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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.927 by dimitri, Tue Dec 18 05:34:41 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  checkpoint59l
8  o moved ptracer ctrl index 17 -> 32  o pkg/salt_plume: added various options for salt plume depth
9      criterion and for vertical distribution of the salt
10    o pkg/ptracers: new version of ptracers pickup:
11      read meta file and write only fields which are needed to restart.
12      ( same logic as main pickup file ; also using pickupStrictlyMatch )
13    o pkg/seaice:
14      - add timescale for melting due to warm mixed layer as a means of
15        setting SEAICE_availHeatFrac more conveniently
16      - add a CPP-flag/runtime parameter check for flooding algorithm
17      - reformulated availHeat in seaice_growth.F to be independent of AREA
18    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
19      unit changes
20    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
21    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
22      SX vector computer.
23    o pkg/seaice:
24      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
25        seaice forcing fields can now be read only through pkg/exf
26      - removed some unused halos
27    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
28    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
29      or U/VICE from U/VWIND before computing U/VSTRESS
30    
31    checkpoint59k
32    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
33      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
34    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
35      all experiments pass when compile with un-initialised var. checking option.
36    o added pkg/salt_plume
37    o script to test restart (for now, in MITgcm_contrib/jmc_script)
38    o pkg/seaice: new read/write pickup version.
39      read meta file and write only fields which are needed to restart.
40      ( same logic as main pickup file ; also using pickupStrictlyMatch )
41    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
42    o lab_sea.hb87: modify the domain & update output.hb87.txt :
43      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
44      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
45      process. Fixed here by closing the domain at the Northern boundary.
46    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
47    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
48      a set of consecutive levels in/from a 3-D array.
49    o pkg/ptracers:
50      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
51      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
52    
53    checkpoint59j
54    o in pkgs: dic, obcs, offline, rbcs:
55      standard way to compute coeff. for time interpolation between 2 time reccords
56      which retains full precision (& make results less dependent on compiler).
57      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
58    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
59      packages instead of reading ice cover and wind speed separately
60    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
61     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
62      to allow to compile customized code before the update)
63    o cleaning-up:
64      - fix CPP instruction syntax in pkg/obcs
65      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
66        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
67      - fix some threads issue in IO parts.
68    o pkg/dic:
69      - add tons of "_d 0" (--> much better testreports !)
70       and then update outputs of tutorial_global_oce_biogeo
71    o pkg/mom_fluxform:
72      add a special version of momentum advection intended to conserve momentum
73      next to a bathymetry step or a coastline edge. (default = off = #undef)
74    o new read/write pickup version:
75      - for now, only implemented for main (mdsio) pickup file.
76      - write out only what is needed to restart; merge pickup_nh , pickup_ph
77        and main pickup together.
78      - read meta file; read only what is needed to restart; stop if a field
79        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
80        if it make sense (even if the restart is not perfect).
81      - if no meta file, assume that pickup to read corresponds exactly to
82        a pickup that would currently be written.
83      - read pickup written in the old format (until checkpoint59i) if it
84        recognizes an old meta file (no field-list).
85      - add a meta file in exp. which starts from a pickup: 2 cases:
86        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
87         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
88        b) a meta file describing the content of the associated pickup file
89         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
90    o pkg/mdsio & pkg/rw:
91      - new routine to read a meta file ; new set of routine to read
92        Multiple-fields file (with meta file).
93    o added open boundary conditions capability for seaice
94        HSNOW, HSALT, UICE, and VICE
95    
96    checkpoint59i
97    o adjoint:
98      * fix multiDimAdvection adjoint
99        (partial recomputation problem by TAF for fVerT(:,:,kDown)
100        and comlev1 size definition (maxpass vs. max. number of tracers)
101      * verification/global_ocean.90x45x15 adjoint now tests
102        NLFS and multiDimAdvection using DST3 (=30)
103      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
104    o pkg/kpp: add "_d 0" to real constant (if missing);
105      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
106      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
107    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
108      for internal parameters related to restart process (formerly from PARAMS.h)
109      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
110    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
111      as argument. (only atm2d & obcs write_pickup have not yet been updated)
112    o pkg/monitor:
113      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
114      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
115      - account for deep Atmosphere factor and density factor (anelastic)
116    o added open boundary conditions capability for seaice HEFF and AREA
117    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
118      thermodynamics
119      - requires a little reorganization, which affects the testreport results
120        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
121        so that now the conservative form is tested
122      - add a few comments
123    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
124    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
125    o add new diagnostics to seaice: advective, diffusive fluxes (only for
126      multidim-advection, for scheme 2 they are not filled) and transports,
127      thermodynamic growth rates
128    o change units of EmPmR (inside the code, + within coupling interface)
129      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
130      Affects results @ truncation level (cg2d match) and update output of
131       experiments: lab_sea(6), global_ocean.90x40x15(10),
132      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
133      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
134      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
135      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
136    
137    checkpoint59h
138    o pkg/exf:
139      - improve vectorization by moving if-statement out of loops in
140        exf_mapfields, exf_radiation
141      - exf_bulkformulae.F: introduce 2D fields and vectorize code
142    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
143    o testreport:
144      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
145        monitor & update offline_exf_seaice exp. output.
146      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
147    o pkg/seaice:
148      - bug fix in the evp solver: boundary conditions were affected be
149        masking of zMax/zMin (changes results)
150      - minor bug fix in boundary conditions in seaice_calc_strainrates
151        (changes results for no_slip)
152      - seaice_lsr.F: make interpolation of eta dependent on boundaries
153      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
154      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
155        stress formulation and no-slip boundary conditions
156    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
157      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
158    o pkg/seaice: a first HSALT time stepping equation has been checked in
159    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
160      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
161      without requiring DO-IF statements
162    o pkg/thsice:
163      use continuous power-law function for partition of energy between lateral
164      melting/freezing and thinning/thickening ; old code using step function
165      still available with #undef THSICE_FRACEN_POWERLAW
166      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
167    o testreport: change AD testing : check against results/output_adm.txt
168      using same scripts as for forward test.
169    
170    checkpoint59g
171    o adjoint testing: in preparation for changing testreport:
172      - output format: cost and grad written on separated lines
173      - ad output results in directory "results" (instead of "results_ad")
174    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
175    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
176    o pkg/ecco: allow user defined cost function contributions
177    o testreport:
178      Allow to choose (per experiment) the list of tested output variables
179       and the main variable (used to issue a pass/FAIL ) ;
180      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
181      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
182      Also modify printing of summary:
183       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
184       b) echo the list of tested variables in the individual summary.txt of
185          each experiment.
