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revision 1.703 by gforget, Fri Jul 14 22:14:28 2006 UTC revision 1.1073 by mlosch, Sat Feb 28 16:57:04 2009 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: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
8    o pkg/ctrl:
9      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
10    o non-hydrostatic (calc_gw.F):
11      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
12      update output of exp. global_ocean.cs32x15.viscA4
13    o remove backward compatibility for thetaMin,phiMin
14      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
15    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
16      interpolated wind field not only for curvilineargrid=.true., but also
17      for a rotated grid (rotateGrid=.true.)
18    o pkg/exf: add capability to bypass interpolation for runoff
19      by setting yet another CPP-flag
20    o eesupp/src, B-grid exchange:
21      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
22    o autodiff
23      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
24      allows to switch to single-prec common blocks;
25      corresponding switch occurs in tamc.h, integer isbyte
26      TAF store directivs "byte" and "kind" seem equivalent;
27      Most tamc.h have been updated correspondingly.
28    
29    checkpoint61i
30    o autodiff:
31      fix autodiff_sore/_restore indices for obcs
32      (spotted by I. Hoteit, M. Mazloff)
33    o pkg/autodiff, pkg/ctrl:
34      Add flag to reduce all tapelev I/O to single-prec.
35      In data.ctrl set
36        doSinglePrecTapelev = .TRUE.
37    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
38      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
39    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
40      real fresh water flux (not yet)
41    o pkg/mdsio & rw:
42     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
43     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
44    o pkg/flt:
45     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
46       init_fixed & ini_varia.
47     - clean-up & simplify linear interpolation S/R:
48       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
49     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
50     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
51     - add vert. coordinate & horiz. indices to output files.
52     - change vertical position in initial condition, from index to depth [m].
53     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
54       (easier to get to a curvilinear grid) ; delX,delY no longer used.
55    o pkg/ggl90: a few modifications:
56     - fix bottom boundary condition, and interpolation of KappaE
57       near top and bottom
58     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
59     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
60     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
61    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
62      (maintain temporary backward compatibility, until next checkpoint)
63    
64    checkpoint61h
65    o pkg/diagnostics with "periodic averaging diagnostics":
66      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
67    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
68    o pkg/obcs: fix loop ranges for balancing code
69    o pkg/flt:
70     - improve criteria for finding which tile owns a float.
71     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
72    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
73      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
74      with ocean biogeo)
75    o pkg/flt:
76     - do some cleaning and fix the restart ;
77     - add output.txt in flt_example/results to get this pkg tested.
78    o genmake2: add an EXTENDED_SRC option and flag.
79       for now, cannot be turned on on command line (only through genmake_local)
80    o pkg/mdsio: read/write vector:
81     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
82     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
83       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
84     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
85      (drop to 4 digits matching for grad). But this test does not look very
86      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
87    
88    checkpoint61g
89    o pkg/flt:
90      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
91       + make OPTIONS file more standard.
92      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
93      - fix _BYTESWAPIO CPP-Flag
94      - standard reading of file-parameter "data.flt"
95      - fix argument list of S/R FLT_RESTART
96      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
97    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
98    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
99      a still unfixed compiler/optimization bug
100    
101    checkpoint61f
102    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
103      update results of global_ocean.cs32x15.icedyn test.
104    o move getcon.F from model/src to pkg/fizhi.
105    o pkg/exf: add parameter for extrapolation of temp up to the surface
106       and option to prevent negative evap (in bulk_largeyeager04 only).
107    o Prather Advection scheme: fix tracer conservation for divergent flow
108      (e.g., when using NonLin Free-Surface).
109    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
110    o gmredi (Visbeck-variable-K):
111     - add more parameters to Visbeck-variable-K.
112     - use a 5 points average for dSigmaR in Visbeck-K calculation
113       (more "homogenous": same stencil and same weights as in dSigmaH)
114     - update output of ideal_2D_oce experiment.
115    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
116      (#undef REAL4_IS_SLOW)
117     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
118       coordinate variable
119     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
120       (surface forcing fields), removes some of the functionality
121     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
122     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
123       probably not all: copy _RS surface flux fields to RL field before
124       calling DIAGNOSTICS_FILL
125     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
126       real*4 (CALL EXCH_*_RS) versions.
127     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
128       (generate new output).
129    
130    checkpoint61e
131    o gmredi (Visbeck-variable-K):
132      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
133      - change computation of Visbeck-K where Slope > Smax :        
134        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
135        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
136    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
137      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
138    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
139    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
140      does not become too large (to avoid precision problems in implicit-diffusion
141      solver); update ideal_2D_oce output.
142    o pkg ggl90:
143      - in ggl90_cal.F: compute only one set of visc/diff, used to
144        step forward TKE/T/S/momentum
145      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
146        have Prandlt =1)
147    o gmredi (fm07):
148      - add lower limit on Transition layer thickness + lower limit on 1/lambda
149      - allow to set few more params from data.gmredi
150    o pkg ggl90:
151          - add missing sqrt(2) factor in computation of mixing length
152            scale in ggl90_calc.F
153            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
154    
155    checkpoint61d
156    o adjoint modifs
157      - adapt to new field rhoInSitu
158      - allow to revert from StoreDynVars2D, StoreDynVars3D
159        to individual fields
160        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
161    o store 3-D (in-situ) density in commom block (DYNVARS.h)
162     - save 1 rho computation.
163     - no longer modify T & S inland when using down_slope pkg.
164    o gad_som : allow to switch to SOM advection for T & S without corresponding
165      pickup files (using new S/R: MDS_CHECK4FILE).
