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Revision 1.62 - (show annotations) (download)
Wed Feb 27 21:19:59 2002 UTC (22 years, 2 months ago) by adcroft
Branch: MAIN
CVS Tags: checkpoint44e_post
Changes since 1.61: +7 -1 lines
Document checkpoint44e_pre,post

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.61 2002/02/15 21:31:57 heimbach 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 checkpoint44e_pre,post
9 o re-wrote convective adjustment to use pre-calculated weights
10 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
11 Adds: model/src/convective_weights.F, convectively_mixtracer.F
12 Original calls to convect() still in place.
13
14 chkpt44d_pre,post
15 o added missing EXCLUDE_MONITOR flags
16 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
17 (incompatible typ in MIN/MAX expressions caused problems
18 on IBM SP3)
19 o in genmake added variable MAKEDEPEND
20 plus resetting for case SunOS
21 o added timer_stats.c routine for IBM SP3
22 o removed variables in dynamics
23 !!! I forgot to create tag chkpt44d_pre !!!
24 !!! But chkpt44d_pre = chkpt44c_post !!!
25
26 chkpt44c_pre,post
27 o few fix (mask in shap_s2, EmPmR in external_field_load,
28 USE_NATURAL_BCS in solve_for_P);
29 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
30
31 checkpoint44b_pre/_post
32 o merge of relevant stuff from the ecco-branch:
33 - genmake: removed $S64 overwrite for case SunOS
34 - pkg/exf: update and corrections for field swapping and obcs
35 - pkg/ecco: parameter lists for the_model_main, the_main_loop
36 harmonized between ECCO and MITgcm
37 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
38 updated checkpointing_lev... lists for obcs
39 - model/src: minor changes in forward_step, plot_field
40 added directive for divided adjoint in the_main_loop
41 - pkg/mdsio: added mdsio_gl_slice
42
43 o check parameters & config (chkpt44a_pre,post)
44 o OBC and NonLin_FrSurf.
45
46 checkpoint44
47 o fix bug in mom_vi_del2uv
48 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
49 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
50 o update AIM experiments (NCEP input files)
51 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
52 o added some stuff for AD
53
54 checkpoint43
55 o added two new advection tests
56 o added global 4x4 degree ocean test
57 o added test of H&S94 with free surface on cube
58 o some final mods for gradient check, adjoint,...
59
60 checkpoint42
61 Fixed AD-related problems:
62 o Store directives up-to-date with re-arranged Adams-Bashforth
63 (mainly thermodynamics.F)
64 o New store directives for multi-dim. advection schemes
65 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
66 * new common block and key passkey
67 (mainly gad_advection.F)
68 o Modified store directives for split of dynamics/thermodynamics
69 for the case ALLOW_KPP
70 o Cleaned argument list for timestep_tracer.F
71
72 checkpoint41
73 o re-formatted/added comments in prologues of key subroutines
74 to work with protex
75
76 checkpoint40
77 o moved calc_gs, calc_gt and calc_tr1 back to model/src
78 o added FLT (floats) package from Arne along with demo. experiment
79 o re-arranged Adams-Bashforth scheme for tracers to allow easier
80 implementation of forward-in-time forcing terms
81 o more mods for non-linear free-surface including new variable
82 o modified multi-dim method to work on cube
83 o bug fix in KPP (from DM)
84
85 checkpoint40pre9
86 o added DST advection schemes
87 o fix MPI bug on SGI's
88 o modifications for non-linear free-surface
89 o fixed conditionals for fixed flow/passive tracer only mode
90 o added tension/strain form of stress tensor
91 o changes to commenting of arguments for TAF/TAMC
92 o added/updated many matlab scripts
93 o added multi-dimensional advection method for tracers
94
95 checkpoint40pre8
96 o new package rw/
97 Added method for dumping intermediate local arrays:
98 mdsio_writetile - same as mdsio_writefield except works from inside
99 bi,bj loop
100 mdsio_writelocal - same as mdsio_writetile except works for local
101 arrays
102 write_local_r? - higher-level wrapper for mdsio_writelocal
103 Controlled by diagFreq. Defaults to zero (ie. no dumps)
104 Example given at end of mom_vecinv.F that dumps some local arrays.
105 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
106 control flux-form versus vector invariant code.
107 Switch is runtime flag vectorInvariantMomentum (defaults to false)
108 or genmake -DISABLE ...
109 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
110 (additional storing is now needed for case vecinv;
111 currently nothing implemented to switch this storing off
112 in case fluxform is used since no CPP flag available).
