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revision 1.747 by dimitri, Mon Nov 20 20:06:43 2006 UTC revision 1.909 by jmc, Tue Nov 13 22:20:29 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 lab_sea.hb87: modify the domain & update output.hb87.txt :
8      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
9      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
10      process. Fixed here by closing the domain at the Northern boundary.
11    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
12    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
13      a set of consecutive levels in/from a 3-D array.
14    o pkg/ptracers:
15      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
16      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
17    
18    checkpoint59j
19    o in pkgs: dic, obcs, offline, rbcs:
20      standard way to compute coeff. for time interpolation between 2 time reccords
21      which retains full precision (& make results less dependent on compiler).
22      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
23    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
24      packages instead of reading ice cover and wind speed separately
25    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
26     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
27      to allow to compile customized code before the update)
28    o cleaning-up:
29      - fix CPP instruction syntax in pkg/obcs
30      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
31        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
32      - fix some threads issue in IO parts.
33    o pkg/dic:
34      - add tons of "_d 0" (--> much better testreports !)
35       and then update outputs of tutorial_global_oce_biogeo
36    o pkg/mom_fluxform:
37      add a special version of momentum advection intended to conserve momentum
38      next to a bathymetry step or a coastline edge. (default = off = #undef)
39    o new read/write pickup version:
40      - for now, only implemented for main (mdsio) pickup file.
41      - write out only what is needed to restart; merge pickup_nh , pickup_ph
42        and main pickup together.
43      - read meta file; read only what is needed to restart; stop if a field
44        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
45        if it make sense (even if the restart is not perfect).
46      - if no meta file, assume that pickup to read corresponds exactly to
47        a pickup that would currently be written.
48      - read pickup written in the old format (until checkpoint59i) if it
49        recognizes an old meta file (no field-list).
50      - add a meta file in exp. which starts from a pickup: 2 cases:
51        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
52         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
53        b) a meta file describing the content of the associated pickup file
54         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
55    o pkg/mdsio & pkg/rw:
56      - new routine to read a meta file ; new set of routine to read
57        Multiple-fields file (with meta file).
58    o added open boundary conditions capability for seaice
59        HSNOW, HSALT, UICE, and VICE
60    
61    checkpoint59i
62    o adjoint:
63      * fix multiDimAdvection adjoint
64        (partial recomputation problem by TAF for fVerT(:,:,kDown)
65        and comlev1 size definition (maxpass vs. max. number of tracers)
66      * verification/global_ocean.90x45x15 adjoint now tests
67        NLFS and multiDimAdvection using DST3 (=30)
68      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
69    o pkg/kpp: add "_d 0" to real constant (if missing);
70      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
71      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
72    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
73      for internal parameters related to restart process (formerly from PARAMS.h)
74      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
75    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
76      as argument. (only atm2d & obcs write_pickup have not yet been updated)
77    o pkg/monitor:
78      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
79      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
80      - account for deep Atmosphere factor and density factor (anelastic)
81    o added open boundary conditions capability for seaice HEFF and AREA
82    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
83      thermodynamics
84      - requires a little reorganization, which affects the testreport results
85        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
86        so that now the conservative form is tested
87      - add a few comments
88    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
89    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
90    o add new diagnostics to seaice: advective, diffusive fluxes (only for
91      multidim-advection, for scheme 2 they are not filled) and transports,
92      thermodynamic growth rates
93    o change units of EmPmR (inside the code, + within coupling interface)
94      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
95      Affects results @ truncation level (cg2d match) and update output of
96       experiments: lab_sea(6), global_ocean.90x40x15(10),
97      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
98      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
99      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
100      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
101    
102    checkpoint59h
103    o pkg/exf:
104      - improve vectorization by moving if-statement out of loops in
105        exf_mapfields, exf_radiation
106      - exf_bulkformulae.F: introduce 2D fields and vectorize code
107    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
108    o testreport:
109      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
110        monitor & update offline_exf_seaice exp. output.
111      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
112    o pkg/seaice:
113      - bug fix in the evp solver: boundary conditions were affected be
114        masking of zMax/zMin (changes results)
115      - minor bug fix in boundary conditions in seaice_calc_strainrates
116        (changes results for no_slip)
117      - seaice_lsr.F: make interpolation of eta dependent on boundaries
118      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
119      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
120        stress formulation and no-slip boundary conditions
121    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
122      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
123    o pkg/seaice: a first HSALT time stepping equation has been checked in
124    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
125      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
126      without requiring DO-IF statements
127    o pkg/thsice:
128      use continuous power-law function for partition of energy between lateral
129      melting/freezing and thinning/thickening ; old code using step function
130      still available with #undef THSICE_FRACEN_POWERLAW
131      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
132    o testreport: change AD testing : check against results/output_adm.txt
133      using same scripts as for forward test.
