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revision 1.822 by mlosch, Fri May 25 12:53:44 2007 UTC revision 1.1154 by jmc, Tue Sep 1 20:45:26 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/mdsio (& pkg/rw): rework high level S/R interface:
8      To avoid mixing type (RS/RL) of input/output array argument,
9      replace single mixed-type array with a pair from each type (RS/RL).
10    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
11      is now implemented for all pkgs (previously only done for the main pickup)
12    
13    checkpoint61u
14    o pkg/obcs:
15      - change OB?eta from _RS to _RL and put them into a separate commen block
16      - add code to read OB?eta from a file via obcs_prescribe_read: the code
17        compiles and does not destroy any other experiments, the data is read
18        properly, but the code is not tested in actual applications
19    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
20      create a meaningful unit attribute for the time coordinate variable
21    o pkg/ebm: add plenty of missing "_d 0" ;
22       update results of experiment global_ocean_ebm (fwd + adjoint tests)
23      Notes: several pieces of code only works for (very) specific set up
24       (domain size, lat range, etc ...); should be documented & stop if one
25       of those assumptions is not meet.
26    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
27       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
28          and offline_exf_seaice (seaicetd + adjoint).
29    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
30       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
31        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
32    o few changes to pass when compiling with strick checking of arguments
33       across S/R (allow to find few bugs in S/R calls).
34  o pkg/seaice:  o pkg/seaice:
35    - allow values of SEAICE_elaticParm > 1   - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
36    - make lsr boundary conditions free slip (by default, changes results of     2d-fields, for slightly better performance
37      lsr solver)  
38    - no slip boundary conditions for lsr will follow  checkpoint61t
39    o pkg/seaice:
40     - remove unused variables in seaice_evp
41     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
42    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
43       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
44       each processor opens a different file (a fix from Matt).
45    o cg2d:
46       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
47       this reduces number of EXCH calls by 2 when using exch2.
48       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
49       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
50    o pkg/thsice:
51       add code for Near Infra-Red albedo (from Jeff)
52       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
53    o ini_model_io:
54       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
55       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
56       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
57    
58    checkpoint61s
59    o pkg/exch2 (exch2_rxN_cube*):
60       remove last BARRIER (no need to synchronise after getting data from shared
61       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
62    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
63      and generate new output (for the 2 tests) using default rotationPeriod.
64    o pkg/exch2:
65      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
66        (was already the case with AUTODIFF_EXCH2 defined)
67      - add bj in exch2 arrays and S/R.
68      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
69        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
70    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
71      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
72        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
73      - verification experiment natl_box.longstep
74    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
75      allow different versions of ifort (8 or 9) and different versions
76       of mpi (mpich or mpich2) to be used with the same optfile.
77      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
78       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
79    o pkg/seaice:
80      fix previous modif (3-level field removed) for old-pickup reading
81    
82    checkpoint61r
83    o pkg/seaice:
84     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
85      1. introduce fields for time step (N-1)
86      2. do not use levels 2 and 3 anymore (but keep them)
87      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
88         includes changes to pkg/thsice/thsice_get_velocity.F,
89         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
90         pkg/obcs/obcs_apply_uvice.F.
91     - completely remove code for leap-frog time stepping for second order
92       advection
93     - adjusted adjoint accordingly;
94       gradient checks have improved by an order of magnitude!
95    
96    checkpoint61q
97    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
98     - the boundary conditions along open boundaries are unclear, because the
99       associated masks are set to zero and are thus treated as closed when
100       applying the slip-boundary conditions.
101     - move initialisation of grid variables from seaice_init_varia to _fixed
102    o adding doc/diags_changes.txt
103    o model/src:
104      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
105       to avoid "_diags" naming if no relation to pkg/diagnostics.
106      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
107       file and only call PLOT_FIELD_XYZ if debugMode=T.
108      remove few PLOT_FIELD_XY calls outside initialisation.
109      remove few unnecessary BARRIER.
110    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
111      of salt_plume package in Southern Ocean
112    o pkg/thsice:
113     - fix hOceMxL in overlap (needed for sea-ice advection);
114       update output of experiment global_ocean.cs32x15.icedyn.
115    o pkg/seaice:
116     - make the (placeholder-)tracer IceAge a little more meaningful
117      by avoiding ridging of age due to convergent ice flow
118     - add diagnostics for surface temperature, atmospheric and oceanic
119       heat flux, and atmospheric and oceanic ice growth
120    
121    checkpoint61p
122    o eesupp (global_max & global_sum):
123     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
124     - remove starting & endding barrier (no longer needed)
125    o pkg/mdsio, writelocal:
126       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
127       (remove the STOP): uses shared buffer IO to store data from all threads
128       and then let master-thread write nThreads tiles.
