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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.868 by jmc, Wed Sep 5 01:55:26 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 new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
8  o moved ptracer ctrl index 17 -> 32    threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
9      (but still depend on the tile decompostion of the domain).
10    o pkg/seaice: change a discretization detail to make the B-grid code
11      "more symmetric". This change is likely to remove all "ridges/leads" that
12      where quasi-aligned with the grid in B-grid solutions. It may also be
13      the solution to the stress coupling issues with the B-grid.
14    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
15      remove .cvsignore from input dir. (since testreport no longer run here).
16    o pkg/thsice:
17     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
18     - fix reshaping of sea-ice just after advection:
19       melt all the ice only if ice-volume is too small.
20     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
21       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
22     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
23    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
24      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
25    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
26      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
27      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
28      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
29      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
30      -> update output.txt
31    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
32     this affects truncation error: -> update output.txt of exp:
33      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
34      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
35    
36    checkpoint59f
37    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
38    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
39      a bounded range (in forward mode)
40    o pkg/ecco, ctrl, autodiff and mom_common:
41     internal parameter controls, completements of implementations
42    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
43    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
44      (not seem any difference in testing results).
45    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
46       at face corners.
47    o pkg/generic_advdiff:
48     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
49      loop range indices for computing vertical advection tendency
50      and do the calculation in the interior only (no overlap) ;
51      for now, only implemented for SOM advection (to save CPU time).
52     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
53    o exch2 adjoint
54      First set of changes:
55      - add exch2 hand-written adjoint templates
56      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
57        This will require cleanup in pkg/autodiff/*.F
58        (changed routines currently kept separate in verif. code/)
59      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
60        that used to hide exch2 or cubed-sphere specific code
61        (commented via 'cph-exch2')
62    o pkg/seaice
63      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
64    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
65       output of global_ocean.cs32x15.thsice .
66    
67    checkpoint59e
68    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
69      for B-grid vector (not yet tested) and C-grid vector (<- only used
70      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
71    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
72      (#ifdef ALLOW_SALT_PLUME)
73    o gather_2d/scatter_2d: removed halo regions
74    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
75      scheme and the corresponding test case (under front_relax dir). For now,
76      only available with Skew-flux form and not yet tested in realistic set-up.
77      adjoint: store directives updated, but gradient checks deteriorated,
78      so maybe GM/Redi adjoint is now broken.
79    o seaice adjoint
80      * add AREA, HEFF, HSNOW as control variable
81        (should not change lab_sea results)
82      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
83    o pkg/seaice:
84      * added computation of saltFlux in seaice_growth;
85        For time being, sea ice salinity is assumed constant
86        contribution of snow flooding to freshening of sea ice is neglected.
87        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
88        defaults to 0.0 in order to maintain backward compatibility.
89        Typical values for SEAICE_salinity are 4 to 10 g/kg.
90      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
91      * added SEAICE_availHeatFrac, which specifies fraction of surface level
92        heat content used to melt or grow ice
93      * commented out cap of HICE: it helps keep ice thinner
94      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
95      * applied OBCS T/S mask to HEFFM sea ice mask
96    
97    checkpoint59d
98    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
99     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
100     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
101    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
102     and change default value of parameter "GM_Small_Number";
103     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
104       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
105       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
106    o pkg/ecco: cost function when applying pkg/smooth to controls
107    o pkg/ctrl: add forcingPrecond run time parameter
108    o pkg/seaice:
109     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
110     - fix bug in metric terms of u-equation in LSR solver (implicit part),
111       changes verification/lab_sea
112     - rearrange implicit part of u-equation in LSR solver to make it easier to
113       read, understand, and debug. This causes changes at the truncation level.
114     - fix (serious) bug in the boundary conditions (sign error in the implicit
115       part) of the LSR solver. Changes all LSR results.
116     - fixed problem with HSNOW initialization to avoid thick snow when AREA
117       is initilized with small values - does not change lab_sea results.
118     - added HsnowFile initialization capability
119    o pkg/smooth: addition to model/src and pkg/ctrl so allow
120     initialization of pkg/smooth and application to control vector
121    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
122    o dependencies: pkg/profiles requires pkg/cal
123    o pkg/profiles:
124     - added option ALLOW_PROFILES_GENERICGRID
125         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
126         that interpolation information (grid points and coefficients) is provided
127         within the netcdf input files.
128         -> sample matlab scripts can be found in MITgcm_contrib/gael
129         that allow you to prepare netcdf input files.
130     - also modified: cleaner include statements, cleaner error print statements,
131       cleaner stops when error, and more tests of the netcdf input files consistency.
132    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
133    o pkg/seaice:
134     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
135       requires a new routine: seaice_diagnostics_fill.F
136     - make sure that seaice does not move if not forced (pressure replacement
137       method, Hibler and Ip, 1995), changes results
138     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
139     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
140       It is turned off by default (=-1.), because it changes the results.
141     - make it possible to read AREA from a file, too.
142    
143    checkpoint59c
144    o add S/R and diagnostics for oceanic mixed-layer depth
145    o move GMRedi call after all vertical mixing schemes (including KPP)
146    o pkg/thsice:
147     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
148      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
149    o pkg/obcs:
150     - bug fix for balance code
151    o pkg/seaice:
152      - allow values of SEAICE_elasticParm > 1
153      - add new parameter SEAICE_evpTauRelax as an alternative
154        to SEAICE_elasticParm
155      - make lsr boundary conditions free slip (by default), changes result
156      - add code for no slip boundary conditions for lsr
157      - set minimum of zeta to zero (and not 4e8) (changes results)
158      - add a cap on AREA after advecting AREA if seaice_growth is not called
159    o change calculation of Visbeck K:
160      - no longer depend on tapering scheme; instead, compute slope (limited
161        by GM_maxSlope). this is equivalent to what was comuted before with
162        clipping or linear tappering.
