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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.896 by jmc, Sun Oct 21 18:56:16 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 adding precip control xx_precip  checkpoint59i
8  o moved ptracer ctrl index 17 -> 32  o adjoint:
9      * fix multiDimAdvection adjoint
10        (partial recomputation problem by TAF for fVerT(:,:,kDown)
11        and comlev1 size definition (maxpass vs. max. number of tracers)
12      * verification/global_ocean.90x45x15 adjoint now tests
13        NLFS and multiDimAdvection using DST3 (=30)
14      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
15    o pkg/kpp: add "_d 0" to real constant (if missing);
16      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
17      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
18    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
19      for internal parameters related to restart process (formerly from PARAMS.h)
20      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
21    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
22      as argument. (only atm2d & obcs write_pickup have not yet been updated)
23    o pkg/monitor:
24      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
25      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
26      - account for deep Atmosphere factor and density factor (anelastic)
27    o added open boundary conditions capability for seaice HEFF and AREA
28    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
29      thermodynamics
30      - requires a little reorganization, which affects the testreport results
31        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
32        so that now the conservative form is tested
33      - add a few comments
34    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
35    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
36    o add new diagnostics to seaice: advective, diffusive fluxes (only for
37      multidim-advection, for scheme 2 they are not filled) and transports,
38      thermodynamic growth rates
39    o change units of EmPmR (inside the code) from m/s to kg/m2/s (mass flux) but
40      leave input file unchanged. Affects results @ truncation level (cg2d match)
41      and update output of experiments: lab_sea(6), global_ocean.90x40x15(10),
42      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
43      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
44      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
45    
46    checkpoint59h
47    o pkg/exf:
48      - improve vectorization by moving if-statement out of loops in
49        exf_mapfields, exf_radiation
50      - exf_bulkformulae.F: introduce 2D fields and vectorize code
51    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
52    o testreport:
53      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
54        monitor & update offline_exf_seaice exp. output.
55      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
56    o pkg/seaice:
57      - bug fix in the evp solver: boundary conditions were affected be
58        masking of zMax/zMin (changes results)
59      - minor bug fix in boundary conditions in seaice_calc_strainrates
60        (changes results for no_slip)
61      - seaice_lsr.F: make interpolation of eta dependent on boundaries
62      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
63      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
64        stress formulation and no-slip boundary conditions
65    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
66      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
67    o pkg/seaice: a first HSALT time stepping equation has been checked in
68    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
69      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
70      without requiring DO-IF statements
71    o pkg/thsice:
72      use continuous power-law function for partition of energy between lateral
73      melting/freezing and thinning/thickening ; old code using step function
74      still available with #undef THSICE_FRACEN_POWERLAW
75      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
76    o testreport: change AD testing : check against results/output_adm.txt
77      using same scripts as for forward test.
78    
79    checkpoint59g
80    o adjoint testing: in preparation for changing testreport:
81      - output format: cost and grad written on separated lines
82      - ad output results in directory "results" (instead of "results_ad")
83    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
84    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
85    o pkg/ecco: allow user defined cost function contributions
86    o testreport:
87      Allow to choose (per experiment) the list of tested output variables
88       and the main variable (used to issue a pass/FAIL ) ;
89      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
90      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
91      Also modify printing of summary:
92       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
93       b) echo the list of tested variables in the individual summary.txt of
94          each experiment.
95    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
96      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
97      (but still depend on the tile decompostion of the domain).
98    o pkg/seaice: change a discretization detail to make the B-grid code
99      "more symmetric". This change is likely to remove all "ridges/leads" that
100      where quasi-aligned with the grid in B-grid solutions. It may also be
101      the solution to the stress coupling issues with the B-grid.
102    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
103      remove .cvsignore from input dir. (since testreport no longer run here).
104    o pkg/thsice:
105     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
106     - fix reshaping of sea-ice just after advection:
107       melt all the ice only if ice-volume is too small.
108     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
109       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
110     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
111    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
112      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
113    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
114      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
115      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
116      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
117      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
118      -> update output.txt
119    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
120     this affects truncation error: -> update output.txt of exp:
121      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
122      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
123    
124    checkpoint59f
125    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
126    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
127      a bounded range (in forward mode)
128    o pkg/ecco, ctrl, autodiff and mom_common:
129     internal parameter controls, completements of implementations
130    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
131    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
132      (not seem any difference in testing results).
133    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
134       at face corners.
135    o pkg/generic_advdiff:
136     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
137      loop range indices for computing vertical advection tendency
138      and do the calculation in the interior only (no overlap) ;
139      for now, only implemented for SOM advection (to save CPU time).
140     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
141    o exch2 adjoint
142      First set of changes:
143      - add exch2 hand-written adjoint templates
144      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
145        This will require cleanup in pkg/autodiff/*.F
146        (changed routines currently kept separate in verif. code/)
147      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
148        that used to hide exch2 or cubed-sphere specific code
149        (commented via 'cph-exch2')
150    o pkg/seaice
151      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
152    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
153       output of global_ocean.cs32x15.thsice .
154    
155    checkpoint59e
156    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
157      for B-grid vector (not yet tested) and C-grid vector (<- only used
158      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
159    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
160      (#ifdef ALLOW_SALT_PLUME)
161    o gather_2d/scatter_2d: removed halo regions
162    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
163      scheme and the corresponding test case (under front_relax dir). For now,
164      only available with Skew-flux form and not yet tested in realistic set-up.
165      adjoint: store directives updated, but gradient checks deteriorated,
166      so maybe GM/Redi adjoint is now broken.
167    o seaice adjoint
168      * add AREA, HEFF, HSNOW as control variable
169        (should not change lab_sea results)
170      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
171    o pkg/seaice:
172      * added computation of saltFlux in seaice_growth;
173        For time being, sea ice salinity is assumed constant
174        contribution of snow flooding to freshening of sea ice is neglected.
175        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
176        defaults to 0.0 in order to maintain backward compatibility.
