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revision 1.637 by mlosch, Tue Mar 21 13:00:33 2006 UTC revision 1.939 by mlosch, Wed Jan 16 09:48:41 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 pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
8      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
9      for now this is only available for the C-grid code and also within
10      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
11    
12    checkpoint59m
13    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
14      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
15    o gad_som : fix flux output (& diagnostics) to have same units as other  
16      advection scheme fluxes (was previously multiplied by deltaT).  
17    o added verification/seaice_obcs both to test seaice open boundaries
18      and to provide an example matlab scrpt for generating them
19    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
20    o pkg/salt_plume: clean up salt_plume_frac.F to
21      remove redundancy in PlumeMethod 1 and 4
22    o pkg/kpp: added saltplume diagnostics
23    o pkg/obcs and pkg/seaice:
24      - do not set uice and vice to zero when OB*icefile are unspecified
25      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
26      - moved seaice tracer obcs after call to seaice_growth
27    o pkg/salt_plume: added various options for salt plume depth
28      criterion and for vertical distribution of the salt
29    
30    checkpoint59l
31    o pkg/ptracers: new version of ptracers pickup:
32      read meta file and write only fields which are needed to restart.
33      ( same logic as main pickup file ; also using pickupStrictlyMatch )
34    o pkg/seaice:
35      - add timescale for melting due to warm mixed layer as a means of
36        setting SEAICE_availHeatFrac more conveniently
37      - add a CPP-flag/runtime parameter check for flooding algorithm
38      - reformulated availHeat in seaice_growth.F to be independent of AREA
39    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
40      unit changes
41    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
42    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
43      SX vector computer.
44    o pkg/seaice:
45      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
46        seaice forcing fields can now be read only through pkg/exf
47      - removed some unused halos
48    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
49    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
50      or U/VICE from U/VWIND before computing U/VSTRESS
51    
52    checkpoint59k
53    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
54      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
55    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
56      all experiments pass when compile with un-initialised var. checking option.
57    o added pkg/salt_plume
58    o script to test restart (for now, in MITgcm_contrib/jmc_script)
59    o pkg/seaice: new read/write pickup version.
60      read meta file and write only fields which are needed to restart.
61      ( same logic as main pickup file ; also using pickupStrictlyMatch )
62    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
63    o lab_sea.hb87: modify the domain & update output.hb87.txt :
64      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
65      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
66      process. Fixed here by closing the domain at the Northern boundary.
67    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
68    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
69      a set of consecutive levels in/from a 3-D array.
70    o pkg/ptracers:
71      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
72      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
73    
74    checkpoint59j
75    o in pkgs: dic, obcs, offline, rbcs:
76      standard way to compute coeff. for time interpolation between 2 time reccords
77      which retains full precision (& make results less dependent on compiler).
78      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
79    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
80      packages instead of reading ice cover and wind speed separately
81    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
82     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
83      to allow to compile customized code before the update)
84    o cleaning-up:
85      - fix CPP instruction syntax in pkg/obcs
86      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
87        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
88      - fix some threads issue in IO parts.
89    o pkg/dic:
90      - add tons of "_d 0" (--> much better testreports !)
91       and then update outputs of tutorial_global_oce_biogeo
92    o pkg/mom_fluxform:
93      add a special version of momentum advection intended to conserve momentum
94      next to a bathymetry step or a coastline edge. (default = off = #undef)
95    o new read/write pickup version:
96      - for now, only implemented for main (mdsio) pickup file.
97      - write out only what is needed to restart; merge pickup_nh , pickup_ph
98        and main pickup together.
99      - read meta file; read only what is needed to restart; stop if a field
100        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
101        if it make sense (even if the restart is not perfect).
102      - if no meta file, assume that pickup to read corresponds exactly to
103        a pickup that would currently be written.
104      - read pickup written in the old format (until checkpoint59i) if it
105        recognizes an old meta file (no field-list).
