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Revision 1.61 - (show annotations) (download)
Fri Feb 15 21:31:57 2002 UTC (22 years, 2 months ago) by heimbach
Branch: MAIN
CVS Tags: chkpt44d_post, checkpoint44e_pre
Branch point for: release1_final
Changes since 1.60: +13 -1 lines
Creating chkpt44d_post
(I forgot to create chkpt44d_pre,
but chkpt44d_pre = chkpt44c_post).

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.60 2002/02/10 20:07:14 jmc Exp $
2
3 Notes on tags used in MITgcmUV
4 ==============================
5
6 o real fresh water flux implemented with non-linear free-surface.
7
8 chkpt44d_pre,post
9 o added missing EXCLUDE_MONITOR flags
10 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
11 (incompatible typ in MIN/MAX expressions caused problems
12 on IBM SP3)
13 o in genmake added variable MAKEDEPEND
14 plus resetting for case SunOS
15 o added timer_stats.c routine for IBM SP3
16 o removed variables in dynamics
17 !!! I forgot to create tag chkpt44d_pre !!!
18 !!! But chkpt44d_pre = chkpt44c_post !!!
19
20 chkpt44c_pre,post
21 o few fix (mask in shap_s2, EmPmR in external_field_load,
22 USE_NATURAL_BCS in solve_for_P);
23 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
24
25 checkpoint44b_pre/_post
26 o merge of relevant stuff from the ecco-branch:
27 - genmake: removed $S64 overwrite for case SunOS
28 - pkg/exf: update and corrections for field swapping and obcs
29 - pkg/ecco: parameter lists for the_model_main, the_main_loop
30 harmonized between ECCO and MITgcm
31 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
32 updated checkpointing_lev... lists for obcs
33 - model/src: minor changes in forward_step, plot_field
34 added directive for divided adjoint in the_main_loop
35 - pkg/mdsio: added mdsio_gl_slice
36
37 o check parameters & config (chkpt44a_pre,post)
38 o OBC and NonLin_FrSurf.
39
40 checkpoint44
41 o fix bug in mom_vi_del2uv
42 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
43 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
44 o update AIM experiments (NCEP input files)
45 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
46 o added some stuff for AD
47
48 checkpoint43
49 o added two new advection tests
50 o added global 4x4 degree ocean test
51 o added test of H&S94 with free surface on cube
52 o some final mods for gradient check, adjoint,...
53
54 checkpoint42
55 Fixed AD-related problems:
56 o Store directives up-to-date with re-arranged Adams-Bashforth
57 (mainly thermodynamics.F)
58 o New store directives for multi-dim. advection schemes
59 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
60 * new common block and key passkey
61 (mainly gad_advection.F)
62 o Modified store directives for split of dynamics/thermodynamics
63 for the case ALLOW_KPP
64 o Cleaned argument list for timestep_tracer.F
65
66 checkpoint41
67 o re-formatted/added comments in prologues of key subroutines
68 to work with protex
69
70 checkpoint40
71 o moved calc_gs, calc_gt and calc_tr1 back to model/src
72 o added FLT (floats) package from Arne along with demo. experiment
73 o re-arranged Adams-Bashforth scheme for tracers to allow easier
74 implementation of forward-in-time forcing terms
75 o more mods for non-linear free-surface including new variable
76 o modified multi-dim method to work on cube
77 o bug fix in KPP (from DM)
78
79 checkpoint40pre9
80 o added DST advection schemes
81 o fix MPI bug on SGI's
82 o modifications for non-linear free-surface
83 o fixed conditionals for fixed flow/passive tracer only mode
84 o added tension/strain form of stress tensor
85 o changes to commenting of arguments for TAF/TAMC
86 o added/updated many matlab scripts
87 o added multi-dimensional advection method for tracers
88
89 checkpoint40pre8
90 o new package rw/
91 Added method for dumping intermediate local arrays:
92 mdsio_writetile - same as mdsio_writefield except works from inside
93 bi,bj loop
94 mdsio_writelocal - same as mdsio_writetile except works for local
95 arrays
96 write_local_r? - higher-level wrapper for mdsio_writelocal
97 Controlled by diagFreq. Defaults to zero (ie. no dumps)
98 Example given at end of mom_vecinv.F that dumps some local arrays.
99 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
100 control flux-form versus vector invariant code.
101 Switch is runtime flag vectorInvariantMomentum (defaults to false)
102 or genmake -DISABLE ...
103 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
104 (additional storing is now needed for case vecinv;
105 currently nothing implemented to switch this storing off
106 in case fluxform is used since no CPP flag available).
