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Revision - (show annotations) (download)
Sun Mar 24 04:23:44 2002 UTC (21 years ago) by heimbach
Branch: release1_final
CVS Tags: release1_final_v1
Changes since 1.61: +12 -2 lines
Creating tag release1_final_v1.

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.61 2002/02/15 21:31:57 heimbach Exp $
3 Notes on tags used in MITgcmUV
4 ==============================
6 release1_final_v1
7 o merged necessary patches:
8 - AD-related changes for GMRedi
9 - fixes i KPP (delZ -> drF)
10 - hook to OBCS songe layer code in external_forcing
11 - errorMessageUnit non-zero in eeboot.F
12 - modified test cost function and carbon verif.
14 release1_final branched from chkpt44d_post
16 chkpt44d_pre,post
17 o added missing EXCLUDE_MONITOR flags
18 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
19 (incompatible typ in MIN/MAX expressions caused problems
20 on IBM SP3)
21 o in genmake added variable MAKEDEPEND
22 plus resetting for case SunOS
23 o added timer_stats.c routine for IBM SP3
24 o removed variables in dynamics
25 !!! I forgot to create tag chkpt44d_pre !!!
26 !!! But chkpt44d_pre = chkpt44c_post !!!
28 o real fresh water flux implemented with non-linear free-surface.
30 chkpt44c_pre,post
31 o few fix (mask in shap_s2, EmPmR in external_field_load,
32 USE_NATURAL_BCS in solve_for_P);
33 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
35 checkpoint44b_pre/_post
36 o merge of relevant stuff from the ecco-branch:
37 - genmake: removed $S64 overwrite for case SunOS
38 - pkg/exf: update and corrections for field swapping and obcs
39 - pkg/ecco: parameter lists for the_model_main, the_main_loop
40 harmonized between ECCO and MITgcm
41 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
42 updated checkpointing_lev... lists for obcs
43 - model/src: minor changes in forward_step, plot_field
44 added directive for divided adjoint in the_main_loop
45 - pkg/mdsio: added mdsio_gl_slice
47 o check parameters & config (chkpt44a_pre,post)
48 o OBC and NonLin_FrSurf.
50 checkpoint44
51 o fix bug in mom_vi_del2uv
52 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
53 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
54 o update AIM experiments (NCEP input files)
55 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
56 o added some stuff for AD
58 checkpoint43
59 o added two new advection tests
60 o added global 4x4 degree ocean test
61 o added test of H&S94 with free surface on cube
62 o some final mods for gradient check, adjoint,...
64 checkpoint42
65 Fixed AD-related problems:
66 o Store directives up-to-date with re-arranged Adams-Bashforth
67 (mainly thermodynamics.F)
68 o New store directives for multi-dim. advection schemes
70 * new common block and key passkey
71 (mainly gad_advection.F)
72 o Modified store directives for split of dynamics/thermodynamics
73 for the case ALLOW_KPP
74 o Cleaned argument list for timestep_tracer.F
76 checkpoint41
77 o re-formatted/added comments in prologues of key subroutines
78 to work with protex
80 checkpoint40
81 o moved calc_gs, calc_gt and calc_tr1 back to model/src
82 o added FLT (floats) package from Arne along with demo. experiment
83 o re-arranged Adams-Bashforth scheme for tracers to allow easier
84 implementation of forward-in-time forcing terms
85 o more mods for non-linear free-surface including new variable
86 o modified multi-dim method to work on cube
87 o bug fix in KPP (from DM)
89 checkpoint40pre9
90 o added DST advection schemes
91 o fix MPI bug on SGI's
92 o modifications for non-linear free-surface
93 o fixed conditionals for fixed flow/passive tracer only mode
94 o added tension/strain form of stress tensor
95 o changes to commenting of arguments for TAF/TAMC
96 o added/updated many matlab scripts
97 o added multi-dimensional advection method for tracers
99 checkpoint40pre8
100 o new package rw/
101 Added method for dumping intermediate local arrays:
102 mdsio_writetile - same as mdsio_writefield except works from inside
103 bi,bj loop
104 mdsio_writelocal - same as mdsio_writetile except works for local
105 arrays
106 write_local_r? - higher-level wrapper for mdsio_writelocal
107 Controlled by diagFreq. Defaults to zero (ie. no dumps)
108 Example given at end of mom_vecinv.F that dumps some local arrays.
109 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
110 control flux-form versus vector invariant code.
111 Switch is runtime flag vectorInvariantMomentum (defaults to false)
112 or genmake -DISABLE ...
