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Revision 1.53.2.6 - (show annotations) (download)
Tue May 21 00:03:29 2002 UTC (22 years ago) by heimbach
Branch: release1
Changes since 1.53.2.5: +3 -1 lines
Further modif's for next patch (p3).

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.53.2.5 2002/05/14 20:42:45 heimbach Exp $
2
3 Notes on tags used in MITgcmUV
4 ==============================
5
6 next patch:
7 o added tangent linear setup to verification/carbon/
8 o added adjoint sensitivity setup to verification/global_ocean...
9 o moved packages_init_variables before convective_adjustment
10
11 release1_p2
12 o fixed array boundary problem for adjoint
13 (related to partial recomputation within subroutine
14 related to dynamics -> calc_viscosity -> mom_...
15 o fixed recomputation in thermodynamics
16 o prepare (but not complete) recomputation problem in impldiff
17 o fixed problem for adjoint of global_max
18 o switched off sponge layer code in external_forcing
19
20 release1_p1
21 o merged necessary patches:
22 - AD-related changes for GMRedi
23 - fixes i KPP (delZ -> drF)
24 - hook to OBCS songe layer code in external_forcing
25 - errorMessageUnit non-zero in eeboot.F
26 - modified test cost function and carbon verif.
27
28 release1_chkpt44d_post = chkpt44d_post
29
30 chkpt44d_pre,post
31 o added missing EXCLUDE_MONITOR flags
32 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
33 (incompatible typ in MIN/MAX expressions caused problems
34 on IBM SP3)
35 o in genmake added variable MAKEDEPEND
36 plus resetting for case SunOS
37 o added timer_stats.c routine for IBM SP3
38 o removed variables in dynamics
39
40 o real fresh water flux implemented with non-linear free-surface.
41
42 chkpt44c_pre,post
43 o few fix (mask in shap_s2, EmPmR in external_field_load,
44 USE_NATURAL_BCS in solve_for_P);
45 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
46
47 checkpoint44b_pre/_post
48 o merge of relevant stuff from the ecco-branch:
49 - genmake: removed $S64 overwrite for case SunOS
50 - pkg/exf: update and corrections for field swapping and obcs
51 - pkg/ecco: parameter lists for the_model_main, the_main_loop
52 harmonized between ECCO and MITgcm
53 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
54 updated checkpointing_lev... lists for obcs
55 - model/src: minor changes in forward_step, plot_field
56 added directive for divided adjoint in the_main_loop
57 - pkg/mdsio: added mdsio_gl_slice
58
59 o check parameters & config (chkpt44a_pre,post)
60 o OBC and NonLin_FrSurf.
61
62 checkpoint44
63 o fix bug in mom_vi_del2uv
64 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
65 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
66 o update AIM experiments (NCEP input files)
67 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
68 o added some stuff for AD
69
70 checkpoint43
71 o added two new advection tests
72 o added global 4x4 degree ocean test
73 o added test of H&S94 with free surface on cube
74 o some final mods for gradient check, adjoint,...
75
76 checkpoint42
77 Fixed AD-related problems:
78 o Store directives up-to-date with re-arranged Adams-Bashforth
79 (mainly thermodynamics.F)
80 o New store directives for multi-dim. advection schemes
81 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
82 * new common block and key passkey
83 (mainly gad_advection.F)
84 o Modified store directives for split of dynamics/thermodynamics
85 for the case ALLOW_KPP
86 o Cleaned argument list for timestep_tracer.F
87
88 checkpoint41
89 o re-formatted/added comments in prologues of key subroutines
90 to work with protex
91
92 checkpoint40
93 o moved calc_gs, calc_gt and calc_tr1 back to model/src
94 o added FLT (floats) package from Arne along with demo. experiment
95 o re-arranged Adams-Bashforth scheme for tracers to allow easier
96 implementation of forward-in-time forcing terms
97 o more mods for non-linear free-surface including new variable
98 o modified multi-dim method to work on cube
99 o bug fix in KPP (from DM)
100
101 checkpoint40pre9
102 o added DST advection schemes
103 o fix MPI bug on SGI's
104 o modifications for non-linear free-surface
105 o fixed conditionals for fixed flow/passive tracer only mode
106 o added tension/strain form of stress tensor
107 o changes to commenting of arguments for TAF/TAMC
108 o added/updated many matlab scripts
109 o added multi-dimensional advection method for tracers
110
111 checkpoint40pre8
112 o new package rw/
113 Added method for dumping intermediate local arrays:
114 mdsio_writetile - same as mdsio_writefield except works from inside
115 bi,bj loop
116 mdsio_writelocal - same as mdsio_writetile except works for local
117 arrays
118 write_local_r? - higher-level wrapper for mdsio_writelocal
119 Controlled by diagFreq. Defaults to zero (ie. no dumps)
120 Example given at end of mom_vecinv.F that dumps some local arrays.
121 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
122 control flux-form versus vector invariant code.
