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Revision 1.299 - (show annotations) (download)
Fri May 21 21:13:34 2004 UTC (20 years ago) by jmc
Branch: MAIN
Changes since 1.298: +5 -1 lines
o new version of coupler for AIM+thSIce and Ocean models
 - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
 - land: change Evaporation of snow
 - aim with thSIce: fix bug in snow-precip.

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.298 2004/05/19 20:38:53 heimbach Exp $
2
3 Notes on tags used in MITgcmUV
4 ==============================
5
6 o new version of coupler for AIM+thSIce and Ocean models
7 - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
8 - land: change Evaporation of snow
9 - aim with thSIce: fix bug in snow-precip.
10 o changes to calc_gw.F
11 - bug fix for w^2 term near the bottom boundary
12 - (hopefully) improve the lateral slip boundary condtions for use with
13 partial/looped cells
14 - because the bug fix changes two verification experiments anyway (exp5
15 and plume on slope), change the lateral boundary condition from half slip
16 to the value of no_slip_sides
17 o ebm package wasnt quite up to the parallel task. Fixed that.
18
19 checkpoint53b_post
20 o Commiting new energy balance model to repository
21 * package is pkg/ebm
22 * verif. is verification/global_ocean_ebm
23 * references are in ebm_driver.F
24 C * X. Wang, P. Stone and J. Marotzke, 1999:
25 C Global thermohaline circulation. Part I:
26 C Sensitivity to atmospheric moisture transport.
27 C J. Climate 12(1), 71-82
28 C * X. Wang, P. Stone and J. Marotzke, 1999:
29 C Global thermohaline circulation. Part II:
30 C Sensitivity with interactive transport.
31 C J. Climate 12(1), 83-91
32 C * M. Nakamura, P. Stone and J. Marotzke, 1994:
33 C Destabilization of the thermohaline circulation
34 C by atmospheric eddy transports.
35 C J. Climate 7(12), 1870-1882
36 o Will need long integration testing.
37 checkpoint53b_pre
38
39 o created pkg/mom_common in preparation for variable viscosity code
40 o renamed and split ini_mnc_io
41 o pkg/land: only liquid water can diffuse or run-off
42 o AIM using land: soil wetness availability account for snow
43 o added printMapIncludesZeros to EEPARMS namelist
44
45 checkpoint53a_post
46 o restore TAMC compatiility for exf_constants.h
47 (no usage of _d in .h)
48 o Additional storing in KPP in an attempt to fix
49 TAMC problem with adjoint of KPP code.
50 (no success...)
51 Identical code works fine with TAF.
52 o Fixed verification/natl_box_adjoint experiments.
53 Initial conditions for Experiments 4 and 5 are now
54 set to "SEAICE_initialHEFF=0", which is more reasonable,
55 and hence gives results closer to that of Experiment 2.
56 Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
57
58 checkpoint53
59 o stable checkpoint with up to date adjoint
60 TLM tests only run for 1st grdchk at the moment. Its unclear if
61 this is a code problem or a problem with resetting code for g_
62 variables that is being autogenerated wrong.
63 Otherwise:
64 o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
65 o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
66 are both still in chaos following their security messes.
67
68 checkpoint52n_post
69 o various build (mostly genmake2) changes including:
70 - ability to build/run more easily within Cygwin and MacOS X
71 - more complicated Makefiles with a stronger dependence on Gnu Make
72 o pkg/seaice modifications
73 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
74 of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
75 and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
76 - changed proxy for geostrophic velocity and updated
77 verification/lab_sea/results/* accordingly
78 - removed ADI dynamic solver from pkg/seaice
79 - replaced all occurrences of 1/CSTICE or 1/CSUICE
80 they caused a segmentation fault under certain circumstances
81 - removed unused field WATR
82 o bug fix in exf-package:
83 - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
84 now reflect that.
85 o small fixes in the cal-package:
86 - set reference date to first of January for the 'model'-calendar
87 - failing of cal_CheckDate in cal_FullDate now actually results in a
88 warning
89 o small modifications in exf-package to increase flexibility:
90 - change climtempfreeze from a constant to a runtime parameter that
91 is specified in data.exf_clim (default = -1.9)
92 - introduce runtime parameter windstressmax (default = 2.0) that is
93 specified in data.exf
94 o fix in pkg/thsice:
95 - update Evap (Tsf changes) to be consistent with Latent heat flux
96 - maintain snow precipitation unchanged (even if Tsf >=0).
97 both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
98
99 checkpoint52m_post
100 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
101 this does not change any of the results, because myIter=0 in swfrac always
102 lead to jwtype=2 (the default anyway), but the call makes little sense
103 as a default
104 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
105 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
106 atmospheric model (AIM) to use it ; add a "slab ocean" component.
107 o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
108 o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
109 o extending useSingleCpuIO option to work with new exch2 I/O format
110 - old-style, missing-tile I/O is still accessible by defining CPP
111 option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
112 o monitor package can write to NetCDF files and/or STDOUT
113 o fix re-definition bug in MNC_GRID_INIT_ALL()
114 o doc/api_reference added
115 - a framework for building an API Reference Manual using all
116 the "protex" comments embedded in the code
117 - see pkg/generic_advdiff, pkg/mnc for examples
118 o MNC:
119 - make myThid the last argument for all subroutines
120 - new default for the grid files: NO halos
121 - add useMNC and other run-time flags
122 - separate per-file-group handling of the unlimited dimension
123 - early initialization of MNC w/ flags read at the eeboot stage
124 and lookup tables set in initialize_fixed
125 - write all MNC output to a freshly-created directory
126 o thermodynamics sea-ice (thsice) is now tested with testreport.
127 o test exp. advect_cs: use the standard cs32 grid ; update output.
128 o Added functionality to grdchk:
129 pick global i,j,k position (or nearest wet) where to perform check.
130
131 checkpoint52l_post
132 o new land formulation:
133 a) use ground enthalpy as prognostic variable to ensure exact
134 energy conservation.
135 b) account for water temperature and for latent heat of freezing
136 in all processes (rain, run-off, ground storage)
137 c) compute surface and ground temperature implicitly.
138 o aim_v23 modification for new land model:
139 a) Treat separately land / ocean / sea-ice surface fluxes
140 to allow implicit computation of land & sea-ice surface temp.
141 b) add snow precipitation.
142 checkpoint52l_pre
143
144 o fix problem (when 1 tile is empty) in min/max monitor.
145 o fix bug in timeAve (u,vZetatave in common block)
146 o no restoring terms under ice for pkg/seaice
147 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
148 o bug fix for pkg/seaice pickups
149 o change MNC call locations and add coordinate attributes
150 o mask vorticity at the corner ; affects global_ocean.cs output
151 o fix ini_curvilinear_grid ; test CS experiments with mpi
152 o aim.5l_cs: modify sea-ice fraction input file ; update output
153 o exf: Adding simple range check routine for exf fields after read
154
155 checkpoint52k_post
156 o removed top-level directory "diags"
157 - we migrated these functions to pkg/timeave a long time ago
158 o fixed bug introduced in pkg/monitor
159 o accuracy ctrlprec = 32 insuffient for gradient checks using
160 averaged fields (I/O via cost_averages)
161 -> use ctrl.h in active_file*.F to control I/O precision.
162 o paramter list of CALL ADTHE_MAIN_LOOP
163 o added initial do_the_model_io to ecco
164 o set all ...Freq to zero after cost_final
165 taveFreq, dumpFreq, pChkptFreq
166 o MAIN and ECCO differentiability restored
167
168 checkpoint52j_post
169 o fix nchklev in tamc.h for global_ocean...
170 o Bringing flow and store directives up-to-date
171 o Really weird thing!
172 call do_the_model_io from the_main_loop with parameters
173 starttime, niter0, instead of mytime, myiter, screws up the adjoint:
174 TAF places a faulty re-call of initialise_varia
175 after cost_final call which should not be there!
176 checkpoint52j_pre
177
178 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
179 error messages
180 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
181 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
182 debug output
183 o modfied mdsio_writefield.F to handle non-global files under exch2
184 o update AIM Cubed-Sphere exp (aim.5l_cs):
185 use land, p*, and Franco.M forcing fields with fractional land-sea mask.
186 o update AIM Equatorial Channel exp:
187 use standard aim_v23 pkg and change the SST fields to be more realistic.
188 o globalFile now works with exch2
189 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
190 mon_vort3.F to make exch2 friendly with >1 tile per cube face
191 o limit timeave output for hi-res integrations
192
193 checkpoint52i_post
194 o removed CPP_EEOPTIONS.h from verification/*/code
195 o updated the tiling for global_ocean_pressure
196 checkpoint52i_pre
197
198 o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
199 the old pkg/aim).