177        Typical values for SEAICE_salinity are 4 to 10 g/kg.
178      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
179      * added SEAICE_availHeatFrac, which specifies fraction of surface level
180        heat content used to melt or grow ice
181      * commented out cap of HICE: it helps keep ice thinner
182      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
183      * applied OBCS T/S mask to HEFFM sea ice mask
184    
185    checkpoint59d
186    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
187     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
188     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
189    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
190     and change default value of parameter "GM_Small_Number";
191     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
192       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
193       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
194    o pkg/ecco: cost function when applying pkg/smooth to controls
195    o pkg/ctrl: add forcingPrecond run time parameter
196    o pkg/seaice:
197     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
198     - fix bug in metric terms of u-equation in LSR solver (implicit part),
199       changes verification/lab_sea
200     - rearrange implicit part of u-equation in LSR solver to make it easier to
201       read, understand, and debug. This causes changes at the truncation level.
202     - fix (serious) bug in the boundary conditions (sign error in the implicit
203       part) of the LSR solver. Changes all LSR results.
204     - fixed problem with HSNOW initialization to avoid thick snow when AREA
205       is initilized with small values - does not change lab_sea results.
206     - added HsnowFile initialization capability
207    o pkg/smooth: addition to model/src and pkg/ctrl so allow
208     initialization of pkg/smooth and application to control vector
209    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
210    o dependencies: pkg/profiles requires pkg/cal
211    o pkg/profiles:
212     - added option ALLOW_PROFILES_GENERICGRID
213         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
214         that interpolation information (grid points and coefficients) is provided
215         within the netcdf input files.
216         -> sample matlab scripts can be found in MITgcm_contrib/gael
217         that allow you to prepare netcdf input files.
218     - also modified: cleaner include statements, cleaner error print statements,
219       cleaner stops when error, and more tests of the netcdf input files consistency.
220    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
221    o pkg/seaice:
222     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
223       requires a new routine: seaice_diagnostics_fill.F
224     - make sure that seaice does not move if not forced (pressure replacement
225       method, Hibler and Ip, 1995), changes results
226     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
227     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
228       It is turned off by default (=-1.), because it changes the results.
229     - make it possible to read AREA from a file, too.
230    
231    checkpoint59c
232    o add S/R and diagnostics for oceanic mixed-layer depth
233    o move GMRedi call after all vertical mixing schemes (including KPP)
234    o pkg/thsice:
235     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
236      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
237    o pkg/obcs:
238     - bug fix for balance code
239    o pkg/seaice:
240      - allow values of SEAICE_elasticParm > 1
241      - add new parameter SEAICE_evpTauRelax as an alternative
242        to SEAICE_elasticParm
243      - make lsr boundary conditions free slip (by default), changes result
244      - add code for no slip boundary conditions for lsr
245      - set minimum of zeta to zero (and not 4e8) (changes results)
246      - add a cap on AREA after advecting AREA if seaice_growth is not called
247    o change calculation of Visbeck K:
248      - no longer depend on tapering scheme; instead, compute slope (limited
249        by GM_maxSlope). this is equivalent to what was comuted before with
250        clipping or linear tappering.
251      - fix vertical averaging (wrong by 1/2 level)
252      - leave the old version (but will not be maintained) within
253        #ifdef OLD_VISBECK_CALC / #endif
254      - update output of exp. ideal_2D_oce
255    o change error catch in calc_r_star to improve vectorization
256    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
257      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
258    o adjoint:
259      Re-organized adjoint checkpointing according to Matt Mazloff
260      (but with modifs/completions/cleanups)
261      Storing is now bundled into large arrays to optimized I/O
262      (and second step in cleanup of the_main_loop)
263    
264    checkpoint59b
265    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
266      - export/import (between ocean & coupler) fields needed for ocean DIC.
267    o pkg/seaice:
268      - get rid of three more exchanges seaice_calc_viscosities (required
269        different loop boundaries in seaice_lsr and seaice_ocean_stress)
270      - bug fix in seaice_ocean_stress (update of lab_sea required)
271      - reduce loop boundaries to necessary minimum also in seaice_evp
272      - go back to the old way of computing deltaC/Z as the adjoint likes that
273        better
274    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
275      passive tracer to an Age Tracer) + update output.txt
276    o pkg/exf:
277      - implement A-grid / C-grid selection for wind-stress input files.
278      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
279      for now, in exf_bulk_largeyeager04.F only :
280      - change implementation for case where windspeed + 2. components wind-stress
281        are read-in. AND use rhoConstFresh to convert evap.
282    o pkg/seaice:
283      - use correct EXCH_UV for wind-forcing (on A-grid).
284      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
285        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
286    o pkg/exf:
287      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
288      EXF_INTERPOLATION:
289      - merge global_with_exf/code version of exf_interp_read.F
290        to the main code ;
291      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
292        reading the file ; Important: This options needs to be defined to recover
293        previous code.
294        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
295      - no longer loose real*8 precision along the way when using exf_iprec=64.
296    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
297      - change discretisation of evp-solver in order to avoid another exchange
298        (changes lab_sea) and clean up a little
299      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
300        help the adjoint (this also changes the results slightly)
301      - add a few "_d 0" where they had been missing in seaice_evp.F
302      - cleaning up: remove unused seaice_calc_rhs.F
303    o pkg/exf: some cleaning-up:
304      - change various "constants" into runtime parameters
305      - cleaned-up Large&Yeager04 routine which should eventually
306        replace exf_bulkformulae.F (changed names of S/R and CPP)
307        and merged various ALLOW_ATM_WIND options
308     only used with thsice pkg (in thsice_get_exf.F):
309      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
310        which are used when useStabilityFct_overIce=TRUE (= the default)
311      - change default values of ice & snow emissivity and scale downward LW
312        by ice & snow emissivity.
313    o pkg/thsice:
314     fix few little problems, in thsice_calc_thickn.F:
315      - growth vertically (and not laterally) if iceFrac == iceMaskMax
316      - melt only laterally if hIce < hThinIce (as the comments say)
317      and in thsice_extend.F:
318      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
319      - start to form ice as soon as the minimum ice-volume is reachable.