186    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
187      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
188      (but still depend on the tile decompostion of the domain).
189    o pkg/seaice: change a discretization detail to make the B-grid code
190      "more symmetric". This change is likely to remove all "ridges/leads" that
191      where quasi-aligned with the grid in B-grid solutions. It may also be
192      the solution to the stress coupling issues with the B-grid.
193    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
194      remove .cvsignore from input dir. (since testreport no longer run here).
195    o pkg/thsice:
196     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
197     - fix reshaping of sea-ice just after advection:
198       melt all the ice only if ice-volume is too small.
199     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
200       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
201     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
202    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
203      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
204    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
205      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
206      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
207      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
208      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
209      -> update output.txt
210    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
211     this affects truncation error: -> update output.txt of exp:
212      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
213      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
214    
215    checkpoint59f
216    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
217    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
218      a bounded range (in forward mode)
219    o pkg/ecco, ctrl, autodiff and mom_common:
220     internal parameter controls, completements of implementations
221    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
222    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
223      (not seem any difference in testing results).
224    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
225       at face corners.
226    o pkg/generic_advdiff:
227     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
228      loop range indices for computing vertical advection tendency
229      and do the calculation in the interior only (no overlap) ;
230      for now, only implemented for SOM advection (to save CPU time).
231     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
232    o exch2 adjoint
233      First set of changes:
234      - add exch2 hand-written adjoint templates
235      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
236        This will require cleanup in pkg/autodiff/*.F
237        (changed routines currently kept separate in verif. code/)
238      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
239        that used to hide exch2 or cubed-sphere specific code
240        (commented via 'cph-exch2')
241    o pkg/seaice
242      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
243    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
244       output of global_ocean.cs32x15.thsice .
245    
246    checkpoint59e
247    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
248      for B-grid vector (not yet tested) and C-grid vector (<- only used
249      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
250    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
251      (#ifdef ALLOW_SALT_PLUME)
252    o gather_2d/scatter_2d: removed halo regions
253    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
254      scheme and the corresponding test case (under front_relax dir). For now,
255      only available with Skew-flux form and not yet tested in realistic set-up.
256      adjoint: store directives updated, but gradient checks deteriorated,
257      so maybe GM/Redi adjoint is now broken.
258    o seaice adjoint
259      * add AREA, HEFF, HSNOW as control variable
260        (should not change lab_sea results)
261      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
262    o pkg/seaice:
263      * added computation of saltFlux in seaice_growth;
264        For time being, sea ice salinity is assumed constant
265        contribution of snow flooding to freshening of sea ice is neglected.
266        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
267        defaults to 0.0 in order to maintain backward compatibility.
268        Typical values for SEAICE_salinity are 4 to 10 g/kg.
269      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
270      * added SEAICE_availHeatFrac, which specifies fraction of surface level
271        heat content used to melt or grow ice
272      * commented out cap of HICE: it helps keep ice thinner
273      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
274      * applied OBCS T/S mask to HEFFM sea ice mask
275    
276    checkpoint59d
277    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
278     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
279     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
280    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
281     and change default value of parameter "GM_Small_Number";
282     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
283       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
284       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
285    o pkg/ecco: cost function when applying pkg/smooth to controls
286    o pkg/ctrl: add forcingPrecond run time parameter
287    o pkg/seaice:
288     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
289     - fix bug in metric terms of u-equation in LSR solver (implicit part),
290       changes verification/lab_sea
291     - rearrange implicit part of u-equation in LSR solver to make it easier to
292       read, understand, and debug. This causes changes at the truncation level.
293     - fix (serious) bug in the boundary conditions (sign error in the implicit
294       part) of the LSR solver. Changes all LSR results.
295     - fixed problem with HSNOW initialization to avoid thick snow when AREA
296       is initilized with small values - does not change lab_sea results.
297     - added HsnowFile initialization capability
298    o pkg/smooth: addition to model/src and pkg/ctrl so allow
299     initialization of pkg/smooth and application to control vector
300    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
301    o dependencies: pkg/profiles requires pkg/cal
302    o pkg/profiles:
303     - added option ALLOW_PROFILES_GENERICGRID
304         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
305         that interpolation information (grid points and coefficients) is provided
306         within the netcdf input files.
307         -> sample matlab scripts can be found in MITgcm_contrib/gael
308         that allow you to prepare netcdf input files.
309     - also modified: cleaner include statements, cleaner error print statements,
310       cleaner stops when error, and more tests of the netcdf input files consistency.
311    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
312    o pkg/seaice:
313     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
314       requires a new routine: seaice_diagnostics_fill.F
315     - make sure that seaice does not move if not forced (pressure replacement
316       method, Hibler and Ip, 1995), changes results
317     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
318     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
319       It is turned off by default (=-1.), because it changes the results.
320     - make it possible to read AREA from a file, too.
321    
322    checkpoint59c
323    o add S/R and diagnostics for oceanic mixed-layer depth
324    o move GMRedi call after all vertical mixing schemes (including KPP)
325    o pkg/thsice:
326     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
327      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
328    o pkg/obcs:
329     - bug fix for balance code
330    o pkg/seaice:
331      - allow values of SEAICE_elasticParm > 1
332      - add new parameter SEAICE_evpTauRelax as an alternative
333        to SEAICE_elasticParm
334      - make lsr boundary conditions free slip (by default), changes result
335      - add code for no slip boundary conditions for lsr
336      - set minimum of zeta to zero (and not 4e8) (changes results)
337      - add a cap on AREA after advecting AREA if seaice_growth is not called
338    o change calculation of Visbeck K:
339      - no longer depend on tapering scheme; instead, compute slope (limited
340        by GM_maxSlope). this is equivalent to what was comuted before with
341        clipping or linear tappering.
342      - fix vertical averaging (wrong by 1/2 level)
343      - leave the old version (but will not be maintained) within
344        #ifdef OLD_VISBECK_CALC / #endif
345      - update output of exp. ideal_2D_oce
346    o change error catch in calc_r_star to improve vectorization
347    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
348      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
349    o adjoint:
350      Re-organized adjoint checkpointing according to Matt Mazloff
351      (but with modifs/completions/cleanups)
352      Storing is now bundled into large arrays to optimized I/O
353      (and second step in cleanup of the_main_loop)
354    
355    checkpoint59b
356    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
357      - export/import (between ocean & coupler) fields needed for ocean DIC.
