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Revision 1.264 - (hide annotations) (download)
Wed Mar 3 05:17:44 2004 UTC (20 years, 2 months ago) by dimitri
Branch: MAIN
Changes since 1.263: +2 -1 lines
o no restoring terms under ice for pkg/seaice
o modfied EXF_EXTERNAL_FLUXES option
o added exf_albedo parameter

1 dimitri 1.264 $Header: /usr/local/gcmpack/MITgcm/doc/tag-index,v 1.263 2004/03/02 08:45:46 dimitri Exp $
2 cnh 1.1
3     Notes on tags used in MITgcmUV
4     ==============================
5 jmc 1.260
6 dimitri 1.264 o no restoring terms under ice for pkg/seaice
7 dimitri 1.263 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
8     o bug fix for pkg/seaice pickups
9 edhill 1.262 o change MNC call locations and add coordinate attributes
10 jmc 1.260 o mask vorticity at the corner ; affects global_ocean.cs output
11     o fix ini_curvilinear_grid ; test CS experiments with mpi
12 jmc 1.259 o aim.5l_cs: modify sea-ice fraction input file ; update output
13 heimbach 1.261 o exf: Adding simple range check routine for exf fields after read
14 adcroft 1.256
15 heimbach 1.257 checkpoint52k_post
16 adcroft 1.256 o removed top-level directory "diags"
17     - we migrated these functions to pkg/timeave a long time ago
18     o fixed bug introduced in pkg/monitor
19 heimbach 1.257 o accuracy ctrlprec = 32 insuffient for gradient checks using
20     averaged fields (I/O via cost_averages)
21     -> use ctrl.h in active_file*.F to control I/O precision.
22     o paramter list of CALL ADTHE_MAIN_LOOP
23     o added initial do_the_model_io to ecco
24     o set all ...Freq to zero after cost_final
25     taveFreq, dumpFreq, pChkptFreq
26 heimbach 1.258 o MAIN and ECCO differentiability restored
27 heimbach 1.255
28     checkpoint52j_post
29     o fix nchklev in tamc.h for global_ocean...
30     o Bringing flow and store directives up-to-date
31     o Really weird thing!
32     call do_the_model_io from the_main_loop with parameters
33     starttime, niter0, instead of mytime, myiter, screws up the adjoint:
34     TAF places a faulty re-call of initialise_varia
35     after cost_final call which should not be there!
36     checkpoint52j_pre
37 jmc 1.253
38 afe 1.254 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
39     error messages
40 jmc 1.253 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
41 afe 1.252 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
42     debug output
43 afe 1.251 o modfied mdsio_writefield.F to handle non-global files under exch2
44 jmc 1.250 o update AIM Cubed-Sphere exp (aim.5l_cs):
45     use land, p*, and Franco.M forcing fields with fractional land-sea mask.
46     o update AIM Equatorial Channel exp:
47     use standard aim_v23 pkg and change the SST fields to be more realistic.
48 afe 1.248 o globalFile now works with exch2
49 afe 1.247 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
50 jmc 1.253 mon_vort3.F to make exch2 friendly with >1 tile per cube face
51 dimitri 1.249 o limit timeave output for hi-res integrations
52 adcroft 1.245
53     checkpoint52i_post
54     o removed CPP_EEOPTIONS.h from verification/*/code
55     o updated the tiling for global_ocean_pressure
56     checkpoint52i_pre
57 jmc 1.246
58     o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
59     the old pkg/aim).
60 afe 1.239
61 dimitri 1.244 checkpoint52h_pre
62 afe 1.243 o shortened offending lines in exch2_send_rx?.template
63 afe 1.242 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
64 edhill 1.240 o genmake2: add build & execute test for NetCDF code
65 afe 1.239 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
66     old grid files, moved CPP_EEMACROS.h to pkg/exch2
67 dimitri 1.238 o added useSingleCPUIO flag to monitor.F and mon_out.F
68 dimitri 1.241 o added temporary hack for sea-ice dynamics on the cube:
69     metric terms are ignored and it is assumed that
70     there is no sea-ice on cube faces 1, 2, 4, and 5.
71 dimitri 1.238
72     checkpoint52f_post
73 afe 1.236 o added exch2 cube routines to pkg/exch2
74     o modified hs94.cs-32x32x5 to use it
75     o added new grid files to hs94.cs-32x32x5
76 dimitri 1.238 checkpoint52f_pre
77 dimitri 1.228
78 jmc 1.235 checkpoint52e_post
79 jmc 1.234 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
80     for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
81 jmc 1.235 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
82     to work with implicit vertical advection and AB ;
83     o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
84     o update output (gad_calc_rhs.F changes affect truncation error) of exp:
85     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
86 jmc 1.233 checkpoint52e_pre
87    
88     o fix bug in impldiff when Nr=1 or Nr=2.
89 jmc 1.232 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
90     o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
91 jmc 1.229 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
92     ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
93 dimitri 1.228 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
94 dimitri 1.231 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
95     o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
96 jmc 1.220
97 jmc 1.226 checkpoint52d_post
98 adcroft 1.230 o re-tiled many expts to allow comparison in multi-processor mode
99     - updated output accordingly
100     - changed hs94.128x64x5 to use intial T from file rather than use the
101     random number generator
102 molod 1.227 o add infrastructure in model routines for fizhi and gridalt packages
103 jmc 1.220 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
104 dimitri 1.222 o changes to permit hi-res, cubed-sphere, configuration
105     - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
106     - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
107     - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
108     of surface winds for the cube
109     (A verification experiment, based on global_ocean.cs32x15, but with
110     pkg/seaice turned on and with on-the-fly interpolation from the NCEP
111     Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
112     complete with example surface forcing files and matlab scripts to look
113     at the output and compare it with that of global_ocean.cs32x15.)
114 jmc 1.223 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
115     but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
116     to conform to the common rule.
117 jmc 1.224 o check-in the first version of the coupler + interfaces for multi-components
118     set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
119     - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
120     - atmosphere: use pkg aim_v23 ; no sea-ice for now.
121     - ocean and atmos. share the same horizontal grid (no interpolation).
122     - exchanges between component and coupler is done in forward_step
123 jmc 1.225 o new verification experiment, cpl_aim+ocn:
124     coupled ocean - AIM atmosphere on cs32 grid.
125 jmc 1.217
126 dimitri 1.219 checkpoint52d_pre
127 jmc 1.217 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
128 jmc 1.218 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
129 heimbach 1.213
130 heimbach 1.216 checkpoint52c_post
131 heimbach 1.213 o Fixing OPTIONS files for use of exf:
132     - ALLOW_ECCO not needed
133     - ECCO_CPPOPTIONS.h should not be included from
134     EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
135     as has been the case in the past
136     - All cal/exf related options are currently set in
137     single header file. Should remain so until we
138     agree on a consistent new policy.
139 heimbach 1.214 o Removed all CPP options for cal package.
140     cal has no more CPP options.
141 heimbach 1.215 o modified STOREs in GAD_ADVECTION
142     o corrected key comp. for passkey
143 heimbach 1.210
144 jmc 1.212 checkpoint52b_post
145     o new version: "thsice" of thermodynamic sea-ice pkg:
146     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
147     - modify fluxes but do not change theta directly;
148     - light cleaning of bulk_force pkg (still needed with thsice).
149     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
150     + output_thsice.txt to test thsice & bulk_force pkgs.
151     o put back grid & coriolis monitor output.
152 jmc 1.211 checkpoint52b_pre
153    
154     o call "do_the_model_io" at the beginning (=> dump initial state)
155     o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
156 heimbach 1.210 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
157     (need info on NUMBER_OF_PTRACERS)
158     o missing PTRACERS headers in some routines
159     o default tamc.h in pkg/autodiff supposed to crash
160     to ensure proper customization
161 dimitri 1.206
162 heimbach 1.209 checkpoint52a_post
163 jmc 1.208 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
164 dimitri 1.207 - moved surfaceTendencyTice from pkg/seaice to main code
165 jmc 1.208 - subroutine FREEZE_SURFACE now limits only surface temperature
166     and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
167     => new output.txt for global_ocean.cs32x15 & global_with_exf
168     - keep the old version of FREEZE for backward compatibility;
169     global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
170 heimbach 1.209 - corresponding modifs for TAF directives
171 dimitri 1.207 o added surface flux output variables to TIMEAVE_STATVARS
172     o time-averaged output for pkg/ptracers
173 heimbach 1.209 o fix problem with ECCO-related divided adjoint
174     snapshot file was missing some ad-variables,
175     but no warning issued by TAF
176 dimitri 1.206
177 dimitri 1.207 checkpoint52a_pre
178 dimitri 1.206 o some bug fixes for #undef REAL4_IS_SLOW
179 heimbach 1.205
180     checkpoint52 = ecco_c52_e35
181     o after testing adjoints of checkpoint51u_post
182 edhill 1.203
183 heimbach 1.204 checkpoint51u_post
184     o this is the post-merge tag of the ecco-branch
185     (needs another clean checkout and re-testing)
186     o various natl_box_adjoint configs and results
187     but no input fields
188     o obcs adjoint not yet merged!
