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revision 1.754 by mlosch, Thu Dec 14 08:23:13 2006 UTC revision 1.914 by dimitri, Thu Nov 29 16:29:12 2007 UTC
# Line 3  $Name$ Line 3  $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
8      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
9    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
10      all experiments pass when compile with un-initilised var. checking option.
11    o added pkg/salt_plume
12    o script to test restart (for now, in MITgcm_contrib/jmc_script)
13    o pkg/seaice: new read/write pickup version.
14      read meta file and write only fields which are needed to restart.
15      ( same logic as main pickup file ; also using pickupStrictlyMatch )
16    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
17    o lab_sea.hb87: modify the domain & update output.hb87.txt :
18      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
19      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
20      process. Fixed here by closing the domain at the Northern boundary.
21    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
22    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
23      a set of consecutive levels in/from a 3-D array.
24    o pkg/ptracers:
25      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
26      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
27    
28    checkpoint59j
29    o in pkgs: dic, obcs, offline, rbcs:
30      standard way to compute coeff. for time interpolation between 2 time reccords
31      which retains full precision (& make results less dependent on compiler).
32      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
33    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
34      packages instead of reading ice cover and wind speed separately
35    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
36     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
37      to allow to compile customized code before the update)
38    o cleaning-up:
39      - fix CPP instruction syntax in pkg/obcs
40      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
41        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
42      - fix some threads issue in IO parts.
43    o pkg/dic:
44      - add tons of "_d 0" (--> much better testreports !)
45       and then update outputs of tutorial_global_oce_biogeo
46    o pkg/mom_fluxform:
47      add a special version of momentum advection intended to conserve momentum
48      next to a bathymetry step or a coastline edge. (default = off = #undef)
49    o new read/write pickup version:
50      - for now, only implemented for main (mdsio) pickup file.
51      - write out only what is needed to restart; merge pickup_nh , pickup_ph
52        and main pickup together.
53      - read meta file; read only what is needed to restart; stop if a field
54        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
55        if it make sense (even if the restart is not perfect).
56      - if no meta file, assume that pickup to read corresponds exactly to
57        a pickup that would currently be written.
58      - read pickup written in the old format (until checkpoint59i) if it
59        recognizes an old meta file (no field-list).
60      - add a meta file in exp. which starts from a pickup: 2 cases:
61        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
62         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
63        b) a meta file describing the content of the associated pickup file
64         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
65    o pkg/mdsio & pkg/rw:
66      - new routine to read a meta file ; new set of routine to read
67        Multiple-fields file (with meta file).
68    o added open boundary conditions capability for seaice
69        HSNOW, HSALT, UICE, and VICE
70    
71    checkpoint59i
72    o adjoint:
73      * fix multiDimAdvection adjoint
74        (partial recomputation problem by TAF for fVerT(:,:,kDown)
75        and comlev1 size definition (maxpass vs. max. number of tracers)
76      * verification/global_ocean.90x45x15 adjoint now tests
77        NLFS and multiDimAdvection using DST3 (=30)
78      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
79    o pkg/kpp: add "_d 0" to real constant (if missing);
80      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
81      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
82    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
83      for internal parameters related to restart process (formerly from PARAMS.h)
84      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
85    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
86      as argument. (only atm2d & obcs write_pickup have not yet been updated)
87    o pkg/monitor:
88      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
89      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
90      - account for deep Atmosphere factor and density factor (anelastic)
91    o added open boundary conditions capability for seaice HEFF and AREA
92    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
93      thermodynamics
94      - requires a little reorganization, which affects the testreport results
95        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
96        so that now the conservative form is tested
97      - add a few comments
98    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
99    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
100    o add new diagnostics to seaice: advective, diffusive fluxes (only for
101      multidim-advection, for scheme 2 they are not filled) and transports,
102      thermodynamic growth rates
103    o change units of EmPmR (inside the code, + within coupling interface)
104      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
105      Affects results @ truncation level (cg2d match) and update output of
106       experiments: lab_sea(6), global_ocean.90x40x15(10),
107      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
108      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
109      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
110      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
111    
112    checkpoint59h
113    o pkg/exf:
114      - improve vectorization by moving if-statement out of loops in
115        exf_mapfields, exf_radiation
116      - exf_bulkformulae.F: introduce 2D fields and vectorize code
117    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
118    o testreport:
119      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
120        monitor & update offline_exf_seaice exp. output.
