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revision 1.760 by jmc, Sun Dec 24 22:30:57 2006 UTC revision 1.865 by jmc, Mon Aug 27 22:21:37 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 pkg/thsice:
8     - fix reshaping of sea-ice just after advection:
9       melt all the ice only if ice-volume is too small.
10     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
11       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
12     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
13    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
14      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
15    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
16      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
17      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
18      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
19      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
20      -> update output.txt
21    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
22     this affects truncation error: -> update output.txt of exp:
23      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
24      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
25    
26    checkpoint59f
27    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
28    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
29      a bounded range (in forward mode)
30    o pkg/ecco, ctrl, autodiff and mom_common:
31     internal parameter controls, completements of implementations
32    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
33    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
34      (not seem any difference in testing results).
35    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
36       at face corners.
37    o pkg/generic_advdiff:
38     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
39      loop range indices for computing vertical advection tendency
40      and do the calculation in the interior only (no overlap) ;
41      for now, only implemented for SOM advection (to save CPU time).
42     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
43    o exch2 adjoint
44      First set of changes:
45      - add exch2 hand-written adjoint templates
46      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
47        This will require cleanup in pkg/autodiff/*.F
48        (changed routines currently kept separate in verif. code/)
49      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
50        that used to hide exch2 or cubed-sphere specific code
51        (commented via 'cph-exch2')
52    o pkg/seaice
53      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
54    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
55       output of global_ocean.cs32x15.thsice .
56    
57    checkpoint59e
58    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
59      for B-grid vector (not yet tested) and C-grid vector (<- only used
60      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
61    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
62      (#ifdef ALLOW_SALT_PLUME)
63    o gather_2d/scatter_2d: removed halo regions
64    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
65      scheme and the corresponding test case (under front_relax dir). For now,
66      only available with Skew-flux form and not yet tested in realistic set-up.
67      adjoint: store directives updated, but gradient checks deteriorated,
68      so maybe GM/Redi adjoint is now broken.
69    o seaice adjoint
70      * add AREA, HEFF, HSNOW as control variable
71        (should not change lab_sea results)
72      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
73    o pkg/seaice:
74      * added computation of saltFlux in seaice_growth;
75        For time being, sea ice salinity is assumed constant
76        contribution of snow flooding to freshening of sea ice is neglected.
77        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
78        defaults to 0.0 in order to maintain backward compatibility.
79        Typical values for SEAICE_salinity are 4 to 10 g/kg.
80      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
81      * added SEAICE_availHeatFrac, which specifies fraction of surface level
82        heat content used to melt or grow ice
83      * commented out cap of HICE: it helps keep ice thinner
84      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
85      * applied OBCS T/S mask to HEFFM sea ice mask
86    
87    checkpoint59d
88    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
89     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
90     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
91    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
92     and change default value of parameter "GM_Small_Number";
93     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
94       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
95       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
96    o pkg/ecco: cost function when applying pkg/smooth to controls
97    o pkg/ctrl: add forcingPrecond run time parameter
98    o pkg/seaice:
99     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
100     - fix bug in metric terms of u-equation in LSR solver (implicit part),
101       changes verification/lab_sea
102     - rearrange implicit part of u-equation in LSR solver to make it easier to
103       read, understand, and debug. This causes changes at the truncation level.
104     - fix (serious) bug in the boundary conditions (sign error in the implicit
105       part) of the LSR solver. Changes all LSR results.
106     - fixed problem with HSNOW initialization to avoid thick snow when AREA
107       is initilized with small values - does not change lab_sea results.
108     - added HsnowFile initialization capability
109    o pkg/smooth: addition to model/src and pkg/ctrl so allow
110     initialization of pkg/smooth and application to control vector
111    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
112    o dependencies: pkg/profiles requires pkg/cal
113    o pkg/profiles:
114     - added option ALLOW_PROFILES_GENERICGRID
115         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
116         that interpolation information (grid points and coefficients) is provided
117         within the netcdf input files.
