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Revision 1.77 - (show annotations) (download)
Fri Jul 12 21:00:23 2002 UTC (18 years, 10 months ago) by jmc
Branch: MAIN
CVS Tags: checkpoint45d_post
Changes since 1.76: +5 -1 lines
import 2 fixes from release1_p5

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.76 2002/07/12 14:52:08 jmc Exp $
2
3 Notes on tags used in MITgcmUV
4 ==============================
5 checkpoint45d_post
6 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
7 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
8 (affects plume_on_slope "cg2d" output)
9 o add new parameter deltaTfreesurf for free-surface time stepping
10 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
11 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
12 o change phiMin in exp1 (to agree with documentation)
13 o add new flags:
14 - T,S forcing inside/outside Adams-Bashforth
15 - turn off temp,salt advection and/or forcing
16 - for each tracer, define internal flag for multiDimAdvection & A-B
17 o monitor: change definition of KE to check conservation of Energy
18
19 checkpoint45c_post
20 o Removed f90 comments ("!")
21 o Modified initialisations to enable exf package for MITgcm
22 (without invoking ECCO_PACKAGE).
23 o modifications to gradient check package (Martin Losch)
24 - enable centered differences
25 - modified format of standard output
26
27 checkpoint45b_post
28 o cleaned exchange calls in cg2d
29 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
30 o included CPP option SINGLE_LAYER_MODE in thermodynamics
31 to configure barotropic setup (Martin Losch)
32 o moved some initialisations within bi,bj loop in dynamics
33 (TAF flow dependency)
34 o in initialise_varia, moved call packages_init_variables
35 before convective_adjustment_init
36 (corresponding adjustment of TAF tape initialisation).
37 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
38
39 checkpoint45a_post
40 o compute Rho over the whole domain (extend iMin,jMin indices)
41 o specific exchange for X-slice domain (case Ny=1)
42 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
43 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
44
45 checkpoint44h_post = checkpoint45
46 o Fix to restore differentiability:
47 place at which packages_init_variables is called in
48 initialise_varia is crucial for reverse control flow.
49 o modifications in GMRedi to enable stable adjoint
50 (corresponding modif's in thermodynamics, dynamics)
51 o added missing hook for sponge layer code in external_forcing
52 o modified test cost functions
53 o storing in gad_advection (plus removal of write(0,*)!
54 o missing headers TR1.h added in convective_adjustment routines
55 o errorMessageUnit set non-equal zero in eeboot
56 (conflict on some platforms, e.g. IBM SP3)
57 o modified carbon verif.
58
59 checkpoint44h_pre
60 o vertical grid option: allow to put the Interface at the middle between
61 2 cell-centers ; replace delZ in pkg/kpp by drF.
62 o GM Advective form: Tracers are advected using the residual transport (=
63 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
64
65 checkpoint44g_post
66 o fix surface correction term in multiDimAdvection (affects plume_on_slope
67 results) ; ifdef missing in thermodynamics.F
68
69 checkpoint44f_pre,checkpoint44f_post
70 o added PTRACERS package
71 This allows an arbitrary number of passive tracers to be integrated
72 forward simultaneously with the dynamicaly model.
73 + Implemented so far:
74 - basic forward algorithm (time-stepping, advection, diffusion, convection)
75 - I/O and checkpointing
76 - GM/Redi *but* using the GM/Redi coefficient of Salt
77 + Not implemented so far:
78 - KPP
79 - OBCS
80 + No specific example supplied (yet) but global_ocean.90x40x15 has the
81 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
82 line in data.pkg.
83 + This package is disabled by default since it increases storage.
84
85
86 o testscript: added -cleanup option
87 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
88 b) enable to filter 2D fields.
89
90 checkpoint44e_pre,post
91 o re-wrote convective adjustment to use pre-calculated weights
92 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
93 Adds: model/src/convective_weights.F, convectively_mixtracer.F
94 Original calls to convect() still in place.
95
96 chkpt44d_pre,post
97 o added missing EXCLUDE_MONITOR flags
98 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
99 (incompatible typ in MIN/MAX expressions caused problems
100 on IBM SP3)
101 o in genmake added variable MAKEDEPEND
102 plus resetting for case SunOS
103 o added timer_stats.c routine for IBM SP3
104 o removed variables in dynamics
105 !!! I forgot to create tag chkpt44d_pre !!!