113
114 checkpoint40pre7
115 o bug fix in dynamics.F
116 calc_viscosity called before k=1,Nr loop.
117 o added some #ifdef's ALLOW_PASSIVE_TRACER
118 o cleaned initialisations in ctrl_map_ini
119 related to TAF
120
121 checkpoint40pre6
122 o split dynamics into thermodynamics & dynamics
123 o corresponding split of calc_diffusivity into
124 calc_diffusivity, calc_viscosity
125 (kpp_calc_diff, kpp_calc_visc).
126 o Added diffkr, kapgm to control variables
127 o bug fix in gmredi_slope_limit for ldd97
128
129 checkpoint40pre5
130 o proper initialization of Adams-Bashforth time stepping
131 + uses forward step for very first step of model (iter=0)
132 o re-generated *all* output since almost all output is modified by this
133 change (sorry but we've been putting this one off for about 2 years)
134 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
135 *not* regenerated since they are already out of date and I don't
136 want to create the impression that they are suddenly working.
137 o removed KAP stuff for DEC's
138 o modified/added many .cvsignore files in */code and */input
139 o added new expt "solid-body.cs-32x32x1"
140 + this uses an alternative form of ini_curvilinear_grid.F which
141 is not necessarily any better than the current one...
142
143 checkpoint40pre4
144 o added re-initialisations of utrans,vtrans,rtrans in
145 calc_common_factors which are crucial for TAF.
146 o extended iMin,jMin range for calc_common_factors,
147 calc_diffusivity
148 o added option ALLOW_PASSIVE_TRACER
149 o a few minor updates and fixes
150
151 checkpoint40pre3
152 o created calc_gtr1.F for gad package
153 o split the_main_loop and re-introduced forward_step
154 o some recomputations of nIter0 for TAMC
155
156 checkpoint40pre2
157 o Updated to latest branch of AJA, JMC
158 o Added gradient check package
159 o Added routines for passive tracer handling
160 o Added carbon sequestration sensitivity experiment
161
162 checkpoint39
163 o Modifications and fixes to support TAMC
164 (mainly missing or wrong directives)
165 o Corrected common blocks when fooling TAMC to produce adjoint I/O
166 in addummy_in_stepping
167 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
168 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
169 o Included following packages:
170 cal: calendar
171 exf: external forcing
172 ecco: essential routines to control use of cal, exf
173 (NB: this is not the full ECCO environment)
174 o disabled some packages by default in genmake
175
176 checkpoint38
177 o see notes_c37_adj.txt
178 o corrected wrong layer index in external_forcing_t
179 o replaced the_main_loop/forward_step by the_main_loop
180 o removed forceoutput from write_state
181 (replaced criteria for initial/final state)
182 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
183
184 checkpoint37
185 o mdsio.F routine split and packaged in pkg/mdsio
186 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
187 used unless genmake -disable=mdsio)
188 o allow a more precise surface-geopotential gradient for the atmosphere
189 taking into account the change in space of Alpha (=1/rho) at the surface.
190 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
191 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
192 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
193 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
194 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
195 o Time-Average diagnostics defined as a pseudo package "timeave".
196 o pickup files : old pickup (before c35) did not work with new code (c35
197 and after) unless activating 2 commented lines in initialise-varia.
198 o Non-Hydrostatic pickup file Pb fixed.
199 o bug with Rigid-lid version (since c35) fixed.
200
201 checkpoint36
202 o implement Crank-Nickelson barotropic time-stepping
203 o recover Time-Average diagnostics
204 o fix Pb in checkpoint (PR#19)
205 o AIM become a standard package ; clean unused CPP_kees
206
207 checkpoint35
208 o subtantial rewrite of dynamics.f
209 o allows staggered time-stepping
210 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
211 o added bottom drag (linear + quadratic)
212
213 checkpoint34
214 o Modified exchange routines for correct reverse simulation.
215 o Added verification output to comply with bug fix in impldiff.F
216 as of c33 (exp2, natl_box).
217 o Corrected store directives in dynamics.F
218 o Corrected array boundaries in impldiff.F
219 o Corrected array dimensions in gmredi.
220 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
221 o Added routine GLOBAL_SUM_INT to global_sum.F
222 o Added mdsio_gl.F for ECCO purposes.