200
201 checkpoint52h_pre
202 o shortened offending lines in exch2_send_rx?.template
203 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
204 o genmake2: add build & execute test for NetCDF code
205 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
206 old grid files, moved CPP_EEMACROS.h to pkg/exch2
207 o added useSingleCPUIO flag to monitor.F and mon_out.F
208 o added temporary hack for sea-ice dynamics on the cube:
209 metric terms are ignored and it is assumed that
210 there is no sea-ice on cube faces 1, 2, 4, and 5.
211
212 checkpoint52f_post
213 o added exch2 cube routines to pkg/exch2
214 o modified hs94.cs-32x32x5 to use it
215 o added new grid files to hs94.cs-32x32x5
216 checkpoint52f_pre
217
218 checkpoint52e_post
219 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
220 for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
221 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
222 to work with implicit vertical advection and AB ;
223 o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
224 o update output (gad_calc_rhs.F changes affect truncation error) of exp:
225 front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
226 checkpoint52e_pre
227
228 o fix bug in impldiff when Nr=1 or Nr=2.
229 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
230 o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
231 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
232 ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
233 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
234 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
235 o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
236
237 checkpoint52d_post
238 o re-tiled many expts to allow comparison in multi-processor mode
239 - updated output accordingly
240 - changed hs94.128x64x5 to use intial T from file rather than use the
241 random number generator
242 o add infrastructure in model routines for fizhi and gridalt packages
243 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
244 o changes to permit hi-res, cubed-sphere, configuration
245 - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
246 - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
247 - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
248 of surface winds for the cube
249 (A verification experiment, based on global_ocean.cs32x15, but with
250 pkg/seaice turned on and with on-the-fly interpolation from the NCEP
251 Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
252 complete with example surface forcing files and matlab scripts to look
253 at the output and compare it with that of global_ocean.cs32x15.)
254 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
255 but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
256 to conform to the common rule.
257 o check-in the first version of the coupler + interfaces for multi-components
258 set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
259 - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
260 - atmosphere: use pkg aim_v23 ; no sea-ice for now.
261 - ocean and atmos. share the same horizontal grid (no interpolation).
262 - exchanges between component and coupler is done in forward_step
263 o new verification experiment, cpl_aim+ocn:
264 coupled ocean - AIM atmosphere on cs32 grid.
265
266 checkpoint52d_pre
267 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
268 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
269
270 checkpoint52c_post
271 o Fixing OPTIONS files for use of exf:
272 - ALLOW_ECCO not needed
273 - ECCO_CPPOPTIONS.h should not be included from
274 EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
275 as has been the case in the past
276 - All cal/exf related options are currently set in
277 single header file. Should remain so until we
278 agree on a consistent new policy.
279 o Removed all CPP options for cal package.
280 cal has no more CPP options.
281 o modified STOREs in GAD_ADVECTION
282 o corrected key comp. for passkey
283
284 checkpoint52b_post
285 o new version: "thsice" of thermodynamic sea-ice pkg:
286 - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
287 - modify fluxes but do not change theta directly;
288 - light cleaning of bulk_force pkg (still needed with thsice).
289 - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
290 + output_thsice.txt to test thsice & bulk_force pkgs.
291 o put back grid & coriolis monitor output.
292 checkpoint52b_pre
293
294 o call "do_the_model_io" at the beginning (=> dump initial state)
295 o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
296 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
297 (need info on NUMBER_OF_PTRACERS)
298 o missing PTRACERS headers in some routines
299 o default tamc.h in pkg/autodiff supposed to crash
300 to ensure proper customization
301
302 checkpoint52a_post
303 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
304 - moved surfaceTendencyTice from pkg/seaice to main code
305 - subroutine FREEZE_SURFACE now limits only surface temperature
306 and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
307 => new output.txt for global_ocean.cs32x15 & global_with_exf
308 - keep the old version of FREEZE for backward compatibility;
309 global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
310 - corresponding modifs for TAF directives
311 o added surface flux output variables to TIMEAVE_STATVARS
312 o time-averaged output for pkg/ptracers
313 o fix problem with ECCO-related divided adjoint
314 snapshot file was missing some ad-variables,
315 but no warning issued by TAF
316
317 checkpoint52a_pre
318 o some bug fixes for #undef REAL4_IS_SLOW
319
320 checkpoint52 = ecco_c52_e35
321 o after testing adjoints of checkpoint51u_post
322
323 checkpoint51u_post
324 o this is the post-merge tag of the ecco-branch
325 (needs another clean checkout and re-testing)
326 o various natl_box_adjoint configs and results
327 but no input fields
328 o obcs adjoint not yet merged!
329 o adding ECCO global 1x1 and 2x2 degree configs
330 o updated/extended some store directives for seaice
331 o pkg/ecco now containes ecco-specific part of cost function
332 o top level routines the_main_loop, forward_step
333 supersede those in model/src/
334 previous input data.cost now in data.ecco
335 (new namelist ecco_cost_nml)
336 o in ctrl/ cleaned some cross-dependencies and updated CPP options
337
338 checkpoint51t_post
339 o this is the pre-merge tag of the ecco-branch
340
341 checkpoint51s_post
342 o cleanup: removed various obsolete #define-s
343 o pkg/grdchk
344 - renamed 'ph-grd 3' to 'grad-res'
345 - merged from ecco-branch
346 (remaining bug fixes for obcs gradient checks)
347 - additional high-precision output for testreport
348 (grep for 'precision_grdchk_result')
349
350 checkpoint51r_post
351 o cleaned up or removed CPP_OPTIONS.h files
352 o updated results for some of the tests to reflect the new
353 optfiles (-ieee: -O0 instead of -O3)
354
355 checkpoint51q_post
356 o cd_code:
357 - moved cd_scheme.F -> cd_code_scheme.F
358 - separate read_checkpoint from cd_code_ini_vars.F
359 - separated cd_code part from write_checkpoint
360 - updated AD_SOURCE, generated .flow
361 - added CD_CODE_VARS.h to the_main_loop
362 - Moving cd_code specific store dir.s to pkg/cd_code
363 o ctrl package totally restructured
364 - pack/unpack now optional and decoupled from
365 xx_/adxx_ I/O
366 - ctrl_pack/unpack cleaned
367 (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
368 - confined inclusion of AD_CONFIG.h to where necessary.
369 o genmake2: changed AD dependencies from SRCFILES to AD_FILES
370
371 checkpoint51p_post
372 o create initial cd_code package
373 - WARNING: the initialization of fields within packages
374 is broken because INI_FIELDS (where READ_CHECKPOINT is
375 called) is called *before* PACKAGES_INIT_VARIABLES.
376 This seems to be backwards since
377 1) its important to initially zero the entire field including
378 the "halo" region
379 2) zeroing needs to be done *before* reading pickup info
380 and the pickup call might or might not happen in any
381 particular run
382 - this needs an overhaul for R2
383 o cleanup verification/*/code/GMREDI_OPTIONS.h
384 o cleanup testreport
385
386 checkpoint51o_post
387 o bringing AD-related verif's up to date with genmake2
388 - carbon/
389 - global_ocean.90x40x15/
390 - hs.94.1x64x5/
391 - (front_relax/ )
392 o (more) consistent directory structure for AD-related verif.'s
393 o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
394 o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
395 o bug fix in find_alpha.F for MDJWF:
396 - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
397 change rho -> rho-rhoConst
398 - replace call find_rho to find_rhonum
399 o initialisation of rFlx extended to full array (required by TAF)
400 and shifted to thermodynamics
401 o removed PTRACERS.h in ptracers routine
402 o added surfacetendencyPtr to S/R parameter list pracers_forcing
403 o Correcting initialisations for fVerU, fVerV.
404 o helping TAF to recognize dependency on kUp for
405 fVerU, fVerV
406 o Replacing delZ by delR in pkg/ctrl/
407 checkpoint51o_pre
408
409 o undid all of cp51 pending some cleanups and discussion
410 o added the [#include "AD_CONFIG.h"] statement to all files that need
411 it for adjoint/tl #defines
412 o re-worked the build logic in genmake2 to support AD_CONFIG.h
413 o removed tools/genmake since it no longer works
414
415 checkpoint51n_post
416 o modifications to make FREEZE flux visible to pkg/kpp
417 - moved surfaceTendencyTice from pkg/seaice to main code
418 - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
419 - subroutine FREEZE now limits only surface temperature
420 (this means new output.txt for global_ocean.90x40x15,
421 global_ocean.cs32x15, and global_with_exf)
422 o added surface flux output variables to TIMEAVE_STATVARS
423
424 checkpoint51n_pre
425 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
426 o added [#include "AD_CONFIG.h"] to all files that use the following
427 defines:
428 - ALLOW_ADJOINT_RUN
429 - ALLOW_TANGENTLINEAR_RUN
430 - ALLOW_ECCO_OPTIMIZATION
431
432 checkpoint51m_post
433 o incorporating changes to get TAMC/TAF working in genmake2
434 - added new TAMC/TAF targets to the Makefile
435 - various cleanups related to package handling
436 - these changes should have no impact on the forward model
437
438 checkpoint51l_post
439 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
440 - faster algorithm for cal_addtime.F
441 - higher precision arithmetic, where needed
442 - pkg/exf *startdate variables changed from calendar date to
443 model integration time
444
445 checkpoint51l_pre
446 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
447 o enable to apply restoring on S & T only in a latitude band.
