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revision 1.685 by baylor, Thu Jun 22 19:39:21 2006 UTC revision 1.874 by jmc, Mon Sep 17 15:28:14 2007 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint59g
8    o adjoint testing: in preparation for changing testreport:
9      - output format: cost and grad written on separated lines
10      - ad output results in directory "results" (instead of "results_ad")
11    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
12    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
13    o pkg/ecco: allow user defined cost function contributions
14    o testreport:
15      Allow to choose (per experiment) the list of tested output variables
16       and the main variable (used to issue a pass/FAIL ) ;
17      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
18      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
19      Also modify printing of summary:
20       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
21       b) echo the list of tested variables in the individual summary.txt of
22          each experiment.
23    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
24      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
25      (but still depend on the tile decompostion of the domain).
26    o pkg/seaice: change a discretization detail to make the B-grid code
27      "more symmetric". This change is likely to remove all "ridges/leads" that
28      where quasi-aligned with the grid in B-grid solutions. It may also be
29      the solution to the stress coupling issues with the B-grid.
30    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
31      remove .cvsignore from input dir. (since testreport no longer run here).
32    o pkg/thsice:
33     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
34     - fix reshaping of sea-ice just after advection:
35       melt all the ice only if ice-volume is too small.
36     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
37       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
38     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
39    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
40      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
41    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
42      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
43      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
44      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
45      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
46      -> update output.txt
47    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
48     this affects truncation error: -> update output.txt of exp:
49      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
50      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
51    
52    checkpoint59f
53    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
54    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
55      a bounded range (in forward mode)
56    o pkg/ecco, ctrl, autodiff and mom_common:
57     internal parameter controls, completements of implementations
58    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
59    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
60      (not seem any difference in testing results).
61    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
62       at face corners.
63    o pkg/generic_advdiff:
64     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
65      loop range indices for computing vertical advection tendency
66      and do the calculation in the interior only (no overlap) ;
67      for now, only implemented for SOM advection (to save CPU time).
68     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
69    o exch2 adjoint
70      First set of changes:
71      - add exch2 hand-written adjoint templates
72      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
73        This will require cleanup in pkg/autodiff/*.F
74        (changed routines currently kept separate in verif. code/)
75      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
76        that used to hide exch2 or cubed-sphere specific code
77        (commented via 'cph-exch2')
78    o pkg/seaice
79      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
80    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
81       output of global_ocean.cs32x15.thsice .
82    
83    checkpoint59e
84    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
85      for B-grid vector (not yet tested) and C-grid vector (<- only used
86      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
87    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
88      (#ifdef ALLOW_SALT_PLUME)
89    o gather_2d/scatter_2d: removed halo regions
90    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
91      scheme and the corresponding test case (under front_relax dir). For now,
92      only available with Skew-flux form and not yet tested in realistic set-up.
93      adjoint: store directives updated, but gradient checks deteriorated,
94      so maybe GM/Redi adjoint is now broken.
95    o seaice adjoint
96      * add AREA, HEFF, HSNOW as control variable
97        (should not change lab_sea results)
98      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
99    o pkg/seaice:
100      * added computation of saltFlux in seaice_growth;
101        For time being, sea ice salinity is assumed constant
102        contribution of snow flooding to freshening of sea ice is neglected.
103        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
104        defaults to 0.0 in order to maintain backward compatibility.
105        Typical values for SEAICE_salinity are 4 to 10 g/kg.
106      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
107      * added SEAICE_availHeatFrac, which specifies fraction of surface level
108        heat content used to melt or grow ice
109      * commented out cap of HICE: it helps keep ice thinner
110      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
111      * applied OBCS T/S mask to HEFFM sea ice mask
112    
113    checkpoint59d
114    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
115     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
116     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
117    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
118     and change default value of parameter "GM_Small_Number";
119     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
120       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
121       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
122    o pkg/ecco: cost function when applying pkg/smooth to controls
123    o pkg/ctrl: add forcingPrecond run time parameter
124    o pkg/seaice:
125     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
126     - fix bug in metric terms of u-equation in LSR solver (implicit part),
127       changes verification/lab_sea
128     - rearrange implicit part of u-equation in LSR solver to make it easier to
129       read, understand, and debug. This causes changes at the truncation level.
