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revision 1.60 by jmc, Sun Feb 10 20:07:14 2002 UTC revision 1.249 by dimitri, Sun Jan 25 00:31:52 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    o globalFile now works with exch2
7    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
8      mon_vort3.F to make exch2 friendly with >1 tile per cube
9      face
10    o limit timeave output for hi-res integrations
11    
12    checkpoint52i_post
13    o removed CPP_EEOPTIONS.h from verification/*/code
14    o updated the tiling for global_ocean_pressure
15    checkpoint52i_pre
16    
17    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
18      the old pkg/aim).
19    
20    checkpoint52h_pre
21    o shortened offending lines in exch2_send_rx?.template
22    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
23    o genmake2: add build & execute test for NetCDF code
24    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
25      old grid files, moved CPP_EEMACROS.h to pkg/exch2
26    o added useSingleCPUIO flag to monitor.F and mon_out.F
27    o added temporary hack for sea-ice dynamics on the cube:
28      metric terms are ignored and it is assumed that
29      there is no sea-ice on cube faces 1, 2, 4, and 5.
30    
31    checkpoint52f_post
32    o added exch2 cube routines to pkg/exch2
33    o modified hs94.cs-32x32x5 to use it
34    o added new grid files to hs94.cs-32x32x5
35    checkpoint52f_pre
36    
37    checkpoint52e_post
38    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
39      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
40    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
41      to work with implicit vertical advection and AB ;
42    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
43    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
44     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
45    checkpoint52e_pre
46    
47    o fix bug in impldiff when Nr=1 or Nr=2.
48    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
49    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
50    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
51      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
52    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
53    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
54    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
55    
56    checkpoint52d_post
57    o re-tiled many expts to allow comparison in multi-processor mode
58      - updated output accordingly
59      - changed hs94.128x64x5 to use intial T from file rather than use the
60        random number generator
61    o add infrastructure in model routines for fizhi and gridalt packages
62    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
63    o changes to permit hi-res, cubed-sphere, configuration
64      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
65      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
66      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
67        of surface winds for the cube
68      (A verification experiment, based on global_ocean.cs32x15, but with
69       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
70       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
71       complete with example surface forcing files and matlab scripts to look
72       at the output and compare it with that of global_ocean.cs32x15.)
73    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
74       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
75       to conform to the common rule.
76    o check-in the first version of the coupler + interfaces for multi-components
77       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
78       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
79       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
80       - ocean and atmos. share the same horizontal grid (no interpolation).
81       - exchanges between component and coupler is done in forward_step
82    o new verification experiment, cpl_aim+ocn:
83       coupled ocean - AIM atmosphere on cs32 grid.
84    
85    checkpoint52d_pre
86    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
87    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
88    
89    checkpoint52c_post
90    o Fixing OPTIONS files for use of exf:
91      - ALLOW_ECCO not needed
92      - ECCO_CPPOPTIONS.h should not be included from
93        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
94        as has been the case in the past
95      - All cal/exf related options are currently set in
96        single header file. Should remain so until we
97        agree on a consistent new policy.
98    o Removed all CPP options for cal package.
99      cal has no more CPP options.
100    o modified STOREs in GAD_ADVECTION
101    o corrected key comp. for passkey
102    
103    checkpoint52b_post
104    o new version: "thsice" of thermodynamic sea-ice pkg:
105     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
106     - modify fluxes but do not change theta directly;
107     - light cleaning of bulk_force pkg (still needed with thsice).
108     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
109       + output_thsice.txt to test thsice & bulk_force pkgs.
110    o put back grid & coriolis monitor output.
111    checkpoint52b_pre
112    
113    o call "do_the_model_io" at the beginning (=> dump initial state)
114    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
115    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
116      (need info on NUMBER_OF_PTRACERS)
117    o missing PTRACERS headers in some routines
118    o default tamc.h in pkg/autodiff supposed to crash
119      to ensure proper customization
120    
121    checkpoint52a_post
122    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
123      - moved surfaceTendencyTice from pkg/seaice to main code
124      - subroutine FREEZE_SURFACE now limits only surface temperature
125        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
126        => new output.txt for global_ocean.cs32x15 & global_with_exf
127      - keep the old version of FREEZE for backward compatibility;
128        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
129      - corresponding modifs for TAF directives
130    o added surface flux output variables to TIMEAVE_STATVARS
131    o time-averaged output for pkg/ptracers
132    o fix problem with ECCO-related divided adjoint
133      snapshot file was missing some ad-variables,
134      but no warning issued by TAF
135    
136    checkpoint52a_pre
137    o some bug fixes for #undef REAL4_IS_SLOW
138    
139    checkpoint52 = ecco_c52_e35
140    o after testing adjoints of checkpoint51u_post
141    
142    checkpoint51u_post
143    o this is the post-merge tag of the ecco-branch
144      (needs another clean checkout and re-testing)
145    o various natl_box_adjoint configs and results
146      but no input fields
147    o obcs adjoint not yet merged!