121      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
122    o pkg/seaice:
123      - bug fix in the evp solver: boundary conditions were affected be
124        masking of zMax/zMin (changes results)
125      - minor bug fix in boundary conditions in seaice_calc_strainrates
126        (changes results for no_slip)
127      - seaice_lsr.F: make interpolation of eta dependent on boundaries
128      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
129      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
130        stress formulation and no-slip boundary conditions
131    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
132      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
133    o pkg/seaice: a first HSALT time stepping equation has been checked in
134    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
135      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
136      without requiring DO-IF statements
137    o pkg/thsice:
138      use continuous power-law function for partition of energy between lateral
139      melting/freezing and thinning/thickening ; old code using step function
140      still available with #undef THSICE_FRACEN_POWERLAW
141      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
142    o testreport: change AD testing : check against results/output_adm.txt
143      using same scripts as for forward test.
144    
145    checkpoint59g
146    o adjoint testing: in preparation for changing testreport:
147      - output format: cost and grad written on separated lines
148      - ad output results in directory "results" (instead of "results_ad")
149    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
150    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
151    o pkg/ecco: allow user defined cost function contributions
152    o testreport:
153      Allow to choose (per experiment) the list of tested output variables
154       and the main variable (used to issue a pass/FAIL ) ;
155      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
156      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
157      Also modify printing of summary:
158       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
159       b) echo the list of tested variables in the individual summary.txt of
160          each experiment.
161    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
162      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
163      (but still depend on the tile decompostion of the domain).
164    o pkg/seaice: change a discretization detail to make the B-grid code
165      "more symmetric". This change is likely to remove all "ridges/leads" that
166      where quasi-aligned with the grid in B-grid solutions. It may also be
167      the solution to the stress coupling issues with the B-grid.
168    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
169      remove .cvsignore from input dir. (since testreport no longer run here).
170    o pkg/thsice:
171     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
172     - fix reshaping of sea-ice just after advection:
173       melt all the ice only if ice-volume is too small.
174     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
175       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
176     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
177    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
178      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
179    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
180      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
181      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
182      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
183      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
184      -> update output.txt
185    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
186     this affects truncation error: -> update output.txt of exp:
187      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
188      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
189    
190    checkpoint59f
191    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
192    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
193      a bounded range (in forward mode)
194    o pkg/ecco, ctrl, autodiff and mom_common:
195     internal parameter controls, completements of implementations
196    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
197    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
198      (not seem any difference in testing results).
199    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
200       at face corners.
201    o pkg/generic_advdiff:
202     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
203      loop range indices for computing vertical advection tendency
204      and do the calculation in the interior only (no overlap) ;
205      for now, only implemented for SOM advection (to save CPU time).
206     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
207    o exch2 adjoint
208      First set of changes:
209      - add exch2 hand-written adjoint templates
210      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
211        This will require cleanup in pkg/autodiff/*.F
212        (changed routines currently kept separate in verif. code/)
213      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
214        that used to hide exch2 or cubed-sphere specific code
215        (commented via 'cph-exch2')
216    o pkg/seaice
217      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
218    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
219       output of global_ocean.cs32x15.thsice .
220    
221    checkpoint59e
222    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
223      for B-grid vector (not yet tested) and C-grid vector (<- only used
224      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
225    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
226      (#ifdef ALLOW_SALT_PLUME)
227    o gather_2d/scatter_2d: removed halo regions
228    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
229      scheme and the corresponding test case (under front_relax dir). For now,
230      only available with Skew-flux form and not yet tested in realistic set-up.
231      adjoint: store directives updated, but gradient checks deteriorated,
232      so maybe GM/Redi adjoint is now broken.
233    o seaice adjoint
234      * add AREA, HEFF, HSNOW as control variable
235        (should not change lab_sea results)
236      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
237    o pkg/seaice:
238      * added computation of saltFlux in seaice_growth;
239        For time being, sea ice salinity is assumed constant
240        contribution of snow flooding to freshening of sea ice is neglected.
241        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
242        defaults to 0.0 in order to maintain backward compatibility.
243        Typical values for SEAICE_salinity are 4 to 10 g/kg.
244      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
245      * added SEAICE_availHeatFrac, which specifies fraction of surface level
246        heat content used to melt or grow ice
247      * commented out cap of HICE: it helps keep ice thinner
248      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
249      * applied OBCS T/S mask to HEFFM sea ice mask
250    
251    checkpoint59d
252    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
253     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
254     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
255    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
256     and change default value of parameter "GM_Small_Number";
257     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
258       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
259       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
260    o pkg/ecco: cost function when applying pkg/smooth to controls
261    o pkg/ctrl: add forcingPrecond run time parameter
262    o pkg/seaice:
263     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
264     - fix bug in metric terms of u-equation in LSR solver (implicit part),
265       changes verification/lab_sea
266     - rearrange implicit part of u-equation in LSR solver to make it easier to
267       read, understand, and debug. This causes changes at the truncation level.
