/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.764 by jmc, Thu Jan 11 00:29:41 2007 UTC revision 1.871 by dimitri, Fri Sep 14 02:07:37 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/seaice: changes for using pkg/seaice with pkg/obcs
8    o pkg/ecco: allow user defined cost function contributions
9    o testreport:
10      Allow to choose (per experiment) the list of tested output variables
11       and the main variable (used to issue a pass/FAIL ) ;
12      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
13      - default is unchange: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
14      Also modify printing of summary:
15       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
16       b) echo the list of tested variables in the individual summary.txt of
17          each experiment.
18    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
19      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
20      (but still depend on the tile decompostion of the domain).
21    o pkg/seaice: change a discretization detail to make the B-grid code
22      "more symmetric". This change is likely to remove all "ridges/leads" that
23      where quasi-aligned with the grid in B-grid solutions. It may also be
24      the solution to the stress coupling issues with the B-grid.
25    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
26      remove .cvsignore from input dir. (since testreport no longer run here).
27    o pkg/thsice:
28     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
29     - fix reshaping of sea-ice just after advection:
30       melt all the ice only if ice-volume is too small.
31     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
32       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
33     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
34    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
35      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
36    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
37      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
38      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
39      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
40      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
41      -> update output.txt
42    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
43     this affects truncation error: -> update output.txt of exp:
44      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
45      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
46    
47    checkpoint59f
48    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
49    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
50      a bounded range (in forward mode)
51    o pkg/ecco, ctrl, autodiff and mom_common:
52     internal parameter controls, completements of implementations
53    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
54    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
55      (not seem any difference in testing results).
56    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
57       at face corners.
58    o pkg/generic_advdiff:
59     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
60      loop range indices for computing vertical advection tendency
61      and do the calculation in the interior only (no overlap) ;
62      for now, only implemented for SOM advection (to save CPU time).
63     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
64    o exch2 adjoint
65      First set of changes:
66      - add exch2 hand-written adjoint templates
67      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
68        This will require cleanup in pkg/autodiff/*.F
69        (changed routines currently kept separate in verif. code/)
70      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
71        that used to hide exch2 or cubed-sphere specific code
72        (commented via 'cph-exch2')
73    o pkg/seaice
74      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
75    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
76       output of global_ocean.cs32x15.thsice .
77    
78    checkpoint59e
79    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
80      for B-grid vector (not yet tested) and C-grid vector (<- only used
81      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
82    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
83      (#ifdef ALLOW_SALT_PLUME)
84    o gather_2d/scatter_2d: removed halo regions
85    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
86      scheme and the corresponding test case (under front_relax dir). For now,
87      only available with Skew-flux form and not yet tested in realistic set-up.
88      adjoint: store directives updated, but gradient checks deteriorated,
89      so maybe GM/Redi adjoint is now broken.
90    o seaice adjoint
91      * add AREA, HEFF, HSNOW as control variable
92        (should not change lab_sea results)
93      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
94    o pkg/seaice:
95      * added computation of saltFlux in seaice_growth;
96        For time being, sea ice salinity is assumed constant
97        contribution of snow flooding to freshening of sea ice is neglected.
98        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
99        defaults to 0.0 in order to maintain backward compatibility.
100        Typical values for SEAICE_salinity are 4 to 10 g/kg.
101      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
102      * added SEAICE_availHeatFrac, which specifies fraction of surface level
103        heat content used to melt or grow ice
104      * commented out cap of HICE: it helps keep ice thinner
105      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
106      * applied OBCS T/S mask to HEFFM sea ice mask
107    
108    checkpoint59d
109    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
110     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
111     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
112    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
113     and change default value of parameter "GM_Small_Number";
114     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
115       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
116       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
117    o pkg/ecco: cost function when applying pkg/smooth to controls
118    o pkg/ctrl: add forcingPrecond run time parameter
119    o pkg/seaice:
120     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
121     - fix bug in metric terms of u-equation in LSR solver (implicit part),
122       changes verification/lab_sea
123     - rearrange implicit part of u-equation in LSR solver to make it easier to
124       read, understand, and debug. This causes changes at the truncation level.
125     - fix (serious) bug in the boundary conditions (sign error in the implicit
126       part) of the LSR solver. Changes all LSR results.
127     - fixed problem with HSNOW initialization to avoid thick snow when AREA
128       is initilized with small values - does not change lab_sea results.
129     - added HsnowFile initialization capability
130    o pkg/smooth: addition to model/src and pkg/ctrl so allow
131     initialization of pkg/smooth and application to control vector
132    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
133    o dependencies: pkg/profiles requires pkg/cal
134    o pkg/profiles:
135     - added option ALLOW_PROFILES_GENERICGRID
136         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
137         that interpolation information (grid points and coefficients) is provided
138         within the netcdf input files.
139         -> sample matlab scripts can be found in MITgcm_contrib/gael
140         that allow you to prepare netcdf input files.
141     - also modified: cleaner include statements, cleaner error print statements,
142       cleaner stops when error, and more tests of the netcdf input files consistency.