148    o adding ECCO global 1x1 and 2x2 degree configs
149    o updated/extended some store directives for seaice
150    o pkg/ecco now containes ecco-specific part of cost function
151    o top level routines the_main_loop, forward_step
152      supersede those in model/src/
153      previous input data.cost now in data.ecco
154      (new namelist ecco_cost_nml)
155    o in ctrl/ cleaned some cross-dependencies and updated CPP options
156    
157    checkpoint51t_post
158    o this is the pre-merge tag of the ecco-branch
159    
160    checkpoint51s_post
161    o cleanup: removed various obsolete #define-s
162    o pkg/grdchk
163      - renamed 'ph-grd 3' to 'grad-res'
164      - merged from ecco-branch
165        (remaining bug fixes for obcs gradient checks)
166      - additional high-precision output for testreport
167        (grep for 'precision_grdchk_result')
168    
169    checkpoint51r_post
170    o cleaned up or removed CPP_OPTIONS.h files
171    o updated results for some of the tests to reflect the new
172      optfiles (-ieee: -O0 instead of -O3)
173    
174    checkpoint51q_post
175    o cd_code:
176      - moved cd_scheme.F -> cd_code_scheme.F
177      - separate read_checkpoint from cd_code_ini_vars.F
178      - separated cd_code part from write_checkpoint
179      - updated AD_SOURCE, generated .flow
180      - added CD_CODE_VARS.h to the_main_loop
181      - Moving cd_code specific store dir.s to pkg/cd_code
182    o ctrl package totally restructured
183      - pack/unpack now optional and decoupled from
184        xx_/adxx_ I/O
185      - ctrl_pack/unpack cleaned
186        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
187      - confined inclusion of AD_CONFIG.h to where necessary.
188    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
189    
190    checkpoint51p_post
191    o create initial cd_code package
192      - WARNING: the initialization of fields within packages
193        is broken because INI_FIELDS (where READ_CHECKPOINT is
194        called) is called *before* PACKAGES_INIT_VARIABLES.
195        This seems to be backwards since
196        1) its important to initially zero the entire field including
197           the "halo" region
198        2) zeroing needs to be done *before* reading pickup info
199           and the pickup call might or might not happen in any
200           particular run
201      - this needs an overhaul for R2
202    o cleanup verification/*/code/GMREDI_OPTIONS.h
203    o cleanup testreport
204    
205    checkpoint51o_post
206    o bringing AD-related verif's up to date with genmake2
207      - carbon/
208      - global_ocean.90x40x15/
209      - hs.94.1x64x5/
210      - (front_relax/ )
211    o (more) consistent directory structure for AD-related verif.'s
212    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
213    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
214    o bug fix in find_alpha.F for MDJWF:
215      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
216        change rho -> rho-rhoConst
217      - replace call find_rho to find_rhonum
218    o initialisation of rFlx extended to full array (required by TAF)
219      and shifted to thermodynamics
220    o removed PTRACERS.h in ptracers routine
221    o added surfacetendencyPtr to S/R parameter list pracers_forcing
222    o Correcting initialisations for fVerU, fVerV.
223    o helping TAF to recognize dependency on kUp for
224      fVerU, fVerV
225    o Replacing delZ by delR in pkg/ctrl/
226    checkpoint51o_pre
227    
228    o undid all of cp51 pending some cleanups and discussion
229    o added the [#include "AD_CONFIG.h"] statement to all files that need
230       it for adjoint/tl #defines
231     o re-worked the build logic in genmake2 to support AD_CONFIG.h
232     o removed tools/genmake since it no longer works
233    
234    checkpoint51n_post
235    o modifications to make FREEZE flux visible to pkg/kpp
236      - moved surfaceTendencyTice from pkg/seaice to main code
237      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
238      - subroutine FREEZE now limits only surface temperature
239        (this means new output.txt for global_ocean.90x40x15,
240         global_ocean.cs32x15, and global_with_exf)
241    o added surface flux output variables to TIMEAVE_STATVARS
242    
243    checkpoint51n_pre
244    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
245    o added [#include "AD_CONFIG.h"] to all files that use the following
246      defines:
247      - ALLOW_ADJOINT_RUN
248      - ALLOW_TANGENTLINEAR_RUN
249      - ALLOW_ECCO_OPTIMIZATION
250    
251    checkpoint51m_post
252    o incorporating changes to get TAMC/TAF working in genmake2
253      - added new TAMC/TAF targets to the Makefile
254      - various cleanups related to package handling
255      - these changes should have no impact on the forward model
256    
257    checkpoint51l_post
258    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
259     - faster algorithm for cal_addtime.F
260     - higher precision arithmetic, where needed
261     - pkg/exf *startdate variables changed from calendar date to
262       model integration time
263    
264    checkpoint51l_pre
265    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
266    o enable to apply restoring on S & T only in a latitude band.
267    o update output (external_forcing_surf modif. change truncation errors)
268       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
269    
270    checkpoint51k_post
271    o change default to: useNHMTerms=.FALSE.
272     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
273       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
274     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
275        exp1, ideal_2D_oce
276     - change data file of oceanic exp (leave the results unchanged for now)
277       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
278    o set gravitySign automatically according to the vertical coordinate used
279      (and change sign: back to "logical" value: +1 when R increases downward)
280    o added an include barrier to the default CPP_OPTIONS.h and
281      removed the #include "PACKAGES_CONFIG.h" from it
282    o fix a bug in mom_fluxform (from chk51j_post)
283    
284    checkpoint51j_post
285    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
286    o adjusted some flow directives (dynamics, thermodynamics)
287    o added cubed-sphere case to test cost function
288    o heckpoint_lev?_directives.h now include
289      pkg-specific directives, whenever those are enabled.
