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revision 1.715 by mlosch, Mon Aug 14 16:53:08 2006 UTC revision 1.886 by jmc, Mon Oct 1 19:30:47 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 shelfice: add a simple boundary layer scheme to reduce noise  o change units of EmPmR (inside the code) from m/s to kg/m2/s (mass flux) but
8      leave input file unchanged. Affects results @ truncation level (cg2d match)
9      and update output of experiments: lab_sea(6), global_ocean.90x40x15(10),
10      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
11      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
12      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
13    
14    checkpoint59h
15    o pkg/exf:
16      - improve vectorization by moving if-statement out of loops in
17        exf_mapfields, exf_radiation
18      - exf_bulkformulae.F: introduce 2D fields and vectorize code
19    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
20    o testreport:
21      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
22        monitor & update offline_exf_seaice exp. output.
23      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
24    o pkg/seaice:
25      - bug fix in the evp solver: boundary conditions were affected be
26        masking of zMax/zMin (changes results)
27      - minor bug fix in boundary conditions in seaice_calc_strainrates
28        (changes results for no_slip)
29      - seaice_lsr.F: make interpolation of eta dependent on boundaries
30      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
31      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
32        stress formulation and no-slip boundary conditions
33    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
34      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
35    o pkg/seaice: a first HSALT time stepping equation has been checked in
36    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
37      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
38      without requiring DO-IF statements
39    o pkg/thsice:
40      use continuous power-law function for partition of energy between lateral
41      melting/freezing and thinning/thickening ; old code using step function
42      still available with #undef THSICE_FRACEN_POWERLAW
43      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
44    o testreport: change AD testing : check against results/output_adm.txt
45      using same scripts as for forward test.
46    
47    checkpoint59g
48    o adjoint testing: in preparation for changing testreport:
49      - output format: cost and grad written on separated lines
50      - ad output results in directory "results" (instead of "results_ad")
51    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
52    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
53    o pkg/ecco: allow user defined cost function contributions
54    o testreport:
55      Allow to choose (per experiment) the list of tested output variables
56       and the main variable (used to issue a pass/FAIL ) ;
57      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
58      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
59      Also modify printing of summary:
60       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
61       b) echo the list of tested variables in the individual summary.txt of
62          each experiment.
63    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
64      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
65      (but still depend on the tile decompostion of the domain).
66    o pkg/seaice: change a discretization detail to make the B-grid code
67      "more symmetric". This change is likely to remove all "ridges/leads" that
68      where quasi-aligned with the grid in B-grid solutions. It may also be
69      the solution to the stress coupling issues with the B-grid.
70    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
71      remove .cvsignore from input dir. (since testreport no longer run here).
72    o pkg/thsice:
73     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
74     - fix reshaping of sea-ice just after advection:
75       melt all the ice only if ice-volume is too small.
76     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
77       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
78     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
79    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
80      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
81    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
82      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
83      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
84      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
85      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
86      -> update output.txt
87    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
88     this affects truncation error: -> update output.txt of exp:
89      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
90      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
91    
92    checkpoint59f
93    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
94    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
95      a bounded range (in forward mode)
96    o pkg/ecco, ctrl, autodiff and mom_common:
97     internal parameter controls, completements of implementations
98    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
99    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
100      (not seem any difference in testing results).
101    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
102       at face corners.
103    o pkg/generic_advdiff:
104     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
105      loop range indices for computing vertical advection tendency
106      and do the calculation in the interior only (no overlap) ;
107      for now, only implemented for SOM advection (to save CPU time).
108     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
109    o exch2 adjoint
110      First set of changes:
111      - add exch2 hand-written adjoint templates
112      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
113        This will require cleanup in pkg/autodiff/*.F
114        (changed routines currently kept separate in verif. code/)
115      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
116        that used to hide exch2 or cubed-sphere specific code
117        (commented via 'cph-exch2')
118    o pkg/seaice
119      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
120    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
121       output of global_ocean.cs32x15.thsice .
122    
123    checkpoint59e
124    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
125      for B-grid vector (not yet tested) and C-grid vector (<- only used
126      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
127    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
128      (#ifdef ALLOW_SALT_PLUME)
129    o gather_2d/scatter_2d: removed halo regions
130    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
131      scheme and the corresponding test case (under front_relax dir). For now,
132      only available with Skew-flux form and not yet tested in realistic set-up.
133      adjoint: store directives updated, but gradient checks deteriorated,
134      so maybe GM/Redi adjoint is now broken.
