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revision 1.32 by adcroft, Thu Nov 30 16:51:40 2000 UTC revision 1.877 by dimitri, Tue Sep 18 21:18:12 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 pkg/seaice: a first HSALT time stepping equation has been checked in
8    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
9      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
10      without requiring DO-IF statements
11    o pkg/thsice:
12      use continuous power-law function for partition of energy between lateral
13      melting/freezing and thinning/thickening ; old code using step function
14      still available with #undef THSICE_FRACEN_POWERLAW
15      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
16    o testreport: change AD testing : check against results/output_adm.txt
17      using same scripts as for forward test.
18    
19    checkpoint59g
20    o adjoint testing: in preparation for changing testreport:
21      - output format: cost and grad written on separated lines
22      - ad output results in directory "results" (instead of "results_ad")
23    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
24    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
25    o pkg/ecco: allow user defined cost function contributions
26    o testreport:
27      Allow to choose (per experiment) the list of tested output variables
28       and the main variable (used to issue a pass/FAIL ) ;
29      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
30      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
31      Also modify printing of summary:
32       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
33       b) echo the list of tested variables in the individual summary.txt of
34          each experiment.
35    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
36      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
37      (but still depend on the tile decompostion of the domain).
38    o pkg/seaice: change a discretization detail to make the B-grid code
39      "more symmetric". This change is likely to remove all "ridges/leads" that
40      where quasi-aligned with the grid in B-grid solutions. It may also be
41      the solution to the stress coupling issues with the B-grid.
42    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
43      remove .cvsignore from input dir. (since testreport no longer run here).
44    o pkg/thsice:
45     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
46     - fix reshaping of sea-ice just after advection:
47       melt all the ice only if ice-volume is too small.
48     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
49       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
50     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
51    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
52      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
53    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
54      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
55      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
56      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
57      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
58      -> update output.txt
59    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
60     this affects truncation error: -> update output.txt of exp:
61      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
62      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
63    
64    checkpoint59f
65    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
66    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
67      a bounded range (in forward mode)
68    o pkg/ecco, ctrl, autodiff and mom_common:
69     internal parameter controls, completements of implementations
70    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
71    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
72      (not seem any difference in testing results).
73    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
74       at face corners.
75    o pkg/generic_advdiff:
76     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
77      loop range indices for computing vertical advection tendency
78      and do the calculation in the interior only (no overlap) ;
79      for now, only implemented for SOM advection (to save CPU time).
80     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
81    o exch2 adjoint
82      First set of changes:
83      - add exch2 hand-written adjoint templates
84      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
85        This will require cleanup in pkg/autodiff/*.F
86        (changed routines currently kept separate in verif. code/)
87      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
88        that used to hide exch2 or cubed-sphere specific code
89        (commented via 'cph-exch2')
90    o pkg/seaice
91      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
92    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
93       output of global_ocean.cs32x15.thsice .
94    
95    checkpoint59e
96    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
97      for B-grid vector (not yet tested) and C-grid vector (<- only used
98      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
99    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
100      (#ifdef ALLOW_SALT_PLUME)
101    o gather_2d/scatter_2d: removed halo regions
102    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
103      scheme and the corresponding test case (under front_relax dir). For now,
104      only available with Skew-flux form and not yet tested in realistic set-up.
105      adjoint: store directives updated, but gradient checks deteriorated,
106      so maybe GM/Redi adjoint is now broken.
107    o seaice adjoint
108      * add AREA, HEFF, HSNOW as control variable
109        (should not change lab_sea results)
110      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
111    o pkg/seaice:
112      * added computation of saltFlux in seaice_growth;
113        For time being, sea ice salinity is assumed constant
114        contribution of snow flooding to freshening of sea ice is neglected.
115        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
116        defaults to 0.0 in order to maintain backward compatibility.
117        Typical values for SEAICE_salinity are 4 to 10 g/kg.
118      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
119      * added SEAICE_availHeatFrac, which specifies fraction of surface level
120        heat content used to melt or grow ice
121      * commented out cap of HICE: it helps keep ice thinner
122      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
123      * applied OBCS T/S mask to HEFFM sea ice mask
124    
125    checkpoint59d
126    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
127     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
128     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
129    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
130     and change default value of parameter "GM_Small_Number";
131     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
132       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
133       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
134    o pkg/ecco: cost function when applying pkg/smooth to controls
135    o pkg/ctrl: add forcingPrecond run time parameter
136    o pkg/seaice:
137     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
138     - fix bug in metric terms of u-equation in LSR solver (implicit part),
139       changes verification/lab_sea
140     - rearrange implicit part of u-equation in LSR solver to make it easier to
141       read, understand, and debug. This causes changes at the truncation level.
142     - fix (serious) bug in the boundary conditions (sign error in the implicit
143       part) of the LSR solver. Changes all LSR results.
144     - fixed problem with HSNOW initialization to avoid thick snow when AREA
145       is initilized with small values - does not change lab_sea results.
146     - added HsnowFile initialization capability
147    o pkg/smooth: addition to model/src and pkg/ctrl so allow
148     initialization of pkg/smooth and application to control vector
149    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
150    o dependencies: pkg/profiles requires pkg/cal
151    o pkg/profiles:
152     - added option ALLOW_PROFILES_GENERICGRID
153         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
154         that interpolation information (grid points and coefficients) is provided
155         within the netcdf input files.
156         -> sample matlab scripts can be found in MITgcm_contrib/gael
157         that allow you to prepare netcdf input files.
158     - also modified: cleaner include statements, cleaner error print statements,
159       cleaner stops when error, and more tests of the netcdf input files consistency.
160    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
161    o pkg/seaice:
162     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
163       requires a new routine: seaice_diagnostics_fill.F
164     - make sure that seaice does not move if not forced (pressure replacement
165       method, Hibler and Ip, 1995), changes results
166     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
167     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
168       It is turned off by default (=-1.), because it changes the results.
169     - make it possible to read AREA from a file, too.
170    
171    checkpoint59c
172    o add S/R and diagnostics for oceanic mixed-layer depth
173    o move GMRedi call after all vertical mixing schemes (including KPP)
174    o pkg/thsice:
175     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
176      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
177    o pkg/obcs:
178     - bug fix for balance code
179    o pkg/seaice:
180      - allow values of SEAICE_elasticParm > 1
181      - add new parameter SEAICE_evpTauRelax as an alternative
182        to SEAICE_elasticParm
183      - make lsr boundary conditions free slip (by default), changes result
184      - add code for no slip boundary conditions for lsr
185      - set minimum of zeta to zero (and not 4e8) (changes results)
186      - add a cap on AREA after advecting AREA if seaice_growth is not called
187    o change calculation of Visbeck K:
188      - no longer depend on tapering scheme; instead, compute slope (limited
189        by GM_maxSlope). this is equivalent to what was comuted before with
190        clipping or linear tappering.
191      - fix vertical averaging (wrong by 1/2 level)
192      - leave the old version (but will not be maintained) within
193        #ifdef OLD_VISBECK_CALC / #endif
194      - update output of exp. ideal_2D_oce
195    o change error catch in calc_r_star to improve vectorization
196    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
197      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
198    o adjoint:
199      Re-organized adjoint checkpointing according to Matt Mazloff
200      (but with modifs/completions/cleanups)
201      Storing is now bundled into large arrays to optimized I/O
202      (and second step in cleanup of the_main_loop)
203    
204    checkpoint59b
205    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
206      - export/import (between ocean & coupler) fields needed for ocean DIC.
207    o pkg/seaice:
208      - get rid of three more exchanges seaice_calc_viscosities (required
209        different loop boundaries in seaice_lsr and seaice_ocean_stress)
210      - bug fix in seaice_ocean_stress (update of lab_sea required)
211      - reduce loop boundaries to necessary minimum also in seaice_evp
212      - go back to the old way of computing deltaC/Z as the adjoint likes that
213        better
214    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
215      passive tracer to an Age Tracer) + update output.txt
216    o pkg/exf:
217      - implement A-grid / C-grid selection for wind-stress input files.
218      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
219      for now, in exf_bulk_largeyeager04.F only :
220      - change implementation for case where windspeed + 2. components wind-stress
221        are read-in. AND use rhoConstFresh to convert evap.
222    o pkg/seaice:
223      - use correct EXCH_UV for wind-forcing (on A-grid).
224      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
225        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
226    o pkg/exf:
227      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
228      EXF_INTERPOLATION:
229      - merge global_with_exf/code version of exf_interp_read.F
230        to the main code ;
231      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
232        reading the file ; Important: This options needs to be defined to recover
233        previous code.
234        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
235      - no longer loose real*8 precision along the way when using exf_iprec=64.
236    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
237      - change discretisation of evp-solver in order to avoid another exchange
238        (changes lab_sea) and clean up a little
239      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
240        help the adjoint (this also changes the results slightly)
241      - add a few "_d 0" where they had been missing in seaice_evp.F
242      - cleaning up: remove unused seaice_calc_rhs.F
243    o pkg/exf: some cleaning-up:
244      - change various "constants" into runtime parameters
245      - cleaned-up Large&Yeager04 routine which should eventually
246        replace exf_bulkformulae.F (changed names of S/R and CPP)
247        and merged various ALLOW_ATM_WIND options
248     only used with thsice pkg (in thsice_get_exf.F):
249      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
250        which are used when useStabilityFct_overIce=TRUE (= the default)
251      - change default values of ice & snow emissivity and scale downward LW
252        by ice & snow emissivity.
253    o pkg/thsice:
254     fix few little problems, in thsice_calc_thickn.F:
255      - growth vertically (and not laterally) if iceFrac == iceMaskMax
256      - melt only laterally if hIce < hThinIce (as the comments say)
257      and in thsice_extend.F:
258      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
259      - start to form ice as soon as the minimum ice-volume is reachable.
260     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
261      and cpl_aim+ocn
262    o pkg/kpp
263     - move computation of surface related input fields to KPP into a new
264       subroutine kpp_forcing_surf.F
265     - remove wrong (within bi,bj loops) EXCH calls.
266     - little cleaning (add argument myThid in last position, cvs header ...)
267     - for now, fix conservation problem by exchanging KPPviscAz (may not
268       be the best fix)
269    o pkg/seaice
270     - check for inconsistent evp parameter/cpp-flag combination
271     - remove leftover errIO flat for obsolete name list error handling
272    o OpenAD
273     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
274    
275    checkpoint59a
276    o pkg/seaice: some parameter clarifications and a little bit of clean up
277    o pkg/thsice: rename run-time parameters:
278       himin       -> hIceMin
279       himin0      -> hThinIce
280       hihig       -> hThickIce
281       i0          -> i0swFrac
282       transCoef   -> bMeltCoef
283       frac_energy -> fracMelting
284      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
285       with default values (for now) that do not change the results.
286      remove old version of thsice vars advection in pkg/seaice.
287    o in FFIELDS.h:
288      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
289      - make pLoad & sIceLoad always available (but still only used if
290         ATMOSPHERIC_LOADING is #define).
291    o pkg/kpp: replaced _KPP_RL with _RL
292    o bug fixes for vertical diffusivity computations when both KPP and
293        3D diffusivity arrays are used.
294    o pkg/seaice: fix bug in evp solver, while doing that
295      - change (improve?) discretization of stress computations for both
296        cgrid-lsr and evp solver
297      - add a new routine to compute strain rates
298      - the above changes lab_sea results
299      - add no slip conditions for evp solver (off by default), lsr-version
300        may follow
301      - fix exchange for shear at Z-points (does not change lab_sea)
302      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
303        (to force the user to pick a time step since there is not "safe" way
304        of choosing it)
305      - add principal stress diagnostics
306      - rearrange fields for evp a little to avoid having to call a: too many
307        exchanges and b: exchanges for stress trensor components which we do
308        not have.
309      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
310        of evp, complete rewrite for lsr case (latter is does not yet work
311        in all cases)
312    o pkg/kpp: add code to have mixing in shelf ice caverns
313      - add myThid to all kpp routines (long overdue)
314    
315    checkpoint59
316    o pkg/exf:
317      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
318        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
319      - move exf header files from lower_case.h to UPPER_CASE.h ;
320        add missing cvs Header & Name
321      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
322      - add namelist param. selectStressGridPosition, exf_monFreq
323      - retire many _CLIM routines, and remove data.exf_clim
324        + params moved to data.exf
325        + climsst, climsss now handled by exf_set_gen, i.e.
326          climss?period=0 refers to constant field,
327          climss?period=-12 to monthly forcing
328      - split up namelists in data.exf
329    o pkg/seaice:
330      - remove seaice_exch and seaice_exch_uv
331      - remove superfluous exchange of theta
332      - add myThid to seaice_budget_ocean/ice
333      - add new interface for atmospheric wind forcing (C-grid only)
334        + new routine
335        + two new field (taux, tauy for stress over ice)
336        + removed one global field (DAIRN) for C-grid case only
337    o pkg/thsise
338      - 2nd set of modifs for thsice adjoint in conjunction with exf
339    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
340    
341    checkpoint58y_post
342    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
343      vertical diffusivity, similar to that in MOM4; turned on using
344      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
345      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
346    o Added capability for 3D specification of background vertical diffusion
347      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
348      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
349      "data" file that contains the 3D vertical diffusivity coefficients.
350    o ice dynamics (pkg/seaice) with thsice thermodynamics:
351      - add code within pkg thsice to advect & diffuse sea-ice fields
352      similar to (and will replace) what has been added in  seaice_advdiff.F,
353      but: - conserving Mass, Heat & Salt.
354           - better when using non-linear advection scheme (not yet fully tested)
355           - can also be used in atmospheric set-up (for now, only the diffusion).
356    
357    checkpoint58x_post
358    o IO option for global-file compact format:
359      - add options when generating topology (utils/exch2/matlab-topology-generator)
360      - add I/O capability (pkg/mdsio).
361      - adapt utils/matlab/rdmds.m to read this format.
362      for now long-line format not yet supported by pkg/mdsio (& exch2).
363    o shelfice: add a few diagnostics
364    
365    checkpoint58w_post
366    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
367      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
368      (and replace horiVertRatio in NH code).
369      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
370                         and tutorial_plume_on_slope (sensitive to truncation)
371    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
372      directly to drive seaice model (C-grid only)
373    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
374     - reintroduce computation of wind from stress,
375     - compute tau (in exf_bulkformulae.F) from windstress averaged to
376       mass points to avoid tau = 0
377     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
378    o rdmnc.m: make it work with "global" files created with gluemnc
379    o rdmnc.m : some improvements in dealing with singleton dimension
380      (tested on all testreport mnc output files).
381    o genmake2: disable pkg/profiles if netcdf test fails.
382    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
383    o move call to cal_readparms up to make calendar parameters/variable available
384      to all packages
385    
386    checkpoint58v_post
387    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
388      useDynP_inEos_Zc tested.
389    o pkg/exf: changes to properly interpolate/mask/scale initial fields
390    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
391      and portions thereof.  See read_cs.txt for description and examples.
392    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
393      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
394      following the great-circle arc between those 2 points.
395    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
396      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
397    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
398     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
399     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
400     - still needs work (not working with some options ; efficiency to improve)
401       and serious testing.
402     - use this scheme for temperature & salinity in 2 advection test exp.:
403       advect_xy & advect_xz, respectively.
404    
405    checkpoint58u_post
406    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
407    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
408    o testreport: add option "-skipdir" to skip some test.
409    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
410      momentum calculation.
411    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
412    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
413      remove checkpoint.F and the_correction_step.F (no longer used);
414      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
415    o add option (linFSConserveTr) to correct for tracer source/sink due to
416      Linear Free surface
417    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
418    o pkg/thsice: fix reading mnc-pickups
419    
420    checkpoint58t_post
421    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
422    o pkg/mdsio:
423     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
424       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
425       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
426     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
427     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
428       either MDS_READ_FIELD or MDS_WRITE_FIELD )
429     - new S/R (to replace MDSWRITEMETA), which allows to write more
430       informations (variable names, time ...) to meta files.
431     - modify rdmds.m to give back the meta file content.
432    o pkg/diagnostics: change vertical interpolation to be safer, and more
433       flexible (define p-levels to interpolate to in data.diagnostics);
434      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
435       diagnostic pointer.
436    o pkg/seaice: more cleaning up of seaice_growth, added many comments
437    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
438    o fix multi-category seaice:
439     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
440       SEAICE_MULTICATEGORY
441     - fix short wave heat flux
442    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
443       and allow to use EVP solver. Change forward lab_sea: test both EVP
444       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
445    o Initial check-in of lab_sea adjoint
446      (very similar to natl_box_adjoint/code_seaice)
447      * used C-grid and EVP solver
448      * used KPP, GM/Redi
449      * uses inAdExact=.TRUE.
