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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.871 by dimitri, Fri Sep 14 02:07:37 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 pkg/seaice: changes for using pkg/seaice with pkg/obcs
8  o moved ptracer ctrl index 17 -> 32  o pkg/ecco: allow user defined cost function contributions
9    o testreport:
10      Allow to choose (per experiment) the list of tested output variables
11       and the main variable (used to issue a pass/FAIL ) ;
12      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
13      - default is unchange: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
14      Also modify printing of summary:
15       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
16       b) echo the list of tested variables in the individual summary.txt of
17          each experiment.
18    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
19      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
20      (but still depend on the tile decompostion of the domain).
21    o pkg/seaice: change a discretization detail to make the B-grid code
22      "more symmetric". This change is likely to remove all "ridges/leads" that
23      where quasi-aligned with the grid in B-grid solutions. It may also be
24      the solution to the stress coupling issues with the B-grid.
25    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
26      remove .cvsignore from input dir. (since testreport no longer run here).
27    o pkg/thsice:
28     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
29     - fix reshaping of sea-ice just after advection:
30       melt all the ice only if ice-volume is too small.
31     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
32       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
33     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
34    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
35      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
36    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
37      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
38      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
39      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
40      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
41      -> update output.txt
42    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
43     this affects truncation error: -> update output.txt of exp:
44      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
45      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
46    
47    checkpoint59f
48    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
49    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
50      a bounded range (in forward mode)
51    o pkg/ecco, ctrl, autodiff and mom_common:
52     internal parameter controls, completements of implementations
53    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
54    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
55      (not seem any difference in testing results).
56    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
57       at face corners.
58    o pkg/generic_advdiff:
59     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
60      loop range indices for computing vertical advection tendency
61      and do the calculation in the interior only (no overlap) ;
62      for now, only implemented for SOM advection (to save CPU time).
63     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
64    o exch2 adjoint
65      First set of changes:
66      - add exch2 hand-written adjoint templates
67      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
68        This will require cleanup in pkg/autodiff/*.F
69        (changed routines currently kept separate in verif. code/)
70      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
71        that used to hide exch2 or cubed-sphere specific code
72        (commented via 'cph-exch2')
73    o pkg/seaice
74      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
75    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
76       output of global_ocean.cs32x15.thsice .
77    
78    checkpoint59e
79    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
80      for B-grid vector (not yet tested) and C-grid vector (<- only used
81      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
82    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
83      (#ifdef ALLOW_SALT_PLUME)
84    o gather_2d/scatter_2d: removed halo regions
85    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
86      scheme and the corresponding test case (under front_relax dir). For now,
87      only available with Skew-flux form and not yet tested in realistic set-up.
88      adjoint: store directives updated, but gradient checks deteriorated,
89      so maybe GM/Redi adjoint is now broken.
90    o seaice adjoint
91      * add AREA, HEFF, HSNOW as control variable
92        (should not change lab_sea results)
93      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
94    o pkg/seaice:
95      * added computation of saltFlux in seaice_growth;
96        For time being, sea ice salinity is assumed constant
97        contribution of snow flooding to freshening of sea ice is neglected.
98        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
99        defaults to 0.0 in order to maintain backward compatibility.
100        Typical values for SEAICE_salinity are 4 to 10 g/kg.
101      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
102      * added SEAICE_availHeatFrac, which specifies fraction of surface level
103        heat content used to melt or grow ice
104      * commented out cap of HICE: it helps keep ice thinner
105      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
106      * applied OBCS T/S mask to HEFFM sea ice mask
107    
108    checkpoint59d
109    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
110     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
111     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
112    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
113     and change default value of parameter "GM_Small_Number";
114     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
115       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
116       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
117    o pkg/ecco: cost function when applying pkg/smooth to controls
118    o pkg/ctrl: add forcingPrecond run time parameter
119    o pkg/seaice:
120     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
121     - fix bug in metric terms of u-equation in LSR solver (implicit part),
122       changes verification/lab_sea
123     - rearrange implicit part of u-equation in LSR solver to make it easier to
124       read, understand, and debug. This causes changes at the truncation level.
125     - fix (serious) bug in the boundary conditions (sign error in the implicit
126       part) of the LSR solver. Changes all LSR results.
127     - fixed problem with HSNOW initialization to avoid thick snow when AREA
128       is initilized with small values - does not change lab_sea results.
129     - added HsnowFile initialization capability
130    o pkg/smooth: addition to model/src and pkg/ctrl so allow
131     initialization of pkg/smooth and application to control vector
132    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
133    o dependencies: pkg/profiles requires pkg/cal
134    o pkg/profiles:
135     - added option ALLOW_PROFILES_GENERICGRID
136         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
137         that interpolation information (grid points and coefficients) is provided
138         within the netcdf input files.
139         -> sample matlab scripts can be found in MITgcm_contrib/gael
140         that allow you to prepare netcdf input files.
141     - also modified: cleaner include statements, cleaner error print statements,
142       cleaner stops when error, and more tests of the netcdf input files consistency.
143    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
144    o pkg/seaice:
145     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
146       requires a new routine: seaice_diagnostics_fill.F
147     - make sure that seaice does not move if not forced (pressure replacement
148       method, Hibler and Ip, 1995), changes results
149     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
150     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
151       It is turned off by default (=-1.), because it changes the results.
152     - make it possible to read AREA from a file, too.
