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revision 1.141 by heimbach, Fri Feb 28 05:21:22 2003 UTC revision 1.208 by jmc, Thu Nov 13 22:51:32 2003 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
7      - moved surfaceTendencyTice from pkg/seaice to main code
8      - subroutine FREEZE_SURFACE now limits only surface temperature
9        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
10        => new output.txt for global_ocean.cs32x15 & global_with_exf
11      - keep the old version of FREEZE for backward compatibility;
12        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
13    o added surface flux output variables to TIMEAVE_STATVARS
14    o time-averaged output for pkg/ptracers
15    
16    checkpoint52a_pre
17    o some bug fixes for #undef REAL4_IS_SLOW
18    
19    checkpoint52 = ecco_c52_e35
20    o after testing adjoints of checkpoint51u_post
21    
22    checkpoint51u_post
23    o this is the post-merge tag of the ecco-branch
24      (needs another clean checkout and re-testing)
25    o various natl_box_adjoint configs and results
26      but no input fields
27    o obcs adjoint not yet merged!
28    o adding ECCO global 1x1 and 2x2 degree configs
29    o updated/extended some store directives for seaice
30    o pkg/ecco now containes ecco-specific part of cost function
31    o top level routines the_main_loop, forward_step
32      supersede those in model/src/
33      previous input data.cost now in data.ecco
34      (new namelist ecco_cost_nml)
35    o in ctrl/ cleaned some cross-dependencies and updated CPP options
36    
37    checkpoint51t_post
38    o this is the pre-merge tag of the ecco-branch
39    
40    checkpoint51s_post
41    o cleanup: removed various obsolete #define-s
42    o pkg/grdchk
43      - renamed 'ph-grd 3' to 'grad-res'
44      - merged from ecco-branch
45        (remaining bug fixes for obcs gradient checks)
46      - additional high-precision output for testreport
47        (grep for 'precision_grdchk_result')
48    
49    checkpoint51r_post
50    o cleaned up or removed CPP_OPTIONS.h files
51    o updated results for some of the tests to reflect the new
52      optfiles (-ieee: -O0 instead of -O3)
53    
54    checkpoint51q_post
55    o cd_code:
56      - moved cd_scheme.F -> cd_code_scheme.F
57      - separate read_checkpoint from cd_code_ini_vars.F
58      - separated cd_code part from write_checkpoint
59      - updated AD_SOURCE, generated .flow
60      - added CD_CODE_VARS.h to the_main_loop
61      - Moving cd_code specific store dir.s to pkg/cd_code
62    o ctrl package totally restructured
63      - pack/unpack now optional and decoupled from
64        xx_/adxx_ I/O
65      - ctrl_pack/unpack cleaned
66        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
67      - confined inclusion of AD_CONFIG.h to where necessary.
68    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
69    
70    checkpoint51p_post
71    o create initial cd_code package
72      - WARNING: the initialization of fields within packages
73        is broken because INI_FIELDS (where READ_CHECKPOINT is
74        called) is called *before* PACKAGES_INIT_VARIABLES.
75        This seems to be backwards since
76        1) its important to initially zero the entire field including
77           the "halo" region
78        2) zeroing needs to be done *before* reading pickup info
79           and the pickup call might or might not happen in any
80           particular run
81      - this needs an overhaul for R2
82    o cleanup verification/*/code/GMREDI_OPTIONS.h
83    o cleanup testreport
84    
85    checkpoint51o_post
86    o bringing AD-related verif's up to date with genmake2
87      - carbon/
88      - global_ocean.90x40x15/
89      - hs.94.1x64x5/
90      - (front_relax/ )
91    o (more) consistent directory structure for AD-related verif.'s
92    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
93    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
94    o bug fix in find_alpha.F for MDJWF:
95      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
96        change rho -> rho-rhoConst
97      - replace call find_rho to find_rhonum
98    o initialisation of rFlx extended to full array (required by TAF)
99      and shifted to thermodynamics
100    o removed PTRACERS.h in ptracers routine
101    o added surfacetendencyPtr to S/R parameter list pracers_forcing
102    o Correcting initialisations for fVerU, fVerV.