448 o update output (external_forcing_surf modif. change truncation errors)
449 global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
450
451 checkpoint51k_post
452 o change default to: useNHMTerms=.FALSE.
453 - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
454 adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
455 - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
456 exp1, ideal_2D_oce
457 - change data file of oceanic exp (leave the results unchanged for now)
458 exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
459 o set gravitySign automatically according to the vertical coordinate used
460 (and change sign: back to "logical" value: +1 when R increases downward)
461 o added an include barrier to the default CPP_OPTIONS.h and
462 removed the #include "PACKAGES_CONFIG.h" from it
463 o fix a bug in mom_fluxform (from chk51j_post)
464
465 checkpoint51j_post
466 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
467 o adjusted some flow directives (dynamics, thermodynamics)
468 o added cubed-sphere case to test cost function
469 o heckpoint_lev?_directives.h now include
470 pkg-specific directives, whenever those are enabled.
471 o Moving pkg-specific flow directives to corresponding pkg
472 Moving pkg-specific differentiation list to corresponding pkg
473 Moving pkg-specific checkpoint-lev storing to corresponding pkg
474 ---> conventions are
475 - pkg_ad.flow
476 - pkg_ad_diff.list
477 - pkg_ad_check_lev?_dir.h
478
479 checkpoint51i_post
480 o merge of the branch-genmake2
481 - knowingly breaks the older genmake
482 - automatic generation of all ALLOW_${PKG_NAME} defines
483 - new testreport supersedes older testscript
484 o large number of package inclusion and header cleanups
485 checkpoint51i_pre
486
487 o new output for adjoin of global ocean vector invariant
488 o fix for checkpoint of thermodynamic seaice and bulk_force
489 o Steph gchem various cleanups
490
491 checkpoint 51h_pre
492 o fixed some single quotes
493 o modify gchem pkg to be more versatile
494 o modifications to clean up dic pkg
495 o add pkg/cfc
496
497 checkpoint51g_post
498 o provide links for ARPACK and ADM*TLM
499 o start removing verification/vero/
500 o update AD-related stuff
501 (in particular some IF-statements in model/src/ routines)
502 o adding to verification/global_ocean.90x40x15/ adjoint of
503 vector invariant setup
504
505 checkpoint51f_post
506 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
507 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
508 of tracer Green's fucntions for ocean inversion project.
509
510 checkpoint51f_pre
511 o Added on-the-fly spatial interpolation capability
512 "USE_EXF_INTERPOLATION" to pkg/exf.
513 - This is a temporary Cartesian-grid hack until
514 the super-duper ESMF coupler becomes available.
515 - See verification/global_with_exf/README for usage example.
516 - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
517 flags and modified pkg/seaice accordingly.
518 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
519 and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
520 non-local transport term.
521
522 checkpoint51e_post
523 o pkg/mom_vecinv:
524 - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
525 - add time-ave diagnostic of vorticity advection.
526 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
527 o atmospheric geopotential: - include water vapor effect;
528 - use p^kappa in p* scaling.
529 o land pkg: read initial state from files.
530 o AIM : add stratospheric drag in the upper level
531
532 checkpoint51d_post
533 o change function ILNBLNK (=> last non-blank char.) to return zero
534 (instead of the string length) when the string. char is empty
535 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
536 o modif's to restore TAMC compatibility
537 - avoid "_d" constructs in PARAMETER declarations
538 - avoid interrupting lines by comment lines
539 o Use cluster local disks for purely local I/O
540 vs. globally visible disks needed for ctrl stuff
541 (merged from ecco-branch)
542 - new active_file_loc... and mdsio_..._loc routines
543 - affected packages: autodiff, ctrl, grdchk, mdsio
544
545 checkpoint51c_post
546 o introducing integer flag debugLevel
547 - debLevZero: suppress all output
548 - debLevA: standard
549 - debLevB: equivalent to current debugMode=.TRUE.
550 o introducing pathname variable mdsioLocalDir for mdsio
551 that can be specified at runtime
552 (relevant for cluster I/O to local disk)
553 `
554 >>>checkpoint51b_post
555 adjoint of ptracers
556 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
557 o extended state in checkpoint_lev?, etc.
558 o alternative ctrl/cost with tr1 or ptracer
559 o new comlev1_bibj_ptracers
560 o new ptracers.flow
561 o made ptracers_forcing same as external_forcing_s
562 o added verification for adjoint with ptracers
563 - adm. grdchk fail so far
564 - tlm. grdchk OK
565 - checked tapelev/comlev recomputations: OK
566 <<<checkpoint51b_pre
567
568 checkpoint51a_post
569 o added code for biogeochemistry package
570 - new pkgs: dic, gchem
571 - new subroutine in ptracers
572 o modify code for biogeo packages
573 - in model/src and pkg/ptracers
574
575 checkpoint51
576 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
577 - autodiff, ctrl, exf, grdchk, seaice
578 kept separate packages
579 - cost, ecco, obcs
580 o updating verification/internal_wave, verification/lab_sea
581 (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
582
583 checkpoint50i_post
584 o Preparing next differentiable checkpoint and sync
585 of MAIN vs. ecco-branch
586 - 1st step: this one is differentiable
587 - 2nd step: next(! not this) checkpoint will have updated packages
588 from ecco-branch)
589
590 checkpoint50h_post
591 o new package "land": provide surface BC for AIM.
592 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
593 o AIM: use true log-P extrapolation for near surface temp (= as in
594 F.Molteni paper) ; update aim.5l_cs output.
595 o New variable in PARM03 for more flexible pickups
596 o somewhat cleaned package initialisation sequence for
597 ctrl/ cost/ ecco/ in packages_... routines
598
599 checkpoint50g_post
600 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
601 - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
602 - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
603 made the default because of faster convergence than ADI
604
605 checkpoint50f_post
606 o exf totally restructured
607 - replaced all exf_set_ routines by one generic exf_set_gen.F
608 and made sure it's still differentiable
609 - split exf_getffields.F into new exf_bulkformulae.F
610 - exf_inscal_/exf_outscal_ suffixes consistent with field names
611 - updated adjoint/makefile and relevant verif. accordingly
612
613 checkpoint50f_pre
614 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
615 + change Evap over land. (update aim.5l_cs output)
616 o added missing .cvsignores and made uniform across expts
617 o changed configuration of tidal_basin_2d expt
618 o added pkg/debug functions for tracing code in fatal crashes
619 o tidied pkg/monitor to use MONITOR_OPTIONS.h
620 o new fn in pkg/monitor to stop model if solution grows too big
621 o removed lots of single quotes from comments
622
623 checkpoint50e_post
624 o make KPP work with PTRACERS
625 - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
626 nearly a copy of kpp_transport_s
627 - there is no analogue to SurfaceTendencyS, so I have to use
628 gPtr(of the surface layer) instead
629 o add a new platform SunFire+mpi (SunFire 15000) to genmake
630 checkpoint50e_pre
631
632 checkpoint50d_post
633 o change kpp output from multiple-record state files to single-record state
634 files analogous to write_state.F
635 o reduce the output frequency of cg3d-related stuff to the monitor frequency,
636 analogous to the cg2d-related output.
637 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
638 so that writing to internal file fn (with length 512) fails.
639 checkpoint50d_pre
640
641 checkpoint50c_post
642 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
643 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
644 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
645 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
646 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
647
648 checkpoint50c_pre
649 Merging from release1_p13:
650 o bug fix for pkg/seaice dynamic solver
651 o Added SEAICE_initialHEFF to pkg/seaice
652
653 checkpoint50b_post
654 o store u*,v* in gU,V instead of in guNm1,gvNm1
655 o in order to put the momForcing out of the Adams-Bashforth:
656 move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
657 to timestep.F
658 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
659 o re-generate output for highly sensitive test-exp:
660 global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
661
662 checkpoint50b_pre
663 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
664 o corrected CPP option mismatch in exf_Bulk... functions for case
665 #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
666
667 checkpoint50a_post
668 o Bug fix for merging between c50 and KPP.
669 ikey was passed from thermodynamics to kpp_calc via
670 common block rather than being recomputed in kpp_calc,
671 in contradiction with new key itdkey.
