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revision 1.390 by jmc, Sun Nov 21 22:22:31 2004 UTC revision 1.857 by jmc, Mon Aug 6 21:44:50 2007 UTC
# Line 1  Line 1 
1  $Header$  $Header$
2    $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o exch2 adjoint
8      First set of changes:
9      - add exch2 hand-written adjoint templates
10      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
11        This will require cleanup in pkg/autodiff/*.F
12        (changed routines currently kept separate in verif. code/)
13      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
14        that used to hide exch2 or cubed-sphere specific code
15        (commented via 'cph-exch2')
16    o pkg/seaice
17      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
18    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
19       output of global_ocean.cs32x15.thsice .
20    
21    checkpoint59e
22    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
23      for B-grid vector (not yet tested) and C-grid vector (<- only used
24      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
25    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
26      (#ifdef ALLOW_SALT_PLUME)
27    o gather_2d/scatter_2d: removed halo regions
28    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
29      scheme and the corresponding test case (under front_relax dir). For now,
30      only available with Skew-flux form and not yet tested in realistic set-up.
31      adjoint: store directives updated, but gradient checks deteriorated,
32      so maybe GM/Redi adjoint is now broken.
33    o seaice adjoint
34      * add AREA, HEFF, HSNOW as control variable
35        (should not change lab_sea results)
36      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
37    o pkg/seaice:
38      * added computation of saltFlux in seaice_growth;
39        For time being, sea ice salinity is assumed constant
40        contribution of snow flooding to freshening of sea ice is neglected.
41        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
42        defaults to 0.0 in order to maintain backward compatibility.
43        Typical values for SEAICE_salinity are 4 to 10 g/kg.
44      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
45      * added SEAICE_availHeatFrac, which specifies fraction of surface level
46        heat content used to melt or grow ice
47      * commented out cap of HICE: it helps keep ice thinner
48      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
49      * applied OBCS T/S mask to HEFFM sea ice mask
50    
51    checkpoint59d
52    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
53     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
54     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
55    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
56     and change default value of parameter "GM_Small_Number";
57     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
58       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
59       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
60    o pkg/ecco: cost function when applying pkg/smooth to controls
61    o pkg/ctrl: add forcingPrecond run time parameter
62    o pkg/seaice:
63     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
64     - fix bug in metric terms of u-equation in LSR solver (implicit part),
65       changes verification/lab_sea
66     - rearrange implicit part of u-equation in LSR solver to make it easier to
67       read, understand, and debug. This causes changes at the truncation level.
68     - fix (serious) bug in the boundary conditions (sign error in the implicit
69       part) of the LSR solver. Changes all LSR results.
70     - fixed problem with HSNOW initialization to avoid thick snow when AREA
71       is initilized with small values - does not change lab_sea results.
72     - added HsnowFile initialization capability
73    o pkg/smooth: addition to model/src and pkg/ctrl so allow
74     initialization of pkg/smooth and application to control vector
75    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
76    o dependencies: pkg/profiles requires pkg/cal
77    o pkg/profiles:
78     - added option ALLOW_PROFILES_GENERICGRID
79         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
80         that interpolation information (grid points and coefficients) is provided
81         within the netcdf input files.
82         -> sample matlab scripts can be found in MITgcm_contrib/gael
83         that allow you to prepare netcdf input files.
84     - also modified: cleaner include statements, cleaner error print statements,
85       cleaner stops when error, and more tests of the netcdf input files consistency.
86    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
87    o pkg/seaice:
88     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
89       requires a new routine: seaice_diagnostics_fill.F
90     - make sure that seaice does not move if not forced (pressure replacement
91       method, Hibler and Ip, 1995), changes results
92     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
93     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
94       It is turned off by default (=-1.), because it changes the results.
95     - make it possible to read AREA from a file, too.
96    
97    checkpoint59c
98    o add S/R and diagnostics for oceanic mixed-layer depth
99    o move GMRedi call after all vertical mixing schemes (including KPP)
100    o pkg/thsice:
101     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
102      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
103    o pkg/obcs:
104     - bug fix for balance code
105    o pkg/seaice:
106      - allow values of SEAICE_elasticParm > 1
107      - add new parameter SEAICE_evpTauRelax as an alternative
108        to SEAICE_elasticParm
109      - make lsr boundary conditions free slip (by default), changes result
110      - add code for no slip boundary conditions for lsr
111      - set minimum of zeta to zero (and not 4e8) (changes results)
112      - add a cap on AREA after advecting AREA if seaice_growth is not called
113    o change calculation of Visbeck K:
114      - no longer depend on tapering scheme; instead, compute slope (limited
115        by GM_maxSlope). this is equivalent to what was comuted before with
116        clipping or linear tappering.
117      - fix vertical averaging (wrong by 1/2 level)
118      - leave the old version (but will not be maintained) within
119        #ifdef OLD_VISBECK_CALC / #endif
120      - update output of exp. ideal_2D_oce
121    o change error catch in calc_r_star to improve vectorization
122    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
123      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
124    o adjoint:
125      Re-organized adjoint checkpointing according to Matt Mazloff
126      (but with modifs/completions/cleanups)
127      Storing is now bundled into large arrays to optimized I/O
128      (and second step in cleanup of the_main_loop)
129    
130    checkpoint59b
131    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
132      - export/import (between ocean & coupler) fields needed for ocean DIC.
133    o pkg/seaice:
134      - get rid of three more exchanges seaice_calc_viscosities (required
135        different loop boundaries in seaice_lsr and seaice_ocean_stress)
136      - bug fix in seaice_ocean_stress (update of lab_sea required)
137      - reduce loop boundaries to necessary minimum also in seaice_evp
138      - go back to the old way of computing deltaC/Z as the adjoint likes that
139        better
140    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
141      passive tracer to an Age Tracer) + update output.txt
142    o pkg/exf:
143      - implement A-grid / C-grid selection for wind-stress input files.
144      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
145      for now, in exf_bulk_largeyeager04.F only :
146      - change implementation for case where windspeed + 2. components wind-stress
147        are read-in. AND use rhoConstFresh to convert evap.
148    o pkg/seaice:
149      - use correct EXCH_UV for wind-forcing (on A-grid).
150      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
151        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
152    o pkg/exf:
153      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
154      EXF_INTERPOLATION:
155      - merge global_with_exf/code version of exf_interp_read.F
156        to the main code ;
157      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
158        reading the file ; Important: This options needs to be defined to recover
159        previous code.
160        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
161      - no longer loose real*8 precision along the way when using exf_iprec=64.
162    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
163      - change discretisation of evp-solver in order to avoid another exchange
164        (changes lab_sea) and clean up a little
165      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
166        help the adjoint (this also changes the results slightly)
167      - add a few "_d 0" where they had been missing in seaice_evp.F
168      - cleaning up: remove unused seaice_calc_rhs.F
169    o pkg/exf: some cleaning-up:
170      - change various "constants" into runtime parameters
171      - cleaned-up Large&Yeager04 routine which should eventually
172        replace exf_bulkformulae.F (changed names of S/R and CPP)
173        and merged various ALLOW_ATM_WIND options
174     only used with thsice pkg (in thsice_get_exf.F):
175      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
176        which are used when useStabilityFct_overIce=TRUE (= the default)
177      - change default values of ice & snow emissivity and scale downward LW
178        by ice & snow emissivity.
