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revision 1.759 by mlosch, Thu Dec 21 10:50:56 2006 UTC revision 1.913 by jmc, Wed Nov 28 16:52:16 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 fix un-initialised variable problem (in mom_vecinv & shap_filt):
8      all experiments pass when compile with un-initilised var. checking option.
9    o added pkg/salt_plume
10    o script to test restart (for now, in MITgcm_contrib/jmc_script)
11    o pkg/seaice: new read/write pickup version.
12      read meta file and write only fields which are needed to restart.
13      ( same logic as main pickup file ; also using pickupStrictlyMatch )
14    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
15    o lab_sea.hb87: modify the domain & update output.hb87.txt :
16      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
17      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
18      process. Fixed here by closing the domain at the Northern boundary.
19    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
20    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
21      a set of consecutive levels in/from a 3-D array.
22    o pkg/ptracers:
23      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
24      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
25    
26    checkpoint59j
27    o in pkgs: dic, obcs, offline, rbcs:
28      standard way to compute coeff. for time interpolation between 2 time reccords
29      which retains full precision (& make results less dependent on compiler).
30      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
31    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
32      packages instead of reading ice cover and wind speed separately
33    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
34     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
35      to allow to compile customized code before the update)
36    o cleaning-up:
37      - fix CPP instruction syntax in pkg/obcs
38      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
39        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
40      - fix some threads issue in IO parts.
41    o pkg/dic:
42      - add tons of "_d 0" (--> much better testreports !)
43       and then update outputs of tutorial_global_oce_biogeo
44    o pkg/mom_fluxform:
45      add a special version of momentum advection intended to conserve momentum
46      next to a bathymetry step or a coastline edge. (default = off = #undef)
47    o new read/write pickup version:
48      - for now, only implemented for main (mdsio) pickup file.
49      - write out only what is needed to restart; merge pickup_nh , pickup_ph
50        and main pickup together.
51      - read meta file; read only what is needed to restart; stop if a field
52        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
53        if it make sense (even if the restart is not perfect).
54      - if no meta file, assume that pickup to read corresponds exactly to
55        a pickup that would currently be written.
56      - read pickup written in the old format (until checkpoint59i) if it
57        recognizes an old meta file (no field-list).
58      - add a meta file in exp. which starts from a pickup: 2 cases:
59        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
60         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
61        b) a meta file describing the content of the associated pickup file
62         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
63    o pkg/mdsio & pkg/rw:
64      - new routine to read a meta file ; new set of routine to read
65        Multiple-fields file (with meta file).
66    o added open boundary conditions capability for seaice
67        HSNOW, HSALT, UICE, and VICE
68    
69    checkpoint59i
70    o adjoint:
71      * fix multiDimAdvection adjoint
72        (partial recomputation problem by TAF for fVerT(:,:,kDown)
73        and comlev1 size definition (maxpass vs. max. number of tracers)
74      * verification/global_ocean.90x45x15 adjoint now tests
75        NLFS and multiDimAdvection using DST3 (=30)
76      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
77    o pkg/kpp: add "_d 0" to real constant (if missing);
78      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
79      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
80    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
81      for internal parameters related to restart process (formerly from PARAMS.h)
82      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
83    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
84      as argument. (only atm2d & obcs write_pickup have not yet been updated)
85    o pkg/monitor:
86      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
87      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
88      - account for deep Atmosphere factor and density factor (anelastic)
89    o added open boundary conditions capability for seaice HEFF and AREA
90    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
91      thermodynamics
92      - requires a little reorganization, which affects the testreport results
93        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
94        so that now the conservative form is tested
95      - add a few comments
96    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
97    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
98    o add new diagnostics to seaice: advective, diffusive fluxes (only for
99      multidim-advection, for scheme 2 they are not filled) and transports,
100      thermodynamic growth rates
101    o change units of EmPmR (inside the code, + within coupling interface)
102      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
103      Affects results @ truncation level (cg2d match) and update output of
104       experiments: lab_sea(6), global_ocean.90x40x15(10),
105      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
106      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
107      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
108      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
109    
110    checkpoint59h
111    o pkg/exf:
112      - improve vectorization by moving if-statement out of loops in
113        exf_mapfields, exf_radiation
114      - exf_bulkformulae.F: introduce 2D fields and vectorize code
115    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
116    o testreport:
117      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
118        monitor & update offline_exf_seaice exp. output.
