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revision 1.746 by jmc, Mon Nov 20 05:19:43 2006 UTC revision 1.877 by dimitri, Tue Sep 18 21:18:12 2007 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice: a first HSALT time stepping equation has been checked in
8    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
9      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
10      without requiring DO-IF statements
11    o pkg/thsice:
12      use continuous power-law function for partition of energy between lateral
13      melting/freezing and thinning/thickening ; old code using step function
14      still available with #undef THSICE_FRACEN_POWERLAW
15      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
16    o testreport: change AD testing : check against results/output_adm.txt
17      using same scripts as for forward test.
18    
19    checkpoint59g
20    o adjoint testing: in preparation for changing testreport:
21      - output format: cost and grad written on separated lines
22      - ad output results in directory "results" (instead of "results_ad")
23    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
24    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
25    o pkg/ecco: allow user defined cost function contributions
26    o testreport:
27      Allow to choose (per experiment) the list of tested output variables
28       and the main variable (used to issue a pass/FAIL ) ;
29      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
30      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
31      Also modify printing of summary:
32       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
33       b) echo the list of tested variables in the individual summary.txt of
34          each experiment.
35    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
36      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
37      (but still depend on the tile decompostion of the domain).
38    o pkg/seaice: change a discretization detail to make the B-grid code
39      "more symmetric". This change is likely to remove all "ridges/leads" that
40      where quasi-aligned with the grid in B-grid solutions. It may also be
41      the solution to the stress coupling issues with the B-grid.
42    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
43      remove .cvsignore from input dir. (since testreport no longer run here).
44    o pkg/thsice:
45     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
46     - fix reshaping of sea-ice just after advection:
47       melt all the ice only if ice-volume is too small.
48     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
49       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
50     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
51    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
52      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
53    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
54      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
55      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
56      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
57      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
58      -> update output.txt
59    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
60     this affects truncation error: -> update output.txt of exp:
61      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
62      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
63    
64    checkpoint59f
65    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
66    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
67      a bounded range (in forward mode)
68    o pkg/ecco, ctrl, autodiff and mom_common:
69     internal parameter controls, completements of implementations
70    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
71    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
72      (not seem any difference in testing results).
73    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
74       at face corners.
75    o pkg/generic_advdiff:
76     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
77      loop range indices for computing vertical advection tendency
78      and do the calculation in the interior only (no overlap) ;
79      for now, only implemented for SOM advection (to save CPU time).
80     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
81    o exch2 adjoint
82      First set of changes:
83      - add exch2 hand-written adjoint templates
84      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
85        This will require cleanup in pkg/autodiff/*.F
86        (changed routines currently kept separate in verif. code/)
87      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
88        that used to hide exch2 or cubed-sphere specific code
89        (commented via 'cph-exch2')
90    o pkg/seaice
91      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
92    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
93       output of global_ocean.cs32x15.thsice .
94    
95    checkpoint59e
96    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
97      for B-grid vector (not yet tested) and C-grid vector (<- only used
98      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
99    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
100      (#ifdef ALLOW_SALT_PLUME)
101    o gather_2d/scatter_2d: removed halo regions
102    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
103      scheme and the corresponding test case (under front_relax dir). For now,
104      only available with Skew-flux form and not yet tested in realistic set-up.
105      adjoint: store directives updated, but gradient checks deteriorated,
106      so maybe GM/Redi adjoint is now broken.
107    o seaice adjoint
108      * add AREA, HEFF, HSNOW as control variable
109        (should not change lab_sea results)
110      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
111    o pkg/seaice:
112      * added computation of saltFlux in seaice_growth;
113        For time being, sea ice salinity is assumed constant
114        contribution of snow flooding to freshening of sea ice is neglected.
115        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
116        defaults to 0.0 in order to maintain backward compatibility.
