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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.876 by jmc, Tue Sep 18 00:12:40 2007 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o adding precip control xx_precip  o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
8  o moved ptracer ctrl index 17 -> 32    in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
9      without requiring DO-IF statements
10    o pkg/thsice:
11      use continuous power-law function for partition of energy between lateral
12      melting/freezing and thinning/thickening ; old code using step function
13      still available with #undef THSICE_FRACEN_POWERLAW
14      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
15    o testreport: change AD testing : check against results/output_adm.txt
16      using same scripts as for forward test.
17    
18    checkpoint59g
19    o adjoint testing: in preparation for changing testreport:
20      - output format: cost and grad written on separated lines
21      - ad output results in directory "results" (instead of "results_ad")
22    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
23    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
24    o pkg/ecco: allow user defined cost function contributions
25    o testreport:
26      Allow to choose (per experiment) the list of tested output variables
27       and the main variable (used to issue a pass/FAIL ) ;
28      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
29      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
30      Also modify printing of summary:
31       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
32       b) echo the list of tested variables in the individual summary.txt of
33          each experiment.
34    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
35      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
36      (but still depend on the tile decompostion of the domain).
37    o pkg/seaice: change a discretization detail to make the B-grid code
38      "more symmetric". This change is likely to remove all "ridges/leads" that
39      where quasi-aligned with the grid in B-grid solutions. It may also be
40      the solution to the stress coupling issues with the B-grid.
41    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
42      remove .cvsignore from input dir. (since testreport no longer run here).
43    o pkg/thsice:
44     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
45     - fix reshaping of sea-ice just after advection:
46       melt all the ice only if ice-volume is too small.
47     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
48       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
49     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
50    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
51      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
52    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
53      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
54      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
55      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
56      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
57      -> update output.txt
58    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
59     this affects truncation error: -> update output.txt of exp:
60      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
61      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
62    
63    checkpoint59f
64    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
65    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
66      a bounded range (in forward mode)
67    o pkg/ecco, ctrl, autodiff and mom_common:
68     internal parameter controls, completements of implementations
69    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
70    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
71      (not seem any difference in testing results).
72    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
73       at face corners.
74    o pkg/generic_advdiff:
75     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
76      loop range indices for computing vertical advection tendency
77      and do the calculation in the interior only (no overlap) ;
78      for now, only implemented for SOM advection (to save CPU time).
79     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
80    o exch2 adjoint
81      First set of changes:
82      - add exch2 hand-written adjoint templates
83      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
84        This will require cleanup in pkg/autodiff/*.F
85        (changed routines currently kept separate in verif. code/)
86      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
87        that used to hide exch2 or cubed-sphere specific code
88        (commented via 'cph-exch2')
89    o pkg/seaice
90      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
91    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
92       output of global_ocean.cs32x15.thsice .
93    
94    checkpoint59e
95    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
96      for B-grid vector (not yet tested) and C-grid vector (<- only used
97      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
98    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
99      (#ifdef ALLOW_SALT_PLUME)
100    o gather_2d/scatter_2d: removed halo regions
101    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
102      scheme and the corresponding test case (under front_relax dir). For now,
103      only available with Skew-flux form and not yet tested in realistic set-up.
104      adjoint: store directives updated, but gradient checks deteriorated,
105      so maybe GM/Redi adjoint is now broken.
106    o seaice adjoint
107      * add AREA, HEFF, HSNOW as control variable
108        (should not change lab_sea results)
109      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
110    o pkg/seaice:
111      * added computation of saltFlux in seaice_growth;
112        For time being, sea ice salinity is assumed constant
113        contribution of snow flooding to freshening of sea ice is neglected.
114        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
115        defaults to 0.0 in order to maintain backward compatibility.
116        Typical values for SEAICE_salinity are 4 to 10 g/kg.
117      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
118      * added SEAICE_availHeatFrac, which specifies fraction of surface level
119        heat content used to melt or grow ice
120      * commented out cap of HICE: it helps keep ice thinner
121      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
122      * applied OBCS T/S mask to HEFFM sea ice mask
123    
124    checkpoint59d
125    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
126     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
127     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
128    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
129     and change default value of parameter "GM_Small_Number";
130     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
131       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
132       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
133    o pkg/ecco: cost function when applying pkg/smooth to controls
134    o pkg/ctrl: add forcingPrecond run time parameter
135    o pkg/seaice:
136     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
137     - fix bug in metric terms of u-equation in LSR solver (implicit part),
138       changes verification/lab_sea
139     - rearrange implicit part of u-equation in LSR solver to make it easier to
140       read, understand, and debug. This causes changes at the truncation level.
141     - fix (serious) bug in the boundary conditions (sign error in the implicit
142       part) of the LSR solver. Changes all LSR results.
143     - fixed problem with HSNOW initialization to avoid thick snow when AREA
144       is initilized with small values - does not change lab_sea results.
145     - added HsnowFile initialization capability
146    o pkg/smooth: addition to model/src and pkg/ctrl so allow
147     initialization of pkg/smooth and application to control vector
148    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
149    o dependencies: pkg/profiles requires pkg/cal
150    o pkg/profiles:
151     - added option ALLOW_PROFILES_GENERICGRID
152         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
153         that interpolation information (grid points and coefficients) is provided
154         within the netcdf input files.
155         -> sample matlab scripts can be found in MITgcm_contrib/gael
156         that allow you to prepare netcdf input files.
157     - also modified: cleaner include statements, cleaner error print statements,
158       cleaner stops when error, and more tests of the netcdf input files consistency.
159    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
160    o pkg/seaice:
161     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
162       requires a new routine: seaice_diagnostics_fill.F
163     - make sure that seaice does not move if not forced (pressure replacement
164       method, Hibler and Ip, 1995), changes results
165     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
166     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
167       It is turned off by default (=-1.), because it changes the results.
168     - make it possible to read AREA from a file, too.