268     - fix (serious) bug in the boundary conditions (sign error in the implicit
269       part) of the LSR solver. Changes all LSR results.
270     - fixed problem with HSNOW initialization to avoid thick snow when AREA
271       is initilized with small values - does not change lab_sea results.
272     - added HsnowFile initialization capability
273    o pkg/smooth: addition to model/src and pkg/ctrl so allow
274     initialization of pkg/smooth and application to control vector
275    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
276    o dependencies: pkg/profiles requires pkg/cal
277    o pkg/profiles:
278     - added option ALLOW_PROFILES_GENERICGRID
279         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
280         that interpolation information (grid points and coefficients) is provided
281         within the netcdf input files.
282         -> sample matlab scripts can be found in MITgcm_contrib/gael
283         that allow you to prepare netcdf input files.
284     - also modified: cleaner include statements, cleaner error print statements,
285       cleaner stops when error, and more tests of the netcdf input files consistency.
286    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
287    o pkg/seaice:
288     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
289       requires a new routine: seaice_diagnostics_fill.F
290     - make sure that seaice does not move if not forced (pressure replacement
291       method, Hibler and Ip, 1995), changes results
292     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
293     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
294       It is turned off by default (=-1.), because it changes the results.
295     - make it possible to read AREA from a file, too.
296    
297    checkpoint59c
298    o add S/R and diagnostics for oceanic mixed-layer depth
299    o move GMRedi call after all vertical mixing schemes (including KPP)
300    o pkg/thsice:
301     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
302      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
303    o pkg/obcs:
304     - bug fix for balance code
305    o pkg/seaice:
306      - allow values of SEAICE_elasticParm > 1
307      - add new parameter SEAICE_evpTauRelax as an alternative
308        to SEAICE_elasticParm
309      - make lsr boundary conditions free slip (by default), changes result
310      - add code for no slip boundary conditions for lsr
311      - set minimum of zeta to zero (and not 4e8) (changes results)
312      - add a cap on AREA after advecting AREA if seaice_growth is not called
313    o change calculation of Visbeck K:
314      - no longer depend on tapering scheme; instead, compute slope (limited
315        by GM_maxSlope). this is equivalent to what was comuted before with
316        clipping or linear tappering.
317      - fix vertical averaging (wrong by 1/2 level)
318      - leave the old version (but will not be maintained) within
319        #ifdef OLD_VISBECK_CALC / #endif
320      - update output of exp. ideal_2D_oce
321    o change error catch in calc_r_star to improve vectorization
322    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
323      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
324    o adjoint:
325      Re-organized adjoint checkpointing according to Matt Mazloff
326      (but with modifs/completions/cleanups)
327      Storing is now bundled into large arrays to optimized I/O
328      (and second step in cleanup of the_main_loop)
329    
330    checkpoint59b
331    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
332      - export/import (between ocean & coupler) fields needed for ocean DIC.
333    o pkg/seaice:
334      - get rid of three more exchanges seaice_calc_viscosities (required
335        different loop boundaries in seaice_lsr and seaice_ocean_stress)
336      - bug fix in seaice_ocean_stress (update of lab_sea required)
337      - reduce loop boundaries to necessary minimum also in seaice_evp
338      - go back to the old way of computing deltaC/Z as the adjoint likes that
339        better
340    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
341      passive tracer to an Age Tracer) + update output.txt
342    o pkg/exf:
343      - implement A-grid / C-grid selection for wind-stress input files.
344      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
345      for now, in exf_bulk_largeyeager04.F only :
346      - change implementation for case where windspeed + 2. components wind-stress
347        are read-in. AND use rhoConstFresh to convert evap.
348    o pkg/seaice:
349      - use correct EXCH_UV for wind-forcing (on A-grid).
350      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
351        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
352    o pkg/exf:
353      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
354      EXF_INTERPOLATION:
355      - merge global_with_exf/code version of exf_interp_read.F
356        to the main code ;
357      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
358        reading the file ; Important: This options needs to be defined to recover
359        previous code.
360        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
361      - no longer loose real*8 precision along the way when using exf_iprec=64.