129    o pkg/mdsio (read/write field):
130     - tiled IO done in 1 piece (all levels at a time);
131     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
132     - multi-threaded: allow to read/write local (non-shared) array
133       (was already working with singleCpuIO ; now works also without);
134       => no longer needs barrier call after reading a file (added inside
135       mds_read/write field).
136     - move barrier calls outside gather/scatter_2d to mds_read/write_field
137    o pkg/obcs/exf
138      - exf_getffieldrec.F: add a few ". _d 0" and
139                            add code to catch the case fldperiod = 0.  
140      - obcs_precribe_read.F: change if statements so that they match
141                              the variable type (_RL)
142      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
143        exf_iprec) as part of namelist EXF_NML_01
144    o pkg/mdsio:
145      - read/write tiled (local) files: read/write 1-level tile chunk at a time
146        (instead of segment of length sNx); expected to speed up tiled IO.
147    o pkg/exch2:
148      - take buffer copy from/to array out of S/R exch2_send/recv into new
149        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
150        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
151      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
152      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
153        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
154        including Topology header file (and common blocks).
155      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
156        remove 2nd exch call in exch2_s3d_rx (no longer needed).
157      - document S/R arg. list (+ update some comments)
158    o pkg/seaice:
159      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
160        temperature and humidity over sea ice based on climatological values.
161      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
162        of LSR (this change is expected to change the results slightly because now
163        it uses slightly difference moduli from the second last LSR solution, but
164        that is more consistent with the stress computations; this part of the code
165        is not tested in the verification experiments)
166      - fix diagnostics for flux of ice in case of B-grid
167      - turn strain rates eij and press into global fields within global
168        common block in SEAICE.h for more straighforward diagnostics
169      - fix diagnostics for principal stress components, press, zeta, eta
170        to give something meaning full
171    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
172      new output (all 4 tests) using default rotationPeriod.
173    o pkg KPP:
174      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
175      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
176        and normal grid from 1 to Nr)
177    o Fix computations of L4rdt in mom_calc_visc.F
178    o eesupp:
179      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
180      should be called before a "stop" if we know that all process are going
181      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
182    
183    checkpoint61o
184    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
185    o model/src/ini_curvilinear_grid.F:
186       compute angleSin/CosC when they are not read from a file
187    o pkg/seaice:
188       add pseudo time stepping for LSOR
189    o pkg/exch2:
190       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
191    o pkg/seaice:
192       Adding separate sea ice albedo, drag coefficients, and HO in Southern
193       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
194    o SingleCpuIO:
195       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
196    o pkg/seaice:
197       put exchanged variable in (local) common block for MPI+Multi-Threads
198       to work (necessary with exch1, and for now with exch2 too).
199    o verification: to get more experiments tested with mpi, mth and mpi+mth,
200      change tiling of:
201       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
202       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
203      update output of exp:
204       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
205       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
206      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
207                       (note: output.txt generated on faulks using only 1 tile)
208    o eesupp & mdsio (SingleCpuIO):
209     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
210       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
211       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
212     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
213     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
214       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
215    o pkg/exch2:
216     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
217       read parameter file "data.exch2" if it exists; otherwise try default regular
218       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
219     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
220       with new code (not to be used, just as a backup solution).
221     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
222       in utils/exch2/input.
223    
224    checkpoint61n
225    o eesupp & mdsio (SingleCpuIO):
226      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
227        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
228        receive real*4 array (instead of real*8) to read/write 32.bit files.
229        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
230         and remove new mapping S/R)
231    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
232      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
233        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
234        when using exch2. Add S/R to map global io-buffer to global model array.
235      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
236    
237    checkpoint61m
238    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
239      and add 3 other S/R for other types (R4,R8,RS).
240      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
241    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
242     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
243     - reduce number of macro definitions (keep only those which are used);
244       can always call directly the corrresponding S/R if needed.
245     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
246       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
247     Fixed wrong type of arg in:
248       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
249       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
250     To fix: global_sum of var in common block is wrong (multi-threaded) in:
251       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
252     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
253    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
254      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
255    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
256    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
257      edges are closed (zero depth); might happen with "blank tiles";
258      for now, disabled if using OBCS.
259    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
260      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
261    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
262      to reduce length of 1.D array print in STDOUT.
263    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
264      + use 48 tiles (16x8): this will allow to test "blank tiles".
265    o start to test MPI + multi-threaded (change testreport to skip tests
266      where number of tiles do not match).
267    o genmake2: add option "-omp" to turn on Open-MP ;
268      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
269    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
270      and keep the original tile numbering. Note: compatible with old
271      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
272    
273    checkpoint61l
274    o Overlaps had been forgotten in calculating ijk keys : fixed
275    o fix cyrus makedepend for gcc 4.4
276    o experiment fizhi-cs-aqualev20:
277      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
278      and generate new output. Note: new output is much closer to the old
279      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
280      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
281    o pkg/fizhi:
282     - change to avoid indices going deliberately over array-bounds
283     - remove unnecessary MPI stuff
284     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
285     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
286       does not go over array-bounds and therefore returns reliable output.