169    
170    checkpoint59c
171    o add S/R and diagnostics for oceanic mixed-layer depth
172    o move GMRedi call after all vertical mixing schemes (including KPP)
173    o pkg/thsice:
174     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
175      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
176    o pkg/obcs:
177     - bug fix for balance code
178    o pkg/seaice:
179      - allow values of SEAICE_elasticParm > 1
180      - add new parameter SEAICE_evpTauRelax as an alternative
181        to SEAICE_elasticParm
182      - make lsr boundary conditions free slip (by default), changes result
183      - add code for no slip boundary conditions for lsr
184      - set minimum of zeta to zero (and not 4e8) (changes results)
185      - add a cap on AREA after advecting AREA if seaice_growth is not called
186    o change calculation of Visbeck K:
187      - no longer depend on tapering scheme; instead, compute slope (limited
188        by GM_maxSlope). this is equivalent to what was comuted before with
189        clipping or linear tappering.
190      - fix vertical averaging (wrong by 1/2 level)
191      - leave the old version (but will not be maintained) within
192        #ifdef OLD_VISBECK_CALC / #endif
193      - update output of exp. ideal_2D_oce
194    o change error catch in calc_r_star to improve vectorization
195    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
196      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
197    o adjoint:
198      Re-organized adjoint checkpointing according to Matt Mazloff
199      (but with modifs/completions/cleanups)
200      Storing is now bundled into large arrays to optimized I/O
201      (and second step in cleanup of the_main_loop)
202    
203    checkpoint59b
204    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
205      - export/import (between ocean & coupler) fields needed for ocean DIC.
206    o pkg/seaice:
207      - get rid of three more exchanges seaice_calc_viscosities (required
208        different loop boundaries in seaice_lsr and seaice_ocean_stress)
209      - bug fix in seaice_ocean_stress (update of lab_sea required)
210      - reduce loop boundaries to necessary minimum also in seaice_evp
211      - go back to the old way of computing deltaC/Z as the adjoint likes that
212        better
213    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
214      passive tracer to an Age Tracer) + update output.txt
215    o pkg/exf:
216      - implement A-grid / C-grid selection for wind-stress input files.
217      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
218      for now, in exf_bulk_largeyeager04.F only :
219      - change implementation for case where windspeed + 2. components wind-stress
220        are read-in. AND use rhoConstFresh to convert evap.
221    o pkg/seaice:
222      - use correct EXCH_UV for wind-forcing (on A-grid).
223      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
224        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
225    o pkg/exf:
226      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
227      EXF_INTERPOLATION:
228      - merge global_with_exf/code version of exf_interp_read.F
229        to the main code ;
230      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
231        reading the file ; Important: This options needs to be defined to recover
232        previous code.
233        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
234      - no longer loose real*8 precision along the way when using exf_iprec=64.
235    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
236      - change discretisation of evp-solver in order to avoid another exchange
237        (changes lab_sea) and clean up a little
238      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
239        help the adjoint (this also changes the results slightly)
240      - add a few "_d 0" where they had been missing in seaice_evp.F
241      - cleaning up: remove unused seaice_calc_rhs.F
242    o pkg/exf: some cleaning-up:
243      - change various "constants" into runtime parameters
244      - cleaned-up Large&Yeager04 routine which should eventually
245        replace exf_bulkformulae.F (changed names of S/R and CPP)
246        and merged various ALLOW_ATM_WIND options
247     only used with thsice pkg (in thsice_get_exf.F):
248      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
249        which are used when useStabilityFct_overIce=TRUE (= the default)
250      - change default values of ice & snow emissivity and scale downward LW
251        by ice & snow emissivity.
252    o pkg/thsice:
253     fix few little problems, in thsice_calc_thickn.F:
254      - growth vertically (and not laterally) if iceFrac == iceMaskMax
255      - melt only laterally if hIce < hThinIce (as the comments say)
256      and in thsice_extend.F:
257      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
258      - start to form ice as soon as the minimum ice-volume is reachable.
259     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
260      and cpl_aim+ocn
261    o pkg/kpp
262     - move computation of surface related input fields to KPP into a new
263       subroutine kpp_forcing_surf.F
264     - remove wrong (within bi,bj loops) EXCH calls.
265     - little cleaning (add argument myThid in last position, cvs header ...)
266     - for now, fix conservation problem by exchanging KPPviscAz (may not
267       be the best fix)
268    o pkg/seaice
269     - check for inconsistent evp parameter/cpp-flag combination
270     - remove leftover errIO flat for obsolete name list error handling
271    o OpenAD
272     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
273    
274    checkpoint59a
275    o pkg/seaice: some parameter clarifications and a little bit of clean up
276    o pkg/thsice: rename run-time parameters:
277       himin       -> hIceMin
278       himin0      -> hThinIce
279       hihig       -> hThickIce
280       i0          -> i0swFrac
281       transCoef   -> bMeltCoef
282       frac_energy -> fracMelting
283      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
284       with default values (for now) that do not change the results.
285      remove old version of thsice vars advection in pkg/seaice.
286    o in FFIELDS.h:
287      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
288      - make pLoad & sIceLoad always available (but still only used if
289         ATMOSPHERIC_LOADING is #define).
290    o pkg/kpp: replaced _KPP_RL with _RL
291    o bug fixes for vertical diffusivity computations when both KPP and
292        3D diffusivity arrays are used.