358    o pkg/seaice:
359      - get rid of three more exchanges seaice_calc_viscosities (required
360        different loop boundaries in seaice_lsr and seaice_ocean_stress)
361      - bug fix in seaice_ocean_stress (update of lab_sea required)
362      - reduce loop boundaries to necessary minimum also in seaice_evp
363      - go back to the old way of computing deltaC/Z as the adjoint likes that
364        better
365    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
366      passive tracer to an Age Tracer) + update output.txt
367    o pkg/exf:
368      - implement A-grid / C-grid selection for wind-stress input files.
369      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
370      for now, in exf_bulk_largeyeager04.F only :
371      - change implementation for case where windspeed + 2. components wind-stress
372        are read-in. AND use rhoConstFresh to convert evap.
373    o pkg/seaice:
374      - use correct EXCH_UV for wind-forcing (on A-grid).
375      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
376        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
377    o pkg/exf:
378      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
379      EXF_INTERPOLATION:
380      - merge global_with_exf/code version of exf_interp_read.F
381        to the main code ;
382      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
383        reading the file ; Important: This options needs to be defined to recover
384        previous code.
385        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
386      - no longer loose real*8 precision along the way when using exf_iprec=64.
387    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
388      - change discretisation of evp-solver in order to avoid another exchange
389        (changes lab_sea) and clean up a little
390      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
391        help the adjoint (this also changes the results slightly)
392      - add a few "_d 0" where they had been missing in seaice_evp.F
393      - cleaning up: remove unused seaice_calc_rhs.F
394    o pkg/exf: some cleaning-up:
395      - change various "constants" into runtime parameters
396      - cleaned-up Large&Yeager04 routine which should eventually
397        replace exf_bulkformulae.F (changed names of S/R and CPP)
398        and merged various ALLOW_ATM_WIND options
399     only used with thsice pkg (in thsice_get_exf.F):
400      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
401        which are used when useStabilityFct_overIce=TRUE (= the default)
402      - change default values of ice & snow emissivity and scale downward LW
403        by ice & snow emissivity.
404    o pkg/thsice:
405     fix few little problems, in thsice_calc_thickn.F:
406      - growth vertically (and not laterally) if iceFrac == iceMaskMax
407      - melt only laterally if hIce < hThinIce (as the comments say)
408      and in thsice_extend.F:
409      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
410      - start to form ice as soon as the minimum ice-volume is reachable.
411     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
412      and cpl_aim+ocn
413    o pkg/kpp
414     - move computation of surface related input fields to KPP into a new
415       subroutine kpp_forcing_surf.F
416     - remove wrong (within bi,bj loops) EXCH calls.
417     - little cleaning (add argument myThid in last position, cvs header ...)
418     - for now, fix conservation problem by exchanging KPPviscAz (may not
419       be the best fix)
420    o pkg/seaice
421     - check for inconsistent evp parameter/cpp-flag combination
422     - remove leftover errIO flat for obsolete name list error handling
423    o OpenAD
424     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
425    
426    checkpoint59a
427    o pkg/seaice: some parameter clarifications and a little bit of clean up
428    o pkg/thsice: rename run-time parameters:
429       himin       -> hIceMin
430       himin0      -> hThinIce
431       hihig       -> hThickIce
432       i0          -> i0swFrac
433       transCoef   -> bMeltCoef
434       frac_energy -> fracMelting
435      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
436       with default values (for now) that do not change the results.
437      remove old version of thsice vars advection in pkg/seaice.
438    o in FFIELDS.h:
439      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
440      - make pLoad & sIceLoad always available (but still only used if
441         ATMOSPHERIC_LOADING is #define).
442    o pkg/kpp: replaced _KPP_RL with _RL
443    o bug fixes for vertical diffusivity computations when both KPP and
444        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
445        are no longer updating the vertical diffusivity array
446        (passed as argument) but are (re-) setting those arrays.
447    o pkg/seaice: fix bug in evp solver, while doing that
448      - change (improve?) discretization of stress computations for both
449        cgrid-lsr and evp solver
450      - add a new routine to compute strain rates
451      - the above changes lab_sea results
452      - add no slip conditions for evp solver (off by default), lsr-version
453        may follow
454      - fix exchange for shear at Z-points (does not change lab_sea)
455      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
456        (to force the user to pick a time step since there is not "safe" way
457        of choosing it)
458      - add principal stress diagnostics
459      - rearrange fields for evp a little to avoid having to call a: too many
460        exchanges and b: exchanges for stress trensor components which we do
461        not have.
462      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
463        of evp, complete rewrite for lsr case (latter is does not yet work
464        in all cases)
465    o pkg/kpp: add code to have mixing in shelf ice caverns
466      - add myThid to all kpp routines (long overdue)
467    
468    checkpoint59
469    o pkg/exf:
470      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
471        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
472      - move exf header files from lower_case.h to UPPER_CASE.h ;
473        add missing cvs Header & Name
474      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
475      - add namelist param. selectStressGridPosition, exf_monFreq
476      - retire many _CLIM routines, and remove data.exf_clim
477        + params moved to data.exf
478        + climsst, climsss now handled by exf_set_gen, i.e.
479          climss?period=0 refers to constant field,
480          climss?period=-12 to monthly forcing
481      - split up namelists in data.exf
482    o pkg/seaice:
483      - remove seaice_exch and seaice_exch_uv
484      - remove superfluous exchange of theta
485      - add myThid to seaice_budget_ocean/ice
486      - add new interface for atmospheric wind forcing (C-grid only)
487        + new routine
488        + two new field (taux, tauy for stress over ice)
489        + removed one global field (DAIRN) for C-grid case only
490    o pkg/thsise
491      - 2nd set of modifs for thsice adjoint in conjunction with exf
492    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
493    
494    checkpoint58y_post
495    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
496      vertical diffusivity, similar to that in MOM4; turned on using
497      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
498      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
499    o Added capability for 3D specification of background vertical diffusion
500      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
501      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
502      "data" file that contains the 3D vertical diffusivity coefficients.
503    o ice dynamics (pkg/seaice) with thsice thermodynamics:
504      - add code within pkg thsice to advect & diffuse sea-ice fields
505      similar to (and will replace) what has been added in  seaice_advdiff.F,
506      but: - conserving Mass, Heat & Salt.
507           - better when using non-linear advection scheme (not yet fully tested)
508           - can also be used in atmospheric set-up (for now, only the diffusion).