320     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
321      and cpl_aim+ocn
322    o pkg/kpp
323     - move computation of surface related input fields to KPP into a new
324       subroutine kpp_forcing_surf.F
325     - remove wrong (within bi,bj loops) EXCH calls.
326     - little cleaning (add argument myThid in last position, cvs header ...)
327     - for now, fix conservation problem by exchanging KPPviscAz (may not
328       be the best fix)
329    o pkg/seaice
330     - check for inconsistent evp parameter/cpp-flag combination
331     - remove leftover errIO flat for obsolete name list error handling
332    o OpenAD
333     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
334    
335    checkpoint59a
336    o pkg/seaice: some parameter clarifications and a little bit of clean up
337    o pkg/thsice: rename run-time parameters:
338       himin       -> hIceMin
339       himin0      -> hThinIce
340       hihig       -> hThickIce
341       i0          -> i0swFrac
342       transCoef   -> bMeltCoef
343       frac_energy -> fracMelting
344      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
345       with default values (for now) that do not change the results.
346      remove old version of thsice vars advection in pkg/seaice.
347    o in FFIELDS.h:
348      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
349      - make pLoad & sIceLoad always available (but still only used if
350         ATMOSPHERIC_LOADING is #define).
351    o pkg/kpp: replaced _KPP_RL with _RL
352    o bug fixes for vertical diffusivity computations when both KPP and
353        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
354        are no longer updating the vertical diffusivity array
355        (passed as argument) but are (re-) setting those arrays.
356    o pkg/seaice: fix bug in evp solver, while doing that
357      - change (improve?) discretization of stress computations for both
358        cgrid-lsr and evp solver
359      - add a new routine to compute strain rates
360      - the above changes lab_sea results
361      - add no slip conditions for evp solver (off by default), lsr-version
362        may follow
363      - fix exchange for shear at Z-points (does not change lab_sea)
364      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
365        (to force the user to pick a time step since there is not "safe" way
366        of choosing it)
367      - add principal stress diagnostics
368      - rearrange fields for evp a little to avoid having to call a: too many
369        exchanges and b: exchanges for stress trensor components which we do
370        not have.
371      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
372        of evp, complete rewrite for lsr case (latter is does not yet work
373        in all cases)
374    o pkg/kpp: add code to have mixing in shelf ice caverns
375      - add myThid to all kpp routines (long overdue)
376    
377    checkpoint59
378    o pkg/exf:
379      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
380        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
381      - move exf header files from lower_case.h to UPPER_CASE.h ;
382        add missing cvs Header & Name
383      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
384      - add namelist param. selectStressGridPosition, exf_monFreq
385      - retire many _CLIM routines, and remove data.exf_clim
386        + params moved to data.exf
387        + climsst, climsss now handled by exf_set_gen, i.e.
388          climss?period=0 refers to constant field,
389          climss?period=-12 to monthly forcing
390      - split up namelists in data.exf
391    o pkg/seaice:
392      - remove seaice_exch and seaice_exch_uv
393      - remove superfluous exchange of theta
394      - add myThid to seaice_budget_ocean/ice
395      - add new interface for atmospheric wind forcing (C-grid only)
396        + new routine
397        + two new field (taux, tauy for stress over ice)
398        + removed one global field (DAIRN) for C-grid case only
399    o pkg/thsise
400      - 2nd set of modifs for thsice adjoint in conjunction with exf
401    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
402    
403    checkpoint58y_post
404    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
405      vertical diffusivity, similar to that in MOM4; turned on using
406      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
407      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
408    o Added capability for 3D specification of background vertical diffusion
409      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
410      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
411      "data" file that contains the 3D vertical diffusivity coefficients.
412    o ice dynamics (pkg/seaice) with thsice thermodynamics:
413      - add code within pkg thsice to advect & diffuse sea-ice fields
414      similar to (and will replace) what has been added in  seaice_advdiff.F,
415      but: - conserving Mass, Heat & Salt.
416           - better when using non-linear advection scheme (not yet fully tested)
417           - can also be used in atmospheric set-up (for now, only the diffusion).
418    
419    checkpoint58x_post
420    o IO option for global-file compact format:
421      - add options when generating topology (utils/exch2/matlab-topology-generator)
422      - add I/O capability (pkg/mdsio).
423      - adapt utils/matlab/rdmds.m to read this format.
424      for now long-line format not yet supported by pkg/mdsio (& exch2).
425    o shelfice: add a few diagnostics
426    
427    checkpoint58w_post
428    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
429      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
430      (and replace horiVertRatio in NH code).
431      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
432                         and tutorial_plume_on_slope (sensitive to truncation)
433    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
434      directly to drive seaice model (C-grid only)
435    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
436     - reintroduce computation of wind from stress,
437     - compute tau (in exf_bulkformulae.F) from windstress averaged to
438       mass points to avoid tau = 0
439     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
440    o rdmnc.m: make it work with "global" files created with gluemnc
441    o rdmnc.m : some improvements in dealing with singleton dimension
442      (tested on all testreport mnc output files).
443    o genmake2: disable pkg/profiles if netcdf test fails.
444    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
445    o move call to cal_readparms up to make calendar parameters/variable available
446      to all packages
447    
448    checkpoint58v_post
449    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
450      useDynP_inEos_Zc tested.
451    o pkg/exf: changes to properly interpolate/mask/scale initial fields
452    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
453      and portions thereof.  See read_cs.txt for description and examples.
454    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
455      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
456      following the great-circle arc between those 2 points.
457    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
458      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
459    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
460     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
461     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
462     - still needs work (not working with some options ; efficiency to improve)
463       and serious testing.
464     - use this scheme for temperature & salinity in 2 advection test exp.:
465       advect_xy & advect_xz, respectively.
466    
467    checkpoint58u_post
468    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
469    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
470    o testreport: add option "-skipdir" to skip some test.
471    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
472      momentum calculation.