130     - fix (serious) bug in the boundary conditions (sign error in the implicit
131       part) of the LSR solver. Changes all LSR results.
132     - fixed problem with HSNOW initialization to avoid thick snow when AREA
133       is initilized with small values - does not change lab_sea results.
134     - added HsnowFile initialization capability
135    o pkg/smooth: addition to model/src and pkg/ctrl so allow
136     initialization of pkg/smooth and application to control vector
137    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
138    o dependencies: pkg/profiles requires pkg/cal
139    o pkg/profiles:
140     - added option ALLOW_PROFILES_GENERICGRID
141         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
142         that interpolation information (grid points and coefficients) is provided
143         within the netcdf input files.
144         -> sample matlab scripts can be found in MITgcm_contrib/gael
145         that allow you to prepare netcdf input files.
146     - also modified: cleaner include statements, cleaner error print statements,
147       cleaner stops when error, and more tests of the netcdf input files consistency.
148    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
149    o pkg/seaice:
150     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
151       requires a new routine: seaice_diagnostics_fill.F
152     - make sure that seaice does not move if not forced (pressure replacement
153       method, Hibler and Ip, 1995), changes results
154     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
155     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
156       It is turned off by default (=-1.), because it changes the results.
157     - make it possible to read AREA from a file, too.
158    
159    checkpoint59c
160    o add S/R and diagnostics for oceanic mixed-layer depth
161    o move GMRedi call after all vertical mixing schemes (including KPP)
162    o pkg/thsice:
163     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
164      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
165    o pkg/obcs:
166     - bug fix for balance code
167    o pkg/seaice:
168      - allow values of SEAICE_elasticParm > 1
169      - add new parameter SEAICE_evpTauRelax as an alternative
170        to SEAICE_elasticParm
171      - make lsr boundary conditions free slip (by default), changes result
172      - add code for no slip boundary conditions for lsr
173      - set minimum of zeta to zero (and not 4e8) (changes results)
174      - add a cap on AREA after advecting AREA if seaice_growth is not called
175    o change calculation of Visbeck K:
176      - no longer depend on tapering scheme; instead, compute slope (limited
177        by GM_maxSlope). this is equivalent to what was comuted before with
178        clipping or linear tappering.
179      - fix vertical averaging (wrong by 1/2 level)
180      - leave the old version (but will not be maintained) within
181        #ifdef OLD_VISBECK_CALC / #endif
182      - update output of exp. ideal_2D_oce
183    o change error catch in calc_r_star to improve vectorization
184    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
185      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
186    o adjoint:
187      Re-organized adjoint checkpointing according to Matt Mazloff
188      (but with modifs/completions/cleanups)
189      Storing is now bundled into large arrays to optimized I/O
190      (and second step in cleanup of the_main_loop)
191    
192    checkpoint59b
193    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
194      - export/import (between ocean & coupler) fields needed for ocean DIC.
195    o pkg/seaice:
196      - get rid of three more exchanges seaice_calc_viscosities (required
197        different loop boundaries in seaice_lsr and seaice_ocean_stress)
198      - bug fix in seaice_ocean_stress (update of lab_sea required)
199      - reduce loop boundaries to necessary minimum also in seaice_evp
200      - go back to the old way of computing deltaC/Z as the adjoint likes that
201        better
202    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
203      passive tracer to an Age Tracer) + update output.txt
204    o pkg/exf:
205      - implement A-grid / C-grid selection for wind-stress input files.
206      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
207      for now, in exf_bulk_largeyeager04.F only :
208      - change implementation for case where windspeed + 2. components wind-stress
209        are read-in. AND use rhoConstFresh to convert evap.
210    o pkg/seaice:
211      - use correct EXCH_UV for wind-forcing (on A-grid).
212      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
213        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
214    o pkg/exf:
215      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
216      EXF_INTERPOLATION:
217      - merge global_with_exf/code version of exf_interp_read.F
218        to the main code ;
219      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
220        reading the file ; Important: This options needs to be defined to recover
221        previous code.
