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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.866 by jmc, Thu Aug 30 21:26:37 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 each tested exp: add a "run" directory with a standard ".cvsignore" file ;
8  o moved ptracer ctrl index 17 -> 32    remove .cvsignore from input dir. (since testreport no longer run here).
9    o pkg/thsice:
10     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
11     - fix reshaping of sea-ice just after advection:
12       melt all the ice only if ice-volume is too small.
13     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
14       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
15     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
16    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
17      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
18    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
19      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
20      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
21      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
22      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
23      -> update output.txt
24    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
25     this affects truncation error: -> update output.txt of exp:
26      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
27      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
28    
29    checkpoint59f
30    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
31    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
32      a bounded range (in forward mode)
33    o pkg/ecco, ctrl, autodiff and mom_common:
34     internal parameter controls, completements of implementations
35    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
36    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
37      (not seem any difference in testing results).
38    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
39       at face corners.
40    o pkg/generic_advdiff:
41     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
42      loop range indices for computing vertical advection tendency
43      and do the calculation in the interior only (no overlap) ;
44      for now, only implemented for SOM advection (to save CPU time).
45     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
46    o exch2 adjoint
47      First set of changes:
48      - add exch2 hand-written adjoint templates
49      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
50        This will require cleanup in pkg/autodiff/*.F
51        (changed routines currently kept separate in verif. code/)
52      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
53        that used to hide exch2 or cubed-sphere specific code
54        (commented via 'cph-exch2')
55    o pkg/seaice
56      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
57    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
58       output of global_ocean.cs32x15.thsice .
59    
60    checkpoint59e
61    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
62      for B-grid vector (not yet tested) and C-grid vector (<- only used
63      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
64    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
65      (#ifdef ALLOW_SALT_PLUME)
66    o gather_2d/scatter_2d: removed halo regions
67    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
68      scheme and the corresponding test case (under front_relax dir). For now,
69      only available with Skew-flux form and not yet tested in realistic set-up.
70      adjoint: store directives updated, but gradient checks deteriorated,
71      so maybe GM/Redi adjoint is now broken.
72    o seaice adjoint
73      * add AREA, HEFF, HSNOW as control variable
74        (should not change lab_sea results)
75      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
76    o pkg/seaice:
77      * added computation of saltFlux in seaice_growth;
78        For time being, sea ice salinity is assumed constant
79        contribution of snow flooding to freshening of sea ice is neglected.
80        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
81        defaults to 0.0 in order to maintain backward compatibility.
82        Typical values for SEAICE_salinity are 4 to 10 g/kg.
83      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
84      * added SEAICE_availHeatFrac, which specifies fraction of surface level
85        heat content used to melt or grow ice
86      * commented out cap of HICE: it helps keep ice thinner
87      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
88      * applied OBCS T/S mask to HEFFM sea ice mask
89    
90    checkpoint59d
91    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
92     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
93     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
94    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
95     and change default value of parameter "GM_Small_Number";
96     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
97       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
98       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
99    o pkg/ecco: cost function when applying pkg/smooth to controls
100    o pkg/ctrl: add forcingPrecond run time parameter
101    o pkg/seaice:
102     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
103     - fix bug in metric terms of u-equation in LSR solver (implicit part),
104       changes verification/lab_sea
105     - rearrange implicit part of u-equation in LSR solver to make it easier to
106       read, understand, and debug. This causes changes at the truncation level.
107     - fix (serious) bug in the boundary conditions (sign error in the implicit
108       part) of the LSR solver. Changes all LSR results.
109     - fixed problem with HSNOW initialization to avoid thick snow when AREA
110       is initilized with small values - does not change lab_sea results.
111     - added HsnowFile initialization capability
112    o pkg/smooth: addition to model/src and pkg/ctrl so allow
113     initialization of pkg/smooth and application to control vector
114    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
115    o dependencies: pkg/profiles requires pkg/cal
116    o pkg/profiles:
117     - added option ALLOW_PROFILES_GENERICGRID
118         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
119         that interpolation information (grid points and coefficients) is provided
120         within the netcdf input files.
121         -> sample matlab scripts can be found in MITgcm_contrib/gael
122         that allow you to prepare netcdf input files.
123     - also modified: cleaner include statements, cleaner error print statements,
124       cleaner stops when error, and more tests of the netcdf input files consistency.
125    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
126    o pkg/seaice:
127     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
128       requires a new routine: seaice_diagnostics_fill.F
129     - make sure that seaice does not move if not forced (pressure replacement
130       method, Hibler and Ip, 1995), changes results
131     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
132     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
133       It is turned off by default (=-1.), because it changes the results.
134     - make it possible to read AREA from a file, too.
135    
136    checkpoint59c
137    o add S/R and diagnostics for oceanic mixed-layer depth
138    o move GMRedi call after all vertical mixing schemes (including KPP)
139    o pkg/thsice:
140     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
141      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
142    o pkg/obcs:
143     - bug fix for balance code
144    o pkg/seaice:
145      - allow values of SEAICE_elasticParm > 1
146      - add new parameter SEAICE_evpTauRelax as an alternative
147        to SEAICE_elasticParm
148      - make lsr boundary conditions free slip (by default), changes result
149      - add code for no slip boundary conditions for lsr
150      - set minimum of zeta to zero (and not 4e8) (changes results)
151      - add a cap on AREA after advecting AREA if seaice_growth is not called
152    o change calculation of Visbeck K:
153      - no longer depend on tapering scheme; instead, compute slope (limited
154        by GM_maxSlope). this is equivalent to what was comuted before with
155        clipping or linear tappering.
