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revision 1.724 by heimbach, Wed Sep 6 18:31:32 2006 UTC revision 1.866 by jmc, Thu Aug 30 21:26:37 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 each tested exp: add a "run" directory with a standard ".cvsignore" file ;
8      remove .cvsignore from input dir. (since testreport no longer run here).
9    o pkg/thsice:
10     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
11     - fix reshaping of sea-ice just after advection:
12       melt all the ice only if ice-volume is too small.
13     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
14       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
15     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
16    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
17      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
18    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
19      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
20      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
21      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
22      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
23      -> update output.txt
24    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
25     this affects truncation error: -> update output.txt of exp:
26      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
27      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
28    
29    checkpoint59f
30    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
31    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
32      a bounded range (in forward mode)
33    o pkg/ecco, ctrl, autodiff and mom_common:
34     internal parameter controls, completements of implementations
35    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
36    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
37      (not seem any difference in testing results).
38    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
39       at face corners.
40    o pkg/generic_advdiff:
41     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
42      loop range indices for computing vertical advection tendency
43      and do the calculation in the interior only (no overlap) ;
44      for now, only implemented for SOM advection (to save CPU time).
45     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
46    o exch2 adjoint
47      First set of changes:
48      - add exch2 hand-written adjoint templates
49      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
50        This will require cleanup in pkg/autodiff/*.F
51        (changed routines currently kept separate in verif. code/)
52      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
53        that used to hide exch2 or cubed-sphere specific code
54        (commented via 'cph-exch2')
55    o pkg/seaice
56      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
57    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
58       output of global_ocean.cs32x15.thsice .
59    
60    checkpoint59e
61    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
62      for B-grid vector (not yet tested) and C-grid vector (<- only used
63      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
64    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
65      (#ifdef ALLOW_SALT_PLUME)
66    o gather_2d/scatter_2d: removed halo regions
67    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
68      scheme and the corresponding test case (under front_relax dir). For now,
69      only available with Skew-flux form and not yet tested in realistic set-up.
70      adjoint: store directives updated, but gradient checks deteriorated,
71      so maybe GM/Redi adjoint is now broken.
72    o seaice adjoint
73      * add AREA, HEFF, HSNOW as control variable
74        (should not change lab_sea results)
75      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
76    o pkg/seaice:
77      * added computation of saltFlux in seaice_growth;
78        For time being, sea ice salinity is assumed constant
79        contribution of snow flooding to freshening of sea ice is neglected.
80        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
81        defaults to 0.0 in order to maintain backward compatibility.
82        Typical values for SEAICE_salinity are 4 to 10 g/kg.
83      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
84      * added SEAICE_availHeatFrac, which specifies fraction of surface level
85        heat content used to melt or grow ice
86      * commented out cap of HICE: it helps keep ice thinner
87      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
88      * applied OBCS T/S mask to HEFFM sea ice mask
89    
90    checkpoint59d
91    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
92     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
93     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
94    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
95     and change default value of parameter "GM_Small_Number";
96     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
97       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
98       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
99    o pkg/ecco: cost function when applying pkg/smooth to controls
100    o pkg/ctrl: add forcingPrecond run time parameter
101    o pkg/seaice:
102     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
103     - fix bug in metric terms of u-equation in LSR solver (implicit part),
104       changes verification/lab_sea
105     - rearrange implicit part of u-equation in LSR solver to make it easier to
106       read, understand, and debug. This causes changes at the truncation level.
107     - fix (serious) bug in the boundary conditions (sign error in the implicit
108       part) of the LSR solver. Changes all LSR results.
109     - fixed problem with HSNOW initialization to avoid thick snow when AREA
110       is initilized with small values - does not change lab_sea results.
111     - added HsnowFile initialization capability
112    o pkg/smooth: addition to model/src and pkg/ctrl so allow
113     initialization of pkg/smooth and application to control vector
114    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
115    o dependencies: pkg/profiles requires pkg/cal
116    o pkg/profiles:
117     - added option ALLOW_PROFILES_GENERICGRID
118         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
119         that interpolation information (grid points and coefficients) is provided
120         within the netcdf input files.