106      - add a meta file in exp. which starts from a pickup: 2 cases:
107        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
108         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
109        b) a meta file describing the content of the associated pickup file
110         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
111    o pkg/mdsio & pkg/rw:
112      - new routine to read a meta file ; new set of routine to read
113        Multiple-fields file (with meta file).
114    o added open boundary conditions capability for seaice
115        HSNOW, HSALT, UICE, and VICE
116    
117    checkpoint59i
118    o adjoint:
119      * fix multiDimAdvection adjoint
120        (partial recomputation problem by TAF for fVerT(:,:,kDown)
121        and comlev1 size definition (maxpass vs. max. number of tracers)
122      * verification/global_ocean.90x45x15 adjoint now tests
123        NLFS and multiDimAdvection using DST3 (=30)
124      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
125    o pkg/kpp: add "_d 0" to real constant (if missing);
126      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
127      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
128    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
129      for internal parameters related to restart process (formerly from PARAMS.h)
130      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
131    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
132      as argument. (only atm2d & obcs write_pickup have not yet been updated)
133    o pkg/monitor:
134      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
135      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
136      - account for deep Atmosphere factor and density factor (anelastic)
137    o added open boundary conditions capability for seaice HEFF and AREA
138    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
139      thermodynamics
140      - requires a little reorganization, which affects the testreport results
141        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
142        so that now the conservative form is tested
143      - add a few comments
144    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
145    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
146    o add new diagnostics to seaice: advective, diffusive fluxes (only for
147      multidim-advection, for scheme 2 they are not filled) and transports,
148      thermodynamic growth rates
149    o change units of EmPmR (inside the code, + within coupling interface)
150      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
151      Affects results @ truncation level (cg2d match) and update output of
152       experiments: lab_sea(6), global_ocean.90x40x15(10),
153      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
154      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
155      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
156      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
157    
158    checkpoint59h
159    o pkg/exf:
160      - improve vectorization by moving if-statement out of loops in
161        exf_mapfields, exf_radiation
162      - exf_bulkformulae.F: introduce 2D fields and vectorize code
163    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
164    o testreport:
165      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
166        monitor & update offline_exf_seaice exp. output.
167      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
168    o pkg/seaice:
169      - bug fix in the evp solver: boundary conditions were affected be
170        masking of zMax/zMin (changes results)
171      - minor bug fix in boundary conditions in seaice_calc_strainrates
172        (changes results for no_slip)
173      - seaice_lsr.F: make interpolation of eta dependent on boundaries
174      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
175      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
176        stress formulation and no-slip boundary conditions
177    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
178      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
179    o pkg/seaice: a first HSALT time stepping equation has been checked in
180    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
181      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
182      without requiring DO-IF statements
183    o pkg/thsice:
184      use continuous power-law function for partition of energy between lateral
185      melting/freezing and thinning/thickening ; old code using step function
186      still available with #undef THSICE_FRACEN_POWERLAW
187      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
188    o testreport: change AD testing : check against results/output_adm.txt
189      using same scripts as for forward test.
190    
191    checkpoint59g
192    o adjoint testing: in preparation for changing testreport:
193      - output format: cost and grad written on separated lines
194      - ad output results in directory "results" (instead of "results_ad")
195    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
196    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
197    o pkg/ecco: allow user defined cost function contributions
198    o testreport:
199      Allow to choose (per experiment) the list of tested output variables
200       and the main variable (used to issue a pass/FAIL ) ;
201      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
202      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
203      Also modify printing of summary:
204       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
205       b) echo the list of tested variables in the individual summary.txt of
206          each experiment.
207    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
208      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
209      (but still depend on the tile decompostion of the domain).
210    o pkg/seaice: change a discretization detail to make the B-grid code
211      "more symmetric". This change is likely to remove all "ridges/leads" that
212      where quasi-aligned with the grid in B-grid solutions. It may also be
213      the solution to the stress coupling issues with the B-grid.
214    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
215      remove .cvsignore from input dir. (since testreport no longer run here).
216    o pkg/thsice:
217     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
218     - fix reshaping of sea-ice just after advection:
219       melt all the ice only if ice-volume is too small.
220     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
221       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
222     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
223    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
224      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
225    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
226      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
227      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
228      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
229      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
230      -> update output.txt
231    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
232     this affects truncation error: -> update output.txt of exp:
233      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
234      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
235    
236    checkpoint59f
237    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
238    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
239      a bounded range (in forward mode)
240    o pkg/ecco, ctrl, autodiff and mom_common:
241     internal parameter controls, completements of implementations
242    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
243    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
244      (not seem any difference in testing results).
245    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
246       at face corners.
247    o pkg/generic_advdiff:
248     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
249      loop range indices for computing vertical advection tendency
250      and do the calculation in the interior only (no overlap) ;
251      for now, only implemented for SOM advection (to save CPU time).
252     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
253    o exch2 adjoint
254      First set of changes:
255      - add exch2 hand-written adjoint templates
256      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
257        This will require cleanup in pkg/autodiff/*.F
258        (changed routines currently kept separate in verif. code/)
259      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
260        that used to hide exch2 or cubed-sphere specific code
261        (commented via 'cph-exch2')
262    o pkg/seaice
263      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
264    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
265       output of global_ocean.cs32x15.thsice .