153    
154    checkpoint59c
155    o add S/R and diagnostics for oceanic mixed-layer depth
156    o move GMRedi call after all vertical mixing schemes (including KPP)
157    o pkg/thsice:
158     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
159      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
160    o pkg/obcs:
161     - bug fix for balance code
162    o pkg/seaice:
163      - allow values of SEAICE_elasticParm > 1
164      - add new parameter SEAICE_evpTauRelax as an alternative
165        to SEAICE_elasticParm
166      - make lsr boundary conditions free slip (by default), changes result
167      - add code for no slip boundary conditions for lsr
168      - set minimum of zeta to zero (and not 4e8) (changes results)
169      - add a cap on AREA after advecting AREA if seaice_growth is not called
170    o change calculation of Visbeck K:
171      - no longer depend on tapering scheme; instead, compute slope (limited
172        by GM_maxSlope). this is equivalent to what was comuted before with
173        clipping or linear tappering.
174      - fix vertical averaging (wrong by 1/2 level)
175      - leave the old version (but will not be maintained) within
176        #ifdef OLD_VISBECK_CALC / #endif
177      - update output of exp. ideal_2D_oce
178    o change error catch in calc_r_star to improve vectorization
179    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
180      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
181    o adjoint:
182      Re-organized adjoint checkpointing according to Matt Mazloff
183      (but with modifs/completions/cleanups)
184      Storing is now bundled into large arrays to optimized I/O
185      (and second step in cleanup of the_main_loop)
186    
187    checkpoint59b
188    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
189      - export/import (between ocean & coupler) fields needed for ocean DIC.
190    o pkg/seaice:
191      - get rid of three more exchanges seaice_calc_viscosities (required
192        different loop boundaries in seaice_lsr and seaice_ocean_stress)
193      - bug fix in seaice_ocean_stress (update of lab_sea required)
194      - reduce loop boundaries to necessary minimum also in seaice_evp
195      - go back to the old way of computing deltaC/Z as the adjoint likes that
196        better
197    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
198      passive tracer to an Age Tracer) + update output.txt
199    o pkg/exf:
200      - implement A-grid / C-grid selection for wind-stress input files.
201      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
202      for now, in exf_bulk_largeyeager04.F only :
203      - change implementation for case where windspeed + 2. components wind-stress
204        are read-in. AND use rhoConstFresh to convert evap.
205    o pkg/seaice:
206      - use correct EXCH_UV for wind-forcing (on A-grid).
207      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
208        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
209    o pkg/exf:
210      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
211      EXF_INTERPOLATION:
212      - merge global_with_exf/code version of exf_interp_read.F
213        to the main code ;
214      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
215        reading the file ; Important: This options needs to be defined to recover
216        previous code.
217        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
218      - no longer loose real*8 precision along the way when using exf_iprec=64.
219    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
220      - change discretisation of evp-solver in order to avoid another exchange
221        (changes lab_sea) and clean up a little
222      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
223        help the adjoint (this also changes the results slightly)
224      - add a few "_d 0" where they had been missing in seaice_evp.F
225      - cleaning up: remove unused seaice_calc_rhs.F
226    o pkg/exf: some cleaning-up:
227      - change various "constants" into runtime parameters
228      - cleaned-up Large&Yeager04 routine which should eventually
229        replace exf_bulkformulae.F (changed names of S/R and CPP)
230        and merged various ALLOW_ATM_WIND options
231     only used with thsice pkg (in thsice_get_exf.F):
232      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
233        which are used when useStabilityFct_overIce=TRUE (= the default)
234      - change default values of ice & snow emissivity and scale downward LW
235        by ice & snow emissivity.
236    o pkg/thsice:
237     fix few little problems, in thsice_calc_thickn.F:
238      - growth vertically (and not laterally) if iceFrac == iceMaskMax
239      - melt only laterally if hIce < hThinIce (as the comments say)
240      and in thsice_extend.F:
241      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
242      - start to form ice as soon as the minimum ice-volume is reachable.
243     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
244      and cpl_aim+ocn
245    o pkg/kpp
246     - move computation of surface related input fields to KPP into a new
247       subroutine kpp_forcing_surf.F
248     - remove wrong (within bi,bj loops) EXCH calls.
249     - little cleaning (add argument myThid in last position, cvs header ...)
250     - for now, fix conservation problem by exchanging KPPviscAz (may not
251       be the best fix)
252    o pkg/seaice
253     - check for inconsistent evp parameter/cpp-flag combination
254     - remove leftover errIO flat for obsolete name list error handling
255    o OpenAD
256     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
257    
258    checkpoint59a
259    o pkg/seaice: some parameter clarifications and a little bit of clean up
260    o pkg/thsice: rename run-time parameters:
261       himin       -> hIceMin
262       himin0      -> hThinIce
263       hihig       -> hThickIce
264       i0          -> i0swFrac
265       transCoef   -> bMeltCoef
266       frac_energy -> fracMelting
267      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
268       with default values (for now) that do not change the results.
269      remove old version of thsice vars advection in pkg/seaice.
270    o in FFIELDS.h:
271      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
272      - make pLoad & sIceLoad always available (but still only used if
273         ATMOSPHERIC_LOADING is #define).
274    o pkg/kpp: replaced _KPP_RL with _RL
275    o bug fixes for vertical diffusivity computations when both KPP and
276        3D diffusivity arrays are used.
277    o pkg/seaice: fix bug in evp solver, while doing that
278      - change (improve?) discretization of stress computations for both
279        cgrid-lsr and evp solver
280      - add a new routine to compute strain rates
281      - the above changes lab_sea results
282      - add no slip conditions for evp solver (off by default), lsr-version
283        may follow
284      - fix exchange for shear at Z-points (does not change lab_sea)
285      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
286        (to force the user to pick a time step since there is not "safe" way
287        of choosing it)
288      - add principal stress diagnostics
289      - rearrange fields for evp a little to avoid having to call a: too many
290        exchanges and b: exchanges for stress trensor components which we do
291        not have.