163      - fix vertical averaging (wrong by 1/2 level)
164      - leave the old version (but will not be maintained) within
165        #ifdef OLD_VISBECK_CALC / #endif
166      - update output of exp. ideal_2D_oce
167    o change error catch in calc_r_star to improve vectorization
168    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
169      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
170    o adjoint:
171      Re-organized adjoint checkpointing according to Matt Mazloff
172      (but with modifs/completions/cleanups)
173      Storing is now bundled into large arrays to optimized I/O
174      (and second step in cleanup of the_main_loop)
175    
176    checkpoint59b
177    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
178      - export/import (between ocean & coupler) fields needed for ocean DIC.
179    o pkg/seaice:
180      - get rid of three more exchanges seaice_calc_viscosities (required
181        different loop boundaries in seaice_lsr and seaice_ocean_stress)
182      - bug fix in seaice_ocean_stress (update of lab_sea required)
183      - reduce loop boundaries to necessary minimum also in seaice_evp
184      - go back to the old way of computing deltaC/Z as the adjoint likes that
185        better
186    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
187      passive tracer to an Age Tracer) + update output.txt
188    o pkg/exf:
189      - implement A-grid / C-grid selection for wind-stress input files.
190      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
191      for now, in exf_bulk_largeyeager04.F only :
192      - change implementation for case where windspeed + 2. components wind-stress
193        are read-in. AND use rhoConstFresh to convert evap.
194    o pkg/seaice:
195      - use correct EXCH_UV for wind-forcing (on A-grid).
196      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
197        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
198    o pkg/exf:
199      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
200      EXF_INTERPOLATION:
201      - merge global_with_exf/code version of exf_interp_read.F
202        to the main code ;
203      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
204        reading the file ; Important: This options needs to be defined to recover
205        previous code.
206        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
207      - no longer loose real*8 precision along the way when using exf_iprec=64.
208    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
209      - change discretisation of evp-solver in order to avoid another exchange
210        (changes lab_sea) and clean up a little
211      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
212        help the adjoint (this also changes the results slightly)
213      - add a few "_d 0" where they had been missing in seaice_evp.F
214      - cleaning up: remove unused seaice_calc_rhs.F
215    o pkg/exf: some cleaning-up:
216      - change various "constants" into runtime parameters
217      - cleaned-up Large&Yeager04 routine which should eventually
218        replace exf_bulkformulae.F (changed names of S/R and CPP)
219        and merged various ALLOW_ATM_WIND options
220     only used with thsice pkg (in thsice_get_exf.F):
221      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
222        which are used when useStabilityFct_overIce=TRUE (= the default)
223      - change default values of ice & snow emissivity and scale downward LW
224        by ice & snow emissivity.
225    o pkg/thsice:
226     fix few little problems, in thsice_calc_thickn.F:
227      - growth vertically (and not laterally) if iceFrac == iceMaskMax
228      - melt only laterally if hIce < hThinIce (as the comments say)
229      and in thsice_extend.F:
230      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
231      - start to form ice as soon as the minimum ice-volume is reachable.
232     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
233      and cpl_aim+ocn
234    o pkg/kpp
235     - move computation of surface related input fields to KPP into a new
236       subroutine kpp_forcing_surf.F
237     - remove wrong (within bi,bj loops) EXCH calls.
238     - little cleaning (add argument myThid in last position, cvs header ...)
239     - for now, fix conservation problem by exchanging KPPviscAz (may not
240       be the best fix)
241    o pkg/seaice
242     - check for inconsistent evp parameter/cpp-flag combination
243     - remove leftover errIO flat for obsolete name list error handling
244    o OpenAD
245     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
246    
247    checkpoint59a
248    o pkg/seaice: some parameter clarifications and a little bit of clean up
249    o pkg/thsice: rename run-time parameters:
250       himin       -> hIceMin
251       himin0      -> hThinIce
252       hihig       -> hThickIce
253       i0          -> i0swFrac
254       transCoef   -> bMeltCoef
255       frac_energy -> fracMelting
256      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
257       with default values (for now) that do not change the results.
258      remove old version of thsice vars advection in pkg/seaice.
259    o in FFIELDS.h:
260      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
261      - make pLoad & sIceLoad always available (but still only used if
262         ATMOSPHERIC_LOADING is #define).
263    o pkg/kpp: replaced _KPP_RL with _RL
264    o bug fixes for vertical diffusivity computations when both KPP and
265        3D diffusivity arrays are used.
266    o pkg/seaice: fix bug in evp solver, while doing that
267      - change (improve?) discretization of stress computations for both
268        cgrid-lsr and evp solver
269      - add a new routine to compute strain rates
270      - the above changes lab_sea results
271      - add no slip conditions for evp solver (off by default), lsr-version
272        may follow
273      - fix exchange for shear at Z-points (does not change lab_sea)
274      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
275        (to force the user to pick a time step since there is not "safe" way
276        of choosing it)
277      - add principal stress diagnostics
278      - rearrange fields for evp a little to avoid having to call a: too many
279        exchanges and b: exchanges for stress trensor components which we do
280        not have.