179    o pkg/thsice:
180     fix few little problems, in thsice_calc_thickn.F:
181      - growth vertically (and not laterally) if iceFrac == iceMaskMax
182      - melt only laterally if hIce < hThinIce (as the comments say)
183      and in thsice_extend.F:
184      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
185      - start to form ice as soon as the minimum ice-volume is reachable.
186     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
187      and cpl_aim+ocn
188    o pkg/kpp
189     - move computation of surface related input fields to KPP into a new
190       subroutine kpp_forcing_surf.F
191     - remove wrong (within bi,bj loops) EXCH calls.
192     - little cleaning (add argument myThid in last position, cvs header ...)
193     - for now, fix conservation problem by exchanging KPPviscAz (may not
194       be the best fix)
195    o pkg/seaice
196     - check for inconsistent evp parameter/cpp-flag combination
197     - remove leftover errIO flat for obsolete name list error handling
198    o OpenAD
199     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
200    
201    checkpoint59a
202    o pkg/seaice: some parameter clarifications and a little bit of clean up
203    o pkg/thsice: rename run-time parameters:
204       himin       -> hIceMin
205       himin0      -> hThinIce
206       hihig       -> hThickIce
207       i0          -> i0swFrac
208       transCoef   -> bMeltCoef
209       frac_energy -> fracMelting
210      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
211       with default values (for now) that do not change the results.
212      remove old version of thsice vars advection in pkg/seaice.
213    o in FFIELDS.h:
214      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
215      - make pLoad & sIceLoad always available (but still only used if
216         ATMOSPHERIC_LOADING is #define).
217    o pkg/kpp: replaced _KPP_RL with _RL
218    o bug fixes for vertical diffusivity computations when both KPP and
219        3D diffusivity arrays are used.
220    o pkg/seaice: fix bug in evp solver, while doing that
221      - change (improve?) discretization of stress computations for both
222        cgrid-lsr and evp solver
223      - add a new routine to compute strain rates
224      - the above changes lab_sea results
225      - add no slip conditions for evp solver (off by default), lsr-version
226        may follow
227      - fix exchange for shear at Z-points (does not change lab_sea)
228      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
229        (to force the user to pick a time step since there is not "safe" way
230        of choosing it)
231      - add principal stress diagnostics
232      - rearrange fields for evp a little to avoid having to call a: too many
233        exchanges and b: exchanges for stress trensor components which we do
234        not have.
235      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
236        of evp, complete rewrite for lsr case (latter is does not yet work
237        in all cases)
238    o pkg/kpp: add code to have mixing in shelf ice caverns
239      - add myThid to all kpp routines (long overdue)
240    
241    checkpoint59
242    o pkg/exf:
243      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
244        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
245      - move exf header files from lower_case.h to UPPER_CASE.h ;
246        add missing cvs Header & Name
247      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
248      - add namelist param. selectStressGridPosition, exf_monFreq
249      - retire many _CLIM routines, and remove data.exf_clim
250        + params moved to data.exf
251        + climsst, climsss now handled by exf_set_gen, i.e.
252          climss?period=0 refers to constant field,
253          climss?period=-12 to monthly forcing
254      - split up namelists in data.exf
255    o pkg/seaice:
256      - remove seaice_exch and seaice_exch_uv
257      - remove superfluous exchange of theta
258      - add myThid to seaice_budget_ocean/ice
259      - add new interface for atmospheric wind forcing (C-grid only)
260        + new routine
261        + two new field (taux, tauy for stress over ice)
262        + removed one global field (DAIRN) for C-grid case only
263    o pkg/thsise
264      - 2nd set of modifs for thsice adjoint in conjunction with exf
265    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
266    
267    checkpoint58y_post
268    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
269      vertical diffusivity, similar to that in MOM4; turned on using
270      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
271      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
272    o Added capability for 3D specification of background vertical diffusion
273      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
274      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
275      "data" file that contains the 3D vertical diffusivity coefficients.
276    o ice dynamics (pkg/seaice) with thsice thermodynamics:
277      - add code within pkg thsice to advect & diffuse sea-ice fields
278      similar to (and will replace) what has been added in  seaice_advdiff.F,
279      but: - conserving Mass, Heat & Salt.
280           - better when using non-linear advection scheme (not yet fully tested)
281           - can also be used in atmospheric set-up (for now, only the diffusion).
282    
283    checkpoint58x_post
284    o IO option for global-file compact format:
285      - add options when generating topology (utils/exch2/matlab-topology-generator)
286      - add I/O capability (pkg/mdsio).
287      - adapt utils/matlab/rdmds.m to read this format.
288      for now long-line format not yet supported by pkg/mdsio (& exch2).
289    o shelfice: add a few diagnostics
290    
291    checkpoint58w_post
292    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
293      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
294      (and replace horiVertRatio in NH code).
295      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
296                         and tutorial_plume_on_slope (sensitive to truncation)
297    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
298      directly to drive seaice model (C-grid only)
299    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
300     - reintroduce computation of wind from stress,
301     - compute tau (in exf_bulkformulae.F) from windstress averaged to
302       mass points to avoid tau = 0
303     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
304    o rdmnc.m: make it work with "global" files created with gluemnc
305    o rdmnc.m : some improvements in dealing with singleton dimension
306      (tested on all testreport mnc output files).
307    o genmake2: disable pkg/profiles if netcdf test fails.
308    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
309    o move call to cal_readparms up to make calendar parameters/variable available
310      to all packages
311    
312    checkpoint58v_post
313    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
314      useDynP_inEos_Zc tested.
315    o pkg/exf: changes to properly interpolate/mask/scale initial fields
316    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
317      and portions thereof.  See read_cs.txt for description and examples.
318    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
319      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
320      following the great-circle arc between those 2 points.
321    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
322      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
323    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
324     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
325     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
326     - still needs work (not working with some options ; efficiency to improve)
327       and serious testing.
328     - use this scheme for temperature & salinity in 2 advection test exp.:
329       advect_xy & advect_xz, respectively.
330    
331    checkpoint58u_post
332    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
333    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
334    o testreport: add option "-skipdir" to skip some test.
335    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
336      momentum calculation.
337    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
338    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
339      remove checkpoint.F and the_correction_step.F (no longer used);
340      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
341    o add option (linFSConserveTr) to correct for tracer source/sink due to
342      Linear Free surface
343    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
344    o pkg/thsice: fix reading mnc-pickups
345    
346    checkpoint58t_post
347    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
348    o pkg/mdsio:
349     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
350       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
351       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
352     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
353     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
354       either MDS_READ_FIELD or MDS_WRITE_FIELD )
355     - new S/R (to replace MDSWRITEMETA), which allows to write more
356       informations (variable names, time ...) to meta files.
357     - modify rdmds.m to give back the meta file content.
358    o pkg/diagnostics: change vertical interpolation to be safer, and more
359       flexible (define p-levels to interpolate to in data.diagnostics);
360      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
361       diagnostic pointer.
362    o pkg/seaice: more cleaning up of seaice_growth, added many comments
363    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
364    o fix multi-category seaice:
365     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
366       SEAICE_MULTICATEGORY
367     - fix short wave heat flux
368    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
369       and allow to use EVP solver. Change forward lab_sea: test both EVP
370       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
371    o Initial check-in of lab_sea adjoint
372      (very similar to natl_box_adjoint/code_seaice)
373      * used C-grid and EVP solver
374      * used KPP, GM/Redi
375      * uses inAdExact=.TRUE.