293    o pkg/seaice: fix bug in evp solver, while doing that
294      - change (improve?) discretization of stress computations for both
295        cgrid-lsr and evp solver
296      - add a new routine to compute strain rates
297      - the above changes lab_sea results
298      - add no slip conditions for evp solver (off by default), lsr-version
299        may follow
300      - fix exchange for shear at Z-points (does not change lab_sea)
301      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
302        (to force the user to pick a time step since there is not "safe" way
303        of choosing it)
304      - add principal stress diagnostics
305      - rearrange fields for evp a little to avoid having to call a: too many
306        exchanges and b: exchanges for stress trensor components which we do
307        not have.
308      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
309        of evp, complete rewrite for lsr case (latter is does not yet work
310        in all cases)
311    o pkg/kpp: add code to have mixing in shelf ice caverns
312      - add myThid to all kpp routines (long overdue)
313    
314    checkpoint59
315    o pkg/exf:
316      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
317        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
318      - move exf header files from lower_case.h to UPPER_CASE.h ;
319        add missing cvs Header & Name
320      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
321      - add namelist param. selectStressGridPosition, exf_monFreq
322      - retire many _CLIM routines, and remove data.exf_clim
323        + params moved to data.exf
324        + climsst, climsss now handled by exf_set_gen, i.e.
325          climss?period=0 refers to constant field,
326          climss?period=-12 to monthly forcing
327      - split up namelists in data.exf
328    o pkg/seaice:
329      - remove seaice_exch and seaice_exch_uv
330      - remove superfluous exchange of theta
331      - add myThid to seaice_budget_ocean/ice
332      - add new interface for atmospheric wind forcing (C-grid only)
333        + new routine
334        + two new field (taux, tauy for stress over ice)
335        + removed one global field (DAIRN) for C-grid case only
336    o pkg/thsise
337      - 2nd set of modifs for thsice adjoint in conjunction with exf
338    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
339    
340    checkpoint58y_post
341    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
342      vertical diffusivity, similar to that in MOM4; turned on using
343      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
344      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
345    o Added capability for 3D specification of background vertical diffusion
346      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
347      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
348      "data" file that contains the 3D vertical diffusivity coefficients.
349    o ice dynamics (pkg/seaice) with thsice thermodynamics:
350      - add code within pkg thsice to advect & diffuse sea-ice fields
351      similar to (and will replace) what has been added in  seaice_advdiff.F,
352      but: - conserving Mass, Heat & Salt.
353           - better when using non-linear advection scheme (not yet fully tested)
354           - can also be used in atmospheric set-up (for now, only the diffusion).
355    
356    checkpoint58x_post
357    o IO option for global-file compact format:
358      - add options when generating topology (utils/exch2/matlab-topology-generator)
359      - add I/O capability (pkg/mdsio).
360      - adapt utils/matlab/rdmds.m to read this format.
361      for now long-line format not yet supported by pkg/mdsio (& exch2).
362    o shelfice: add a few diagnostics
363    
364    checkpoint58w_post
365    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
366      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
367      (and replace horiVertRatio in NH code).
368      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
369                         and tutorial_plume_on_slope (sensitive to truncation)
370    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
371      directly to drive seaice model (C-grid only)
372    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
373     - reintroduce computation of wind from stress,
374     - compute tau (in exf_bulkformulae.F) from windstress averaged to
375       mass points to avoid tau = 0
376     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
377    o rdmnc.m: make it work with "global" files created with gluemnc
378    o rdmnc.m : some improvements in dealing with singleton dimension
379      (tested on all testreport mnc output files).
380    o genmake2: disable pkg/profiles if netcdf test fails.
381    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
382    o move call to cal_readparms up to make calendar parameters/variable available
383      to all packages
384    
385    checkpoint58v_post
386    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
387      useDynP_inEos_Zc tested.
388    o pkg/exf: changes to properly interpolate/mask/scale initial fields
389    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
390      and portions thereof.  See read_cs.txt for description and examples.
391    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
392      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
393      following the great-circle arc between those 2 points.
394    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
395      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
396    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
397     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
398     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
399     - still needs work (not working with some options ; efficiency to improve)
400       and serious testing.
401     - use this scheme for temperature & salinity in 2 advection test exp.:
402       advect_xy & advect_xz, respectively.
403    
404    checkpoint58u_post
405    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
406    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
407    o testreport: add option "-skipdir" to skip some test.
408    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
409      momentum calculation.
410    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
411    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
412      remove checkpoint.F and the_correction_step.F (no longer used);
413      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
414    o add option (linFSConserveTr) to correct for tracer source/sink due to
415      Linear Free surface
416    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
417    o pkg/thsice: fix reading mnc-pickups
418    
419    checkpoint58t_post
420    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
421    o pkg/mdsio:
422     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
423       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
424       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
425     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
426     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
427       either MDS_READ_FIELD or MDS_WRITE_FIELD )
428     - new S/R (to replace MDSWRITEMETA), which allows to write more
429       informations (variable names, time ...) to meta files.
430     - modify rdmds.m to give back the meta file content.
431    o pkg/diagnostics: change vertical interpolation to be safer, and more
432       flexible (define p-levels to interpolate to in data.diagnostics);
433      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
434       diagnostic pointer.
435    o pkg/seaice: more cleaning up of seaice_growth, added many comments
436    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
437    o fix multi-category seaice:
438     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
439       SEAICE_MULTICATEGORY
440     - fix short wave heat flux
441    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
442       and allow to use EVP solver. Change forward lab_sea: test both EVP
443       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
444    o Initial check-in of lab_sea adjoint
445      (very similar to natl_box_adjoint/code_seaice)
446      * used C-grid and EVP solver
447      * used KPP, GM/Redi
448      * uses inAdExact=.TRUE.
449      * gradient checks fail for both ADM and TLM
450        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
451        f.d. gradients actually seem more problematic than ADM, TLM gradients;
452        issue is related to forward mismatch between g77 an ifort
453    o pkg/seaice: overhaul of thermodynamics
454     - growth.F and groatb.F are replaced by new routine seaice_growth.F
455     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
456     - move a few global fields out of SEAICE.h into seaice_growth.F and
457       make them 2D (FICE/QNETO/ ...)