134    
135    checkpoint59g
136    o adjoint testing: in preparation for changing testreport:
137      - output format: cost and grad written on separated lines
138      - ad output results in directory "results" (instead of "results_ad")
139    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
140    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
141    o pkg/ecco: allow user defined cost function contributions
142    o testreport:
143      Allow to choose (per experiment) the list of tested output variables
144       and the main variable (used to issue a pass/FAIL ) ;
145      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
146      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
147      Also modify printing of summary:
148       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
149       b) echo the list of tested variables in the individual summary.txt of
150          each experiment.
151    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
152      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
153      (but still depend on the tile decompostion of the domain).
154    o pkg/seaice: change a discretization detail to make the B-grid code
155      "more symmetric". This change is likely to remove all "ridges/leads" that
156      where quasi-aligned with the grid in B-grid solutions. It may also be
157      the solution to the stress coupling issues with the B-grid.
158    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
159      remove .cvsignore from input dir. (since testreport no longer run here).
160    o pkg/thsice:
161     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
162     - fix reshaping of sea-ice just after advection:
163       melt all the ice only if ice-volume is too small.
164     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
165       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
166     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
167    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
168      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
169    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
170      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
171      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
172      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
173      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
174      -> update output.txt
175    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
176     this affects truncation error: -> update output.txt of exp:
177      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
178      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
179    
180    checkpoint59f
181    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
182    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
183      a bounded range (in forward mode)
184    o pkg/ecco, ctrl, autodiff and mom_common:
185     internal parameter controls, completements of implementations
186    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
187    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
188      (not seem any difference in testing results).
189    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
190       at face corners.
191    o pkg/generic_advdiff:
192     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
193      loop range indices for computing vertical advection tendency
194      and do the calculation in the interior only (no overlap) ;
195      for now, only implemented for SOM advection (to save CPU time).
196     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
197    o exch2 adjoint
198      First set of changes:
199      - add exch2 hand-written adjoint templates
200      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
201        This will require cleanup in pkg/autodiff/*.F
202        (changed routines currently kept separate in verif. code/)
203      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
204        that used to hide exch2 or cubed-sphere specific code
205        (commented via 'cph-exch2')
206    o pkg/seaice
207      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
208    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
209       output of global_ocean.cs32x15.thsice .
210    
211    checkpoint59e
212    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
213      for B-grid vector (not yet tested) and C-grid vector (<- only used
214      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
215    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
216      (#ifdef ALLOW_SALT_PLUME)
217    o gather_2d/scatter_2d: removed halo regions
218    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
219      scheme and the corresponding test case (under front_relax dir). For now,
220      only available with Skew-flux form and not yet tested in realistic set-up.
221      adjoint: store directives updated, but gradient checks deteriorated,
222      so maybe GM/Redi adjoint is now broken.
223    o seaice adjoint
224      * add AREA, HEFF, HSNOW as control variable
225        (should not change lab_sea results)
226      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
227    o pkg/seaice:
228      * added computation of saltFlux in seaice_growth;
229        For time being, sea ice salinity is assumed constant
230        contribution of snow flooding to freshening of sea ice is neglected.
231        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
232        defaults to 0.0 in order to maintain backward compatibility.
233        Typical values for SEAICE_salinity are 4 to 10 g/kg.
234      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
235      * added SEAICE_availHeatFrac, which specifies fraction of surface level
236        heat content used to melt or grow ice
237      * commented out cap of HICE: it helps keep ice thinner
238      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
239      * applied OBCS T/S mask to HEFFM sea ice mask
240    
241    checkpoint59d
242    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
243     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
244     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
245    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
246     and change default value of parameter "GM_Small_Number";
247     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
248       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
249       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
250    o pkg/ecco: cost function when applying pkg/smooth to controls
251    o pkg/ctrl: add forcingPrecond run time parameter
252    o pkg/seaice:
253     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
254     - fix bug in metric terms of u-equation in LSR solver (implicit part),
255       changes verification/lab_sea
256     - rearrange implicit part of u-equation in LSR solver to make it easier to
257       read, understand, and debug. This causes changes at the truncation level.
258     - fix (serious) bug in the boundary conditions (sign error in the implicit
259       part) of the LSR solver. Changes all LSR results.
260     - fixed problem with HSNOW initialization to avoid thick snow when AREA
261       is initilized with small values - does not change lab_sea results.