376      * gradient checks fail for both ADM and TLM
377        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
378        f.d. gradients actually seem more problematic than ADM, TLM gradients;
379        issue is related to forward mismatch between g77 an ifort
380    o pkg/seaice: overhaul of thermodynamics
381     - growth.F and groatb.F are replaced by new routine seaice_growth.F
382     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
383     - move a few global fields out of SEAICE.h into seaice_growth.F and
384       make them 2D (FICE/QNETO/ ...)
385     - remove FO (it is the same as QNETO)
386     - introduce a few local fields to avoid modifying external fields such
387       as atemp, etc.
388    
389    checkpoint58s_post
390    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
391      changed exf_set_gen.F so that
392        genperiod=0 means input file is one time-constant field and
393        genperiod=-12 means input file contains 12 monthly means
394    o CG2D: use pre-computed solver main-diagonal (stored in common block);
395      this affects truncation error ; generate new output file for exp. which
396      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
397        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
398        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
399        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
400        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
401        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
402    o start implementation of deep-atmosphere and anelastic formulation
403    o verification: remove 2nd copy of input files and use script "prepare_run"
404      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
405    o mom_common/vecinv/fluxform: fix a few initialisation isssues
406    o profiles: fix for multithreaded case
407    
408    o diagnostics: rename few diags:
409      s/'PRESSURE'/'RCENTER '/g
410      s/'TICE    '/'oceFreez'/g
411      s/'TAUX    '/'oceTAUX '/g
412      s/'TAUY    '/'oceTAUY '/g
413      s/'SWFLUX  '/'oceQsw  '/g
414      s/DIFx/DFxE/g
415      s/DIFy/DFyE/g
416      and add few ocean-forcing diagnostics:
417      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
418    o modifications to pkg/seaice/growth.F and budget.F, which change results of
419      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
420      as actual snow thickness.  It now refers everywhere to effective snow
421      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
422    
423    checkpoint58r_post
424    o modifications to pkg/seaice/growth.F, which change results of
425      lab_sea experiment: fixes pertain to melting snow over open water, to
426      masking EVAP under sea ice, and to using the correct AREA variable for
427      computations of EVAP, PRECIP, HSNOW, and GHEFF
428    o add ability to read bathy, salt, and theta using MNC (off by def)
429    o add flooding algorithm and advection of HSNOW for pkg/seaice;
430      both are turned off by default and do no change any results
431    o seaice advection with pkg/thsice: a step toward the use of non-linear
432      advection scheme, but #ifdef or commented out for now (requires more EXCH).
433    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
434      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
435      in natl_box (affects results @ truncation level: update output.txt)
436    o multi-threading and IO:
437      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
438      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
439        (needed to work with SingleCpuIO): tested in all verif. exp.
440    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
441      affects the results (but none of the verification test uses this scheme).
442    o Adding some pkg/diagnostics capability to pkg/seaice
443      (will certainly be subject to changes)
444    o ctrl: adding new control variables:
445      lwflux, lwdown, evap, snowprecip, apressure, runoff
446    
447    checkpoint58q_post
448    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
449      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
450      high_res_cube configuration by 4% on Columbia.
451    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
452      add (in global_with_exf/code) a version of EXF_INTERP_READ without
453      dynamical allocation (seems to work in multi-threaded).
454    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
455      single CPU io) so that TAF does not have to see EESUPPORT.h
456    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
457    
458    checkpoint58p_post
459    o obcs: stop if obcs is used with useCDscheme = .true.
460    o shelfice:
461     - fix a sign error so that no slip at shelfice interface works
462     - remove stop for combination non-hydrostatic code and shelfice. That does
463       not mean, that the results are correct, but at least they are numerically
464       stable
465    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
466    o added adjoint exch routined for all exch*3d* routines
467      and updated flow directives
468    
469    checkpoint58o_post
470    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
471      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
472    o change controling S/R for writing pickup file (new S/R do_write_pickup)
473      and clean-up reading/writing of pickup files.
474    o fix local version of read/write pickup (NH part) in rotating_tank/code
475    o simplify EXCH interface:
476     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
477     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
478    o added the regrid package
479    o shelfice:
480     - add a simple boundary layer scheme to reduce noise
481     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
482    
483    checkpoint58n_post
484    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
485       local variable (not in common block).
486    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
487      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
488      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
489        to work with SingleCpuIO.
490    o add "_d 0" to real constant of pkg/cfc subroutines ;
491       update exp. cfc_exemple & tutorial_cfc_offline output files.
492    o multi-threading and IO:
493      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
494        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
495      - barrier before and after reading.
496      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
497      - avoid using MDS_WRITELOCAL for LAND pkg output.
498      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
499        common-block variables ; Allows multi-threading with master-thread IO.
500    o change default MAX_NO_THREADS from 32 to 4 ;
501      and stop cleanly when MAX_NO_THREADS is too small.
502    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
503    
504    checkpoint58m_post
505    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
506       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
507    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
508       keep global_ocean.90x40x15 (for AD testing) with former secondary test
509       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
510    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
511        add MITgcm_tutorials (= code + all the tutorials)
512    o ecco, option to compute cost for total ssh (mean+anom)
513    o consistent with addition of ptracer and ssh in pkg/profiles
514    o profiles: adding ptracer and ssh
515    o testreport: change multi-test output-file name
516      (from output.txt.{name} to output.{name}.txt)
517    o profiles: now ok for mutli-tiles case
518    o seaice: add 4 parameters for different advection schemes for area,
519      (effective) seaice thickness, enthalphy, and snow height. Their default
520      is the standard parameter SEAICEadvScheme
521    o calc_gw:
522     - add cosFacU in zonal viscous flux (harmonic.visc.).
523     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
524       of tutorial_plume_on_slope.
525    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
526    o calc_gw: true flux-form, account for horizontal grid spacing.
527      update rotating_tank results, but not plume_on_slope (affected at
528      truncation level, 11 digits).
529    
530    checkpoint58l_post
531    o calc_gw:
532     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
533     - remove side-drag for now (need to fix it); update plume_on_slope results.
534     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
535    o commit code to make SST/SSS weights spatially variable
536      (based on either variable in-situ or variable initial T/S weights)
537    o pkg/ecco:
538      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
539        now based on horizontally varying weights wthetaLev, wsaltLev
540      * cost_averagesflags now returns year indices in addition to day, month
541      * sflux balance is performed on annual basis
542        (sflxumm, sfluxmm2, bal_sfluxmm)
543      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
544        including separate counting and multipliers
545    o pkg/rbcs
546      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
547    
548    checkpoint58k_post
549    o testreport:
550     - always build in dir. "build" (if not there, mkdir build instead of building
551       & running in input)
552     - run in dir run (if it exists), in build otherwise.
553     - call prepare_run (if input/prepare_run exists)
554     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
555    o pkg/exf modifications to interpolation and rotation routines for more
556       reasonable treatment of North Pole singularity: for tracers North Pole
557       value is set to northernmost zonal-mean value, for zonal velocity it is
558       set to zero, and for meridional velocity it is set to northernmost value.
559    o pkg/exf/exf_check_range.F
560     - add tile index to diagnostics and move stop statement to the very
561       end of the routine.
