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Revision 1.53.2.4 - (show annotations) (download)
Wed Apr 17 01:48:17 2002 UTC (22 years, 1 month ago) by heimbach
Branch: release1
CVS Tags: release1_p2
Changes since 1.53.2.3: +10 -2 lines
Creating release1_p2
o partial recomputation bug fix for adjoint (kappar...)
o switched-off sponge layer code
o recomputation fix in thermodynamics

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.53.2.3 2002/04/08 20:27:12 heimbach Exp $
2
3 Notes on tags used in MITgcmUV
4 ==============================
5
6 release1_p2
7 o fixed array boundary problem for adjoint
8 (related to partial recomputation within subroutine
9 related to dynamics -> calc_viscosity -> mom_...
10 o fixed recomputation in thermodynamics
11 o prepare (but not complete) recomputation problem in impldiff
12 o fixed problem for adjoint of global_max
13 o switched off sponge layer code in external_forcing
14
15 release1_p1
16 o merged necessary patches:
17 - AD-related changes for GMRedi
18 - fixes i KPP (delZ -> drF)
19 - hook to OBCS songe layer code in external_forcing
20 - errorMessageUnit non-zero in eeboot.F
21 - modified test cost function and carbon verif.
22
23 release1_chkpt44d_post = chkpt44d_post
24
25 chkpt44d_pre,post
26 o added missing EXCLUDE_MONITOR flags
27 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
28 (incompatible typ in MIN/MAX expressions caused problems
29 on IBM SP3)
30 o in genmake added variable MAKEDEPEND
31 plus resetting for case SunOS
32 o added timer_stats.c routine for IBM SP3
33 o removed variables in dynamics
34
35 o real fresh water flux implemented with non-linear free-surface.
36
37 chkpt44c_pre,post
38 o few fix (mask in shap_s2, EmPmR in external_field_load,
39 USE_NATURAL_BCS in solve_for_P);
40 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
41
42 checkpoint44b_pre/_post
43 o merge of relevant stuff from the ecco-branch:
44 - genmake: removed $S64 overwrite for case SunOS
45 - pkg/exf: update and corrections for field swapping and obcs
46 - pkg/ecco: parameter lists for the_model_main, the_main_loop
47 harmonized between ECCO and MITgcm
48 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
49 updated checkpointing_lev... lists for obcs
50 - model/src: minor changes in forward_step, plot_field
51 added directive for divided adjoint in the_main_loop
52 - pkg/mdsio: added mdsio_gl_slice
53
54 o check parameters & config (chkpt44a_pre,post)
55 o OBC and NonLin_FrSurf.
56
57 checkpoint44
58 o fix bug in mom_vi_del2uv
59 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
60 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
61 o update AIM experiments (NCEP input files)
62 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
63 o added some stuff for AD
64
65 checkpoint43
66 o added two new advection tests
67 o added global 4x4 degree ocean test
68 o added test of H&S94 with free surface on cube
69 o some final mods for gradient check, adjoint,...
70
71 checkpoint42
72 Fixed AD-related problems:
73 o Store directives up-to-date with re-arranged Adams-Bashforth
74 (mainly thermodynamics.F)
75 o New store directives for multi-dim. advection schemes
76 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
77 * new common block and key passkey
78 (mainly gad_advection.F)
79 o Modified store directives for split of dynamics/thermodynamics
80 for the case ALLOW_KPP
81 o Cleaned argument list for timestep_tracer.F
82
83 checkpoint41
84 o re-formatted/added comments in prologues of key subroutines
85 to work with protex
86
87 checkpoint40
88 o moved calc_gs, calc_gt and calc_tr1 back to model/src
89 o added FLT (floats) package from Arne along with demo. experiment
90 o re-arranged Adams-Bashforth scheme for tracers to allow easier
91 implementation of forward-in-time forcing terms
92 o more mods for non-linear free-surface including new variable
93 o modified multi-dim method to work on cube
94 o bug fix in KPP (from DM)
95
96 checkpoint40pre9
97 o added DST advection schemes
98 o fix MPI bug on SGI's
99 o modifications for non-linear free-surface
100 o fixed conditionals for fixed flow/passive tracer only mode
101 o added tension/strain form of stress tensor
102 o changes to commenting of arguments for TAF/TAMC
103 o added/updated many matlab scripts
104 o added multi-dimensional advection method for tracers
105
106 checkpoint40pre8
107 o new package rw/
108 Added method for dumping intermediate local arrays:
109 mdsio_writetile - same as mdsio_writefield except works from inside
110 bi,bj loop
111 mdsio_writelocal - same as mdsio_writetile except works for local
112 arrays
113 write_local_r? - higher-level wrapper for mdsio_writelocal
114 Controlled by diagFreq. Defaults to zero (ie. no dumps)
115 Example given at end of mom_vecinv.F that dumps some local arrays.
116 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
117 control flux-form versus vector invariant code.
