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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.863 by jmc, Thu Aug 23 19:37:08 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  o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
8  o moved ptracer ctrl index 17 -> 32    forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
9      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
10      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
11      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
12      -> update output.txt
13    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
14     this affects truncation error: -> update output.txt of exp:
15      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
16      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
17    
18    checkpoint59f
19    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
20    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
21      a bounded range (in forward mode)
22    o pkg/ecco, ctrl, autodiff and mom_common:
23     internal parameter controls, completements of implementations
24    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
25    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
26      (not seem any difference in testing results).
27    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
28       at face corners.
29    o pkg/generic_advdiff:
30     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
31      loop range indices for computing vertical advection tendency
32      and do the calculation in the interior only (no overlap) ;
33      for now, only implemented for SOM advection (to save CPU time).
34     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
35    o exch2 adjoint
36      First set of changes:
37      - add exch2 hand-written adjoint templates
38      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
39        This will require cleanup in pkg/autodiff/*.F
40        (changed routines currently kept separate in verif. code/)
41      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
42        that used to hide exch2 or cubed-sphere specific code
43        (commented via 'cph-exch2')
44    o pkg/seaice
45      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
46    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
47       output of global_ocean.cs32x15.thsice .
48    
49    checkpoint59e
50    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
51      for B-grid vector (not yet tested) and C-grid vector (<- only used
52      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
53    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
54      (#ifdef ALLOW_SALT_PLUME)
55    o gather_2d/scatter_2d: removed halo regions
56    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
57      scheme and the corresponding test case (under front_relax dir). For now,
58      only available with Skew-flux form and not yet tested in realistic set-up.
59      adjoint: store directives updated, but gradient checks deteriorated,
60      so maybe GM/Redi adjoint is now broken.
61    o seaice adjoint
62      * add AREA, HEFF, HSNOW as control variable
63        (should not change lab_sea results)
64      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
65    o pkg/seaice:
66      * added computation of saltFlux in seaice_growth;
67        For time being, sea ice salinity is assumed constant
68        contribution of snow flooding to freshening of sea ice is neglected.
69        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
70        defaults to 0.0 in order to maintain backward compatibility.
71        Typical values for SEAICE_salinity are 4 to 10 g/kg.
72      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
73      * added SEAICE_availHeatFrac, which specifies fraction of surface level
74        heat content used to melt or grow ice
75      * commented out cap of HICE: it helps keep ice thinner
76      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
77      * applied OBCS T/S mask to HEFFM sea ice mask
78    
79    checkpoint59d
80    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
81     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
82     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
83    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
84     and change default value of parameter "GM_Small_Number";
85     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
86       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
87       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
88    o pkg/ecco: cost function when applying pkg/smooth to controls
89    o pkg/ctrl: add forcingPrecond run time parameter
90    o pkg/seaice:
91     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
92     - fix bug in metric terms of u-equation in LSR solver (implicit part),
93       changes verification/lab_sea
94     - rearrange implicit part of u-equation in LSR solver to make it easier to
95       read, understand, and debug. This causes changes at the truncation level.
96     - fix (serious) bug in the boundary conditions (sign error in the implicit
97       part) of the LSR solver. Changes all LSR results.
98     - fixed problem with HSNOW initialization to avoid thick snow when AREA
99       is initilized with small values - does not change lab_sea results.
100     - added HsnowFile initialization capability
101    o pkg/smooth: addition to model/src and pkg/ctrl so allow
102     initialization of pkg/smooth and application to control vector
103    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
104    o dependencies: pkg/profiles requires pkg/cal
105    o pkg/profiles:
106     - added option ALLOW_PROFILES_GENERICGRID
107         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
108         that interpolation information (grid points and coefficients) is provided
109         within the netcdf input files.
110         -> sample matlab scripts can be found in MITgcm_contrib/gael
111         that allow you to prepare netcdf input files.
112     - also modified: cleaner include statements, cleaner error print statements,
113       cleaner stops when error, and more tests of the netcdf input files consistency.
114    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
115    o pkg/seaice:
116     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
117       requires a new routine: seaice_diagnostics_fill.F
118     - make sure that seaice does not move if not forced (pressure replacement
119       method, Hibler and Ip, 1995), changes results
120     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
121     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
122       It is turned off by default (=-1.), because it changes the results.
123     - make it possible to read AREA from a file, too.
124    
125    checkpoint59c
126    o add S/R and diagnostics for oceanic mixed-layer depth
127    o move GMRedi call after all vertical mixing schemes (including KPP)
128    o pkg/thsice:
129     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
130      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
131    o pkg/obcs:
132     - bug fix for balance code
133    o pkg/seaice:
134      - allow values of SEAICE_elasticParm > 1
135      - add new parameter SEAICE_evpTauRelax as an alternative
136        to SEAICE_elasticParm
137      - make lsr boundary conditions free slip (by default), changes result
138      - add code for no slip boundary conditions for lsr
139      - set minimum of zeta to zero (and not 4e8) (changes results)
140      - add a cap on AREA after advecting AREA if seaice_growth is not called
141    o change calculation of Visbeck K:
142      - no longer depend on tapering scheme; instead, compute slope (limited
143        by GM_maxSlope). this is equivalent to what was comuted before with
144        clipping or linear tappering.