458     - remove FO (it is the same as QNETO)
459     - introduce a few local fields to avoid modifying external fields such
460       as atemp, etc.
461    
462    checkpoint58s_post
463    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
464      changed exf_set_gen.F so that
465        genperiod=0 means input file is one time-constant field and
466        genperiod=-12 means input file contains 12 monthly means
467    o CG2D: use pre-computed solver main-diagonal (stored in common block);
468      this affects truncation error ; generate new output file for exp. which
469      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
470        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
471        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
472        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
473        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
474        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
475    o start implementation of deep-atmosphere and anelastic formulation
476    o verification: remove 2nd copy of input files and use script "prepare_run"
477      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
478    o mom_common/vecinv/fluxform: fix a few initialisation isssues
479    o profiles: fix for multithreaded case
480    
481    o diagnostics: rename few diags:
482      s/'PRESSURE'/'RCENTER '/g
483      s/'TICE    '/'oceFreez'/g
484      s/'TAUX    '/'oceTAUX '/g
485      s/'TAUY    '/'oceTAUY '/g
486      s/'SWFLUX  '/'oceQsw  '/g
487      s/DIFx/DFxE/g
488      s/DIFy/DFyE/g
489      and add few ocean-forcing diagnostics:
490      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
491    o modifications to pkg/seaice/growth.F and budget.F, which change results of
492      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
493      as actual snow thickness.  It now refers everywhere to effective snow
494      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
495    
496    checkpoint58r_post
497    o modifications to pkg/seaice/growth.F, which change results of
498      lab_sea experiment: fixes pertain to melting snow over open water, to
499      masking EVAP under sea ice, and to using the correct AREA variable for
500      computations of EVAP, PRECIP, HSNOW, and GHEFF
501    o add ability to read bathy, salt, and theta using MNC (off by def)
502    o add flooding algorithm and advection of HSNOW for pkg/seaice;
503      both are turned off by default and do no change any results
504    o seaice advection with pkg/thsice: a step toward the use of non-linear
505      advection scheme, but #ifdef or commented out for now (requires more EXCH).
506    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
507      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
508      in natl_box (affects results @ truncation level: update output.txt)
509    o multi-threading and IO:
510      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
511      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
512        (needed to work with SingleCpuIO): tested in all verif. exp.
513    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
514      affects the results (but none of the verification test uses this scheme).
515    o Adding some pkg/diagnostics capability to pkg/seaice
516      (will certainly be subject to changes)
517    o ctrl: adding new control variables:
518      lwflux, lwdown, evap, snowprecip, apressure, runoff
519    
520    checkpoint58q_post
521    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
522      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
523      high_res_cube configuration by 4% on Columbia.
524    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
525      add (in global_with_exf/code) a version of EXF_INTERP_READ without
526      dynamical allocation (seems to work in multi-threaded).
527    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
528      single CPU io) so that TAF does not have to see EESUPPORT.h
529    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
530    
531    checkpoint58p_post
532    o obcs: stop if obcs is used with useCDscheme = .true.
533    o shelfice:
534     - fix a sign error so that no slip at shelfice interface works
535     - remove stop for combination non-hydrostatic code and shelfice. That does
536       not mean, that the results are correct, but at least they are numerically
537       stable
538    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
539    o added adjoint exch routined for all exch*3d* routines
540      and updated flow directives
541    
542    checkpoint58o_post
543    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
544      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
545    o change controling S/R for writing pickup file (new S/R do_write_pickup)
546      and clean-up reading/writing of pickup files.
547    o fix local version of read/write pickup (NH part) in rotating_tank/code
548    o simplify EXCH interface:
549     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
550     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
551    o added the regrid package
552    o shelfice:
553     - add a simple boundary layer scheme to reduce noise
554     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
555    
556    checkpoint58n_post
557    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
558       local variable (not in common block).
559    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
560      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
561      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
562        to work with SingleCpuIO.
563    o add "_d 0" to real constant of pkg/cfc subroutines ;
564       update exp. cfc_exemple & tutorial_cfc_offline output files.
565    o multi-threading and IO:
566      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
567        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
568      - barrier before and after reading.
569      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
570      - avoid using MDS_WRITELOCAL for LAND pkg output.
571      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
572        common-block variables ; Allows multi-threading with master-thread IO.
573    o change default MAX_NO_THREADS from 32 to 4 ;
574      and stop cleanly when MAX_NO_THREADS is too small.
575    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
576    
577    checkpoint58m_post
578    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
579       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
580    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
581       keep global_ocean.90x40x15 (for AD testing) with former secondary test
582       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
583    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
584        add MITgcm_tutorials (= code + all the tutorials)
585    o ecco, option to compute cost for total ssh (mean+anom)
586    o consistent with addition of ptracer and ssh in pkg/profiles
587    o profiles: adding ptracer and ssh
588    o testreport: change multi-test output-file name
589      (from output.txt.{name} to output.{name}.txt)
590    o profiles: now ok for mutli-tiles case
591    o seaice: add 4 parameters for different advection schemes for area,
592      (effective) seaice thickness, enthalphy, and snow height. Their default
593      is the standard parameter SEAICEadvScheme
594    o calc_gw:
595     - add cosFacU in zonal viscous flux (harmonic.visc.).
596     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
597       of tutorial_plume_on_slope.
598    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
599    o calc_gw: true flux-form, account for horizontal grid spacing.
600      update rotating_tank results, but not plume_on_slope (affected at
601      truncation level, 11 digits).
