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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.891 by dimitri, Thu Oct 11 10:30:34 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 added open boundary conditions capability for seaice HEFF and AREA
8  o moved ptracer ctrl index 17 -> 32  o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
9      thermodynamics
10      - requires a little reorganization, which affects the testreport results
11        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
12        so that now the conservative form is tested
13      - add a few comments
14    o add missing cvs $Header$ or $Name$ in eesupp/*, pkg/* & verification/code*
15    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
16    o add new diagnostics to seaice: advective, diffusive fluxes (only for
17      multidim-advection, for scheme 2 they are not filled) and transports,
18      thermodynamic growth rates
19    o change units of EmPmR (inside the code) from m/s to kg/m2/s (mass flux) but
20      leave input file unchanged. Affects results @ truncation level (cg2d match)
21      and update output of experiments: lab_sea(6), global_ocean.90x40x15(10),
22      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
23      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
24      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
25    
26    checkpoint59h
27    o pkg/exf:
28      - improve vectorization by moving if-statement out of loops in
29        exf_mapfields, exf_radiation
30      - exf_bulkformulae.F: introduce 2D fields and vectorize code
31    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
32    o testreport:
33      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
34        monitor & update offline_exf_seaice exp. output.
35      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
36    o pkg/seaice:
37      - bug fix in the evp solver: boundary conditions were affected be
38        masking of zMax/zMin (changes results)
39      - minor bug fix in boundary conditions in seaice_calc_strainrates
40        (changes results for no_slip)
41      - seaice_lsr.F: make interpolation of eta dependent on boundaries
42      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
43      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
44        stress formulation and no-slip boundary conditions
45    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
46      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
47    o pkg/seaice: a first HSALT time stepping equation has been checked in
48    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
49      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
50      without requiring DO-IF statements
51    o pkg/thsice:
52      use continuous power-law function for partition of energy between lateral
53      melting/freezing and thinning/thickening ; old code using step function
54      still available with #undef THSICE_FRACEN_POWERLAW
55      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
56    o testreport: change AD testing : check against results/output_adm.txt
57      using same scripts as for forward test.
58    
59    checkpoint59g
60    o adjoint testing: in preparation for changing testreport:
61      - output format: cost and grad written on separated lines
62      - ad output results in directory "results" (instead of "results_ad")
63    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
64    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
65    o pkg/ecco: allow user defined cost function contributions
66    o testreport:
67      Allow to choose (per experiment) the list of tested output variables
68       and the main variable (used to issue a pass/FAIL ) ;
69      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
70      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
71      Also modify printing of summary:
72       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
73       b) echo the list of tested variables in the individual summary.txt of
74          each experiment.
75    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
76      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
77      (but still depend on the tile decompostion of the domain).
78    o pkg/seaice: change a discretization detail to make the B-grid code
79      "more symmetric". This change is likely to remove all "ridges/leads" that
80      where quasi-aligned with the grid in B-grid solutions. It may also be
81      the solution to the stress coupling issues with the B-grid.
82    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
83      remove .cvsignore from input dir. (since testreport no longer run here).
84    o pkg/thsice:
85     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
86     - fix reshaping of sea-ice just after advection:
87       melt all the ice only if ice-volume is too small.
88     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
89       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
90     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
91    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
92      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
93    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
94      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
95      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
96      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
97      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
98      -> update output.txt
99    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
100     this affects truncation error: -> update output.txt of exp:
101      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
102      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
103    
104    checkpoint59f
105    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
106    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
107      a bounded range (in forward mode)
108    o pkg/ecco, ctrl, autodiff and mom_common:
109     internal parameter controls, completements of implementations
110    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
111    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
112      (not seem any difference in testing results).
113    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
114       at face corners.
115    o pkg/generic_advdiff:
116     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
117      loop range indices for computing vertical advection tendency
118      and do the calculation in the interior only (no overlap) ;
119      for now, only implemented for SOM advection (to save CPU time).
120     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
121    o exch2 adjoint
122      First set of changes:
123      - add exch2 hand-written adjoint templates
124      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
125        This will require cleanup in pkg/autodiff/*.F
126        (changed routines currently kept separate in verif. code/)
127      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
128        that used to hide exch2 or cubed-sphere specific code
129        (commented via 'cph-exch2')
130    o pkg/seaice
131      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
132    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
133       output of global_ocean.cs32x15.thsice .
134    
135    checkpoint59e
136    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
137      for B-grid vector (not yet tested) and C-grid vector (<- only used
138      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
139    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
140      (#ifdef ALLOW_SALT_PLUME)
141    o gather_2d/scatter_2d: removed halo regions
142    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
143      scheme and the corresponding test case (under front_relax dir). For now,
144      only available with Skew-flux form and not yet tested in realistic set-up.
145      adjoint: store directives updated, but gradient checks deteriorated,
146      so maybe GM/Redi adjoint is now broken.
147    o seaice adjoint
148      * add AREA, HEFF, HSNOW as control variable
149        (should not change lab_sea results)
150      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
151    o pkg/seaice:
152      * added computation of saltFlux in seaice_growth;
153        For time being, sea ice salinity is assumed constant
154        contribution of snow flooding to freshening of sea ice is neglected.
155        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
156        defaults to 0.0 in order to maintain backward compatibility.
157        Typical values for SEAICE_salinity are 4 to 10 g/kg.
158      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
159      * added SEAICE_availHeatFrac, which specifies fraction of surface level
160        heat content used to melt or grow ice
161      * commented out cap of HICE: it helps keep ice thinner
162      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
163      * applied OBCS T/S mask to HEFFM sea ice mask
164    
165    checkpoint59d
166    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
167     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
168     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
169    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
170     and change default value of parameter "GM_Small_Number";
171     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
172       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
173       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
174    o pkg/ecco: cost function when applying pkg/smooth to controls
175    o pkg/ctrl: add forcingPrecond run time parameter
176    o pkg/seaice:
177     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
178     - fix bug in metric terms of u-equation in LSR solver (implicit part),
179       changes verification/lab_sea
180     - rearrange implicit part of u-equation in LSR solver to make it easier to
181       read, understand, and debug. This causes changes at the truncation level.