135    o seaice adjoint
136      * add AREA, HEFF, HSNOW as control variable
137        (should not change lab_sea results)
138      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
139    o pkg/seaice:
140      * added computation of saltFlux in seaice_growth;
141        For time being, sea ice salinity is assumed constant
142        contribution of snow flooding to freshening of sea ice is neglected.
143        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
144        defaults to 0.0 in order to maintain backward compatibility.
145        Typical values for SEAICE_salinity are 4 to 10 g/kg.
146      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
147      * added SEAICE_availHeatFrac, which specifies fraction of surface level
148        heat content used to melt or grow ice
149      * commented out cap of HICE: it helps keep ice thinner
150      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
151      * applied OBCS T/S mask to HEFFM sea ice mask
152    
153    checkpoint59d
154    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
155     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
156     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
157    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
158     and change default value of parameter "GM_Small_Number";
159     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
160       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
161       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
162    o pkg/ecco: cost function when applying pkg/smooth to controls
163    o pkg/ctrl: add forcingPrecond run time parameter
164    o pkg/seaice:
165     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
166     - fix bug in metric terms of u-equation in LSR solver (implicit part),
167       changes verification/lab_sea
168     - rearrange implicit part of u-equation in LSR solver to make it easier to
169       read, understand, and debug. This causes changes at the truncation level.
170     - fix (serious) bug in the boundary conditions (sign error in the implicit
171       part) of the LSR solver. Changes all LSR results.
172     - fixed problem with HSNOW initialization to avoid thick snow when AREA
173       is initilized with small values - does not change lab_sea results.
174     - added HsnowFile initialization capability
175    o pkg/smooth: addition to model/src and pkg/ctrl so allow
176     initialization of pkg/smooth and application to control vector
177    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
178    o dependencies: pkg/profiles requires pkg/cal
179    o pkg/profiles:
180     - added option ALLOW_PROFILES_GENERICGRID
181         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
182         that interpolation information (grid points and coefficients) is provided
183         within the netcdf input files.
184         -> sample matlab scripts can be found in MITgcm_contrib/gael
185         that allow you to prepare netcdf input files.
186     - also modified: cleaner include statements, cleaner error print statements,
187       cleaner stops when error, and more tests of the netcdf input files consistency.
188    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
189    o pkg/seaice:
190     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
191       requires a new routine: seaice_diagnostics_fill.F
192     - make sure that seaice does not move if not forced (pressure replacement
193       method, Hibler and Ip, 1995), changes results
194     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
195     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
196       It is turned off by default (=-1.), because it changes the results.
197     - make it possible to read AREA from a file, too.
198    
199    checkpoint59c
200    o add S/R and diagnostics for oceanic mixed-layer depth
201    o move GMRedi call after all vertical mixing schemes (including KPP)
202    o pkg/thsice:
203     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
204      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
205    o pkg/obcs:
206     - bug fix for balance code
207    o pkg/seaice:
208      - allow values of SEAICE_elasticParm > 1
209      - add new parameter SEAICE_evpTauRelax as an alternative
210        to SEAICE_elasticParm
211      - make lsr boundary conditions free slip (by default), changes result
212      - add code for no slip boundary conditions for lsr
213      - set minimum of zeta to zero (and not 4e8) (changes results)
214      - add a cap on AREA after advecting AREA if seaice_growth is not called
215    o change calculation of Visbeck K:
216      - no longer depend on tapering scheme; instead, compute slope (limited
217        by GM_maxSlope). this is equivalent to what was comuted before with
218        clipping or linear tappering.
219      - fix vertical averaging (wrong by 1/2 level)
220      - leave the old version (but will not be maintained) within
221        #ifdef OLD_VISBECK_CALC / #endif
222      - update output of exp. ideal_2D_oce
223    o change error catch in calc_r_star to improve vectorization
224    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
225      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
226    o adjoint:
227      Re-organized adjoint checkpointing according to Matt Mazloff
228      (but with modifs/completions/cleanups)
229      Storing is now bundled into large arrays to optimized I/O
230      (and second step in cleanup of the_main_loop)
231    
232    checkpoint59b
233    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
234      - export/import (between ocean & coupler) fields needed for ocean DIC.
235    o pkg/seaice:
236      - get rid of three more exchanges seaice_calc_viscosities (required
237        different loop boundaries in seaice_lsr and seaice_ocean_stress)
238      - bug fix in seaice_ocean_stress (update of lab_sea required)
239      - reduce loop boundaries to necessary minimum also in seaice_evp
240      - go back to the old way of computing deltaC/Z as the adjoint likes that
241        better
242    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
243      passive tracer to an Age Tracer) + update output.txt
244    o pkg/exf:
245      - implement A-grid / C-grid selection for wind-stress input files.