189     o adding ECCO global 1x1 and 2x2 degree configs
190     o updated/extended some store directives for seaice
191     o pkg/ecco now containes ecco-specific part of cost function
192     o top level routines the_main_loop, forward_step
193     supersede those in model/src/
194     previous input data.cost now in data.ecco
195     (new namelist ecco_cost_nml)
196     o in ctrl/ cleaned some cross-dependencies and updated CPP options
197    
198     checkpoint51t_post
199     o this is the pre-merge tag of the ecco-branch
200    
201 edhill 1.203 checkpoint51s_post
202     o cleanup: removed various obsolete #define-s
203 heimbach 1.204 o pkg/grdchk
204     - renamed 'ph-grd 3' to 'grad-res'
205     - merged from ecco-branch
206     (remaining bug fixes for obcs gradient checks)
207     - additional high-precision output for testreport
208     (grep for 'precision_grdchk_result')
209 edhill 1.202
210     checkpoint51r_post
211     o cleaned up or removed CPP_OPTIONS.h files
212     o updated results for some of the tests to reflect the new
213     optfiles (-ieee: -O0 instead of -O3)
214 heimbach 1.201
215     checkpoint51q_post
216     o cd_code:
217     - moved cd_scheme.F -> cd_code_scheme.F
218     - separate read_checkpoint from cd_code_ini_vars.F
219     - separated cd_code part from write_checkpoint
220     - updated AD_SOURCE, generated .flow
221     - added CD_CODE_VARS.h to the_main_loop
222     - Moving cd_code specific store dir.s to pkg/cd_code
223     o ctrl package totally restructured
224     - pack/unpack now optional and decoupled from
225     xx_/adxx_ I/O
226     - ctrl_pack/unpack cleaned
227     (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
228     - confined inclusion of AD_CONFIG.h to where necessary.
229     o genmake2: changed AD dependencies from SRCFILES to AD_FILES
230 edhill 1.198
231 edhill 1.200 checkpoint51p_post
232 edhill 1.198 o create initial cd_code package
233 edhill 1.199 - WARNING: the initialization of fields within packages
234     is broken because INI_FIELDS (where READ_CHECKPOINT is
235     called) is called *before* PACKAGES_INIT_VARIABLES.
236     This seems to be backwards since
237     1) its important to initially zero the entire field including
238     the "halo" region
239     2) zeroing needs to be done *before* reading pickup info
240     and the pickup call might or might not happen in any
241     particular run
242     - this needs an overhaul for R2
243 edhill 1.198 o cleanup verification/*/code/GMREDI_OPTIONS.h
244     o cleanup testreport
245 heimbach 1.196
246     checkpoint51o_post
247     o bringing AD-related verif's up to date with genmake2
248     - carbon/
249     - global_ocean.90x40x15/
250     - hs.94.1x64x5/
251     - (front_relax/ )
252     o (more) consistent directory structure for AD-related verif.'s
253     o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
254     o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
255     o bug fix in find_alpha.F for MDJWF:
256     - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
257     change rho -> rho-rhoConst
258     - replace call find_rho to find_rhonum
259     o initialisation of rFlx extended to full array (required by TAF)
260     and shifted to thermodynamics
261     o removed PTRACERS.h in ptracers routine
262     o added surfacetendencyPtr to S/R parameter list pracers_forcing
263     o Correcting initialisations for fVerU, fVerV.
264     o helping TAF to recognize dependency on kUp for
265     fVerU, fVerV
266     o Replacing delZ by delR in pkg/ctrl/
267     checkpoint51o_pre
268 dimitri 1.192
269 edhill 1.195 o undid all of cp51 pending some cleanups and discussion
270 heimbach 1.197 o added the [#include "AD_CONFIG.h"] statement to all files that need
271     it for adjoint/tl #defines
272     o re-worked the build logic in genmake2 to support AD_CONFIG.h
273     o removed tools/genmake since it no longer works
274 dimitri 1.194
275     checkpoint51n_post
276     o modifications to make FREEZE flux visible to pkg/kpp
277     - moved surfaceTendencyTice from pkg/seaice to main code
278     - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
279     - subroutine FREEZE now limits only surface temperature
280     (this means new output.txt for global_ocean.90x40x15,
281     global_ocean.cs32x15, and global_with_exf)
282     o added surface flux output variables to TIMEAVE_STATVARS
283    
284     checkpoint51n_pre
285 dimitri 1.192 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
286 edhill 1.193 o added [#include "AD_CONFIG.h"] to all files that use the following
287     defines:
288     - ALLOW_ADJOINT_RUN
289     - ALLOW_TANGENTLINEAR_RUN
290     - ALLOW_ECCO_OPTIMIZATION
291 edhill 1.190
292 edhill 1.191 checkpoint51m_post
293 edhill 1.190 o incorporating changes to get TAMC/TAF working in genmake2
294     - added new TAMC/TAF targets to the Makefile
295     - various cleanups related to package handling
296 edhill 1.191 - these changes should have no impact on the forward model
297 dimitri 1.189
298     checkpoint51l_post
299     o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
300     - faster algorithm for cal_addtime.F
301     - higher precision arithmetic, where needed
302     - pkg/exf *startdate variables changed from calendar date to
303     model integration time
304    
305     checkpoint51l_pre
306 jmc 1.188 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
307     o enable to apply restoring on S & T only in a latitude band.
308     o update output (external_forcing_surf modif. change truncation errors)
309     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
310 edhill 1.186
311 jmc 1.187 checkpoint51k_post
312     o change default to: useNHMTerms=.FALSE.
313     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
314     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
315     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
316     exp1, ideal_2D_oce
317     - change data file of oceanic exp (leave the results unchanged for now)
318     exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
319     o set gravitySign automatically according to the vertical coordinate used
320     (and change sign: back to "logical" value: +1 when R increases downward)
321 edhill 1.186 o added an include barrier to the default CPP_OPTIONS.h and
322     removed the #include "PACKAGES_CONFIG.h" from it
323 jmc 1.187 o fix a bug in mom_fluxform (from chk51j_post)
324 heimbach 1.185
325     checkpoint51j_post
326     o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
327     o adjusted some flow directives (dynamics, thermodynamics)
328     o added cubed-sphere case to test cost function
329     o heckpoint_lev?_directives.h now include
330     pkg-specific directives, whenever those are enabled.
331     o Moving pkg-specific flow directives to corresponding pkg
332     Moving pkg-specific differentiation list to corresponding pkg
333     Moving pkg-specific checkpoint-lev storing to corresponding pkg
334     ---> conventions are
335     - pkg_ad.flow
336     - pkg_ad_diff.list
337     - pkg_ad_check_lev?_dir.h
338 stephd 1.181
339 edhill 1.184 checkpoint51i_post
340     o merge of the branch-genmake2
341     - knowingly breaks the older genmake
342     - automatic generation of all ALLOW_${PKG_NAME} defines
343     - new testreport supersedes older testscript
344     o large number of package inclusion and header cleanups
345     checkpoint51i_pre
346    
347 edhill 1.183 o new output for adjoin of global ocean vector invariant
348     o fix for checkpoint of thermodynamic seaice and bulk_force
349     o Steph gchem various cleanups
350    
351 stephd 1.181 checkpoint 51h_pre
352 edhill 1.183 o fixed some single quotes
353 stephd 1.181 o modify gchem pkg to be more versatile
354     o modifications to clean up dic pkg
355     o add pkg/cfc
356 heimbach 1.182
357     checkpoint51g_post
358     o provide links for ARPACK and ADM*TLM
359     o start removing verification/vero/
360     o update AD-related stuff
361     (in particular some IF-statements in model/src/ routines)
362     o adding to verification/global_ocean.90x40x15/ adjoint of
363     vector invariant setup
364 dimitri 1.177
365 heimbach 1.180 checkpoint51f_post
366 jmc 1.179 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
367 dimitri 1.178 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
368 dimitri 1.177 of tracer Green's fucntions for ocean inversion project.
369 dimitri 1.175
370 dimitri 1.176 checkpoint51f_pre
371 dimitri 1.175 o Added on-the-fly spatial interpolation capability
372     "USE_EXF_INTERPOLATION" to pkg/exf.
373 dimitri 1.176 - This is a temporary Cartesian-grid hack until
374 dimitri 1.175 the super-duper ESMF coupler becomes available.
375 dimitri 1.176 - See verification/global_with_exf/README for usage example.
376     - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
377     flags and modified pkg/seaice accordingly.
378 dimitri 1.175 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
379     and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
380     non-local transport term.
381 heimbach 1.172
382 jmc 1.174 checkpoint51e_post
383     o pkg/mom_vecinv:
384     - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
385     - add time-ave diagnostic of vorticity advection.
386     o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
387     o atmospheric geopotential: - include water vapor effect;
388     - use p^kappa in p* scaling.
389 jmc 1.173 o land pkg: read initial state from files.