222        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
223      - no longer loose real*8 precision along the way when using exf_iprec=64.
224    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
225      - change discretisation of evp-solver in order to avoid another exchange
226        (changes lab_sea) and clean up a little
227      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
228        help the adjoint (this also changes the results slightly)
229      - add a few "_d 0" where they had been missing in seaice_evp.F
230      - cleaning up: remove unused seaice_calc_rhs.F
231    o pkg/exf: some cleaning-up:
232      - change various "constants" into runtime parameters
233      - cleaned-up Large&Yeager04 routine which should eventually
234        replace exf_bulkformulae.F (changed names of S/R and CPP)
235        and merged various ALLOW_ATM_WIND options
236     only used with thsice pkg (in thsice_get_exf.F):
237      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
238        which are used when useStabilityFct_overIce=TRUE (= the default)
239      - change default values of ice & snow emissivity and scale downward LW
240        by ice & snow emissivity.
241    o pkg/thsice:
242     fix few little problems, in thsice_calc_thickn.F:
243      - growth vertically (and not laterally) if iceFrac == iceMaskMax
244      - melt only laterally if hIce < hThinIce (as the comments say)
245      and in thsice_extend.F:
246      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
247      - start to form ice as soon as the minimum ice-volume is reachable.
248     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
249      and cpl_aim+ocn
250    o pkg/kpp
251     - move computation of surface related input fields to KPP into a new
252       subroutine kpp_forcing_surf.F
253     - remove wrong (within bi,bj loops) EXCH calls.
254     - little cleaning (add argument myThid in last position, cvs header ...)
255     - for now, fix conservation problem by exchanging KPPviscAz (may not
256       be the best fix)
257    o pkg/seaice
258     - check for inconsistent evp parameter/cpp-flag combination
259     - remove leftover errIO flat for obsolete name list error handling
260    o OpenAD
261     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
262    
263    checkpoint59a
264    o pkg/seaice: some parameter clarifications and a little bit of clean up
265    o pkg/thsice: rename run-time parameters:
266       himin       -> hIceMin
267       himin0      -> hThinIce
268       hihig       -> hThickIce
269       i0          -> i0swFrac
270       transCoef   -> bMeltCoef
271       frac_energy -> fracMelting
272      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
273       with default values (for now) that do not change the results.
274      remove old version of thsice vars advection in pkg/seaice.
275    o in FFIELDS.h:
276      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
277      - make pLoad & sIceLoad always available (but still only used if
278         ATMOSPHERIC_LOADING is #define).
279    o pkg/kpp: replaced _KPP_RL with _RL
280    o bug fixes for vertical diffusivity computations when both KPP and
281        3D diffusivity arrays are used.
282    o pkg/seaice: fix bug in evp solver, while doing that
283      - change (improve?) discretization of stress computations for both
284        cgrid-lsr and evp solver
285      - add a new routine to compute strain rates
286      - the above changes lab_sea results
287      - add no slip conditions for evp solver (off by default), lsr-version
288        may follow
289      - fix exchange for shear at Z-points (does not change lab_sea)
290      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
291        (to force the user to pick a time step since there is not "safe" way
292        of choosing it)
293      - add principal stress diagnostics
294      - rearrange fields for evp a little to avoid having to call a: too many
295        exchanges and b: exchanges for stress trensor components which we do
296        not have.
297      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
298        of evp, complete rewrite for lsr case (latter is does not yet work
299        in all cases)
300    o pkg/kpp: add code to have mixing in shelf ice caverns
301      - add myThid to all kpp routines (long overdue)
302    
303    checkpoint59
304    o pkg/exf:
305      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
306        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
307      - move exf header files from lower_case.h to UPPER_CASE.h ;
308        add missing cvs Header & Name
309      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
310      - add namelist param. selectStressGridPosition, exf_monFreq
311      - retire many _CLIM routines, and remove data.exf_clim
312        + params moved to data.exf
313        + climsst, climsss now handled by exf_set_gen, i.e.