113 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
114 (additional storing is now needed for case vecinv;
115 currently nothing implemented to switch this storing off
116 in case fluxform is used since no CPP flag available).
118 checkpoint40pre7
119 o bug fix in dynamics.F
120 calc_viscosity called before k=1,Nr loop.
121 o added some #ifdef's ALLOW_PASSIVE_TRACER
122 o cleaned initialisations in ctrl_map_ini
123 related to TAF
125 checkpoint40pre6
126 o split dynamics into thermodynamics & dynamics
127 o corresponding split of calc_diffusivity into
128 calc_diffusivity, calc_viscosity
129 (kpp_calc_diff, kpp_calc_visc).
130 o Added diffkr, kapgm to control variables
131 o bug fix in gmredi_slope_limit for ldd97
133 checkpoint40pre5
134 o proper initialization of Adams-Bashforth time stepping
135 + uses forward step for very first step of model (iter=0)
136 o re-generated *all* output since almost all output is modified by this
137 change (sorry but we've been putting this one off for about 2 years)
138 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
139 *not* regenerated since they are already out of date and I don't
140 want to create the impression that they are suddenly working.
141 o removed KAP stuff for DEC's
142 o modified/added many .cvsignore files in */code and */input
143 o added new expt "solid-body.cs-32x32x1"
144 + this uses an alternative form of ini_curvilinear_grid.F which
145 is not necessarily any better than the current one...
147 checkpoint40pre4
148 o added re-initialisations of utrans,vtrans,rtrans in
149 calc_common_factors which are crucial for TAF.
150 o extended iMin,jMin range for calc_common_factors,
151 calc_diffusivity
152 o added option ALLOW_PASSIVE_TRACER
153 o a few minor updates and fixes
155 checkpoint40pre3
156 o created calc_gtr1.F for gad package
157 o split the_main_loop and re-introduced forward_step
158 o some recomputations of nIter0 for TAMC
160 checkpoint40pre2
161 o Updated to latest branch of AJA, JMC
162 o Added gradient check package
163 o Added routines for passive tracer handling
164 o Added carbon sequestration sensitivity experiment
166 checkpoint39
167 o Modifications and fixes to support TAMC
168 (mainly missing or wrong directives)
169 o Corrected common blocks when fooling TAMC to produce adjoint I/O
170 in addummy_in_stepping
171 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
172 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
173 o Included following packages:
174 cal: calendar
175 exf: external forcing
176 ecco: essential routines to control use of cal, exf
177 (NB: this is not the full ECCO environment)
178 o disabled some packages by default in genmake
180 checkpoint38
181 o see notes_c37_adj.txt
182 o corrected wrong layer index in external_forcing_t
183 o replaced the_main_loop/forward_step by the_main_loop
184 o removed forceoutput from write_state
185 (replaced criteria for initial/final state)
186 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
188 checkpoint37
189 o mdsio.F routine split and packaged in pkg/mdsio
190 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
191 used unless genmake -disable=mdsio)
192 o allow a more precise surface-geopotential gradient for the atmosphere
193 taking into account the change in space of Alpha (=1/rho) at the surface.
194 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
195 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
196 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
197 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
198 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
199 o Time-Average diagnostics defined as a pseudo package "timeave".
200 o pickup files : old pickup (before c35) did not work with new code (c35
201 and after) unless activating 2 commented lines in initialise-varia.
202 o Non-Hydrostatic pickup file Pb fixed.
203 o bug with Rigid-lid version (since c35) fixed.
205 checkpoint36
206 o implement Crank-Nickelson barotropic time-stepping
207 o recover Time-Average diagnostics
208 o fix Pb in checkpoint (PR#19)
209 o AIM become a standard package ; clean unused CPP_kees
211 checkpoint35
212 o subtantial rewrite of dynamics.f
213 o allows staggered time-stepping
214 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
215 o added bottom drag (linear + quadratic)
217 checkpoint34
218 o Modified exchange routines for correct reverse simulation.
219 o Added verification output to comply with bug fix in impldiff.F
220 as of c33 (exp2, natl_box).
221 o Corrected store directives in dynamics.F
222 o Corrected array boundaries in impldiff.F
223 o Corrected array dimensions in gmredi.
224 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
225 o Added routine GLOBAL_SUM_INT to global_sum.F
226 o Added mdsio_gl.F for ECCO purposes.