602    
603    checkpoint58l_post
604    o calc_gw:
605     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
606     - remove side-drag for now (need to fix it); update plume_on_slope results.
607     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
608    o commit code to make SST/SSS weights spatially variable
609      (based on either variable in-situ or variable initial T/S weights)
610    o pkg/ecco:
611      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
612        now based on horizontally varying weights wthetaLev, wsaltLev
613      * cost_averagesflags now returns year indices in addition to day, month
614      * sflux balance is performed on annual basis
615        (sflxumm, sfluxmm2, bal_sfluxmm)
616      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
617        including separate counting and multipliers
618    o pkg/rbcs
619      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
620    
621    checkpoint58k_post
622    o testreport:
623     - always build in dir. "build" (if not there, mkdir build instead of building
624       & running in input)
625     - run in dir run (if it exists), in build otherwise.
626     - call prepare_run (if input/prepare_run exists)
627     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
628    o pkg/exf modifications to interpolation and rotation routines for more
629       reasonable treatment of North Pole singularity: for tracers North Pole
630       value is set to northernmost zonal-mean value, for zonal velocity it is
631       set to zero, and for meridional velocity it is set to northernmost value.
632    o pkg/exf/exf_check_range.F
633     - add tile index to diagnostics and move stop statement to the very
634       end of the routine.
635    o pkg/diagnostics: (diagnostics_main_init.F)
636      define title of isomorphic variables according to the current config.
637    o pkg/thsice with pkg/seaice dynamics:
638    - fix domain of computation (interior only, required for exf) and do exchanges
639    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
640    o towards a standard way of dealing with multi-threading in MONITOR
641      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
642    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
643       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
644    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
645    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
646    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
647       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
648    o tracer advection:
649     - clean-up and simplify calc_common_factors.F
650     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
651       advection subroutine (but still not used within DST advection S/R)
652    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
653    
654    checkpoint58j_post
655    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
656      from file (collects calls previously in FORWARD_STEP)
657    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
658    o adjoint store dir. adjusted accordingly
659    o genmake2
660      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
661    
662    checkpoint58i_post
663    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
664      on wind stress (SEAICEstressFactor defaults to 1.)
665    o Total number of Timers is finite (<=40): comment out 2 non-essential one
666      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
667    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
668      on CS-grid: no longer loosing mass.
669    o exf & curvilinear-grid: no longer modify longitude xC & xG.
670    o pkg/ggl90: fix sloppy output and fix a bug
671    o pkg/seaice: added SEAICEuseEVPpickup parameter
672      - Set to false in order to start EVP solver with
673        non-EVP pickup files when using SEAICEuseEVP
674      - fix sign error in diffusion in seaice_calc_rhs
675    
676    checkpoint58h_post
677    * Modifications for bottom topography control
678      o replace hFacC by _hFacC at various places
679      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
680      o add non-self-adjoint cg2d_nsa
681      o update autodiff support routines
682      o re-initialise hfac after ctrl_depth_ini
683      o works for 5x5 box, doesnt work for global_ocean.90x40x15
684    * Adding verification for 5x5 box (4-layer) bottom topography control
685    
686    checkpoint58g_post
687    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
688       used for mean seasonal cycle, mean diurnal cycle); add an example
689       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
690    o pkg/ggl90:
691      - add parameter (minimum surface kinetic energy)
692      - fix bug (avoiding division by zero)
693    o couple pkg/thsice to pkg/seaice:
694      - modify advection in seaice to accomodate new scalar fields to be advected
695      - only muliDimAdection scheme work with seaice/thsice
696      - mapping of thsice-variables to seaice-variables, back and forth
697      - does not break the verification experiments, but does not give the
698        desired results either
699    o pkg/seaice
700      - make (default) second order advection a bit less confusing?
701    
702    checkpoint58f_post
703    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
704      to pkg/seaice):
705      - new routines thsice_map_exf and thsice_get_exf provide the interface
706      - add an additional formal parameter to thsice_solve4temp
707    o pkg/exf:
708      - add new fields wspeed, snowprecip (to be able to couple to thsice)
709      - correct Stefan-Boltzmann constant
710      - new parameter for longwave surface emittance
711      - separate some stuff from exf_bulkformulae into new routines  
712        exf_radiation, exf_wind
713      - add new parameters and constants: longwave emissivity for ocean, ice
714        and snow, evaporation parameters over ice
715      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
716        either wind from stress or stress from wind
717    o pkg/thSIce:
718    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
719    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
720       and THSICE_CALC_THICKN
721    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
722    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
723      to make debugging easier.
724    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
725    o pkg/bulk_force:
726      - clean-up comments and parameters ;
727      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
728    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
729      generate new output for test-experiment: aim.5l_cs.thSI
730    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
731      testreport accordingly
732    
733    checkpoint58e_post
734    o SEAICE_CGRID adjoint done
735    o R_STAR adjoint implemented.
736      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
737      * need to sort out init. of h0facc, etc.
738    o Make pkg/profile fully independent of ecco,cost, etc. stuff
739      to be able to use it in pure forward.
740    
741    checkpoint58d_post
742    o upgrade simple test-experiment to tutorial example:
743     step.1: duplicate the experiment and (step.2) will remove the old copy.
744      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
745      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
746      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
747      tutorial_global_oce_biogeo    <- copy of dic_example
748      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
749      tutorial_plume_on_slope       <- copy of plume_on_slope
750      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
751      tutorial_global_oce_optim     <- empty for now (David ?)
752      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
753     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
754    o correct a sign problem in cost_scat.F
755    o obcs and ptracers: fix boundary conditions for advections schemes
756      with larger stencil
757    o thsice adjoint: start
758    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
759      completeness
760    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
761      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
762    o ptracers adjoint:
763      * avoid extensive recomputatations
764      * fix missing re-init. of gptr (missed by TAF)
765    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
766      me to turn off the excessive output to STDOUT that this package produces
767    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
768      and add those terms in Vector-Invariant formulation.