292      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
293        of evp, complete rewrite for lsr case (latter is does not yet work
294        in all cases)
295    o pkg/kpp: add code to have mixing in shelf ice caverns
296      - add myThid to all kpp routines (long overdue)
297    
298    checkpoint59
299    o pkg/exf:
300      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
301        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
302      - move exf header files from lower_case.h to UPPER_CASE.h ;
303        add missing cvs Header & Name
304      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
305      - add namelist param. selectStressGridPosition, exf_monFreq
306      - retire many _CLIM routines, and remove data.exf_clim
307        + params moved to data.exf
308        + climsst, climsss now handled by exf_set_gen, i.e.
309          climss?period=0 refers to constant field,
310          climss?period=-12 to monthly forcing
311      - split up namelists in data.exf
312    o pkg/seaice:
313      - remove seaice_exch and seaice_exch_uv
314      - remove superfluous exchange of theta
315      - add myThid to seaice_budget_ocean/ice
316      - add new interface for atmospheric wind forcing (C-grid only)
317        + new routine
318        + two new field (taux, tauy for stress over ice)
319        + removed one global field (DAIRN) for C-grid case only
320    o pkg/thsise
321      - 2nd set of modifs for thsice adjoint in conjunction with exf
322    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
323    
324    checkpoint58y_post
325    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
326      vertical diffusivity, similar to that in MOM4; turned on using
327      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
328      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
329    o Added capability for 3D specification of background vertical diffusion
330      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
331      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
332      "data" file that contains the 3D vertical diffusivity coefficients.
333    o ice dynamics (pkg/seaice) with thsice thermodynamics:
334      - add code within pkg thsice to advect & diffuse sea-ice fields
335      similar to (and will replace) what has been added in  seaice_advdiff.F,
336      but: - conserving Mass, Heat & Salt.
337           - better when using non-linear advection scheme (not yet fully tested)
338           - can also be used in atmospheric set-up (for now, only the diffusion).
339    
340    checkpoint58x_post
341    o IO option for global-file compact format:
342      - add options when generating topology (utils/exch2/matlab-topology-generator)
343      - add I/O capability (pkg/mdsio).
344      - adapt utils/matlab/rdmds.m to read this format.
345      for now long-line format not yet supported by pkg/mdsio (& exch2).
346    o shelfice: add a few diagnostics
347    
348    checkpoint58w_post
349    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
350      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
351      (and replace horiVertRatio in NH code).
352      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
353                         and tutorial_plume_on_slope (sensitive to truncation)
354    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
355      directly to drive seaice model (C-grid only)
356    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
357     - reintroduce computation of wind from stress,
358     - compute tau (in exf_bulkformulae.F) from windstress averaged to
359       mass points to avoid tau = 0
360     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
361    o rdmnc.m: make it work with "global" files created with gluemnc
362    o rdmnc.m : some improvements in dealing with singleton dimension
363      (tested on all testreport mnc output files).
364    o genmake2: disable pkg/profiles if netcdf test fails.
365    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
366    o move call to cal_readparms up to make calendar parameters/variable available
367      to all packages
368    
369    checkpoint58v_post
370    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
371      useDynP_inEos_Zc tested.
372    o pkg/exf: changes to properly interpolate/mask/scale initial fields
373    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
374      and portions thereof.  See read_cs.txt for description and examples.
375    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
376      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
377      following the great-circle arc between those 2 points.
378    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
379      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
380    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
381     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
382     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
383     - still needs work (not working with some options ; efficiency to improve)
384       and serious testing.
385     - use this scheme for temperature & salinity in 2 advection test exp.:
386       advect_xy & advect_xz, respectively.
387    
388    checkpoint58u_post
389    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
390    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
391    o testreport: add option "-skipdir" to skip some test.
392    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
393      momentum calculation.
394    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
395    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
396      remove checkpoint.F and the_correction_step.F (no longer used);
397      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
398    o add option (linFSConserveTr) to correct for tracer source/sink due to
399      Linear Free surface
400    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
401    o pkg/thsice: fix reading mnc-pickups
402    
403    checkpoint58t_post
404    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
405    o pkg/mdsio:
406     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
407       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
408       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
409     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
410     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
411       either MDS_READ_FIELD or MDS_WRITE_FIELD )
412     - new S/R (to replace MDSWRITEMETA), which allows to write more
413       informations (variable names, time ...) to meta files.
414     - modify rdmds.m to give back the meta file content.
415    o pkg/diagnostics: change vertical interpolation to be safer, and more
416       flexible (define p-levels to interpolate to in data.diagnostics);
417      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
418       diagnostic pointer.
419    o pkg/seaice: more cleaning up of seaice_growth, added many comments
420    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
421    o fix multi-category seaice:
422     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
423       SEAICE_MULTICATEGORY
424     - fix short wave heat flux
425    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
426       and allow to use EVP solver. Change forward lab_sea: test both EVP
427       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
428    o Initial check-in of lab_sea adjoint
429      (very similar to natl_box_adjoint/code_seaice)
430      * used C-grid and EVP solver
431      * used KPP, GM/Redi
432      * uses inAdExact=.TRUE.
433      * gradient checks fail for both ADM and TLM
434        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
435        f.d. gradients actually seem more problematic than ADM, TLM gradients;
436        issue is related to forward mismatch between g77 an ifort
437    o pkg/seaice: overhaul of thermodynamics
438     - growth.F and groatb.F are replaced by new routine seaice_growth.F
439     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
440     - move a few global fields out of SEAICE.h into seaice_growth.F and
441       make them 2D (FICE/QNETO/ ...)
442     - remove FO (it is the same as QNETO)
443     - introduce a few local fields to avoid modifying external fields such
444       as atemp, etc.
