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revision 1.794 by mlosch, Thu Apr 19 15:49:24 2007 UTC revision 1.961 by mlosch, Mon Feb 25 20:59:01 2008 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o add a flag writePickupAtEnd (default=true) to be able to suppress
8      writing a pickup at the last timestep
9    o pkg/profiles:
10      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
11      (for "less than 32 characters name" compiler requirement)
12    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
13      conditions that have a different sampling frequency than S/T/U/V obcs
14    o pkg/diagnostics (stats-diags):
15      - fix global Min/Max in case 1 processor get only empty tiles
16    o genmake2: replace (4 times)
17         make genmake_tc_1.o >> genmake_warnings 2>&1
18      with
19         COMM="$CC $CFLAGS -c genmake_tc_1.c"
20         echo $COMM >> genmake_warnings
21         $COMM >> genmake_warnings 2>&1
22      to make genmake2 always see the value of CC as specified in the optfile.
23    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
24      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
25      - modify verification advect_cs test to test SOM-advection on CS-grid.
26    o pkg/ctrl:
27      - Rewrite of ctrl_map_ini_ecco.F,
28        introducing a generic routine (ctrl_map_ini_gen.F).
29      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
30    
31    checkpoint59n
32    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
33      number in dedicate array "hdiag":
34      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
35        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
36      - many small changes (integer format) for large number of diagnostics
37      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
38        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
39    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
40      usingSphericalGrid, this allows to define the rotated grid coordinates
41      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
42      geographical coordinates according to the inverse of the rotation defined
43      by the Euler angles, so that Coriolis parameter and online-interpolation by
44      exf works with the geographical coordinates on XC/YC/XG/YG.
45      Naturally, this feature does not work with all packages, so some
46      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
47      profiles), because there the coordinates are assumed to be regular
48      spherical grid coordinates.
49    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
50      - introduce isopycnal diffusion coefficient control.
51    o tools/adjoint_options:
52      - additional control vector components.
53    o pkg/mnc: have mnc create marginally meaning full coordinate variables
54      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
55    o pkg/mypackage:
56      - add example of read/write pickup for state-var ;
57      - add entry points to the main code for state-vars diags & write-pickup.
58    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
59      transitions for useExfYearlyFields
60      - add new subroutine that determines the file to read from for
61        use*YearlyFields = .TRUE. and .FALSE.
62      - add a verification experiment to global_with_exf that tests
63        useExfYearlyFields with USE_EXF_INTERPOLATION defined
64    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
65      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
66      subroutines (which could be generated from a template, because they are
67      almost identical), for now they are included in obcs_prescribe_read.F for
68      simplicity
69    o pkg/exf:
70      - add a little more diagnostic to exf_interp_read (in analogy to
71        mds_read_field, can be turned off with debugLevel < debugLevA=1)
72      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
73        ugly but fast by unrolling short inner loops, inserting a unroll=8
74        directive in routine lagran, and splitting a loop and making do while the
75        outermost loop (the latter requires the intoduction of index arrays)
76    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
77    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
78      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
79    o verification/seaice_obcs: updated for restart test and latest options
80    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
81      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
82      for now this is only available for the C-grid code and also within
83      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
84    
85    checkpoint59m
86    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
87      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
88    o gad_som : fix flux output (& diagnostics) to have same units as other  
89      advection scheme fluxes (was previously multiplied by deltaT).  
90    o added verification/seaice_obcs both to test seaice open boundaries
91      and to provide an example matlab scrpt for generating them
92    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
93    o pkg/salt_plume: clean up salt_plume_frac.F to
94      remove redundancy in PlumeMethod 1 and 4
95    o pkg/kpp: added saltplume diagnostics
96    o pkg/obcs and pkg/seaice:
97      - do not set uice and vice to zero when OB*icefile are unspecified
98      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
99      - moved seaice tracer obcs after call to seaice_growth
100    o pkg/salt_plume: added various options for salt plume depth
101      criterion and for vertical distribution of the salt
102    
103    checkpoint59l
104    o pkg/ptracers: new version of ptracers pickup:
105      read meta file and write only fields which are needed to restart.