156      - fix vertical averaging (wrong by 1/2 level)
157      - leave the old version (but will not be maintained) within
158        #ifdef OLD_VISBECK_CALC / #endif
159      - update output of exp. ideal_2D_oce
160    o change error catch in calc_r_star to improve vectorization
161    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
162      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
163    o adjoint:
164      Re-organized adjoint checkpointing according to Matt Mazloff
165      (but with modifs/completions/cleanups)
166      Storing is now bundled into large arrays to optimized I/O
167      (and second step in cleanup of the_main_loop)
168    
169    checkpoint59b
170    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
171      - export/import (between ocean & coupler) fields needed for ocean DIC.
172    o pkg/seaice:
173      - get rid of three more exchanges seaice_calc_viscosities (required
174        different loop boundaries in seaice_lsr and seaice_ocean_stress)
175      - bug fix in seaice_ocean_stress (update of lab_sea required)
176      - reduce loop boundaries to necessary minimum also in seaice_evp
177      - go back to the old way of computing deltaC/Z as the adjoint likes that
178        better
179    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
180      passive tracer to an Age Tracer) + update output.txt
181    o pkg/exf:
182      - implement A-grid / C-grid selection for wind-stress input files.
183      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
184      for now, in exf_bulk_largeyeager04.F only :
185      - change implementation for case where windspeed + 2. components wind-stress
186        are read-in. AND use rhoConstFresh to convert evap.
187    o pkg/seaice:
188      - use correct EXCH_UV for wind-forcing (on A-grid).
189      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
190        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
191    o pkg/exf:
192      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
193      EXF_INTERPOLATION:
194      - merge global_with_exf/code version of exf_interp_read.F
195        to the main code ;
196      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
197        reading the file ; Important: This options needs to be defined to recover
198        previous code.
199        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
200      - no longer loose real*8 precision along the way when using exf_iprec=64.
201    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
202      - change discretisation of evp-solver in order to avoid another exchange
203        (changes lab_sea) and clean up a little
204      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
205        help the adjoint (this also changes the results slightly)
206      - add a few "_d 0" where they had been missing in seaice_evp.F
207      - cleaning up: remove unused seaice_calc_rhs.F
208    o pkg/exf: some cleaning-up:
209      - change various "constants" into runtime parameters
210      - cleaned-up Large&Yeager04 routine which should eventually
211        replace exf_bulkformulae.F (changed names of S/R and CPP)
212        and merged various ALLOW_ATM_WIND options
213     only used with thsice pkg (in thsice_get_exf.F):
214      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
215        which are used when useStabilityFct_overIce=TRUE (= the default)
216      - change default values of ice & snow emissivity and scale downward LW
217        by ice & snow emissivity.
218    o pkg/thsice:
219     fix few little problems, in thsice_calc_thickn.F:
220      - growth vertically (and not laterally) if iceFrac == iceMaskMax
221      - melt only laterally if hIce < hThinIce (as the comments say)
222      and in thsice_extend.F:
223      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
224      - start to form ice as soon as the minimum ice-volume is reachable.
225     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
226      and cpl_aim+ocn
227    o pkg/kpp
228     - move computation of surface related input fields to KPP into a new
229       subroutine kpp_forcing_surf.F
230     - remove wrong (within bi,bj loops) EXCH calls.
231     - little cleaning (add argument myThid in last position, cvs header ...)
232     - for now, fix conservation problem by exchanging KPPviscAz (may not
233       be the best fix)
234    o pkg/seaice
235     - check for inconsistent evp parameter/cpp-flag combination
236     - remove leftover errIO flat for obsolete name list error handling
237    o OpenAD
238     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
239    
240    checkpoint59a
241    o pkg/seaice: some parameter clarifications and a little bit of clean up
242    o pkg/thsice: rename run-time parameters:
243       himin       -> hIceMin
244       himin0      -> hThinIce
245       hihig       -> hThickIce
246       i0          -> i0swFrac
247       transCoef   -> bMeltCoef
248       frac_energy -> fracMelting
249      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
250       with default values (for now) that do not change the results.
251      remove old version of thsice vars advection in pkg/seaice.
252    o in FFIELDS.h:
253      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
254      - make pLoad & sIceLoad always available (but still only used if
255         ATMOSPHERIC_LOADING is #define).
256    o pkg/kpp: replaced _KPP_RL with _RL
257    o bug fixes for vertical diffusivity computations when both KPP and
258        3D diffusivity arrays are used.
259    o pkg/seaice: fix bug in evp solver, while doing that
260      - change (improve?) discretization of stress computations for both
261        cgrid-lsr and evp solver
262      - add a new routine to compute strain rates
263      - the above changes lab_sea results
264      - add no slip conditions for evp solver (off by default), lsr-version
265        may follow
266      - fix exchange for shear at Z-points (does not change lab_sea)
267      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
268        (to force the user to pick a time step since there is not "safe" way
269        of choosing it)
270      - add principal stress diagnostics
271      - rearrange fields for evp a little to avoid having to call a: too many
272        exchanges and b: exchanges for stress trensor components which we do
273        not have.
274      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
275        of evp, complete rewrite for lsr case (latter is does not yet work
276        in all cases)
277    o pkg/kpp: add code to have mixing in shelf ice caverns
278      - add myThid to all kpp routines (long overdue)
279    
280    checkpoint59
281    o pkg/exf:
282      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
283        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
284      - move exf header files from lower_case.h to UPPER_CASE.h ;
285        add missing cvs Header & Name
286      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
287      - add namelist param. selectStressGridPosition, exf_monFreq
288      - retire many _CLIM routines, and remove data.exf_clim
289        + params moved to data.exf
290        + climsst, climsss now handled by exf_set_gen, i.e.
