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revision 1.121 by heimbach, Tue Jan 21 19:44:45 2003 UTC revision 1.286 by dimitri, Mon May 3 07:12:25 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 pkg/seaice modifications
7      - changed proxy for geostrophic velocity and updated
8        verification/lab_sea/results/* accordingly
9      - removed ADI dynamic solver from pkg/seaice
10      - replaced all occurrences of 1/CSTICE or 1/CSUICE
11        they caused a segmentation fault under certain circumstances
12      - removed unused field WATR
13    o bug fix in exf-package:
14      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
15         now reflect that.
16    o small fixes in the cal-package:
17      - set reference date to first of January for the 'model'-calendar
18      - failing of cal_CheckDate in cal_FullDate now actually results in a
19        warning
20    o small modifications in exf-package to increase flexibility:
21      - change climtempfreeze from a constant to a runtime parameter that
22        is specified in data.exf_clim (default = -1.9)
23      - introduce runtime parameter windstressmax (default = 2.0) that is
24        specified in data.exf
25    o fix in pkg/thsice:
26      - update Evap (Tsf changes) to be consistent with Latent heat flux
27      - maintain snow precipitation unchanged (even if Tsf >=0).
28     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
29    
30    checkpoint52m_post
31    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
32      this does not change any of the results, because myIter=0 in swfrac always
33      lead to jwtype=2 (the default anyway), but the call makes little sense
34      as a default
35    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
36    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
37      atmospheric model (AIM) to use it ; add a "slab ocean" component.
38    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
39    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
40    o extending useSingleCpuIO option to work with new exch2 I/O format
41      - old-style, missing-tile I/O is still accessible by defining CPP
42        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
43    o monitor package can write to NetCDF files and/or STDOUT
44    o fix re-definition bug in MNC_GRID_INIT_ALL()
45    o doc/api_reference added
46      - a framework for building an API Reference Manual using all
47        the "protex" comments embedded in the code
48      - see pkg/generic_advdiff, pkg/mnc for examples
49    o MNC:
50      - make myThid the last argument for all subroutines
51      - new default for the grid files: NO halos
52      - add useMNC and other run-time flags
53      - separate per-file-group handling of the unlimited dimension
54      - early initialization of MNC w/ flags read at the eeboot stage
55        and lookup tables set in initialize_fixed
56      - write all MNC output to a freshly-created directory
57    o thermodynamics sea-ice (thsice) is now tested with testreport.
58    o test exp. advect_cs: use the standard cs32 grid ; update output.
59    o Added functionality to grdchk:
60      pick global i,j,k position (or nearest wet) where to perform check.
61    
62    checkpoint52l_post
63    o new land formulation:
64      a) use ground enthalpy as prognostic variable to ensure exact
65         energy conservation.
66      b) account for water temperature and for latent heat of freezing
67         in all processes (rain, run-off, ground storage)
68      c) compute surface and ground temperature implicitly.
69    o aim_v23 modification for new land model:
70      a) Treat separately land / ocean / sea-ice surface fluxes
71         to allow implicit computation of land & sea-ice surface temp.
72      b) add snow precipitation.
73    checkpoint52l_pre
74    
75    o fix problem (when 1 tile is empty) in min/max monitor.
76    o fix bug in timeAve (u,vZetatave in common block)
77    o no restoring terms under ice for pkg/seaice
78    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
79    o bug fix for pkg/seaice pickups
80    o change MNC call locations and add coordinate attributes
81    o mask vorticity at the corner ; affects global_ocean.cs output
82    o fix ini_curvilinear_grid ; test CS experiments with mpi
83    o aim.5l_cs: modify sea-ice fraction input file ; update output
84    o exf: Adding simple range check routine for exf fields after read
85    
86    checkpoint52k_post
87    o removed top-level directory "diags"
88      - we migrated these functions to pkg/timeave a long time ago
89    o fixed bug introduced in pkg/monitor
90    o accuracy ctrlprec = 32 insuffient for gradient checks using
91      averaged fields (I/O via cost_averages)
92      -> use ctrl.h in active_file*.F to control I/O precision.
