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revision 1.757 by mlosch, Wed Dec 20 12:27:02 2006 UTC revision 1.907 by jmc, Fri Nov 9 15:42:54 2007 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint59j
8    o in pkgs: dic, obcs, offline, rbcs:
9      standard way to compute coeff. for time interpolation between 2 time reccords
10      which retains full precision (& make results less dependent on compiler).
11      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
12    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
13      packages instead of reading ice cover and wind speed separately
14    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
15     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
16      to allow to compile customized code before the update)
17    o cleaning-up:
18      - fix CPP instruction syntax in pkg/obcs
19      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
20        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
21      - fix some threads issue in IO parts.
22    o pkg/dic:
23      - add tons of "_d 0" (--> much better testreports !)
24       and then update outputs of tutorial_global_oce_biogeo
25    o pkg/mom_fluxform:
26      add a special version of momentum advection intended to conserve momentum
27      next to a bathymetry step or a coastline edge. (default = off = #undef)
28    o new read/write pickup version:
29      - for now, only implemented for main (mdsio) pickup file.
30      - write out only what is needed to restart; merge pickup_nh , pickup_ph
31        and main pickup together.
32      - read meta file; read only what is needed to restart; stop if a field
33        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
34        if it make sense (even if the restart is not perfect).
35      - if no meta file, assume that pickup to read corresponds exactly to
36        a pickup that would currently be written.
37      - read pickup written in the old format (until checkpoint59i) if it
38        recognizes an old meta file (no field-list).
39      - add a meta file in exp. which starts from a pickup: 2 cases:
40        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
41         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
42        b) a meta file describing the content of the associated pickup file
43         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
44    o pkg/mdsio & pkg/rw:
45      - new routine to read a meta file ; new set of routine to read
46        Multiple-fields file (with meta file).
47    o added open boundary conditions capability for seaice
48        HSNOW, HSALT, UICE, and VICE
49    
50    checkpoint59i
51    o adjoint:
52      * fix multiDimAdvection adjoint
53        (partial recomputation problem by TAF for fVerT(:,:,kDown)
54        and comlev1 size definition (maxpass vs. max. number of tracers)
55      * verification/global_ocean.90x45x15 adjoint now tests
56        NLFS and multiDimAdvection using DST3 (=30)
57      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
58    o pkg/kpp: add "_d 0" to real constant (if missing);
59      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
60      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
61    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
62      for internal parameters related to restart process (formerly from PARAMS.h)
63      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
64    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
65      as argument. (only atm2d & obcs write_pickup have not yet been updated)
66    o pkg/monitor:
67      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
68      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
69      - account for deep Atmosphere factor and density factor (anelastic)
70    o added open boundary conditions capability for seaice HEFF and AREA
71    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
72      thermodynamics
73      - requires a little reorganization, which affects the testreport results
74        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
75        so that now the conservative form is tested
76      - add a few comments
77    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
78    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
79    o add new diagnostics to seaice: advective, diffusive fluxes (only for
80      multidim-advection, for scheme 2 they are not filled) and transports,
81      thermodynamic growth rates
82    o change units of EmPmR (inside the code, + within coupling interface)
83      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
84      Affects results @ truncation level (cg2d match) and update output of
85       experiments: lab_sea(6), global_ocean.90x40x15(10),
86      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
87      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
88      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
89      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
90    
91    checkpoint59h
92    o pkg/exf:
93      - improve vectorization by moving if-statement out of loops in
94        exf_mapfields, exf_radiation
95      - exf_bulkformulae.F: introduce 2D fields and vectorize code
96    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
97    o testreport:
98      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
99        monitor & update offline_exf_seaice exp. output.
100      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
101    o pkg/seaice:
102      - bug fix in the evp solver: boundary conditions were affected be
103        masking of zMax/zMin (changes results)
104      - minor bug fix in boundary conditions in seaice_calc_strainrates
105        (changes results for no_slip)
106      - seaice_lsr.F: make interpolation of eta dependent on boundaries
107      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
108      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
109        stress formulation and no-slip boundary conditions
110    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
111      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
112    o pkg/seaice: a first HSALT time stepping equation has been checked in
113    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
114      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
115      without requiring DO-IF statements
116    o pkg/thsice:
117      use continuous power-law function for partition of energy between lateral
118      melting/freezing and thinning/thickening ; old code using step function
119      still available with #undef THSICE_FRACEN_POWERLAW
120      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
121    o testreport: change AD testing : check against results/output_adm.txt
122      using same scripts as for forward test.