119      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
120    o pkg/seaice:
121      - bug fix in the evp solver: boundary conditions were affected be
122        masking of zMax/zMin (changes results)
123      - minor bug fix in boundary conditions in seaice_calc_strainrates
124        (changes results for no_slip)
125      - seaice_lsr.F: make interpolation of eta dependent on boundaries
126      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
127      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
128        stress formulation and no-slip boundary conditions
129    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
130      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
131    o pkg/seaice: a first HSALT time stepping equation has been checked in
132    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
133      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
134      without requiring DO-IF statements
135    o pkg/thsice:
136      use continuous power-law function for partition of energy between lateral
137      melting/freezing and thinning/thickening ; old code using step function
138      still available with #undef THSICE_FRACEN_POWERLAW
139      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
140    o testreport: change AD testing : check against results/output_adm.txt
141      using same scripts as for forward test.
142    
143    checkpoint59g
144    o adjoint testing: in preparation for changing testreport:
145      - output format: cost and grad written on separated lines
146      - ad output results in directory "results" (instead of "results_ad")
147    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
148    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
149    o pkg/ecco: allow user defined cost function contributions
150    o testreport:
151      Allow to choose (per experiment) the list of tested output variables
152       and the main variable (used to issue a pass/FAIL ) ;
153      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
154      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
155      Also modify printing of summary:
156       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
157       b) echo the list of tested variables in the individual summary.txt of
158          each experiment.
159    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
160      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
161      (but still depend on the tile decompostion of the domain).
162    o pkg/seaice: change a discretization detail to make the B-grid code
163      "more symmetric". This change is likely to remove all "ridges/leads" that
164      where quasi-aligned with the grid in B-grid solutions. It may also be
165      the solution to the stress coupling issues with the B-grid.
166    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
167      remove .cvsignore from input dir. (since testreport no longer run here).
168    o pkg/thsice:
169     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
170     - fix reshaping of sea-ice just after advection:
171       melt all the ice only if ice-volume is too small.
172     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
173       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
174     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
175    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
176      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
177    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
178      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
179      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
180      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
181      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
182      -> update output.txt
183    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
184     this affects truncation error: -> update output.txt of exp:
185      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
186      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
187    
188    checkpoint59f
189    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
190    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
191      a bounded range (in forward mode)
192    o pkg/ecco, ctrl, autodiff and mom_common:
193     internal parameter controls, completements of implementations
194    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
195    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
196      (not seem any difference in testing results).
197    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
198       at face corners.
199    o pkg/generic_advdiff:
200     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
201      loop range indices for computing vertical advection tendency
202      and do the calculation in the interior only (no overlap) ;
203      for now, only implemented for SOM advection (to save CPU time).
204     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
205    o exch2 adjoint
206      First set of changes:
207      - add exch2 hand-written adjoint templates
208      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
209        This will require cleanup in pkg/autodiff/*.F
210        (changed routines currently kept separate in verif. code/)
211      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
212        that used to hide exch2 or cubed-sphere specific code
213        (commented via 'cph-exch2')
214    o pkg/seaice
215      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
216    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
217       output of global_ocean.cs32x15.thsice .
218    
219    checkpoint59e
220    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
221      for B-grid vector (not yet tested) and C-grid vector (<- only used
222      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
223    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
224      (#ifdef ALLOW_SALT_PLUME)
225    o gather_2d/scatter_2d: removed halo regions
226    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
227      scheme and the corresponding test case (under front_relax dir). For now,
228      only available with Skew-flux form and not yet tested in realistic set-up.
229      adjoint: store directives updated, but gradient checks deteriorated,
230      so maybe GM/Redi adjoint is now broken.
231    o seaice adjoint
232      * add AREA, HEFF, HSNOW as control variable
233        (should not change lab_sea results)
234      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
235    o pkg/seaice:
236      * added computation of saltFlux in seaice_growth;
237        For time being, sea ice salinity is assumed constant
238        contribution of snow flooding to freshening of sea ice is neglected.
239        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
240        defaults to 0.0 in order to maintain backward compatibility.