509    
510    checkpoint58x_post
511    o IO option for global-file compact format:
512      - add options when generating topology (utils/exch2/matlab-topology-generator)
513      - add I/O capability (pkg/mdsio).
514      - adapt utils/matlab/rdmds.m to read this format.
515      for now long-line format not yet supported by pkg/mdsio (& exch2).
516    o shelfice: add a few diagnostics
517    
518    checkpoint58w_post
519    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
520      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
521      (and replace horiVertRatio in NH code).
522      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
523                         and tutorial_plume_on_slope (sensitive to truncation)
524    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
525      directly to drive seaice model (C-grid only)
526    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
527     - reintroduce computation of wind from stress,
528     - compute tau (in exf_bulkformulae.F) from windstress averaged to
529       mass points to avoid tau = 0
530     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
531    o rdmnc.m: make it work with "global" files created with gluemnc
532    o rdmnc.m : some improvements in dealing with singleton dimension
533      (tested on all testreport mnc output files).
534    o genmake2: disable pkg/profiles if netcdf test fails.
535    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
536    o move call to cal_readparms up to make calendar parameters/variable available
537      to all packages
538    
539    checkpoint58v_post
540    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
541      useDynP_inEos_Zc tested.
542    o pkg/exf: changes to properly interpolate/mask/scale initial fields
543    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
544      and portions thereof.  See read_cs.txt for description and examples.
545    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
546      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
547      following the great-circle arc between those 2 points.
548    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
549      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
550    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
551     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
552     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
553     - still needs work (not working with some options ; efficiency to improve)
554       and serious testing.
555     - use this scheme for temperature & salinity in 2 advection test exp.:
556       advect_xy & advect_xz, respectively.
557    
558    checkpoint58u_post
559    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
560    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
561    o testreport: add option "-skipdir" to skip some test.
562    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
563      momentum calculation.
564    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
565    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
566      remove checkpoint.F and the_correction_step.F (no longer used);
567      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
568    o add option (linFSConserveTr) to correct for tracer source/sink due to
569      Linear Free surface
570    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
571    o pkg/thsice: fix reading mnc-pickups
572    
573    checkpoint58t_post
574    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
575    o pkg/mdsio:
576     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
577       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
578       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
579     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
580     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
581       either MDS_READ_FIELD or MDS_WRITE_FIELD )
582     - new S/R (to replace MDSWRITEMETA), which allows to write more
583       informations (variable names, time ...) to meta files.
584     - modify rdmds.m to give back the meta file content.
585    o pkg/diagnostics: change vertical interpolation to be safer, and more
586       flexible (define p-levels to interpolate to in data.diagnostics);
587      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
588       diagnostic pointer.
589    o pkg/seaice: more cleaning up of seaice_growth, added many comments
590    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
591    o fix multi-category seaice:
592     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
593       SEAICE_MULTICATEGORY
594     - fix short wave heat flux
595    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
596       and allow to use EVP solver. Change forward lab_sea: test both EVP
597       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
598    o Initial check-in of lab_sea adjoint
599      (very similar to natl_box_adjoint/code_seaice)
600      * used C-grid and EVP solver
601      * used KPP, GM/Redi
602      * uses inAdExact=.TRUE.
603      * gradient checks fail for both ADM and TLM
604        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
605        f.d. gradients actually seem more problematic than ADM, TLM gradients;
606        issue is related to forward mismatch between g77 an ifort
607    o pkg/seaice: overhaul of thermodynamics
608     - growth.F and groatb.F are replaced by new routine seaice_growth.F
609     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
610     - move a few global fields out of SEAICE.h into seaice_growth.F and
611       make them 2D (FICE/QNETO/ ...)
612     - remove FO (it is the same as QNETO)
613     - introduce a few local fields to avoid modifying external fields such
614       as atemp, etc.
615    
616    checkpoint58s_post
617    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
618      changed exf_set_gen.F so that
619        genperiod=0 means input file is one time-constant field and
620        genperiod=-12 means input file contains 12 monthly means
621    o CG2D: use pre-computed solver main-diagonal (stored in common block);
622      this affects truncation error ; generate new output file for exp. which
623      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
624        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
625        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
626        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
627        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
628        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
629    o start implementation of deep-atmosphere and anelastic formulation
630    o verification: remove 2nd copy of input files and use script "prepare_run"
631      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
632    o mom_common/vecinv/fluxform: fix a few initialisation isssues
633    o profiles: fix for multithreaded case
634    
635    o diagnostics: rename few diags:
636      s/'PRESSURE'/'RCENTER '/g
637      s/'TICE    '/'oceFreez'/g
638      s/'TAUX    '/'oceTAUX '/g
639      s/'TAUY    '/'oceTAUY '/g
640      s/'SWFLUX  '/'oceQsw  '/g
641      s/DIFx/DFxE/g
642      s/DIFy/DFyE/g
643      and add few ocean-forcing diagnostics:
644      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
645    o modifications to pkg/seaice/growth.F and budget.F, which change results of
646      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
647      as actual snow thickness.  It now refers everywhere to effective snow
648      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
649    
650    checkpoint58r_post
651    o modifications to pkg/seaice/growth.F, which change results of
652      lab_sea experiment: fixes pertain to melting snow over open water, to
653      masking EVAP under sea ice, and to using the correct AREA variable for
654      computations of EVAP, PRECIP, HSNOW, and GHEFF
655    o add ability to read bathy, salt, and theta using MNC (off by def)
656    o add flooding algorithm and advection of HSNOW for pkg/seaice;
657      both are turned off by default and do no change any results
658    o seaice advection with pkg/thsice: a step toward the use of non-linear
659      advection scheme, but #ifdef or commented out for now (requires more EXCH).
660    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
661      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
662      in natl_box (affects results @ truncation level: update output.txt)
663    o multi-threading and IO:
664      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
665      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
666        (needed to work with SingleCpuIO): tested in all verif. exp.
667    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
668      affects the results (but none of the verification test uses this scheme).
669    o Adding some pkg/diagnostics capability to pkg/seaice
670      (will certainly be subject to changes)
671    o ctrl: adding new control variables:
672      lwflux, lwdown, evap, snowprecip, apressure, runoff
673    
674    checkpoint58q_post
675    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
676      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
677      high_res_cube configuration by 4% on Columbia.
678    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
679      add (in global_with_exf/code) a version of EXF_INTERP_READ without
680      dynamical allocation (seems to work in multi-threaded).
681    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
682      single CPU io) so that TAF does not have to see EESUPPORT.h
683    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
684    
685    checkpoint58p_post
686    o obcs: stop if obcs is used with useCDscheme = .true.