562    o pkg/diagnostics: (diagnostics_main_init.F)
563      define title of isomorphic variables according to the current config.
564    o pkg/thsice with pkg/seaice dynamics:
565    - fix domain of computation (interior only, required for exf) and do exchanges
566    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
567    o towards a standard way of dealing with multi-threading in MONITOR
568      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
569    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
570       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
571    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
572    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
573    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
574       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
575    o tracer advection:
576     - clean-up and simplify calc_common_factors.F
577     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
578       advection subroutine (but still not used within DST advection S/R)
579    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
580    
581    checkpoint58j_post
582    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
583      from file (collects calls previously in FORWARD_STEP)
584    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
585    o adjoint store dir. adjusted accordingly
586    o genmake2
587      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
588    
589    checkpoint58i_post
590    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
591      on wind stress (SEAICEstressFactor defaults to 1.)
592    o Total number of Timers is finite (<=40): comment out 2 non-essential one
593      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
594    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
595      on CS-grid: no longer loosing mass.
596    o exf & curvilinear-grid: no longer modify longitude xC & xG.
597    o pkg/ggl90: fix sloppy output and fix a bug
598    o pkg/seaice: added SEAICEuseEVPpickup parameter
599      - Set to false in order to start EVP solver with
600        non-EVP pickup files when using SEAICEuseEVP
601      - fix sign error in diffusion in seaice_calc_rhs
602    
603    checkpoint58h_post
604    * Modifications for bottom topography control
605      o replace hFacC by _hFacC at various places
606      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
607      o add non-self-adjoint cg2d_nsa
608      o update autodiff support routines
609      o re-initialise hfac after ctrl_depth_ini
610      o works for 5x5 box, doesnt work for global_ocean.90x40x15
611    * Adding verification for 5x5 box (4-layer) bottom topography control
612    
613    checkpoint58g_post
614    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
615       used for mean seasonal cycle, mean diurnal cycle); add an example
616       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
617    o pkg/ggl90:
618      - add parameter (minimum surface kinetic energy)
619      - fix bug (avoiding division by zero)
620    o couple pkg/thsice to pkg/seaice:
621      - modify advection in seaice to accomodate new scalar fields to be advected
622      - only muliDimAdection scheme work with seaice/thsice
623      - mapping of thsice-variables to seaice-variables, back and forth
624      - does not break the verification experiments, but does not give the
625        desired results either
626    o pkg/seaice
627      - make (default) second order advection a bit less confusing?
628    
629    checkpoint58f_post
630    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
631      to pkg/seaice):
632      - new routines thsice_map_exf and thsice_get_exf provide the interface
633      - add an additional formal parameter to thsice_solve4temp
634    o pkg/exf:
635      - add new fields wspeed, snowprecip (to be able to couple to thsice)
636      - correct Stefan-Boltzmann constant
637      - new parameter for longwave surface emittance
638      - separate some stuff from exf_bulkformulae into new routines  
639        exf_radiation, exf_wind
640      - add new parameters and constants: longwave emissivity for ocean, ice
641        and snow, evaporation parameters over ice
642      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
643        either wind from stress or stress from wind
644    o pkg/thSIce:
645    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
646    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
647       and THSICE_CALC_THICKN
648    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
649    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
650      to make debugging easier.
651    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
652    o pkg/bulk_force:
653      - clean-up comments and parameters ;
654      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
655    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
656      generate new output for test-experiment: aim.5l_cs.thSI
657    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
658      testreport accordingly
659    
660    checkpoint58e_post
661    o SEAICE_CGRID adjoint done
662    o R_STAR adjoint implemented.
663      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
664      * need to sort out init. of h0facc, etc.
665    o Make pkg/profile fully independent of ecco,cost, etc. stuff
666      to be able to use it in pure forward.
667    
668    checkpoint58d_post
669    o upgrade simple test-experiment to tutorial example:
670     step.1: duplicate the experiment and (step.2) will remove the old copy.
671      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
672      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
673      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
674      tutorial_global_oce_biogeo    <- copy of dic_example
675      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
676      tutorial_plume_on_slope       <- copy of plume_on_slope
677      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
678      tutorial_global_oce_optim     <- empty for now (David ?)
679      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
680     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
681    o correct a sign problem in cost_scat.F
682    o obcs and ptracers: fix boundary conditions for advections schemes
683      with larger stencil
684    o thsice adjoint: start
685    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
686      completeness
687    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
688      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
689    o ptracers adjoint:
690      * avoid extensive recomputatations
691      * fix missing re-init. of gptr (missed by TAF)
692    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
693      me to turn off the excessive output to STDOUT that this package produces
694    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
695      and add those terms in Vector-Invariant formulation.
696    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
697      if the control period (xx_hfluxperiod etc) is 0
698    o in profiles pkg, clean routines and fix details
699    o in ecco pkg, reading ssh data:
700      fix problem in case the model does not start at iter0=0
701    o fix mnc-pickup/restart for ptracers
702    o new package prifiles:
703      code to compute profile-based cost by Gael Forget
704      (modifs in ecco, ctrl, autodiff)
705    o Benign bug fix in initialization (spotted by M. Mazloff) of
706      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
707    
708    checkpoint58c_post
709    o adjoint: finish NLFS adjoint and provide reference output in
710      verification/global_ocean.90x40x15/results_ad_nlfs
711    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
712      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
713      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
714      with SEAICE_CGRID defined.
715    o move calendarDumps from "data" to "data.cal" and clean-up the code
716      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
717    o add useEXF & useCAL flags (for now, set in hard-coded way)
718    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
719      (were missing in NH mode, and wrong in quasihydrostatic mode).
720      waiting for Chris updated version of calc_gw to add those CALLs.
721    o fix bug in quasihydrostatic S/R ;
722      add a test for this option: global_ocean.90x40x15.qshyd
723    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
724      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
725    o add on/off flag useOffLine for package OFFLINE
726    o seaice:
727      - modify advection so that it works also on the C-grid
728      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
729        problem in multi-tile runs with C-grid
730      - add flags for clipping ice velocities and/or masking solver forcing
731      - fix drag (ocean on ice) formulation and a bug that caused noise in the
732        C-grid solver
733      - added a few comments to seaice_diffusion.F
734      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
735        are now exclusive)
736      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
737        required re-ordering the code a little:
738       + make DAIRN global variable (defined in SEAICE)
739       + move computation of the viscosities eta and zeta into a new separate
740         routine (because I need to recompute them in seaice_ocean_stress.F)
741    
742    checkpoint58b_post
743    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
744      update output.txt of exp. aim.5l_cs.thSI
745    o various mnc cleanups and improvements:
746      + shrink lookup tables by factor of ~4
747      + better error reporting when running out of lookup space
748      + able to handle longer path/file names (up to 500 chars)
749    o adjoint:
750      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
751      - TBD: "hidden" mom_vecinv recomp. in dynamics
752    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
753     (allow to differentiate between forcing components using new integer flags:
754      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
755     and add new flag to put Dissipation tendency out of Adams-Bashforth.
756    o ecco
757      - enable trend removal from SSH anomaly obs.