182     - fix (serious) bug in the boundary conditions (sign error in the implicit
183       part) of the LSR solver. Changes all LSR results.
184     - fixed problem with HSNOW initialization to avoid thick snow when AREA
185       is initilized with small values - does not change lab_sea results.
186     - added HsnowFile initialization capability
187    o pkg/smooth: addition to model/src and pkg/ctrl so allow
188     initialization of pkg/smooth and application to control vector
189    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
190    o dependencies: pkg/profiles requires pkg/cal
191    o pkg/profiles:
192     - added option ALLOW_PROFILES_GENERICGRID
193         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
194         that interpolation information (grid points and coefficients) is provided
195         within the netcdf input files.
196         -> sample matlab scripts can be found in MITgcm_contrib/gael
197         that allow you to prepare netcdf input files.
198     - also modified: cleaner include statements, cleaner error print statements,
199       cleaner stops when error, and more tests of the netcdf input files consistency.
200    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
201    o pkg/seaice:
202     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
203       requires a new routine: seaice_diagnostics_fill.F
204     - make sure that seaice does not move if not forced (pressure replacement
205       method, Hibler and Ip, 1995), changes results
206     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
207     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
208       It is turned off by default (=-1.), because it changes the results.
209     - make it possible to read AREA from a file, too.
210    
211    checkpoint59c
212    o add S/R and diagnostics for oceanic mixed-layer depth
213    o move GMRedi call after all vertical mixing schemes (including KPP)
214    o pkg/thsice:
215     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
216      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
217    o pkg/obcs:
218     - bug fix for balance code
219    o pkg/seaice:
220      - allow values of SEAICE_elasticParm > 1
221      - add new parameter SEAICE_evpTauRelax as an alternative
222        to SEAICE_elasticParm
223      - make lsr boundary conditions free slip (by default), changes result
224      - add code for no slip boundary conditions for lsr
225      - set minimum of zeta to zero (and not 4e8) (changes results)
226      - add a cap on AREA after advecting AREA if seaice_growth is not called
227    o change calculation of Visbeck K:
228      - no longer depend on tapering scheme; instead, compute slope (limited
229        by GM_maxSlope). this is equivalent to what was comuted before with
230        clipping or linear tappering.
231      - fix vertical averaging (wrong by 1/2 level)
232      - leave the old version (but will not be maintained) within
233        #ifdef OLD_VISBECK_CALC / #endif
234      - update output of exp. ideal_2D_oce
235    o change error catch in calc_r_star to improve vectorization
236    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
237      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
238    o adjoint:
239      Re-organized adjoint checkpointing according to Matt Mazloff
240      (but with modifs/completions/cleanups)
241      Storing is now bundled into large arrays to optimized I/O
242      (and second step in cleanup of the_main_loop)
243    
244    checkpoint59b
245    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
246      - export/import (between ocean & coupler) fields needed for ocean DIC.
247    o pkg/seaice:
248      - get rid of three more exchanges seaice_calc_viscosities (required
249        different loop boundaries in seaice_lsr and seaice_ocean_stress)
250      - bug fix in seaice_ocean_stress (update of lab_sea required)
251      - reduce loop boundaries to necessary minimum also in seaice_evp
252      - go back to the old way of computing deltaC/Z as the adjoint likes that
253        better
254    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
255      passive tracer to an Age Tracer) + update output.txt
256    o pkg/exf:
257      - implement A-grid / C-grid selection for wind-stress input files.
258      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
259      for now, in exf_bulk_largeyeager04.F only :
260      - change implementation for case where windspeed + 2. components wind-stress
261        are read-in. AND use rhoConstFresh to convert evap.
262    o pkg/seaice:
263      - use correct EXCH_UV for wind-forcing (on A-grid).
264      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
265        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
266    o pkg/exf:
267      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
268      EXF_INTERPOLATION:
269      - merge global_with_exf/code version of exf_interp_read.F
270        to the main code ;
271      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
272        reading the file ; Important: This options needs to be defined to recover
273        previous code.
274        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
275      - no longer loose real*8 precision along the way when using exf_iprec=64.
276    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
277      - change discretisation of evp-solver in order to avoid another exchange
278        (changes lab_sea) and clean up a little
279      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
280        help the adjoint (this also changes the results slightly)
281      - add a few "_d 0" where they had been missing in seaice_evp.F
282      - cleaning up: remove unused seaice_calc_rhs.F
283    o pkg/exf: some cleaning-up:
284      - change various "constants" into runtime parameters
285      - cleaned-up Large&Yeager04 routine which should eventually
286        replace exf_bulkformulae.F (changed names of S/R and CPP)
287        and merged various ALLOW_ATM_WIND options
288     only used with thsice pkg (in thsice_get_exf.F):
289      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
290        which are used when useStabilityFct_overIce=TRUE (= the default)
291      - change default values of ice & snow emissivity and scale downward LW
292        by ice & snow emissivity.
293    o pkg/thsice:
294     fix few little problems, in thsice_calc_thickn.F:
295      - growth vertically (and not laterally) if iceFrac == iceMaskMax
296      - melt only laterally if hIce < hThinIce (as the comments say)
297      and in thsice_extend.F:
298      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
299      - start to form ice as soon as the minimum ice-volume is reachable.
300     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
301      and cpl_aim+ocn
302    o pkg/kpp
303     - move computation of surface related input fields to KPP into a new
304       subroutine kpp_forcing_surf.F
305     - remove wrong (within bi,bj loops) EXCH calls.
306     - little cleaning (add argument myThid in last position, cvs header ...)