473    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
474    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
475      remove checkpoint.F and the_correction_step.F (no longer used);
476      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
477    o add option (linFSConserveTr) to correct for tracer source/sink due to
478      Linear Free surface
479    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
480    o pkg/thsice: fix reading mnc-pickups
481    
482    checkpoint58t_post
483    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
484    o pkg/mdsio:
485     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
486       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
487       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
488     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
489     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
490       either MDS_READ_FIELD or MDS_WRITE_FIELD )
491     - new S/R (to replace MDSWRITEMETA), which allows to write more
492       informations (variable names, time ...) to meta files.
493     - modify rdmds.m to give back the meta file content.
494    o pkg/diagnostics: change vertical interpolation to be safer, and more
495       flexible (define p-levels to interpolate to in data.diagnostics);
496      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
497       diagnostic pointer.
498    o pkg/seaice: more cleaning up of seaice_growth, added many comments
499    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
500    o fix multi-category seaice:
501     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
502       SEAICE_MULTICATEGORY
503     - fix short wave heat flux
504    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
505       and allow to use EVP solver. Change forward lab_sea: test both EVP
506       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
507    o Initial check-in of lab_sea adjoint
508      (very similar to natl_box_adjoint/code_seaice)
509      * used C-grid and EVP solver
510      * used KPP, GM/Redi
511      * uses inAdExact=.TRUE.
512      * gradient checks fail for both ADM and TLM
513        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
514        f.d. gradients actually seem more problematic than ADM, TLM gradients;
515        issue is related to forward mismatch between g77 an ifort
516    o pkg/seaice: overhaul of thermodynamics
517     - growth.F and groatb.F are replaced by new routine seaice_growth.F
518     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
519     - move a few global fields out of SEAICE.h into seaice_growth.F and
520       make them 2D (FICE/QNETO/ ...)
521     - remove FO (it is the same as QNETO)
522     - introduce a few local fields to avoid modifying external fields such
523       as atemp, etc.
524    
525    checkpoint58s_post
526    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
527      changed exf_set_gen.F so that
528        genperiod=0 means input file is one time-constant field and
529        genperiod=-12 means input file contains 12 monthly means
530    o CG2D: use pre-computed solver main-diagonal (stored in common block);
531      this affects truncation error ; generate new output file for exp. which
532      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
533        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
534        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
535        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
536        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
537        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
538    o start implementation of deep-atmosphere and anelastic formulation
539    o verification: remove 2nd copy of input files and use script "prepare_run"
540      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
541    o mom_common/vecinv/fluxform: fix a few initialisation isssues
542    o profiles: fix for multithreaded case
543    
544    o diagnostics: rename few diags:
545      s/'PRESSURE'/'RCENTER '/g
546      s/'TICE    '/'oceFreez'/g
547      s/'TAUX    '/'oceTAUX '/g
548      s/'TAUY    '/'oceTAUY '/g
549      s/'SWFLUX  '/'oceQsw  '/g
550      s/DIFx/DFxE/g
551      s/DIFy/DFyE/g
552      and add few ocean-forcing diagnostics:
553      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
554    o modifications to pkg/seaice/growth.F and budget.F, which change results of
555      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
556      as actual snow thickness.  It now refers everywhere to effective snow
557      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
558    
559    checkpoint58r_post
560    o modifications to pkg/seaice/growth.F, which change results of
561      lab_sea experiment: fixes pertain to melting snow over open water, to
562      masking EVAP under sea ice, and to using the correct AREA variable for
563      computations of EVAP, PRECIP, HSNOW, and GHEFF
564    o add ability to read bathy, salt, and theta using MNC (off by def)
565    o add flooding algorithm and advection of HSNOW for pkg/seaice;
566      both are turned off by default and do no change any results
567    o seaice advection with pkg/thsice: a step toward the use of non-linear
568      advection scheme, but #ifdef or commented out for now (requires more EXCH).
569    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
570      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
571      in natl_box (affects results @ truncation level: update output.txt)
572    o multi-threading and IO:
573      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
574      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
575        (needed to work with SingleCpuIO): tested in all verif. exp.
576    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
577      affects the results (but none of the verification test uses this scheme).
578    o Adding some pkg/diagnostics capability to pkg/seaice
579      (will certainly be subject to changes)
580    o ctrl: adding new control variables:
581      lwflux, lwdown, evap, snowprecip, apressure, runoff
582    
583    checkpoint58q_post
584    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
585      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
586      high_res_cube configuration by 4% on Columbia.
587    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
588      add (in global_with_exf/code) a version of EXF_INTERP_READ without
589      dynamical allocation (seems to work in multi-threaded).
590    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
591      single CPU io) so that TAF does not have to see EESUPPORT.h
592    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
593    
594    checkpoint58p_post
595    o obcs: stop if obcs is used with useCDscheme = .true.
596    o shelfice:
597     - fix a sign error so that no slip at shelfice interface works
598     - remove stop for combination non-hydrostatic code and shelfice. That does
599       not mean, that the results are correct, but at least they are numerically
600       stable
601    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
602    o added adjoint exch routined for all exch*3d* routines
603      and updated flow directives
604    
605    checkpoint58o_post
606    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
607      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
608    o change controling S/R for writing pickup file (new S/R do_write_pickup)
609      and clean-up reading/writing of pickup files.
610    o fix local version of read/write pickup (NH part) in rotating_tank/code
611    o simplify EXCH interface:
612     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
613     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
614    o added the regrid package
615    o shelfice:
616     - add a simple boundary layer scheme to reduce noise
617     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
618    
619    checkpoint58n_post
620    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
621       local variable (not in common block).
622    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
623      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
624      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
625        to work with SingleCpuIO.
626    o add "_d 0" to real constant of pkg/cfc subroutines ;
627       update exp. cfc_exemple & tutorial_cfc_offline output files.
628    o multi-threading and IO:
629      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
630        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
631      - barrier before and after reading.
632      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
633      - avoid using MDS_WRITELOCAL for LAND pkg output.
634      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
635        common-block variables ; Allows multi-threading with master-thread IO.
636    o change default MAX_NO_THREADS from 32 to 4 ;
637      and stop cleanly when MAX_NO_THREADS is too small.
