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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.862 by jmc, Tue Aug 21 14:39:43 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  checkpoint59f
8  o moved ptracer ctrl index 17 -> 32  o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
9    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
10      a bounded range (in forward mode)
11    o pkg/ecco, ctrl, autodiff and mom_common:
12     internal parameter controls, completements of implementations
13    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
14    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
15      (not seem any difference in testing results).
16    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
17       at face corners.
18    o pkg/generic_advdiff:
19     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
20      loop range indices for computing vertical advection tendency
21      and do the calculation in the interior only (no overlap) ;
22      for now, only implemented for SOM advection (to save CPU time).
23     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
24    o exch2 adjoint
25      First set of changes:
26      - add exch2 hand-written adjoint templates
27      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
28        This will require cleanup in pkg/autodiff/*.F
29        (changed routines currently kept separate in verif. code/)
30      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
31        that used to hide exch2 or cubed-sphere specific code
32        (commented via 'cph-exch2')
33    o pkg/seaice
34      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
35    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
36       output of global_ocean.cs32x15.thsice .
37    
38    checkpoint59e
39    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
40      for B-grid vector (not yet tested) and C-grid vector (<- only used
41      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
42    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
43      (#ifdef ALLOW_SALT_PLUME)
44    o gather_2d/scatter_2d: removed halo regions
45    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
46      scheme and the corresponding test case (under front_relax dir). For now,
47      only available with Skew-flux form and not yet tested in realistic set-up.
48      adjoint: store directives updated, but gradient checks deteriorated,
49      so maybe GM/Redi adjoint is now broken.
50    o seaice adjoint
51      * add AREA, HEFF, HSNOW as control variable
52        (should not change lab_sea results)
53      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
54    o pkg/seaice:
55      * added computation of saltFlux in seaice_growth;
56        For time being, sea ice salinity is assumed constant
57        contribution of snow flooding to freshening of sea ice is neglected.
58        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
59        defaults to 0.0 in order to maintain backward compatibility.
60        Typical values for SEAICE_salinity are 4 to 10 g/kg.
61      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
62      * added SEAICE_availHeatFrac, which specifies fraction of surface level
63        heat content used to melt or grow ice
64      * commented out cap of HICE: it helps keep ice thinner
65      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
66      * applied OBCS T/S mask to HEFFM sea ice mask
67    
68    checkpoint59d
69    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
70     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
71     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
72    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
73     and change default value of parameter "GM_Small_Number";
74     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
75       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
76       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
77    o pkg/ecco: cost function when applying pkg/smooth to controls
78    o pkg/ctrl: add forcingPrecond run time parameter
79    o pkg/seaice:
80     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
81     - fix bug in metric terms of u-equation in LSR solver (implicit part),
82       changes verification/lab_sea
83     - rearrange implicit part of u-equation in LSR solver to make it easier to
84       read, understand, and debug. This causes changes at the truncation level.
85     - fix (serious) bug in the boundary conditions (sign error in the implicit
86       part) of the LSR solver. Changes all LSR results.
87     - fixed problem with HSNOW initialization to avoid thick snow when AREA
88       is initilized with small values - does not change lab_sea results.
89     - added HsnowFile initialization capability
90    o pkg/smooth: addition to model/src and pkg/ctrl so allow
91     initialization of pkg/smooth and application to control vector
92    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
93    o dependencies: pkg/profiles requires pkg/cal
94    o pkg/profiles:
95     - added option ALLOW_PROFILES_GENERICGRID
96         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
97         that interpolation information (grid points and coefficients) is provided
98         within the netcdf input files.
99         -> sample matlab scripts can be found in MITgcm_contrib/gael
100         that allow you to prepare netcdf input files.
101     - also modified: cleaner include statements, cleaner error print statements,
102       cleaner stops when error, and more tests of the netcdf input files consistency.
103    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
104    o pkg/seaice:
105     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
106       requires a new routine: seaice_diagnostics_fill.F
107     - make sure that seaice does not move if not forced (pressure replacement
108       method, Hibler and Ip, 1995), changes results
109     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
110     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
111       It is turned off by default (=-1.), because it changes the results.
112     - make it possible to read AREA from a file, too.
113    
114    checkpoint59c
115    o add S/R and diagnostics for oceanic mixed-layer depth
116    o move GMRedi call after all vertical mixing schemes (including KPP)
117    o pkg/thsice:
118     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
119      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
120    o pkg/obcs:
121     - bug fix for balance code
122    o pkg/seaice:
123      - allow values of SEAICE_elasticParm > 1
124      - add new parameter SEAICE_evpTauRelax as an alternative
125        to SEAICE_elasticParm
126      - make lsr boundary conditions free slip (by default), changes result
127      - add code for no slip boundary conditions for lsr
128      - set minimum of zeta to zero (and not 4e8) (changes results)
129      - add a cap on AREA after advecting AREA if seaice_growth is not called
130    o change calculation of Visbeck K:
131      - no longer depend on tapering scheme; instead, compute slope (limited
132        by GM_maxSlope). this is equivalent to what was comuted before with
133        clipping or linear tappering.
134      - fix vertical averaging (wrong by 1/2 level)
135      - leave the old version (but will not be maintained) within
136        #ifdef OLD_VISBECK_CALC / #endif
137      - update output of exp. ideal_2D_oce
138    o change error catch in calc_r_star to improve vectorization
139    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
140      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
141    o adjoint:
142      Re-organized adjoint checkpointing according to Matt Mazloff
143      (but with modifs/completions/cleanups)
144      Storing is now bundled into large arrays to optimized I/O
145      (and second step in cleanup of the_main_loop)
146    
147    checkpoint59b
148    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
149      - export/import (between ocean & coupler) fields needed for ocean DIC.