450      * gradient checks fail for both ADM and TLM
451        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
452        f.d. gradients actually seem more problematic than ADM, TLM gradients;
453        issue is related to forward mismatch between g77 an ifort
454    o pkg/seaice: overhaul of thermodynamics
455     - growth.F and groatb.F are replaced by new routine seaice_growth.F
456     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
457     - move a few global fields out of SEAICE.h into seaice_growth.F and
458       make them 2D (FICE/QNETO/ ...)
459     - remove FO (it is the same as QNETO)
460     - introduce a few local fields to avoid modifying external fields such
461       as atemp, etc.
462    
463    checkpoint58s_post
464    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
465      changed exf_set_gen.F so that
466        genperiod=0 means input file is one time-constant field and
467        genperiod=-12 means input file contains 12 monthly means
468    o CG2D: use pre-computed solver main-diagonal (stored in common block);
469      this affects truncation error ; generate new output file for exp. which
470      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
471        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
472        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
473        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
474        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
475        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
476    o start implementation of deep-atmosphere and anelastic formulation
477    o verification: remove 2nd copy of input files and use script "prepare_run"
478      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
479    o mom_common/vecinv/fluxform: fix a few initialisation isssues
480    o profiles: fix for multithreaded case
481    
482    o diagnostics: rename few diags:
483      s/'PRESSURE'/'RCENTER '/g
484      s/'TICE    '/'oceFreez'/g
485      s/'TAUX    '/'oceTAUX '/g
486      s/'TAUY    '/'oceTAUY '/g
487      s/'SWFLUX  '/'oceQsw  '/g
488      s/DIFx/DFxE/g
489      s/DIFy/DFyE/g
490      and add few ocean-forcing diagnostics:
491      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
492    o modifications to pkg/seaice/growth.F and budget.F, which change results of
493      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
494      as actual snow thickness.  It now refers everywhere to effective snow
495      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
496    
497    checkpoint58r_post
498    o modifications to pkg/seaice/growth.F, which change results of
499      lab_sea experiment: fixes pertain to melting snow over open water, to
500      masking EVAP under sea ice, and to using the correct AREA variable for
501      computations of EVAP, PRECIP, HSNOW, and GHEFF
502    o add ability to read bathy, salt, and theta using MNC (off by def)
503    o add flooding algorithm and advection of HSNOW for pkg/seaice;
504      both are turned off by default and do no change any results
505    o seaice advection with pkg/thsice: a step toward the use of non-linear
506      advection scheme, but #ifdef or commented out for now (requires more EXCH).
507    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
508      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
509      in natl_box (affects results @ truncation level: update output.txt)
510    o multi-threading and IO:
511      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
512      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
513        (needed to work with SingleCpuIO): tested in all verif. exp.
514    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
515      affects the results (but none of the verification test uses this scheme).
516    o Adding some pkg/diagnostics capability to pkg/seaice
517      (will certainly be subject to changes)
518    o ctrl: adding new control variables:
519      lwflux, lwdown, evap, snowprecip, apressure, runoff
520    
521    checkpoint58q_post
522    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
523      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
524      high_res_cube configuration by 4% on Columbia.
525    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
526      add (in global_with_exf/code) a version of EXF_INTERP_READ without
527      dynamical allocation (seems to work in multi-threaded).
528    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
529      single CPU io) so that TAF does not have to see EESUPPORT.h
530    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
531    
532    checkpoint58p_post
533    o obcs: stop if obcs is used with useCDscheme = .true.
534    o shelfice:
535     - fix a sign error so that no slip at shelfice interface works
536     - remove stop for combination non-hydrostatic code and shelfice. That does
537       not mean, that the results are correct, but at least they are numerically
538       stable
539    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
540    o added adjoint exch routined for all exch*3d* routines
541      and updated flow directives
542    
543    checkpoint58o_post
544    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
545      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
546    o change controling S/R for writing pickup file (new S/R do_write_pickup)
547      and clean-up reading/writing of pickup files.
548    o fix local version of read/write pickup (NH part) in rotating_tank/code
549    o simplify EXCH interface:
550     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
551     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
552    o added the regrid package
553    o shelfice:
554     - add a simple boundary layer scheme to reduce noise
555     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
556    
557    checkpoint58n_post
558    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
559       local variable (not in common block).
560    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
561      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
562      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
563        to work with SingleCpuIO.
564    o add "_d 0" to real constant of pkg/cfc subroutines ;
565       update exp. cfc_exemple & tutorial_cfc_offline output files.
566    o multi-threading and IO:
567      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
568        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
569      - barrier before and after reading.
570      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
571      - avoid using MDS_WRITELOCAL for LAND pkg output.
572      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
573        common-block variables ; Allows multi-threading with master-thread IO.
574    o change default MAX_NO_THREADS from 32 to 4 ;
575      and stop cleanly when MAX_NO_THREADS is too small.
576    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
577    
578    checkpoint58m_post
579    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
580       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
581    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
582       keep global_ocean.90x40x15 (for AD testing) with former secondary test
583       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
584    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
585        add MITgcm_tutorials (= code + all the tutorials)
586    o ecco, option to compute cost for total ssh (mean+anom)
587    o consistent with addition of ptracer and ssh in pkg/profiles
588    o profiles: adding ptracer and ssh
589    o testreport: change multi-test output-file name
590      (from output.txt.{name} to output.{name}.txt)
591    o profiles: now ok for mutli-tiles case
592    o seaice: add 4 parameters for different advection schemes for area,
593      (effective) seaice thickness, enthalphy, and snow height. Their default
594      is the standard parameter SEAICEadvScheme
595    o calc_gw:
596     - add cosFacU in zonal viscous flux (harmonic.visc.).
597     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
598       of tutorial_plume_on_slope.
599    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
600    o calc_gw: true flux-form, account for horizontal grid spacing.
601      update rotating_tank results, but not plume_on_slope (affected at
602      truncation level, 11 digits).
603    
604    checkpoint58l_post
605    o calc_gw:
606     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
607     - remove side-drag for now (need to fix it); update plume_on_slope results.
608     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
609    o commit code to make SST/SSS weights spatially variable
610      (based on either variable in-situ or variable initial T/S weights)
611    o pkg/ecco:
612      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
613        now based on horizontally varying weights wthetaLev, wsaltLev
614      * cost_averagesflags now returns year indices in addition to day, month
615      * sflux balance is performed on annual basis
616        (sflxumm, sfluxmm2, bal_sfluxmm)
617      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
618        including separate counting and multipliers
619    o pkg/rbcs
620      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
621    
622    checkpoint58k_post
623    o testreport:
624     - always build in dir. "build" (if not there, mkdir build instead of building
625       & running in input)
626     - run in dir run (if it exists), in build otherwise.
627     - call prepare_run (if input/prepare_run exists)
628     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
629    o pkg/exf modifications to interpolation and rotation routines for more
630       reasonable treatment of North Pole singularity: for tracers North Pole
631       value is set to northernmost zonal-mean value, for zonal velocity it is
632       set to zero, and for meridional velocity it is set to northernmost value.
633    o pkg/exf/exf_check_range.F
634     - add tile index to diagnostics and move stop statement to the very
635       end of the routine.
636    o pkg/diagnostics: (diagnostics_main_init.F)
637      define title of isomorphic variables according to the current config.
638    o pkg/thsice with pkg/seaice dynamics:
639    - fix domain of computation (interior only, required for exf) and do exchanges
640    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
641    o towards a standard way of dealing with multi-threading in MONITOR
642      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
643    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
644       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
645    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
646    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
647    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
648       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
649    o tracer advection:
650     - clean-up and simplify calc_common_factors.F
651     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
652       advection subroutine (but still not used within DST advection S/R)
653    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
654    
655    checkpoint58j_post
656    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
657      from file (collects calls previously in FORWARD_STEP)
658    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
659    o adjoint store dir. adjusted accordingly
660    o genmake2
661      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
662    
663    checkpoint58i_post
664    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
665      on wind stress (SEAICEstressFactor defaults to 1.)
666    o Total number of Timers is finite (<=40): comment out 2 non-essential one
667      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
668    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
669      on CS-grid: no longer loosing mass.
670    o exf & curvilinear-grid: no longer modify longitude xC & xG.
671    o pkg/ggl90: fix sloppy output and fix a bug
672    o pkg/seaice: added SEAICEuseEVPpickup parameter
673      - Set to false in order to start EVP solver with
674        non-EVP pickup files when using SEAICEuseEVP
675      - fix sign error in diffusion in seaice_calc_rhs
676    
677    checkpoint58h_post
678    * Modifications for bottom topography control
679      o replace hFacC by _hFacC at various places
680      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
681      o add non-self-adjoint cg2d_nsa
682      o update autodiff support routines
683      o re-initialise hfac after ctrl_depth_ini
684      o works for 5x5 box, doesnt work for global_ocean.90x40x15
685    * Adding verification for 5x5 box (4-layer) bottom topography control
686    
687    checkpoint58g_post
688    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
689       used for mean seasonal cycle, mean diurnal cycle); add an example
690       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
691    o pkg/ggl90:
692      - add parameter (minimum surface kinetic energy)
693      - fix bug (avoiding division by zero)
694    o couple pkg/thsice to pkg/seaice:
695      - modify advection in seaice to accomodate new scalar fields to be advected
696      - only muliDimAdection scheme work with seaice/thsice
697      - mapping of thsice-variables to seaice-variables, back and forth
698      - does not break the verification experiments, but does not give the
699        desired results either
700    o pkg/seaice
701      - make (default) second order advection a bit less confusing?
702    
703    checkpoint58f_post
704    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
705      to pkg/seaice):
706      - new routines thsice_map_exf and thsice_get_exf provide the interface
707      - add an additional formal parameter to thsice_solve4temp
708    o pkg/exf:
709      - add new fields wspeed, snowprecip (to be able to couple to thsice)
710      - correct Stefan-Boltzmann constant
711      - new parameter for longwave surface emittance
712      - separate some stuff from exf_bulkformulae into new routines  
713        exf_radiation, exf_wind
714      - add new parameters and constants: longwave emissivity for ocean, ice
715        and snow, evaporation parameters over ice
716      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
717        either wind from stress or stress from wind
718    o pkg/thSIce:
719    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
720    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
721       and THSICE_CALC_THICKN
722    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
723    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
724      to make debugging easier.
725    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
726    o pkg/bulk_force:
727      - clean-up comments and parameters ;
728      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
729    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
730      generate new output for test-experiment: aim.5l_cs.thSI
731    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
732      testreport accordingly
733    
734    checkpoint58e_post
735    o SEAICE_CGRID adjoint done
736    o R_STAR adjoint implemented.
737      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
738      * need to sort out init. of h0facc, etc.
739    o Make pkg/profile fully independent of ecco,cost, etc. stuff
740      to be able to use it in pure forward.
741    
742    checkpoint58d_post
743    o upgrade simple test-experiment to tutorial example:
744     step.1: duplicate the experiment and (step.2) will remove the old copy.
745      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
746      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
747      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
748      tutorial_global_oce_biogeo    <- copy of dic_example
749      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
750      tutorial_plume_on_slope       <- copy of plume_on_slope
751      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
752      tutorial_global_oce_optim     <- empty for now (David ?)
753      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
754     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
755    o correct a sign problem in cost_scat.F
756    o obcs and ptracers: fix boundary conditions for advections schemes
757      with larger stencil
758    o thsice adjoint: start
759    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
760      completeness
761    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
762      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
763    o ptracers adjoint:
764      * avoid extensive recomputatations
765      * fix missing re-init. of gptr (missed by TAF)
766    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
767      me to turn off the excessive output to STDOUT that this package produces
768    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
769      and add those terms in Vector-Invariant formulation.
770    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
771      if the control period (xx_hfluxperiod etc) is 0
772    o in profiles pkg, clean routines and fix details
773    o in ecco pkg, reading ssh data:
774      fix problem in case the model does not start at iter0=0
775    o fix mnc-pickup/restart for ptracers
776    o new package prifiles:
777      code to compute profile-based cost by Gael Forget
778      (modifs in ecco, ctrl, autodiff)
779    o Benign bug fix in initialization (spotted by M. Mazloff) of
780      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
781    
782    checkpoint58c_post
783    o adjoint: finish NLFS adjoint and provide reference output in
784      verification/global_ocean.90x40x15/results_ad_nlfs
785    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
786      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
787      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
788      with SEAICE_CGRID defined.
789    o move calendarDumps from "data" to "data.cal" and clean-up the code
790      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
791    o add useEXF & useCAL flags (for now, set in hard-coded way)
792    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
793      (were missing in NH mode, and wrong in quasihydrostatic mode).
794      waiting for Chris updated version of calc_gw to add those CALLs.
795    o fix bug in quasihydrostatic S/R ;
796      add a test for this option: global_ocean.90x40x15.qshyd
797    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
798      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
799    o add on/off flag useOffLine for package OFFLINE
800    o seaice:
801      - modify advection so that it works also on the C-grid
802      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
803        problem in multi-tile runs with C-grid
804      - add flags for clipping ice velocities and/or masking solver forcing
805      - fix drag (ocean on ice) formulation and a bug that caused noise in the
806        C-grid solver
807      - added a few comments to seaice_diffusion.F
808      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
809        are now exclusive)
810      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
811        required re-ordering the code a little:
812       + make DAIRN global variable (defined in SEAICE)
813       + move computation of the viscosities eta and zeta into a new separate
814         routine (because I need to recompute them in seaice_ocean_stress.F)
815    
816    checkpoint58b_post
817    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
818      update output.txt of exp. aim.5l_cs.thSI
819    o various mnc cleanups and improvements:
820      + shrink lookup tables by factor of ~4
821      + better error reporting when running out of lookup space
822      + able to handle longer path/file names (up to 500 chars)
823    o adjoint:
824      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
825      - TBD: "hidden" mom_vecinv recomp. in dynamics
826    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
827     (allow to differentiate between forcing components using new integer flags:
828      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
829     and add new flag to put Dissipation tendency out of Adams-Bashforth.
830    o ecco
831      - enable trend removal from SSH anomaly obs.
832    o adjoint
833      - a fix for PmEpR when #undef EXACT_CONSERV
834      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
835      - try to fix "hidden" recomp. in forward_step for NLFS
836        (NLFS seems broken sometimes after I checked it in)
837    o seaice:
838     - add c-grid version of the dynamic solver:
839       + three new routines that are the c-grid substitute lsr, dynsolver
840         and ostres
841       + put a few fields that were local to dynsolver into global common
842         blocks, so that I can move the computation of stresses etc into
843         seaice_lsr (saves coding but may break the adjoint).
844     - replace more hardwired parameters by runtime parameters
845     - add ice masks that mask the rhs of the implicit solvers where there
846       is no ice (commented out in seaice_dynsolver, because i am not sure
847       if this works properly), eventually this should replace the clipping
848       of ice velocities in seaice_dynsolver to +/-40cm/s.
849    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
850      include it only where its needed
851    o move balancing of fluxes before the call of external_forcing_surf
852    o seaice:
853      - correct units of turning angles (now they are really in degrees)
854      - move computation of GWATX/Y out of main routine into dynsolver
855      - initialize GWATX/Y in seaice_init
856    o Apply mask on Fresh-Water flux (needed for SSH forcing).
857      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
858    o seaice: add runtime flags for turning angles (default to zero)
859    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
860      and trend from exf forcing and ctrl control adjustments
861    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
862      (since checkpoint57x_post)
863    o change the default rotation period to 86164.s = the Earth rotation
864    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
865      and based on a reference stratification. Tested within hs94.cs-32x32x5.
866    o seaice advection: add code for choosing between the default (2nd order
867      central differences) and multiDim advection schemes provided by
868      pkg/generic_advdiff
869    o seaice:
870      - removed all references to SEAICE_GRID.h fields from
871        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
872        (cubed-sphere configuration will change a little)
873      - grid computations in seaice_init are obsolete now.
874      - cleaned up code a little so that is easier to read (hopefully).
875      - added new (better?) discretizations of default advection and diffusion
876        (turn on with SEAICEuseFluxForm)
877      - replace 1 in 3d global fields by kSurface in growth.F
878      
879    checkpoint58a_post
880    o seaice:
881      - bug fix in advect.F
882    o shelfice:
883      - separate shelfice load anomaly from pload (breaks with time
884        dependent forcing), => introduce constant field shelficeLoadAnomaly.
885        Its default is 0., but it may be computed more cleverly from (unknown)
886        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
887        done offline. A good approximation of the pressure load anomaly is
888        necessary to avoid large initial adjustment processes underneath
889        deep-reaching shelfice.
890      - small fix in ISOMIP shelfice_thermodynamics
891      - add more sophisticated thermodynamics of Hellmer (1989), this is
892        now the default
893      - give a few constants more intuitive names
894    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
895      if bulk formulae are used in long integration (especially EmPmR). Turn
896      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
897      if balancePrintMean, the imbalance that is substracted is printed to
898      STDOUT.
899    o fix bug (typo) in obcs_apply_eta.F
900    o add a new package shelfice which enables us to model the circulation
901      underneath shelf-ice with draughts of hundreds of meters.
