I/O package that supports direct-access records (mdsio.F)
745 o Split-up mid-level I/O routines
746 o Updated input data for experiments 0,1,2,4 and 5
747 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
749 checkpoint20
750 o Tidied up open-boundaries some more
751 o Added non-hydrostatic code
752 o Fixed some input data
753 o Modified MPI start-up to work in "coupled" context.
755 checkpoint19
756 o Tidied up directory structure for verification experiments.
757 o Added new code for open boundaries.
758 o Corrected advective terms near boundaries.
759 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
760 o Implemented free-slip/no-slip BCs and del^4 dissipation.
761 o Split default parameters out of ini_parms.F into set_defaults.F.
763 checkpoint18
764 o Further changes for optional code generation with
765 CPP - ugh!
767 checkpoint17
768 o Beginning to incorporating modularity
769 for supporting atmos. and ocean configs.
770 o Small changes for TAMC complinace
771 o New ultra simple test case. Barotropic box
772 configuration "exp0".
774 checkpoint16
775 o Minor changes to exchange routines to support
776 accumulation in reverse mode. Adjoint of an
777 assignment is an addition.
778 o Changes to support compilation by TAMC (LR(1)
779 syntax) and by g77 under Linux ( 72 character
780 limit ).
782 checkpoint15
783 Rewrote exchange routines to allow
784 o General tile <-> tile connectivity.
785 o TAMC reverse mode flag ( is this really needed? )
786 o Variable width overlap and exchange region widths.
787 o Hooks for sharing data via DMA, Arctic, Memory Channel,
788 shmput/shmget, VIA, SYSV shmem and every other cool
789 communication method.
791 checkpoint14
792 Consistent isomorphism chages made. These allow dynamical core
793 to support both pressure and meters as a vertical coordinate.
795 checkpoint13
796 Release which corrects global_max problem and a couple
797 of KGM time-averaging diagnostic errors. Also contains
798 a double-gyre experiment setup as well as the baseline
799 4 degree global template. The double gyre template is
800 organised to allow it to be applied automatically to
801 the baseline configuration.
803 branch-point-rdot
804 A few tidy-ups have been made bt the real point of this
805 check-point (excuse the pun) is to allow a branch to be
806 made for the purposes of adding the rDot alterations.
807 I don't want to commit the rDot to the main-trunk until
808 we've actually tested it...
810 checkpoint12
811 Tidy up and added generic genmake script (formerly
812 configure script).
813 Released to testers.
815 checkpoint11
816 Re-arranged initialise() and introduced ini_vertical_grid()
817 and ini_masks_etc().
819 checkpoint10
820 Introduced the configure script.
821 Separated out the diags package.
822 Added template for writing time-averages of tile/intermediate quantities.
823 Updated SIZE.h in exp2 and made the data big-endian.
825 checkpoint9
826 MPI fix. Filename changes (meta/data). salbin*y stuff.
827 General tidy-up.
828 SST.bin SSS.bin added to verification/exp2
830 checkpoint8
831 Inludes time-dependant forcing and time-averaging.
832 Works at 4x4 and 2.8125x2.8125 global
834 checkpoint7-4degree-ref
835 Branch from checkpoint7. Released for application to
836 global modeling and general modeling - process studies, regional
837 model etc..
838 Configured for verification/exp2 - 4 degree global, two process.
840 checkpoint7
841 Created by cnh
842 Simple 4 degree global simulation
843 configuration.
844 Includes climatological wind,
845 hydrography, bathymetry etc
846 Does not include Heat Flux and E-P
848 checkpoint6
849 Created by cnh
850 merged checkpoint5 with CD and
851 spherical polar code.
852 Still some problems with GM Redi
853 abd full topography.
855 checkpoint5
856 Created by AJA
857 contains updates to GM Redi
858 and reordered timestepping loop
859 for Implicit Diffusion.
861 checkpoint4
862 Created by cnh
863 Contains memory saving macros ( _rdxc etc..) for when
864 grid variations are limited.
865 Contains polynomial coeffs for EOS and knudsen program
866 for generation.
868 checkpoint3
869 Created by cnh
870 Added extra flags for runtime options
871 Added this file
872 Added implicit free-surface
873 Added pre-conditioner
874 Put compare01 into repository ( compare01/... )
875 Put data and eedata into repository ( verification/exp1 )
877 checkpoint2
878 Created by AJA
879 Added GM/Redi
881 checkpoint1
882 Created by AJA
883 Restructured kloop in dynamics.F
884 Added non-linear EOS
886 baseline
887 Original checked in code

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