287     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
288       this S/R has 4 output arguments, which are used inside "get_alarm";
289       when it is called with the same variable "ndum" in place of several
290       output arguments, this produces weird side effect inside "get_alarm"
291      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
292       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
293       address) and produces error.
294    o tools/gemake2: (March 27-29 2009)
295      with option "-mpi": link *_mpi files from "MODS" dir (this is what
296      testreport does).
297    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
298    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
299       update lab_sea.lsr & lab_sea.salt_plume results
300    o pkg/seaice:
301      Major overhaul of the LSOR solver: change discretization from original
302      finite differences to finite volume. The old routine is still in the
303      file seaice_lsr.F and can be turned on with the CPP-flag
304      SEAICE_OLD_AND_BAD_DISCRETIZATION
305      Along with this change, the discretization of the strain rates is changed.
306      The same flag turns on the old discretization in seaice_calc_strainrates.F
307      All verification experiments with seaice are affected (except for
308      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
309      results by setting the above flag.
310      Further changes involve changes in defaults:
311      - ALLOW_FLOODING is defined and turned on by default
312      - SEAICEadvSnow = .true. is now the default
313      - SEAICEadvSalt = .true. is now the default
314      - SEAICEadvAge  = .true. is now the default
315      - SEAICE_clipVelocities  = .false. is now the default
316                                         (as per J. Zhang's recommendation)
317      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
318        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
319      - seaice_growth: replace computation of UG by a simple copy from wspeed
320    
321    checkpoint61k
322    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
323      seaice_lsr: fixed a few metric terms,
324                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
325                  add more debugging diagnostics
326      seaice_evp: removed superfluous many metric terms of FV discretization
327                  of stress divergence
328                  affects lab_sea, lab_sea.hb87
329      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
330                  of stress divergence for non-evp solver
331                  (this part is not tested anywhere)
332      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
333                  they were effectively only half slip
334                  affects lab_sea.hb87
335      updated all relevant verification experiments (except lab_sea//output_adm.txt
336        which was left over, but fails at level 7 & 6)
337    
338    checkpoint61j
339    o pkg/seaice: turn a few hard wired parameters into run time parameters
340    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
341      time in seconds as promised by the usints in seaice_monitor and exf_monitor
342    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
343      that are not cubed-sphere grids
344    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
345    o pkg/ctrl:
346      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
347    o non-hydrostatic (calc_gw.F):
348      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
349      update output of exp. global_ocean.cs32x15.viscA4
350    o remove backward compatibility for thetaMin,phiMin
351      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
352    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
353      interpolated wind field not only for curvilineargrid=.true., but also
354      for a rotated grid (rotateGrid=.true.)
355    o pkg/exf: add capability to bypass interpolation for runoff
356      by setting yet another CPP-flag
357    o eesupp/src, B-grid exchange:
358      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
359    o autodiff
360      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
361      allows to switch to single-prec common blocks;
362      corresponding switch occurs in tamc.h, integer isbyte
363      TAF store directivs "byte" and "kind" seem equivalent;
364      Most tamc.h have been updated correspondingly.
365    
366    checkpoint61i
367    o autodiff:
368      fix autodiff_sore/_restore indices for obcs
369      (spotted by I. Hoteit, M. Mazloff)
370    o pkg/autodiff, pkg/ctrl:
371      Add flag to reduce all tapelev I/O to single-prec.
372      In data.ctrl set
373        doSinglePrecTapelev = .TRUE.
374    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
375      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
376    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
377      real fresh water flux (not yet)
378    o pkg/mdsio & rw:
379     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
380     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
381    o pkg/flt:
382     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
383       init_fixed & ini_varia.
384     - clean-up & simplify linear interpolation S/R:
385       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
386     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
387     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
388     - add vert. coordinate & horiz. indices to output files.
389     - change vertical position in initial condition, from index to depth [m].
390     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
391       (easier to get to a curvilinear grid) ; delX,delY no longer used.
392    o pkg/ggl90: a few modifications:
393     - fix bottom boundary condition, and interpolation of KappaE
394       near top and bottom
395     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
396     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
397     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
398    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
399      (maintain temporary backward compatibility, until next checkpoint)
400    
401    checkpoint61h
402    o pkg/diagnostics with "periodic averaging diagnostics":
403      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
404    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
405    o pkg/obcs: fix loop ranges for balancing code
406    o pkg/flt:
407     - improve criteria for finding which tile owns a float.