291          climss?period=0 refers to constant field,
292          climss?period=-12 to monthly forcing
293      - split up namelists in data.exf
294    o pkg/seaice:
295      - remove seaice_exch and seaice_exch_uv
296      - remove superfluous exchange of theta
297      - add myThid to seaice_budget_ocean/ice
298      - add new interface for atmospheric wind forcing (C-grid only)
299        + new routine
300        + two new field (taux, tauy for stress over ice)
301        + removed one global field (DAIRN) for C-grid case only
302    o pkg/thsise
303      - 2nd set of modifs for thsice adjoint in conjunction with exf
304    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
305    
306    checkpoint58y_post
307    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
308      vertical diffusivity, similar to that in MOM4; turned on using
309      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
310      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
311    o Added capability for 3D specification of background vertical diffusion
312      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
313      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
314      "data" file that contains the 3D vertical diffusivity coefficients.
315    o ice dynamics (pkg/seaice) with thsice thermodynamics:
316      - add code within pkg thsice to advect & diffuse sea-ice fields
317      similar to (and will replace) what has been added in  seaice_advdiff.F,
318      but: - conserving Mass, Heat & Salt.
319           - better when using non-linear advection scheme (not yet fully tested)
320           - can also be used in atmospheric set-up (for now, only the diffusion).
321    
322    checkpoint58x_post
323    o IO option for global-file compact format:
324      - add options when generating topology (utils/exch2/matlab-topology-generator)
325      - add I/O capability (pkg/mdsio).
326      - adapt utils/matlab/rdmds.m to read this format.
327      for now long-line format not yet supported by pkg/mdsio (& exch2).
328    o shelfice: add a few diagnostics
329    
330    checkpoint58w_post
331    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
332      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
333      (and replace horiVertRatio in NH code).
334      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
335                         and tutorial_plume_on_slope (sensitive to truncation)
336    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
337      directly to drive seaice model (C-grid only)
338    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
339     - reintroduce computation of wind from stress,
340     - compute tau (in exf_bulkformulae.F) from windstress averaged to
341       mass points to avoid tau = 0
342     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
343    o rdmnc.m: make it work with "global" files created with gluemnc
344    o rdmnc.m : some improvements in dealing with singleton dimension
345      (tested on all testreport mnc output files).
346    o genmake2: disable pkg/profiles if netcdf test fails.
347    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
348    o move call to cal_readparms up to make calendar parameters/variable available
349      to all packages
350    
351    checkpoint58v_post
352    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
353      useDynP_inEos_Zc tested.
354    o pkg/exf: changes to properly interpolate/mask/scale initial fields
355    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
356      and portions thereof.  See read_cs.txt for description and examples.
357    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
358      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
359      following the great-circle arc between those 2 points.
360    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
361      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
362    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
363     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
364     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
365     - still needs work (not working with some options ; efficiency to improve)
366       and serious testing.
367     - use this scheme for temperature & salinity in 2 advection test exp.:
368       advect_xy & advect_xz, respectively.
369    
370    checkpoint58u_post
371    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
372    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
373    o testreport: add option "-skipdir" to skip some test.
374    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
375      momentum calculation.
376    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
377    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
378      remove checkpoint.F and the_correction_step.F (no longer used);
379      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
380    o add option (linFSConserveTr) to correct for tracer source/sink due to
381      Linear Free surface
382    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
383    o pkg/thsice: fix reading mnc-pickups
384    
385    checkpoint58t_post
386    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
387    o pkg/mdsio:
388     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
389       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
390       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
391     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
392     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
393       either MDS_READ_FIELD or MDS_WRITE_FIELD )
394     - new S/R (to replace MDSWRITEMETA), which allows to write more
395       informations (variable names, time ...) to meta files.
396     - modify rdmds.m to give back the meta file content.
397    o pkg/diagnostics: change vertical interpolation to be safer, and more
398       flexible (define p-levels to interpolate to in data.diagnostics);
399      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
400       diagnostic pointer.
401    o pkg/seaice: more cleaning up of seaice_growth, added many comments
402    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
403    o fix multi-category seaice:
404     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
405       SEAICE_MULTICATEGORY
406     - fix short wave heat flux
407    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
408       and allow to use EVP solver. Change forward lab_sea: test both EVP
409       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
410    o Initial check-in of lab_sea adjoint
411      (very similar to natl_box_adjoint/code_seaice)
412      * used C-grid and EVP solver
413      * used KPP, GM/Redi
414      * uses inAdExact=.TRUE.
415      * gradient checks fail for both ADM and TLM
416        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
417        f.d. gradients actually seem more problematic than ADM, TLM gradients;
418        issue is related to forward mismatch between g77 an ifort
419    o pkg/seaice: overhaul of thermodynamics
420     - growth.F and groatb.F are replaced by new routine seaice_growth.F
421     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
422     - move a few global fields out of SEAICE.h into seaice_growth.F and
423       make them 2D (FICE/QNETO/ ...)
424     - remove FO (it is the same as QNETO)
425     - introduce a few local fields to avoid modifying external fields such
426       as atemp, etc.
