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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.848 by dimitri, Fri Jul 6 02:37:34 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 gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
8  o moved ptracer ctrl index 17 -> 32    scheme and the corresponding test case (under front_relax dir). For now,
9      only available with Skew-flux form and not yet tested in realistic set-up.
10      adjoint: store directives updated, but gradient checks deteriorated,
11      so maybe GM/Redi adjoint is now broken.
12    o seaice adjoint
13      * add AREA, HEFF, HSNOW as control variable
14        (should not change lab_sea results)
15      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
16    o pkg/seaice:
17      * added computation of saltFlux in seaice_growth;
18        For time being, sea ice salinity is assumed constant
19        contribution of snow flooding to freshening of sea ice is neglected.
20        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
21        defaults to 0.0 in order to maintain backward compatibility.
22        Typical values for SEAICE_salinity are 4 to 10 g/kg.
23      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
24      * added SEAICE_availHeatFrac, which specifies fraction of surface level
25        heat content used to melt or grow ice
26    
27    checkpoint59d
28    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
29     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
30     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
31    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
32     and change default value of parameter "GM_Small_Number";
33     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
34       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
35       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
36    o pkg/ecco: cost function when applying pkg/smooth to controls
37    o pkg/ctrl: add forcingPrecond run time parameter
38    o pkg/seaice:
39     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
40     - fix bug in metric terms of u-equation in LSR solver (implicit part),
41       changes verification/lab_sea
42     - rearrange implicit part of u-equation in LSR solver to make it easier to
43       read, understand, and debug. This causes changes at the truncation level.
44     - fix (serious) bug in the boundary conditions (sign error in the implicit
45       part) of the LSR solver. Changes all LSR results.
46     - fixed problem with HSNOW initialization to avoid thick snow when AREA
47       is initilized with small values - does not change lab_sea results.
48     - added HsnowFile initialization capability
49    o pkg/smooth: addition to model/src and pkg/ctrl so allow
50     initialization of pkg/smooth and application to control vector
51    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
52    o dependencies: pkg/profiles requires pkg/cal
53    o pkg/profiles:
54     - added option ALLOW_PROFILES_GENERICGRID
55         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
56         that interpolation information (grid points and coefficients) is provided
57         within the netcdf input files.
58         -> sample matlab scripts can be found in MITgcm_contrib/gael
59         that allow you to prepare netcdf input files.
60     - also modified: cleaner include statements, cleaner error print statements,
61       cleaner stops when error, and more tests of the netcdf input files consistency.
62    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
63    o pkg/seaice:
64     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
65       requires a new routine: seaice_diagnostics_fill.F
66     - make sure that seaice does not move if not forced (pressure replacement
67       method, Hibler and Ip, 1995), changes results
68     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
69     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
70       It is turned off by default (=-1.), because it changes the results.
71     - make it possible to read AREA from a file, too.
72    
73    checkpoint59c
74    o add S/R and diagnostics for oceanic mixed-layer depth
75    o move GMRedi call after all vertical mixing schemes (including KPP)
76    o pkg/thsice:
77     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
78      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
79    o pkg/obcs:
80     - bug fix for balance code
81    o pkg/seaice:
82      - allow values of SEAICE_elasticParm > 1
83      - add new parameter SEAICE_evpTauRelax as an alternative
84        to SEAICE_elasticParm
85      - make lsr boundary conditions free slip (by default), changes result
86      - add code for no slip boundary conditions for lsr
87      - set minimum of zeta to zero (and not 4e8) (changes results)
88      - add a cap on AREA after advecting AREA if seaice_growth is not called
89    o change calculation of Visbeck K:
90      - no longer depend on tapering scheme; instead, compute slope (limited
91        by GM_maxSlope). this is equivalent to what was comuted before with
92        clipping or linear tappering.
93      - fix vertical averaging (wrong by 1/2 level)
94      - leave the old version (but will not be maintained) within
95        #ifdef OLD_VISBECK_CALC / #endif
96      - update output of exp. ideal_2D_oce
97    o change error catch in calc_r_star to improve vectorization
98    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
99      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
100    o adjoint:
101      Re-organized adjoint checkpointing according to Matt Mazloff
102      (but with modifs/completions/cleanups)
103      Storing is now bundled into large arrays to optimized I/O
104      (and second step in cleanup of the_main_loop)
105    
106    checkpoint59b
107    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
108      - export/import (between ocean & coupler) fields needed for ocean DIC.
109    o pkg/seaice:
110      - get rid of three more exchanges seaice_calc_viscosities (required
111        different loop boundaries in seaice_lsr and seaice_ocean_stress)
112      - bug fix in seaice_ocean_stress (update of lab_sea required)
113      - reduce loop boundaries to necessary minimum also in seaice_evp
114      - go back to the old way of computing deltaC/Z as the adjoint likes that
115        better
116    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
117      passive tracer to an Age Tracer) + update output.txt
118    o pkg/exf:
119      - implement A-grid / C-grid selection for wind-stress input files.
120      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
121      for now, in exf_bulk_largeyeager04.F only :
122      - change implementation for case where windspeed + 2. components wind-stress
123        are read-in. AND use rhoConstFresh to convert evap.
124    o pkg/seaice:
125      - use correct EXCH_UV for wind-forcing (on A-grid).