408     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
409    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
410      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
411      with ocean biogeo)
412    o pkg/flt:
413     - do some cleaning and fix the restart ;
414     - add output.txt in flt_example/results to get this pkg tested.
415    o genmake2: add an EXTENDED_SRC option and flag.
416       for now, cannot be turned on on command line (only through genmake_local)
417    o pkg/mdsio: read/write vector:
418     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
419     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
420       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
421     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
422      (drop to 4 digits matching for grad). But this test does not look very
423      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
424    
425    checkpoint61g
426    o pkg/flt:
427      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
428       + make OPTIONS file more standard.
429      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
430      - fix _BYTESWAPIO CPP-Flag
431      - standard reading of file-parameter "data.flt"
432      - fix argument list of S/R FLT_RESTART
433      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
434    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
435    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
436      a still unfixed compiler/optimization bug
437    
438    checkpoint61f
439    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
440      update results of global_ocean.cs32x15.icedyn test.
441    o move getcon.F from model/src to pkg/fizhi.
442    o pkg/exf: add parameter for extrapolation of temp up to the surface
443       and option to prevent negative evap (in bulk_largeyeager04 only).
444    o Prather Advection scheme: fix tracer conservation for divergent flow
445      (e.g., when using NonLin Free-Surface).
446    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
447    o gmredi (Visbeck-variable-K):
448     - add more parameters to Visbeck-variable-K.
449     - use a 5 points average for dSigmaR in Visbeck-K calculation
450       (more "homogenous": same stencil and same weights as in dSigmaH)
451     - update output of ideal_2D_oce experiment.
452    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
453      (#undef REAL4_IS_SLOW)
454     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
455       coordinate variable
456     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
457       (surface forcing fields), removes some of the functionality
458     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
459     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
460       probably not all: copy _RS surface flux fields to RL field before
461       calling DIAGNOSTICS_FILL
462     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
463       real*4 (CALL EXCH_*_RS) versions.
464     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
465       (generate new output).
466    
467    checkpoint61e
468    o gmredi (Visbeck-variable-K):
469      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
470      - change computation of Visbeck-K where Slope > Smax :        
471        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
472        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
473    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
474      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
475    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
476    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
477      does not become too large (to avoid precision problems in implicit-diffusion
478      solver); update ideal_2D_oce output.
479    o pkg ggl90:
480      - in ggl90_cal.F: compute only one set of visc/diff, used to
481        step forward TKE/T/S/momentum
482      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
483        have Prandlt =1)
484    o gmredi (fm07):
485      - add lower limit on Transition layer thickness + lower limit on 1/lambda
486      - allow to set few more params from data.gmredi
487    o pkg ggl90:
488          - add missing sqrt(2) factor in computation of mixing length
489            scale in ggl90_calc.F
490            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
491    
492    checkpoint61d
493    o adjoint modifs
494      - adapt to new field rhoInSitu
495      - allow to revert from StoreDynVars2D, StoreDynVars3D
496        to individual fields
497        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
498    o store 3-D (in-situ) density in commom block (DYNVARS.h)
499     - save 1 rho computation.
500     - no longer modify T & S inland when using down_slope pkg.
501    o gad_som : allow to switch to SOM advection for T & S without corresponding
502      pickup files (using new S/R: MDS_CHECK4FILE).
503    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
504      (for useSingleCpuIO to work in multi-threaded)
505    o pkg/shelfice:
506     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
507       with SHELFICEtopoFile in data.shelfice
508     - move code for reading ice shelf topography and modifying hFacC into separate
509       subroutines of the shelfice package
510     - separate initialisation of "fixed" and "variable" variables
511     - kTopC is not (yet) replaced by kSurfC, although this is possible
512    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
513    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
514      and rename:
515      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
516      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
517    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
518    
519    checkpoint61c
520    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
521      to add mass source/sink of fluid in the interior (3-D generalisation
522      of oceanic real-fresh water flux).
523    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
524    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
525    o new pkg: down_slope
526      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
527      - presently, modify T & S inland (dwnslp_calc_rho.F).
528        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
529      - implementation for ocean in P-coords not tested.
530      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
531    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
532      (to facilitate conversion of oceanic pkg to p-coordinate).
533    o change FIND_RHO to FIND_RHO_2D :
534      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
535    o new pkg: cheapaml
536    
537    checkpoint61b
538    o exch2:
539      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
540      - no longer depend on the order sequence (N,S,E,W).
541      - 3rd exchange no longer needed (tested with 24 tiles).
542      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
543      - exch_UV_A-grid readily available (but not yet tested).
544      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
545      (both are no longer needed) in exch_uv: no effect in forward run; but
546       get truncation error differences with adjoint exch.
547    o exch2:
548     - change index-bounds storage (moved from target to local tile,
549       more intuitive this way) ; rename/remove some variables.
