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revision 1.703 by gforget, Fri Jul 14 22:14:28 2006 UTC revision 1.867 by mlosch, Fri Aug 31 14:06:57 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: change a discretization detail to make the B-grid code
8      "more symmetric". This change is likely to remove all "ridges/leads" that
9      where quasi-aligned with the grid in B-grid solutions. It may also be
10      the solution to the stress coupling issues with the B-grid.
11    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
12      remove .cvsignore from input dir. (since testreport no longer run here).
13    o pkg/thsice:
14     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
15     - fix reshaping of sea-ice just after advection:
16       melt all the ice only if ice-volume is too small.
17     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
18       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
19     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
20    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
21      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
22    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
23      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
24      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
25      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
26      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
27      -> update output.txt
28    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
29     this affects truncation error: -> update output.txt of exp:
30      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
31      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
32    
33    checkpoint59f
34    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
35    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
36      a bounded range (in forward mode)
37    o pkg/ecco, ctrl, autodiff and mom_common:
38     internal parameter controls, completements of implementations
39    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
40    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
41      (not seem any difference in testing results).
42    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
43       at face corners.
44    o pkg/generic_advdiff:
45     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
46      loop range indices for computing vertical advection tendency
47      and do the calculation in the interior only (no overlap) ;
48      for now, only implemented for SOM advection (to save CPU time).
49     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
50    o exch2 adjoint
51      First set of changes:
52      - add exch2 hand-written adjoint templates
53      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
54        This will require cleanup in pkg/autodiff/*.F
55        (changed routines currently kept separate in verif. code/)
56      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
57        that used to hide exch2 or cubed-sphere specific code
58        (commented via 'cph-exch2')
59    o pkg/seaice
60      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
61    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
62       output of global_ocean.cs32x15.thsice .
63    
64    checkpoint59e
65    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
66      for B-grid vector (not yet tested) and C-grid vector (<- only used
67      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
68    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
69      (#ifdef ALLOW_SALT_PLUME)
70    o gather_2d/scatter_2d: removed halo regions
71    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
72      scheme and the corresponding test case (under front_relax dir). For now,
73      only available with Skew-flux form and not yet tested in realistic set-up.
74      adjoint: store directives updated, but gradient checks deteriorated,
75      so maybe GM/Redi adjoint is now broken.
76    o seaice adjoint
77      * add AREA, HEFF, HSNOW as control variable
78        (should not change lab_sea results)
79      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
80    o pkg/seaice:
81      * added computation of saltFlux in seaice_growth;
82        For time being, sea ice salinity is assumed constant
83        contribution of snow flooding to freshening of sea ice is neglected.
84        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
85        defaults to 0.0 in order to maintain backward compatibility.
86        Typical values for SEAICE_salinity are 4 to 10 g/kg.
87      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
88      * added SEAICE_availHeatFrac, which specifies fraction of surface level
89        heat content used to melt or grow ice
90      * commented out cap of HICE: it helps keep ice thinner
91      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
92      * applied OBCS T/S mask to HEFFM sea ice mask
93    
94    checkpoint59d
95    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
96     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
97     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
98    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
99     and change default value of parameter "GM_Small_Number";
100     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
101       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
102       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
103    o pkg/ecco: cost function when applying pkg/smooth to controls
104    o pkg/ctrl: add forcingPrecond run time parameter
105    o pkg/seaice:
106     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
107     - fix bug in metric terms of u-equation in LSR solver (implicit part),
108       changes verification/lab_sea
109     - rearrange implicit part of u-equation in LSR solver to make it easier to
110       read, understand, and debug. This causes changes at the truncation level.
111     - fix (serious) bug in the boundary conditions (sign error in the implicit
112       part) of the LSR solver. Changes all LSR results.
113     - fixed problem with HSNOW initialization to avoid thick snow when AREA
114       is initilized with small values - does not change lab_sea results.
115     - added HsnowFile initialization capability
116    o pkg/smooth: addition to model/src and pkg/ctrl so allow
117     initialization of pkg/smooth and application to control vector
118    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
119    o dependencies: pkg/profiles requires pkg/cal
120    o pkg/profiles:
121     - added option ALLOW_PROFILES_GENERICGRID
122         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
123         that interpolation information (grid points and coefficients) is provided
124         within the netcdf input files.
125         -> sample matlab scripts can be found in MITgcm_contrib/gael
126         that allow you to prepare netcdf input files.
