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revision 1.757 by mlosch, Wed Dec 20 12:27:02 2006 UTC revision 1.847 by heimbach, Thu Jun 28 00:35:07 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 gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
8      scheme and the corresponding test case (under front_relax dir). For now,
9      only available with Skew-flux form and not yet tested in realistic set-up.
10      adjoint: store directives updated, but gradient checks deteriorated,
11      so maybe GM/Redi adjoint is now broken.
12    o seaice adjoint
13      * add AREA, HEFF, HSNOW as control variable
14        (should not change lab_sea results)
15      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
16    o pkg/seaice: added computation of saltFlux in seaice_growth;
17       For time being, sea ice salinity is assumed constant
18       contribution of snow flooding to freshening of sea ice is neglected.
19       SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
20       defaults to 0.0 in order to maintain backward compatibility.
21       Typical values for SEAICE_salinity are 4 to 10 g/kg.
22    
23    checkpoint59d
24    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
25     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
26     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
27    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
28     and change default value of parameter "GM_Small_Number";
29     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
30       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
31       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
32    o pkg/ecco: cost function when applying pkg/smooth to controls
33    o pkg/ctrl: add forcingPrecond run time parameter
34    o pkg/seaice:
35     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
36     - fix bug in metric terms of u-equation in LSR solver (implicit part),
37       changes verification/lab_sea
38     - rearrange implicit part of u-equation in LSR solver to make it easier to
39       read, understand, and debug. This causes changes at the truncation level.
40     - fix (serious) bug in the boundary conditions (sign error in the implicit
41       part) of the LSR solver. Changes all LSR results.
42     - fixed problem with HSNOW initialization to avoid thick snow when AREA
43       is initilized with small values - does not change lab_sea results.
44     - added HsnowFile initialization capability
45    o pkg/smooth: addition to model/src and pkg/ctrl so allow
46     initialization of pkg/smooth and application to control vector
47    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
48    o dependencies: pkg/profiles requires pkg/cal
49    o pkg/profiles:
50     - added option ALLOW_PROFILES_GENERICGRID
51         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
52         that interpolation information (grid points and coefficients) is provided
53         within the netcdf input files.
54         -> sample matlab scripts can be found in MITgcm_contrib/gael
55         that allow you to prepare netcdf input files.
56     - also modified: cleaner include statements, cleaner error print statements,
57       cleaner stops when error, and more tests of the netcdf input files consistency.
58    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
59    o pkg/seaice:
60     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
61       requires a new routine: seaice_diagnostics_fill.F
62     - make sure that seaice does not move if not forced (pressure replacement
63       method, Hibler and Ip, 1995), changes results
64     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
65     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
66       It is turned off by default (=-1.), because it changes the results.
67     - make it possible to read AREA from a file, too.
68    
69    checkpoint59c
70    o add S/R and diagnostics for oceanic mixed-layer depth
71    o move GMRedi call after all vertical mixing schemes (including KPP)
72    o pkg/thsice:
73     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
74      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
75    o pkg/obcs:
76     - bug fix for balance code
77    o pkg/seaice:
78      - allow values of SEAICE_elasticParm > 1
79      - add new parameter SEAICE_evpTauRelax as an alternative
80        to SEAICE_elasticParm
81      - make lsr boundary conditions free slip (by default), changes result
82      - add code for no slip boundary conditions for lsr
83      - set minimum of zeta to zero (and not 4e8) (changes results)
84      - add a cap on AREA after advecting AREA if seaice_growth is not called
85    o change calculation of Visbeck K:
86      - no longer depend on tapering scheme; instead, compute slope (limited
87        by GM_maxSlope). this is equivalent to what was comuted before with
88        clipping or linear tappering.
89      - fix vertical averaging (wrong by 1/2 level)
90      - leave the old version (but will not be maintained) within
91        #ifdef OLD_VISBECK_CALC / #endif
92      - update output of exp. ideal_2D_oce
93    o change error catch in calc_r_star to improve vectorization
94    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
95      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
96    o adjoint:
97      Re-organized adjoint checkpointing according to Matt Mazloff
98      (but with modifs/completions/cleanups)
99      Storing is now bundled into large arrays to optimized I/O
100      (and second step in cleanup of the_main_loop)
101    
102    checkpoint59b
103    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
104      - export/import (between ocean & coupler) fields needed for ocean DIC.
105    o pkg/seaice:
106      - get rid of three more exchanges seaice_calc_viscosities (required
107        different loop boundaries in seaice_lsr and seaice_ocean_stress)
108      - bug fix in seaice_ocean_stress (update of lab_sea required)
109      - reduce loop boundaries to necessary minimum also in seaice_evp
110      - go back to the old way of computing deltaC/Z as the adjoint likes that
111        better
112    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
113      passive tracer to an Age Tracer) + update output.txt
114    o pkg/exf:
115      - implement A-grid / C-grid selection for wind-stress input files.
