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revision 1.747 by dimitri, Mon Nov 20 20:06:43 2006 UTC revision 1.897 by dimitri, Tue Oct 23 08:25:28 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 added open boundary conditions capability for seaice HSNOW and HSALT
8    
9    checkpoint59i
10    o adjoint:
11      * fix multiDimAdvection adjoint
12        (partial recomputation problem by TAF for fVerT(:,:,kDown)
13        and comlev1 size definition (maxpass vs. max. number of tracers)
14      * verification/global_ocean.90x45x15 adjoint now tests
15        NLFS and multiDimAdvection using DST3 (=30)
16      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
17    o pkg/kpp: add "_d 0" to real constant (if missing);
18      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
19      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
20    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
21      for internal parameters related to restart process (formerly from PARAMS.h)
22      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
23    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
24      as argument. (only atm2d & obcs write_pickup have not yet been updated)
25    o pkg/monitor:
26      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
27      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
28      - account for deep Atmosphere factor and density factor (anelastic)
29    o added open boundary conditions capability for seaice HEFF and AREA
30    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
31      thermodynamics
32      - requires a little reorganization, which affects the testreport results
33        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
34        so that now the conservative form is tested
35      - add a few comments
36    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
37    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
38    o add new diagnostics to seaice: advective, diffusive fluxes (only for
39      multidim-advection, for scheme 2 they are not filled) and transports,
40      thermodynamic growth rates
41    o change units of EmPmR (inside the code) from m/s to kg/m2/s (mass flux) but
42      leave input file unchanged. Affects results @ truncation level (cg2d match)
43      and update output of experiments: lab_sea(6), global_ocean.90x40x15(10),
44      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
45      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
46      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
47    
48    checkpoint59h
49    o pkg/exf:
50      - improve vectorization by moving if-statement out of loops in
51        exf_mapfields, exf_radiation
52      - exf_bulkformulae.F: introduce 2D fields and vectorize code
53    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
54    o testreport:
55      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
56        monitor & update offline_exf_seaice exp. output.
57      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
58    o pkg/seaice:
59      - bug fix in the evp solver: boundary conditions were affected be
60        masking of zMax/zMin (changes results)
61      - minor bug fix in boundary conditions in seaice_calc_strainrates
62        (changes results for no_slip)
63      - seaice_lsr.F: make interpolation of eta dependent on boundaries
64      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
65      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
66        stress formulation and no-slip boundary conditions
67    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
68      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
69    o pkg/seaice: a first HSALT time stepping equation has been checked in
70    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
71      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
72      without requiring DO-IF statements
73    o pkg/thsice:
74      use continuous power-law function for partition of energy between lateral
75      melting/freezing and thinning/thickening ; old code using step function
76      still available with #undef THSICE_FRACEN_POWERLAW
77      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
78    o testreport: change AD testing : check against results/output_adm.txt
79      using same scripts as for forward test.
80    
81    checkpoint59g
82    o adjoint testing: in preparation for changing testreport:
83      - output format: cost and grad written on separated lines
84      - ad output results in directory "results" (instead of "results_ad")
85    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
86    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
87    o pkg/ecco: allow user defined cost function contributions
88    o testreport:
89      Allow to choose (per experiment) the list of tested output variables
90       and the main variable (used to issue a pass/FAIL ) ;
91      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
92      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
93      Also modify printing of summary:
94       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
95       b) echo the list of tested variables in the individual summary.txt of
96          each experiment.
97    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
98      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
99      (but still depend on the tile decompostion of the domain).
100    o pkg/seaice: change a discretization detail to make the B-grid code
101      "more symmetric". This change is likely to remove all "ridges/leads" that
102      where quasi-aligned with the grid in B-grid solutions. It may also be
103      the solution to the stress coupling issues with the B-grid.
104    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
105      remove .cvsignore from input dir. (since testreport no longer run here).
106    o pkg/thsice:
107     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
108     - fix reshaping of sea-ice just after advection:
109       melt all the ice only if ice-volume is too small.