362    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
363      - change discretisation of evp-solver in order to avoid another exchange
364        (changes lab_sea) and clean up a little
365      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
366        help the adjoint (this also changes the results slightly)
367      - add a few "_d 0" where they had been missing in seaice_evp.F
368      - cleaning up: remove unused seaice_calc_rhs.F
369    o pkg/exf: some cleaning-up:
370      - change various "constants" into runtime parameters
371      - cleaned-up Large&Yeager04 routine which should eventually
372        replace exf_bulkformulae.F (changed names of S/R and CPP)
373        and merged various ALLOW_ATM_WIND options
374     only used with thsice pkg (in thsice_get_exf.F):
375      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
376        which are used when useStabilityFct_overIce=TRUE (= the default)
377      - change default values of ice & snow emissivity and scale downward LW
378        by ice & snow emissivity.
379    o pkg/thsice:
380     fix few little problems, in thsice_calc_thickn.F:
381      - growth vertically (and not laterally) if iceFrac == iceMaskMax
382      - melt only laterally if hIce < hThinIce (as the comments say)
383      and in thsice_extend.F:
384      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
385      - start to form ice as soon as the minimum ice-volume is reachable.
386     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
387      and cpl_aim+ocn
388    o pkg/kpp
389     - move computation of surface related input fields to KPP into a new
390       subroutine kpp_forcing_surf.F
391     - remove wrong (within bi,bj loops) EXCH calls.
392     - little cleaning (add argument myThid in last position, cvs header ...)
393     - for now, fix conservation problem by exchanging KPPviscAz (may not
394       be the best fix)
395    o pkg/seaice
396     - check for inconsistent evp parameter/cpp-flag combination
397     - remove leftover errIO flat for obsolete name list error handling
398    o OpenAD
399     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
400    
401    checkpoint59a
402    o pkg/seaice: some parameter clarifications and a little bit of clean up
403    o pkg/thsice: rename run-time parameters:
404       himin       -> hIceMin
405       himin0      -> hThinIce
406       hihig       -> hThickIce
407       i0          -> i0swFrac
408       transCoef   -> bMeltCoef
409       frac_energy -> fracMelting
410      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
411       with default values (for now) that do not change the results.
412      remove old version of thsice vars advection in pkg/seaice.
413    o in FFIELDS.h:
414      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
415      - make pLoad & sIceLoad always available (but still only used if
416         ATMOSPHERIC_LOADING is #define).
417    o pkg/kpp: replaced _KPP_RL with _RL
418    o bug fixes for vertical diffusivity computations when both KPP and
419        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
420        are no longer updating the vertical diffusivity array
421        (passed as argument) but are (re-) setting those arrays.
422    o pkg/seaice: fix bug in evp solver, while doing that
423      - change (improve?) discretization of stress computations for both
424        cgrid-lsr and evp solver
425      - add a new routine to compute strain rates
426      - the above changes lab_sea results
427      - add no slip conditions for evp solver (off by default), lsr-version
428        may follow
429      - fix exchange for shear at Z-points (does not change lab_sea)
430      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
431        (to force the user to pick a time step since there is not "safe" way
432        of choosing it)
433      - add principal stress diagnostics
434      - rearrange fields for evp a little to avoid having to call a: too many
435        exchanges and b: exchanges for stress trensor components which we do
436        not have.
437      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
438        of evp, complete rewrite for lsr case (latter is does not yet work
439        in all cases)
440    o pkg/kpp: add code to have mixing in shelf ice caverns
441      - add myThid to all kpp routines (long overdue)
442    
443    checkpoint59
444    o pkg/exf:
445      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
446        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
447      - move exf header files from lower_case.h to UPPER_CASE.h ;
448        add missing cvs Header & Name
449      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
450      - add namelist param. selectStressGridPosition, exf_monFreq
451      - retire many _CLIM routines, and remove data.exf_clim
452        + params moved to data.exf
453        + climsst, climsss now handled by exf_set_gen, i.e.
454          climss?period=0 refers to constant field,
455          climss?period=-12 to monthly forcing
456      - split up namelists in data.exf
457    o pkg/seaice:
458      - remove seaice_exch and seaice_exch_uv
459      - remove superfluous exchange of theta
460      - add myThid to seaice_budget_ocean/ice
461      - add new interface for atmospheric wind forcing (C-grid only)
462        + new routine
463        + two new field (taux, tauy for stress over ice)
464        + removed one global field (DAIRN) for C-grid case only
465    o pkg/thsise
466      - 2nd set of modifs for thsice adjoint in conjunction with exf
467    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
468    
469    checkpoint58y_post
470    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
471      vertical diffusivity, similar to that in MOM4; turned on using
472      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
473      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
474    o Added capability for 3D specification of background vertical diffusion
475      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
476      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
477      "data" file that contains the 3D vertical diffusivity coefficients.