281      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
282        of evp, complete rewrite for lsr case (latter is does not yet work
283        in all cases)
284    o pkg/kpp: add code to have mixing in shelf ice caverns
285      - add myThid to all kpp routines (long overdue)
286    
287    checkpoint59
288    o pkg/exf:
289      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
290        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
291      - move exf header files from lower_case.h to UPPER_CASE.h ;
292        add missing cvs Header & Name
293      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
294      - add namelist param. selectStressGridPosition, exf_monFreq
295      - retire many _CLIM routines, and remove data.exf_clim
296        + params moved to data.exf
297        + climsst, climsss now handled by exf_set_gen, i.e.
298          climss?period=0 refers to constant field,
299          climss?period=-12 to monthly forcing
300      - split up namelists in data.exf
301    o pkg/seaice:
302      - remove seaice_exch and seaice_exch_uv
303      - remove superfluous exchange of theta
304      - add myThid to seaice_budget_ocean/ice
305      - add new interface for atmospheric wind forcing (C-grid only)
306        + new routine
307        + two new field (taux, tauy for stress over ice)
308        + removed one global field (DAIRN) for C-grid case only
309    o pkg/thsise
310      - 2nd set of modifs for thsice adjoint in conjunction with exf
311    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
312    
313    checkpoint58y_post
314    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
315      vertical diffusivity, similar to that in MOM4; turned on using
316      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
317      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
318    o Added capability for 3D specification of background vertical diffusion
319      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
320      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
321      "data" file that contains the 3D vertical diffusivity coefficients.
322    o ice dynamics (pkg/seaice) with thsice thermodynamics:
323      - add code within pkg thsice to advect & diffuse sea-ice fields
324      similar to (and will replace) what has been added in  seaice_advdiff.F,
325      but: - conserving Mass, Heat & Salt.
326           - better when using non-linear advection scheme (not yet fully tested)
327           - can also be used in atmospheric set-up (for now, only the diffusion).
328    
329    checkpoint58x_post
330    o IO option for global-file compact format:
331      - add options when generating topology (utils/exch2/matlab-topology-generator)
332      - add I/O capability (pkg/mdsio).
333      - adapt utils/matlab/rdmds.m to read this format.
334      for now long-line format not yet supported by pkg/mdsio (& exch2).
335    o shelfice: add a few diagnostics
336    
337    checkpoint58w_post
338    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
339      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
340      (and replace horiVertRatio in NH code).
341      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
342                         and tutorial_plume_on_slope (sensitive to truncation)
343    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
344      directly to drive seaice model (C-grid only)
345    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
346     - reintroduce computation of wind from stress,
347     - compute tau (in exf_bulkformulae.F) from windstress averaged to
348       mass points to avoid tau = 0
349     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
350    o rdmnc.m: make it work with "global" files created with gluemnc
351    o rdmnc.m : some improvements in dealing with singleton dimension
352      (tested on all testreport mnc output files).
353    o genmake2: disable pkg/profiles if netcdf test fails.
354    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
355    o move call to cal_readparms up to make calendar parameters/variable available
356      to all packages
357    
358    checkpoint58v_post
359    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
360      useDynP_inEos_Zc tested.
361    o pkg/exf: changes to properly interpolate/mask/scale initial fields
362    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
363      and portions thereof.  See read_cs.txt for description and examples.
364    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
365      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
366      following the great-circle arc between those 2 points.
367    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
368      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
369    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
370     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
371     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
372     - still needs work (not working with some options ; efficiency to improve)
373       and serious testing.
374     - use this scheme for temperature & salinity in 2 advection test exp.:
375       advect_xy & advect_xz, respectively.
376    
377    checkpoint58u_post
378    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
379    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
380    o testreport: add option "-skipdir" to skip some test.
381    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
382      momentum calculation.
383    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
384    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
385      remove checkpoint.F and the_correction_step.F (no longer used);
386      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
387    o add option (linFSConserveTr) to correct for tracer source/sink due to
388      Linear Free surface
389    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
390    o pkg/thsice: fix reading mnc-pickups
391    
392    checkpoint58t_post
393    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
394    o pkg/mdsio:
395     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
396       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
397       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
398     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
399     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
400       either MDS_READ_FIELD or MDS_WRITE_FIELD )
401     - new S/R (to replace MDSWRITEMETA), which allows to write more
402       informations (variable names, time ...) to meta files.
403     - modify rdmds.m to give back the meta file content.
404    o pkg/diagnostics: change vertical interpolation to be safer, and more
405       flexible (define p-levels to interpolate to in data.diagnostics);
406      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
407       diagnostic pointer.
408    o pkg/seaice: more cleaning up of seaice_growth, added many comments
409    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
410    o fix multi-category seaice:
411     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
412       SEAICE_MULTICATEGORY
413     - fix short wave heat flux
414    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
415       and allow to use EVP solver. Change forward lab_sea: test both EVP
416       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
417    o Initial check-in of lab_sea adjoint
418      (very similar to natl_box_adjoint/code_seaice)
419      * used C-grid and EVP solver
420      * used KPP, GM/Redi
421      * uses inAdExact=.TRUE.
422      * gradient checks fail for both ADM and TLM
423        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
424        f.d. gradients actually seem more problematic than ADM, TLM gradients;
425        issue is related to forward mismatch between g77 an ifort
426    o pkg/seaice: overhaul of thermodynamics
427     - growth.F and groatb.F are replaced by new routine seaice_growth.F
428     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
429     - move a few global fields out of SEAICE.h into seaice_growth.F and
430       make them 2D (FICE/QNETO/ ...)
431     - remove FO (it is the same as QNETO)
432     - introduce a few local fields to avoid modifying external fields such
433       as atemp, etc.