687    o shelfice:
688     - fix a sign error so that no slip at shelfice interface works
689     - remove stop for combination non-hydrostatic code and shelfice. That does
690       not mean, that the results are correct, but at least they are numerically
691       stable
692    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
693    o added adjoint exch routined for all exch*3d* routines
694      and updated flow directives
695    
696    checkpoint58o_post
697    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
698      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
699    o change controling S/R for writing pickup file (new S/R do_write_pickup)
700      and clean-up reading/writing of pickup files.
701    o fix local version of read/write pickup (NH part) in rotating_tank/code
702    o simplify EXCH interface:
703     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
704     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
705    o added the regrid package
706    o shelfice:
707     - add a simple boundary layer scheme to reduce noise
708     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
709    
710    checkpoint58n_post
711    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
712       local variable (not in common block).
713    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
714      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
715      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
716        to work with SingleCpuIO.
717    o add "_d 0" to real constant of pkg/cfc subroutines ;
718       update exp. cfc_exemple & tutorial_cfc_offline output files.
719    o multi-threading and IO:
720      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
721        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
722      - barrier before and after reading.
723      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
724      - avoid using MDS_WRITELOCAL for LAND pkg output.
725      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
726        common-block variables ; Allows multi-threading with master-thread IO.
727    o change default MAX_NO_THREADS from 32 to 4 ;
728      and stop cleanly when MAX_NO_THREADS is too small.
729    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
730    
731    checkpoint58m_post
732    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
733       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
734    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
735       keep global_ocean.90x40x15 (for AD testing) with former secondary test
736       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
737    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
738        add MITgcm_tutorials (= code + all the tutorials)
739    o ecco, option to compute cost for total ssh (mean+anom)
740    o consistent with addition of ptracer and ssh in pkg/profiles
741    o profiles: adding ptracer and ssh
742    o testreport: change multi-test output-file name
743      (from output.txt.{name} to output.{name}.txt)
744    o profiles: now ok for mutli-tiles case
745    o seaice: add 4 parameters for different advection schemes for area,
746      (effective) seaice thickness, enthalphy, and snow height. Their default
747      is the standard parameter SEAICEadvScheme
748    o calc_gw:
749     - add cosFacU in zonal viscous flux (harmonic.visc.).
750     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
751       of tutorial_plume_on_slope.
752    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
753    o calc_gw: true flux-form, account for horizontal grid spacing.
754      update rotating_tank results, but not plume_on_slope (affected at
755      truncation level, 11 digits).
756    
757    checkpoint58l_post
758    o calc_gw:
759     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
760     - remove side-drag for now (need to fix it); update plume_on_slope results.
761     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
762    o commit code to make SST/SSS weights spatially variable
763      (based on either variable in-situ or variable initial T/S weights)
764    o pkg/ecco:
765      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
766        now based on horizontally varying weights wthetaLev, wsaltLev
767      * cost_averagesflags now returns year indices in addition to day, month
768      * sflux balance is performed on annual basis
769        (sflxumm, sfluxmm2, bal_sfluxmm)
770      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
771        including separate counting and multipliers
772    o pkg/rbcs
773      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
774    
775    checkpoint58k_post
776    o testreport:
777     - always build in dir. "build" (if not there, mkdir build instead of building
778       & running in input)
779     - run in dir run (if it exists), in build otherwise.
780     - call prepare_run (if input/prepare_run exists)
781     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
782    o pkg/exf modifications to interpolation and rotation routines for more
783       reasonable treatment of North Pole singularity: for tracers North Pole
784       value is set to northernmost zonal-mean value, for zonal velocity it is
785       set to zero, and for meridional velocity it is set to northernmost value.
786    o pkg/exf/exf_check_range.F
787     - add tile index to diagnostics and move stop statement to the very
788       end of the routine.
789    o pkg/diagnostics: (diagnostics_main_init.F)
790      define title of isomorphic variables according to the current config.
791    o pkg/thsice with pkg/seaice dynamics:
792    - fix domain of computation (interior only, required for exf) and do exchanges
793    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
794    o towards a standard way of dealing with multi-threading in MONITOR
795      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
796    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
797       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
798    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
799    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
800    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
801       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
802    o tracer advection:
803     - clean-up and simplify calc_common_factors.F
804     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
805       advection subroutine (but still not used within DST advection S/R)
806    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
807    
808    checkpoint58j_post
809    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
810      from file (collects calls previously in FORWARD_STEP)
811    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
812    o adjoint store dir. adjusted accordingly
813    o genmake2
814      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
815    
816    checkpoint58i_post
817    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
818      on wind stress (SEAICEstressFactor defaults to 1.)
819    o Total number of Timers is finite (<=40): comment out 2 non-essential one
820      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
821    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
822      on CS-grid: no longer loosing mass.
823    o exf & curvilinear-grid: no longer modify longitude xC & xG.
824    o pkg/ggl90: fix sloppy output and fix a bug
825    o pkg/seaice: added SEAICEuseEVPpickup parameter
826      - Set to false in order to start EVP solver with
827        non-EVP pickup files when using SEAICEuseEVP
828      - fix sign error in diffusion in seaice_calc_rhs
829    
830    checkpoint58h_post
831    * Modifications for bottom topography control
832      o replace hFacC by _hFacC at various places
833      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
834      o add non-self-adjoint cg2d_nsa
835      o update autodiff support routines
836      o re-initialise hfac after ctrl_depth_ini
837      o works for 5x5 box, doesnt work for global_ocean.90x40x15
838    * Adding verification for 5x5 box (4-layer) bottom topography control
839    
840    checkpoint58g_post
841    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
842       used for mean seasonal cycle, mean diurnal cycle); add an example
843       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
844    o pkg/ggl90:
845      - add parameter (minimum surface kinetic energy)
846      - fix bug (avoiding division by zero)
847    o couple pkg/thsice to pkg/seaice:
848      - modify advection in seaice to accomodate new scalar fields to be advected
849      - only muliDimAdection scheme work with seaice/thsice
850      - mapping of thsice-variables to seaice-variables, back and forth
851      - does not break the verification experiments, but does not give the
852        desired results either
853    o pkg/seaice
854      - make (default) second order advection a bit less confusing?