126      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
127        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
128    o pkg/exf:
129      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
130      EXF_INTERPOLATION:
131      - merge global_with_exf/code version of exf_interp_read.F
132        to the main code ;
133      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
134        reading the file ; Important: This options needs to be defined to recover
135        previous code.
136        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
137      - no longer loose real*8 precision along the way when using exf_iprec=64.
138    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
139      - change discretisation of evp-solver in order to avoid another exchange
140        (changes lab_sea) and clean up a little
141      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
142        help the adjoint (this also changes the results slightly)
143      - add a few "_d 0" where they had been missing in seaice_evp.F
144      - cleaning up: remove unused seaice_calc_rhs.F
145    o pkg/exf: some cleaning-up:
146      - change various "constants" into runtime parameters
147      - cleaned-up Large&Yeager04 routine which should eventually
148        replace exf_bulkformulae.F (changed names of S/R and CPP)
149        and merged various ALLOW_ATM_WIND options
150     only used with thsice pkg (in thsice_get_exf.F):
151      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
152        which are used when useStabilityFct_overIce=TRUE (= the default)
153      - change default values of ice & snow emissivity and scale downward LW
154        by ice & snow emissivity.
155    o pkg/thsice:
156     fix few little problems, in thsice_calc_thickn.F:
157      - growth vertically (and not laterally) if iceFrac == iceMaskMax
158      - melt only laterally if hIce < hThinIce (as the comments say)
159      and in thsice_extend.F:
160      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
161      - start to form ice as soon as the minimum ice-volume is reachable.
162     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
163      and cpl_aim+ocn
164    o pkg/kpp
165     - move computation of surface related input fields to KPP into a new
166       subroutine kpp_forcing_surf.F
167     - remove wrong (within bi,bj loops) EXCH calls.
168     - little cleaning (add argument myThid in last position, cvs header ...)
169     - for now, fix conservation problem by exchanging KPPviscAz (may not
170       be the best fix)
171    o pkg/seaice
172     - check for inconsistent evp parameter/cpp-flag combination
173     - remove leftover errIO flat for obsolete name list error handling
174    o OpenAD
175     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
176    
177    checkpoint59a
178    o pkg/seaice: some parameter clarifications and a little bit of clean up
179    o pkg/thsice: rename run-time parameters:
180       himin       -> hIceMin
181       himin0      -> hThinIce
182       hihig       -> hThickIce
183       i0          -> i0swFrac
184       transCoef   -> bMeltCoef
185       frac_energy -> fracMelting
186      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
187       with default values (for now) that do not change the results.
188      remove old version of thsice vars advection in pkg/seaice.
189    o in FFIELDS.h:
190      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
191      - make pLoad & sIceLoad always available (but still only used if
192         ATMOSPHERIC_LOADING is #define).
193    o pkg/kpp: replaced _KPP_RL with _RL
194    o bug fixes for vertical diffusivity computations when both KPP and
195        3D diffusivity arrays are used.
196    o pkg/seaice: fix bug in evp solver, while doing that
197      - change (improve?) discretization of stress computations for both
198        cgrid-lsr and evp solver
199      - add a new routine to compute strain rates
200      - the above changes lab_sea results
201      - add no slip conditions for evp solver (off by default), lsr-version
202        may follow
203      - fix exchange for shear at Z-points (does not change lab_sea)
204      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
205        (to force the user to pick a time step since there is not "safe" way
206        of choosing it)
207      - add principal stress diagnostics
208      - rearrange fields for evp a little to avoid having to call a: too many
209        exchanges and b: exchanges for stress trensor components which we do
210        not have.
211      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
212        of evp, complete rewrite for lsr case (latter is does not yet work
213        in all cases)
214    o pkg/kpp: add code to have mixing in shelf ice caverns
215      - add myThid to all kpp routines (long overdue)
216    
217    checkpoint59
218    o pkg/exf:
219      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
220        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
221      - move exf header files from lower_case.h to UPPER_CASE.h ;
222        add missing cvs Header & Name
223      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
224      - add namelist param. selectStressGridPosition, exf_monFreq
225      - retire many _CLIM routines, and remove data.exf_clim
226        + params moved to data.exf
227        + climsst, climsss now handled by exf_set_gen, i.e.
228          climss?period=0 refers to constant field,
229          climss?period=-12 to monthly forcing
230      - split up namelists in data.exf
231    o pkg/seaice:
232      - remove seaice_exch and seaice_exch_uv
233      - remove superfluous exchange of theta
234      - add myThid to seaice_budget_ocean/ice
235      - add new interface for atmospheric wind forcing (C-grid only)
236        + new routine
237        + two new field (taux, tauy for stress over ice)
238        + removed one global field (DAIRN) for C-grid case only
239    o pkg/thsise
240      - 2nd set of modifs for thsice adjoint in conjunction with exf
241    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
242    
243    checkpoint58y_post
244    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
245      vertical diffusivity, similar to that in MOM4; turned on using
246      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
247      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
248    o Added capability for 3D specification of background vertical diffusion
249      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
250      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
251      "data" file that contains the 3D vertical diffusivity coefficients.
252    o ice dynamics (pkg/seaice) with thsice thermodynamics:
253      - add code within pkg thsice to advect & diffuse sea-ice fields
254      similar to (and will replace) what has been added in  seaice_advdiff.F,
255      but: - conserving Mass, Heat & Salt.