434    
435    checkpoint58s_post
436    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
437      changed exf_set_gen.F so that
438        genperiod=0 means input file is one time-constant field and
439        genperiod=-12 means input file contains 12 monthly means
440    o CG2D: use pre-computed solver main-diagonal (stored in common block);
441      this affects truncation error ; generate new output file for exp. which
442      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
443        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
444        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
445        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
446        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
447        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
448    o start implementation of deep-atmosphere and anelastic formulation
449    o verification: remove 2nd copy of input files and use script "prepare_run"
450      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
451    o mom_common/vecinv/fluxform: fix a few initialisation isssues
452    o profiles: fix for multithreaded case
453    
454    o diagnostics: rename few diags:
455      s/'PRESSURE'/'RCENTER '/g
456      s/'TICE    '/'oceFreez'/g
457      s/'TAUX    '/'oceTAUX '/g
458      s/'TAUY    '/'oceTAUY '/g
459      s/'SWFLUX  '/'oceQsw  '/g
460      s/DIFx/DFxE/g
461      s/DIFy/DFyE/g
462      and add few ocean-forcing diagnostics:
463      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
464    o modifications to pkg/seaice/growth.F and budget.F, which change results of
465      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
466      as actual snow thickness.  It now refers everywhere to effective snow
467      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
468    
469    checkpoint58r_post
470    o modifications to pkg/seaice/growth.F, which change results of
471      lab_sea experiment: fixes pertain to melting snow over open water, to
472      masking EVAP under sea ice, and to using the correct AREA variable for
473      computations of EVAP, PRECIP, HSNOW, and GHEFF
474    o add ability to read bathy, salt, and theta using MNC (off by def)
475    o add flooding algorithm and advection of HSNOW for pkg/seaice;
476      both are turned off by default and do no change any results
477    o seaice advection with pkg/thsice: a step toward the use of non-linear
478      advection scheme, but #ifdef or commented out for now (requires more EXCH).
479    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
480      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
481      in natl_box (affects results @ truncation level: update output.txt)
482    o multi-threading and IO:
483      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
484      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
485        (needed to work with SingleCpuIO): tested in all verif. exp.
486    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
487      affects the results (but none of the verification test uses this scheme).
488    o Adding some pkg/diagnostics capability to pkg/seaice
489      (will certainly be subject to changes)
490    o ctrl: adding new control variables:
491      lwflux, lwdown, evap, snowprecip, apressure, runoff
492    
493    checkpoint58q_post
494    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
495      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
496      high_res_cube configuration by 4% on Columbia.
497    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
498      add (in global_with_exf/code) a version of EXF_INTERP_READ without
499      dynamical allocation (seems to work in multi-threaded).
500    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
501      single CPU io) so that TAF does not have to see EESUPPORT.h
502    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
503    
504    checkpoint58p_post
505    o obcs: stop if obcs is used with useCDscheme = .true.
506    o shelfice:
507     - fix a sign error so that no slip at shelfice interface works
508     - remove stop for combination non-hydrostatic code and shelfice. That does
509       not mean, that the results are correct, but at least they are numerically
510       stable
511    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
512    o added adjoint exch routined for all exch*3d* routines
513      and updated flow directives
514    
515    checkpoint58o_post
516    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
517      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
518    o change controling S/R for writing pickup file (new S/R do_write_pickup)
519      and clean-up reading/writing of pickup files.
520    o fix local version of read/write pickup (NH part) in rotating_tank/code
521    o simplify EXCH interface:
522     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
523     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
524    o added the regrid package
525    o shelfice:
526     - add a simple boundary layer scheme to reduce noise
527     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
528    
529    checkpoint58n_post
530    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
531       local variable (not in common block).
532    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
533      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
534      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
535        to work with SingleCpuIO.
536    o add "_d 0" to real constant of pkg/cfc subroutines ;
537       update exp. cfc_exemple & tutorial_cfc_offline output files.
538    o multi-threading and IO:
539      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
540        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
541      - barrier before and after reading.
542      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
543      - avoid using MDS_WRITELOCAL for LAND pkg output.
544      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
545        common-block variables ; Allows multi-threading with master-thread IO.
546    o change default MAX_NO_THREADS from 32 to 4 ;
547      and stop cleanly when MAX_NO_THREADS is too small.
548    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
549    
550    checkpoint58m_post
551    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
552       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
553    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
554       keep global_ocean.90x40x15 (for AD testing) with former secondary test
555       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
556    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
557        add MITgcm_tutorials (= code + all the tutorials)
558    o ecco, option to compute cost for total ssh (mean+anom)
559    o consistent with addition of ptracer and ssh in pkg/profiles
560    o profiles: adding ptracer and ssh
561    o testreport: change multi-test output-file name
562      (from output.txt.{name} to output.{name}.txt)
563    o profiles: now ok for mutli-tiles case
564    o seaice: add 4 parameters for different advection schemes for area,
565      (effective) seaice thickness, enthalphy, and snow height. Their default
566      is the standard parameter SEAICEadvScheme
567    o calc_gw:
568     - add cosFacU in zonal viscous flux (harmonic.visc.).
569     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
570       of tutorial_plume_on_slope.
571    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
572    o calc_gw: true flux-form, account for horizontal grid spacing.
573      update rotating_tank results, but not plume_on_slope (affected at
574      truncation level, 11 digits).
575    
576    checkpoint58l_post
577    o calc_gw:
578     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
579     - remove side-drag for now (need to fix it); update plume_on_slope results.
580     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
581    o commit code to make SST/SSS weights spatially variable
582      (based on either variable in-situ or variable initial T/S weights)
583    o pkg/ecco:
584      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
585        now based on horizontally varying weights wthetaLev, wsaltLev
586      * cost_averagesflags now returns year indices in addition to day, month
587      * sflux balance is performed on annual basis
588        (sflxumm, sfluxmm2, bal_sfluxmm)
589      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
590        including separate counting and multipliers
591    o pkg/rbcs
592      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
593    
594    checkpoint58k_post
595    o testreport:
596     - always build in dir. "build" (if not there, mkdir build instead of building
597       & running in input)
598     - run in dir run (if it exists), in build otherwise.