150    o pkg/seaice:
151      - get rid of three more exchanges seaice_calc_viscosities (required
152        different loop boundaries in seaice_lsr and seaice_ocean_stress)
153      - bug fix in seaice_ocean_stress (update of lab_sea required)
154      - reduce loop boundaries to necessary minimum also in seaice_evp
155      - go back to the old way of computing deltaC/Z as the adjoint likes that
156        better
157    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
158      passive tracer to an Age Tracer) + update output.txt
159    o pkg/exf:
160      - implement A-grid / C-grid selection for wind-stress input files.
161      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
162      for now, in exf_bulk_largeyeager04.F only :
163      - change implementation for case where windspeed + 2. components wind-stress
164        are read-in. AND use rhoConstFresh to convert evap.
165    o pkg/seaice:
166      - use correct EXCH_UV for wind-forcing (on A-grid).
167      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
168        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
169    o pkg/exf:
170      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
171      EXF_INTERPOLATION:
172      - merge global_with_exf/code version of exf_interp_read.F
173        to the main code ;
174      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
175        reading the file ; Important: This options needs to be defined to recover
176        previous code.
177        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
178      - no longer loose real*8 precision along the way when using exf_iprec=64.
179    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
180      - change discretisation of evp-solver in order to avoid another exchange
181        (changes lab_sea) and clean up a little
182      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
183        help the adjoint (this also changes the results slightly)
184      - add a few "_d 0" where they had been missing in seaice_evp.F
185      - cleaning up: remove unused seaice_calc_rhs.F
186    o pkg/exf: some cleaning-up:
187      - change various "constants" into runtime parameters
188      - cleaned-up Large&Yeager04 routine which should eventually
189        replace exf_bulkformulae.F (changed names of S/R and CPP)
190        and merged various ALLOW_ATM_WIND options
191     only used with thsice pkg (in thsice_get_exf.F):
192      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
193        which are used when useStabilityFct_overIce=TRUE (= the default)
194      - change default values of ice & snow emissivity and scale downward LW
195        by ice & snow emissivity.
196    o pkg/thsice:
197     fix few little problems, in thsice_calc_thickn.F:
198      - growth vertically (and not laterally) if iceFrac == iceMaskMax
199      - melt only laterally if hIce < hThinIce (as the comments say)
200      and in thsice_extend.F:
201      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
202      - start to form ice as soon as the minimum ice-volume is reachable.
203     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
204      and cpl_aim+ocn
205    o pkg/kpp
206     - move computation of surface related input fields to KPP into a new
207       subroutine kpp_forcing_surf.F
208     - remove wrong (within bi,bj loops) EXCH calls.
209     - little cleaning (add argument myThid in last position, cvs header ...)
210     - for now, fix conservation problem by exchanging KPPviscAz (may not
211       be the best fix)
212    o pkg/seaice
213     - check for inconsistent evp parameter/cpp-flag combination
214     - remove leftover errIO flat for obsolete name list error handling
215    o OpenAD
216     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
217    
218    checkpoint59a
219    o pkg/seaice: some parameter clarifications and a little bit of clean up
220    o pkg/thsice: rename run-time parameters:
221       himin       -> hIceMin
222       himin0      -> hThinIce
223       hihig       -> hThickIce
224       i0          -> i0swFrac
225       transCoef   -> bMeltCoef
226       frac_energy -> fracMelting
227      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
228       with default values (for now) that do not change the results.
229      remove old version of thsice vars advection in pkg/seaice.
230    o in FFIELDS.h:
231      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
232      - make pLoad & sIceLoad always available (but still only used if
233         ATMOSPHERIC_LOADING is #define).
234    o pkg/kpp: replaced _KPP_RL with _RL
235    o bug fixes for vertical diffusivity computations when both KPP and
236        3D diffusivity arrays are used.
237    o pkg/seaice: fix bug in evp solver, while doing that
238      - change (improve?) discretization of stress computations for both
239        cgrid-lsr and evp solver
240      - add a new routine to compute strain rates
241      - the above changes lab_sea results
242      - add no slip conditions for evp solver (off by default), lsr-version
243        may follow
244      - fix exchange for shear at Z-points (does not change lab_sea)
245      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
246        (to force the user to pick a time step since there is not "safe" way
247        of choosing it)
248      - add principal stress diagnostics
249      - rearrange fields for evp a little to avoid having to call a: too many
250        exchanges and b: exchanges for stress trensor components which we do
251        not have.
252      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
253        of evp, complete rewrite for lsr case (latter is does not yet work
254        in all cases)
255    o pkg/kpp: add code to have mixing in shelf ice caverns
256      - add myThid to all kpp routines (long overdue)
257    
258    checkpoint59
259    o pkg/exf:
260      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
261        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
262      - move exf header files from lower_case.h to UPPER_CASE.h ;
263        add missing cvs Header & Name
264      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
265      - add namelist param. selectStressGridPosition, exf_monFreq
266      - retire many _CLIM routines, and remove data.exf_clim
267        + params moved to data.exf
268        + climsst, climsss now handled by exf_set_gen, i.e.
