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-revision 1.747 by dimitri,
Mon Nov 20 20:06:43 2006 UTC
+revision 1.862 by jmc,
Tue Aug 21 14:39:43 2007 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ checkpoint59f
+ o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
+ o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
+   a bounded range (in forward mode)
+ o pkg/ecco, ctrl, autodiff and mom_common:
+  internal parameter controls, completements of implementations
+ o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
+ o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
+   (not seem any difference in testing results).
+ o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
+    at face corners.
+ o pkg/generic_advdiff:
+  - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
+   loop range indices for computing vertical advection tendency
+   and do the calculation in the interior only (no overlap) ;
+   for now, only implemented for SOM advection (to save CPU time).
+  - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
+ o exch2 adjoint
+   First set of changes:
+   - add exch2 hand-written adjoint templates
+   - exch2 hand-written no longer use TAF-flag 'nownew_arg'
+     This will require cleanup in pkg/autodiff/*.F
+     (changed routines currently kept separate in verif. code/)
+   - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
+     that used to hide exch2 or cubed-sphere specific code
+     (commented via 'cph-exch2')
+ o pkg/seaice
+   - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
+ o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
+    output of global_ocean.cs32x15.thsice .
+ checkpoint59e
+ o exch2: new S/R that only use the cube-tracer (center-position) exchange:
+   for B-grid vector (not yet tested) and C-grid vector (<- only used
+   when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
+ o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
+   (#ifdef ALLOW_SALT_PLUME)
+ o gather_2d/scatter_2d: removed halo regions
+ o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
+   scheme and the corresponding test case (under front_relax dir). For now,
+   only available with Skew-flux form and not yet tested in realistic set-up.
+   adjoint: store directives updated, but gradient checks deteriorated,
+   so maybe GM/Redi adjoint is now broken.
+ o seaice adjoint
+   * add AREA, HEFF, HSNOW as control variable
+     (should not change lab_sea results)
+   * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
+ o pkg/seaice:
+   * added computation of saltFlux in seaice_growth;
+     For time being, sea ice salinity is assumed constant
+     contribution of snow flooding to freshening of sea ice is neglected.
+     SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
+     defaults to 0.0 in order to maintain backward compatibility.
+     Typical values for SEAICE_salinity are 4 to 10 g/kg.
+   * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
+   * added SEAICE_availHeatFrac, which specifies fraction of surface level
+     heat content used to melt or grow ice
+   * commented out cap of HICE: it helps keep ice thinner
+   * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
+   * applied OBCS T/S mask to HEFFM sea ice mask
+ checkpoint59d
+ o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
+  for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
+  (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
+ o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
+  and change default value of parameter "GM_Small_Number";
+  update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
+    global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
+    tutorial_global_oce_biogeo, tutorial_global_oce_latlon
+ o pkg/ecco: cost function when applying pkg/smooth to controls
+ o pkg/ctrl: add forcingPrecond run time parameter
+ o pkg/seaice:
+  - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
+  - fix bug in metric terms of u-equation in LSR solver (implicit part),
+    changes verification/lab_sea
+  - rearrange implicit part of u-equation in LSR solver to make it easier to
+    read, understand, and debug. This causes changes at the truncation level.
+  - fix (serious) bug in the boundary conditions (sign error in the implicit
+    part) of the LSR solver. Changes all LSR results.
+  - fixed problem with HSNOW initialization to avoid thick snow when AREA
+    is initilized with small values - does not change lab_sea results.
+  - added HsnowFile initialization capability
+ o pkg/smooth: addition to model/src and pkg/ctrl so allow
+  initialization of pkg/smooth and application to control vector
+ o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
+ o dependencies: pkg/profiles requires pkg/cal
+ o pkg/profiles:
+  - added option ALLOW_PROFILES_GENERICGRID
+      -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
+      that interpolation information (grid points and coefficients) is provided
+      within the netcdf input files.
+      -> sample matlab scripts can be found in MITgcm_contrib/gael
+      that allow you to prepare netcdf input files.
+  - also modified: cleaner include statements, cleaner error print statements,
+    cleaner stops when error, and more tests of the netcdf input files consistency.
+ o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
+ o pkg/seaice:
+  - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
+    requires a new routine: seaice_diagnostics_fill.F
+  - make sure that seaice does not move if not forced (pressure replacement
+    method, Hibler and Ip, 1995), changes results
+  - and new damping criterion for EVP solver according to Hunke, JCP, 2001
+  - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
+    It is turned off by default (=-1.), because it changes the results.