117        Typical values for SEAICE_salinity are 4 to 10 g/kg.
118      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
119      * added SEAICE_availHeatFrac, which specifies fraction of surface level
120        heat content used to melt or grow ice
121      * commented out cap of HICE: it helps keep ice thinner
122      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
123      * applied OBCS T/S mask to HEFFM sea ice mask
124    
125    checkpoint59d
126    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
127     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
128     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
129    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
130     and change default value of parameter "GM_Small_Number";
131     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
132       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
133       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
134    o pkg/ecco: cost function when applying pkg/smooth to controls
135    o pkg/ctrl: add forcingPrecond run time parameter
136    o pkg/seaice:
137     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
138     - fix bug in metric terms of u-equation in LSR solver (implicit part),
139       changes verification/lab_sea
140     - rearrange implicit part of u-equation in LSR solver to make it easier to
141       read, understand, and debug. This causes changes at the truncation level.
142     - fix (serious) bug in the boundary conditions (sign error in the implicit
143       part) of the LSR solver. Changes all LSR results.
144     - fixed problem with HSNOW initialization to avoid thick snow when AREA
145       is initilized with small values - does not change lab_sea results.
146     - added HsnowFile initialization capability
147    o pkg/smooth: addition to model/src and pkg/ctrl so allow
148     initialization of pkg/smooth and application to control vector
149    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
150    o dependencies: pkg/profiles requires pkg/cal
151    o pkg/profiles:
152     - added option ALLOW_PROFILES_GENERICGRID
153         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
154         that interpolation information (grid points and coefficients) is provided
155         within the netcdf input files.
156         -> sample matlab scripts can be found in MITgcm_contrib/gael
157         that allow you to prepare netcdf input files.
158     - also modified: cleaner include statements, cleaner error print statements,
159       cleaner stops when error, and more tests of the netcdf input files consistency.
160    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
161    o pkg/seaice:
162     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
163       requires a new routine: seaice_diagnostics_fill.F
164     - make sure that seaice does not move if not forced (pressure replacement
165       method, Hibler and Ip, 1995), changes results
166     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
167     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
168       It is turned off by default (=-1.), because it changes the results.
169     - make it possible to read AREA from a file, too.
170    
171    checkpoint59c
172    o add S/R and diagnostics for oceanic mixed-layer depth
173    o move GMRedi call after all vertical mixing schemes (including KPP)
174    o pkg/thsice:
175     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
176      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
177    o pkg/obcs:
178     - bug fix for balance code
179    o pkg/seaice:
180      - allow values of SEAICE_elasticParm > 1
181      - add new parameter SEAICE_evpTauRelax as an alternative
182        to SEAICE_elasticParm
183      - make lsr boundary conditions free slip (by default), changes result
184      - add code for no slip boundary conditions for lsr
185      - set minimum of zeta to zero (and not 4e8) (changes results)
186      - add a cap on AREA after advecting AREA if seaice_growth is not called
187    o change calculation of Visbeck K:
188      - no longer depend on tapering scheme; instead, compute slope (limited
189        by GM_maxSlope). this is equivalent to what was comuted before with
190        clipping or linear tappering.
191      - fix vertical averaging (wrong by 1/2 level)
192      - leave the old version (but will not be maintained) within
193        #ifdef OLD_VISBECK_CALC / #endif
194      - update output of exp. ideal_2D_oce
195    o change error catch in calc_r_star to improve vectorization
196    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
197      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
198    o adjoint:
199      Re-organized adjoint checkpointing according to Matt Mazloff
200      (but with modifs/completions/cleanups)
201      Storing is now bundled into large arrays to optimized I/O
202      (and second step in cleanup of the_main_loop)
203    
204    checkpoint59b
205    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
206      - export/import (between ocean & coupler) fields needed for ocean DIC.