758    o adjoint
759      - a fix for PmEpR when #undef EXACT_CONSERV
760      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
761      - try to fix "hidden" recomp. in forward_step for NLFS
762        (NLFS seems broken sometimes after I checked it in)
763    o seaice:
764     - add c-grid version of the dynamic solver:
765       + three new routines that are the c-grid substitute lsr, dynsolver
766         and ostres
767       + put a few fields that were local to dynsolver into global common
768         blocks, so that I can move the computation of stresses etc into
769         seaice_lsr (saves coding but may break the adjoint).
770     - replace more hardwired parameters by runtime parameters
771     - add ice masks that mask the rhs of the implicit solvers where there
772       is no ice (commented out in seaice_dynsolver, because i am not sure
773       if this works properly), eventually this should replace the clipping
774       of ice velocities in seaice_dynsolver to +/-40cm/s.
775    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
776      include it only where its needed
777    o move balancing of fluxes before the call of external_forcing_surf
778    o seaice:
779      - correct units of turning angles (now they are really in degrees)
780      - move computation of GWATX/Y out of main routine into dynsolver
781      - initialize GWATX/Y in seaice_init
782    o Apply mask on Fresh-Water flux (needed for SSH forcing).
783      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
784    o seaice: add runtime flags for turning angles (default to zero)
785    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
786      and trend from exf forcing and ctrl control adjustments
787    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
788      (since checkpoint57x_post)
789    o change the default rotation period to 86164.s = the Earth rotation
790    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
791      and based on a reference stratification. Tested within hs94.cs-32x32x5.
792    o seaice advection: add code for choosing between the default (2nd order
793      central differences) and multiDim advection schemes provided by
794      pkg/generic_advdiff
795    o seaice:
796      - removed all references to SEAICE_GRID.h fields from
797        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
798        (cubed-sphere configuration will change a little)
799      - grid computations in seaice_init are obsolete now.
800      - cleaned up code a little so that is easier to read (hopefully).
801      - added new (better?) discretizations of default advection and diffusion
802        (turn on with SEAICEuseFluxForm)
803      - replace 1 in 3d global fields by kSurface in growth.F
804      
805    checkpoint58a_post
806    o seaice:
807      - bug fix in advect.F
808    o shelfice:
809      - separate shelfice load anomaly from pload (breaks with time
810        dependent forcing), => introduce constant field shelficeLoadAnomaly.
811        Its default is 0., but it may be computed more cleverly from (unknown)
812        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
813        done offline. A good approximation of the pressure load anomaly is
814        necessary to avoid large initial adjustment processes underneath
815        deep-reaching shelfice.
816      - small fix in ISOMIP shelfice_thermodynamics
817      - add more sophisticated thermodynamics of Hellmer (1989), this is
818        now the default
819      - give a few constants more intuitive names
820    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
821      if bulk formulae are used in long integration (especially EmPmR). Turn
822      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
823      if balancePrintMean, the imbalance that is substracted is printed to
824      STDOUT.
825    o fix bug (typo) in obcs_apply_eta.F
826    o add a new package shelfice which enables us to model the circulation
827      underneath shelf-ice with draughts of hundreds of meters.
828     - works
829     - to do: + include improved thermodynamics
830              + check whether kSurfC (from model/inc/SURFACE.h) can be used
831                instead of new field kTopC
832              + can we use topoFile, Ro_surf and existing code in ini_depth.F
833                instead of new field R_shelfIce and new code in ini_depth.F
834                and ini_mask_etc.F?
835              + adjust vertical mixing schemes?
836    o seaice pkg:
837     - add a cpp-flag to include a simple formula for a salinity dependent
838       freezing point of sea water at the surface
839     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
840       meridional stresses are now different (and hopefully correct)
841    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
842       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
843       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
844    o pkg/diagnostics: add options and parameters for regional-statistics
845       diagnostics ; define regions by reading a region-mask from a file
846       (might add other options later)
847    o pkg/bulk_force:
848     - add option and parameters to use AIM surface-flux formulae.
849     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
850       others forcing fields (defined in PARM05, parameter file "data") are loaded
851       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
852     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
853     - use the right EXCH call for uwind,vwind (to work on CS-grid).
854     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
855       and parameters (note: calcWindStress replaces .NOT.readwindstress).
856     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
857    
858    checkpoint58
859    o add "--embed-source" option to genmake2 which, when the supporting
860      tools can be compiled (as determined by genmake2) will turn on the
861      embed_files package which then embeds the entire MITgcm source code
862      (*.[fFhc] + Makefile) used for the build within the executable
863      - requested by CNH but off by default
864      - adds a paltry <9MB to the mitgcmuv executable in most cases
865      - only writes the output when useEMBEDSRC in eedata is true
866    o clean up 3-dim. relaxation codes:
867      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
868      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
869      * Thanks to Tom Haine for testing!
870    
871    checkpoint57z_post
872    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
873      affects output (@ truncation level) of exp. plume_on_slope ; updated.
874    o fix the pickup behavior for obcs in combination with ptracers
875    o fix a bug in ptracers_external_fields_load
876    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
877      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
878    o transfered surface NH pressure to eta field (if exactConserv).
879    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
880         and update lab_sea output.txt file.
881    o completing 3-dim. relaxation code: additional term
882         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
883      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
884      * At compile time, in "EXF_OPTIONS.h" set
885          #define  ALLOW_CLIMTEMP_RELAXATION
886          #define  ALLOW_CLIMSALT_RELAXATION
887      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
888          tauThetaClimRelax3Dim = 15552000.0,
889          tauSaltClimRelax3Dim  = 15552000.0,
890      * 3 cases:
891          1) Use a constant-in-time 3-dim. field
892          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
893          3) Real-time relax. to time-evolving prescribed field
894    o Adding Laplacian-type smoothness constraint on
895      initial and boundary (forcing) controls (ic, bc)
896      * enable at compile-time via
897        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
898      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
899      * Absolute scale somewhat unclear so far
900      * no area weighting was included since no other cost term does so far
901    
902    checkpoint57y_post
903    First step for a NLFS adjoint
904    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
905    o new init. routines for calc_r_star, calc_surf_dr
906    o still need to deal with ini_masks_etc
907    o testreport seemed happy
908    checkpoint57y_pre
909    
910    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
911    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
912    o add new offset feature to offline pkg (plus minor cleanup)
913    o cfc fixes for final year of integration
914    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
915      be in GCHEM_OPTIONS).
916    
917    checkpoint57x_post
918    o fix testreport Pb in multiple test experiment.
919    o cleanup our namelist syntax in verification:
920      - make it more F95 standards compliant (some work still needed)
921      - allows the vast majority of our tests to work with gfortran
922    o Non-Hydrostatic:
923     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
924     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
925    o Allow to apply AB on T,S rather than on AB(gT,gS):
926     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
927     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
928       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
929     - need a "clever" read_pickup to restart from the other AB formulation
930    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
931    o remove some unused variables (reduces number of compiler warnings)
932    o adjoint
933      * Disable useVariableViscosity for adjoint for time being
934        (there are a number of extensive recomputations)
935      * Initialize certain variables needed for adjoint
936    
937    checkpoint57w_post
938    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
939                 fix the singleCpuIO RS version of MDSWRITEFIELD
940       and add a WARNING if using globalFiles=T with multi-processors.
941    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
942      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
943    o tracer advection scheme:
944      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
945       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
946       was not very convenient).
947      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
948       (further tests needed for the implicit DST & Flux-Limiter schemes).