246      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
247      for now, in exf_bulk_largeyeager04.F only :
248      - change implementation for case where windspeed + 2. components wind-stress
249        are read-in. AND use rhoConstFresh to convert evap.
250    o pkg/seaice:
251      - use correct EXCH_UV for wind-forcing (on A-grid).
252      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
253        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
254    o pkg/exf:
255      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
256      EXF_INTERPOLATION:
257      - merge global_with_exf/code version of exf_interp_read.F
258        to the main code ;
259      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
260        reading the file ; Important: This options needs to be defined to recover
261        previous code.
262        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
263      - no longer loose real*8 precision along the way when using exf_iprec=64.
264    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
265      - change discretisation of evp-solver in order to avoid another exchange
266        (changes lab_sea) and clean up a little
267      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
268        help the adjoint (this also changes the results slightly)
269      - add a few "_d 0" where they had been missing in seaice_evp.F
270      - cleaning up: remove unused seaice_calc_rhs.F
271    o pkg/exf: some cleaning-up:
272      - change various "constants" into runtime parameters
273      - cleaned-up Large&Yeager04 routine which should eventually
274        replace exf_bulkformulae.F (changed names of S/R and CPP)
275        and merged various ALLOW_ATM_WIND options
276     only used with thsice pkg (in thsice_get_exf.F):
277      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
278        which are used when useStabilityFct_overIce=TRUE (= the default)
279      - change default values of ice & snow emissivity and scale downward LW
280        by ice & snow emissivity.
281    o pkg/thsice:
282     fix few little problems, in thsice_calc_thickn.F:
283      - growth vertically (and not laterally) if iceFrac == iceMaskMax
284      - melt only laterally if hIce < hThinIce (as the comments say)
285      and in thsice_extend.F:
286      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
287      - start to form ice as soon as the minimum ice-volume is reachable.
288     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
289      and cpl_aim+ocn
290    o pkg/kpp
291     - move computation of surface related input fields to KPP into a new
292       subroutine kpp_forcing_surf.F
293     - remove wrong (within bi,bj loops) EXCH calls.
294     - little cleaning (add argument myThid in last position, cvs header ...)
295     - for now, fix conservation problem by exchanging KPPviscAz (may not
296       be the best fix)
297    o pkg/seaice
298     - check for inconsistent evp parameter/cpp-flag combination
299     - remove leftover errIO flat for obsolete name list error handling
300    o OpenAD
301     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
302    
303    checkpoint59a
304    o pkg/seaice: some parameter clarifications and a little bit of clean up
305    o pkg/thsice: rename run-time parameters:
306       himin       -> hIceMin
307       himin0      -> hThinIce
308       hihig       -> hThickIce
309       i0          -> i0swFrac
310       transCoef   -> bMeltCoef
311       frac_energy -> fracMelting
312      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
313       with default values (for now) that do not change the results.
314      remove old version of thsice vars advection in pkg/seaice.
315    o in FFIELDS.h:
316      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
317      - make pLoad & sIceLoad always available (but still only used if
318         ATMOSPHERIC_LOADING is #define).
319    o pkg/kpp: replaced _KPP_RL with _RL
320    o bug fixes for vertical diffusivity computations when both KPP and
321        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
322        are no longer updating the vertical diffusivity array
323        (passed as argument) but are (re-) setting those arrays.
324    o pkg/seaice: fix bug in evp solver, while doing that
325      - change (improve?) discretization of stress computations for both
326        cgrid-lsr and evp solver
327      - add a new routine to compute strain rates
328      - the above changes lab_sea results
329      - add no slip conditions for evp solver (off by default), lsr-version
330        may follow
331      - fix exchange for shear at Z-points (does not change lab_sea)
332      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
333        (to force the user to pick a time step since there is not "safe" way
334        of choosing it)
335      - add principal stress diagnostics
336      - rearrange fields for evp a little to avoid having to call a: too many
337        exchanges and b: exchanges for stress trensor components which we do
338        not have.
339      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
340        of evp, complete rewrite for lsr case (latter is does not yet work
341        in all cases)
342    o pkg/kpp: add code to have mixing in shelf ice caverns
343      - add myThid to all kpp routines (long overdue)
344    
345    checkpoint59
346    o pkg/exf:
347      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
348        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
349      - move exf header files from lower_case.h to UPPER_CASE.h ;
350        add missing cvs Header & Name
351      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
352      - add namelist param. selectStressGridPosition, exf_monFreq
353      - retire many _CLIM routines, and remove data.exf_clim
354        + params moved to data.exf
355        + climsst, climsss now handled by exf_set_gen, i.e.