110     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
111       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
112     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
113    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
114      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
115    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
116      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
117      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
118      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
119      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
120      -> update output.txt
121    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
122     this affects truncation error: -> update output.txt of exp:
123      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
124      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
125    
126    checkpoint59f
127    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
128    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
129      a bounded range (in forward mode)
130    o pkg/ecco, ctrl, autodiff and mom_common:
131     internal parameter controls, completements of implementations
132    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
133    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
134      (not seem any difference in testing results).
135    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
136       at face corners.
137    o pkg/generic_advdiff:
138     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
139      loop range indices for computing vertical advection tendency
140      and do the calculation in the interior only (no overlap) ;
141      for now, only implemented for SOM advection (to save CPU time).
142     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
143    o exch2 adjoint
144      First set of changes:
145      - add exch2 hand-written adjoint templates
146      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
147        This will require cleanup in pkg/autodiff/*.F
148        (changed routines currently kept separate in verif. code/)
149      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
150        that used to hide exch2 or cubed-sphere specific code
151        (commented via 'cph-exch2')
152    o pkg/seaice
153      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
154    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
155       output of global_ocean.cs32x15.thsice .
156    
157    checkpoint59e
158    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
159      for B-grid vector (not yet tested) and C-grid vector (<- only used
160      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
161    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
162      (#ifdef ALLOW_SALT_PLUME)
163    o gather_2d/scatter_2d: removed halo regions
164    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
165      scheme and the corresponding test case (under front_relax dir). For now,
166      only available with Skew-flux form and not yet tested in realistic set-up.
167      adjoint: store directives updated, but gradient checks deteriorated,
168      so maybe GM/Redi adjoint is now broken.
169    o seaice adjoint
170      * add AREA, HEFF, HSNOW as control variable
171        (should not change lab_sea results)
172      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
173    o pkg/seaice:
174      * added computation of saltFlux in seaice_growth;
175        For time being, sea ice salinity is assumed constant
176        contribution of snow flooding to freshening of sea ice is neglected.
177        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
178        defaults to 0.0 in order to maintain backward compatibility.
179        Typical values for SEAICE_salinity are 4 to 10 g/kg.
180      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
181      * added SEAICE_availHeatFrac, which specifies fraction of surface level
182        heat content used to melt or grow ice
183      * commented out cap of HICE: it helps keep ice thinner
184      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
185      * applied OBCS T/S mask to HEFFM sea ice mask
186    
187    checkpoint59d
188    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
189     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
190     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
191    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
192     and change default value of parameter "GM_Small_Number";
193     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
194       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
195       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
196    o pkg/ecco: cost function when applying pkg/smooth to controls
197    o pkg/ctrl: add forcingPrecond run time parameter
198    o pkg/seaice:
199     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
200     - fix bug in metric terms of u-equation in LSR solver (implicit part),
201       changes verification/lab_sea
202     - rearrange implicit part of u-equation in LSR solver to make it easier to
203       read, understand, and debug. This causes changes at the truncation level.
204     - fix (serious) bug in the boundary conditions (sign error in the implicit
205       part) of the LSR solver. Changes all LSR results.
206     - fixed problem with HSNOW initialization to avoid thick snow when AREA
207       is initilized with small values - does not change lab_sea results.
208     - added HsnowFile initialization capability
209    o pkg/smooth: addition to model/src and pkg/ctrl so allow
210     initialization of pkg/smooth and application to control vector
211    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
212    o dependencies: pkg/profiles requires pkg/cal
213    o pkg/profiles:
214     - added option ALLOW_PROFILES_GENERICGRID
215         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
216         that interpolation information (grid points and coefficients) is provided
217         within the netcdf input files.
218         -> sample matlab scripts can be found in MITgcm_contrib/gael
219         that allow you to prepare netcdf input files.
220     - also modified: cleaner include statements, cleaner error print statements,
221       cleaner stops when error, and more tests of the netcdf input files consistency.
222    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
223    o pkg/seaice:
224     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
225       requires a new routine: seaice_diagnostics_fill.F
226     - make sure that seaice does not move if not forced (pressure replacement
227       method, Hibler and Ip, 1995), changes results
228     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
229     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
230       It is turned off by default (=-1.), because it changes the results.
231     - make it possible to read AREA from a file, too.