269          climss?period=0 refers to constant field,
270          climss?period=-12 to monthly forcing
271      - split up namelists in data.exf
272    o pkg/seaice:
273      - remove seaice_exch and seaice_exch_uv
274      - remove superfluous exchange of theta
275      - add myThid to seaice_budget_ocean/ice
276      - add new interface for atmospheric wind forcing (C-grid only)
277        + new routine
278        + two new field (taux, tauy for stress over ice)
279        + removed one global field (DAIRN) for C-grid case only
280    o pkg/thsise
281      - 2nd set of modifs for thsice adjoint in conjunction with exf
282    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
283    
284    checkpoint58y_post
285    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
286      vertical diffusivity, similar to that in MOM4; turned on using
287      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
288      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
289    o Added capability for 3D specification of background vertical diffusion
290      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
291      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
292      "data" file that contains the 3D vertical diffusivity coefficients.
293    o ice dynamics (pkg/seaice) with thsice thermodynamics:
294      - add code within pkg thsice to advect & diffuse sea-ice fields
295      similar to (and will replace) what has been added in  seaice_advdiff.F,
296      but: - conserving Mass, Heat & Salt.
297           - better when using non-linear advection scheme (not yet fully tested)
298           - can also be used in atmospheric set-up (for now, only the diffusion).
299    
300    checkpoint58x_post
301    o IO option for global-file compact format:
302      - add options when generating topology (utils/exch2/matlab-topology-generator)
303      - add I/O capability (pkg/mdsio).
304      - adapt utils/matlab/rdmds.m to read this format.
305      for now long-line format not yet supported by pkg/mdsio (& exch2).
306    o shelfice: add a few diagnostics
307    
308    checkpoint58w_post
309    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
310      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
311      (and replace horiVertRatio in NH code).
312      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
313                         and tutorial_plume_on_slope (sensitive to truncation)
314    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
315      directly to drive seaice model (C-grid only)
316    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
317     - reintroduce computation of wind from stress,
318     - compute tau (in exf_bulkformulae.F) from windstress averaged to
319       mass points to avoid tau = 0
320     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
321    o rdmnc.m: make it work with "global" files created with gluemnc
322    o rdmnc.m : some improvements in dealing with singleton dimension
323      (tested on all testreport mnc output files).
324    o genmake2: disable pkg/profiles if netcdf test fails.
325    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
326    o move call to cal_readparms up to make calendar parameters/variable available
327      to all packages
328    
329    checkpoint58v_post
330    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
331      useDynP_inEos_Zc tested.
332    o pkg/exf: changes to properly interpolate/mask/scale initial fields
333    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
334      and portions thereof.  See read_cs.txt for description and examples.
335    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
336      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
337      following the great-circle arc between those 2 points.
338    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
339      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
340    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
341     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
342     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
343     - still needs work (not working with some options ; efficiency to improve)
344       and serious testing.
345     - use this scheme for temperature & salinity in 2 advection test exp.:
346       advect_xy & advect_xz, respectively.
347    
348    checkpoint58u_post
349    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
350    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
351    o testreport: add option "-skipdir" to skip some test.
352    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
353      momentum calculation.
354    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
355    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
356      remove checkpoint.F and the_correction_step.F (no longer used);
357      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
358    o add option (linFSConserveTr) to correct for tracer source/sink due to
359      Linear Free surface
360    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
361    o pkg/thsice: fix reading mnc-pickups
362    
363    checkpoint58t_post
364    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
365    o pkg/mdsio:
366     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
367       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
368       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
369     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
370     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
371       either MDS_READ_FIELD or MDS_WRITE_FIELD )
372     - new S/R (to replace MDSWRITEMETA), which allows to write more
373       informations (variable names, time ...) to meta files.
374     - modify rdmds.m to give back the meta file content.
375    o pkg/diagnostics: change vertical interpolation to be safer, and more
376       flexible (define p-levels to interpolate to in data.diagnostics);
377      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
378       diagnostic pointer.
379    o pkg/seaice: more cleaning up of seaice_growth, added many comments
380    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
381    o fix multi-category seaice:
382     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
383       SEAICE_MULTICATEGORY
384     - fix short wave heat flux
385    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
386       and allow to use EVP solver. Change forward lab_sea: test both EVP
387       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
388    o Initial check-in of lab_sea adjoint
389      (very similar to natl_box_adjoint/code_seaice)
390      * used C-grid and EVP solver
391      * used KPP, GM/Redi
392      * uses inAdExact=.TRUE.
393      * gradient checks fail for both ADM and TLM
394        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
395        f.d. gradients actually seem more problematic than ADM, TLM gradients;
396        issue is related to forward mismatch between g77 an ifort
397    o pkg/seaice: overhaul of thermodynamics
398     - growth.F and groatb.F are replaced by new routine seaice_growth.F
399     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
400     - move a few global fields out of SEAICE.h into seaice_growth.F and
401       make them 2D (FICE/QNETO/ ...)
402     - remove FO (it is the same as QNETO)
403     - introduce a few local fields to avoid modifying external fields such
404       as atemp, etc.