166    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
167      (for useSingleCpuIO to work in multi-threaded)
168    o pkg/shelfice:
169     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
170       with SHELFICEtopoFile in data.shelfice
171     - move code for reading ice shelf topography and modifying hFacC into separate
172       subroutines of the shelfice package
173     - separate initialisation of "fixed" and "variable" variables
174     - kTopC is not (yet) replaced by kSurfC, although this is possible
175    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
176    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
177      and rename:
178      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
179      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
180    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
181    
182    checkpoint61c
183    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
184      to add mass source/sink of fluid in the interior (3-D generalisation
185      of oceanic real-fresh water flux).
186    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
187    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
188    o new pkg: down_slope
189      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
190      - presently, modify T & S inland (dwnslp_calc_rho.F).
191        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
192      - implementation for ocean in P-coords not tested.
193      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
194    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
195      (to facilitate conversion of oceanic pkg to p-coordinate).
196    o change FIND_RHO to FIND_RHO_2D :
197      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
198    o new pkg: cheapaml
199    
200    checkpoint61b
201    o exch2:
202      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
203      - no longer depend on the order sequence (N,S,E,W).
204      - 3rd exchange no longer needed (tested with 24 tiles).
205      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
206      - exch_UV_A-grid readily available (but not yet tested).
207      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
208      (both are no longer needed) in exch_uv: no effect in forward run; but
209       get truncation error differences with adjoint exch.
210    o exch2:
211     - change index-bounds storage (moved from target to local tile,
212       more intuitive this way) ; rename/remove some variables.
213     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
214    
215    checkpoint61a
216    o exch2/matlab-topology-generator:
217      fix bug in index bounds for N-S internal exchange (hard to tell if this
218      had any effect on the solution).
219    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
220      is exceeded
221    o testreport: modify syntax of awk, so that it works also with
222      awk, and not only with nawk and gawk
223    
224    checkpoint61
225    o autodiff
226      Change default for TAF usage by removing argument '-nonew_arg'
227      This changes TAF subroutine argument list (ordering of active var.)
228      Omission of this flag leads to incompatibility w.r.t. TAMC
229      To restore TAMC-compatibility, need following modifs:
230      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
231      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
232      Tested TAF version is 1.9.22
233      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
234    
235    checkpoint60
236    --->>> This is the last checkpoint for which generating the adjoint
237    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
238    --->>> by default.
239    --->>> Future checkpoints will ommit this flag by default.
240    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
241    o pkg/grdchk: Add gradient check to etan0 perturbations.
242    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
243    o pkg/autodiff: more flexibility in zeroadj.
244      model/src: modifying do_oceanic_phys.F accordingly.
245    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
246    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
247      special setup of gmredi for which the adjoint is stable
248      enough for parameter optimization.
249    o bridging the gap between eddy stress and GM.
250      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
251          along with a change in CPP option (now ALLOW_EDDYPSI).
252      -> when using GM w/ GM_AdvForm:
253          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
254          is applied either in the tracer Eq. or in momentum Eq.
255          depending on data.gmredi (intro. GM_InMomAsStress).
256      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
257      The key modifications are in model/src/taueddy_external_forcing.F
258      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
259    
260    checkpoint59r
261    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
262      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
263      fix option to read coriolis(@ cell-corner) from files with CS-grid.
264    o pkg/mnc: add some attributes to standard 1D-coordinate variables
265    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
266      mass points, when using mnc for output
267      - add runtime parameter (missing_value, missing_value_int) to override
268        default (which is the value of getcon('UNDEF'))
269    o pkg/mnc: prepare mnc for the actual use of missing values with the
270      diagnostics package: small fix in mnc_cw_readwrite.template and more
271      initialisation of never used fields
272      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
273      versions
274    o pkg/thsice/thsice_ini_vars.F added default initial values so that
275      thermodynamics sea ice solver does not blow up when some initial fields
276      are missing.
277    o move from external_forcing_surf.F to ini_forcing.F
278      the p-coord. hack consisting in using pLoad to set phi0surf ;
279      update output of tutorial_global_oce_in_p (affected @ truncation level).
280    o Freshen up a bit hs94.1x64x5, notably:
281      remove rotationPeriod and tRef=5*0. (adjoint only), and add
282      exactConserv=.TRUE.
283    o pkg/generic_advdiff:
284      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
285      applies to files where Temperature & Salinity 2nd Order moments are used.
286    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
287      this uses a dynamically allocated internal state data structure
288      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
289      and requires a fortran 90 compiler
290    
291    checkpoint59q
292    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
293       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
294    o Refresh tutorial_global_oce_biogeo, notably:
295      - change bathymetry (put back seamounts in ACC, use hFacs)
296      - change EOS (POLY3 --> JMD95Z)
297      - use Bryan-Lewis vertical diffusivity
298      - use multidimensional advection
299      - remove old virtual virtual in dic pkg, now done through ptracer pkg
300      - change a couple of parameters in dic pkg
301    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
302    o pkg/obcs: change default to OBCSfixTopo = .true.,
303      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
304      - replace "debugMode" with "debugLevel .GE. debLevB"
305    o implementation of TAF directives for gchem,cfc,dic
306    o remove "exp5" (replaced by tutorial_deep_convection).
307    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
308      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
309      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
310      --> changes results in exp4, seaice_obcs
311    o tutorial_deep_convection :
312      update the set-up and increase resolution and domain size ; start
313      from pseudo initial conditions = output at t=120mn in order to see
314      something happening when running testreport.
315    o pkg/seaice: add os7mp as an advection scheme
316                  add check for advection schemes
317                  add a flag for restoring T and S underneath sea ice
318    o pkg/my82: add netcdf-support and diagnostics
319    o thsice pkg:
320      - Now hsMax limits snow height by turning it into ice following
321        flooding scheme (and now conserving energy)
322      - Slight rewriting of the formula in thsice_calc_thick.F
323      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
324      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
325    
326    checkpoint59p
327    o gchem / dic / cfc :
328      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
329      - add new parameter files: "data.dic" & "data.cfc" ;
330      - various re-arrangement in initialisation & header file ;
331      - fix tutorial_global_oce_biogeo for multi-threaded test.