290    o Moving pkg-specific flow directives to corresponding pkg
291      Moving pkg-specific differentiation list to corresponding pkg
292      Moving pkg-specific checkpoint-lev storing to corresponding pkg
293      ---> conventions are
294           - pkg_ad.flow
295           - pkg_ad_diff.list
296           - pkg_ad_check_lev?_dir.h
297    
298    checkpoint51i_post
299    o merge of the branch-genmake2
300      - knowingly breaks the older genmake
301      - automatic generation of all ALLOW_${PKG_NAME} defines
302      - new testreport supersedes older testscript
303    o large number of package inclusion and header cleanups
304    checkpoint51i_pre
305    
306    o new output for adjoin of global ocean vector invariant
307    o fix for checkpoint of thermodynamic seaice and bulk_force
308    o Steph gchem various cleanups
309    
310    checkpoint 51h_pre
311    o fixed some single quotes
312    o modify gchem pkg to be more versatile
313    o modifications to clean up dic pkg
314    o add pkg/cfc
315    
316    checkpoint51g_post
317    o provide links for ARPACK and ADM*TLM
318    o start removing verification/vero/
319    o update AD-related stuff
320      (in particular some IF-statements in model/src/ routines)
321    o adding to verification/global_ocean.90x40x15/ adjoint of
322      vector invariant setup
323    
324    checkpoint51f_post
325    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
326    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
327      of tracer Green's fucntions for ocean inversion project.
328    
329    checkpoint51f_pre
330    o Added on-the-fly spatial interpolation capability
331        "USE_EXF_INTERPOLATION" to pkg/exf.
332      - This is a temporary Cartesian-grid hack until
333        the super-duper ESMF coupler becomes available.
334      - See verification/global_with_exf/README for usage example.
335      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
336        flags and modified pkg/seaice accordingly.
337    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
338        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
339        non-local transport term.
340    
341    checkpoint51e_post
342    o pkg/mom_vecinv:
343      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
344      - add time-ave diagnostic of vorticity advection.
345    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
346    o atmospheric geopotential: - include water vapor effect;
347                                - use p^kappa in p* scaling.
348    o land pkg: read initial state from files.
349    o AIM : add stratospheric drag in the upper level
350    
351    checkpoint51d_post
352    o change function ILNBLNK (=> last non-blank char.) to return zero
353      (instead of the string length) when the string. char is empty
354    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
355    o modif's to restore TAMC compatibility
356      - avoid "_d" constructs in PARAMETER declarations
357      - avoid interrupting lines by comment lines
358    o Use cluster local disks for purely local I/O
359      vs. globally visible disks needed for ctrl stuff
360      (merged from ecco-branch)
361      - new active_file_loc... and mdsio_..._loc routines
362      - affected packages: autodiff, ctrl, grdchk, mdsio
363    
364    checkpoint51c_post
365    o introducing integer flag debugLevel
366      - debLevZero: suppress all output
367      - debLevA: standard
368      - debLevB: equivalent to current debugMode=.TRUE.
369    o introducing pathname variable mdsioLocalDir for mdsio
370      that can be specified at runtime
371      (relevant for cluster I/O to local disk)
372    `
373    >>>checkpoint51b_post
374    adjoint of ptracers
375    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
376    o extended state in checkpoint_lev?, etc.
377    o alternative ctrl/cost with tr1 or ptracer
378    o new comlev1_bibj_ptracers
379    o new ptracers.flow
380    o made ptracers_forcing same as external_forcing_s
381    o added verification for adjoint with ptracers
382      - adm. grdchk fail so far
383      - tlm. grdchk OK
384      - checked tapelev/comlev recomputations: OK
385    <<<checkpoint51b_pre
386    
387    checkpoint51a_post
388    o added code for biogeochemistry package
389      - new pkgs: dic, gchem
390      - new subroutine in ptracers
391    o modify code for biogeo packages
392      - in model/src and pkg/ptracers
393    
394    checkpoint51
395    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
396      - autodiff, ctrl, exf, grdchk, seaice
397      kept separate packages
398      - cost, ecco, obcs
399    o updating verification/internal_wave, verification/lab_sea
400      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
401    
402    checkpoint50i_post
403    o Preparing next differentiable checkpoint and sync
404      of MAIN vs. ecco-branch
405      - 1st step: this one is differentiable
406      - 2nd step: next(! not this) checkpoint will have updated packages
407                  from ecco-branch)
408    
409    checkpoint50h_post
410    o new package "land": provide surface BC for AIM.
411    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
412    o AIM: use true log-P extrapolation for near surface temp (= as in
413        F.Molteni paper) ; update aim.5l_cs output.
414    o New variable in PARM03 for more flexible pickups
415    o somewhat cleaned package initialisation sequence for
416      ctrl/ cost/ ecco/ in packages_... routines
417    
418    checkpoint50g_post
419    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
420      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
421      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
422        made the default because of faster convergence than ADI
423    
424    checkpoint50f_post
425    o exf totally restructured
426      - replaced all exf_set_ routines by one generic exf_set_gen.F
427        and made sure it's still differentiable
428      - split exf_getffields.F into new exf_bulkformulae.F
429      - exf_inscal_/exf_outscal_ suffixes consistent with field names
430      - updated adjoint/makefile and relevant verif. accordingly
431    
432    checkpoint50f_pre
433     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
434          + change Evap over land. (update aim.5l_cs output)
435     o added missing .cvsignores and made uniform across expts
436     o changed configuration of tidal_basin_2d expt
437     o added pkg/debug functions for tracing code in fatal crashes
438     o tidied pkg/monitor to use MONITOR_OPTIONS.h
439     o new fn in pkg/monitor to stop model if solution grows too big
440     o removed lots of single quotes from comments
441    
442    checkpoint50e_post
443    o make KPP work with PTRACERS
444     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
445       nearly a copy of kpp_transport_s
446     - there is no analogue to SurfaceTendencyS, so I have to use
447       gPtr(of the surface layer) instead
448    o add a new platform SunFire+mpi (SunFire 15000) to genmake
449    checkpoint50e_pre
450    
451    checkpoint50d_post
452    o change kpp output from multiple-record state files to single-record state
453      files analogous to write_state.F
454    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
455      analogous to the cg2d-related output.
