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revision 1.765 by jmc, Fri Jan 12 19:18:24 2007 UTC revision 1.895 by heimbach, Fri Oct 19 21:03:09 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 adjoint:
8      * fix multiDimAdvection adjoint
9        (partial recomputation problem by TAF for fVerT(:,:,kDown)
10        and comlev1 size definition (maxpass vs. max. number of tracers)
11      * verification/global_ocean.90x45x15 adjoint now tests
12        NLFS and multiDimAdvection using DST3 (=30)
13      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
14    o pkg/kpp: add "_d 0" to real constant (if missing);
15      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
16      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
17    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
18      for internal parameters related to restart process (formerly from PARAMS.h)
19      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
20    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
21      as argument. (only atm2d & obcs write_pickup have not yet been updated)
22    o pkg/monitor:
23      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
24      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
25      - account for deep Atmosphere factor and density factor (anelastic)
26    o added open boundary conditions capability for seaice HEFF and AREA
27    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
28      thermodynamics
29      - requires a little reorganization, which affects the testreport results
30        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
31        so that now the conservative form is tested
32      - add a few comments
33    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
34    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
35    o add new diagnostics to seaice: advective, diffusive fluxes (only for
36      multidim-advection, for scheme 2 they are not filled) and transports,
37      thermodynamic growth rates
38    o change units of EmPmR (inside the code) from m/s to kg/m2/s (mass flux) but
39      leave input file unchanged. Affects results @ truncation level (cg2d match)
40      and update output of experiments: lab_sea(6), global_ocean.90x40x15(10),
41      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
42      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
43      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
44    
45    checkpoint59h
46    o pkg/exf:
47      - improve vectorization by moving if-statement out of loops in
48        exf_mapfields, exf_radiation
49      - exf_bulkformulae.F: introduce 2D fields and vectorize code
50    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
51    o testreport:
52      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
53        monitor & update offline_exf_seaice exp. output.
54      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
55    o pkg/seaice:
56      - bug fix in the evp solver: boundary conditions were affected be
57        masking of zMax/zMin (changes results)
58      - minor bug fix in boundary conditions in seaice_calc_strainrates
59        (changes results for no_slip)
60      - seaice_lsr.F: make interpolation of eta dependent on boundaries
61      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
62      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
63        stress formulation and no-slip boundary conditions
64    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
65      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
66    o pkg/seaice: a first HSALT time stepping equation has been checked in
67    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
68      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
69      without requiring DO-IF statements
70    o pkg/thsice:
71      use continuous power-law function for partition of energy between lateral
72      melting/freezing and thinning/thickening ; old code using step function
73      still available with #undef THSICE_FRACEN_POWERLAW
74      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
75    o testreport: change AD testing : check against results/output_adm.txt
76      using same scripts as for forward test.
77    
78    checkpoint59g
79    o adjoint testing: in preparation for changing testreport:
80      - output format: cost and grad written on separated lines
81      - ad output results in directory "results" (instead of "results_ad")
82    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
83    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
84    o pkg/ecco: allow user defined cost function contributions
85    o testreport:
86      Allow to choose (per experiment) the list of tested output variables
87       and the main variable (used to issue a pass/FAIL ) ;
88      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
89      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
90      Also modify printing of summary:
91       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
92       b) echo the list of tested variables in the individual summary.txt of
93          each experiment.
94    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
95      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
96      (but still depend on the tile decompostion of the domain).
97    o pkg/seaice: change a discretization detail to make the B-grid code
98      "more symmetric". This change is likely to remove all "ridges/leads" that
99      where quasi-aligned with the grid in B-grid solutions. It may also be
100      the solution to the stress coupling issues with the B-grid.
101    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
102      remove .cvsignore from input dir. (since testreport no longer run here).
103    o pkg/thsice:
104     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
105     - fix reshaping of sea-ice just after advection:
106       melt all the ice only if ice-volume is too small.
107     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
108       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
109     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
110    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
111      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
112    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
113      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
114      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
115      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
116      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
117      -> update output.txt
118    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
119     this affects truncation error: -> update output.txt of exp:
120      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
121      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
122    
123    checkpoint59f
124    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
125    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
126      a bounded range (in forward mode)
127    o pkg/ecco, ctrl, autodiff and mom_common:
128     internal parameter controls, completements of implementations
129    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
130    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
131      (not seem any difference in testing results).
132    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
133       at face corners.
134    o pkg/generic_advdiff:
135     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
136      loop range indices for computing vertical advection tendency
137      and do the calculation in the interior only (no overlap) ;
138      for now, only implemented for SOM advection (to save CPU time).