+  - make it possible to read AREA from a file, too.
+ checkpoint59c
+ o add S/R and diagnostics for oceanic mixed-layer depth
+ o move GMRedi call after all vertical mixing schemes (including KPP)
+ o pkg/thsice:
+  - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
+   (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
+ o pkg/obcs:
+  - bug fix for balance code
+ o pkg/seaice:
+   - allow values of SEAICE_elasticParm > 1
+   - add new parameter SEAICE_evpTauRelax as an alternative
+     to SEAICE_elasticParm
+   - make lsr boundary conditions free slip (by default), changes result
+   - add code for no slip boundary conditions for lsr
+   - set minimum of zeta to zero (and not 4e8) (changes results)
+   - add a cap on AREA after advecting AREA if seaice_growth is not called
+ o change calculation of Visbeck K:
+   - no longer depend on tapering scheme; instead, compute slope (limited
+     by GM_maxSlope). this is equivalent to what was comuted before with
+     clipping or linear tappering.
+   - fix vertical averaging (wrong by 1/2 level)
+   - leave the old version (but will not be maintained) within
+     #ifdef OLD_VISBECK_CALC / #endif
+   - update output of exp. ideal_2D_oce
+ o change error catch in calc_r_star to improve vectorization
+ o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
+   add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
+ o adjoint:
+   Re-organized adjoint checkpointing according to Matt Mazloff
+   (but with modifs/completions/cleanups)
+   Storing is now bundled into large arrays to optimized I/O
+   (and second step in cleanup of the_main_loop)
+ checkpoint59b
+ o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
+   - export/import (between ocean & coupler) fields needed for ocean DIC.
+ o pkg/seaice:
+   - get rid of three more exchanges seaice_calc_viscosities (required
+     different loop boundaries in seaice_lsr and seaice_ocean_stress)
+   - bug fix in seaice_ocean_stress (update of lab_sea required)
+   - reduce loop boundaries to necessary minimum also in seaice_evp
+   - go back to the old way of computing deltaC/Z as the adjoint likes that
+     better
+ o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
+   passive tracer to an Age Tracer) + update output.txt
+ o pkg/exf:
+   - implement A-grid / C-grid selection for wind-stress input files.
+   - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
+   for now, in exf_bulk_largeyeager04.F only :
+   - change implementation for case where windspeed + 2. components wind-stress
+     are read-in. AND use rhoConstFresh to convert evap.
+ o pkg/seaice:
+   - use correct EXCH_UV for wind-forcing (on A-grid).
+   - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
+     SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
+ o pkg/exf:
+   - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
+   EXF_INTERPOLATION:
+   - merge global_with_exf/code version of exf_interp_read.F
+     to the main code ;
+   - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
+     reading the file ; Important: This options needs to be defined to recover
+     previous code.
+     otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
+   - no longer loose real*8 precision along the way when using exf_iprec=64.
+ o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
+   - change discretisation of evp-solver in order to avoid another exchange
+     (changes lab_sea) and clean up a little
+   - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
+     help the adjoint (this also changes the results slightly)
+   - add a few "_d 0" where they had been missing in seaice_evp.F
+   - cleaning up: remove unused seaice_calc_rhs.F
+ o pkg/exf: some cleaning-up:
+   - change various "constants" into runtime parameters
+   - cleaned-up Large&Yeager04 routine which should eventually
+     replace exf_bulkformulae.F (changed names of S/R and CPP)
+     and merged various ALLOW_ATM_WIND options
+  only used with thsice pkg (in thsice_get_exf.F):
+   - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
+     which are used when useStabilityFct_overIce=TRUE (= the default)
+   - change default values of ice & snow emissivity and scale downward LW
+     by ice & snow emissivity.
+ o pkg/thsice:
+  fix few little problems, in thsice_calc_thickn.F:
+   - growth vertically (and not laterally) if iceFrac == iceMaskMax
+   - melt only laterally if hIce < hThinIce (as the comments say)
+   and in thsice_extend.F:
+   - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
+   - start to form ice as soon as the minimum ice-volume is reachable.
+  update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
+   and cpl_aim+ocn
+ o pkg/kpp
+  - move computation of surface related input fields to KPP into a new
+    subroutine kpp_forcing_surf.F
+  - remove wrong (within bi,bj loops) EXCH calls.
+  - little cleaning (add argument myThid in last position, cvs header ...)