307     - for now, fix conservation problem by exchanging KPPviscAz (may not
308       be the best fix)
309    o pkg/seaice
310     - check for inconsistent evp parameter/cpp-flag combination
311     - remove leftover errIO flat for obsolete name list error handling
312    o OpenAD
313     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
314    
315    checkpoint59a
316    o pkg/seaice: some parameter clarifications and a little bit of clean up
317    o pkg/thsice: rename run-time parameters:
318       himin       -> hIceMin
319       himin0      -> hThinIce
320       hihig       -> hThickIce
321       i0          -> i0swFrac
322       transCoef   -> bMeltCoef
323       frac_energy -> fracMelting
324      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
325       with default values (for now) that do not change the results.
326      remove old version of thsice vars advection in pkg/seaice.
327    o in FFIELDS.h:
328      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
329      - make pLoad & sIceLoad always available (but still only used if
330         ATMOSPHERIC_LOADING is #define).
331    o pkg/kpp: replaced _KPP_RL with _RL
332    o bug fixes for vertical diffusivity computations when both KPP and
333        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
334        are no longer updating the vertical diffusivity array
335        (passed as argument) but are (re-) setting those arrays.
336    o pkg/seaice: fix bug in evp solver, while doing that
337      - change (improve?) discretization of stress computations for both
338        cgrid-lsr and evp solver
339      - add a new routine to compute strain rates
340      - the above changes lab_sea results
341      - add no slip conditions for evp solver (off by default), lsr-version
342        may follow
343      - fix exchange for shear at Z-points (does not change lab_sea)
344      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
345        (to force the user to pick a time step since there is not "safe" way
346        of choosing it)
347      - add principal stress diagnostics
348      - rearrange fields for evp a little to avoid having to call a: too many
349        exchanges and b: exchanges for stress trensor components which we do
350        not have.
351      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
352        of evp, complete rewrite for lsr case (latter is does not yet work
353        in all cases)
354    o pkg/kpp: add code to have mixing in shelf ice caverns
355      - add myThid to all kpp routines (long overdue)
356    
357    checkpoint59
358    o pkg/exf:
359      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
360        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
361      - move exf header files from lower_case.h to UPPER_CASE.h ;
362        add missing cvs Header & Name
363      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
364      - add namelist param. selectStressGridPosition, exf_monFreq
365      - retire many _CLIM routines, and remove data.exf_clim
366        + params moved to data.exf
367        + climsst, climsss now handled by exf_set_gen, i.e.
368          climss?period=0 refers to constant field,
369          climss?period=-12 to monthly forcing
370      - split up namelists in data.exf
371    o pkg/seaice:
372      - remove seaice_exch and seaice_exch_uv
373      - remove superfluous exchange of theta
374      - add myThid to seaice_budget_ocean/ice
375      - add new interface for atmospheric wind forcing (C-grid only)
376        + new routine
377        + two new field (taux, tauy for stress over ice)
378        + removed one global field (DAIRN) for C-grid case only
379    o pkg/thsise
380      - 2nd set of modifs for thsice adjoint in conjunction with exf
381    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
382    
383    checkpoint58y_post
384    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
385      vertical diffusivity, similar to that in MOM4; turned on using
386      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
387      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
388    o Added capability for 3D specification of background vertical diffusion
389      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
390      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
391      "data" file that contains the 3D vertical diffusivity coefficients.
392    o ice dynamics (pkg/seaice) with thsice thermodynamics:
393      - add code within pkg thsice to advect & diffuse sea-ice fields
394      similar to (and will replace) what has been added in  seaice_advdiff.F,
395      but: - conserving Mass, Heat & Salt.
396           - better when using non-linear advection scheme (not yet fully tested)
397           - can also be used in atmospheric set-up (for now, only the diffusion).
398    
399    checkpoint58x_post
400    o IO option for global-file compact format:
401      - add options when generating topology (utils/exch2/matlab-topology-generator)
402      - add I/O capability (pkg/mdsio).
403      - adapt utils/matlab/rdmds.m to read this format.
404      for now long-line format not yet supported by pkg/mdsio (& exch2).
405    o shelfice: add a few diagnostics
406    
407    checkpoint58w_post
408    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
409      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
410      (and replace horiVertRatio in NH code).
411      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
412                         and tutorial_plume_on_slope (sensitive to truncation)
413    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
414      directly to drive seaice model (C-grid only)
415    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
416     - reintroduce computation of wind from stress,
417     - compute tau (in exf_bulkformulae.F) from windstress averaged to
418       mass points to avoid tau = 0
419     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
420    o rdmnc.m: make it work with "global" files created with gluemnc
421    o rdmnc.m : some improvements in dealing with singleton dimension
422      (tested on all testreport mnc output files).
423    o genmake2: disable pkg/profiles if netcdf test fails.
424    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
425    o move call to cal_readparms up to make calendar parameters/variable available
426      to all packages
427    
428    checkpoint58v_post
429    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
430      useDynP_inEos_Zc tested.
431    o pkg/exf: changes to properly interpolate/mask/scale initial fields
432    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
433      and portions thereof.  See read_cs.txt for description and examples.
434    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
435      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
436      following the great-circle arc between those 2 points.
437    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
438      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
439    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
440     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
441     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
442     - still needs work (not working with some options ; efficiency to improve)
443       and serious testing.
444     - use this scheme for temperature & salinity in 2 advection test exp.:
445       advect_xy & advect_xz, respectively.
446    
447    checkpoint58u_post
448    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
449    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
450    o testreport: add option "-skipdir" to skip some test.
451    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
452      momentum calculation.
453    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
454    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
455      remove checkpoint.F and the_correction_step.F (no longer used);
456      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
457    o add option (linFSConserveTr) to correct for tracer source/sink due to
458      Linear Free surface
459    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
460    o pkg/thsice: fix reading mnc-pickups
461    
462    checkpoint58t_post
463    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
464    o pkg/mdsio:
465     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
466       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
467       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
468     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
469     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
470       either MDS_READ_FIELD or MDS_WRITE_FIELD )
471     - new S/R (to replace MDSWRITEMETA), which allows to write more
472       informations (variable names, time ...) to meta files.
473     - modify rdmds.m to give back the meta file content.