143    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
144    o pkg/seaice:
145     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
146       requires a new routine: seaice_diagnostics_fill.F
147     - make sure that seaice does not move if not forced (pressure replacement
148       method, Hibler and Ip, 1995), changes results
149     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
150     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
151       It is turned off by default (=-1.), because it changes the results.
152     - make it possible to read AREA from a file, too.
153    
154    checkpoint59c
155    o add S/R and diagnostics for oceanic mixed-layer depth
156    o move GMRedi call after all vertical mixing schemes (including KPP)
157    o pkg/thsice:
158     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
159      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
160    o pkg/obcs:
161     - bug fix for balance code
162    o pkg/seaice:
163      - allow values of SEAICE_elasticParm > 1
164      - add new parameter SEAICE_evpTauRelax as an alternative
165        to SEAICE_elasticParm
166      - make lsr boundary conditions free slip (by default), changes result
167      - add code for no slip boundary conditions for lsr
168      - set minimum of zeta to zero (and not 4e8) (changes results)
169      - add a cap on AREA after advecting AREA if seaice_growth is not called
170    o change calculation of Visbeck K:
171      - no longer depend on tapering scheme; instead, compute slope (limited
172        by GM_maxSlope). this is equivalent to what was comuted before with
173        clipping or linear tappering.
174      - fix vertical averaging (wrong by 1/2 level)
175      - leave the old version (but will not be maintained) within
176        #ifdef OLD_VISBECK_CALC / #endif
177      - update output of exp. ideal_2D_oce
178    o change error catch in calc_r_star to improve vectorization
179    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
180      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
181    o adjoint:
182      Re-organized adjoint checkpointing according to Matt Mazloff
183      (but with modifs/completions/cleanups)
184      Storing is now bundled into large arrays to optimized I/O
185      (and second step in cleanup of the_main_loop)
186    
187    checkpoint59b
188    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
189      - export/import (between ocean & coupler) fields needed for ocean DIC.
190    o pkg/seaice:
191      - get rid of three more exchanges seaice_calc_viscosities (required
192        different loop boundaries in seaice_lsr and seaice_ocean_stress)
193      - bug fix in seaice_ocean_stress (update of lab_sea required)
194      - reduce loop boundaries to necessary minimum also in seaice_evp
195      - go back to the old way of computing deltaC/Z as the adjoint likes that
196        better
197    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
198      passive tracer to an Age Tracer) + update output.txt
199    o pkg/exf:
200      - implement A-grid / C-grid selection for wind-stress input files.
201      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
202      for now, in exf_bulk_largeyeager04.F only :
203      - change implementation for case where windspeed + 2. components wind-stress
204        are read-in. AND use rhoConstFresh to convert evap.
205    o pkg/seaice:
206      - use correct EXCH_UV for wind-forcing (on A-grid).
207      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
208        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
209    o pkg/exf:
210      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
211      EXF_INTERPOLATION:
212      - merge global_with_exf/code version of exf_interp_read.F
213        to the main code ;
214      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
215        reading the file ; Important: This options needs to be defined to recover
216        previous code.
217        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
218      - no longer loose real*8 precision along the way when using exf_iprec=64.
219    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
220      - change discretisation of evp-solver in order to avoid another exchange
221        (changes lab_sea) and clean up a little
222      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
223        help the adjoint (this also changes the results slightly)
224      - add a few "_d 0" where they had been missing in seaice_evp.F
225      - cleaning up: remove unused seaice_calc_rhs.F
226    o pkg/exf: some cleaning-up:
227      - change various "constants" into runtime parameters
228      - cleaned-up Large&Yeager04 routine which should eventually
229        replace exf_bulkformulae.F (changed names of S/R and CPP)
230        and merged various ALLOW_ATM_WIND options
231     only used with thsice pkg (in thsice_get_exf.F):
232      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
233        which are used when useStabilityFct_overIce=TRUE (= the default)
234      - change default values of ice & snow emissivity and scale downward LW
235        by ice & snow emissivity.
236    o pkg/thsice:
237     fix few little problems, in thsice_calc_thickn.F:
238      - growth vertically (and not laterally) if iceFrac == iceMaskMax
239      - melt only laterally if hIce < hThinIce (as the comments say)
240      and in thsice_extend.F:
241      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
242      - start to form ice as soon as the minimum ice-volume is reachable.
243     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
244      and cpl_aim+ocn
245    o pkg/kpp
246     - move computation of surface related input fields to KPP into a new
247       subroutine kpp_forcing_surf.F
248     - remove wrong (within bi,bj loops) EXCH calls.
249     - little cleaning (add argument myThid in last position, cvs header ...)
250     - for now, fix conservation problem by exchanging KPPviscAz (may not
251       be the best fix)
252    o pkg/seaice
253     - check for inconsistent evp parameter/cpp-flag combination
254     - remove leftover errIO flat for obsolete name list error handling
255    o OpenAD
256     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
257    
258    checkpoint59a
259    o pkg/seaice: some parameter clarifications and a little bit of clean up
260    o pkg/thsice: rename run-time parameters:
261       himin       -> hIceMin
262       himin0      -> hThinIce
263       hihig       -> hThickIce
264       i0          -> i0swFrac
265       transCoef   -> bMeltCoef
266       frac_energy -> fracMelting
267      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
268       with default values (for now) that do not change the results.