405    
406    checkpoint58s_post
407    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
408      changed exf_set_gen.F so that
409        genperiod=0 means input file is one time-constant field and
410        genperiod=-12 means input file contains 12 monthly means
411    o CG2D: use pre-computed solver main-diagonal (stored in common block);
412      this affects truncation error ; generate new output file for exp. which
413      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
414        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
415        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
416        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
417        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
418        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
419    o start implementation of deep-atmosphere and anelastic formulation
420    o verification: remove 2nd copy of input files and use script "prepare_run"
421      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
422    o mom_common/vecinv/fluxform: fix a few initialisation isssues
423    o profiles: fix for multithreaded case
424    
425    o diagnostics: rename few diags:
426      s/'PRESSURE'/'RCENTER '/g
427      s/'TICE    '/'oceFreez'/g
428      s/'TAUX    '/'oceTAUX '/g
429      s/'TAUY    '/'oceTAUY '/g
430      s/'SWFLUX  '/'oceQsw  '/g
431      s/DIFx/DFxE/g
432      s/DIFy/DFyE/g
433      and add few ocean-forcing diagnostics:
434      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
435    o modifications to pkg/seaice/growth.F and budget.F, which change results of
436      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
437      as actual snow thickness.  It now refers everywhere to effective snow
438      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
439    
440    checkpoint58r_post
441    o modifications to pkg/seaice/growth.F, which change results of
442      lab_sea experiment: fixes pertain to melting snow over open water, to
443      masking EVAP under sea ice, and to using the correct AREA variable for
444      computations of EVAP, PRECIP, HSNOW, and GHEFF
445    o add ability to read bathy, salt, and theta using MNC (off by def)
446    o add flooding algorithm and advection of HSNOW for pkg/seaice;
447      both are turned off by default and do no change any results
448    o seaice advection with pkg/thsice: a step toward the use of non-linear
449      advection scheme, but #ifdef or commented out for now (requires more EXCH).
450    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
451      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
452      in natl_box (affects results @ truncation level: update output.txt)
453    o multi-threading and IO:
454      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
455      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
456        (needed to work with SingleCpuIO): tested in all verif. exp.
457    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
458      affects the results (but none of the verification test uses this scheme).
459    o Adding some pkg/diagnostics capability to pkg/seaice
460      (will certainly be subject to changes)
461    o ctrl: adding new control variables:
462      lwflux, lwdown, evap, snowprecip, apressure, runoff
463    
464    checkpoint58q_post
465    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
466      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
467      high_res_cube configuration by 4% on Columbia.
468    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
469      add (in global_with_exf/code) a version of EXF_INTERP_READ without
470      dynamical allocation (seems to work in multi-threaded).
471    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
472      single CPU io) so that TAF does not have to see EESUPPORT.h
473    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
474    
475    checkpoint58p_post
476    o obcs: stop if obcs is used with useCDscheme = .true.
477    o shelfice:
478     - fix a sign error so that no slip at shelfice interface works
479     - remove stop for combination non-hydrostatic code and shelfice. That does
480       not mean, that the results are correct, but at least they are numerically
481       stable
482    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
483    o added adjoint exch routined for all exch*3d* routines
484      and updated flow directives
485    
486    checkpoint58o_post
487    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
488      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
489    o change controling S/R for writing pickup file (new S/R do_write_pickup)
490      and clean-up reading/writing of pickup files.
491    o fix local version of read/write pickup (NH part) in rotating_tank/code
492    o simplify EXCH interface:
493     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
494     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
495    o added the regrid package
496    o shelfice:
497     - add a simple boundary layer scheme to reduce noise
498     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
499    
500    checkpoint58n_post
501    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
502       local variable (not in common block).
503    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
504      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
505      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
506        to work with SingleCpuIO.
507    o add "_d 0" to real constant of pkg/cfc subroutines ;
508       update exp. cfc_exemple & tutorial_cfc_offline output files.
509    o multi-threading and IO:
510      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
511        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
512      - barrier before and after reading.
513      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
514      - avoid using MDS_WRITELOCAL for LAND pkg output.
515      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
516        common-block variables ; Allows multi-threading with master-thread IO.
517    o change default MAX_NO_THREADS from 32 to 4 ;
518      and stop cleanly when MAX_NO_THREADS is too small.
519    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
520    
521    checkpoint58m_post
522    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
523       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
524    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
525       keep global_ocean.90x40x15 (for AD testing) with former secondary test
526       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
527    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
528        add MITgcm_tutorials (= code + all the tutorials)
529    o ecco, option to compute cost for total ssh (mean+anom)
530    o consistent with addition of ptracer and ssh in pkg/profiles
531    o profiles: adding ptracer and ssh
532    o testreport: change multi-test output-file name
533      (from output.txt.{name} to output.{name}.txt)
534    o profiles: now ok for mutli-tiles case
535    o seaice: add 4 parameters for different advection schemes for area,
536      (effective) seaice thickness, enthalphy, and snow height. Their default
537      is the standard parameter SEAICEadvScheme
538    o calc_gw:
539     - add cosFacU in zonal viscous flux (harmonic.visc.).
540     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
541       of tutorial_plume_on_slope.
542    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
543    o calc_gw: true flux-form, account for horizontal grid spacing.
544      update rotating_tank results, but not plume_on_slope (affected at
545      truncation level, 11 digits).
546    
547    checkpoint58l_post
548    o calc_gw:
549     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
550     - remove side-drag for now (need to fix it); update plume_on_slope results.
551     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
552    o commit code to make SST/SSS weights spatially variable
553      (based on either variable in-situ or variable initial T/S weights)
554    o pkg/ecco:
555      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
556        now based on horizontally varying weights wthetaLev, wsaltLev
557      * cost_averagesflags now returns year indices in addition to day, month
558      * sflux balance is performed on annual basis
559        (sflxumm, sfluxmm2, bal_sfluxmm)
560      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
561        including separate counting and multipliers
562    o pkg/rbcs
563      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
564    
565    checkpoint58k_post
566    o testreport:
567     - always build in dir. "build" (if not there, mkdir build instead of building
568       & running in input)
569     - run in dir run (if it exists), in build otherwise.