266    
267    checkpoint59e
268    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
269      for B-grid vector (not yet tested) and C-grid vector (<- only used
270      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
271    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
272      (#ifdef ALLOW_SALT_PLUME)
273    o gather_2d/scatter_2d: removed halo regions
274    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
275      scheme and the corresponding test case (under front_relax dir). For now,
276      only available with Skew-flux form and not yet tested in realistic set-up.
277      adjoint: store directives updated, but gradient checks deteriorated,
278      so maybe GM/Redi adjoint is now broken.
279    o seaice adjoint
280      * add AREA, HEFF, HSNOW as control variable
281        (should not change lab_sea results)
282      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
283    o pkg/seaice:
284      * added computation of saltFlux in seaice_growth;
285        For time being, sea ice salinity is assumed constant
286        contribution of snow flooding to freshening of sea ice is neglected.
287        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
288        defaults to 0.0 in order to maintain backward compatibility.
289        Typical values for SEAICE_salinity are 4 to 10 g/kg.
290      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
291      * added SEAICE_availHeatFrac, which specifies fraction of surface level
292        heat content used to melt or grow ice
293      * commented out cap of HICE: it helps keep ice thinner
294      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
295      * applied OBCS T/S mask to HEFFM sea ice mask
296    
297    checkpoint59d
298    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
299     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
300     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
301    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
302     and change default value of parameter "GM_Small_Number";
303     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
304       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
305       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
306    o pkg/ecco: cost function when applying pkg/smooth to controls
307    o pkg/ctrl: add forcingPrecond run time parameter
308    o pkg/seaice:
309     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
310     - fix bug in metric terms of u-equation in LSR solver (implicit part),
311       changes verification/lab_sea
312     - rearrange implicit part of u-equation in LSR solver to make it easier to
313       read, understand, and debug. This causes changes at the truncation level.
314     - fix (serious) bug in the boundary conditions (sign error in the implicit
315       part) of the LSR solver. Changes all LSR results.
316     - fixed problem with HSNOW initialization to avoid thick snow when AREA
317       is initilized with small values - does not change lab_sea results.
318     - added HsnowFile initialization capability
319    o pkg/smooth: addition to model/src and pkg/ctrl so allow
320     initialization of pkg/smooth and application to control vector
321    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
322    o dependencies: pkg/profiles requires pkg/cal
323    o pkg/profiles:
324     - added option ALLOW_PROFILES_GENERICGRID
325         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
326         that interpolation information (grid points and coefficients) is provided
327         within the netcdf input files.
328         -> sample matlab scripts can be found in MITgcm_contrib/gael
329         that allow you to prepare netcdf input files.
330     - also modified: cleaner include statements, cleaner error print statements,
331       cleaner stops when error, and more tests of the netcdf input files consistency.
332    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
333    o pkg/seaice:
334     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
335       requires a new routine: seaice_diagnostics_fill.F
336     - make sure that seaice does not move if not forced (pressure replacement
337       method, Hibler and Ip, 1995), changes results
338     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
339     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
340       It is turned off by default (=-1.), because it changes the results.
341     - make it possible to read AREA from a file, too.
342    
343    checkpoint59c
344    o add S/R and diagnostics for oceanic mixed-layer depth
345    o move GMRedi call after all vertical mixing schemes (including KPP)
346    o pkg/thsice:
347     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
348      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
349    o pkg/obcs:
350     - bug fix for balance code
351    o pkg/seaice:
352      - allow values of SEAICE_elasticParm > 1
353      - add new parameter SEAICE_evpTauRelax as an alternative
354        to SEAICE_elasticParm
355      - make lsr boundary conditions free slip (by default), changes result
356      - add code for no slip boundary conditions for lsr
357      - set minimum of zeta to zero (and not 4e8) (changes results)
358      - add a cap on AREA after advecting AREA if seaice_growth is not called
359    o change calculation of Visbeck K:
360      - no longer depend on tapering scheme; instead, compute slope (limited
361        by GM_maxSlope). this is equivalent to what was comuted before with
362        clipping or linear tappering.
363      - fix vertical averaging (wrong by 1/2 level)
364      - leave the old version (but will not be maintained) within
365        #ifdef OLD_VISBECK_CALC / #endif
366      - update output of exp. ideal_2D_oce
367    o change error catch in calc_r_star to improve vectorization
368    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
369      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
370    o adjoint:
371      Re-organized adjoint checkpointing according to Matt Mazloff
372      (but with modifs/completions/cleanups)
373      Storing is now bundled into large arrays to optimized I/O
374      (and second step in cleanup of the_main_loop)
375    
376    checkpoint59b
377    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
378      - export/import (between ocean & coupler) fields needed for ocean DIC.
