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revision 1.122 by jmc, Thu Jan 23 15:35:48 2003 UTC revision 1.235 by jmc, Wed Jan 7 22:26:05 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint52e_post
7    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
8      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
9    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
10      to work with implicit vertical advection and AB ;
11    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
12    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
13     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
14    checkpoint52e_pre
15    
16    o fix bug in impldiff when Nr=1 or Nr=2.
17    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
18    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
19    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
20      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
21    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
22    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
23    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
24    
25    checkpoint52d_post
26    o re-tiled many expts to allow comparison in multi-processor mode
27      - updated output accordingly
28      - changed hs94.128x64x5 to use intial T from file rather than use the
29        random number generator
30    o add infrastructure in model routines for fizhi and gridalt packages
31    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
32    o changes to permit hi-res, cubed-sphere, configuration
33      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
34      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
35      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
36        of surface winds for the cube
37      (A verification experiment, based on global_ocean.cs32x15, but with
38       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
39       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
40       complete with example surface forcing files and matlab scripts to look
41       at the output and compare it with that of global_ocean.cs32x15.)
42    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
43       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
44       to conform to the common rule.
45    o check-in the first version of the coupler + interfaces for multi-components
46       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
47       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
48       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
49       - ocean and atmos. share the same horizontal grid (no interpolation).
50       - exchanges between component and coupler is done in forward_step
51    o new verification experiment, cpl_aim+ocn:
52       coupled ocean - AIM atmosphere on cs32 grid.
53    
54    checkpoint52d_pre
55    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
56    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
57    
58    checkpoint52c_post
59    o Fixing OPTIONS files for use of exf:
60      - ALLOW_ECCO not needed
61      - ECCO_CPPOPTIONS.h should not be included from
62        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
63        as has been the case in the past
64      - All cal/exf related options are currently set in
65        single header file. Should remain so until we
66        agree on a consistent new policy.
67    o Removed all CPP options for cal package.
68      cal has no more CPP options.
69    o modified STOREs in GAD_ADVECTION
70    o corrected key comp. for passkey
71    
72    checkpoint52b_post
73    o new version: "thsice" of thermodynamic sea-ice pkg:
74     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
75     - modify fluxes but do not change theta directly;
76     - light cleaning of bulk_force pkg (still needed with thsice).
77     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
78       + output_thsice.txt to test thsice & bulk_force pkgs.
79    o put back grid & coriolis monitor output.
80    checkpoint52b_pre
81    
82    o call "do_the_model_io" at the beginning (=> dump initial state)
83    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
84    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
85      (need info on NUMBER_OF_PTRACERS)
86    o missing PTRACERS headers in some routines
87    o default tamc.h in pkg/autodiff supposed to crash
88      to ensure proper customization
89    
90    checkpoint52a_post
91    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
92      - moved surfaceTendencyTice from pkg/seaice to main code
93      - subroutine FREEZE_SURFACE now limits only surface temperature
94        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
95        => new output.txt for global_ocean.cs32x15 & global_with_exf
96      - keep the old version of FREEZE for backward compatibility;
97        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
98      - corresponding modifs for TAF directives
99    o added surface flux output variables to TIMEAVE_STATVARS
100    o time-averaged output for pkg/ptracers
101    o fix problem with ECCO-related divided adjoint
102      snapshot file was missing some ad-variables,
103      but no warning issued by TAF
104    
105    checkpoint52a_pre
106    o some bug fixes for #undef REAL4_IS_SLOW
107    
108    checkpoint52 = ecco_c52_e35
109    o after testing adjoints of checkpoint51u_post
110    
111    checkpoint51u_post
112    o this is the post-merge tag of the ecco-branch
113      (needs another clean checkout and re-testing)
114    o various natl_box_adjoint configs and results
115      but no input fields
116    o obcs adjoint not yet merged!