570     - call prepare_run (if input/prepare_run exists)
571     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
572    o pkg/exf modifications to interpolation and rotation routines for more
573       reasonable treatment of North Pole singularity: for tracers North Pole
574       value is set to northernmost zonal-mean value, for zonal velocity it is
575       set to zero, and for meridional velocity it is set to northernmost value.
576    o pkg/exf/exf_check_range.F
577     - add tile index to diagnostics and move stop statement to the very
578       end of the routine.
579    o pkg/diagnostics: (diagnostics_main_init.F)
580      define title of isomorphic variables according to the current config.
581    o pkg/thsice with pkg/seaice dynamics:
582    - fix domain of computation (interior only, required for exf) and do exchanges
583    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
584    o towards a standard way of dealing with multi-threading in MONITOR
585      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
586    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
587       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
588    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
589    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
590    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
591       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
592    o tracer advection:
593     - clean-up and simplify calc_common_factors.F
594     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
595       advection subroutine (but still not used within DST advection S/R)
596    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
597    
598    checkpoint58j_post
599    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
600      from file (collects calls previously in FORWARD_STEP)
601    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
602    o adjoint store dir. adjusted accordingly
603    o genmake2
604      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
605    
606    checkpoint58i_post
607    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
608      on wind stress (SEAICEstressFactor defaults to 1.)
609    o Total number of Timers is finite (<=40): comment out 2 non-essential one
610      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
611    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
612      on CS-grid: no longer loosing mass.
613    o exf & curvilinear-grid: no longer modify longitude xC & xG.
614    o pkg/ggl90: fix sloppy output and fix a bug
615    o pkg/seaice: added SEAICEuseEVPpickup parameter
616      - Set to false in order to start EVP solver with
617        non-EVP pickup files when using SEAICEuseEVP
618      - fix sign error in diffusion in seaice_calc_rhs
619    
620    checkpoint58h_post
621    * Modifications for bottom topography control
622      o replace hFacC by _hFacC at various places
623      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
624      o add non-self-adjoint cg2d_nsa
625      o update autodiff support routines
626      o re-initialise hfac after ctrl_depth_ini
627      o works for 5x5 box, doesnt work for global_ocean.90x40x15
628    * Adding verification for 5x5 box (4-layer) bottom topography control
629    
630    checkpoint58g_post
631    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
632       used for mean seasonal cycle, mean diurnal cycle); add an example
633       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
634    o pkg/ggl90:
635      - add parameter (minimum surface kinetic energy)
636      - fix bug (avoiding division by zero)
637    o couple pkg/thsice to pkg/seaice:
638      - modify advection in seaice to accomodate new scalar fields to be advected
639      - only muliDimAdection scheme work with seaice/thsice
640      - mapping of thsice-variables to seaice-variables, back and forth
641      - does not break the verification experiments, but does not give the
642        desired results either
643    o pkg/seaice
644      - make (default) second order advection a bit less confusing?
645    
646    checkpoint58f_post
647    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
648      to pkg/seaice):
649      - new routines thsice_map_exf and thsice_get_exf provide the interface
650      - add an additional formal parameter to thsice_solve4temp
651    o pkg/exf:
652      - add new fields wspeed, snowprecip (to be able to couple to thsice)
653      - correct Stefan-Boltzmann constant
654      - new parameter for longwave surface emittance
655      - separate some stuff from exf_bulkformulae into new routines  
656        exf_radiation, exf_wind
657      - add new parameters and constants: longwave emissivity for ocean, ice
658        and snow, evaporation parameters over ice
659      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
660        either wind from stress or stress from wind
661    o pkg/thSIce:
662    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
663    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
664       and THSICE_CALC_THICKN
665    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
666    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
667      to make debugging easier.
668    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
669    o pkg/bulk_force:
670      - clean-up comments and parameters ;
671      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
672    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
673      generate new output for test-experiment: aim.5l_cs.thSI
674    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
675      testreport accordingly
676    
677    checkpoint58e_post
678    o SEAICE_CGRID adjoint done
679    o R_STAR adjoint implemented.
680      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
681      * need to sort out init. of h0facc, etc.
682    o Make pkg/profile fully independent of ecco,cost, etc. stuff
683      to be able to use it in pure forward.
684    
685    checkpoint58d_post
686    o upgrade simple test-experiment to tutorial example:
687     step.1: duplicate the experiment and (step.2) will remove the old copy.
688      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
689      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
690      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
691      tutorial_global_oce_biogeo    <- copy of dic_example
692      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
693      tutorial_plume_on_slope       <- copy of plume_on_slope
694      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
695      tutorial_global_oce_optim     <- empty for now (David ?)
696      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
697     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
698    o correct a sign problem in cost_scat.F
699    o obcs and ptracers: fix boundary conditions for advections schemes
700      with larger stencil
701    o thsice adjoint: start
702    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
703      completeness
704    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
705      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
706    o ptracers adjoint:
707      * avoid extensive recomputatations
708      * fix missing re-init. of gptr (missed by TAF)
709    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
710      me to turn off the excessive output to STDOUT that this package produces
711    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
712      and add those terms in Vector-Invariant formulation.
713    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
714      if the control period (xx_hfluxperiod etc) is 0
715    o in profiles pkg, clean routines and fix details
716    o in ecco pkg, reading ssh data:
717      fix problem in case the model does not start at iter0=0
718    o fix mnc-pickup/restart for ptracers
719    o new package prifiles:
720      code to compute profile-based cost by Gael Forget
721      (modifs in ecco, ctrl, autodiff)
722    o Benign bug fix in initialization (spotted by M. Mazloff) of
723      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
724    
725    checkpoint58c_post
726    o adjoint: finish NLFS adjoint and provide reference output in
727      verification/global_ocean.90x40x15/results_ad_nlfs
728    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
729      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
730      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
731      with SEAICE_CGRID defined.