145      - fix vertical averaging (wrong by 1/2 level)
146      - leave the old version (but will not be maintained) within
147        #ifdef OLD_VISBECK_CALC / #endif
148      - update output of exp. ideal_2D_oce
149    o change error catch in calc_r_star to improve vectorization
150    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
151      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
152    o adjoint:
153      Re-organized adjoint checkpointing according to Matt Mazloff
154      (but with modifs/completions/cleanups)
155      Storing is now bundled into large arrays to optimized I/O
156      (and second step in cleanup of the_main_loop)
157    
158    checkpoint59b
159    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
160      - export/import (between ocean & coupler) fields needed for ocean DIC.
161    o pkg/seaice:
162      - get rid of three more exchanges seaice_calc_viscosities (required
163        different loop boundaries in seaice_lsr and seaice_ocean_stress)
164      - bug fix in seaice_ocean_stress (update of lab_sea required)
165      - reduce loop boundaries to necessary minimum also in seaice_evp
166      - go back to the old way of computing deltaC/Z as the adjoint likes that
167        better
168    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
169      passive tracer to an Age Tracer) + update output.txt
170    o pkg/exf:
171      - implement A-grid / C-grid selection for wind-stress input files.
172      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
173      for now, in exf_bulk_largeyeager04.F only :
174      - change implementation for case where windspeed + 2. components wind-stress
175        are read-in. AND use rhoConstFresh to convert evap.
176    o pkg/seaice:
177      - use correct EXCH_UV for wind-forcing (on A-grid).
178      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
179        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
180    o pkg/exf:
181      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
182      EXF_INTERPOLATION:
183      - merge global_with_exf/code version of exf_interp_read.F
184        to the main code ;
185      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
186        reading the file ; Important: This options needs to be defined to recover
187        previous code.
188        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
189      - no longer loose real*8 precision along the way when using exf_iprec=64.
190    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
191      - change discretisation of evp-solver in order to avoid another exchange
192        (changes lab_sea) and clean up a little
193      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
194        help the adjoint (this also changes the results slightly)
195      - add a few "_d 0" where they had been missing in seaice_evp.F
196      - cleaning up: remove unused seaice_calc_rhs.F
197    o pkg/exf: some cleaning-up:
198      - change various "constants" into runtime parameters
199      - cleaned-up Large&Yeager04 routine which should eventually
200        replace exf_bulkformulae.F (changed names of S/R and CPP)
201        and merged various ALLOW_ATM_WIND options
202     only used with thsice pkg (in thsice_get_exf.F):
203      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
204        which are used when useStabilityFct_overIce=TRUE (= the default)
205      - change default values of ice & snow emissivity and scale downward LW
206        by ice & snow emissivity.
207    o pkg/thsice:
208     fix few little problems, in thsice_calc_thickn.F:
209      - growth vertically (and not laterally) if iceFrac == iceMaskMax
210      - melt only laterally if hIce < hThinIce (as the comments say)
211      and in thsice_extend.F:
212      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
213      - start to form ice as soon as the minimum ice-volume is reachable.
214     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
215      and cpl_aim+ocn
216    o pkg/kpp
217     - move computation of surface related input fields to KPP into a new
218       subroutine kpp_forcing_surf.F
219     - remove wrong (within bi,bj loops) EXCH calls.
220     - little cleaning (add argument myThid in last position, cvs header ...)
221     - for now, fix conservation problem by exchanging KPPviscAz (may not
222       be the best fix)
223    o pkg/seaice
224     - check for inconsistent evp parameter/cpp-flag combination
225     - remove leftover errIO flat for obsolete name list error handling
226    o OpenAD
227     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
228    
229    checkpoint59a
230    o pkg/seaice: some parameter clarifications and a little bit of clean up
231    o pkg/thsice: rename run-time parameters:
232       himin       -> hIceMin
233       himin0      -> hThinIce
234       hihig       -> hThickIce
235       i0          -> i0swFrac
236       transCoef   -> bMeltCoef
237       frac_energy -> fracMelting
238      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
239       with default values (for now) that do not change the results.
240      remove old version of thsice vars advection in pkg/seaice.
241    o in FFIELDS.h:
242      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
243      - make pLoad & sIceLoad always available (but still only used if
244         ATMOSPHERIC_LOADING is #define).
245    o pkg/kpp: replaced _KPP_RL with _RL
246    o bug fixes for vertical diffusivity computations when both KPP and
247        3D diffusivity arrays are used.
248    o pkg/seaice: fix bug in evp solver, while doing that
249      - change (improve?) discretization of stress computations for both
250        cgrid-lsr and evp solver
251      - add a new routine to compute strain rates
252      - the above changes lab_sea results
253      - add no slip conditions for evp solver (off by default), lsr-version
254        may follow
255      - fix exchange for shear at Z-points (does not change lab_sea)
256      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
257        (to force the user to pick a time step since there is not "safe" way
258        of choosing it)
259      - add principal stress diagnostics
260      - rearrange fields for evp a little to avoid having to call a: too many
261        exchanges and b: exchanges for stress trensor components which we do
262        not have.
263      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
264        of evp, complete rewrite for lsr case (latter is does not yet work
265        in all cases)
266    o pkg/kpp: add code to have mixing in shelf ice caverns
267      - add myThid to all kpp routines (long overdue)
268    
269    checkpoint59
270    o pkg/exf:
271      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
272        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
273      - move exf header files from lower_case.h to UPPER_CASE.h ;
274        add missing cvs Header & Name
275      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
276      - add namelist param. selectStressGridPosition, exf_monFreq
277      - retire many _CLIM routines, and remove data.exf_clim
278        + params moved to data.exf
279        + climsst, climsss now handled by exf_set_gen, i.e.