107
108 checkpoint40pre7
109 o bug fix in dynamics.F
110 calc_viscosity called before k=1,Nr loop.
111 o added some #ifdef's ALLOW_PASSIVE_TRACER
112 o cleaned initialisations in ctrl_map_ini
113 related to TAF
114
115 checkpoint40pre6
116 o split dynamics into thermodynamics & dynamics
117 o corresponding split of calc_diffusivity into
118 calc_diffusivity, calc_viscosity
119 (kpp_calc_diff, kpp_calc_visc).
120 o Added diffkr, kapgm to control variables
121 o bug fix in gmredi_slope_limit for ldd97
122
123 checkpoint40pre5
124 o proper initialization of Adams-Bashforth time stepping
125 + uses forward step for very first step of model (iter=0)
126 o re-generated *all* output since almost all output is modified by this
127 change (sorry but we've been putting this one off for about 2 years)
128 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
129 *not* regenerated since they are already out of date and I don't
130 want to create the impression that they are suddenly working.
131 o removed KAP stuff for DEC's
132 o modified/added many .cvsignore files in */code and */input
133 o added new expt "solid-body.cs-32x32x1"
134 + this uses an alternative form of ini_curvilinear_grid.F which
135 is not necessarily any better than the current one...
136
137 checkpoint40pre4
138 o added re-initialisations of utrans,vtrans,rtrans in
139 calc_common_factors which are crucial for TAF.
140 o extended iMin,jMin range for calc_common_factors,
141 calc_diffusivity
142 o added option ALLOW_PASSIVE_TRACER
143 o a few minor updates and fixes
144
145 checkpoint40pre3
146 o created calc_gtr1.F for gad package
147 o split the_main_loop and re-introduced forward_step
148 o some recomputations of nIter0 for TAMC
149
150 checkpoint40pre2
151 o Updated to latest branch of AJA, JMC
152 o Added gradient check package
153 o Added routines for passive tracer handling
154 o Added carbon sequestration sensitivity experiment
155
156 checkpoint39
157 o Modifications and fixes to support TAMC
158 (mainly missing or wrong directives)
159 o Corrected common blocks when fooling TAMC to produce adjoint I/O
160 in addummy_in_stepping
161 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
162 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
163 o Included following packages:
164 cal: calendar
165 exf: external forcing
166 ecco: essential routines to control use of cal, exf
167 (NB: this is not the full ECCO environment)
168 o disabled some packages by default in genmake
169
170 checkpoint38
171 o see notes_c37_adj.txt
172 o corrected wrong layer index in external_forcing_t
173 o replaced the_main_loop/forward_step by the_main_loop
174 o removed forceoutput from write_state
175 (replaced criteria for initial/final state)
176 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
177
178 checkpoint37
179 o mdsio.F routine split and packaged in pkg/mdsio
180 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
181 used unless genmake -disable=mdsio)
182 o allow a more precise surface-geopotential gradient for the atmosphere
183 taking into account the change in space of Alpha (=1/rho) at the surface.
184 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
185 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
186 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
187 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
188 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
189 o Time-Average diagnostics defined as a pseudo package "timeave".
190 o pickup files : old pickup (before c35) did not work with new code (c35
191 and after) unless activating 2 commented lines in initialise-varia.
192 o Non-Hydrostatic pickup file Pb fixed.
193 o bug with Rigid-lid version (since c35) fixed.
194
195 checkpoint36
196 o implement Crank-Nickelson barotropic time-stepping
197 o recover Time-Average diagnostics
198 o fix Pb in checkpoint (PR#19)
199 o AIM become a standard package ; clean unused CPP_kees
200
201 checkpoint35
202 o subtantial rewrite of dynamics.f
203 o allows staggered time-stepping
204 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
205 o added bottom drag (linear + quadratic)
206
207 checkpoint34
208 o Modified exchange routines for correct reverse simulation.
209 o Added verification output to comply with bug fix in impldiff.F
210 as of c33 (exp2, natl_box).
211 o Corrected store directives in dynamics.F
212 o Corrected array boundaries in impldiff.F
213 o Corrected array dimensions in gmredi.
214 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
215 o Added routine GLOBAL_SUM_INT to global_sum.F
216 o Added mdsio_gl.F for ECCO purposes.