106      ( same logic as main pickup file ; also using pickupStrictlyMatch )
107    o pkg/seaice:
108      - add timescale for melting due to warm mixed layer as a means of
109        setting SEAICE_availHeatFrac more conveniently
110      - add a CPP-flag/runtime parameter check for flooding algorithm
111      - reformulated availHeat in seaice_growth.F to be independent of AREA
112    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
113      unit changes
114    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
115    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
116      SX vector computer.
117    o pkg/seaice:
118      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
119        seaice forcing fields can now be read only through pkg/exf
120      - removed some unused halos
121    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
122    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
123      or U/VICE from U/VWIND before computing U/VSTRESS
124    
125    checkpoint59k
126    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
127      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
128    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
129      all experiments pass when compile with un-initialised var. checking option.
130    o added pkg/salt_plume
131    o script to test restart (for now, in MITgcm_contrib/jmc_script)
132    o pkg/seaice: new read/write pickup version.
133      read meta file and write only fields which are needed to restart.
134      ( same logic as main pickup file ; also using pickupStrictlyMatch )
135    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
136    o lab_sea.hb87: modify the domain & update output.hb87.txt :
137      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
138      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
139      process. Fixed here by closing the domain at the Northern boundary.
140    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
141    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
142      a set of consecutive levels in/from a 3-D array.
143    o pkg/ptracers:
144      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
145      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
146    
147    checkpoint59j
148    o in pkgs: dic, obcs, offline, rbcs:
149      standard way to compute coeff. for time interpolation between 2 time reccords
150      which retains full precision (& make results less dependent on compiler).
151      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
152    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
153      packages instead of reading ice cover and wind speed separately
154    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
155     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
156      to allow to compile customized code before the update)
157    o cleaning-up:
158      - fix CPP instruction syntax in pkg/obcs
159      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
160        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
161      - fix some threads issue in IO parts.
162    o pkg/dic:
163      - add tons of "_d 0" (--> much better testreports !)
164       and then update outputs of tutorial_global_oce_biogeo
165    o pkg/mom_fluxform:
166      add a special version of momentum advection intended to conserve momentum
167      next to a bathymetry step or a coastline edge. (default = off = #undef)
168    o new read/write pickup version:
169      - for now, only implemented for main (mdsio) pickup file.
170      - write out only what is needed to restart; merge pickup_nh , pickup_ph
171        and main pickup together.
172      - read meta file; read only what is needed to restart; stop if a field
173        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
174        if it make sense (even if the restart is not perfect).
175      - if no meta file, assume that pickup to read corresponds exactly to
176        a pickup that would currently be written.
177      - read pickup written in the old format (until checkpoint59i) if it
178        recognizes an old meta file (no field-list).
179      - add a meta file in exp. which starts from a pickup: 2 cases:
180        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
181         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
182        b) a meta file describing the content of the associated pickup file
183         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
184    o pkg/mdsio & pkg/rw:
185      - new routine to read a meta file ; new set of routine to read
186        Multiple-fields file (with meta file).
187    o added open boundary conditions capability for seaice
188        HSNOW, HSALT, UICE, and VICE
189    
190    checkpoint59i
191    o adjoint:
192      * fix multiDimAdvection adjoint
193        (partial recomputation problem by TAF for fVerT(:,:,kDown)
194        and comlev1 size definition (maxpass vs. max. number of tracers)
195      * verification/global_ocean.90x45x15 adjoint now tests
196        NLFS and multiDimAdvection using DST3 (=30)
197      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
198    o pkg/kpp: add "_d 0" to real constant (if missing);
199      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
200      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
201    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
202      for internal parameters related to restart process (formerly from PARAMS.h)
203      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
204    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
205      as argument. (only atm2d & obcs write_pickup have not yet been updated)
206    o pkg/monitor:
207      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
208      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
209      - account for deep Atmosphere factor and density factor (anelastic)
210    o added open boundary conditions capability for seaice HEFF and AREA
211    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
212      thermodynamics
213      - requires a little reorganization, which affects the testreport results
214        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
215        so that now the conservative form is tested
216      - add a few comments
217    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
218    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
219    o add new diagnostics to seaice: advective, diffusive fluxes (only for
220      multidim-advection, for scheme 2 they are not filled) and transports,
221      thermodynamic growth rates
222    o change units of EmPmR (inside the code, + within coupling interface)
223      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
224      Affects results @ truncation level (cg2d match) and update output of
225       experiments: lab_sea(6), global_ocean.90x40x15(10),
226      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
227      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
228      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
229      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
230    
231    checkpoint59h
232    o pkg/exf:
233      - improve vectorization by moving if-statement out of loops in
234        exf_mapfields, exf_radiation
235      - exf_bulkformulae.F: introduce 2D fields and vectorize code
236    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
237    o testreport:
238      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
239        monitor & update offline_exf_seaice exp. output.