280          climss?period=0 refers to constant field,
281          climss?period=-12 to monthly forcing
282      - split up namelists in data.exf
283    o pkg/seaice:
284      - remove seaice_exch and seaice_exch_uv
285      - remove superfluous exchange of theta
286      - add myThid to seaice_budget_ocean/ice
287      - add new interface for atmospheric wind forcing (C-grid only)
288        + new routine
289        + two new field (taux, tauy for stress over ice)
290        + removed one global field (DAIRN) for C-grid case only
291    o pkg/thsise
292      - 2nd set of modifs for thsice adjoint in conjunction with exf
293    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
294    
295    checkpoint58y_post
296    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
297      vertical diffusivity, similar to that in MOM4; turned on using
298      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
299      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
300    o Added capability for 3D specification of background vertical diffusion
301      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
302      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
303      "data" file that contains the 3D vertical diffusivity coefficients.
304    o ice dynamics (pkg/seaice) with thsice thermodynamics:
305      - add code within pkg thsice to advect & diffuse sea-ice fields
306      similar to (and will replace) what has been added in  seaice_advdiff.F,
307      but: - conserving Mass, Heat & Salt.
308           - better when using non-linear advection scheme (not yet fully tested)
309           - can also be used in atmospheric set-up (for now, only the diffusion).
310    
311    checkpoint58x_post
312    o IO option for global-file compact format:
313      - add options when generating topology (utils/exch2/matlab-topology-generator)
314      - add I/O capability (pkg/mdsio).
315      - adapt utils/matlab/rdmds.m to read this format.
316      for now long-line format not yet supported by pkg/mdsio (& exch2).
317    o shelfice: add a few diagnostics
318    
319    checkpoint58w_post
320    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
321      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
322      (and replace horiVertRatio in NH code).
323      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
324                         and tutorial_plume_on_slope (sensitive to truncation)
325    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
326      directly to drive seaice model (C-grid only)
327    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
328     - reintroduce computation of wind from stress,
329     - compute tau (in exf_bulkformulae.F) from windstress averaged to
330       mass points to avoid tau = 0
331     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
332    o rdmnc.m: make it work with "global" files created with gluemnc
333    o rdmnc.m : some improvements in dealing with singleton dimension
334      (tested on all testreport mnc output files).
335    o genmake2: disable pkg/profiles if netcdf test fails.
336    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
337    o move call to cal_readparms up to make calendar parameters/variable available
338      to all packages
339    
340    checkpoint58v_post
341    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
342      useDynP_inEos_Zc tested.
343    o pkg/exf: changes to properly interpolate/mask/scale initial fields
344    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
345      and portions thereof.  See read_cs.txt for description and examples.
346    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
347      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
348      following the great-circle arc between those 2 points.
349    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
350      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
351    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
352     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
353     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
354     - still needs work (not working with some options ; efficiency to improve)
355       and serious testing.
356     - use this scheme for temperature & salinity in 2 advection test exp.:
357       advect_xy & advect_xz, respectively.
358    
359    checkpoint58u_post
360    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
361    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
362    o testreport: add option "-skipdir" to skip some test.
363    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
364      momentum calculation.
365    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
366    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
367      remove checkpoint.F and the_correction_step.F (no longer used);
368      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
369    o add option (linFSConserveTr) to correct for tracer source/sink due to
370      Linear Free surface
371    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
372    o pkg/thsice: fix reading mnc-pickups
373    
374    checkpoint58t_post
375    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
376    o pkg/mdsio:
377     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
378       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
379       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
380     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
381     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
382       either MDS_READ_FIELD or MDS_WRITE_FIELD )
383     - new S/R (to replace MDSWRITEMETA), which allows to write more
384       informations (variable names, time ...) to meta files.
385     - modify rdmds.m to give back the meta file content.
386    o pkg/diagnostics: change vertical interpolation to be safer, and more
387       flexible (define p-levels to interpolate to in data.diagnostics);
388      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
389       diagnostic pointer.
390    o pkg/seaice: more cleaning up of seaice_growth, added many comments
391    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
392    o fix multi-category seaice:
393     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
394       SEAICE_MULTICATEGORY
395     - fix short wave heat flux
396    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
397       and allow to use EVP solver. Change forward lab_sea: test both EVP
398       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
399    o Initial check-in of lab_sea adjoint
400      (very similar to natl_box_adjoint/code_seaice)
401      * used C-grid and EVP solver
402      * used KPP, GM/Redi
403      * uses inAdExact=.TRUE.
404      * gradient checks fail for both ADM and TLM
405        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
406        f.d. gradients actually seem more problematic than ADM, TLM gradients;
407        issue is related to forward mismatch between g77 an ifort
408    o pkg/seaice: overhaul of thermodynamics
409     - growth.F and groatb.F are replaced by new routine seaice_growth.F
410     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
411     - move a few global fields out of SEAICE.h into seaice_growth.F and
412       make them 2D (FICE/QNETO/ ...)
413     - remove FO (it is the same as QNETO)
414     - introduce a few local fields to avoid modifying external fields such
415       as atemp, etc.