207    o pkg/seaice:
208      - get rid of three more exchanges seaice_calc_viscosities (required
209        different loop boundaries in seaice_lsr and seaice_ocean_stress)
210      - bug fix in seaice_ocean_stress (update of lab_sea required)
211      - reduce loop boundaries to necessary minimum also in seaice_evp
212      - go back to the old way of computing deltaC/Z as the adjoint likes that
213        better
214    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
215      passive tracer to an Age Tracer) + update output.txt
216    o pkg/exf:
217      - implement A-grid / C-grid selection for wind-stress input files.
218      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
219      for now, in exf_bulk_largeyeager04.F only :
220      - change implementation for case where windspeed + 2. components wind-stress
221        are read-in. AND use rhoConstFresh to convert evap.
222    o pkg/seaice:
223      - use correct EXCH_UV for wind-forcing (on A-grid).
224      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
225        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
226    o pkg/exf:
227      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
228      EXF_INTERPOLATION:
229      - merge global_with_exf/code version of exf_interp_read.F
230        to the main code ;
231      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
232        reading the file ; Important: This options needs to be defined to recover
233        previous code.
234        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
235      - no longer loose real*8 precision along the way when using exf_iprec=64.
236    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
237      - change discretisation of evp-solver in order to avoid another exchange
238        (changes lab_sea) and clean up a little
239      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
240        help the adjoint (this also changes the results slightly)
241      - add a few "_d 0" where they had been missing in seaice_evp.F
242      - cleaning up: remove unused seaice_calc_rhs.F
243    o pkg/exf: some cleaning-up:
244      - change various "constants" into runtime parameters
245      - cleaned-up Large&Yeager04 routine which should eventually
246        replace exf_bulkformulae.F (changed names of S/R and CPP)
247        and merged various ALLOW_ATM_WIND options
248     only used with thsice pkg (in thsice_get_exf.F):
249      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
250        which are used when useStabilityFct_overIce=TRUE (= the default)
251      - change default values of ice & snow emissivity and scale downward LW
252        by ice & snow emissivity.
253    o pkg/thsice:
254     fix few little problems, in thsice_calc_thickn.F:
255      - growth vertically (and not laterally) if iceFrac == iceMaskMax
256      - melt only laterally if hIce < hThinIce (as the comments say)
257      and in thsice_extend.F:
258      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
259      - start to form ice as soon as the minimum ice-volume is reachable.
260     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
261      and cpl_aim+ocn
262    o pkg/kpp
263     - move computation of surface related input fields to KPP into a new
264       subroutine kpp_forcing_surf.F
265     - remove wrong (within bi,bj loops) EXCH calls.
266     - little cleaning (add argument myThid in last position, cvs header ...)
267     - for now, fix conservation problem by exchanging KPPviscAz (may not
268       be the best fix)
269    o pkg/seaice
270     - check for inconsistent evp parameter/cpp-flag combination
271     - remove leftover errIO flat for obsolete name list error handling
272    o OpenAD
273     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
274    
275    checkpoint59a
276    o pkg/seaice: some parameter clarifications and a little bit of clean up
277    o pkg/thsice: rename run-time parameters:
278       himin       -> hIceMin
279       himin0      -> hThinIce
280       hihig       -> hThickIce
281       i0          -> i0swFrac
282       transCoef   -> bMeltCoef
283       frac_energy -> fracMelting
284      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
285       with default values (for now) that do not change the results.
286      remove old version of thsice vars advection in pkg/seaice.
287    o in FFIELDS.h:
288      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
289      - make pLoad & sIceLoad always available (but still only used if
290         ATMOSPHERIC_LOADING is #define).
291    o pkg/kpp: replaced _KPP_RL with _RL
292    o bug fixes for vertical diffusivity computations when both KPP and
293        3D diffusivity arrays are used.