672 New key ikppkey created, and tamc.h headers updated.
673
674 checkpoint50
675 - 2nd step of merge with ecco-branch:
676 merge changes in ecco-branch back into main trunk
677 - bug fix in find_alpha
678 - more storing in gmredi_calc_tensor.F, kpp_routines.F
679 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
680 - merged some sliced AD support routines
681
682 checkpoint49
683 merged from ecco-branch:
684 o exf:
685 - Enable initialisation of forcing fields to constant
686 (runtime) values.
687 - in exf_getffields.F
688 Reduce i-/j-loop to interior domain, discarding overlaps.
689 That also fixes wrong TAF-key computations for key_1, key_2
690 with bulf formulae.
691 - exf_init.F modify #ifdef for exf_init_evap
692 - exf_getffieldrec.F, ctrl_getrec.F
693 The following INT-usages are not safe:
694 fldsecs = int(fldsecs/fldperiod)*fldperiod
695 fldcount = int(fldsecs/fldperiod) + 1
696 and were modified.
697 o autodiff: checkpoint_lev...
698 - updated storing for bulk formulae (some arrays were missing)
699 - added state for seaice package
700 - synchronized with main branch
701 o DIVA:
702 Modif.s in
703 - the_main_loop.F
704 - the_model_main.F
705 and added cost_final_restore.F cost_final_store.F
706 o With these changes, it is possible to fully separate
707 the first forward run to compute the cost function (mdthe_main_loop)
708 and adjoint runs over individual DIVA intervals (adthe_main_loop)
709 into separate model executions.
710 This enables better tuning of DIVA to given queue sizes.
711 o Loss of cost function value in consecutive DIVA runs is
712 fixed by storing to 'costfinal' file.
713 o Appropriate call of ctrl_unpack/_pack,grdchk_main at
714 beginning/end of adjoint integration is accounted for.
715 The current changes apply to TAF-1.4.26.
716 TAF has one remaining bug, requiring one manual change
717 (see MITgcm manual).
718 o cal: synchronized between MAIN and ecco-branch
719
720 checkpoint48i_post
721 o Changes to restore differentiability of code w.r.t. previous tag
722 (mostly adding new routines to make list and replacing
723 pressure by totPhiHyd).
724 o Updated and merged grdchk package
725 - has both ADM and TLM checks
726 - works for single- and multi-proc.
727 - output cleaned
728 - worked successfully for parallel DIVA
729 o genmake:
730 - Adding -platform=SP4
731 - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
732 o Modif. for DIVA:
733 ctrl_unpack should not be called in intermediate DIVA interval.
734 (similar thing would apply for active files such as
735 tbar, sbar, psbar, which should not be reinitialised;
736 only relevant for ecco-branch)
737
738 checkpoint48h_post
739 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
740 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
741 o Added SEAICE_initialHEFF to pkg/seaice
742 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
743
744 checkpoint48g_post
745 --- EOS:
746 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
747 store total Potential in totPhyHyd for diagnostics & EOS.
748 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
749 --- Pressure/geopotential gradient:
750 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
751 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
752 ( changes results of global_ocean_pressure )
753 o NLFS + z-coord.: add eta*Rho' contribution.
754 o accurate phiHyd when using interface-W at the middle between 2 centers
755 ( changes results of ideal_2D_oce )
756 o includes r* 2nd term in potential gradient.
757
758 checkpoint48f_post
759 Merging from release1_p12:
760 o Modifications for using pkg/exf with pkg/seaice
761 - improved description of the various forcing configurations
762 - added basic radiation bulk formulae to pkg/exf
763 - units/sign fix for evap computation in exf_getffields.F
764 - updated verification/global_with_exf/results/output.txt
765 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
766 (SBO) core products, including oceanic mass, center-of-mass,
767 angular, and bottom pressure (see pkg/sbo/README.sbo).
768 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
769 to avoid negative values in shallow regions.
770 - updated verification/natl_box/results/output.txt
771 - updated verification/lab_sea/results/output.txt
772 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
773 o Added useSingleCpuIO option (see PARAMS.h).
774 o Updated useSingleCpuIO option in mdsio_writefield.F to
775 work with multi-field files, e.g., for single-file pickup.
776 o pkg/seaice:
777 - bug fix in growth.F: QNET for no shortwave case
778 - added HeffFile for specifying initial sea-ice thickness
779 - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
780 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
781 kpp_transport_t.F, forward_step.F, and the_main_loop.F
782 o pkg/seaice:
783 - adjoint-friendly modifications
784 - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
785
786 checkpoint48e_post
787 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
788 o dynamics: change definition of computational domain & adapt mom_fluxform
789 accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
790 o following exp works with Olx=Oly=2 (and pass through checkbounds option):
791 adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
792 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
793 global_ocean.90x40x15 global_with_exf global_ocean_pressure
794 inverted_barometer solid-body.cs-32x32x1
795 (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
796
797 checkpoint48d_post
798 o in preparation for r*:
799 a) use pre-computed gradient of hydrostatic potential:
800 changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
801 b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
802 => affects results of glob_oce_pressure (different truncation error)
803 update output.txt of ideal_2D_oce & global_ocean_pressure
804
805 checkpoint48d_pre
806 o in preparation for r*:
807 new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
808 pass the 2 comp. of the grad. as arguments to momentum S/R.
809 but for the moment, only used if it does not change the results.
810 o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
811
812 checkpoint48c_post
813 Modifications in treatment of initial flux forcing controls
814 to avoid extra storing of flux fields.
815
816 checkpoint48c_pre
817 o Added tidal_basin_2d experiment (currently 1D!)
818 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
819
820 checkpoint48b_post
821 o r* coordinate added in #ifdef NONLIN_FRSURF block.
822 (modification to pressure gradient not yet implemented)
823 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
824 (for U & V) that are used for vertical advection of momentum.
825
826 checkpoint48a_post
827 o In preparation for r*, use temp. array to compute vertical transport
828 in flux-form momentum pkg. => change results of few test-exp.
829 Update output of: exp4, exp5, front_relax, global_ocean_pressure,
830 lab_sea, natl_box & plume_on_slope
831
832 checkpoint48
833 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
834
835 checkpoint47j_post
836 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
837 o moved adexch from forward_step to addummy_in_stepping
838 o added exch in ctrl_map_...
839 o aveFreq.=0. at end of cost_final to avoid overwrite in
840 reverse checkpointing loop
841 o Yet more changes in gmredi:
842 * adgmredi_calc_tensor
843 avoiding all recomputation of gmredi_slope_limit
844 * adgmredi_x/y/rtransport
845 added flag for excessive storing to avoid recomp. of
846 u/v/rtans, dTdx/y/z
847 -> this is not really necessary and very memory-consuming
848 * adgmredi_slope_psi:
849 consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
850 * gmredi_slope_limit
851 re-activated full calculation of taperfct for case 'ac02'
852 o updating verification/ adjoints of carbon, global_ocean.90x40x15
853
854 checkpoint47i_post
855 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
856 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
857 default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
858 o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
859 o gmredi: fix few bugs.
860
861 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
862 This will be a good checkpoint to plug into the ecco-branch.
863 o few modif.'s to get latest version adjointed
864 (mainly kick out code in ini_linear_phisurf)
865 o modif's to run adjoint with exactConserv
866 o case GM_BOLUS_ADVEC should be cleaned
867 S/R gmredi_slope_psi should be cleaned
868 o verification/carbon now has exactConserv=.TRUE.
869
870 checkpoint47g_post
871 o time-average AIM output: becomes independent from statvars time-average
872 (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
873 o After TAF bug fix:
874 Tested adjoint of gmredi package.
875 Tests were done with checkpoint47 rather than with latest
876 checkpoint47f_post since the latter is broken for the adjoint
877 verification/carbon/ contains both ADM and TLM gradient checks.
878 Here they are, before they get changed/lost/stolen.
879 Mostly modif.'s to fix numerical sensitivities.
880 Gradient checks OK for
881 - GM_taper_scheme:
882 * clipping
883 * ac02
884 * linear
885 * glw91
886 * dm95
887 * ldd97
888 - GMREDI_OPTIONS:
889 * GM_VISBECK_VARIABLE_K
890 * GM_NON_UNITY_DIAGONAL
891 * GM_EXTRA_DIAGONAL
892 * GM_BOLUS_ADVEC
893 in conjunction with data.gmredi parameters to be checked in
894 in a few minutes under verification/carbon/code/
895
896 checkpoint47f_post
897 Merging from release1_p10:
898 o modifications for using pkg/exf with pkg/seaice
899 - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
900 and SEAICE_EXTERNAL_FLUXES
901 - pkg/exf CPP options EXF_READ_EVAP and
902 EXF_NO_BULK_COMPUTATIONS
903 - usage examples are Experiments 8 and 9 in
904 verification/lab_sea/README
905 - verification/lab_sea default experiment now uses
906 pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
907
908 checkpoint47e_post
909 o created a tag prior to creating a branch
910
911 checkpoint47d_post
912 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
913 at the bottom boundary had an erroneous half slip boundary condition
914 o added bottom drag and no slip boundary condition capabilities to
915 oceanic pressure coordinates code
916 o added new verification experiment global_ocean_pressure, this experiment is
917 also described in the tutorial section of the manual
918 checkpoint47d_pre
919
920 checkpoint47c_post
921 o Added a verification experiment for a global cubed-sphere ocean run
922 - verification/global_ocean.cubed32x32x30
923 - uses pkg/therm_seaice and pkg/bulk_forcing
924
925 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
926 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
927 when using P-coordinate; only implemented for atmospheric config.
