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revision 1.766 by jmc, Tue Jan 16 19:45:13 2007 UTC revision 1.881 by dimitri, Sat Sep 22 17:55:31 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/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
8    o testreport:
9      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
10        monitor & update offline_exf_seaice exp. output.
11      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
12    o pkg/seaice:
13      - bug fix in the evp solver: boundary conditions were affected be
14        masking of zMax/zMin (changes results)
15      - minor bug fix in boundary conditions in seaice_calc_strainrates
16        (changes results for no_slip)
17      - seaice_lsr.F: make interpolation of eta dependent on boundaries
18      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
19      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
20        stress formulation and no-slip boundary conditions
21    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
22      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
23    o pkg/seaice: a first HSALT time stepping equation has been checked in
24    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
25      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
26      without requiring DO-IF statements
27    o pkg/thsice:
28      use continuous power-law function for partition of energy between lateral
29      melting/freezing and thinning/thickening ; old code using step function
30      still available with #undef THSICE_FRACEN_POWERLAW
31      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
32    o testreport: change AD testing : check against results/output_adm.txt
33      using same scripts as for forward test.
34    
35    checkpoint59g
36    o adjoint testing: in preparation for changing testreport:
37      - output format: cost and grad written on separated lines
38      - ad output results in directory "results" (instead of "results_ad")
39    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
40    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
41    o pkg/ecco: allow user defined cost function contributions
42    o testreport:
43      Allow to choose (per experiment) the list of tested output variables
44       and the main variable (used to issue a pass/FAIL ) ;
45      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
46      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
47      Also modify printing of summary:
48       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
49       b) echo the list of tested variables in the individual summary.txt of
50          each experiment.
51    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
52      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
53      (but still depend on the tile decompostion of the domain).
54    o pkg/seaice: change a discretization detail to make the B-grid code
55      "more symmetric". This change is likely to remove all "ridges/leads" that
56      where quasi-aligned with the grid in B-grid solutions. It may also be
57      the solution to the stress coupling issues with the B-grid.
58    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
59      remove .cvsignore from input dir. (since testreport no longer run here).
60    o pkg/thsice:
61     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
62     - fix reshaping of sea-ice just after advection:
63       melt all the ice only if ice-volume is too small.
64     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
65       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
66     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
67    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
68      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
69    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
70      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
71      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
72      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
73      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
74      -> update output.txt
75    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
76     this affects truncation error: -> update output.txt of exp:
77      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
78      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
79    
80    checkpoint59f
81    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
82    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
83      a bounded range (in forward mode)
84    o pkg/ecco, ctrl, autodiff and mom_common:
85     internal parameter controls, completements of implementations
86    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
87    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
88      (not seem any difference in testing results).
89    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
90       at face corners.
91    o pkg/generic_advdiff:
92     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
93      loop range indices for computing vertical advection tendency
94      and do the calculation in the interior only (no overlap) ;
95      for now, only implemented for SOM advection (to save CPU time).
96     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
97    o exch2 adjoint
98      First set of changes:
99      - add exch2 hand-written adjoint templates
100      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
101        This will require cleanup in pkg/autodiff/*.F
102        (changed routines currently kept separate in verif. code/)
103      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
104        that used to hide exch2 or cubed-sphere specific code
105        (commented via 'cph-exch2')
106    o pkg/seaice
107      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
108    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
109       output of global_ocean.cs32x15.thsice .
110    
111    checkpoint59e
112    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
113      for B-grid vector (not yet tested) and C-grid vector (<- only used
114      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
115    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
116      (#ifdef ALLOW_SALT_PLUME)
117    o gather_2d/scatter_2d: removed halo regions
118    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
119      scheme and the corresponding test case (under front_relax dir). For now,
120      only available with Skew-flux form and not yet tested in realistic set-up.
121      adjoint: store directives updated, but gradient checks deteriorated,
122      so maybe GM/Redi adjoint is now broken.