240      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
241    o pkg/seaice:
242      - bug fix in the evp solver: boundary conditions were affected be
243        masking of zMax/zMin (changes results)
244      - minor bug fix in boundary conditions in seaice_calc_strainrates
245        (changes results for no_slip)
246      - seaice_lsr.F: make interpolation of eta dependent on boundaries
247      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
248      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
249        stress formulation and no-slip boundary conditions
250    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
251      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
252    o pkg/seaice: a first HSALT time stepping equation has been checked in
253    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
254      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
255      without requiring DO-IF statements
256    o pkg/thsice:
257      use continuous power-law function for partition of energy between lateral
258      melting/freezing and thinning/thickening ; old code using step function
259      still available with #undef THSICE_FRACEN_POWERLAW
260      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
261    o testreport: change AD testing : check against results/output_adm.txt
262      using same scripts as for forward test.
263    
264    checkpoint59g
265    o adjoint testing: in preparation for changing testreport:
266      - output format: cost and grad written on separated lines
267      - ad output results in directory "results" (instead of "results_ad")
268    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
269    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
270    o pkg/ecco: allow user defined cost function contributions
271    o testreport:
272      Allow to choose (per experiment) the list of tested output variables
273       and the main variable (used to issue a pass/FAIL ) ;
274      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
275      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
276      Also modify printing of summary:
277       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
278       b) echo the list of tested variables in the individual summary.txt of
279          each experiment.
280    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
281      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
282      (but still depend on the tile decompostion of the domain).
283    o pkg/seaice: change a discretization detail to make the B-grid code
284      "more symmetric". This change is likely to remove all "ridges/leads" that
285      where quasi-aligned with the grid in B-grid solutions. It may also be
286      the solution to the stress coupling issues with the B-grid.
287    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
288      remove .cvsignore from input dir. (since testreport no longer run here).
289    o pkg/thsice:
290     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
291     - fix reshaping of sea-ice just after advection:
292       melt all the ice only if ice-volume is too small.
293     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
294       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
295     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
296    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
297      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
298    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
299      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
300      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
301      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
302      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
303      -> update output.txt
304    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
305     this affects truncation error: -> update output.txt of exp:
306      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
307      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
308    
309    checkpoint59f
310    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
311    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
312      a bounded range (in forward mode)
313    o pkg/ecco, ctrl, autodiff and mom_common:
314     internal parameter controls, completements of implementations
315    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
316    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
317      (not seem any difference in testing results).
318    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
319       at face corners.
320    o pkg/generic_advdiff:
321     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
322      loop range indices for computing vertical advection tendency
323      and do the calculation in the interior only (no overlap) ;
324      for now, only implemented for SOM advection (to save CPU time).
325     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
326    o exch2 adjoint
327      First set of changes:
328      - add exch2 hand-written adjoint templates
329      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
330        This will require cleanup in pkg/autodiff/*.F
331        (changed routines currently kept separate in verif. code/)
332      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
333        that used to hide exch2 or cubed-sphere specific code
334        (commented via 'cph-exch2')
335    o pkg/seaice
336      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
337    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
338       output of global_ocean.cs32x15.thsice .
339    
340    checkpoint59e
341    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
342      for B-grid vector (not yet tested) and C-grid vector (<- only used
343      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
344    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
345      (#ifdef ALLOW_SALT_PLUME)
346    o gather_2d/scatter_2d: removed halo regions
347    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
348      scheme and the corresponding test case (under front_relax dir). For now,
349      only available with Skew-flux form and not yet tested in realistic set-up.
350      adjoint: store directives updated, but gradient checks deteriorated,
351      so maybe GM/Redi adjoint is now broken.
352    o seaice adjoint
353      * add AREA, HEFF, HSNOW as control variable
354        (should not change lab_sea results)
355      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
356    o pkg/seaice:
357      * added computation of saltFlux in seaice_growth;
358        For time being, sea ice salinity is assumed constant
359        contribution of snow flooding to freshening of sea ice is neglected.
360        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
361        defaults to 0.0 in order to maintain backward compatibility.