638    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
639    
640    checkpoint58m_post
641    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
642       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
643    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
644       keep global_ocean.90x40x15 (for AD testing) with former secondary test
645       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
646    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
647        add MITgcm_tutorials (= code + all the tutorials)
648    o ecco, option to compute cost for total ssh (mean+anom)
649    o consistent with addition of ptracer and ssh in pkg/profiles
650    o profiles: adding ptracer and ssh
651    o testreport: change multi-test output-file name
652      (from output.txt.{name} to output.{name}.txt)
653    o profiles: now ok for mutli-tiles case
654    o seaice: add 4 parameters for different advection schemes for area,
655      (effective) seaice thickness, enthalphy, and snow height. Their default
656      is the standard parameter SEAICEadvScheme
657    o calc_gw:
658     - add cosFacU in zonal viscous flux (harmonic.visc.).
659     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
660       of tutorial_plume_on_slope.
661    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
662    o calc_gw: true flux-form, account for horizontal grid spacing.
663      update rotating_tank results, but not plume_on_slope (affected at
664      truncation level, 11 digits).
665    
666    checkpoint58l_post
667    o calc_gw:
668     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
669     - remove side-drag for now (need to fix it); update plume_on_slope results.
670     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
671    o commit code to make SST/SSS weights spatially variable
672      (based on either variable in-situ or variable initial T/S weights)
673    o pkg/ecco:
674      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
675        now based on horizontally varying weights wthetaLev, wsaltLev
676      * cost_averagesflags now returns year indices in addition to day, month
677      * sflux balance is performed on annual basis
678        (sflxumm, sfluxmm2, bal_sfluxmm)
679      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
680        including separate counting and multipliers
681    o pkg/rbcs
682      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
683    
684    checkpoint58k_post
685    o testreport:
686     - always build in dir. "build" (if not there, mkdir build instead of building
687       & running in input)
688     - run in dir run (if it exists), in build otherwise.
689     - call prepare_run (if input/prepare_run exists)
690     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
691    o pkg/exf modifications to interpolation and rotation routines for more
692       reasonable treatment of North Pole singularity: for tracers North Pole
693       value is set to northernmost zonal-mean value, for zonal velocity it is
694       set to zero, and for meridional velocity it is set to northernmost value.
695    o pkg/exf/exf_check_range.F
696     - add tile index to diagnostics and move stop statement to the very
697       end of the routine.
698    o pkg/diagnostics: (diagnostics_main_init.F)
699      define title of isomorphic variables according to the current config.
700    o pkg/thsice with pkg/seaice dynamics:
701    - fix domain of computation (interior only, required for exf) and do exchanges
702    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
703    o towards a standard way of dealing with multi-threading in MONITOR
704      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
705    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
706       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
707    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
708    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
709    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
710       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
711    o tracer advection:
712     - clean-up and simplify calc_common_factors.F
713     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
714       advection subroutine (but still not used within DST advection S/R)
715    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
716    
717    checkpoint58j_post
718    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
719      from file (collects calls previously in FORWARD_STEP)
720    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
721    o adjoint store dir. adjusted accordingly
722    o genmake2
723      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
724    
725    checkpoint58i_post
726    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
727      on wind stress (SEAICEstressFactor defaults to 1.)
728    o Total number of Timers is finite (<=40): comment out 2 non-essential one
729      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
730    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
731      on CS-grid: no longer loosing mass.
732    o exf & curvilinear-grid: no longer modify longitude xC & xG.
733    o pkg/ggl90: fix sloppy output and fix a bug
734    o pkg/seaice: added SEAICEuseEVPpickup parameter
735      - Set to false in order to start EVP solver with
736        non-EVP pickup files when using SEAICEuseEVP
737      - fix sign error in diffusion in seaice_calc_rhs
738    
739    checkpoint58h_post
740    * Modifications for bottom topography control
741      o replace hFacC by _hFacC at various places
742      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
743      o add non-self-adjoint cg2d_nsa
744      o update autodiff support routines
745      o re-initialise hfac after ctrl_depth_ini
746      o works for 5x5 box, doesnt work for global_ocean.90x40x15
747    * Adding verification for 5x5 box (4-layer) bottom topography control
748    
749    checkpoint58g_post
750    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
751       used for mean seasonal cycle, mean diurnal cycle); add an example
752       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
753    o pkg/ggl90:
754      - add parameter (minimum surface kinetic energy)
755      - fix bug (avoiding division by zero)
756    o couple pkg/thsice to pkg/seaice:
757      - modify advection in seaice to accomodate new scalar fields to be advected
758      - only muliDimAdection scheme work with seaice/thsice
759      - mapping of thsice-variables to seaice-variables, back and forth
760      - does not break the verification experiments, but does not give the
761        desired results either
762    o pkg/seaice
763      - make (default) second order advection a bit less confusing?
764    
765    checkpoint58f_post
766    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
767      to pkg/seaice):
768      - new routines thsice_map_exf and thsice_get_exf provide the interface
769      - add an additional formal parameter to thsice_solve4temp
770    o pkg/exf:
771      - add new fields wspeed, snowprecip (to be able to couple to thsice)
772      - correct Stefan-Boltzmann constant
773      - new parameter for longwave surface emittance
774      - separate some stuff from exf_bulkformulae into new routines  
775        exf_radiation, exf_wind
776      - add new parameters and constants: longwave emissivity for ocean, ice
777        and snow, evaporation parameters over ice
778      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
779        either wind from stress or stress from wind
780    o pkg/thSIce:
781    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
782    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
783       and THSICE_CALC_THICKN
784    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
785    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
786      to make debugging easier.
787    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
788    o pkg/bulk_force:
789      - clean-up comments and parameters ;
790      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
791    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
792      generate new output for test-experiment: aim.5l_cs.thSI
793    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
794      testreport accordingly
795    
796    checkpoint58e_post
797    o SEAICE_CGRID adjoint done
798    o R_STAR adjoint implemented.
799      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
800      * need to sort out init. of h0facc, etc.
801    o Make pkg/profile fully independent of ecco,cost, etc. stuff
802      to be able to use it in pure forward.