332    o pkg/dic: test for "pickup_dic" file when restarting ;
333      if no pickup-file, can restart with a re-initialised pH (same as it did
334      before) providing pickupStrictlyMatch is set to False.
335    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
336      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
337    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
338      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
339    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
340     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
341       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
342    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
343       scheme to use for vorticty-term ;
344     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
345       (with default selectVortScheme, return to original discretisation)
346     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
347    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
348    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
349      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
350      also fix diagnostics VISCAHW & VISCA4W.
351    
352    checkpoint59o
353    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
354    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
355      move a few statemens out the main loop into separate loops
356    o pkg/shelfice:
357      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
358        (kg/m^2/s), does not break tests, because in verification/isomip,
359        rhoConstFresh=rhoConst (by accident)
360      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
361      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
362        new file model/src/seawater.F, so that they are available for all pkgs.
363      - convert potential temperature into in-situ temperature. This changes the
364        isomip tests => update tests
365    o add a flag writePickupAtEnd (default=true) to be able to suppress
366      writing a pickup at the last timestep
367    o tools/mpack-1.6 :
368      - disable automake (not working) and autoconf (not needed).
369      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
370        also cleaner with much less compilation warnings.
371    o pkg/profiles:
372      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
373      (for "less than 32 characters name" compiler requirement)
374    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
375      conditions that have a different sampling frequency than S/T/U/V obcs
376    o pkg/diagnostics (stats-diags):
377      - fix global Min/Max in case 1 processor get only empty tiles
378    o genmake2: replace (4 times)
379         make genmake_tc_1.o >> genmake_warnings 2>&1
380      with
381         COMM="$CC $CFLAGS -c genmake_tc_1.c"
382         echo $COMM >> genmake_warnings
383         $COMM >> genmake_warnings 2>&1
384      to make genmake2 always see the value of CC as specified in the optfile.
385    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
386      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
387      - modify verification advect_cs test to test SOM-advection on CS-grid.
388    o pkg/ctrl:
389      - Rewrite of ctrl_map_ini_ecco.F,
390        introducing a generic routine (ctrl_map_ini_gen.F).
391      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
392    
393    checkpoint59n
394    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
395      number in dedicate array "hdiag":
396      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
397        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
398      - many small changes (integer format) for large number of diagnostics
399      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
400        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
401    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
402      usingSphericalGrid, this allows to define the rotated grid coordinates
403      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
404      geographical coordinates according to the inverse of the rotation defined
405      by the Euler angles, so that Coriolis parameter and online-interpolation by
406      exf works with the geographical coordinates on XC/YC/XG/YG.
407      Naturally, this feature does not work with all packages, so some
408      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
409      profiles), because there the coordinates are assumed to be regular
410      spherical grid coordinates.
411    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
412      - introduce isopycnal diffusion coefficient control.
413    o tools/adjoint_options:
414      - additional control vector components.
415    o pkg/mnc: have mnc create marginally meaning full coordinate variables
416      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
417    o pkg/mypackage:
418      - add example of read/write pickup for state-var ;
419      - add entry points to the main code for state-vars diags & write-pickup.
420    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
421      transitions for useExfYearlyFields
422      - add new subroutine that determines the file to read from for
423        use*YearlyFields = .TRUE. and .FALSE.
424      - add a verification experiment to global_with_exf that tests
425        useExfYearlyFields with USE_EXF_INTERPOLATION defined
426    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
427      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
428      subroutines (which could be generated from a template, because they are
429      almost identical), for now they are included in obcs_prescribe_read.F for
430      simplicity
431    o pkg/exf:
432      - add a little more diagnostic to exf_interp_read (in analogy to
433        mds_read_field, can be turned off with debugLevel < debugLevA=1)
434      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
435        ugly but fast by unrolling short inner loops, inserting a unroll=8
436        directive in routine lagran, and splitting a loop and making do while the
437        outermost loop (the latter requires the intoduction of index arrays)
438    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
439    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
440      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
441    o verification/seaice_obcs: updated for restart test and latest options
442    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
443      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
444      for now this is only available for the C-grid code and also within
445      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
446    
447    checkpoint59m
448    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
449      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
450    o gad_som : fix flux output (& diagnostics) to have same units as other  
451      advection scheme fluxes (was previously multiplied by deltaT).  
452    o added verification/seaice_obcs both to test seaice open boundaries
453      and to provide an example matlab scrpt for generating them
454    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
455    o pkg/salt_plume: clean up salt_plume_frac.F to
456      remove redundancy in PlumeMethod 1 and 4
457    o pkg/kpp: added saltplume diagnostics
458    o pkg/obcs and pkg/seaice:
459      - do not set uice and vice to zero when OB*icefile are unspecified
460      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
461      - moved seaice tracer obcs after call to seaice_growth
462    o pkg/salt_plume: added various options for salt plume depth
463      criterion and for vertical distribution of the salt
464    
465    checkpoint59l
466    o pkg/ptracers: new version of ptracers pickup:
467      read meta file and write only fields which are needed to restart.