106 !!! But chkpt44d_pre = chkpt44c_post !!!
107
108 o real fresh water flux implemented with non-linear free-surface.
109
110 chkpt44c_pre,post
111 o few fix (mask in shap_s2, EmPmR in external_field_load,
112 USE_NATURAL_BCS in solve_for_P);
113 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
114
115 checkpoint44b_pre/_post
116 o merge of relevant stuff from the ecco-branch:
117 - genmake: removed $S64 overwrite for case SunOS
118 - pkg/exf: update and corrections for field swapping and obcs
119 - pkg/ecco: parameter lists for the_model_main, the_main_loop
120 harmonized between ECCO and MITgcm
121 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
122 updated checkpointing_lev... lists for obcs
123 - model/src: minor changes in forward_step, plot_field
124 added directive for divided adjoint in the_main_loop
125 - pkg/mdsio: added mdsio_gl_slice
126
127 o check parameters & config (chkpt44a_pre,post)
128 o OBC and NonLin_FrSurf.
129
130 checkpoint44
131 o fix bug in mom_vi_del2uv
132 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
133 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
134 o update AIM experiments (NCEP input files)
135 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
136 o added some stuff for AD
137
138 checkpoint43
139 o added two new advection tests
140 o added global 4x4 degree ocean test
141 o added test of H&S94 with free surface on cube
142 o some final mods for gradient check, adjoint,...
143
144 checkpoint42
145 Fixed AD-related problems:
146 o Store directives up-to-date with re-arranged Adams-Bashforth
147 (mainly thermodynamics.F)
148 o New store directives for multi-dim. advection schemes
149 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
150 * new common block and key passkey
151 (mainly gad_advection.F)
152 o Modified store directives for split of dynamics/thermodynamics
153 for the case ALLOW_KPP
154 o Cleaned argument list for timestep_tracer.F
155
156 checkpoint41
157 o re-formatted/added comments in prologues of key subroutines
158 to work with protex
159
160 checkpoint40
161 o moved calc_gs, calc_gt and calc_tr1 back to model/src
162 o added FLT (floats) package from Arne along with demo. experiment
163 o re-arranged Adams-Bashforth scheme for tracers to allow easier
164 implementation of forward-in-time forcing terms
165 o more mods for non-linear free-surface including new variable
166 o modified multi-dim method to work on cube
167 o bug fix in KPP (from DM)
168
169 checkpoint40pre9
170 o added DST advection schemes
171 o fix MPI bug on SGI's
172 o modifications for non-linear free-surface
173 o fixed conditionals for fixed flow/passive tracer only mode
174 o added tension/strain form of stress tensor
175 o changes to commenting of arguments for TAF/TAMC
176 o added/updated many matlab scripts
177 o added multi-dimensional advection method for tracers
178
179 checkpoint40pre8
180 o new package rw/
181 Added method for dumping intermediate local arrays:
182 mdsio_writetile - same as mdsio_writefield except works from inside
183 bi,bj loop
184 mdsio_writelocal - same as mdsio_writetile except works for local
185 arrays
186 write_local_r? - higher-level wrapper for mdsio_writelocal
187 Controlled by diagFreq. Defaults to zero (ie. no dumps)
188 Example given at end of mom_vecinv.F that dumps some local arrays.
189 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
190 control flux-form versus vector invariant code.
191 Switch is runtime flag vectorInvariantMomentum (defaults to false)
192 or genmake -DISABLE ...
193 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
194 (additional storing is now needed for case vecinv;
195 currently nothing implemented to switch this storing off
196 in case fluxform is used since no CPP flag available).
197
198 checkpoint40pre7
199 o bug fix in dynamics.F
200 calc_viscosity called before k=1,Nr loop.
201 o added some #ifdef's ALLOW_PASSIVE_TRACER
202 o cleaned initialisations in ctrl_map_ini
203 related to TAF
204
205 checkpoint40pre6
206 o split dynamics into thermodynamics & dynamics
207 o corresponding split of calc_diffusivity into
208 calc_diffusivity, calc_viscosity
209 (kpp_calc_diff, kpp_calc_visc).