599     - call prepare_run (if input/prepare_run exists)
600     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
601    o pkg/exf modifications to interpolation and rotation routines for more
602       reasonable treatment of North Pole singularity: for tracers North Pole
603       value is set to northernmost zonal-mean value, for zonal velocity it is
604       set to zero, and for meridional velocity it is set to northernmost value.
605    o pkg/exf/exf_check_range.F
606     - add tile index to diagnostics and move stop statement to the very
607       end of the routine.
608    o pkg/diagnostics: (diagnostics_main_init.F)
609      define title of isomorphic variables according to the current config.
610    o pkg/thsice with pkg/seaice dynamics:
611    - fix domain of computation (interior only, required for exf) and do exchanges
612    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
613    o towards a standard way of dealing with multi-threading in MONITOR
614      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
615    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
616       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
617    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
618    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
619    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
620       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
621    o tracer advection:
622     - clean-up and simplify calc_common_factors.F
623     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
624       advection subroutine (but still not used within DST advection S/R)
625    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
626    
627    checkpoint58j_post
628    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
629      from file (collects calls previously in FORWARD_STEP)
630    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
631    o adjoint store dir. adjusted accordingly
632    o genmake2
633      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
634    
635    checkpoint58i_post
636    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
637      on wind stress (SEAICEstressFactor defaults to 1.)
638    o Total number of Timers is finite (<=40): comment out 2 non-essential one
639      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
640    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
641      on CS-grid: no longer loosing mass.
642    o exf & curvilinear-grid: no longer modify longitude xC & xG.
643    o pkg/ggl90: fix sloppy output and fix a bug
644    o pkg/seaice: added SEAICEuseEVPpickup parameter
645      - Set to false in order to start EVP solver with
646        non-EVP pickup files when using SEAICEuseEVP
647      - fix sign error in diffusion in seaice_calc_rhs
648    
649    checkpoint58h_post
650    * Modifications for bottom topography control
651      o replace hFacC by _hFacC at various places
652      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
653      o add non-self-adjoint cg2d_nsa
654      o update autodiff support routines
655      o re-initialise hfac after ctrl_depth_ini
656      o works for 5x5 box, doesnt work for global_ocean.90x40x15
657    * Adding verification for 5x5 box (4-layer) bottom topography control
658    
659    checkpoint58g_post
660    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
661       used for mean seasonal cycle, mean diurnal cycle); add an example
662       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
663    o pkg/ggl90:
664      - add parameter (minimum surface kinetic energy)
665      - fix bug (avoiding division by zero)
666    o couple pkg/thsice to pkg/seaice:
667      - modify advection in seaice to accomodate new scalar fields to be advected
668      - only muliDimAdection scheme work with seaice/thsice
669      - mapping of thsice-variables to seaice-variables, back and forth
670      - does not break the verification experiments, but does not give the
671        desired results either
672    o pkg/seaice
673      - make (default) second order advection a bit less confusing?
674    
675    checkpoint58f_post
676    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
677      to pkg/seaice):
678      - new routines thsice_map_exf and thsice_get_exf provide the interface
679      - add an additional formal parameter to thsice_solve4temp
680    o pkg/exf:
681      - add new fields wspeed, snowprecip (to be able to couple to thsice)
682      - correct Stefan-Boltzmann constant
683      - new parameter for longwave surface emittance
684      - separate some stuff from exf_bulkformulae into new routines  
685        exf_radiation, exf_wind
686      - add new parameters and constants: longwave emissivity for ocean, ice
687        and snow, evaporation parameters over ice
688      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
689        either wind from stress or stress from wind
690    o pkg/thSIce:
691    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
692    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
693       and THSICE_CALC_THICKN
694    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
695    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
696      to make debugging easier.
697    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
698    o pkg/bulk_force:
699      - clean-up comments and parameters ;
700      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
701    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
702      generate new output for test-experiment: aim.5l_cs.thSI
703    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
704      testreport accordingly
705    
706    checkpoint58e_post
707    o SEAICE_CGRID adjoint done
708    o R_STAR adjoint implemented.
709      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
710      * need to sort out init. of h0facc, etc.
711    o Make pkg/profile fully independent of ecco,cost, etc. stuff
712      to be able to use it in pure forward.
713    
714    checkpoint58d_post
715    o upgrade simple test-experiment to tutorial example:
716     step.1: duplicate the experiment and (step.2) will remove the old copy.
717      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
718      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
719      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
720      tutorial_global_oce_biogeo    <- copy of dic_example
721      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
722      tutorial_plume_on_slope       <- copy of plume_on_slope
723      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
724      tutorial_global_oce_optim     <- empty for now (David ?)
725      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
726     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
727    o correct a sign problem in cost_scat.F
728    o obcs and ptracers: fix boundary conditions for advections schemes
729      with larger stencil
730    o thsice adjoint: start
731    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
732      completeness
733    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
734      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
735    o ptracers adjoint:
736      * avoid extensive recomputatations
737      * fix missing re-init. of gptr (missed by TAF)
738    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
739      me to turn off the excessive output to STDOUT that this package produces
740    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
741      and add those terms in Vector-Invariant formulation.