117    o adding ECCO global 1x1 and 2x2 degree configs
118    o updated/extended some store directives for seaice
119    o pkg/ecco now containes ecco-specific part of cost function
120    o top level routines the_main_loop, forward_step
121      supersede those in model/src/
122      previous input data.cost now in data.ecco
123      (new namelist ecco_cost_nml)
124    o in ctrl/ cleaned some cross-dependencies and updated CPP options
125    
126    checkpoint51t_post
127    o this is the pre-merge tag of the ecco-branch
128    
129    checkpoint51s_post
130    o cleanup: removed various obsolete #define-s
131    o pkg/grdchk
132      - renamed 'ph-grd 3' to 'grad-res'
133      - merged from ecco-branch
134        (remaining bug fixes for obcs gradient checks)
135      - additional high-precision output for testreport
136        (grep for 'precision_grdchk_result')
137    
138    checkpoint51r_post
139    o cleaned up or removed CPP_OPTIONS.h files
140    o updated results for some of the tests to reflect the new
141      optfiles (-ieee: -O0 instead of -O3)
142    
143    checkpoint51q_post
144    o cd_code:
145      - moved cd_scheme.F -> cd_code_scheme.F
146      - separate read_checkpoint from cd_code_ini_vars.F
147      - separated cd_code part from write_checkpoint
148      - updated AD_SOURCE, generated .flow
149      - added CD_CODE_VARS.h to the_main_loop
150      - Moving cd_code specific store dir.s to pkg/cd_code
151    o ctrl package totally restructured
152      - pack/unpack now optional and decoupled from
153        xx_/adxx_ I/O
154      - ctrl_pack/unpack cleaned
155        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
156      - confined inclusion of AD_CONFIG.h to where necessary.
157    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
158    
159    checkpoint51p_post
160    o create initial cd_code package
161      - WARNING: the initialization of fields within packages
162        is broken because INI_FIELDS (where READ_CHECKPOINT is
163        called) is called *before* PACKAGES_INIT_VARIABLES.
164        This seems to be backwards since
165        1) its important to initially zero the entire field including
166           the "halo" region
167        2) zeroing needs to be done *before* reading pickup info
168           and the pickup call might or might not happen in any
169           particular run
170      - this needs an overhaul for R2
171    o cleanup verification/*/code/GMREDI_OPTIONS.h
172    o cleanup testreport
173    
174    checkpoint51o_post
175    o bringing AD-related verif's up to date with genmake2
176      - carbon/
177      - global_ocean.90x40x15/
178      - hs.94.1x64x5/
179      - (front_relax/ )
180    o (more) consistent directory structure for AD-related verif.'s
181    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
182    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
183    o bug fix in find_alpha.F for MDJWF:
184      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
185        change rho -> rho-rhoConst
186      - replace call find_rho to find_rhonum
187    o initialisation of rFlx extended to full array (required by TAF)
188      and shifted to thermodynamics
189    o removed PTRACERS.h in ptracers routine
190    o added surfacetendencyPtr to S/R parameter list pracers_forcing
191    o Correcting initialisations for fVerU, fVerV.
192    o helping TAF to recognize dependency on kUp for
193      fVerU, fVerV
194    o Replacing delZ by delR in pkg/ctrl/
195    checkpoint51o_pre
196    
197    o undid all of cp51 pending some cleanups and discussion
198    o added the [#include "AD_CONFIG.h"] statement to all files that need
199       it for adjoint/tl #defines
200     o re-worked the build logic in genmake2 to support AD_CONFIG.h
201     o removed tools/genmake since it no longer works
202    
203    checkpoint51n_post
204    o modifications to make FREEZE flux visible to pkg/kpp
205      - moved surfaceTendencyTice from pkg/seaice to main code
206      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
207      - subroutine FREEZE now limits only surface temperature
208        (this means new output.txt for global_ocean.90x40x15,
209         global_ocean.cs32x15, and global_with_exf)
210    o added surface flux output variables to TIMEAVE_STATVARS
211    
212    checkpoint51n_pre
213    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
214    o added [#include "AD_CONFIG.h"] to all files that use the following
215      defines:
216      - ALLOW_ADJOINT_RUN
217      - ALLOW_TANGENTLINEAR_RUN
218      - ALLOW_ECCO_OPTIMIZATION
219    
220    checkpoint51m_post
221    o incorporating changes to get TAMC/TAF working in genmake2
222      - added new TAMC/TAF targets to the Makefile
223      - various cleanups related to package handling
224      - these changes should have no impact on the forward model
225    
226    checkpoint51l_post
227    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
228     - faster algorithm for cal_addtime.F
229     - higher precision arithmetic, where needed
230     - pkg/exf *startdate variables changed from calendar date to
231       model integration time
232    
233    checkpoint51l_pre
234    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
235    o enable to apply restoring on S & T only in a latitude band.
236    o update output (external_forcing_surf modif. change truncation errors)
237       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
238    
239    checkpoint51k_post
240    o change default to: useNHMTerms=.FALSE.
241     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
242       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
243     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
244        exp1, ideal_2D_oce
245     - change data file of oceanic exp (leave the results unchanged for now)
246       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
247    o set gravitySign automatically according to the vertical coordinate used
248      (and change sign: back to "logical" value: +1 when R increases downward)
249    o added an include barrier to the default CPP_OPTIONS.h and
250      removed the #include "PACKAGES_CONFIG.h" from it
251    o fix a bug in mom_fluxform (from chk51j_post)
252    
253    checkpoint51j_post
254    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
255    o adjusted some flow directives (dynamics, thermodynamics)
256    o added cubed-sphere case to test cost function
257    o heckpoint_lev?_directives.h now include
258      pkg-specific directives, whenever those are enabled.