210 o Added diffkr, kapgm to control variables
211 o bug fix in gmredi_slope_limit for ldd97
212
213 checkpoint40pre5
214 o proper initialization of Adams-Bashforth time stepping
215 + uses forward step for very first step of model (iter=0)
216 o re-generated *all* output since almost all output is modified by this
217 change (sorry but we've been putting this one off for about 2 years)
218 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
219 *not* regenerated since they are already out of date and I don't
220 want to create the impression that they are suddenly working.
221 o removed KAP stuff for DEC's
222 o modified/added many .cvsignore files in */code and */input
223 o added new expt "solid-body.cs-32x32x1"
224 + this uses an alternative form of ini_curvilinear_grid.F which
225 is not necessarily any better than the current one...
226
227 checkpoint40pre4
228 o added re-initialisations of utrans,vtrans,rtrans in
229 calc_common_factors which are crucial for TAF.
230 o extended iMin,jMin range for calc_common_factors,
231 calc_diffusivity
232 o added option ALLOW_PASSIVE_TRACER
233 o a few minor updates and fixes
234
235 checkpoint40pre3
236 o created calc_gtr1.F for gad package
237 o split the_main_loop and re-introduced forward_step
238 o some recomputations of nIter0 for TAMC
239
240 checkpoint40pre2
241 o Updated to latest branch of AJA, JMC
242 o Added gradient check package
243 o Added routines for passive tracer handling
244 o Added carbon sequestration sensitivity experiment
245
246 checkpoint39
247 o Modifications and fixes to support TAMC
248 (mainly missing or wrong directives)
249 o Corrected common blocks when fooling TAMC to produce adjoint I/O
250 in addummy_in_stepping
251 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
252 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
253 o Included following packages:
254 cal: calendar
255 exf: external forcing
256 ecco: essential routines to control use of cal, exf
257 (NB: this is not the full ECCO environment)
258 o disabled some packages by default in genmake
259
260 checkpoint38
261 o see notes_c37_adj.txt
262 o corrected wrong layer index in external_forcing_t
263 o replaced the_main_loop/forward_step by the_main_loop
264 o removed forceoutput from write_state
265 (replaced criteria for initial/final state)
266 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
267
268 checkpoint37
269 o mdsio.F routine split and packaged in pkg/mdsio
270 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
271 used unless genmake -disable=mdsio)
272 o allow a more precise surface-geopotential gradient for the atmosphere
273 taking into account the change in space of Alpha (=1/rho) at the surface.
274 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
275 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
276 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
277 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
278 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
279 o Time-Average diagnostics defined as a pseudo package "timeave".
280 o pickup files : old pickup (before c35) did not work with new code (c35
281 and after) unless activating 2 commented lines in initialise-varia.
282 o Non-Hydrostatic pickup file Pb fixed.
283 o bug with Rigid-lid version (since c35) fixed.
284
285 checkpoint36
286 o implement Crank-Nickelson barotropic time-stepping
287 o recover Time-Average diagnostics
288 o fix Pb in checkpoint (PR#19)
289 o AIM become a standard package ; clean unused CPP_kees
290
291 checkpoint35
292 o subtantial rewrite of dynamics.f
293 o allows staggered time-stepping
294 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
295 o added bottom drag (linear + quadratic)
296
297 checkpoint34
298 o Modified exchange routines for correct reverse simulation.
299 o Added verification output to comply with bug fix in impldiff.F
300 as of c33 (exp2, natl_box).
301 o Corrected store directives in dynamics.F
302 o Corrected array boundaries in impldiff.F
303 o Corrected array dimensions in gmredi.
304 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
305 o Added routine GLOBAL_SUM_INT to global_sum.F
306 o Added mdsio_gl.F for ECCO purposes.
307
308 checkpoint33
309 o Fixed bug in lower BC in impldiff.F
310 o Fixed confusion about units of forcing arrays in FFIELDS.h
311 namely Fu,Fv,Qnet,Qsw,EmPmR:
312 - Removed verification/natl_box/code/external_fields_scale.F
313 (did not differ from that in model/src)
314 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
315 (see FFIELDS.h for description)
316 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
317 kpp_calc.F and kpp_transport_t.F
318 - Removed model/src/external_fields_scale.F and calls to it
319 - verification/natl_box uses flux data with "atmospheric" sign so
320 a special version of external_fields_load.F is used to
321 change the data as it's read in. This way, the arrays
322 have the right units and signs at all times tha a user could
323 possibly use them.