294    o pkg/seaice: fix bug in evp solver, while doing that
295      - change (improve?) discretization of stress computations for both
296        cgrid-lsr and evp solver
297      - add a new routine to compute strain rates
298      - the above changes lab_sea results
299      - add no slip conditions for evp solver (off by default), lsr-version
300        may follow
301      - fix exchange for shear at Z-points (does not change lab_sea)
302      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
303        (to force the user to pick a time step since there is not "safe" way
304        of choosing it)
305      - add principal stress diagnostics
306      - rearrange fields for evp a little to avoid having to call a: too many
307        exchanges and b: exchanges for stress trensor components which we do
308        not have.
309      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
310        of evp, complete rewrite for lsr case (latter is does not yet work
311        in all cases)
312    o pkg/kpp: add code to have mixing in shelf ice caverns
313      - add myThid to all kpp routines (long overdue)
314    
315    checkpoint59
316    o pkg/exf:
317      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
318        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
319      - move exf header files from lower_case.h to UPPER_CASE.h ;
320        add missing cvs Header & Name
321      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
322      - add namelist param. selectStressGridPosition, exf_monFreq
323      - retire many _CLIM routines, and remove data.exf_clim
324        + params moved to data.exf
325        + climsst, climsss now handled by exf_set_gen, i.e.
326          climss?period=0 refers to constant field,
327          climss?period=-12 to monthly forcing
328      - split up namelists in data.exf
329    o pkg/seaice:
330      - remove seaice_exch and seaice_exch_uv
331      - remove superfluous exchange of theta
332      - add myThid to seaice_budget_ocean/ice
333      - add new interface for atmospheric wind forcing (C-grid only)
334        + new routine
335        + two new field (taux, tauy for stress over ice)
336        + removed one global field (DAIRN) for C-grid case only
337    o pkg/thsise
338      - 2nd set of modifs for thsice adjoint in conjunction with exf
339    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
340    
341    checkpoint58y_post
342    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
343      vertical diffusivity, similar to that in MOM4; turned on using
344      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
345      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
346    o Added capability for 3D specification of background vertical diffusion
347      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
348      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
349      "data" file that contains the 3D vertical diffusivity coefficients.
350    o ice dynamics (pkg/seaice) with thsice thermodynamics:
351      - add code within pkg thsice to advect & diffuse sea-ice fields
352      similar to (and will replace) what has been added in  seaice_advdiff.F,
353      but: - conserving Mass, Heat & Salt.
354           - better when using non-linear advection scheme (not yet fully tested)
355           - can also be used in atmospheric set-up (for now, only the diffusion).
356    
357    checkpoint58x_post
358    o IO option for global-file compact format:
359      - add options when generating topology (utils/exch2/matlab-topology-generator)
360      - add I/O capability (pkg/mdsio).
361      - adapt utils/matlab/rdmds.m to read this format.
362      for now long-line format not yet supported by pkg/mdsio (& exch2).
363    o shelfice: add a few diagnostics
364    
365    checkpoint58w_post
366    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
367      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
368      (and replace horiVertRatio in NH code).
369      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
370                         and tutorial_plume_on_slope (sensitive to truncation)
371    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
372      directly to drive seaice model (C-grid only)
373    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
374     - reintroduce computation of wind from stress,
375     - compute tau (in exf_bulkformulae.F) from windstress averaged to
376       mass points to avoid tau = 0
377     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
378    o rdmnc.m: make it work with "global" files created with gluemnc
379    o rdmnc.m : some improvements in dealing with singleton dimension
380      (tested on all testreport mnc output files).
381    o genmake2: disable pkg/profiles if netcdf test fails.
382    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
383    o move call to cal_readparms up to make calendar parameters/variable available
384      to all packages
385    
386    checkpoint58v_post
387    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
388      useDynP_inEos_Zc tested.
389    o pkg/exf: changes to properly interpolate/mask/scale initial fields
390    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
391      and portions thereof.  See read_cs.txt for description and examples.
392    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
393      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
394      following the great-circle arc between those 2 points.