456    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
457      so that writing to internal file fn (with length 512) fails.
458    checkpoint50d_pre
459    
460    checkpoint50c_post
461    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
462    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
463    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
464    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
465    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
466    
467    checkpoint50c_pre
468    Merging from release1_p13:
469    o bug fix for pkg/seaice dynamic solver
470    o Added SEAICE_initialHEFF to pkg/seaice
471    
472    checkpoint50b_post
473    o store u*,v* in gU,V instead of in guNm1,gvNm1
474    o in order to put the momForcing out of the Adams-Bashforth:
475      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
476      to timestep.F
477    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
478    o re-generate output for highly sensitive test-exp:
479       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
480    
481    checkpoint50b_pre
482    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
483    o corrected CPP option mismatch in exf_Bulk... functions for case
484      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
485    
486    checkpoint50a_post
487    o Bug fix for merging between c50 and KPP.
488      ikey was passed from thermodynamics to kpp_calc via
489      common block rather than being recomputed in kpp_calc,
490      in contradiction with new key itdkey.
491      New key ikppkey created, and tamc.h headers updated.
492    
493    checkpoint50
494    - 2nd step of merge with ecco-branch:
495      merge changes in ecco-branch back into main trunk
496    - bug fix in find_alpha
497    - more storing in gmredi_calc_tensor.F, kpp_routines.F
498    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
499    - merged some sliced AD support routines
500    
501    checkpoint49
502    merged from ecco-branch:
503    o exf:
504      - Enable initialisation of forcing fields to constant
505        (runtime) values.
506      - in exf_getffields.F
507        Reduce i-/j-loop to interior domain, discarding overlaps.
508        That also fixes wrong TAF-key computations for key_1, key_2
509        with bulf formulae.
510      - exf_init.F modify #ifdef for exf_init_evap
511      - exf_getffieldrec.F, ctrl_getrec.F
512        The following INT-usages are not safe:
513          fldsecs  = int(fldsecs/fldperiod)*fldperiod
514          fldcount = int(fldsecs/fldperiod) + 1
515        and were modified.
516    o autodiff: checkpoint_lev...
517      - updated storing for bulk formulae (some arrays were missing)
518      - added state for seaice package
519      - synchronized with main branch
520    o DIVA:
521      Modif.s in
522      - the_main_loop.F
523      - the_model_main.F
524      and added cost_final_restore.F cost_final_store.F
525      o With these changes, it is possible to fully separate
526        the first forward run to compute the cost function (mdthe_main_loop)
527        and adjoint runs over individual DIVA intervals (adthe_main_loop)
528        into separate model executions.
529        This enables better tuning of DIVA to given queue sizes.
530      o Loss of cost function value in consecutive DIVA runs is
531        fixed by storing to 'costfinal' file.
532      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
533        beginning/end of adjoint integration is accounted for.
534      The current changes apply to TAF-1.4.26.
535      TAF has one remaining bug, requiring one manual change
536      (see MITgcm manual).
537    o cal: synchronized between MAIN and ecco-branch
538    
539    checkpoint48i_post
540    o Changes to restore differentiability of code w.r.t. previous tag
541      (mostly adding new routines to make list and replacing
542      pressure by totPhiHyd).
543    o Updated and merged grdchk package
544      - has both ADM and TLM checks
545      - works for single- and multi-proc.
546      - output cleaned
547      - worked successfully for parallel DIVA
548    o genmake:
549      - Adding -platform=SP4
550      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
551    o Modif. for DIVA:
552      ctrl_unpack should not be called in intermediate DIVA interval.
553      (similar thing would apply for active files such as
554      tbar, sbar, psbar, which should not be reinitialised;
555      only relevant for ecco-branch)
556    
557    checkpoint48h_post
558    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
559    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
560    o Added SEAICE_initialHEFF to pkg/seaice
561    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
562    
563    checkpoint48g_post
564    --- EOS:
565    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
566      store total Potential in totPhyHyd for diagnostics & EOS.
567    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
568    --- Pressure/geopotential gradient:
569    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
570    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
571      ( changes results of global_ocean_pressure )
572    o NLFS + z-coord.: add eta*Rho' contribution.
573    o accurate phiHyd when using interface-W at the middle between 2 centers
574     ( changes results of ideal_2D_oce )
575    o includes r* 2nd term in potential gradient.
576    
577    checkpoint48f_post
578    Merging from release1_p12:
579    o Modifications for using pkg/exf with pkg/seaice
580      - improved description of the various forcing configurations
581      - added basic radiation bulk formulae to pkg/exf
582      - units/sign fix for evap computation in exf_getffields.F
583      - updated verification/global_with_exf/results/output.txt
584    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
585      (SBO) core products, including oceanic mass, center-of-mass,
586      angular, and bottom pressure (see pkg/sbo/README.sbo).
587    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
588      to avoid negative values in shallow regions.
589      - updated verification/natl_box/results/output.txt
590      - updated verification/lab_sea/results/output.txt
591    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
592    o Added useSingleCpuIO option (see PARAMS.h).
593    o Updated useSingleCpuIO option in mdsio_writefield.F to
594      work with multi-field files, e.g., for single-file pickup.