217
218 checkpoint33
219 o Fixed bug in lower BC in impldiff.F
220 o Fixed confusion about units of forcing arrays in FFIELDS.h
221 namely Fu,Fv,Qnet,Qsw,EmPmR:
222 - Removed verification/natl_box/code/external_fields_scale.F
223 (did not differ from that in model/src)
224 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
225 (see FFIELDS.h for description)
226 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
227 kpp_calc.F and kpp_transport_t.F
228 - Removed model/src/external_fields_scale.F and calls to it
229 - verification/natl_box uses flux data with "atmospheric" sign so
230 a special version of external_fields_load.F is used to
231 change the data as it's read in. This way, the arrays
232 have the right units and signs at all times tha a user could
233 possibly use them.
234 o Corrected genmake to delete a temporary file during configuration
235
236 checkpoint32
237 o Scaling of forcing fields moved from external_forcing.F to
238 external_fields_scale.F, called directly after loading fields.
239 o Surface relaxation terms added to surface tendency fields in
240 extra subroutine.
241 o impldiff.F changed to avoid storing by TAMC of huge intermediate
242 fields.
243 o Changes in GMRedi to comply with packaging structure.
244 o Modifications and bug fixes in KPP package.
245 o Verification experiment for KPP added (verification/nat_box/)
246
247 checkpoint31
248 o Packages interface brought in line with defined standard
249 -> new routines packages_...F
250 -> changes in initialise_fixed.F, initialise_varia.F
251 -> enables initialisation interface for ECCO package
252 o Rescaling of external forcing fields immediately after read
253 (removed from external_forcing.F)
254 -> new: surface_fields_scale.F
255 -> affects ini_foorcing.F, external_fields_load.F
256 o Computation of surface tendencies before tendency updates.
257 -> new: external_forcing_surf.F
258 o Change of variable names useGMRedi, useKPP, useECCO
259 o Further changes in dynamics.F, impldiff.F for TAMC
260 o Tested for experiments 0, 2, 4.
261 - not yet tested for GMRedi.
262 - not yet tested for KPP.
263
264 checkpoint30
265 o Updates for OBCs
266 o New experiment for test OBCs (internal_wave)
267 o New output.txt in verification/exp4/results/
268 o Updates for KPP: calculation of viscosity corrected, new variables
269 kpp_dumpFreq and kpp_taveFreq
270 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
271 and entry for T90 in genmake
272
273 checkpoint29
274 o packaged KPP and GM/Redi
275
276 checkpoint28
277 o Corrected initialization of hFacMin for difference vertical coordinates
278 o Modified calculation of partial cell thickness to more robust algorithm
279 o config_summary.F: replaced write_1D_... by write_0D_...
280 read_write.F: added subroutines write_0D_...
281 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
282 included some initialisations required for TAMC.
283 o routine calc_isoslopes: modified sqrt computation to make it
284 differentiable for zero argument.
285 o routines dynamics, impldiff:
286 included store directives and tape key computations required for TAMC.
287 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
288
289 checkpoint27
290 o fixed calc_isoslopes() to so that cancellation of terms in tensor
291 formulation works properly with variable resolution.
292 o restructured the calling tree between the_model_main() and dynamics()
293 o split initialise() into initialise_fixed() and initialise_varia()
294 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
295 in new routine ini_psurf()
296
297 checkpoint26
298 o moved some #ifdef in optional routines to encompass everything
299 except the argument declarations. This was using up some memory.
300 o fixed macros like _ADT to work with both versions of Linux cpp
301 o cleaned up some unused and uninitialized variables
302 (helps when debugging with strict compile options)
303 o split up CPP_EEOPTIONS.h into options and macros
304 (macros are now in eesupp/inc/CPP_EEMACROS.h)
305 o patch for 2 processor JAM mode
306
307 checkpoint25
308 o updates for OBCs and NH
309 o dramatically reduced memory usage
310 o added "JAM" routines for use on Artic network
311 o parameterization of convection by implicit vertical diffusion
312 o added a diagnostic of convective index
313 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
314 (this is was partly for OBCs and NH but also in anticipation of
315 an explicit free-surface option)
316 o initial state input files for U and V
317
318 checkpoint24
319 o Removed some spurious "REAL"s
320 o Updated KPP to latest version from JPL
321 o Added a COS(latitude) in horizontal viscosity
322
323 checkpoint23
324 o Added del^4 diffusion for salt and temperature
325 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
326
327 checkpoint22
328 o Made many small changes: implicit none, format(i5), etc...