93    o paramter list of CALL ADTHE_MAIN_LOOP
94    o added initial do_the_model_io to ecco
95    o set all ...Freq to zero after cost_final
96      taveFreq, dumpFreq, pChkptFreq
97    o MAIN and ECCO differentiability restored
98    
99    checkpoint52j_post
100    o fix nchklev in tamc.h for global_ocean...
101    o Bringing flow and store directives up-to-date
102    o Really weird thing!
103      call do_the_model_io from the_main_loop with parameters
104      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
105      TAF places a faulty re-call of initialise_varia
106      after cost_final call which should not be there!
107    checkpoint52j_pre
108    
109    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
110      error messages
111    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
112    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
113      debug output
114    o modfied mdsio_writefield.F to handle non-global files under exch2
115    o update AIM Cubed-Sphere exp (aim.5l_cs):
116      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
117    o update AIM Equatorial Channel exp:
118      use standard aim_v23 pkg and change the SST fields to be more realistic.
119    o globalFile now works with exch2
120    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
121      mon_vort3.F to make exch2 friendly with >1 tile per cube face
122    o limit timeave output for hi-res integrations
123    
124    checkpoint52i_post
125    o removed CPP_EEOPTIONS.h from verification/*/code
126    o updated the tiling for global_ocean_pressure
127    checkpoint52i_pre
128    
129    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
130      the old pkg/aim).
131    
132    checkpoint52h_pre
133    o shortened offending lines in exch2_send_rx?.template
134    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
135    o genmake2: add build & execute test for NetCDF code
136    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
137      old grid files, moved CPP_EEMACROS.h to pkg/exch2
138    o added useSingleCPUIO flag to monitor.F and mon_out.F
139    o added temporary hack for sea-ice dynamics on the cube:
140      metric terms are ignored and it is assumed that
141      there is no sea-ice on cube faces 1, 2, 4, and 5.
142    
143    checkpoint52f_post
144    o added exch2 cube routines to pkg/exch2
145    o modified hs94.cs-32x32x5 to use it
146    o added new grid files to hs94.cs-32x32x5
147    checkpoint52f_pre
148    
149    checkpoint52e_post
150    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
151      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
152    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
153      to work with implicit vertical advection and AB ;
154    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
155    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
156     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
157    checkpoint52e_pre
158    
159    o fix bug in impldiff when Nr=1 or Nr=2.
160    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
161    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
162    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
163      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
164    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
165    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
166    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
167    
168    checkpoint52d_post
169    o re-tiled many expts to allow comparison in multi-processor mode
170      - updated output accordingly
171      - changed hs94.128x64x5 to use intial T from file rather than use the
172        random number generator
173    o add infrastructure in model routines for fizhi and gridalt packages
174    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
175    o changes to permit hi-res, cubed-sphere, configuration
176      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
177      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
178      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
179        of surface winds for the cube
180      (A verification experiment, based on global_ocean.cs32x15, but with
181       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
182       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
183       complete with example surface forcing files and matlab scripts to look
184       at the output and compare it with that of global_ocean.cs32x15.)
185    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
186       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
187       to conform to the common rule.
188    o check-in the first version of the coupler + interfaces for multi-components
189       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
190       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
191       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
192       - ocean and atmos. share the same horizontal grid (no interpolation).
193       - exchanges between component and coupler is done in forward_step
194    o new verification experiment, cpl_aim+ocn:
195       coupled ocean - AIM atmosphere on cs32 grid.
196    
197    checkpoint52d_pre
198    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
199    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
200    
201    checkpoint52c_post
202    o Fixing OPTIONS files for use of exf:
203      - ALLOW_ECCO not needed
204      - ECCO_CPPOPTIONS.h should not be included from
205        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
206        as has been the case in the past
207      - All cal/exf related options are currently set in
208        single header file. Should remain so until we
209        agree on a consistent new policy.
210    o Removed all CPP options for cal package.
211      cal has no more CPP options.
212    o modified STOREs in GAD_ADVECTION
213    o corrected key comp. for passkey
214    
215    checkpoint52b_post
216    o new version: "thsice" of thermodynamic sea-ice pkg:
217     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
218     - modify fluxes but do not change theta directly;
219     - light cleaning of bulk_force pkg (still needed with thsice).