+  - for now, fix conservation problem by exchanging KPPviscAz (may not
+    be the best fix)
+ o pkg/seaice
+  - check for inconsistent evp parameter/cpp-flag combination
+  - remove leftover errIO flat for obsolete name list error handling
+ o OpenAD
+  - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
+ checkpoint59a
+ o pkg/seaice: some parameter clarifications and a little bit of clean up
+ o pkg/thsice: rename run-time parameters:
+    himin       -> hIceMin
+    himin0      -> hThinIce
+    hihig       -> hThickIce
+    i0          -> i0swFrac
+    transCoef   -> bMeltCoef
+    frac_energy -> fracMelting
+   add new parameters: hNewIceMax, fracFreezing, dhSnowLin
+    with default values (for now) that do not change the results.
+   remove old version of thsice vars advection in pkg/seaice.
+ o in FFIELDS.h:
+   - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
+   - make pLoad & sIceLoad always available (but still only used if
+      ATMOSPHERIC_LOADING is #define).
+ o pkg/kpp: replaced _KPP_RL with _RL
+ o bug fixes for vertical diffusivity computations when both KPP and
+D diffusivity arrays are used.
+ o pkg/seaice: fix bug in evp solver, while doing that
+   - change (improve?) discretization of stress computations for both
+     cgrid-lsr and evp solver
+   - add a new routine to compute strain rates
+   - the above changes lab_sea results
+   - add no slip conditions for evp solver (off by default), lsr-version
+     may follow
+   - fix exchange for shear at Z-points (does not change lab_sea)
+   - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
+     (to force the user to pick a time step since there is not "safe" way
+     of choosing it)
+   - add principal stress diagnostics
+   - rearrange fields for evp a little to avoid having to call a: too many
+     exchanges and b: exchanges for stress trensor components which we do
+     not have.
+   - modify Hibler+Bryan (1987) stress coupling so that it reuses information
+     of evp, complete rewrite for lsr case (latter is does not yet work
+     in all cases)
+ o pkg/kpp: add code to have mixing in shelf ice caverns
+   - add myThid to all kpp routines (long overdue)
+ checkpoint59
+ o pkg/exf:
+   - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
+     ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
+   - move exf header files from lower_case.h to UPPER_CASE.h ;
+     add missing cvs Header & Name
+   - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
+   - add namelist param. selectStressGridPosition, exf_monFreq
+   - retire many _CLIM routines, and remove data.exf_clim
+     + params moved to data.exf
+     + climsst, climsss now handled by exf_set_gen, i.e.
+       climss?period=0 refers to constant field,
+       climss?period=-12 to monthly forcing
+   - split up namelists in data.exf
+ o pkg/seaice:
+   - remove seaice_exch and seaice_exch_uv
+   - remove superfluous exchange of theta
+   - add myThid to seaice_budget_ocean/ice
+   - add new interface for atmospheric wind forcing (C-grid only)
+     + new routine
+     + two new field (taux, tauy for stress over ice)
+     + removed one global field (DAIRN) for C-grid case only
+ o pkg/thsise
+   - 2nd set of modifs for thsice adjoint in conjunction with exf
+ o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
+ checkpoint58y_post
+ o Added capability for latitudinal dependence of Bryan and Lewis, 1979
+   vertical diffusivity, similar to that in MOM4; turned on using
+   #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
+   diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
+ o Added capability for 3D specification of background vertical diffusion
+   coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
+   in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
+   "data" file that contains the 3D vertical diffusivity coefficients.
+ o ice dynamics (pkg/seaice) with thsice thermodynamics:
+   - add code within pkg thsice to advect & diffuse sea-ice fields
+   similar to (and will replace) what has been added in  seaice_advdiff.F,
+   but: - conserving Mass, Heat & Salt.
+        - better when using non-linear advection scheme (not yet fully tested)
+        - can also be used in atmospheric set-up (for now, only the diffusion).
+ checkpoint58x_post
+ o IO option for global-file compact format:
+   - add options when generating topology (utils/exch2/matlab-topology-generator)
+   - add I/O capability (pkg/mdsio).
+   - adapt utils/matlab/rdmds.m to read this format.
+   for now long-line format not yet supported by pkg/mdsio (& exch2).
+ o shelfice: add a few diagnostics
+ checkpoint58w_post
+ o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
+   rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
+   (and replace horiVertRatio in NH code).
