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Revision 1.53.2.2 - (show annotations) (download)
Mon Apr 8 20:10:36 2002 UTC (22 years, 1 month ago) by heimbach
Branch: release1
CVS Tags: release1_chkpt44d_post
Changes since 1.53.2.1: +44 -3 lines
Changes encapsulated by checkpoint43a-release1mods and chkpt44d_post
on the main trunk.
These are:

 o added missing EXCLUDE_MONITOR flags
 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
   (incompatible typ in MIN/MAX expressions caused problems
   on IBM SP3)
 o in genmake added variable MAKEDEPEND
   plus resetting for case SunOS
 o added timer_stats.c routine for IBM SP3
 o removed variables in dynamics
 o real fresh water flux implemented with non-linear free-surface.
 o few fix (mask in shap_s2, EmPmR in external_field_load,
   USE_NATURAL_BCS in solve_for_P);
 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
 o merge of relevant stuff from the ecco-branch:
   - genmake: removed $S64 overwrite for case SunOS
   - pkg/exf: update and corrections for field swapping and obcs
   - pkg/ecco: parameter lists for the_model_main, the_main_loop
               harmonized between ECCO and MITgcm
   - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
                   updated checkpointing_lev... lists for obcs
   - model/src: minor changes in forward_step, plot_field
                added directive for divided adjoint in the_main_loop
   - pkg/mdsio: added mdsio_gl_slice
 o check parameters & config (chkpt44a_pre,post)
 o OBC and NonLin_FrSurf.
 o fix bug in mom_vi_del2uv
 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
 o update AIM experiments (NCEP input files)
 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
 o added some stuff for AD

These were merged with
cvs co -r release1 -P MITgcm
cd MITgcm
cvs update -kk
cvs update -j checkpoint43a-release1mods -j chkpt44d_post -d -P -kk

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

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