379    o pkg/seaice:
380      - get rid of three more exchanges seaice_calc_viscosities (required
381        different loop boundaries in seaice_lsr and seaice_ocean_stress)
382      - bug fix in seaice_ocean_stress (update of lab_sea required)
383      - reduce loop boundaries to necessary minimum also in seaice_evp
384      - go back to the old way of computing deltaC/Z as the adjoint likes that
385        better
386    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
387      passive tracer to an Age Tracer) + update output.txt
388    o pkg/exf:
389      - implement A-grid / C-grid selection for wind-stress input files.
390      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
391      for now, in exf_bulk_largeyeager04.F only :
392      - change implementation for case where windspeed + 2. components wind-stress
393        are read-in. AND use rhoConstFresh to convert evap.
394    o pkg/seaice:
395      - use correct EXCH_UV for wind-forcing (on A-grid).
396      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
397        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
398    o pkg/exf:
399      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
400      EXF_INTERPOLATION:
401      - merge global_with_exf/code version of exf_interp_read.F
402        to the main code ;
403      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
404        reading the file ; Important: This options needs to be defined to recover
405        previous code.
406        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
407      - no longer loose real*8 precision along the way when using exf_iprec=64.
408    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
409      - change discretisation of evp-solver in order to avoid another exchange
410        (changes lab_sea) and clean up a little
411      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
412        help the adjoint (this also changes the results slightly)
413      - add a few "_d 0" where they had been missing in seaice_evp.F
414      - cleaning up: remove unused seaice_calc_rhs.F
415    o pkg/exf: some cleaning-up:
416      - change various "constants" into runtime parameters
417      - cleaned-up Large&Yeager04 routine which should eventually
418        replace exf_bulkformulae.F (changed names of S/R and CPP)
419        and merged various ALLOW_ATM_WIND options
420     only used with thsice pkg (in thsice_get_exf.F):
421      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
422        which are used when useStabilityFct_overIce=TRUE (= the default)
423      - change default values of ice & snow emissivity and scale downward LW
424        by ice & snow emissivity.
425    o pkg/thsice:
426     fix few little problems, in thsice_calc_thickn.F:
427      - growth vertically (and not laterally) if iceFrac == iceMaskMax
428      - melt only laterally if hIce < hThinIce (as the comments say)
429      and in thsice_extend.F:
430      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
431      - start to form ice as soon as the minimum ice-volume is reachable.
432     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
433      and cpl_aim+ocn
434    o pkg/kpp
435     - move computation of surface related input fields to KPP into a new
436       subroutine kpp_forcing_surf.F
437     - remove wrong (within bi,bj loops) EXCH calls.
438     - little cleaning (add argument myThid in last position, cvs header ...)
439     - for now, fix conservation problem by exchanging KPPviscAz (may not
440       be the best fix)
441    o pkg/seaice
442     - check for inconsistent evp parameter/cpp-flag combination
443     - remove leftover errIO flat for obsolete name list error handling
444    o OpenAD
445     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
446    
447    checkpoint59a
448    o pkg/seaice: some parameter clarifications and a little bit of clean up
449    o pkg/thsice: rename run-time parameters:
450       himin       -> hIceMin
451       himin0      -> hThinIce
452       hihig       -> hThickIce
453       i0          -> i0swFrac
454       transCoef   -> bMeltCoef
455       frac_energy -> fracMelting
456      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
457       with default values (for now) that do not change the results.
458      remove old version of thsice vars advection in pkg/seaice.
459    o in FFIELDS.h:
460      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
461      - make pLoad & sIceLoad always available (but still only used if
462         ATMOSPHERIC_LOADING is #define).
463    o pkg/kpp: replaced _KPP_RL with _RL
464    o bug fixes for vertical diffusivity computations when both KPP and
465        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
466        are no longer updating the vertical diffusivity array
467        (passed as argument) but are (re-) setting those arrays.
468    o pkg/seaice: fix bug in evp solver, while doing that
469      - change (improve?) discretization of stress computations for both
470        cgrid-lsr and evp solver
471      - add a new routine to compute strain rates
472      - the above changes lab_sea results
473      - add no slip conditions for evp solver (off by default), lsr-version
474        may follow
475      - fix exchange for shear at Z-points (does not change lab_sea)
476      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
477        (to force the user to pick a time step since there is not "safe" way
478        of choosing it)
479      - add principal stress diagnostics
480      - rearrange fields for evp a little to avoid having to call a: too many
481        exchanges and b: exchanges for stress trensor components which we do
482        not have.