232    
233    checkpoint59c
234    o add S/R and diagnostics for oceanic mixed-layer depth
235    o move GMRedi call after all vertical mixing schemes (including KPP)
236    o pkg/thsice:
237     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
238      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
239    o pkg/obcs:
240     - bug fix for balance code
241    o pkg/seaice:
242      - allow values of SEAICE_elasticParm > 1
243      - add new parameter SEAICE_evpTauRelax as an alternative
244        to SEAICE_elasticParm
245      - make lsr boundary conditions free slip (by default), changes result
246      - add code for no slip boundary conditions for lsr
247      - set minimum of zeta to zero (and not 4e8) (changes results)
248      - add a cap on AREA after advecting AREA if seaice_growth is not called
249    o change calculation of Visbeck K:
250      - no longer depend on tapering scheme; instead, compute slope (limited
251        by GM_maxSlope). this is equivalent to what was comuted before with
252        clipping or linear tappering.
253      - fix vertical averaging (wrong by 1/2 level)
254      - leave the old version (but will not be maintained) within
255        #ifdef OLD_VISBECK_CALC / #endif
256      - update output of exp. ideal_2D_oce
257    o change error catch in calc_r_star to improve vectorization
258    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
259      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
260    o adjoint:
261      Re-organized adjoint checkpointing according to Matt Mazloff
262      (but with modifs/completions/cleanups)
263      Storing is now bundled into large arrays to optimized I/O
264      (and second step in cleanup of the_main_loop)
265    
266    checkpoint59b
267    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
268      - export/import (between ocean & coupler) fields needed for ocean DIC.
269    o pkg/seaice:
270      - get rid of three more exchanges seaice_calc_viscosities (required
271        different loop boundaries in seaice_lsr and seaice_ocean_stress)
272      - bug fix in seaice_ocean_stress (update of lab_sea required)
273      - reduce loop boundaries to necessary minimum also in seaice_evp
274      - go back to the old way of computing deltaC/Z as the adjoint likes that
275        better
276    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
277      passive tracer to an Age Tracer) + update output.txt
278    o pkg/exf:
279      - implement A-grid / C-grid selection for wind-stress input files.
280      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
281      for now, in exf_bulk_largeyeager04.F only :
282      - change implementation for case where windspeed + 2. components wind-stress
283        are read-in. AND use rhoConstFresh to convert evap.
284    o pkg/seaice:
285      - use correct EXCH_UV for wind-forcing (on A-grid).
286      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
287        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
288    o pkg/exf:
289      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
290      EXF_INTERPOLATION:
291      - merge global_with_exf/code version of exf_interp_read.F
292        to the main code ;
293      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
294        reading the file ; Important: This options needs to be defined to recover
295        previous code.
296        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
297      - no longer loose real*8 precision along the way when using exf_iprec=64.
298    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
299      - change discretisation of evp-solver in order to avoid another exchange
300        (changes lab_sea) and clean up a little
301      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
302        help the adjoint (this also changes the results slightly)
303      - add a few "_d 0" where they had been missing in seaice_evp.F
304      - cleaning up: remove unused seaice_calc_rhs.F
305    o pkg/exf: some cleaning-up:
306      - change various "constants" into runtime parameters
307      - cleaned-up Large&Yeager04 routine which should eventually
308        replace exf_bulkformulae.F (changed names of S/R and CPP)
309        and merged various ALLOW_ATM_WIND options
310     only used with thsice pkg (in thsice_get_exf.F):
311      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
312        which are used when useStabilityFct_overIce=TRUE (= the default)
313      - change default values of ice & snow emissivity and scale downward LW
314        by ice & snow emissivity.
315    o pkg/thsice:
316     fix few little problems, in thsice_calc_thickn.F:
317      - growth vertically (and not laterally) if iceFrac == iceMaskMax
318      - melt only laterally if hIce < hThinIce (as the comments say)
319      and in thsice_extend.F:
320      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
321      - start to form ice as soon as the minimum ice-volume is reachable.
322     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
323      and cpl_aim+ocn
324    o pkg/kpp
325     - move computation of surface related input fields to KPP into a new
326       subroutine kpp_forcing_surf.F
327     - remove wrong (within bi,bj loops) EXCH calls.
328     - little cleaning (add argument myThid in last position, cvs header ...)