127     - also modified: cleaner include statements, cleaner error print statements,
128       cleaner stops when error, and more tests of the netcdf input files consistency.
129    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
130    o pkg/seaice:
131     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
132       requires a new routine: seaice_diagnostics_fill.F
133     - make sure that seaice does not move if not forced (pressure replacement
134       method, Hibler and Ip, 1995), changes results
135     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
136     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
137       It is turned off by default (=-1.), because it changes the results.
138     - make it possible to read AREA from a file, too.
139    
140    checkpoint59c
141    o add S/R and diagnostics for oceanic mixed-layer depth
142    o move GMRedi call after all vertical mixing schemes (including KPP)
143    o pkg/thsice:
144     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
145      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
146    o pkg/obcs:
147     - bug fix for balance code
148    o pkg/seaice:
149      - allow values of SEAICE_elasticParm > 1
150      - add new parameter SEAICE_evpTauRelax as an alternative
151        to SEAICE_elasticParm
152      - make lsr boundary conditions free slip (by default), changes result
153      - add code for no slip boundary conditions for lsr
154      - set minimum of zeta to zero (and not 4e8) (changes results)
155      - add a cap on AREA after advecting AREA if seaice_growth is not called
156    o change calculation of Visbeck K:
157      - no longer depend on tapering scheme; instead, compute slope (limited
158        by GM_maxSlope). this is equivalent to what was comuted before with
159        clipping or linear tappering.
160      - fix vertical averaging (wrong by 1/2 level)
161      - leave the old version (but will not be maintained) within
162        #ifdef OLD_VISBECK_CALC / #endif
163      - update output of exp. ideal_2D_oce
164    o change error catch in calc_r_star to improve vectorization
165    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
166      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
167    o adjoint:
168      Re-organized adjoint checkpointing according to Matt Mazloff
169      (but with modifs/completions/cleanups)
170      Storing is now bundled into large arrays to optimized I/O
171      (and second step in cleanup of the_main_loop)
172    
173    checkpoint59b
174    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
175      - export/import (between ocean & coupler) fields needed for ocean DIC.
176    o pkg/seaice:
177      - get rid of three more exchanges seaice_calc_viscosities (required
178        different loop boundaries in seaice_lsr and seaice_ocean_stress)
179      - bug fix in seaice_ocean_stress (update of lab_sea required)
180      - reduce loop boundaries to necessary minimum also in seaice_evp
181      - go back to the old way of computing deltaC/Z as the adjoint likes that
182        better
183    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
184      passive tracer to an Age Tracer) + update output.txt
185    o pkg/exf:
186      - implement A-grid / C-grid selection for wind-stress input files.
187      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
188      for now, in exf_bulk_largeyeager04.F only :
189      - change implementation for case where windspeed + 2. components wind-stress
190        are read-in. AND use rhoConstFresh to convert evap.
191    o pkg/seaice:
192      - use correct EXCH_UV for wind-forcing (on A-grid).
193      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
194        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
195    o pkg/exf:
196      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
197      EXF_INTERPOLATION:
198      - merge global_with_exf/code version of exf_interp_read.F
199        to the main code ;
200      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
201        reading the file ; Important: This options needs to be defined to recover
202        previous code.
203        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
204      - no longer loose real*8 precision along the way when using exf_iprec=64.
205    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
206      - change discretisation of evp-solver in order to avoid another exchange
207        (changes lab_sea) and clean up a little
208      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
209        help the adjoint (this also changes the results slightly)
210      - add a few "_d 0" where they had been missing in seaice_evp.F
211      - cleaning up: remove unused seaice_calc_rhs.F
212    o pkg/exf: some cleaning-up:
213      - change various "constants" into runtime parameters
214      - cleaned-up Large&Yeager04 routine which should eventually
215        replace exf_bulkformulae.F (changed names of S/R and CPP)
216        and merged various ALLOW_ATM_WIND options
217     only used with thsice pkg (in thsice_get_exf.F):
218      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
219        which are used when useStabilityFct_overIce=TRUE (= the default)
220      - change default values of ice & snow emissivity and scale downward LW
221        by ice & snow emissivity.
222    o pkg/thsice:
223     fix few little problems, in thsice_calc_thickn.F:
224      - growth vertically (and not laterally) if iceFrac == iceMaskMax
225      - melt only laterally if hIce < hThinIce (as the comments say)
226      and in thsice_extend.F:
227      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
228      - start to form ice as soon as the minimum ice-volume is reachable.