256           - better when using non-linear advection scheme (not yet fully tested)
257           - can also be used in atmospheric set-up (for now, only the diffusion).
258    
259    checkpoint58x_post
260    o IO option for global-file compact format:
261      - add options when generating topology (utils/exch2/matlab-topology-generator)
262      - add I/O capability (pkg/mdsio).
263      - adapt utils/matlab/rdmds.m to read this format.
264      for now long-line format not yet supported by pkg/mdsio (& exch2).
265    o shelfice: add a few diagnostics
266    
267    checkpoint58w_post
268    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
269      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
270      (and replace horiVertRatio in NH code).
271      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
272                         and tutorial_plume_on_slope (sensitive to truncation)
273    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
274      directly to drive seaice model (C-grid only)
275    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
276     - reintroduce computation of wind from stress,
277     - compute tau (in exf_bulkformulae.F) from windstress averaged to
278       mass points to avoid tau = 0
279     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
280    o rdmnc.m: make it work with "global" files created with gluemnc
281    o rdmnc.m : some improvements in dealing with singleton dimension
282      (tested on all testreport mnc output files).
283    o genmake2: disable pkg/profiles if netcdf test fails.
284    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
285    o move call to cal_readparms up to make calendar parameters/variable available
286      to all packages
287    
288    checkpoint58v_post
289    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
290      useDynP_inEos_Zc tested.
291    o pkg/exf: changes to properly interpolate/mask/scale initial fields
292    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
293      and portions thereof.  See read_cs.txt for description and examples.
294    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
295      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
296      following the great-circle arc between those 2 points.
297    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
298      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
299    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
300     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
301     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
302     - still needs work (not working with some options ; efficiency to improve)
303       and serious testing.
304     - use this scheme for temperature & salinity in 2 advection test exp.:
305       advect_xy & advect_xz, respectively.
306    
307    checkpoint58u_post
308    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
309    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
310    o testreport: add option "-skipdir" to skip some test.
311    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
312      momentum calculation.
313    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
314    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
315      remove checkpoint.F and the_correction_step.F (no longer used);
316      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
317    o add option (linFSConserveTr) to correct for tracer source/sink due to
318      Linear Free surface
319    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
320    o pkg/thsice: fix reading mnc-pickups
321    
322    checkpoint58t_post
323    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
324    o pkg/mdsio:
325     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
326       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
327       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
328     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
329     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
330       either MDS_READ_FIELD or MDS_WRITE_FIELD )
331     - new S/R (to replace MDSWRITEMETA), which allows to write more
332       informations (variable names, time ...) to meta files.
333     - modify rdmds.m to give back the meta file content.
334    o pkg/diagnostics: change vertical interpolation to be safer, and more
335       flexible (define p-levels to interpolate to in data.diagnostics);
336      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
337       diagnostic pointer.
338    o pkg/seaice: more cleaning up of seaice_growth, added many comments
339    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
340    o fix multi-category seaice:
341     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
342       SEAICE_MULTICATEGORY
343     - fix short wave heat flux
344    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
345       and allow to use EVP solver. Change forward lab_sea: test both EVP
346       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
347    o Initial check-in of lab_sea adjoint
348      (very similar to natl_box_adjoint/code_seaice)
349      * used C-grid and EVP solver
350      * used KPP, GM/Redi
351      * uses inAdExact=.TRUE.
352      * gradient checks fail for both ADM and TLM
353        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
354        f.d. gradients actually seem more problematic than ADM, TLM gradients;
355        issue is related to forward mismatch between g77 an ifort
356    o pkg/seaice: overhaul of thermodynamics
357     - growth.F and groatb.F are replaced by new routine seaice_growth.F
358     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
359     - move a few global fields out of SEAICE.h into seaice_growth.F and
360       make them 2D (FICE/QNETO/ ...)
361     - remove FO (it is the same as QNETO)
362     - introduce a few local fields to avoid modifying external fields such
363       as atemp, etc.
364    
365    checkpoint58s_post
366    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
367      changed exf_set_gen.F so that
368        genperiod=0 means input file is one time-constant field and
369        genperiod=-12 means input file contains 12 monthly means
370    o CG2D: use pre-computed solver main-diagonal (stored in common block);
371      this affects truncation error ; generate new output file for exp. which
372      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
373        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
374        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
375        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
376        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
377        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
378    o start implementation of deep-atmosphere and anelastic formulation
379    o verification: remove 2nd copy of input files and use script "prepare_run"
380      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
381    o mom_common/vecinv/fluxform: fix a few initialisation isssues
382    o profiles: fix for multithreaded case
383    
384    o diagnostics: rename few diags:
385      s/'PRESSURE'/'RCENTER '/g
386      s/'TICE    '/'oceFreez'/g
387      s/'TAUX    '/'oceTAUX '/g
388      s/'TAUY    '/'oceTAUY '/g
389      s/'SWFLUX  '/'oceQsw  '/g
390      s/DIFx/DFxE/g
391      s/DIFy/DFyE/g
392      and add few ocean-forcing diagnostics:
393      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
394    o modifications to pkg/seaice/growth.F and budget.F, which change results of
395      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
396      as actual snow thickness.  It now refers everywhere to effective snow
397      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
398    
399    checkpoint58r_post
400    o modifications to pkg/seaice/growth.F, which change results of
401      lab_sea experiment: fixes pertain to melting snow over open water, to
402      masking EVAP under sea ice, and to using the correct AREA variable for
403      computations of EVAP, PRECIP, HSNOW, and GHEFF
404    o add ability to read bathy, salt, and theta using MNC (off by def)
405    o add flooding algorithm and advection of HSNOW for pkg/seaice;
406      both are turned off by default and do no change any results
407    o seaice advection with pkg/thsice: a step toward the use of non-linear
408      advection scheme, but #ifdef or commented out for now (requires more EXCH).