902     - works
903     - to do: + include improved thermodynamics
904              + check whether kSurfC (from model/inc/SURFACE.h) can be used
905                instead of new field kTopC
906              + can we use topoFile, Ro_surf and existing code in ini_depth.F
907                instead of new field R_shelfIce and new code in ini_depth.F
908                and ini_mask_etc.F?
909              + adjust vertical mixing schemes?
910    o seaice pkg:
911     - add a cpp-flag to include a simple formula for a salinity dependent
912       freezing point of sea water at the surface
913     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
914       meridional stresses are now different (and hopefully correct)
915    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
916       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
917       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
918    o pkg/diagnostics: add options and parameters for regional-statistics
919       diagnostics ; define regions by reading a region-mask from a file
920       (might add other options later)
921    o pkg/bulk_force:
922     - add option and parameters to use AIM surface-flux formulae.
923     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
924       others forcing fields (defined in PARM05, parameter file "data") are loaded
925       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
926     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
927     - use the right EXCH call for uwind,vwind (to work on CS-grid).
928     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
929       and parameters (note: calcWindStress replaces .NOT.readwindstress).
930     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
931    
932    checkpoint58
933    o add "--embed-source" option to genmake2 which, when the supporting
934      tools can be compiled (as determined by genmake2) will turn on the
935      embed_files package which then embeds the entire MITgcm source code
936      (*.[fFhc] + Makefile) used for the build within the executable
937      - requested by CNH but off by default
938      - adds a paltry <9MB to the mitgcmuv executable in most cases
939      - only writes the output when useEMBEDSRC in eedata is true
940    o clean up 3-dim. relaxation codes:
941      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
942      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
943      * Thanks to Tom Haine for testing!
944    
945    checkpoint57z_post
946    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
947      affects output (@ truncation level) of exp. plume_on_slope ; updated.
948    o fix the pickup behavior for obcs in combination with ptracers
949    o fix a bug in ptracers_external_fields_load
950    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
951      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
952    o transfered surface NH pressure to eta field (if exactConserv).
953    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
954         and update lab_sea output.txt file.
955    o completing 3-dim. relaxation code: additional term
956         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
957      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
958      * At compile time, in "EXF_OPTIONS.h" set
959          #define  ALLOW_CLIMTEMP_RELAXATION
960          #define  ALLOW_CLIMSALT_RELAXATION
961      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
962          tauThetaClimRelax3Dim = 15552000.0,
963          tauSaltClimRelax3Dim  = 15552000.0,
964      * 3 cases:
965          1) Use a constant-in-time 3-dim. field
966          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
967          3) Real-time relax. to time-evolving prescribed field
968    o Adding Laplacian-type smoothness constraint on
969      initial and boundary (forcing) controls (ic, bc)
970      * enable at compile-time via
971        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
972      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
973      * Absolute scale somewhat unclear so far
974      * no area weighting was included since no other cost term does so far
975    
976    checkpoint57y_post
977    First step for a NLFS adjoint
978    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
979    o new init. routines for calc_r_star, calc_surf_dr
980    o still need to deal with ini_masks_etc
981    o testreport seemed happy
982    checkpoint57y_pre
983    
984    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
985    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
986    o add new offset feature to offline pkg (plus minor cleanup)
987    o cfc fixes for final year of integration
988    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
989      be in GCHEM_OPTIONS).
990    
991    checkpoint57x_post
992    o fix testreport Pb in multiple test experiment.
993    o cleanup our namelist syntax in verification:
994      - make it more F95 standards compliant (some work still needed)
995      - allows the vast majority of our tests to work with gfortran
996    o Non-Hydrostatic:
997     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
998     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
999    o Allow to apply AB on T,S rather than on AB(gT,gS):
1000     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
1001     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
1002       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
1003     - need a "clever" read_pickup to restart from the other AB formulation
1004    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
1005    o remove some unused variables (reduces number of compiler warnings)
1006    o adjoint
1007      * Disable useVariableViscosity for adjoint for time being
1008        (there are a number of extensive recomputations)
1009      * Initialize certain variables needed for adjoint
1010    
1011    checkpoint57w_post
1012    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
1013                 fix the singleCpuIO RS version of MDSWRITEFIELD
1014       and add a WARNING if using globalFiles=T with multi-processors.
1015    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
1016      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
1017    o tracer advection scheme:
1018      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
1019       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
1020       was not very convenient).
1021      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
1022       (further tests needed for the implicit DST & Flux-Limiter schemes).
1023    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
1024      and sRef for convenience, handy, when you want to initialize
1025      ptracers in a large domain with a constant non-zero value. Also,
1026      untangle ptracers_init.F a little.
1027    
1028    checkpoint57v_post
1029    o change dome exp. to use variable viscosity in side-drag terms.
1030    o remove all the files from the cfc_offline test since they are now
1031      incorporated into tutorial_cfc_offline which has been producing
1032      identical results for a few days of testing
1033    o add new parameter: sideDragFactor to enable half-slip-side BC
1034      and change side-drag S/R to use viscosity from mom_calc_visc
1035      (can switch back by setting sideDragFactor=0.); affects results at
1036      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
1037       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
1038    o vorticity & strain are now computed without masking, to account for
1039      no-slip-side BC in variable viscosity calculation ; mask is applied
1040      anyway later on, before computing advection/coriolis terms.
1041    o modify exp4 to test new obcs support for reading from external files
1042      and for passive tracers
1043    o fix behavior of ptracers_monitor when monitor output is written to a
1044      netcdf-file; still not independent of monitor.F (writes in the same
1045      file).
1046    o change default value of tRef (put a uniform, meaningful value for ocean
1047      & atmos) and initialize sRef (was missing, as Martin mentioned).
1048    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
1049      to be proportional to enstrophy dissipation length.  Thus,
1050       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
1051      This is now consistent with Smagorinsky and with the manual.
1052    
1053    checkpoint57u_post
1054    o OBCS and PTRACERS: add open boundary support for passive tracers
1055      - either use homogenous (pseudo) v.Neumann conditions or prescribe
1056        OB-values from file; this is not different from the way theta and salinity
1057        are treated
1058      - however, Orlanski-radiation conditions are not supported, and the model
1059        will stop if you use pTracers and Orlanski at the same time.
1060      - beefed up the rountine obcs_external_fields_load: now only those open
1061        boundary values are overwritten with values from files for which there
1062        are really files, otherwise the OB-fields remain untouched. This makes
1063        it possible to use different OBs at different ends of the domain (as
1064        with EXF)
1065    o reduce number of exch calls in shap_filt (s2).
1066    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1067      truncation level) 4/5 MLAdjust test results (11&12 digits match).
1068    
1069    checkpoint57t_post
1070    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1071    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1072      same truncation, independent of the face number: affects affects several
1073      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1074    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1075      note that biharmonic viscosity + no-slip was not tested in any experiment.
1076    o fix bug in non-linear free-surf side-drag ; generate new output for
1077      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1078    o make mnc honor the writeBinaryPrec flag for most kinds of output
1079    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1080    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1081      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1082    o add brackets in multi-terms sum to get same truncation, independent of
1083      the face number (manage to get exactly same value of gU,gV at the cs-edge)
1084      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1085    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
1086      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1087      a maximum grid-scale Reynolds number.  Also, changes all length calculations
1088      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1089      Suggested values of viscosity parameters found in mom_calc_visc.
1090      Many new viscosity diagnostics available.
1091    
1092    checkpoint57s_post
1093    o Add clearing-house for viscosity calculations, mom_calc_visc and
1094      correct numerous bugs in LeithD and Smagorinsky discretizations.  
1095      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1096      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1097      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1098      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
1099      The Strain-Tension form is now called with useStrainTensonVisc=.true.
1100      ViscAhStrain and viscAhTension are now retired.
1101    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1102    o In response to JMC's bug report, genmake2 now ignores any soft-links
1103      that it finds in the *current* directory when searching for files.
1104      Soft-links found in any other source directories will still work as
1105      they did before.
1106    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1107      a C routine to unlimit the stack size
1108    o mnc-ify pkg/aim snapshot vars
1109    o mnc-ify pkg/land as requested by Daniel
1110    o various changes to mnc including:
1111      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1112      - output can now be grouped so that all files within a group
1113          change the ITER portion of their names in lock-step together
1114      - can now read ("global") PER-FACE (in addition to PER-TILE) files
1115          and works with both EXCH1 and EXCH2 (but needs more testing)
1116      - writing works for all verification test cases w/ g77 on Linux
1117    
1118    checkpoint57r_post
1119    o make MNC variable initialization happen earlier
1120    o add diagnostics for (almost) each term of the momentum Eq.
1121    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1122    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1123    o remove MINIMAL_TAVE_OUTPUT option ;
1124      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1125    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1126      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1127    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1128    o add time-dependent SST, SSS control
1129    o cost terms in ecco/ modularized (new cost_generic.F)
1130    o cost_averages routines are modularized (new cost_averagesgeneric.F)
1131    o new infrastructure for seaice model vs. obs misfits in seaice/
1132      * driver from the_main_loop.F is seaice_cost_driver.F
1133      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1134      * gradient check in Exp. 6a of natl_box_adjoint/
1135    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1136      (see README file)
1137    
1138    checkpoint57q_post
1139    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1140    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1141      - bug was reported by Jean-Michel and Ian Fenty
1142    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1143      update exp. cpl_aim+ocn output.
1144    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1145      Needed for high-res. runs with large global files
1146      to be able to limit tapelev size
1147    o Changed some tests for adjoint:
1148      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1149      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1150      * global_ocean.90x40x15/ back to default 3-level checkpointing
1151    o Modifications to enable scripted COMMON to MODULE conversion
1152      * verification/OpenAD/code/ has necessary scripts and description;
1153      * converts, compiles and runs successfully;
1154    
1155    checkpoint57p_post
1156    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1157    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1158      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1159    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1160    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1161      (was already the case for dissipation with mom_vecinv,
1162       and also the case for grad.PhiHyd when staggered-timeStep)
1163      This will allow to put dissipation out-off the AB time-stepping.
1164     Unfortunately, affects truncation error. Update output of exp. that "fails"
1165      (cg2d matching number) and leave the others for later: front_relax(10),
1166      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1167      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1168    
1169    checkpoint57o_post
1170    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1171      (2) its ready to be documented during the 20050801 DocFest
1172    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1173      for ideal_2D_oce and lab_sea on linux_ia32_g77
1174    o set to #undef CTRL_SET_OLD_MAXCVARS_30
1175      in global1x1_tot/code_seaice_adj to access indices 32, 33
1176      (worth another tag)
1177    
1178    checkpoint57n_post
1179    o adding precip control xx_precip 32
1180    o adding swflux control xx_swflux 33
1181    o Replacing 10 forcing penalty cost routines by 1 generic.
1182    o Implementing partitioning in time-mean and variable adjustment
1183      for atmos. state.
1184    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1185    o in natl_box_adjoint:
1186      * updated exp 1 to 10
1187        (but does not have time-mean vs. variable split results yet)
1188    o updated global1x1/*_seaice_adj/
1189      to incorporate latest changes
1190    o enable useSingleCpuIO for mdsio vector routines
1191      (applies in particular to tapelev I/O)
1192    o removed inefficient K-loop in all active_file*control*.F
1193    
1194    checkpoint57m_post
1195    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
1196      and advect_cs (use EXCH-2 and standard cs-32 grid files).
1197    o pkg/exch2: filling of face-corner halo regions is optional
1198      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
1199    
1200    checkpoint57l_post
1201     tag before updating tutorials (pre-release-2)
1202    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
1203       for output and interpolation of input fields onto model grid)
1204    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
1205       Affects results of exp. rotating_tank ; update output.txt.
1206    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
1207          and taking the square quantity and/or using a fraction-weight field.
1208    o fix aim_diagnostics_init.F mate numbers.
1209    o add mnc output capability to diagnostics/diagstat and update
1210      our cvsignore files for the ACSII output generated
1211    
1212    checkpoint57k_post
1213    o lab_sea now uses diagnostics package and provides a suite of
1214      new EXF diagnostics output.
1215    
1216    checkpoint57j_post
1217    o exf
1218      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
1219        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
1220        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
1221      * extended diagnostics output
1222        - now includes all EXF variables
1223        - hs, hl moved to common block
1224        - separate S/R for diagnostics, called after ctrl vector is added
1225        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
1226        - EXFqnet contains true Qnet (i.e. includes qsw)
1227      * updated verif. lab_sea, global_with_exf
1228      * Rearranging hflux (exf_mapfields -> exf_getforcing)
1229        to ensure that diagnostics sees a true EXFqnet
1230    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
1231    o diagnostics pkg: change pointers so that 1 diagnostic can be used
1232      several times with different frequencies.
1233    o mnc-ify the thsice package as requested by Daniel Enderton
1234      - the monitor--MNC output needs work
1235      - many attributes need to be added (most are currently blank)
1236    o mnc-ify theaim_v23 package as requested by Daniel Enderton
1237      - many attributes need to be added (most are currently blank)
1238    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
1239    o add Sadourny like discretization to the 4th.O vorticity advection scheme
1240    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
1241      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
1242         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
1243    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
1244     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
1245    
1246    checkpoint57i_post
1247    o Diagnostics package was changed: diagnostic allocation is now deactivated
1248      by setting an empty file name in the namelist (used to be by setting 0 frequency)
1249    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
1250      add 1rst Order upwind vertical Shear.
1251    o add a quick fix for A/B checkpointing in OFFLINE mode
1252    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
1253      end-run around the C/Fortran linking horror in eesup/src/timers.F
1254    o added pkg/runclock: allows user to terminate run based on wall clock
1255    o added non-hydrostatic scaling parameter: nh_am2
1256    o pkg/my82: futile attempt to make results compiler-independent by adding
1257      some "_d 0", etc. no effect.
1258    o for mnc output, fill the 'T' coordinate var with myTime and create a
1259      separate 'iter' variable for iteration count
1260    o pkg/diagnostics:
1261      add new capability: output of Global/Regional & per-level statistics ;
1262      tested against monitor output (including land & thSIce) on various exp.
1263    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
1264    
1265    checkpoint57h_done
1266      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
1267      data.diagnostics, data.gchem, data.ptracers) is done.
1268    
1269    o pkg/diagnostics: prepare for Global/Regional statistics.
1270      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
1271    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
1272      and rename it: DIFFERENT_MULTIPLE
1273    
1274    checkpoint57h_post
1275    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
1276    o pkg/diagnostics: change output frequency, now in seconds (instead
1277      of Nb of iterations). This requires to change data.diagnostics.
1278    checkpoint57h_pre
1279    
1280    o in mnc, let the user create the output dir if both mnc_outdir_date
1281      and mnc_outdir_num are false
1282    o add fflags() to pkg/diagnostics which allows one to specify, on a
1283      per-file basis, the file precision [default behavior is unchanged]
1284    o added diagnostics to pkg/kpp, including computation of mixed layer
1285      depth based on a temperature/density criterion
1286    o updated verification/natl_box to test the new pkg/kpp diagnostics
1287    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
1288    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
1289    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
1290      not mnc -- this mistake was found by JMC and is now corrected
1291    
1292    checkpoint57g_post
1293    o add Adams-Bashforth 3rd Order time stepping:
1294      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
1295      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
1296    checkpoint57g_pre
1297    
1298    o make lambda[Theta,Salt]ClimRelax spatially varying
1299      (default remains spatially uniform constant based on tau)
1300    o added new control variables
1301      * init. uVel, vVel, etanN
1302      * lambda[Theta,Salt]ClimRelax
1303    o separate masks used for ctrl_pack/unpack 'from write_grid' output
1304      (suggested by G. Forget)
1305    
1306    checkpoint57f_post
1307    o add parameter "baseTime" = model base time = time at iteration zero
1308      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
1309      account for baseTime shift
1310    o move Coriolis arrays from PARAMS.h to GRID.h
1311    checkpoint57f_pre
1312    
1313    o mnc-ifying the seaice package
1314    o introduced an alternative length scale calculation for use in the limiting
1315      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
1316    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
1317    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
1318      as well as grad(vort3).  Made it compatible with both approximate form
1319      for the cubed sphere and full form of these gradients.  Added flag
1320      useFullLeith to select between approximate and full form.  
1321    o add "d0" in getcon.F to reduce differences between compilers/platforms
1322      update output.txt of exp. fizhi-gridalt-hs
1323    o change port_rand funtion to allow to set the seed.
1324    o fix obscure MNC bug involving conversion between reals and integers
1325      - it caused no problems with certain (eg. gcc, ifc) compilers but the
1326        new version is now more standards-compliant
1327    o adjoint-related modifications
1328      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
1329      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
1330      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
1331    
1332    checkpoint57e_post
1333    o Adding eddy stress controls a la Ferreira et al.