742    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
743      if the control period (xx_hfluxperiod etc) is 0
744    o in profiles pkg, clean routines and fix details
745    o in ecco pkg, reading ssh data:
746      fix problem in case the model does not start at iter0=0
747    o fix mnc-pickup/restart for ptracers
748    o new package prifiles:
749      code to compute profile-based cost by Gael Forget
750      (modifs in ecco, ctrl, autodiff)
751    o Benign bug fix in initialization (spotted by M. Mazloff) of
752      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
753    
754    checkpoint58c_post
755    o adjoint: finish NLFS adjoint and provide reference output in
756      verification/global_ocean.90x40x15/results_ad_nlfs
757    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
758      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
759      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
760      with SEAICE_CGRID defined.
761    o move calendarDumps from "data" to "data.cal" and clean-up the code
762      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
763    o add useEXF & useCAL flags (for now, set in hard-coded way)
764    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
765      (were missing in NH mode, and wrong in quasihydrostatic mode).
766      waiting for Chris updated version of calc_gw to add those CALLs.
767    o fix bug in quasihydrostatic S/R ;
768      add a test for this option: global_ocean.90x40x15.qshyd
769    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
770      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
771    o add on/off flag useOffLine for package OFFLINE
772    o seaice:
773      - modify advection so that it works also on the C-grid
774      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
775        problem in multi-tile runs with C-grid
776      - add flags for clipping ice velocities and/or masking solver forcing
777      - fix drag (ocean on ice) formulation and a bug that caused noise in the
778        C-grid solver
779      - added a few comments to seaice_diffusion.F
780      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
781        are now exclusive)
782      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
783        required re-ordering the code a little:
784       + make DAIRN global variable (defined in SEAICE)
785       + move computation of the viscosities eta and zeta into a new separate
786         routine (because I need to recompute them in seaice_ocean_stress.F)
787    
788    checkpoint58b_post
789    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
790      update output.txt of exp. aim.5l_cs.thSI
791    o various mnc cleanups and improvements:
792      + shrink lookup tables by factor of ~4
793      + better error reporting when running out of lookup space
794      + able to handle longer path/file names (up to 500 chars)
795    o adjoint:
796      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
797      - TBD: "hidden" mom_vecinv recomp. in dynamics
798    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
799     (allow to differentiate between forcing components using new integer flags:
800      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
801     and add new flag to put Dissipation tendency out of Adams-Bashforth.
802    o ecco
803      - enable trend removal from SSH anomaly obs.
804    o adjoint
805      - a fix for PmEpR when #undef EXACT_CONSERV
806      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
807      - try to fix "hidden" recomp. in forward_step for NLFS
808        (NLFS seems broken sometimes after I checked it in)
809    o seaice:
810     - add c-grid version of the dynamic solver:
811       + three new routines that are the c-grid substitute lsr, dynsolver
812         and ostres
813       + put a few fields that were local to dynsolver into global common
814         blocks, so that I can move the computation of stresses etc into
815         seaice_lsr (saves coding but may break the adjoint).
816     - replace more hardwired parameters by runtime parameters
817     - add ice masks that mask the rhs of the implicit solvers where there
818       is no ice (commented out in seaice_dynsolver, because i am not sure
819       if this works properly), eventually this should replace the clipping
820       of ice velocities in seaice_dynsolver to +/-40cm/s.
821    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
822      include it only where its needed
823    o move balancing of fluxes before the call of external_forcing_surf
824    o seaice:
825      - correct units of turning angles (now they are really in degrees)
826      - move computation of GWATX/Y out of main routine into dynsolver
827      - initialize GWATX/Y in seaice_init
828    o Apply mask on Fresh-Water flux (needed for SSH forcing).
829      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
830    o seaice: add runtime flags for turning angles (default to zero)
831    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
832      and trend from exf forcing and ctrl control adjustments
833    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
834      (since checkpoint57x_post)
835    o change the default rotation period to 86164.s = the Earth rotation
836    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
837      and based on a reference stratification. Tested within hs94.cs-32x32x5.
838    o seaice advection: add code for choosing between the default (2nd order
839      central differences) and multiDim advection schemes provided by
840      pkg/generic_advdiff
841    o seaice:
842      - removed all references to SEAICE_GRID.h fields from
843        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
844        (cubed-sphere configuration will change a little)
845      - grid computations in seaice_init are obsolete now.
846      - cleaned up code a little so that is easier to read (hopefully).
847      - added new (better?) discretizations of default advection and diffusion
848        (turn on with SEAICEuseFluxForm)
849      - replace 1 in 3d global fields by kSurface in growth.F
850      
851    checkpoint58a_post
852    o seaice:
853      - bug fix in advect.F
854    o shelfice:
855      - separate shelfice load anomaly from pload (breaks with time
856        dependent forcing), => introduce constant field shelficeLoadAnomaly.
857        Its default is 0., but it may be computed more cleverly from (unknown)
858        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
859        done offline. A good approximation of the pressure load anomaly is
860        necessary to avoid large initial adjustment processes underneath
861        deep-reaching shelfice.
862      - small fix in ISOMIP shelfice_thermodynamics
863      - add more sophisticated thermodynamics of Hellmer (1989), this is
864        now the default
865      - give a few constants more intuitive names
866    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
867      if bulk formulae are used in long integration (especially EmPmR). Turn
868      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
869      if balancePrintMean, the imbalance that is substracted is printed to
870      STDOUT.
871    o fix bug (typo) in obcs_apply_eta.F
872    o add a new package shelfice which enables us to model the circulation
873      underneath shelf-ice with draughts of hundreds of meters.
874     - works
875     - to do: + include improved thermodynamics
876              + check whether kSurfC (from model/inc/SURFACE.h) can be used
877                instead of new field kTopC
878              + can we use topoFile, Ro_surf and existing code in ini_depth.F
879                instead of new field R_shelfIce and new code in ini_depth.F
880                and ini_mask_etc.F?