229     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
230      and cpl_aim+ocn
231    o pkg/kpp
232     - move computation of surface related input fields to KPP into a new
233       subroutine kpp_forcing_surf.F
234     - remove wrong (within bi,bj loops) EXCH calls.
235     - little cleaning (add argument myThid in last position, cvs header ...)
236     - for now, fix conservation problem by exchanging KPPviscAz (may not
237       be the best fix)
238    o pkg/seaice
239     - check for inconsistent evp parameter/cpp-flag combination
240     - remove leftover errIO flat for obsolete name list error handling
241    o OpenAD
242     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
243    
244    checkpoint59a
245    o pkg/seaice: some parameter clarifications and a little bit of clean up
246    o pkg/thsice: rename run-time parameters:
247       himin       -> hIceMin
248       himin0      -> hThinIce
249       hihig       -> hThickIce
250       i0          -> i0swFrac
251       transCoef   -> bMeltCoef
252       frac_energy -> fracMelting
253      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
254       with default values (for now) that do not change the results.
255      remove old version of thsice vars advection in pkg/seaice.
256    o in FFIELDS.h:
257      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
258      - make pLoad & sIceLoad always available (but still only used if
259         ATMOSPHERIC_LOADING is #define).
260    o pkg/kpp: replaced _KPP_RL with _RL
261    o bug fixes for vertical diffusivity computations when both KPP and
262        3D diffusivity arrays are used.
263    o pkg/seaice: fix bug in evp solver, while doing that
264      - change (improve?) discretization of stress computations for both
265        cgrid-lsr and evp solver
266      - add a new routine to compute strain rates
267      - the above changes lab_sea results
268      - add no slip conditions for evp solver (off by default), lsr-version
269        may follow
270      - fix exchange for shear at Z-points (does not change lab_sea)
271      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
272        (to force the user to pick a time step since there is not "safe" way
273        of choosing it)
274      - add principal stress diagnostics
275      - rearrange fields for evp a little to avoid having to call a: too many
276        exchanges and b: exchanges for stress trensor components which we do
277        not have.
278      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
279        of evp, complete rewrite for lsr case (latter is does not yet work
280        in all cases)
281    o pkg/kpp: add code to have mixing in shelf ice caverns
282      - add myThid to all kpp routines (long overdue)
283    
284    checkpoint59
285    o pkg/exf:
286      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
287        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
288      - move exf header files from lower_case.h to UPPER_CASE.h ;
289        add missing cvs Header & Name
290      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
291      - add namelist param. selectStressGridPosition, exf_monFreq
292      - retire many _CLIM routines, and remove data.exf_clim
293        + params moved to data.exf
294        + climsst, climsss now handled by exf_set_gen, i.e.
295          climss?period=0 refers to constant field,
296          climss?period=-12 to monthly forcing
297      - split up namelists in data.exf
298    o pkg/seaice:
299      - remove seaice_exch and seaice_exch_uv
300      - remove superfluous exchange of theta
301      - add myThid to seaice_budget_ocean/ice
302      - add new interface for atmospheric wind forcing (C-grid only)
303        + new routine
304        + two new field (taux, tauy for stress over ice)
305        + removed one global field (DAIRN) for C-grid case only
306    o pkg/thsise
307      - 2nd set of modifs for thsice adjoint in conjunction with exf
308    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
309    
310    checkpoint58y_post
311    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
312      vertical diffusivity, similar to that in MOM4; turned on using
313      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
314      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
315    o Added capability for 3D specification of background vertical diffusion
316      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
317      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
318      "data" file that contains the 3D vertical diffusivity coefficients.
319    o ice dynamics (pkg/seaice) with thsice thermodynamics:
320      - add code within pkg thsice to advect & diffuse sea-ice fields
321      similar to (and will replace) what has been added in  seaice_advdiff.F,
322      but: - conserving Mass, Heat & Salt.
323           - better when using non-linear advection scheme (not yet fully tested)
324           - can also be used in atmospheric set-up (for now, only the diffusion).
325    
326    checkpoint58x_post
327    o IO option for global-file compact format:
328      - add options when generating topology (utils/exch2/matlab-topology-generator)
329      - add I/O capability (pkg/mdsio).
330      - adapt utils/matlab/rdmds.m to read this format.
331      for now long-line format not yet supported by pkg/mdsio (& exch2).