262     - added HsnowFile initialization capability
263    o pkg/smooth: addition to model/src and pkg/ctrl so allow
264     initialization of pkg/smooth and application to control vector
265    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
266    o dependencies: pkg/profiles requires pkg/cal
267    o pkg/profiles:
268     - added option ALLOW_PROFILES_GENERICGRID
269         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
270         that interpolation information (grid points and coefficients) is provided
271         within the netcdf input files.
272         -> sample matlab scripts can be found in MITgcm_contrib/gael
273         that allow you to prepare netcdf input files.
274     - also modified: cleaner include statements, cleaner error print statements,
275       cleaner stops when error, and more tests of the netcdf input files consistency.
276    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
277    o pkg/seaice:
278     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
279       requires a new routine: seaice_diagnostics_fill.F
280     - make sure that seaice does not move if not forced (pressure replacement
281       method, Hibler and Ip, 1995), changes results
282     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
283     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
284       It is turned off by default (=-1.), because it changes the results.
285     - make it possible to read AREA from a file, too.
286    
287    checkpoint59c
288    o add S/R and diagnostics for oceanic mixed-layer depth
289    o move GMRedi call after all vertical mixing schemes (including KPP)
290    o pkg/thsice:
291     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
292      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
293    o pkg/obcs:
294     - bug fix for balance code
295    o pkg/seaice:
296      - allow values of SEAICE_elasticParm > 1
297      - add new parameter SEAICE_evpTauRelax as an alternative
298        to SEAICE_elasticParm
299      - make lsr boundary conditions free slip (by default), changes result
300      - add code for no slip boundary conditions for lsr
301      - set minimum of zeta to zero (and not 4e8) (changes results)
302      - add a cap on AREA after advecting AREA if seaice_growth is not called
303    o change calculation of Visbeck K:
304      - no longer depend on tapering scheme; instead, compute slope (limited
305        by GM_maxSlope). this is equivalent to what was comuted before with
306        clipping or linear tappering.
307      - fix vertical averaging (wrong by 1/2 level)
308      - leave the old version (but will not be maintained) within
309        #ifdef OLD_VISBECK_CALC / #endif
310      - update output of exp. ideal_2D_oce
311    o change error catch in calc_r_star to improve vectorization
312    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
313      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
314    o adjoint:
315      Re-organized adjoint checkpointing according to Matt Mazloff
316      (but with modifs/completions/cleanups)
317      Storing is now bundled into large arrays to optimized I/O
318      (and second step in cleanup of the_main_loop)
319    
320    checkpoint59b
321    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
322      - export/import (between ocean & coupler) fields needed for ocean DIC.
323    o pkg/seaice:
324      - get rid of three more exchanges seaice_calc_viscosities (required
325        different loop boundaries in seaice_lsr and seaice_ocean_stress)
326      - bug fix in seaice_ocean_stress (update of lab_sea required)
327      - reduce loop boundaries to necessary minimum also in seaice_evp
328      - go back to the old way of computing deltaC/Z as the adjoint likes that
329        better
330    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
331      passive tracer to an Age Tracer) + update output.txt
332    o pkg/exf:
333      - implement A-grid / C-grid selection for wind-stress input files.
334      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
335      for now, in exf_bulk_largeyeager04.F only :
336      - change implementation for case where windspeed + 2. components wind-stress
337        are read-in. AND use rhoConstFresh to convert evap.
338    o pkg/seaice:
339      - use correct EXCH_UV for wind-forcing (on A-grid).
340      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
341        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
342    o pkg/exf:
343      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
344      EXF_INTERPOLATION:
345      - merge global_with_exf/code version of exf_interp_read.F
346        to the main code ;
347      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
348        reading the file ; Important: This options needs to be defined to recover
349        previous code.
350        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
351      - no longer loose real*8 precision along the way when using exf_iprec=64.
352    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
353      - change discretisation of evp-solver in order to avoid another exchange
354        (changes lab_sea) and clean up a little
355      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
356        help the adjoint (this also changes the results slightly)
357      - add a few "_d 0" where they had been missing in seaice_evp.F
358      - cleaning up: remove unused seaice_calc_rhs.F
359    o pkg/exf: some cleaning-up:
360      - change various "constants" into runtime parameters
361      - cleaned-up Large&Yeager04 routine which should eventually
362        replace exf_bulkformulae.F (changed names of S/R and CPP)
363        and merged various ALLOW_ATM_WIND options
364     only used with thsice pkg (in thsice_get_exf.F):
365      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
366        which are used when useStabilityFct_overIce=TRUE (= the default)
367      - change default values of ice & snow emissivity and scale downward LW
368        by ice & snow emissivity.