259    o Moving pkg-specific flow directives to corresponding pkg
260      Moving pkg-specific differentiation list to corresponding pkg
261      Moving pkg-specific checkpoint-lev storing to corresponding pkg
262      ---> conventions are
263           - pkg_ad.flow
264           - pkg_ad_diff.list
265           - pkg_ad_check_lev?_dir.h
266    
267    checkpoint51i_post
268    o merge of the branch-genmake2
269      - knowingly breaks the older genmake
270      - automatic generation of all ALLOW_${PKG_NAME} defines
271      - new testreport supersedes older testscript
272    o large number of package inclusion and header cleanups
273    checkpoint51i_pre
274    
275    o new output for adjoin of global ocean vector invariant
276    o fix for checkpoint of thermodynamic seaice and bulk_force
277    o Steph gchem various cleanups
278    
279    checkpoint 51h_pre
280    o fixed some single quotes
281    o modify gchem pkg to be more versatile
282    o modifications to clean up dic pkg
283    o add pkg/cfc
284    
285    checkpoint51g_post
286    o provide links for ARPACK and ADM*TLM
287    o start removing verification/vero/
288    o update AD-related stuff
289      (in particular some IF-statements in model/src/ routines)
290    o adding to verification/global_ocean.90x40x15/ adjoint of
291      vector invariant setup
292    
293    checkpoint51f_post
294    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
295    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
296      of tracer Green's fucntions for ocean inversion project.
297    
298    checkpoint51f_pre
299    o Added on-the-fly spatial interpolation capability
300        "USE_EXF_INTERPOLATION" to pkg/exf.
301      - This is a temporary Cartesian-grid hack until
302        the super-duper ESMF coupler becomes available.
303      - See verification/global_with_exf/README for usage example.
304      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
305        flags and modified pkg/seaice accordingly.
306    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
307        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
308        non-local transport term.
309    
310    checkpoint51e_post
311    o pkg/mom_vecinv:
312      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
313      - add time-ave diagnostic of vorticity advection.
314    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
315    o atmospheric geopotential: - include water vapor effect;
316                                - use p^kappa in p* scaling.
317    o land pkg: read initial state from files.
318    o AIM : add stratospheric drag in the upper level
319    
320    checkpoint51d_post
321    o change function ILNBLNK (=> last non-blank char.) to return zero
322      (instead of the string length) when the string. char is empty
323    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
324    o modif's to restore TAMC compatibility
325      - avoid "_d" constructs in PARAMETER declarations
326      - avoid interrupting lines by comment lines
327    o Use cluster local disks for purely local I/O
328      vs. globally visible disks needed for ctrl stuff
329      (merged from ecco-branch)
330      - new active_file_loc... and mdsio_..._loc routines
331      - affected packages: autodiff, ctrl, grdchk, mdsio
332    
333    checkpoint51c_post
334    o introducing integer flag debugLevel
335      - debLevZero: suppress all output
336      - debLevA: standard
337      - debLevB: equivalent to current debugMode=.TRUE.
338    o introducing pathname variable mdsioLocalDir for mdsio
339      that can be specified at runtime
340      (relevant for cluster I/O to local disk)
341    `
342    >>>checkpoint51b_post
343    adjoint of ptracers
344    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
345    o extended state in checkpoint_lev?, etc.
346    o alternative ctrl/cost with tr1 or ptracer
347    o new comlev1_bibj_ptracers
348    o new ptracers.flow
349    o made ptracers_forcing same as external_forcing_s
350    o added verification for adjoint with ptracers
351      - adm. grdchk fail so far
352      - tlm. grdchk OK
353      - checked tapelev/comlev recomputations: OK
354    <<<checkpoint51b_pre
355    
356    checkpoint51a_post
357    o added code for biogeochemistry package
358      - new pkgs: dic, gchem
359      - new subroutine in ptracers
360    o modify code for biogeo packages
361      - in model/src and pkg/ptracers
362    
363    checkpoint51
364    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
365      - autodiff, ctrl, exf, grdchk, seaice
366      kept separate packages
367      - cost, ecco, obcs
368    o updating verification/internal_wave, verification/lab_sea
369      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
370    
371    checkpoint50i_post
372    o Preparing next differentiable checkpoint and sync
373      of MAIN vs. ecco-branch
374      - 1st step: this one is differentiable
375      - 2nd step: next(! not this) checkpoint will have updated packages
376                  from ecco-branch)
377    
378    checkpoint50h_post
379    o new package "land": provide surface BC for AIM.