220     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
221       + output_thsice.txt to test thsice & bulk_force pkgs.
222    o put back grid & coriolis monitor output.
223    checkpoint52b_pre
224    
225    o call "do_the_model_io" at the beginning (=> dump initial state)
226    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
227    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
228      (need info on NUMBER_OF_PTRACERS)
229    o missing PTRACERS headers in some routines
230    o default tamc.h in pkg/autodiff supposed to crash
231      to ensure proper customization
232    
233    checkpoint52a_post
234    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
235      - moved surfaceTendencyTice from pkg/seaice to main code
236      - subroutine FREEZE_SURFACE now limits only surface temperature
237        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
238        => new output.txt for global_ocean.cs32x15 & global_with_exf
239      - keep the old version of FREEZE for backward compatibility;
240        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
241      - corresponding modifs for TAF directives
242    o added surface flux output variables to TIMEAVE_STATVARS
243    o time-averaged output for pkg/ptracers
244    o fix problem with ECCO-related divided adjoint
245      snapshot file was missing some ad-variables,
246      but no warning issued by TAF
247    
248    checkpoint52a_pre
249    o some bug fixes for #undef REAL4_IS_SLOW
250    
251    checkpoint52 = ecco_c52_e35
252    o after testing adjoints of checkpoint51u_post
253    
254    checkpoint51u_post
255    o this is the post-merge tag of the ecco-branch
256      (needs another clean checkout and re-testing)
257    o various natl_box_adjoint configs and results
258      but no input fields
259    o obcs adjoint not yet merged!
260    o adding ECCO global 1x1 and 2x2 degree configs
261    o updated/extended some store directives for seaice
262    o pkg/ecco now containes ecco-specific part of cost function
263    o top level routines the_main_loop, forward_step
264      supersede those in model/src/
265      previous input data.cost now in data.ecco
266      (new namelist ecco_cost_nml)
267    o in ctrl/ cleaned some cross-dependencies and updated CPP options
268    
269    checkpoint51t_post
270    o this is the pre-merge tag of the ecco-branch
271    
272    checkpoint51s_post
273    o cleanup: removed various obsolete #define-s
274    o pkg/grdchk
275      - renamed 'ph-grd 3' to 'grad-res'
276      - merged from ecco-branch
277        (remaining bug fixes for obcs gradient checks)
278      - additional high-precision output for testreport
279        (grep for 'precision_grdchk_result')
280    
281    checkpoint51r_post
282    o cleaned up or removed CPP_OPTIONS.h files
283    o updated results for some of the tests to reflect the new
284      optfiles (-ieee: -O0 instead of -O3)
285    
286    checkpoint51q_post
287    o cd_code:
288      - moved cd_scheme.F -> cd_code_scheme.F
289      - separate read_checkpoint from cd_code_ini_vars.F
290      - separated cd_code part from write_checkpoint
291      - updated AD_SOURCE, generated .flow
292      - added CD_CODE_VARS.h to the_main_loop
293      - Moving cd_code specific store dir.s to pkg/cd_code
294    o ctrl package totally restructured
295      - pack/unpack now optional and decoupled from
296        xx_/adxx_ I/O
297      - ctrl_pack/unpack cleaned
298        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
299      - confined inclusion of AD_CONFIG.h to where necessary.
300    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
301    
302    checkpoint51p_post
303    o create initial cd_code package
304      - WARNING: the initialization of fields within packages
305        is broken because INI_FIELDS (where READ_CHECKPOINT is
306        called) is called *before* PACKAGES_INIT_VARIABLES.
307        This seems to be backwards since
308        1) its important to initially zero the entire field including
309           the "halo" region
310        2) zeroing needs to be done *before* reading pickup info
311           and the pickup call might or might not happen in any
312           particular run
313      - this needs an overhaul for R2
314    o cleanup verification/*/code/GMREDI_OPTIONS.h
315    o cleanup testreport
316    
317    checkpoint51o_post
318    o bringing AD-related verif's up to date with genmake2
319      - carbon/
320      - global_ocean.90x40x15/
321      - hs.94.1x64x5/
322      - (front_relax/ )
323    o (more) consistent directory structure for AD-related verif.'s
324    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
325    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
326    o bug fix in find_alpha.F for MDJWF:
327      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
328        change rho -> rho-rhoConst
329      - replace call find_rho to find_rhonum
330    o initialisation of rFlx extended to full array (required by TAF)
331      and shifted to thermodynamics
332    o removed PTRACERS.h in ptracers routine
333    o added surfacetendencyPtr to S/R parameter list pracers_forcing
334    o Correcting initialisations for fVerU, fVerV.