241        Typical values for SEAICE_salinity are 4 to 10 g/kg.
242      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
243      * added SEAICE_availHeatFrac, which specifies fraction of surface level
244        heat content used to melt or grow ice
245      * commented out cap of HICE: it helps keep ice thinner
246      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
247      * applied OBCS T/S mask to HEFFM sea ice mask
248    
249    checkpoint59d
250    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
251     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
252     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
253    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
254     and change default value of parameter "GM_Small_Number";
255     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
256       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
257       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
258    o pkg/ecco: cost function when applying pkg/smooth to controls
259    o pkg/ctrl: add forcingPrecond run time parameter
260    o pkg/seaice:
261     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
262     - fix bug in metric terms of u-equation in LSR solver (implicit part),
263       changes verification/lab_sea
264     - rearrange implicit part of u-equation in LSR solver to make it easier to
265       read, understand, and debug. This causes changes at the truncation level.
266     - fix (serious) bug in the boundary conditions (sign error in the implicit
267       part) of the LSR solver. Changes all LSR results.
268     - fixed problem with HSNOW initialization to avoid thick snow when AREA
269       is initilized with small values - does not change lab_sea results.
270     - added HsnowFile initialization capability
271    o pkg/smooth: addition to model/src and pkg/ctrl so allow
272     initialization of pkg/smooth and application to control vector
273    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
274    o dependencies: pkg/profiles requires pkg/cal
275    o pkg/profiles:
276     - added option ALLOW_PROFILES_GENERICGRID
277         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
278         that interpolation information (grid points and coefficients) is provided
279         within the netcdf input files.
280         -> sample matlab scripts can be found in MITgcm_contrib/gael
281         that allow you to prepare netcdf input files.
282     - also modified: cleaner include statements, cleaner error print statements,
283       cleaner stops when error, and more tests of the netcdf input files consistency.
284    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
285    o pkg/seaice:
286     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
287       requires a new routine: seaice_diagnostics_fill.F
288     - make sure that seaice does not move if not forced (pressure replacement
289       method, Hibler and Ip, 1995), changes results
290     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
291     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
292       It is turned off by default (=-1.), because it changes the results.
293     - make it possible to read AREA from a file, too.
294    
295    checkpoint59c
296    o add S/R and diagnostics for oceanic mixed-layer depth
297    o move GMRedi call after all vertical mixing schemes (including KPP)
298    o pkg/thsice:
299     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
300      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
301    o pkg/obcs:
302     - bug fix for balance code
303    o pkg/seaice:
304      - allow values of SEAICE_elasticParm > 1
305      - add new parameter SEAICE_evpTauRelax as an alternative
306        to SEAICE_elasticParm
307      - make lsr boundary conditions free slip (by default), changes result
308      - add code for no slip boundary conditions for lsr
309      - set minimum of zeta to zero (and not 4e8) (changes results)
310      - add a cap on AREA after advecting AREA if seaice_growth is not called
311    o change calculation of Visbeck K:
312      - no longer depend on tapering scheme; instead, compute slope (limited
313        by GM_maxSlope). this is equivalent to what was comuted before with
314        clipping or linear tappering.
315      - fix vertical averaging (wrong by 1/2 level)
316      - leave the old version (but will not be maintained) within
317        #ifdef OLD_VISBECK_CALC / #endif
318      - update output of exp. ideal_2D_oce
319    o change error catch in calc_r_star to improve vectorization
320    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
321      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
322    o adjoint:
323      Re-organized adjoint checkpointing according to Matt Mazloff
324      (but with modifs/completions/cleanups)
325      Storing is now bundled into large arrays to optimized I/O
326      (and second step in cleanup of the_main_loop)
327    
328    checkpoint59b
329    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
330      - export/import (between ocean & coupler) fields needed for ocean DIC.
331    o pkg/seaice:
332      - get rid of three more exchanges seaice_calc_viscosities (required
333        different loop boundaries in seaice_lsr and seaice_ocean_stress)
334      - bug fix in seaice_ocean_stress (update of lab_sea required)
335      - reduce loop boundaries to necessary minimum also in seaice_evp
336      - go back to the old way of computing deltaC/Z as the adjoint likes that
337        better
338    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
339      passive tracer to an Age Tracer) + update output.txt
340    o pkg/exf:
341      - implement A-grid / C-grid selection for wind-stress input files.
342      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
343      for now, in exf_bulk_largeyeager04.F only :
344      - change implementation for case where windspeed + 2. components wind-stress
345        are read-in. AND use rhoConstFresh to convert evap.
346    o pkg/seaice:
347      - use correct EXCH_UV for wind-forcing (on A-grid).