1334    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
1335    
1336    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
1337      update output.txt of exp. fizhi-gridalt-hs
1338    o add more "Z" dimensions and associated coordinate vars to MNC
1339    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
1340    o parameter calendarDumps: when set, approximate months (30-31 days) and years
1341      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
1342      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
1343      months and years.  Requires pkg/cal.
1344    o diagnostics: add pickup functionality
1345      - off by default for backwards compatibility
1346      - current version only uses MDSIO -- MNC will be added
1347    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
1348    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
1349    
1350    checkpoint57d_post
1351    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
1352    o modify verification/ideal_2D_oce so that it tests the creation of mnc
1353      output from the diagnostics package
1354    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
1355    o make genmake2 more portable by using ".$FS" instead of ".f" for more
1356      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
1357    o add coordinate variables to the MNC output from the diagnostics package
1358    o change MNC-flags default value: true when useMNC=TRUE
1359    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
1360      the ability (off by default) to read the grid information using MNC
1361    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
1362    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
1363    o do snap-shot diagnostics at the middle of the time-interval (instead of
1364      at the end).
1365    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
1366      new test for AIM with thSIce + slab-ocean
1367    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
1368    o move state variable diagnostics to the beginning of the time step ;
1369      (note: still needs some work specially for snap-shot diagnostics)
1370      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
1371    
1372    checkpoint57c_post
1373    o Change testing option (-ieee) to get closer agreement between g77 & ifort
1374    o generate new output.txt files on faulks with g77 & the new -ieee option
1375    checkpoint57c_pre
1376    
1377    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
1378      update output.txt of exp. global_ocean.90x40x15
1379    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
1380      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
1381    o add saltFlux(+File) forcing capability with periodicExternalForcing
1382    o allow to use pkg diagnostics for GM-Redi & ThSIce output
1383    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
1384    o improvements for the MNC output from DIAGNOSTICS:
1385      - correct handling of the unlimitied dimension
1386      - all dims now have associated coordinate variables
1387      - variables located at U, V, and Corner ("Z") points are now written
1388        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
1389        *all* data points are output
1390    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
1391    o added pkg/seaice/seaice_monitor.F
1392    o mdsio_readfield.F can now read files visible only to master MPI process.
1393    o pkg/seaice: some test code for ice-modified ocean stress
1394    o exf_getffields interpolation defaults to bilinear for all scalar forcing
1395      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
1396      spurious negative numbers for precipitation and humidity.  Will cause
1397      some small numerical differences for integrations using pkg/exf/exf_interp.F.
1398    o pkg/ctrl/
1399      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
1400        May be enabled via doPackDiag
1401      *  introduce z-scaling of
1402         + gradient (doZscalePack) and
1403         + control (doZscaleUnpack)
1404    o pkg/mdsio/
1405      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
1406      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
1407    
1408    checkpoint57b_post
1409    o simplify options in diagnostics_fill arguments (remove weird combinations)
1410    o fix MNC coordinate variables so that they now contain per-face index
1411      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
1412      general, EXCH2 grids are only aligned to a "local" coordinate system
1413    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
1414    o Implement instantaneous output within pkg diagnostics:
1415      setting a negative frequency in data.diagnostics produces
1416     "snap-shot" output (as opposed to time-average if freq > 0)
1417    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
1418      NOTE: change ptracer diagnostics name: use 2 characters to work with
1419            more than 9 tracers. Add also diagnostics of advect & diffus flux.
1420    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
1421      becomes the coordinate variable for the 'T' dimension
1422    o add CF-style coordinate variables to MNC
1423      - just a first cut:  numbers are meaningless on the cubesphere and
1424        missing along the T axis but otherwise it works!
1425    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
1426    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
1427    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
1428      this is based directly on what the model compute, so that the content of
1429      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
1430    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
1431    o clean up build options files for SunOS, in particular
1432      - remove -traditional from xmakedepend
1433      - change -xarch=v9 to -xarch=native for f77
1434      - restore use of make (not gmake)
1435      - add CC=gcc if using g77
1436    o changes per discussion of AM, JMC, & EH3 today:
1437      - move redundant "grid" variables out of "state" -- in preparation of
1438        creating proper CF-style coordinate variables and in recognition
1439        that any/all grid variables can be easily copied (eg. w/NCO) from
1440        the grid files into any of the other NetCDF files
1441      - *always* output grid variables with MDSIO (this will eventually be
1442        changed)
1443      - output MNC grid file if useMNC is true
1444    o every instance of _END_MASTER() has been found and replaced with
1445      _END_MASTER( myThid ) in order to satisfy certain picky Sun
1446      preprocessors
1447    o re-arrange diagnostics pkg initialisation:
1448     - allow each package to extend the available diagnostics list
1449     - add some checking and fix small problems (multi-threaded, ...)
1450     - new S/R diagnostics_fill (replace fill_diagnostics):
1451       look through the short list of active diag. (instead of the long list)
1452       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
1453    
1454    checkpoint57a_post
1455    o this set of changes restores TAMC compatibility
1456      tested for global_ocean.90x40x15 adjoint on trough
1457      (what a pain)
1458    
1459    checkpoint57a_pre
1460    o some modifs in tools/build_options for sunos
1461    o call ctrl_pack for ctrl at end for optimcycle=0
1462    
1463    checkpoint57
1464    o add horizontal bi-harmonic viscosity for vertical velocity
1465      - new parameter viscA4W (defaults to viscA4)
1466      - affects only non-hydrostatic code
1467      - to be done: no-slip lateral boundary conditions
1468    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
1469    o implement Implicit Vertical advection for pTracers
1470    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
1471      (implemented also for implicit vertical diffusion & advection)
1472    o OBCS: extend application of tracer open boundary conditions
1473      to a strip beyond the boundary of width Olx/Oly
1474    o add call monitor to TAF set of required calls (flow directives)
1475      and include in natl_box_adjoint
1476    o untangle a few ifdefs related to cost, ctrl, autodiff
1477      untangel a few ALLOW_ECCO_OPTIMIZATION
1478    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
1479      (theta2, salt2 in ecco_cost_weights)
1480    
1481    checkpoint56c_post
1482    o OBCS as control variables
1483      - update ctrl_ad_diff.list, obcs_ad_diff.list
1484      - remove balance of obcs controls from default
1485      - fix index bug nobcs in ctrl_init
1486      - fix dummy fields filen in ctrl_pack
1487      - add dummy weights for obcs
1488    o lsopt: comment out fort.94 output
1489    o optim:
1490      - remove unnecessary header files
1491      - adjusted namelists
1492      - add xerbla.F to Makefile
1493    o exf:
1494      - multiple modifications of exf_check_range
1495      - unit change in exf_init_runoff from [m/year] to [m/s]
1496    o mdsio:
1497      - i/o-vector change debugLevel from debLevA to debLevB
1498    
1499    checkpoint56b_post
1500    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
1501      is called from DO_THE_MODEL_IO
1502      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
1503      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
1504      - clean up PTRACERS_WRITE_TIMEAVE a little
1505    o add another verification experiment that tests both the cfc-pkg and
1506      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
1507      reactive tendencies treated inline with regular timestepping
1508    o testreport previously did a lousy job of comparing small numbers, so
1509      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
1510      implemented in the little c-progam tmp_cmpnum.c which is embedded in
1511      testreport.
1512    o ptracers_monitor: bug fix for MPI
1513    
1514    checkpoint56a_post
1515    o GCHEM: finish reorganizating the package
1516      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
1517        (introduces another 3D-array for each passive tracer, but only if
1518        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
1519        gchemTendency is not needed because the timestep is done separately)
1520      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
1521      - GCHEM is now---more or less cleanly---separate from PTRACERS
1522      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
1523        so clear to me how that should be done in a general way.
1524    o CFC: improve formatting of output in CFC_ATMOS
1525    o PTRACERS:
1526      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
1527        that ALL experiments with ptracers enable can be checked. This makes
1528        GCHEM_MONITOR obsolete.
1529      - include a runtime parameter PTRACERS_monitorFreq that defaults to
1530        monitorFreq
1531      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
1532    o add PTRACERS (PTR0[1-5]) to testreport output
1533    o exf_check_range:
1534      * default changed to .TRUE.
1535      * will check values for niter0 if debLevA, every timestep if debLevB
1536      * STOP in exf_check_range if 'out of range'
1537      * range chosen generous to allow for potential extema
1538      TBD: a version with stricter range
1539           permitted range would be runtime parameters
1540    o GMredi:
1541      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
1542      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
1543      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
1544    o GCHEM:
1545      - move call to GCHEM_FORCING_SEP, so that it is now called before
1546        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
1547      - introduced a useGCHEM runtime flag and applied it everywhere.
1548      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
1549        this flag is now only visible within GCHEM-pkg routines.
1550      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
1551        be replaced by a 3D array that is computed before thermodynamics; for
1552        this, the tracer ID iTracer had to be included into the parameter list
1553        of ptracers_forcing
1554      - set up forward_step to call gchem_forcing, that will replace
1555        gchem_forcing_int in ptracers_forcing
1556      - cleaning up
1557    o small cleaning of exch2: remove files that are also in eesupp/src
1558    
1559    checkpoint56
1560    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
1561    o mnc: cleanup "full" files--fixes out-of-memory problem
1562    o ECCO-GODAE
1563      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
1564      * fully merged and updated from SIO code
1565        windstress sign change affects
1566        - exf_inscal_[u/v]stress
1567        - sign of xx_tau[u/v] adjustments
1568        - signs in cost_scat
1569      * ctrl_get_gen: avoid update of tau[u/v] for first few days
1570      * natl_box_adjoint updated and compressed
1571      * 2-level checkpoint switch added
1572        (tested in EXP. 1 of natl_box_adjoint)
1573      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
1574    o SVD
1575      * first complete, non-hacked version for SVD calculations
1576      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
1577        performed via direct access files admtlm_vector.it????
1578        (via ctrl_[un]pack)
1579      * optimcycle is used for ARPACK iteration counter
1580        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
1581      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
1582        and add linear transforms where necessary
1583      * controls are initial/final SST, SSS (can be extended; need to check
1584        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
1585    o mdsio: filename info to both stderr, stdout
1586    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
1587      from sign change
1588    
1589    checkpoint55j_post
1590    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
1591      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
1592    o add consistent build directories and .cvsignore files to verification
1593    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
1594    o make all subroutines 30 or less characters in length for certain older
1595      compilers to work (a thorough search only turns up two routines in
1596      pkg/ptracers)
1597    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
1598      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
1599    
1600    checkpoint55i_post
1601    o change arrays for total vertical diffusivity (2.D if explicit,
1602      3.D if implicit) ; each ptracer uses its own background value.
1603    o added mnc/NetCDF output capability to ocn_compon_interf
1604      - added bits to verification/cpl_aim+ocn so that it can run on
1605        ITRDA and other clusters without the mpirun "-wd" option
1606    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
1607      configuration
1608    o give MNC the ability to create additional files rather than
1609      exceeding a specified file size limit "MNC_MAX_FILESIZE"
1610      - the default is just less than 2GB which is a practical limit
1611        on many systems
1612    o Compute the non-local term using either KPP vertical diffusivity (=default)
1613       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
1614    
1615    checkpoint55h_post
1616    o add verification test "vermix"
1617    o remove all the *_ioinc flags and replace with the single global
1618      outputTypesInclusive flag
1619    o allow to set a vertical profile of vertical diffusivity for T & S
1620    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
1621    o useMNC moved from data.mnc to data.pkg
1622    
1623    checkpoint55g_post
1624    o Renaming carbon AD experiments to comply with testreport conventions
1625    o Updating adjoint of Held-Suarez hs94.1x64x5
1626    o Fixing directives for non-ECCO forward_step, after ECCO directives
1627      have been fixed to avoid recomp. of do_oceanic_phys
1628      Works well for global_ocean.90x40x15,
1629      but recomp. issue remains for carbon
1630    o Updating adjoint output for natl_box_adjoint after
1631      pkg/ecco has been modified (see taga c55d_post)
1632    
1633    checkpoint55f_post
1634    o rename to timeave_init_fixed
1635    
1636    checkpoint55e_post
1637    o some delicate re-shuffle of store directives to avoid one
1638      extra call of do_oceanic_physics
1639      affects ecco_the_main_loop.F, do_oceanic_physics.F
1640      checkpoint_lev1_directives.h
1641    o NB: this may break global_ocean adjoint temporarily,
1642      but it is clear how to fix it. Will do later, need this now.
1643    
1644    checkpoint55d_post
1645    o ECCO specific cost function terms (up-to-date with 1x1 runs)
1646    o ecco_cost_weights is modified to 1x1 runs
1647    o modifs to allow observations to be read in as
1648      single file or yearly files
1649    o enable to read exf forcing fields as either
1650      single file or yearly files (flag useExfYearlyFields)
1651    checkpoint55d_pre
1652    
1653    o switch between 2-level and 3-level checkpointing
1654    o add ability of MNC to write local and "partial" (eg. 2D slices where
1655      the full 3D field is never actually stored) arrays to NetCDF files
1656      with the correct (that is, the complete multi-dimensional) set of
1657      array indicies
1658      - used in mom_vecinv() to write the diagFreq output
1659      - tested (demonstrated) in verification/aim.5l_cs
1660    o further mnc-ification
1661      - add verification/lab_sea to the list with mnc setups
1662      - fix undefined mnc v-names in cd_code
1663      - add kpp to mnc output (both snapshot and timeave)
1664    o non-hydrostatic code
1665      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
1666        in calc_gw.F
1667      - defaults to viscAh
1668      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
1669        friction or Leith) in non-hydrostatic mode, as long as there is
1670        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
1671    o pkg/cost
1672      extend simple cost functions to treat time mean quantities
1673      (T,U,V) via cost_accumulate_state from cost_tile
1674    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
1675        be 2 times larger than the minimum size the advection scheme requires.
1676        now get a perfect conservation of salt in advect_cs test-exp (updated)
1677    o GGL90 (Gaspar's TKE mixed layer)
1678      - add horizontal diffusion of TKE, requires exchanges in
1679        do_fields_blocking_exchanges, horizontal diffusivity is zero by
1680        default. In OPA there is no horizontal diffusion of TKE but the
1681        mixing coefficients are computed from a horizontal average of TKE of
1682        6 points or so. I think that diffusion has a little more physical
1683        justification.
1684      - clean up ggl90_calc in the hope of reducing memory usage (this hope
1685        was in vain)
1686      - mask tke-variable in ggl90_init
1687    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
1688    o fix biharmonic diffusion on CS-grid.
1689    o more obcs stuff
1690      - added obcs_external_fields_load as an alternative to the EXF-pkg option
1691        for reading boundary values. This routine is called from
1692        obcs_prescribe_read
1693      - updated obcs_check
1694      - changed sponge layer relaxation parameter units for days to seconds
1695      - turned off sponge layer by default
1696      - changed argument list of OBCS_CALC to myTime+deltaTclock
1697      - fixed about 35 bugs in obcs_external_fields_load
1698    
1699    checkpoint55c_post
1700    o obcs stuff
1701      - new runtime flags useOBCSprescribe, useOBCSbalance
1702      - re-arranged obcs_calc
1703      - moved exf_getobcs to obcs_prescibe_read
1704        obcs_prescibe_read is called after ORLANSKI stuff
1705        and independent of it (executable can contain all).
1706      - updated obcs_check
1707      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
1708        These may be necessary only if tangential velocities are
1709        prescribed at OB, not sure, needs testing.
1710    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
1711      which simplifies the calls and passes the ifc check-bounds test
1712    
1713    checkpoint55b_post
1714    o add a 2D scalar, Z location, exchange_2 routine.
1715    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
1716      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
1717      affects advect_cs results (for the wrong reason): update output.txt
1718    o use a more standard discretization for biharmonic viscosity ;
1719     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
1720      affects results of dome set-up: update output.txt
1721    o fix gad_advection.F (CubedSphere part), back to version 1.23
1722    o fix bug in mom_vi_del2uv.F (CubedSphere part).