139     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
140    o exch2 adjoint
141      First set of changes:
142      - add exch2 hand-written adjoint templates
143      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
144        This will require cleanup in pkg/autodiff/*.F
145        (changed routines currently kept separate in verif. code/)
146      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
147        that used to hide exch2 or cubed-sphere specific code
148        (commented via 'cph-exch2')
149    o pkg/seaice
150      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
151    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
152       output of global_ocean.cs32x15.thsice .
153    
154    checkpoint59e
155    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
156      for B-grid vector (not yet tested) and C-grid vector (<- only used
157      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
158    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
159      (#ifdef ALLOW_SALT_PLUME)
160    o gather_2d/scatter_2d: removed halo regions
161    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
162      scheme and the corresponding test case (under front_relax dir). For now,
163      only available with Skew-flux form and not yet tested in realistic set-up.
164      adjoint: store directives updated, but gradient checks deteriorated,
165      so maybe GM/Redi adjoint is now broken.
166    o seaice adjoint
167      * add AREA, HEFF, HSNOW as control variable
168        (should not change lab_sea results)
169      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
170    o pkg/seaice:
171      * added computation of saltFlux in seaice_growth;
172        For time being, sea ice salinity is assumed constant
173        contribution of snow flooding to freshening of sea ice is neglected.
174        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
175        defaults to 0.0 in order to maintain backward compatibility.
176        Typical values for SEAICE_salinity are 4 to 10 g/kg.
177      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
178      * added SEAICE_availHeatFrac, which specifies fraction of surface level
179        heat content used to melt or grow ice
180      * commented out cap of HICE: it helps keep ice thinner
181      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
182      * applied OBCS T/S mask to HEFFM sea ice mask
183    
184    checkpoint59d
185    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
186     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
187     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
188    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
189     and change default value of parameter "GM_Small_Number";
190     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
191       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
192       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
193    o pkg/ecco: cost function when applying pkg/smooth to controls
194    o pkg/ctrl: add forcingPrecond run time parameter
195    o pkg/seaice:
196     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
197     - fix bug in metric terms of u-equation in LSR solver (implicit part),
198       changes verification/lab_sea
199     - rearrange implicit part of u-equation in LSR solver to make it easier to
200       read, understand, and debug. This causes changes at the truncation level.
201     - fix (serious) bug in the boundary conditions (sign error in the implicit
202       part) of the LSR solver. Changes all LSR results.
203     - fixed problem with HSNOW initialization to avoid thick snow when AREA
204       is initilized with small values - does not change lab_sea results.
205     - added HsnowFile initialization capability
206    o pkg/smooth: addition to model/src and pkg/ctrl so allow
207     initialization of pkg/smooth and application to control vector
208    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
209    o dependencies: pkg/profiles requires pkg/cal
210    o pkg/profiles:
211     - added option ALLOW_PROFILES_GENERICGRID
212         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
213         that interpolation information (grid points and coefficients) is provided
214         within the netcdf input files.
215         -> sample matlab scripts can be found in MITgcm_contrib/gael
216         that allow you to prepare netcdf input files.
217     - also modified: cleaner include statements, cleaner error print statements,
218       cleaner stops when error, and more tests of the netcdf input files consistency.
219    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
220    o pkg/seaice:
221     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
222       requires a new routine: seaice_diagnostics_fill.F
223     - make sure that seaice does not move if not forced (pressure replacement
224       method, Hibler and Ip, 1995), changes results
225     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
226     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
227       It is turned off by default (=-1.), because it changes the results.
228     - make it possible to read AREA from a file, too.
229    
230    checkpoint59c
231    o add S/R and diagnostics for oceanic mixed-layer depth
232    o move GMRedi call after all vertical mixing schemes (including KPP)
233    o pkg/thsice:
234     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
235      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
236    o pkg/obcs:
237     - bug fix for balance code
238    o pkg/seaice:
239      - allow values of SEAICE_elasticParm > 1
240      - add new parameter SEAICE_evpTauRelax as an alternative
241        to SEAICE_elasticParm
242      - make lsr boundary conditions free slip (by default), changes result
243      - add code for no slip boundary conditions for lsr
244      - set minimum of zeta to zero (and not 4e8) (changes results)
245      - add a cap on AREA after advecting AREA if seaice_growth is not called
246    o change calculation of Visbeck K:
247      - no longer depend on tapering scheme; instead, compute slope (limited
248        by GM_maxSlope). this is equivalent to what was comuted before with
249        clipping or linear tappering.