390     o AIM : add stratospheric drag in the upper level
391    
392 heimbach 1.172 checkpoint51d_post
393 jmc 1.173 o change function ILNBLNK (=> last non-blank char.) to return zero
394     (instead of the string length) when the string. char is empty
395 jmc 1.171 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
396 heimbach 1.172 o modif's to restore TAMC compatibility
397     - avoid "_d" constructs in PARAMETER declarations
398     - avoid interrupting lines by comment lines
399     o Use cluster local disks for purely local I/O
400     vs. globally visible disks needed for ctrl stuff
401     (merged from ecco-branch)
402     - new active_file_loc... and mdsio_..._loc routines
403     - affected packages: autodiff, ctrl, grdchk, mdsio
404 heimbach 1.169
405 heimbach 1.170 checkpoint51c_post
406     o introducing integer flag debugLevel
407     - debLevZero: suppress all output
408     - debLevA: standard
409     - debLevB: equivalent to current debugMode=.TRUE.
410     o introducing pathname variable mdsioLocalDir for mdsio
411     that can be specified at runtime
412     (relevant for cluster I/O to local disk)
413     `
414 heimbach 1.169 >>>checkpoint51b_post
415     adjoint of ptracers
416     o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
417     o extended state in checkpoint_lev?, etc.
418     o alternative ctrl/cost with tr1 or ptracer
419     o new comlev1_bibj_ptracers
420     o new ptracers.flow
421     o made ptracers_forcing same as external_forcing_s
422     o added verification for adjoint with ptracers
423     - adm. grdchk fail so far
424     - tlm. grdchk OK
425     - checked tapelev/comlev recomputations: OK
426     <<<checkpoint51b_pre
427 stephd 1.168
428     checkpoint51a_post
429     o added code for biogeochemistry package
430     - new pkgs: dic, gchem
431     - new subroutine in ptracers
432     o modify code for biogeo packages
433     - in model/src and pkg/ptracers
434 heimbach 1.166
435     checkpoint51
436     o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
437     - autodiff, ctrl, exf, grdchk, seaice
438     kept separate packages
439     - cost, ecco, obcs
440 heimbach 1.167 o updating verification/internal_wave, verification/lab_sea
441     (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
442 heimbach 1.165
443     checkpoint50i_post
444     o Preparing next differentiable checkpoint and sync
445     of MAIN vs. ecco-branch
446     - 1st step: this one is differentiable
447     - 2nd step: next(! not this) checkpoint will have updated packages
448     from ecco-branch)
449 jmc 1.161
450 heimbach 1.164 checkpoint50h_post
451 jmc 1.163 o new package "land": provide surface BC for AIM.
452     o pkg/ptracers: apply exchange to all tracers after reading a pickup.
453 jmc 1.161 o AIM: use true log-P extrapolation for near surface temp (= as in
454     F.Molteni paper) ; update aim.5l_cs output.
455 adcroft 1.162 o New variable in PARM03 for more flexible pickups
456 heimbach 1.164 o somewhat cleaned package initialisation sequence for
457     ctrl/ cost/ ecco/ in packages_... routines
458 dimitri 1.160
459     checkpoint50g_post
460     o merged with release1_p17 (pkg/seaice and verification/lab_sea)
461     - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
462     - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
463     made the default because of faster convergence than ADI
464 heimbach 1.159
465     checkpoint50f_post
466     o exf totally restructured
467     - replaced all exf_set_ routines by one generic exf_set_gen.F
468     and made sure it's still differentiable
469     - split exf_getffields.F into new exf_bulkformulae.F
470     - exf_inscal_/exf_outscal_ suffixes consistent with field names
471     - updated adjoint/makefile and relevant verif. accordingly
472 adcroft 1.156
473 heimbach 1.158 checkpoint50f_pre
474 jmc 1.157 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
475     + change Evap over land. (update aim.5l_cs output)
476 adcroft 1.156 o added missing .cvsignores and made uniform across expts
477     o changed configuration of tidal_basin_2d expt
478     o added pkg/debug functions for tracing code in fatal crashes
479     o tidied pkg/monitor to use MONITOR_OPTIONS.h
480     o new fn in pkg/monitor to stop model if solution grows too big
481     o removed lots of single quotes from comments
482    
483 mlosch 1.155 checkpoint50e_post
484     o make KPP work with PTRACERS
485     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
486     nearly a copy of kpp_transport_s
487     - there is no analogue to SurfaceTendencyS, so I have to use
488     gPtr(of the surface layer) instead
489     o add a new platform SunFire+mpi (SunFire 15000) to genmake
490     checkpoint50e_pre
491    
492     checkpoint50d_post
493 mlosch 1.154 o change kpp output from multiple-record state files to single-record state
494     files analogous to write_state.F
495     o reduce the output frequency of cg3d-related stuff to the monitor frequency,
496     analogous to the cg2d-related output.
497 mlosch 1.155 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
498     so that writing to internal file fn (with length 512) fails.
499 mlosch 1.154 checkpoint50d_pre
500 jmc 1.151
501 jmc 1.153 checkpoint50c_post
502     o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
503 jmc 1.152 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
504 jmc 1.151 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
505     o bug fixed in convective adjustment diagnostic (multi-tile set-up).
506     o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
507 dimitri 1.150
508     checkpoint50c_pre
509     Merging from release1_p13:
510     o bug fix for pkg/seaice dynamic solver
511     o Added SEAICE_initialHEFF to pkg/seaice
512 jmc 1.149
513     checkpoint50b_post
514     o store u*,v* in gU,V instead of in guNm1,gvNm1
515     o in order to put the momForcing out of the Adams-Bashforth:
516     move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
517     to timestep.F
518     o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
519     o re-generate output for highly sensitive test-exp:
520     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
521 heimbach 1.146
522 jmc 1.148 checkpoint50b_pre
523 jmc 1.147 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
524 heimbach 1.146 o corrected CPP option mismatch in exf_Bulk... functions for case
525     #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
526 heimbach 1.145
527     checkpoint50a_post
528     o Bug fix for merging between c50 and KPP.
529     ikey was passed from thermodynamics to kpp_calc via
530     common block rather than being recomputed in kpp_calc,
531     in contradiction with new key itdkey.
532     New key ikppkey created, and tamc.h headers updated.
533 heimbach 1.143
534 heimbach 1.144 checkpoint50
535     - 2nd step of merge with ecco-branch:
536     merge changes in ecco-branch back into main trunk
537     - bug fix in find_alpha
538     - more storing in gmredi_calc_tensor.F, kpp_routines.F
539     - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
540     - merged some sliced AD support routines
541    
542 heimbach 1.143 checkpoint49
543     merged from ecco-branch:
544     o exf:
545     - Enable initialisation of forcing fields to constant
546     (runtime) values.
547     - in exf_getffields.F
548     Reduce i-/j-loop to interior domain, discarding overlaps.
549     That also fixes wrong TAF-key computations for key_1, key_2
550     with bulf formulae.
551     - exf_init.F modify #ifdef for exf_init_evap
552     - exf_getffieldrec.F, ctrl_getrec.F
553     The following INT-usages are not safe:
554     fldsecs = int(fldsecs/fldperiod)*fldperiod
555     fldcount = int(fldsecs/fldperiod) + 1
556     and were modified.
557     o autodiff: checkpoint_lev...
558     - updated storing for bulk formulae (some arrays were missing)
559     - added state for seaice package
560     - synchronized with main branch
561     o DIVA:
562     Modif.s in
563 heimbach 1.144 - the_main_loop.F
564     - the_model_main.F
565 heimbach 1.143 and added cost_final_restore.F cost_final_store.F
566     o With these changes, it is possible to fully separate
567     the first forward run to compute the cost function (mdthe_main_loop)
568     and adjoint runs over individual DIVA intervals (adthe_main_loop)
569     into separate model executions.
570     This enables better tuning of DIVA to given queue sizes.
571     o Loss of cost function value in consecutive DIVA runs is
572     fixed by storing to 'costfinal' file.
573     o Appropriate call of ctrl_unpack/_pack,grdchk_main at
574     beginning/end of adjoint integration is accounted for.
575     The current changes apply to TAF-1.4.26.
576     TAF has one remaining bug, requiring one manual change
577     (see MITgcm manual).
578     o cal: synchronized between MAIN and ecco-branch
579 heimbach 1.141
580 heimbach 1.142 checkpoint48i_post
581 heimbach 1.141 o Changes to restore differentiability of code w.r.t. previous tag
582     (mostly adding new routines to make list and replacing
583     pressure by totPhiHyd).
584     o Updated and merged grdchk package
585     - has both ADM and TLM checks
586     - works for single- and multi-proc.
587     - output cleaned
588     - worked successfully for parallel DIVA
589     o genmake:
590     - Adding -platform=SP4
591     - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
592     o Modif. for DIVA:
593     ctrl_unpack should not be called in intermediate DIVA interval.
594     (similar thing would apply for active files such as
595     tbar, sbar, psbar, which should not be reinitialised;
596     only relevant for ecco-branch)
597 dimitri 1.136
598 heimbach 1.140 checkpoint48h_post
599 jmc 1.137 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
600 dimitri 1.136 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
601     o Added SEAICE_initialHEFF to pkg/seaice
602 dimitri 1.139 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
603 jmc 1.135
604     checkpoint48g_post
605     --- EOS:
606     o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
607     store total Potential in totPhyHyd for diagnostics & EOS.