474    o pkg/diagnostics: change vertical interpolation to be safer, and more
475       flexible (define p-levels to interpolate to in data.diagnostics);
476      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
477       diagnostic pointer.
478    o pkg/seaice: more cleaning up of seaice_growth, added many comments
479    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
480    o fix multi-category seaice:
481     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
482       SEAICE_MULTICATEGORY
483     - fix short wave heat flux
484    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
485       and allow to use EVP solver. Change forward lab_sea: test both EVP
486       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
487    o Initial check-in of lab_sea adjoint
488      (very similar to natl_box_adjoint/code_seaice)
489      * used C-grid and EVP solver
490      * used KPP, GM/Redi
491      * uses inAdExact=.TRUE.
492      * gradient checks fail for both ADM and TLM
493        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
494        f.d. gradients actually seem more problematic than ADM, TLM gradients;
495        issue is related to forward mismatch between g77 an ifort
496    o pkg/seaice: overhaul of thermodynamics
497     - growth.F and groatb.F are replaced by new routine seaice_growth.F
498     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
499     - move a few global fields out of SEAICE.h into seaice_growth.F and
500       make them 2D (FICE/QNETO/ ...)
501     - remove FO (it is the same as QNETO)
502     - introduce a few local fields to avoid modifying external fields such
503       as atemp, etc.
504    
505    checkpoint58s_post
506    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
507      changed exf_set_gen.F so that
508        genperiod=0 means input file is one time-constant field and
509        genperiod=-12 means input file contains 12 monthly means
510    o CG2D: use pre-computed solver main-diagonal (stored in common block);
511      this affects truncation error ; generate new output file for exp. which
512      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
513        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
514        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
515        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
516        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
517        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
518    o start implementation of deep-atmosphere and anelastic formulation
519    o verification: remove 2nd copy of input files and use script "prepare_run"
520      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
521    o mom_common/vecinv/fluxform: fix a few initialisation isssues
522    o profiles: fix for multithreaded case
523    
524    o diagnostics: rename few diags:
525      s/'PRESSURE'/'RCENTER '/g
526      s/'TICE    '/'oceFreez'/g
527      s/'TAUX    '/'oceTAUX '/g
528      s/'TAUY    '/'oceTAUY '/g
529      s/'SWFLUX  '/'oceQsw  '/g
530      s/DIFx/DFxE/g
531      s/DIFy/DFyE/g
532      and add few ocean-forcing diagnostics:
533      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
534    o modifications to pkg/seaice/growth.F and budget.F, which change results of
535      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
536      as actual snow thickness.  It now refers everywhere to effective snow
537      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
538    
539    checkpoint58r_post
540    o modifications to pkg/seaice/growth.F, which change results of
541      lab_sea experiment: fixes pertain to melting snow over open water, to
542      masking EVAP under sea ice, and to using the correct AREA variable for
543      computations of EVAP, PRECIP, HSNOW, and GHEFF
544    o add ability to read bathy, salt, and theta using MNC (off by def)
545    o add flooding algorithm and advection of HSNOW for pkg/seaice;
546      both are turned off by default and do no change any results
547    o seaice advection with pkg/thsice: a step toward the use of non-linear
548      advection scheme, but #ifdef or commented out for now (requires more EXCH).
549    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
550      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
551      in natl_box (affects results @ truncation level: update output.txt)
552    o multi-threading and IO:
553      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
554      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
555        (needed to work with SingleCpuIO): tested in all verif. exp.
556    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
557      affects the results (but none of the verification test uses this scheme).
558    o Adding some pkg/diagnostics capability to pkg/seaice
559      (will certainly be subject to changes)
560    o ctrl: adding new control variables:
561      lwflux, lwdown, evap, snowprecip, apressure, runoff
562    
563    checkpoint58q_post
564    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
565      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
566      high_res_cube configuration by 4% on Columbia.
567    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
568      add (in global_with_exf/code) a version of EXF_INTERP_READ without
569      dynamical allocation (seems to work in multi-threaded).
570    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
571      single CPU io) so that TAF does not have to see EESUPPORT.h
572    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
573    
574    checkpoint58p_post
575    o obcs: stop if obcs is used with useCDscheme = .true.
576    o shelfice:
577     - fix a sign error so that no slip at shelfice interface works
578     - remove stop for combination non-hydrostatic code and shelfice. That does
579       not mean, that the results are correct, but at least they are numerically
580       stable
581    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
582    o added adjoint exch routined for all exch*3d* routines
583      and updated flow directives
584    
585    checkpoint58o_post
586    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
587      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
588    o change controling S/R for writing pickup file (new S/R do_write_pickup)
589      and clean-up reading/writing of pickup files.
590    o fix local version of read/write pickup (NH part) in rotating_tank/code
591    o simplify EXCH interface:
592     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
593     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
594    o added the regrid package
595    o shelfice:
596     - add a simple boundary layer scheme to reduce noise
597     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
598    
599    checkpoint58n_post
600    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
601       local variable (not in common block).
602    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
603      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
604      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
605        to work with SingleCpuIO.
606    o add "_d 0" to real constant of pkg/cfc subroutines ;
607       update exp. cfc_exemple & tutorial_cfc_offline output files.
608    o multi-threading and IO:
609      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
610        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
611      - barrier before and after reading.
612      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
613      - avoid using MDS_WRITELOCAL for LAND pkg output.
614      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
615        common-block variables ; Allows multi-threading with master-thread IO.
616    o change default MAX_NO_THREADS from 32 to 4 ;
617      and stop cleanly when MAX_NO_THREADS is too small.