409    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
410      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
411      in natl_box (affects results @ truncation level: update output.txt)
412    o multi-threading and IO:
413      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
414      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
415        (needed to work with SingleCpuIO): tested in all verif. exp.
416    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
417      affects the results (but none of the verification test uses this scheme).
418    o Adding some pkg/diagnostics capability to pkg/seaice
419      (will certainly be subject to changes)
420    o ctrl: adding new control variables:
421      lwflux, lwdown, evap, snowprecip, apressure, runoff
422    
423    checkpoint58q_post
424    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
425      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
426      high_res_cube configuration by 4% on Columbia.
427    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
428      add (in global_with_exf/code) a version of EXF_INTERP_READ without
429      dynamical allocation (seems to work in multi-threaded).
430    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
431      single CPU io) so that TAF does not have to see EESUPPORT.h
432    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
433    
434    checkpoint58p_post
435    o obcs: stop if obcs is used with useCDscheme = .true.
436    o shelfice:
437     - fix a sign error so that no slip at shelfice interface works
438     - remove stop for combination non-hydrostatic code and shelfice. That does
439       not mean, that the results are correct, but at least they are numerically
440       stable
441    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
442    o added adjoint exch routined for all exch*3d* routines
443      and updated flow directives
444    
445    checkpoint58o_post
446    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
447      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
448    o change controling S/R for writing pickup file (new S/R do_write_pickup)
449      and clean-up reading/writing of pickup files.
450    o fix local version of read/write pickup (NH part) in rotating_tank/code
451    o simplify EXCH interface:
452     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
453     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
454    o added the regrid package
455    o shelfice:
456     - add a simple boundary layer scheme to reduce noise
457     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
458    
459    checkpoint58n_post
460    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
461       local variable (not in common block).
462    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
463      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
464      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
465        to work with SingleCpuIO.
466    o add "_d 0" to real constant of pkg/cfc subroutines ;
467       update exp. cfc_exemple & tutorial_cfc_offline output files.
468    o multi-threading and IO:
469      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
470        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
471      - barrier before and after reading.
472      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
473      - avoid using MDS_WRITELOCAL for LAND pkg output.
474      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
475        common-block variables ; Allows multi-threading with master-thread IO.
476    o change default MAX_NO_THREADS from 32 to 4 ;
477      and stop cleanly when MAX_NO_THREADS is too small.
478    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
479    
480    checkpoint58m_post
481    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
482       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
483    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
484       keep global_ocean.90x40x15 (for AD testing) with former secondary test
485       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
486    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
487        add MITgcm_tutorials (= code + all the tutorials)
488    o ecco, option to compute cost for total ssh (mean+anom)
489    o consistent with addition of ptracer and ssh in pkg/profiles
490    o profiles: adding ptracer and ssh
491    o testreport: change multi-test output-file name
492      (from output.txt.{name} to output.{name}.txt)
493    o profiles: now ok for mutli-tiles case
494    o seaice: add 4 parameters for different advection schemes for area,
495      (effective) seaice thickness, enthalphy, and snow height. Their default
496      is the standard parameter SEAICEadvScheme
497    o calc_gw:
498     - add cosFacU in zonal viscous flux (harmonic.visc.).
499     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
500       of tutorial_plume_on_slope.
501    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
502    o calc_gw: true flux-form, account for horizontal grid spacing.
503      update rotating_tank results, but not plume_on_slope (affected at
504      truncation level, 11 digits).
505    
506    checkpoint58l_post
507    o calc_gw:
508     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
509     - remove side-drag for now (need to fix it); update plume_on_slope results.
510     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
511    o commit code to make SST/SSS weights spatially variable
512      (based on either variable in-situ or variable initial T/S weights)
513    o pkg/ecco:
514      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
515        now based on horizontally varying weights wthetaLev, wsaltLev
516      * cost_averagesflags now returns year indices in addition to day, month
517      * sflux balance is performed on annual basis
518        (sflxumm, sfluxmm2, bal_sfluxmm)
519      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
520        including separate counting and multipliers
521    o pkg/rbcs
522      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
523    
524    checkpoint58k_post
525    o testreport:
526     - always build in dir. "build" (if not there, mkdir build instead of building
527       & running in input)
528     - run in dir run (if it exists), in build otherwise.
529     - call prepare_run (if input/prepare_run exists)
530     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
531    o pkg/exf modifications to interpolation and rotation routines for more
532       reasonable treatment of North Pole singularity: for tracers North Pole
533       value is set to northernmost zonal-mean value, for zonal velocity it is
534       set to zero, and for meridional velocity it is set to northernmost value.
535    o pkg/exf/exf_check_range.F
536     - add tile index to diagnostics and move stop statement to the very
537       end of the routine.
538    o pkg/diagnostics: (diagnostics_main_init.F)
539      define title of isomorphic variables according to the current config.