332    o shelfice: add a few diagnostics
333    
334    checkpoint58w_post
335    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
336      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
337      (and replace horiVertRatio in NH code).
338      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
339                         and tutorial_plume_on_slope (sensitive to truncation)
340    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
341      directly to drive seaice model (C-grid only)
342    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
343     - reintroduce computation of wind from stress,
344     - compute tau (in exf_bulkformulae.F) from windstress averaged to
345       mass points to avoid tau = 0
346     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
347    o rdmnc.m: make it work with "global" files created with gluemnc
348    o rdmnc.m : some improvements in dealing with singleton dimension
349      (tested on all testreport mnc output files).
350    o genmake2: disable pkg/profiles if netcdf test fails.
351    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
352    o move call to cal_readparms up to make calendar parameters/variable available
353      to all packages
354    
355    checkpoint58v_post
356    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
357      useDynP_inEos_Zc tested.
358    o pkg/exf: changes to properly interpolate/mask/scale initial fields
359    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
360      and portions thereof.  See read_cs.txt for description and examples.
361    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
362      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
363      following the great-circle arc between those 2 points.
364    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
365      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
366    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
367     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
368     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
369     - still needs work (not working with some options ; efficiency to improve)
370       and serious testing.
371     - use this scheme for temperature & salinity in 2 advection test exp.:
372       advect_xy & advect_xz, respectively.
373    
374    checkpoint58u_post
375    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
376    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
377    o testreport: add option "-skipdir" to skip some test.
378    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
379      momentum calculation.
380    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
381    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
382      remove checkpoint.F and the_correction_step.F (no longer used);
383      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
384    o add option (linFSConserveTr) to correct for tracer source/sink due to
385      Linear Free surface
386    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
387    o pkg/thsice: fix reading mnc-pickups
388    
389    checkpoint58t_post
390    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
391    o pkg/mdsio:
392     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
393       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
394       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
395     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
396     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
397       either MDS_READ_FIELD or MDS_WRITE_FIELD )
398     - new S/R (to replace MDSWRITEMETA), which allows to write more
399       informations (variable names, time ...) to meta files.
400     - modify rdmds.m to give back the meta file content.
401    o pkg/diagnostics: change vertical interpolation to be safer, and more
402       flexible (define p-levels to interpolate to in data.diagnostics);
403      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
404       diagnostic pointer.
405    o pkg/seaice: more cleaning up of seaice_growth, added many comments
406    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
407    o fix multi-category seaice:
408     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
409       SEAICE_MULTICATEGORY
410     - fix short wave heat flux
411    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
412       and allow to use EVP solver. Change forward lab_sea: test both EVP
413       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
414    o Initial check-in of lab_sea adjoint
415      (very similar to natl_box_adjoint/code_seaice)
416      * used C-grid and EVP solver
417      * used KPP, GM/Redi
418      * uses inAdExact=.TRUE.
419      * gradient checks fail for both ADM and TLM
420        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
421        f.d. gradients actually seem more problematic than ADM, TLM gradients;
422        issue is related to forward mismatch between g77 an ifort
423    o pkg/seaice: overhaul of thermodynamics
424     - growth.F and groatb.F are replaced by new routine seaice_growth.F
425     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
426     - move a few global fields out of SEAICE.h into seaice_growth.F and
427       make them 2D (FICE/QNETO/ ...)
428     - remove FO (it is the same as QNETO)
429     - introduce a few local fields to avoid modifying external fields such
430       as atemp, etc.