118 Switch is runtime flag vectorInvariantMomentum (defaults to false)
119 or genmake -DISABLE ...
120 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
121 (additional storing is now needed for case vecinv;
122 currently nothing implemented to switch this storing off
123 in case fluxform is used since no CPP flag available).
124
125 checkpoint40pre7
126 o bug fix in dynamics.F
127 calc_viscosity called before k=1,Nr loop.
128 o added some #ifdef's ALLOW_PASSIVE_TRACER
129 o cleaned initialisations in ctrl_map_ini
130 related to TAF
131
132 checkpoint40pre6
133 o split dynamics into thermodynamics & dynamics
134 o corresponding split of calc_diffusivity into
135 calc_diffusivity, calc_viscosity
136 (kpp_calc_diff, kpp_calc_visc).
137 o Added diffkr, kapgm to control variables
138 o bug fix in gmredi_slope_limit for ldd97
139
140 checkpoint40pre5
141 o proper initialization of Adams-Bashforth time stepping
142 + uses forward step for very first step of model (iter=0)
143 o re-generated *all* output since almost all output is modified by this
144 change (sorry but we've been putting this one off for about 2 years)
145 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
146 *not* regenerated since they are already out of date and I don't
147 want to create the impression that they are suddenly working.
148 o removed KAP stuff for DEC's
149 o modified/added many .cvsignore files in */code and */input
150 o added new expt "solid-body.cs-32x32x1"
151 + this uses an alternative form of ini_curvilinear_grid.F which
152 is not necessarily any better than the current one...
153
154 checkpoint40pre4
155 o added re-initialisations of utrans,vtrans,rtrans in
156 calc_common_factors which are crucial for TAF.
157 o extended iMin,jMin range for calc_common_factors,
158 calc_diffusivity
159 o added option ALLOW_PASSIVE_TRACER
160 o a few minor updates and fixes
161
162 checkpoint40pre3
163 o created calc_gtr1.F for gad package
164 o split the_main_loop and re-introduced forward_step
165 o some recomputations of nIter0 for TAMC
166
167 checkpoint40pre2
168 o Updated to latest branch of AJA, JMC
169 o Added gradient check package
170 o Added routines for passive tracer handling
171 o Added carbon sequestration sensitivity experiment
172
173 checkpoint39
174 o Modifications and fixes to support TAMC
175 (mainly missing or wrong directives)
176 o Corrected common blocks when fooling TAMC to produce adjoint I/O
177 in addummy_in_stepping
178 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
179 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
180 o Included following packages:
181 cal: calendar
182 exf: external forcing
183 ecco: essential routines to control use of cal, exf
184 (NB: this is not the full ECCO environment)
185 o disabled some packages by default in genmake
186
187 checkpoint38
188 o see notes_c37_adj.txt
189 o corrected wrong layer index in external_forcing_t
190 o replaced the_main_loop/forward_step by the_main_loop
191 o removed forceoutput from write_state
192 (replaced criteria for initial/final state)
193 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
194
195 checkpoint37
196 o mdsio.F routine split and packaged in pkg/mdsio
197 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
198 used unless genmake -disable=mdsio)
199 o allow a more precise surface-geopotential gradient for the atmosphere
200 taking into account the change in space of Alpha (=1/rho) at the surface.
201 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
202 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
203 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
204 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
205 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
206 o Time-Average diagnostics defined as a pseudo package "timeave".
207 o pickup files : old pickup (before c35) did not work with new code (c35
208 and after) unless activating 2 commented lines in initialise-varia.
209 o Non-Hydrostatic pickup file Pb fixed.
210 o bug with Rigid-lid version (since c35) fixed.
211
212 checkpoint36
213 o implement Crank-Nickelson barotropic time-stepping
214 o recover Time-Average diagnostics
215 o fix Pb in checkpoint (PR#19)
216 o AIM become a standard package ; clean unused CPP_kees
217
218 checkpoint35
219 o subtantial rewrite of dynamics.f
220 o allows staggered time-stepping
221 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
222 o added bottom drag (linear + quadratic)
223
224 checkpoint34
225 o Modified exchange routines for correct reverse simulation.
226 o Added verification output to comply with bug fix in impldiff.F
227 as of c33 (exp2, natl_box).
228 o Corrected store directives in dynamics.F
229 o Corrected array boundaries in impldiff.F
230 o Corrected array dimensions in gmredi.