228 checkpoint33
229 o Fixed bug in lower BC in impldiff.F
230 o Fixed confusion about units of forcing arrays in FFIELDS.h
231 namely Fu,Fv,Qnet,Qsw,EmPmR:
232 - Removed verification/natl_box/code/external_fields_scale.F
233 (did not differ from that in model/src)
234 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
235 (see FFIELDS.h for description)
236 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
237 kpp_calc.F and kpp_transport_t.F
238 - Removed model/src/external_fields_scale.F and calls to it
239 - verification/natl_box uses flux data with "atmospheric" sign so
240 a special version of external_fields_load.F is used to
241 change the data as it's read in. This way, the arrays
242 have the right units and signs at all times tha a user could
243 possibly use them.
244 o Corrected genmake to delete a temporary file during configuration
246 checkpoint32
247 o Scaling of forcing fields moved from external_forcing.F to
248 external_fields_scale.F, called directly after loading fields.
249 o Surface relaxation terms added to surface tendency fields in
250 extra subroutine.
251 o impldiff.F changed to avoid storing by TAMC of huge intermediate
252 fields.
253 o Changes in GMRedi to comply with packaging structure.
254 o Modifications and bug fixes in KPP package.
255 o Verification experiment for KPP added (verification/nat_box/)
257 checkpoint31
258 o Packages interface brought in line with defined standard
259 -> new routines packages_...F
260 -> changes in initialise_fixed.F, initialise_varia.F
261 -> enables initialisation interface for ECCO package
262 o Rescaling of external forcing fields immediately after read
263 (removed from external_forcing.F)
264 -> new: surface_fields_scale.F
265 -> affects ini_foorcing.F, external_fields_load.F
266 o Computation of surface tendencies before tendency updates.
267 -> new: external_forcing_surf.F
268 o Change of variable names useGMRedi, useKPP, useECCO
269 o Further changes in dynamics.F, impldiff.F for TAMC
270 o Tested for experiments 0, 2, 4.
271 - not yet tested for GMRedi.
272 - not yet tested for KPP.
274 checkpoint30
275 o Updates for OBCs
276 o New experiment for test OBCs (internal_wave)
277 o New output.txt in verification/exp4/results/
278 o Updates for KPP: calculation of viscosity corrected, new variables
279 kpp_dumpFreq and kpp_taveFreq
280 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
281 and entry for T90 in genmake
283 checkpoint29
284 o packaged KPP and GM/Redi
286 checkpoint28
287 o Corrected initialization of hFacMin for difference vertical coordinates
288 o Modified calculation of partial cell thickness to more robust algorithm
289 o config_summary.F: replaced write_1D_... by write_0D_...
290 read_write.F: added subroutines write_0D_...
291 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
292 included some initialisations required for TAMC.
293 o routine calc_isoslopes: modified sqrt computation to make it
294 differentiable for zero argument.
295 o routines dynamics, impldiff:
296 included store directives and tape key computations required for TAMC.
297 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
299 checkpoint27
300 o fixed calc_isoslopes() to so that cancellation of terms in tensor
301 formulation works properly with variable resolution.
302 o restructured the calling tree between the_model_main() and dynamics()
303 o split initialise() into initialise_fixed() and initialise_varia()
304 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
305 in new routine ini_psurf()
307 checkpoint26
308 o moved some #ifdef in optional routines to encompass everything
309 except the argument declarations. This was using up some memory.
310 o fixed macros like _ADT to work with both versions of Linux cpp
311 o cleaned up some unused and uninitialized variables
312 (helps when debugging with strict compile options)
313 o split up CPP_EEOPTIONS.h into options and macros
314 (macros are now in eesupp/inc/CPP_EEMACROS.h)
315 o patch for 2 processor JAM mode
317 checkpoint25
318 o updates for OBCs and NH
319 o dramatically reduced memory usage
320 o added "JAM" routines for use on Artic network
321 o parameterization of convection by implicit vertical diffusion
322 o added a diagnostic of convective index
323 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
324 (this is was partly for OBCs and NH but also in anticipation of
325 an explicit free-surface option)
326 o initial state input files for U and V
328 checkpoint24
329 o Removed some spurious "REAL"s
330 o Updated KPP to latest version from JPL
331 o Added a COS(latitude) in horizontal viscosity
333 checkpoint23
334 o Added del^4 diffusion for salt and temperature
335 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
337 checkpoint22
338 o Made many small changes: implicit none, format(i5), etc...