803    
804    checkpoint58d_post
805    o upgrade simple test-experiment to tutorial example:
806     step.1: duplicate the experiment and (step.2) will remove the old copy.
807      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
808      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
809      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
810      tutorial_global_oce_biogeo    <- copy of dic_example
811      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
812      tutorial_plume_on_slope       <- copy of plume_on_slope
813      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
814      tutorial_global_oce_optim     <- empty for now (David ?)
815      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
816     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
817    o correct a sign problem in cost_scat.F
818    o obcs and ptracers: fix boundary conditions for advections schemes
819      with larger stencil
820    o thsice adjoint: start
821    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
822      completeness
823    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
824      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
825    o ptracers adjoint:
826      * avoid extensive recomputatations
827      * fix missing re-init. of gptr (missed by TAF)
828    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
829      me to turn off the excessive output to STDOUT that this package produces
830    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
831      and add those terms in Vector-Invariant formulation.
832    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
833      if the control period (xx_hfluxperiod etc) is 0
834    o in profiles pkg, clean routines and fix details
835    o in ecco pkg, reading ssh data:
836      fix problem in case the model does not start at iter0=0
837    o fix mnc-pickup/restart for ptracers
838    o new package prifiles:
839      code to compute profile-based cost by Gael Forget
840      (modifs in ecco, ctrl, autodiff)
841    o Benign bug fix in initialization (spotted by M. Mazloff) of
842      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
843    
844    checkpoint58c_post
845    o adjoint: finish NLFS adjoint and provide reference output in
846      verification/global_ocean.90x40x15/results_ad_nlfs
847    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
848      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
849      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
850      with SEAICE_CGRID defined.
851    o move calendarDumps from "data" to "data.cal" and clean-up the code
852      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
853    o add useEXF & useCAL flags (for now, set in hard-coded way)
854    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
855      (were missing in NH mode, and wrong in quasihydrostatic mode).
856      waiting for Chris updated version of calc_gw to add those CALLs.
857    o fix bug in quasihydrostatic S/R ;
858      add a test for this option: global_ocean.90x40x15.qshyd
859    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
860      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
861    o add on/off flag useOffLine for package OFFLINE
862    o seaice:
863      - modify advection so that it works also on the C-grid
864      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
865        problem in multi-tile runs with C-grid
866      - add flags for clipping ice velocities and/or masking solver forcing
867      - fix drag (ocean on ice) formulation and a bug that caused noise in the
868        C-grid solver
869      - added a few comments to seaice_diffusion.F
870      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
871        are now exclusive)
872      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
873        required re-ordering the code a little:
874       + make DAIRN global variable (defined in SEAICE)
875       + move computation of the viscosities eta and zeta into a new separate
876         routine (because I need to recompute them in seaice_ocean_stress.F)
877    
878    checkpoint58b_post
879    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
880      update output.txt of exp. aim.5l_cs.thSI
881    o various mnc cleanups and improvements:
882      + shrink lookup tables by factor of ~4
883      + better error reporting when running out of lookup space
884      + able to handle longer path/file names (up to 500 chars)
885    o adjoint:
886      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
887      - TBD: "hidden" mom_vecinv recomp. in dynamics
888    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
889     (allow to differentiate between forcing components using new integer flags:
890      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
891     and add new flag to put Dissipation tendency out of Adams-Bashforth.
892    o ecco
893      - enable trend removal from SSH anomaly obs.
894    o adjoint
895      - a fix for PmEpR when #undef EXACT_CONSERV
896      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
897      - try to fix "hidden" recomp. in forward_step for NLFS
898        (NLFS seems broken sometimes after I checked it in)
899    o seaice:
900     - add c-grid version of the dynamic solver:
901       + three new routines that are the c-grid substitute lsr, dynsolver
902         and ostres
903       + put a few fields that were local to dynsolver into global common
904         blocks, so that I can move the computation of stresses etc into
905         seaice_lsr (saves coding but may break the adjoint).
906     - replace more hardwired parameters by runtime parameters
907     - add ice masks that mask the rhs of the implicit solvers where there
908       is no ice (commented out in seaice_dynsolver, because i am not sure
909       if this works properly), eventually this should replace the clipping
910       of ice velocities in seaice_dynsolver to +/-40cm/s.
911    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
912      include it only where its needed
913    o move balancing of fluxes before the call of external_forcing_surf
914    o seaice:
915      - correct units of turning angles (now they are really in degrees)
916      - move computation of GWATX/Y out of main routine into dynsolver
917      - initialize GWATX/Y in seaice_init
918    o Apply mask on Fresh-Water flux (needed for SSH forcing).
919      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
920    o seaice: add runtime flags for turning angles (default to zero)
921    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
922      and trend from exf forcing and ctrl control adjustments
923    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
924      (since checkpoint57x_post)
925    o change the default rotation period to 86164.s = the Earth rotation
926    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
927      and based on a reference stratification. Tested within hs94.cs-32x32x5.
928    o seaice advection: add code for choosing between the default (2nd order
929      central differences) and multiDim advection schemes provided by
930      pkg/generic_advdiff
931    o seaice:
932      - removed all references to SEAICE_GRID.h fields from
933        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
934        (cubed-sphere configuration will change a little)
935      - grid computations in seaice_init are obsolete now.
936      - cleaned up code a little so that is easier to read (hopefully).
937      - added new (better?) discretizations of default advection and diffusion
938        (turn on with SEAICEuseFluxForm)
939      - replace 1 in 3d global fields by kSurface in growth.F
940      
941    checkpoint58a_post
942    o seaice:
943      - bug fix in advect.F
944    o shelfice:
945      - separate shelfice load anomaly from pload (breaks with time
946        dependent forcing), => introduce constant field shelficeLoadAnomaly.
947        Its default is 0., but it may be computed more cleverly from (unknown)
948        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
949        done offline. A good approximation of the pressure load anomaly is
950        necessary to avoid large initial adjustment processes underneath
951        deep-reaching shelfice.