329     - for now, fix conservation problem by exchanging KPPviscAz (may not
330       be the best fix)
331    o pkg/seaice
332     - check for inconsistent evp parameter/cpp-flag combination
333     - remove leftover errIO flat for obsolete name list error handling
334    o OpenAD
335     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
336    
337    checkpoint59a
338    o pkg/seaice: some parameter clarifications and a little bit of clean up
339    o pkg/thsice: rename run-time parameters:
340       himin       -> hIceMin
341       himin0      -> hThinIce
342       hihig       -> hThickIce
343       i0          -> i0swFrac
344       transCoef   -> bMeltCoef
345       frac_energy -> fracMelting
346      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
347       with default values (for now) that do not change the results.
348      remove old version of thsice vars advection in pkg/seaice.
349    o in FFIELDS.h:
350      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
351      - make pLoad & sIceLoad always available (but still only used if
352         ATMOSPHERIC_LOADING is #define).
353    o pkg/kpp: replaced _KPP_RL with _RL
354    o bug fixes for vertical diffusivity computations when both KPP and
355        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
356        are no longer updating the vertical diffusivity array
357        (passed as argument) but are (re-) setting those arrays.
358    o pkg/seaice: fix bug in evp solver, while doing that
359      - change (improve?) discretization of stress computations for both
360        cgrid-lsr and evp solver
361      - add a new routine to compute strain rates
362      - the above changes lab_sea results
363      - add no slip conditions for evp solver (off by default), lsr-version
364        may follow
365      - fix exchange for shear at Z-points (does not change lab_sea)
366      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
367        (to force the user to pick a time step since there is not "safe" way
368        of choosing it)
369      - add principal stress diagnostics
370      - rearrange fields for evp a little to avoid having to call a: too many
371        exchanges and b: exchanges for stress trensor components which we do
372        not have.
373      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
374        of evp, complete rewrite for lsr case (latter is does not yet work
375        in all cases)
376    o pkg/kpp: add code to have mixing in shelf ice caverns
377      - add myThid to all kpp routines (long overdue)
378    
379    checkpoint59
380    o pkg/exf:
381      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
382        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
383      - move exf header files from lower_case.h to UPPER_CASE.h ;
384        add missing cvs Header & Name
385      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
386      - add namelist param. selectStressGridPosition, exf_monFreq
387      - retire many _CLIM routines, and remove data.exf_clim
388        + params moved to data.exf
389        + climsst, climsss now handled by exf_set_gen, i.e.
390          climss?period=0 refers to constant field,
391          climss?period=-12 to monthly forcing
392      - split up namelists in data.exf
393    o pkg/seaice:
394      - remove seaice_exch and seaice_exch_uv
395      - remove superfluous exchange of theta
396      - add myThid to seaice_budget_ocean/ice
397      - add new interface for atmospheric wind forcing (C-grid only)
398        + new routine
399        + two new field (taux, tauy for stress over ice)
400        + removed one global field (DAIRN) for C-grid case only
401    o pkg/thsise
402      - 2nd set of modifs for thsice adjoint in conjunction with exf
403    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
404    
405    checkpoint58y_post
406    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
407      vertical diffusivity, similar to that in MOM4; turned on using
408      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
409      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
410    o Added capability for 3D specification of background vertical diffusion
411      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
412      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
413      "data" file that contains the 3D vertical diffusivity coefficients.
414    o ice dynamics (pkg/seaice) with thsice thermodynamics:
415      - add code within pkg thsice to advect & diffuse sea-ice fields
416      similar to (and will replace) what has been added in  seaice_advdiff.F,
417      but: - conserving Mass, Heat & Salt.
418           - better when using non-linear advection scheme (not yet fully tested)
419           - can also be used in atmospheric set-up (for now, only the diffusion).
420    
421    checkpoint58x_post
422    o IO option for global-file compact format:
423      - add options when generating topology (utils/exch2/matlab-topology-generator)
424      - add I/O capability (pkg/mdsio).
425      - adapt utils/matlab/rdmds.m to read this format.
426      for now long-line format not yet supported by pkg/mdsio (& exch2).
427    o shelfice: add a few diagnostics
428    
429    checkpoint58w_post
430    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
431      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
432      (and replace horiVertRatio in NH code).