732    o move calendarDumps from "data" to "data.cal" and clean-up the code
733      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
734    o add useEXF & useCAL flags (for now, set in hard-coded way)
735    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
736      (were missing in NH mode, and wrong in quasihydrostatic mode).
737      waiting for Chris updated version of calc_gw to add those CALLs.
738    o fix bug in quasihydrostatic S/R ;
739      add a test for this option: global_ocean.90x40x15.qshyd
740    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
741      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
742    o add on/off flag useOffLine for package OFFLINE
743    o seaice:
744      - modify advection so that it works also on the C-grid
745      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
746        problem in multi-tile runs with C-grid
747      - add flags for clipping ice velocities and/or masking solver forcing
748      - fix drag (ocean on ice) formulation and a bug that caused noise in the
749        C-grid solver
750      - added a few comments to seaice_diffusion.F
751      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
752        are now exclusive)
753      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
754        required re-ordering the code a little:
755       + make DAIRN global variable (defined in SEAICE)
756       + move computation of the viscosities eta and zeta into a new separate
757         routine (because I need to recompute them in seaice_ocean_stress.F)
758    
759    checkpoint58b_post
760    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
761      update output.txt of exp. aim.5l_cs.thSI
762    o various mnc cleanups and improvements:
763      + shrink lookup tables by factor of ~4
764      + better error reporting when running out of lookup space
765      + able to handle longer path/file names (up to 500 chars)
766    o adjoint:
767      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
768      - TBD: "hidden" mom_vecinv recomp. in dynamics
769    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
770     (allow to differentiate between forcing components using new integer flags:
771      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
772     and add new flag to put Dissipation tendency out of Adams-Bashforth.
773    o ecco
774      - enable trend removal from SSH anomaly obs.
775    o adjoint
776      - a fix for PmEpR when #undef EXACT_CONSERV
777      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
778      - try to fix "hidden" recomp. in forward_step for NLFS
779        (NLFS seems broken sometimes after I checked it in)
780    o seaice:
781     - add c-grid version of the dynamic solver:
782       + three new routines that are the c-grid substitute lsr, dynsolver
783         and ostres
784       + put a few fields that were local to dynsolver into global common
785         blocks, so that I can move the computation of stresses etc into
786         seaice_lsr (saves coding but may break the adjoint).
787     - replace more hardwired parameters by runtime parameters
788     - add ice masks that mask the rhs of the implicit solvers where there
789       is no ice (commented out in seaice_dynsolver, because i am not sure
790       if this works properly), eventually this should replace the clipping
791       of ice velocities in seaice_dynsolver to +/-40cm/s.
792    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
793      include it only where its needed
794    o move balancing of fluxes before the call of external_forcing_surf
795    o seaice:
796      - correct units of turning angles (now they are really in degrees)
797      - move computation of GWATX/Y out of main routine into dynsolver
798      - initialize GWATX/Y in seaice_init
799    o Apply mask on Fresh-Water flux (needed for SSH forcing).
800      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
801    o seaice: add runtime flags for turning angles (default to zero)
802    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
803      and trend from exf forcing and ctrl control adjustments
804    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
805      (since checkpoint57x_post)
806    o change the default rotation period to 86164.s = the Earth rotation
807    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
808      and based on a reference stratification. Tested within hs94.cs-32x32x5.
809    o seaice advection: add code for choosing between the default (2nd order
810      central differences) and multiDim advection schemes provided by
811      pkg/generic_advdiff
812    o seaice:
813      - removed all references to SEAICE_GRID.h fields from
814        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
815        (cubed-sphere configuration will change a little)
816      - grid computations in seaice_init are obsolete now.
817      - cleaned up code a little so that is easier to read (hopefully).
818      - added new (better?) discretizations of default advection and diffusion
819        (turn on with SEAICEuseFluxForm)
820      - replace 1 in 3d global fields by kSurface in growth.F
821      
822    checkpoint58a_post
823    o seaice:
824      - bug fix in advect.F
825    o shelfice:
826      - separate shelfice load anomaly from pload (breaks with time
827        dependent forcing), => introduce constant field shelficeLoadAnomaly.
828        Its default is 0., but it may be computed more cleverly from (unknown)
829        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
830        done offline. A good approximation of the pressure load anomaly is
831        necessary to avoid large initial adjustment processes underneath
832        deep-reaching shelfice.
833      - small fix in ISOMIP shelfice_thermodynamics
834      - add more sophisticated thermodynamics of Hellmer (1989), this is
835        now the default
836      - give a few constants more intuitive names
837    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
838      if bulk formulae are used in long integration (especially EmPmR). Turn
839      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
840      if balancePrintMean, the imbalance that is substracted is printed to
841      STDOUT.
842    o fix bug (typo) in obcs_apply_eta.F
843    o add a new package shelfice which enables us to model the circulation
844      underneath shelf-ice with draughts of hundreds of meters.
845     - works
846     - to do: + include improved thermodynamics
847              + check whether kSurfC (from model/inc/SURFACE.h) can be used
848                instead of new field kTopC
849              + can we use topoFile, Ro_surf and existing code in ini_depth.F
850                instead of new field R_shelfIce and new code in ini_depth.F
851                and ini_mask_etc.F?