540    o pkg/thsice with pkg/seaice dynamics:
541    - fix domain of computation (interior only, required for exf) and do exchanges
542    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
543    o towards a standard way of dealing with multi-threading in MONITOR
544      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
545    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
546       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
547    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
548    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
549    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
550       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
551    o tracer advection:
552     - clean-up and simplify calc_common_factors.F
553     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
554       advection subroutine (but still not used within DST advection S/R)
555    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
556    
557    checkpoint58j_post
558    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
559      from file (collects calls previously in FORWARD_STEP)
560    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
561    o adjoint store dir. adjusted accordingly
562    o genmake2
563      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
564    
565    checkpoint58i_post
566    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
567      on wind stress (SEAICEstressFactor defaults to 1.)
568    o Total number of Timers is finite (<=40): comment out 2 non-essential one
569      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
570    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
571      on CS-grid: no longer loosing mass.
572    o exf & curvilinear-grid: no longer modify longitude xC & xG.
573    o pkg/ggl90: fix sloppy output and fix a bug
574    o pkg/seaice: added SEAICEuseEVPpickup parameter
575      - Set to false in order to start EVP solver with
576        non-EVP pickup files when using SEAICEuseEVP
577      - fix sign error in diffusion in seaice_calc_rhs
578    
579    checkpoint58h_post
580    * Modifications for bottom topography control
581      o replace hFacC by _hFacC at various places
582      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
583      o add non-self-adjoint cg2d_nsa
584      o update autodiff support routines
585      o re-initialise hfac after ctrl_depth_ini
586      o works for 5x5 box, doesnt work for global_ocean.90x40x15
587    * Adding verification for 5x5 box (4-layer) bottom topography control
588    
589    checkpoint58g_post
590    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
591       used for mean seasonal cycle, mean diurnal cycle); add an example
592       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
593    o pkg/ggl90:
594      - add parameter (minimum surface kinetic energy)
595      - fix bug (avoiding division by zero)
596    o couple pkg/thsice to pkg/seaice:
597      - modify advection in seaice to accomodate new scalar fields to be advected
598      - only muliDimAdection scheme work with seaice/thsice
599      - mapping of thsice-variables to seaice-variables, back and forth
600      - does not break the verification experiments, but does not give the
601        desired results either
602    o pkg/seaice
603      - make (default) second order advection a bit less confusing?
604    
605    checkpoint58f_post
606    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
607      to pkg/seaice):
608      - new routines thsice_map_exf and thsice_get_exf provide the interface
609      - add an additional formal parameter to thsice_solve4temp
610    o pkg/exf:
611      - add new fields wspeed, snowprecip (to be able to couple to thsice)
612      - correct Stefan-Boltzmann constant
613      - new parameter for longwave surface emittance
614      - separate some stuff from exf_bulkformulae into new routines  
615        exf_radiation, exf_wind
616      - add new parameters and constants: longwave emissivity for ocean, ice
617        and snow, evaporation parameters over ice
618      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
619        either wind from stress or stress from wind
620    o pkg/thSIce:
621    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
622    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
623       and THSICE_CALC_THICKN
624    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
625    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
626      to make debugging easier.
627    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
628    o pkg/bulk_force:
629      - clean-up comments and parameters ;
630      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
631    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
632      generate new output for test-experiment: aim.5l_cs.thSI
633    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
634      testreport accordingly
635    
636    checkpoint58e_post
637    o SEAICE_CGRID adjoint done
638    o R_STAR adjoint implemented.
639      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
640      * need to sort out init. of h0facc, etc.
641    o Make pkg/profile fully independent of ecco,cost, etc. stuff
642      to be able to use it in pure forward.
643    
644    checkpoint58d_post
645    o upgrade simple test-experiment to tutorial example:
646     step.1: duplicate the experiment and (step.2) will remove the old copy.
647      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
648      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
649      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
650      tutorial_global_oce_biogeo    <- copy of dic_example
651      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
652      tutorial_plume_on_slope       <- copy of plume_on_slope
653      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
654      tutorial_global_oce_optim     <- empty for now (David ?)
655      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
656     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
657    o correct a sign problem in cost_scat.F
658    o obcs and ptracers: fix boundary conditions for advections schemes
659      with larger stencil
660    o thsice adjoint: start
661    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
662      completeness
663    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
664      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
665    o ptracers adjoint:
666      * avoid extensive recomputatations
667      * fix missing re-init. of gptr (missed by TAF)
668    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
669      me to turn off the excessive output to STDOUT that this package produces
670    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
671      and add those terms in Vector-Invariant formulation.
672    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
673      if the control period (xx_hfluxperiod etc) is 0
674    o in profiles pkg, clean routines and fix details
675    o in ecco pkg, reading ssh data:
676      fix problem in case the model does not start at iter0=0
677    o fix mnc-pickup/restart for ptracers
678    o new package prifiles:
679      code to compute profile-based cost by Gael Forget
680      (modifs in ecco, ctrl, autodiff)
681    o Benign bug fix in initialization (spotted by M. Mazloff) of
682      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
683    
684    checkpoint58c_post
685    o adjoint: finish NLFS adjoint and provide reference output in
686      verification/global_ocean.90x40x15/results_ad_nlfs
687    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
688      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
689      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
690      with SEAICE_CGRID defined.
691    o move calendarDumps from "data" to "data.cal" and clean-up the code
692      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
693    o add useEXF & useCAL flags (for now, set in hard-coded way)
694    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
695      (were missing in NH mode, and wrong in quasihydrostatic mode).