123 Switch is runtime flag vectorInvariantMomentum (defaults to false)
124 or genmake -DISABLE ...
125 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
126 (additional storing is now needed for case vecinv;
127 currently nothing implemented to switch this storing off
128 in case fluxform is used since no CPP flag available).
129
130 checkpoint40pre7
131 o bug fix in dynamics.F
132 calc_viscosity called before k=1,Nr loop.
133 o added some #ifdef's ALLOW_PASSIVE_TRACER
134 o cleaned initialisations in ctrl_map_ini
135 related to TAF
136
137 checkpoint40pre6
138 o split dynamics into thermodynamics & dynamics
139 o corresponding split of calc_diffusivity into
140 calc_diffusivity, calc_viscosity
141 (kpp_calc_diff, kpp_calc_visc).
142 o Added diffkr, kapgm to control variables
143 o bug fix in gmredi_slope_limit for ldd97
144
145 checkpoint40pre5
146 o proper initialization of Adams-Bashforth time stepping
147 + uses forward step for very first step of model (iter=0)
148 o re-generated *all* output since almost all output is modified by this
149 change (sorry but we've been putting this one off for about 2 years)
150 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
151 *not* regenerated since they are already out of date and I don't
152 want to create the impression that they are suddenly working.
153 o removed KAP stuff for DEC's
154 o modified/added many .cvsignore files in */code and */input
155 o added new expt "solid-body.cs-32x32x1"
156 + this uses an alternative form of ini_curvilinear_grid.F which
157 is not necessarily any better than the current one...
158
159 checkpoint40pre4
160 o added re-initialisations of utrans,vtrans,rtrans in
161 calc_common_factors which are crucial for TAF.
162 o extended iMin,jMin range for calc_common_factors,
163 calc_diffusivity
164 o added option ALLOW_PASSIVE_TRACER
165 o a few minor updates and fixes
166
167 checkpoint40pre3
168 o created calc_gtr1.F for gad package
169 o split the_main_loop and re-introduced forward_step
170 o some recomputations of nIter0 for TAMC
171
172 checkpoint40pre2
173 o Updated to latest branch of AJA, JMC
174 o Added gradient check package
175 o Added routines for passive tracer handling
176 o Added carbon sequestration sensitivity experiment
177
178 checkpoint39
179 o Modifications and fixes to support TAMC
180 (mainly missing or wrong directives)
181 o Corrected common blocks when fooling TAMC to produce adjoint I/O
182 in addummy_in_stepping
183 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
184 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
185 o Included following packages:
186 cal: calendar
187 exf: external forcing
188 ecco: essential routines to control use of cal, exf
189 (NB: this is not the full ECCO environment)
190 o disabled some packages by default in genmake
191
192 checkpoint38
193 o see notes_c37_adj.txt
194 o corrected wrong layer index in external_forcing_t
195 o replaced the_main_loop/forward_step by the_main_loop
196 o removed forceoutput from write_state
197 (replaced criteria for initial/final state)
198 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
199
200 checkpoint37
201 o mdsio.F routine split and packaged in pkg/mdsio
202 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
203 used unless genmake -disable=mdsio)
204 o allow a more precise surface-geopotential gradient for the atmosphere
205 taking into account the change in space of Alpha (=1/rho) at the surface.
206 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
207 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
208 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
209 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
210 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
211 o Time-Average diagnostics defined as a pseudo package "timeave".
212 o pickup files : old pickup (before c35) did not work with new code (c35
213 and after) unless activating 2 commented lines in initialise-varia.
214 o Non-Hydrostatic pickup file Pb fixed.
215 o bug with Rigid-lid version (since c35) fixed.
216
217 checkpoint36
218 o implement Crank-Nickelson barotropic time-stepping
219 o recover Time-Average diagnostics
220 o fix Pb in checkpoint (PR#19)
221 o AIM become a standard package ; clean unused CPP_kees
222
223 checkpoint35
224 o subtantial rewrite of dynamics.f
225 o allows staggered time-stepping
226 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
227 o added bottom drag (linear + quadratic)
228
229 checkpoint34
230 o Modified exchange routines for correct reverse simulation.
231 o Added verification output to comply with bug fix in impldiff.F
232 as of c33 (exp2, natl_box).
233 o Corrected store directives in dynamics.F
234 o Corrected array boundaries in impldiff.F
235 o Corrected array dimensions in gmredi.