269      remove old version of thsice vars advection in pkg/seaice.
270    o in FFIELDS.h:
271      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
272      - make pLoad & sIceLoad always available (but still only used if
273         ATMOSPHERIC_LOADING is #define).
274    o pkg/kpp: replaced _KPP_RL with _RL
275    o bug fixes for vertical diffusivity computations when both KPP and
276        3D diffusivity arrays are used.
277    o pkg/seaice: fix bug in evp solver, while doing that
278      - change (improve?) discretization of stress computations for both
279        cgrid-lsr and evp solver
280      - add a new routine to compute strain rates
281      - the above changes lab_sea results
282      - add no slip conditions for evp solver (off by default), lsr-version
283        may follow
284      - fix exchange for shear at Z-points (does not change lab_sea)
285      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
286        (to force the user to pick a time step since there is not "safe" way
287        of choosing it)
288      - add principal stress diagnostics
289      - rearrange fields for evp a little to avoid having to call a: too many
290        exchanges and b: exchanges for stress trensor components which we do
291        not have.
292      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
293        of evp, complete rewrite for lsr case (latter is does not yet work
294        in all cases)
295    o pkg/kpp: add code to have mixing in shelf ice caverns
296      - add myThid to all kpp routines (long overdue)
297    
298    checkpoint59
299    o pkg/exf:
300      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
301        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
302      - move exf header files from lower_case.h to UPPER_CASE.h ;
303        add missing cvs Header & Name
304      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
305      - add namelist param. selectStressGridPosition, exf_monFreq
306      - retire many _CLIM routines, and remove data.exf_clim
307        + params moved to data.exf
308        + climsst, climsss now handled by exf_set_gen, i.e.
309          climss?period=0 refers to constant field,
310          climss?period=-12 to monthly forcing
311      - split up namelists in data.exf
312    o pkg/seaice:
313      - remove seaice_exch and seaice_exch_uv
314      - remove superfluous exchange of theta
315      - add myThid to seaice_budget_ocean/ice
316      - add new interface for atmospheric wind forcing (C-grid only)
317        + new routine
318        + two new field (taux, tauy for stress over ice)
319        + removed one global field (DAIRN) for C-grid case only
320    o pkg/thsise
321      - 2nd set of modifs for thsice adjoint in conjunction with exf
322    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
323    
324    checkpoint58y_post
325    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
326      vertical diffusivity, similar to that in MOM4; turned on using
327      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
328      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
329    o Added capability for 3D specification of background vertical diffusion
330      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
331      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
332      "data" file that contains the 3D vertical diffusivity coefficients.
333    o ice dynamics (pkg/seaice) with thsice thermodynamics:
334      - add code within pkg thsice to advect & diffuse sea-ice fields
335      similar to (and will replace) what has been added in  seaice_advdiff.F,
336      but: - conserving Mass, Heat & Salt.
337           - better when using non-linear advection scheme (not yet fully tested)
338           - can also be used in atmospheric set-up (for now, only the diffusion).
339    
340    checkpoint58x_post
341    o IO option for global-file compact format:
342      - add options when generating topology (utils/exch2/matlab-topology-generator)
343      - add I/O capability (pkg/mdsio).
344      - adapt utils/matlab/rdmds.m to read this format.
345      for now long-line format not yet supported by pkg/mdsio (& exch2).
346    o shelfice: add a few diagnostics
347    
348    checkpoint58w_post
349    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
350      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
351      (and replace horiVertRatio in NH code).
352      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
353                         and tutorial_plume_on_slope (sensitive to truncation)
354    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
355      directly to drive seaice model (C-grid only)
356    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
357     - reintroduce computation of wind from stress,
358     - compute tau (in exf_bulkformulae.F) from windstress averaged to
359       mass points to avoid tau = 0
360     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
361    o rdmnc.m: make it work with "global" files created with gluemnc
362    o rdmnc.m : some improvements in dealing with singleton dimension
363      (tested on all testreport mnc output files).
364    o genmake2: disable pkg/profiles if netcdf test fails.
365    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
366    o move call to cal_readparms up to make calendar parameters/variable available
367      to all packages
368    
369    checkpoint58v_post
370    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
371      useDynP_inEos_Zc tested.
372    o pkg/exf: changes to properly interpolate/mask/scale initial fields
373    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
374      and portions thereof.  See read_cs.txt for description and examples.
375    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
376      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
377      following the great-circle arc between those 2 points.
378    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
379      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
380    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
381     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
382     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
383     - still needs work (not working with some options ; efficiency to improve)
384       and serious testing.
385     - use this scheme for temperature & salinity in 2 advection test exp.:
386       advect_xy & advect_xz, respectively.
387    
388    checkpoint58u_post
389    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
390  o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.  o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
391  o testreport: add option "-skipdir" to skip some test.  o testreport: add option "-skipdir" to skip some test.
392  o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent  o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
Legend:
Removed from v.1.764  
changed lines
  Added in v.1.871
  ViewVC Help
Powered by ViewVC 1.1.22