369    o pkg/thsice:
370     fix few little problems, in thsice_calc_thickn.F:
371      - growth vertically (and not laterally) if iceFrac == iceMaskMax
372      - melt only laterally if hIce < hThinIce (as the comments say)
373      and in thsice_extend.F:
374      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
375      - start to form ice as soon as the minimum ice-volume is reachable.
376     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
377      and cpl_aim+ocn
378    o pkg/kpp
379     - move computation of surface related input fields to KPP into a new
380       subroutine kpp_forcing_surf.F
381     - remove wrong (within bi,bj loops) EXCH calls.
382     - little cleaning (add argument myThid in last position, cvs header ...)
383     - for now, fix conservation problem by exchanging KPPviscAz (may not
384       be the best fix)
385    o pkg/seaice
386     - check for inconsistent evp parameter/cpp-flag combination
387     - remove leftover errIO flat for obsolete name list error handling
388    o OpenAD
389     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
390    
391    checkpoint59a
392    o pkg/seaice: some parameter clarifications and a little bit of clean up
393    o pkg/thsice: rename run-time parameters:
394       himin       -> hIceMin
395       himin0      -> hThinIce
396       hihig       -> hThickIce
397       i0          -> i0swFrac
398       transCoef   -> bMeltCoef
399       frac_energy -> fracMelting
400      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
401       with default values (for now) that do not change the results.
402      remove old version of thsice vars advection in pkg/seaice.
403    o in FFIELDS.h:
404      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
405      - make pLoad & sIceLoad always available (but still only used if
406         ATMOSPHERIC_LOADING is #define).
407    o pkg/kpp: replaced _KPP_RL with _RL
408    o bug fixes for vertical diffusivity computations when both KPP and
409        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
410        are no longer updating the vertical diffusivity array
411        (passed as argument) but are (re-) setting those arrays.
412    o pkg/seaice: fix bug in evp solver, while doing that
413      - change (improve?) discretization of stress computations for both
414        cgrid-lsr and evp solver
415      - add a new routine to compute strain rates
416      - the above changes lab_sea results
417      - add no slip conditions for evp solver (off by default), lsr-version
418        may follow
419      - fix exchange for shear at Z-points (does not change lab_sea)
420      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
421        (to force the user to pick a time step since there is not "safe" way
422        of choosing it)
423      - add principal stress diagnostics
424      - rearrange fields for evp a little to avoid having to call a: too many
425        exchanges and b: exchanges for stress trensor components which we do
426        not have.
427      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
428        of evp, complete rewrite for lsr case (latter is does not yet work
429        in all cases)
430    o pkg/kpp: add code to have mixing in shelf ice caverns
431      - add myThid to all kpp routines (long overdue)
432    
433    checkpoint59
434    o pkg/exf:
435      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
436        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
437      - move exf header files from lower_case.h to UPPER_CASE.h ;
438        add missing cvs Header & Name
439      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
440      - add namelist param. selectStressGridPosition, exf_monFreq
441      - retire many _CLIM routines, and remove data.exf_clim
442        + params moved to data.exf
443        + climsst, climsss now handled by exf_set_gen, i.e.
444          climss?period=0 refers to constant field,
445          climss?period=-12 to monthly forcing
446      - split up namelists in data.exf
447    o pkg/seaice:
448      - remove seaice_exch and seaice_exch_uv
449      - remove superfluous exchange of theta
450      - add myThid to seaice_budget_ocean/ice
451      - add new interface for atmospheric wind forcing (C-grid only)
452        + new routine
453        + two new field (taux, tauy for stress over ice)
454        + removed one global field (DAIRN) for C-grid case only
455    o pkg/thsise
456      - 2nd set of modifs for thsice adjoint in conjunction with exf
457    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
458    
459    checkpoint58y_post
460    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
461      vertical diffusivity, similar to that in MOM4; turned on using
462      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
463      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
464    o Added capability for 3D specification of background vertical diffusion
465      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
466      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
467      "data" file that contains the 3D vertical diffusivity coefficients.
468    o ice dynamics (pkg/seaice) with thsice thermodynamics:
469      - add code within pkg thsice to advect & diffuse sea-ice fields
470      similar to (and will replace) what has been added in  seaice_advdiff.F,
471      but: - conserving Mass, Heat & Salt.
472           - better when using non-linear advection scheme (not yet fully tested)
473           - can also be used in atmospheric set-up (for now, only the diffusion).
474    
475    checkpoint58x_post
476    o IO option for global-file compact format:
477      - add options when generating topology (utils/exch2/matlab-topology-generator)
478      - add I/O capability (pkg/mdsio).