445    
446    checkpoint58s_post
447    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
448      changed exf_set_gen.F so that
449        genperiod=0 means input file is one time-constant field and
450        genperiod=-12 means input file contains 12 monthly means
451    o CG2D: use pre-computed solver main-diagonal (stored in common block);
452      this affects truncation error ; generate new output file for exp. which
453      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
454        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
455        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
456        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
457        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
458        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
459    o start implementation of deep-atmosphere and anelastic formulation
460    o verification: remove 2nd copy of input files and use script "prepare_run"
461      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
462    o mom_common/vecinv/fluxform: fix a few initialisation isssues
463    o profiles: fix for multithreaded case
464    
465    o diagnostics: rename few diags:
466      s/'PRESSURE'/'RCENTER '/g
467      s/'TICE    '/'oceFreez'/g
468      s/'TAUX    '/'oceTAUX '/g
469      s/'TAUY    '/'oceTAUY '/g
470      s/'SWFLUX  '/'oceQsw  '/g
471      s/DIFx/DFxE/g
472      s/DIFy/DFyE/g
473      and add few ocean-forcing diagnostics:
474      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
475    o modifications to pkg/seaice/growth.F and budget.F, which change results of
476      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
477      as actual snow thickness.  It now refers everywhere to effective snow
478      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
479    
480    checkpoint58r_post
481    o modifications to pkg/seaice/growth.F, which change results of
482      lab_sea experiment: fixes pertain to melting snow over open water, to
483      masking EVAP under sea ice, and to using the correct AREA variable for
484      computations of EVAP, PRECIP, HSNOW, and GHEFF
485    o add ability to read bathy, salt, and theta using MNC (off by def)
486    o add flooding algorithm and advection of HSNOW for pkg/seaice;
487      both are turned off by default and do no change any results
488    o seaice advection with pkg/thsice: a step toward the use of non-linear
489      advection scheme, but #ifdef or commented out for now (requires more EXCH).
490    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
491      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
492      in natl_box (affects results @ truncation level: update output.txt)
493    o multi-threading and IO:
494      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
495      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
496        (needed to work with SingleCpuIO): tested in all verif. exp.
497    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
498      affects the results (but none of the verification test uses this scheme).
499    o Adding some pkg/diagnostics capability to pkg/seaice
500      (will certainly be subject to changes)
501    o ctrl: adding new control variables:
502      lwflux, lwdown, evap, snowprecip, apressure, runoff
503    
504    checkpoint58q_post
505    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
506      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
507      high_res_cube configuration by 4% on Columbia.
508    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
509      add (in global_with_exf/code) a version of EXF_INTERP_READ without
510      dynamical allocation (seems to work in multi-threaded).
511    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
512      single CPU io) so that TAF does not have to see EESUPPORT.h
513    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
514    
515    checkpoint58p_post
516    o obcs: stop if obcs is used with useCDscheme = .true.
517    o shelfice:
518     - fix a sign error so that no slip at shelfice interface works
519     - remove stop for combination non-hydrostatic code and shelfice. That does
520       not mean, that the results are correct, but at least they are numerically
521       stable
522    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
523    o added adjoint exch routined for all exch*3d* routines
524      and updated flow directives
525    
526    checkpoint58o_post
527    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
528      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
529    o change controling S/R for writing pickup file (new S/R do_write_pickup)
530      and clean-up reading/writing of pickup files.
531    o fix local version of read/write pickup (NH part) in rotating_tank/code
532    o simplify EXCH interface:
533     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
534     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
535    o added the regrid package
536    o shelfice:
537     - add a simple boundary layer scheme to reduce noise
538     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
539    
540    checkpoint58n_post
541    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
542       local variable (not in common block).
543    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
544      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
545      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
546        to work with SingleCpuIO.
547    o add "_d 0" to real constant of pkg/cfc subroutines ;
548       update exp. cfc_exemple & tutorial_cfc_offline output files.
549    o multi-threading and IO:
550      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
551        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
552      - barrier before and after reading.
553      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
554      - avoid using MDS_WRITELOCAL for LAND pkg output.
555      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
556        common-block variables ; Allows multi-threading with master-thread IO.
557    o change default MAX_NO_THREADS from 32 to 4 ;
558      and stop cleanly when MAX_NO_THREADS is too small.
559    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
560    
561    checkpoint58m_post
562    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
563       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
564    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
565       keep global_ocean.90x40x15 (for AD testing) with former secondary test
566       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
567    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
568        add MITgcm_tutorials (= code + all the tutorials)
569    o ecco, option to compute cost for total ssh (mean+anom)
570    o consistent with addition of ptracer and ssh in pkg/profiles
571    o profiles: adding ptracer and ssh
572    o testreport: change multi-test output-file name
573      (from output.txt.{name} to output.{name}.txt)
574    o profiles: now ok for mutli-tiles case
575    o seaice: add 4 parameters for different advection schemes for area,
576      (effective) seaice thickness, enthalphy, and snow height. Their default
577      is the standard parameter SEAICEadvScheme
578    o calc_gw:
579     - add cosFacU in zonal viscous flux (harmonic.visc.).
580     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
581       of tutorial_plume_on_slope.
582    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
583    o calc_gw: true flux-form, account for horizontal grid spacing.
584      update rotating_tank results, but not plume_on_slope (affected at
585      truncation level, 11 digits).
586    
587    checkpoint58l_post
588    o calc_gw:
589     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
590     - remove side-drag for now (need to fix it); update plume_on_slope results.