123    o seaice adjoint
124      * add AREA, HEFF, HSNOW as control variable
125        (should not change lab_sea results)
126      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
127    o pkg/seaice:
128      * added computation of saltFlux in seaice_growth;
129        For time being, sea ice salinity is assumed constant
130        contribution of snow flooding to freshening of sea ice is neglected.
131        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
132        defaults to 0.0 in order to maintain backward compatibility.
133        Typical values for SEAICE_salinity are 4 to 10 g/kg.
134      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
135      * added SEAICE_availHeatFrac, which specifies fraction of surface level
136        heat content used to melt or grow ice
137      * commented out cap of HICE: it helps keep ice thinner
138      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
139      * applied OBCS T/S mask to HEFFM sea ice mask
140    
141    checkpoint59d
142    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
143     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
144     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
145    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
146     and change default value of parameter "GM_Small_Number";
147     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
148       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
149       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
150    o pkg/ecco: cost function when applying pkg/smooth to controls
151    o pkg/ctrl: add forcingPrecond run time parameter
152    o pkg/seaice:
153     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
154     - fix bug in metric terms of u-equation in LSR solver (implicit part),
155       changes verification/lab_sea
156     - rearrange implicit part of u-equation in LSR solver to make it easier to
157       read, understand, and debug. This causes changes at the truncation level.
158     - fix (serious) bug in the boundary conditions (sign error in the implicit
159       part) of the LSR solver. Changes all LSR results.
160     - fixed problem with HSNOW initialization to avoid thick snow when AREA
161       is initilized with small values - does not change lab_sea results.
162     - added HsnowFile initialization capability
163    o pkg/smooth: addition to model/src and pkg/ctrl so allow
164     initialization of pkg/smooth and application to control vector
165    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
166    o dependencies: pkg/profiles requires pkg/cal
167    o pkg/profiles:
168     - added option ALLOW_PROFILES_GENERICGRID
169         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
170         that interpolation information (grid points and coefficients) is provided
171         within the netcdf input files.
172         -> sample matlab scripts can be found in MITgcm_contrib/gael
173         that allow you to prepare netcdf input files.
174     - also modified: cleaner include statements, cleaner error print statements,
175       cleaner stops when error, and more tests of the netcdf input files consistency.
176    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
177    o pkg/seaice:
178     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
179       requires a new routine: seaice_diagnostics_fill.F
180     - make sure that seaice does not move if not forced (pressure replacement
181       method, Hibler and Ip, 1995), changes results
182     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
183     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
184       It is turned off by default (=-1.), because it changes the results.
185     - make it possible to read AREA from a file, too.
186    
187    checkpoint59c
188    o add S/R and diagnostics for oceanic mixed-layer depth
189    o move GMRedi call after all vertical mixing schemes (including KPP)
190    o pkg/thsice:
191     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
192      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
193    o pkg/obcs:
194     - bug fix for balance code
195    o pkg/seaice:
196      - allow values of SEAICE_elasticParm > 1
197      - add new parameter SEAICE_evpTauRelax as an alternative
198        to SEAICE_elasticParm
199      - make lsr boundary conditions free slip (by default), changes result
200      - add code for no slip boundary conditions for lsr
201      - set minimum of zeta to zero (and not 4e8) (changes results)
202      - add a cap on AREA after advecting AREA if seaice_growth is not called
203    o change calculation of Visbeck K:
204      - no longer depend on tapering scheme; instead, compute slope (limited
205        by GM_maxSlope). this is equivalent to what was comuted before with
206        clipping or linear tappering.
207      - fix vertical averaging (wrong by 1/2 level)
208      - leave the old version (but will not be maintained) within
209        #ifdef OLD_VISBECK_CALC / #endif
210      - update output of exp. ideal_2D_oce
211    o change error catch in calc_r_star to improve vectorization
212    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
213      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
214    o adjoint:
215      Re-organized adjoint checkpointing according to Matt Mazloff
216      (but with modifs/completions/cleanups)
217      Storing is now bundled into large arrays to optimized I/O
218      (and second step in cleanup of the_main_loop)
219    
220    checkpoint59b
221    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
222      - export/import (between ocean & coupler) fields needed for ocean DIC.