550     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
551    
552    checkpoint61a
553    o exch2/matlab-topology-generator:
554      fix bug in index bounds for N-S internal exchange (hard to tell if this
555      had any effect on the solution).
556    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
557      is exceeded
558    o testreport: modify syntax of awk, so that it works also with
559      awk, and not only with nawk and gawk
560    
561    checkpoint61
562    o autodiff
563      Change default for TAF usage by removing argument '-nonew_arg'
564      This changes TAF subroutine argument list (ordering of active var.)
565      Omission of this flag leads to incompatibility w.r.t. TAMC
566      To restore TAMC-compatibility, need following modifs:
567      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
568      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
569      Tested TAF version is 1.9.22
570      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
571    
572    checkpoint60
573    --->>> This is the last checkpoint for which generating the adjoint
574    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
575    --->>> by default.
576    --->>> Future checkpoints will ommit this flag by default.
577    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
578    o pkg/grdchk: Add gradient check to etan0 perturbations.
579    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
580    o pkg/autodiff: more flexibility in zeroadj.
581      model/src: modifying do_oceanic_phys.F accordingly.
582    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
583    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
584      special setup of gmredi for which the adjoint is stable
585      enough for parameter optimization.
586    o bridging the gap between eddy stress and GM.
587      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
588          along with a change in CPP option (now ALLOW_EDDYPSI).
589      -> when using GM w/ GM_AdvForm:
590          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
591          is applied either in the tracer Eq. or in momentum Eq.
592          depending on data.gmredi (intro. GM_InMomAsStress).
593      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
594      The key modifications are in model/src/taueddy_external_forcing.F
595      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
596    
597    checkpoint59r
598    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
599      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
600      fix option to read coriolis(@ cell-corner) from files with CS-grid.
601    o pkg/mnc: add some attributes to standard 1D-coordinate variables
602    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
603      mass points, when using mnc for output
604      - add runtime parameter (missing_value, missing_value_int) to override
605        default (which is the value of getcon('UNDEF'))
606    o pkg/mnc: prepare mnc for the actual use of missing values with the
607      diagnostics package: small fix in mnc_cw_readwrite.template and more
608      initialisation of never used fields
609      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
610      versions
611    o pkg/thsice/thsice_ini_vars.F added default initial values so that
612      thermodynamics sea ice solver does not blow up when some initial fields
613      are missing.
614    o move from external_forcing_surf.F to ini_forcing.F
615      the p-coord. hack consisting in using pLoad to set phi0surf ;
616      update output of tutorial_global_oce_in_p (affected @ truncation level).
617    o Freshen up a bit hs94.1x64x5, notably:
618      remove rotationPeriod and tRef=5*0. (adjoint only), and add
619      exactConserv=.TRUE.
620    o pkg/generic_advdiff:
621      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
622      applies to files where Temperature & Salinity 2nd Order moments are used.
623    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
624      this uses a dynamically allocated internal state data structure
625      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
626      and requires a fortran 90 compiler
627    
628    checkpoint59q
629    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
630       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
631    o Refresh tutorial_global_oce_biogeo, notably:
632      - change bathymetry (put back seamounts in ACC, use hFacs)
633      - change EOS (POLY3 --> JMD95Z)
634      - use Bryan-Lewis vertical diffusivity
635      - use multidimensional advection
636      - remove old virtual virtual in dic pkg, now done through ptracer pkg
637      - change a couple of parameters in dic pkg
638    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
639    o pkg/obcs: change default to OBCSfixTopo = .true.,
640      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
641      - replace "debugMode" with "debugLevel .GE. debLevB"
642    o implementation of TAF directives for gchem,cfc,dic
643    o remove "exp5" (replaced by tutorial_deep_convection).
644    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
645      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
646      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
647      --> changes results in exp4, seaice_obcs
648    o tutorial_deep_convection :
649      update the set-up and increase resolution and domain size ; start
650      from pseudo initial conditions = output at t=120mn in order to see
651      something happening when running testreport.
652    o pkg/seaice: add os7mp as an advection scheme
653                  add check for advection schemes
654                  add a flag for restoring T and S underneath sea ice
655    o pkg/my82: add netcdf-support and diagnostics
656    o thsice pkg:
657      - Now hsMax limits snow height by turning it into ice following
658        flooding scheme (and now conserving energy)
659      - Slight rewriting of the formula in thsice_calc_thick.F
660      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
661      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
662    
663    checkpoint59p
664    o gchem / dic / cfc :
665      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
666      - add new parameter files: "data.dic" & "data.cfc" ;
667      - various re-arrangement in initialisation & header file ;
668      - fix tutorial_global_oce_biogeo for multi-threaded test.