952      - small fix in ISOMIP shelfice_thermodynamics
953      - add more sophisticated thermodynamics of Hellmer (1989), this is
954        now the default
955      - give a few constants more intuitive names
956    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
957      if bulk formulae are used in long integration (especially EmPmR). Turn
958      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
959      if balancePrintMean, the imbalance that is substracted is printed to
960      STDOUT.
961    o fix bug (typo) in obcs_apply_eta.F
962    o add a new package shelfice which enables us to model the circulation
963      underneath shelf-ice with draughts of hundreds of meters.
964     - works
965     - to do: + include improved thermodynamics
966              + check whether kSurfC (from model/inc/SURFACE.h) can be used
967                instead of new field kTopC
968              + can we use topoFile, Ro_surf and existing code in ini_depth.F
969                instead of new field R_shelfIce and new code in ini_depth.F
970                and ini_mask_etc.F?
971              + adjust vertical mixing schemes?
972    o seaice pkg:
973     - add a cpp-flag to include a simple formula for a salinity dependent
974       freezing point of sea water at the surface
975     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
976       meridional stresses are now different (and hopefully correct)
977    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
978       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
979       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
980    o pkg/diagnostics: add options and parameters for regional-statistics
981       diagnostics ; define regions by reading a region-mask from a file
982       (might add other options later)
983    o pkg/bulk_force:
984     - add option and parameters to use AIM surface-flux formulae.
985     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
986       others forcing fields (defined in PARM05, parameter file "data") are loaded
987       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
988     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
989     - use the right EXCH call for uwind,vwind (to work on CS-grid).
990     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
991       and parameters (note: calcWindStress replaces .NOT.readwindstress).
992     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
993    
994    checkpoint58
995    o add "--embed-source" option to genmake2 which, when the supporting
996      tools can be compiled (as determined by genmake2) will turn on the
997      embed_files package which then embeds the entire MITgcm source code
998      (*.[fFhc] + Makefile) used for the build within the executable
999      - requested by CNH but off by default
1000      - adds a paltry <9MB to the mitgcmuv executable in most cases
1001      - only writes the output when useEMBEDSRC in eedata is true
1002    o clean up 3-dim. relaxation codes:
1003      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
1004      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
1005      * Thanks to Tom Haine for testing!
1006    
1007    checkpoint57z_post
1008    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
1009      affects output (@ truncation level) of exp. plume_on_slope ; updated.
1010    o fix the pickup behavior for obcs in combination with ptracers
1011    o fix a bug in ptracers_external_fields_load
1012    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
1013      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
1014    o transfered surface NH pressure to eta field (if exactConserv).
1015    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
1016         and update lab_sea output.txt file.
1017    o completing 3-dim. relaxation code: additional term
1018         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
1019      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
1020      * At compile time, in "EXF_OPTIONS.h" set
1021          #define  ALLOW_CLIMTEMP_RELAXATION
1022          #define  ALLOW_CLIMSALT_RELAXATION
1023      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
1024          tauThetaClimRelax3Dim = 15552000.0,
1025          tauSaltClimRelax3Dim  = 15552000.0,
1026      * 3 cases:
1027          1) Use a constant-in-time 3-dim. field
1028          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
1029          3) Real-time relax. to time-evolving prescribed field
1030    o Adding Laplacian-type smoothness constraint on
1031      initial and boundary (forcing) controls (ic, bc)
1032      * enable at compile-time via
1033        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
1034      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
1035      * Absolute scale somewhat unclear so far
1036      * no area weighting was included since no other cost term does so far
1037    
1038    checkpoint57y_post
1039    First step for a NLFS adjoint
1040    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
1041    o new init. routines for calc_r_star, calc_surf_dr
1042    o still need to deal with ini_masks_etc
1043    o testreport seemed happy
1044    checkpoint57y_pre
1045    
1046    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
1047    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
1048    o add new offset feature to offline pkg (plus minor cleanup)
1049    o cfc fixes for final year of integration
1050    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
1051      be in GCHEM_OPTIONS).
1052    
1053    checkpoint57x_post
1054    o fix testreport Pb in multiple test experiment.
1055    o cleanup our namelist syntax in verification:
1056      - make it more F95 standards compliant (some work still needed)
1057      - allows the vast majority of our tests to work with gfortran
1058    o Non-Hydrostatic:
1059     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
1060     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
1061    o Allow to apply AB on T,S rather than on AB(gT,gS):
1062     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
1063     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
1064       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
1065     - need a "clever" read_pickup to restart from the other AB formulation
1066    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
1067    o remove some unused variables (reduces number of compiler warnings)
1068    o adjoint
1069      * Disable useVariableViscosity for adjoint for time being
1070        (there are a number of extensive recomputations)
1071      * Initialize certain variables needed for adjoint
1072    
1073    checkpoint57w_post
1074    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
1075                 fix the singleCpuIO RS version of MDSWRITEFIELD
1076       and add a WARNING if using globalFiles=T with multi-processors.
1077    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
1078      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
1079    o tracer advection scheme:
1080      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
1081       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
1082       was not very convenient).
1083      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
1084       (further tests needed for the implicit DST & Flux-Limiter schemes).
1085    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
1086      and sRef for convenience, handy, when you want to initialize
1087      ptracers in a large domain with a constant non-zero value. Also,
1088      untangle ptracers_init.F a little.
1089    
1090    checkpoint57v_post
1091    o change dome exp. to use variable viscosity in side-drag terms.
1092    o remove all the files from the cfc_offline test since they are now
1093      incorporated into tutorial_cfc_offline which has been producing
1094      identical results for a few days of testing
1095    o add new parameter: sideDragFactor to enable half-slip-side BC
1096      and change side-drag S/R to use viscosity from mom_calc_visc
1097      (can switch back by setting sideDragFactor=0.); affects results at
1098      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
1099       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
1100    o vorticity & strain are now computed without masking, to account for
1101      no-slip-side BC in variable viscosity calculation ; mask is applied
1102      anyway later on, before computing advection/coriolis terms.
1103    o modify exp4 to test new obcs support for reading from external files
1104      and for passive tracers
1105    o fix behavior of ptracers_monitor when monitor output is written to a
1106      netcdf-file; still not independent of monitor.F (writes in the same
1107      file).