103    o helping TAF to recognize dependency on kUp for
104      fVerU, fVerV
105    o Replacing delZ by delR in pkg/ctrl/
106    checkpoint51o_pre
107    
108    o undid all of cp51 pending some cleanups and discussion
109    o added the [#include "AD_CONFIG.h"] statement to all files that need
110       it for adjoint/tl #defines
111     o re-worked the build logic in genmake2 to support AD_CONFIG.h
112     o removed tools/genmake since it no longer works
113    
114    checkpoint51n_post
115    o modifications to make FREEZE flux visible to pkg/kpp
116      - moved surfaceTendencyTice from pkg/seaice to main code
117      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
118      - subroutine FREEZE now limits only surface temperature
119        (this means new output.txt for global_ocean.90x40x15,
120         global_ocean.cs32x15, and global_with_exf)
121    o added surface flux output variables to TIMEAVE_STATVARS
122    
123    checkpoint51n_pre
124    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
125    o added [#include "AD_CONFIG.h"] to all files that use the following
126      defines:
127      - ALLOW_ADJOINT_RUN
128      - ALLOW_TANGENTLINEAR_RUN
129      - ALLOW_ECCO_OPTIMIZATION
130    
131    checkpoint51m_post
132    o incorporating changes to get TAMC/TAF working in genmake2
133      - added new TAMC/TAF targets to the Makefile
134      - various cleanups related to package handling
135      - these changes should have no impact on the forward model
136    
137    checkpoint51l_post
138    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
139     - faster algorithm for cal_addtime.F
140     - higher precision arithmetic, where needed
141     - pkg/exf *startdate variables changed from calendar date to
142       model integration time
143    
144    checkpoint51l_pre
145    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
146    o enable to apply restoring on S & T only in a latitude band.
147    o update output (external_forcing_surf modif. change truncation errors)
148       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
149    
150    checkpoint51k_post
151    o change default to: useNHMTerms=.FALSE.
152     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
153       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
154     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
155        exp1, ideal_2D_oce
156     - change data file of oceanic exp (leave the results unchanged for now)
157       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
158    o set gravitySign automatically according to the vertical coordinate used
159      (and change sign: back to "logical" value: +1 when R increases downward)
160    o added an include barrier to the default CPP_OPTIONS.h and
161      removed the #include "PACKAGES_CONFIG.h" from it
162    o fix a bug in mom_fluxform (from chk51j_post)
163    
164    checkpoint51j_post
165    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
166    o adjusted some flow directives (dynamics, thermodynamics)
167    o added cubed-sphere case to test cost function
168    o heckpoint_lev?_directives.h now include
169      pkg-specific directives, whenever those are enabled.
170    o Moving pkg-specific flow directives to corresponding pkg
171      Moving pkg-specific differentiation list to corresponding pkg
172      Moving pkg-specific checkpoint-lev storing to corresponding pkg
173      ---> conventions are
174           - pkg_ad.flow
175           - pkg_ad_diff.list
176           - pkg_ad_check_lev?_dir.h
177    
178    checkpoint51i_post
179    o merge of the branch-genmake2
180      - knowingly breaks the older genmake
181      - automatic generation of all ALLOW_${PKG_NAME} defines
182      - new testreport supersedes older testscript
183    o large number of package inclusion and header cleanups
184    checkpoint51i_pre
185    
186    o new output for adjoin of global ocean vector invariant
187    o fix for checkpoint of thermodynamic seaice and bulk_force
188    o Steph gchem various cleanups
189    
190    checkpoint 51h_pre
191    o fixed some single quotes
192    o modify gchem pkg to be more versatile
193    o modifications to clean up dic pkg
194    o add pkg/cfc
195    
196    checkpoint51g_post
197    o provide links for ARPACK and ADM*TLM
198    o start removing verification/vero/
199    o update AD-related stuff
200      (in particular some IF-statements in model/src/ routines)
201    o adding to verification/global_ocean.90x40x15/ adjoint of
202      vector invariant setup
203    
204    checkpoint51f_post
205    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
206    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
207      of tracer Green's fucntions for ocean inversion project.