1723    
1724    checkpoint55a_post
1725    o merged code to
1726      * prescribe/read time-dependent open boundaries
1727        (works in conjunction with exf, cal)
1728      * sponge layer code for open boundaries
1729      * each boundary N/S/E/W now has its own CPP option
1730        (healthy for the adjoint)
1731    
1732    checkpoint55
1733    o up-to-date adjoint of previous breaks
1734      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
1735      - global_ocean_ebm: adjoint still needs fix (TLM ok)
1736      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
1737      - carbon: * remove tr1-related adjoint verification
1738                * add ptracer as control variable
1739    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
1740      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
1741    
1742    checkpoint54f_post
1743    o in verification/carbin/ remove experiment related to
1744      ALLOW_PASSIVE_TRACER (array tr1 etc)
1745      code_ad/ input_ad/ results_ad
1746    
1747    o add two new packages
1748      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
1749        + subject to optimization (memory)
1750      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
1751        + subject to reordering (many GOTOs in the original code)
1752        + so far opps is called for every (i,j) point, and then operates in
1753          the vertical; one may want to reorder the scheme in order operate in
1754          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
1755          fields)
1756    o overhaul of IO so that we now have flags for MDSIO and/or MNC
1757      - all verification tests compile and run with linux_ia32_g77
1758      - defaults are compatible with current input files--nothing
1759        should change if you were not previously using MNC
1760      - MNC output has been added in numerous places (eg. timeave)
1761        but there are still a few writes not yet do-able with MNC
1762        (this is in progress)
1763      - flags now allow for either/or/both use of MDSIO and MNC and
1764        documentation will soon follow
1765      - numerous small formatting cleanups for ProTeX
1766    o add version info (via BUILD_INFO.h) to MNC and stdout
1767    
1768    checkpoint54e_post
1769    o add two new packages
1770      - pp81 (Packanowski and Philander, 1981), Richardson number and
1771        stratification dependent mixing
1772      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
1773      - these scheme operate in a similar manner as KPP (without ghat, of
1774        course), however there is only one diffusivity that is used for both
1775        temperature and salinity (and passive tracers)ç
1776    o add offline package
1777    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
1778      provided by Stephanie Dutkiewicz
1779    o genmake2: add ability to search for C compilers and cleanup test output
1780      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
1781    
1782    checkpoint54d_post
1783    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
1784    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
1785      leading to additional shift by 5 days each year of integration
1786       (i.e. leading to considerable offset over the years)
1787    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
1788    o start with no AB and no initial filtering (staggerTimeStep):
1789      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
1790    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
1791      (external loading & cpl import/export stay in forward_step.F)
1792    o update coupling interface to work with new staggerTimeStep
1793    o change MDSIO ptracers_pickup.
1794    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
1795    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
1796    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
1797    
1798    checkpoint54c_post
1799    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
1800      this affects (truncation error) output.txt of test-exp:
1801       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
1802    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
1803    o change Qnet to always be the net heat flux, (+upward).
1804      affects (truncation error) output of natl_box exp.: updated
1805    o define the max number of passive tracers in PTRACERS_SIZE.h
1806    o start to test mnc routinely in exp0
1807    o add sea-ice loading (sIceLoad) as a new forcing field.
1808    
1809    checkpoint54b_post
1810    o add testreport "-j JOBS" option for parallel builds (tested and pretty
1811       impressive on Altix and Opteron systems)
1812    o diagnostics can now write NetCDF files through the mnc package
1813    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
1814    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
1815    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
1816      affects (truncation error) output of lab_sea & natl_box exp.: updated
1817    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
1818    
1819    checkpoint54a_post
1820    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
1821    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
1822    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
1823    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
1824      + internal_wave (shift in writing cg2d_ini_res)
1825    checkpoint54a_pre
1826    
1827    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
1828      - modified verification/lab_sea and natl_box_adjoint accordingly
1829    
1830    checkpoint54
1831    checkpoint53g_post
1832    o prepare splitting of thermodynamics: store convect.counter in common block
1833    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
1834      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
1835    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
1836    o new parameter "nShapS": allow to treat differently S from T (nShapT)
1837    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
1838    o restore adjointability
1839    
1840    checkpoint53f_post
1841    o modifications that affect AIM experiment results (update output.txt):
1842      - no advection of S at top interface Nr (pkg/generic_advdiff)
1843      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
1844    o AIM pkg:
1845      - include stability function into surf.Flux derivative relative to Tsurf
1846      - calculate clear-sky radiation & surface temp. change (for diagnostics)
1847    
1848    checkpoint53e_post
1849    o merged cylindrical coord configuration
1850    o added rotating_tank experiment
1851    checkpoint53e_pre
1852    
1853    checkpoint53d_post
1854    o faulks upgraded: re-generate output.txt that have changed:
1855       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
1856    o Added Bryan and Lewis, 1979, vertical diffusivity profile
1857    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
1858    o added Sadourny discretization of Coriolis
1859      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
1860      - re-enabled use of omega3 (useAbsVorticity)
1861    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
1862      vector-invariant equations
1863      - note: does *NOT* yet use same variable visc. for no-slip BC's.
1864    o recoded the lateral boundary conditions for non-hydrostatic w, this time
1865      hopefully without new bugs
1866      - still to do: biharmonic friction for non-hydrostatic w
1867    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
1868    o regenerated output for global_ocean_ebm (using -ieee)
1869    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
1870      of mom_common/
1871      - simple re-arrangement of instructions within computing loop
1872    checkpoint53d_pre
1873    
1874    checkpoint53c_post
1875    o new version of coupler for AIM+thSIce and Ocean models
1876     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
1877     - land: change Evaporation of snow
1878     - aim with thSIce: fix bug in snow-precip.
1879    o changes to calc_gw.F
1880     - bug fix for w^2 term near the bottom boundary
1881     - (hopefully) improve the lateral slip boundary condtions for use with
1882        partial/looped cells
1883      - because the bug fix changes two verification experiments anyway (exp5
1884        and plume on slope), change the lateral boundary condition from half slip
1885        to the value of no_slip_sides
1886    o ebm package wasnt quite up to the parallel task. Fixed that.
1887    o Adjoint of EBM package + verification
1888      * TLM OK
1889      * ADM not sufficient accuracy yet (needs further testing)
1890    
1891    checkpoint53b_post
1892    o Commiting new energy balance model to repository
1893      * package is pkg/ebm
1894      * verif. is verification/global_ocean_ebm
1895      * references are in ebm_driver.F
1896    C      * X. Wang, P. Stone and J. Marotzke, 1999:
1897    C        Global thermohaline circulation. Part I:
1898    C        Sensitivity to atmospheric moisture transport.
1899    C        J. Climate 12(1), 71-82
1900    C      * X. Wang, P. Stone and J. Marotzke, 1999:
1901    C        Global thermohaline circulation. Part II:
1902    C        Sensitivity with interactive transport.
1903    C        J. Climate 12(1), 83-91
1904    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
1905    C        Destabilization of the thermohaline circulation
1906    C        by atmospheric eddy transports.
1907    C        J. Climate 7(12), 1870-1882
1908    o Will need long integration testing.
1909    checkpoint53b_pre
1910    
1911    o created pkg/mom_common in preparation for variable viscosity code
1912    o renamed and split ini_mnc_io
1913    o pkg/land: only liquid water can diffuse or run-off
1914    o AIM using land: soil wetness availability account for snow
1915    o added printMapIncludesZeros to EEPARMS namelist
1916    
1917    checkpoint53a_post
1918    o restore TAMC compatiility for exf_constants.h
1919      (no usage of _d in .h)
1920    o Additional storing in KPP in an attempt to fix
1921      TAMC problem with adjoint of KPP code.
1922      (no success...)
1923      Identical code works fine with TAF.
1924    o Fixed verification/natl_box_adjoint experiments.
1925      Initial conditions for Experiments 4 and 5 are now
1926      set to "SEAICE_initialHEFF=0", which is more reasonable,
1927      and hence gives results closer to that of Experiment 2.
1928      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
1929    
1930    checkpoint53
1931    o stable checkpoint with up to date adjoint
1932      TLM tests only run for 1st grdchk at the moment. Its unclear if
1933      this is a code problem or a problem with resetting code for g_
1934      variables that is being autogenerated wrong.
1935      Otherwise:
1936       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
1937       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
1938         are both still in chaos following their security messes.
1939    
1940    checkpoint52n_post
1941    o various build (mostly genmake2) changes including:
1942      - ability to build/run more easily within Cygwin and MacOS X
1943      - more complicated Makefiles with a stronger dependence on Gnu Make
1944    o pkg/seaice modifications
1945      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
1946        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
1947        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
1948      - changed proxy for geostrophic velocity and updated
1949        verification/lab_sea/results/* accordingly
1950      - removed ADI dynamic solver from pkg/seaice
1951      - replaced all occurrences of 1/CSTICE or 1/CSUICE
1952        they caused a segmentation fault under certain circumstances
1953      - removed unused field WATR
1954    o bug fix in exf-package:
1955      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
1956         now reflect that.
1957    o small fixes in the cal-package:
1958      - set reference date to first of January for the 'model'-calendar
1959      - failing of cal_CheckDate in cal_FullDate now actually results in a
1960        warning
1961    o small modifications in exf-package to increase flexibility:
1962      - change climtempfreeze from a constant to a runtime parameter that
1963        is specified in data.exf_clim (default = -1.9)
1964      - introduce runtime parameter windstressmax (default = 2.0) that is
1965        specified in data.exf
1966    o fix in pkg/thsice:
1967      - update Evap (Tsf changes) to be consistent with Latent heat flux
1968      - maintain snow precipitation unchanged (even if Tsf >=0).
1969     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
1970    
1971    checkpoint52m_post
1972    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
1973      this does not change any of the results, because myIter=0 in swfrac always
1974      lead to jwtype=2 (the default anyway), but the call makes little sense
1975      as a default
1976    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
1977    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
1978      atmospheric model (AIM) to use it ; add a "slab ocean" component.
1979    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
1980    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
1981    o extending useSingleCpuIO option to work with new exch2 I/O format
1982      - old-style, missing-tile I/O is still accessible by defining CPP
1983        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
1984    o monitor package can write to NetCDF files and/or STDOUT
1985    o fix re-definition bug in MNC_GRID_INIT_ALL()
1986    o doc/api_reference added
1987      - a framework for building an API Reference Manual using all
1988        the "protex" comments embedded in the code
1989      - see pkg/generic_advdiff, pkg/mnc for examples
1990    o MNC:
1991      - make myThid the last argument for all subroutines
1992      - new default for the grid files: NO halos
1993      - add useMNC and other run-time flags
1994      - separate per-file-group handling of the unlimited dimension
1995      - early initialization of MNC w/ flags read at the eeboot stage
1996        and lookup tables set in initialize_fixed
1997      - write all MNC output to a freshly-created directory
1998    o thermodynamics sea-ice (thsice) is now tested with testreport.
1999    o test exp. advect_cs: use the standard cs32 grid ; update output.
2000    o Added functionality to grdchk:
2001      pick global i,j,k position (or nearest wet) where to perform check.
2002    
2003    checkpoint52l_post
2004    o new land formulation:
2005      a) use ground enthalpy as prognostic variable to ensure exact
2006         energy conservation.
2007      b) account for water temperature and for latent heat of freezing
2008         in all processes (rain, run-off, ground storage)
2009      c) compute surface and ground temperature implicitly.
2010    o aim_v23 modification for new land model:
2011      a) Treat separately land / ocean / sea-ice surface fluxes
2012         to allow implicit computation of land & sea-ice surface temp.
2013      b) add snow precipitation.
2014    checkpoint52l_pre
2015    
2016    o fix problem (when 1 tile is empty) in min/max monitor.
2017    o fix bug in timeAve (u,vZetatave in common block)
2018    o no restoring terms under ice for pkg/seaice
2019    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
2020    o bug fix for pkg/seaice pickups
2021    o change MNC call locations and add coordinate attributes
2022    o mask vorticity at the corner ; affects global_ocean.cs output
2023    o fix ini_curvilinear_grid ; test CS experiments with mpi
2024    o aim.5l_cs: modify sea-ice fraction input file ; update output
2025    o exf: Adding simple range check routine for exf fields after read
2026    
2027    checkpoint52k_post
2028    o removed top-level directory "diags"
2029      - we migrated these functions to pkg/timeave a long time ago
2030    o fixed bug introduced in pkg/monitor
2031    o accuracy ctrlprec = 32 insuffient for gradient checks using
2032      averaged fields (I/O via cost_averages)
2033      -> use ctrl.h in active_file*.F to control I/O precision.
2034    o paramter list of CALL ADTHE_MAIN_LOOP
2035    o added initial do_the_model_io to ecco
2036    o set all ...Freq to zero after cost_final
2037      taveFreq, dumpFreq, pChkptFreq
2038    o MAIN and ECCO differentiability restored
2039    
2040    checkpoint52j_post
2041    o fix nchklev in tamc.h for global_ocean...
2042    o Bringing flow and store directives up-to-date
2043    o Really weird thing!
2044      call do_the_model_io from the_main_loop with parameters
2045      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
2046      TAF places a faulty re-call of initialise_varia
2047      after cost_final call which should not be there!
2048    checkpoint52j_pre
2049    
2050    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
2051      error messages
2052    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
2053    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
2054      debug output
2055    o modfied mdsio_writefield.F to handle non-global files under exch2
2056    o update AIM Cubed-Sphere exp (aim.5l_cs):
2057      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
2058    o update AIM Equatorial Channel exp:
2059      use standard aim_v23 pkg and change the SST fields to be more realistic.
2060    o globalFile now works with exch2
2061    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
2062      mon_vort3.F to make exch2 friendly with >1 tile per cube face
2063    o limit timeave output for hi-res integrations
2064    
2065    checkpoint52i_post
2066    o removed CPP_EEOPTIONS.h from verification/*/code
2067    o updated the tiling for global_ocean_pressure
2068    checkpoint52i_pre
2069    
2070    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
2071      the old pkg/aim).
2072    
2073    checkpoint52h_pre
2074    o shortened offending lines in exch2_send_rx?.template
2075    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
2076    o genmake2: add build & execute test for NetCDF code
2077    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
2078      old grid files, moved CPP_EEMACROS.h to pkg/exch2
2079    o added useSingleCPUIO flag to monitor.F and mon_out.F
2080    o added temporary hack for sea-ice dynamics on the cube:
2081      metric terms are ignored and it is assumed that
2082      there is no sea-ice on cube faces 1, 2, 4, and 5.
2083    
2084    checkpoint52f_post
2085    o added exch2 cube routines to pkg/exch2
2086    o modified hs94.cs-32x32x5 to use it
2087    o added new grid files to hs94.cs-32x32x5
2088    checkpoint52f_pre
2089    
2090    checkpoint52e_post
2091    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
2092      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
2093    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
2094      to work with implicit vertical advection and AB ;
2095    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
2096    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
2097     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
2098    checkpoint52e_pre
2099    
2100    o fix bug in impldiff when Nr=1 or Nr=2.
2101    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
2102    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
2103    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
2104      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
2105    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
2106    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
2107    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
2108    
2109    checkpoint52d_post
2110    o re-tiled many expts to allow comparison in multi-processor mode
2111      - updated output accordingly
2112      - changed hs94.128x64x5 to use intial T from file rather than use the
2113        random number generator
2114    o add infrastructure in model routines for fizhi and gridalt packages
2115    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
2116    o changes to permit hi-res, cubed-sphere, configuration
2117      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
2118      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
2119      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
2120        of surface winds for the cube
2121      (A verification experiment, based on global_ocean.cs32x15, but with
2122       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
2123       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
2124       complete with example surface forcing files and matlab scripts to look
2125       at the output and compare it with that of global_ocean.cs32x15.)
2126    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
2127       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
2128       to conform to the common rule.
2129    o check-in the first version of the coupler + interfaces for multi-components
2130       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
2131       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
2132       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
2133       - ocean and atmos. share the same horizontal grid (no interpolation).
2134       - exchanges between component and coupler is done in forward_step
2135    o new verification experiment, cpl_aim+ocn:
2136       coupled ocean - AIM atmosphere on cs32 grid.
2137    
2138    checkpoint52d_pre
2139    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
2140    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
2141    
2142    checkpoint52c_post
2143    o Fixing OPTIONS files for use of exf:
2144      - ALLOW_ECCO not needed
2145      - ECCO_CPPOPTIONS.h should not be included from
2146        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
2147        as has been the case in the past
2148      - All cal/exf related options are currently set in
2149        single header file. Should remain so until we
2150        agree on a consistent new policy.
2151    o Removed all CPP options for cal package.
2152      cal has no more CPP options.
2153    o modified STOREs in GAD_ADVECTION
2154    o corrected key comp. for passkey
2155    
2156    checkpoint52b_post
2157    o new version: "thsice" of thermodynamic sea-ice pkg:
2158     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
2159     - modify fluxes but do not change theta directly;
2160     - light cleaning of bulk_force pkg (still needed with thsice).
2161     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
2162       + output_thsice.txt to test thsice & bulk_force pkgs.
2163    o put back grid & coriolis monitor output.