123    
124    checkpoint59g
125    o adjoint testing: in preparation for changing testreport:
126      - output format: cost and grad written on separated lines
127      - ad output results in directory "results" (instead of "results_ad")
128    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
129    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
130    o pkg/ecco: allow user defined cost function contributions
131    o testreport:
132      Allow to choose (per experiment) the list of tested output variables
133       and the main variable (used to issue a pass/FAIL ) ;
134      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
135      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
136      Also modify printing of summary:
137       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
138       b) echo the list of tested variables in the individual summary.txt of
139          each experiment.
140    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
141      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
142      (but still depend on the tile decompostion of the domain).
143    o pkg/seaice: change a discretization detail to make the B-grid code
144      "more symmetric". This change is likely to remove all "ridges/leads" that
145      where quasi-aligned with the grid in B-grid solutions. It may also be
146      the solution to the stress coupling issues with the B-grid.
147    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
148      remove .cvsignore from input dir. (since testreport no longer run here).
149    o pkg/thsice:
150     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
151     - fix reshaping of sea-ice just after advection:
152       melt all the ice only if ice-volume is too small.
153     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
154       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
155     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
156    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
157      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
158    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
159      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
160      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
161      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
162      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
163      -> update output.txt
164    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
165     this affects truncation error: -> update output.txt of exp:
166      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
167      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
168    
169    checkpoint59f
170    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
171    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
172      a bounded range (in forward mode)
173    o pkg/ecco, ctrl, autodiff and mom_common:
174     internal parameter controls, completements of implementations
175    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
176    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
177      (not seem any difference in testing results).
178    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
179       at face corners.
180    o pkg/generic_advdiff:
181     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
182      loop range indices for computing vertical advection tendency
183      and do the calculation in the interior only (no overlap) ;
184      for now, only implemented for SOM advection (to save CPU time).
185     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
186    o exch2 adjoint
187      First set of changes:
188      - add exch2 hand-written adjoint templates
189      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
190        This will require cleanup in pkg/autodiff/*.F
191        (changed routines currently kept separate in verif. code/)
192      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
193        that used to hide exch2 or cubed-sphere specific code
194        (commented via 'cph-exch2')
195    o pkg/seaice
196      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
197    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
198       output of global_ocean.cs32x15.thsice .
199    
200    checkpoint59e
201    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
202      for B-grid vector (not yet tested) and C-grid vector (<- only used
203      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
204    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
205      (#ifdef ALLOW_SALT_PLUME)
206    o gather_2d/scatter_2d: removed halo regions
207    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
208      scheme and the corresponding test case (under front_relax dir). For now,
209      only available with Skew-flux form and not yet tested in realistic set-up.
210      adjoint: store directives updated, but gradient checks deteriorated,
211      so maybe GM/Redi adjoint is now broken.
212    o seaice adjoint
213      * add AREA, HEFF, HSNOW as control variable
214        (should not change lab_sea results)
215      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
216    o pkg/seaice:
217      * added computation of saltFlux in seaice_growth;
218        For time being, sea ice salinity is assumed constant
219        contribution of snow flooding to freshening of sea ice is neglected.
220        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
221        defaults to 0.0 in order to maintain backward compatibility.
222        Typical values for SEAICE_salinity are 4 to 10 g/kg.
223      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
224      * added SEAICE_availHeatFrac, which specifies fraction of surface level
225        heat content used to melt or grow ice
226      * commented out cap of HICE: it helps keep ice thinner
227      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
228      * applied OBCS T/S mask to HEFFM sea ice mask
229    
230    checkpoint59d
231    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
232     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
233     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
234    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
235     and change default value of parameter "GM_Small_Number";
236     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
237       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
238       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
239    o pkg/ecco: cost function when applying pkg/smooth to controls
240    o pkg/ctrl: add forcingPrecond run time parameter
241    o pkg/seaice:
242     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
243     - fix bug in metric terms of u-equation in LSR solver (implicit part),
244       changes verification/lab_sea
245     - rearrange implicit part of u-equation in LSR solver to make it easier to
246       read, understand, and debug. This causes changes at the truncation level.