324 o Corrected genmake to delete a temporary file during configuration
325
326 checkpoint32
327 o Scaling of forcing fields moved from external_forcing.F to
328 external_fields_scale.F, called directly after loading fields.
329 o Surface relaxation terms added to surface tendency fields in
330 extra subroutine.
331 o impldiff.F changed to avoid storing by TAMC of huge intermediate
332 fields.
333 o Changes in GMRedi to comply with packaging structure.
334 o Modifications and bug fixes in KPP package.
335 o Verification experiment for KPP added (verification/nat_box/)
336
337 checkpoint31
338 o Packages interface brought in line with defined standard
339 -> new routines packages_...F
340 -> changes in initialise_fixed.F, initialise_varia.F
341 -> enables initialisation interface for ECCO package
342 o Rescaling of external forcing fields immediately after read
343 (removed from external_forcing.F)
344 -> new: surface_fields_scale.F
345 -> affects ini_foorcing.F, external_fields_load.F
346 o Computation of surface tendencies before tendency updates.
347 -> new: external_forcing_surf.F
348 o Change of variable names useGMRedi, useKPP, useECCO
349 o Further changes in dynamics.F, impldiff.F for TAMC
350 o Tested for experiments 0, 2, 4.
351 - not yet tested for GMRedi.
352 - not yet tested for KPP.
353
354 checkpoint30
355 o Updates for OBCs
356 o New experiment for test OBCs (internal_wave)
357 o New output.txt in verification/exp4/results/
358 o Updates for KPP: calculation of viscosity corrected, new variables
359 kpp_dumpFreq and kpp_taveFreq
360 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
361 and entry for T90 in genmake
362
363 checkpoint29
364 o packaged KPP and GM/Redi
365
366 checkpoint28
367 o Corrected initialization of hFacMin for difference vertical coordinates
368 o Modified calculation of partial cell thickness to more robust algorithm
369 o config_summary.F: replaced write_1D_... by write_0D_...
370 read_write.F: added subroutines write_0D_...
371 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
372 included some initialisations required for TAMC.
373 o routine calc_isoslopes: modified sqrt computation to make it
374 differentiable for zero argument.
375 o routines dynamics, impldiff:
376 included store directives and tape key computations required for TAMC.
377 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
378
379 checkpoint27
380 o fixed calc_isoslopes() to so that cancellation of terms in tensor
381 formulation works properly with variable resolution.
382 o restructured the calling tree between the_model_main() and dynamics()
383 o split initialise() into initialise_fixed() and initialise_varia()
384 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
385 in new routine ini_psurf()
386
387 checkpoint26
388 o moved some #ifdef in optional routines to encompass everything
389 except the argument declarations. This was using up some memory.
390 o fixed macros like _ADT to work with both versions of Linux cpp
391 o cleaned up some unused and uninitialized variables
392 (helps when debugging with strict compile options)
393 o split up CPP_EEOPTIONS.h into options and macros
394 (macros are now in eesupp/inc/CPP_EEMACROS.h)
395 o patch for 2 processor JAM mode
396
397 checkpoint25
398 o updates for OBCs and NH
399 o dramatically reduced memory usage
400 o added "JAM" routines for use on Artic network
401 o parameterization of convection by implicit vertical diffusion
402 o added a diagnostic of convective index
403 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
404 (this is was partly for OBCs and NH but also in anticipation of
405 an explicit free-surface option)
406 o initial state input files for U and V
407
408 checkpoint24
409 o Removed some spurious "REAL"s
410 o Updated KPP to latest version from JPL
411 o Added a COS(latitude) in horizontal viscosity
412
413 checkpoint23
414 o Added del^4 diffusion for salt and temperature
415 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
416
417 checkpoint22
418 o Made many small changes: implicit none, format(i5), etc...
419 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
420
421 checkpoint21
422 o Introduced new I/O package that supports direct-access records (mdsio.F)
423 o Split-up mid-level I/O routines
424 o Updated input data for experiments 0,1,2,4 and 5
425 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
426
427 checkpoint20
428 o Tidied up open-boundaries some more
429 o Added non-hydrostatic code
430 o Fixed some input data
431 o Modified MPI start-up to work in "coupled" context.