478    o ice dynamics (pkg/seaice) with thsice thermodynamics:
479      - add code within pkg thsice to advect & diffuse sea-ice fields
480      similar to (and will replace) what has been added in  seaice_advdiff.F,
481      but: - conserving Mass, Heat & Salt.
482           - better when using non-linear advection scheme (not yet fully tested)
483           - can also be used in atmospheric set-up (for now, only the diffusion).
484    
485    checkpoint58x_post
486    o IO option for global-file compact format:
487      - add options when generating topology (utils/exch2/matlab-topology-generator)
488      - add I/O capability (pkg/mdsio).
489      - adapt utils/matlab/rdmds.m to read this format.
490      for now long-line format not yet supported by pkg/mdsio (& exch2).
491    o shelfice: add a few diagnostics
492    
493    checkpoint58w_post
494    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
495      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
496      (and replace horiVertRatio in NH code).
497      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
498                         and tutorial_plume_on_slope (sensitive to truncation)
499    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
500      directly to drive seaice model (C-grid only)
501    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
502     - reintroduce computation of wind from stress,
503     - compute tau (in exf_bulkformulae.F) from windstress averaged to
504       mass points to avoid tau = 0
505     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
506    o rdmnc.m: make it work with "global" files created with gluemnc
507    o rdmnc.m : some improvements in dealing with singleton dimension
508      (tested on all testreport mnc output files).
509    o genmake2: disable pkg/profiles if netcdf test fails.
510    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
511    o move call to cal_readparms up to make calendar parameters/variable available
512      to all packages
513    
514    checkpoint58v_post
515    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
516      useDynP_inEos_Zc tested.
517    o pkg/exf: changes to properly interpolate/mask/scale initial fields
518    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
519      and portions thereof.  See read_cs.txt for description and examples.
520    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
521      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
522      following the great-circle arc between those 2 points.
523    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
524      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
525    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
526     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
527     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
528     - still needs work (not working with some options ; efficiency to improve)
529       and serious testing.
530     - use this scheme for temperature & salinity in 2 advection test exp.:
531       advect_xy & advect_xz, respectively.
532    
533    checkpoint58u_post
534    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
535    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
536    o testreport: add option "-skipdir" to skip some test.
537    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
538      momentum calculation.
539    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
540    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
541      remove checkpoint.F and the_correction_step.F (no longer used);
542      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
543    o add option (linFSConserveTr) to correct for tracer source/sink due to
544      Linear Free surface
545    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
546    o pkg/thsice: fix reading mnc-pickups
547    
548    checkpoint58t_post
549    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
550    o pkg/mdsio:
551     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
552       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
553       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
554     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
555     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
556       either MDS_READ_FIELD or MDS_WRITE_FIELD )
557     - new S/R (to replace MDSWRITEMETA), which allows to write more
558       informations (variable names, time ...) to meta files.
559     - modify rdmds.m to give back the meta file content.
560    o pkg/diagnostics: change vertical interpolation to be safer, and more
561       flexible (define p-levels to interpolate to in data.diagnostics);
562      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
563       diagnostic pointer.
564    o pkg/seaice: more cleaning up of seaice_growth, added many comments
565    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
566    o fix multi-category seaice:
567     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
568       SEAICE_MULTICATEGORY
569     - fix short wave heat flux
570    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
571       and allow to use EVP solver. Change forward lab_sea: test both EVP
572       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
573    o Initial check-in of lab_sea adjoint
574      (very similar to natl_box_adjoint/code_seaice)
575      * used C-grid and EVP solver
576      * used KPP, GM/Redi
577      * uses inAdExact=.TRUE.
578      * gradient checks fail for both ADM and TLM
579        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
580        f.d. gradients actually seem more problematic than ADM, TLM gradients;
581        issue is related to forward mismatch between g77 an ifort
582    o pkg/seaice: overhaul of thermodynamics
583     - growth.F and groatb.F are replaced by new routine seaice_growth.F
584     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
585     - move a few global fields out of SEAICE.h into seaice_growth.F and
586       make them 2D (FICE/QNETO/ ...)
587     - remove FO (it is the same as QNETO)
588     - introduce a few local fields to avoid modifying external fields such
589       as atemp, etc.
590    
591  checkpoint58s_post  checkpoint58s_post
592  o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F  o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
593    changed exf_set_gen.F so that    changed exf_set_gen.F so that
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