769    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
770      if the control period (xx_hfluxperiod etc) is 0
771    o in profiles pkg, clean routines and fix details
772    o in ecco pkg, reading ssh data:
773      fix problem in case the model does not start at iter0=0
774    o fix mnc-pickup/restart for ptracers
775    o new package prifiles:
776      code to compute profile-based cost by Gael Forget
777      (modifs in ecco, ctrl, autodiff)
778    o Benign bug fix in initialization (spotted by M. Mazloff) of
779      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
780    
781    checkpoint58c_post
782    o adjoint: finish NLFS adjoint and provide reference output in
783      verification/global_ocean.90x40x15/results_ad_nlfs
784    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
785      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
786      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
787      with SEAICE_CGRID defined.
788    o move calendarDumps from "data" to "data.cal" and clean-up the code
789      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
790    o add useEXF & useCAL flags (for now, set in hard-coded way)
791    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
792      (were missing in NH mode, and wrong in quasihydrostatic mode).
793      waiting for Chris updated version of calc_gw to add those CALLs.
794    o fix bug in quasihydrostatic S/R ;
795      add a test for this option: global_ocean.90x40x15.qshyd
796    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
797      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
798    o add on/off flag useOffLine for package OFFLINE
799    o seaice:
800      - modify advection so that it works also on the C-grid
801      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
802        problem in multi-tile runs with C-grid
803      - add flags for clipping ice velocities and/or masking solver forcing
804      - fix drag (ocean on ice) formulation and a bug that caused noise in the
805        C-grid solver
806      - added a few comments to seaice_diffusion.F
807      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
808        are now exclusive)
809      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
810        required re-ordering the code a little:
811       + make DAIRN global variable (defined in SEAICE)
812       + move computation of the viscosities eta and zeta into a new separate
813         routine (because I need to recompute them in seaice_ocean_stress.F)
814    
815    checkpoint58b_post
816    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
817      update output.txt of exp. aim.5l_cs.thSI
818    o various mnc cleanups and improvements:
819      + shrink lookup tables by factor of ~4
820      + better error reporting when running out of lookup space
821      + able to handle longer path/file names (up to 500 chars)
822    o adjoint:
823      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
824      - TBD: "hidden" mom_vecinv recomp. in dynamics
825    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
826     (allow to differentiate between forcing components using new integer flags:
827      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
828     and add new flag to put Dissipation tendency out of Adams-Bashforth.
829    o ecco
830      - enable trend removal from SSH anomaly obs.
831    o adjoint
832      - a fix for PmEpR when #undef EXACT_CONSERV
833      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
834      - try to fix "hidden" recomp. in forward_step for NLFS
835        (NLFS seems broken sometimes after I checked it in)
836    o seaice:
837     - add c-grid version of the dynamic solver:
838       + three new routines that are the c-grid substitute lsr, dynsolver
839         and ostres
840       + put a few fields that were local to dynsolver into global common
841         blocks, so that I can move the computation of stresses etc into
842         seaice_lsr (saves coding but may break the adjoint).
843     - replace more hardwired parameters by runtime parameters
844     - add ice masks that mask the rhs of the implicit solvers where there
845       is no ice (commented out in seaice_dynsolver, because i am not sure
846       if this works properly), eventually this should replace the clipping
847       of ice velocities in seaice_dynsolver to +/-40cm/s.
848    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
849      include it only where its needed
850    o move balancing of fluxes before the call of external_forcing_surf
851    o seaice:
852      - correct units of turning angles (now they are really in degrees)
853      - move computation of GWATX/Y out of main routine into dynsolver
854      - initialize GWATX/Y in seaice_init
855    o Apply mask on Fresh-Water flux (needed for SSH forcing).
856      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
857    o seaice: add runtime flags for turning angles (default to zero)
858    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
859      and trend from exf forcing and ctrl control adjustments
860    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
861      (since checkpoint57x_post)
862    o change the default rotation period to 86164.s = the Earth rotation
863    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
864      and based on a reference stratification. Tested within hs94.cs-32x32x5.
865    o seaice advection: add code for choosing between the default (2nd order
866      central differences) and multiDim advection schemes provided by
867      pkg/generic_advdiff
868    o seaice:
869      - removed all references to SEAICE_GRID.h fields from
870        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
871        (cubed-sphere configuration will change a little)
872      - grid computations in seaice_init are obsolete now.
873      - cleaned up code a little so that is easier to read (hopefully).
874      - added new (better?) discretizations of default advection and diffusion
875        (turn on with SEAICEuseFluxForm)
876      - replace 1 in 3d global fields by kSurface in growth.F
877      
878    checkpoint58a_post
879    o seaice:
880      - bug fix in advect.F
881    o shelfice:
882      - separate shelfice load anomaly from pload (breaks with time
883        dependent forcing), => introduce constant field shelficeLoadAnomaly.
884        Its default is 0., but it may be computed more cleverly from (unknown)
885        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
886        done offline. A good approximation of the pressure load anomaly is
887        necessary to avoid large initial adjustment processes underneath
888        deep-reaching shelfice.
889      - small fix in ISOMIP shelfice_thermodynamics
890      - add more sophisticated thermodynamics of Hellmer (1989), this is
891        now the default
892      - give a few constants more intuitive names
893    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
894      if bulk formulae are used in long integration (especially EmPmR). Turn
895      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
896      if balancePrintMean, the imbalance that is substracted is printed to
897      STDOUT.
898    o fix bug (typo) in obcs_apply_eta.F
899    o add a new package shelfice which enables us to model the circulation
900      underneath shelf-ice with draughts of hundreds of meters.