618    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
619    
620    checkpoint58m_post
621    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
622       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
623    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
624       keep global_ocean.90x40x15 (for AD testing) with former secondary test
625       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
626    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
627        add MITgcm_tutorials (= code + all the tutorials)
628    o ecco, option to compute cost for total ssh (mean+anom)
629    o consistent with addition of ptracer and ssh in pkg/profiles
630    o profiles: adding ptracer and ssh
631    o testreport: change multi-test output-file name
632      (from output.txt.{name} to output.{name}.txt)
633    o profiles: now ok for mutli-tiles case
634    o seaice: add 4 parameters for different advection schemes for area,
635      (effective) seaice thickness, enthalphy, and snow height. Their default
636      is the standard parameter SEAICEadvScheme
637    o calc_gw:
638     - add cosFacU in zonal viscous flux (harmonic.visc.).
639     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
640       of tutorial_plume_on_slope.
641    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
642    o calc_gw: true flux-form, account for horizontal grid spacing.
643      update rotating_tank results, but not plume_on_slope (affected at
644      truncation level, 11 digits).
645    
646    checkpoint58l_post
647    o calc_gw:
648     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
649     - remove side-drag for now (need to fix it); update plume_on_slope results.
650     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
651    o commit code to make SST/SSS weights spatially variable
652      (based on either variable in-situ or variable initial T/S weights)
653    o pkg/ecco:
654      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
655        now based on horizontally varying weights wthetaLev, wsaltLev
656      * cost_averagesflags now returns year indices in addition to day, month
657      * sflux balance is performed on annual basis
658        (sflxumm, sfluxmm2, bal_sfluxmm)
659      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
660        including separate counting and multipliers
661    o pkg/rbcs
662      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
663    
664    checkpoint58k_post
665    o testreport:
666     - always build in dir. "build" (if not there, mkdir build instead of building
667       & running in input)
668     - run in dir run (if it exists), in build otherwise.
669     - call prepare_run (if input/prepare_run exists)
670     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
671    o pkg/exf modifications to interpolation and rotation routines for more
672       reasonable treatment of North Pole singularity: for tracers North Pole
673       value is set to northernmost zonal-mean value, for zonal velocity it is
674       set to zero, and for meridional velocity it is set to northernmost value.
675    o pkg/exf/exf_check_range.F
676     - add tile index to diagnostics and move stop statement to the very
677       end of the routine.
678    o pkg/diagnostics: (diagnostics_main_init.F)
679      define title of isomorphic variables according to the current config.
680    o pkg/thsice with pkg/seaice dynamics:
681    - fix domain of computation (interior only, required for exf) and do exchanges
682    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
683    o towards a standard way of dealing with multi-threading in MONITOR
684      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
685    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
686       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
687    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
688    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
689    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
690       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
691    o tracer advection:
692     - clean-up and simplify calc_common_factors.F
693     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
694       advection subroutine (but still not used within DST advection S/R)
695    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
696    
697    checkpoint58j_post
698    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
699      from file (collects calls previously in FORWARD_STEP)
700    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
701    o adjoint store dir. adjusted accordingly
702    o genmake2
703      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
704    
705    checkpoint58i_post
706    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
707      on wind stress (SEAICEstressFactor defaults to 1.)
708    o Total number of Timers is finite (<=40): comment out 2 non-essential one
709      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
710    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
711      on CS-grid: no longer loosing mass.
712    o exf & curvilinear-grid: no longer modify longitude xC & xG.
713    o pkg/ggl90: fix sloppy output and fix a bug
714    o pkg/seaice: added SEAICEuseEVPpickup parameter
715      - Set to false in order to start EVP solver with
716        non-EVP pickup files when using SEAICEuseEVP
717      - fix sign error in diffusion in seaice_calc_rhs
718    
719    checkpoint58h_post
720    * Modifications for bottom topography control
721      o replace hFacC by _hFacC at various places
722      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
723      o add non-self-adjoint cg2d_nsa
724      o update autodiff support routines
725      o re-initialise hfac after ctrl_depth_ini
726      o works for 5x5 box, doesnt work for global_ocean.90x40x15
727    * Adding verification for 5x5 box (4-layer) bottom topography control
728    
729    checkpoint58g_post
730    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
731       used for mean seasonal cycle, mean diurnal cycle); add an example
732       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
733    o pkg/ggl90:
734      - add parameter (minimum surface kinetic energy)
735      - fix bug (avoiding division by zero)
736    o couple pkg/thsice to pkg/seaice:
737      - modify advection in seaice to accomodate new scalar fields to be advected
738      - only muliDimAdection scheme work with seaice/thsice
739      - mapping of thsice-variables to seaice-variables, back and forth
740      - does not break the verification experiments, but does not give the
741        desired results either
742    o pkg/seaice
743      - make (default) second order advection a bit less confusing?
744    
745    checkpoint58f_post
746    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
747      to pkg/seaice):
748      - new routines thsice_map_exf and thsice_get_exf provide the interface
749      - add an additional formal parameter to thsice_solve4temp
750    o pkg/exf:
751      - add new fields wspeed, snowprecip (to be able to couple to thsice)
752      - correct Stefan-Boltzmann constant
753      - new parameter for longwave surface emittance
754      - separate some stuff from exf_bulkformulae into new routines  
755        exf_radiation, exf_wind
756      - add new parameters and constants: longwave emissivity for ocean, ice
757        and snow, evaporation parameters over ice
758      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
759        either wind from stress or stress from wind
760    o pkg/thSIce:
761    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
762    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
763       and THSICE_CALC_THICKN
764    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
765    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
766      to make debugging easier.
767    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
768    o pkg/bulk_force:
769      - clean-up comments and parameters ;
770      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
771    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
772      generate new output for test-experiment: aim.5l_cs.thSI
773    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
774      testreport accordingly
775    
776    checkpoint58e_post
777    o SEAICE_CGRID adjoint done
778    o R_STAR adjoint implemented.
779      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
780      * need to sort out init. of h0facc, etc.
781    o Make pkg/profile fully independent of ecco,cost, etc. stuff
782      to be able to use it in pure forward.
783    
784    checkpoint58d_post
785    o upgrade simple test-experiment to tutorial example:
786     step.1: duplicate the experiment and (step.2) will remove the old copy.