468      ( same logic as main pickup file ; also using pickupStrictlyMatch )
469    o pkg/seaice:
470      - add timescale for melting due to warm mixed layer as a means of
471        setting SEAICE_availHeatFrac more conveniently
472      - add a CPP-flag/runtime parameter check for flooding algorithm
473      - reformulated availHeat in seaice_growth.F to be independent of AREA
474    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
475      unit changes
476    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
477    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
478      SX vector computer.
479    o pkg/seaice:
480      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
481        seaice forcing fields can now be read only through pkg/exf
482      - removed some unused halos
483    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
484    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
485      or U/VICE from U/VWIND before computing U/VSTRESS
486    
487    checkpoint59k
488    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
489      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
490    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
491      all experiments pass when compile with un-initialised var. checking option.
492    o added pkg/salt_plume
493    o script to test restart (for now, in MITgcm_contrib/jmc_script)
494    o pkg/seaice: new read/write pickup version.
495      read meta file and write only fields which are needed to restart.
496      ( same logic as main pickup file ; also using pickupStrictlyMatch )
497    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
498    o lab_sea.hb87: modify the domain & update output.hb87.txt :
499      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
500      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
501      process. Fixed here by closing the domain at the Northern boundary.
502    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
503    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
504      a set of consecutive levels in/from a 3-D array.
505    o pkg/ptracers:
506      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
507      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
508    
509    checkpoint59j
510    o in pkgs: dic, obcs, offline, rbcs:
511      standard way to compute coeff. for time interpolation between 2 time reccords
512      which retains full precision (& make results less dependent on compiler).
513      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
514    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
515      packages instead of reading ice cover and wind speed separately
516    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
517     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
518      to allow to compile customized code before the update)
519    o cleaning-up:
520      - fix CPP instruction syntax in pkg/obcs
521      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
522        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
523      - fix some threads issue in IO parts.
524    o pkg/dic:
525      - add tons of "_d 0" (--> much better testreports !)
526       and then update outputs of tutorial_global_oce_biogeo
527    o pkg/mom_fluxform:
528      add a special version of momentum advection intended to conserve momentum
529      next to a bathymetry step or a coastline edge. (default = off = #undef)
530    o new read/write pickup version:
531      - for now, only implemented for main (mdsio) pickup file.
532      - write out only what is needed to restart; merge pickup_nh , pickup_ph
533        and main pickup together.
534      - read meta file; read only what is needed to restart; stop if a field
535        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
536        if it make sense (even if the restart is not perfect).
537      - if no meta file, assume that pickup to read corresponds exactly to
538        a pickup that would currently be written.
539      - read pickup written in the old format (until checkpoint59i) if it
540        recognizes an old meta file (no field-list).
541      - add a meta file in exp. which starts from a pickup: 2 cases:
542        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
543         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
544        b) a meta file describing the content of the associated pickup file
545         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
546    o pkg/mdsio & pkg/rw:
547      - new routine to read a meta file ; new set of routine to read
548        Multiple-fields file (with meta file).
549    o added open boundary conditions capability for seaice
550        HSNOW, HSALT, UICE, and VICE
551    
552    checkpoint59i
553    o adjoint:
554      * fix multiDimAdvection adjoint
555        (partial recomputation problem by TAF for fVerT(:,:,kDown)
556        and comlev1 size definition (maxpass vs. max. number of tracers)
557      * verification/global_ocean.90x45x15 adjoint now tests
558        NLFS and multiDimAdvection using DST3 (=30)
559      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
560    o pkg/kpp: add "_d 0" to real constant (if missing);
561      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
562      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
563    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
564      for internal parameters related to restart process (formerly from PARAMS.h)
565      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
566    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
567      as argument. (only atm2d & obcs write_pickup have not yet been updated)
568    o pkg/monitor:
569      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
570      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
571      - account for deep Atmosphere factor and density factor (anelastic)
572    o added open boundary conditions capability for seaice HEFF and AREA
573    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
574      thermodynamics
575      - requires a little reorganization, which affects the testreport results
576        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
577        so that now the conservative form is tested
578      - add a few comments
579    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
580    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
581    o add new diagnostics to seaice: advective, diffusive fluxes (only for
582      multidim-advection, for scheme 2 they are not filled) and transports,
583      thermodynamic growth rates
584    o change units of EmPmR (inside the code, + within coupling interface)
585      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
586      Affects results @ truncation level (cg2d match) and update output of
587       experiments: lab_sea(6), global_ocean.90x40x15(10),
588      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
589      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
590      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
591      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
592    
593    checkpoint59h
594    o pkg/exf:
595      - improve vectorization by moving if-statement out of loops in
596        exf_mapfields, exf_radiation
597      - exf_bulkformulae.F: introduce 2D fields and vectorize code
598    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
599    o testreport:
600      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
601        monitor & update offline_exf_seaice exp. output.
602      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
603    o pkg/seaice:
604      - bug fix in the evp solver: boundary conditions were affected be
605        masking of zMax/zMin (changes results)
606      - minor bug fix in boundary conditions in seaice_calc_strainrates
607        (changes results for no_slip)
608      - seaice_lsr.F: make interpolation of eta dependent on boundaries
609      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
610      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
611        stress formulation and no-slip boundary conditions
612    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
613      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
614    o pkg/seaice: a first HSALT time stepping equation has been checked in
615    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
616      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
617      without requiring DO-IF statements
618    o pkg/thsice:
619      use continuous power-law function for partition of energy between lateral
620      melting/freezing and thinning/thickening ; old code using step function
621      still available with #undef THSICE_FRACEN_POWERLAW
622      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
623    o testreport: change AD testing : check against results/output_adm.txt
624      using same scripts as for forward test.
625    
626    checkpoint59g
627    o adjoint testing: in preparation for changing testreport:
628      - output format: cost and grad written on separated lines
629      - ad output results in directory "results" (instead of "results_ad")
630    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
631    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
632    o pkg/ecco: allow user defined cost function contributions
633    o testreport:
634      Allow to choose (per experiment) the list of tested output variables
635       and the main variable (used to issue a pass/FAIL ) ;
636      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
637      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
638      Also modify printing of summary:
639       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
640       b) echo the list of tested variables in the individual summary.txt of
641          each experiment.