427    
428    checkpoint58s_post
429    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
430      changed exf_set_gen.F so that
431        genperiod=0 means input file is one time-constant field and
432        genperiod=-12 means input file contains 12 monthly means
433    o CG2D: use pre-computed solver main-diagonal (stored in common block);
434      this affects truncation error ; generate new output file for exp. which
435      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
436        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
437        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
438        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
439        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
440        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
441    o start implementation of deep-atmosphere and anelastic formulation
442    o verification: remove 2nd copy of input files and use script "prepare_run"
443      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
444    o mom_common/vecinv/fluxform: fix a few initialisation isssues
445    o profiles: fix for multithreaded case
446    
447    o diagnostics: rename few diags:
448      s/'PRESSURE'/'RCENTER '/g
449      s/'TICE    '/'oceFreez'/g
450      s/'TAUX    '/'oceTAUX '/g
451      s/'TAUY    '/'oceTAUY '/g
452      s/'SWFLUX  '/'oceQsw  '/g
453      s/DIFx/DFxE/g
454      s/DIFy/DFyE/g
455      and add few ocean-forcing diagnostics:
456      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
457    o modifications to pkg/seaice/growth.F and budget.F, which change results of
458      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
459      as actual snow thickness.  It now refers everywhere to effective snow
460      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
461    
462    checkpoint58r_post
463    o modifications to pkg/seaice/growth.F, which change results of
464      lab_sea experiment: fixes pertain to melting snow over open water, to
465      masking EVAP under sea ice, and to using the correct AREA variable for
466      computations of EVAP, PRECIP, HSNOW, and GHEFF
467    o add ability to read bathy, salt, and theta using MNC (off by def)
468    o add flooding algorithm and advection of HSNOW for pkg/seaice;
469      both are turned off by default and do no change any results
470    o seaice advection with pkg/thsice: a step toward the use of non-linear
471      advection scheme, but #ifdef or commented out for now (requires more EXCH).
472    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
473      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
474      in natl_box (affects results @ truncation level: update output.txt)
475    o multi-threading and IO:
476      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
477      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
478        (needed to work with SingleCpuIO): tested in all verif. exp.
479    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
480      affects the results (but none of the verification test uses this scheme).
481    o Adding some pkg/diagnostics capability to pkg/seaice
482      (will certainly be subject to changes)
483    o ctrl: adding new control variables:
484      lwflux, lwdown, evap, snowprecip, apressure, runoff
485    
486    checkpoint58q_post
487    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
488      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
489      high_res_cube configuration by 4% on Columbia.
490    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
491      add (in global_with_exf/code) a version of EXF_INTERP_READ without
492      dynamical allocation (seems to work in multi-threaded).
493    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
494      single CPU io) so that TAF does not have to see EESUPPORT.h
495    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
496    
497    checkpoint58p_post
498    o obcs: stop if obcs is used with useCDscheme = .true.
499    o shelfice:
500     - fix a sign error so that no slip at shelfice interface works
501     - remove stop for combination non-hydrostatic code and shelfice. That does
502       not mean, that the results are correct, but at least they are numerically
503       stable
504    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
505    o added adjoint exch routined for all exch*3d* routines
506      and updated flow directives
507    
508    checkpoint58o_post
509    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
510      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
511    o change controling S/R for writing pickup file (new S/R do_write_pickup)
512      and clean-up reading/writing of pickup files.
513    o fix local version of read/write pickup (NH part) in rotating_tank/code
514    o simplify EXCH interface:
515     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
516     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
517    o added the regrid package
518    o shelfice:
519     - add a simple boundary layer scheme to reduce noise
520     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
521    
522    checkpoint58n_post
523    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
524       local variable (not in common block).
525    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
526      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
527      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
528        to work with SingleCpuIO.
529    o add "_d 0" to real constant of pkg/cfc subroutines ;
530       update exp. cfc_exemple & tutorial_cfc_offline output files.
531    o multi-threading and IO:
532      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
533        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
534      - barrier before and after reading.
535      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
536      - avoid using MDS_WRITELOCAL for LAND pkg output.
537      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
538        common-block variables ; Allows multi-threading with master-thread IO.
539    o change default MAX_NO_THREADS from 32 to 4 ;
540      and stop cleanly when MAX_NO_THREADS is too small.
541    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
542    
543    checkpoint58m_post
544    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
545       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
546    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
547       keep global_ocean.90x40x15 (for AD testing) with former secondary test
548       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
549    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
550        add MITgcm_tutorials (= code + all the tutorials)
551    o ecco, option to compute cost for total ssh (mean+anom)
552    o consistent with addition of ptracer and ssh in pkg/profiles
553    o profiles: adding ptracer and ssh
554    o testreport: change multi-test output-file name
555      (from output.txt.{name} to output.{name}.txt)
556    o profiles: now ok for mutli-tiles case
557    o seaice: add 4 parameters for different advection schemes for area,
558      (effective) seaice thickness, enthalphy, and snow height. Their default
559      is the standard parameter SEAICEadvScheme
560    o calc_gw:
561     - add cosFacU in zonal viscous flux (harmonic.visc.).
562     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
563       of tutorial_plume_on_slope.
564    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
565    o calc_gw: true flux-form, account for horizontal grid spacing.
566      update rotating_tank results, but not plume_on_slope (affected at
567      truncation level, 11 digits).
568    
569    checkpoint58l_post
570    o calc_gw:
571     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
572     - remove side-drag for now (need to fix it); update plume_on_slope results.
573     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
574    o commit code to make SST/SSS weights spatially variable
575      (based on either variable in-situ or variable initial T/S weights)
576    o pkg/ecco:
577      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
578        now based on horizontally varying weights wthetaLev, wsaltLev
579      * cost_averagesflags now returns year indices in addition to day, month
580      * sflux balance is performed on annual basis
581        (sflxumm, sfluxmm2, bal_sfluxmm)
582      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
583        including separate counting and multipliers
584    o pkg/rbcs
585      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
586    
587    checkpoint58k_post
588    o testreport:
589     - always build in dir. "build" (if not there, mkdir build instead of building
590       & running in input)
591     - run in dir run (if it exists), in build otherwise.