608     o fix restart and overlap Pb when using Z-coord and EOS funct. of P
609     --- Pressure/geopotential gradient:
610     o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
611     o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
612     ( changes results of global_ocean_pressure )
613     o NLFS + z-coord.: add eta*Rho' contribution.
614     o accurate phiHyd when using interface-W at the middle between 2 centers
615     ( changes results of ideal_2D_oce )
616     o includes r* 2nd term in potential gradient.
617 dimitri 1.134
618     checkpoint48f_post
619     Merging from release1_p12:
620     o Modifications for using pkg/exf with pkg/seaice
621     - improved description of the various forcing configurations
622     - added basic radiation bulk formulae to pkg/exf
623     - units/sign fix for evap computation in exf_getffields.F
624     - updated verification/global_with_exf/results/output.txt
625     o Added pkg/sbo for computing IERS Special Bureau for the Oceans
626     (SBO) core products, including oceanic mass, center-of-mass,
627     angular, and bottom pressure (see pkg/sbo/README.sbo).
628     o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
629     to avoid negative values in shallow regions.
630     - updated verification/natl_box/results/output.txt
631     - updated verification/lab_sea/results/output.txt
632     o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
633     o Added useSingleCpuIO option (see PARAMS.h).
634     o Updated useSingleCpuIO option in mdsio_writefield.F to
635     work with multi-field files, e.g., for single-file pickup.
636     o pkg/seaice:
637     - bug fix in growth.F: QNET for no shortwave case
638     - added HeffFile for specifying initial sea-ice thickness
639     - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
640     o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
641     kpp_transport_t.F, forward_step.F, and the_main_loop.F
642     o pkg/seaice:
643     - adjoint-friendly modifications
644     - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
645 jmc 1.131
646 jmc 1.133 checkpoint48e_post
647 jmc 1.131 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
648 jmc 1.132 o dynamics: change definition of computational domain & adapt mom_fluxform
649     accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
650     o following exp works with Olx=Oly=2 (and pass through checkbounds option):
651     adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
652 jmc 1.133 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
653 jmc 1.132 global_ocean.90x40x15 global_with_exf global_ocean_pressure
654     inverted_barometer solid-body.cs-32x32x1
655     (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
656 jmc 1.130
657     checkpoint48d_post
658     o in preparation for r*:
659     a) use pre-computed gradient of hydrostatic potential:
660     changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
661     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
662     => affects results of glob_oce_pressure (different truncation error)
663     update output.txt of ideal_2D_oce & global_ocean_pressure
664 jmc 1.129
665     checkpoint48d_pre
666     o in preparation for r*:
667     new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
668     pass the 2 comp. of the grad. as arguments to momentum S/R.
669     but for the moment, only used if it does not change the results.
670     o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
671 jmc 1.126
672 heimbach 1.128 checkpoint48c_post
673     Modifications in treatment of initial flux forcing controls
674     to avoid extra storing of flux fields.
675    
676     checkpoint48c_pre
677 adcroft 1.127 o Added tidal_basin_2d experiment (currently 1D!)
678 jmc 1.126 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
679 jmc 1.124
680 jmc 1.125 checkpoint48b_post
681 jmc 1.124 o r* coordinate added in #ifdef NONLIN_FRSURF block.
682     (modification to pressure gradient not yet implemented)
683     o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
684     (for U & V) that are used for vertical advection of momentum.
685 jmc 1.123
686     checkpoint48a_post
687     o In preparation for r*, use temp. array to compute vertical transport
688     in flux-form momentum pkg. => change results of few test-exp.
689     Update output of: exp4, exp5, front_relax, global_ocean_pressure,
690     lab_sea, natl_box & plume_on_slope
691 jmc 1.122
692     checkpoint48
693     o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
694 heimbach 1.121
695     checkpoint47j_post
696 jmc 1.120 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
697 heimbach 1.121 o moved adexch from forward_step to addummy_in_stepping
698     o added exch in ctrl_map_...
699     o aveFreq.=0. at end of cost_final to avoid overwrite in
700     reverse checkpointing loop
701     o Yet more changes in gmredi:
702     * adgmredi_calc_tensor
703     avoiding all recomputation of gmredi_slope_limit
704     * adgmredi_x/y/rtransport
705     added flag for excessive storing to avoid recomp. of
706     u/v/rtans, dTdx/y/z
707     -> this is not really necessary and very memory-consuming
708     * adgmredi_slope_psi:
709     consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
710     * gmredi_slope_limit
711     re-activated full calculation of taperfct for case 'ac02'
712     o updating verification/ adjoints of carbon, global_ocean.90x40x15
713 heimbach 1.116
714 jmc 1.119 checkpoint47i_post
715     o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
716     o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
717     default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
718     o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
719     o gmredi: fix few bugs.
720    
721 adcroft 1.118 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
722 heimbach 1.116 This will be a good checkpoint to plug into the ecco-branch.
723     o few modif.'s to get latest version adjointed
724     (mainly kick out code in ini_linear_phisurf)
725     o modif's to run adjoint with exactConserv
726     o case GM_BOLUS_ADVEC should be cleaned
727     S/R gmredi_slope_psi should be cleaned
728     o verification/carbon now has exactConserv=.TRUE.
729 jmc 1.114
730 heimbach 1.115 checkpoint47g_post
731 jmc 1.114 o time-average AIM output: becomes independent from statvars time-average
732     (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
733 heimbach 1.115 o After TAF bug fix:
734     Tested adjoint of gmredi package.
735     Tests were done with checkpoint47 rather than with latest
736     checkpoint47f_post since the latter is broken for the adjoint
737     verification/carbon/ contains both ADM and TLM gradient checks.
738     Here they are, before they get changed/lost/stolen.
739     Mostly modif.'s to fix numerical sensitivities.
740     Gradient checks OK for
741     - GM_taper_scheme:
742     * clipping
743     * ac02
744     * linear
745     * glw91
746     * dm95
747     * ldd97
748     - GMREDI_OPTIONS:
749     * GM_VISBECK_VARIABLE_K
750     * GM_NON_UNITY_DIAGONAL
751     * GM_EXTRA_DIAGONAL
752     * GM_BOLUS_ADVEC
753     in conjunction with data.gmredi parameters to be checked in
754     in a few minutes under verification/carbon/code/
755 cheisey 1.112
756 dimitri 1.113 checkpoint47f_post
757     Merging from release1_p10:
758     o modifications for using pkg/exf with pkg/seaice
759     - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
760     and SEAICE_EXTERNAL_FLUXES
761     - pkg/exf CPP options EXF_READ_EVAP and
762     EXF_NO_BULK_COMPUTATIONS
763     - usage examples are Experiments 8 and 9 in
764     verification/lab_sea/README
765     - verification/lab_sea default experiment now uses
766     pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
767    
768 cheisey 1.112 checkpoint47e_post
769     o created a tag prior to creating a branch
770    
771 mlosch 1.111 checkpoint47d_post
772     o fixed bug in the oceanic pressure coordinates code: vertical viscosity
773     at the bottom boundary had an erroneous half slip boundary condition
774     o added bottom drag and no slip boundary condition capabilities to
775     oceanic pressure coordinates code
776     o added new verification experiment global_ocean_pressure, this experiment is
777     also described in the tutorial section of the manual
778     checkpoint47d_pre
779 cheisey 1.110
780     checkpoint47c_post
781     o Added a verification experiment for a global cubed-sphere ocean run
782     - verification/global_ocean.cubed32x32x30
783     - uses pkg/therm_seaice and pkg/bulk_forcing
784 jmc 1.109
785     o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
786     o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
787     when using P-coordinate; only implemented for atmospheric config.
788     o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
789     NOTES: requires option NONLIN_FRSURF to be "#define".
790     o update advect_xz/results/output.txt (left from checkpoint44g_post)
791 dimitri 1.108
792     checkpoint47b_post
793     Merging from release1_p9:
794     o pkg/seaice
795     - removed GOTO's and added taf directives
796     - double precision constants to reduce the g77 (Linux)
797     to F77 (SGI) differences reported in release1_p8
798     o tools/genmake
799     - added SGI options
800     o verification/testscript
801     - updated to that of checkpoint47a_post
802     o verification/global_ocean.90x40x15/input/eedata
803     - modified for SGI f77 compatibility
804     o verification/lab_sea
805     - added description of sea-ice model
806     - added missing matlab routines
807     - added test of thermodynamics parallelization
808 jmc 1.105
809 jmc 1.106 checkpoint47a_post
810 jmc 1.105 o new pkg: aim_v23
811     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
812     for now, keep the same surface forcing as before.
813     - Part-Cell implemented into AIM; check that Heat & Water are conserved
814     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
815     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
816     o add diagnostic of surface correction term in monitor output
817 jmc 1.106
818     o bulk_force and therm_seaice
819 cheisey 1.107 - Two packages: bulk_force (Bulk forcing)
820     and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
821     - Earlier integration from Stephaine Dutkiewicz
822     and Patrick Heimbach.