483      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
484        of evp, complete rewrite for lsr case (latter is does not yet work
485        in all cases)
486    o pkg/kpp: add code to have mixing in shelf ice caverns
487      - add myThid to all kpp routines (long overdue)
488    
489    checkpoint59
490    o pkg/exf:
491      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
492        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
493      - move exf header files from lower_case.h to UPPER_CASE.h ;
494        add missing cvs Header & Name
495      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
496      - add namelist param. selectStressGridPosition, exf_monFreq
497      - retire many _CLIM routines, and remove data.exf_clim
498        + params moved to data.exf
499        + climsst, climsss now handled by exf_set_gen, i.e.
500          climss?period=0 refers to constant field,
501          climss?period=-12 to monthly forcing
502      - split up namelists in data.exf
503    o pkg/seaice:
504      - remove seaice_exch and seaice_exch_uv
505      - remove superfluous exchange of theta
506      - add myThid to seaice_budget_ocean/ice
507      - add new interface for atmospheric wind forcing (C-grid only)
508        + new routine
509        + two new field (taux, tauy for stress over ice)
510        + removed one global field (DAIRN) for C-grid case only
511    o pkg/thsise
512      - 2nd set of modifs for thsice adjoint in conjunction with exf
513    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
514    
515    checkpoint58y_post
516    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
517      vertical diffusivity, similar to that in MOM4; turned on using
518      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
519      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
520    o Added capability for 3D specification of background vertical diffusion
521      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
522      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
523      "data" file that contains the 3D vertical diffusivity coefficients.
524    o ice dynamics (pkg/seaice) with thsice thermodynamics:
525      - add code within pkg thsice to advect & diffuse sea-ice fields
526      similar to (and will replace) what has been added in  seaice_advdiff.F,
527      but: - conserving Mass, Heat & Salt.
528           - better when using non-linear advection scheme (not yet fully tested)
529           - can also be used in atmospheric set-up (for now, only the diffusion).
530    
531    checkpoint58x_post
532    o IO option for global-file compact format:
533      - add options when generating topology (utils/exch2/matlab-topology-generator)
534      - add I/O capability (pkg/mdsio).
535      - adapt utils/matlab/rdmds.m to read this format.
536      for now long-line format not yet supported by pkg/mdsio (& exch2).
537    o shelfice: add a few diagnostics
538    
539    checkpoint58w_post
540    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
541      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
542      (and replace horiVertRatio in NH code).
543      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
544                         and tutorial_plume_on_slope (sensitive to truncation)
545    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
546      directly to drive seaice model (C-grid only)
547    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
548     - reintroduce computation of wind from stress,
549     - compute tau (in exf_bulkformulae.F) from windstress averaged to
550       mass points to avoid tau = 0
551     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
552    o rdmnc.m: make it work with "global" files created with gluemnc
553    o rdmnc.m : some improvements in dealing with singleton dimension
554      (tested on all testreport mnc output files).
555    o genmake2: disable pkg/profiles if netcdf test fails.
556    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
557    o move call to cal_readparms up to make calendar parameters/variable available
558      to all packages
559    
560    checkpoint58v_post
561    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
562      useDynP_inEos_Zc tested.
563    o pkg/exf: changes to properly interpolate/mask/scale initial fields
564    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
565      and portions thereof.  See read_cs.txt for description and examples.
566    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
567      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
568      following the great-circle arc between those 2 points.
569    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
570      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
571    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
572     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
573     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
574     - still needs work (not working with some options ; efficiency to improve)
575       and serious testing.
576     - use this scheme for temperature & salinity in 2 advection test exp.:
577       advect_xy & advect_xz, respectively.
578    
579    checkpoint58u_post
580    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
581    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
582    o testreport: add option "-skipdir" to skip some test.
583    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
584      momentum calculation.
585    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
586    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
587      remove checkpoint.F and the_correction_step.F (no longer used);
588      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
589    o add option (linFSConserveTr) to correct for tracer source/sink due to
590      Linear Free surface
591    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
592    o pkg/thsice: fix reading mnc-pickups
593    
594    checkpoint58t_post
595    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
596    o pkg/mdsio:
597     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
598       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
599       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
600     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
601     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
602       either MDS_READ_FIELD or MDS_WRITE_FIELD )
603     - new S/R (to replace MDSWRITEMETA), which allows to write more
604       informations (variable names, time ...) to meta files.