356          climss?period=0 refers to constant field,
357          climss?period=-12 to monthly forcing
358      - split up namelists in data.exf
359    o pkg/seaice:
360      - remove seaice_exch and seaice_exch_uv
361      - remove superfluous exchange of theta
362      - add myThid to seaice_budget_ocean/ice
363      - add new interface for atmospheric wind forcing (C-grid only)
364        + new routine
365        + two new field (taux, tauy for stress over ice)
366        + removed one global field (DAIRN) for C-grid case only
367    o pkg/thsise
368      - 2nd set of modifs for thsice adjoint in conjunction with exf
369    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
370    
371    checkpoint58y_post
372    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
373      vertical diffusivity, similar to that in MOM4; turned on using
374      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
375      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
376    o Added capability for 3D specification of background vertical diffusion
377      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
378      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
379      "data" file that contains the 3D vertical diffusivity coefficients.
380    o ice dynamics (pkg/seaice) with thsice thermodynamics:
381      - add code within pkg thsice to advect & diffuse sea-ice fields
382      similar to (and will replace) what has been added in  seaice_advdiff.F,
383      but: - conserving Mass, Heat & Salt.
384           - better when using non-linear advection scheme (not yet fully tested)
385           - can also be used in atmospheric set-up (for now, only the diffusion).
386    
387    checkpoint58x_post
388    o IO option for global-file compact format:
389      - add options when generating topology (utils/exch2/matlab-topology-generator)
390      - add I/O capability (pkg/mdsio).
391      - adapt utils/matlab/rdmds.m to read this format.
392      for now long-line format not yet supported by pkg/mdsio (& exch2).
393    o shelfice: add a few diagnostics
394    
395    checkpoint58w_post
396    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
397      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
398      (and replace horiVertRatio in NH code).
399      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
400                         and tutorial_plume_on_slope (sensitive to truncation)
401    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
402      directly to drive seaice model (C-grid only)
403    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
404     - reintroduce computation of wind from stress,
405     - compute tau (in exf_bulkformulae.F) from windstress averaged to
406       mass points to avoid tau = 0
407     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
408    o rdmnc.m: make it work with "global" files created with gluemnc
409    o rdmnc.m : some improvements in dealing with singleton dimension
410      (tested on all testreport mnc output files).
411    o genmake2: disable pkg/profiles if netcdf test fails.
412    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
413    o move call to cal_readparms up to make calendar parameters/variable available
414      to all packages
415    
416    checkpoint58v_post
417    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
418      useDynP_inEos_Zc tested.
419    o pkg/exf: changes to properly interpolate/mask/scale initial fields
420    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
421      and portions thereof.  See read_cs.txt for description and examples.
422    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
423      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
424      following the great-circle arc between those 2 points.
425    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
426      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
427    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
428     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
429     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
430     - still needs work (not working with some options ; efficiency to improve)
431       and serious testing.
432     - use this scheme for temperature & salinity in 2 advection test exp.:
433       advect_xy & advect_xz, respectively.
434    
435    checkpoint58u_post
436    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
437    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
438    o testreport: add option "-skipdir" to skip some test.
439    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
440      momentum calculation.
441    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
442    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
443      remove checkpoint.F and the_correction_step.F (no longer used);
444      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
445    o add option (linFSConserveTr) to correct for tracer source/sink due to
446      Linear Free surface
447    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
448    o pkg/thsice: fix reading mnc-pickups
449    
450    checkpoint58t_post
451    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
452    o pkg/mdsio:
453     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
454       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
455       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
456     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
457     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
458       either MDS_READ_FIELD or MDS_WRITE_FIELD )
459     - new S/R (to replace MDSWRITEMETA), which allows to write more
460       informations (variable names, time ...) to meta files.
461     - modify rdmds.m to give back the meta file content.
462    o pkg/diagnostics: change vertical interpolation to be safer, and more
463       flexible (define p-levels to interpolate to in data.diagnostics);
464      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
465       diagnostic pointer.
466    o pkg/seaice: more cleaning up of seaice_growth, added many comments
467    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
468    o fix multi-category seaice:
469     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
470       SEAICE_MULTICATEGORY
471     - fix short wave heat flux
472    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
473       and allow to use EVP solver. Change forward lab_sea: test both EVP
474       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
475    o Initial check-in of lab_sea adjoint
476      (very similar to natl_box_adjoint/code_seaice)
477      * used C-grid and EVP solver
478      * used KPP, GM/Redi
479      * uses inAdExact=.TRUE.