314          climss?period=0 refers to constant field,
315          climss?period=-12 to monthly forcing
316      - split up namelists in data.exf
317    o pkg/seaice:
318      - remove seaice_exch and seaice_exch_uv
319      - remove superfluous exchange of theta
320      - add myThid to seaice_budget_ocean/ice
321      - add new interface for atmospheric wind forcing (C-grid only)
322        + new routine
323        + two new field (taux, tauy for stress over ice)
324        + removed one global field (DAIRN) for C-grid case only
325    o pkg/thsise
326      - 2nd set of modifs for thsice adjoint in conjunction with exf
327    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
328    
329    checkpoint58y_post
330    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
331      vertical diffusivity, similar to that in MOM4; turned on using
332      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
333      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
334    o Added capability for 3D specification of background vertical diffusion
335      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
336      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
337      "data" file that contains the 3D vertical diffusivity coefficients.
338    o ice dynamics (pkg/seaice) with thsice thermodynamics:
339      - add code within pkg thsice to advect & diffuse sea-ice fields
340      similar to (and will replace) what has been added in  seaice_advdiff.F,
341      but: - conserving Mass, Heat & Salt.
342           - better when using non-linear advection scheme (not yet fully tested)
343           - can also be used in atmospheric set-up (for now, only the diffusion).
344    
345    checkpoint58x_post
346    o IO option for global-file compact format:
347      - add options when generating topology (utils/exch2/matlab-topology-generator)
348      - add I/O capability (pkg/mdsio).
349      - adapt utils/matlab/rdmds.m to read this format.
350      for now long-line format not yet supported by pkg/mdsio (& exch2).
351    o shelfice: add a few diagnostics
352    
353    checkpoint58w_post
354    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
355      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
356      (and replace horiVertRatio in NH code).
357      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
358                         and tutorial_plume_on_slope (sensitive to truncation)
359    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
360      directly to drive seaice model (C-grid only)
361    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
362     - reintroduce computation of wind from stress,
363     - compute tau (in exf_bulkformulae.F) from windstress averaged to
364       mass points to avoid tau = 0
365     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
366    o rdmnc.m: make it work with "global" files created with gluemnc
367    o rdmnc.m : some improvements in dealing with singleton dimension
368      (tested on all testreport mnc output files).
369    o genmake2: disable pkg/profiles if netcdf test fails.
370    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
371    o move call to cal_readparms up to make calendar parameters/variable available
372      to all packages
373    
374    checkpoint58v_post
375    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
376      useDynP_inEos_Zc tested.
377    o pkg/exf: changes to properly interpolate/mask/scale initial fields
378    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
379      and portions thereof.  See read_cs.txt for description and examples.
380    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
381      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
382      following the great-circle arc between those 2 points.
383    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
384      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
385    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
386     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
387     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
388     - still needs work (not working with some options ; efficiency to improve)
389       and serious testing.
390     - use this scheme for temperature & salinity in 2 advection test exp.:
391       advect_xy & advect_xz, respectively.
392    
393    checkpoint58u_post
394    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
395    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
396    o testreport: add option "-skipdir" to skip some test.
397    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
398      momentum calculation.
399    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
400    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
401      remove checkpoint.F and the_correction_step.F (no longer used);
402      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
403    o add option (linFSConserveTr) to correct for tracer source/sink due to
404      Linear Free surface
405    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
406    o pkg/thsice: fix reading mnc-pickups
407    
408    checkpoint58t_post
409    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
410    o pkg/mdsio:
411     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
412       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
413       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
414     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
415     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
416       either MDS_READ_FIELD or MDS_WRITE_FIELD )
417     - new S/R (to replace MDSWRITEMETA), which allows to write more
418       informations (variable names, time ...) to meta files.
419     - modify rdmds.m to give back the meta file content.
420    o pkg/diagnostics: change vertical interpolation to be safer, and more
421       flexible (define p-levels to interpolate to in data.diagnostics);
422      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
423       diagnostic pointer.