605     - modify rdmds.m to give back the meta file content.
606    o pkg/diagnostics: change vertical interpolation to be safer, and more
607       flexible (define p-levels to interpolate to in data.diagnostics);
608      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
609       diagnostic pointer.
610    o pkg/seaice: more cleaning up of seaice_growth, added many comments
611    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
612    o fix multi-category seaice:
613     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
614       SEAICE_MULTICATEGORY
615     - fix short wave heat flux
616    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
617       and allow to use EVP solver. Change forward lab_sea: test both EVP
618       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
619    o Initial check-in of lab_sea adjoint
620      (very similar to natl_box_adjoint/code_seaice)
621      * used C-grid and EVP solver
622      * used KPP, GM/Redi
623      * uses inAdExact=.TRUE.
624      * gradient checks fail for both ADM and TLM
625        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
626        f.d. gradients actually seem more problematic than ADM, TLM gradients;
627        issue is related to forward mismatch between g77 an ifort
628    o pkg/seaice: overhaul of thermodynamics
629     - growth.F and groatb.F are replaced by new routine seaice_growth.F
630     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
631     - move a few global fields out of SEAICE.h into seaice_growth.F and
632       make them 2D (FICE/QNETO/ ...)
633     - remove FO (it is the same as QNETO)
634     - introduce a few local fields to avoid modifying external fields such
635       as atemp, etc.
636    
637    checkpoint58s_post
638    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
639      changed exf_set_gen.F so that
640        genperiod=0 means input file is one time-constant field and
641        genperiod=-12 means input file contains 12 monthly means
642    o CG2D: use pre-computed solver main-diagonal (stored in common block);
643      this affects truncation error ; generate new output file for exp. which
644      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
645        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
646        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
647        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
648        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
649        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
650    o start implementation of deep-atmosphere and anelastic formulation
651    o verification: remove 2nd copy of input files and use script "prepare_run"
652      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
653    o mom_common/vecinv/fluxform: fix a few initialisation isssues
654    o profiles: fix for multithreaded case
655    
656    o diagnostics: rename few diags:
657      s/'PRESSURE'/'RCENTER '/g
658      s/'TICE    '/'oceFreez'/g
659      s/'TAUX    '/'oceTAUX '/g
660      s/'TAUY    '/'oceTAUY '/g
661      s/'SWFLUX  '/'oceQsw  '/g
662      s/DIFx/DFxE/g
663      s/DIFy/DFyE/g
664      and add few ocean-forcing diagnostics:
665      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
666    o modifications to pkg/seaice/growth.F and budget.F, which change results of
667      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
668      as actual snow thickness.  It now refers everywhere to effective snow
669      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
670    
671    checkpoint58r_post
672    o modifications to pkg/seaice/growth.F, which change results of
673      lab_sea experiment: fixes pertain to melting snow over open water, to
674      masking EVAP under sea ice, and to using the correct AREA variable for
675      computations of EVAP, PRECIP, HSNOW, and GHEFF
676    o add ability to read bathy, salt, and theta using MNC (off by def)
677    o add flooding algorithm and advection of HSNOW for pkg/seaice;
678      both are turned off by default and do no change any results
679    o seaice advection with pkg/thsice: a step toward the use of non-linear
680      advection scheme, but #ifdef or commented out for now (requires more EXCH).
681    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
682      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
683      in natl_box (affects results @ truncation level: update output.txt)
684    o multi-threading and IO:
685      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
686      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
687        (needed to work with SingleCpuIO): tested in all verif. exp.
688    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
689      affects the results (but none of the verification test uses this scheme).
690    o Adding some pkg/diagnostics capability to pkg/seaice
691      (will certainly be subject to changes)
692    o ctrl: adding new control variables:
693      lwflux, lwdown, evap, snowprecip, apressure, runoff
694    
695    checkpoint58q_post
696    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
697      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
698      high_res_cube configuration by 4% on Columbia.
699    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
700      add (in global_with_exf/code) a version of EXF_INTERP_READ without
701      dynamical allocation (seems to work in multi-threaded).
702    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
703      single CPU io) so that TAF does not have to see EESUPPORT.h
704    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
705    
706    checkpoint58p_post
707    o obcs: stop if obcs is used with useCDscheme = .true.