595    o pkg/seaice:
596      - bug fix in growth.F: QNET for no shortwave case
597      - added HeffFile for specifying initial sea-ice thickness
598      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
599    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
600      kpp_transport_t.F, forward_step.F, and the_main_loop.F
601    o pkg/seaice:
602      - adjoint-friendly modifications
603      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
604    
605    checkpoint48e_post
606    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
607    o dynamics: change definition of computational domain & adapt mom_fluxform
608      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
609    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
610        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
611        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
612        global_ocean.90x40x15 global_with_exf global_ocean_pressure
613        inverted_barometer solid-body.cs-32x32x1
614      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
615    
616    checkpoint48d_post
617    o in preparation for r*:
618     a) use pre-computed gradient of hydrostatic potential:
619        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
620     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
621        => affects results of glob_oce_pressure (different truncation error)  
622      update output.txt of ideal_2D_oce & global_ocean_pressure
623    
624    checkpoint48d_pre
625    o in preparation for r*:
626      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
627      pass the 2 comp. of the grad. as arguments to momentum S/R.
628      but for the moment, only used if it does not change the results.
629    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
630    
631    checkpoint48c_post
632    Modifications in treatment of initial flux forcing controls
633    to avoid extra storing of flux fields.
634    
635    checkpoint48c_pre
636    o Added tidal_basin_2d experiment (currently 1D!)
637    o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
638    
639    checkpoint48b_post
640    o r* coordinate added in #ifdef NONLIN_FRSURF block.
641     (modification to pressure gradient not yet implemented)
642    o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
643      (for U & V) that are used for vertical advection of momentum.
644    
645    checkpoint48a_post
646    o In preparation for r*, use temp. array to compute vertical transport
647       in flux-form momentum pkg. => change results of few test-exp.
648      Update output of: exp4, exp5, front_relax, global_ocean_pressure,
649                        lab_sea, natl_box & plume_on_slope
650    
651    checkpoint48
652    o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
653    
654    checkpoint47j_post
655    o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
656    o moved adexch from forward_step to addummy_in_stepping
657    o added exch in ctrl_map_...
658    o aveFreq.=0. at end of cost_final to avoid overwrite in
659      reverse checkpointing loop
660    o Yet more changes in gmredi:
661      * adgmredi_calc_tensor
662        avoiding all recomputation of gmredi_slope_limit
663      * adgmredi_x/y/rtransport
664        added flag for excessive storing to avoid recomp. of
665        u/v/rtans, dTdx/y/z
666        -> this is not really necessary and very memory-consuming
667      * adgmredi_slope_psi:
668        consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
669      * gmredi_slope_limit
670        re-activated full calculation of taperfct for case 'ac02'
671    o updating verification/ adjoints of carbon, global_ocean.90x40x15
672    
673    checkpoint47i_post
674    o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
675    o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
676      default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
677    o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
678    o gmredi: fix few bugs.
679    
680    checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
681    This will be a good checkpoint to plug into the ecco-branch.
682    o few modif.'s to get latest version adjointed
683      (mainly kick out code in ini_linear_phisurf)
684    o modif's to run adjoint with exactConserv
685    o case GM_BOLUS_ADVEC should be cleaned
686      S/R gmredi_slope_psi should be cleaned
687    o verification/carbon now has exactConserv=.TRUE.
688    
689    checkpoint47g_post
690    o time-average AIM output: becomes independent from statvars time-average
691      (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
692    o After TAF bug fix:
693      Tested adjoint of gmredi package.
694      Tests were done with checkpoint47 rather than with latest
695      checkpoint47f_post since the latter is broken for the adjoint
696      verification/carbon/ contains both ADM and TLM gradient checks.
697    Here they are, before they get changed/lost/stolen.
698    Mostly modif.'s to fix numerical sensitivities.
699    Gradient checks OK for
700    - GM_taper_scheme:
701      * clipping
702      * ac02
703      * linear
704      * glw91
705      * dm95
706      * ldd97
707    - GMREDI_OPTIONS:
708      * GM_VISBECK_VARIABLE_K
709      * GM_NON_UNITY_DIAGONAL
710      * GM_EXTRA_DIAGONAL
711      * GM_BOLUS_ADVEC
712    in conjunction with data.gmredi parameters to be checked in
713    in a few minutes under verification/carbon/code/
714    
715    checkpoint47f_post
716    Merging from release1_p10:
717    o modifications for using pkg/exf with pkg/seaice
718      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
719        and SEAICE_EXTERNAL_FLUXES
720      - pkg/exf CPP options EXF_READ_EVAP and
721        EXF_NO_BULK_COMPUTATIONS
722      - usage examples are Experiments 8 and 9 in
723        verification/lab_sea/README
724      - verification/lab_sea default experiment now uses
725        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
726    
727    checkpoint47e_post
728    o created a tag prior to creating a branch
729    
730    checkpoint47d_post
731    o fixed bug in the oceanic pressure coordinates code: vertical viscosity
732      at the bottom boundary had an erroneous half slip boundary condition
733    o added bottom drag and no slip boundary condition capabilities to
734      oceanic pressure coordinates code
735    o added new verification experiment global_ocean_pressure, this experiment is
736      also described in the tutorial section of the manual
737    checkpoint47d_pre
738    
739    checkpoint47c_post
740    o Added a verification experiment for a global cubed-sphere ocean run
741      -  verification/global_ocean.cubed32x32x30
742      -  uses pkg/therm_seaice and pkg/bulk_forcing
743    
744    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
745    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
746      when using P-coordinate; only implemented for atmospheric config.