339 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
341 checkpoint21
342 o Introduced new I/O package that supports direct-access records (mdsio.F)
343 o Split-up mid-level I/O routines
344 o Updated input data for experiments 0,1,2,4 and 5
345 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
347 checkpoint20
348 o Tidied up open-boundaries some more
349 o Added non-hydrostatic code
350 o Fixed some input data
351 o Modified MPI start-up to work in "coupled" context.
353 checkpoint19
354 o Tidied up directory structure for verification experiments.
355 o Added new code for open boundaries.
356 o Corrected advective terms near boundaries.
357 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
358 o Implemented free-slip/no-slip BCs and del^4 dissipation.
359 o Split default parameters out of ini_parms.F into set_defaults.F.
361 checkpoint18
362 o Further changes for optional code generation with
363 CPP - ugh!
365 checkpoint17
366 o Beginning to incorporating modularity
367 for supporting atmos. and ocean configs.
368 o Small changes for TAMC complinace
369 o New ultra simple test case. Barotropic box
370 configuration "exp0".
372 checkpoint16
373 o Minor changes to exchange routines to support
374 accumulation in reverse mode. Adjoint of an
375 assignment is an addition.
376 o Changes to support compilation by TAMC (LR(1)
377 syntax) and by g77 under Linux ( 72 character
378 limit ).
380 checkpoint15
381 Rewrote exchange routines to allow
382 o General tile <-> tile connectivity.
383 o TAMC reverse mode flag ( is this really needed? )
384 o Variable width overlap and exchange region widths.
385 o Hooks for sharing data via DMA, Arctic, Memory Channel,
386 shmput/shmget, VIA, SYSV shmem and every other cool
387 communication method.
389 checkpoint14
390 Consistent isomorphism chages made. These allow dynamical core
391 to support both pressure and meters as a vertical coordinate.
393 checkpoint13
394 Release which corrects global_max problem and a couple
395 of KGM time-averaging diagnostic errors. Also contains
396 a double-gyre experiment setup as well as the baseline
397 4 degree global template. The double gyre template is
398 organised to allow it to be applied automatically to
399 the baseline configuration.
401 branch-point-rdot
402 A few tidy-ups have been made bt the real point of this
403 check-point (excuse the pun) is to allow a branch to be
404 made for the purposes of adding the rDot alterations.
405 I don't want to commit the rDot to the main-trunk until
406 we've actually tested it...
408 checkpoint12
409 Tidy up and added generic genmake script (formerly
410 configure script).
411 Released to testers.
413 checkpoint11
414 Re-arranged initialise() and introduced ini_vertical_grid()
415 and ini_masks_etc().
417 checkpoint10
418 Introduced the configure script.
419 Separated out the diags package.
420 Added template for writing time-averages of tile/intermediate quantities.
421 Updated SIZE.h in exp2 and made the data big-endian.
423 checkpoint9
424 MPI fix. Filename changes (meta/data). salbin*y stuff.
425 General tidy-up.
426 SST.bin SSS.bin added to verification/exp2
428 checkpoint8
429 Inludes time-dependant forcing and time-averaging.
430 Works at 4x4 and 2.8125x2.8125 global
432 checkpoint7-4degree-ref
433 Branch from checkpoint7. Released for application to
434 global modeling and general modeling - process studies, regional
435 model etc..
436 Configured for verification/exp2 - 4 degree global, two process.
438 checkpoint7
439 Created by cnh
440 Simple 4 degree global simulation
441 configuration.
442 Includes climatological wind,
443 hydrography, bathymetry etc
444 Does not include Heat Flux and E-P
446 checkpoint6
447 Created by cnh
448 merged checkpoint5 with CD and
449 spherical polar code.
450 Still some problems with GM Redi
451 abd full topography.
453 checkpoint5
454 Created by AJA
455 contains updates to GM Redi
456 and reordered timestepping loop
457 for Implicit Diffusion.
459 checkpoint4
460 Created by cnh
461 Contains memory saving macros ( _rdxc etc..) for when
462 grid variations are limited.
463 Contains polynomial coeffs for EOS and knudsen program
464 for generation.
466 checkpoint3
467 Created by cnh
468 Added extra flags for runtime options
469 Added this file
470 Added implicit free-surface
471 Added pre-conditioner
472 Put compare01 into repository ( compare01/... )
473 Put data and eedata into repository ( verification/exp1 )
475 checkpoint2
476 Created by AJA
477 Added GM/Redi
479 checkpoint1
480 Created by AJA
481 Restructured kloop in dynamics.F
482 Added non-linear EOS
484 baseline
485 Original checked in code

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