696      waiting for Chris updated version of calc_gw to add those CALLs.
697    o fix bug in quasihydrostatic S/R ;
698      add a test for this option: global_ocean.90x40x15.qshyd
699    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
700      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
701    o add on/off flag useOffLine for package OFFLINE
702    o seaice:
703      - modify advection so that it works also on the C-grid
704      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
705        problem in multi-tile runs with C-grid
706      - add flags for clipping ice velocities and/or masking solver forcing
707      - fix drag (ocean on ice) formulation and a bug that caused noise in the
708        C-grid solver
709      - added a few comments to seaice_diffusion.F
710      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
711        are now exclusive)
712      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
713        required re-ordering the code a little:
714       + make DAIRN global variable (defined in SEAICE)
715       + move computation of the viscosities eta and zeta into a new separate
716         routine (because I need to recompute them in seaice_ocean_stress.F)
717    
718    checkpoint58b_post
719    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
720      update output.txt of exp. aim.5l_cs.thSI
721    o various mnc cleanups and improvements:
722      + shrink lookup tables by factor of ~4
723      + better error reporting when running out of lookup space
724      + able to handle longer path/file names (up to 500 chars)
725    o adjoint:
726      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
727      - TBD: "hidden" mom_vecinv recomp. in dynamics
728    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
729     (allow to differentiate between forcing components using new integer flags:
730      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
731     and add new flag to put Dissipation tendency out of Adams-Bashforth.
732    o ecco
733      - enable trend removal from SSH anomaly obs.
734    o adjoint
735      - a fix for PmEpR when #undef EXACT_CONSERV
736      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
737      - try to fix "hidden" recomp. in forward_step for NLFS
738        (NLFS seems broken sometimes after I checked it in)
739    o seaice:
740     - add c-grid version of the dynamic solver:
741       + three new routines that are the c-grid substitute lsr, dynsolver
742         and ostres
743       + put a few fields that were local to dynsolver into global common
744         blocks, so that I can move the computation of stresses etc into
745         seaice_lsr (saves coding but may break the adjoint).
746     - replace more hardwired parameters by runtime parameters
747     - add ice masks that mask the rhs of the implicit solvers where there
748       is no ice (commented out in seaice_dynsolver, because i am not sure
749       if this works properly), eventually this should replace the clipping
750       of ice velocities in seaice_dynsolver to +/-40cm/s.
751    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
752      include it only where its needed
753    o move balancing of fluxes before the call of external_forcing_surf
754    o seaice:
755      - correct units of turning angles (now they are really in degrees)
756      - move computation of GWATX/Y out of main routine into dynsolver
757      - initialize GWATX/Y in seaice_init
758    o Apply mask on Fresh-Water flux (needed for SSH forcing).
759      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
760    o seaice: add runtime flags for turning angles (default to zero)
761    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
762      and trend from exf forcing and ctrl control adjustments
763    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
764      (since checkpoint57x_post)
765    o change the default rotation period to 86164.s = the Earth rotation
766    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
767      and based on a reference stratification. Tested within hs94.cs-32x32x5.
768    o seaice advection: add code for choosing between the default (2nd order
769      central differences) and multiDim advection schemes provided by
770      pkg/generic_advdiff
771    o seaice:
772      - removed all references to SEAICE_GRID.h fields from
773        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
774        (cubed-sphere configuration will change a little)
775      - grid computations in seaice_init are obsolete now.
776      - cleaned up code a little so that is easier to read (hopefully).
777      - added new (better?) discretizations of default advection and diffusion
778        (turn on with SEAICEuseFluxForm)
779      - replace 1 in 3d global fields by kSurface in growth.F
780      
781    checkpoint58a_post
782    o seaice:
783      - bug fix in advect.F
784    o shelfice:
785      - separate shelfice load anomaly from pload (breaks with time
786        dependent forcing), => introduce constant field shelficeLoadAnomaly.
787        Its default is 0., but it may be computed more cleverly from (unknown)
788        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
789        done offline. A good approximation of the pressure load anomaly is
790        necessary to avoid large initial adjustment processes underneath
791        deep-reaching shelfice.
792      - small fix in ISOMIP shelfice_thermodynamics
793      - add more sophisticated thermodynamics of Hellmer (1989), this is
794        now the default
795      - give a few constants more intuitive names
796    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
797      if bulk formulae are used in long integration (especially EmPmR). Turn
798      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
799      if balancePrintMean, the imbalance that is substracted is printed to
800      STDOUT.
801    o fix bug (typo) in obcs_apply_eta.F
802    o add a new package shelfice which enables us to model the circulation
803      underneath shelf-ice with draughts of hundreds of meters.
804     - works
805     - to do: + include improved thermodynamics
806              + check whether kSurfC (from model/inc/SURFACE.h) can be used
807                instead of new field kTopC
808              + can we use topoFile, Ro_surf and existing code in ini_depth.F
809                instead of new field R_shelfIce and new code in ini_depth.F
810                and ini_mask_etc.F?
811              + adjust vertical mixing schemes?
812    o seaice pkg:
813     - add a cpp-flag to include a simple formula for a salinity dependent
814       freezing point of sea water at the surface
815     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
816       meridional stresses are now different (and hopefully correct)
817    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
818       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
819       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
820    o pkg/diagnostics: add options and parameters for regional-statistics
821       diagnostics ; define regions by reading a region-mask from a file
822       (might add other options later)
823    o pkg/bulk_force:
824     - add option and parameters to use AIM surface-flux formulae.