208    
209    checkpoint51f_pre
210    o Added on-the-fly spatial interpolation capability
211        "USE_EXF_INTERPOLATION" to pkg/exf.
212      - This is a temporary Cartesian-grid hack until
213        the super-duper ESMF coupler becomes available.
214      - See verification/global_with_exf/README for usage example.
215      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
216        flags and modified pkg/seaice accordingly.
217    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
218        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
219        non-local transport term.
220    
221    checkpoint51e_post
222    o pkg/mom_vecinv:
223      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
224      - add time-ave diagnostic of vorticity advection.
225    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
226    o atmospheric geopotential: - include water vapor effect;
227                                - use p^kappa in p* scaling.
228    o land pkg: read initial state from files.
229    o AIM : add stratospheric drag in the upper level
230    
231    checkpoint51d_post
232    o change function ILNBLNK (=> last non-blank char.) to return zero
233      (instead of the string length) when the string. char is empty
234    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
235    o modif's to restore TAMC compatibility
236      - avoid "_d" constructs in PARAMETER declarations
237      - avoid interrupting lines by comment lines
238    o Use cluster local disks for purely local I/O
239      vs. globally visible disks needed for ctrl stuff
240      (merged from ecco-branch)
241      - new active_file_loc... and mdsio_..._loc routines
242      - affected packages: autodiff, ctrl, grdchk, mdsio
243    
244    checkpoint51c_post
245    o introducing integer flag debugLevel
246      - debLevZero: suppress all output
247      - debLevA: standard
248      - debLevB: equivalent to current debugMode=.TRUE.
249    o introducing pathname variable mdsioLocalDir for mdsio
250      that can be specified at runtime
251      (relevant for cluster I/O to local disk)
252    `
253    >>>checkpoint51b_post
254    adjoint of ptracers
255    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
256    o extended state in checkpoint_lev?, etc.
257    o alternative ctrl/cost with tr1 or ptracer
258    o new comlev1_bibj_ptracers
259    o new ptracers.flow
260    o made ptracers_forcing same as external_forcing_s
261    o added verification for adjoint with ptracers
262      - adm. grdchk fail so far
263      - tlm. grdchk OK
264      - checked tapelev/comlev recomputations: OK
265    <<<checkpoint51b_pre
266    
267    checkpoint51a_post
268    o added code for biogeochemistry package
269      - new pkgs: dic, gchem
270      - new subroutine in ptracers
271    o modify code for biogeo packages
272      - in model/src and pkg/ptracers
273    
274    checkpoint51
275    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
276      - autodiff, ctrl, exf, grdchk, seaice
277      kept separate packages
278      - cost, ecco, obcs
279    o updating verification/internal_wave, verification/lab_sea
280      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
281    
282    checkpoint50i_post
283    o Preparing next differentiable checkpoint and sync
284      of MAIN vs. ecco-branch
285      - 1st step: this one is differentiable
286      - 2nd step: next(! not this) checkpoint will have updated packages
287                  from ecco-branch)
288    
289    checkpoint50h_post
290    o new package "land": provide surface BC for AIM.
291    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
292    o AIM: use true log-P extrapolation for near surface temp (= as in
293        F.Molteni paper) ; update aim.5l_cs output.
294    o New variable in PARM03 for more flexible pickups
295    o somewhat cleaned package initialisation sequence for
296      ctrl/ cost/ ecco/ in packages_... routines
297    
298    checkpoint50g_post
299    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
300      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
301      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
302        made the default because of faster convergence than ADI
303    
304    checkpoint50f_post
305    o exf totally restructured
306      - replaced all exf_set_ routines by one generic exf_set_gen.F
307        and made sure it's still differentiable
308      - split exf_getffields.F into new exf_bulkformulae.F
309      - exf_inscal_/exf_outscal_ suffixes consistent with field names
310      - updated adjoint/makefile and relevant verif. accordingly
311    
312    checkpoint50f_pre
313     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
314          + change Evap over land. (update aim.5l_cs output)
315     o added missing .cvsignores and made uniform across expts
316     o changed configuration of tidal_basin_2d expt
317     o added pkg/debug functions for tracing code in fatal crashes
318     o tidied pkg/monitor to use MONITOR_OPTIONS.h
319     o new fn in pkg/monitor to stop model if solution grows too big
320     o removed lots of single quotes from comments
321    
322    checkpoint50e_post
323    o make KPP work with PTRACERS
324     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
325       nearly a copy of kpp_transport_s
326     - there is no analogue to SurfaceTendencyS, so I have to use
327       gPtr(of the surface layer) instead
328    o add a new platform SunFire+mpi (SunFire 15000) to genmake
329    checkpoint50e_pre
330    
331    checkpoint50d_post
332    o change kpp output from multiple-record state files to single-record state
333      files analogous to write_state.F
334    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
335      analogous to the cg2d-related output.