928 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
929 NOTES: requires option NONLIN_FRSURF to be "#define".
930 o update advect_xz/results/output.txt (left from checkpoint44g_post)
931
932 checkpoint47b_post
933 Merging from release1_p9:
934 o pkg/seaice
935 - removed GOTO's and added taf directives
936 - double precision constants to reduce the g77 (Linux)
937 to F77 (SGI) differences reported in release1_p8
938 o tools/genmake
939 - added SGI options
940 o verification/testscript
941 - updated to that of checkpoint47a_post
942 o verification/global_ocean.90x40x15/input/eedata
943 - modified for SGI f77 compatibility
944 o verification/lab_sea
945 - added description of sea-ice model
946 - added missing matlab routines
947 - added test of thermodynamics parallelization
948
949 checkpoint47a_post
950 o new pkg: aim_v23
951 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
952 for now, keep the same surface forcing as before.
953 - Part-Cell implemented into AIM; check that Heat & Water are conserved
954 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
955 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
956 o add diagnostic of surface correction term in monitor output
957
958 o bulk_force and therm_seaice
959 - Two packages: bulk_force (Bulk forcing)
960 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
961 - Earlier integration from Stephaine Dutkiewicz
962 and Patrick Heimbach.
963 - Two ifdef statements for compile time,
964 ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
965
966 checkpoint47
967 differentiable version of checkpoint46n_post
968 o bug fix in quasihydrostaticterms
969 o * "clean" adjoint code (in terms of extensive recomputations)
970 can now be obtained for all GMREDI options (i.e. for
971 - GM_VISBECK_VARIABLE_K
972 - GM_NON_UNITY_DIAGONAL
973 - GM_EXTRA_DIAGONAL
974 - GM_BOLUS_ADVEC )
975 * However, wrong gradient check problem remains unsolved.
976 * New CPP options have been introduced for different
977 tapering schemes
978 o external_fields_load now part of differentiation list
979 o pressure needs multiple storing;
980 would be nice to have store_pressure at beginning or
981 end of forward_step, e.g. by having phiHyd global (5-dim.)
982 (NB: pressure is needed for certain cases in find_rho,
983 which is also invoked through convective_adjustment).
984 o recomputations in find_rho for cases
985 'JMD95'/'UNESCO' or 'MDJWF' are OK.
986 o #define ATMOSPHERIC_LOADING should be differentiable
987 o ini_forcing shifted to begining of initialise_varia
988 o Incorporating QNVS line search routines into MITgcm
989 (this is separate code, and therefore not under pkg)
990 lsopt/, optim/
991 o Updated verification/carbon/
992 - #define GM_VISBECK_VARIABLE_K
993 - GM_taper_scheme = 'ldd97'
994
995 checkpoint46n_post
996 Merging from release1_p8:
997 o verification/natl_box:
998 updating new external_fields_load routine
999 o New package: pkg/seaice
1000 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
1001 The sea-ice code is based on Hibler (1979-1980).
1002 Two sea-ice dynamic solvers, ADI and LSR, are included.
1003 In addition to computing prognostic sea-ice variables and diagnosing
1004 the forcing/external data fields that drive the ocean model,
1005 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
1006 The implied surface heat flux is then stored in variable
1007 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
1008 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
1009 non-local transport term. Because this call precedes model
1010 thermodynamics, temperature under sea-ice may not be "exactly" at
1011 the freezing point by the time theta is dumped or time-averaged.
1012 N.B.: fairly large differences in accuracy occur across
1013 different platforms/compilers; comparison between
1014 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
1015 generated output gives:
1016 T S U V
1017 C D M c m s m s m s m s
1018 n p a R g m m e . m m e . m m e . m m e .
1019 f n k u 2 i a a d i a a d i a a d i a a d
1020 g d e n d n x n . n x n . n x n . n x n .
1021
1022 Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
1023 o GAD:
1024 - generated new common blocks to account for call of
1025 same gad routines with differing traceridentities
1026 (needed to modify tracerIdentity indices in GAD.h)
1027 - generated separate common blocks for case useCubedSphereExchange
1028 (Department of Futurology)
1029 - parameter lists to gmredi_?transport: added tracerIdentity
1030 - added new key indices to tamc.h
1031 o external_fields_load:
1032 - added this routine to TAF list
1033 - needed to make some common blocks global and additional storing
1034 along the same lines as exf package (checkpoint_lev?_directives.h)
1035 o exf:
1036 updated external forcing package
1037 - bug fixes carried over from ecco-branch
1038 (missing OBCS_OPTIONS.h in two routines)
1039 - enable easy to use "no forcing".
1040 - added exf I/O for atmospheric loading
1041 - added exf I/O for runoff data
1042 - transfered scaling between exf <-> MITgcm to exf namelist
1043 o Adding new verification experiment global_with_exf.
1044 This verification experiment is almost identical to the
1045 global_ocean.90x40x15 experiment, except that it uses
1046 the exf (and cal) package instead of the
1047 external_fields_load routine (cf README file).
1048
1049 checkpoint46m_post
1050 o modified testscript to return -- when there are no lines of "%MON" output
1051 o added new flag "quasiHydrostatic" for QH mode
1052 and new routine quasihydrostaticterms()
1053 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
1054 New routine: mom_u_coriolis_nh()
1055 o fixed sign of non-hydrostatic metric terms in u and v equations.
1056 Depend on correct sign of gravitySign.
1057 o added work.pc* to .cvsignore in aim directories using ifc
1058 o introduced flag for controllin non-hydrostatic metric terms
1059 o removed gravitySign from PARM04
1060 o switched to g77/ifc from pgf77 in aim experiments
1061
1062 checkpoint46l_post
1063 o made convective adjustment work with pressure coordinates:
1064 - changed the direction of k-loop in convective_adjustment.F for the
1065 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
1066 - adjusted the reference pressure k-index in convective_adjustment.F
1067 - adjusted the convection condition in convect.F (in analogy to
1068 calc_ivdc.F)
1069 - convective_adjustment no longer computes anything on the halos
1070 - removed the warnings about negative salinity from find_rho.F and
1071 find_alpha.F; instead the new routine look_for_neg_salinity, called
1072 at the beginning of find_rho, find_alpha, and find_beta, does a
1073 check of the entire slice, if CPP-option
1074 CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
1075 checkpoint46l_pre
1076
1077 checkpoint46k_post
1078 o fixed the verification/global_ocean.90x40x15 experiment:
1079 - new bathymetry (the world according to A., JMC, and M.)
1080 - new initial fields and forcing fields (*.bin files)
1081 - new POLY3.COEFFS (for the next release one should switch to a full
1082 equation of state: JMD95P or MDJWF)
1083 - fixed several errors and redundancies in the data file
1084 - experiment uses looped cells
1085 - added matlab directory with diagnostic scripts for plotting of output
1086
1087 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
1088 - read AIM physics parameters from a file (data.aimphys)
1089 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
1090
1091 checkpoint46j_post
1092 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
1093 o move wVel computation at the end of the time step, in S/R integr_continuity
1094 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
1095 o update timeave pkg for wVel diagnostic.
1096 checkpoint46j_pre
1097
1098 checkpoint46i_post
1099 o Clean up AIM package (and keep the results unchanged):
1100 include CPP_OPTION and use IMPLICT NONE in all routines ;
1101 declare all the variables _RL ; use _d 0 for all numerical constants.
1102 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
1103
1104 checkpoint46h_post
1105 o cleaned up the use of rhoNil and rhoConst.
1106 - rhoNil should only appear in the LINEAR equation of state, everywhere
1107 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
1108 and the dynamical equations are all divided by rhoConst
1109 o introduced new parameter rhoConstFresh, a reference density of fresh
1110 water, to remove the fresh water flux's dependence on rhoNil. The default
1111 value is 999.8 kg/m^3
1112 o cleanup up external_forcing.F and external_forcing_surf.F
1113 - can now be used by both OCEANIC and OCEANICP
1114 checkpoint46h_pre
1115
1116 Added code to convert surface volume flux (fresh water) into
1117 a mass flux when using P coordinates in the ocean (OCEANICP).