416    
417    checkpoint58s_post
418    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
419      changed exf_set_gen.F so that
420        genperiod=0 means input file is one time-constant field and
421        genperiod=-12 means input file contains 12 monthly means
422    o CG2D: use pre-computed solver main-diagonal (stored in common block);
423      this affects truncation error ; generate new output file for exp. which
424      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
425        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
426        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
427        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
428        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
429        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
430    o start implementation of deep-atmosphere and anelastic formulation
431    o verification: remove 2nd copy of input files and use script "prepare_run"
432      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
433    o mom_common/vecinv/fluxform: fix a few initialisation isssues
434    o profiles: fix for multithreaded case
435    
436    o diagnostics: rename few diags:
437      s/'PRESSURE'/'RCENTER '/g
438      s/'TICE    '/'oceFreez'/g
439      s/'TAUX    '/'oceTAUX '/g
440      s/'TAUY    '/'oceTAUY '/g
441      s/'SWFLUX  '/'oceQsw  '/g
442      s/DIFx/DFxE/g
443      s/DIFy/DFyE/g
444      and add few ocean-forcing diagnostics:
445      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
446    o modifications to pkg/seaice/growth.F and budget.F, which change results of
447      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
448      as actual snow thickness.  It now refers everywhere to effective snow
449      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
450    
451    checkpoint58r_post
452    o modifications to pkg/seaice/growth.F, which change results of
453      lab_sea experiment: fixes pertain to melting snow over open water, to
454      masking EVAP under sea ice, and to using the correct AREA variable for
455      computations of EVAP, PRECIP, HSNOW, and GHEFF
456    o add ability to read bathy, salt, and theta using MNC (off by def)
457    o add flooding algorithm and advection of HSNOW for pkg/seaice;
458      both are turned off by default and do no change any results
459    o seaice advection with pkg/thsice: a step toward the use of non-linear
460      advection scheme, but #ifdef or commented out for now (requires more EXCH).
461    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
462      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
463      in natl_box (affects results @ truncation level: update output.txt)
464    o multi-threading and IO:
465      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
466      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
467        (needed to work with SingleCpuIO): tested in all verif. exp.
468    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
469      affects the results (but none of the verification test uses this scheme).
470    o Adding some pkg/diagnostics capability to pkg/seaice
471      (will certainly be subject to changes)
472    o ctrl: adding new control variables:
473      lwflux, lwdown, evap, snowprecip, apressure, runoff
474    
475    checkpoint58q_post
476    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
477      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
478      high_res_cube configuration by 4% on Columbia.
479    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
480      add (in global_with_exf/code) a version of EXF_INTERP_READ without
481      dynamical allocation (seems to work in multi-threaded).
482    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
483      single CPU io) so that TAF does not have to see EESUPPORT.h
484    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
485    
486    checkpoint58p_post
487    o obcs: stop if obcs is used with useCDscheme = .true.
488    o shelfice:
489     - fix a sign error so that no slip at shelfice interface works
490     - remove stop for combination non-hydrostatic code and shelfice. That does
491       not mean, that the results are correct, but at least they are numerically
492       stable
493    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
494    o added adjoint exch routined for all exch*3d* routines
495      and updated flow directives
496    
497    checkpoint58o_post
498    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
499      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
500    o change controling S/R for writing pickup file (new S/R do_write_pickup)
501      and clean-up reading/writing of pickup files.
502    o fix local version of read/write pickup (NH part) in rotating_tank/code
503    o simplify EXCH interface:
504     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
505     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
506    o added the regrid package
507    o shelfice:
508     - add a simple boundary layer scheme to reduce noise
509     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
510    
511    checkpoint58n_post
512    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
513       local variable (not in common block).
514    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
515      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
516      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
517        to work with SingleCpuIO.
518    o add "_d 0" to real constant of pkg/cfc subroutines ;
519       update exp. cfc_exemple & tutorial_cfc_offline output files.
520    o multi-threading and IO:
521      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
522        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
523      - barrier before and after reading.
524      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
525      - avoid using MDS_WRITELOCAL for LAND pkg output.
526      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
527        common-block variables ; Allows multi-threading with master-thread IO.
528    o change default MAX_NO_THREADS from 32 to 4 ;
529      and stop cleanly when MAX_NO_THREADS is too small.
530    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
531    
532    checkpoint58m_post
533    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
534       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
535    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
536       keep global_ocean.90x40x15 (for AD testing) with former secondary test
537       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
538    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
539        add MITgcm_tutorials (= code + all the tutorials)
540    o ecco, option to compute cost for total ssh (mean+anom)
541    o consistent with addition of ptracer and ssh in pkg/profiles
542    o profiles: adding ptracer and ssh
543    o testreport: change multi-test output-file name
544      (from output.txt.{name} to output.{name}.txt)
545    o profiles: now ok for mutli-tiles case
546    o seaice: add 4 parameters for different advection schemes for area,
547      (effective) seaice thickness, enthalphy, and snow height. Their default
548      is the standard parameter SEAICEadvScheme
549    o calc_gw:
550     - add cosFacU in zonal viscous flux (harmonic.visc.).
551     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
552       of tutorial_plume_on_slope.
553    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
554    o calc_gw: true flux-form, account for horizontal grid spacing.
555      update rotating_tank results, but not plume_on_slope (affected at
556      truncation level, 11 digits).
557    
558    checkpoint58l_post
559    o calc_gw:
560     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
561     - remove side-drag for now (need to fix it); update plume_on_slope results.
562     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
563    o commit code to make SST/SSS weights spatially variable
564      (based on either variable in-situ or variable initial T/S weights)
565    o pkg/ecco:
566      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
567        now based on horizontally varying weights wthetaLev, wsaltLev
568      * cost_averagesflags now returns year indices in addition to day, month
569      * sflux balance is performed on annual basis
570        (sflxumm, sfluxmm2, bal_sfluxmm)
571      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
572        including separate counting and multipliers
573    o pkg/rbcs
574      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
575    
576    checkpoint58k_post
577    o testreport:
578     - always build in dir. "build" (if not there, mkdir build instead of building
579       & running in input)
580     - run in dir run (if it exists), in build otherwise.