480      * gradient checks fail for both ADM and TLM
481        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
482        f.d. gradients actually seem more problematic than ADM, TLM gradients;
483        issue is related to forward mismatch between g77 an ifort
484    o pkg/seaice: overhaul of thermodynamics
485     - growth.F and groatb.F are replaced by new routine seaice_growth.F
486     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
487     - move a few global fields out of SEAICE.h into seaice_growth.F and
488       make them 2D (FICE/QNETO/ ...)
489     - remove FO (it is the same as QNETO)
490     - introduce a few local fields to avoid modifying external fields such
491       as atemp, etc.
492    
493    checkpoint58s_post
494    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
495      changed exf_set_gen.F so that
496        genperiod=0 means input file is one time-constant field and
497        genperiod=-12 means input file contains 12 monthly means
498    o CG2D: use pre-computed solver main-diagonal (stored in common block);
499      this affects truncation error ; generate new output file for exp. which
500      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
501        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
502        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
503        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
504        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
505        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
506    o start implementation of deep-atmosphere and anelastic formulation
507    o verification: remove 2nd copy of input files and use script "prepare_run"
508      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
509    o mom_common/vecinv/fluxform: fix a few initialisation isssues
510    o profiles: fix for multithreaded case
511    
512    o diagnostics: rename few diags:
513      s/'PRESSURE'/'RCENTER '/g
514      s/'TICE    '/'oceFreez'/g
515      s/'TAUX    '/'oceTAUX '/g
516      s/'TAUY    '/'oceTAUY '/g
517      s/'SWFLUX  '/'oceQsw  '/g
518      s/DIFx/DFxE/g
519      s/DIFy/DFyE/g
520      and add few ocean-forcing diagnostics:
521      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
522    o modifications to pkg/seaice/growth.F and budget.F, which change results of
523      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
524      as actual snow thickness.  It now refers everywhere to effective snow
525      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
526    
527    checkpoint58r_post
528    o modifications to pkg/seaice/growth.F, which change results of
529      lab_sea experiment: fixes pertain to melting snow over open water, to
530      masking EVAP under sea ice, and to using the correct AREA variable for
531      computations of EVAP, PRECIP, HSNOW, and GHEFF
532    o add ability to read bathy, salt, and theta using MNC (off by def)
533    o add flooding algorithm and advection of HSNOW for pkg/seaice;
534      both are turned off by default and do no change any results
535    o seaice advection with pkg/thsice: a step toward the use of non-linear
536      advection scheme, but #ifdef or commented out for now (requires more EXCH).
537    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
538      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
539      in natl_box (affects results @ truncation level: update output.txt)
540    o multi-threading and IO:
541      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
542      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
543        (needed to work with SingleCpuIO): tested in all verif. exp.
544    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
545      affects the results (but none of the verification test uses this scheme).
546    o Adding some pkg/diagnostics capability to pkg/seaice
547      (will certainly be subject to changes)
548    o ctrl: adding new control variables:
549      lwflux, lwdown, evap, snowprecip, apressure, runoff
550    
551    checkpoint58q_post
552    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
553      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
554      high_res_cube configuration by 4% on Columbia.
555    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
556      add (in global_with_exf/code) a version of EXF_INTERP_READ without
557      dynamical allocation (seems to work in multi-threaded).
558    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
559      single CPU io) so that TAF does not have to see EESUPPORT.h
560    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
561    
562    checkpoint58p_post
563    o obcs: stop if obcs is used with useCDscheme = .true.
564    o shelfice:
565     - fix a sign error so that no slip at shelfice interface works
566     - remove stop for combination non-hydrostatic code and shelfice. That does
567       not mean, that the results are correct, but at least they are numerically
568       stable
569    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
570    o added adjoint exch routined for all exch*3d* routines
571      and updated flow directives
572    
573    checkpoint58o_post
574    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
575      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
576    o change controling S/R for writing pickup file (new S/R do_write_pickup)
577      and clean-up reading/writing of pickup files.
578    o fix local version of read/write pickup (NH part) in rotating_tank/code
579    o simplify EXCH interface:
580     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
581     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
582    o added the regrid package
583    o shelfice:
584     - add a simple boundary layer scheme to reduce noise
585     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
586    
587  checkpoint58n_post  checkpoint58n_post
588  o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to  o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
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