2164    checkpoint52b_pre
2165    
2166    o call "do_the_model_io" at the beginning (=> dump initial state)
2167    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
2168    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
2169      (need info on NUMBER_OF_PTRACERS)
2170    o missing PTRACERS headers in some routines
2171    o default tamc.h in pkg/autodiff supposed to crash
2172      to ensure proper customization
2173    
2174    checkpoint52a_post
2175    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
2176      - moved surfaceTendencyTice from pkg/seaice to main code
2177      - subroutine FREEZE_SURFACE now limits only surface temperature
2178        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
2179        => new output.txt for global_ocean.cs32x15 & global_with_exf
2180      - keep the old version of FREEZE for backward compatibility;
2181        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
2182      - corresponding modifs for TAF directives
2183    o added surface flux output variables to TIMEAVE_STATVARS
2184    o time-averaged output for pkg/ptracers
2185    o fix problem with ECCO-related divided adjoint
2186      snapshot file was missing some ad-variables,
2187      but no warning issued by TAF
2188    
2189    checkpoint52a_pre
2190    o some bug fixes for #undef REAL4_IS_SLOW
2191    
2192    checkpoint52 = ecco_c52_e35
2193    o after testing adjoints of checkpoint51u_post
2194    
2195    checkpoint51u_post
2196    o this is the post-merge tag of the ecco-branch
2197      (needs another clean checkout and re-testing)
2198    o various natl_box_adjoint configs and results
2199      but no input fields
2200    o obcs adjoint not yet merged!
2201    o adding ECCO global 1x1 and 2x2 degree configs
2202    o updated/extended some store directives for seaice
2203    o pkg/ecco now containes ecco-specific part of cost function
2204    o top level routines the_main_loop, forward_step
2205      supersede those in model/src/
2206      previous input data.cost now in data.ecco
2207      (new namelist ecco_cost_nml)
2208    o in ctrl/ cleaned some cross-dependencies and updated CPP options
2209    
2210    checkpoint51t_post
2211    o this is the pre-merge tag of the ecco-branch
2212    
2213    checkpoint51s_post
2214    o cleanup: removed various obsolete #define-s
2215    o pkg/grdchk
2216      - renamed 'ph-grd 3' to 'grad-res'
2217      - merged from ecco-branch
2218        (remaining bug fixes for obcs gradient checks)
2219      - additional high-precision output for testreport
2220        (grep for 'precision_grdchk_result')
2221    
2222    checkpoint51r_post
2223    o cleaned up or removed CPP_OPTIONS.h files
2224    o updated results for some of the tests to reflect the new
2225      optfiles (-ieee: -O0 instead of -O3)
2226    
2227    checkpoint51q_post
2228    o cd_code:
2229      - moved cd_scheme.F -> cd_code_scheme.F
2230      - separate read_checkpoint from cd_code_ini_vars.F
2231      - separated cd_code part from write_checkpoint
2232      - updated AD_SOURCE, generated .flow
2233      - added CD_CODE_VARS.h to the_main_loop
2234      - Moving cd_code specific store dir.s to pkg/cd_code
2235    o ctrl package totally restructured
2236      - pack/unpack now optional and decoupled from
2237        xx_/adxx_ I/O
2238      - ctrl_pack/unpack cleaned
2239        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
2240      - confined inclusion of AD_CONFIG.h to where necessary.
2241    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
2242    
2243    checkpoint51p_post
2244    o create initial cd_code package
2245      - WARNING: the initialization of fields within packages
2246        is broken because INI_FIELDS (where READ_CHECKPOINT is
2247        called) is called *before* PACKAGES_INIT_VARIABLES.
2248        This seems to be backwards since
2249        1) its important to initially zero the entire field including
2250           the "halo" region
2251        2) zeroing needs to be done *before* reading pickup info
2252           and the pickup call might or might not happen in any
2253           particular run
2254      - this needs an overhaul for R2
2255    o cleanup verification/*/code/GMREDI_OPTIONS.h
2256    o cleanup testreport
2257    
2258    checkpoint51o_post
2259    o bringing AD-related verif's up to date with genmake2
2260      - carbon/
2261      - global_ocean.90x40x15/
2262      - hs.94.1x64x5/
2263      - (front_relax/ )
2264    o (more) consistent directory structure for AD-related verif.'s
2265    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
2266    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
2267    o bug fix in find_alpha.F for MDJWF:
2268      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
2269        change rho -> rho-rhoConst
2270      - replace call find_rho to find_rhonum
2271    o initialisation of rFlx extended to full array (required by TAF)
2272      and shifted to thermodynamics
2273    o removed PTRACERS.h in ptracers routine
2274    o added surfacetendencyPtr to S/R parameter list pracers_forcing
2275    o Correcting initialisations for fVerU, fVerV.
2276    o helping TAF to recognize dependency on kUp for
2277      fVerU, fVerV
2278    o Replacing delZ by delR in pkg/ctrl/
2279    checkpoint51o_pre
2280    
2281    o undid all of cp51 pending some cleanups and discussion
2282    o added the [#include "AD_CONFIG.h"] statement to all files that need
2283       it for adjoint/tl #defines
2284     o re-worked the build logic in genmake2 to support AD_CONFIG.h
2285     o removed tools/genmake since it no longer works
2286    
2287    checkpoint51n_post
2288    o modifications to make FREEZE flux visible to pkg/kpp
2289      - moved surfaceTendencyTice from pkg/seaice to main code
2290      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
2291      - subroutine FREEZE now limits only surface temperature
2292        (this means new output.txt for global_ocean.90x40x15,
2293         global_ocean.cs32x15, and global_with_exf)
2294    o added surface flux output variables to TIMEAVE_STATVARS
2295    
2296    checkpoint51n_pre
2297    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
2298    o added [#include "AD_CONFIG.h"] to all files that use the following
2299      defines:
2300      - ALLOW_ADJOINT_RUN
2301      - ALLOW_TANGENTLINEAR_RUN
2302      - ALLOW_ECCO_OPTIMIZATION
2303    
2304    checkpoint51m_post
2305    o incorporating changes to get TAMC/TAF working in genmake2
2306      - added new TAMC/TAF targets to the Makefile
2307      - various cleanups related to package handling
2308      - these changes should have no impact on the forward model
2309    
2310    checkpoint51l_post
2311    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
2312     - faster algorithm for cal_addtime.F
2313     - higher precision arithmetic, where needed
2314     - pkg/exf *startdate variables changed from calendar date to
2315       model integration time
2316    
2317    checkpoint51l_pre
2318    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
2319    o enable to apply restoring on S & T only in a latitude band.
2320    o update output (external_forcing_surf modif. change truncation errors)
2321       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
2322    
2323    checkpoint51k_post
2324    o change default to: useNHMTerms=.FALSE.
2325     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
2326       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
2327     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
2328        exp1, ideal_2D_oce
2329     - change data file of oceanic exp (leave the results unchanged for now)
2330       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
2331    o set gravitySign automatically according to the vertical coordinate used
2332      (and change sign: back to "logical" value: +1 when R increases downward)
2333    o added an include barrier to the default CPP_OPTIONS.h and
2334      removed the #include "PACKAGES_CONFIG.h" from it
2335    o fix a bug in mom_fluxform (from chk51j_post)
2336    
2337    checkpoint51j_post
2338    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
2339    o adjusted some flow directives (dynamics, thermodynamics)
2340    o added cubed-sphere case to test cost function
2341    o heckpoint_lev?_directives.h now include
2342      pkg-specific directives, whenever those are enabled.
2343    o Moving pkg-specific flow directives to corresponding pkg
2344      Moving pkg-specific differentiation list to corresponding pkg
2345      Moving pkg-specific checkpoint-lev storing to corresponding pkg
2346      ---> conventions are
2347           - pkg_ad.flow
2348           - pkg_ad_diff.list
2349           - pkg_ad_check_lev?_dir.h
2350    
2351    checkpoint51i_post
2352    o merge of the branch-genmake2
2353      - knowingly breaks the older genmake
2354      - automatic generation of all ALLOW_${PKG_NAME} defines
2355      - new testreport supersedes older testscript
2356    o large number of package inclusion and header cleanups
2357    checkpoint51i_pre
2358    
2359    o new output for adjoin of global ocean vector invariant
2360    o fix for checkpoint of thermodynamic seaice and bulk_force
2361    o Steph gchem various cleanups
2362    
2363    checkpoint 51h_pre
2364    o fixed some single quotes
2365    o modify gchem pkg to be more versatile
2366    o modifications to clean up dic pkg
2367    o add pkg/cfc
2368    
2369    checkpoint51g_post
2370    o provide links for ARPACK and ADM*TLM
2371    o start removing verification/vero/
2372    o update AD-related stuff
2373      (in particular some IF-statements in model/src/ routines)
2374    o adding to verification/global_ocean.90x40x15/ adjoint of
2375      vector invariant setup
2376    
2377    checkpoint51f_post
2378    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
2379    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
2380      of tracer Green's fucntions for ocean inversion project.
2381    
2382    checkpoint51f_pre
2383    o Added on-the-fly spatial interpolation capability
2384        "USE_EXF_INTERPOLATION" to pkg/exf.
2385      - This is a temporary Cartesian-grid hack until
2386        the super-duper ESMF coupler becomes available.
2387      - See verification/global_with_exf/README for usage example.
2388      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
2389        flags and modified pkg/seaice accordingly.
2390    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
2391        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
2392        non-local transport term.
2393    
2394    checkpoint51e_post
2395    o pkg/mom_vecinv:
2396      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
2397      - add time-ave diagnostic of vorticity advection.
2398    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
2399    o atmospheric geopotential: - include water vapor effect;
2400                                - use p^kappa in p* scaling.
2401    o land pkg: read initial state from files.
2402    o AIM : add stratospheric drag in the upper level
2403    
2404    checkpoint51d_post
2405    o change function ILNBLNK (=> last non-blank char.) to return zero
2406      (instead of the string length) when the string. char is empty
2407    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
2408    o modif's to restore TAMC compatibility
2409      - avoid "_d" constructs in PARAMETER declarations
2410      - avoid interrupting lines by comment lines
2411    o Use cluster local disks for purely local I/O
2412      vs. globally visible disks needed for ctrl stuff
2413      (merged from ecco-branch)
2414      - new active_file_loc... and mdsio_..._loc routines
2415      - affected packages: autodiff, ctrl, grdchk, mdsio
2416    
2417    checkpoint51c_post
2418    o introducing integer flag debugLevel
2419      - debLevZero: suppress all output
2420      - debLevA: standard
2421      - debLevB: equivalent to current debugMode=.TRUE.
2422    o introducing pathname variable mdsioLocalDir for mdsio
2423      that can be specified at runtime
2424      (relevant for cluster I/O to local disk)
2425    `
2426    >>>checkpoint51b_post
2427    adjoint of ptracers
2428    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
2429    o extended state in checkpoint_lev?, etc.
2430    o alternative ctrl/cost with tr1 or ptracer
2431    o new comlev1_bibj_ptracers
2432    o new ptracers.flow
2433    o made ptracers_forcing same as external_forcing_s
2434    o added verification for adjoint with ptracers
2435      - adm. grdchk fail so far
2436      - tlm. grdchk OK
2437      - checked tapelev/comlev recomputations: OK
2438    <<<checkpoint51b_pre
2439    
2440    checkpoint51a_post
2441    o added code for biogeochemistry package
2442      - new pkgs: dic, gchem
2443      - new subroutine in ptracers
2444    o modify code for biogeo packages
2445      - in model/src and pkg/ptracers
2446    
2447    checkpoint51
2448    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
2449      - autodiff, ctrl, exf, grdchk, seaice
2450      kept separate packages
2451      - cost, ecco, obcs
2452    o updating verification/internal_wave, verification/lab_sea
2453      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
2454    
2455    checkpoint50i_post
2456    o Preparing next differentiable checkpoint and sync
2457      of MAIN vs. ecco-branch
2458      - 1st step: this one is differentiable
2459      - 2nd step: next(! not this) checkpoint will have updated packages
2460                  from ecco-branch)
2461    
2462    checkpoint50h_post
2463    o new package "land": provide surface BC for AIM.
2464    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
2465    o AIM: use true log-P extrapolation for near surface temp (= as in
2466        F.Molteni paper) ; update aim.5l_cs output.
2467    o New variable in PARM03 for more flexible pickups
2468    o somewhat cleaned package initialisation sequence for
2469      ctrl/ cost/ ecco/ in packages_... routines
2470    
2471    checkpoint50g_post
2472    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
2473      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
2474      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
2475        made the default because of faster convergence than ADI
2476    
2477    checkpoint50f_post
2478    o exf totally restructured
2479      - replaced all exf_set_ routines by one generic exf_set_gen.F
2480        and made sure it's still differentiable
2481      - split exf_getffields.F into new exf_bulkformulae.F
2482      - exf_inscal_/exf_outscal_ suffixes consistent with field names
2483      - updated adjoint/makefile and relevant verif. accordingly
2484    
2485    checkpoint50f_pre
2486     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
2487          + change Evap over land. (update aim.5l_cs output)
2488     o added missing .cvsignores and made uniform across expts
2489     o changed configuration of tidal_basin_2d expt
2490     o added pkg/debug functions for tracing code in fatal crashes
2491     o tidied pkg/monitor to use MONITOR_OPTIONS.h
2492     o new fn in pkg/monitor to stop model if solution grows too big
2493     o removed lots of single quotes from comments
2494    
2495    checkpoint50e_post
2496    o make KPP work with PTRACERS
2497     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
2498       nearly a copy of kpp_transport_s
2499     - there is no analogue to SurfaceTendencyS, so I have to use
2500       gPtr(of the surface layer) instead
2501    o add a new platform SunFire+mpi (SunFire 15000) to genmake
2502    checkpoint50e_pre
2503    
2504    checkpoint50d_post
2505    o change kpp output from multiple-record state files to single-record state
2506      files analogous to write_state.F
2507    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
2508      analogous to the cg2d-related output.
2509    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
2510      so that writing to internal file fn (with length 512) fails.
2511    checkpoint50d_pre
2512    
2513    checkpoint50c_post
2514    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
2515    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
2516    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
2517    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
2518    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
2519    
2520    checkpoint50c_pre
2521    Merging from release1_p13:
2522    o bug fix for pkg/seaice dynamic solver
2523    o Added SEAICE_initialHEFF to pkg/seaice
2524    
2525    checkpoint50b_post
2526    o store u*,v* in gU,V instead of in guNm1,gvNm1
2527    o in order to put the momForcing out of the Adams-Bashforth:
2528      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
2529      to timestep.F
2530    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
2531    o re-generate output for highly sensitive test-exp:
2532       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
2533    
2534    checkpoint50b_pre
2535    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
2536    o corrected CPP option mismatch in exf_Bulk... functions for case
2537      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
2538    
2539    checkpoint50a_post
2540    o Bug fix for merging between c50 and KPP.
2541      ikey was passed from thermodynamics to kpp_calc via
2542      common block rather than being recomputed in kpp_calc,
2543      in contradiction with new key itdkey.
2544      New key ikppkey created, and tamc.h headers updated.
2545    
2546    checkpoint50
2547    - 2nd step of merge with ecco-branch:
2548      merge changes in ecco-branch back into main trunk
2549    - bug fix in find_alpha
2550    - more storing in gmredi_calc_tensor.F, kpp_routines.F
2551    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
2552    - merged some sliced AD support routines
2553    
2554    checkpoint49
2555    merged from ecco-branch:
2556    o exf:
2557      - Enable initialisation of forcing fields to constant
2558        (runtime) values.
2559      - in exf_getffields.F
2560        Reduce i-/j-loop to interior domain, discarding overlaps.
2561        That also fixes wrong TAF-key computations for key_1, key_2
2562        with bulf formulae.
2563      - exf_init.F modify #ifdef for exf_init_evap
2564      - exf_getffieldrec.F, ctrl_getrec.F
2565        The following INT-usages are not safe:
2566          fldsecs  = int(fldsecs/fldperiod)*fldperiod
2567          fldcount = int(fldsecs/fldperiod) + 1
2568        and were modified.
2569    o autodiff: checkpoint_lev...
2570      - updated storing for bulk formulae (some arrays were missing)
2571      - added state for seaice package
2572      - synchronized with main branch
2573    o DIVA:
2574      Modif.s in
2575      - the_main_loop.F
2576      - the_model_main.F
2577      and added cost_final_restore.F cost_final_store.F
2578      o With these changes, it is possible to fully separate
2579        the first forward run to compute the cost function (mdthe_main_loop)
2580        and adjoint runs over individual DIVA intervals (adthe_main_loop)
2581        into separate model executions.
2582        This enables better tuning of DIVA to given queue sizes.
2583      o Loss of cost function value in consecutive DIVA runs is
2584        fixed by storing to 'costfinal' file.
2585      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
2586        beginning/end of adjoint integration is accounted for.
2587      The current changes apply to TAF-1.4.26.
2588      TAF has one remaining bug, requiring one manual change
2589      (see MITgcm manual).