250      - fix vertical averaging (wrong by 1/2 level)
251      - leave the old version (but will not be maintained) within
252        #ifdef OLD_VISBECK_CALC / #endif
253      - update output of exp. ideal_2D_oce
254    o change error catch in calc_r_star to improve vectorization
255    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
256      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
257    o adjoint:
258      Re-organized adjoint checkpointing according to Matt Mazloff
259      (but with modifs/completions/cleanups)
260      Storing is now bundled into large arrays to optimized I/O
261      (and second step in cleanup of the_main_loop)
262    
263    checkpoint59b
264    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
265      - export/import (between ocean & coupler) fields needed for ocean DIC.
266    o pkg/seaice:
267      - get rid of three more exchanges seaice_calc_viscosities (required
268        different loop boundaries in seaice_lsr and seaice_ocean_stress)
269      - bug fix in seaice_ocean_stress (update of lab_sea required)
270      - reduce loop boundaries to necessary minimum also in seaice_evp
271      - go back to the old way of computing deltaC/Z as the adjoint likes that
272        better
273    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
274      passive tracer to an Age Tracer) + update output.txt
275    o pkg/exf:
276      - implement A-grid / C-grid selection for wind-stress input files.
277      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
278      for now, in exf_bulk_largeyeager04.F only :
279      - change implementation for case where windspeed + 2. components wind-stress
280        are read-in. AND use rhoConstFresh to convert evap.
281    o pkg/seaice:
282      - use correct EXCH_UV for wind-forcing (on A-grid).
283      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
284        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
285    o pkg/exf:
286      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
287      EXF_INTERPOLATION:
288      - merge global_with_exf/code version of exf_interp_read.F
289        to the main code ;
290      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
291        reading the file ; Important: This options needs to be defined to recover
292        previous code.
293        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
294      - no longer loose real*8 precision along the way when using exf_iprec=64.
295    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
296      - change discretisation of evp-solver in order to avoid another exchange
297        (changes lab_sea) and clean up a little
298      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
299        help the adjoint (this also changes the results slightly)
300      - add a few "_d 0" where they had been missing in seaice_evp.F
301      - cleaning up: remove unused seaice_calc_rhs.F
302    o pkg/exf: some cleaning-up:
303      - change various "constants" into runtime parameters
304      - cleaned-up Large&Yeager04 routine which should eventually
305        replace exf_bulkformulae.F (changed names of S/R and CPP)
306        and merged various ALLOW_ATM_WIND options
307     only used with thsice pkg (in thsice_get_exf.F):
308      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
309        which are used when useStabilityFct_overIce=TRUE (= the default)
310      - change default values of ice & snow emissivity and scale downward LW
311        by ice & snow emissivity.
312    o pkg/thsice:
313     fix few little problems, in thsice_calc_thickn.F:
314      - growth vertically (and not laterally) if iceFrac == iceMaskMax
315      - melt only laterally if hIce < hThinIce (as the comments say)
316      and in thsice_extend.F:
317      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
318      - start to form ice as soon as the minimum ice-volume is reachable.
319     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
320      and cpl_aim+ocn
321    o pkg/kpp
322     - move computation of surface related input fields to KPP into a new
323       subroutine kpp_forcing_surf.F
324     - remove wrong (within bi,bj loops) EXCH calls.
325     - little cleaning (add argument myThid in last position, cvs header ...)
326     - for now, fix conservation problem by exchanging KPPviscAz (may not
327       be the best fix)
328    o pkg/seaice
329     - check for inconsistent evp parameter/cpp-flag combination
330     - remove leftover errIO flat for obsolete name list error handling
331    o OpenAD
332     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
333    
334    checkpoint59a
335    o pkg/seaice: some parameter clarifications and a little bit of clean up
336    o pkg/thsice: rename run-time parameters:
337       himin       -> hIceMin
338       himin0      -> hThinIce
339       hihig       -> hThickIce
340       i0          -> i0swFrac
341       transCoef   -> bMeltCoef
342       frac_energy -> fracMelting
343      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
344       with default values (for now) that do not change the results.
345      remove old version of thsice vars advection in pkg/seaice.
346    o in FFIELDS.h:
347      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
348      - make pLoad & sIceLoad always available (but still only used if
349         ATMOSPHERIC_LOADING is #define).
350    o pkg/kpp: replaced _KPP_RL with _RL
351    o bug fixes for vertical diffusivity computations when both KPP and
352        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
353        are no longer updating the vertical diffusivity array
354        (passed as argument) but are (re-) setting those arrays.