1118 Note: It assumes you have set rho0=rhoConst=density of fresh water.
1119
1120 checkpoint46g_post
1121 o Include a new diagnostic variable phiHydLow for the ocean model
1122 - in z-coordinates, it is the bottom pressure anomaly
1123 - in p-coordinates, it is the sea surface elevation
1124 - in both cases, these variable have global drift, reflecting the mass
1125 drift in z-coordinates and the volume drift in p-coordinates
1126 - included time averaging for phiHydLow, be aware of the drift!
1127 o depth-dependent computation of Bo_surf for pressure coordinates
1128 in the ocean (buoyancyRelation='OCEANICP')
1129 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
1130 Theta, Salinity, and Pressure in the parameter list. This routine is
1131 presently contained in find_rho.F. This routine does not give the
1132 correct density for 'POLY3', which would be a z-dependent reference
1133 density.
1134 o cleaned up find_rho
1135 - removed obsolete 'eqn' from the parameter list.
1136 o added two new verification experiments: gop and goz
1137 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
1138 checkpoint46g_pre
1139
1140 checkpoint46f_post
1141 o Enable tangent linear (forward mode) gradient checks:
1142 - extended active file handling to g_... files
1143 - added TANGENT_SIMULATION to theSimulationMode
1144 - extended grdchk package accordingly
1145 o added tangent linear setup in verification/carbon/code_ftl
1146 o added adjoint setup in verification/front_relax/code_ad
1147
1148 checkpoint46e_post
1149 o Added new equation of state -> MDJWF
1150 - EOS of McDougall et al., 2002, JAOT, submitted
1151 - caveat: the equation of state is only valid for a smaller (more
1152 realistic?) range of values than JMD95P/Z and UNESCO
1153 - added masks to the calculation of pressure in store_pressure
1154 - added more check values for density in check_eos (ini_eos.F), some of
1155 the old check values are out of the range of the MDJWF-eos, so don't
1156 expect perfect matches for those
1157 checkpoint46e_pre
1158
1159 checkpoint46d_post
1160 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
1161 'OCEANICP', also initialised field pressure correctly in ini_eos in the
1162 case of pressure coordinates. eosType='JMD95Z' in
1163 combination with buoyancyRelation='OCEANICP' now causes an error.
1164 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
1165 in find_alpha/beta.
1166 checkpoint46d_pre
1167
1168 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
1169 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
1170
1171 checkpoint46c_post
1172 o Changes necessary for ocean in p-coordinates
1173 - Added new buoyancy relation = 'OCEANICP'
1174 - Added new parameters = gravitySign (this used to be contained inside
1175 the factor dRdZ which I added when we first switched to R coordinates).
1176 X GM/Redi is not compatible (yet)
1177 X bottom drag and no-slip need to be debugged.
1178 checkpoint46c_pre
1179
1180 checkpoint46b_post
1181 o Added new equation of state -> JMD95Z and JMD95P
1182 - EOS of Jackett and McDougall, 1995, JAOT
1183 - moved all EOS parameters into EOS.h
1184 - new routines ini_eos.F, store_pressure.F
1185 o Added UNESCO EOS, but not recommended because it requires
1186 in-situ temperature (see JMD95)
1187 o Modified formatting for knudsen2.f in utils/knudsen2 and added
1188 unesco.f to be used with POLY3
1189 checkpoint46b_pre
1190
1191 checkpoint46a_post
1192 o Added (atmospheric) pressure loading
1193 - new field in FFIELDS.h, etc...
1194 - new cpp flag ATMOSPHERIC_LOADING
1195 o Changed hFacC to _hFacC in calc_phi_hyd.F
1196 o Added SHORTWAVE_HEATING to some files for consistency
1197 checkpoint46a_pre
1198
1199 checkpoint46
1200 further merges from release1_p5
1201 o new ctrl package
1202 - adopted from ECCO environment to enable optimization
1203 - added Eliassen Palm fluxes to controls
1204 o added Eliassen Palm flux controls to gradient check package
1205 o cost package
1206 - Compatible with new ctrl package
1207 - added Eliassen Palm cost hooks
1208 - modif's of existing cost functions
1209 o Adjoint-related bug fixes in kpp:
1210 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
1211 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
1212 o autodiff package
1213 - flow directives:
1214 + new for S/R do_the_model_io
1215 + enhanced for S/R checkpoint
1216 + new gmredi.flow
1217 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
1218 disable adcommon.h/g_common.h by default.
1219 - fixed problem for adjoint of global_max
1220 o modified verification/carbon/
1221 o New setup for adjoint of global_ocean
1222 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
1223 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
1224 o incorporated hooks for sponge layer code (external_forcing.F)
1225
1226 checkpoint45d_post
1227 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
1228 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
1229 (affects plume_on_slope "cg2d" output)
1230 o add new parameter deltaTfreesurf for free-surface time stepping
1231 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
1232 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
1233 o change phiMin in exp1 (to agree with documentation)
1234 o add new flags:
1235 - T,S forcing inside/outside Adams-Bashforth
1236 - turn off temp,salt advection and/or forcing
1237 - for each tracer, define internal flag for multiDimAdvection & A-B
1238 o monitor: change definition of KE to check conservation of Energy
1239
1240 checkpoint45c_post
1241 o Removed f90 comments ("!")
1242 o Modified initialisations to enable exf package for MITgcm
1243 (without invoking ECCO_PACKAGE).
1244 o modifications to gradient check package (Martin Losch)
1245 - enable centered differences
1246 - modified format of standard output
1247
1248 checkpoint45b_post
1249 o cleaned exchange calls in cg2d
1250 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
1251 o included CPP option SINGLE_LAYER_MODE in thermodynamics
1252 to configure barotropic setup (Martin Losch)
1253 o moved some initialisations within bi,bj loop in dynamics
1254 (TAF flow dependency)
1255 o in initialise_varia, moved call packages_init_variables
1256 before convective_adjustment_init
1257 (corresponding adjustment of TAF tape initialisation).
1258 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
1259
1260 checkpoint45a_post
1261 o compute Rho over the whole domain (extend iMin,jMin indices)
1262 o specific exchange for X-slice domain (case Ny=1)
1263 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
1264 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
1265
1266 checkpoint44h_post = checkpoint45
1267 o Fix to restore differentiability:
1268 place at which packages_init_variables is called in
1269 initialise_varia is crucial for reverse control flow.
1270 o modifications in GMRedi to enable stable adjoint
1271 (corresponding modif's in thermodynamics, dynamics)
1272 o added missing hook for sponge layer code in external_forcing
1273 o modified test cost functions
1274 o storing in gad_advection (plus removal of write(0,*)!
1275 o missing headers TR1.h added in convective_adjustment routines
1276 o errorMessageUnit set non-equal zero in eeboot
1277 (conflict on some platforms, e.g. IBM SP3)
1278 o modified carbon verif.
1279
1280 checkpoint44h_pre
1281 o vertical grid option: allow to put the Interface at the middle between
1282 2 cell-centers ; replace delZ in pkg/kpp by drF.
1283 o GM Advective form: Tracers are advected using the residual transport (=
1284 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
1285
1286 checkpoint44g_post
1287 o fix surface correction term in multiDimAdvection (affects plume_on_slope
1288 results) ; ifdef missing in thermodynamics.F
1289
1290 checkpoint44f_pre,checkpoint44f_post
1291 o added PTRACERS package
1292 This allows an arbitrary number of passive tracers to be integrated
1293 forward simultaneously with the dynamicaly model.
1294 + Implemented so far:
1295 - basic forward algorithm (time-stepping, advection, diffusion, convection)
1296 - I/O and checkpointing
1297 - GM/Redi *but* using the GM/Redi coefficient of Salt
1298 + Not implemented so far:
1299 - KPP
1300 - OBCS
1301 + No specific example supplied (yet) but global_ocean.90x40x15 has the
1302 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
1303 line in data.pkg.
1304 + This package is disabled by default since it increases storage.
1305
1306
1307 o testscript: added -cleanup option
1308 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
1309 b) enable to filter 2D fields.
1310
1311 checkpoint44e_pre,post
1312 o re-wrote convective adjustment to use pre-calculated weights
1313 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
1314 Adds: model/src/convective_weights.F, convectively_mixtracer.F
1315 Original calls to convect() still in place.
1316
1317 chkpt44d_pre,post
1318 o added missing EXCLUDE_MONITOR flags
1319 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
1320 (incompatible typ in MIN/MAX expressions caused problems
1321 on IBM SP3)
1322 o in genmake added variable MAKEDEPEND
1323 plus resetting for case SunOS
1324 o added timer_stats.c routine for IBM SP3
1325 o removed variables in dynamics
1326 !!! I forgot to create tag chkpt44d_pre !!!
1327 !!! But chkpt44d_pre = chkpt44c_post !!!
1328
1329 o real fresh water flux implemented with non-linear free-surface.