823     - Two ifdef statements for compile time,
824     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
825 heimbach 1.104
826     checkpoint47
827     differentiable version of checkpoint46n_post
828     o bug fix in quasihydrostaticterms
829     o * "clean" adjoint code (in terms of extensive recomputations)
830     can now be obtained for all GMREDI options (i.e. for
831     - GM_VISBECK_VARIABLE_K
832     - GM_NON_UNITY_DIAGONAL
833     - GM_EXTRA_DIAGONAL
834     - GM_BOLUS_ADVEC )
835     * However, wrong gradient check problem remains unsolved.
836     * New CPP options have been introduced for different
837     tapering schemes
838     o external_fields_load now part of differentiation list
839     o pressure needs multiple storing;
840     would be nice to have store_pressure at beginning or
841     end of forward_step, e.g. by having phiHyd global (5-dim.)
842     (NB: pressure is needed for certain cases in find_rho,
843     which is also invoked through convective_adjustment).
844     o recomputations in find_rho for cases
845     'JMD95'/'UNESCO' or 'MDJWF' are OK.
846     o #define ATMOSPHERIC_LOADING should be differentiable
847     o ini_forcing shifted to begining of initialise_varia
848     o Incorporating QNVS line search routines into MITgcm
849     (this is separate code, and therefore not under pkg)
850     lsopt/, optim/
851     o Updated verification/carbon/
852     - #define GM_VISBECK_VARIABLE_K
853     - GM_taper_scheme = 'ldd97'
854 heimbach 1.103
855     checkpoint46n_post
856     Merging from release1_p8:
857     o verification/natl_box:
858     updating new external_fields_load routine
859     o New package: pkg/seaice
860     Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
861     The sea-ice code is based on Hibler (1979-1980).
862     Two sea-ice dynamic solvers, ADI and LSR, are included.
863     In addition to computing prognostic sea-ice variables and diagnosing
864     the forcing/external data fields that drive the ocean model,
865     SEAICE_MODEL also sets theta to the freezing point under sea-ice.
866     The implied surface heat flux is then stored in variable
867     surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
868     kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
869     non-local transport term. Because this call precedes model
870     thermodynamics, temperature under sea-ice may not be "exactly" at
871     the freezing point by the time theta is dumped or time-averaged.
872     N.B.: fairly large differences in accuracy occur across
873     different platforms/compilers; comparison between
874     g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
875     generated output gives:
876     T S U V
877     C D M c m s m s m s m s
878     n p a R g m m e . m m e . m m e . m m e .
879     f n k u 2 i a a d i a a d i a a d i a a d
880     g d e n d n x n . n x n . n x n . n x n .
881    
882     Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
883     o GAD:
884     - generated new common blocks to account for call of
885     same gad routines with differing traceridentities
886     (needed to modify tracerIdentity indices in GAD.h)
887     - generated separate common blocks for case useCubedSphereExchange
888     (Department of Futurology)
889     - parameter lists to gmredi_?transport: added tracerIdentity
890     - added new key indices to tamc.h
891     o external_fields_load:
892     - added this routine to TAF list
893     - needed to make some common blocks global and additional storing
894     along the same lines as exf package (checkpoint_lev?_directives.h)
895     o exf:
896     updated external forcing package
897     - bug fixes carried over from ecco-branch
898     (missing OBCS_OPTIONS.h in two routines)
899     - enable easy to use "no forcing".
900     - added exf I/O for atmospheric loading
901     - added exf I/O for runoff data
902     - transfered scaling between exf <-> MITgcm to exf namelist
903     o Adding new verification experiment global_with_exf.
904     This verification experiment is almost identical to the
905     global_ocean.90x40x15 experiment, except that it uses
906     the exf (and cal) package instead of the
907     external_fields_load routine (cf README file).
908 adcroft 1.94
909 adcroft 1.102 checkpoint46m_post
910 adcroft 1.101 o modified testscript to return -- when there are no lines of "%MON" output
911 adcroft 1.100 o added new flag "quasiHydrostatic" for QH mode
912     and new routine quasihydrostaticterms()
913 adcroft 1.99 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
914     New routine: mom_u_coriolis_nh()
915 adcroft 1.98 o fixed sign of non-hydrostatic metric terms in u and v equations.
916     Depend on correct sign of gravitySign.
917 adcroft 1.97 o added work.pc* to .cvsignore in aim directories using ifc
918 adcroft 1.96 o introduced flag for controllin non-hydrostatic metric terms
919 adcroft 1.95 o removed gravitySign from PARM04
920 adcroft 1.94 o switched to g77/ifc from pgf77 in aim experiments
921 mlosch 1.93
922     checkpoint46l_post
923     o made convective adjustment work with pressure coordinates:
924     - changed the direction of k-loop in convective_adjustment.F for the
925     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
926     - adjusted the reference pressure k-index in convective_adjustment.F
927     - adjusted the convection condition in convect.F (in analogy to
928     calc_ivdc.F)
929     - convective_adjustment no longer computes anything on the halos
930     - removed the warnings about negative salinity from find_rho.F and
931     find_alpha.F; instead the new routine look_for_neg_salinity, called
932     at the beginning of find_rho, find_alpha, and find_beta, does a
933     check of the entire slice, if CPP-option
934     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
935     checkpoint46l_pre
936 mlosch 1.91
937 mlosch 1.92 checkpoint46k_post
938 mlosch 1.91 o fixed the verification/global_ocean.90x40x15 experiment:
939     - new bathymetry (the world according to A., JMC, and M.)
940     - new initial fields and forcing fields (*.bin files)
941     - new POLY3.COEFFS (for the next release one should switch to a full
942     equation of state: JMD95P or MDJWF)
943     - fixed several errors and redundancies in the data file
944     - experiment uses looped cells
945     - added matlab directory with diagnostic scripts for plotting of output
946 jmc 1.90
947     o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
948     - read AIM physics parameters from a file (data.aimphys)
949     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
950 jmc 1.89
951     checkpoint46j_post
952     o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
953     o move wVel computation at the end of the time step, in S/R integr_continuity
954     o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
955     o update timeave pkg for wVel diagnostic.
956     checkpoint46j_pre
957 mlosch 1.87
958 jmc 1.88 checkpoint46i_post
959     o Clean up AIM package (and keep the results unchanged):
960     include CPP_OPTION and use IMPLICT NONE in all routines ;
961     declare all the variables _RL ; use _d 0 for all numerical constants.
962     use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
963 mlosch 1.87
964     checkpoint46h_post
965     o cleaned up the use of rhoNil and rhoConst.
966     - rhoNil should only appear in the LINEAR equation of state, everywhere
967     else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
968     and the dynamical equations are all divided by rhoConst
969     o introduced new parameter rhoConstFresh, a reference density of fresh
970     water, to remove the fresh water flux's dependence on rhoNil. The default
971     value is 999.8 kg/m^3
972     o cleanup up external_forcing.F and external_forcing_surf.F
973     - can now be used by both OCEANIC and OCEANICP
974     checkpoint46h_pre
975    
976     Added code to convert surface volume flux (fresh water) into
977     a mass flux when using P coordinates in the ocean (OCEANICP).
978     Note: It assumes you have set rho0=rhoConst=density of fresh water.
979 mlosch 1.86
980     checkpoint46g_post
981     o Include a new diagnostic variable phiHydLow for the ocean model
982     - in z-coordinates, it is the bottom pressure anomaly
983     - in p-coordinates, it is the sea surface elevation
984     - in both cases, these variable have global drift, reflecting the mass
985     drift in z-coordinates and the volume drift in p-coordinates
986     - included time averaging for phiHydLow, be aware of the drift!
987     o depth-dependent computation of Bo_surf for pressure coordinates
988     in the ocean (buoyancyRelation='OCEANICP')
989     - requires a new routine (FIND_RHO_SCALAR) to compute density with only
990     Theta, Salinity, and Pressure in the parameter list. This routine is
991     presently contained in find_rho.F. This routine does not give the
992     correct density for 'POLY3', which would be a z-dependent reference
993     density.
994     o cleaned up find_rho
995     - removed obsolete 'eqn' from the parameter list.
996     o added two new verification experiments: gop and goz
997     (4x4 degree global ocean, 15 layers in pressure and height coordinates)
998     checkpoint46g_pre
999 heimbach 1.85
1000     checkpoint46f_post
1001     o Enable tangent linear (forward mode) gradient checks:
1002     - extended active file handling to g_... files
1003     - added TANGENT_SIMULATION to theSimulationMode
1004     - extended grdchk package accordingly
1005     o added tangent linear setup in verification/carbon/code_ftl
1006     o added adjoint setup in verification/front_relax/code_ad
1007 mlosch 1.82
1008 cnh 1.84 checkpoint46e_post
1009 mlosch 1.83 o Added new equation of state -> MDJWF
1010     - EOS of McDougall et al., 2002, JAOT, submitted
1011     - caveat: the equation of state is only valid for a smaller (more
1012     realistic?) range of values than JMD95P/Z and UNESCO
1013     - added masks to the calculation of pressure in store_pressure
1014     - added more check values for density in check_eos (ini_eos.F), some of
1015     the old check values are out of the range of the MDJWF-eos, so don't
1016     expect perfect matches for those
1017 cnh 1.84 checkpoint46e_pre
1018 mlosch 1.83
1019 mlosch 1.82 checkpoint46d_post
1020     o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
1021     'OCEANICP', also initialised field pressure correctly in ini_eos in the
1022     case of pressure coordinates. eosType='JMD95Z' in
1023     combination with buoyancyRelation='OCEANICP' now causes an error.