855    
856    checkpoint58f_post
857    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
858      to pkg/seaice):
859      - new routines thsice_map_exf and thsice_get_exf provide the interface
860      - add an additional formal parameter to thsice_solve4temp
861    o pkg/exf:
862      - add new fields wspeed, snowprecip (to be able to couple to thsice)
863      - correct Stefan-Boltzmann constant
864      - new parameter for longwave surface emittance
865      - separate some stuff from exf_bulkformulae into new routines  
866        exf_radiation, exf_wind
867      - add new parameters and constants: longwave emissivity for ocean, ice
868        and snow, evaporation parameters over ice
869      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
870        either wind from stress or stress from wind
871    o pkg/thSIce:
872    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
873    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
874       and THSICE_CALC_THICKN
875    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
876    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
877      to make debugging easier.
878    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
879    o pkg/bulk_force:
880      - clean-up comments and parameters ;
881      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
882    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
883      generate new output for test-experiment: aim.5l_cs.thSI
884    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
885      testreport accordingly
886    
887    checkpoint58e_post
888    o SEAICE_CGRID adjoint done
889    o R_STAR adjoint implemented.
890      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
891      * need to sort out init. of h0facc, etc.
892    o Make pkg/profile fully independent of ecco,cost, etc. stuff
893      to be able to use it in pure forward.
894    
895    checkpoint58d_post
896    o upgrade simple test-experiment to tutorial example:
897     step.1: duplicate the experiment and (step.2) will remove the old copy.
898      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
899      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
900      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
901      tutorial_global_oce_biogeo    <- copy of dic_example
902      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
903      tutorial_plume_on_slope       <- copy of plume_on_slope
904      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
905      tutorial_global_oce_optim     <- empty for now (David ?)
906      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
907     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
908    o correct a sign problem in cost_scat.F
909    o obcs and ptracers: fix boundary conditions for advections schemes
910      with larger stencil
911    o thsice adjoint: start
912    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
913      completeness
914    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
915      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
916    o ptracers adjoint:
917      * avoid extensive recomputatations
918      * fix missing re-init. of gptr (missed by TAF)
919    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
920      me to turn off the excessive output to STDOUT that this package produces
921    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
922      and add those terms in Vector-Invariant formulation.
923    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
924      if the control period (xx_hfluxperiod etc) is 0
925    o in profiles pkg, clean routines and fix details
926    o in ecco pkg, reading ssh data:
927      fix problem in case the model does not start at iter0=0
928    o fix mnc-pickup/restart for ptracers
929    o new package prifiles:
930      code to compute profile-based cost by Gael Forget
931      (modifs in ecco, ctrl, autodiff)
932    o Benign bug fix in initialization (spotted by M. Mazloff) of
933      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
934    
935    checkpoint58c_post
936    o adjoint: finish NLFS adjoint and provide reference output in
937      verification/global_ocean.90x40x15/results_ad_nlfs
938    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
939      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
940      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
941      with SEAICE_CGRID defined.
942    o move calendarDumps from "data" to "data.cal" and clean-up the code
943      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
944    o add useEXF & useCAL flags (for now, set in hard-coded way)
945    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
946      (were missing in NH mode, and wrong in quasihydrostatic mode).
947      waiting for Chris updated version of calc_gw to add those CALLs.
948    o fix bug in quasihydrostatic S/R ;
949      add a test for this option: global_ocean.90x40x15.qshyd
950    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
951      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
952    o add on/off flag useOffLine for package OFFLINE
953    o seaice:
954      - modify advection so that it works also on the C-grid
955      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
956        problem in multi-tile runs with C-grid
957      - add flags for clipping ice velocities and/or masking solver forcing
958      - fix drag (ocean on ice) formulation and a bug that caused noise in the
959        C-grid solver
960      - added a few comments to seaice_diffusion.F
961      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
962        are now exclusive)
963      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
964        required re-ordering the code a little:
965       + make DAIRN global variable (defined in SEAICE)
966       + move computation of the viscosities eta and zeta into a new separate
967         routine (because I need to recompute them in seaice_ocean_stress.F)
968    
969    checkpoint58b_post
970    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
971      update output.txt of exp. aim.5l_cs.thSI
972    o various mnc cleanups and improvements:
973      + shrink lookup tables by factor of ~4
974      + better error reporting when running out of lookup space
975      + able to handle longer path/file names (up to 500 chars)
976    o adjoint:
977      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
978      - TBD: "hidden" mom_vecinv recomp. in dynamics
979    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
980     (allow to differentiate between forcing components using new integer flags:
981      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
982     and add new flag to put Dissipation tendency out of Adams-Bashforth.
983    o ecco
984      - enable trend removal from SSH anomaly obs.
985    o adjoint
986      - a fix for PmEpR when #undef EXACT_CONSERV
987      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
988      - try to fix "hidden" recomp. in forward_step for NLFS
989        (NLFS seems broken sometimes after I checked it in)
990    o seaice:
991     - add c-grid version of the dynamic solver:
992       + three new routines that are the c-grid substitute lsr, dynsolver
993         and ostres
994       + put a few fields that were local to dynsolver into global common
995         blocks, so that I can move the computation of stresses etc into
996         seaice_lsr (saves coding but may break the adjoint).
997     - replace more hardwired parameters by runtime parameters
998     - add ice masks that mask the rhs of the implicit solvers where there
999       is no ice (commented out in seaice_dynsolver, because i am not sure
1000       if this works properly), eventually this should replace the clipping
1001       of ice velocities in seaice_dynsolver to +/-40cm/s.
1002    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
1003      include it only where its needed
1004    o move balancing of fluxes before the call of external_forcing_surf
1005    o seaice:
1006      - correct units of turning angles (now they are really in degrees)
1007      - move computation of GWATX/Y out of main routine into dynsolver
1008      - initialize GWATX/Y in seaice_init
1009    o Apply mask on Fresh-Water flux (needed for SSH forcing).
1010      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
1011    o seaice: add runtime flags for turning angles (default to zero)
1012    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
1013      and trend from exf forcing and ctrl control adjustments
1014    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
1015      (since checkpoint57x_post)
1016    o change the default rotation period to 86164.s = the Earth rotation
1017    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
1018      and based on a reference stratification. Tested within hs94.cs-32x32x5.
1019    o seaice advection: add code for choosing between the default (2nd order
1020      central differences) and multiDim advection schemes provided by
1021      pkg/generic_advdiff
1022    o seaice:
1023      - removed all references to SEAICE_GRID.h fields from
1024        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
1025        (cubed-sphere configuration will change a little)
1026      - grid computations in seaice_init are obsolete now.
1027      - cleaned up code a little so that is easier to read (hopefully).