747    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
748      NOTES: requires option NONLIN_FRSURF to be "#define".
749    o update advect_xz/results/output.txt (left from checkpoint44g_post)
750    
751    checkpoint47b_post
752    Merging from release1_p9:
753    o pkg/seaice
754      - removed GOTO's and added taf directives
755      - double precision constants to reduce the g77 (Linux)
756        to F77 (SGI) differences reported in release1_p8
757    o tools/genmake
758      - added SGI options
759    o verification/testscript
760      - updated to that of checkpoint47a_post
761    o verification/global_ocean.90x40x15/input/eedata
762      - modified for SGI f77 compatibility
763    o verification/lab_sea
764      - added description of sea-ice model
765      - added missing matlab routines
766      - added test of thermodynamics parallelization
767    
768    checkpoint47a_post
769    o new pkg: aim_v23
770     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
771       for now, keep the same surface forcing as before.
772     - Part-Cell implemented into AIM; check that Heat & Water are conserved
773     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
774     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
775    o add diagnostic of surface correction term in monitor output
776    
777    o bulk_force and therm_seaice
778    - Two packages:  bulk_force (Bulk forcing)
779      and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
780    - Earlier integration from Stephaine Dutkiewicz
781      and Patrick Heimbach.
782    - Two ifdef statements for compile time,
783       ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
784    
785    checkpoint47
786    differentiable version of checkpoint46n_post
787    o bug fix in quasihydrostaticterms
788    o * "clean" adjoint code (in terms of extensive recomputations)
789        can now be obtained for all GMREDI options (i.e. for
790        - GM_VISBECK_VARIABLE_K
791        - GM_NON_UNITY_DIAGONAL
792        - GM_EXTRA_DIAGONAL
793        - GM_BOLUS_ADVEC )
794      * However, wrong gradient check problem remains unsolved.
795      * New CPP options have been introduced for different
796        tapering schemes
797    o external_fields_load now part of differentiation list
798    o pressure needs multiple storing;
799      would be nice to have store_pressure at beginning or
800      end of forward_step, e.g. by having phiHyd global (5-dim.)
801      (NB: pressure is needed for certain cases in find_rho,
802      which is also invoked through convective_adjustment).
803    o recomputations in find_rho for cases
804     'JMD95'/'UNESCO' or 'MDJWF' are OK.
805    o #define ATMOSPHERIC_LOADING should be differentiable
806    o ini_forcing shifted to begining of initialise_varia
807    o Incorporating QNVS line search routines into MITgcm
808      (this is separate code, and therefore not under pkg)
809      lsopt/, optim/
810    o Updated verification/carbon/
811      - #define GM_VISBECK_VARIABLE_K
812      - GM_taper_scheme    = 'ldd97'    
813    
814    checkpoint46n_post
815    Merging from release1_p8:
816    o verification/natl_box:
817      updating new external_fields_load routine
818    o New package: pkg/seaice
819      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
820      The sea-ice code is based on Hibler (1979-1980).
821      Two sea-ice dynamic solvers, ADI and LSR, are included.
822      In addition to computing prognostic sea-ice variables and diagnosing
823      the forcing/external data fields that drive the ocean model,
824      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
825      The implied surface heat flux is then stored in variable
826      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
827      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
828      non-local transport term.  Because this call precedes model
829      thermodynamics, temperature under sea-ice may not be "exactly" at
830      the freezing point by the time theta is dumped or time-averaged.
831      N.B.: fairly large differences in accuracy occur across
832            different platforms/compilers; comparison between
833            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
834            generated output gives:
835       T           S           U           V
836      C D M    c        m  s        m  s        m  s        m  s
837      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
838      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
839      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
840    
841      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
842    o GAD:
843      - generated new common blocks to account for call of
844        same gad routines with differing traceridentities
845        (needed to modify tracerIdentity indices in GAD.h)
846      - generated separate common blocks for case useCubedSphereExchange
847        (Department of Futurology)
848      - parameter lists to gmredi_?transport: added tracerIdentity
849      - added new key indices to tamc.h
850    o external_fields_load:
851      - added this routine to TAF list
852      - needed to make some common blocks global and additional storing
853        along the same lines as exf package (checkpoint_lev?_directives.h)
854    o exf:
855      updated external forcing package
856      - bug fixes carried over from ecco-branch
857        (missing OBCS_OPTIONS.h in two routines)
858      - enable easy to use "no forcing".
859      - added exf I/O for atmospheric loading
860      - added exf I/O for runoff data
861      - transfered scaling between exf <-> MITgcm to exf namelist
862    o Adding new verification experiment global_with_exf.
863      This verification experiment is almost identical to the
864      global_ocean.90x40x15 experiment, except that it uses
865      the exf (and cal) package instead of the
866      external_fields_load routine (cf README file).
867    
868    checkpoint46m_post
869    o modified testscript to return -- when there are no lines of "%MON" output
870    o added new flag "quasiHydrostatic" for QH mode
871      and new routine quasihydrostaticterms()
872    o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
873      New routine: mom_u_coriolis_nh()
874    o fixed sign of non-hydrostatic metric terms in u and v equations.
875      Depend on correct sign of gravitySign.
876    o added work.pc* to .cvsignore in aim directories using ifc
877    o introduced flag for controllin non-hydrostatic metric terms
878    o removed gravitySign from PARM04
879    o switched to g77/ifc from pgf77 in aim experiments
880    
881    checkpoint46l_post
882    o made convective adjustment work with pressure coordinates:
883     - changed the direction of k-loop in convective_adjustment.F for the
884       case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
885     - adjusted the reference pressure k-index in convective_adjustment.F
886     - adjusted the convection condition in convect.F (in analogy to
887       calc_ivdc.F)
888     - convective_adjustment no longer computes anything on the halos
889     - removed the warnings about negative salinity from find_rho.F and
890       find_alpha.F; instead the new routine look_for_neg_salinity, called
891       at the beginning of find_rho, find_alpha, and find_beta, does a
892       check of the entire slice, if CPP-option
893       CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
894    checkpoint46l_pre
895    
896    checkpoint46k_post
897    o fixed the verification/global_ocean.90x40x15 experiment:
898     - new bathymetry (the world according to A., JMC, and M.)