787      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
788      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
789      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
790      tutorial_global_oce_biogeo    <- copy of dic_example
791      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
792      tutorial_plume_on_slope       <- copy of plume_on_slope
793      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
794      tutorial_global_oce_optim     <- empty for now (David ?)
795      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
796     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
797    o correct a sign problem in cost_scat.F
798    o obcs and ptracers: fix boundary conditions for advections schemes
799      with larger stencil
800    o thsice adjoint: start
801    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
802      completeness
803    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
804      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
805    o ptracers adjoint:
806      * avoid extensive recomputatations
807      * fix missing re-init. of gptr (missed by TAF)
808    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
809      me to turn off the excessive output to STDOUT that this package produces
810    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
811      and add those terms in Vector-Invariant formulation.
812    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
813      if the control period (xx_hfluxperiod etc) is 0
814    o in profiles pkg, clean routines and fix details
815    o in ecco pkg, reading ssh data:
816      fix problem in case the model does not start at iter0=0
817    o fix mnc-pickup/restart for ptracers
818    o new package prifiles:
819      code to compute profile-based cost by Gael Forget
820      (modifs in ecco, ctrl, autodiff)
821    o Benign bug fix in initialization (spotted by M. Mazloff) of
822      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
823    
824    checkpoint58c_post
825    o adjoint: finish NLFS adjoint and provide reference output in
826      verification/global_ocean.90x40x15/results_ad_nlfs
827    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
828      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
829      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
830      with SEAICE_CGRID defined.
831    o move calendarDumps from "data" to "data.cal" and clean-up the code
832      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
833    o add useEXF & useCAL flags (for now, set in hard-coded way)
834    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
835      (were missing in NH mode, and wrong in quasihydrostatic mode).
836      waiting for Chris updated version of calc_gw to add those CALLs.
837    o fix bug in quasihydrostatic S/R ;
838      add a test for this option: global_ocean.90x40x15.qshyd
839    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
840      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
841    o add on/off flag useOffLine for package OFFLINE
842    o seaice:
843      - modify advection so that it works also on the C-grid
844      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
845        problem in multi-tile runs with C-grid
846      - add flags for clipping ice velocities and/or masking solver forcing
847      - fix drag (ocean on ice) formulation and a bug that caused noise in the
848        C-grid solver
849      - added a few comments to seaice_diffusion.F
850      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
851        are now exclusive)
852      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
853        required re-ordering the code a little:
854       + make DAIRN global variable (defined in SEAICE)
855       + move computation of the viscosities eta and zeta into a new separate
856         routine (because I need to recompute them in seaice_ocean_stress.F)
857    
858    checkpoint58b_post
859    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
860      update output.txt of exp. aim.5l_cs.thSI
861    o various mnc cleanups and improvements:
862      + shrink lookup tables by factor of ~4
863      + better error reporting when running out of lookup space
864      + able to handle longer path/file names (up to 500 chars)
865    o adjoint:
866      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
867      - TBD: "hidden" mom_vecinv recomp. in dynamics
868    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
869     (allow to differentiate between forcing components using new integer flags:
870      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
871     and add new flag to put Dissipation tendency out of Adams-Bashforth.
872    o ecco
873      - enable trend removal from SSH anomaly obs.
874    o adjoint
875      - a fix for PmEpR when #undef EXACT_CONSERV
876      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
877      - try to fix "hidden" recomp. in forward_step for NLFS
878        (NLFS seems broken sometimes after I checked it in)
879    o seaice:
880     - add c-grid version of the dynamic solver:
881       + three new routines that are the c-grid substitute lsr, dynsolver
882         and ostres
883       + put a few fields that were local to dynsolver into global common
884         blocks, so that I can move the computation of stresses etc into
885         seaice_lsr (saves coding but may break the adjoint).
886     - replace more hardwired parameters by runtime parameters
887     - add ice masks that mask the rhs of the implicit solvers where there
888       is no ice (commented out in seaice_dynsolver, because i am not sure
889       if this works properly), eventually this should replace the clipping
890       of ice velocities in seaice_dynsolver to +/-40cm/s.
891    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
892      include it only where its needed
893    o move balancing of fluxes before the call of external_forcing_surf
894    o seaice:
895      - correct units of turning angles (now they are really in degrees)
896      - move computation of GWATX/Y out of main routine into dynsolver
897      - initialize GWATX/Y in seaice_init
898    o Apply mask on Fresh-Water flux (needed for SSH forcing).
899      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
900    o seaice: add runtime flags for turning angles (default to zero)
901    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
902      and trend from exf forcing and ctrl control adjustments
903    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
904      (since checkpoint57x_post)
905    o change the default rotation period to 86164.s = the Earth rotation
906    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
907      and based on a reference stratification. Tested within hs94.cs-32x32x5.
908    o seaice advection: add code for choosing between the default (2nd order
909      central differences) and multiDim advection schemes provided by
910      pkg/generic_advdiff
911    o seaice:
912      - removed all references to SEAICE_GRID.h fields from
913        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
914        (cubed-sphere configuration will change a little)
915      - grid computations in seaice_init are obsolete now.
916      - cleaned up code a little so that is easier to read (hopefully).
917      - added new (better?) discretizations of default advection and diffusion
918        (turn on with SEAICEuseFluxForm)
919      - replace 1 in 3d global fields by kSurface in growth.F
920      
921    checkpoint58a_post
922    o seaice:
923      - bug fix in advect.F
924    o shelfice:
925      - separate shelfice load anomaly from pload (breaks with time
926        dependent forcing), => introduce constant field shelficeLoadAnomaly.
927        Its default is 0., but it may be computed more cleverly from (unknown)
928        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
929        done offline. A good approximation of the pressure load anomaly is
930        necessary to avoid large initial adjustment processes underneath
931        deep-reaching shelfice.