581     - call prepare_run (if input/prepare_run exists)
582     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
583    o pkg/exf modifications to interpolation and rotation routines for more
584       reasonable treatment of North Pole singularity: for tracers North Pole
585       value is set to northernmost zonal-mean value, for zonal velocity it is
586       set to zero, and for meridional velocity it is set to northernmost value.
587    o pkg/exf/exf_check_range.F
588     - add tile index to diagnostics and move stop statement to the very
589       end of the routine.
590    o pkg/diagnostics: (diagnostics_main_init.F)
591      define title of isomorphic variables according to the current config.
592    o pkg/thsice with pkg/seaice dynamics:
593    - fix domain of computation (interior only, required for exf) and do exchanges
594    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
595    o towards a standard way of dealing with multi-threading in MONITOR
596      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
597    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
598       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
599    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
600    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
601    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
602       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
603    o tracer advection:
604     - clean-up and simplify calc_common_factors.F
605     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
606       advection subroutine (but still not used within DST advection S/R)
607    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
608    
609    checkpoint58j_post
610    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
611      from file (collects calls previously in FORWARD_STEP)
612    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
613    o adjoint store dir. adjusted accordingly
614    o genmake2
615      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
616    
617    checkpoint58i_post
618    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
619      on wind stress (SEAICEstressFactor defaults to 1.)
620    o Total number of Timers is finite (<=40): comment out 2 non-essential one
621      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
622    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
623      on CS-grid: no longer loosing mass.
624    o exf & curvilinear-grid: no longer modify longitude xC & xG.
625    o pkg/ggl90: fix sloppy output and fix a bug
626    o pkg/seaice: added SEAICEuseEVPpickup parameter
627      - Set to false in order to start EVP solver with
628        non-EVP pickup files when using SEAICEuseEVP
629      - fix sign error in diffusion in seaice_calc_rhs
630    
631    checkpoint58h_post
632    * Modifications for bottom topography control
633      o replace hFacC by _hFacC at various places
634      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
635      o add non-self-adjoint cg2d_nsa
636      o update autodiff support routines
637      o re-initialise hfac after ctrl_depth_ini
638      o works for 5x5 box, doesnt work for global_ocean.90x40x15
639    * Adding verification for 5x5 box (4-layer) bottom topography control
640    
641    checkpoint58g_post
642    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
643       used for mean seasonal cycle, mean diurnal cycle); add an example
644       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
645    o pkg/ggl90:
646      - add parameter (minimum surface kinetic energy)
647      - fix bug (avoiding division by zero)
648    o couple pkg/thsice to pkg/seaice:
649      - modify advection in seaice to accomodate new scalar fields to be advected
650      - only muliDimAdection scheme work with seaice/thsice
651      - mapping of thsice-variables to seaice-variables, back and forth
652      - does not break the verification experiments, but does not give the
653        desired results either
654    o pkg/seaice
655      - make (default) second order advection a bit less confusing?
656    
657    checkpoint58f_post
658    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
659      to pkg/seaice):
660      - new routines thsice_map_exf and thsice_get_exf provide the interface
661      - add an additional formal parameter to thsice_solve4temp
662    o pkg/exf:
663      - add new fields wspeed, snowprecip (to be able to couple to thsice)
664      - correct Stefan-Boltzmann constant
665      - new parameter for longwave surface emittance
666      - separate some stuff from exf_bulkformulae into new routines  
667        exf_radiation, exf_wind
668      - add new parameters and constants: longwave emissivity for ocean, ice
669        and snow, evaporation parameters over ice
670      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
671        either wind from stress or stress from wind
672    o pkg/thSIce:
673    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
674    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
675       and THSICE_CALC_THICKN
676    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
677    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
678      to make debugging easier.
679    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
680    o pkg/bulk_force:
681      - clean-up comments and parameters ;
682      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
683    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
684      generate new output for test-experiment: aim.5l_cs.thSI
685    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
686      testreport accordingly
687    
688    checkpoint58e_post
689    o SEAICE_CGRID adjoint done
690    o R_STAR adjoint implemented.
691      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
692      * need to sort out init. of h0facc, etc.
693    o Make pkg/profile fully independent of ecco,cost, etc. stuff
694      to be able to use it in pure forward.
695    
696    checkpoint58d_post
697    o upgrade simple test-experiment to tutorial example:
698     step.1: duplicate the experiment and (step.2) will remove the old copy.
699      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
700      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
701      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
702      tutorial_global_oce_biogeo    <- copy of dic_example
703      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
704      tutorial_plume_on_slope       <- copy of plume_on_slope
705      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
706      tutorial_global_oce_optim     <- empty for now (David ?)
707      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
708     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
709    o correct a sign problem in cost_scat.F
710    o obcs and ptracers: fix boundary conditions for advections schemes
711      with larger stencil
712    o thsice adjoint: start
713    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
714      completeness
715    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
716      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
717    o ptracers adjoint:
718      * avoid extensive recomputatations
719      * fix missing re-init. of gptr (missed by TAF)
720    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
721      me to turn off the excessive output to STDOUT that this package produces
722    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
723      and add those terms in Vector-Invariant formulation.
724    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
725      if the control period (xx_hfluxperiod etc) is 0
726    o in profiles pkg, clean routines and fix details
727    o in ecco pkg, reading ssh data:
728      fix problem in case the model does not start at iter0=0
729    o fix mnc-pickup/restart for ptracers
730    o new package prifiles:
731      code to compute profile-based cost by Gael Forget
732      (modifs in ecco, ctrl, autodiff)
733    o Benign bug fix in initialization (spotted by M. Mazloff) of
734      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
735    
736    checkpoint58c_post
737    o adjoint: finish NLFS adjoint and provide reference output in
738      verification/global_ocean.90x40x15/results_ad_nlfs
739    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
740      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
741      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
742      with SEAICE_CGRID defined.