591     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
592    o commit code to make SST/SSS weights spatially variable
593      (based on either variable in-situ or variable initial T/S weights)
594    o pkg/ecco:
595      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
596        now based on horizontally varying weights wthetaLev, wsaltLev
597      * cost_averagesflags now returns year indices in addition to day, month
598      * sflux balance is performed on annual basis
599        (sflxumm, sfluxmm2, bal_sfluxmm)
600      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
601        including separate counting and multipliers
602    o pkg/rbcs
603      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
604    
605    checkpoint58k_post
606    o testreport:
607     - always build in dir. "build" (if not there, mkdir build instead of building
608       & running in input)
609     - run in dir run (if it exists), in build otherwise.
610     - call prepare_run (if input/prepare_run exists)
611     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
612    o pkg/exf modifications to interpolation and rotation routines for more
613       reasonable treatment of North Pole singularity: for tracers North Pole
614       value is set to northernmost zonal-mean value, for zonal velocity it is
615       set to zero, and for meridional velocity it is set to northernmost value.
616    o pkg/exf/exf_check_range.F
617     - add tile index to diagnostics and move stop statement to the very
618       end of the routine.
619    o pkg/diagnostics: (diagnostics_main_init.F)
620      define title of isomorphic variables according to the current config.
621    o pkg/thsice with pkg/seaice dynamics:
622    - fix domain of computation (interior only, required for exf) and do exchanges
623    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
624    o towards a standard way of dealing with multi-threading in MONITOR
625      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
626    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
627       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
628    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
629    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
630    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
631       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
632    o tracer advection:
633     - clean-up and simplify calc_common_factors.F
634     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
635       advection subroutine (but still not used within DST advection S/R)
636    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
637    
638    checkpoint58j_post
639    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
640      from file (collects calls previously in FORWARD_STEP)
641    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
642    o adjoint store dir. adjusted accordingly
643    o genmake2
644      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
645    
646    checkpoint58i_post
647    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
648      on wind stress (SEAICEstressFactor defaults to 1.)
649    o Total number of Timers is finite (<=40): comment out 2 non-essential one
650      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
651    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
652      on CS-grid: no longer loosing mass.
653    o exf & curvilinear-grid: no longer modify longitude xC & xG.
654    o pkg/ggl90: fix sloppy output and fix a bug
655    o pkg/seaice: added SEAICEuseEVPpickup parameter
656      - Set to false in order to start EVP solver with
657        non-EVP pickup files when using SEAICEuseEVP
658      - fix sign error in diffusion in seaice_calc_rhs
659    
660    checkpoint58h_post
661    * Modifications for bottom topography control
662      o replace hFacC by _hFacC at various places
663      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
664      o add non-self-adjoint cg2d_nsa
665      o update autodiff support routines
666      o re-initialise hfac after ctrl_depth_ini
667      o works for 5x5 box, doesnt work for global_ocean.90x40x15
668    * Adding verification for 5x5 box (4-layer) bottom topography control
669    
670    checkpoint58g_post
671    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
672       used for mean seasonal cycle, mean diurnal cycle); add an example
673       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
674    o pkg/ggl90:
675      - add parameter (minimum surface kinetic energy)
676      - fix bug (avoiding division by zero)
677    o couple pkg/thsice to pkg/seaice:
678      - modify advection in seaice to accomodate new scalar fields to be advected
679      - only muliDimAdection scheme work with seaice/thsice
680      - mapping of thsice-variables to seaice-variables, back and forth
681      - does not break the verification experiments, but does not give the
682        desired results either
683    o pkg/seaice
684      - make (default) second order advection a bit less confusing?
685    
686    checkpoint58f_post
687    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
688      to pkg/seaice):
689      - new routines thsice_map_exf and thsice_get_exf provide the interface
690      - add an additional formal parameter to thsice_solve4temp
691    o pkg/exf:
692      - add new fields wspeed, snowprecip (to be able to couple to thsice)
693      - correct Stefan-Boltzmann constant
694      - new parameter for longwave surface emittance
695      - separate some stuff from exf_bulkformulae into new routines  
696        exf_radiation, exf_wind
697      - add new parameters and constants: longwave emissivity for ocean, ice
698        and snow, evaporation parameters over ice
699      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
700        either wind from stress or stress from wind
701    o pkg/thSIce:
702    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
703    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
704       and THSICE_CALC_THICKN
705    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
706    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
707      to make debugging easier.
708    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
709    o pkg/bulk_force:
710      - clean-up comments and parameters ;
711      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
712    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
713      generate new output for test-experiment: aim.5l_cs.thSI
714    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
715      testreport accordingly
716    
717    checkpoint58e_post
718    o SEAICE_CGRID adjoint done
719    o R_STAR adjoint implemented.
720      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
721      * need to sort out init. of h0facc, etc.
722    o Make pkg/profile fully independent of ecco,cost, etc. stuff
723      to be able to use it in pure forward.
724    
725    checkpoint58d_post
726    o upgrade simple test-experiment to tutorial example:
727     step.1: duplicate the experiment and (step.2) will remove the old copy.
728      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
729      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
730      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
731      tutorial_global_oce_biogeo    <- copy of dic_example
732      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
733      tutorial_plume_on_slope       <- copy of plume_on_slope
734      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
735      tutorial_global_oce_optim     <- empty for now (David ?)
736      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
737     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
738    o correct a sign problem in cost_scat.F
739    o obcs and ptracers: fix boundary conditions for advections schemes
740      with larger stencil
741    o thsice adjoint: start
742    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
743      completeness
744    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
745      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
746    o ptracers adjoint:
747      * avoid extensive recomputatations
748      * fix missing re-init. of gptr (missed by TAF)
749    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
750      me to turn off the excessive output to STDOUT that this package produces
751    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
752      and add those terms in Vector-Invariant formulation.