932      - small fix in ISOMIP shelfice_thermodynamics
933      - add more sophisticated thermodynamics of Hellmer (1989), this is
934        now the default
935      - give a few constants more intuitive names
936    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
937      if bulk formulae are used in long integration (especially EmPmR). Turn
938      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
939      if balancePrintMean, the imbalance that is substracted is printed to
940      STDOUT.
941    o fix bug (typo) in obcs_apply_eta.F
942    o add a new package shelfice which enables us to model the circulation
943      underneath shelf-ice with draughts of hundreds of meters.
944     - works
945     - to do: + include improved thermodynamics
946              + check whether kSurfC (from model/inc/SURFACE.h) can be used
947                instead of new field kTopC
948              + can we use topoFile, Ro_surf and existing code in ini_depth.F
949                instead of new field R_shelfIce and new code in ini_depth.F
950                and ini_mask_etc.F?
951              + adjust vertical mixing schemes?
952    o seaice pkg:
953     - add a cpp-flag to include a simple formula for a salinity dependent
954       freezing point of sea water at the surface
955     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
956       meridional stresses are now different (and hopefully correct)
957    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
958       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
959       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
960    o pkg/diagnostics: add options and parameters for regional-statistics
961       diagnostics ; define regions by reading a region-mask from a file
962       (might add other options later)
963    o pkg/bulk_force:
964     - add option and parameters to use AIM surface-flux formulae.
965     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
966       others forcing fields (defined in PARM05, parameter file "data") are loaded
967       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
968     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
969     - use the right EXCH call for uwind,vwind (to work on CS-grid).
970     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
971       and parameters (note: calcWindStress replaces .NOT.readwindstress).
972     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
973    
974    checkpoint58
975    o add "--embed-source" option to genmake2 which, when the supporting
976      tools can be compiled (as determined by genmake2) will turn on the
977      embed_files package which then embeds the entire MITgcm source code
978      (*.[fFhc] + Makefile) used for the build within the executable
979      - requested by CNH but off by default
980      - adds a paltry <9MB to the mitgcmuv executable in most cases
981      - only writes the output when useEMBEDSRC in eedata is true
982    o clean up 3-dim. relaxation codes:
983      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
984      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
985      * Thanks to Tom Haine for testing!
986    
987    checkpoint57z_post
988    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
989      affects output (@ truncation level) of exp. plume_on_slope ; updated.
990    o fix the pickup behavior for obcs in combination with ptracers
991    o fix a bug in ptracers_external_fields_load
992    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
993      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
994    o transfered surface NH pressure to eta field (if exactConserv).
995    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
996         and update lab_sea output.txt file.
997    o completing 3-dim. relaxation code: additional term
998         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
999      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
1000      * At compile time, in "EXF_OPTIONS.h" set
1001          #define  ALLOW_CLIMTEMP_RELAXATION
1002          #define  ALLOW_CLIMSALT_RELAXATION
1003      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
1004          tauThetaClimRelax3Dim = 15552000.0,
1005          tauSaltClimRelax3Dim  = 15552000.0,
1006      * 3 cases:
1007          1) Use a constant-in-time 3-dim. field
1008          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
1009          3) Real-time relax. to time-evolving prescribed field
1010    o Adding Laplacian-type smoothness constraint on
1011      initial and boundary (forcing) controls (ic, bc)
1012      * enable at compile-time via
1013        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
1014      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
1015      * Absolute scale somewhat unclear so far
1016      * no area weighting was included since no other cost term does so far
1017    
1018    checkpoint57y_post
1019    First step for a NLFS adjoint
1020    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
1021    o new init. routines for calc_r_star, calc_surf_dr
1022    o still need to deal with ini_masks_etc
1023    o testreport seemed happy
1024    checkpoint57y_pre
1025    
1026    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
1027    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
1028    o add new offset feature to offline pkg (plus minor cleanup)
1029    o cfc fixes for final year of integration
1030    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
1031      be in GCHEM_OPTIONS).
1032    
1033    checkpoint57x_post
1034    o fix testreport Pb in multiple test experiment.
1035    o cleanup our namelist syntax in verification:
1036      - make it more F95 standards compliant (some work still needed)
1037      - allows the vast majority of our tests to work with gfortran
1038    o Non-Hydrostatic:
1039     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
1040     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
1041    o Allow to apply AB on T,S rather than on AB(gT,gS):
1042     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
1043     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
1044       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
1045     - need a "clever" read_pickup to restart from the other AB formulation
1046    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
1047    o remove some unused variables (reduces number of compiler warnings)
1048    o adjoint
1049      * Disable useVariableViscosity for adjoint for time being
1050        (there are a number of extensive recomputations)
1051      * Initialize certain variables needed for adjoint
1052    
1053    checkpoint57w_post
1054    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
1055                 fix the singleCpuIO RS version of MDSWRITEFIELD
1056       and add a WARNING if using globalFiles=T with multi-processors.
1057    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
1058      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
1059    o tracer advection scheme:
1060      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
1061       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
1062       was not very convenient).
1063      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
1064       (further tests needed for the implicit DST & Flux-Limiter schemes).
1065    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
1066      and sRef for convenience, handy, when you want to initialize
1067      ptracers in a large domain with a constant non-zero value. Also,
1068      untangle ptracers_init.F a little.
1069    
1070    checkpoint57v_post
1071    o change dome exp. to use variable viscosity in side-drag terms.
1072    o remove all the files from the cfc_offline test since they are now
1073      incorporated into tutorial_cfc_offline which has been producing
1074      identical results for a few days of testing
1075    o add new parameter: sideDragFactor to enable half-slip-side BC
1076      and change side-drag S/R to use viscosity from mom_calc_visc
1077      (can switch back by setting sideDragFactor=0.); affects results at
1078      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
1079       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
1080    o vorticity & strain are now computed without masking, to account for
1081      no-slip-side BC in variable viscosity calculation ; mask is applied
1082      anyway later on, before computing advection/coriolis terms.
1083    o modify exp4 to test new obcs support for reading from external files
1084      and for passive tracers
1085    o fix behavior of ptracers_monitor when monitor output is written to a
1086      netcdf-file; still not independent of monitor.F (writes in the same
1087      file).