424    o pkg/seaice: more cleaning up of seaice_growth, added many comments
425    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
426    o fix multi-category seaice:
427     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
428       SEAICE_MULTICATEGORY
429     - fix short wave heat flux
430    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
431       and allow to use EVP solver. Change forward lab_sea: test both EVP
432       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
433    o Initial check-in of lab_sea adjoint
434      (very similar to natl_box_adjoint/code_seaice)
435      * used C-grid and EVP solver
436      * used KPP, GM/Redi
437      * uses inAdExact=.TRUE.
438      * gradient checks fail for both ADM and TLM
439        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
440        f.d. gradients actually seem more problematic than ADM, TLM gradients;
441        issue is related to forward mismatch between g77 an ifort
442    o pkg/seaice: overhaul of thermodynamics
443     - growth.F and groatb.F are replaced by new routine seaice_growth.F
444     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
445     - move a few global fields out of SEAICE.h into seaice_growth.F and
446       make them 2D (FICE/QNETO/ ...)
447     - remove FO (it is the same as QNETO)
448     - introduce a few local fields to avoid modifying external fields such
449       as atemp, etc.
450    
451    checkpoint58s_post
452    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
453      changed exf_set_gen.F so that
454        genperiod=0 means input file is one time-constant field and
455        genperiod=-12 means input file contains 12 monthly means
456    o CG2D: use pre-computed solver main-diagonal (stored in common block);
457      this affects truncation error ; generate new output file for exp. which
458      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
459        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
460        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
461        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
462        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
463        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
464    o start implementation of deep-atmosphere and anelastic formulation
465    o verification: remove 2nd copy of input files and use script "prepare_run"
466      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
467    o mom_common/vecinv/fluxform: fix a few initialisation isssues
468    o profiles: fix for multithreaded case
469    
470    o diagnostics: rename few diags:
471      s/'PRESSURE'/'RCENTER '/g
472      s/'TICE    '/'oceFreez'/g
473      s/'TAUX    '/'oceTAUX '/g
474      s/'TAUY    '/'oceTAUY '/g
475      s/'SWFLUX  '/'oceQsw  '/g
476      s/DIFx/DFxE/g
477      s/DIFy/DFyE/g
478      and add few ocean-forcing diagnostics:
479      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
480    o modifications to pkg/seaice/growth.F and budget.F, which change results of
481      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
482      as actual snow thickness.  It now refers everywhere to effective snow
483      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
484    
485    checkpoint58r_post
486    o modifications to pkg/seaice/growth.F, which change results of
487      lab_sea experiment: fixes pertain to melting snow over open water, to
488      masking EVAP under sea ice, and to using the correct AREA variable for
489      computations of EVAP, PRECIP, HSNOW, and GHEFF
490    o add ability to read bathy, salt, and theta using MNC (off by def)
491    o add flooding algorithm and advection of HSNOW for pkg/seaice;
492      both are turned off by default and do no change any results
493    o seaice advection with pkg/thsice: a step toward the use of non-linear
494      advection scheme, but #ifdef or commented out for now (requires more EXCH).
495    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
496      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
497      in natl_box (affects results @ truncation level: update output.txt)
498    o multi-threading and IO:
499      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
500      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
501        (needed to work with SingleCpuIO): tested in all verif. exp.
502    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
503      affects the results (but none of the verification test uses this scheme).
504    o Adding some pkg/diagnostics capability to pkg/seaice
505      (will certainly be subject to changes)
506    o ctrl: adding new control variables:
507      lwflux, lwdown, evap, snowprecip, apressure, runoff
508    
509    checkpoint58q_post
510    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
511      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
512      high_res_cube configuration by 4% on Columbia.
513    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
514      add (in global_with_exf/code) a version of EXF_INTERP_READ without
515      dynamical allocation (seems to work in multi-threaded).
516    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
517      single CPU io) so that TAF does not have to see EESUPPORT.h
518    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
519    
520    checkpoint58p_post
521    o obcs: stop if obcs is used with useCDscheme = .true.