899     - new initial fields and forcing fields (*.bin files)
900     - new POLY3.COEFFS (for the next release one should switch to a full
901       equation of state: JMD95P or MDJWF)
902     - fixed several errors and redundancies in the data file
903     - experiment uses looped cells
904     - added matlab directory with diagnostic scripts for plotting of output
905    
906    o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
907     - read AIM physics parameters from a file (data.aimphys)
908     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
909    
910    checkpoint46j_post
911    o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
912    o move wVel computation at the end of the time step, in S/R integr_continuity
913    o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
914    o update timeave pkg for wVel diagnostic.
915    checkpoint46j_pre
916    
917    checkpoint46i_post
918    o Clean up AIM package (and keep the results unchanged):
919      include CPP_OPTION and use IMPLICT NONE in all routines ;
920      declare all the variables _RL ; use _d 0 for all numerical constants.
921      use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
922    
923    checkpoint46h_post
924    o cleaned up the use of rhoNil and rhoConst.
925      - rhoNil should only appear in the LINEAR equation of state, everywhere
926        else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
927        and the dynamical equations are all divided by rhoConst
928    o introduced new parameter rhoConstFresh, a reference density of fresh
929      water, to remove the fresh water flux's dependence on rhoNil. The default
930      value is 999.8 kg/m^3
931    o cleanup up external_forcing.F and external_forcing_surf.F
932      - can now be used by both OCEANIC and OCEANICP
933    checkpoint46h_pre
934    
935     Added code to convert surface volume flux (fresh water) into
936     a mass flux when using P coordinates in the ocean (OCEANICP).
937     Note: It assumes you have set rho0=rhoConst=density of fresh water.
938    
939    checkpoint46g_post
940    o Include a new diagnostic variable phiHydLow for the ocean model
941      - in z-coordinates, it is the bottom pressure anomaly
942      - in p-coordinates, it is the sea surface elevation
943      - in both cases, these variable have global drift, reflecting the mass
944        drift in z-coordinates and the volume drift in p-coordinates
945      - included time averaging for phiHydLow, be aware of the drift!
946    o depth-dependent computation of Bo_surf for pressure coordinates
947      in the ocean (buoyancyRelation='OCEANICP')
948      - requires a new routine (FIND_RHO_SCALAR) to compute density with only
949        Theta, Salinity, and Pressure in the parameter list. This routine is
950        presently contained in find_rho.F. This routine does not give the
951        correct density for 'POLY3', which would be a z-dependent reference
952        density.
953    o cleaned up find_rho
954      - removed obsolete 'eqn' from the parameter list.
955    o added two new verification experiments: gop and goz
956      (4x4 degree global ocean, 15 layers in pressure and height coordinates)
957    checkpoint46g_pre
958    
959    checkpoint46f_post
960    o Enable tangent linear (forward mode) gradient checks:
961      - extended active file handling to g_... files
962      - added TANGENT_SIMULATION to theSimulationMode
963      - extended grdchk package accordingly
964    o added tangent linear setup in verification/carbon/code_ftl
965    o added adjoint setup in verification/front_relax/code_ad
966    
967    checkpoint46e_post
968    o Added new equation of state -> MDJWF
969      - EOS of McDougall et al., 2002, JAOT, submitted
970      - caveat: the equation of state is only valid for a smaller (more
971        realistic?) range of values than JMD95P/Z and UNESCO
972      - added masks to the calculation of pressure in store_pressure
973      - added more check values for density in check_eos (ini_eos.F), some of
974        the old check values are out of the range of the MDJWF-eos, so don't
975        expect perfect matches for those
976    checkpoint46e_pre
977    
978    checkpoint46d_post
979    o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
980      'OCEANICP', also initialised field pressure correctly in ini_eos in the
981      case of pressure coordinates. eosType='JMD95Z' in
982      combination with buoyancyRelation='OCEANICP' now causes an error.
983    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
984      in find_alpha/beta.
985    checkpoint46d_pre
986    
987    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
988      so that JMD95Z and JMD95P give approptiate static stability in find_rho.
989    
990    checkpoint46c_post
991    o Changes necessary for ocean in p-coordinates
992     -  Added new buoyancy relation = 'OCEANICP'
993     -  Added new parameters = gravitySign (this used to be contained inside
994        the factor dRdZ which I added when we first switched to R coordinates).
995     X GM/Redi is not compatible (yet)
996     X bottom drag and no-slip need to be debugged.
997    checkpoint46c_pre
998    
999    checkpoint46b_post
1000    o Added new equation of state -> JMD95Z and JMD95P
1001      - EOS of Jackett and McDougall, 1995, JAOT
1002      - moved all EOS parameters into EOS.h
1003      - new routines ini_eos.F, store_pressure.F
1004    o Added UNESCO EOS, but not recommended because it requires
1005      in-situ temperature (see JMD95)
1006    o Modified formatting for knudsen2.f in utils/knudsen2 and added
1007      unesco.f to be used with POLY3
1008    checkpoint46b_pre
1009    
1010    checkpoint46a_post
1011    o Added (atmospheric) pressure loading
1012      - new field in FFIELDS.h, etc...