335    o helping TAF to recognize dependency on kUp for
336      fVerU, fVerV
337    o Replacing delZ by delR in pkg/ctrl/
338    checkpoint51o_pre
339    
340    o undid all of cp51 pending some cleanups and discussion
341    o added the [#include "AD_CONFIG.h"] statement to all files that need
342       it for adjoint/tl #defines
343     o re-worked the build logic in genmake2 to support AD_CONFIG.h
344     o removed tools/genmake since it no longer works
345    
346    checkpoint51n_post
347    o modifications to make FREEZE flux visible to pkg/kpp
348      - moved surfaceTendencyTice from pkg/seaice to main code
349      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
350      - subroutine FREEZE now limits only surface temperature
351        (this means new output.txt for global_ocean.90x40x15,
352         global_ocean.cs32x15, and global_with_exf)
353    o added surface flux output variables to TIMEAVE_STATVARS
354    
355    checkpoint51n_pre
356    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
357    o added [#include "AD_CONFIG.h"] to all files that use the following
358      defines:
359      - ALLOW_ADJOINT_RUN
360      - ALLOW_TANGENTLINEAR_RUN
361      - ALLOW_ECCO_OPTIMIZATION
362    
363    checkpoint51m_post
364    o incorporating changes to get TAMC/TAF working in genmake2
365      - added new TAMC/TAF targets to the Makefile
366      - various cleanups related to package handling
367      - these changes should have no impact on the forward model
368    
369    checkpoint51l_post
370    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
371     - faster algorithm for cal_addtime.F
372     - higher precision arithmetic, where needed
373     - pkg/exf *startdate variables changed from calendar date to
374       model integration time
375    
376    checkpoint51l_pre
377    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
378    o enable to apply restoring on S & T only in a latitude band.
379    o update output (external_forcing_surf modif. change truncation errors)
380       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
381    
382    checkpoint51k_post
383    o change default to: useNHMTerms=.FALSE.
384     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
385       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
386     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
387        exp1, ideal_2D_oce
388     - change data file of oceanic exp (leave the results unchanged for now)
389       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
390    o set gravitySign automatically according to the vertical coordinate used
391      (and change sign: back to "logical" value: +1 when R increases downward)
392    o added an include barrier to the default CPP_OPTIONS.h and
393      removed the #include "PACKAGES_CONFIG.h" from it
394    o fix a bug in mom_fluxform (from chk51j_post)
395    
396    checkpoint51j_post
397    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
398    o adjusted some flow directives (dynamics, thermodynamics)
399    o added cubed-sphere case to test cost function
400    o heckpoint_lev?_directives.h now include
401      pkg-specific directives, whenever those are enabled.
402    o Moving pkg-specific flow directives to corresponding pkg
403      Moving pkg-specific differentiation list to corresponding pkg
404      Moving pkg-specific checkpoint-lev storing to corresponding pkg
405      ---> conventions are
406           - pkg_ad.flow
407           - pkg_ad_diff.list
408           - pkg_ad_check_lev?_dir.h
409    
410    checkpoint51i_post
411    o merge of the branch-genmake2
412      - knowingly breaks the older genmake
413      - automatic generation of all ALLOW_${PKG_NAME} defines
414      - new testreport supersedes older testscript
415    o large number of package inclusion and header cleanups
416    checkpoint51i_pre
417    
418    o new output for adjoin of global ocean vector invariant
419    o fix for checkpoint of thermodynamic seaice and bulk_force
420    o Steph gchem various cleanups
421    
422    checkpoint 51h_pre
423    o fixed some single quotes
424    o modify gchem pkg to be more versatile
425    o modifications to clean up dic pkg
426    o add pkg/cfc
427    
428    checkpoint51g_post
429    o provide links for ARPACK and ADM*TLM
430    o start removing verification/vero/
431    o update AD-related stuff
432      (in particular some IF-statements in model/src/ routines)
433    o adding to verification/global_ocean.90x40x15/ adjoint of
434      vector invariant setup
435    
436    checkpoint51f_post
437    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
438    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
439      of tracer Green's fucntions for ocean inversion project.