852              + adjust vertical mixing schemes?
853    o seaice pkg:
854     - add a cpp-flag to include a simple formula for a salinity dependent
855       freezing point of sea water at the surface
856     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
857       meridional stresses are now different (and hopefully correct)
858    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
859       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
860       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
861    o pkg/diagnostics: add options and parameters for regional-statistics
862       diagnostics ; define regions by reading a region-mask from a file
863       (might add other options later)
864    o pkg/bulk_force:
865     - add option and parameters to use AIM surface-flux formulae.
866     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
867       others forcing fields (defined in PARM05, parameter file "data") are loaded
868       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
869     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
870     - use the right EXCH call for uwind,vwind (to work on CS-grid).
871     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
872       and parameters (note: calcWindStress replaces .NOT.readwindstress).
873     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
874    
875    checkpoint58
876    o add "--embed-source" option to genmake2 which, when the supporting
877      tools can be compiled (as determined by genmake2) will turn on the
878      embed_files package which then embeds the entire MITgcm source code
879      (*.[fFhc] + Makefile) used for the build within the executable
880      - requested by CNH but off by default
881      - adds a paltry <9MB to the mitgcmuv executable in most cases
882      - only writes the output when useEMBEDSRC in eedata is true
883    o clean up 3-dim. relaxation codes:
884      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
885      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
886      * Thanks to Tom Haine for testing!
887    
888    checkpoint57z_post
889    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
890      affects output (@ truncation level) of exp. plume_on_slope ; updated.
891    o fix the pickup behavior for obcs in combination with ptracers
892    o fix a bug in ptracers_external_fields_load
893    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
894      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
895    o transfered surface NH pressure to eta field (if exactConserv).
896    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
897         and update lab_sea output.txt file.
898    o completing 3-dim. relaxation code: additional term
899         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
900      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
901      * At compile time, in "EXF_OPTIONS.h" set
902          #define  ALLOW_CLIMTEMP_RELAXATION
903          #define  ALLOW_CLIMSALT_RELAXATION
904      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
905          tauThetaClimRelax3Dim = 15552000.0,
906          tauSaltClimRelax3Dim  = 15552000.0,
907      * 3 cases:
908          1) Use a constant-in-time 3-dim. field
909          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
910          3) Real-time relax. to time-evolving prescribed field
911    o Adding Laplacian-type smoothness constraint on
912      initial and boundary (forcing) controls (ic, bc)
913      * enable at compile-time via
914        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
915      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
916      * Absolute scale somewhat unclear so far
917      * no area weighting was included since no other cost term does so far
918    
919    checkpoint57y_post
920    First step for a NLFS adjoint
921    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
922    o new init. routines for calc_r_star, calc_surf_dr
923    o still need to deal with ini_masks_etc
924    o testreport seemed happy
925    checkpoint57y_pre
926    
927    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
928    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
929    o add new offset feature to offline pkg (plus minor cleanup)
930    o cfc fixes for final year of integration
931    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
932      be in GCHEM_OPTIONS).
933    
934    checkpoint57x_post
935    o fix testreport Pb in multiple test experiment.
936    o cleanup our namelist syntax in verification:
937      - make it more F95 standards compliant (some work still needed)
938      - allows the vast majority of our tests to work with gfortran
939    o Non-Hydrostatic:
940     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
941     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
942    o Allow to apply AB on T,S rather than on AB(gT,gS):
943     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
944     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
945       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
946     - need a "clever" read_pickup to restart from the other AB formulation
947    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
948    o remove some unused variables (reduces number of compiler warnings)
949    o adjoint
950      * Disable useVariableViscosity for adjoint for time being
951        (there are a number of extensive recomputations)
952      * Initialize certain variables needed for adjoint
953    
954    checkpoint57w_post
955    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
956                 fix the singleCpuIO RS version of MDSWRITEFIELD
957       and add a WARNING if using globalFiles=T with multi-processors.
958    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
959      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
960    o tracer advection scheme:
961      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
962       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
963       was not very convenient).
964      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
965       (further tests needed for the implicit DST & Flux-Limiter schemes).
966    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
967      and sRef for convenience, handy, when you want to initialize
968      ptracers in a large domain with a constant non-zero value. Also,
969      untangle ptracers_init.F a little.
970    
971    checkpoint57v_post
972    o change dome exp. to use variable viscosity in side-drag terms.
973    o remove all the files from the cfc_offline test since they are now
974      incorporated into tutorial_cfc_offline which has been producing
975      identical results for a few days of testing
976    o add new parameter: sideDragFactor to enable half-slip-side BC
977      and change side-drag S/R to use viscosity from mom_calc_visc
978      (can switch back by setting sideDragFactor=0.); affects results at
979      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
980       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
981    o vorticity & strain are now computed without masking, to account for
982      no-slip-side BC in variable viscosity calculation ; mask is applied
983      anyway later on, before computing advection/coriolis terms.
984    o modify exp4 to test new obcs support for reading from external files
985      and for passive tracers
986    o fix behavior of ptracers_monitor when monitor output is written to a
987      netcdf-file; still not independent of monitor.F (writes in the same
988      file).
989    o change default value of tRef (put a uniform, meaningful value for ocean
990      & atmos) and initialize sRef (was missing, as Martin mentioned).
991    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
992      to be proportional to enstrophy dissipation length.  Thus,
993       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
994      This is now consistent with Smagorinsky and with the manual.
995    
996    checkpoint57u_post
997    o OBCS and PTRACERS: add open boundary support for passive tracers
998      - either use homogenous (pseudo) v.Neumann conditions or prescribe
999        OB-values from file; this is not different from the way theta and salinity
1000        are treated
1001      - however, Orlanski-radiation conditions are not supported, and the model
1002        will stop if you use pTracers and Orlanski at the same time.