1330
1331 chkpt44c_pre,post
1332 o few fix (mask in shap_s2, EmPmR in external_field_load,
1333 USE_NATURAL_BCS in solve_for_P);
1334 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
1335
1336 checkpoint44b_pre/_post
1337 o merge of relevant stuff from the ecco-branch:
1338 - genmake: removed $S64 overwrite for case SunOS
1339 - pkg/exf: update and corrections for field swapping and obcs
1340 - pkg/ecco: parameter lists for the_model_main, the_main_loop
1341 harmonized between ECCO and MITgcm
1342 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
1343 updated checkpointing_lev... lists for obcs
1344 - model/src: minor changes in forward_step, plot_field
1345 added directive for divided adjoint in the_main_loop
1346 - pkg/mdsio: added mdsio_gl_slice
1347
1348 o check parameters & config (chkpt44a_pre,post)
1349 o OBC and NonLin_FrSurf.
1350
1351 checkpoint44
1352 o fix bug in mom_vi_del2uv
1353 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
1354 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
1355 o update AIM experiments (NCEP input files)
1356 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
1357 o added some stuff for AD
1358
1359 checkpoint43
1360 o added two new advection tests
1361 o added global 4x4 degree ocean test
1362 o added test of H&S94 with free surface on cube
1363 o some final mods for gradient check, adjoint,...
1364
1365 checkpoint42
1366 Fixed AD-related problems:
1367 o Store directives up-to-date with re-arranged Adams-Bashforth
1368 (mainly thermodynamics.F)
1369 o New store directives for multi-dim. advection schemes
1370 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
1371 * new common block and key passkey
1372 (mainly gad_advection.F)
1373 o Modified store directives for split of dynamics/thermodynamics
1374 for the case ALLOW_KPP
1375 o Cleaned argument list for timestep_tracer.F
1376
1377 checkpoint41
1378 o re-formatted/added comments in prologues of key subroutines
1379 to work with protex
1380
1381 checkpoint40
1382 o moved calc_gs, calc_gt and calc_tr1 back to model/src
1383 o added FLT (floats) package from Arne along with demo. experiment
1384 o re-arranged Adams-Bashforth scheme for tracers to allow easier
1385 implementation of forward-in-time forcing terms
1386 o more mods for non-linear free-surface including new variable
1387 o modified multi-dim method to work on cube
1388 o bug fix in KPP (from DM)
1389
1390 checkpoint40pre9
1391 o added DST advection schemes
1392 o fix MPI bug on SGI's
1393 o modifications for non-linear free-surface
1394 o fixed conditionals for fixed flow/passive tracer only mode
1395 o added tension/strain form of stress tensor
1396 o changes to commenting of arguments for TAF/TAMC
1397 o added/updated many matlab scripts
1398 o added multi-dimensional advection method for tracers
1399
1400 checkpoint40pre8
1401 o new package rw/
1402 Added method for dumping intermediate local arrays:
1403 mdsio_writetile - same as mdsio_writefield except works from inside
1404 bi,bj loop
1405 mdsio_writelocal - same as mdsio_writetile except works for local
1406 arrays
1407 write_local_r? - higher-level wrapper for mdsio_writelocal
1408 Controlled by diagFreq. Defaults to zero (ie. no dumps)
1409 Example given at end of mom_vecinv.F that dumps some local arrays.
1410 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
1411 control flux-form versus vector invariant code.
1412 Switch is runtime flag vectorInvariantMomentum (defaults to false)
1413 or genmake -DISABLE ...
1414 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
1415 (additional storing is now needed for case vecinv;
1416 currently nothing implemented to switch this storing off
1417 in case fluxform is used since no CPP flag available).
1418
1419 checkpoint40pre7
1420 o bug fix in dynamics.F
1421 calc_viscosity called before k=1,Nr loop.
1422 o added some #ifdef's ALLOW_PASSIVE_TRACER
1423 o cleaned initialisations in ctrl_map_ini
1424 related to TAF
1425
1426 checkpoint40pre6
1427 o split dynamics into thermodynamics & dynamics
1428 o corresponding split of calc_diffusivity into
1429 calc_diffusivity, calc_viscosity
1430 (kpp_calc_diff, kpp_calc_visc).
1431 o Added diffkr, kapgm to control variables
1432 o bug fix in gmredi_slope_limit for ldd97
1433
1434 checkpoint40pre5
1435 o proper initialization of Adams-Bashforth time stepping
1436 + uses forward step for very first step of model (iter=0)
1437 o re-generated *all* output since almost all output is modified by this
1438 change (sorry but we've been putting this one off for about 2 years)
1439 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
1440 *not* regenerated since they are already out of date and I don't
1441 want to create the impression that they are suddenly working.
1442 o removed KAP stuff for DEC's
1443 o modified/added many .cvsignore files in */code and */input
1444 o added new expt "solid-body.cs-32x32x1"
1445 + this uses an alternative form of ini_curvilinear_grid.F which
1446 is not necessarily any better than the current one...
1447
1448 checkpoint40pre4
1449 o added re-initialisations of utrans,vtrans,rtrans in
1450 calc_common_factors which are crucial for TAF.
1451 o extended iMin,jMin range for calc_common_factors,
1452 calc_diffusivity
1453 o added option ALLOW_PASSIVE_TRACER
1454 o a few minor updates and fixes
1455
1456 checkpoint40pre3
1457 o created calc_gtr1.F for gad package
1458 o split the_main_loop and re-introduced forward_step
1459 o some recomputations of nIter0 for TAMC
1460
1461 checkpoint40pre2
1462 o Updated to latest branch of AJA, JMC
1463 o Added gradient check package
1464 o Added routines for passive tracer handling
1465 o Added carbon sequestration sensitivity experiment
1466
1467 checkpoint39
1468 o Modifications and fixes to support TAMC
1469 (mainly missing or wrong directives)
1470 o Corrected common blocks when fooling TAMC to produce adjoint I/O
1471 in addummy_in_stepping
1472 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
1473 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
1474 o Included following packages:
1475 cal: calendar
1476 exf: external forcing
1477 ecco: essential routines to control use of cal, exf
1478 (NB: this is not the full ECCO environment)
1479 o disabled some packages by default in genmake
1480
1481 checkpoint38
1482 o see notes_c37_adj.txt
1483 o corrected wrong layer index in external_forcing_t
1484 o replaced the_main_loop/forward_step by the_main_loop
1485 o removed forceoutput from write_state
1486 (replaced criteria for initial/final state)
1487 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
1488
1489 checkpoint37
1490 o mdsio.F routine split and packaged in pkg/mdsio
1491 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
1492 used unless genmake -disable=mdsio)
1493 o allow a more precise surface-geopotential gradient for the atmosphere
1494 taking into account the change in space of Alpha (=1/rho) at the surface.
1495 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
1496 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
1497 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
1498 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
1499 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
1500 o Time-Average diagnostics defined as a pseudo package "timeave".
1501 o pickup files : old pickup (before c35) did not work with new code (c35
1502 and after) unless activating 2 commented lines in initialise-varia.
1503 o Non-Hydrostatic pickup file Pb fixed.
1504 o bug with Rigid-lid version (since c35) fixed.
1505
1506 checkpoint36
1507 o implement Crank-Nickelson barotropic time-stepping
1508 o recover Time-Average diagnostics
1509 o fix Pb in checkpoint (PR#19)
1510 o AIM become a standard package ; clean unused CPP_kees
1511
1512 checkpoint35
1513 o subtantial rewrite of dynamics.f
1514 o allows staggered time-stepping
1515 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
1516 o added bottom drag (linear + quadratic)
1517
1518 checkpoint34
1519 o Modified exchange routines for correct reverse simulation.
1520 o Added verification output to comply with bug fix in impldiff.F
1521 as of c33 (exp2, natl_box).
1522 o Corrected store directives in dynamics.F
1523 o Corrected array boundaries in impldiff.F
1524 o Corrected array dimensions in gmredi.
1525 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
1526 o Added routine GLOBAL_SUM_INT to global_sum.F
1527 o Added mdsio_gl.F for ECCO purposes.
1528
1529 checkpoint33
1530 o Fixed bug in lower BC in impldiff.F
1531 o Fixed confusion about units of forcing arrays in FFIELDS.h
1532 namely Fu,Fv,Qnet,Qsw,EmPmR:
1533 - Removed verification/natl_box/code/external_fields_scale.F
1534 (did not differ from that in model/src)
1535 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
1536 (see FFIELDS.h for description)
1537 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
1538 kpp_calc.F and kpp_transport_t.F
1539 - Removed model/src/external_fields_scale.F and calls to it
1540 - verification/natl_box uses flux data with "atmospheric" sign so
1541 a special version of external_fields_load.F is used to
1542 change the data as it's read in. This way, the arrays
1543 have the right units and signs at all times tha a user could
1544 possibly use them.
1545 o Corrected genmake to delete a temporary file during configuration
1546
1547 checkpoint32
1548 o Scaling of forcing fields moved from external_forcing.F to
1549 external_fields_scale.F, called directly after loading fields.