395    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
396      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
397    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
398     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
399     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
400     - still needs work (not working with some options ; efficiency to improve)
401       and serious testing.
402     - use this scheme for temperature & salinity in 2 advection test exp.:
403       advect_xy & advect_xz, respectively.
404    
405    checkpoint58u_post
406    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
407    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
408    o testreport: add option "-skipdir" to skip some test.
409    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
410      momentum calculation.
411    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
412    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
413      remove checkpoint.F and the_correction_step.F (no longer used);
414      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
415    o add option (linFSConserveTr) to correct for tracer source/sink due to
416      Linear Free surface
417    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
418    o pkg/thsice: fix reading mnc-pickups
419    
420    checkpoint58t_post
421    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
422    o pkg/mdsio:
423     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
424       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
425       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
426     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
427     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
428       either MDS_READ_FIELD or MDS_WRITE_FIELD )
429     - new S/R (to replace MDSWRITEMETA), which allows to write more
430       informations (variable names, time ...) to meta files.
431     - modify rdmds.m to give back the meta file content.
432    o pkg/diagnostics: change vertical interpolation to be safer, and more
433       flexible (define p-levels to interpolate to in data.diagnostics);
434      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
435       diagnostic pointer.
436    o pkg/seaice: more cleaning up of seaice_growth, added many comments
437    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
438    o fix multi-category seaice:
439     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
440       SEAICE_MULTICATEGORY
441     - fix short wave heat flux
442    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
443       and allow to use EVP solver. Change forward lab_sea: test both EVP
444       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
445    o Initial check-in of lab_sea adjoint
446      (very similar to natl_box_adjoint/code_seaice)
447      * used C-grid and EVP solver
448      * used KPP, GM/Redi
449      * uses inAdExact=.TRUE.
450      * gradient checks fail for both ADM and TLM
451        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
452        f.d. gradients actually seem more problematic than ADM, TLM gradients;
453        issue is related to forward mismatch between g77 an ifort
454    o pkg/seaice: overhaul of thermodynamics
455     - growth.F and groatb.F are replaced by new routine seaice_growth.F
456     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
457     - move a few global fields out of SEAICE.h into seaice_growth.F and
458       make them 2D (FICE/QNETO/ ...)
459     - remove FO (it is the same as QNETO)
460     - introduce a few local fields to avoid modifying external fields such
461       as atemp, etc.
462    
463    checkpoint58s_post
464    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
465      changed exf_set_gen.F so that
466        genperiod=0 means input file is one time-constant field and
467        genperiod=-12 means input file contains 12 monthly means
468    o CG2D: use pre-computed solver main-diagonal (stored in common block);
469      this affects truncation error ; generate new output file for exp. which
470      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
471        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
472        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
473        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
474        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
475        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
476    o start implementation of deep-atmosphere and anelastic formulation
477    o verification: remove 2nd copy of input files and use script "prepare_run"
478      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
479    o mom_common/vecinv/fluxform: fix a few initialisation isssues
480    o profiles: fix for multithreaded case
481    
482  o diagnostics: rename few diags:  o diagnostics: rename few diags:
483    s/'PRESSURE'/'RCENTER '/g    s/'PRESSURE'/'RCENTER '/g
484    s/'TICE    '/'oceFreez'/g    s/'TICE    '/'oceFreez'/g
# Line 14  o diagnostics: rename few diags: Line 489  o diagnostics: rename few diags:
489    s/DIFy/DFyE/g    s/DIFy/DFyE/g
490    and add few ocean-forcing diagnostics:    and add few ocean-forcing diagnostics:
491    atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS    atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
492    o modifications to pkg/seaice/growth.F and budget.F, which change results of
493      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
494      as actual snow thickness.  It now refers everywhere to effective snow
495      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
496    
497  checkpoint58r_post  checkpoint58r_post
498  o modifications to pkg/seaice/growth.F, which change results of  o modifications to pkg/seaice/growth.F, which change results of
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