247     - fix (serious) bug in the boundary conditions (sign error in the implicit
248       part) of the LSR solver. Changes all LSR results.
249     - fixed problem with HSNOW initialization to avoid thick snow when AREA
250       is initilized with small values - does not change lab_sea results.
251     - added HsnowFile initialization capability
252    o pkg/smooth: addition to model/src and pkg/ctrl so allow
253     initialization of pkg/smooth and application to control vector
254    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
255    o dependencies: pkg/profiles requires pkg/cal
256    o pkg/profiles:
257     - added option ALLOW_PROFILES_GENERICGRID
258         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
259         that interpolation information (grid points and coefficients) is provided
260         within the netcdf input files.
261         -> sample matlab scripts can be found in MITgcm_contrib/gael
262         that allow you to prepare netcdf input files.
263     - also modified: cleaner include statements, cleaner error print statements,
264       cleaner stops when error, and more tests of the netcdf input files consistency.
265    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
266    o pkg/seaice:
267     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
268       requires a new routine: seaice_diagnostics_fill.F
269     - make sure that seaice does not move if not forced (pressure replacement
270       method, Hibler and Ip, 1995), changes results
271     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
272     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
273       It is turned off by default (=-1.), because it changes the results.
274     - make it possible to read AREA from a file, too.
275    
276    checkpoint59c
277    o add S/R and diagnostics for oceanic mixed-layer depth
278    o move GMRedi call after all vertical mixing schemes (including KPP)
279    o pkg/thsice:
280     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
281      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
282    o pkg/obcs:
283     - bug fix for balance code
284    o pkg/seaice:
285      - allow values of SEAICE_elasticParm > 1
286      - add new parameter SEAICE_evpTauRelax as an alternative
287        to SEAICE_elasticParm
288      - make lsr boundary conditions free slip (by default), changes result
289      - add code for no slip boundary conditions for lsr
290      - set minimum of zeta to zero (and not 4e8) (changes results)
291      - add a cap on AREA after advecting AREA if seaice_growth is not called
292    o change calculation of Visbeck K:
293      - no longer depend on tapering scheme; instead, compute slope (limited
294        by GM_maxSlope). this is equivalent to what was comuted before with
295        clipping or linear tappering.
296      - fix vertical averaging (wrong by 1/2 level)
297      - leave the old version (but will not be maintained) within
298        #ifdef OLD_VISBECK_CALC / #endif
299      - update output of exp. ideal_2D_oce
300    o change error catch in calc_r_star to improve vectorization
301    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
302      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
303    o adjoint:
304      Re-organized adjoint checkpointing according to Matt Mazloff
305      (but with modifs/completions/cleanups)
306      Storing is now bundled into large arrays to optimized I/O
307      (and second step in cleanup of the_main_loop)
308    
309    checkpoint59b
310    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
311      - export/import (between ocean & coupler) fields needed for ocean DIC.
312    o pkg/seaice:
313      - get rid of three more exchanges seaice_calc_viscosities (required
314        different loop boundaries in seaice_lsr and seaice_ocean_stress)
315      - bug fix in seaice_ocean_stress (update of lab_sea required)
316      - reduce loop boundaries to necessary minimum also in seaice_evp
317      - go back to the old way of computing deltaC/Z as the adjoint likes that
318        better
319    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
320      passive tracer to an Age Tracer) + update output.txt
321    o pkg/exf:
322      - implement A-grid / C-grid selection for wind-stress input files.
323      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
324      for now, in exf_bulk_largeyeager04.F only :
325      - change implementation for case where windspeed + 2. components wind-stress
326        are read-in. AND use rhoConstFresh to convert evap.
327    o pkg/seaice:
328      - use correct EXCH_UV for wind-forcing (on A-grid).
329      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
330        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
331    o pkg/exf:
332      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
333      EXF_INTERPOLATION:
334      - merge global_with_exf/code version of exf_interp_read.F
335        to the main code ;
336      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
337        reading the file ; Important: This options needs to be defined to recover
338        previous code.
339        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
340      - no longer loose real*8 precision along the way when using exf_iprec=64.