753    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
754      if the control period (xx_hfluxperiod etc) is 0
755    o in profiles pkg, clean routines and fix details
756    o in ecco pkg, reading ssh data:
757      fix problem in case the model does not start at iter0=0
758    o fix mnc-pickup/restart for ptracers
759    o new package prifiles:
760      code to compute profile-based cost by Gael Forget
761      (modifs in ecco, ctrl, autodiff)
762    o Benign bug fix in initialization (spotted by M. Mazloff) of
763      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
764    
765    checkpoint58c_post
766    o adjoint: finish NLFS adjoint and provide reference output in
767      verification/global_ocean.90x40x15/results_ad_nlfs
768    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
769      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
770      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
771      with SEAICE_CGRID defined.
772    o move calendarDumps from "data" to "data.cal" and clean-up the code
773      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
774    o add useEXF & useCAL flags (for now, set in hard-coded way)
775    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
776      (were missing in NH mode, and wrong in quasihydrostatic mode).
777      waiting for Chris updated version of calc_gw to add those CALLs.
778    o fix bug in quasihydrostatic S/R ;
779      add a test for this option: global_ocean.90x40x15.qshyd
780    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
781      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
782    o add on/off flag useOffLine for package OFFLINE
783    o seaice:
784      - modify advection so that it works also on the C-grid
785      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
786        problem in multi-tile runs with C-grid
787      - add flags for clipping ice velocities and/or masking solver forcing
788      - fix drag (ocean on ice) formulation and a bug that caused noise in the
789        C-grid solver
790      - added a few comments to seaice_diffusion.F
791      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
792        are now exclusive)
793      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
794        required re-ordering the code a little:
795       + make DAIRN global variable (defined in SEAICE)
796       + move computation of the viscosities eta and zeta into a new separate
797         routine (because I need to recompute them in seaice_ocean_stress.F)
798    
799    checkpoint58b_post
800    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
801      update output.txt of exp. aim.5l_cs.thSI
802    o various mnc cleanups and improvements:
803      + shrink lookup tables by factor of ~4
804      + better error reporting when running out of lookup space
805      + able to handle longer path/file names (up to 500 chars)
806    o adjoint:
807      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
808      - TBD: "hidden" mom_vecinv recomp. in dynamics
809    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
810     (allow to differentiate between forcing components using new integer flags:
811      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
812     and add new flag to put Dissipation tendency out of Adams-Bashforth.
813    o ecco
814      - enable trend removal from SSH anomaly obs.
815    o adjoint
816      - a fix for PmEpR when #undef EXACT_CONSERV
817      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
818      - try to fix "hidden" recomp. in forward_step for NLFS
819        (NLFS seems broken sometimes after I checked it in)
820    o seaice:
821     - add c-grid version of the dynamic solver:
822       + three new routines that are the c-grid substitute lsr, dynsolver
823         and ostres
824       + put a few fields that were local to dynsolver into global common
825         blocks, so that I can move the computation of stresses etc into
826         seaice_lsr (saves coding but may break the adjoint).
827     - replace more hardwired parameters by runtime parameters
828     - add ice masks that mask the rhs of the implicit solvers where there
829       is no ice (commented out in seaice_dynsolver, because i am not sure
830       if this works properly), eventually this should replace the clipping
831       of ice velocities in seaice_dynsolver to +/-40cm/s.
832    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
833      include it only where its needed
834    o move balancing of fluxes before the call of external_forcing_surf
835    o seaice:
836      - correct units of turning angles (now they are really in degrees)
837      - move computation of GWATX/Y out of main routine into dynsolver
838      - initialize GWATX/Y in seaice_init
839    o Apply mask on Fresh-Water flux (needed for SSH forcing).
840      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
841    o seaice: add runtime flags for turning angles (default to zero)
842    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
843      and trend from exf forcing and ctrl control adjustments
844    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
845      (since checkpoint57x_post)
846    o change the default rotation period to 86164.s = the Earth rotation
847    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
848      and based on a reference stratification. Tested within hs94.cs-32x32x5.
849    o seaice advection: add code for choosing between the default (2nd order
850      central differences) and multiDim advection schemes provided by
851      pkg/generic_advdiff
852    o seaice:
853      - removed all references to SEAICE_GRID.h fields from
854        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
855        (cubed-sphere configuration will change a little)
856      - grid computations in seaice_init are obsolete now.
857      - cleaned up code a little so that is easier to read (hopefully).
858      - added new (better?) discretizations of default advection and diffusion
859        (turn on with SEAICEuseFluxForm)
860      - replace 1 in 3d global fields by kSurface in growth.F
861      
862    checkpoint58a_post
863    o seaice:
864      - bug fix in advect.F
865    o shelfice:
866      - separate shelfice load anomaly from pload (breaks with time
867        dependent forcing), => introduce constant field shelficeLoadAnomaly.
868        Its default is 0., but it may be computed more cleverly from (unknown)
869        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
870        done offline. A good approximation of the pressure load anomaly is
871        necessary to avoid large initial adjustment processes underneath
872        deep-reaching shelfice.
873      - small fix in ISOMIP shelfice_thermodynamics
874      - add more sophisticated thermodynamics of Hellmer (1989), this is
875        now the default
876      - give a few constants more intuitive names
877    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
878      if bulk formulae are used in long integration (especially EmPmR). Turn
879      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
880      if balancePrintMean, the imbalance that is substracted is printed to
881      STDOUT.
882    o fix bug (typo) in obcs_apply_eta.F
883    o add a new package shelfice which enables us to model the circulation
884      underneath shelf-ice with draughts of hundreds of meters.