901     - works
902     - to do: + include improved thermodynamics
903              + check whether kSurfC (from model/inc/SURFACE.h) can be used
904                instead of new field kTopC
905              + can we use topoFile, Ro_surf and existing code in ini_depth.F
906                instead of new field R_shelfIce and new code in ini_depth.F
907                and ini_mask_etc.F?
908              + adjust vertical mixing schemes?
909    o seaice pkg:
910     - add a cpp-flag to include a simple formula for a salinity dependent
911       freezing point of sea water at the surface
912     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
913       meridional stresses are now different (and hopefully correct)
914    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
915       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
916       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
917    o pkg/diagnostics: add options and parameters for regional-statistics
918       diagnostics ; define regions by reading a region-mask from a file
919       (might add other options later)
920    o pkg/bulk_force:
921     - add option and parameters to use AIM surface-flux formulae.
922     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
923       others forcing fields (defined in PARM05, parameter file "data") are loaded
924       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
925     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
926     - use the right EXCH call for uwind,vwind (to work on CS-grid).
927     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
928       and parameters (note: calcWindStress replaces .NOT.readwindstress).
929     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
930    
931    checkpoint58
932    o add "--embed-source" option to genmake2 which, when the supporting
933      tools can be compiled (as determined by genmake2) will turn on the
934      embed_files package which then embeds the entire MITgcm source code
935      (*.[fFhc] + Makefile) used for the build within the executable
936      - requested by CNH but off by default
937      - adds a paltry <9MB to the mitgcmuv executable in most cases
938      - only writes the output when useEMBEDSRC in eedata is true
939    o clean up 3-dim. relaxation codes:
940      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
941      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
942      * Thanks to Tom Haine for testing!
943    
944    checkpoint57z_post
945    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
946      affects output (@ truncation level) of exp. plume_on_slope ; updated.
947    o fix the pickup behavior for obcs in combination with ptracers
948    o fix a bug in ptracers_external_fields_load
949    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
950      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
951    o transfered surface NH pressure to eta field (if exactConserv).
952    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
953         and update lab_sea output.txt file.
954    o completing 3-dim. relaxation code: additional term
955         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
956      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
957      * At compile time, in "EXF_OPTIONS.h" set
958          #define  ALLOW_CLIMTEMP_RELAXATION
959          #define  ALLOW_CLIMSALT_RELAXATION
960      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
961          tauThetaClimRelax3Dim = 15552000.0,
962          tauSaltClimRelax3Dim  = 15552000.0,
963      * 3 cases:
964          1) Use a constant-in-time 3-dim. field
965          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
966          3) Real-time relax. to time-evolving prescribed field
967    o Adding Laplacian-type smoothness constraint on
968      initial and boundary (forcing) controls (ic, bc)
969      * enable at compile-time via
970        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
971      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
972      * Absolute scale somewhat unclear so far
973      * no area weighting was included since no other cost term does so far
974    
975    checkpoint57y_post
976    First step for a NLFS adjoint
977    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
978    o new init. routines for calc_r_star, calc_surf_dr
979    o still need to deal with ini_masks_etc
980    o testreport seemed happy
981    checkpoint57y_pre
982    
983    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
984    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
985    o add new offset feature to offline pkg (plus minor cleanup)
986    o cfc fixes for final year of integration
987    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
988      be in GCHEM_OPTIONS).
989    
990    checkpoint57x_post
991    o fix testreport Pb in multiple test experiment.
992    o cleanup our namelist syntax in verification:
993      - make it more F95 standards compliant (some work still needed)
994      - allows the vast majority of our tests to work with gfortran
995    o Non-Hydrostatic:
996     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
997     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
998    o Allow to apply AB on T,S rather than on AB(gT,gS):
999     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
1000     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
1001       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
1002     - need a "clever" read_pickup to restart from the other AB formulation
1003    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
1004    o remove some unused variables (reduces number of compiler warnings)
1005    o adjoint
1006      * Disable useVariableViscosity for adjoint for time being
1007        (there are a number of extensive recomputations)
1008      * Initialize certain variables needed for adjoint
1009    
1010    checkpoint57w_post
1011    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
1012                 fix the singleCpuIO RS version of MDSWRITEFIELD
1013       and add a WARNING if using globalFiles=T with multi-processors.
1014    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
1015      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
1016    o tracer advection scheme:
1017      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
1018       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
1019       was not very convenient).
1020      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
1021       (further tests needed for the implicit DST & Flux-Limiter schemes).
1022    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
1023      and sRef for convenience, handy, when you want to initialize
1024      ptracers in a large domain with a constant non-zero value. Also,
1025      untangle ptracers_init.F a little.
1026    
1027    checkpoint57v_post
1028    o change dome exp. to use variable viscosity in side-drag terms.
1029    o remove all the files from the cfc_offline test since they are now
1030      incorporated into tutorial_cfc_offline which has been producing
1031      identical results for a few days of testing
1032    o add new parameter: sideDragFactor to enable half-slip-side BC
1033      and change side-drag S/R to use viscosity from mom_calc_visc
1034      (can switch back by setting sideDragFactor=0.); affects results at
1035      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
1036       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
1037    o vorticity & strain are now computed without masking, to account for
1038      no-slip-side BC in variable viscosity calculation ; mask is applied
1039      anyway later on, before computing advection/coriolis terms.
1040    o modify exp4 to test new obcs support for reading from external files
1041      and for passive tracers
1042    o fix behavior of ptracers_monitor when monitor output is written to a
1043      netcdf-file; still not independent of monitor.F (writes in the same
1044      file).
1045    o change default value of tRef (put a uniform, meaningful value for ocean
1046      & atmos) and initialize sRef (was missing, as Martin mentioned).