341    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
342      - change discretisation of evp-solver in order to avoid another exchange
343        (changes lab_sea) and clean up a little
344      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
345        help the adjoint (this also changes the results slightly)
346      - add a few "_d 0" where they had been missing in seaice_evp.F
347      - cleaning up: remove unused seaice_calc_rhs.F
348    o pkg/exf: some cleaning-up:
349      - change various "constants" into runtime parameters
350      - cleaned-up Large&Yeager04 routine which should eventually
351        replace exf_bulkformulae.F (changed names of S/R and CPP)
352        and merged various ALLOW_ATM_WIND options
353     only used with thsice pkg (in thsice_get_exf.F):
354      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
355        which are used when useStabilityFct_overIce=TRUE (= the default)
356      - change default values of ice & snow emissivity and scale downward LW
357        by ice & snow emissivity.
358    o pkg/thsice:
359     fix few little problems, in thsice_calc_thickn.F:
360      - growth vertically (and not laterally) if iceFrac == iceMaskMax
361      - melt only laterally if hIce < hThinIce (as the comments say)
362      and in thsice_extend.F:
363      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
364      - start to form ice as soon as the minimum ice-volume is reachable.
365     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
366      and cpl_aim+ocn
367    o pkg/kpp
368     - move computation of surface related input fields to KPP into a new
369       subroutine kpp_forcing_surf.F
370     - remove wrong (within bi,bj loops) EXCH calls.
371     - little cleaning (add argument myThid in last position, cvs header ...)
372     - for now, fix conservation problem by exchanging KPPviscAz (may not
373       be the best fix)
374    o pkg/seaice
375     - check for inconsistent evp parameter/cpp-flag combination
376     - remove leftover errIO flat for obsolete name list error handling
377    o OpenAD
378     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
379    
380    checkpoint59a
381    o pkg/seaice: some parameter clarifications and a little bit of clean up
382    o pkg/thsice: rename run-time parameters:
383       himin       -> hIceMin
384       himin0      -> hThinIce
385       hihig       -> hThickIce
386       i0          -> i0swFrac
387       transCoef   -> bMeltCoef
388       frac_energy -> fracMelting
389      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
390       with default values (for now) that do not change the results.
391      remove old version of thsice vars advection in pkg/seaice.
392    o in FFIELDS.h:
393      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
394      - make pLoad & sIceLoad always available (but still only used if
395         ATMOSPHERIC_LOADING is #define).
396    o pkg/kpp: replaced _KPP_RL with _RL
397    o bug fixes for vertical diffusivity computations when both KPP and
398        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
399        are no longer updating the vertical diffusivity array
400        (passed as argument) but are (re-) setting those arrays.
401    o pkg/seaice: fix bug in evp solver, while doing that
402      - change (improve?) discretization of stress computations for both
403        cgrid-lsr and evp solver
404      - add a new routine to compute strain rates
405      - the above changes lab_sea results
406      - add no slip conditions for evp solver (off by default), lsr-version
407        may follow
408      - fix exchange for shear at Z-points (does not change lab_sea)
409      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
410        (to force the user to pick a time step since there is not "safe" way
411        of choosing it)
412      - add principal stress diagnostics
413      - rearrange fields for evp a little to avoid having to call a: too many
414        exchanges and b: exchanges for stress trensor components which we do
415        not have.
416      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
417        of evp, complete rewrite for lsr case (latter is does not yet work
418        in all cases)
419    o pkg/kpp: add code to have mixing in shelf ice caverns
420      - add myThid to all kpp routines (long overdue)
421    
422    checkpoint59
423    o pkg/exf:
424      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
425        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
426      - move exf header files from lower_case.h to UPPER_CASE.h ;
427        add missing cvs Header & Name
428      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
429      - add namelist param. selectStressGridPosition, exf_monFreq
430      - retire many _CLIM routines, and remove data.exf_clim
431        + params moved to data.exf
432        + climsst, climsss now handled by exf_set_gen, i.e.
433          climss?period=0 refers to constant field,
434          climss?period=-12 to monthly forcing
435      - split up namelists in data.exf
436    o pkg/seaice:
437      - remove seaice_exch and seaice_exch_uv
438      - remove superfluous exchange of theta
439      - add myThid to seaice_budget_ocean/ice
440      - add new interface for atmospheric wind forcing (C-grid only)
441        + new routine
442        + two new field (taux, tauy for stress over ice)
443        + removed one global field (DAIRN) for C-grid case only
444    o pkg/thsise
445      - 2nd set of modifs for thsice adjoint in conjunction with exf
446    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
447    
448    checkpoint58y_post
449    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
450      vertical diffusivity, similar to that in MOM4; turned on using
451      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
452      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
453    o Added capability for 3D specification of background vertical diffusion
454      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
455      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
456      "data" file that contains the 3D vertical diffusivity coefficients.