329 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
330
331 checkpoint21
332 o Introduced new I/O package that supports direct-access records (mdsio.F)
333 o Split-up mid-level I/O routines
334 o Updated input data for experiments 0,1,2,4 and 5
335 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
336
337 checkpoint20
338 o Tidied up open-boundaries some more
339 o Added non-hydrostatic code
340 o Fixed some input data
341 o Modified MPI start-up to work in "coupled" context.
342
343 checkpoint19
344 o Tidied up directory structure for verification experiments.
345 o Added new code for open boundaries.
346 o Corrected advective terms near boundaries.
347 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
348 o Implemented free-slip/no-slip BCs and del^4 dissipation.
349 o Split default parameters out of ini_parms.F into set_defaults.F.
350
351 checkpoint18
352 o Further changes for optional code generation with
353 CPP - ugh!
354
355 checkpoint17
356 o Beginning to incorporating modularity
357 for supporting atmos. and ocean configs.
358 o Small changes for TAMC complinace
359 o New ultra simple test case. Barotropic box
360 configuration "exp0".
361
362 checkpoint16
363 o Minor changes to exchange routines to support
364 accumulation in reverse mode. Adjoint of an
365 assignment is an addition.
366 o Changes to support compilation by TAMC (LR(1)
367 syntax) and by g77 under Linux ( 72 character
368 limit ).
369
370 checkpoint15
371 Rewrote exchange routines to allow
372 o General tile <-> tile connectivity.
373 o TAMC reverse mode flag ( is this really needed? )
374 o Variable width overlap and exchange region widths.
375 o Hooks for sharing data via DMA, Arctic, Memory Channel,
376 shmput/shmget, VIA, SYSV shmem and every other cool
377 communication method.
378
379 checkpoint14
380 Consistent isomorphism chages made. These allow dynamical core
381 to support both pressure and meters as a vertical coordinate.
382
383 checkpoint13
384 Release which corrects global_max problem and a couple
385 of KGM time-averaging diagnostic errors. Also contains
386 a double-gyre experiment setup as well as the baseline
387 4 degree global template. The double gyre template is
388 organised to allow it to be applied automatically to
389 the baseline configuration.
390
391 branch-point-rdot
392 A few tidy-ups have been made bt the real point of this
393 check-point (excuse the pun) is to allow a branch to be
394 made for the purposes of adding the rDot alterations.
395 I don't want to commit the rDot to the main-trunk until
396 we've actually tested it...
397
398 checkpoint12
399 Tidy up and added generic genmake script (formerly
400 configure script).
401 Released to testers.
402
403 checkpoint11
404 Re-arranged initialise() and introduced ini_vertical_grid()
405 and ini_masks_etc().
406
407 checkpoint10
408 Introduced the configure script.
409 Separated out the diags package.
410 Added template for writing time-averages of tile/intermediate quantities.
411 Updated SIZE.h in exp2 and made the data big-endian.
412
413 checkpoint9
414 MPI fix. Filename changes (meta/data). salbin*y stuff.
415 General tidy-up.
416 SST.bin SSS.bin added to verification/exp2
417
418 checkpoint8
419 Inludes time-dependant forcing and time-averaging.
420 Works at 4x4 and 2.8125x2.8125 global
421
422 checkpoint7-4degree-ref
423 Branch from checkpoint7. Released for application to
424 global modeling and general modeling - process studies, regional
425 model etc..
426 Configured for verification/exp2 - 4 degree global, two process.
427
428 checkpoint7
429 Created by cnh
430 Simple 4 degree global simulation
431 configuration.
432 Includes climatological wind,
433 hydrography, bathymetry etc
434 Does not include Heat Flux and E-P
435
436 checkpoint6
437 Created by cnh
438 merged checkpoint5 with CD and
439 spherical polar code.
440 Still some problems with GM Redi
441 abd full topography.
442
443 checkpoint5
444 Created by AJA
445 contains updates to GM Redi
446 and reordered timestepping loop
447 for Implicit Diffusion.
448
449 checkpoint4
450 Created by cnh
451 Contains memory saving macros ( _rdxc etc..) for when
452 grid variations are limited.
453 Contains polynomial coeffs for EOS and knudsen program
454 for generation.
455
456 checkpoint3
457 Created by cnh
458 Added extra flags for runtime options
459 Added this file
460 Added implicit free-surface
461 Added pre-conditioner
462 Put compare01 into repository ( compare01/... )
463 Put data and eedata into repository ( verification/exp1 )
464
465 checkpoint2
466 Created by AJA
467 Added GM/Redi
468
469 checkpoint1
470 Created by AJA
471 Restructured kloop in dynamics.F
472 Added non-linear EOS
473
474 baseline
475 Original checked in code

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