231 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
232 o Added routine GLOBAL_SUM_INT to global_sum.F
233 o Added mdsio_gl.F for ECCO purposes.
234
235 checkpoint33
236 o Fixed bug in lower BC in impldiff.F
237 o Fixed confusion about units of forcing arrays in FFIELDS.h
238 namely Fu,Fv,Qnet,Qsw,EmPmR:
239 - Removed verification/natl_box/code/external_fields_scale.F
240 (did not differ from that in model/src)
241 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
242 (see FFIELDS.h for description)
243 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
244 kpp_calc.F and kpp_transport_t.F
245 - Removed model/src/external_fields_scale.F and calls to it
246 - verification/natl_box uses flux data with "atmospheric" sign so
247 a special version of external_fields_load.F is used to
248 change the data as it's read in. This way, the arrays
249 have the right units and signs at all times tha a user could
250 possibly use them.
251 o Corrected genmake to delete a temporary file during configuration
252
253 checkpoint32
254 o Scaling of forcing fields moved from external_forcing.F to
255 external_fields_scale.F, called directly after loading fields.
256 o Surface relaxation terms added to surface tendency fields in
257 extra subroutine.
258 o impldiff.F changed to avoid storing by TAMC of huge intermediate
259 fields.
260 o Changes in GMRedi to comply with packaging structure.
261 o Modifications and bug fixes in KPP package.
262 o Verification experiment for KPP added (verification/nat_box/)
263
264 checkpoint31
265 o Packages interface brought in line with defined standard
266 -> new routines packages_...F
267 -> changes in initialise_fixed.F, initialise_varia.F
268 -> enables initialisation interface for ECCO package
269 o Rescaling of external forcing fields immediately after read
270 (removed from external_forcing.F)
271 -> new: surface_fields_scale.F
272 -> affects ini_foorcing.F, external_fields_load.F
273 o Computation of surface tendencies before tendency updates.
274 -> new: external_forcing_surf.F
275 o Change of variable names useGMRedi, useKPP, useECCO
276 o Further changes in dynamics.F, impldiff.F for TAMC
277 o Tested for experiments 0, 2, 4.
278 - not yet tested for GMRedi.
279 - not yet tested for KPP.
280
281 checkpoint30
282 o Updates for OBCs
283 o New experiment for test OBCs (internal_wave)
284 o New output.txt in verification/exp4/results/
285 o Updates for KPP: calculation of viscosity corrected, new variables
286 kpp_dumpFreq and kpp_taveFreq
287 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
288 and entry for T90 in genmake
289
290 checkpoint29
291 o packaged KPP and GM/Redi
292
293 checkpoint28
294 o Corrected initialization of hFacMin for difference vertical coordinates
295 o Modified calculation of partial cell thickness to more robust algorithm
296 o config_summary.F: replaced write_1D_... by write_0D_...
297 read_write.F: added subroutines write_0D_...
298 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
299 included some initialisations required for TAMC.
300 o routine calc_isoslopes: modified sqrt computation to make it
301 differentiable for zero argument.
302 o routines dynamics, impldiff:
303 included store directives and tape key computations required for TAMC.
304 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
305
306 checkpoint27
307 o fixed calc_isoslopes() to so that cancellation of terms in tensor
308 formulation works properly with variable resolution.
309 o restructured the calling tree between the_model_main() and dynamics()
310 o split initialise() into initialise_fixed() and initialise_varia()
311 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
312 in new routine ini_psurf()
313
314 checkpoint26
315 o moved some #ifdef in optional routines to encompass everything
316 except the argument declarations. This was using up some memory.
317 o fixed macros like _ADT to work with both versions of Linux cpp
318 o cleaned up some unused and uninitialized variables
319 (helps when debugging with strict compile options)
320 o split up CPP_EEOPTIONS.h into options and macros
321 (macros are now in eesupp/inc/CPP_EEMACROS.h)
322 o patch for 2 processor JAM mode
323
324 checkpoint25
325 o updates for OBCs and NH
326 o dramatically reduced memory usage
327 o added "JAM" routines for use on Artic network
328 o parameterization of convection by implicit vertical diffusion
329 o added a diagnostic of convective index
330 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
331 (this is was partly for OBCs and NH but also in anticipation of
332 an explicit free-surface option)
333 o initial state input files for U and V
334
335 checkpoint24
336 o Removed some spurious "REAL"s
337 o Updated KPP to latest version from JPL
338 o Added a COS(latitude) in horizontal viscosity
339
340 checkpoint23
341 o Added del^4 diffusion for salt and temperature
342 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
343
344 checkpoint22
345 o Made many small changes: implicit none, format(i5), etc...