1047    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
1048      to be proportional to enstrophy dissipation length.  Thus,
1049       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
1050      This is now consistent with Smagorinsky and with the manual.
1051    
1052    checkpoint57u_post
1053    o OBCS and PTRACERS: add open boundary support for passive tracers
1054      - either use homogenous (pseudo) v.Neumann conditions or prescribe
1055        OB-values from file; this is not different from the way theta and salinity
1056        are treated
1057      - however, Orlanski-radiation conditions are not supported, and the model
1058        will stop if you use pTracers and Orlanski at the same time.
1059      - beefed up the rountine obcs_external_fields_load: now only those open
1060        boundary values are overwritten with values from files for which there
1061        are really files, otherwise the OB-fields remain untouched. This makes
1062        it possible to use different OBs at different ends of the domain (as
1063        with EXF)
1064    o reduce number of exch calls in shap_filt (s2).
1065    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1066      truncation level) 4/5 MLAdjust test results (11&12 digits match).
1067    
1068    checkpoint57t_post
1069    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1070    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1071      same truncation, independent of the face number: affects affects several
1072      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1073    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1074      note that biharmonic viscosity + no-slip was not tested in any experiment.
1075    o fix bug in non-linear free-surf side-drag ; generate new output for
1076      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1077    o make mnc honor the writeBinaryPrec flag for most kinds of output
1078    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1079    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1080      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1081    o add brackets in multi-terms sum to get same truncation, independent of
1082      the face number (manage to get exactly same value of gU,gV at the cs-edge)
1083      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1084    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
1085      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1086      a maximum grid-scale Reynolds number.  Also, changes all length calculations
1087      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1088      Suggested values of viscosity parameters found in mom_calc_visc.
1089      Many new viscosity diagnostics available.
1090    
1091    checkpoint57s_post
1092    o Add clearing-house for viscosity calculations, mom_calc_visc and
1093      correct numerous bugs in LeithD and Smagorinsky discretizations.  
1094      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1095      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1096      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1097      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
1098      The Strain-Tension form is now called with useStrainTensonVisc=.true.
1099      ViscAhStrain and viscAhTension are now retired.
1100    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1101    o In response to JMC's bug report, genmake2 now ignores any soft-links
1102      that it finds in the *current* directory when searching for files.
1103      Soft-links found in any other source directories will still work as
1104      they did before.
1105    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1106      a C routine to unlimit the stack size
1107    o mnc-ify pkg/aim snapshot vars
1108    o mnc-ify pkg/land as requested by Daniel
1109    o various changes to mnc including:
1110      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1111      - output can now be grouped so that all files within a group
1112          change the ITER portion of their names in lock-step together
1113      - can now read ("global") PER-FACE (in addition to PER-TILE) files
1114          and works with both EXCH1 and EXCH2 (but needs more testing)
1115      - writing works for all verification test cases w/ g77 on Linux
1116    
1117    checkpoint57r_post
1118    o make MNC variable initialization happen earlier
1119    o add diagnostics for (almost) each term of the momentum Eq.
1120    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1121    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1122    o remove MINIMAL_TAVE_OUTPUT option ;
1123      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1124    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1125      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1126    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1127    o add time-dependent SST, SSS control
1128    o cost terms in ecco/ modularized (new cost_generic.F)
1129    o cost_averages routines are modularized (new cost_averagesgeneric.F)
1130    o new infrastructure for seaice model vs. obs misfits in seaice/
1131      * driver from the_main_loop.F is seaice_cost_driver.F
1132      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1133      * gradient check in Exp. 6a of natl_box_adjoint/
1134    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1135      (see README file)
1136    
1137    checkpoint57q_post
1138    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1139    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1140      - bug was reported by Jean-Michel and Ian Fenty
1141    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1142      update exp. cpl_aim+ocn output.
1143    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1144      Needed for high-res. runs with large global files
1145      to be able to limit tapelev size
1146    o Changed some tests for adjoint:
1147      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1148      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1149      * global_ocean.90x40x15/ back to default 3-level checkpointing
1150    o Modifications to enable scripted COMMON to MODULE conversion
1151      * verification/OpenAD/code/ has necessary scripts and description;
1152      * converts, compiles and runs successfully;
1153    
1154    checkpoint57p_post
1155    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1156    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1157      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1158    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1159    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1160      (was already the case for dissipation with mom_vecinv,
1161       and also the case for grad.PhiHyd when staggered-timeStep)
1162      This will allow to put dissipation out-off the AB time-stepping.
1163     Unfortunately, affects truncation error. Update output of exp. that "fails"
1164      (cg2d matching number) and leave the others for later: front_relax(10),
1165      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1166      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1167    
1168    checkpoint57o_post
1169    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1170      (2) its ready to be documented during the 20050801 DocFest
1171    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1172      for ideal_2D_oce and lab_sea on linux_ia32_g77
1173    o set to #undef CTRL_SET_OLD_MAXCVARS_30
1174      in global1x1_tot/code_seaice_adj to access indices 32, 33
1175      (worth another tag)
1176    
1177    checkpoint57n_post
1178    o adding precip control xx_precip 32
1179    o adding swflux control xx_swflux 33
1180    o Replacing 10 forcing penalty cost routines by 1 generic.
1181    o Implementing partitioning in time-mean and variable adjustment
1182      for atmos. state.
1183    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1184  o in natl_box_adjoint:  o in natl_box_adjoint:
1185    * updated: results_bulk/    * updated exp 1 to 10
1186    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
1187    o updated global1x1/*_seaice_adj/
1188      to incorporate latest changes
1189    o enable useSingleCpuIO for mdsio vector routines
1190      (applies in particular to tapelev I/O)
1191    o removed inefficient K-loop in all active_file*control*.F
1192    
1193  checkpoint57m_post  checkpoint57m_post
1194  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
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