669    o pkg/dic: test for "pickup_dic" file when restarting ;
670      if no pickup-file, can restart with a re-initialised pH (same as it did
671      before) providing pickupStrictlyMatch is set to False.
672    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
673      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
674    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
675      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
676    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
677     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
678       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
679    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
680       scheme to use for vorticty-term ;
681     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
682       (with default selectVortScheme, return to original discretisation)
683     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
684    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
685    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
686      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
687      also fix diagnostics VISCAHW & VISCA4W.
688    
689    checkpoint59o
690    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
691    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
692      move a few statemens out the main loop into separate loops
693    o pkg/shelfice:
694      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
695        (kg/m^2/s), does not break tests, because in verification/isomip,
696        rhoConstFresh=rhoConst (by accident)
697      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
698      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
699        new file model/src/seawater.F, so that they are available for all pkgs.
700      - convert potential temperature into in-situ temperature. This changes the
701        isomip tests => update tests
702    o add a flag writePickupAtEnd (default=true) to be able to suppress
703      writing a pickup at the last timestep
704    o tools/mpack-1.6 :
705      - disable automake (not working) and autoconf (not needed).
706      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
707        also cleaner with much less compilation warnings.
708    o pkg/profiles:
709      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
710      (for "less than 32 characters name" compiler requirement)
711    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
712      conditions that have a different sampling frequency than S/T/U/V obcs
713    o pkg/diagnostics (stats-diags):
714      - fix global Min/Max in case 1 processor get only empty tiles
715    o genmake2: replace (4 times)
716         make genmake_tc_1.o >> genmake_warnings 2>&1
717      with
718         COMM="$CC $CFLAGS -c genmake_tc_1.c"
719         echo $COMM >> genmake_warnings
720         $COMM >> genmake_warnings 2>&1
721      to make genmake2 always see the value of CC as specified in the optfile.
722    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
723      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
724      - modify verification advect_cs test to test SOM-advection on CS-grid.
725    o pkg/ctrl:
726      - Rewrite of ctrl_map_ini_ecco.F,
727        introducing a generic routine (ctrl_map_ini_gen.F).
728      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
729    
730    checkpoint59n
731    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
732      number in dedicate array "hdiag":
733      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
734        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
735      - many small changes (integer format) for large number of diagnostics
736      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
737        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
738    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
739      usingSphericalGrid, this allows to define the rotated grid coordinates
740      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
741      geographical coordinates according to the inverse of the rotation defined
742      by the Euler angles, so that Coriolis parameter and online-interpolation by
743      exf works with the geographical coordinates on XC/YC/XG/YG.
744      Naturally, this feature does not work with all packages, so some
745      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
746      profiles), because there the coordinates are assumed to be regular
747      spherical grid coordinates.
748    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
749      - introduce isopycnal diffusion coefficient control.
750    o tools/adjoint_options:
751      - additional control vector components.
752    o pkg/mnc: have mnc create marginally meaning full coordinate variables
753      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
754    o pkg/mypackage:
755      - add example of read/write pickup for state-var ;
756      - add entry points to the main code for state-vars diags & write-pickup.
757    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
758      transitions for useExfYearlyFields
759      - add new subroutine that determines the file to read from for
760        use*YearlyFields = .TRUE. and .FALSE.
761      - add a verification experiment to global_with_exf that tests
762        useExfYearlyFields with USE_EXF_INTERPOLATION defined
763    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
764      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
765      subroutines (which could be generated from a template, because they are
766      almost identical), for now they are included in obcs_prescribe_read.F for
767      simplicity
768    o pkg/exf:
769      - add a little more diagnostic to exf_interp_read (in analogy to
770        mds_read_field, can be turned off with debugLevel < debugLevA=1)
771      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
772        ugly but fast by unrolling short inner loops, inserting a unroll=8
773        directive in routine lagran, and splitting a loop and making do while the
774        outermost loop (the latter requires the intoduction of index arrays)
775    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
776    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
777      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
778    o verification/seaice_obcs: updated for restart test and latest options
779    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
780      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
781      for now this is only available for the C-grid code and also within
782      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
783    
784    checkpoint59m
785    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
786      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
787    o gad_som : fix flux output (& diagnostics) to have same units as other  
788      advection scheme fluxes (was previously multiplied by deltaT).  
789    o added verification/seaice_obcs both to test seaice open boundaries
790      and to provide an example matlab scrpt for generating them
791    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
792    o pkg/salt_plume: clean up salt_plume_frac.F to
793      remove redundancy in PlumeMethod 1 and 4
794    o pkg/kpp: added saltplume diagnostics
795    o pkg/obcs and pkg/seaice:
796      - do not set uice and vice to zero when OB*icefile are unspecified
797      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
798      - moved seaice tracer obcs after call to seaice_growth
799    o pkg/salt_plume: added various options for salt plume depth
800      criterion and for vertical distribution of the salt
801    
802    checkpoint59l
803    o pkg/ptracers: new version of ptracers pickup:
804      read meta file and write only fields which are needed to restart.