1108    o change default value of tRef (put a uniform, meaningful value for ocean
1109      & atmos) and initialize sRef (was missing, as Martin mentioned).
1110    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
1111      to be proportional to enstrophy dissipation length.  Thus,
1112       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
1113      This is now consistent with Smagorinsky and with the manual.
1114    
1115    checkpoint57u_post
1116    o OBCS and PTRACERS: add open boundary support for passive tracers
1117      - either use homogenous (pseudo) v.Neumann conditions or prescribe
1118        OB-values from file; this is not different from the way theta and salinity
1119        are treated
1120      - however, Orlanski-radiation conditions are not supported, and the model
1121        will stop if you use pTracers and Orlanski at the same time.
1122      - beefed up the rountine obcs_external_fields_load: now only those open
1123        boundary values are overwritten with values from files for which there
1124        are really files, otherwise the OB-fields remain untouched. This makes
1125        it possible to use different OBs at different ends of the domain (as
1126        with EXF)
1127    o reduce number of exch calls in shap_filt (s2).
1128    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1129      truncation level) 4/5 MLAdjust test results (11&12 digits match).
1130    
1131    checkpoint57t_post
1132    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1133    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1134      same truncation, independent of the face number: affects affects several
1135      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1136    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1137      note that biharmonic viscosity + no-slip was not tested in any experiment.
1138    o fix bug in non-linear free-surf side-drag ; generate new output for
1139      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1140    o make mnc honor the writeBinaryPrec flag for most kinds of output
1141    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1142    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1143      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1144    o add brackets in multi-terms sum to get same truncation, independent of
1145      the face number (manage to get exactly same value of gU,gV at the cs-edge)
1146      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1147    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
1148      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1149      a maximum grid-scale Reynolds number.  Also, changes all length calculations
1150      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1151      Suggested values of viscosity parameters found in mom_calc_visc.
1152      Many new viscosity diagnostics available.
1153    
1154    checkpoint57s_post
1155    o Add clearing-house for viscosity calculations, mom_calc_visc and
1156      correct numerous bugs in LeithD and Smagorinsky discretizations.  
1157      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1158      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1159      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1160      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
1161      The Strain-Tension form is now called with useStrainTensonVisc=.true.
1162      ViscAhStrain and viscAhTension are now retired.
1163    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1164    o In response to JMC's bug report, genmake2 now ignores any soft-links
1165      that it finds in the *current* directory when searching for files.
1166      Soft-links found in any other source directories will still work as
1167      they did before.
1168    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1169      a C routine to unlimit the stack size
1170    o mnc-ify pkg/aim snapshot vars
1171    o mnc-ify pkg/land as requested by Daniel
1172    o various changes to mnc including:
1173      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1174      - output can now be grouped so that all files within a group
1175          change the ITER portion of their names in lock-step together
1176      - can now read ("global") PER-FACE (in addition to PER-TILE) files
1177          and works with both EXCH1 and EXCH2 (but needs more testing)
1178      - writing works for all verification test cases w/ g77 on Linux
1179    
1180    checkpoint57r_post
1181    o make MNC variable initialization happen earlier
1182    o add diagnostics for (almost) each term of the momentum Eq.
1183    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1184    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1185    o remove MINIMAL_TAVE_OUTPUT option ;
1186      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1187    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1188      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1189    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1190    o add time-dependent SST, SSS control
1191    o cost terms in ecco/ modularized (new cost_generic.F)
1192    o cost_averages routines are modularized (new cost_averagesgeneric.F)
1193    o new infrastructure for seaice model vs. obs misfits in seaice/
1194      * driver from the_main_loop.F is seaice_cost_driver.F
1195      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1196      * gradient check in Exp. 6a of natl_box_adjoint/
1197    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1198      (see README file)
1199    
1200    checkpoint57q_post
1201    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1202    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1203      - bug was reported by Jean-Michel and Ian Fenty
1204    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1205      update exp. cpl_aim+ocn output.
1206    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1207      Needed for high-res. runs with large global files
1208      to be able to limit tapelev size
1209    o Changed some tests for adjoint:
1210      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1211      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1212      * global_ocean.90x40x15/ back to default 3-level checkpointing
1213    o Modifications to enable scripted COMMON to MODULE conversion
1214      * verification/OpenAD/code/ has necessary scripts and description;
1215      * converts, compiles and runs successfully;
1216    
1217    checkpoint57p_post
1218    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1219    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1220      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1221    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1222    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1223      (was already the case for dissipation with mom_vecinv,
1224       and also the case for grad.PhiHyd when staggered-timeStep)
1225      This will allow to put dissipation out-off the AB time-stepping.
1226     Unfortunately, affects truncation error. Update output of exp. that "fails"
1227      (cg2d matching number) and leave the others for later: front_relax(10),
1228      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1229      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1230    
1231    checkpoint57o_post
1232    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1233      (2) its ready to be documented during the 20050801 DocFest
1234    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1235      for ideal_2D_oce and lab_sea on linux_ia32_g77
1236    o set to #undef CTRL_SET_OLD_MAXCVARS_30
1237      in global1x1_tot/code_seaice_adj to access indices 32, 33
1238      (worth another tag)
1239    
1240    checkpoint57n_post
1241    o adding precip control xx_precip 32
1242    o adding swflux control xx_swflux 33
1243    o Replacing 10 forcing penalty cost routines by 1 generic.
1244    o Implementing partitioning in time-mean and variable adjustment
1245      for atmos. state.
1246    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1247  o in natl_box_adjoint:  o in natl_box_adjoint:
1248    * updated: results_bulk/    * updated exp 1 to 10
1249    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
1250    o updated global1x1/*_seaice_adj/
1251      to incorporate latest changes
1252    o enable useSingleCpuIO for mdsio vector routines
1253      (applies in particular to tapelev I/O)
1254    o removed inefficient K-loop in all active_file*control*.F
1255    
1256  checkpoint57m_post  checkpoint57m_post
1257  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
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