121         -> sample matlab scripts can be found in MITgcm_contrib/gael
122         that allow you to prepare netcdf input files.
123     - also modified: cleaner include statements, cleaner error print statements,
124       cleaner stops when error, and more tests of the netcdf input files consistency.
125    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
126    o pkg/seaice:
127     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
128       requires a new routine: seaice_diagnostics_fill.F
129     - make sure that seaice does not move if not forced (pressure replacement
130       method, Hibler and Ip, 1995), changes results
131     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
132     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
133       It is turned off by default (=-1.), because it changes the results.
134     - make it possible to read AREA from a file, too.
135    
136    checkpoint59c
137    o add S/R and diagnostics for oceanic mixed-layer depth
138    o move GMRedi call after all vertical mixing schemes (including KPP)
139    o pkg/thsice:
140     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
141      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
142    o pkg/obcs:
143     - bug fix for balance code
144    o pkg/seaice:
145      - allow values of SEAICE_elasticParm > 1
146      - add new parameter SEAICE_evpTauRelax as an alternative
147        to SEAICE_elasticParm
148      - make lsr boundary conditions free slip (by default), changes result
149      - add code for no slip boundary conditions for lsr
150      - set minimum of zeta to zero (and not 4e8) (changes results)
151      - add a cap on AREA after advecting AREA if seaice_growth is not called
152    o change calculation of Visbeck K:
153      - no longer depend on tapering scheme; instead, compute slope (limited
154        by GM_maxSlope). this is equivalent to what was comuted before with
155        clipping or linear tappering.
156      - fix vertical averaging (wrong by 1/2 level)
157      - leave the old version (but will not be maintained) within
158        #ifdef OLD_VISBECK_CALC / #endif
159      - update output of exp. ideal_2D_oce
160    o change error catch in calc_r_star to improve vectorization
161    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
162      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
163    o adjoint:
164      Re-organized adjoint checkpointing according to Matt Mazloff
165      (but with modifs/completions/cleanups)
166      Storing is now bundled into large arrays to optimized I/O
167      (and second step in cleanup of the_main_loop)
168    
169    checkpoint59b
170    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
171      - export/import (between ocean & coupler) fields needed for ocean DIC.
172    o pkg/seaice:
173      - get rid of three more exchanges seaice_calc_viscosities (required
174        different loop boundaries in seaice_lsr and seaice_ocean_stress)
175      - bug fix in seaice_ocean_stress (update of lab_sea required)
176      - reduce loop boundaries to necessary minimum also in seaice_evp
177      - go back to the old way of computing deltaC/Z as the adjoint likes that
178        better
179    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
180      passive tracer to an Age Tracer) + update output.txt
181    o pkg/exf:
182      - implement A-grid / C-grid selection for wind-stress input files.
183      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
184      for now, in exf_bulk_largeyeager04.F only :
185      - change implementation for case where windspeed + 2. components wind-stress
186        are read-in. AND use rhoConstFresh to convert evap.
187    o pkg/seaice:
188      - use correct EXCH_UV for wind-forcing (on A-grid).
189      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
190        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
191    o pkg/exf:
192      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
193      EXF_INTERPOLATION:
194      - merge global_with_exf/code version of exf_interp_read.F
195        to the main code ;
196      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
197        reading the file ; Important: This options needs to be defined to recover
198        previous code.
199        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
200      - no longer loose real*8 precision along the way when using exf_iprec=64.