348      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
349        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
350    o pkg/exf:
351      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
352      EXF_INTERPOLATION:
353      - merge global_with_exf/code version of exf_interp_read.F
354        to the main code ;
355      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
356        reading the file ; Important: This options needs to be defined to recover
357        previous code.
358        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
359      - no longer loose real*8 precision along the way when using exf_iprec=64.
360    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
361      - change discretisation of evp-solver in order to avoid another exchange
362        (changes lab_sea) and clean up a little
363      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
364        help the adjoint (this also changes the results slightly)
365      - add a few "_d 0" where they had been missing in seaice_evp.F
366      - cleaning up: remove unused seaice_calc_rhs.F
367    o pkg/exf: some cleaning-up:
368      - change various "constants" into runtime parameters
369      - cleaned-up Large&Yeager04 routine which should eventually
370        replace exf_bulkformulae.F (changed names of S/R and CPP)
371        and merged various ALLOW_ATM_WIND options
372     only used with thsice pkg (in thsice_get_exf.F):
373      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
374        which are used when useStabilityFct_overIce=TRUE (= the default)
375      - change default values of ice & snow emissivity and scale downward LW
376        by ice & snow emissivity.
377    o pkg/thsice:
378     fix few little problems, in thsice_calc_thickn.F:
379      - growth vertically (and not laterally) if iceFrac == iceMaskMax
380      - melt only laterally if hIce < hThinIce (as the comments say)
381      and in thsice_extend.F:
382      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
383      - start to form ice as soon as the minimum ice-volume is reachable.
384     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
385      and cpl_aim+ocn
386    o pkg/kpp
387     - move computation of surface related input fields to KPP into a new
388       subroutine kpp_forcing_surf.F
389     - remove wrong (within bi,bj loops) EXCH calls.
390     - little cleaning (add argument myThid in last position, cvs header ...)
391     - for now, fix conservation problem by exchanging KPPviscAz (may not
392       be the best fix)
393    o pkg/seaice
394     - check for inconsistent evp parameter/cpp-flag combination
395     - remove leftover errIO flat for obsolete name list error handling
396    o OpenAD
397     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
398    
399    checkpoint59a
400    o pkg/seaice: some parameter clarifications and a little bit of clean up
401    o pkg/thsice: rename run-time parameters:
402       himin       -> hIceMin
403       himin0      -> hThinIce
404       hihig       -> hThickIce
405       i0          -> i0swFrac
406       transCoef   -> bMeltCoef
407       frac_energy -> fracMelting
408      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
409       with default values (for now) that do not change the results.
410      remove old version of thsice vars advection in pkg/seaice.
411    o in FFIELDS.h:
412      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
413      - make pLoad & sIceLoad always available (but still only used if
414         ATMOSPHERIC_LOADING is #define).
415    o pkg/kpp: replaced _KPP_RL with _RL
416    o bug fixes for vertical diffusivity computations when both KPP and
417        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
418        are no longer updating the vertical diffusivity array
419        (passed as argument) but are (re-) setting those arrays.
420    o pkg/seaice: fix bug in evp solver, while doing that
421      - change (improve?) discretization of stress computations for both
422        cgrid-lsr and evp solver
423      - add a new routine to compute strain rates
424      - the above changes lab_sea results
425      - add no slip conditions for evp solver (off by default), lsr-version
426        may follow
427      - fix exchange for shear at Z-points (does not change lab_sea)
428      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
429        (to force the user to pick a time step since there is not "safe" way
430        of choosing it)
431      - add principal stress diagnostics
432      - rearrange fields for evp a little to avoid having to call a: too many
433        exchanges and b: exchanges for stress trensor components which we do
434        not have.
435      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
436        of evp, complete rewrite for lsr case (latter is does not yet work
437        in all cases)
438    o pkg/kpp: add code to have mixing in shelf ice caverns
439      - add myThid to all kpp routines (long overdue)
440    
441    checkpoint59
442    o pkg/exf:
443      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
444        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
445      - move exf header files from lower_case.h to UPPER_CASE.h ;
446        add missing cvs Header & Name
447      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
448      - add namelist param. selectStressGridPosition, exf_monFreq
449      - retire many _CLIM routines, and remove data.exf_clim
450        + params moved to data.exf
451        + climsst, climsss now handled by exf_set_gen, i.e.