440    
441    checkpoint51f_pre
442    o Added on-the-fly spatial interpolation capability
443        "USE_EXF_INTERPOLATION" to pkg/exf.
444      - This is a temporary Cartesian-grid hack until
445        the super-duper ESMF coupler becomes available.
446      - See verification/global_with_exf/README for usage example.
447      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
448        flags and modified pkg/seaice accordingly.
449    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
450        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
451        non-local transport term.
452    
453    checkpoint51e_post
454    o pkg/mom_vecinv:
455      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
456      - add time-ave diagnostic of vorticity advection.
457    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
458    o atmospheric geopotential: - include water vapor effect;
459                                - use p^kappa in p* scaling.
460    o land pkg: read initial state from files.
461    o AIM : add stratospheric drag in the upper level
462    
463    checkpoint51d_post
464    o change function ILNBLNK (=> last non-blank char.) to return zero
465      (instead of the string length) when the string. char is empty
466    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
467    o modif's to restore TAMC compatibility
468      - avoid "_d" constructs in PARAMETER declarations
469      - avoid interrupting lines by comment lines
470    o Use cluster local disks for purely local I/O
471      vs. globally visible disks needed for ctrl stuff
472      (merged from ecco-branch)
473      - new active_file_loc... and mdsio_..._loc routines
474      - affected packages: autodiff, ctrl, grdchk, mdsio
475    
476    checkpoint51c_post
477    o introducing integer flag debugLevel
478      - debLevZero: suppress all output
479      - debLevA: standard
480      - debLevB: equivalent to current debugMode=.TRUE.
481    o introducing pathname variable mdsioLocalDir for mdsio
482      that can be specified at runtime
483      (relevant for cluster I/O to local disk)
484    `
485    >>>checkpoint51b_post
486    adjoint of ptracers
487    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
488    o extended state in checkpoint_lev?, etc.
489    o alternative ctrl/cost with tr1 or ptracer
490    o new comlev1_bibj_ptracers
491    o new ptracers.flow
492    o made ptracers_forcing same as external_forcing_s
493    o added verification for adjoint with ptracers
494      - adm. grdchk fail so far
495      - tlm. grdchk OK
496      - checked tapelev/comlev recomputations: OK
497    <<<checkpoint51b_pre
498    
499    checkpoint51a_post
500    o added code for biogeochemistry package
501      - new pkgs: dic, gchem
502      - new subroutine in ptracers
503    o modify code for biogeo packages
504      - in model/src and pkg/ptracers
505    
506    checkpoint51
507    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
508      - autodiff, ctrl, exf, grdchk, seaice
509      kept separate packages
510      - cost, ecco, obcs
511    o updating verification/internal_wave, verification/lab_sea
512      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
513    
514    checkpoint50i_post
515    o Preparing next differentiable checkpoint and sync
516      of MAIN vs. ecco-branch
517      - 1st step: this one is differentiable
518      - 2nd step: next(! not this) checkpoint will have updated packages
519                  from ecco-branch)
520    
521    checkpoint50h_post
522    o new package "land": provide surface BC for AIM.