336    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
337      so that writing to internal file fn (with length 512) fails.
338    checkpoint50d_pre
339    
340    checkpoint50c_post
341    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
342    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
343    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
344    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
345    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
346    
347    checkpoint50c_pre
348    Merging from release1_p13:
349    o bug fix for pkg/seaice dynamic solver
350    o Added SEAICE_initialHEFF to pkg/seaice
351    
352    checkpoint50b_post
353    o store u*,v* in gU,V instead of in guNm1,gvNm1
354    o in order to put the momForcing out of the Adams-Bashforth:
355      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
356      to timestep.F
357    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
358    o re-generate output for highly sensitive test-exp:
359       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
360    
361    checkpoint50b_pre
362    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
363    o corrected CPP option mismatch in exf_Bulk... functions for case
364      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
365    
366    checkpoint50a_post
367    o Bug fix for merging between c50 and KPP.
368      ikey was passed from thermodynamics to kpp_calc via
369      common block rather than being recomputed in kpp_calc,
370      in contradiction with new key itdkey.
371      New key ikppkey created, and tamc.h headers updated.
372    
373    checkpoint50
374    - 2nd step of merge with ecco-branch:
375      merge changes in ecco-branch back into main trunk
376    - bug fix in find_alpha
377    - more storing in gmredi_calc_tensor.F, kpp_routines.F
378    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
379    - merged some sliced AD support routines
380    
381  checkpoint49  checkpoint49
382    merged from ecco-branch:
383    o exf:
384      - Enable initialisation of forcing fields to constant
385        (runtime) values.
386      - in exf_getffields.F
387        Reduce i-/j-loop to interior domain, discarding overlaps.
388        That also fixes wrong TAF-key computations for key_1, key_2
389        with bulf formulae.
390      - exf_init.F modify #ifdef for exf_init_evap
391      - exf_getffieldrec.F, ctrl_getrec.F
392        The following INT-usages are not safe:
393          fldsecs  = int(fldsecs/fldperiod)*fldperiod
394          fldcount = int(fldsecs/fldperiod) + 1
395        and were modified.
396    o autodiff: checkpoint_lev...
397      - updated storing for bulk formulae (some arrays were missing)
398      - added state for seaice package
399      - synchronized with main branch
400    o DIVA:
401      Modif.s in
402      - the_main_loop.F
403      - the_model_main.F
404      and added cost_final_restore.F cost_final_store.F
405      o With these changes, it is possible to fully separate
406        the first forward run to compute the cost function (mdthe_main_loop)
407        and adjoint runs over individual DIVA intervals (adthe_main_loop)
408        into separate model executions.
409        This enables better tuning of DIVA to given queue sizes.
410      o Loss of cost function value in consecutive DIVA runs is
411        fixed by storing to 'costfinal' file.
412      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
413        beginning/end of adjoint integration is accounted for.
414      The current changes apply to TAF-1.4.26.
415      TAF has one remaining bug, requiring one manual change
416      (see MITgcm manual).
417    o cal: synchronized between MAIN and ecco-branch
418    
419    checkpoint48i_post
420  o Changes to restore differentiability of code w.r.t. previous tag  o Changes to restore differentiability of code w.r.t. previous tag
421    (mostly adding new routines to make list and replacing    (mostly adding new routines to make list and replacing
422    pressure by totPhiHyd).    pressure by totPhiHyd).

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