362        Typical values for SEAICE_salinity are 4 to 10 g/kg.
363      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
364      * added SEAICE_availHeatFrac, which specifies fraction of surface level
365        heat content used to melt or grow ice
366      * commented out cap of HICE: it helps keep ice thinner
367      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
368      * applied OBCS T/S mask to HEFFM sea ice mask
369    
370    checkpoint59d
371    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
372     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
373     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
374    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
375     and change default value of parameter "GM_Small_Number";
376     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
377       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
378       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
379    o pkg/ecco: cost function when applying pkg/smooth to controls
380    o pkg/ctrl: add forcingPrecond run time parameter
381    o pkg/seaice:
382     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
383     - fix bug in metric terms of u-equation in LSR solver (implicit part),
384       changes verification/lab_sea
385     - rearrange implicit part of u-equation in LSR solver to make it easier to
386       read, understand, and debug. This causes changes at the truncation level.
387     - fix (serious) bug in the boundary conditions (sign error in the implicit
388       part) of the LSR solver. Changes all LSR results.
389     - fixed problem with HSNOW initialization to avoid thick snow when AREA
390       is initilized with small values - does not change lab_sea results.
391     - added HsnowFile initialization capability
392    o pkg/smooth: addition to model/src and pkg/ctrl so allow
393     initialization of pkg/smooth and application to control vector
394    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
395    o dependencies: pkg/profiles requires pkg/cal
396    o pkg/profiles:
397     - added option ALLOW_PROFILES_GENERICGRID
398         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
399         that interpolation information (grid points and coefficients) is provided
400         within the netcdf input files.
401         -> sample matlab scripts can be found in MITgcm_contrib/gael
402         that allow you to prepare netcdf input files.
403     - also modified: cleaner include statements, cleaner error print statements,
404       cleaner stops when error, and more tests of the netcdf input files consistency.
405    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
406    o pkg/seaice:
407     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
408       requires a new routine: seaice_diagnostics_fill.F
409     - make sure that seaice does not move if not forced (pressure replacement
410       method, Hibler and Ip, 1995), changes results
411     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
412     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
413       It is turned off by default (=-1.), because it changes the results.
414     - make it possible to read AREA from a file, too.
415    
416    checkpoint59c
417    o add S/R and diagnostics for oceanic mixed-layer depth
418    o move GMRedi call after all vertical mixing schemes (including KPP)
419    o pkg/thsice:
420     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
421      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
422    o pkg/obcs:
423     - bug fix for balance code
424    o pkg/seaice:
425      - allow values of SEAICE_elasticParm > 1
426      - add new parameter SEAICE_evpTauRelax as an alternative
427        to SEAICE_elasticParm
428      - make lsr boundary conditions free slip (by default), changes result
429      - add code for no slip boundary conditions for lsr
430      - set minimum of zeta to zero (and not 4e8) (changes results)
431      - add a cap on AREA after advecting AREA if seaice_growth is not called
432    o change calculation of Visbeck K:
433      - no longer depend on tapering scheme; instead, compute slope (limited
434        by GM_maxSlope). this is equivalent to what was comuted before with
435        clipping or linear tappering.
436      - fix vertical averaging (wrong by 1/2 level)
437      - leave the old version (but will not be maintained) within
438        #ifdef OLD_VISBECK_CALC / #endif
439      - update output of exp. ideal_2D_oce
440    o change error catch in calc_r_star to improve vectorization
441    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
442      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
443    o adjoint:
444      Re-organized adjoint checkpointing according to Matt Mazloff
445      (but with modifs/completions/cleanups)
446      Storing is now bundled into large arrays to optimized I/O
447      (and second step in cleanup of the_main_loop)
448    
449    checkpoint59b
450    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
451      - export/import (between ocean & coupler) fields needed for ocean DIC.
452    o pkg/seaice:
453      - get rid of three more exchanges seaice_calc_viscosities (required
454        different loop boundaries in seaice_lsr and seaice_ocean_stress)
455      - bug fix in seaice_ocean_stress (update of lab_sea required)
456      - reduce loop boundaries to necessary minimum also in seaice_evp
457      - go back to the old way of computing deltaC/Z as the adjoint likes that
458        better
459    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
460      passive tracer to an Age Tracer) + update output.txt
461    o pkg/exf:
462      - implement A-grid / C-grid selection for wind-stress input files.