642    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
643      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
644      (but still depend on the tile decompostion of the domain).
645    o pkg/seaice: change a discretization detail to make the B-grid code
646      "more symmetric". This change is likely to remove all "ridges/leads" that
647      where quasi-aligned with the grid in B-grid solutions. It may also be
648      the solution to the stress coupling issues with the B-grid.
649    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
650      remove .cvsignore from input dir. (since testreport no longer run here).
651    o pkg/thsice:
652     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
653     - fix reshaping of sea-ice just after advection:
654       melt all the ice only if ice-volume is too small.
655     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
656       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
657     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
658    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
659      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
660    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
661      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
662      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
663      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
664      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
665      -> update output.txt
666    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
667     this affects truncation error: -> update output.txt of exp:
668      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
669      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
670    
671    checkpoint59f
672    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
673    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
674      a bounded range (in forward mode)
675    o pkg/ecco, ctrl, autodiff and mom_common:
676     internal parameter controls, completements of implementations
677    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
678    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
679      (not seem any difference in testing results).
680    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
681       at face corners.
682    o pkg/generic_advdiff:
683     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
684      loop range indices for computing vertical advection tendency
685      and do the calculation in the interior only (no overlap) ;
686      for now, only implemented for SOM advection (to save CPU time).
687     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
688    o exch2 adjoint
689      First set of changes:
690      - add exch2 hand-written adjoint templates
691      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
692        This will require cleanup in pkg/autodiff/*.F
693        (changed routines currently kept separate in verif. code/)
694      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
695        that used to hide exch2 or cubed-sphere specific code
696        (commented via 'cph-exch2')
697    o pkg/seaice
698      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
699    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
700       output of global_ocean.cs32x15.thsice .
701    
702    checkpoint59e
703    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
704      for B-grid vector (not yet tested) and C-grid vector (<- only used
705      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
706    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
707      (#ifdef ALLOW_SALT_PLUME)
708    o gather_2d/scatter_2d: removed halo regions
709    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
710      scheme and the corresponding test case (under front_relax dir). For now,
711      only available with Skew-flux form and not yet tested in realistic set-up.
712      adjoint: store directives updated, but gradient checks deteriorated,
713      so maybe GM/Redi adjoint is now broken.
714    o seaice adjoint
715      * add AREA, HEFF, HSNOW as control variable
716        (should not change lab_sea results)
717      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
718    o pkg/seaice:
719      * added computation of saltFlux in seaice_growth;
720        For time being, sea ice salinity is assumed constant
721        contribution of snow flooding to freshening of sea ice is neglected.
722        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
723        defaults to 0.0 in order to maintain backward compatibility.
724        Typical values for SEAICE_salinity are 4 to 10 g/kg.
725      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
726      * added SEAICE_availHeatFrac, which specifies fraction of surface level
727        heat content used to melt or grow ice
728      * commented out cap of HICE: it helps keep ice thinner
729      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
730      * applied OBCS T/S mask to HEFFM sea ice mask
731    
732    checkpoint59d
733    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
734     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
735     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
736    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
737     and change default value of parameter "GM_Small_Number";
738     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
739       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
740       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
741    o pkg/ecco: cost function when applying pkg/smooth to controls
742    o pkg/ctrl: add forcingPrecond run time parameter
743    o pkg/seaice:
744     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
745     - fix bug in metric terms of u-equation in LSR solver (implicit part),
746       changes verification/lab_sea
747     - rearrange implicit part of u-equation in LSR solver to make it easier to
748       read, understand, and debug. This causes changes at the truncation level.
749     - fix (serious) bug in the boundary conditions (sign error in the implicit
750       part) of the LSR solver. Changes all LSR results.
751     - fixed problem with HSNOW initialization to avoid thick snow when AREA
752       is initilized with small values - does not change lab_sea results.
753     - added HsnowFile initialization capability
754    o pkg/smooth: addition to model/src and pkg/ctrl so allow
755     initialization of pkg/smooth and application to control vector
756    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
757    o dependencies: pkg/profiles requires pkg/cal
758    o pkg/profiles:
759     - added option ALLOW_PROFILES_GENERICGRID
760         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
761         that interpolation information (grid points and coefficients) is provided
762         within the netcdf input files.
763         -> sample matlab scripts can be found in MITgcm_contrib/gael
764         that allow you to prepare netcdf input files.
765     - also modified: cleaner include statements, cleaner error print statements,
766       cleaner stops when error, and more tests of the netcdf input files consistency.
767    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
768    o pkg/seaice:
769     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
770       requires a new routine: seaice_diagnostics_fill.F
771     - make sure that seaice does not move if not forced (pressure replacement
772       method, Hibler and Ip, 1995), changes results
773     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
774     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
775       It is turned off by default (=-1.), because it changes the results.
776     - make it possible to read AREA from a file, too.
777    
778    checkpoint59c
779    o add S/R and diagnostics for oceanic mixed-layer depth
780    o move GMRedi call after all vertical mixing schemes (including KPP)
781    o pkg/thsice:
782     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
783      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
784    o pkg/obcs:
785     - bug fix for balance code
786    o pkg/seaice:
787      - allow values of SEAICE_elasticParm > 1
788      - add new parameter SEAICE_evpTauRelax as an alternative
789        to SEAICE_elasticParm
790      - make lsr boundary conditions free slip (by default), changes result
791      - add code for no slip boundary conditions for lsr
792      - set minimum of zeta to zero (and not 4e8) (changes results)
793      - add a cap on AREA after advecting AREA if seaice_growth is not called
794    o change calculation of Visbeck K:
795      - no longer depend on tapering scheme; instead, compute slope (limited
796        by GM_maxSlope). this is equivalent to what was comuted before with
797        clipping or linear tappering.