431    
432    checkpoint58s_post
433    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
434      changed exf_set_gen.F so that
435        genperiod=0 means input file is one time-constant field and
436        genperiod=-12 means input file contains 12 monthly means
437    o CG2D: use pre-computed solver main-diagonal (stored in common block);
438      this affects truncation error ; generate new output file for exp. which
439      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
440        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
441        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
442        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
443        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
444        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
445    o start implementation of deep-atmosphere and anelastic formulation
446    o verification: remove 2nd copy of input files and use script "prepare_run"
447      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
448    o mom_common/vecinv/fluxform: fix a few initialisation isssues
449    o profiles: fix for multithreaded case
450    
451    o diagnostics: rename few diags:
452      s/'PRESSURE'/'RCENTER '/g
453      s/'TICE    '/'oceFreez'/g
454      s/'TAUX    '/'oceTAUX '/g
455      s/'TAUY    '/'oceTAUY '/g
456      s/'SWFLUX  '/'oceQsw  '/g
457      s/DIFx/DFxE/g
458      s/DIFy/DFyE/g
459      and add few ocean-forcing diagnostics:
460      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
461    o modifications to pkg/seaice/growth.F and budget.F, which change results of
462      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
463      as actual snow thickness.  It now refers everywhere to effective snow
464      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
465    
466    checkpoint58r_post
467    o modifications to pkg/seaice/growth.F, which change results of
468      lab_sea experiment: fixes pertain to melting snow over open water, to
469      masking EVAP under sea ice, and to using the correct AREA variable for
470      computations of EVAP, PRECIP, HSNOW, and GHEFF
471    o add ability to read bathy, salt, and theta using MNC (off by def)
472    o add flooding algorithm and advection of HSNOW for pkg/seaice;
473      both are turned off by default and do no change any results
474    o seaice advection with pkg/thsice: a step toward the use of non-linear
475      advection scheme, but #ifdef or commented out for now (requires more EXCH).
476    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
477      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
478      in natl_box (affects results @ truncation level: update output.txt)
479    o multi-threading and IO:
480      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
481      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
482        (needed to work with SingleCpuIO): tested in all verif. exp.
483    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
484      affects the results (but none of the verification test uses this scheme).
485    o Adding some pkg/diagnostics capability to pkg/seaice
486      (will certainly be subject to changes)
487    o ctrl: adding new control variables:
488      lwflux, lwdown, evap, snowprecip, apressure, runoff
489    
490    checkpoint58q_post
491    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
492      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
493      high_res_cube configuration by 4% on Columbia.
494    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
495      add (in global_with_exf/code) a version of EXF_INTERP_READ without
496      dynamical allocation (seems to work in multi-threaded).
497    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
498      single CPU io) so that TAF does not have to see EESUPPORT.h
499    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
500    
501    checkpoint58p_post
502    o obcs: stop if obcs is used with useCDscheme = .true.
503    o shelfice:
504     - fix a sign error so that no slip at shelfice interface works
505     - remove stop for combination non-hydrostatic code and shelfice. That does
506       not mean, that the results are correct, but at least they are numerically
507       stable
508    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
509    o added adjoint exch routined for all exch*3d* routines
510      and updated flow directives
511    
512    checkpoint58o_post
513    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
514      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
515    o change controling S/R for writing pickup file (new S/R do_write_pickup)
516      and clean-up reading/writing of pickup files.
517    o fix local version of read/write pickup (NH part) in rotating_tank/code
518    o simplify EXCH interface:
519     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
520     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
521    o added the regrid package
522    o shelfice:
523     - add a simple boundary layer scheme to reduce noise
524     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
525    
526    checkpoint58n_post
527    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
528       local variable (not in common block).
529    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
530      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
531      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
532        to work with SingleCpuIO.
533    o add "_d 0" to real constant of pkg/cfc subroutines ;
534       update exp. cfc_exemple & tutorial_cfc_offline output files.
535    o multi-threading and IO:
536      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
537        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
538      - barrier before and after reading.
539      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
540      - avoid using MDS_WRITELOCAL for LAND pkg output.
541      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
542        common-block variables ; Allows multi-threading with master-thread IO.
543    o change default MAX_NO_THREADS from 32 to 4 ;
544      and stop cleanly when MAX_NO_THREADS is too small.
545    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
546    
547    checkpoint58m_post
548    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
549       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
550    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
551       keep global_ocean.90x40x15 (for AD testing) with former secondary test
552       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
553    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
554        add MITgcm_tutorials (= code + all the tutorials)
555    o ecco, option to compute cost for total ssh (mean+anom)
556    o consistent with addition of ptracer and ssh in pkg/profiles
557  o profiles: adding ptracer and ssh  o profiles: adding ptracer and ssh
558  o testreport: change multi-test output-file name  o testreport: change multi-test output-file name
559    (from output.txt.{name} to output.{name}.txt)    (from output.txt.{name} to output.{name}.txt)
560  o profiles: now ok for mutli-threaded case  o profiles: now ok for mutli-tiles case
561  o seaice: add 4 parameters for different advection schemes for area,  o seaice: add 4 parameters for different advection schemes for area,
562    (effective) seaice thickness, enthalphy, and snow height. Their default    (effective) seaice thickness, enthalphy, and snow height. Their default
563    is the standard parameter SEAICEadvScheme    is the standard parameter SEAICEadvScheme
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