949    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
950      and sRef for convenience, handy, when you want to initialize
951      ptracers in a large domain with a constant non-zero value. Also,
952      untangle ptracers_init.F a little.
953    
954    checkpoint57v_post
955    o change dome exp. to use variable viscosity in side-drag terms.
956    o remove all the files from the cfc_offline test since they are now
957      incorporated into tutorial_cfc_offline which has been producing
958      identical results for a few days of testing
959    o add new parameter: sideDragFactor to enable half-slip-side BC
960      and change side-drag S/R to use viscosity from mom_calc_visc
961      (can switch back by setting sideDragFactor=0.); affects results at
962      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
963       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
964    o vorticity & strain are now computed without masking, to account for
965      no-slip-side BC in variable viscosity calculation ; mask is applied
966      anyway later on, before computing advection/coriolis terms.
967    o modify exp4 to test new obcs support for reading from external files
968      and for passive tracers
969    o fix behavior of ptracers_monitor when monitor output is written to a
970      netcdf-file; still not independent of monitor.F (writes in the same
971      file).
972    o change default value of tRef (put a uniform, meaningful value for ocean
973      & atmos) and initialize sRef (was missing, as Martin mentioned).
974    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
975      to be proportional to enstrophy dissipation length.  Thus,
976       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
977      This is now consistent with Smagorinsky and with the manual.
978    
979    checkpoint57u_post
980    o OBCS and PTRACERS: add open boundary support for passive tracers
981      - either use homogenous (pseudo) v.Neumann conditions or prescribe
982        OB-values from file; this is not different from the way theta and salinity
983        are treated
984      - however, Orlanski-radiation conditions are not supported, and the model
985        will stop if you use pTracers and Orlanski at the same time.
986      - beefed up the rountine obcs_external_fields_load: now only those open
987        boundary values are overwritten with values from files for which there
988        are really files, otherwise the OB-fields remain untouched. This makes
989        it possible to use different OBs at different ends of the domain (as
990        with EXF)
991    o reduce number of exch calls in shap_filt (s2).
992    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
993      truncation level) 4/5 MLAdjust test results (11&12 digits match).
994    
995    checkpoint57t_post
996    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
997    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
998      same truncation, independent of the face number: affects affects several
999      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1000    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1001      note that biharmonic viscosity + no-slip was not tested in any experiment.
1002    o fix bug in non-linear free-surf side-drag ; generate new output for
1003      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1004    o make mnc honor the writeBinaryPrec flag for most kinds of output
1005    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1006    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1007      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1008    o add brackets in multi-terms sum to get same truncation, independent of
1009      the face number (manage to get exactly same value of gU,gV at the cs-edge)
1010      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1011    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
1012      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1013      a maximum grid-scale Reynolds number.  Also, changes all length calculations
1014      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1015      Suggested values of viscosity parameters found in mom_calc_visc.
1016      Many new viscosity diagnostics available.
1017    
1018    checkpoint57s_post
1019    o Add clearing-house for viscosity calculations, mom_calc_visc and
1020      correct numerous bugs in LeithD and Smagorinsky discretizations.  
1021      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1022      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1023      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1024      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
1025      The Strain-Tension form is now called with useStrainTensonVisc=.true.
1026      ViscAhStrain and viscAhTension are now retired.
1027    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1028    o In response to JMC's bug report, genmake2 now ignores any soft-links
1029      that it finds in the *current* directory when searching for files.
1030      Soft-links found in any other source directories will still work as
1031      they did before.
1032    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1033      a C routine to unlimit the stack size
1034    o mnc-ify pkg/aim snapshot vars
1035    o mnc-ify pkg/land as requested by Daniel
1036    o various changes to mnc including:
1037      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1038      - output can now be grouped so that all files within a group
1039          change the ITER portion of their names in lock-step together
1040      - can now read ("global") PER-FACE (in addition to PER-TILE) files
1041          and works with both EXCH1 and EXCH2 (but needs more testing)
1042      - writing works for all verification test cases w/ g77 on Linux
1043    
1044    checkpoint57r_post
1045    o make MNC variable initialization happen earlier
1046    o add diagnostics for (almost) each term of the momentum Eq.
1047    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1048    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1049    o remove MINIMAL_TAVE_OUTPUT option ;
1050      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1051    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1052      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1053    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1054    o add time-dependent SST, SSS control
1055    o cost terms in ecco/ modularized (new cost_generic.F)
1056    o cost_averages routines are modularized (new cost_averagesgeneric.F)
1057    o new infrastructure for seaice model vs. obs misfits in seaice/
1058      * driver from the_main_loop.F is seaice_cost_driver.F
1059      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1060      * gradient check in Exp. 6a of natl_box_adjoint/
1061    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1062      (see README file)
1063    
1064    checkpoint57q_post
1065    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1066    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1067      - bug was reported by Jean-Michel and Ian Fenty
1068    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1069      update exp. cpl_aim+ocn output.
1070    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1071      Needed for high-res. runs with large global files
1072      to be able to limit tapelev size
1073    o Changed some tests for adjoint:
1074      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1075      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1076      * global_ocean.90x40x15/ back to default 3-level checkpointing
1077    o Modifications to enable scripted COMMON to MODULE conversion
1078      * verification/OpenAD/code/ has necessary scripts and description;
1079      * converts, compiles and runs successfully;
1080    
1081    checkpoint57p_post
1082    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1083    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1084      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1085    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1086    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1087      (was already the case for dissipation with mom_vecinv,
1088       and also the case for grad.PhiHyd when staggered-timeStep)
1089      This will allow to put dissipation out-off the AB time-stepping.
1090     Unfortunately, affects truncation error. Update output of exp. that "fails"
1091      (cg2d matching number) and leave the others for later: front_relax(10),
1092      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1093      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1094    
1095    checkpoint57o_post
1096    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1097      (2) its ready to be documented during the 20050801 DocFest
1098    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1099      for ideal_2D_oce and lab_sea on linux_ia32_g77
1100    o set to #undef CTRL_SET_OLD_MAXCVARS_30
1101      in global1x1_tot/code_seaice_adj to access indices 32, 33
1102      (worth another tag)
1103    
1104    checkpoint57n_post
1105    o adding precip control xx_precip 32
1106    o adding swflux control xx_swflux 33
1107    o Replacing 10 forcing penalty cost routines by 1 generic.
1108    o Implementing partitioning in time-mean and variable adjustment
1109      for atmos. state.
1110    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1111    o in natl_box_adjoint:
1112      * updated exp 1 to 10
1113        (but does not have time-mean vs. variable split results yet)
1114    o updated global1x1/*_seaice_adj/
1115      to incorporate latest changes
1116    o enable useSingleCpuIO for mdsio vector routines
1117      (applies in particular to tapelev I/O)
1118    o removed inefficient K-loop in all active_file*control*.F
1119    
1120    checkpoint57m_post
1121    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
1122      and advect_cs (use EXCH-2 and standard cs-32 grid files).
1123    o pkg/exch2: filling of face-corner halo regions is optional
1124      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
1125    
1126    checkpoint57l_post
1127     tag before updating tutorials (pre-release-2)
1128    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
1129       for output and interpolation of input fields onto model grid)
1130    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
1131       Affects results of exp. rotating_tank ; update output.txt.
1132    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
1133          and taking the square quantity and/or using a fraction-weight field.