592     - call prepare_run (if input/prepare_run exists)
593     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
594    o pkg/exf modifications to interpolation and rotation routines for more
595       reasonable treatment of North Pole singularity: for tracers North Pole
596       value is set to northernmost zonal-mean value, for zonal velocity it is
597       set to zero, and for meridional velocity it is set to northernmost value.
598    o pkg/exf/exf_check_range.F
599     - add tile index to diagnostics and move stop statement to the very
600       end of the routine.
601    o pkg/diagnostics: (diagnostics_main_init.F)
602      define title of isomorphic variables according to the current config.
603    o pkg/thsice with pkg/seaice dynamics:
604    - fix domain of computation (interior only, required for exf) and do exchanges
605    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
606    o towards a standard way of dealing with multi-threading in MONITOR
607      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
608    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
609       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
610    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
611    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
612    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
613       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
614    o tracer advection:
615     - clean-up and simplify calc_common_factors.F
616     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
617       advection subroutine (but still not used within DST advection S/R)
618    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
619    
620    checkpoint58j_post
621    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
622      from file (collects calls previously in FORWARD_STEP)
623    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
624    o adjoint store dir. adjusted accordingly
625    o genmake2
626      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
627    
628    checkpoint58i_post
629    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
630      on wind stress (SEAICEstressFactor defaults to 1.)
631    o Total number of Timers is finite (<=40): comment out 2 non-essential one
632      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
633    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
634      on CS-grid: no longer loosing mass.
635    o exf & curvilinear-grid: no longer modify longitude xC & xG.
636    o pkg/ggl90: fix sloppy output and fix a bug
637    o pkg/seaice: added SEAICEuseEVPpickup parameter
638      - Set to false in order to start EVP solver with
639        non-EVP pickup files when using SEAICEuseEVP
640      - fix sign error in diffusion in seaice_calc_rhs
641    
642    checkpoint58h_post
643    * Modifications for bottom topography control
644      o replace hFacC by _hFacC at various places
645      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
646      o add non-self-adjoint cg2d_nsa
647      o update autodiff support routines
648      o re-initialise hfac after ctrl_depth_ini
649      o works for 5x5 box, doesnt work for global_ocean.90x40x15
650    * Adding verification for 5x5 box (4-layer) bottom topography control
651    
652    checkpoint58g_post
653    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
654       used for mean seasonal cycle, mean diurnal cycle); add an example
655       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
656    o pkg/ggl90:
657      - add parameter (minimum surface kinetic energy)
658      - fix bug (avoiding division by zero)
659    o couple pkg/thsice to pkg/seaice:
660      - modify advection in seaice to accomodate new scalar fields to be advected
661      - only muliDimAdection scheme work with seaice/thsice
662      - mapping of thsice-variables to seaice-variables, back and forth
663      - does not break the verification experiments, but does not give the
664        desired results either
665    o pkg/seaice
666      - make (default) second order advection a bit less confusing?
667    
668    checkpoint58f_post
669    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
670      to pkg/seaice):
671      - new routines thsice_map_exf and thsice_get_exf provide the interface
672      - add an additional formal parameter to thsice_solve4temp
673    o pkg/exf:
674      - add new fields wspeed, snowprecip (to be able to couple to thsice)
675      - correct Stefan-Boltzmann constant
676      - new parameter for longwave surface emittance
677      - separate some stuff from exf_bulkformulae into new routines  
678        exf_radiation, exf_wind
679      - add new parameters and constants: longwave emissivity for ocean, ice
680        and snow, evaporation parameters over ice
681      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
682        either wind from stress or stress from wind
683    o pkg/thSIce:
684    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
685    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
686       and THSICE_CALC_THICKN
687    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
688    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
689      to make debugging easier.
690    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
691    o pkg/bulk_force:
692      - clean-up comments and parameters ;
693      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
694    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
695      generate new output for test-experiment: aim.5l_cs.thSI
696    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
697      testreport accordingly
698    
699    checkpoint58e_post
700    o SEAICE_CGRID adjoint done
701    o R_STAR adjoint implemented.
702      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
703      * need to sort out init. of h0facc, etc.
704    o Make pkg/profile fully independent of ecco,cost, etc. stuff
705      to be able to use it in pure forward.
706    
707    checkpoint58d_post
708    o upgrade simple test-experiment to tutorial example:
709     step.1: duplicate the experiment and (step.2) will remove the old copy.
710      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
711      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
712      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
713      tutorial_global_oce_biogeo    <- copy of dic_example
714      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
715      tutorial_plume_on_slope       <- copy of plume_on_slope
716      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
717      tutorial_global_oce_optim     <- empty for now (David ?)
718      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
719     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
720    o correct a sign problem in cost_scat.F
721    o obcs and ptracers: fix boundary conditions for advections schemes
722      with larger stencil
723    o thsice adjoint: start
724    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
725      completeness
726    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
727      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
728    o ptracers adjoint:
729      * avoid extensive recomputatations
730      * fix missing re-init. of gptr (missed by TAF)
731    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
732      me to turn off the excessive output to STDOUT that this package produces
733    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
734      and add those terms in Vector-Invariant formulation.