223    o pkg/seaice:
224      - get rid of three more exchanges seaice_calc_viscosities (required
225        different loop boundaries in seaice_lsr and seaice_ocean_stress)
226      - bug fix in seaice_ocean_stress (update of lab_sea required)
227      - reduce loop boundaries to necessary minimum also in seaice_evp
228      - go back to the old way of computing deltaC/Z as the adjoint likes that
229        better
230    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
231      passive tracer to an Age Tracer) + update output.txt
232    o pkg/exf:
233      - implement A-grid / C-grid selection for wind-stress input files.
234      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
235      for now, in exf_bulk_largeyeager04.F only :
236      - change implementation for case where windspeed + 2. components wind-stress
237        are read-in. AND use rhoConstFresh to convert evap.
238    o pkg/seaice:
239      - use correct EXCH_UV for wind-forcing (on A-grid).
240      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
241        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
242    o pkg/exf:
243      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
244      EXF_INTERPOLATION:
245      - merge global_with_exf/code version of exf_interp_read.F
246        to the main code ;
247      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
248        reading the file ; Important: This options needs to be defined to recover
249        previous code.
250        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
251      - no longer loose real*8 precision along the way when using exf_iprec=64.
252    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
253      - change discretisation of evp-solver in order to avoid another exchange
254        (changes lab_sea) and clean up a little
255      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
256        help the adjoint (this also changes the results slightly)
257      - add a few "_d 0" where they had been missing in seaice_evp.F
258      - cleaning up: remove unused seaice_calc_rhs.F
259    o pkg/exf: some cleaning-up:
260      - change various "constants" into runtime parameters
261      - cleaned-up Large&Yeager04 routine which should eventually
262        replace exf_bulkformulae.F (changed names of S/R and CPP)
263        and merged various ALLOW_ATM_WIND options
264     only used with thsice pkg (in thsice_get_exf.F):
265      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
266        which are used when useStabilityFct_overIce=TRUE (= the default)
267      - change default values of ice & snow emissivity and scale downward LW
268        by ice & snow emissivity.
269    o pkg/thsice:
270     fix few little problems, in thsice_calc_thickn.F:
271      - growth vertically (and not laterally) if iceFrac == iceMaskMax
272      - melt only laterally if hIce < hThinIce (as the comments say)
273      and in thsice_extend.F:
274      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
275      - start to form ice as soon as the minimum ice-volume is reachable.
276     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
277      and cpl_aim+ocn
278    o pkg/kpp
279     - move computation of surface related input fields to KPP into a new
280       subroutine kpp_forcing_surf.F
281     - remove wrong (within bi,bj loops) EXCH calls.
282     - little cleaning (add argument myThid in last position, cvs header ...)
283     - for now, fix conservation problem by exchanging KPPviscAz (may not
284       be the best fix)
285    o pkg/seaice
286     - check for inconsistent evp parameter/cpp-flag combination
287     - remove leftover errIO flat for obsolete name list error handling
288    o OpenAD
289     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
290    
291    checkpoint59a
292    o pkg/seaice: some parameter clarifications and a little bit of clean up
293    o pkg/thsice: rename run-time parameters:
294       himin       -> hIceMin
295       himin0      -> hThinIce
296       hihig       -> hThickIce
297       i0          -> i0swFrac
298       transCoef   -> bMeltCoef
299       frac_energy -> fracMelting
300      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
301       with default values (for now) that do not change the results.
302      remove old version of thsice vars advection in pkg/seaice.
303    o in FFIELDS.h:
304      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
305      - make pLoad & sIceLoad always available (but still only used if
306         ATMOSPHERIC_LOADING is #define).
307    o pkg/kpp: replaced _KPP_RL with _RL
308    o bug fixes for vertical diffusivity computations when both KPP and
309        3D diffusivity arrays are used.