885     - works
886     - to do: + include improved thermodynamics
887              + check whether kSurfC (from model/inc/SURFACE.h) can be used
888                instead of new field kTopC
889              + can we use topoFile, Ro_surf and existing code in ini_depth.F
890                instead of new field R_shelfIce and new code in ini_depth.F
891                and ini_mask_etc.F?
892              + adjust vertical mixing schemes?
893    o seaice pkg:
894     - add a cpp-flag to include a simple formula for a salinity dependent
895       freezing point of sea water at the surface
896     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
897       meridional stresses are now different (and hopefully correct)
898    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
899       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
900       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
901    o pkg/diagnostics: add options and parameters for regional-statistics
902       diagnostics ; define regions by reading a region-mask from a file
903       (might add other options later)
904    o pkg/bulk_force:
905     - add option and parameters to use AIM surface-flux formulae.
906     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
907       others forcing fields (defined in PARM05, parameter file "data") are loaded
908       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
909     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
910     - use the right EXCH call for uwind,vwind (to work on CS-grid).
911     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
912       and parameters (note: calcWindStress replaces .NOT.readwindstress).
913     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
914    
915    checkpoint58
916    o add "--embed-source" option to genmake2 which, when the supporting
917      tools can be compiled (as determined by genmake2) will turn on the
918      embed_files package which then embeds the entire MITgcm source code
919      (*.[fFhc] + Makefile) used for the build within the executable
920      - requested by CNH but off by default
921      - adds a paltry <9MB to the mitgcmuv executable in most cases
922      - only writes the output when useEMBEDSRC in eedata is true
923    o clean up 3-dim. relaxation codes:
924      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
925      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
926      * Thanks to Tom Haine for testing!
927    
928    checkpoint57z_post
929    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
930      affects output (@ truncation level) of exp. plume_on_slope ; updated.
931    o fix the pickup behavior for obcs in combination with ptracers
932    o fix a bug in ptracers_external_fields_load
933    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
934      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
935    o transfered surface NH pressure to eta field (if exactConserv).
936    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
937         and update lab_sea output.txt file.
938    o completing 3-dim. relaxation code: additional term
939         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
940      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
941      * At compile time, in "EXF_OPTIONS.h" set
942          #define  ALLOW_CLIMTEMP_RELAXATION
943          #define  ALLOW_CLIMSALT_RELAXATION
944      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
945          tauThetaClimRelax3Dim = 15552000.0,
946          tauSaltClimRelax3Dim  = 15552000.0,
947      * 3 cases:
948          1) Use a constant-in-time 3-dim. field
949          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
950          3) Real-time relax. to time-evolving prescribed field
951    o Adding Laplacian-type smoothness constraint on
952      initial and boundary (forcing) controls (ic, bc)
953      * enable at compile-time via
954        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
955      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
956      * Absolute scale somewhat unclear so far
957      * no area weighting was included since no other cost term does so far
958    
959    checkpoint57y_post
960    First step for a NLFS adjoint
961    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
962    o new init. routines for calc_r_star, calc_surf_dr
963    o still need to deal with ini_masks_etc
964    o testreport seemed happy
965    checkpoint57y_pre
966    
967    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
968    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
969    o add new offset feature to offline pkg (plus minor cleanup)
970    o cfc fixes for final year of integration
971    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
972      be in GCHEM_OPTIONS).
973    
974    checkpoint57x_post
975    o fix testreport Pb in multiple test experiment.
976    o cleanup our namelist syntax in verification:
977      - make it more F95 standards compliant (some work still needed)
978      - allows the vast majority of our tests to work with gfortran
979    o Non-Hydrostatic:
980     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
981     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
982    o Allow to apply AB on T,S rather than on AB(gT,gS):
983     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
984     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
985       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
986     - need a "clever" read_pickup to restart from the other AB formulation
987    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
988    o remove some unused variables (reduces number of compiler warnings)
989    o adjoint
990      * Disable useVariableViscosity for adjoint for time being
991        (there are a number of extensive recomputations)
992      * Initialize certain variables needed for adjoint
993    
994    checkpoint57w_post
995    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
996                 fix the singleCpuIO RS version of MDSWRITEFIELD
997       and add a WARNING if using globalFiles=T with multi-processors.
998    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
999      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
1000    o tracer advection scheme:
1001      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
1002       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
1003       was not very convenient).
1004      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
1005       (further tests needed for the implicit DST & Flux-Limiter schemes).
1006    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
1007      and sRef for convenience, handy, when you want to initialize
1008      ptracers in a large domain with a constant non-zero value. Also,
1009      untangle ptracers_init.F a little.
1010    
1011    checkpoint57v_post
1012    o change dome exp. to use variable viscosity in side-drag terms.
1013    o remove all the files from the cfc_offline test since they are now
1014      incorporated into tutorial_cfc_offline which has been producing
1015      identical results for a few days of testing
1016    o add new parameter: sideDragFactor to enable half-slip-side BC
1017      and change side-drag S/R to use viscosity from mom_calc_visc
1018      (can switch back by setting sideDragFactor=0.); affects results at
1019      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
1020       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
1021    o vorticity & strain are now computed without masking, to account for
1022      no-slip-side BC in variable viscosity calculation ; mask is applied
1023      anyway later on, before computing advection/coriolis terms.
1024    o modify exp4 to test new obcs support for reading from external files
1025      and for passive tracers
1026    o fix behavior of ptracers_monitor when monitor output is written to a
1027      netcdf-file; still not independent of monitor.F (writes in the same
1028      file).
1029    o change default value of tRef (put a uniform, meaningful value for ocean
1030      & atmos) and initialize sRef (was missing, as Martin mentioned).
