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revision 1.770 by jmc, Thu Feb 8 00:12:37 2007 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 new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
8      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  checkpoint58v_post
359  o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get  o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
360    useDynP_inEos_Zc tested.    useDynP_inEos_Zc tested.

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