380    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
381    o AIM: use true log-P extrapolation for near surface temp (= as in
382        F.Molteni paper) ; update aim.5l_cs output.
383    o New variable in PARM03 for more flexible pickups
384    o somewhat cleaned package initialisation sequence for
385      ctrl/ cost/ ecco/ in packages_... routines
386    
387    checkpoint50g_post
388    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
389      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
390      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
391        made the default because of faster convergence than ADI
392    
393    checkpoint50f_post
394    o exf totally restructured
395      - replaced all exf_set_ routines by one generic exf_set_gen.F
396        and made sure it's still differentiable
397      - split exf_getffields.F into new exf_bulkformulae.F
398      - exf_inscal_/exf_outscal_ suffixes consistent with field names
399      - updated adjoint/makefile and relevant verif. accordingly
400    
401    checkpoint50f_pre
402     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
403          + change Evap over land. (update aim.5l_cs output)
404     o added missing .cvsignores and made uniform across expts
405     o changed configuration of tidal_basin_2d expt
406     o added pkg/debug functions for tracing code in fatal crashes
407     o tidied pkg/monitor to use MONITOR_OPTIONS.h
408     o new fn in pkg/monitor to stop model if solution grows too big
409     o removed lots of single quotes from comments
410    
411    checkpoint50e_post
412    o make KPP work with PTRACERS
413     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
414       nearly a copy of kpp_transport_s
415     - there is no analogue to SurfaceTendencyS, so I have to use
416       gPtr(of the surface layer) instead
417    o add a new platform SunFire+mpi (SunFire 15000) to genmake
418    checkpoint50e_pre
419    
420    checkpoint50d_post
421    o change kpp output from multiple-record state files to single-record state
422      files analogous to write_state.F
423    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
424      analogous to the cg2d-related output.
425    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
426      so that writing to internal file fn (with length 512) fails.
427    checkpoint50d_pre
428    
429    checkpoint50c_post
430    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
431    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
432    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
433    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
434    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
435    
436    checkpoint50c_pre
437    Merging from release1_p13:
438    o bug fix for pkg/seaice dynamic solver
439    o Added SEAICE_initialHEFF to pkg/seaice
440    
441    checkpoint50b_post
442    o store u*,v* in gU,V instead of in guNm1,gvNm1
443    o in order to put the momForcing out of the Adams-Bashforth:
444      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
445      to timestep.F
446    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
447    o re-generate output for highly sensitive test-exp:
448       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
449    
450    checkpoint50b_pre
451    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
452    o corrected CPP option mismatch in exf_Bulk... functions for case
453      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
454    
455    checkpoint50a_post
456    o Bug fix for merging between c50 and KPP.
457      ikey was passed from thermodynamics to kpp_calc via
458      common block rather than being recomputed in kpp_calc,
459      in contradiction with new key itdkey.
460      New key ikppkey created, and tamc.h headers updated.
461    
462    checkpoint50
463    - 2nd step of merge with ecco-branch:
464      merge changes in ecco-branch back into main trunk
465    - bug fix in find_alpha
466    - more storing in gmredi_calc_tensor.F, kpp_routines.F
467    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
468    - merged some sliced AD support routines
469    
470    checkpoint49
471    merged from ecco-branch:
472    o exf:
473      - Enable initialisation of forcing fields to constant
474        (runtime) values.
475      - in exf_getffields.F
476        Reduce i-/j-loop to interior domain, discarding overlaps.
477        That also fixes wrong TAF-key computations for key_1, key_2
478        with bulf formulae.
479      - exf_init.F modify #ifdef for exf_init_evap
480      - exf_getffieldrec.F, ctrl_getrec.F
481        The following INT-usages are not safe:
482          fldsecs  = int(fldsecs/fldperiod)*fldperiod
483          fldcount = int(fldsecs/fldperiod) + 1
484        and were modified.
485    o autodiff: checkpoint_lev...
486      - updated storing for bulk formulae (some arrays were missing)
487      - added state for seaice package
488      - synchronized with main branch
489    o DIVA:
490      Modif.s in
491      - the_main_loop.F
492      - the_model_main.F
493      and added cost_final_restore.F cost_final_store.F
494      o With these changes, it is possible to fully separate
495        the first forward run to compute the cost function (mdthe_main_loop)
496        and adjoint runs over individual DIVA intervals (adthe_main_loop)
497        into separate model executions.