1031    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
1032      to be proportional to enstrophy dissipation length.  Thus,
1033       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
1034      This is now consistent with Smagorinsky and with the manual.
1035    
1036    checkpoint57u_post
1037    o OBCS and PTRACERS: add open boundary support for passive tracers
1038      - either use homogenous (pseudo) v.Neumann conditions or prescribe
1039        OB-values from file; this is not different from the way theta and salinity
1040        are treated
1041      - however, Orlanski-radiation conditions are not supported, and the model
1042        will stop if you use pTracers and Orlanski at the same time.
1043      - beefed up the rountine obcs_external_fields_load: now only those open
1044        boundary values are overwritten with values from files for which there
1045        are really files, otherwise the OB-fields remain untouched. This makes
1046        it possible to use different OBs at different ends of the domain (as
1047        with EXF)
1048    o reduce number of exch calls in shap_filt (s2).
1049    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1050      truncation level) 4/5 MLAdjust test results (11&12 digits match).
1051    
1052    checkpoint57t_post
1053    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1054    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1055      same truncation, independent of the face number: affects affects several
1056      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1057    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1058      note that biharmonic viscosity + no-slip was not tested in any experiment.
1059    o fix bug in non-linear free-surf side-drag ; generate new output for
1060      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1061    o make mnc honor the writeBinaryPrec flag for most kinds of output
1062    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1063    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1064      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1065    o add brackets in multi-terms sum to get same truncation, independent of
1066      the face number (manage to get exactly same value of gU,gV at the cs-edge)
1067      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1068    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
1069      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1070      a maximum grid-scale Reynolds number.  Also, changes all length calculations
1071      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1072      Suggested values of viscosity parameters found in mom_calc_visc.
1073      Many new viscosity diagnostics available.
1074    
1075    checkpoint57s_post
1076    o Add clearing-house for viscosity calculations, mom_calc_visc and
1077      correct numerous bugs in LeithD and Smagorinsky discretizations.  
1078      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1079      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1080      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1081      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
1082      The Strain-Tension form is now called with useStrainTensonVisc=.true.
1083      ViscAhStrain and viscAhTension are now retired.
1084    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1085    o In response to JMC's bug report, genmake2 now ignores any soft-links
1086      that it finds in the *current* directory when searching for files.
1087      Soft-links found in any other source directories will still work as
1088      they did before.
1089    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1090      a C routine to unlimit the stack size
1091    o mnc-ify pkg/aim snapshot vars
1092    o mnc-ify pkg/land as requested by Daniel
1093    o various changes to mnc including:
1094      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1095      - output can now be grouped so that all files within a group
1096          change the ITER portion of their names in lock-step together
1097      - can now read ("global") PER-FACE (in addition to PER-TILE) files
1098          and works with both EXCH1 and EXCH2 (but needs more testing)
1099      - writing works for all verification test cases w/ g77 on Linux
1100    
1101    checkpoint57r_post
1102    o make MNC variable initialization happen earlier
1103    o add diagnostics for (almost) each term of the momentum Eq.
1104    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1105    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1106    o remove MINIMAL_TAVE_OUTPUT option ;
1107      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1108    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1109      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1110    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1111    o add time-dependent SST, SSS control
1112    o cost terms in ecco/ modularized (new cost_generic.F)
1113    o cost_averages routines are modularized (new cost_averagesgeneric.F)
1114    o new infrastructure for seaice model vs. obs misfits in seaice/
1115      * driver from the_main_loop.F is seaice_cost_driver.F
1116      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1117      * gradient check in Exp. 6a of natl_box_adjoint/
1118    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1119      (see README file)
1120    
1121    checkpoint57q_post
1122    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1123    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1124      - bug was reported by Jean-Michel and Ian Fenty
1125    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1126      update exp. cpl_aim+ocn output.
1127    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1128      Needed for high-res. runs with large global files
1129      to be able to limit tapelev size
1130    o Changed some tests for adjoint:
1131      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1132      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1133      * global_ocean.90x40x15/ back to default 3-level checkpointing
1134    o Modifications to enable scripted COMMON to MODULE conversion
1135      * verification/OpenAD/code/ has necessary scripts and description;
1136      * converts, compiles and runs successfully;
1137    
1138    checkpoint57p_post
1139    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1140    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1141      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1142    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1143    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1144      (was already the case for dissipation with mom_vecinv,
1145       and also the case for grad.PhiHyd when staggered-timeStep)
1146      This will allow to put dissipation out-off the AB time-stepping.
1147     Unfortunately, affects truncation error. Update output of exp. that "fails"
1148      (cg2d matching number) and leave the others for later: front_relax(10),
1149      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1150      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1151    
1152    checkpoint57o_post
1153    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1154      (2) its ready to be documented during the 20050801 DocFest
1155    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1156      for ideal_2D_oce and lab_sea on linux_ia32_g77
1157    o set to #undef CTRL_SET_OLD_MAXCVARS_30
1158      in global1x1_tot/code_seaice_adj to access indices 32, 33
1159      (worth another tag)
1160    
1161    checkpoint57n_post
1162    o adding precip control xx_precip 32
1163    o adding swflux control xx_swflux 33
1164    o Replacing 10 forcing penalty cost routines by 1 generic.
1165    o Implementing partitioning in time-mean and variable adjustment
1166      for atmos. state.
1167    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1168  o in natl_box_adjoint:  o in natl_box_adjoint:
1169    * updated: results_bulk/    * updated exp 1 to 10
1170    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
1171    o updated global1x1/*_seaice_adj/
1172      to incorporate latest changes
1173    o enable useSingleCpuIO for mdsio vector routines
1174      (applies in particular to tapelev I/O)
1175    o removed inefficient K-loop in all active_file*control*.F
1176    
1177  checkpoint57m_post  checkpoint57m_post
1178  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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