1028      - added new (better?) discretizations of default advection and diffusion
1029        (turn on with SEAICEuseFluxForm)
1030      - replace 1 in 3d global fields by kSurface in growth.F
1031      
1032    checkpoint58a_post
1033    o seaice:
1034      - bug fix in advect.F
1035    o shelfice:
1036      - separate shelfice load anomaly from pload (breaks with time
1037        dependent forcing), => introduce constant field shelficeLoadAnomaly.
1038        Its default is 0., but it may be computed more cleverly from (unknown)
1039        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
1040        done offline. A good approximation of the pressure load anomaly is
1041        necessary to avoid large initial adjustment processes underneath
1042        deep-reaching shelfice.
1043      - small fix in ISOMIP shelfice_thermodynamics
1044      - add more sophisticated thermodynamics of Hellmer (1989), this is
1045        now the default
1046      - give a few constants more intuitive names
1047    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
1048      if bulk formulae are used in long integration (especially EmPmR). Turn
1049      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
1050      if balancePrintMean, the imbalance that is substracted is printed to
1051      STDOUT.
1052    o fix bug (typo) in obcs_apply_eta.F
1053    o add a new package shelfice which enables us to model the circulation
1054      underneath shelf-ice with draughts of hundreds of meters.
1055     - works
1056     - to do: + include improved thermodynamics
1057              + check whether kSurfC (from model/inc/SURFACE.h) can be used
1058                instead of new field kTopC
1059              + can we use topoFile, Ro_surf and existing code in ini_depth.F
1060                instead of new field R_shelfIce and new code in ini_depth.F
1061                and ini_mask_etc.F?
1062              + adjust vertical mixing schemes?
1063    o seaice pkg:
1064     - add a cpp-flag to include a simple formula for a salinity dependent
1065       freezing point of sea water at the surface
1066     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
1067       meridional stresses are now different (and hopefully correct)
1068    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
1069       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
1070       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
1071    o pkg/diagnostics: add options and parameters for regional-statistics
1072       diagnostics ; define regions by reading a region-mask from a file
1073       (might add other options later)
1074    o pkg/bulk_force:
1075     - add option and parameters to use AIM surface-flux formulae.
1076     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
1077       others forcing fields (defined in PARM05, parameter file "data") are loaded
1078       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
1079     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
1080     - use the right EXCH call for uwind,vwind (to work on CS-grid).
1081     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
1082       and parameters (note: calcWindStress replaces .NOT.readwindstress).
1083     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
1084    
1085    checkpoint58
1086    o add "--embed-source" option to genmake2 which, when the supporting
1087      tools can be compiled (as determined by genmake2) will turn on the
1088      embed_files package which then embeds the entire MITgcm source code
1089      (*.[fFhc] + Makefile) used for the build within the executable
1090      - requested by CNH but off by default
1091      - adds a paltry <9MB to the mitgcmuv executable in most cases
1092      - only writes the output when useEMBEDSRC in eedata is true
1093    o clean up 3-dim. relaxation codes:
1094      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
1095      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
1096      * Thanks to Tom Haine for testing!
1097    
1098    checkpoint57z_post
1099    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
1100      affects output (@ truncation level) of exp. plume_on_slope ; updated.
1101    o fix the pickup behavior for obcs in combination with ptracers
1102    o fix a bug in ptracers_external_fields_load
1103    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
1104      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
1105    o transfered surface NH pressure to eta field (if exactConserv).
1106    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
1107         and update lab_sea output.txt file.
1108    o completing 3-dim. relaxation code: additional term
1109         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
1110      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
1111      * At compile time, in "EXF_OPTIONS.h" set
1112          #define  ALLOW_CLIMTEMP_RELAXATION
1113          #define  ALLOW_CLIMSALT_RELAXATION
1114      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
1115          tauThetaClimRelax3Dim = 15552000.0,
1116          tauSaltClimRelax3Dim  = 15552000.0,
1117      * 3 cases:
1118          1) Use a constant-in-time 3-dim. field
1119          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
1120          3) Real-time relax. to time-evolving prescribed field
1121    o Adding Laplacian-type smoothness constraint on
1122      initial and boundary (forcing) controls (ic, bc)
1123      * enable at compile-time via
1124        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
1125      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
1126      * Absolute scale somewhat unclear so far
1127      * no area weighting was included since no other cost term does so far
1128    
1129    checkpoint57y_post
1130    First step for a NLFS adjoint
1131    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
1132    o new init. routines for calc_r_star, calc_surf_dr
1133    o still need to deal with ini_masks_etc
1134    o testreport seemed happy
1135    checkpoint57y_pre
1136    
1137    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
1138    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
1139    o add new offset feature to offline pkg (plus minor cleanup)
1140    o cfc fixes for final year of integration
1141    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
1142      be in GCHEM_OPTIONS).
1143    
1144    checkpoint57x_post
1145    o fix testreport Pb in multiple test experiment.
1146    o cleanup our namelist syntax in verification:
1147      - make it more F95 standards compliant (some work still needed)
1148      - allows the vast majority of our tests to work with gfortran
1149    o Non-Hydrostatic:
1150     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
1151     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
1152    o Allow to apply AB on T,S rather than on AB(gT,gS):
1153     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
1154     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
1155       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
1156     - need a "clever" read_pickup to restart from the other AB formulation
1157    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
1158    o remove some unused variables (reduces number of compiler warnings)
1159    o adjoint
1160      * Disable useVariableViscosity for adjoint for time being
1161        (there are a number of extensive recomputations)
1162      * Initialize certain variables needed for adjoint
1163    
1164    checkpoint57w_post
1165    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
1166                 fix the singleCpuIO RS version of MDSWRITEFIELD
1167       and add a WARNING if using globalFiles=T with multi-processors.
1168    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
1169      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
1170    o tracer advection scheme:
1171      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
1172       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
1173       was not very convenient).
1174      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
1175       (further tests needed for the implicit DST & Flux-Limiter schemes).
1176    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
1177      and sRef for convenience, handy, when you want to initialize
1178      ptracers in a large domain with a constant non-zero value. Also,
1179      untangle ptracers_init.F a little.
1180    
1181    checkpoint57v_post
1182    o change dome exp. to use variable viscosity in side-drag terms.