201    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
202      - change discretisation of evp-solver in order to avoid another exchange
203        (changes lab_sea) and clean up a little
204      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
205        help the adjoint (this also changes the results slightly)
206      - add a few "_d 0" where they had been missing in seaice_evp.F
207      - cleaning up: remove unused seaice_calc_rhs.F
208    o pkg/exf: some cleaning-up:
209      - change various "constants" into runtime parameters
210      - cleaned-up Large&Yeager04 routine which should eventually
211        replace exf_bulkformulae.F (changed names of S/R and CPP)
212        and merged various ALLOW_ATM_WIND options
213     only used with thsice pkg (in thsice_get_exf.F):
214      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
215        which are used when useStabilityFct_overIce=TRUE (= the default)
216      - change default values of ice & snow emissivity and scale downward LW
217        by ice & snow emissivity.
218    o pkg/thsice:
219     fix few little problems, in thsice_calc_thickn.F:
220      - growth vertically (and not laterally) if iceFrac == iceMaskMax
221      - melt only laterally if hIce < hThinIce (as the comments say)
222      and in thsice_extend.F:
223      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
224      - start to form ice as soon as the minimum ice-volume is reachable.
225     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
226      and cpl_aim+ocn
227    o pkg/kpp
228     - move computation of surface related input fields to KPP into a new
229       subroutine kpp_forcing_surf.F
230     - remove wrong (within bi,bj loops) EXCH calls.
231     - little cleaning (add argument myThid in last position, cvs header ...)
232     - for now, fix conservation problem by exchanging KPPviscAz (may not
233       be the best fix)
234    o pkg/seaice
235     - check for inconsistent evp parameter/cpp-flag combination
236     - remove leftover errIO flat for obsolete name list error handling
237    o OpenAD
238     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
239    
240    checkpoint59a
241    o pkg/seaice: some parameter clarifications and a little bit of clean up
242    o pkg/thsice: rename run-time parameters:
243       himin       -> hIceMin
244       himin0      -> hThinIce
245       hihig       -> hThickIce
246       i0          -> i0swFrac
247       transCoef   -> bMeltCoef
248       frac_energy -> fracMelting
249      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
250       with default values (for now) that do not change the results.
251      remove old version of thsice vars advection in pkg/seaice.
252    o in FFIELDS.h:
253      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
254      - make pLoad & sIceLoad always available (but still only used if
255         ATMOSPHERIC_LOADING is #define).
256    o pkg/kpp: replaced _KPP_RL with _RL
257    o bug fixes for vertical diffusivity computations when both KPP and
258        3D diffusivity arrays are used.
259    o pkg/seaice: fix bug in evp solver, while doing that
260      - change (improve?) discretization of stress computations for both
261        cgrid-lsr and evp solver
262      - add a new routine to compute strain rates
263      - the above changes lab_sea results
264      - add no slip conditions for evp solver (off by default), lsr-version
265        may follow
266      - fix exchange for shear at Z-points (does not change lab_sea)
267      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
268        (to force the user to pick a time step since there is not "safe" way
269        of choosing it)
270      - add principal stress diagnostics
271      - rearrange fields for evp a little to avoid having to call a: too many
272        exchanges and b: exchanges for stress trensor components which we do
273        not have.
274      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
275        of evp, complete rewrite for lsr case (latter is does not yet work
276        in all cases)
277    o pkg/kpp: add code to have mixing in shelf ice caverns
278      - add myThid to all kpp routines (long overdue)
279    
280    checkpoint59
281    o pkg/exf:
282      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
283        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
284      - move exf header files from lower_case.h to UPPER_CASE.h ;
285        add missing cvs Header & Name
286      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
287      - add namelist param. selectStressGridPosition, exf_monFreq
288      - retire many _CLIM routines, and remove data.exf_clim
289        + params moved to data.exf
290        + climsst, climsss now handled by exf_set_gen, i.e.