1013      - new cpp flag ATMOSPHERIC_LOADING
1014    o Changed hFacC to _hFacC in calc_phi_hyd.F
1015    o Added SHORTWAVE_HEATING to some files for consistency
1016    checkpoint46a_pre
1017    
1018    checkpoint46
1019    further merges from release1_p5
1020    o new ctrl package
1021      - adopted from ECCO environment to enable optimization
1022      - added Eliassen Palm fluxes to controls
1023    o added Eliassen Palm flux controls to gradient check package
1024    o cost package
1025      - Compatible with new ctrl package
1026      - added Eliassen Palm cost hooks
1027      - modif's of existing cost functions
1028    o Adjoint-related bug fixes in kpp:
1029      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
1030      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
1031    o autodiff package
1032      - flow directives:
1033        + new for S/R do_the_model_io
1034        + enhanced for S/R checkpoint
1035        + new gmredi.flow
1036      - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
1037        disable adcommon.h/g_common.h by default.
1038      - fixed problem for adjoint of global_max
1039    o modified verification/carbon/
1040    o New setup for adjoint of global_ocean
1041    o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
1042    o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
1043    o incorporated hooks for sponge layer code (external_forcing.F)
1044    
1045    checkpoint45d_post
1046    o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
1047    o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
1048      (affects plume_on_slope "cg2d" output)
1049    o add new parameter deltaTfreesurf for free-surface time stepping
1050    o exchange gT,gS when using staggerTimeStep & GM & Oly<4
1051    o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
1052    o change phiMin in exp1 (to agree with documentation)
1053    o add new flags:
1054     - T,S forcing inside/outside Adams-Bashforth
1055     - turn off temp,salt advection and/or forcing
1056     - for each tracer, define internal flag for multiDimAdvection & A-B
1057    o monitor: change definition of KE to check conservation of Energy
1058    
1059    checkpoint45c_post
1060    o Removed f90 comments ("!")
1061    o Modified initialisations to enable exf package for MITgcm
1062      (without invoking ECCO_PACKAGE).
1063    o modifications to gradient check package (Martin Losch)
1064      - enable centered differences
1065      - modified format of standard output
1066    
1067    checkpoint45b_post
1068    o cleaned exchange calls in cg2d
1069    o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
1070    o included CPP option SINGLE_LAYER_MODE in thermodynamics
1071      to configure barotropic setup (Martin Losch)
1072    o moved some initialisations within bi,bj loop in dynamics
1073      (TAF flow dependency)
1074    o in initialise_varia, moved call packages_init_variables
1075      before convective_adjustment_init
1076      (corresponding adjustment of TAF tape initialisation).
1077    o in calc_diffusivity/calc_viscosity extended domain to full overlap.
1078    
1079    checkpoint45a_post
1080    o compute Rho over the whole domain (extend iMin,jMin indices)
1081    o specific exchange for X-slice domain (case Ny=1)
1082    o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
1083    o solve_for_pressure : set cg2d_x to zero where OBCS are applied
1084    
1085    checkpoint44h_post = checkpoint45
1086    o Fix to restore differentiability:
1087      place at which packages_init_variables is called in
1088      initialise_varia is crucial for reverse control flow.
1089    o modifications in GMRedi to enable stable adjoint
1090      (corresponding modif's in thermodynamics, dynamics)
1091    o added missing hook for sponge layer code in external_forcing
1092    o modified test cost functions
1093    o storing in gad_advection (plus removal of write(0,*)!
1094    o missing headers TR1.h added in convective_adjustment routines
1095    o errorMessageUnit set non-equal zero in eeboot
1096      (conflict on some platforms, e.g. IBM SP3)
1097    o modified carbon verif.
1098    
1099    checkpoint44h_pre
1100    o vertical grid option: allow to put the Interface at the middle between
1101      2 cell-centers ; replace delZ in pkg/kpp by drF.
1102    o GM Advective form: Tracers are advected using the residual transport (=
1103      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
1104    
1105    checkpoint44g_post
1106    o fix surface correction term in multiDimAdvection (affects plume_on_slope
1107      results) ; ifdef missing in thermodynamics.F
1108    
1109    checkpoint44f_pre,checkpoint44f_post
1110    o added PTRACERS package
1111      This allows an arbitrary number of passive tracers to be integrated
1112      forward simultaneously with the dynamicaly model.
1113      + Implemented so far:
1114        - basic forward algorithm (time-stepping, advection, diffusion, convection)
1115        - I/O and checkpointing
1116        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
1117      + Not implemented so far:
1118        - KPP
1119        - OBCS
1120      + No specific example supplied (yet) but global_ocean.90x40x15 has the
1121        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
1122        line in data.pkg.
1123      + This package is disabled by default since it increases storage.
1124    
1125    
1126    o testscript: added -cleanup option
1127    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
1128                 b) enable to filter 2D fields.
1129    
1130    checkpoint44e_pre,post
1131    o re-wrote convective adjustment to use pre-calculated weights
1132      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
1133      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
1134      Original calls to convect() still in place.
1135    
1136    chkpt44d_pre,post
1137    o added missing EXCLUDE_MONITOR flags
1138    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
1139      (incompatible typ in MIN/MAX expressions caused problems
1140      on IBM SP3)
1141    o in genmake added variable MAKEDEPEND
1142      plus resetting for case SunOS
1143    o added timer_stats.c routine for IBM SP3
1144    o removed variables in dynamics
1145    !!! I forgot to create tag chkpt44d_pre !!!
1146    !!! But chkpt44d_pre = chkpt44c_post    !!!
1147    
1148  o real fresh water flux implemented with non-linear free-surface.  o real fresh water flux implemented with non-linear free-surface.
1149    
1150  chkpt44c_pre,post  chkpt44c_pre,post

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