1550 o Surface relaxation terms added to surface tendency fields in
1551 extra subroutine.
1552 o impldiff.F changed to avoid storing by TAMC of huge intermediate
1553 fields.
1554 o Changes in GMRedi to comply with packaging structure.
1555 o Modifications and bug fixes in KPP package.
1556 o Verification experiment for KPP added (verification/nat_box/)
1557
1558 checkpoint31
1559 o Packages interface brought in line with defined standard
1560 -> new routines packages_...F
1561 -> changes in initialise_fixed.F, initialise_varia.F
1562 -> enables initialisation interface for ECCO package
1563 o Rescaling of external forcing fields immediately after read
1564 (removed from external_forcing.F)
1565 -> new: surface_fields_scale.F
1566 -> affects ini_foorcing.F, external_fields_load.F
1567 o Computation of surface tendencies before tendency updates.
1568 -> new: external_forcing_surf.F
1569 o Change of variable names useGMRedi, useKPP, useECCO
1570 o Further changes in dynamics.F, impldiff.F for TAMC
1571 o Tested for experiments 0, 2, 4.
1572 - not yet tested for GMRedi.
1573 - not yet tested for KPP.
1574
1575 checkpoint30
1576 o Updates for OBCs
1577 o New experiment for test OBCs (internal_wave)
1578 o New output.txt in verification/exp4/results/
1579 o Updates for KPP: calculation of viscosity corrected, new variables
1580 kpp_dumpFreq and kpp_taveFreq
1581 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
1582 and entry for T90 in genmake
1583
1584 checkpoint29
1585 o packaged KPP and GM/Redi
1586
1587 checkpoint28
1588 o Corrected initialization of hFacMin for difference vertical coordinates
1589 o Modified calculation of partial cell thickness to more robust algorithm
1590 o config_summary.F: replaced write_1D_... by write_0D_...
1591 read_write.F: added subroutines write_0D_...
1592 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
1593 included some initialisations required for TAMC.
1594 o routine calc_isoslopes: modified sqrt computation to make it
1595 differentiable for zero argument.
1596 o routines dynamics, impldiff:
1597 included store directives and tape key computations required for TAMC.
1598 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
1599
1600 checkpoint27
1601 o fixed calc_isoslopes() to so that cancellation of terms in tensor
1602 formulation works properly with variable resolution.
1603 o restructured the calling tree between the_model_main() and dynamics()
1604 o split initialise() into initialise_fixed() and initialise_varia()
1605 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
1606 in new routine ini_psurf()
1607
1608 checkpoint26
1609 o moved some #ifdef in optional routines to encompass everything
1610 except the argument declarations. This was using up some memory.
1611 o fixed macros like _ADT to work with both versions of Linux cpp
1612 o cleaned up some unused and uninitialized variables
1613 (helps when debugging with strict compile options)
1614 o split up CPP_EEOPTIONS.h into options and macros
1615 (macros are now in eesupp/inc/CPP_EEMACROS.h)
1616 o patch for 2 processor JAM mode
1617
1618 checkpoint25
1619 o updates for OBCs and NH
1620 o dramatically reduced memory usage
1621 o added "JAM" routines for use on Artic network
1622 o parameterization of convection by implicit vertical diffusion
1623 o added a diagnostic of convective index
1624 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
1625 (this is was partly for OBCs and NH but also in anticipation of
1626 an explicit free-surface option)
1627 o initial state input files for U and V
1628
1629 checkpoint24
1630 o Removed some spurious "REAL"s
1631 o Updated KPP to latest version from JPL
1632 o Added a COS(latitude) in horizontal viscosity
1633
1634 checkpoint23
1635 o Added del^4 diffusion for salt and temperature
1636 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
1637
1638 checkpoint22
1639 o Made many small changes: implicit none, format(i5), etc...
1640 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
1641
1642 checkpoint21
1643 o Introduced new I/O package that supports direct-access records (mdsio.F)
1644 o Split-up mid-level I/O routines
1645 o Updated input data for experiments 0,1,2,4 and 5
1646 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
1647
1648 checkpoint20
1649 o Tidied up open-boundaries some more
1650 o Added non-hydrostatic code
1651 o Fixed some input data
1652 o Modified MPI start-up to work in "coupled" context.
1653
1654 checkpoint19
1655 o Tidied up directory structure for verification experiments.
1656 o Added new code for open boundaries.
1657 o Corrected advective terms near boundaries.
1658 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
1659 o Implemented free-slip/no-slip BCs and del^4 dissipation.
1660 o Split default parameters out of ini_parms.F into set_defaults.F.
1661
1662 checkpoint18
1663 o Further changes for optional code generation with
1664 CPP - ugh!
1665
1666 checkpoint17
1667 o Beginning to incorporating modularity
1668 for supporting atmos. and ocean configs.
1669 o Small changes for TAMC complinace
1670 o New ultra simple test case. Barotropic box
1671 configuration "exp0".
1672
1673 checkpoint16
1674 o Minor changes to exchange routines to support
1675 accumulation in reverse mode. Adjoint of an
1676 assignment is an addition.
1677 o Changes to support compilation by TAMC (LR(1)
1678 syntax) and by g77 under Linux ( 72 character
1679 limit ).
1680
1681 checkpoint15
1682 Rewrote exchange routines to allow
1683 o General tile <-> tile connectivity.
1684 o TAMC reverse mode flag ( is this really needed? )
1685 o Variable width overlap and exchange region widths.
1686 o Hooks for sharing data via DMA, Arctic, Memory Channel,
1687 shmput/shmget, VIA, SYSV shmem and every other cool
1688 communication method.
1689
1690 checkpoint14
1691 Consistent isomorphism chages made. These allow dynamical core
1692 to support both pressure and meters as a vertical coordinate.
1693
1694 checkpoint13
1695 Release which corrects global_max problem and a couple
1696 of KGM time-averaging diagnostic errors. Also contains
1697 a double-gyre experiment setup as well as the baseline
1698 4 degree global template. The double gyre template is
1699 organised to allow it to be applied automatically to
1700 the baseline configuration.
1701
1702 branch-point-rdot
1703 A few tidy-ups have been made bt the real point of this
1704 check-point (excuse the pun) is to allow a branch to be
1705 made for the purposes of adding the rDot alterations.
1706 I don't want to commit the rDot to the main-trunk until
1707 we've actually tested it...
1708
1709 checkpoint12
1710 Tidy up and added generic genmake script (formerly
1711 configure script).
1712 Released to testers.
1713
1714 checkpoint11
1715 Re-arranged initialise() and introduced ini_vertical_grid()
1716 and ini_masks_etc().
1717
1718 checkpoint10
1719 Introduced the configure script.
1720 Separated out the diags package.
1721 Added template for writing time-averages of tile/intermediate quantities.
1722 Updated SIZE.h in exp2 and made the data big-endian.
1723
1724 checkpoint9
1725 MPI fix. Filename changes (meta/data). salbin*y stuff.
1726 General tidy-up.
1727 SST.bin SSS.bin added to verification/exp2
1728
1729 checkpoint8
1730 Inludes time-dependant forcing and time-averaging.
1731 Works at 4x4 and 2.8125x2.8125 global
1732
1733 checkpoint7-4degree-ref
1734 Branch from checkpoint7. Released for application to
1735 global modeling and general modeling - process studies, regional
1736 model etc..
1737 Configured for verification/exp2 - 4 degree global, two process.
1738
1739 checkpoint7
1740 Created by cnh
1741 Simple 4 degree global simulation
1742 configuration.
1743 Includes climatological wind,
1744 hydrography, bathymetry etc
1745 Does not include Heat Flux and E-P
1746
1747 checkpoint6
1748 Created by cnh
1749 merged checkpoint5 with CD and
1750 spherical polar code.
1751 Still some problems with GM Redi
1752 abd full topography.
1753
1754 checkpoint5
1755 Created by AJA
1756 contains updates to GM Redi
1757 and reordered timestepping loop
1758 for Implicit Diffusion.
1759
1760 checkpoint4
1761 Created by cnh
1762 Contains memory saving macros ( _rdxc etc..) for when
1763 grid variations are limited.
1764 Contains polynomial coeffs for EOS and knudsen program
1765 for generation.
1766
1767 checkpoint3
1768 Created by cnh
1769 Added extra flags for runtime options
1770 Added this file
1771 Added implicit free-surface
1772 Added pre-conditioner
1773 Put compare01 into repository ( compare01/... )
1774 Put data and eedata into repository ( verification/exp1 )
1775
1776 checkpoint2
1777 Created by AJA
1778 Added GM/Redi
1779
1780 checkpoint1
1781 Created by AJA
1782 Restructured kloop in dynamics.F
1783 Added non-linear EOS
1784
1785 baseline
1786 Original checked in code

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