881              + adjust vertical mixing schemes?
882    o seaice pkg:
883     - add a cpp-flag to include a simple formula for a salinity dependent
884       freezing point of sea water at the surface
885     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
886       meridional stresses are now different (and hopefully correct)
887    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
888       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
889       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
890    o pkg/diagnostics: add options and parameters for regional-statistics
891       diagnostics ; define regions by reading a region-mask from a file
892       (might add other options later)
893    o pkg/bulk_force:
894     - add option and parameters to use AIM surface-flux formulae.
895     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
896       others forcing fields (defined in PARM05, parameter file "data") are loaded
897       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
898     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
899     - use the right EXCH call for uwind,vwind (to work on CS-grid).
900     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
901       and parameters (note: calcWindStress replaces .NOT.readwindstress).
902     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
903    
904    checkpoint58
905    o add "--embed-source" option to genmake2 which, when the supporting
906      tools can be compiled (as determined by genmake2) will turn on the
907      embed_files package which then embeds the entire MITgcm source code
908      (*.[fFhc] + Makefile) used for the build within the executable
909      - requested by CNH but off by default
910      - adds a paltry <9MB to the mitgcmuv executable in most cases
911      - only writes the output when useEMBEDSRC in eedata is true
912    o clean up 3-dim. relaxation codes:
913      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
914      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
915      * Thanks to Tom Haine for testing!
916    
917    checkpoint57z_post
918    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
919      affects output (@ truncation level) of exp. plume_on_slope ; updated.
920    o fix the pickup behavior for obcs in combination with ptracers
921    o fix a bug in ptracers_external_fields_load
922    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
923      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
924    o transfered surface NH pressure to eta field (if exactConserv).
925    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
926         and update lab_sea output.txt file.
927    o completing 3-dim. relaxation code: additional term
928         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
929      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
930      * At compile time, in "EXF_OPTIONS.h" set
931          #define  ALLOW_CLIMTEMP_RELAXATION
932          #define  ALLOW_CLIMSALT_RELAXATION
933      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
934          tauThetaClimRelax3Dim = 15552000.0,
935          tauSaltClimRelax3Dim  = 15552000.0,
936      * 3 cases:
937          1) Use a constant-in-time 3-dim. field
938          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
939          3) Real-time relax. to time-evolving prescribed field
940    o Adding Laplacian-type smoothness constraint on
941      initial and boundary (forcing) controls (ic, bc)
942      * enable at compile-time via
943        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
944      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
945      * Absolute scale somewhat unclear so far
946      * no area weighting was included since no other cost term does so far
947    
948    checkpoint57y_post
949    First step for a NLFS adjoint
950    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
951    o new init. routines for calc_r_star, calc_surf_dr
952    o still need to deal with ini_masks_etc
953    o testreport seemed happy
954    checkpoint57y_pre
955    
956    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
957    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
958    o add new offset feature to offline pkg (plus minor cleanup)
959    o cfc fixes for final year of integration
960    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
961      be in GCHEM_OPTIONS).
962    
963    checkpoint57x_post
964    o fix testreport Pb in multiple test experiment.
965    o cleanup our namelist syntax in verification:
966      - make it more F95 standards compliant (some work still needed)
967      - allows the vast majority of our tests to work with gfortran
968    o Non-Hydrostatic:
969     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
970     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
971    o Allow to apply AB on T,S rather than on AB(gT,gS):
972     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
973     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
974       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
975     - need a "clever" read_pickup to restart from the other AB formulation
976    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
977    o remove some unused variables (reduces number of compiler warnings)
978    o adjoint
979      * Disable useVariableViscosity for adjoint for time being
980        (there are a number of extensive recomputations)
981      * Initialize certain variables needed for adjoint
982    
983    checkpoint57w_post
984    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
985                 fix the singleCpuIO RS version of MDSWRITEFIELD
986       and add a WARNING if using globalFiles=T with multi-processors.
987    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
988      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
989    o tracer advection scheme:
990      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
991       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
992       was not very convenient).
993      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
994       (further tests needed for the implicit DST & Flux-Limiter schemes).
995    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
996      and sRef for convenience, handy, when you want to initialize
997      ptracers in a large domain with a constant non-zero value. Also,
998      untangle ptracers_init.F a little.
999    
1000    checkpoint57v_post
1001    o change dome exp. to use variable viscosity in side-drag terms.
1002    o remove all the files from the cfc_offline test since they are now
1003      incorporated into tutorial_cfc_offline which has been producing
1004      identical results for a few days of testing
1005    o add new parameter: sideDragFactor to enable half-slip-side BC
1006      and change side-drag S/R to use viscosity from mom_calc_visc
1007      (can switch back by setting sideDragFactor=0.); affects results at
1008      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
1009       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
1010    o vorticity & strain are now computed without masking, to account for
1011      no-slip-side BC in variable viscosity calculation ; mask is applied
1012      anyway later on, before computing advection/coriolis terms.
1013    o modify exp4 to test new obcs support for reading from external files
1014      and for passive tracers
1015    o fix behavior of ptracers_monitor when monitor output is written to a
1016      netcdf-file; still not independent of monitor.F (writes in the same
1017      file).
1018    o change default value of tRef (put a uniform, meaningful value for ocean
1019      & atmos) and initialize sRef (was missing, as Martin mentioned).