118         -> sample matlab scripts can be found in MITgcm_contrib/gael
119         that allow you to prepare netcdf input files.
120     - also modified: cleaner include statements, cleaner error print statements,
121       cleaner stops when error, and more tests of the netcdf input files consistency.
122    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
123    o pkg/seaice:
124     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
125       requires a new routine: seaice_diagnostics_fill.F
126     - make sure that seaice does not move if not forced (pressure replacement
127       method, Hibler and Ip, 1995), changes results
128     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
129     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
130       It is turned off by default (=-1.), because it changes the results.
131     - make it possible to read AREA from a file, too.
132    
133    checkpoint59c
134    o add S/R and diagnostics for oceanic mixed-layer depth
135    o move GMRedi call after all vertical mixing schemes (including KPP)
136    o pkg/thsice:
137     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
138      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
139    o pkg/obcs:
140     - bug fix for balance code
141    o pkg/seaice:
142      - allow values of SEAICE_elasticParm > 1
143      - add new parameter SEAICE_evpTauRelax as an alternative
144        to SEAICE_elasticParm
145      - make lsr boundary conditions free slip (by default), changes result
146      - add code for no slip boundary conditions for lsr
147      - set minimum of zeta to zero (and not 4e8) (changes results)
148      - add a cap on AREA after advecting AREA if seaice_growth is not called
149    o change calculation of Visbeck K:
150      - no longer depend on tapering scheme; instead, compute slope (limited
151        by GM_maxSlope). this is equivalent to what was comuted before with
152        clipping or linear tappering.
153      - fix vertical averaging (wrong by 1/2 level)
154      - leave the old version (but will not be maintained) within
155        #ifdef OLD_VISBECK_CALC / #endif
156      - update output of exp. ideal_2D_oce
157    o change error catch in calc_r_star to improve vectorization
158    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
159      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
160    o adjoint:
161      Re-organized adjoint checkpointing according to Matt Mazloff
162      (but with modifs/completions/cleanups)
163      Storing is now bundled into large arrays to optimized I/O
164      (and second step in cleanup of the_main_loop)
165    
166    checkpoint59b
167    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
168      - export/import (between ocean & coupler) fields needed for ocean DIC.
169    o pkg/seaice:
170      - get rid of three more exchanges seaice_calc_viscosities (required
171        different loop boundaries in seaice_lsr and seaice_ocean_stress)
172      - bug fix in seaice_ocean_stress (update of lab_sea required)
173      - reduce loop boundaries to necessary minimum also in seaice_evp
174      - go back to the old way of computing deltaC/Z as the adjoint likes that
175        better
176    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
177      passive tracer to an Age Tracer) + update output.txt
178    o pkg/exf:
179      - implement A-grid / C-grid selection for wind-stress input files.
180      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
181      for now, in exf_bulk_largeyeager04.F only :
182      - change implementation for case where windspeed + 2. components wind-stress
183        are read-in. AND use rhoConstFresh to convert evap.
184    o pkg/seaice:
185      - use correct EXCH_UV for wind-forcing (on A-grid).
186      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
187        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
188    o pkg/exf:
189      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
190      EXF_INTERPOLATION:
191      - merge global_with_exf/code version of exf_interp_read.F
192        to the main code ;
193      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
194        reading the file ; Important: This options needs to be defined to recover
195        previous code.
196        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
197      - no longer loose real*8 precision along the way when using exf_iprec=64.
198    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
199      - change discretisation of evp-solver in order to avoid another exchange
200        (changes lab_sea) and clean up a little
201      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
202        help the adjoint (this also changes the results slightly)
203      - add a few "_d 0" where they had been missing in seaice_evp.F
204      - cleaning up: remove unused seaice_calc_rhs.F
205    o pkg/exf: some cleaning-up:
206      - change various "constants" into runtime parameters
207      - cleaned-up Large&Yeager04 routine which should eventually
208        replace exf_bulkformulae.F (changed names of S/R and CPP)
209        and merged various ALLOW_ATM_WIND options
210     only used with thsice pkg (in thsice_get_exf.F):
211      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
212        which are used when useStabilityFct_overIce=TRUE (= the default)
213      - change default values of ice & snow emissivity and scale downward LW
214        by ice & snow emissivity.