523    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
524    o AIM: use true log-P extrapolation for near surface temp (= as in
525        F.Molteni paper) ; update aim.5l_cs output.
526    o New variable in PARM03 for more flexible pickups
527    o somewhat cleaned package initialisation sequence for
528      ctrl/ cost/ ecco/ in packages_... routines
529    
530    checkpoint50g_post
531    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
532      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
533      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
534        made the default because of faster convergence than ADI
535    
536    checkpoint50f_post
537    o exf totally restructured
538      - replaced all exf_set_ routines by one generic exf_set_gen.F
539        and made sure it's still differentiable
540      - split exf_getffields.F into new exf_bulkformulae.F
541      - exf_inscal_/exf_outscal_ suffixes consistent with field names
542      - updated adjoint/makefile and relevant verif. accordingly
543    
544    checkpoint50f_pre
545     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
546          + change Evap over land. (update aim.5l_cs output)
547     o added missing .cvsignores and made uniform across expts
548     o changed configuration of tidal_basin_2d expt
549     o added pkg/debug functions for tracing code in fatal crashes
550     o tidied pkg/monitor to use MONITOR_OPTIONS.h
551     o new fn in pkg/monitor to stop model if solution grows too big
552     o removed lots of single quotes from comments
553    
554    checkpoint50e_post
555    o make KPP work with PTRACERS
556     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
557       nearly a copy of kpp_transport_s
558     - there is no analogue to SurfaceTendencyS, so I have to use
559       gPtr(of the surface layer) instead
560    o add a new platform SunFire+mpi (SunFire 15000) to genmake
561    checkpoint50e_pre
562    
563    checkpoint50d_post
564    o change kpp output from multiple-record state files to single-record state
565      files analogous to write_state.F
566    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
567      analogous to the cg2d-related output.
568    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
569      so that writing to internal file fn (with length 512) fails.
570    checkpoint50d_pre
571    
572    checkpoint50c_post
573    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
574    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
575    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
576    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
577    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
578    
579    checkpoint50c_pre
580    Merging from release1_p13:
581    o bug fix for pkg/seaice dynamic solver
582    o Added SEAICE_initialHEFF to pkg/seaice
583    
584    checkpoint50b_post
585    o store u*,v* in gU,V instead of in guNm1,gvNm1
586    o in order to put the momForcing out of the Adams-Bashforth:
587      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
588      to timestep.F
589    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
590    o re-generate output for highly sensitive test-exp:
591       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
592    
593    checkpoint50b_pre
594    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
595    o corrected CPP option mismatch in exf_Bulk... functions for case
596      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
597    
598    checkpoint50a_post
599    o Bug fix for merging between c50 and KPP.
600      ikey was passed from thermodynamics to kpp_calc via
601      common block rather than being recomputed in kpp_calc,
602      in contradiction with new key itdkey.
603      New key ikppkey created, and tamc.h headers updated.
604    
605    checkpoint50
606    - 2nd step of merge with ecco-branch:
607      merge changes in ecco-branch back into main trunk
608    - bug fix in find_alpha
609    - more storing in gmredi_calc_tensor.F, kpp_routines.F
610    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
611    - merged some sliced AD support routines
612    
613    checkpoint49
614    merged from ecco-branch:
615    o exf:
616      - Enable initialisation of forcing fields to constant
617        (runtime) values.
618      - in exf_getffields.F
619        Reduce i-/j-loop to interior domain, discarding overlaps.
620        That also fixes wrong TAF-key computations for key_1, key_2
621        with bulf formulae.
622      - exf_init.F modify #ifdef for exf_init_evap
623      - exf_getffieldrec.F, ctrl_getrec.F
624        The following INT-usages are not safe:
625          fldsecs  = int(fldsecs/fldperiod)*fldperiod
626          fldcount = int(fldsecs/fldperiod) + 1
627        and were modified.
628    o autodiff: checkpoint_lev...
629      - updated storing for bulk formulae (some arrays were missing)
630      - added state for seaice package
631      - synchronized with main branch
632    o DIVA:
633      Modif.s in
634      - the_main_loop.F
635      - the_model_main.F
636      and added cost_final_restore.F cost_final_store.F
637      o With these changes, it is possible to fully separate
638        the first forward run to compute the cost function (mdthe_main_loop)
639        and adjoint runs over individual DIVA intervals (adthe_main_loop)
640        into separate model executions.
641        This enables better tuning of DIVA to given queue sizes.
642      o Loss of cost function value in consecutive DIVA runs is
643        fixed by storing to 'costfinal' file.
644      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
645        beginning/end of adjoint integration is accounted for.
646      The current changes apply to TAF-1.4.26.
647      TAF has one remaining bug, requiring one manual change
648      (see MITgcm manual).
649    o cal: synchronized between MAIN and ecco-branch
650    
651    checkpoint48i_post
652    o Changes to restore differentiability of code w.r.t. previous tag
653      (mostly adding new routines to make list and replacing
654      pressure by totPhiHyd).