743    o move calendarDumps from "data" to "data.cal" and clean-up the code
744      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
745    o add useEXF & useCAL flags (for now, set in hard-coded way)
746    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
747      (were missing in NH mode, and wrong in quasihydrostatic mode).
748      waiting for Chris updated version of calc_gw to add those CALLs.
749    o fix bug in quasihydrostatic S/R ;
750      add a test for this option: global_ocean.90x40x15.qshyd
751    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
752      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
753    o add on/off flag useOffLine for package OFFLINE
754    o seaice:
755      - modify advection so that it works also on the C-grid
756      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
757        problem in multi-tile runs with C-grid
758      - add flags for clipping ice velocities and/or masking solver forcing
759      - fix drag (ocean on ice) formulation and a bug that caused noise in the
760        C-grid solver
761      - added a few comments to seaice_diffusion.F
762      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
763        are now exclusive)
764      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
765        required re-ordering the code a little:
766       + make DAIRN global variable (defined in SEAICE)
767       + move computation of the viscosities eta and zeta into a new separate
768         routine (because I need to recompute them in seaice_ocean_stress.F)
769    
770    checkpoint58b_post
771    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
772      update output.txt of exp. aim.5l_cs.thSI
773    o various mnc cleanups and improvements:
774      + shrink lookup tables by factor of ~4
775      + better error reporting when running out of lookup space
776      + able to handle longer path/file names (up to 500 chars)
777    o adjoint:
778      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
779      - TBD: "hidden" mom_vecinv recomp. in dynamics
780    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
781     (allow to differentiate between forcing components using new integer flags:
782      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
783     and add new flag to put Dissipation tendency out of Adams-Bashforth.
784    o ecco
785      - enable trend removal from SSH anomaly obs.
786    o adjoint
787      - a fix for PmEpR when #undef EXACT_CONSERV
788      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
789      - try to fix "hidden" recomp. in forward_step for NLFS
790        (NLFS seems broken sometimes after I checked it in)
791    o seaice:
792     - add c-grid version of the dynamic solver:
793       + three new routines that are the c-grid substitute lsr, dynsolver
794         and ostres
795       + put a few fields that were local to dynsolver into global common
796         blocks, so that I can move the computation of stresses etc into
797         seaice_lsr (saves coding but may break the adjoint).
798     - replace more hardwired parameters by runtime parameters
799     - add ice masks that mask the rhs of the implicit solvers where there
800       is no ice (commented out in seaice_dynsolver, because i am not sure
801       if this works properly), eventually this should replace the clipping
802       of ice velocities in seaice_dynsolver to +/-40cm/s.
803    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
804      include it only where its needed
805    o move balancing of fluxes before the call of external_forcing_surf
806    o seaice:
807      - correct units of turning angles (now they are really in degrees)
808      - move computation of GWATX/Y out of main routine into dynsolver
809      - initialize GWATX/Y in seaice_init
810    o Apply mask on Fresh-Water flux (needed for SSH forcing).
811      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
812    o seaice: add runtime flags for turning angles (default to zero)
813    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
814      and trend from exf forcing and ctrl control adjustments
815    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
816      (since checkpoint57x_post)
817    o change the default rotation period to 86164.s = the Earth rotation
818    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
819      and based on a reference stratification. Tested within hs94.cs-32x32x5.
820    o seaice advection: add code for choosing between the default (2nd order
821      central differences) and multiDim advection schemes provided by
822      pkg/generic_advdiff
823    o seaice:
824      - removed all references to SEAICE_GRID.h fields from
825        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
826        (cubed-sphere configuration will change a little)
827      - grid computations in seaice_init are obsolete now.
828      - cleaned up code a little so that is easier to read (hopefully).
829      - added new (better?) discretizations of default advection and diffusion
830        (turn on with SEAICEuseFluxForm)
831      - replace 1 in 3d global fields by kSurface in growth.F
832      
833    checkpoint58a_post
834    o seaice:
835      - bug fix in advect.F
836    o shelfice:
837      - separate shelfice load anomaly from pload (breaks with time
838        dependent forcing), => introduce constant field shelficeLoadAnomaly.
839        Its default is 0., but it may be computed more cleverly from (unknown)
840        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
841        done offline. A good approximation of the pressure load anomaly is
842        necessary to avoid large initial adjustment processes underneath
843        deep-reaching shelfice.
844      - small fix in ISOMIP shelfice_thermodynamics
845      - add more sophisticated thermodynamics of Hellmer (1989), this is
846        now the default
847      - give a few constants more intuitive names
848    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
849      if bulk formulae are used in long integration (especially EmPmR). Turn
850      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
851      if balancePrintMean, the imbalance that is substracted is printed to
852      STDOUT.
853    o fix bug (typo) in obcs_apply_eta.F
854    o add a new package shelfice which enables us to model the circulation
855      underneath shelf-ice with draughts of hundreds of meters.
856     - works
857     - to do: + include improved thermodynamics
858              + check whether kSurfC (from model/inc/SURFACE.h) can be used
859                instead of new field kTopC
860              + can we use topoFile, Ro_surf and existing code in ini_depth.F
861                instead of new field R_shelfIce and new code in ini_depth.F
862                and ini_mask_etc.F?