2590    o cal: synchronized between MAIN and ecco-branch
2591    
2592    checkpoint48i_post
2593    o Changes to restore differentiability of code w.r.t. previous tag
2594      (mostly adding new routines to make list and replacing
2595      pressure by totPhiHyd).
2596    o Updated and merged grdchk package
2597      - has both ADM and TLM checks
2598      - works for single- and multi-proc.
2599      - output cleaned
2600      - worked successfully for parallel DIVA
2601    o genmake:
2602      - Adding -platform=SP4
2603      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
2604    o Modif. for DIVA:
2605      ctrl_unpack should not be called in intermediate DIVA interval.
2606      (similar thing would apply for active files such as
2607      tbar, sbar, psbar, which should not be reinitialised;
2608      only relevant for ecco-branch)
2609    
2610    checkpoint48h_post
2611    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
2612    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
2613    o Added SEAICE_initialHEFF to pkg/seaice
2614    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
2615    
2616    checkpoint48g_post
2617    --- EOS:
2618    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
2619      store total Potential in totPhyHyd for diagnostics & EOS.
2620    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
2621    --- Pressure/geopotential gradient:
2622    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
2623    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
2624      ( changes results of global_ocean_pressure )
2625    o NLFS + z-coord.: add eta*Rho' contribution.
2626    o accurate phiHyd when using interface-W at the middle between 2 centers
2627     ( changes results of ideal_2D_oce )
2628    o includes r* 2nd term in potential gradient.
2629    
2630    checkpoint48f_post
2631    Merging from release1_p12:
2632    o Modifications for using pkg/exf with pkg/seaice
2633      - improved description of the various forcing configurations
2634      - added basic radiation bulk formulae to pkg/exf
2635      - units/sign fix for evap computation in exf_getffields.F
2636      - updated verification/global_with_exf/results/output.txt
2637    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
2638      (SBO) core products, including oceanic mass, center-of-mass,
2639      angular, and bottom pressure (see pkg/sbo/README.sbo).
2640    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
2641      to avoid negative values in shallow regions.
2642      - updated verification/natl_box/results/output.txt
2643      - updated verification/lab_sea/results/output.txt
2644    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
2645    o Added useSingleCpuIO option (see PARAMS.h).
2646    o Updated useSingleCpuIO option in mdsio_writefield.F to
2647      work with multi-field files, e.g., for single-file pickup.
2648    o pkg/seaice:
2649      - bug fix in growth.F: QNET for no shortwave case
2650      - added HeffFile for specifying initial sea-ice thickness
2651      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
2652    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
2653      kpp_transport_t.F, forward_step.F, and the_main_loop.F
2654    o pkg/seaice:
2655      - adjoint-friendly modifications
2656      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
2657    
2658    checkpoint48e_post
2659    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
2660    o dynamics: change definition of computational domain & adapt mom_fluxform
2661      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
2662    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
2663        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
2664        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
2665        global_ocean.90x40x15 global_with_exf global_ocean_pressure
2666        inverted_barometer solid-body.cs-32x32x1
2667      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
2668    
2669    checkpoint48d_post
2670    o in preparation for r*:
2671     a) use pre-computed gradient of hydrostatic potential:
2672        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
2673     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
2674        => affects results of glob_oce_pressure (different truncation error)  
2675      update output.txt of ideal_2D_oce & global_ocean_pressure
2676    
2677    checkpoint48d_pre
2678    o in preparation for r*:
2679      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
2680      pass the 2 comp. of the grad. as arguments to momentum S/R.
2681      but for the moment, only used if it does not change the results.
2682    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
2683    
2684    checkpoint48c_post
2685    Modifications in treatment of initial flux forcing controls
2686    to avoid extra storing of flux fields.
2687    
2688    checkpoint48c_pre
2689    o Added tidal_basin_2d experiment (currently 1D!)
2690    o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
2691    
2692    checkpoint48b_post
2693    o r* coordinate added in #ifdef NONLIN_FRSURF block.
2694     (modification to pressure gradient not yet implemented)
2695    o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
2696      (for U & V) that are used for vertical advection of momentum.
2697    
2698    checkpoint48a_post
2699    o In preparation for r*, use temp. array to compute vertical transport
2700       in flux-form momentum pkg. => change results of few test-exp.
2701      Update output of: exp4, exp5, front_relax, global_ocean_pressure,
2702                        lab_sea, natl_box & plume_on_slope
2703    
2704    checkpoint48
2705    o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
2706    
2707    checkpoint47j_post
2708    o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
2709    o moved adexch from forward_step to addummy_in_stepping
2710    o added exch in ctrl_map_...
2711    o aveFreq.=0. at end of cost_final to avoid overwrite in
2712      reverse checkpointing loop
2713    o Yet more changes in gmredi:
2714      * adgmredi_calc_tensor
2715        avoiding all recomputation of gmredi_slope_limit
2716      * adgmredi_x/y/rtransport
2717        added flag for excessive storing to avoid recomp. of
2718        u/v/rtans, dTdx/y/z
2719        -> this is not really necessary and very memory-consuming
2720      * adgmredi_slope_psi:
2721        consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
2722      * gmredi_slope_limit
2723        re-activated full calculation of taperfct for case 'ac02'
2724    o updating verification/ adjoints of carbon, global_ocean.90x40x15
2725    
2726    checkpoint47i_post
2727    o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
2728    o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
2729      default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
2730    o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
2731    o gmredi: fix few bugs.
2732    
2733    checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
2734    This will be a good checkpoint to plug into the ecco-branch.
2735    o few modif.'s to get latest version adjointed
2736      (mainly kick out code in ini_linear_phisurf)
2737    o modif's to run adjoint with exactConserv
2738    o case GM_BOLUS_ADVEC should be cleaned
2739      S/R gmredi_slope_psi should be cleaned
2740    o verification/carbon now has exactConserv=.TRUE.
2741    
2742    checkpoint47g_post
2743    o time-average AIM output: becomes independent from statvars time-average
2744      (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
2745    o After TAF bug fix:
2746      Tested adjoint of gmredi package.
2747      Tests were done with checkpoint47 rather than with latest
2748      checkpoint47f_post since the latter is broken for the adjoint
2749      verification/carbon/ contains both ADM and TLM gradient checks.
2750    Here they are, before they get changed/lost/stolen.
2751    Mostly modif.'s to fix numerical sensitivities.
2752    Gradient checks OK for
2753    - GM_taper_scheme:
2754      * clipping
2755      * ac02
2756      * linear
2757      * glw91
2758      * dm95
2759      * ldd97
2760    - GMREDI_OPTIONS:
2761      * GM_VISBECK_VARIABLE_K
2762      * GM_NON_UNITY_DIAGONAL
2763      * GM_EXTRA_DIAGONAL
2764      * GM_BOLUS_ADVEC
2765    in conjunction with data.gmredi parameters to be checked in
2766    in a few minutes under verification/carbon/code/
2767    
2768    checkpoint47f_post
2769    Merging from release1_p10:
2770    o modifications for using pkg/exf with pkg/seaice
2771      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
2772        and SEAICE_EXTERNAL_FLUXES
2773      - pkg/exf CPP options EXF_READ_EVAP and
2774        EXF_NO_BULK_COMPUTATIONS
2775      - usage examples are Experiments 8 and 9 in
2776        verification/lab_sea/README
2777      - verification/lab_sea default experiment now uses
2778        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
2779    
2780    checkpoint47e_post
2781    o created a tag prior to creating a branch
2782    
2783    checkpoint47d_post
2784    o fixed bug in the oceanic pressure coordinates code: vertical viscosity
2785      at the bottom boundary had an erroneous half slip boundary condition
2786    o added bottom drag and no slip boundary condition capabilities to
2787      oceanic pressure coordinates code
2788    o added new verification experiment global_ocean_pressure, this experiment is
2789      also described in the tutorial section of the manual
2790    checkpoint47d_pre
2791    
2792    checkpoint47c_post
2793    o Added a verification experiment for a global cubed-sphere ocean run
2794      -  verification/global_ocean.cubed32x32x30
2795      -  uses pkg/therm_seaice and pkg/bulk_forcing
2796    
2797    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
2798    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
2799      when using P-coordinate; only implemented for atmospheric config.
2800    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
2801      NOTES: requires option NONLIN_FRSURF to be "#define".
2802    o update advect_xz/results/output.txt (left from checkpoint44g_post)
2803    
2804    checkpoint47b_post
2805    Merging from release1_p9:
2806    o pkg/seaice
2807      - removed GOTO's and added taf directives
2808      - double precision constants to reduce the g77 (Linux)
2809        to F77 (SGI) differences reported in release1_p8
2810    o tools/genmake
2811      - added SGI options
2812    o verification/testscript
2813      - updated to that of checkpoint47a_post
2814    o verification/global_ocean.90x40x15/input/eedata
2815      - modified for SGI f77 compatibility
2816    o verification/lab_sea
2817      - added description of sea-ice model
2818      - added missing matlab routines
2819      - added test of thermodynamics parallelization
2820    
2821    checkpoint47a_post
2822    o new pkg: aim_v23
2823     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
2824       for now, keep the same surface forcing as before.
2825     - Part-Cell implemented into AIM; check that Heat & Water are conserved
2826     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
2827     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
2828    o add diagnostic of surface correction term in monitor output
2829    
2830    o bulk_force and therm_seaice
2831    - Two packages:  bulk_force (Bulk forcing)
2832      and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
2833    - Earlier integration from Stephaine Dutkiewicz
2834      and Patrick Heimbach.
2835    - Two ifdef statements for compile time,
2836       ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
2837    
2838    checkpoint47
2839    differentiable version of checkpoint46n_post
2840    o bug fix in quasihydrostaticterms
2841    o * "clean" adjoint code (in terms of extensive recomputations)
2842        can now be obtained for all GMREDI options (i.e. for
2843        - GM_VISBECK_VARIABLE_K
2844        - GM_NON_UNITY_DIAGONAL
2845        - GM_EXTRA_DIAGONAL
2846        - GM_BOLUS_ADVEC )
2847      * However, wrong gradient check problem remains unsolved.
2848      * New CPP options have been introduced for different
2849        tapering schemes
2850    o external_fields_load now part of differentiation list
2851    o pressure needs multiple storing;
2852      would be nice to have store_pressure at beginning or
2853      end of forward_step, e.g. by having phiHyd global (5-dim.)
2854      (NB: pressure is needed for certain cases in find_rho,
2855      which is also invoked through convective_adjustment).
2856    o recomputations in find_rho for cases
2857     'JMD95'/'UNESCO' or 'MDJWF' are OK.
2858    o #define ATMOSPHERIC_LOADING should be differentiable
2859    o ini_forcing shifted to begining of initialise_varia
2860    o Incorporating QNVS line search routines into MITgcm
2861      (this is separate code, and therefore not under pkg)
2862      lsopt/, optim/
2863    o Updated verification/carbon/
2864      - #define GM_VISBECK_VARIABLE_K
2865      - GM_taper_scheme    = 'ldd97'    
2866    
2867    checkpoint46n_post
2868    Merging from release1_p8:
2869    o verification/natl_box:
2870      updating new external_fields_load routine
2871    o New package: pkg/seaice
2872      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
2873      The sea-ice code is based on Hibler (1979-1980).
2874      Two sea-ice dynamic solvers, ADI and LSR, are included.
2875      In addition to computing prognostic sea-ice variables and diagnosing
2876      the forcing/external data fields that drive the ocean model,
2877      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
2878      The implied surface heat flux is then stored in variable
2879      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
2880      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
2881      non-local transport term.  Because this call precedes model
2882      thermodynamics, temperature under sea-ice may not be "exactly" at
2883      the freezing point by the time theta is dumped or time-averaged.
2884      N.B.: fairly large differences in accuracy occur across
2885            different platforms/compilers; comparison between
2886            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
2887            generated output gives:
2888       T           S           U           V
2889      C D M    c        m  s        m  s        m  s        m  s
2890      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
2891      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
2892      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
2893    
2894      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
2895    o GAD:
2896      - generated new common blocks to account for call of
2897        same gad routines with differing traceridentities
2898        (needed to modify tracerIdentity indices in GAD.h)
2899      - generated separate common blocks for case useCubedSphereExchange
2900        (Department of Futurology)
2901      - parameter lists to gmredi_?transport: added tracerIdentity
2902      - added new key indices to tamc.h
2903    o external_fields_load:
2904      - added this routine to TAF list
2905      - needed to make some common blocks global and additional storing
2906        along the same lines as exf package (checkpoint_lev?_directives.h)
2907    o exf:
2908      updated external forcing package
2909      - bug fixes carried over from ecco-branch
2910        (missing OBCS_OPTIONS.h in two routines)
2911      - enable easy to use "no forcing".
2912      - added exf I/O for atmospheric loading
2913      - added exf I/O for runoff data
2914      - transfered scaling between exf <-> MITgcm to exf namelist
2915    o Adding new verification experiment global_with_exf.
2916      This verification experiment is almost identical to the
2917      global_ocean.90x40x15 experiment, except that it uses
2918      the exf (and cal) package instead of the
2919      external_fields_load routine (cf README file).
2920    
2921    checkpoint46m_post
2922    o modified testscript to return -- when there are no lines of "%MON" output
2923    o added new flag "quasiHydrostatic" for QH mode
2924      and new routine quasihydrostaticterms()
2925    o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
2926      New routine: mom_u_coriolis_nh()
2927    o fixed sign of non-hydrostatic metric terms in u and v equations.
2928      Depend on correct sign of gravitySign.
2929    o added work.pc* to .cvsignore in aim directories using ifc
2930    o introduced flag for controllin non-hydrostatic metric terms
2931    o removed gravitySign from PARM04
2932    o switched to g77/ifc from pgf77 in aim experiments
2933    
2934    checkpoint46l_post
2935    o made convective adjustment work with pressure coordinates:
2936     - changed the direction of k-loop in convective_adjustment.F for the
2937       case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
2938     - adjusted the reference pressure k-index in convective_adjustment.F
2939     - adjusted the convection condition in convect.F (in analogy to
2940       calc_ivdc.F)
2941     - convective_adjustment no longer computes anything on the halos
2942     - removed the warnings about negative salinity from find_rho.F and
2943       find_alpha.F; instead the new routine look_for_neg_salinity, called
2944       at the beginning of find_rho, find_alpha, and find_beta, does a
2945       check of the entire slice, if CPP-option
2946       CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
2947    checkpoint46l_pre
2948    
2949    checkpoint46k_post
2950    o fixed the verification/global_ocean.90x40x15 experiment:
2951     - new bathymetry (the world according to A., JMC, and M.)
2952     - new initial fields and forcing fields (*.bin files)
2953     - new POLY3.COEFFS (for the next release one should switch to a full
2954       equation of state: JMD95P or MDJWF)
2955     - fixed several errors and redundancies in the data file
2956     - experiment uses looped cells
2957     - added matlab directory with diagnostic scripts for plotting of output
2958    
2959    o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
2960     - read AIM physics parameters from a file (data.aimphys)
2961     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
2962    
2963    checkpoint46j_post
2964    o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
2965    o move wVel computation at the end of the time step, in S/R integr_continuity
2966    o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
2967    o update timeave pkg for wVel diagnostic.
2968    checkpoint46j_pre
2969    
2970    checkpoint46i_post
2971    o Clean up AIM package (and keep the results unchanged):
2972      include CPP_OPTION and use IMPLICT NONE in all routines ;
2973      declare all the variables _RL ; use _d 0 for all numerical constants.
2974      use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
2975    
2976    checkpoint46h_post
2977    o cleaned up the use of rhoNil and rhoConst.
2978      - rhoNil should only appear in the LINEAR equation of state, everywhere
2979        else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
2980        and the dynamical equations are all divided by rhoConst
2981    o introduced new parameter rhoConstFresh, a reference density of fresh
2982      water, to remove the fresh water flux's dependence on rhoNil. The default
2983      value is 999.8 kg/m^3
2984    o cleanup up external_forcing.F and external_forcing_surf.F
2985      - can now be used by both OCEANIC and OCEANICP
2986    checkpoint46h_pre
2987    
2988     Added code to convert surface volume flux (fresh water) into
2989     a mass flux when using P coordinates in the ocean (OCEANICP).
2990     Note: It assumes you have set rho0=rhoConst=density of fresh water.
2991    
2992    checkpoint46g_post
2993    o Include a new diagnostic variable phiHydLow for the ocean model
2994      - in z-coordinates, it is the bottom pressure anomaly
2995      - in p-coordinates, it is the sea surface elevation
2996      - in both cases, these variable have global drift, reflecting the mass
2997        drift in z-coordinates and the volume drift in p-coordinates
2998      - included time averaging for phiHydLow, be aware of the drift!