735    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
736      if the control period (xx_hfluxperiod etc) is 0
737    o in profiles pkg, clean routines and fix details
738    o in ecco pkg, reading ssh data:
739      fix problem in case the model does not start at iter0=0
740    o fix mnc-pickup/restart for ptracers
741    o new package prifiles:
742      code to compute profile-based cost by Gael Forget
743      (modifs in ecco, ctrl, autodiff)
744    o Benign bug fix in initialization (spotted by M. Mazloff) of
745      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
746    
747    checkpoint58c_post
748    o adjoint: finish NLFS adjoint and provide reference output in
749      verification/global_ocean.90x40x15/results_ad_nlfs
750    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
751      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
752      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
753      with SEAICE_CGRID defined.
754    o move calendarDumps from "data" to "data.cal" and clean-up the code
755      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
756    o add useEXF & useCAL flags (for now, set in hard-coded way)
757    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
758      (were missing in NH mode, and wrong in quasihydrostatic mode).
759      waiting for Chris updated version of calc_gw to add those CALLs.
760    o fix bug in quasihydrostatic S/R ;
761      add a test for this option: global_ocean.90x40x15.qshyd
762    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
763      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
764    o add on/off flag useOffLine for package OFFLINE
765    o seaice:
766      - modify advection so that it works also on the C-grid
767      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
768        problem in multi-tile runs with C-grid
769      - add flags for clipping ice velocities and/or masking solver forcing
770      - fix drag (ocean on ice) formulation and a bug that caused noise in the
771        C-grid solver
772      - added a few comments to seaice_diffusion.F
773      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
774        are now exclusive)
775      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
776        required re-ordering the code a little:
777       + make DAIRN global variable (defined in SEAICE)
778       + move computation of the viscosities eta and zeta into a new separate
779         routine (because I need to recompute them in seaice_ocean_stress.F)
780    
781    checkpoint58b_post
782    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
783      update output.txt of exp. aim.5l_cs.thSI
784    o various mnc cleanups and improvements:
785      + shrink lookup tables by factor of ~4
786      + better error reporting when running out of lookup space
787      + able to handle longer path/file names (up to 500 chars)
788    o adjoint:
789      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
790      - TBD: "hidden" mom_vecinv recomp. in dynamics
791    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
792     (allow to differentiate between forcing components using new integer flags:
793      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
794     and add new flag to put Dissipation tendency out of Adams-Bashforth.
795    o ecco
796      - enable trend removal from SSH anomaly obs.
797    o adjoint
798      - a fix for PmEpR when #undef EXACT_CONSERV
799      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
800      - try to fix "hidden" recomp. in forward_step for NLFS
801        (NLFS seems broken sometimes after I checked it in)
802    o seaice:
803     - add c-grid version of the dynamic solver:
804       + three new routines that are the c-grid substitute lsr, dynsolver
805         and ostres
806       + put a few fields that were local to dynsolver into global common
807         blocks, so that I can move the computation of stresses etc into
808         seaice_lsr (saves coding but may break the adjoint).
809     - replace more hardwired parameters by runtime parameters
810     - add ice masks that mask the rhs of the implicit solvers where there
811       is no ice (commented out in seaice_dynsolver, because i am not sure
812       if this works properly), eventually this should replace the clipping
813       of ice velocities in seaice_dynsolver to +/-40cm/s.
814    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
815      include it only where its needed
816    o move balancing of fluxes before the call of external_forcing_surf
817    o seaice:
818      - correct units of turning angles (now they are really in degrees)
819      - move computation of GWATX/Y out of main routine into dynsolver
820      - initialize GWATX/Y in seaice_init
821    o Apply mask on Fresh-Water flux (needed for SSH forcing).
822      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
823    o seaice: add runtime flags for turning angles (default to zero)
824    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
825      and trend from exf forcing and ctrl control adjustments
826    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
827      (since checkpoint57x_post)
828    o change the default rotation period to 86164.s = the Earth rotation
829    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
830      and based on a reference stratification. Tested within hs94.cs-32x32x5.
831    o seaice advection: add code for choosing between the default (2nd order
832      central differences) and multiDim advection schemes provided by
833      pkg/generic_advdiff
834    o seaice:
835      - removed all references to SEAICE_GRID.h fields from
836        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
837        (cubed-sphere configuration will change a little)
838      - grid computations in seaice_init are obsolete now.
839      - cleaned up code a little so that is easier to read (hopefully).
840      - added new (better?) discretizations of default advection and diffusion
841        (turn on with SEAICEuseFluxForm)
842      - replace 1 in 3d global fields by kSurface in growth.F
843      
844    checkpoint58a_post
845    o seaice:
846      - bug fix in advect.F
847    o shelfice:
848      - separate shelfice load anomaly from pload (breaks with time
849        dependent forcing), => introduce constant field shelficeLoadAnomaly.
850        Its default is 0., but it may be computed more cleverly from (unknown)
851        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
852        done offline. A good approximation of the pressure load anomaly is
853        necessary to avoid large initial adjustment processes underneath
854        deep-reaching shelfice.
855      - small fix in ISOMIP shelfice_thermodynamics
856      - add more sophisticated thermodynamics of Hellmer (1989), this is
857        now the default
858      - give a few constants more intuitive names
859    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
860      if bulk formulae are used in long integration (especially EmPmR). Turn
861      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
862      if balancePrintMean, the imbalance that is substracted is printed to
863      STDOUT.
864    o fix bug (typo) in obcs_apply_eta.F
865    o add a new package shelfice which enables us to model the circulation
866      underneath shelf-ice with draughts of hundreds of meters.
867     - works
868     - to do: + include improved thermodynamics
869              + check whether kSurfC (from model/inc/SURFACE.h) can be used
870                instead of new field kTopC
871              + can we use topoFile, Ro_surf and existing code in ini_depth.F
872                instead of new field R_shelfIce and new code in ini_depth.F
873                and ini_mask_etc.F?