522    o shelfice:
523     - fix a sign error so that no slip at shelfice interface works
524     - remove stop for combination non-hydrostatic code and shelfice. That does
525       not mean, that the results are correct, but at least they are numerically
526       stable
527    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
528    o added adjoint exch routined for all exch*3d* routines
529      and updated flow directives
530    
531    checkpoint58o_post
532    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
533      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
534    o change controling S/R for writing pickup file (new S/R do_write_pickup)
535      and clean-up reading/writing of pickup files.
536    o fix local version of read/write pickup (NH part) in rotating_tank/code
537    o simplify EXCH interface:
538     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
539     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
540    o added the regrid package
541    o shelfice:
542     - add a simple boundary layer scheme to reduce noise
543     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
544    
545    checkpoint58n_post
546    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
547       local variable (not in common block).
548    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
549      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
550      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
551        to work with SingleCpuIO.
552    o add "_d 0" to real constant of pkg/cfc subroutines ;
553       update exp. cfc_exemple & tutorial_cfc_offline output files.
554    o multi-threading and IO:
555      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
556        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
557      - barrier before and after reading.
558      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
559      - avoid using MDS_WRITELOCAL for LAND pkg output.
560      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
561        common-block variables ; Allows multi-threading with master-thread IO.
562    o change default MAX_NO_THREADS from 32 to 4 ;
563      and stop cleanly when MAX_NO_THREADS is too small.
564    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
565    
566    checkpoint58m_post
567    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
568       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
569    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
570       keep global_ocean.90x40x15 (for AD testing) with former secondary test
571       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
572    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
573        add MITgcm_tutorials (= code + all the tutorials)
574    o ecco, option to compute cost for total ssh (mean+anom)
575    o consistent with addition of ptracer and ssh in pkg/profiles
576    o profiles: adding ptracer and ssh
577    o testreport: change multi-test output-file name
578      (from output.txt.{name} to output.{name}.txt)
579    o profiles: now ok for mutli-tiles case
580    o seaice: add 4 parameters for different advection schemes for area,
581      (effective) seaice thickness, enthalphy, and snow height. Their default
582      is the standard parameter SEAICEadvScheme
583    o calc_gw:
584     - add cosFacU in zonal viscous flux (harmonic.visc.).
585     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
586       of tutorial_plume_on_slope.
587    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
588    o calc_gw: true flux-form, account for horizontal grid spacing.
589      update rotating_tank results, but not plume_on_slope (affected at
590      truncation level, 11 digits).
591    
592    checkpoint58l_post
593    o calc_gw:
594     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
595     - remove side-drag for now (need to fix it); update plume_on_slope results.
596     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
597    o commit code to make SST/SSS weights spatially variable
598      (based on either variable in-situ or variable initial T/S weights)
599    o pkg/ecco:
600      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
601        now based on horizontally varying weights wthetaLev, wsaltLev
602      * cost_averagesflags now returns year indices in addition to day, month
603      * sflux balance is performed on annual basis
604        (sflxumm, sfluxmm2, bal_sfluxmm)
605      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
606        including separate counting and multipliers
607    o pkg/rbcs
608      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
609    
610    checkpoint58k_post
611    o testreport:
612     - always build in dir. "build" (if not there, mkdir build instead of building
613       & running in input)
614     - run in dir run (if it exists), in build otherwise.
615     - call prepare_run (if input/prepare_run exists)
616     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
617    o pkg/exf modifications to interpolation and rotation routines for more
618       reasonable treatment of North Pole singularity: for tracers North Pole
619       value is set to northernmost zonal-mean value, for zonal velocity it is
620       set to zero, and for meridional velocity it is set to northernmost value.
621    o pkg/exf/exf_check_range.F
622     - add tile index to diagnostics and move stop statement to the very
623       end of the routine.
624    o pkg/diagnostics: (diagnostics_main_init.F)
625      define title of isomorphic variables according to the current config.
626    o pkg/thsice with pkg/seaice dynamics:
627    - fix domain of computation (interior only, required for exf) and do exchanges
628    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
629    o towards a standard way of dealing with multi-threading in MONITOR
630      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
631  o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)  o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
632     to W momentum equation in nonhydrostatic and quasihydrostatic runs.       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
633  o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.  o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
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