433      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
434                         and tutorial_plume_on_slope (sensitive to truncation)
435    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
436      directly to drive seaice model (C-grid only)
437    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
438     - reintroduce computation of wind from stress,
439     - compute tau (in exf_bulkformulae.F) from windstress averaged to
440       mass points to avoid tau = 0
441     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
442    o rdmnc.m: make it work with "global" files created with gluemnc
443    o rdmnc.m : some improvements in dealing with singleton dimension
444      (tested on all testreport mnc output files).
445    o genmake2: disable pkg/profiles if netcdf test fails.
446    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
447    o move call to cal_readparms up to make calendar parameters/variable available
448      to all packages
449    
450    checkpoint58v_post
451    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
452      useDynP_inEos_Zc tested.
453    o pkg/exf: changes to properly interpolate/mask/scale initial fields
454    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
455      and portions thereof.  See read_cs.txt for description and examples.
456    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
457      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
458      following the great-circle arc between those 2 points.
459    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
460      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
461    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
462     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
463     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
464     - still needs work (not working with some options ; efficiency to improve)
465       and serious testing.
466     - use this scheme for temperature & salinity in 2 advection test exp.:
467       advect_xy & advect_xz, respectively.
468    
469    checkpoint58u_post
470    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
471    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
472    o testreport: add option "-skipdir" to skip some test.
473    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
474      momentum calculation.
475    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
476    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
477      remove checkpoint.F and the_correction_step.F (no longer used);
478      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
479    o add option (linFSConserveTr) to correct for tracer source/sink due to
480      Linear Free surface
481    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
482    o pkg/thsice: fix reading mnc-pickups
483    
484    checkpoint58t_post
485    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
486    o pkg/mdsio:
487     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
488       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
489       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
490     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
491     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
492       either MDS_READ_FIELD or MDS_WRITE_FIELD )
493     - new S/R (to replace MDSWRITEMETA), which allows to write more
494       informations (variable names, time ...) to meta files.
495     - modify rdmds.m to give back the meta file content.
496    o pkg/diagnostics: change vertical interpolation to be safer, and more
497       flexible (define p-levels to interpolate to in data.diagnostics);
498      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
499       diagnostic pointer.
500    o pkg/seaice: more cleaning up of seaice_growth, added many comments
501    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
502    o fix multi-category seaice:
503     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
504       SEAICE_MULTICATEGORY
505     - fix short wave heat flux
506    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
507       and allow to use EVP solver. Change forward lab_sea: test both EVP
508       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
509    o Initial check-in of lab_sea adjoint
510      (very similar to natl_box_adjoint/code_seaice)
511      * used C-grid and EVP solver
512      * used KPP, GM/Redi
513      * uses inAdExact=.TRUE.
514      * gradient checks fail for both ADM and TLM
515        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
516        f.d. gradients actually seem more problematic than ADM, TLM gradients;
517        issue is related to forward mismatch between g77 an ifort
518    o pkg/seaice: overhaul of thermodynamics
519     - growth.F and groatb.F are replaced by new routine seaice_growth.F
520     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
521     - move a few global fields out of SEAICE.h into seaice_growth.F and
522       make them 2D (FICE/QNETO/ ...)
523     - remove FO (it is the same as QNETO)
524     - introduce a few local fields to avoid modifying external fields such
525       as atemp, etc.
526    
527    checkpoint58s_post
528    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
529      changed exf_set_gen.F so that
530        genperiod=0 means input file is one time-constant field and
531        genperiod=-12 means input file contains 12 monthly means
532    o CG2D: use pre-computed solver main-diagonal (stored in common block);
533      this affects truncation error ; generate new output file for exp. which
534      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
535        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
536        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
537        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
538        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
539        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
540    o start implementation of deep-atmosphere and anelastic formulation
541    o verification: remove 2nd copy of input files and use script "prepare_run"
542      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
543    o mom_common/vecinv/fluxform: fix a few initialisation isssues
544    o profiles: fix for multithreaded case
545    
546  o diagnostics: rename few diags:  o diagnostics: rename few diags:
547    s/'PRESSURE'/'RCENTER '/g    s/'PRESSURE'/'RCENTER '/g
548    s/'TICE    '/'oceFreez'/g    s/'TICE    '/'oceFreez'/g
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