498        This enables better tuning of DIVA to given queue sizes.
499      o Loss of cost function value in consecutive DIVA runs is
500        fixed by storing to 'costfinal' file.
501      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
502        beginning/end of adjoint integration is accounted for.
503      The current changes apply to TAF-1.4.26.
504      TAF has one remaining bug, requiring one manual change
505      (see MITgcm manual).
506    o cal: synchronized between MAIN and ecco-branch
507    
508    checkpoint48i_post
509    o Changes to restore differentiability of code w.r.t. previous tag
510      (mostly adding new routines to make list and replacing
511      pressure by totPhiHyd).
512    o Updated and merged grdchk package
513      - has both ADM and TLM checks
514      - works for single- and multi-proc.
515      - output cleaned
516      - worked successfully for parallel DIVA
517    o genmake:
518      - Adding -platform=SP4
519      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
520    o Modif. for DIVA:
521      ctrl_unpack should not be called in intermediate DIVA interval.
522      (similar thing would apply for active files such as
523      tbar, sbar, psbar, which should not be reinitialised;
524      only relevant for ecco-branch)
525    
526    checkpoint48h_post
527    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
528    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
529    o Added SEAICE_initialHEFF to pkg/seaice
530    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
531    
532    checkpoint48g_post
533    --- EOS:
534    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
535      store total Potential in totPhyHyd for diagnostics & EOS.
536    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
537    --- Pressure/geopotential gradient:
538    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
539    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
540      ( changes results of global_ocean_pressure )
541    o NLFS + z-coord.: add eta*Rho' contribution.
542    o accurate phiHyd when using interface-W at the middle between 2 centers
543     ( changes results of ideal_2D_oce )
544    o includes r* 2nd term in potential gradient.
545    
546    checkpoint48f_post
547    Merging from release1_p12:
548    o Modifications for using pkg/exf with pkg/seaice
549      - improved description of the various forcing configurations
550      - added basic radiation bulk formulae to pkg/exf
551      - units/sign fix for evap computation in exf_getffields.F
552      - updated verification/global_with_exf/results/output.txt
553    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
554      (SBO) core products, including oceanic mass, center-of-mass,
555      angular, and bottom pressure (see pkg/sbo/README.sbo).
556    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
557      to avoid negative values in shallow regions.
558      - updated verification/natl_box/results/output.txt
559      - updated verification/lab_sea/results/output.txt
560    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
561    o Added useSingleCpuIO option (see PARAMS.h).
562    o Updated useSingleCpuIO option in mdsio_writefield.F to
563      work with multi-field files, e.g., for single-file pickup.
564    o pkg/seaice:
565      - bug fix in growth.F: QNET for no shortwave case
566      - added HeffFile for specifying initial sea-ice thickness
567      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
568    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
569      kpp_transport_t.F, forward_step.F, and the_main_loop.F
570    o pkg/seaice:
571      - adjoint-friendly modifications
572      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
573    
574    checkpoint48e_post
575    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
576    o dynamics: change definition of computational domain & adapt mom_fluxform
577      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
578    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
579        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
580        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
581        global_ocean.90x40x15 global_with_exf global_ocean_pressure
582        inverted_barometer solid-body.cs-32x32x1
583      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
584    
585    checkpoint48d_post
586    o in preparation for r*:
587     a) use pre-computed gradient of hydrostatic potential:
588        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
589     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
590        => affects results of glob_oce_pressure (different truncation error)  
591      update output.txt of ideal_2D_oce & global_ocean_pressure
592    
593    checkpoint48d_pre
594    o in preparation for r*:
595      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
596      pass the 2 comp. of the grad. as arguments to momentum S/R.
597      but for the moment, only used if it does not change the results.
598    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
599    
600    checkpoint48c_post
601    Modifications in treatment of initial flux forcing controls
602    to avoid extra storing of flux fields.
603    
604    checkpoint48c_pre
605    o Added tidal_basin_2d experiment (currently 1D!)
606    o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
607    
608    checkpoint48b_post
609    o r* coordinate added in #ifdef NONLIN_FRSURF block.
610     (modification to pressure gradient not yet implemented)
611    o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
612      (for U & V) that are used for vertical advection of momentum.
613    
614    checkpoint48a_post
615    o In preparation for r*, use temp. array to compute vertical transport
616       in flux-form momentum pkg. => change results of few test-exp.
617      Update output of: exp4, exp5, front_relax, global_ocean_pressure,
618                        lab_sea, natl_box & plume_on_slope
619    
620  checkpoint48  checkpoint48
621  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
622    
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