1183    o remove all the files from the cfc_offline test since they are now
1184      incorporated into tutorial_cfc_offline which has been producing
1185      identical results for a few days of testing
1186    o add new parameter: sideDragFactor to enable half-slip-side BC
1187      and change side-drag S/R to use viscosity from mom_calc_visc
1188      (can switch back by setting sideDragFactor=0.); affects results at
1189      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
1190       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
1191    o vorticity & strain are now computed without masking, to account for
1192      no-slip-side BC in variable viscosity calculation ; mask is applied
1193      anyway later on, before computing advection/coriolis terms.
1194    o modify exp4 to test new obcs support for reading from external files
1195      and for passive tracers
1196    o fix behavior of ptracers_monitor when monitor output is written to a
1197      netcdf-file; still not independent of monitor.F (writes in the same
1198      file).
1199    o change default value of tRef (put a uniform, meaningful value for ocean
1200      & atmos) and initialize sRef (was missing, as Martin mentioned).
1201    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
1202      to be proportional to enstrophy dissipation length.  Thus,
1203       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
1204      This is now consistent with Smagorinsky and with the manual.
1205    
1206    checkpoint57u_post
1207    o OBCS and PTRACERS: add open boundary support for passive tracers
1208      - either use homogenous (pseudo) v.Neumann conditions or prescribe
1209        OB-values from file; this is not different from the way theta and salinity
1210        are treated
1211      - however, Orlanski-radiation conditions are not supported, and the model
1212        will stop if you use pTracers and Orlanski at the same time.
1213      - beefed up the rountine obcs_external_fields_load: now only those open
1214        boundary values are overwritten with values from files for which there
1215        are really files, otherwise the OB-fields remain untouched. This makes
1216        it possible to use different OBs at different ends of the domain (as
1217        with EXF)
1218    o reduce number of exch calls in shap_filt (s2).
1219    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1220      truncation level) 4/5 MLAdjust test results (11&12 digits match).
1221    
1222    checkpoint57t_post
1223    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1224    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1225      same truncation, independent of the face number: affects affects several
1226      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1227    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1228      note that biharmonic viscosity + no-slip was not tested in any experiment.
1229    o fix bug in non-linear free-surf side-drag ; generate new output for
1230      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1231    o make mnc honor the writeBinaryPrec flag for most kinds of output
1232    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1233    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1234      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1235    o add brackets in multi-terms sum to get same truncation, independent of
1236      the face number (manage to get exactly same value of gU,gV at the cs-edge)
1237      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1238    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
1239      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1240      a maximum grid-scale Reynolds number.  Also, changes all length calculations
1241      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1242      Suggested values of viscosity parameters found in mom_calc_visc.
1243      Many new viscosity diagnostics available.
1244    
1245    checkpoint57s_post
1246    o Add clearing-house for viscosity calculations, mom_calc_visc and
1247      correct numerous bugs in LeithD and Smagorinsky discretizations.  
1248      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1249      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1250      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1251      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
1252      The Strain-Tension form is now called with useStrainTensonVisc=.true.
1253      ViscAhStrain and viscAhTension are now retired.
1254    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1255    o In response to JMC's bug report, genmake2 now ignores any soft-links
1256      that it finds in the *current* directory when searching for files.
1257      Soft-links found in any other source directories will still work as
1258      they did before.
1259    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1260      a C routine to unlimit the stack size
1261    o mnc-ify pkg/aim snapshot vars
1262    o mnc-ify pkg/land as requested by Daniel
1263    o various changes to mnc including:
1264      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1265      - output can now be grouped so that all files within a group
1266          change the ITER portion of their names in lock-step together
1267      - can now read ("global") PER-FACE (in addition to PER-TILE) files
1268          and works with both EXCH1 and EXCH2 (but needs more testing)
1269      - writing works for all verification test cases w/ g77 on Linux
1270    
1271    checkpoint57r_post
1272    o make MNC variable initialization happen earlier
1273    o add diagnostics for (almost) each term of the momentum Eq.
1274    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1275    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1276    o remove MINIMAL_TAVE_OUTPUT option ;
1277      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1278    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1279      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1280    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1281    o add time-dependent SST, SSS control
1282    o cost terms in ecco/ modularized (new cost_generic.F)
1283    o cost_averages routines are modularized (new cost_averagesgeneric.F)
1284    o new infrastructure for seaice model vs. obs misfits in seaice/
1285      * driver from the_main_loop.F is seaice_cost_driver.F
1286      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1287      * gradient check in Exp. 6a of natl_box_adjoint/
1288    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1289      (see README file)
1290    
1291    checkpoint57q_post
1292    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1293    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1294      - bug was reported by Jean-Michel and Ian Fenty
1295    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1296      update exp. cpl_aim+ocn output.
1297    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1298      Needed for high-res. runs with large global files
1299      to be able to limit tapelev size
1300    o Changed some tests for adjoint:
1301      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1302      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1303      * global_ocean.90x40x15/ back to default 3-level checkpointing
1304    o Modifications to enable scripted COMMON to MODULE conversion
1305      * verification/OpenAD/code/ has necessary scripts and description;
1306      * converts, compiles and runs successfully;
1307    
1308    checkpoint57p_post
1309    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1310    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1311      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1312    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1313    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1314      (was already the case for dissipation with mom_vecinv,
1315       and also the case for grad.PhiHyd when staggered-timeStep)
1316      This will allow to put dissipation out-off the AB time-stepping.
1317     Unfortunately, affects truncation error. Update output of exp. that "fails"
1318      (cg2d matching number) and leave the others for later: front_relax(10),
1319      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1320      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1321    
1322    checkpoint57o_post
1323    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1324      (2) its ready to be documented during the 20050801 DocFest
1325    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1326      for ideal_2D_oce and lab_sea on linux_ia32_g77
1327    o set to #undef CTRL_SET_OLD_MAXCVARS_30
1328      in global1x1_tot/code_seaice_adj to access indices 32, 33
1329      (worth another tag)
1330    
1331    checkpoint57n_post
1332    o adding precip control xx_precip 32
1333    o adding swflux control xx_swflux 33
1334    o Replacing 10 forcing penalty cost routines by 1 generic.
1335    o Implementing partitioning in time-mean and variable adjustment
1336      for atmos. state.
1337    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1338  o in natl_box_adjoint:  o in natl_box_adjoint:
1339    * updated: results_bulk/    * updated exp 1 to 10
1340    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
1341    o updated global1x1/*_seaice_adj/
1342      to incorporate latest changes
1343    o enable useSingleCpuIO for mdsio vector routines
1344      (applies in particular to tapelev I/O)
1345    o removed inefficient K-loop in all active_file*control*.F
1346    
1347  checkpoint57m_post  checkpoint57m_post
1348  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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