291          climss?period=0 refers to constant field,
292          climss?period=-12 to monthly forcing
293      - split up namelists in data.exf
294    o pkg/seaice:
295      - remove seaice_exch and seaice_exch_uv
296      - remove superfluous exchange of theta
297      - add myThid to seaice_budget_ocean/ice
298      - add new interface for atmospheric wind forcing (C-grid only)
299        + new routine
300        + two new field (taux, tauy for stress over ice)
301        + removed one global field (DAIRN) for C-grid case only
302    o pkg/thsise
303      - 2nd set of modifs for thsice adjoint in conjunction with exf
304    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
305    
306    checkpoint58y_post
307    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
308      vertical diffusivity, similar to that in MOM4; turned on using
309      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
310      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
311    o Added capability for 3D specification of background vertical diffusion
312      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
313      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
314      "data" file that contains the 3D vertical diffusivity coefficients.
315    o ice dynamics (pkg/seaice) with thsice thermodynamics:
316      - add code within pkg thsice to advect & diffuse sea-ice fields
317      similar to (and will replace) what has been added in  seaice_advdiff.F,
318      but: - conserving Mass, Heat & Salt.
319           - better when using non-linear advection scheme (not yet fully tested)
320           - can also be used in atmospheric set-up (for now, only the diffusion).
321    
322    checkpoint58x_post
323    o IO option for global-file compact format:
324      - add options when generating topology (utils/exch2/matlab-topology-generator)
325      - add I/O capability (pkg/mdsio).
326      - adapt utils/matlab/rdmds.m to read this format.
327      for now long-line format not yet supported by pkg/mdsio (& exch2).
328    o shelfice: add a few diagnostics
329    
330    checkpoint58w_post
331    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
332      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
333      (and replace horiVertRatio in NH code).
334      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
335                         and tutorial_plume_on_slope (sensitive to truncation)
336    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
337      directly to drive seaice model (C-grid only)
338    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
339     - reintroduce computation of wind from stress,
340     - compute tau (in exf_bulkformulae.F) from windstress averaged to
341       mass points to avoid tau = 0
342     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
343    o rdmnc.m: make it work with "global" files created with gluemnc
344    o rdmnc.m : some improvements in dealing with singleton dimension
345      (tested on all testreport mnc output files).
346    o genmake2: disable pkg/profiles if netcdf test fails.
347    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
348    o move call to cal_readparms up to make calendar parameters/variable available
349      to all packages
350    
351    checkpoint58v_post
352    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
353      useDynP_inEos_Zc tested.
354    o pkg/exf: changes to properly interpolate/mask/scale initial fields
355    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
356      and portions thereof.  See read_cs.txt for description and examples.
357    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
358      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
359      following the great-circle arc between those 2 points.
360    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
361      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
362    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
363     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
364     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
365     - still needs work (not working with some options ; efficiency to improve)
366       and serious testing.
367     - use this scheme for temperature & salinity in 2 advection test exp.:
368       advect_xy & advect_xz, respectively.
369    
370    checkpoint58u_post
371    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
372    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
373    o testreport: add option "-skipdir" to skip some test.
374    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
375      momentum calculation.
376    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
377    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
378      remove checkpoint.F and the_correction_step.F (no longer used);
379      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
380    o add option (linFSConserveTr) to correct for tracer source/sink due to
381      Linear Free surface
382    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
383    o pkg/thsice: fix reading mnc-pickups
384    
385    checkpoint58t_post
386    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
387    o pkg/mdsio:
388     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
389       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
390       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
391     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
392     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
393       either MDS_READ_FIELD or MDS_WRITE_FIELD )
394     - new S/R (to replace MDSWRITEMETA), which allows to write more
395       informations (variable names, time ...) to meta files.
396     - modify rdmds.m to give back the meta file content.
397    o pkg/diagnostics: change vertical interpolation to be safer, and more
398       flexible (define p-levels to interpolate to in data.diagnostics);
399      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
400       diagnostic pointer.
401    o pkg/seaice: more cleaning up of seaice_growth, added many comments
402    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
403    o fix multi-category seaice:
404     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
405       SEAICE_MULTICATEGORY
406     - fix short wave heat flux
407    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
408       and allow to use EVP solver. Change forward lab_sea: test both EVP
409       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
410    o Initial check-in of lab_sea adjoint
411      (very similar to natl_box_adjoint/code_seaice)
412      * used C-grid and EVP solver
413      * used KPP, GM/Redi
414      * uses inAdExact=.TRUE.