863              + adjust vertical mixing schemes?
864    o seaice pkg:
865     - add a cpp-flag to include a simple formula for a salinity dependent
866       freezing point of sea water at the surface
867     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
868       meridional stresses are now different (and hopefully correct)
869    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
870       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
871       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
872    o pkg/diagnostics: add options and parameters for regional-statistics
873       diagnostics ; define regions by reading a region-mask from a file
874       (might add other options later)
875    o pkg/bulk_force:
876     - add option and parameters to use AIM surface-flux formulae.
877     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
878       others forcing fields (defined in PARM05, parameter file "data") are loaded
879       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
880     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
881     - use the right EXCH call for uwind,vwind (to work on CS-grid).
882     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
883       and parameters (note: calcWindStress replaces .NOT.readwindstress).
884     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
885    
886    checkpoint58
887    o add "--embed-source" option to genmake2 which, when the supporting
888      tools can be compiled (as determined by genmake2) will turn on the
889      embed_files package which then embeds the entire MITgcm source code
890      (*.[fFhc] + Makefile) used for the build within the executable
891      - requested by CNH but off by default
892      - adds a paltry <9MB to the mitgcmuv executable in most cases
893      - only writes the output when useEMBEDSRC in eedata is true
894    o clean up 3-dim. relaxation codes:
895      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
896      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
897      * Thanks to Tom Haine for testing!
898    
899    checkpoint57z_post
900    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
901      affects output (@ truncation level) of exp. plume_on_slope ; updated.
902    o fix the pickup behavior for obcs in combination with ptracers
903    o fix a bug in ptracers_external_fields_load
904    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
905      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
906    o transfered surface NH pressure to eta field (if exactConserv).
907    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
908         and update lab_sea output.txt file.
909    o completing 3-dim. relaxation code: additional term
910         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
911      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
912      * At compile time, in "EXF_OPTIONS.h" set
913          #define  ALLOW_CLIMTEMP_RELAXATION
914          #define  ALLOW_CLIMSALT_RELAXATION
915      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
916          tauThetaClimRelax3Dim = 15552000.0,
917          tauSaltClimRelax3Dim  = 15552000.0,
918      * 3 cases:
919          1) Use a constant-in-time 3-dim. field
920          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
921          3) Real-time relax. to time-evolving prescribed field
922    o Adding Laplacian-type smoothness constraint on
923      initial and boundary (forcing) controls (ic, bc)
924      * enable at compile-time via
925        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
926      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
927      * Absolute scale somewhat unclear so far
928      * no area weighting was included since no other cost term does so far
929    
930    checkpoint57y_post
931    First step for a NLFS adjoint
932    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
933    o new init. routines for calc_r_star, calc_surf_dr
934    o still need to deal with ini_masks_etc
935    o testreport seemed happy
936    checkpoint57y_pre
937    
938    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
939    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
940    o add new offset feature to offline pkg (plus minor cleanup)
941    o cfc fixes for final year of integration
942    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
943      be in GCHEM_OPTIONS).
944    
945    checkpoint57x_post
946    o fix testreport Pb in multiple test experiment.
947    o cleanup our namelist syntax in verification:
948      - make it more F95 standards compliant (some work still needed)
949      - allows the vast majority of our tests to work with gfortran
950    o Non-Hydrostatic:
951     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
952     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
953    o Allow to apply AB on T,S rather than on AB(gT,gS):
954     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
955     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
956       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
957     - need a "clever" read_pickup to restart from the other AB formulation
958    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
959    o remove some unused variables (reduces number of compiler warnings)
960    o adjoint
961      * Disable useVariableViscosity for adjoint for time being
962        (there are a number of extensive recomputations)
963      * Initialize certain variables needed for adjoint
964    
965    checkpoint57w_post
966    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
967                 fix the singleCpuIO RS version of MDSWRITEFIELD
968       and add a WARNING if using globalFiles=T with multi-processors.
969    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
970      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
971    o tracer advection scheme:
972      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
973       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
974       was not very convenient).
975      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
976       (further tests needed for the implicit DST & Flux-Limiter schemes).
977    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
978      and sRef for convenience, handy, when you want to initialize
979      ptracers in a large domain with a constant non-zero value. Also,
980      untangle ptracers_init.F a little.
981    
982    checkpoint57v_post
983    o change dome exp. to use variable viscosity in side-drag terms.
984    o remove all the files from the cfc_offline test since they are now
985      incorporated into tutorial_cfc_offline which has been producing
986      identical results for a few days of testing
987    o add new parameter: sideDragFactor to enable half-slip-side BC
988      and change side-drag S/R to use viscosity from mom_calc_visc
989      (can switch back by setting sideDragFactor=0.); affects results at
990      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
991       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
992    o vorticity & strain are now computed without masking, to account for
993      no-slip-side BC in variable viscosity calculation ; mask is applied
994      anyway later on, before computing advection/coriolis terms.
995    o modify exp4 to test new obcs support for reading from external files
996      and for passive tracers
997    o fix behavior of ptracers_monitor when monitor output is written to a
998      netcdf-file; still not independent of monitor.F (writes in the same
999      file).
1000    o change default value of tRef (put a uniform, meaningful value for ocean
1001      & atmos) and initialize sRef (was missing, as Martin mentioned).