452          climss?period=0 refers to constant field,
453          climss?period=-12 to monthly forcing
454      - split up namelists in data.exf
455    o pkg/seaice:
456      - remove seaice_exch and seaice_exch_uv
457      - remove superfluous exchange of theta
458      - add myThid to seaice_budget_ocean/ice
459      - add new interface for atmospheric wind forcing (C-grid only)
460        + new routine
461        + two new field (taux, tauy for stress over ice)
462        + removed one global field (DAIRN) for C-grid case only
463    o pkg/thsise
464      - 2nd set of modifs for thsice adjoint in conjunction with exf
465    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
466    
467    checkpoint58y_post
468    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
469      vertical diffusivity, similar to that in MOM4; turned on using
470      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
471      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
472    o Added capability for 3D specification of background vertical diffusion
473      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
474      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
475      "data" file that contains the 3D vertical diffusivity coefficients.
476    o ice dynamics (pkg/seaice) with thsice thermodynamics:
477      - add code within pkg thsice to advect & diffuse sea-ice fields
478      similar to (and will replace) what has been added in  seaice_advdiff.F,
479      but: - conserving Mass, Heat & Salt.
480           - better when using non-linear advection scheme (not yet fully tested)
481           - can also be used in atmospheric set-up (for now, only the diffusion).
482    
483    checkpoint58x_post
484    o IO option for global-file compact format:
485      - add options when generating topology (utils/exch2/matlab-topology-generator)
486      - add I/O capability (pkg/mdsio).
487      - adapt utils/matlab/rdmds.m to read this format.
488      for now long-line format not yet supported by pkg/mdsio (& exch2).
489    o shelfice: add a few diagnostics
490    
491    checkpoint58w_post
492    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
493      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
494      (and replace horiVertRatio in NH code).
495      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
496                         and tutorial_plume_on_slope (sensitive to truncation)
497    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
498      directly to drive seaice model (C-grid only)
499    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
500     - reintroduce computation of wind from stress,
501     - compute tau (in exf_bulkformulae.F) from windstress averaged to
502       mass points to avoid tau = 0
503     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
504    o rdmnc.m: make it work with "global" files created with gluemnc
505    o rdmnc.m : some improvements in dealing with singleton dimension
506      (tested on all testreport mnc output files).
507    o genmake2: disable pkg/profiles if netcdf test fails.
508    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
509    o move call to cal_readparms up to make calendar parameters/variable available
510      to all packages
511    
512    checkpoint58v_post
513    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
514      useDynP_inEos_Zc tested.
515    o pkg/exf: changes to properly interpolate/mask/scale initial fields
516    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
517      and portions thereof.  See read_cs.txt for description and examples.
518    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
519      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
520      following the great-circle arc between those 2 points.
521    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
522      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
523    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
524     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
525     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
526     - still needs work (not working with some options ; efficiency to improve)
527       and serious testing.
528     - use this scheme for temperature & salinity in 2 advection test exp.:
529       advect_xy & advect_xz, respectively.
530    
531    checkpoint58u_post
532    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
533    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
534    o testreport: add option "-skipdir" to skip some test.
535    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
536      momentum calculation.
537    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
538    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
539      remove checkpoint.F and the_correction_step.F (no longer used);
540      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
541    o add option (linFSConserveTr) to correct for tracer source/sink due to
542      Linear Free surface
543    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
544    o pkg/thsice: fix reading mnc-pickups
545    
546    checkpoint58t_post
547    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
548    o pkg/mdsio:
549     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
550       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
551       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
552     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
553     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
554       either MDS_READ_FIELD or MDS_WRITE_FIELD )
555     - new S/R (to replace MDSWRITEMETA), which allows to write more
556       informations (variable names, time ...) to meta files.
557     - modify rdmds.m to give back the meta file content.
558    o pkg/diagnostics: change vertical interpolation to be safer, and more
559       flexible (define p-levels to interpolate to in data.diagnostics);
560      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
561       diagnostic pointer.
562  o pkg/seaice: more cleaning up of seaice_growth, added many comments  o pkg/seaice: more cleaning up of seaice_growth, added many comments
563  o pkg/exf: put runoff0 and runoff into the appropriate common block  o pkg/exf: put runoff0 and runoff1 into the appropriate common block
564  o fix multi-category seaice:  o fix multi-category seaice:
565   - change cpp flag SEAICE_MULTILEVEL to more meaningful name:   - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
566     SEAICE_MULTICATEGORY     SEAICE_MULTICATEGORY
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