798      - fix vertical averaging (wrong by 1/2 level)
799      - leave the old version (but will not be maintained) within
800        #ifdef OLD_VISBECK_CALC / #endif
801      - update output of exp. ideal_2D_oce
802    o change error catch in calc_r_star to improve vectorization
803    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
804      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
805    o adjoint:
806      Re-organized adjoint checkpointing according to Matt Mazloff
807      (but with modifs/completions/cleanups)
808      Storing is now bundled into large arrays to optimized I/O
809      (and second step in cleanup of the_main_loop)
810    
811    checkpoint59b
812    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
813      - export/import (between ocean & coupler) fields needed for ocean DIC.
814    o pkg/seaice:
815      - get rid of three more exchanges seaice_calc_viscosities (required
816        different loop boundaries in seaice_lsr and seaice_ocean_stress)
817      - bug fix in seaice_ocean_stress (update of lab_sea required)
818      - reduce loop boundaries to necessary minimum also in seaice_evp
819      - go back to the old way of computing deltaC/Z as the adjoint likes that
820        better
821    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
822      passive tracer to an Age Tracer) + update output.txt
823    o pkg/exf:
824      - implement A-grid / C-grid selection for wind-stress input files.
825      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
826      for now, in exf_bulk_largeyeager04.F only :
827      - change implementation for case where windspeed + 2. components wind-stress
828        are read-in. AND use rhoConstFresh to convert evap.
829    o pkg/seaice:
830      - use correct EXCH_UV for wind-forcing (on A-grid).
831      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
832        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
833    o pkg/exf:
834      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
835      EXF_INTERPOLATION:
836      - merge global_with_exf/code version of exf_interp_read.F
837        to the main code ;
838      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
839        reading the file ; Important: This options needs to be defined to recover
840        previous code.
841        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
842      - no longer loose real*8 precision along the way when using exf_iprec=64.
843    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
844      - change discretisation of evp-solver in order to avoid another exchange
845        (changes lab_sea) and clean up a little
846      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
847        help the adjoint (this also changes the results slightly)
848      - add a few "_d 0" where they had been missing in seaice_evp.F
849      - cleaning up: remove unused seaice_calc_rhs.F
850    o pkg/exf: some cleaning-up:
851      - change various "constants" into runtime parameters
852      - cleaned-up Large&Yeager04 routine which should eventually
853        replace exf_bulkformulae.F (changed names of S/R and CPP)
854        and merged various ALLOW_ATM_WIND options
855     only used with thsice pkg (in thsice_get_exf.F):
856      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
857        which are used when useStabilityFct_overIce=TRUE (= the default)
858      - change default values of ice & snow emissivity and scale downward LW
859        by ice & snow emissivity.
860    o pkg/thsice:
861     fix few little problems, in thsice_calc_thickn.F:
862      - growth vertically (and not laterally) if iceFrac == iceMaskMax
863      - melt only laterally if hIce < hThinIce (as the comments say)
864      and in thsice_extend.F:
865      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
866      - start to form ice as soon as the minimum ice-volume is reachable.
867     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
868      and cpl_aim+ocn
869    o pkg/kpp
870     - move computation of surface related input fields to KPP into a new
871       subroutine kpp_forcing_surf.F
872     - remove wrong (within bi,bj loops) EXCH calls.
873     - little cleaning (add argument myThid in last position, cvs header ...)
874     - for now, fix conservation problem by exchanging KPPviscAz (may not
875       be the best fix)
876    o pkg/seaice
877     - check for inconsistent evp parameter/cpp-flag combination
878     - remove leftover errIO flat for obsolete name list error handling
879    o OpenAD
880     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
881    
882    checkpoint59a
883    o pkg/seaice: some parameter clarifications and a little bit of clean up
884    o pkg/thsice: rename run-time parameters:
885       himin       -> hIceMin
886       himin0      -> hThinIce
887       hihig       -> hThickIce
888       i0          -> i0swFrac
889       transCoef   -> bMeltCoef
890       frac_energy -> fracMelting
891      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
892       with default values (for now) that do not change the results.
893      remove old version of thsice vars advection in pkg/seaice.
894    o in FFIELDS.h:
895      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
896      - make pLoad & sIceLoad always available (but still only used if
897         ATMOSPHERIC_LOADING is #define).
898    o pkg/kpp: replaced _KPP_RL with _RL
899    o bug fixes for vertical diffusivity computations when both KPP and
900        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
901        are no longer updating the vertical diffusivity array
902        (passed as argument) but are (re-) setting those arrays.
903    o pkg/seaice: fix bug in evp solver, while doing that
904      - change (improve?) discretization of stress computations for both
905        cgrid-lsr and evp solver
906      - add a new routine to compute strain rates
907      - the above changes lab_sea results
908      - add no slip conditions for evp solver (off by default), lsr-version
909        may follow
910      - fix exchange for shear at Z-points (does not change lab_sea)
911      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
912        (to force the user to pick a time step since there is not "safe" way
913        of choosing it)
914      - add principal stress diagnostics
915      - rearrange fields for evp a little to avoid having to call a: too many
916        exchanges and b: exchanges for stress trensor components which we do
917        not have.
918      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
919        of evp, complete rewrite for lsr case (latter is does not yet work
920        in all cases)
921    o pkg/kpp: add code to have mixing in shelf ice caverns
922      - add myThid to all kpp routines (long overdue)
923    
924    checkpoint59
925    o pkg/exf:
926      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
927        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
928      - move exf header files from lower_case.h to UPPER_CASE.h ;
929        add missing cvs Header & Name
930      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
931      - add namelist param. selectStressGridPosition, exf_monFreq
932      - retire many _CLIM routines, and remove data.exf_clim
933        + params moved to data.exf
934        + climsst, climsss now handled by exf_set_gen, i.e.