223
224 checkpoint33
225 o Fixed bug in lower BC in impldiff.F
226 o Fixed confusion about units of forcing arrays in FFIELDS.h
227 namely Fu,Fv,Qnet,Qsw,EmPmR:
228 - Removed verification/natl_box/code/external_fields_scale.F
229 (did not differ from that in model/src)
230 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
231 (see FFIELDS.h for description)
232 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
233 kpp_calc.F and kpp_transport_t.F
234 - Removed model/src/external_fields_scale.F and calls to it
235 - verification/natl_box uses flux data with "atmospheric" sign so
236 a special version of external_fields_load.F is used to
237 change the data as it's read in. This way, the arrays
238 have the right units and signs at all times tha a user could
239 possibly use them.
240 o Corrected genmake to delete a temporary file during configuration
241
242 checkpoint32
243 o Scaling of forcing fields moved from external_forcing.F to
244 external_fields_scale.F, called directly after loading fields.
245 o Surface relaxation terms added to surface tendency fields in
246 extra subroutine.
247 o impldiff.F changed to avoid storing by TAMC of huge intermediate
248 fields.
249 o Changes in GMRedi to comply with packaging structure.
250 o Modifications and bug fixes in KPP package.
251 o Verification experiment for KPP added (verification/nat_box/)
252
253 checkpoint31
254 o Packages interface brought in line with defined standard
255 -> new routines packages_...F
256 -> changes in initialise_fixed.F, initialise_varia.F
257 -> enables initialisation interface for ECCO package
258 o Rescaling of external forcing fields immediately after read
259 (removed from external_forcing.F)
260 -> new: surface_fields_scale.F
261 -> affects ini_foorcing.F, external_fields_load.F
262 o Computation of surface tendencies before tendency updates.
263 -> new: external_forcing_surf.F
264 o Change of variable names useGMRedi, useKPP, useECCO
265 o Further changes in dynamics.F, impldiff.F for TAMC
266 o Tested for experiments 0, 2, 4.
267 - not yet tested for GMRedi.
268 - not yet tested for KPP.
269
270 checkpoint30
271 o Updates for OBCs
272 o New experiment for test OBCs (internal_wave)
273 o New output.txt in verification/exp4/results/
274 o Updates for KPP: calculation of viscosity corrected, new variables
275 kpp_dumpFreq and kpp_taveFreq
276 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
277 and entry for T90 in genmake
278
279 checkpoint29
280 o packaged KPP and GM/Redi
281
282 checkpoint28
283 o Corrected initialization of hFacMin for difference vertical coordinates
284 o Modified calculation of partial cell thickness to more robust algorithm
285 o config_summary.F: replaced write_1D_... by write_0D_...
286 read_write.F: added subroutines write_0D_...
287 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
288 included some initialisations required for TAMC.
289 o routine calc_isoslopes: modified sqrt computation to make it
290 differentiable for zero argument.
291 o routines dynamics, impldiff:
292 included store directives and tape key computations required for TAMC.
293 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
294
295 checkpoint27
296 o fixed calc_isoslopes() to so that cancellation of terms in tensor
297 formulation works properly with variable resolution.
298 o restructured the calling tree between the_model_main() and dynamics()
299 o split initialise() into initialise_fixed() and initialise_varia()
300 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
301 in new routine ini_psurf()
302
303 checkpoint26
304 o moved some #ifdef in optional routines to encompass everything
305 except the argument declarations. This was using up some memory.
306 o fixed macros like _ADT to work with both versions of Linux cpp
307 o cleaned up some unused and uninitialized variables
308 (helps when debugging with strict compile options)
309 o split up CPP_EEOPTIONS.h into options and macros
310 (macros are now in eesupp/inc/CPP_EEMACROS.h)
311 o patch for 2 processor JAM mode
312
313 checkpoint25
314 o updates for OBCs and NH
315 o dramatically reduced memory usage
316 o added "JAM" routines for use on Artic network
317 o parameterization of convection by implicit vertical diffusion
318 o added a diagnostic of convective index
319 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
320 (this is was partly for OBCs and NH but also in anticipation of
321 an explicit free-surface option)
322 o initial state input files for U and V
323
324 checkpoint24
325 o Removed some spurious "REAL"s
326 o Updated KPP to latest version from JPL
327 o Added a COS(latitude) in horizontal viscosity
328
329 checkpoint23
330 o Added del^4 diffusion for salt and temperature
331 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
332
333 checkpoint22
334 o Made many small changes: implicit none, format(i5), etc...
335 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
336
337 checkpoint21
338 o Introduced new I/O package that supports direct-access records (mdsio.F)
339 o Split-up mid-level I/O routines
340 o Updated input data for experiments 0,1,2,4 and 5
341 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
342
343 checkpoint20
344 o Tidied up open-boundaries some more
345 o Added non-hydrostatic code
346 o Fixed some input data
347 o Modified MPI start-up to work in "coupled" context.