+   Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
+                      and tutorial_plume_on_slope (sensitive to truncation)
+ o seaice: if ALLOW_ATM_WIND is undefined use wind stress
+   directly to drive seaice model (C-grid only)
+ o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
+  - reintroduce computation of wind from stress,
+  - compute tau (in exf_bulkformulae.F) from windstress averaged to
+    mass points to avoid tau = 0
+  - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
+ o rdmnc.m: make it work with "global" files created with gluemnc
+ o rdmnc.m : some improvements in dealing with singleton dimension
+   (tested on all testreport mnc output files).
+ o genmake2: disable pkg/profiles if netcdf test fails.
+ o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
+ o move call to cal_readparms up to make calendar parameters/variable available
+   to all packages
+ checkpoint58v_post
+ o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
+   useDynP_inEos_Zc tested.
+ o pkg/exf: changes to properly interpolate/mask/scale initial fields
+ o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
+   and portions thereof.  See read_cs.txt for description and examples.
+ o utils/matlab/cs_grid/bk_line: to compute transport through passages,
+   add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
+   following the great-circle arc between those 2 points.
+ o trap un-initialized variable with pathscale compiler on weddell.mit.edu
+   (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
+ o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
+  - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
+  - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
+  - still needs work (not working with some options ; efficiency to improve)
+    and serious testing.
+  - use this scheme for temperature & salinity in 2 advection test exp.:
+    advect_xy & advect_xz, respectively.
+ checkpoint58u_post
+ o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
+ o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
+ o testreport: add option "-skipdir" to skip some test.
+ o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
+   momentum calculation.
+ o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
+ o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
+   remove checkpoint.F and the_correction_step.F (no longer used);
+   do the k loop inside CYCLE_TRACER (supposed to be more efficient).
+ o add option (linFSConserveTr) to correct for tracer source/sink due to
+   Linear Free surface
+ o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
+ o pkg/thsice: fix reading mnc-pickups
+ checkpoint58t_post
+ o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
+ o pkg/mdsio:
+  - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
+    move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
+    mdsio_write_field.F (S/R MDS_WRITE_FIELD);
+  - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
+  - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
+    either MDS_READ_FIELD or MDS_WRITE_FIELD )
+  - new S/R (to replace MDSWRITEMETA), which allows to write more
+    informations (variable names, time ...) to meta files.
+  - modify rdmds.m to give back the meta file content.
+ o pkg/diagnostics: change vertical interpolation to be safer, and more
+    flexible (define p-levels to interpolate to in data.diagnostics);
+   add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
+    diagnostic pointer.
+ o pkg/seaice: more cleaning up of seaice_growth, added many comments
+ o pkg/exf: put runoff0 and runoff1 into the appropriate common block
+ o fix multi-category seaice:
+  - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
+    SEAICE_MULTICATEGORY
+  - fix short wave heat flux
+ o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
+    and allow to use EVP solver. Change forward lab_sea: test both EVP
+    solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
+ o Initial check-in of lab_sea adjoint
+   (very similar to natl_box_adjoint/code_seaice)
+   * used C-grid and EVP solver
+   * used KPP, GM/Redi
+   * uses inAdExact=.TRUE.
+   * gradient checks fail for both ADM and TLM
+     due to sensitive snow melt code in seaice_grwoth (look for "JZ")
+     f.d. gradients actually seem more problematic than ADM, TLM gradients;
+     issue is related to forward mismatch between g77 an ifort
+ o pkg/seaice: overhaul of thermodynamics
+  - growth.F and groatb.F are replaced by new routine seaice_growth.F
+  - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
+  - move a few global fields out of SEAICE.h into seaice_growth.F and
+    make them 2D (FICE/QNETO/ ...)
+  - remove FO (it is the same as QNETO)
+  - introduce a few local fields to avoid modifying external fields such
+    as atemp, etc.
+ checkpoint58s_post
+ o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
+   changed exf_set_gen.F so that
+     genperiod=0 means input file is one time-constant field and
+     genperiod=-12 means input file contains 12 monthly means
+ o CG2D: use pre-computed solver main-diagonal (stored in common block);
+   this affects truncation error ; generate new output file for exp. which
+   fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
+     global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
+     ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
+     MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
+     tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
+     vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
+ o start implementation of deep-atmosphere and anelastic formulation
+ o verification: remove 2nd copy of input files and use script "prepare_run"
+   to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
+ o mom_common/vecinv/fluxform: fix a few initialisation isssues
+ o profiles: fix for multithreaded case
  o diagnostics: rename few diags:
    s/'PRESSURE'/'RCENTER '/g
    s/'TICE    '/'oceFreez'/g

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