215    o pkg/thsice:
216     fix few little problems, in thsice_calc_thickn.F:
217      - growth vertically (and not laterally) if iceFrac == iceMaskMax
218      - melt only laterally if hIce < hThinIce (as the comments say)
219      and in thsice_extend.F:
220      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
221      - start to form ice as soon as the minimum ice-volume is reachable.
222     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
223      and cpl_aim+ocn
224    o pkg/kpp
225     - move computation of surface related input fields to KPP into a new
226       subroutine kpp_forcing_surf.F
227     - remove wrong (within bi,bj loops) EXCH calls.
228     - little cleaning (add argument myThid in last position, cvs header ...)
229     - for now, fix conservation problem by exchanging KPPviscAz (may not
230       be the best fix)
231    o pkg/seaice
232     - check for inconsistent evp parameter/cpp-flag combination
233     - remove leftover errIO flat for obsolete name list error handling
234    o OpenAD
235     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
236    
237    checkpoint59a
238    o pkg/seaice: some parameter clarifications and a little bit of clean up
239    o pkg/thsice: rename run-time parameters:
240       himin       -> hIceMin
241       himin0      -> hThinIce
242       hihig       -> hThickIce
243       i0          -> i0swFrac
244       transCoef   -> bMeltCoef
245       frac_energy -> fracMelting
246      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
247       with default values (for now) that do not change the results.
248      remove old version of thsice vars advection in pkg/seaice.
249    o in FFIELDS.h:
250      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
251      - make pLoad & sIceLoad always available (but still only used if
252         ATMOSPHERIC_LOADING is #define).
253    o pkg/kpp: replaced _KPP_RL with _RL
254    o bug fixes for vertical diffusivity computations when both KPP and
255        3D diffusivity arrays are used.
256    o pkg/seaice: fix bug in evp solver, while doing that
257      - change (improve?) discretization of stress computations for both
258        cgrid-lsr and evp solver
259      - add a new routine to compute strain rates
260      - the above changes lab_sea results
261      - add no slip conditions for evp solver (off by default), lsr-version
262        may follow
263      - fix exchange for shear at Z-points (does not change lab_sea)
264      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
265        (to force the user to pick a time step since there is not "safe" way
266        of choosing it)
267      - add principal stress diagnostics
268      - rearrange fields for evp a little to avoid having to call a: too many
269        exchanges and b: exchanges for stress trensor components which we do
270        not have.
271      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
272        of evp, complete rewrite for lsr case (latter is does not yet work
273        in all cases)
274    o pkg/kpp: add code to have mixing in shelf ice caverns
275      - add myThid to all kpp routines (long overdue)
276    
277    checkpoint59
278    o pkg/exf:
279      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
280        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
281      - move exf header files from lower_case.h to UPPER_CASE.h ;
282        add missing cvs Header & Name
283      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
284      - add namelist param. selectStressGridPosition, exf_monFreq
285      - retire many _CLIM routines, and remove data.exf_clim
286        + params moved to data.exf
287        + climsst, climsss now handled by exf_set_gen, i.e.
288          climss?period=0 refers to constant field,
289          climss?period=-12 to monthly forcing
290      - split up namelists in data.exf
291    o pkg/seaice:
292      - remove seaice_exch and seaice_exch_uv
293      - remove superfluous exchange of theta
294      - add myThid to seaice_budget_ocean/ice
295      - add new interface for atmospheric wind forcing (C-grid only)
296        + new routine
297        + two new field (taux, tauy for stress over ice)
298        + removed one global field (DAIRN) for C-grid case only
299    o pkg/thsise
300      - 2nd set of modifs for thsice adjoint in conjunction with exf
301    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
302    
303    checkpoint58y_post
304    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
305      vertical diffusivity, similar to that in MOM4; turned on using
306      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
307      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
308    o Added capability for 3D specification of background vertical diffusion
309      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
310      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
311      "data" file that contains the 3D vertical diffusivity coefficients.