935          climss?period=0 refers to constant field,
936          climss?period=-12 to monthly forcing
937      - split up namelists in data.exf
938    o pkg/seaice:
939      - remove seaice_exch and seaice_exch_uv
940      - remove superfluous exchange of theta
941      - add myThid to seaice_budget_ocean/ice
942      - add new interface for atmospheric wind forcing (C-grid only)
943        + new routine
944        + two new field (taux, tauy for stress over ice)
945        + removed one global field (DAIRN) for C-grid case only
946    o pkg/thsise
947      - 2nd set of modifs for thsice adjoint in conjunction with exf
948    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
949    
950    checkpoint58y_post
951    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
952      vertical diffusivity, similar to that in MOM4; turned on using
953      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
954      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
955    o Added capability for 3D specification of background vertical diffusion
956      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
957      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
958      "data" file that contains the 3D vertical diffusivity coefficients.
959    o ice dynamics (pkg/seaice) with thsice thermodynamics:
960      - add code within pkg thsice to advect & diffuse sea-ice fields
961      similar to (and will replace) what has been added in  seaice_advdiff.F,
962      but: - conserving Mass, Heat & Salt.
963           - better when using non-linear advection scheme (not yet fully tested)
964           - can also be used in atmospheric set-up (for now, only the diffusion).
965    
966    checkpoint58x_post
967    o IO option for global-file compact format:
968      - add options when generating topology (utils/exch2/matlab-topology-generator)
969      - add I/O capability (pkg/mdsio).
970      - adapt utils/matlab/rdmds.m to read this format.
971      for now long-line format not yet supported by pkg/mdsio (& exch2).
972    o shelfice: add a few diagnostics
973    
974    checkpoint58w_post
975    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
976      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
977      (and replace horiVertRatio in NH code).
978      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
979                         and tutorial_plume_on_slope (sensitive to truncation)
980    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
981      directly to drive seaice model (C-grid only)
982    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
983     - reintroduce computation of wind from stress,
984     - compute tau (in exf_bulkformulae.F) from windstress averaged to
985       mass points to avoid tau = 0
986     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
987    o rdmnc.m: make it work with "global" files created with gluemnc
988    o rdmnc.m : some improvements in dealing with singleton dimension
989      (tested on all testreport mnc output files).
990    o genmake2: disable pkg/profiles if netcdf test fails.
991    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
992    o move call to cal_readparms up to make calendar parameters/variable available
993      to all packages
994    
995    checkpoint58v_post
996    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
997      useDynP_inEos_Zc tested.
998    o pkg/exf: changes to properly interpolate/mask/scale initial fields
999    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
1000      and portions thereof.  See read_cs.txt for description and examples.
1001    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
1002      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
1003      following the great-circle arc between those 2 points.
1004    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
1005      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
1006    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
1007     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
1008     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
1009     - still needs work (not working with some options ; efficiency to improve)
1010       and serious testing.
1011     - use this scheme for temperature & salinity in 2 advection test exp.:
1012       advect_xy & advect_xz, respectively.
1013    
1014    checkpoint58u_post
1015    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
1016    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
1017    o testreport: add option "-skipdir" to skip some test.
1018    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
1019      momentum calculation.
1020    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
1021    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
1022      remove checkpoint.F and the_correction_step.F (no longer used);
1023      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
1024    o add option (linFSConserveTr) to correct for tracer source/sink due to
1025      Linear Free surface
1026    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
1027    o pkg/thsice: fix reading mnc-pickups
1028    
1029    checkpoint58t_post
1030    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
1031    o pkg/mdsio:
1032     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
1033       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
1034       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
1035     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
1036     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
1037       either MDS_READ_FIELD or MDS_WRITE_FIELD )
1038     - new S/R (to replace MDSWRITEMETA), which allows to write more
1039       informations (variable names, time ...) to meta files.
1040     - modify rdmds.m to give back the meta file content.
1041    o pkg/diagnostics: change vertical interpolation to be safer, and more
1042       flexible (define p-levels to interpolate to in data.diagnostics);
1043      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
1044       diagnostic pointer.
1045    o pkg/seaice: more cleaning up of seaice_growth, added many comments
1046    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
1047    o fix multi-category seaice:
1048     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
1049       SEAICE_MULTICATEGORY
1050     - fix short wave heat flux
1051    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
1052       and allow to use EVP solver. Change forward lab_sea: test both EVP
1053       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
1054    o Initial check-in of lab_sea adjoint
1055      (very similar to natl_box_adjoint/code_seaice)
1056      * used C-grid and EVP solver
1057      * used KPP, GM/Redi
1058      * uses inAdExact=.TRUE.
1059      * gradient checks fail for both ADM and TLM
1060        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
1061        f.d. gradients actually seem more problematic than ADM, TLM gradients;
1062        issue is related to forward mismatch between g77 an ifort
1063    o pkg/seaice: overhaul of thermodynamics
1064     - growth.F and groatb.F are replaced by new routine seaice_growth.F
1065     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
1066     - move a few global fields out of SEAICE.h into seaice_growth.F and
1067       make them 2D (FICE/QNETO/ ...)
1068     - remove FO (it is the same as QNETO)
1069     - introduce a few local fields to avoid modifying external fields such
1070       as atemp, etc.