310    o pkg/seaice: fix bug in evp solver, while doing that
311      - change (improve?) discretization of stress computations for both
312        cgrid-lsr and evp solver
313      - add a new routine to compute strain rates
314      - the above changes lab_sea results
315      - add no slip conditions for evp solver (off by default), lsr-version
316        may follow
317      - fix exchange for shear at Z-points (does not change lab_sea)
318      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
319        (to force the user to pick a time step since there is not "safe" way
320        of choosing it)
321      - add principal stress diagnostics
322      - rearrange fields for evp a little to avoid having to call a: too many
323        exchanges and b: exchanges for stress trensor components which we do
324        not have.
325      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
326        of evp, complete rewrite for lsr case (latter is does not yet work
327        in all cases)
328    o pkg/kpp: add code to have mixing in shelf ice caverns
329      - add myThid to all kpp routines (long overdue)
330    
331    checkpoint59
332    o pkg/exf:
333      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
334        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
335      - move exf header files from lower_case.h to UPPER_CASE.h ;
336        add missing cvs Header & Name
337      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
338      - add namelist param. selectStressGridPosition, exf_monFreq
339      - retire many _CLIM routines, and remove data.exf_clim
340        + params moved to data.exf
341        + climsst, climsss now handled by exf_set_gen, i.e.
342          climss?period=0 refers to constant field,
343          climss?period=-12 to monthly forcing
344      - split up namelists in data.exf
345    o pkg/seaice:
346      - remove seaice_exch and seaice_exch_uv
347      - remove superfluous exchange of theta
348      - add myThid to seaice_budget_ocean/ice
349      - add new interface for atmospheric wind forcing (C-grid only)
350        + new routine
351        + two new field (taux, tauy for stress over ice)
352        + removed one global field (DAIRN) for C-grid case only
353    o pkg/thsise
354      - 2nd set of modifs for thsice adjoint in conjunction with exf
355    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
356    
357    checkpoint58y_post
358    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
359      vertical diffusivity, similar to that in MOM4; turned on using
360      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
361      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
362    o Added capability for 3D specification of background vertical diffusion
363      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
364      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
365      "data" file that contains the 3D vertical diffusivity coefficients.
366    o ice dynamics (pkg/seaice) with thsice thermodynamics:
367      - add code within pkg thsice to advect & diffuse sea-ice fields
368      similar to (and will replace) what has been added in  seaice_advdiff.F,
369      but: - conserving Mass, Heat & Salt.
370           - better when using non-linear advection scheme (not yet fully tested)
371           - can also be used in atmospheric set-up (for now, only the diffusion).
372    
373    checkpoint58x_post
374    o IO option for global-file compact format:
375      - add options when generating topology (utils/exch2/matlab-topology-generator)
376      - add I/O capability (pkg/mdsio).
377      - adapt utils/matlab/rdmds.m to read this format.
378      for now long-line format not yet supported by pkg/mdsio (& exch2).
379    o shelfice: add a few diagnostics
380    
381    checkpoint58w_post
382    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
383      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
384      (and replace horiVertRatio in NH code).
385      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
386                         and tutorial_plume_on_slope (sensitive to truncation)
387    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
388      directly to drive seaice model (C-grid only)
389    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
390     - reintroduce computation of wind from stress,
391     - compute tau (in exf_bulkformulae.F) from windstress averaged to
392       mass points to avoid tau = 0
393     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
394    o rdmnc.m: make it work with "global" files created with gluemnc
395    o rdmnc.m : some improvements in dealing with singleton dimension
396      (tested on all testreport mnc output files).
397    o genmake2: disable pkg/profiles if netcdf test fails.
398    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
399    o move call to cal_readparms up to make calendar parameters/variable available
400      to all packages
401    
402    checkpoint58v_post
403    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
404      useDynP_inEos_Zc tested.
405    o pkg/exf: changes to properly interpolate/mask/scale initial fields
406    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
407      and portions thereof.  See read_cs.txt for description and examples.
408    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
409      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
410      following the great-circle arc between those 2 points.
411    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
412      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
413  o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in  o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
414   - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)   - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
415   - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)   - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
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