116      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
117      for now, in exf_bulk_largeyeager04.F only :
118      - change implementation for case where windspeed + 2. components wind-stress
119        are read-in. AND use rhoConstFresh to convert evap.
120    o pkg/seaice:
121      - use correct EXCH_UV for wind-forcing (on A-grid).
122      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
123        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
124    o pkg/exf:
125      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
126      EXF_INTERPOLATION:
127      - merge global_with_exf/code version of exf_interp_read.F
128        to the main code ;
129      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
130        reading the file ; Important: This options needs to be defined to recover
131        previous code.
132        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
133      - no longer loose real*8 precision along the way when using exf_iprec=64.
134    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
135      - change discretisation of evp-solver in order to avoid another exchange
136        (changes lab_sea) and clean up a little
137      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
138        help the adjoint (this also changes the results slightly)
139      - add a few "_d 0" where they had been missing in seaice_evp.F
140      - cleaning up: remove unused seaice_calc_rhs.F
141    o pkg/exf: some cleaning-up:
142      - change various "constants" into runtime parameters
143      - cleaned-up Large&Yeager04 routine which should eventually
144        replace exf_bulkformulae.F (changed names of S/R and CPP)
145        and merged various ALLOW_ATM_WIND options
146     only used with thsice pkg (in thsice_get_exf.F):
147      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
148        which are used when useStabilityFct_overIce=TRUE (= the default)
149      - change default values of ice & snow emissivity and scale downward LW
150        by ice & snow emissivity.
151    o pkg/thsice:
152     fix few little problems, in thsice_calc_thickn.F:
153      - growth vertically (and not laterally) if iceFrac == iceMaskMax
154      - melt only laterally if hIce < hThinIce (as the comments say)
155      and in thsice_extend.F:
156      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
157      - start to form ice as soon as the minimum ice-volume is reachable.
158     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
159      and cpl_aim+ocn
160    o pkg/kpp
161     - move computation of surface related input fields to KPP into a new
162       subroutine kpp_forcing_surf.F
163     - remove wrong (within bi,bj loops) EXCH calls.
164     - little cleaning (add argument myThid in last position, cvs header ...)
165     - for now, fix conservation problem by exchanging KPPviscAz (may not
166       be the best fix)
167    o pkg/seaice
168     - check for inconsistent evp parameter/cpp-flag combination
169     - remove leftover errIO flat for obsolete name list error handling
170    o OpenAD
171     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
172    
173    checkpoint59a
174    o pkg/seaice: some parameter clarifications and a little bit of clean up
175    o pkg/thsice: rename run-time parameters:
176       himin       -> hIceMin
177       himin0      -> hThinIce
178       hihig       -> hThickIce
179       i0          -> i0swFrac
180       transCoef   -> bMeltCoef
181       frac_energy -> fracMelting
182      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
183       with default values (for now) that do not change the results.
184      remove old version of thsice vars advection in pkg/seaice.
185    o in FFIELDS.h:
186      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
187      - make pLoad & sIceLoad always available (but still only used if
188         ATMOSPHERIC_LOADING is #define).
189    o pkg/kpp: replaced _KPP_RL with _RL
190    o bug fixes for vertical diffusivity computations when both KPP and
191        3D diffusivity arrays are used.
192    o pkg/seaice: fix bug in evp solver, while doing that
193      - change (improve?) discretization of stress computations for both
194        cgrid-lsr and evp solver
195      - add a new routine to compute strain rates
196      - the above changes lab_sea results
197      - add no slip conditions for evp solver (off by default), lsr-version
198        may follow
199      - fix exchange for shear at Z-points (does not change lab_sea)
200      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
201        (to force the user to pick a time step since there is not "safe" way
202        of choosing it)
203      - add principal stress diagnostics
204      - rearrange fields for evp a little to avoid having to call a: too many
205        exchanges and b: exchanges for stress trensor components which we do
206        not have.
207      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
208        of evp, complete rewrite for lsr case (latter is does not yet work
209        in all cases)
210    o pkg/kpp: add code to have mixing in shelf ice caverns
211      - add myThid to all kpp routines (long overdue)
212    
213    checkpoint59
214    o pkg/exf:
215      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
216        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
217      - move exf header files from lower_case.h to UPPER_CASE.h ;
218        add missing cvs Header & Name
219      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
220      - add namelist param. selectStressGridPosition, exf_monFreq
221      - retire many _CLIM routines, and remove data.exf_clim
222        + params moved to data.exf
223        + climsst, climsss now handled by exf_set_gen, i.e.