1134    o fix aim_diagnostics_init.F mate numbers.
1135    o add mnc output capability to diagnostics/diagstat and update
1136      our cvsignore files for the ACSII output generated
1137    
1138    checkpoint57k_post
1139    o lab_sea now uses diagnostics package and provides a suite of
1140      new EXF diagnostics output.
1141    
1142    checkpoint57j_post
1143    o exf
1144      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
1145        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
1146        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
1147      * extended diagnostics output
1148        - now includes all EXF variables
1149        - hs, hl moved to common block
1150        - separate S/R for diagnostics, called after ctrl vector is added
1151        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
1152        - EXFqnet contains true Qnet (i.e. includes qsw)
1153      * updated verif. lab_sea, global_with_exf
1154      * Rearranging hflux (exf_mapfields -> exf_getforcing)
1155        to ensure that diagnostics sees a true EXFqnet
1156    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
1157    o diagnostics pkg: change pointers so that 1 diagnostic can be used
1158      several times with different frequencies.
1159    o mnc-ify the thsice package as requested by Daniel Enderton
1160      - the monitor--MNC output needs work
1161      - many attributes need to be added (most are currently blank)
1162    o mnc-ify theaim_v23 package as requested by Daniel Enderton
1163      - many attributes need to be added (most are currently blank)
1164    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
1165    o add Sadourny like discretization to the 4th.O vorticity advection scheme
1166    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
1167      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
1168         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
1169    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
1170     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
1171    
1172    checkpoint57i_post
1173    o Diagnostics package was changed: diagnostic allocation is now deactivated
1174      by setting an empty file name in the namelist (used to be by setting 0 frequency)
1175    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
1176      add 1rst Order upwind vertical Shear.
1177    o add a quick fix for A/B checkpointing in OFFLINE mode
1178    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
1179      end-run around the C/Fortran linking horror in eesup/src/timers.F
1180    o added pkg/runclock: allows user to terminate run based on wall clock
1181    o added non-hydrostatic scaling parameter: nh_am2
1182    o pkg/my82: futile attempt to make results compiler-independent by adding
1183      some "_d 0", etc. no effect.
1184    o for mnc output, fill the 'T' coordinate var with myTime and create a
1185      separate 'iter' variable for iteration count
1186    o pkg/diagnostics:
1187      add new capability: output of Global/Regional & per-level statistics ;
1188      tested against monitor output (including land & thSIce) on various exp.
1189    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
1190    
1191    checkpoint57h_done
1192      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
1193      data.diagnostics, data.gchem, data.ptracers) is done.
1194    
1195    o pkg/diagnostics: prepare for Global/Regional statistics.
1196      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
1197    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
1198      and rename it: DIFFERENT_MULTIPLE
1199    
1200    checkpoint57h_post
1201    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
1202    o pkg/diagnostics: change output frequency, now in seconds (instead
1203      of Nb of iterations). This requires to change data.diagnostics.
1204    checkpoint57h_pre
1205    
1206    o in mnc, let the user create the output dir if both mnc_outdir_date
1207      and mnc_outdir_num are false
1208    o add fflags() to pkg/diagnostics which allows one to specify, on a
1209      per-file basis, the file precision [default behavior is unchanged]
1210    o added diagnostics to pkg/kpp, including computation of mixed layer
1211      depth based on a temperature/density criterion
1212    o updated verification/natl_box to test the new pkg/kpp diagnostics
1213    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
1214    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
1215    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
1216      not mnc -- this mistake was found by JMC and is now corrected
1217    
1218    checkpoint57g_post
1219    o add Adams-Bashforth 3rd Order time stepping:
1220      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
1221      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
1222    checkpoint57g_pre
1223    
1224    o make lambda[Theta,Salt]ClimRelax spatially varying
1225      (default remains spatially uniform constant based on tau)
1226    o added new control variables
1227      * init. uVel, vVel, etanN
1228      * lambda[Theta,Salt]ClimRelax
1229    o separate masks used for ctrl_pack/unpack 'from write_grid' output
1230      (suggested by G. Forget)
1231    
1232    checkpoint57f_post
1233    o add parameter "baseTime" = model base time = time at iteration zero
1234      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
1235      account for baseTime shift
1236    o move Coriolis arrays from PARAMS.h to GRID.h
1237    checkpoint57f_pre
1238    
1239    o mnc-ifying the seaice package
1240    o introduced an alternative length scale calculation for use in the limiting
1241      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
1242    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
1243    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
1244      as well as grad(vort3).  Made it compatible with both approximate form
1245      for the cubed sphere and full form of these gradients.  Added flag
1246      useFullLeith to select between approximate and full form.  
1247    o add "d0" in getcon.F to reduce differences between compilers/platforms
1248      update output.txt of exp. fizhi-gridalt-hs
1249    o change port_rand funtion to allow to set the seed.
1250    o fix obscure MNC bug involving conversion between reals and integers
1251      - it caused no problems with certain (eg. gcc, ifc) compilers but the
1252        new version is now more standards-compliant
1253    o adjoint-related modifications
1254      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
1255      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
1256      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
1257    
1258    checkpoint57e_post
1259    o Adding eddy stress controls a la Ferreira et al.
1260    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
1261    
1262    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
1263      update output.txt of exp. fizhi-gridalt-hs
1264    o add more "Z" dimensions and associated coordinate vars to MNC
1265    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
1266    o parameter calendarDumps: when set, approximate months (30-31 days) and years
1267      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
1268      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
1269      months and years.  Requires pkg/cal.
1270    o diagnostics: add pickup functionality
1271      - off by default for backwards compatibility
1272      - current version only uses MDSIO -- MNC will be added
1273    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
1274    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
1275    
1276    checkpoint57d_post
1277    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
1278    o modify verification/ideal_2D_oce so that it tests the creation of mnc
1279      output from the diagnostics package
1280    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
1281    o make genmake2 more portable by using ".$FS" instead of ".f" for more
1282      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
1283    o add coordinate variables to the MNC output from the diagnostics package
1284    o change MNC-flags default value: true when useMNC=TRUE
1285    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
1286      the ability (off by default) to read the grid information using MNC
1287    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
1288    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
1289    o do snap-shot diagnostics at the middle of the time-interval (instead of
1290      at the end).
1291    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
1292      new test for AIM with thSIce + slab-ocean
1293    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
1294    o move state variable diagnostics to the beginning of the time step ;
1295      (note: still needs some work specially for snap-shot diagnostics)
1296      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
1297    
1298    checkpoint57c_post
1299    o Change testing option (-ieee) to get closer agreement between g77 & ifort
1300    o generate new output.txt files on faulks with g77 & the new -ieee option
1301    checkpoint57c_pre
1302    
1303    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
1304      update output.txt of exp. global_ocean.90x40x15
1305    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
1306      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
1307    o add saltFlux(+File) forcing capability with periodicExternalForcing
1308    o allow to use pkg diagnostics for GM-Redi & ThSIce output
1309    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
1310    o improvements for the MNC output from DIAGNOSTICS:
1311      - correct handling of the unlimitied dimension
1312      - all dims now have associated coordinate variables
1313      - variables located at U, V, and Corner ("Z") points are now written
1314        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
1315        *all* data points are output
1316    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
1317    o added pkg/seaice/seaice_monitor.F
1318    o mdsio_readfield.F can now read files visible only to master MPI process.