479      - adapt utils/matlab/rdmds.m to read this format.
480      for now long-line format not yet supported by pkg/mdsio (& exch2).
481    o shelfice: add a few diagnostics
482    
483    checkpoint58w_post
484    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
485      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
486      (and replace horiVertRatio in NH code).
487      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
488                         and tutorial_plume_on_slope (sensitive to truncation)
489    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
490      directly to drive seaice model (C-grid only)
491    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
492     - reintroduce computation of wind from stress,
493     - compute tau (in exf_bulkformulae.F) from windstress averaged to
494       mass points to avoid tau = 0
495     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
496    o rdmnc.m: make it work with "global" files created with gluemnc
497    o rdmnc.m : some improvements in dealing with singleton dimension
498      (tested on all testreport mnc output files).
499    o genmake2: disable pkg/profiles if netcdf test fails.
500    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
501    o move call to cal_readparms up to make calendar parameters/variable available
502      to all packages
503    
504    checkpoint58v_post
505    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
506      useDynP_inEos_Zc tested.
507    o pkg/exf: changes to properly interpolate/mask/scale initial fields
508    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
509      and portions thereof.  See read_cs.txt for description and examples.
510    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
511      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
512      following the great-circle arc between those 2 points.
513    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
514      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
515    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
516     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
517     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
518     - still needs work (not working with some options ; efficiency to improve)
519       and serious testing.
520     - use this scheme for temperature & salinity in 2 advection test exp.:
521       advect_xy & advect_xz, respectively.
522    
523    checkpoint58u_post
524    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
525    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
526    o testreport: add option "-skipdir" to skip some test.
527    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
528      momentum calculation.
529    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
530    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
531      remove checkpoint.F and the_correction_step.F (no longer used);
532      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
533    o add option (linFSConserveTr) to correct for tracer source/sink due to
534      Linear Free surface
535    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
536    o pkg/thsice: fix reading mnc-pickups
537    
538    checkpoint58t_post
539    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
540    o pkg/mdsio:
541     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
542       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
543       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
544     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
545     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
546       either MDS_READ_FIELD or MDS_WRITE_FIELD )
547     - new S/R (to replace MDSWRITEMETA), which allows to write more
548       informations (variable names, time ...) to meta files.
549     - modify rdmds.m to give back the meta file content.
550    o pkg/diagnostics: change vertical interpolation to be safer, and more
551       flexible (define p-levels to interpolate to in data.diagnostics);
552      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
553       diagnostic pointer.
554    o pkg/seaice: more cleaning up of seaice_growth, added many comments
555    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
556    o fix multi-category seaice:
557     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
558       SEAICE_MULTICATEGORY
559     - fix short wave heat flux
560    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
561       and allow to use EVP solver. Change forward lab_sea: test both EVP
562       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
563    o Initial check-in of lab_sea adjoint
564      (very similar to natl_box_adjoint/code_seaice)
565      * used C-grid and EVP solver
566      * used KPP, GM/Redi
567      * uses inAdExact=.TRUE.
568      * gradient checks fail for both ADM and TLM
569        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
570        f.d. gradients actually seem more problematic than ADM, TLM gradients;
571        issue is related to forward mismatch between g77 an ifort
572    o pkg/seaice: overhaul of thermodynamics
573     - growth.F and groatb.F are replaced by new routine seaice_growth.F
574     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
575     - move a few global fields out of SEAICE.h into seaice_growth.F and
576       make them 2D (FICE/QNETO/ ...)
577     - remove FO (it is the same as QNETO)
578     - introduce a few local fields to avoid modifying external fields such
579       as atemp, etc.
580    
581    checkpoint58s_post
582    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
583      changed exf_set_gen.F so that
584        genperiod=0 means input file is one time-constant field and
585        genperiod=-12 means input file contains 12 monthly means
586    o CG2D: use pre-computed solver main-diagonal (stored in common block);
587      this affects truncation error ; generate new output file for exp. which
588      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
589        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
590        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
591        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
592        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
593        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
594    o start implementation of deep-atmosphere and anelastic formulation
595    o verification: remove 2nd copy of input files and use script "prepare_run"
596      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
597    o mom_common/vecinv/fluxform: fix a few initialisation isssues
598    o profiles: fix for multithreaded case
599    
600  o diagnostics: rename few diags:  o diagnostics: rename few diags:
601    s/'PRESSURE'/'RCENTER '/g    s/'PRESSURE'/'RCENTER '/g
602    s/'TICE    '/'oceFreez'/g    s/'TICE    '/'oceFreez'/g
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