655    o Updated and merged grdchk package
656      - has both ADM and TLM checks
657      - works for single- and multi-proc.
658      - output cleaned
659      - worked successfully for parallel DIVA
660    o genmake:
661      - Adding -platform=SP4
662      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
663    o Modif. for DIVA:
664      ctrl_unpack should not be called in intermediate DIVA interval.
665      (similar thing would apply for active files such as
666      tbar, sbar, psbar, which should not be reinitialised;
667      only relevant for ecco-branch)
668    
669    checkpoint48h_post
670    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
671    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
672    o Added SEAICE_initialHEFF to pkg/seaice
673    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
674    
675    checkpoint48g_post
676    --- EOS:
677    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
678      store total Potential in totPhyHyd for diagnostics & EOS.
679    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
680    --- Pressure/geopotential gradient:
681    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
682    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
683      ( changes results of global_ocean_pressure )
684    o NLFS + z-coord.: add eta*Rho' contribution.
685    o accurate phiHyd when using interface-W at the middle between 2 centers
686     ( changes results of ideal_2D_oce )
687    o includes r* 2nd term in potential gradient.
688    
689    checkpoint48f_post
690    Merging from release1_p12:
691    o Modifications for using pkg/exf with pkg/seaice
692      - improved description of the various forcing configurations
693      - added basic radiation bulk formulae to pkg/exf
694      - units/sign fix for evap computation in exf_getffields.F
695      - updated verification/global_with_exf/results/output.txt
696    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
697      (SBO) core products, including oceanic mass, center-of-mass,
698      angular, and bottom pressure (see pkg/sbo/README.sbo).
699    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
700      to avoid negative values in shallow regions.
701      - updated verification/natl_box/results/output.txt
702      - updated verification/lab_sea/results/output.txt
703    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
704    o Added useSingleCpuIO option (see PARAMS.h).
705    o Updated useSingleCpuIO option in mdsio_writefield.F to
706      work with multi-field files, e.g., for single-file pickup.
707    o pkg/seaice:
708      - bug fix in growth.F: QNET for no shortwave case
709      - added HeffFile for specifying initial sea-ice thickness
710      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
711    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
712      kpp_transport_t.F, forward_step.F, and the_main_loop.F
713    o pkg/seaice:
714      - adjoint-friendly modifications
715      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
716    
717    checkpoint48e_post
718    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
719    o dynamics: change definition of computational domain & adapt mom_fluxform
720      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
721    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
722        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
723        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
724        global_ocean.90x40x15 global_with_exf global_ocean_pressure
725        inverted_barometer solid-body.cs-32x32x1
726      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
727    
728    checkpoint48d_post
729    o in preparation for r*:
730     a) use pre-computed gradient of hydrostatic potential:
731        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
732     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
733        => affects results of glob_oce_pressure (different truncation error)  
734      update output.txt of ideal_2D_oce & global_ocean_pressure
735    
736    checkpoint48d_pre
737    o in preparation for r*:
738      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
739      pass the 2 comp. of the grad. as arguments to momentum S/R.
740      but for the moment, only used if it does not change the results.
741    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
742    
743    checkpoint48c_post
744    Modifications in treatment of initial flux forcing controls
745    to avoid extra storing of flux fields.
746    
747    checkpoint48c_pre
748    o Added tidal_basin_2d experiment (currently 1D!)
749    o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
750    
751    checkpoint48b_post
752    o r* coordinate added in #ifdef NONLIN_FRSURF block.
753     (modification to pressure gradient not yet implemented)
754    o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
755      (for U & V) that are used for vertical advection of momentum.
756    
757    checkpoint48a_post
758    o In preparation for r*, use temp. array to compute vertical transport
759       in flux-form momentum pkg. => change results of few test-exp.
760      Update output of: exp4, exp5, front_relax, global_ocean_pressure,
761                        lab_sea, natl_box & plume_on_slope
762    
763    checkpoint48
764    o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
765    
766  checkpoint47j_post  checkpoint47j_post
767  o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.  o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
768  o moved adexch from forward_step to addummy_in_stepping  o moved adexch from forward_step to addummy_in_stepping

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