432
433 checkpoint19
434 o Tidied up directory structure for verification experiments.
435 o Added new code for open boundaries.
436 o Corrected advective terms near boundaries.
437 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
438 o Implemented free-slip/no-slip BCs and del^4 dissipation.
439 o Split default parameters out of ini_parms.F into set_defaults.F.
440
441 checkpoint18
442 o Further changes for optional code generation with
443 CPP - ugh!
444
445 checkpoint17
446 o Beginning to incorporating modularity
447 for supporting atmos. and ocean configs.
448 o Small changes for TAMC complinace
449 o New ultra simple test case. Barotropic box
450 configuration "exp0".
451
452 checkpoint16
453 o Minor changes to exchange routines to support
454 accumulation in reverse mode. Adjoint of an
455 assignment is an addition.
456 o Changes to support compilation by TAMC (LR(1)
457 syntax) and by g77 under Linux ( 72 character
458 limit ).
459
460 checkpoint15
461 Rewrote exchange routines to allow
462 o General tile <-> tile connectivity.
463 o TAMC reverse mode flag ( is this really needed? )
464 o Variable width overlap and exchange region widths.
465 o Hooks for sharing data via DMA, Arctic, Memory Channel,
466 shmput/shmget, VIA, SYSV shmem and every other cool
467 communication method.
468
469 checkpoint14
470 Consistent isomorphism chages made. These allow dynamical core
471 to support both pressure and meters as a vertical coordinate.
472
473 checkpoint13
474 Release which corrects global_max problem and a couple
475 of KGM time-averaging diagnostic errors. Also contains
476 a double-gyre experiment setup as well as the baseline
477 4 degree global template. The double gyre template is
478 organised to allow it to be applied automatically to
479 the baseline configuration.
480
481 branch-point-rdot
482 A few tidy-ups have been made bt the real point of this
483 check-point (excuse the pun) is to allow a branch to be
484 made for the purposes of adding the rDot alterations.
485 I don't want to commit the rDot to the main-trunk until
486 we've actually tested it...
487
488 checkpoint12
489 Tidy up and added generic genmake script (formerly
490 configure script).
491 Released to testers.
492
493 checkpoint11
494 Re-arranged initialise() and introduced ini_vertical_grid()
495 and ini_masks_etc().
496
497 checkpoint10
498 Introduced the configure script.
499 Separated out the diags package.
500 Added template for writing time-averages of tile/intermediate quantities.
501 Updated SIZE.h in exp2 and made the data big-endian.
502
503 checkpoint9
504 MPI fix. Filename changes (meta/data). salbin*y stuff.
505 General tidy-up.
506 SST.bin SSS.bin added to verification/exp2
507
508 checkpoint8
509 Inludes time-dependant forcing and time-averaging.
510 Works at 4x4 and 2.8125x2.8125 global
511
512 checkpoint7-4degree-ref
513 Branch from checkpoint7. Released for application to
514 global modeling and general modeling - process studies, regional
515 model etc..
516 Configured for verification/exp2 - 4 degree global, two process.
517
518 checkpoint7
519 Created by cnh
520 Simple 4 degree global simulation
521 configuration.
522 Includes climatological wind,
523 hydrography, bathymetry etc
524 Does not include Heat Flux and E-P
525
526 checkpoint6
527 Created by cnh
528 merged checkpoint5 with CD and
529 spherical polar code.
530 Still some problems with GM Redi
531 abd full topography.
532
533 checkpoint5
534 Created by AJA
535 contains updates to GM Redi
536 and reordered timestepping loop
537 for Implicit Diffusion.
538
539 checkpoint4
540 Created by cnh
541 Contains memory saving macros ( _rdxc etc..) for when
542 grid variations are limited.
543 Contains polynomial coeffs for EOS and knudsen program
544 for generation.
545
546 checkpoint3
547 Created by cnh
548 Added extra flags for runtime options
549 Added this file
550 Added implicit free-surface
551 Added pre-conditioner
552 Put compare01 into repository ( compare01/... )
553 Put data and eedata into repository ( verification/exp1 )
554
555 checkpoint2
556 Created by AJA
557 Added GM/Redi
558
559 checkpoint1
560 Created by AJA
561 Restructured kloop in dynamics.F
562 Added non-linear EOS
563
564 baseline
565 Original checked in code

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