1071    
1072    checkpoint58s_post
1073    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
1074      changed exf_set_gen.F so that
1075        genperiod=0 means input file is one time-constant field and
1076        genperiod=-12 means input file contains 12 monthly means
1077    o CG2D: use pre-computed solver main-diagonal (stored in common block);
1078      this affects truncation error ; generate new output file for exp. which
1079      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
1080        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
1081        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
1082        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
1083        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
1084        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
1085    o start implementation of deep-atmosphere and anelastic formulation
1086    o verification: remove 2nd copy of input files and use script "prepare_run"
1087      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
1088    o mom_common/vecinv/fluxform: fix a few initialisation isssues
1089    o profiles: fix for multithreaded case
1090    
1091    o diagnostics: rename few diags:
1092      s/'PRESSURE'/'RCENTER '/g
1093      s/'TICE    '/'oceFreez'/g
1094      s/'TAUX    '/'oceTAUX '/g
1095      s/'TAUY    '/'oceTAUY '/g
1096      s/'SWFLUX  '/'oceQsw  '/g
1097      s/DIFx/DFxE/g
1098      s/DIFy/DFyE/g
1099      and add few ocean-forcing diagnostics:
1100      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
1101    o modifications to pkg/seaice/growth.F and budget.F, which change results of
1102      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
1103      as actual snow thickness.  It now refers everywhere to effective snow
1104      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
1105    
1106    checkpoint58r_post
1107    o modifications to pkg/seaice/growth.F, which change results of
1108      lab_sea experiment: fixes pertain to melting snow over open water, to
1109      masking EVAP under sea ice, and to using the correct AREA variable for
1110      computations of EVAP, PRECIP, HSNOW, and GHEFF
1111    o add ability to read bathy, salt, and theta using MNC (off by def)
1112    o add flooding algorithm and advection of HSNOW for pkg/seaice;
1113      both are turned off by default and do no change any results
1114    o seaice advection with pkg/thsice: a step toward the use of non-linear
1115      advection scheme, but #ifdef or commented out for now (requires more EXCH).
1116    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
1117      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
1118      in natl_box (affects results @ truncation level: update output.txt)
1119    o multi-threading and IO:
1120      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
1121      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
1122        (needed to work with SingleCpuIO): tested in all verif. exp.
1123    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
1124      affects the results (but none of the verification test uses this scheme).
1125    o Adding some pkg/diagnostics capability to pkg/seaice
1126      (will certainly be subject to changes)
1127    o ctrl: adding new control variables:
1128      lwflux, lwdown, evap, snowprecip, apressure, runoff
1129    
1130    checkpoint58q_post
1131    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
1132      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
1133      high_res_cube configuration by 4% on Columbia.
1134    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
1135      add (in global_with_exf/code) a version of EXF_INTERP_READ without
1136      dynamical allocation (seems to work in multi-threaded).
1137    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
1138      single CPU io) so that TAF does not have to see EESUPPORT.h
1139    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
1140    
1141    checkpoint58p_post
1142    o obcs: stop if obcs is used with useCDscheme = .true.
1143    o shelfice:
1144     - fix a sign error so that no slip at shelfice interface works
1145     - remove stop for combination non-hydrostatic code and shelfice. That does
1146       not mean, that the results are correct, but at least they are numerically
1147       stable
1148    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
1149    o added adjoint exch routined for all exch*3d* routines
1150      and updated flow directives
1151    
1152    checkpoint58o_post
1153    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
1154      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
1155    o change controling S/R for writing pickup file (new S/R do_write_pickup)
1156      and clean-up reading/writing of pickup files.
1157    o fix local version of read/write pickup (NH part) in rotating_tank/code
1158    o simplify EXCH interface:
1159     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
1160     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
1161    o added the regrid package
1162    o shelfice:
1163     - add a simple boundary layer scheme to reduce noise
1164     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
1165    
1166    checkpoint58n_post
1167    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
1168       local variable (not in common block).
1169    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
1170      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
1171      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
1172        to work with SingleCpuIO.
1173    o add "_d 0" to real constant of pkg/cfc subroutines ;
1174       update exp. cfc_exemple & tutorial_cfc_offline output files.
1175    o multi-threading and IO:
1176      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
1177        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
1178      - barrier before and after reading.
1179      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
1180      - avoid using MDS_WRITELOCAL for LAND pkg output.
1181      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
1182        common-block variables ; Allows multi-threading with master-thread IO.
1183    o change default MAX_NO_THREADS from 32 to 4 ;
1184      and stop cleanly when MAX_NO_THREADS is too small.
1185    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
1186    
1187    checkpoint58m_post
1188    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
1189       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
1190    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
1191       keep global_ocean.90x40x15 (for AD testing) with former secondary test
1192       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
1193    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
1194        add MITgcm_tutorials (= code + all the tutorials)
1195    o ecco, option to compute cost for total ssh (mean+anom)
1196    o consistent with addition of ptracer and ssh in pkg/profiles
1197  o profiles: adding ptracer and ssh  o profiles: adding ptracer and ssh
1198  o testreport: change multi-test output-file name  o testreport: change multi-test output-file name
1199    (from output.txt.{name} to output.{name}.txt)    (from output.txt.{name} to output.{name}.txt)
1200  o profiles: now ok for mutli-threaded case  o profiles: now ok for mutli-tiles case
1201  o seaice: add 4 parameters for different advection schemes for area,  o seaice: add 4 parameters for different advection schemes for area,
1202    (effective) seaice thickness, enthalphy, and snow height. Their default    (effective) seaice thickness, enthalphy, and snow height. Their default
1203    is the standard parameter SEAICEadvScheme    is the standard parameter SEAICEadvScheme
# Line 1191  o add two new packages Line 2381  o add two new packages
2381    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2382    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2383      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2384      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2385  o add offline package  o add offline package
2386  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2387    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz
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