224          climss?period=0 refers to constant field,
225          climss?period=-12 to monthly forcing
226      - split up namelists in data.exf
227    o pkg/seaice:
228      - remove seaice_exch and seaice_exch_uv
229      - remove superfluous exchange of theta
230      - add myThid to seaice_budget_ocean/ice
231      - add new interface for atmospheric wind forcing (C-grid only)
232        + new routine
233        + two new field (taux, tauy for stress over ice)
234        + removed one global field (DAIRN) for C-grid case only
235    o pkg/thsise
236      - 2nd set of modifs for thsice adjoint in conjunction with exf
237    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
238    
239    checkpoint58y_post
240    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
241      vertical diffusivity, similar to that in MOM4; turned on using
242      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
243      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
244    o Added capability for 3D specification of background vertical diffusion
245      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
246      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
247      "data" file that contains the 3D vertical diffusivity coefficients.
248    o ice dynamics (pkg/seaice) with thsice thermodynamics:
249      - add code within pkg thsice to advect & diffuse sea-ice fields
250      similar to (and will replace) what has been added in  seaice_advdiff.F,
251      but: - conserving Mass, Heat & Salt.
252           - better when using non-linear advection scheme (not yet fully tested)
253           - can also be used in atmospheric set-up (for now, only the diffusion).
254    
255    checkpoint58x_post
256    o IO option for global-file compact format:
257      - add options when generating topology (utils/exch2/matlab-topology-generator)
258      - add I/O capability (pkg/mdsio).
259      - adapt utils/matlab/rdmds.m to read this format.
260      for now long-line format not yet supported by pkg/mdsio (& exch2).
261    o shelfice: add a few diagnostics
262    
263    checkpoint58w_post
264    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
265      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
266      (and replace horiVertRatio in NH code).
267      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
268                         and tutorial_plume_on_slope (sensitive to truncation)
269    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
270      directly to drive seaice model (C-grid only)
271    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
272     - reintroduce computation of wind from stress,
273     - compute tau (in exf_bulkformulae.F) from windstress averaged to
274       mass points to avoid tau = 0
275     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
276    o rdmnc.m: make it work with "global" files created with gluemnc
277    o rdmnc.m : some improvements in dealing with singleton dimension
278      (tested on all testreport mnc output files).
279    o genmake2: disable pkg/profiles if netcdf test fails.
280    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
281    o move call to cal_readparms up to make calendar parameters/variable available
282      to all packages
283    
284    checkpoint58v_post
285    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
286      useDynP_inEos_Zc tested.
287    o pkg/exf: changes to properly interpolate/mask/scale initial fields
288    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
289      and portions thereof.  See read_cs.txt for description and examples.
290    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
291      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
292      following the great-circle arc between those 2 points.
293    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
294      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
295    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
296     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
297     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
298     - still needs work (not working with some options ; efficiency to improve)
299       and serious testing.
300     - use this scheme for temperature & salinity in 2 advection test exp.:
301       advect_xy & advect_xz, respectively.
302    
303    checkpoint58u_post
304    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
305    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
306    o testreport: add option "-skipdir" to skip some test.
307    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
308      momentum calculation.
309    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
310    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
311      remove checkpoint.F and the_correction_step.F (no longer used);
312      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
313    o add option (linFSConserveTr) to correct for tracer source/sink due to
314      Linear Free surface
315    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
316    o pkg/thsice: fix reading mnc-pickups
317    
318    checkpoint58t_post
319    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
320    o pkg/mdsio:
321     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
322       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
323       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
324     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
325     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
326       either MDS_READ_FIELD or MDS_WRITE_FIELD )
327     - new S/R (to replace MDSWRITEMETA), which allows to write more
328       informations (variable names, time ...) to meta files.
329     - modify rdmds.m to give back the meta file content.
330    o pkg/diagnostics: change vertical interpolation to be safer, and more
331       flexible (define p-levels to interpolate to in data.diagnostics);
332      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
333       diagnostic pointer.
334    o pkg/seaice: more cleaning up of seaice_growth, added many comments
335    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
336  o fix multi-category seaice:  o fix multi-category seaice:
337   - change cpp flag SEAICE_MULTILEVEL to more meaningful name:   - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
338     SEAICE_MULTICATEGORY     SEAICE_MULTICATEGORY
339   - fix short wave heat flux   - fix short wave heat flux
340    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
341       and allow to use EVP solver. Change forward lab_sea: test both EVP
342       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
343  o Initial check-in of lab_sea adjoint  o Initial check-in of lab_sea adjoint
344    (very similar to natl_box_adjoint/code_seaice)    (very similar to natl_box_adjoint/code_seaice)
345    * used C-grid and EVP solver    * used C-grid and EVP solver

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