1319    o pkg/seaice: some test code for ice-modified ocean stress
1320    o exf_getffields interpolation defaults to bilinear for all scalar forcing
1321      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
1322      spurious negative numbers for precipitation and humidity.  Will cause
1323      some small numerical differences for integrations using pkg/exf/exf_interp.F.
1324    o pkg/ctrl/
1325      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
1326        May be enabled via doPackDiag
1327      *  introduce z-scaling of
1328         + gradient (doZscalePack) and
1329         + control (doZscaleUnpack)
1330    o pkg/mdsio/
1331      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
1332      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
1333    
1334    checkpoint57b_post
1335    o simplify options in diagnostics_fill arguments (remove weird combinations)
1336    o fix MNC coordinate variables so that they now contain per-face index
1337      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
1338      general, EXCH2 grids are only aligned to a "local" coordinate system
1339    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
1340    o Implement instantaneous output within pkg diagnostics:
1341      setting a negative frequency in data.diagnostics produces
1342     "snap-shot" output (as opposed to time-average if freq > 0)
1343    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
1344      NOTE: change ptracer diagnostics name: use 2 characters to work with
1345            more than 9 tracers. Add also diagnostics of advect & diffus flux.
1346    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
1347      becomes the coordinate variable for the 'T' dimension
1348    o add CF-style coordinate variables to MNC
1349      - just a first cut:  numbers are meaningless on the cubesphere and
1350        missing along the T axis but otherwise it works!
1351    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
1352    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
1353    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
1354      this is based directly on what the model compute, so that the content of
1355      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
1356    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
1357    o clean up build options files for SunOS, in particular
1358      - remove -traditional from xmakedepend
1359      - change -xarch=v9 to -xarch=native for f77
1360      - restore use of make (not gmake)
1361      - add CC=gcc if using g77
1362    o changes per discussion of AM, JMC, & EH3 today:
1363      - move redundant "grid" variables out of "state" -- in preparation of
1364        creating proper CF-style coordinate variables and in recognition
1365        that any/all grid variables can be easily copied (eg. w/NCO) from
1366        the grid files into any of the other NetCDF files
1367      - *always* output grid variables with MDSIO (this will eventually be
1368        changed)
1369      - output MNC grid file if useMNC is true
1370    o every instance of _END_MASTER() has been found and replaced with
1371      _END_MASTER( myThid ) in order to satisfy certain picky Sun
1372      preprocessors
1373    o re-arrange diagnostics pkg initialisation:
1374     - allow each package to extend the available diagnostics list
1375     - add some checking and fix small problems (multi-threaded, ...)
1376     - new S/R diagnostics_fill (replace fill_diagnostics):
1377       look through the short list of active diag. (instead of the long list)
1378       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
1379    
1380    checkpoint57a_post
1381    o this set of changes restores TAMC compatibility
1382      tested for global_ocean.90x40x15 adjoint on trough
1383      (what a pain)
1384    
1385    checkpoint57a_pre
1386    o some modifs in tools/build_options for sunos
1387    o call ctrl_pack for ctrl at end for optimcycle=0
1388    
1389    checkpoint57
1390    o add horizontal bi-harmonic viscosity for vertical velocity
1391      - new parameter viscA4W (defaults to viscA4)
1392      - affects only non-hydrostatic code
1393      - to be done: no-slip lateral boundary conditions
1394    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
1395    o implement Implicit Vertical advection for pTracers
1396    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
1397      (implemented also for implicit vertical diffusion & advection)
1398    o OBCS: extend application of tracer open boundary conditions
1399      to a strip beyond the boundary of width Olx/Oly
1400    o add call monitor to TAF set of required calls (flow directives)
1401      and include in natl_box_adjoint
1402    o untangle a few ifdefs related to cost, ctrl, autodiff
1403      untangel a few ALLOW_ECCO_OPTIMIZATION
1404    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
1405      (theta2, salt2 in ecco_cost_weights)
1406    
1407    checkpoint56c_post
1408    o OBCS as control variables
1409      - update ctrl_ad_diff.list, obcs_ad_diff.list
1410      - remove balance of obcs controls from default
1411      - fix index bug nobcs in ctrl_init
1412      - fix dummy fields filen in ctrl_pack
1413      - add dummy weights for obcs
1414    o lsopt: comment out fort.94 output
1415    o optim:
1416      - remove unnecessary header files
1417      - adjusted namelists
1418      - add xerbla.F to Makefile
1419    o exf:
1420      - multiple modifications of exf_check_range
1421      - unit change in exf_init_runoff from [m/year] to [m/s]
1422    o mdsio:
1423      - i/o-vector change debugLevel from debLevA to debLevB
1424    
1425    checkpoint56b_post
1426    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
1427      is called from DO_THE_MODEL_IO
1428      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
1429      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
1430      - clean up PTRACERS_WRITE_TIMEAVE a little
1431    o add another verification experiment that tests both the cfc-pkg and
1432      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
1433      reactive tendencies treated inline with regular timestepping
1434    o testreport previously did a lousy job of comparing small numbers, so
1435      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
1436      implemented in the little c-progam tmp_cmpnum.c which is embedded in
1437      testreport.
1438    o ptracers_monitor: bug fix for MPI
1439    
1440    checkpoint56a_post
1441    o GCHEM: finish reorganizating the package
1442      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
1443        (introduces another 3D-array for each passive tracer, but only if
1444        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
1445        gchemTendency is not needed because the timestep is done separately)
1446      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
1447      - GCHEM is now---more or less cleanly---separate from PTRACERS
1448      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
1449        so clear to me how that should be done in a general way.
1450    o CFC: improve formatting of output in CFC_ATMOS
1451    o PTRACERS:
1452      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
1453        that ALL experiments with ptracers enable can be checked. This makes
1454        GCHEM_MONITOR obsolete.
1455      - include a runtime parameter PTRACERS_monitorFreq that defaults to
1456        monitorFreq
1457      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
1458    o add PTRACERS (PTR0[1-5]) to testreport output
1459    o exf_check_range:
1460      * default changed to .TRUE.
1461      * will check values for niter0 if debLevA, every timestep if debLevB
1462      * STOP in exf_check_range if 'out of range'
1463      * range chosen generous to allow for potential extema
1464      TBD: a version with stricter range
1465           permitted range would be runtime parameters
1466  o GMredi:  o GMredi:
1467    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
1468    - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.    - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
# Line 11  o GCHEM: Line 1471  o GCHEM:
1471    - move call to GCHEM_FORCING_SEP, so that it is now called before    - move call to GCHEM_FORCING_SEP, so that it is now called before
1472      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
1473    - introduced a useGCHEM runtime flag and applied it everywhere.    - introduced a useGCHEM runtime flag and applied it everywhere.
1474      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
1475        this flag is now only visible within GCHEM-pkg routines.
1476      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
1477        be replaced by a 3D array that is computed before thermodynamics; for
1478        this, the tracer ID iTracer had to be included into the parameter list
1479        of ptracers_forcing
1480      - set up forward_step to call gchem_forcing, that will replace
1481        gchem_forcing_int in ptracers_forcing
1482      - cleaning up
1483  o small cleaning of exch2: remove files that are also in eesupp/src  o small cleaning of exch2: remove files that are also in eesupp/src
1484    
1485  checkpoint56  checkpoint56

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