346 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
347
348 checkpoint21
349 o Introduced new I/O package that supports direct-access records (mdsio.F)
350 o Split-up mid-level I/O routines
351 o Updated input data for experiments 0,1,2,4 and 5
352 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
353
354 checkpoint20
355 o Tidied up open-boundaries some more
356 o Added non-hydrostatic code
357 o Fixed some input data
358 o Modified MPI start-up to work in "coupled" context.
359
360 checkpoint19
361 o Tidied up directory structure for verification experiments.
362 o Added new code for open boundaries.
363 o Corrected advective terms near boundaries.
364 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
365 o Implemented free-slip/no-slip BCs and del^4 dissipation.
366 o Split default parameters out of ini_parms.F into set_defaults.F.
367
368 checkpoint18
369 o Further changes for optional code generation with
370 CPP - ugh!
371
372 checkpoint17
373 o Beginning to incorporating modularity
374 for supporting atmos. and ocean configs.
375 o Small changes for TAMC complinace
376 o New ultra simple test case. Barotropic box
377 configuration "exp0".
378
379 checkpoint16
380 o Minor changes to exchange routines to support
381 accumulation in reverse mode. Adjoint of an
382 assignment is an addition.
383 o Changes to support compilation by TAMC (LR(1)
384 syntax) and by g77 under Linux ( 72 character
385 limit ).
386
387 checkpoint15
388 Rewrote exchange routines to allow
389 o General tile <-> tile connectivity.
390 o TAMC reverse mode flag ( is this really needed? )
391 o Variable width overlap and exchange region widths.
392 o Hooks for sharing data via DMA, Arctic, Memory Channel,
393 shmput/shmget, VIA, SYSV shmem and every other cool
394 communication method.
395
396 checkpoint14
397 Consistent isomorphism chages made. These allow dynamical core
398 to support both pressure and meters as a vertical coordinate.
399
400 checkpoint13
401 Release which corrects global_max problem and a couple
402 of KGM time-averaging diagnostic errors. Also contains
403 a double-gyre experiment setup as well as the baseline
404 4 degree global template. The double gyre template is
405 organised to allow it to be applied automatically to
406 the baseline configuration.
407
408 branch-point-rdot
409 A few tidy-ups have been made bt the real point of this
410 check-point (excuse the pun) is to allow a branch to be
411 made for the purposes of adding the rDot alterations.
412 I don't want to commit the rDot to the main-trunk until
413 we've actually tested it...
414
415 checkpoint12
416 Tidy up and added generic genmake script (formerly
417 configure script).
418 Released to testers.
419
420 checkpoint11
421 Re-arranged initialise() and introduced ini_vertical_grid()
422 and ini_masks_etc().
423
424 checkpoint10
425 Introduced the configure script.
426 Separated out the diags package.
427 Added template for writing time-averages of tile/intermediate quantities.
428 Updated SIZE.h in exp2 and made the data big-endian.
429
430 checkpoint9
431 MPI fix. Filename changes (meta/data). salbin*y stuff.
432 General tidy-up.
433 SST.bin SSS.bin added to verification/exp2
434
435 checkpoint8
436 Inludes time-dependant forcing and time-averaging.
437 Works at 4x4 and 2.8125x2.8125 global
438
439 checkpoint7-4degree-ref
440 Branch from checkpoint7. Released for application to
441 global modeling and general modeling - process studies, regional
442 model etc..
443 Configured for verification/exp2 - 4 degree global, two process.
444
445 checkpoint7
446 Created by cnh
447 Simple 4 degree global simulation
448 configuration.
449 Includes climatological wind,
450 hydrography, bathymetry etc
451 Does not include Heat Flux and E-P
452
453 checkpoint6
454 Created by cnh
455 merged checkpoint5 with CD and
456 spherical polar code.
457 Still some problems with GM Redi
458 abd full topography.
459
460 checkpoint5
461 Created by AJA
462 contains updates to GM Redi
463 and reordered timestepping loop
464 for Implicit Diffusion.
465
466 checkpoint4
467 Created by cnh
468 Contains memory saving macros ( _rdxc etc..) for when
469 grid variations are limited.
470 Contains polynomial coeffs for EOS and knudsen program
471 for generation.
472
473 checkpoint3
474 Created by cnh
475 Added extra flags for runtime options
476 Added this file
477 Added implicit free-surface
478 Added pre-conditioner
479 Put compare01 into repository ( compare01/... )
480 Put data and eedata into repository ( verification/exp1 )
481
482 checkpoint2
483 Created by AJA
484 Added GM/Redi
485
486 checkpoint1
487 Created by AJA
488 Restructured kloop in dynamics.F
489 Added non-linear EOS
490
491 baseline
492 Original checked in code

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