1024     o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
1025     in find_alpha/beta.
1026     checkpoint46d_pre
1027    
1028     o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
1029     so that JMD95Z and JMD95P give approptiate static stability in find_rho.
1030 adcroft 1.81
1031     checkpoint46c_post
1032     o Changes necessary for ocean in p-coordinates
1033     - Added new buoyancy relation = 'OCEANICP'
1034     - Added new parameters = gravitySign (this used to be contained inside
1035     the factor dRdZ which I added when we first switched to R coordinates).
1036     X GM/Redi is not compatible (yet)
1037     X bottom drag and no-slip need to be debugged.
1038     checkpoint46c_pre
1039 mlosch 1.80
1040     checkpoint46b_post
1041     o Added new equation of state -> JMD95Z and JMD95P
1042 mlosch 1.83 - EOS of Jackett and McDougall, 1995, JAOT
1043 mlosch 1.80 - moved all EOS parameters into EOS.h
1044     - new routines ini_eos.F, store_pressure.F
1045     o Added UNESCO EOS, but not recommended because it requires
1046     in-situ temperature (see JMD95)
1047     o Modified formatting for knudsen2.f in utils/knudsen2 and added
1048     unesco.f to be used with POLY3
1049     checkpoint46b_pre
1050 mlosch 1.79
1051     checkpoint46a_post
1052     o Added (atmospheric) pressure loading
1053     - new field in FFIELDS.h, etc...
1054     - new cpp flag ATMOSPHERIC_LOADING
1055     o Changed hFacC to _hFacC in calc_phi_hyd.F
1056     o Added SHORTWAVE_HEATING to some files for consistency
1057     checkpoint46a_pre
1058 heimbach 1.78
1059     checkpoint46
1060     further merges from release1_p5
1061     o new ctrl package
1062     - adopted from ECCO environment to enable optimization
1063     - added Eliassen Palm fluxes to controls
1064     o added Eliassen Palm flux controls to gradient check package
1065     o cost package
1066     - Compatible with new ctrl package
1067     - added Eliassen Palm cost hooks
1068     - modif's of existing cost functions
1069     o Adjoint-related bug fixes in kpp:
1070     - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
1071     - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
1072     o autodiff package
1073     - flow directives:
1074     + new for S/R do_the_model_io
1075     + enhanced for S/R checkpoint
1076     + new gmredi.flow
1077     - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
1078     disable adcommon.h/g_common.h by default.
1079     - fixed problem for adjoint of global_max
1080     o modified verification/carbon/
1081     o New setup for adjoint of global_ocean
1082     o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
1083     o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
1084     o incorporated hooks for sponge layer code (external_forcing.F)
1085    
1086 jmc 1.77 checkpoint45d_post
1087     o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
1088 jmc 1.76 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
1089     (affects plume_on_slope "cg2d" output)
1090 jmc 1.77 o add new parameter deltaTfreesurf for free-surface time stepping
1091     o exchange gT,gS when using staggerTimeStep & GM & Oly<4
1092 jmc 1.75 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
1093 jmc 1.74 o change phiMin in exp1 (to agree with documentation)
1094     o add new flags:
1095     - T,S forcing inside/outside Adams-Bashforth
1096     - turn off temp,salt advection and/or forcing
1097     - for each tracer, define internal flag for multiDimAdvection & A-B
1098     o monitor: change definition of KE to check conservation of Energy
1099 heimbach 1.73
1100     checkpoint45c_post
1101     o Removed f90 comments ("!")
1102     o Modified initialisations to enable exf package for MITgcm
1103     (without invoking ECCO_PACKAGE).
1104     o modifications to gradient check package (Martin Losch)
1105     - enable centered differences
1106     - modified format of standard output
1107 heimbach 1.72
1108     checkpoint45b_post
1109     o cleaned exchange calls in cg2d
1110     o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
1111     o included CPP option SINGLE_LAYER_MODE in thermodynamics
1112     to configure barotropic setup (Martin Losch)
1113     o moved some initialisations within bi,bj loop in dynamics
1114     (TAF flow dependency)
1115     o in initialise_varia, moved call packages_init_variables
1116     before convective_adjustment_init
1117     (corresponding adjustment of TAF tape initialisation).
1118     o in calc_diffusivity/calc_viscosity extended domain to full overlap.
1119 jmc 1.70
1120 jmc 1.71 checkpoint45a_post
1121     o compute Rho over the whole domain (extend iMin,jMin indices)
1122     o specific exchange for X-slice domain (case Ny=1)
1123 jmc 1.70 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
1124     o solve_for_pressure : set cg2d_x to zero where OBCS are applied
1125 jmc 1.67
1126 heimbach 1.69 checkpoint44h_post = checkpoint45
1127     o Fix to restore differentiability:
1128     place at which packages_init_variables is called in
1129     initialise_varia is crucial for reverse control flow.
1130     o modifications in GMRedi to enable stable adjoint
1131     (corresponding modif's in thermodynamics, dynamics)
1132     o added missing hook for sponge layer code in external_forcing
1133     o modified test cost functions
1134     o storing in gad_advection (plus removal of write(0,*)!
1135     o missing headers TR1.h added in convective_adjustment routines
1136     o errorMessageUnit set non-equal zero in eeboot
1137     (conflict on some platforms, e.g. IBM SP3)
1138     o modified carbon verif.
1139    
1140     checkpoint44h_pre
1141 jmc 1.68 o vertical grid option: allow to put the Interface at the middle between
1142     2 cell-centers ; replace delZ in pkg/kpp by drF.
1143 jmc 1.67 o GM Advective form: Tracers are advected using the residual transport (=
1144     Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
1145 jmc 1.66
1146     checkpoint44g_post
1147     o fix surface correction term in multiDimAdvection (affects plume_on_slope
1148     results) ; ifdef missing in thermodynamics.F
1149 adcroft 1.65
1150     checkpoint44f_pre,checkpoint44f_post
1151     o added PTRACERS package
1152     This allows an arbitrary number of passive tracers to be integrated
1153     forward simultaneously with the dynamicaly model.
1154     + Implemented so far:
1155     - basic forward algorithm (time-stepping, advection, diffusion, convection)
1156     - I/O and checkpointing
1157     - GM/Redi *but* using the GM/Redi coefficient of Salt
1158     + Not implemented so far:
1159     - KPP
1160     - OBCS
1161     + No specific example supplied (yet) but global_ocean.90x40x15 has the
1162     necessary data.ptracer file. Simply use -enable=ptracers and uncomment
1163     line in data.pkg.
1164     + This package is disabled by default since it increases storage.
1165    
1166 jmc 1.60
1167 adcroft 1.64 o testscript: added -cleanup option
1168 jmc 1.63 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
1169     b) enable to filter 2D fields.
1170 adcroft 1.62
1171     checkpoint44e_pre,post
1172     o re-wrote convective adjustment to use pre-calculated weights
1173     Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
1174     Adds: model/src/convective_weights.F, convectively_mixtracer.F
1175     Original calls to convect() still in place.
1176 heimbach 1.61
1177     chkpt44d_pre,post
1178     o added missing EXCLUDE_MONITOR flags
1179     o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
1180     (incompatible typ in MIN/MAX expressions caused problems
1181     on IBM SP3)
1182     o in genmake added variable MAKEDEPEND
1183     plus resetting for case SunOS
1184     o added timer_stats.c routine for IBM SP3
1185     o removed variables in dynamics
1186     !!! I forgot to create tag chkpt44d_pre !!!
1187     !!! But chkpt44d_pre = chkpt44c_post !!!
1188 jmc 1.63
1189     o real fresh water flux implemented with non-linear free-surface.
1190 heimbach 1.58
1191 jmc 1.59 chkpt44c_pre,post
1192     o few fix (mask in shap_s2, EmPmR in external_field_load,
1193     USE_NATURAL_BCS in solve_for_P);
1194     o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
1195    
1196 heimbach 1.58 checkpoint44b_pre/_post
1197     o merge of relevant stuff from the ecco-branch:
1198     - genmake: removed $S64 overwrite for case SunOS
1199     - pkg/exf: update and corrections for field swapping and obcs
1200     - pkg/ecco: parameter lists for the_model_main, the_main_loop
1201     harmonized between ECCO and MITgcm
1202     - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
1203     updated checkpointing_lev... lists for obcs
1204     - model/src: minor changes in forward_step, plot_field
1205     added directive for divided adjoint in the_main_loop
1206     - pkg/mdsio: added mdsio_gl_slice
1207 jmc 1.57
1208     o check parameters & config (chkpt44a_pre,post)
1209 jmc 1.56 o OBC and NonLin_FrSurf.