355    o pkg/seaice: fix bug in evp solver, while doing that
356      - change (improve?) discretization of stress computations for both
357        cgrid-lsr and evp solver
358      - add a new routine to compute strain rates
359      - the above changes lab_sea results
360      - add no slip conditions for evp solver (off by default), lsr-version
361        may follow
362      - fix exchange for shear at Z-points (does not change lab_sea)
363      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
364        (to force the user to pick a time step since there is not "safe" way
365        of choosing it)
366      - add principal stress diagnostics
367      - rearrange fields for evp a little to avoid having to call a: too many
368        exchanges and b: exchanges for stress trensor components which we do
369        not have.
370      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
371        of evp, complete rewrite for lsr case (latter is does not yet work
372        in all cases)
373    o pkg/kpp: add code to have mixing in shelf ice caverns
374      - add myThid to all kpp routines (long overdue)
375    
376    checkpoint59
377    o pkg/exf:
378      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
379        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
380      - move exf header files from lower_case.h to UPPER_CASE.h ;
381        add missing cvs Header & Name
382      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
383      - add namelist param. selectStressGridPosition, exf_monFreq
384      - retire many _CLIM routines, and remove data.exf_clim
385        + params moved to data.exf
386        + climsst, climsss now handled by exf_set_gen, i.e.
387          climss?period=0 refers to constant field,
388          climss?period=-12 to monthly forcing
389      - split up namelists in data.exf
390    o pkg/seaice:
391      - remove seaice_exch and seaice_exch_uv
392      - remove superfluous exchange of theta
393      - add myThid to seaice_budget_ocean/ice
394      - add new interface for atmospheric wind forcing (C-grid only)
395        + new routine
396        + two new field (taux, tauy for stress over ice)
397        + removed one global field (DAIRN) for C-grid case only
398    o pkg/thsise
399      - 2nd set of modifs for thsice adjoint in conjunction with exf
400    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
401    
402    checkpoint58y_post
403    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
404      vertical diffusivity, similar to that in MOM4; turned on using
405      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
406      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
407    o Added capability for 3D specification of background vertical diffusion
408      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
409      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
410      "data" file that contains the 3D vertical diffusivity coefficients.
411    o ice dynamics (pkg/seaice) with thsice thermodynamics:
412      - add code within pkg thsice to advect & diffuse sea-ice fields
413      similar to (and will replace) what has been added in  seaice_advdiff.F,
414      but: - conserving Mass, Heat & Salt.
415           - better when using non-linear advection scheme (not yet fully tested)
416           - can also be used in atmospheric set-up (for now, only the diffusion).
417    
418    checkpoint58x_post
419    o IO option for global-file compact format:
420      - add options when generating topology (utils/exch2/matlab-topology-generator)
421      - add I/O capability (pkg/mdsio).
422      - adapt utils/matlab/rdmds.m to read this format.
423      for now long-line format not yet supported by pkg/mdsio (& exch2).
424    o shelfice: add a few diagnostics
425    
426    checkpoint58w_post
427    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
428      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
429      (and replace horiVertRatio in NH code).
430      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
431                         and tutorial_plume_on_slope (sensitive to truncation)
432    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
433      directly to drive seaice model (C-grid only)
434    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
435     - reintroduce computation of wind from stress,
436     - compute tau (in exf_bulkformulae.F) from windstress averaged to
437       mass points to avoid tau = 0
438     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
439    o rdmnc.m: make it work with "global" files created with gluemnc
440    o rdmnc.m : some improvements in dealing with singleton dimension
441      (tested on all testreport mnc output files).
442    o genmake2: disable pkg/profiles if netcdf test fails.
443    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
444    o move call to cal_readparms up to make calendar parameters/variable available
445      to all packages
446    
447    checkpoint58v_post
448    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
449      useDynP_inEos_Zc tested.
450    o pkg/exf: changes to properly interpolate/mask/scale initial fields
451    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
452      and portions thereof.  See read_cs.txt for description and examples.
453    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
454      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
455      following the great-circle arc between those 2 points.
456    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
457      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
458    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
459     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
460     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
461     - still needs work (not working with some options ; efficiency to improve)
462       and serious testing.
463     - use this scheme for temperature & salinity in 2 advection test exp.:
464       advect_xy & advect_xz, respectively.
465    
466  checkpoint58u_post  checkpoint58u_post
467  o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.  o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
468  o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.  o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
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