2999    o depth-dependent computation of Bo_surf for pressure coordinates
3000      in the ocean (buoyancyRelation='OCEANICP')
3001      - requires a new routine (FIND_RHO_SCALAR) to compute density with only
3002        Theta, Salinity, and Pressure in the parameter list. This routine is
3003        presently contained in find_rho.F. This routine does not give the
3004        correct density for 'POLY3', which would be a z-dependent reference
3005        density.
3006    o cleaned up find_rho
3007      - removed obsolete 'eqn' from the parameter list.
3008    o added two new verification experiments: gop and goz
3009      (4x4 degree global ocean, 15 layers in pressure and height coordinates)
3010    checkpoint46g_pre
3011    
3012    checkpoint46f_post
3013    o Enable tangent linear (forward mode) gradient checks:
3014      - extended active file handling to g_... files
3015      - added TANGENT_SIMULATION to theSimulationMode
3016      - extended grdchk package accordingly
3017    o added tangent linear setup in verification/carbon/code_ftl
3018    o added adjoint setup in verification/front_relax/code_ad
3019    
3020    checkpoint46e_post
3021    o Added new equation of state -> MDJWF
3022      - EOS of McDougall et al., 2002, JAOT, submitted
3023      - caveat: the equation of state is only valid for a smaller (more
3024        realistic?) range of values than JMD95P/Z and UNESCO
3025      - added masks to the calculation of pressure in store_pressure
3026      - added more check values for density in check_eos (ini_eos.F), some of
3027        the old check values are out of the range of the MDJWF-eos, so don't
3028        expect perfect matches for those
3029    checkpoint46e_pre
3030    
3031    checkpoint46d_post
3032    o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
3033      'OCEANICP', also initialised field pressure correctly in ini_eos in the
3034      case of pressure coordinates. eosType='JMD95Z' in
3035      combination with buoyancyRelation='OCEANICP' now causes an error.
3036    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
3037      in find_alpha/beta.
3038    checkpoint46d_pre
3039    
3040    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
3041      so that JMD95Z and JMD95P give approptiate static stability in find_rho.
3042    
3043    checkpoint46c_post
3044    o Changes necessary for ocean in p-coordinates
3045     -  Added new buoyancy relation = 'OCEANICP'
3046     -  Added new parameters = gravitySign (this used to be contained inside
3047        the factor dRdZ which I added when we first switched to R coordinates).
3048     X GM/Redi is not compatible (yet)
3049     X bottom drag and no-slip need to be debugged.
3050    checkpoint46c_pre
3051    
3052    checkpoint46b_post
3053    o Added new equation of state -> JMD95Z and JMD95P
3054      - EOS of Jackett and McDougall, 1995, JAOT
3055      - moved all EOS parameters into EOS.h
3056      - new routines ini_eos.F, store_pressure.F
3057    o Added UNESCO EOS, but not recommended because it requires
3058      in-situ temperature (see JMD95)
3059    o Modified formatting for knudsen2.f in utils/knudsen2 and added
3060      unesco.f to be used with POLY3
3061    checkpoint46b_pre
3062    
3063    checkpoint46a_post
3064    o Added (atmospheric) pressure loading
3065      - new field in FFIELDS.h, etc...
3066      - new cpp flag ATMOSPHERIC_LOADING
3067    o Changed hFacC to _hFacC in calc_phi_hyd.F
3068    o Added SHORTWAVE_HEATING to some files for consistency
3069    checkpoint46a_pre
3070    
3071    checkpoint46
3072    further merges from release1_p5
3073    o new ctrl package
3074      - adopted from ECCO environment to enable optimization
3075      - added Eliassen Palm fluxes to controls
3076    o added Eliassen Palm flux controls to gradient check package
3077    o cost package
3078      - Compatible with new ctrl package
3079      - added Eliassen Palm cost hooks
3080      - modif's of existing cost functions
3081    o Adjoint-related bug fixes in kpp:
3082      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
3083      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
3084    o autodiff package
3085      - flow directives:
3086        + new for S/R do_the_model_io
3087        + enhanced for S/R checkpoint
3088        + new gmredi.flow
3089      - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
3090        disable adcommon.h/g_common.h by default.
3091      - fixed problem for adjoint of global_max
3092    o modified verification/carbon/
3093    o New setup for adjoint of global_ocean
3094    o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
3095    o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
3096    o incorporated hooks for sponge layer code (external_forcing.F)
3097    
3098    checkpoint45d_post
3099    o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
3100    o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
3101      (affects plume_on_slope "cg2d" output)
3102    o add new parameter deltaTfreesurf for free-surface time stepping
3103    o exchange gT,gS when using staggerTimeStep & GM & Oly<4
3104    o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
3105    o change phiMin in exp1 (to agree with documentation)
3106    o add new flags:
3107     - T,S forcing inside/outside Adams-Bashforth
3108     - turn off temp,salt advection and/or forcing
3109     - for each tracer, define internal flag for multiDimAdvection & A-B
3110    o monitor: change definition of KE to check conservation of Energy
3111    
3112    checkpoint45c_post
3113    o Removed f90 comments ("!")
3114    o Modified initialisations to enable exf package for MITgcm
3115      (without invoking ECCO_PACKAGE).
3116    o modifications to gradient check package (Martin Losch)
3117      - enable centered differences
3118      - modified format of standard output
3119    
3120    checkpoint45b_post
3121    o cleaned exchange calls in cg2d
3122    o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
3123    o included CPP option SINGLE_LAYER_MODE in thermodynamics
3124      to configure barotropic setup (Martin Losch)
3125    o moved some initialisations within bi,bj loop in dynamics
3126      (TAF flow dependency)
3127    o in initialise_varia, moved call packages_init_variables
3128      before convective_adjustment_init
3129      (corresponding adjustment of TAF tape initialisation).
3130    o in calc_diffusivity/calc_viscosity extended domain to full overlap.
3131    
3132    checkpoint45a_post
3133    o compute Rho over the whole domain (extend iMin,jMin indices)
3134    o specific exchange for X-slice domain (case Ny=1)
3135    o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
3136    o solve_for_pressure : set cg2d_x to zero where OBCS are applied
3137    
3138    checkpoint44h_post = checkpoint45
3139    o Fix to restore differentiability:
3140      place at which packages_init_variables is called in
3141      initialise_varia is crucial for reverse control flow.
3142    o modifications in GMRedi to enable stable adjoint
3143      (corresponding modif's in thermodynamics, dynamics)
3144    o added missing hook for sponge layer code in external_forcing
3145    o modified test cost functions
3146    o storing in gad_advection (plus removal of write(0,*)!
3147    o missing headers TR1.h added in convective_adjustment routines
3148    o errorMessageUnit set non-equal zero in eeboot
3149      (conflict on some platforms, e.g. IBM SP3)
3150    o modified carbon verif.
3151    
3152    checkpoint44h_pre
3153    o vertical grid option: allow to put the Interface at the middle between
3154      2 cell-centers ; replace delZ in pkg/kpp by drF.
3155    o GM Advective form: Tracers are advected using the residual transport (=
3156      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
3157    
3158    checkpoint44g_post
3159    o fix surface correction term in multiDimAdvection (affects plume_on_slope
3160      results) ; ifdef missing in thermodynamics.F
3161    
3162    checkpoint44f_pre,checkpoint44f_post
3163    o added PTRACERS package
3164      This allows an arbitrary number of passive tracers to be integrated
3165      forward simultaneously with the dynamicaly model.
3166      + Implemented so far:
3167        - basic forward algorithm (time-stepping, advection, diffusion, convection)
3168        - I/O and checkpointing
3169        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
3170      + Not implemented so far:
3171        - KPP
3172        - OBCS
3173      + No specific example supplied (yet) but global_ocean.90x40x15 has the
3174        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
3175        line in data.pkg.
3176      + This package is disabled by default since it increases storage.
3177    
3178    
3179    o testscript: added -cleanup option
3180    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
3181                 b) enable to filter 2D fields.
3182    
3183    checkpoint44e_pre,post
3184    o re-wrote convective adjustment to use pre-calculated weights
3185      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
3186      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
3187      Original calls to convect() still in place.
3188    
3189    chkpt44d_pre,post
3190    o added missing EXCLUDE_MONITOR flags
3191    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
3192      (incompatible typ in MIN/MAX expressions caused problems
3193      on IBM SP3)
3194    o in genmake added variable MAKEDEPEND
3195      plus resetting for case SunOS
3196    o added timer_stats.c routine for IBM SP3
3197    o removed variables in dynamics
3198    !!! I forgot to create tag chkpt44d_pre !!!
3199    !!! But chkpt44d_pre = chkpt44c_post    !!!
3200    
3201    o real fresh water flux implemented with non-linear free-surface.
3202    
3203    chkpt44c_pre,post
3204    o few fix (mask in shap_s2, EmPmR in external_field_load,
3205      USE_NATURAL_BCS in solve_for_P);
3206    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
3207    
3208    checkpoint44b_pre/_post
3209    o merge of relevant stuff from the ecco-branch:
3210      - genmake: removed $S64 overwrite for case SunOS
3211      - pkg/exf: update and corrections for field swapping and obcs
3212      - pkg/ecco: parameter lists for the_model_main, the_main_loop
3213                  harmonized between ECCO and MITgcm
3214      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
3215                      updated checkpointing_lev... lists for obcs
3216      - model/src: minor changes in forward_step, plot_field
3217                   added directive for divided adjoint in the_main_loop
3218      - pkg/mdsio: added mdsio_gl_slice
3219    
3220    o check parameters & config (chkpt44a_pre,post)
3221    o OBC and NonLin_FrSurf.
3222    
3223    checkpoint44
3224    o fix bug in mom_vi_del2uv
3225    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
3226    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
3227    o update AIM experiments (NCEP input files)
3228    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
3229    o added some stuff for AD
3230    
3231    checkpoint43
3232    o added two new advection tests
3233    o added global 4x4 degree ocean test
3234    o added test of H&S94 with free surface on cube
3235    o some final mods for gradient check, adjoint,...
3236    
3237    checkpoint42
3238      Fixed AD-related problems:
3239    o Store directives up-to-date with re-arranged Adams-Bashforth
3240      (mainly thermodynamics.F)
3241    o New store directives for multi-dim. advection schemes
3242      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
3243      * new common block and key passkey
3244      (mainly gad_advection.F)
3245    o Modified store directives for split of dynamics/thermodynamics
3246      for the case ALLOW_KPP
3247    o Cleaned argument list for timestep_tracer.F
3248    
3249    checkpoint41
3250    o re-formatted/added comments in prologues of key subroutines
3251      to work with protex
3252    
3253    checkpoint40
3254    o moved calc_gs, calc_gt and calc_tr1 back to model/src
3255    o added FLT (floats) package from Arne along with demo. experiment
3256    o re-arranged Adams-Bashforth scheme for tracers to allow easier
3257      implementation of forward-in-time forcing terms
3258    o more mods for non-linear free-surface including new variable
3259    o modified multi-dim method to work on cube
3260    o bug fix in KPP (from DM)
3261    
3262    checkpoint40pre9
3263    o added DST advection schemes
3264    o fix MPI bug on SGI's
3265    o modifications for non-linear free-surface
3266    o fixed conditionals for fixed flow/passive tracer only mode
3267    o added tension/strain form of stress tensor
3268    o changes to commenting of arguments for TAF/TAMC
3269    o added/updated many matlab scripts
3270    o added multi-dimensional advection method for tracers
3271      
3272    checkpoint40pre8
3273    o new package rw/
3274      Added method for dumping intermediate local arrays:
3275      mdsio_writetile - same as mdsio_writefield except works from inside
3276                        bi,bj loop
3277      mdsio_writelocal - same as mdsio_writetile except works for local
3278                         arrays
3279      write_local_r? - higher-level wrapper for mdsio_writelocal
3280      Controlled by diagFreq. Defaults to zero (ie. no dumps)
3281      Example given at end of mom_vecinv.F that dumps some local arrays.
3282    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
3283      control flux-form versus vector invariant code.
3284      Switch is runtime flag vectorInvariantMomentum (defaults to false)
3285      or genmake -DISABLE ...
3286    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
3287      (additional storing is now needed for case vecinv;
3288      currently nothing implemented to switch this storing off
3289      in case fluxform is used since no CPP flag available).
3290    
3291    checkpoint40pre7
3292    o bug fix in dynamics.F
3293      calc_viscosity called before k=1,Nr loop.
3294    o added some #ifdef's ALLOW_PASSIVE_TRACER
3295    o cleaned initialisations in ctrl_map_ini
3296      related to TAF
3297    
3298    checkpoint40pre6
3299    o split dynamics into thermodynamics & dynamics
3300    o corresponding split of calc_diffusivity into
3301      calc_diffusivity, calc_viscosity
3302      (kpp_calc_diff, kpp_calc_visc).
3303    o Added diffkr, kapgm to control variables
3304    o bug fix in gmredi_slope_limit for ldd97
3305    
3306    checkpoint40pre5
3307    o proper initialization of Adams-Bashforth time stepping
3308      + uses forward step for very first step of model (iter=0)
3309    o re-generated *all* output since almost all output is modified by this
3310      change (sorry but we've been putting this one off for about 2 years)
3311      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
3312        *not* regenerated since they are already out of date and I don't
3313        want to create the impression that they are suddenly working.
3314    o removed KAP stuff for DEC's
3315    o modified/added many .cvsignore files in */code and */input
3316    o added new expt "solid-body.cs-32x32x1"
3317      + this uses an alternative form of ini_curvilinear_grid.F which
3318        is not necessarily any better than the current one...
3319    
3320    checkpoint40pre4
3321    o added re-initialisations of utrans,vtrans,rtrans in
3322      calc_common_factors which are crucial for TAF.
3323    o extended iMin,jMin range for calc_common_factors,
3324      calc_diffusivity
3325    o added option ALLOW_PASSIVE_TRACER
3326    o a few minor updates and fixes
3327    
3328    checkpoint40pre3
3329    o created calc_gtr1.F for gad package
3330    o split the_main_loop and re-introduced forward_step
3331    o some recomputations of nIter0 for TAMC
3332    
3333    checkpoint40pre2
3334    o Updated to latest branch of AJA, JMC
3335    o Added gradient check package
3336    o Added routines for passive tracer handling
3337    o Added carbon sequestration sensitivity experiment
3338    
3339    checkpoint39
3340     o Modifications and fixes to support TAMC
3341       (mainly missing or wrong directives)
3342     o Corrected common blocks when fooling TAMC to produce adjoint I/O
3343       in addummy_in_stepping
3344     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
3345     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
3346     o Included following packages:
3347       cal: calendar
3348       exf: external forcing
3349       ecco: essential routines to control use of cal, exf
3350             (NB: this is not the full ECCO environment)
3351     o disabled some packages by default in genmake
3352    
3353    checkpoint38
3354     o see notes_c37_adj.txt
3355     o corrected wrong layer index in external_forcing_t
3356     o replaced the_main_loop/forward_step by the_main_loop
3357     o removed forceoutput from write_state
3358       (replaced criteria for initial/final state)
3359     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
3360    
3361    checkpoint37
3362     o mdsio.F routine split and packaged in pkg/mdsio
3363       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
3364        used unless genmake -disable=mdsio)
3365     o allow a more precise surface-geopotential gradient for the atmosphere
3366       taking into account the change in space of Alpha (=1/rho) at the surface.
3367     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
3368       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
3369     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
3370       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
3371       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
3372     o Time-Average diagnostics defined as a pseudo package "timeave".
3373     o pickup files : old pickup (before c35) did not work with new code (c35
3374       and after) unless activating 2 commented lines in initialise-varia.
3375     o Non-Hydrostatic pickup file Pb fixed.
3376     o bug with Rigid-lid version (since c35) fixed.  
3377    
3378    checkpoint36
3379     o implement Crank-Nickelson barotropic time-stepping
3380     o recover Time-Average diagnostics
3381     o fix Pb in checkpoint (PR#19)
3382     o AIM become a standard package ; clean unused CPP_kees
3383    
3384    checkpoint35
3385     o subtantial rewrite of dynamics.f
3386     o allows staggered time-stepping
3387     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
3388     o added bottom drag (linear + quadratic)
3389    
3390    checkpoint34
3391     o Modified exchange routines for correct reverse simulation.
3392     o Added verification output to comply with bug fix in impldiff.F
3393       as of c33 (exp2, natl_box).
3394     o Corrected store directives in dynamics.F
3395     o Corrected array boundaries in impldiff.F
3396     o Corrected array dimensions in gmredi.
3397       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
3398     o Added routine GLOBAL_SUM_INT to global_sum.F
3399     o Added mdsio_gl.F for ECCO purposes.
3400    
3401  checkpoint33  checkpoint33
3402   o Fixed bug in lower BC in impldiff.F   o Fixed bug in lower BC in impldiff.F
3403   o Fixed confusion about units of forcing arrays in FFIELDS.h   o Fixed confusion about units of forcing arrays in FFIELDS.h

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