1210    
1211 heimbach 1.55 checkpoint44
1212 jmc 1.54 o fix bug in mom_vi_del2uv
1213 jmc 1.56 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
1214     o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
1215     o update AIM experiments (NCEP input files)
1216     o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
1217 heimbach 1.55 o added some stuff for AD
1218 adcroft 1.53
1219     checkpoint43
1220     o added two new advection tests
1221     o added global 4x4 degree ocean test
1222     o added test of H&S94 with free surface on cube
1223     o some final mods for gradient check, adjoint,...
1224 heimbach 1.52
1225     checkpoint42
1226     Fixed AD-related problems:
1227     o Store directives up-to-date with re-arranged Adams-Bashforth
1228     (mainly thermodynamics.F)
1229     o New store directives for multi-dim. advection schemes
1230     * new CPP flag ALLOW_MULTI_DIM_ADVECTION
1231     * new common block and key passkey
1232     (mainly gad_advection.F)
1233     o Modified store directives for split of dynamics/thermodynamics
1234     for the case ALLOW_KPP
1235     o Cleaned argument list for timestep_tracer.F
1236 adcroft 1.51
1237     checkpoint41
1238     o re-formatted/added comments in prologues of key subroutines
1239     to work with protex
1240 heimbach 1.47
1241 adcroft 1.50 checkpoint40
1242     o moved calc_gs, calc_gt and calc_tr1 back to model/src
1243     o added FLT (floats) package from Arne along with demo. experiment
1244     o re-arranged Adams-Bashforth scheme for tracers to allow easier
1245     implementation of forward-in-time forcing terms
1246     o more mods for non-linear free-surface including new variable
1247     o modified multi-dim method to work on cube
1248     o bug fix in KPP (from DM)
1249    
1250 adcroft 1.49 checkpoint40pre9
1251     o added DST advection schemes
1252     o fix MPI bug on SGI's
1253     o modifications for non-linear free-surface
1254     o fixed conditionals for fixed flow/passive tracer only mode
1255     o added tension/strain form of stress tensor
1256     o changes to commenting of arguments for TAF/TAMC
1257     o added/updated many matlab scripts
1258 adcroft 1.50 o added multi-dimensional advection method for tracers
1259 adcroft 1.49
1260 adcroft 1.48 checkpoint40pre8
1261 heimbach 1.47 o new package rw/
1262     Added method for dumping intermediate local arrays:
1263     mdsio_writetile - same as mdsio_writefield except works from inside
1264     bi,bj loop
1265     mdsio_writelocal - same as mdsio_writetile except works for local
1266     arrays
1267     write_local_r? - higher-level wrapper for mdsio_writelocal
1268     Controlled by diagFreq. Defaults to zero (ie. no dumps)
1269     Example given at end of mom_vecinv.F that dumps some local arrays.
1270     o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
1271     control flux-form versus vector invariant code.
1272     Switch is runtime flag vectorInvariantMomentum (defaults to false)
1273     or genmake -DISABLE ...
1274     o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
1275     (additional storing is now needed for case vecinv;
1276     currently nothing implemented to switch this storing off
1277     in case fluxform is used since no CPP flag available).
1278 heimbach 1.46
1279     checkpoint40pre7
1280     o bug fix in dynamics.F
1281     calc_viscosity called before k=1,Nr loop.
1282     o added some #ifdef's ALLOW_PASSIVE_TRACER
1283     o cleaned initialisations in ctrl_map_ini
1284     related to TAF
1285 heimbach 1.45
1286     checkpoint40pre6
1287     o split dynamics into thermodynamics & dynamics
1288     o corresponding split of calc_diffusivity into
1289     calc_diffusivity, calc_viscosity
1290     (kpp_calc_diff, kpp_calc_visc).
1291     o Added diffkr, kapgm to control variables
1292     o bug fix in gmredi_slope_limit for ldd97
1293 adcroft 1.44
1294     checkpoint40pre5
1295     o proper initialization of Adams-Bashforth time stepping
1296     + uses forward step for very first step of model (iter=0)
1297     o re-generated *all* output since almost all output is modified by this
1298     change (sorry but we've been putting this one off for about 2 years)
1299     + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
1300     *not* regenerated since they are already out of date and I don't
1301     want to create the impression that they are suddenly working.
1302     o removed KAP stuff for DEC's
1303     o modified/added many .cvsignore files in */code and */input
1304     o added new expt "solid-body.cs-32x32x1"
1305     + this uses an alternative form of ini_curvilinear_grid.F which
1306     is not necessarily any better than the current one...
1307 heimbach 1.43
1308     checkpoint40pre4
1309     o added re-initialisations of utrans,vtrans,rtrans in
1310     calc_common_factors which are crucial for TAF.
1311     o extended iMin,jMin range for calc_common_factors,
1312     calc_diffusivity
1313     o added option ALLOW_PASSIVE_TRACER
1314     o a few minor updates and fixes
1315    
1316 heimbach 1.42 checkpoint40pre3
1317     o created calc_gtr1.F for gad package
1318     o split the_main_loop and re-introduced forward_step
1319     o some recomputations of nIter0 for TAMC
1320    
1321 heimbach 1.41 checkpoint40pre2
1322     o Updated to latest branch of AJA, JMC
1323     o Added gradient check package
1324     o Added routines for passive tracer handling
1325     o Added carbon sequestration sensitivity experiment
1326    
1327 heimbach 1.39 checkpoint39
1328     o Modifications and fixes to support TAMC
1329     (mainly missing or wrong directives)
1330     o Corrected common blocks when fooling TAMC to produce adjoint I/O
1331     in addummy_in_stepping
1332     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
1333     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
1334     o Included following packages:
1335     cal: calendar
1336     exf: external forcing
1337     ecco: essential routines to control use of cal, exf
1338     (NB: this is not the full ECCO environment)
1339 heimbach 1.40 o disabled some packages by default in genmake
1340 heimbach 1.39
1341 heimbach 1.38 checkpoint38
1342     o see notes_c37_adj.txt
1343     o corrected wrong layer index in external_forcing_t
1344     o replaced the_main_loop/forward_step by the_main_loop
1345     o removed forceoutput from write_state
1346     (replaced criteria for initial/final state)
1347     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
1348 jmc 1.36
1349 jmc 1.37 checkpoint37
1350     o mdsio.F routine split and packaged in pkg/mdsio
1351     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
1352     used unless genmake -disable=mdsio)
1353     o allow a more precise surface-geopotential gradient for the atmosphere
1354     taking into account the change in space of Alpha (=1/rho) at the surface.
1355     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
1356     (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
1357     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
1358     Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
1359     [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
1360     o Time-Average diagnostics defined as a pseudo package "timeave".
1361     o pickup files : old pickup (before c35) did not work with new code (c35
1362     and after) unless activating 2 commented lines in initialise-varia.
1363     o Non-Hydrostatic pickup file Pb fixed.
1364     o bug with Rigid-lid version (since c35) fixed.
1365    
1366 jmc 1.36 checkpoint36
1367 jmc 1.37 o implement Crank-Nickelson barotropic time-stepping
1368 jmc 1.36 o recover Time-Average diagnostics
1369     o fix Pb in checkpoint (PR#19)
1370     o AIM become a standard package ; clean unused CPP_kees
1371 jmc 1.35
1372     checkpoint35
1373     o subtantial rewrite of dynamics.f
1374     o allows staggered time-stepping
1375     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
1376     o added bottom drag (linear + quadratic)
1377 heimbach 1.33
1378     checkpoint34
1379     o Modified exchange routines for correct reverse simulation.
1380     o Added verification output to comply with bug fix in impldiff.F
1381     as of c33 (exp2, natl_box).
1382     o Corrected store directives in dynamics.F
1383     o Corrected array boundaries in impldiff.F
1384     o Corrected array dimensions in gmredi.
1385     Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
1386 heimbach 1.34 o Added routine GLOBAL_SUM_INT to global_sum.F
1387 heimbach 1.33 o Added mdsio_gl.F for ECCO purposes.
1388 adcroft 1.32
1389     checkpoint33
1390     o Fixed bug in lower BC in impldiff.F
1391     o Fixed confusion about units of forcing arrays in FFIELDS.h
1392     namely Fu,Fv,Qnet,Qsw,EmPmR:
1393     - Removed verification/natl_box/code/external_fields_scale.F
1394     (did not differ from that in model/src)
1395     - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
1396     (see FFIELDS.h for description)
1397     - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
1398     kpp_calc.F and kpp_transport_t.F
1399     - Removed model/src/external_fields_scale.F and calls to it
1400     - verification/natl_box uses flux data with "atmospheric" sign so
1401     a special version of external_fields_load.F is used to
1402     change the data as it's read in. This way, the arrays
1403     have the right units and signs at all times tha a user could
1404     possibly use them.
1405     o Corrected genmake to delete a temporary file during configuration
1406 heimbach 1.31
1407     checkpoint32
1408     o Scaling of forcing fields moved from external_forcing.F to
1409     external_fields_scale.F, called directly after loading fields.
1410     o Surface relaxation terms added to surface tendency fields in
1411     extra subroutine.
1412     o impldiff.F changed to avoid storing by TAMC of huge intermediate
1413     fields.
1414     o Changes in GMRedi to comply with packaging structure.
1415     o Modifications and bug fixes in KPP package.