457    o ice dynamics (pkg/seaice) with thsice thermodynamics:
458      - add code within pkg thsice to advect & diffuse sea-ice fields
459      similar to (and will replace) what has been added in  seaice_advdiff.F,
460      but: - conserving Mass, Heat & Salt.
461           - better when using non-linear advection scheme (not yet fully tested)
462           - can also be used in atmospheric set-up (for now, only the diffusion).
463    
464    checkpoint58x_post
465    o IO option for global-file compact format:
466      - add options when generating topology (utils/exch2/matlab-topology-generator)
467      - add I/O capability (pkg/mdsio).
468      - adapt utils/matlab/rdmds.m to read this format.
469      for now long-line format not yet supported by pkg/mdsio (& exch2).
470    o shelfice: add a few diagnostics
471    
472    checkpoint58w_post
473    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
474      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
475      (and replace horiVertRatio in NH code).
476      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
477                         and tutorial_plume_on_slope (sensitive to truncation)
478    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
479      directly to drive seaice model (C-grid only)
480    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
481     - reintroduce computation of wind from stress,
482     - compute tau (in exf_bulkformulae.F) from windstress averaged to
483       mass points to avoid tau = 0
484     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
485    o rdmnc.m: make it work with "global" files created with gluemnc
486    o rdmnc.m : some improvements in dealing with singleton dimension
487      (tested on all testreport mnc output files).
488    o genmake2: disable pkg/profiles if netcdf test fails.
489    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
490    o move call to cal_readparms up to make calendar parameters/variable available
491      to all packages
492    
493    checkpoint58v_post
494    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
495      useDynP_inEos_Zc tested.
496    o pkg/exf: changes to properly interpolate/mask/scale initial fields
497    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
498      and portions thereof.  See read_cs.txt for description and examples.
499    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
500      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
501      following the great-circle arc between those 2 points.
502    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
503      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
504    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
505     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
506     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
507     - still needs work (not working with some options ; efficiency to improve)
508       and serious testing.
509     - use this scheme for temperature & salinity in 2 advection test exp.:
510       advect_xy & advect_xz, respectively.
511    
512    checkpoint58u_post
513    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
514    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
515    o testreport: add option "-skipdir" to skip some test.
516    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
517      momentum calculation.
518    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
519    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
520      remove checkpoint.F and the_correction_step.F (no longer used);
521      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
522    o add option (linFSConserveTr) to correct for tracer source/sink due to
523      Linear Free surface
524    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
525    o pkg/thsice: fix reading mnc-pickups
526    
527    checkpoint58t_post
528    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
529    o pkg/mdsio:
530     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
531       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
532       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
533     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
534     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
535       either MDS_READ_FIELD or MDS_WRITE_FIELD )
536     - new S/R (to replace MDSWRITEMETA), which allows to write more
537       informations (variable names, time ...) to meta files.
538     - modify rdmds.m to give back the meta file content.
539    o pkg/diagnostics: change vertical interpolation to be safer, and more
540       flexible (define p-levels to interpolate to in data.diagnostics);
541      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
542       diagnostic pointer.
543    o pkg/seaice: more cleaning up of seaice_growth, added many comments
544    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
545  o fix multi-category seaice:  o fix multi-category seaice:
546   - change cpp flag SEAICE_MULTILEVEL to more meaningful name:   - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
547     SEAICE_MULTICATEGORY     SEAICE_MULTICATEGORY
548   - fix short wave heat flux   - fix short wave heat flux
549    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
550       and allow to use EVP solver. Change forward lab_sea: test both EVP
551       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
552  o Initial check-in of lab_sea adjoint  o Initial check-in of lab_sea adjoint
553    (very similar to natl_box_adjoint/code_seaice)    (very similar to natl_box_adjoint/code_seaice)
554    * used C-grid and EVP solver    * used C-grid and EVP solver
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