415      * gradient checks fail for both ADM and TLM
416        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
417        f.d. gradients actually seem more problematic than ADM, TLM gradients;
418        issue is related to forward mismatch between g77 an ifort
419    o pkg/seaice: overhaul of thermodynamics
420     - growth.F and groatb.F are replaced by new routine seaice_growth.F
421     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
422     - move a few global fields out of SEAICE.h into seaice_growth.F and
423       make them 2D (FICE/QNETO/ ...)
424     - remove FO (it is the same as QNETO)
425     - introduce a few local fields to avoid modifying external fields such
426       as atemp, etc.
427    
428    checkpoint58s_post
429    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
430      changed exf_set_gen.F so that
431        genperiod=0 means input file is one time-constant field and
432        genperiod=-12 means input file contains 12 monthly means
433    o CG2D: use pre-computed solver main-diagonal (stored in common block);
434      this affects truncation error ; generate new output file for exp. which
435      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
436        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
437        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
438        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
439        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
440        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
441    o start implementation of deep-atmosphere and anelastic formulation
442    o verification: remove 2nd copy of input files and use script "prepare_run"
443      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
444    o mom_common/vecinv/fluxform: fix a few initialisation isssues
445    o profiles: fix for multithreaded case
446    
447    o diagnostics: rename few diags:
448      s/'PRESSURE'/'RCENTER '/g
449      s/'TICE    '/'oceFreez'/g
450      s/'TAUX    '/'oceTAUX '/g
451      s/'TAUY    '/'oceTAUY '/g
452      s/'SWFLUX  '/'oceQsw  '/g
453      s/DIFx/DFxE/g
454      s/DIFy/DFyE/g
455      and add few ocean-forcing diagnostics:
456      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
457    o modifications to pkg/seaice/growth.F and budget.F, which change results of
458      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
459      as actual snow thickness.  It now refers everywhere to effective snow
460      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
461    
462    checkpoint58r_post
463    o modifications to pkg/seaice/growth.F, which change results of
464      lab_sea experiment: fixes pertain to melting snow over open water, to
465      masking EVAP under sea ice, and to using the correct AREA variable for
466      computations of EVAP, PRECIP, HSNOW, and GHEFF
467    o add ability to read bathy, salt, and theta using MNC (off by def)
468    o add flooding algorithm and advection of HSNOW for pkg/seaice;
469      both are turned off by default and do no change any results
470    o seaice advection with pkg/thsice: a step toward the use of non-linear
471      advection scheme, but #ifdef or commented out for now (requires more EXCH).
472    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
473      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
474      in natl_box (affects results @ truncation level: update output.txt)
475    o multi-threading and IO:
476      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
477      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
478        (needed to work with SingleCpuIO): tested in all verif. exp.
479    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
480      affects the results (but none of the verification test uses this scheme).
481    o Adding some pkg/diagnostics capability to pkg/seaice
482      (will certainly be subject to changes)
483    o ctrl: adding new control variables:
484      lwflux, lwdown, evap, snowprecip, apressure, runoff
485    
486    checkpoint58q_post
487    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
488      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
489      high_res_cube configuration by 4% on Columbia.
490    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
491      add (in global_with_exf/code) a version of EXF_INTERP_READ without
492      dynamical allocation (seems to work in multi-threaded).
493    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
494      single CPU io) so that TAF does not have to see EESUPPORT.h
495    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
496    
497    checkpoint58p_post
498    o obcs: stop if obcs is used with useCDscheme = .true.
499  o shelfice:  o shelfice:
500   - fix a sign error so that no slip at shelfice interface works   - fix a sign error so that no slip at shelfice interface works
501   - remove stop for combination non-hydrostatic code and shelfice. That does   - remove stop for combination non-hydrostatic code and shelfice. That does
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