312    o ice dynamics (pkg/seaice) with thsice thermodynamics:
313      - add code within pkg thsice to advect & diffuse sea-ice fields
314      similar to (and will replace) what has been added in  seaice_advdiff.F,
315      but: - conserving Mass, Heat & Salt.
316           - better when using non-linear advection scheme (not yet fully tested)
317           - can also be used in atmospheric set-up (for now, only the diffusion).
318    
319    checkpoint58x_post
320    o IO option for global-file compact format:
321      - add options when generating topology (utils/exch2/matlab-topology-generator)
322      - add I/O capability (pkg/mdsio).
323      - adapt utils/matlab/rdmds.m to read this format.
324      for now long-line format not yet supported by pkg/mdsio (& exch2).
325    o shelfice: add a few diagnostics
326    
327    checkpoint58w_post
328    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
329      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
330      (and replace horiVertRatio in NH code).
331      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
332                         and tutorial_plume_on_slope (sensitive to truncation)
333    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
334      directly to drive seaice model (C-grid only)
335    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
336     - reintroduce computation of wind from stress,
337     - compute tau (in exf_bulkformulae.F) from windstress averaged to
338       mass points to avoid tau = 0
339     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
340    o rdmnc.m: make it work with "global" files created with gluemnc
341    o rdmnc.m : some improvements in dealing with singleton dimension
342      (tested on all testreport mnc output files).
343    o genmake2: disable pkg/profiles if netcdf test fails.
344    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
345    o move call to cal_readparms up to make calendar parameters/variable available
346      to all packages
347    
348    checkpoint58v_post
349    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
350      useDynP_inEos_Zc tested.
351    o pkg/exf: changes to properly interpolate/mask/scale initial fields
352    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
353      and portions thereof.  See read_cs.txt for description and examples.
354    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
355      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
356      following the great-circle arc between those 2 points.
357    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
358      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
359    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
360     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
361     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
362     - still needs work (not working with some options ; efficiency to improve)
363       and serious testing.
364     - use this scheme for temperature & salinity in 2 advection test exp.:
365       advect_xy & advect_xz, respectively.
366    
367    checkpoint58u_post
368    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
369    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
370    o testreport: add option "-skipdir" to skip some test.
371    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
372      momentum calculation.
373    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
374    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
375      remove checkpoint.F and the_correction_step.F (no longer used);
376      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
377    o add option (linFSConserveTr) to correct for tracer source/sink due to
378      Linear Free surface
379    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
380    o pkg/thsice: fix reading mnc-pickups
381    
382    checkpoint58t_post
383    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
384    o pkg/mdsio:
385     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
386       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
387       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
388     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
389     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
390       either MDS_READ_FIELD or MDS_WRITE_FIELD )
391     - new S/R (to replace MDSWRITEMETA), which allows to write more
392       informations (variable names, time ...) to meta files.
393     - modify rdmds.m to give back the meta file content.
394  o pkg/diagnostics: change vertical interpolation to be safer, and more  o pkg/diagnostics: change vertical interpolation to be safer, and more
395     flexible (define p-levels to interpolate to in data.diagnostics);     flexible (define p-levels to interpolate to in data.diagnostics);
396    add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right    add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
397     diagnostic pointer.     diagnostic pointer.
398  o pkg/seaice: more cleaning up of seaice_growth, added many comments  o pkg/seaice: more cleaning up of seaice_growth, added many comments
399  o pkg/exf: put runoff0 and runoff into the appropriate common block  o pkg/exf: put runoff0 and runoff1 into the appropriate common block
400  o fix multi-category seaice:  o fix multi-category seaice:
401   - change cpp flag SEAICE_MULTILEVEL to more meaningful name:   - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
402     SEAICE_MULTICATEGORY     SEAICE_MULTICATEGORY
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