805      ( same logic as main pickup file ; also using pickupStrictlyMatch )
806    o pkg/seaice:
807      - add timescale for melting due to warm mixed layer as a means of
808        setting SEAICE_availHeatFrac more conveniently
809      - add a CPP-flag/runtime parameter check for flooding algorithm
810      - reformulated availHeat in seaice_growth.F to be independent of AREA
811    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
812      unit changes
813    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
814    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
815      SX vector computer.
816    o pkg/seaice:
817      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
818        seaice forcing fields can now be read only through pkg/exf
819      - removed some unused halos
820    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
821    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
822      or U/VICE from U/VWIND before computing U/VSTRESS
823    
824    checkpoint59k
825    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
826      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
827    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
828      all experiments pass when compile with un-initialised var. checking option.
829    o added pkg/salt_plume
830    o script to test restart (for now, in MITgcm_contrib/jmc_script)
831    o pkg/seaice: new read/write pickup version.
832      read meta file and write only fields which are needed to restart.
833      ( same logic as main pickup file ; also using pickupStrictlyMatch )
834    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
835    o lab_sea.hb87: modify the domain & update output.hb87.txt :
836      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
837      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
838      process. Fixed here by closing the domain at the Northern boundary.
839    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
840    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
841      a set of consecutive levels in/from a 3-D array.
842    o pkg/ptracers:
843      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
844      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
845    
846    checkpoint59j
847    o in pkgs: dic, obcs, offline, rbcs:
848      standard way to compute coeff. for time interpolation between 2 time reccords
849      which retains full precision (& make results less dependent on compiler).
850      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
851    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
852      packages instead of reading ice cover and wind speed separately
853    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
854     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
855      to allow to compile customized code before the update)
856    o cleaning-up:
857      - fix CPP instruction syntax in pkg/obcs
858      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
859        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
860      - fix some threads issue in IO parts.
861    o pkg/dic:
862      - add tons of "_d 0" (--> much better testreports !)
863       and then update outputs of tutorial_global_oce_biogeo
864    o pkg/mom_fluxform:
865      add a special version of momentum advection intended to conserve momentum
866      next to a bathymetry step or a coastline edge. (default = off = #undef)
867    o new read/write pickup version:
868      - for now, only implemented for main (mdsio) pickup file.
869      - write out only what is needed to restart; merge pickup_nh , pickup_ph
870        and main pickup together.
871      - read meta file; read only what is needed to restart; stop if a field
872        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
873        if it make sense (even if the restart is not perfect).
874      - if no meta file, assume that pickup to read corresponds exactly to
875        a pickup that would currently be written.
876      - read pickup written in the old format (until checkpoint59i) if it
877        recognizes an old meta file (no field-list).
878      - add a meta file in exp. which starts from a pickup: 2 cases:
879        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
880         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
881        b) a meta file describing the content of the associated pickup file
882         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
883    o pkg/mdsio & pkg/rw:
884      - new routine to read a meta file ; new set of routine to read
885        Multiple-fields file (with meta file).
886    o added open boundary conditions capability for seaice
887        HSNOW, HSALT, UICE, and VICE
888    
889    checkpoint59i
890    o adjoint:
891      * fix multiDimAdvection adjoint
892        (partial recomputation problem by TAF for fVerT(:,:,kDown)
893        and comlev1 size definition (maxpass vs. max. number of tracers)
894      * verification/global_ocean.90x45x15 adjoint now tests
895        NLFS and multiDimAdvection using DST3 (=30)
896      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
897    o pkg/kpp: add "_d 0" to real constant (if missing);
898      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
899      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
900    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
901      for internal parameters related to restart process (formerly from PARAMS.h)
902      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
903    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
904      as argument. (only atm2d & obcs write_pickup have not yet been updated)
905    o pkg/monitor:
906      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
907      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
908      - account for deep Atmosphere factor and density factor (anelastic)
909    o added open boundary conditions capability for seaice HEFF and AREA
910    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
911      thermodynamics
912      - requires a little reorganization, which affects the testreport results
913        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
914        so that now the conservative form is tested
915      - add a few comments
916    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
917    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
918    o add new diagnostics to seaice: advective, diffusive fluxes (only for
919      multidim-advection, for scheme 2 they are not filled) and transports,
920      thermodynamic growth rates
921    o change units of EmPmR (inside the code, + within coupling interface)
922      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
923      Affects results @ truncation level (cg2d match) and update output of
924       experiments: lab_sea(6), global_ocean.90x40x15(10),
925      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
926      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
927      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
928      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
929    
930    checkpoint59h
931    o pkg/exf:
932      - improve vectorization by moving if-statement out of loops in
933        exf_mapfields, exf_radiation
934      - exf_bulkformulae.F: introduce 2D fields and vectorize code
935    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
936    o testreport:
937      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
938        monitor & update offline_exf_seaice exp. output.