236 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
237 o Added routine GLOBAL_SUM_INT to global_sum.F
238 o Added mdsio_gl.F for ECCO purposes.
239
240 checkpoint33
241 o Fixed bug in lower BC in impldiff.F
242 o Fixed confusion about units of forcing arrays in FFIELDS.h
243 namely Fu,Fv,Qnet,Qsw,EmPmR:
244 - Removed verification/natl_box/code/external_fields_scale.F
245 (did not differ from that in model/src)
246 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
247 (see FFIELDS.h for description)
248 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
249 kpp_calc.F and kpp_transport_t.F
250 - Removed model/src/external_fields_scale.F and calls to it
251 - verification/natl_box uses flux data with "atmospheric" sign so
252 a special version of external_fields_load.F is used to
253 change the data as it's read in. This way, the arrays
254 have the right units and signs at all times tha a user could
255 possibly use them.
256 o Corrected genmake to delete a temporary file during configuration
257
258 checkpoint32
259 o Scaling of forcing fields moved from external_forcing.F to
260 external_fields_scale.F, called directly after loading fields.
261 o Surface relaxation terms added to surface tendency fields in
262 extra subroutine.
263 o impldiff.F changed to avoid storing by TAMC of huge intermediate
264 fields.
265 o Changes in GMRedi to comply with packaging structure.
266 o Modifications and bug fixes in KPP package.
267 o Verification experiment for KPP added (verification/nat_box/)
268
269 checkpoint31
270 o Packages interface brought in line with defined standard
271 -> new routines packages_...F
272 -> changes in initialise_fixed.F, initialise_varia.F
273 -> enables initialisation interface for ECCO package
274 o Rescaling of external forcing fields immediately after read
275 (removed from external_forcing.F)
276 -> new: surface_fields_scale.F
277 -> affects ini_foorcing.F, external_fields_load.F
278 o Computation of surface tendencies before tendency updates.
279 -> new: external_forcing_surf.F
280 o Change of variable names useGMRedi, useKPP, useECCO
281 o Further changes in dynamics.F, impldiff.F for TAMC
282 o Tested for experiments 0, 2, 4.
283 - not yet tested for GMRedi.
284 - not yet tested for KPP.
285
286 checkpoint30
287 o Updates for OBCs
288 o New experiment for test OBCs (internal_wave)
289 o New output.txt in verification/exp4/results/
290 o Updates for KPP: calculation of viscosity corrected, new variables
291 kpp_dumpFreq and kpp_taveFreq
292 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
293 and entry for T90 in genmake
294
295 checkpoint29
296 o packaged KPP and GM/Redi
297
298 checkpoint28
299 o Corrected initialization of hFacMin for difference vertical coordinates
300 o Modified calculation of partial cell thickness to more robust algorithm
301 o config_summary.F: replaced write_1D_... by write_0D_...
302 read_write.F: added subroutines write_0D_...
303 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
304 included some initialisations required for TAMC.
305 o routine calc_isoslopes: modified sqrt computation to make it
306 differentiable for zero argument.
307 o routines dynamics, impldiff:
308 included store directives and tape key computations required for TAMC.
309 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
310
311 checkpoint27
312 o fixed calc_isoslopes() to so that cancellation of terms in tensor
313 formulation works properly with variable resolution.
314 o restructured the calling tree between the_model_main() and dynamics()
315 o split initialise() into initialise_fixed() and initialise_varia()
316 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
317 in new routine ini_psurf()
318
319 checkpoint26
320 o moved some #ifdef in optional routines to encompass everything
321 except the argument declarations. This was using up some memory.
322 o fixed macros like _ADT to work with both versions of Linux cpp
323 o cleaned up some unused and uninitialized variables
324 (helps when debugging with strict compile options)
325 o split up CPP_EEOPTIONS.h into options and macros
326 (macros are now in eesupp/inc/CPP_EEMACROS.h)
327 o patch for 2 processor JAM mode
328
329 checkpoint25
330 o updates for OBCs and NH
331 o dramatically reduced memory usage
332 o added "JAM" routines for use on Artic network
333 o parameterization of convection by implicit vertical diffusion
334 o added a diagnostic of convective index
335 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
336 (this is was partly for OBCs and NH but also in anticipation of
337 an explicit free-surface option)
338 o initial state input files for U and V
339
340 checkpoint24
341 o Removed some spurious "REAL"s
342 o Updated KPP to latest version from JPL
343 o Added a COS(latitude) in horizontal viscosity
344
345 checkpoint23
346 o Added del^4 diffusion for salt and temperature
347 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
348
349 checkpoint22
350 o Made many small changes: implicit none, format(i5), etc...