463      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
464      for now, in exf_bulk_largeyeager04.F only :
465      - change implementation for case where windspeed + 2. components wind-stress
466        are read-in. AND use rhoConstFresh to convert evap.
467    o pkg/seaice:
468      - use correct EXCH_UV for wind-forcing (on A-grid).
469      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
470        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
471    o pkg/exf:
472      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
473      EXF_INTERPOLATION:
474      - merge global_with_exf/code version of exf_interp_read.F
475        to the main code ;
476      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
477        reading the file ; Important: This options needs to be defined to recover
478        previous code.
479        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
480      - no longer loose real*8 precision along the way when using exf_iprec=64.
481    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
482      - change discretisation of evp-solver in order to avoid another exchange
483        (changes lab_sea) and clean up a little
484      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
485        help the adjoint (this also changes the results slightly)
486      - add a few "_d 0" where they had been missing in seaice_evp.F
487      - cleaning up: remove unused seaice_calc_rhs.F
488    o pkg/exf: some cleaning-up:
489      - change various "constants" into runtime parameters
490      - cleaned-up Large&Yeager04 routine which should eventually
491        replace exf_bulkformulae.F (changed names of S/R and CPP)
492        and merged various ALLOW_ATM_WIND options
493     only used with thsice pkg (in thsice_get_exf.F):
494      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
495        which are used when useStabilityFct_overIce=TRUE (= the default)
496      - change default values of ice & snow emissivity and scale downward LW
497        by ice & snow emissivity.
498    o pkg/thsice:
499     fix few little problems, in thsice_calc_thickn.F:
500      - growth vertically (and not laterally) if iceFrac == iceMaskMax
501      - melt only laterally if hIce < hThinIce (as the comments say)
502      and in thsice_extend.F:
503      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
504      - start to form ice as soon as the minimum ice-volume is reachable.
505     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
506      and cpl_aim+ocn
507    o pkg/kpp
508     - move computation of surface related input fields to KPP into a new
509       subroutine kpp_forcing_surf.F
510     - remove wrong (within bi,bj loops) EXCH calls.
511     - little cleaning (add argument myThid in last position, cvs header ...)
512     - for now, fix conservation problem by exchanging KPPviscAz (may not
513       be the best fix)
514    o pkg/seaice
515     - check for inconsistent evp parameter/cpp-flag combination
516     - remove leftover errIO flat for obsolete name list error handling
517    o OpenAD
518     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
519    
520    checkpoint59a
521    o pkg/seaice: some parameter clarifications and a little bit of clean up
522    o pkg/thsice: rename run-time parameters:
523       himin       -> hIceMin
524       himin0      -> hThinIce
525       hihig       -> hThickIce
526       i0          -> i0swFrac
527       transCoef   -> bMeltCoef
528       frac_energy -> fracMelting
529      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
530       with default values (for now) that do not change the results.
531      remove old version of thsice vars advection in pkg/seaice.
532    o in FFIELDS.h:
533      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
534      - make pLoad & sIceLoad always available (but still only used if
535         ATMOSPHERIC_LOADING is #define).
536    o pkg/kpp: replaced _KPP_RL with _RL
537    o bug fixes for vertical diffusivity computations when both KPP and
538        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
539        are no longer updating the vertical diffusivity array
540        (passed as argument) but are (re-) setting those arrays.
541    o pkg/seaice: fix bug in evp solver, while doing that
542      - change (improve?) discretization of stress computations for both
543        cgrid-lsr and evp solver
544      - add a new routine to compute strain rates
545      - the above changes lab_sea results
546      - add no slip conditions for evp solver (off by default), lsr-version
547        may follow
548      - fix exchange for shear at Z-points (does not change lab_sea)
549      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
550        (to force the user to pick a time step since there is not "safe" way
551        of choosing it)
552      - add principal stress diagnostics
553      - rearrange fields for evp a little to avoid having to call a: too many
554        exchanges and b: exchanges for stress trensor components which we do
555        not have.
556      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
557        of evp, complete rewrite for lsr case (latter is does not yet work
558        in all cases)
559  o pkg/kpp: add code to have mixing in shelf ice caverns  o pkg/kpp: add code to have mixing in shelf ice caverns
560      - add myThid to all kpp routines (long overdue)
561    
562  checkpoint59  checkpoint59
563  o pkg/exf:  o pkg/exf:

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