1002    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
1003      to be proportional to enstrophy dissipation length.  Thus,
1004       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
1005      This is now consistent with Smagorinsky and with the manual.
1006    
1007    checkpoint57u_post
1008    o OBCS and PTRACERS: add open boundary support for passive tracers
1009      - either use homogenous (pseudo) v.Neumann conditions or prescribe
1010        OB-values from file; this is not different from the way theta and salinity
1011        are treated
1012      - however, Orlanski-radiation conditions are not supported, and the model
1013        will stop if you use pTracers and Orlanski at the same time.
1014      - beefed up the rountine obcs_external_fields_load: now only those open
1015        boundary values are overwritten with values from files for which there
1016        are really files, otherwise the OB-fields remain untouched. This makes
1017        it possible to use different OBs at different ends of the domain (as
1018        with EXF)
1019    o reduce number of exch calls in shap_filt (s2).
1020    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1021      truncation level) 4/5 MLAdjust test results (11&12 digits match).
1022    
1023    checkpoint57t_post
1024    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1025    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1026      same truncation, independent of the face number: affects affects several
1027      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1028    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1029      note that biharmonic viscosity + no-slip was not tested in any experiment.
1030    o fix bug in non-linear free-surf side-drag ; generate new output for
1031      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1032    o make mnc honor the writeBinaryPrec flag for most kinds of output
1033    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1034    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1035      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1036    o add brackets in multi-terms sum to get same truncation, independent of
1037      the face number (manage to get exactly same value of gU,gV at the cs-edge)
1038      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1039    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
1040      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1041      a maximum grid-scale Reynolds number.  Also, changes all length calculations
1042      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1043      Suggested values of viscosity parameters found in mom_calc_visc.
1044      Many new viscosity diagnostics available.
1045    
1046    checkpoint57s_post
1047    o Add clearing-house for viscosity calculations, mom_calc_visc and
1048      correct numerous bugs in LeithD and Smagorinsky discretizations.  
1049      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1050      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1051      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1052      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
1053      The Strain-Tension form is now called with useStrainTensonVisc=.true.
1054      ViscAhStrain and viscAhTension are now retired.
1055    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1056    o In response to JMC's bug report, genmake2 now ignores any soft-links
1057      that it finds in the *current* directory when searching for files.
1058      Soft-links found in any other source directories will still work as
1059      they did before.
1060    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1061      a C routine to unlimit the stack size
1062    o mnc-ify pkg/aim snapshot vars
1063    o mnc-ify pkg/land as requested by Daniel
1064    o various changes to mnc including:
1065      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1066      - output can now be grouped so that all files within a group
1067          change the ITER portion of their names in lock-step together
1068      - can now read ("global") PER-FACE (in addition to PER-TILE) files
1069          and works with both EXCH1 and EXCH2 (but needs more testing)
1070      - writing works for all verification test cases w/ g77 on Linux
1071    
1072    checkpoint57r_post
1073    o make MNC variable initialization happen earlier
1074    o add diagnostics for (almost) each term of the momentum Eq.
1075    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1076    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1077    o remove MINIMAL_TAVE_OUTPUT option ;
1078      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1079    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1080      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1081    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1082    o add time-dependent SST, SSS control
1083    o cost terms in ecco/ modularized (new cost_generic.F)
1084    o cost_averages routines are modularized (new cost_averagesgeneric.F)
1085    o new infrastructure for seaice model vs. obs misfits in seaice/
1086      * driver from the_main_loop.F is seaice_cost_driver.F
1087      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1088      * gradient check in Exp. 6a of natl_box_adjoint/
1089    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1090      (see README file)
1091    
1092    checkpoint57q_post
1093    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1094    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1095      - bug was reported by Jean-Michel and Ian Fenty
1096    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1097      update exp. cpl_aim+ocn output.
1098    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1099      Needed for high-res. runs with large global files
1100      to be able to limit tapelev size
1101    o Changed some tests for adjoint:
1102      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1103      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1104      * global_ocean.90x40x15/ back to default 3-level checkpointing
1105    o Modifications to enable scripted COMMON to MODULE conversion
1106      * verification/OpenAD/code/ has necessary scripts and description;
1107      * converts, compiles and runs successfully;
1108    
1109    checkpoint57p_post
1110    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1111    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1112      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1113    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1114    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1115      (was already the case for dissipation with mom_vecinv,
1116       and also the case for grad.PhiHyd when staggered-timeStep)
1117      This will allow to put dissipation out-off the AB time-stepping.
1118     Unfortunately, affects truncation error. Update output of exp. that "fails"
1119      (cg2d matching number) and leave the others for later: front_relax(10),
1120      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1121      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1122    
1123    checkpoint57o_post
1124    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1125      (2) its ready to be documented during the 20050801 DocFest
1126    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1127      for ideal_2D_oce and lab_sea on linux_ia32_g77
1128    o set to #undef CTRL_SET_OLD_MAXCVARS_30
1129      in global1x1_tot/code_seaice_adj to access indices 32, 33
1130      (worth another tag)
1131    
1132    checkpoint57n_post
1133    o adding precip control xx_precip 32
1134    o adding swflux control xx_swflux 33
1135    o Replacing 10 forcing penalty cost routines by 1 generic.
1136    o Implementing partitioning in time-mean and variable adjustment
1137      for atmos. state.
1138    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1139  o in natl_box_adjoint:  o in natl_box_adjoint:
1140    * updated: results_bulk/    * updated exp 1 to 10
1141    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
1142    o updated global1x1/*_seaice_adj/
1143      to incorporate latest changes
1144    o enable useSingleCpuIO for mdsio vector routines
1145      (applies in particular to tapelev I/O)
1146    o removed inefficient K-loop in all active_file*control*.F
1147    
1148  checkpoint57m_post  checkpoint57m_post
1149  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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