825     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
826       others forcing fields (defined in PARM05, parameter file "data") are loaded
827       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
828     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
829     - use the right EXCH call for uwind,vwind (to work on CS-grid).
830     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
831       and parameters (note: calcWindStress replaces .NOT.readwindstress).
832     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
833    
834    checkpoint58
835    o add "--embed-source" option to genmake2 which, when the supporting
836      tools can be compiled (as determined by genmake2) will turn on the
837      embed_files package which then embeds the entire MITgcm source code
838      (*.[fFhc] + Makefile) used for the build within the executable
839      - requested by CNH but off by default
840      - adds a paltry <9MB to the mitgcmuv executable in most cases
841      - only writes the output when useEMBEDSRC in eedata is true
842    o clean up 3-dim. relaxation codes:
843      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
844      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
845      * Thanks to Tom Haine for testing!
846    
847    checkpoint57z_post
848    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
849      affects output (@ truncation level) of exp. plume_on_slope ; updated.
850    o fix the pickup behavior for obcs in combination with ptracers
851    o fix a bug in ptracers_external_fields_load
852    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
853      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
854    o transfered surface NH pressure to eta field (if exactConserv).
855    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
856         and update lab_sea output.txt file.
857    o completing 3-dim. relaxation code: additional term
858         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
859      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
860      * At compile time, in "EXF_OPTIONS.h" set
861          #define  ALLOW_CLIMTEMP_RELAXATION
862          #define  ALLOW_CLIMSALT_RELAXATION
863      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
864          tauThetaClimRelax3Dim = 15552000.0,
865          tauSaltClimRelax3Dim  = 15552000.0,
866      * 3 cases:
867          1) Use a constant-in-time 3-dim. field
868          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
869          3) Real-time relax. to time-evolving prescribed field
870    o Adding Laplacian-type smoothness constraint on
871      initial and boundary (forcing) controls (ic, bc)
872      * enable at compile-time via
873        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
874      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
875      * Absolute scale somewhat unclear so far
876      * no area weighting was included since no other cost term does so far
877    
878    checkpoint57y_post
879    First step for a NLFS adjoint
880    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
881    o new init. routines for calc_r_star, calc_surf_dr
882    o still need to deal with ini_masks_etc
883    o testreport seemed happy
884    checkpoint57y_pre
885    
886    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
887    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
888    o add new offset feature to offline pkg (plus minor cleanup)
889    o cfc fixes for final year of integration
890    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
891      be in GCHEM_OPTIONS).
892    
893    checkpoint57x_post
894    o fix testreport Pb in multiple test experiment.
895    o cleanup our namelist syntax in verification:
896      - make it more F95 standards compliant (some work still needed)
897      - allows the vast majority of our tests to work with gfortran
898    o Non-Hydrostatic:
899     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
900     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
901    o Allow to apply AB on T,S rather than on AB(gT,gS):
902     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
903     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
904       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
905     - need a "clever" read_pickup to restart from the other AB formulation
906    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
907    o remove some unused variables (reduces number of compiler warnings)
908    o adjoint
909      * Disable useVariableViscosity for adjoint for time being
910        (there are a number of extensive recomputations)
911      * Initialize certain variables needed for adjoint
912    
913    checkpoint57w_post
914    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
915                 fix the singleCpuIO RS version of MDSWRITEFIELD
916       and add a WARNING if using globalFiles=T with multi-processors.
917    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
918      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
919    o tracer advection scheme:
920      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
921       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
922       was not very convenient).
923      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
924       (further tests needed for the implicit DST & Flux-Limiter schemes).
925    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
926      and sRef for convenience, handy, when you want to initialize
927      ptracers in a large domain with a constant non-zero value. Also,
928      untangle ptracers_init.F a little.
929    
930    checkpoint57v_post
931    o change dome exp. to use variable viscosity in side-drag terms.
932    o remove all the files from the cfc_offline test since they are now
933      incorporated into tutorial_cfc_offline which has been producing
934      identical results for a few days of testing
935    o add new parameter: sideDragFactor to enable half-slip-side BC
936      and change side-drag S/R to use viscosity from mom_calc_visc
937      (can switch back by setting sideDragFactor=0.); affects results at
938      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
939       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
940    o vorticity & strain are now computed without masking, to account for
941      no-slip-side BC in variable viscosity calculation ; mask is applied
942      anyway later on, before computing advection/coriolis terms.
943    o modify exp4 to test new obcs support for reading from external files
944      and for passive tracers
945    o fix behavior of ptracers_monitor when monitor output is written to a
946      netcdf-file; still not independent of monitor.F (writes in the same
947      file).
948    o change default value of tRef (put a uniform, meaningful value for ocean
949      & atmos) and initialize sRef (was missing, as Martin mentioned).
950    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
951      to be proportional to enstrophy dissipation length.  Thus,
952       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
953      This is now consistent with Smagorinsky and with the manual.
954    
955    checkpoint57u_post
956    o OBCS and PTRACERS: add open boundary support for passive tracers
957      - either use homogenous (pseudo) v.Neumann conditions or prescribe
958        OB-values from file; this is not different from the way theta and salinity
959        are treated
960      - however, Orlanski-radiation conditions are not supported, and the model
961        will stop if you use pTracers and Orlanski at the same time.