351 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
352
353 checkpoint21
354 o Introduced new I/O package that supports direct-access records (mdsio.F)
355 o Split-up mid-level I/O routines
356 o Updated input data for experiments 0,1,2,4 and 5
357 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
358
359 checkpoint20
360 o Tidied up open-boundaries some more
361 o Added non-hydrostatic code
362 o Fixed some input data
363 o Modified MPI start-up to work in "coupled" context.
364
365 checkpoint19
366 o Tidied up directory structure for verification experiments.
367 o Added new code for open boundaries.
368 o Corrected advective terms near boundaries.
369 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
370 o Implemented free-slip/no-slip BCs and del^4 dissipation.
371 o Split default parameters out of ini_parms.F into set_defaults.F.
372
373 checkpoint18
374 o Further changes for optional code generation with
375 CPP - ugh!
376
377 checkpoint17
378 o Beginning to incorporating modularity
379 for supporting atmos. and ocean configs.
380 o Small changes for TAMC complinace
381 o New ultra simple test case. Barotropic box
382 configuration "exp0".
383
384 checkpoint16
385 o Minor changes to exchange routines to support
386 accumulation in reverse mode. Adjoint of an
387 assignment is an addition.
388 o Changes to support compilation by TAMC (LR(1)
389 syntax) and by g77 under Linux ( 72 character
390 limit ).
391
392 checkpoint15
393 Rewrote exchange routines to allow
394 o General tile <-> tile connectivity.
395 o TAMC reverse mode flag ( is this really needed? )
396 o Variable width overlap and exchange region widths.
397 o Hooks for sharing data via DMA, Arctic, Memory Channel,
398 shmput/shmget, VIA, SYSV shmem and every other cool
399 communication method.
400
401 checkpoint14
402 Consistent isomorphism chages made. These allow dynamical core
403 to support both pressure and meters as a vertical coordinate.
404
405 checkpoint13
406 Release which corrects global_max problem and a couple
407 of KGM time-averaging diagnostic errors. Also contains
408 a double-gyre experiment setup as well as the baseline
409 4 degree global template. The double gyre template is
410 organised to allow it to be applied automatically to
411 the baseline configuration.
412
413 branch-point-rdot
414 A few tidy-ups have been made bt the real point of this
415 check-point (excuse the pun) is to allow a branch to be
416 made for the purposes of adding the rDot alterations.
417 I don't want to commit the rDot to the main-trunk until
418 we've actually tested it...
419
420 checkpoint12
421 Tidy up and added generic genmake script (formerly
422 configure script).
423 Released to testers.
424
425 checkpoint11
426 Re-arranged initialise() and introduced ini_vertical_grid()
427 and ini_masks_etc().
428
429 checkpoint10
430 Introduced the configure script.
431 Separated out the diags package.
432 Added template for writing time-averages of tile/intermediate quantities.
433 Updated SIZE.h in exp2 and made the data big-endian.
434
435 checkpoint9
436 MPI fix. Filename changes (meta/data). salbin*y stuff.
437 General tidy-up.
438 SST.bin SSS.bin added to verification/exp2
439
440 checkpoint8
441 Inludes time-dependant forcing and time-averaging.
442 Works at 4x4 and 2.8125x2.8125 global
443
444 checkpoint7-4degree-ref
445 Branch from checkpoint7. Released for application to
446 global modeling and general modeling - process studies, regional
447 model etc..
448 Configured for verification/exp2 - 4 degree global, two process.
449
450 checkpoint7
451 Created by cnh
452 Simple 4 degree global simulation
453 configuration.
454 Includes climatological wind,
455 hydrography, bathymetry etc
456 Does not include Heat Flux and E-P
457
458 checkpoint6
459 Created by cnh
460 merged checkpoint5 with CD and
461 spherical polar code.
462 Still some problems with GM Redi
463 abd full topography.
464
465 checkpoint5
466 Created by AJA
467 contains updates to GM Redi
468 and reordered timestepping loop
469 for Implicit Diffusion.
470
471 checkpoint4
472 Created by cnh
473 Contains memory saving macros ( _rdxc etc..) for when
474 grid variations are limited.
475 Contains polynomial coeffs for EOS and knudsen program
476 for generation.
477
478 checkpoint3
479 Created by cnh
480 Added extra flags for runtime options
481 Added this file
482 Added implicit free-surface
483 Added pre-conditioner
484 Put compare01 into repository ( compare01/... )
485 Put data and eedata into repository ( verification/exp1 )
486
487 checkpoint2
488 Created by AJA
489 Added GM/Redi
490
491 checkpoint1
492 Created by AJA
493 Restructured kloop in dynamics.F
494 Added non-linear EOS
495
496 baseline
497 Original checked in code

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