874              + adjust vertical mixing schemes?
875    o seaice pkg:
876     - add a cpp-flag to include a simple formula for a salinity dependent
877       freezing point of sea water at the surface
878     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
879       meridional stresses are now different (and hopefully correct)
880    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
881       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
882       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
883    o pkg/diagnostics: add options and parameters for regional-statistics
884       diagnostics ; define regions by reading a region-mask from a file
885       (might add other options later)
886    o pkg/bulk_force:
887     - add option and parameters to use AIM surface-flux formulae.
888     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
889       others forcing fields (defined in PARM05, parameter file "data") are loaded
890       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
891     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
892     - use the right EXCH call for uwind,vwind (to work on CS-grid).
893     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
894       and parameters (note: calcWindStress replaces .NOT.readwindstress).
895     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
896    
897    checkpoint58
898    o add "--embed-source" option to genmake2 which, when the supporting
899      tools can be compiled (as determined by genmake2) will turn on the
900      embed_files package which then embeds the entire MITgcm source code
901      (*.[fFhc] + Makefile) used for the build within the executable
902      - requested by CNH but off by default
903      - adds a paltry <9MB to the mitgcmuv executable in most cases
904      - only writes the output when useEMBEDSRC in eedata is true
905    o clean up 3-dim. relaxation codes:
906      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
907      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
908      * Thanks to Tom Haine for testing!
909    
910    checkpoint57z_post
911    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
912      affects output (@ truncation level) of exp. plume_on_slope ; updated.
913    o fix the pickup behavior for obcs in combination with ptracers
914    o fix a bug in ptracers_external_fields_load
915    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
916      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
917    o transfered surface NH pressure to eta field (if exactConserv).
918    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
919         and update lab_sea output.txt file.
920    o completing 3-dim. relaxation code: additional term
921         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
922      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
923      * At compile time, in "EXF_OPTIONS.h" set
924          #define  ALLOW_CLIMTEMP_RELAXATION
925          #define  ALLOW_CLIMSALT_RELAXATION
926      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
927          tauThetaClimRelax3Dim = 15552000.0,
928          tauSaltClimRelax3Dim  = 15552000.0,
929      * 3 cases:
930          1) Use a constant-in-time 3-dim. field
931          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
932          3) Real-time relax. to time-evolving prescribed field
933    o Adding Laplacian-type smoothness constraint on
934      initial and boundary (forcing) controls (ic, bc)
935      * enable at compile-time via
936        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
937      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
938      * Absolute scale somewhat unclear so far
939      * no area weighting was included since no other cost term does so far
940    
941    checkpoint57y_post
942    First step for a NLFS adjoint
943    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
944    o new init. routines for calc_r_star, calc_surf_dr
945    o still need to deal with ini_masks_etc
946    o testreport seemed happy
947    checkpoint57y_pre
948    
949    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
950    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
951    o add new offset feature to offline pkg (plus minor cleanup)
952    o cfc fixes for final year of integration
953    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
954      be in GCHEM_OPTIONS).
955    
956    checkpoint57x_post
957    o fix testreport Pb in multiple test experiment.
958    o cleanup our namelist syntax in verification:
959      - make it more F95 standards compliant (some work still needed)
960      - allows the vast majority of our tests to work with gfortran
961    o Non-Hydrostatic:
962     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
963     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
964    o Allow to apply AB on T,S rather than on AB(gT,gS):
965     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
966     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
967       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
968     - need a "clever" read_pickup to restart from the other AB formulation
969    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
970    o remove some unused variables (reduces number of compiler warnings)
971    o adjoint
972      * Disable useVariableViscosity for adjoint for time being
973        (there are a number of extensive recomputations)
974      * Initialize certain variables needed for adjoint
975    
976    checkpoint57w_post
977    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
978                 fix the singleCpuIO RS version of MDSWRITEFIELD
979       and add a WARNING if using globalFiles=T with multi-processors.
980    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
981      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
982    o tracer advection scheme:
983      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
984       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
985       was not very convenient).
986      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
987       (further tests needed for the implicit DST & Flux-Limiter schemes).
988    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
989      and sRef for convenience, handy, when you want to initialize
990      ptracers in a large domain with a constant non-zero value. Also,
991      untangle ptracers_init.F a little.
992    
993    checkpoint57v_post
994    o change dome exp. to use variable viscosity in side-drag terms.
995    o remove all the files from the cfc_offline test since they are now
996      incorporated into tutorial_cfc_offline which has been producing
997      identical results for a few days of testing
998    o add new parameter: sideDragFactor to enable half-slip-side BC
999      and change side-drag S/R to use viscosity from mom_calc_visc
1000      (can switch back by setting sideDragFactor=0.); affects results at
1001      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
1002       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
1003    o vorticity & strain are now computed without masking, to account for
1004      no-slip-side BC in variable viscosity calculation ; mask is applied
1005      anyway later on, before computing advection/coriolis terms.
1006    o modify exp4 to test new obcs support for reading from external files
1007      and for passive tracers
1008    o fix behavior of ptracers_monitor when monitor output is written to a
1009      netcdf-file; still not independent of monitor.F (writes in the same
1010      file).
1011    o change default value of tRef (put a uniform, meaningful value for ocean
1012      & atmos) and initialize sRef (was missing, as Martin mentioned).