708    o shelfice:
709     - fix a sign error so that no slip at shelfice interface works
710     - remove stop for combination non-hydrostatic code and shelfice. That does
711       not mean, that the results are correct, but at least they are numerically
712       stable
713    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
714    o added adjoint exch routined for all exch*3d* routines
715      and updated flow directives
716    
717    checkpoint58o_post
718    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
719      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
720    o change controling S/R for writing pickup file (new S/R do_write_pickup)
721      and clean-up reading/writing of pickup files.
722    o fix local version of read/write pickup (NH part) in rotating_tank/code
723    o simplify EXCH interface:
724     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
725     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
726    o added the regrid package
727    o shelfice:
728     - add a simple boundary layer scheme to reduce noise
729     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
730    
731    checkpoint58n_post
732    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
733       local variable (not in common block).
734    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
735      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
736      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
737        to work with SingleCpuIO.
738    o add "_d 0" to real constant of pkg/cfc subroutines ;
739       update exp. cfc_exemple & tutorial_cfc_offline output files.
740    o multi-threading and IO:
741      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
742        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
743      - barrier before and after reading.
744      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
745      - avoid using MDS_WRITELOCAL for LAND pkg output.
746      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
747        common-block variables ; Allows multi-threading with master-thread IO.
748    o change default MAX_NO_THREADS from 32 to 4 ;
749      and stop cleanly when MAX_NO_THREADS is too small.
750    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
751    
752    checkpoint58m_post
753    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
754       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
755    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
756       keep global_ocean.90x40x15 (for AD testing) with former secondary test
757       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
758    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
759        add MITgcm_tutorials (= code + all the tutorials)
760    o ecco, option to compute cost for total ssh (mean+anom)
761    o consistent with addition of ptracer and ssh in pkg/profiles
762    o profiles: adding ptracer and ssh
763    o testreport: change multi-test output-file name
764      (from output.txt.{name} to output.{name}.txt)
765    o profiles: now ok for mutli-tiles case
766    o seaice: add 4 parameters for different advection schemes for area,
767      (effective) seaice thickness, enthalphy, and snow height. Their default
768      is the standard parameter SEAICEadvScheme
769    o calc_gw:
770     - add cosFacU in zonal viscous flux (harmonic.visc.).
771     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
772       of tutorial_plume_on_slope.
773    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
774    o calc_gw: true flux-form, account for horizontal grid spacing.
775      update rotating_tank results, but not plume_on_slope (affected at
776      truncation level, 11 digits).
777    
778    checkpoint58l_post
779    o calc_gw:
780     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
781     - remove side-drag for now (need to fix it); update plume_on_slope results.
782     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
783    o commit code to make SST/SSS weights spatially variable
784      (based on either variable in-situ or variable initial T/S weights)
785    o pkg/ecco:
786      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
787        now based on horizontally varying weights wthetaLev, wsaltLev
788      * cost_averagesflags now returns year indices in addition to day, month
789      * sflux balance is performed on annual basis
790        (sflxumm, sfluxmm2, bal_sfluxmm)
791      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
792        including separate counting and multipliers
793    o pkg/rbcs
794      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
795    
796    checkpoint58k_post
797    o testreport:
798     - always build in dir. "build" (if not there, mkdir build instead of building
799       & running in input)
800     - run in dir run (if it exists), in build otherwise.
801     - call prepare_run (if input/prepare_run exists)
802     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
803    o pkg/exf modifications to interpolation and rotation routines for more
804       reasonable treatment of North Pole singularity: for tracers North Pole
805       value is set to northernmost zonal-mean value, for zonal velocity it is
806       set to zero, and for meridional velocity it is set to northernmost value.
807    o pkg/exf/exf_check_range.F
808     - add tile index to diagnostics and move stop statement to the very
809       end of the routine.
810    o pkg/diagnostics: (diagnostics_main_init.F)
811      define title of isomorphic variables according to the current config.
812    o pkg/thsice with pkg/seaice dynamics:
813    - fix domain of computation (interior only, required for exf) and do exchanges
814    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
815    o towards a standard way of dealing with multi-threading in MONITOR
816      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
817    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
818       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
819    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
820    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
821    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
822       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
823    o tracer advection:
824     - clean-up and simplify calc_common_factors.F
825     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
826       advection subroutine (but still not used within DST advection S/R)
827    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
828    
829    checkpoint58j_post
830    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
831      from file (collects calls previously in FORWARD_STEP)
832    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
833    o adjoint store dir. adjusted accordingly
834    o genmake2
835      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
836    
837    checkpoint58i_post
838    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
839      on wind stress (SEAICEstressFactor defaults to 1.)