348
349 checkpoint19
350 o Tidied up directory structure for verification experiments.
351 o Added new code for open boundaries.
352 o Corrected advective terms near boundaries.
353 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
354 o Implemented free-slip/no-slip BCs and del^4 dissipation.
355 o Split default parameters out of ini_parms.F into set_defaults.F.
356
357 checkpoint18
358 o Further changes for optional code generation with
359 CPP - ugh!
360
361 checkpoint17
362 o Beginning to incorporating modularity
363 for supporting atmos. and ocean configs.
364 o Small changes for TAMC complinace
365 o New ultra simple test case. Barotropic box
366 configuration "exp0".
367
368 checkpoint16
369 o Minor changes to exchange routines to support
370 accumulation in reverse mode. Adjoint of an
371 assignment is an addition.
372 o Changes to support compilation by TAMC (LR(1)
373 syntax) and by g77 under Linux ( 72 character
374 limit ).
375
376 checkpoint15
377 Rewrote exchange routines to allow
378 o General tile <-> tile connectivity.
379 o TAMC reverse mode flag ( is this really needed? )
380 o Variable width overlap and exchange region widths.
381 o Hooks for sharing data via DMA, Arctic, Memory Channel,
382 shmput/shmget, VIA, SYSV shmem and every other cool
383 communication method.
384
385 checkpoint14
386 Consistent isomorphism chages made. These allow dynamical core
387 to support both pressure and meters as a vertical coordinate.
388
389 checkpoint13
390 Release which corrects global_max problem and a couple
391 of KGM time-averaging diagnostic errors. Also contains
392 a double-gyre experiment setup as well as the baseline
393 4 degree global template. The double gyre template is
394 organised to allow it to be applied automatically to
395 the baseline configuration.
396
397 branch-point-rdot
398 A few tidy-ups have been made bt the real point of this
399 check-point (excuse the pun) is to allow a branch to be
400 made for the purposes of adding the rDot alterations.
401 I don't want to commit the rDot to the main-trunk until
402 we've actually tested it...
403
404 checkpoint12
405 Tidy up and added generic genmake script (formerly
406 configure script).
407 Released to testers.
408
409 checkpoint11
410 Re-arranged initialise() and introduced ini_vertical_grid()
411 and ini_masks_etc().
412
413 checkpoint10
414 Introduced the configure script.
415 Separated out the diags package.
416 Added template for writing time-averages of tile/intermediate quantities.
417 Updated SIZE.h in exp2 and made the data big-endian.
418
419 checkpoint9
420 MPI fix. Filename changes (meta/data). salbin*y stuff.
421 General tidy-up.
422 SST.bin SSS.bin added to verification/exp2
423
424 checkpoint8
425 Inludes time-dependant forcing and time-averaging.
426 Works at 4x4 and 2.8125x2.8125 global
427
428 checkpoint7-4degree-ref
429 Branch from checkpoint7. Released for application to
430 global modeling and general modeling - process studies, regional
431 model etc..
432 Configured for verification/exp2 - 4 degree global, two process.
433
434 checkpoint7
435 Created by cnh
436 Simple 4 degree global simulation
437 configuration.
438 Includes climatological wind,
439 hydrography, bathymetry etc
440 Does not include Heat Flux and E-P
441
442 checkpoint6
443 Created by cnh
444 merged checkpoint5 with CD and
445 spherical polar code.
446 Still some problems with GM Redi
447 abd full topography.
448
449 checkpoint5
450 Created by AJA
451 contains updates to GM Redi
452 and reordered timestepping loop
453 for Implicit Diffusion.
454
455 checkpoint4
456 Created by cnh
457 Contains memory saving macros ( _rdxc etc..) for when
458 grid variations are limited.
459 Contains polynomial coeffs for EOS and knudsen program
460 for generation.
461
462 checkpoint3
463 Created by cnh
464 Added extra flags for runtime options
465 Added this file
466 Added implicit free-surface
467 Added pre-conditioner
468 Put compare01 into repository ( compare01/... )
469 Put data and eedata into repository ( verification/exp1 )
470
471 checkpoint2
472 Created by AJA
473 Added GM/Redi
474
475 checkpoint1
476 Created by AJA
477 Restructured kloop in dynamics.F
478 Added non-linear EOS
479
480 baseline
481 Original checked in code

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