1020    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
1021      to be proportional to enstrophy dissipation length.  Thus,
1022       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
1023      This is now consistent with Smagorinsky and with the manual.
1024    
1025    checkpoint57u_post
1026    o OBCS and PTRACERS: add open boundary support for passive tracers
1027      - either use homogenous (pseudo) v.Neumann conditions or prescribe
1028        OB-values from file; this is not different from the way theta and salinity
1029        are treated
1030      - however, Orlanski-radiation conditions are not supported, and the model
1031        will stop if you use pTracers and Orlanski at the same time.
1032      - beefed up the rountine obcs_external_fields_load: now only those open
1033        boundary values are overwritten with values from files for which there
1034        are really files, otherwise the OB-fields remain untouched. This makes
1035        it possible to use different OBs at different ends of the domain (as
1036        with EXF)
1037    o reduce number of exch calls in shap_filt (s2).
1038    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1039      truncation level) 4/5 MLAdjust test results (11&12 digits match).
1040    
1041    checkpoint57t_post
1042    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1043    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1044      same truncation, independent of the face number: affects affects several
1045      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1046    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1047      note that biharmonic viscosity + no-slip was not tested in any experiment.
1048    o fix bug in non-linear free-surf side-drag ; generate new output for
1049      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1050    o make mnc honor the writeBinaryPrec flag for most kinds of output
1051    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1052    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1053      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1054    o add brackets in multi-terms sum to get same truncation, independent of
1055      the face number (manage to get exactly same value of gU,gV at the cs-edge)
1056      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1057    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
1058      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1059      a maximum grid-scale Reynolds number.  Also, changes all length calculations
1060      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1061      Suggested values of viscosity parameters found in mom_calc_visc.
1062      Many new viscosity diagnostics available.
1063    
1064    checkpoint57s_post
1065    o Add clearing-house for viscosity calculations, mom_calc_visc and
1066      correct numerous bugs in LeithD and Smagorinsky discretizations.  
1067      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1068      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1069      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1070      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
1071      The Strain-Tension form is now called with useStrainTensonVisc=.true.
1072      ViscAhStrain and viscAhTension are now retired.
1073    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1074    o In response to JMC's bug report, genmake2 now ignores any soft-links
1075      that it finds in the *current* directory when searching for files.
1076      Soft-links found in any other source directories will still work as
1077      they did before.
1078    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1079      a C routine to unlimit the stack size
1080    o mnc-ify pkg/aim snapshot vars
1081    o mnc-ify pkg/land as requested by Daniel
1082    o various changes to mnc including:
1083      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1084      - output can now be grouped so that all files within a group
1085          change the ITER portion of their names in lock-step together
1086      - can now read ("global") PER-FACE (in addition to PER-TILE) files
1087          and works with both EXCH1 and EXCH2 (but needs more testing)
1088      - writing works for all verification test cases w/ g77 on Linux
1089    
1090    checkpoint57r_post
1091    o make MNC variable initialization happen earlier
1092    o add diagnostics for (almost) each term of the momentum Eq.
1093    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1094    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1095    o remove MINIMAL_TAVE_OUTPUT option ;
1096      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1097    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1098      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1099    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1100    o add time-dependent SST, SSS control
1101    o cost terms in ecco/ modularized (new cost_generic.F)
1102    o cost_averages routines are modularized (new cost_averagesgeneric.F)
1103    o new infrastructure for seaice model vs. obs misfits in seaice/
1104      * driver from the_main_loop.F is seaice_cost_driver.F
1105      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1106      * gradient check in Exp. 6a of natl_box_adjoint/
1107    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1108      (see README file)
1109    
1110    checkpoint57q_post
1111    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1112    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1113      - bug was reported by Jean-Michel and Ian Fenty
1114    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1115      update exp. cpl_aim+ocn output.
1116    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1117      Needed for high-res. runs with large global files
1118      to be able to limit tapelev size
1119    o Changed some tests for adjoint:
1120      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1121      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1122      * global_ocean.90x40x15/ back to default 3-level checkpointing
1123    o Modifications to enable scripted COMMON to MODULE conversion
1124      * verification/OpenAD/code/ has necessary scripts and description;
1125      * converts, compiles and runs successfully;
1126    
1127    checkpoint57p_post
1128    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1129    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1130      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1131    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1132    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1133      (was already the case for dissipation with mom_vecinv,
1134       and also the case for grad.PhiHyd when staggered-timeStep)
1135      This will allow to put dissipation out-off the AB time-stepping.
1136     Unfortunately, affects truncation error. Update output of exp. that "fails"
1137      (cg2d matching number) and leave the others for later: front_relax(10),
1138      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1139      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1140    
1141    checkpoint57o_post
1142    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1143      (2) its ready to be documented during the 20050801 DocFest
1144    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1145      for ideal_2D_oce and lab_sea on linux_ia32_g77
1146    o set to #undef CTRL_SET_OLD_MAXCVARS_30
1147      in global1x1_tot/code_seaice_adj to access indices 32, 33
1148      (worth another tag)
1149    
1150    checkpoint57n_post
1151    o adding precip control xx_precip 32
1152    o adding swflux control xx_swflux 33
1153    o Replacing 10 forcing penalty cost routines by 1 generic.
1154    o Implementing partitioning in time-mean and variable adjustment
1155      for atmos. state.
1156    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1157  o in natl_box_adjoint:  o in natl_box_adjoint:
1158    * updated: results_bulk/    * updated exp 1 to 10
1159    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
1160    o updated global1x1/*_seaice_adj/
1161      to incorporate latest changes
1162    o enable useSingleCpuIO for mdsio vector routines
1163      (applies in particular to tapelev I/O)
1164    o removed inefficient K-loop in all active_file*control*.F
1165    
1166  checkpoint57m_post  checkpoint57m_post
1167  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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