1088    o change default value of tRef (put a uniform, meaningful value for ocean
1089      & atmos) and initialize sRef (was missing, as Martin mentioned).
1090    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
1091      to be proportional to enstrophy dissipation length.  Thus,
1092       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
1093      This is now consistent with Smagorinsky and with the manual.
1094    
1095    checkpoint57u_post
1096    o OBCS and PTRACERS: add open boundary support for passive tracers
1097      - either use homogenous (pseudo) v.Neumann conditions or prescribe
1098        OB-values from file; this is not different from the way theta and salinity
1099        are treated
1100      - however, Orlanski-radiation conditions are not supported, and the model
1101        will stop if you use pTracers and Orlanski at the same time.
1102      - beefed up the rountine obcs_external_fields_load: now only those open
1103        boundary values are overwritten with values from files for which there
1104        are really files, otherwise the OB-fields remain untouched. This makes
1105        it possible to use different OBs at different ends of the domain (as
1106        with EXF)
1107    o reduce number of exch calls in shap_filt (s2).
1108    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1109      truncation level) 4/5 MLAdjust test results (11&12 digits match).
1110    
1111    checkpoint57t_post
1112    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1113    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1114      same truncation, independent of the face number: affects affects several
1115      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1116    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1117      note that biharmonic viscosity + no-slip was not tested in any experiment.
1118    o fix bug in non-linear free-surf side-drag ; generate new output for
1119      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1120    o make mnc honor the writeBinaryPrec flag for most kinds of output
1121    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1122    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1123      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1124    o add brackets in multi-terms sum to get same truncation, independent of
1125      the face number (manage to get exactly same value of gU,gV at the cs-edge)
1126      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1127    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
1128      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1129      a maximum grid-scale Reynolds number.  Also, changes all length calculations
1130      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1131      Suggested values of viscosity parameters found in mom_calc_visc.
1132      Many new viscosity diagnostics available.
1133    
1134    checkpoint57s_post
1135    o Add clearing-house for viscosity calculations, mom_calc_visc and
1136      correct numerous bugs in LeithD and Smagorinsky discretizations.  
1137      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1138      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1139      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1140      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
1141      The Strain-Tension form is now called with useStrainTensonVisc=.true.
1142      ViscAhStrain and viscAhTension are now retired.
1143    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1144    o In response to JMC's bug report, genmake2 now ignores any soft-links
1145      that it finds in the *current* directory when searching for files.
1146      Soft-links found in any other source directories will still work as
1147      they did before.
1148    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1149      a C routine to unlimit the stack size
1150    o mnc-ify pkg/aim snapshot vars
1151    o mnc-ify pkg/land as requested by Daniel
1152    o various changes to mnc including:
1153      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1154      - output can now be grouped so that all files within a group
1155          change the ITER portion of their names in lock-step together
1156      - can now read ("global") PER-FACE (in addition to PER-TILE) files
1157          and works with both EXCH1 and EXCH2 (but needs more testing)
1158      - writing works for all verification test cases w/ g77 on Linux
1159    
1160    checkpoint57r_post
1161    o make MNC variable initialization happen earlier
1162    o add diagnostics for (almost) each term of the momentum Eq.
1163    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1164    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1165    o remove MINIMAL_TAVE_OUTPUT option ;
1166      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1167    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1168      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1169    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1170    o add time-dependent SST, SSS control
1171    o cost terms in ecco/ modularized (new cost_generic.F)
1172    o cost_averages routines are modularized (new cost_averagesgeneric.F)
1173    o new infrastructure for seaice model vs. obs misfits in seaice/
1174      * driver from the_main_loop.F is seaice_cost_driver.F
1175      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1176      * gradient check in Exp. 6a of natl_box_adjoint/
1177    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1178      (see README file)
1179    
1180    checkpoint57q_post
1181    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1182    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1183      - bug was reported by Jean-Michel and Ian Fenty
1184    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1185      update exp. cpl_aim+ocn output.
1186    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1187      Needed for high-res. runs with large global files
1188      to be able to limit tapelev size
1189    o Changed some tests for adjoint:
1190      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1191      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1192      * global_ocean.90x40x15/ back to default 3-level checkpointing
1193    o Modifications to enable scripted COMMON to MODULE conversion
1194      * verification/OpenAD/code/ has necessary scripts and description;
1195      * converts, compiles and runs successfully;
1196    
1197    checkpoint57p_post
1198    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1199    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1200      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1201    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1202    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1203      (was already the case for dissipation with mom_vecinv,
1204       and also the case for grad.PhiHyd when staggered-timeStep)
1205      This will allow to put dissipation out-off the AB time-stepping.
1206     Unfortunately, affects truncation error. Update output of exp. that "fails"
1207      (cg2d matching number) and leave the others for later: front_relax(10),
1208      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1209      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1210    
1211    checkpoint57o_post
1212    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1213      (2) its ready to be documented during the 20050801 DocFest
1214    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1215      for ideal_2D_oce and lab_sea on linux_ia32_g77
1216    o set to #undef CTRL_SET_OLD_MAXCVARS_30
1217      in global1x1_tot/code_seaice_adj to access indices 32, 33
1218      (worth another tag)
1219    
1220    checkpoint57n_post
1221    o adding precip control xx_precip 32
1222    o adding swflux control xx_swflux 33
1223    o Replacing 10 forcing penalty cost routines by 1 generic.
1224    o Implementing partitioning in time-mean and variable adjustment
1225      for atmos. state.
1226    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1227  o in natl_box_adjoint:  o in natl_box_adjoint:
1228    * updated: results_bulk/    * updated exp 1 to 10
1229    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
1230    o updated global1x1/*_seaice_adj/
1231      to incorporate latest changes
1232    o enable useSingleCpuIO for mdsio vector routines
1233      (applies in particular to tapelev I/O)
1234    o removed inefficient K-loop in all active_file*control*.F
1235    
1236  checkpoint57m_post  checkpoint57m_post
1237  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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