1013    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
1014      to be proportional to enstrophy dissipation length.  Thus,
1015       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
1016      This is now consistent with Smagorinsky and with the manual.
1017    
1018    checkpoint57u_post
1019    o OBCS and PTRACERS: add open boundary support for passive tracers
1020      - either use homogenous (pseudo) v.Neumann conditions or prescribe
1021        OB-values from file; this is not different from the way theta and salinity
1022        are treated
1023      - however, Orlanski-radiation conditions are not supported, and the model
1024        will stop if you use pTracers and Orlanski at the same time.
1025      - beefed up the rountine obcs_external_fields_load: now only those open
1026        boundary values are overwritten with values from files for which there
1027        are really files, otherwise the OB-fields remain untouched. This makes
1028        it possible to use different OBs at different ends of the domain (as
1029        with EXF)
1030    o reduce number of exch calls in shap_filt (s2).
1031    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1032      truncation level) 4/5 MLAdjust test results (11&12 digits match).
1033    
1034    checkpoint57t_post
1035    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1036    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1037      same truncation, independent of the face number: affects affects several
1038      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1039    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1040      note that biharmonic viscosity + no-slip was not tested in any experiment.
1041    o fix bug in non-linear free-surf side-drag ; generate new output for
1042      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1043    o make mnc honor the writeBinaryPrec flag for most kinds of output
1044    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1045    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1046      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1047    o add brackets in multi-terms sum to get same truncation, independent of
1048      the face number (manage to get exactly same value of gU,gV at the cs-edge)
1049      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1050    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
1051      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1052      a maximum grid-scale Reynolds number.  Also, changes all length calculations
1053      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1054      Suggested values of viscosity parameters found in mom_calc_visc.
1055      Many new viscosity diagnostics available.
1056    
1057    checkpoint57s_post
1058    o Add clearing-house for viscosity calculations, mom_calc_visc and
1059      correct numerous bugs in LeithD and Smagorinsky discretizations.  
1060      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1061      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1062      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1063      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
1064      The Strain-Tension form is now called with useStrainTensonVisc=.true.
1065      ViscAhStrain and viscAhTension are now retired.
1066    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1067    o In response to JMC's bug report, genmake2 now ignores any soft-links
1068      that it finds in the *current* directory when searching for files.
1069      Soft-links found in any other source directories will still work as
1070      they did before.
1071    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1072      a C routine to unlimit the stack size
1073    o mnc-ify pkg/aim snapshot vars
1074    o mnc-ify pkg/land as requested by Daniel
1075    o various changes to mnc including:
1076      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1077      - output can now be grouped so that all files within a group
1078          change the ITER portion of their names in lock-step together
1079      - can now read ("global") PER-FACE (in addition to PER-TILE) files
1080          and works with both EXCH1 and EXCH2 (but needs more testing)
1081      - writing works for all verification test cases w/ g77 on Linux
1082    
1083    checkpoint57r_post
1084    o make MNC variable initialization happen earlier
1085    o add diagnostics for (almost) each term of the momentum Eq.
1086    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1087    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1088    o remove MINIMAL_TAVE_OUTPUT option ;
1089      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1090    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1091      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1092    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1093    o add time-dependent SST, SSS control
1094    o cost terms in ecco/ modularized (new cost_generic.F)
1095    o cost_averages routines are modularized (new cost_averagesgeneric.F)
1096    o new infrastructure for seaice model vs. obs misfits in seaice/
1097      * driver from the_main_loop.F is seaice_cost_driver.F
1098      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1099      * gradient check in Exp. 6a of natl_box_adjoint/
1100    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1101      (see README file)
1102    
1103    checkpoint57q_post
1104    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1105    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1106      - bug was reported by Jean-Michel and Ian Fenty
1107    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1108      update exp. cpl_aim+ocn output.
1109    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1110      Needed for high-res. runs with large global files
1111      to be able to limit tapelev size
1112    o Changed some tests for adjoint:
1113      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1114      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1115      * global_ocean.90x40x15/ back to default 3-level checkpointing
1116    o Modifications to enable scripted COMMON to MODULE conversion
1117      * verification/OpenAD/code/ has necessary scripts and description;
1118      * converts, compiles and runs successfully;
1119    
1120    checkpoint57p_post
1121    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1122    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1123      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1124    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1125    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1126      (was already the case for dissipation with mom_vecinv,
1127       and also the case for grad.PhiHyd when staggered-timeStep)
1128      This will allow to put dissipation out-off the AB time-stepping.
1129     Unfortunately, affects truncation error. Update output of exp. that "fails"
1130      (cg2d matching number) and leave the others for later: front_relax(10),
1131      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1132      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1133    
1134    checkpoint57o_post
1135    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1136      (2) its ready to be documented during the 20050801 DocFest
1137    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1138      for ideal_2D_oce and lab_sea on linux_ia32_g77
1139    o set to #undef CTRL_SET_OLD_MAXCVARS_30
1140      in global1x1_tot/code_seaice_adj to access indices 32, 33
1141      (worth another tag)
1142    
1143    checkpoint57n_post
1144    o adding precip control xx_precip 32
1145    o adding swflux control xx_swflux 33
1146    o Replacing 10 forcing penalty cost routines by 1 generic.
1147    o Implementing partitioning in time-mean and variable adjustment
1148      for atmos. state.
1149    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1150  o in natl_box_adjoint:  o in natl_box_adjoint:
1151    * updated: results_bulk/    * updated exp 1 to 10
1152    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
1153    o updated global1x1/*_seaice_adj/
1154      to incorporate latest changes
1155    o enable useSingleCpuIO for mdsio vector routines
1156      (applies in particular to tapelev I/O)
1157    o removed inefficient K-loop in all active_file*control*.F
1158    
1159  checkpoint57m_post  checkpoint57m_post
1160  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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