1003      - beefed up the rountine obcs_external_fields_load: now only those open
1004        boundary values are overwritten with values from files for which there
1005        are really files, otherwise the OB-fields remain untouched. This makes
1006        it possible to use different OBs at different ends of the domain (as
1007        with EXF)
1008    o reduce number of exch calls in shap_filt (s2).
1009    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1010      truncation level) 4/5 MLAdjust test results (11&12 digits match).
1011    
1012    checkpoint57t_post
1013    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1014    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1015      same truncation, independent of the face number: affects affects several
1016      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1017    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1018      note that biharmonic viscosity + no-slip was not tested in any experiment.
1019    o fix bug in non-linear free-surf side-drag ; generate new output for
1020      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1021    o make mnc honor the writeBinaryPrec flag for most kinds of output
1022    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1023    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1024      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1025    o add brackets in multi-terms sum to get same truncation, independent of
1026      the face number (manage to get exactly same value of gU,gV at the cs-edge)
1027      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1028    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
1029      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1030      a maximum grid-scale Reynolds number.  Also, changes all length calculations
1031      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1032      Suggested values of viscosity parameters found in mom_calc_visc.
1033      Many new viscosity diagnostics available.
1034    
1035    checkpoint57s_post
1036    o Add clearing-house for viscosity calculations, mom_calc_visc and
1037      correct numerous bugs in LeithD and Smagorinsky discretizations.  
1038      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1039      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1040      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1041      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
1042      The Strain-Tension form is now called with useStrainTensonVisc=.true.
1043      ViscAhStrain and viscAhTension are now retired.
1044    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1045    o In response to JMC's bug report, genmake2 now ignores any soft-links
1046      that it finds in the *current* directory when searching for files.
1047      Soft-links found in any other source directories will still work as
1048      they did before.
1049    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1050      a C routine to unlimit the stack size
1051    o mnc-ify pkg/aim snapshot vars
1052    o mnc-ify pkg/land as requested by Daniel
1053    o various changes to mnc including:
1054      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1055      - output can now be grouped so that all files within a group
1056          change the ITER portion of their names in lock-step together
1057      - can now read ("global") PER-FACE (in addition to PER-TILE) files
1058          and works with both EXCH1 and EXCH2 (but needs more testing)
1059      - writing works for all verification test cases w/ g77 on Linux
1060    
1061    checkpoint57r_post
1062    o make MNC variable initialization happen earlier
1063    o add diagnostics for (almost) each term of the momentum Eq.
1064    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1065    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1066    o remove MINIMAL_TAVE_OUTPUT option ;
1067      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1068    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1069      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1070    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1071    o add time-dependent SST, SSS control
1072    o cost terms in ecco/ modularized (new cost_generic.F)
1073    o cost_averages routines are modularized (new cost_averagesgeneric.F)
1074    o new infrastructure for seaice model vs. obs misfits in seaice/
1075      * driver from the_main_loop.F is seaice_cost_driver.F
1076      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1077      * gradient check in Exp. 6a of natl_box_adjoint/
1078    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1079      (see README file)
1080    
1081    checkpoint57q_post
1082    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1083    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1084      - bug was reported by Jean-Michel and Ian Fenty
1085    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1086      update exp. cpl_aim+ocn output.
1087    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1088      Needed for high-res. runs with large global files
1089      to be able to limit tapelev size
1090    o Changed some tests for adjoint:
1091      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1092      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1093      * global_ocean.90x40x15/ back to default 3-level checkpointing
1094    o Modifications to enable scripted COMMON to MODULE conversion
1095      * verification/OpenAD/code/ has necessary scripts and description;
1096      * converts, compiles and runs successfully;
1097    
1098    checkpoint57p_post
1099    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1100    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1101      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1102    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1103    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1104      (was already the case for dissipation with mom_vecinv,
1105       and also the case for grad.PhiHyd when staggered-timeStep)
1106      This will allow to put dissipation out-off the AB time-stepping.
1107     Unfortunately, affects truncation error. Update output of exp. that "fails"
1108      (cg2d matching number) and leave the others for later: front_relax(10),
1109      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1110      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1111    
1112    checkpoint57o_post
1113    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1114      (2) its ready to be documented during the 20050801 DocFest
1115    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1116      for ideal_2D_oce and lab_sea on linux_ia32_g77
1117    o set to #undef CTRL_SET_OLD_MAXCVARS_30
1118      in global1x1_tot/code_seaice_adj to access indices 32, 33
1119      (worth another tag)
1120    
1121    checkpoint57n_post
1122    o adding precip control xx_precip 32
1123    o adding swflux control xx_swflux 33
1124    o Replacing 10 forcing penalty cost routines by 1 generic.
1125    o Implementing partitioning in time-mean and variable adjustment
1126      for atmos. state.
1127    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1128  o in natl_box_adjoint:  o in natl_box_adjoint:
1129    * updated: results_bulk/    * updated exp 1 to 10
1130    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
1131    o updated global1x1/*_seaice_adj/
1132      to incorporate latest changes
1133    o enable useSingleCpuIO for mdsio vector routines
1134      (applies in particular to tapelev I/O)
1135    o removed inefficient K-loop in all active_file*control*.F
1136    
1137  checkpoint57m_post  checkpoint57m_post
1138  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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