1416     o Verification experiment for KPP added (verification/nat_box/)
1417 heimbach 1.30
1418     checkpoint31
1419     o Packages interface brought in line with defined standard
1420     -> new routines packages_...F
1421     -> changes in initialise_fixed.F, initialise_varia.F
1422     -> enables initialisation interface for ECCO package
1423     o Rescaling of external forcing fields immediately after read
1424     (removed from external_forcing.F)
1425     -> new: surface_fields_scale.F
1426     -> affects ini_foorcing.F, external_fields_load.F
1427     o Computation of surface tendencies before tendency updates.
1428     -> new: external_forcing_surf.F
1429     o Change of variable names useGMRedi, useKPP, useECCO
1430     o Further changes in dynamics.F, impldiff.F for TAMC
1431     o Tested for experiments 0, 2, 4.
1432     - not yet tested for GMRedi.
1433     - not yet tested for KPP.
1434 adcroft 1.29
1435     checkpoint30
1436     o Updates for OBCs
1437     o New experiment for test OBCs (internal_wave)
1438     o New output.txt in verification/exp4/results/
1439     o Updates for KPP: calculation of viscosity corrected, new variables
1440     kpp_dumpFreq and kpp_taveFreq
1441     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
1442     and entry for T90 in genmake
1443 adcroft 1.28
1444     checkpoint29
1445     o packaged KPP and GM/Redi
1446 heimbach 1.27
1447     checkpoint28
1448     o Corrected initialization of hFacMin for difference vertical coordinates
1449     o Modified calculation of partial cell thickness to more robust algorithm
1450     o config_summary.F: replaced write_1D_... by write_0D_...
1451     read_write.F: added subroutines write_0D_...
1452     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
1453     included some initialisations required for TAMC.
1454     o routine calc_isoslopes: modified sqrt computation to make it
1455     differentiable for zero argument.
1456     o routines dynamics, impldiff:
1457     included store directives and tape key computations required for TAMC.
1458     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
1459 adcroft 1.26
1460     checkpoint27
1461     o fixed calc_isoslopes() to so that cancellation of terms in tensor
1462     formulation works properly with variable resolution.
1463     o restructured the calling tree between the_model_main() and dynamics()
1464     o split initialise() into initialise_fixed() and initialise_varia()
1465     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
1466     in new routine ini_psurf()
1467 adcroft 1.25
1468     checkpoint26
1469     o moved some #ifdef in optional routines to encompass everything
1470     except the argument declarations. This was using up some memory.
1471     o fixed macros like _ADT to work with both versions of Linux cpp
1472     o cleaned up some unused and uninitialized variables
1473     (helps when debugging with strict compile options)
1474     o split up CPP_EEOPTIONS.h into options and macros
1475     (macros are now in eesupp/inc/CPP_EEMACROS.h)
1476     o patch for 2 processor JAM mode
1477 adcroft 1.24
1478     checkpoint25
1479     o updates for OBCs and NH
1480     o dramatically reduced memory usage
1481     o added "JAM" routines for use on Artic network
1482     o parameterization of convection by implicit vertical diffusion
1483     o added a diagnostic of convective index
1484     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
1485     (this is was partly for OBCs and NH but also in anticipation of
1486     an explicit free-surface option)
1487     o initial state input files for U and V
1488 adcroft 1.23
1489     checkpoint24
1490     o Removed some spurious "REAL"s
1491     o Updated KPP to latest version from JPL
1492     o Added a COS(latitude) in horizontal viscosity
1493 adcroft 1.22
1494     checkpoint23
1495     o Added del^4 diffusion for salt and temperature
1496     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
1497 adcroft 1.21
1498     checkpoint22
1499     o Made many small changes: implicit none, format(i5), etc...
1500     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
1501 adcroft 1.20
1502     checkpoint21
1503     o Introduced new I/O package that supports direct-access records (mdsio.F)
1504     o Split-up mid-level I/O routines
1505     o Updated input data for experiments 0,1,2,4 and 5
1506     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
1507 adcroft 1.18
1508 adcroft 1.19 checkpoint20
1509     o Tidied up open-boundaries some more
1510     o Added non-hydrostatic code
1511     o Fixed some input data
1512     o Modified MPI start-up to work in "coupled" context.
1513    
1514 adcroft 1.18 checkpoint19
1515     o Tidied up directory structure for verification experiments.
1516     o Added new code for open boundaries.
1517     o Corrected advective terms near boundaries.
1518     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
1519     o Implemented free-slip/no-slip BCs and del^4 dissipation.
1520 adcroft 1.19 o Split default parameters out of ini_parms.F into set_defaults.F.
1521 cnh 1.17
1522     checkpoint18
1523     o Further changes for optional code generation with
1524     CPP - ugh!
1525 cnh 1.16
1526     checkpoint17
1527     o Beginning to incorporating modularity
1528     for supporting atmos. and ocean configs.
1529     o Small changes for TAMC complinace
1530     o New ultra simple test case. Barotropic box
1531     configuration "exp0".
1532 cnh 1.15
1533     checkpoint16
1534     o Minor changes to exchange routines to support
1535     accumulation in reverse mode. Adjoint of an
1536     assignment is an addition.
1537     o Changes to support compilation by TAMC (LR(1)
1538     syntax) and by g77 under Linux ( 72 character
1539     limit ).
1540 cnh 1.14
1541     checkpoint15
1542     Rewrote exchange routines to allow
1543     o General tile <-> tile connectivity.
1544     o TAMC reverse mode flag ( is this really needed? )
1545     o Variable width overlap and exchange region widths.
1546     o Hooks for sharing data via DMA, Arctic, Memory Channel,
1547     shmput/shmget, VIA, SYSV shmem and every other cool
1548     communication method.
1549 cnh 1.13
1550     checkpoint14
1551     Consistent isomorphism chages made. These allow dynamical core
1552     to support both pressure and meters as a vertical coordinate.
1553 cnh 1.12
1554     checkpoint13
1555     Release which corrects global_max problem and a couple
1556     of KGM time-averaging diagnostic errors. Also contains
1557     a double-gyre experiment setup as well as the baseline
1558     4 degree global template. The double gyre template is
1559     organised to allow it to be applied automatically to
1560     the baseline configuration.
1561 adcroft 1.11
1562     branch-point-rdot
1563     A few tidy-ups have been made bt the real point of this
1564     check-point (excuse the pun) is to allow a branch to be
1565     made for the purposes of adding the rDot alterations.
1566     I don't want to commit the rDot to the main-trunk until
1567     we've actually tested it...
1568 cnh 1.10
1569     checkpoint12
1570     Tidy up and added generic genmake script (formerly
1571     configure script).
1572     Released to testers.
1573 adcroft 1.9
1574     checkpoint11
1575     Re-arranged initialise() and introduced ini_vertical_grid()
1576     and ini_masks_etc().
1577 adcroft 1.8
1578     checkpoint10
1579     Introduced the configure script.
1580     Separated out the diags package.
1581     Added template for writing time-averages of tile/intermediate quantities.
1582     Updated SIZE.h in exp2 and made the data big-endian.
1583 adcroft 1.7
1584     checkpoint9
1585     MPI fix. Filename changes (meta/data). salbin*y stuff.
1586     General tidy-up.
1587     SST.bin SSS.bin added to verification/exp2
1588 adcroft 1.6
1589     checkpoint8
1590     Inludes time-dependant forcing and time-averaging.
1591     Works at 4x4 and 2.8125x2.8125 global
1592    
1593     checkpoint7-4degree-ref
1594     Branch from checkpoint7. Released for application to
1595     global modeling and general modeling - process studies, regional
1596     model etc..
1597     Configured for verification/exp2 - 4 degree global, two process.
1598 cnh 1.5
1599     checkpoint7
1600     Created by cnh
1601     Simple 4 degree global simulation
1602     configuration.
1603     Includes climatological wind,
1604     hydrography, bathymetry etc
1605     Does not include Heat Flux and E-P
1606 cnh 1.4
1607     checkpoint6
1608     Created by cnh
1609     merged checkpoint5 with CD and
1610     spherical polar code.
1611     Still some problems with GM Redi
1612     abd full topography.
1613 cnh 1.3
1614     checkpoint5
1615     Created by AJA
1616     contains updates to GM Redi
1617     and reordered timestepping loop
1618     for Implicit Diffusion.
1619 cnh 1.2
1620     checkpoint4
1621     Created by cnh
1622     Contains memory saving macros ( _rdxc etc..) for when
1623     grid variations are limited.
1624     Contains polynomial coeffs for EOS and knudsen program
1625     for generation.
1626    
1627 cnh 1.1 checkpoint3
1628     Created by cnh
1629     Added extra flags for runtime options
1630     Added this file
1631     Added implicit free-surface
1632     Added pre-conditioner
1633     Put compare01 into repository ( compare01/... )
1634     Put data and eedata into repository ( verification/exp1 )
1635    
1636     checkpoint2
1637     Created by AJA
1638     Added GM/Redi
1639    
1640     checkpoint1
1641     Created by AJA
1642     Restructured kloop in dynamics.F
1643     Added non-linear EOS
1644    
1645 cnh 1.2 baseline
1646     Original checked in code
1647 cnh 1.1

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