840    o Total number of Timers is finite (<=40): comment out 2 non-essential one
841      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
842    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
843      on CS-grid: no longer loosing mass.
844    o exf & curvilinear-grid: no longer modify longitude xC & xG.
845    o pkg/ggl90: fix sloppy output and fix a bug
846    o pkg/seaice: added SEAICEuseEVPpickup parameter
847      - Set to false in order to start EVP solver with
848        non-EVP pickup files when using SEAICEuseEVP
849      - fix sign error in diffusion in seaice_calc_rhs
850    
851    checkpoint58h_post
852    * Modifications for bottom topography control
853      o replace hFacC by _hFacC at various places
854      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
855      o add non-self-adjoint cg2d_nsa
856      o update autodiff support routines
857      o re-initialise hfac after ctrl_depth_ini
858      o works for 5x5 box, doesnt work for global_ocean.90x40x15
859    * Adding verification for 5x5 box (4-layer) bottom topography control
860    
861    checkpoint58g_post
862    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
863       used for mean seasonal cycle, mean diurnal cycle); add an example
864       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
865    o pkg/ggl90:
866      - add parameter (minimum surface kinetic energy)
867      - fix bug (avoiding division by zero)
868    o couple pkg/thsice to pkg/seaice:
869      - modify advection in seaice to accomodate new scalar fields to be advected
870      - only muliDimAdection scheme work with seaice/thsice
871      - mapping of thsice-variables to seaice-variables, back and forth
872      - does not break the verification experiments, but does not give the
873        desired results either
874    o pkg/seaice
875      - make (default) second order advection a bit less confusing?
876    
877    checkpoint58f_post
878    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
879      to pkg/seaice):
880      - new routines thsice_map_exf and thsice_get_exf provide the interface
881      - add an additional formal parameter to thsice_solve4temp
882    o pkg/exf:
883      - add new fields wspeed, snowprecip (to be able to couple to thsice)
884      - correct Stefan-Boltzmann constant
885      - new parameter for longwave surface emittance
886      - separate some stuff from exf_bulkformulae into new routines  
887        exf_radiation, exf_wind
888      - add new parameters and constants: longwave emissivity for ocean, ice
889        and snow, evaporation parameters over ice
890      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
891        either wind from stress or stress from wind
892    o pkg/thSIce:
893    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
894    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
895       and THSICE_CALC_THICKN
896    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
897    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
898      to make debugging easier.
899    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
900    o pkg/bulk_force:
901      - clean-up comments and parameters ;
902      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
903    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
904      generate new output for test-experiment: aim.5l_cs.thSI
905    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
906      testreport accordingly
907    
908    checkpoint58e_post
909    o SEAICE_CGRID adjoint done
910    o R_STAR adjoint implemented.
911      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
912      * need to sort out init. of h0facc, etc.
913    o Make pkg/profile fully independent of ecco,cost, etc. stuff
914      to be able to use it in pure forward.
915    
916    checkpoint58d_post
917    o upgrade simple test-experiment to tutorial example:
918     step.1: duplicate the experiment and (step.2) will remove the old copy.
919      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
920      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
921      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
922      tutorial_global_oce_biogeo    <- copy of dic_example
923      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
924      tutorial_plume_on_slope       <- copy of plume_on_slope
925      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
926      tutorial_global_oce_optim     <- empty for now (David ?)
927      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
928     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
929    o correct a sign problem in cost_scat.F
930    o obcs and ptracers: fix boundary conditions for advections schemes
931      with larger stencil
932    o thsice adjoint: start
933    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
934      completeness
935    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
936      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
937    o ptracers adjoint:
938      * avoid extensive recomputatations
939      * fix missing re-init. of gptr (missed by TAF)
940    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
941      me to turn off the excessive output to STDOUT that this package produces
942    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
943      and add those terms in Vector-Invariant formulation.
944    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
945      if the control period (xx_hfluxperiod etc) is 0
946    o in profiles pkg, clean routines and fix details
947    o in ecco pkg, reading ssh data:
948      fix problem in case the model does not start at iter0=0
949    o fix mnc-pickup/restart for ptracers
950    o new package prifiles:
951      code to compute profile-based cost by Gael Forget
952      (modifs in ecco, ctrl, autodiff)
953    o Benign bug fix in initialization (spotted by M. Mazloff) of
954      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
955    
956    checkpoint58c_post
957    o adjoint: finish NLFS adjoint and provide reference output in
958      verification/global_ocean.90x40x15/results_ad_nlfs
959  o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the  o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
960    documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in    documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
961    SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only    SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only

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