962      - beefed up the rountine obcs_external_fields_load: now only those open
963        boundary values are overwritten with values from files for which there
964        are really files, otherwise the OB-fields remain untouched. This makes
965        it possible to use different OBs at different ends of the domain (as
966        with EXF)
967    o reduce number of exch calls in shap_filt (s2).
968    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
969      truncation level) 4/5 MLAdjust test results (11&12 digits match).
970    
971    checkpoint57t_post
972    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
973    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
974      same truncation, independent of the face number: affects affects several
975      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
976    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
977      note that biharmonic viscosity + no-slip was not tested in any experiment.
978    o fix bug in non-linear free-surf side-drag ; generate new output for
979      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
980    o make mnc honor the writeBinaryPrec flag for most kinds of output
981    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
982    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
983      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
984    o add brackets in multi-terms sum to get same truncation, independent of
985      the face number (manage to get exactly same value of gU,gV at the cs-edge)
986      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
987    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
988      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
989      a maximum grid-scale Reynolds number.  Also, changes all length calculations
990      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
991      Suggested values of viscosity parameters found in mom_calc_visc.
992      Many new viscosity diagnostics available.
993    
994    checkpoint57s_post
995    o Add clearing-house for viscosity calculations, mom_calc_visc and
996      correct numerous bugs in LeithD and Smagorinsky discretizations.  
997      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
998      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
999      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1000      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
1001      The Strain-Tension form is now called with useStrainTensonVisc=.true.
1002      ViscAhStrain and viscAhTension are now retired.
1003    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1004    o In response to JMC's bug report, genmake2 now ignores any soft-links
1005      that it finds in the *current* directory when searching for files.
1006      Soft-links found in any other source directories will still work as
1007      they did before.
1008    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1009      a C routine to unlimit the stack size
1010    o mnc-ify pkg/aim snapshot vars
1011    o mnc-ify pkg/land as requested by Daniel
1012    o various changes to mnc including:
1013      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1014      - output can now be grouped so that all files within a group
1015          change the ITER portion of their names in lock-step together
1016      - can now read ("global") PER-FACE (in addition to PER-TILE) files
1017          and works with both EXCH1 and EXCH2 (but needs more testing)
1018      - writing works for all verification test cases w/ g77 on Linux
1019    
1020    checkpoint57r_post
1021    o make MNC variable initialization happen earlier
1022    o add diagnostics for (almost) each term of the momentum Eq.
1023    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1024    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1025    o remove MINIMAL_TAVE_OUTPUT option ;
1026      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1027    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1028      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1029    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1030    o add time-dependent SST, SSS control
1031    o cost terms in ecco/ modularized (new cost_generic.F)
1032    o cost_averages routines are modularized (new cost_averagesgeneric.F)
1033    o new infrastructure for seaice model vs. obs misfits in seaice/
1034      * driver from the_main_loop.F is seaice_cost_driver.F
1035      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1036      * gradient check in Exp. 6a of natl_box_adjoint/
1037    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1038      (see README file)
1039    
1040    checkpoint57q_post
1041    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1042    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1043      - bug was reported by Jean-Michel and Ian Fenty
1044    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1045      update exp. cpl_aim+ocn output.
1046    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1047      Needed for high-res. runs with large global files
1048      to be able to limit tapelev size
1049    o Changed some tests for adjoint:
1050      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1051      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1052      * global_ocean.90x40x15/ back to default 3-level checkpointing
1053    o Modifications to enable scripted COMMON to MODULE conversion
1054      * verification/OpenAD/code/ has necessary scripts and description;
1055      * converts, compiles and runs successfully;
1056    
1057    checkpoint57p_post
1058    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1059    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1060      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1061    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1062    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1063      (was already the case for dissipation with mom_vecinv,
1064       and also the case for grad.PhiHyd when staggered-timeStep)
1065      This will allow to put dissipation out-off the AB time-stepping.
1066     Unfortunately, affects truncation error. Update output of exp. that "fails"
1067      (cg2d matching number) and leave the others for later: front_relax(10),
1068      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1069      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1070    
1071    checkpoint57o_post
1072    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1073      (2) its ready to be documented during the 20050801 DocFest
1074    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1075      for ideal_2D_oce and lab_sea on linux_ia32_g77
1076    o set to #undef CTRL_SET_OLD_MAXCVARS_30
1077      in global1x1_tot/code_seaice_adj to access indices 32, 33
1078      (worth another tag)
1079    
1080    checkpoint57n_post
1081    o adding precip control xx_precip 32
1082    o adding swflux control xx_swflux 33
1083    o Replacing 10 forcing penalty cost routines by 1 generic.
1084    o Implementing partitioning in time-mean and variable adjustment
1085      for atmos. state.
1086    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1087  o in natl_box_adjoint:  o in natl_box_adjoint:
1088    * updated: results_bulk/    * updated exp 1 to 10
1089    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
1090    o updated global1x1/*_seaice_adj/
1091      to incorporate latest changes
1092    o enable useSingleCpuIO for mdsio vector routines
1093      (applies in particular to tapelev I/O)
1094    o removed inefficient K-loop in all active_file*control*.F
1095    
1096  checkpoint57m_post  checkpoint57m_post
1097  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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