939      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
940    o pkg/seaice:
941      - bug fix in the evp solver: boundary conditions were affected be
942        masking of zMax/zMin (changes results)
943      - minor bug fix in boundary conditions in seaice_calc_strainrates
944        (changes results for no_slip)
945      - seaice_lsr.F: make interpolation of eta dependent on boundaries
946      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
947      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
948        stress formulation and no-slip boundary conditions
949    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
950      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
951    o pkg/seaice: a first HSALT time stepping equation has been checked in
952    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
953      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
954      without requiring DO-IF statements
955    o pkg/thsice:
956      use continuous power-law function for partition of energy between lateral
957      melting/freezing and thinning/thickening ; old code using step function
958      still available with #undef THSICE_FRACEN_POWERLAW
959      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
960    o testreport: change AD testing : check against results/output_adm.txt
961      using same scripts as for forward test.
962    
963    checkpoint59g
964    o adjoint testing: in preparation for changing testreport:
965      - output format: cost and grad written on separated lines
966      - ad output results in directory "results" (instead of "results_ad")
967    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
968    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
969    o pkg/ecco: allow user defined cost function contributions
970    o testreport:
971      Allow to choose (per experiment) the list of tested output variables
972       and the main variable (used to issue a pass/FAIL ) ;
973      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
974      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
975      Also modify printing of summary:
976       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
977       b) echo the list of tested variables in the individual summary.txt of
978          each experiment.
979    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
980      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
981      (but still depend on the tile decompostion of the domain).
982    o pkg/seaice: change a discretization detail to make the B-grid code
983      "more symmetric". This change is likely to remove all "ridges/leads" that
984      where quasi-aligned with the grid in B-grid solutions. It may also be
985      the solution to the stress coupling issues with the B-grid.
986    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
987      remove .cvsignore from input dir. (since testreport no longer run here).
988    o pkg/thsice:
989     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
990     - fix reshaping of sea-ice just after advection:
991       melt all the ice only if ice-volume is too small.
992     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
993       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
994     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
995    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
996      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
997    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
998      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
999      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
1000      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
1001      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
1002      -> update output.txt
1003    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
1004     this affects truncation error: -> update output.txt of exp:
1005      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
1006      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
1007    
1008    checkpoint59f
1009    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
1010    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
1011      a bounded range (in forward mode)
1012    o pkg/ecco, ctrl, autodiff and mom_common:
1013     internal parameter controls, completements of implementations
1014    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
1015    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
1016      (not seem any difference in testing results).
1017    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
1018       at face corners.
1019    o pkg/generic_advdiff:
1020     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
1021      loop range indices for computing vertical advection tendency
1022      and do the calculation in the interior only (no overlap) ;
1023      for now, only implemented for SOM advection (to save CPU time).
1024     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
1025    o exch2 adjoint
1026      First set of changes:
1027      - add exch2 hand-written adjoint templates
1028      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
1029        This will require cleanup in pkg/autodiff/*.F
1030        (changed routines currently kept separate in verif. code/)
1031      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
1032        that used to hide exch2 or cubed-sphere specific code
1033        (commented via 'cph-exch2')
1034    o pkg/seaice
1035      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
1036    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
1037       output of global_ocean.cs32x15.thsice .
1038    
1039    checkpoint59e
1040    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
1041      for B-grid vector (not yet tested) and C-grid vector (<- only used
1042      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
1043    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
1044      (#ifdef ALLOW_SALT_PLUME)
1045    o gather_2d/scatter_2d: removed halo regions
1046    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
1047      scheme and the corresponding test case (under front_relax dir). For now,
1048      only available with Skew-flux form and not yet tested in realistic set-up.
1049      adjoint: store directives updated, but gradient checks deteriorated,
1050      so maybe GM/Redi adjoint is now broken.
1051    o seaice adjoint
1052      * add AREA, HEFF, HSNOW as control variable
1053        (should not change lab_sea results)
1054      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
1055    o pkg/seaice:
1056      * added computation of saltFlux in seaice_growth;
1057        For time being, sea ice salinity is assumed constant
1058        contribution of snow flooding to freshening of sea ice is neglected.
1059        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
1060        defaults to 0.0 in order to maintain backward compatibility.
1061        Typical values for SEAICE_salinity are 4 to 10 g/kg.
1062      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
1063      * added SEAICE_availHeatFrac, which specifies fraction of surface level
1064        heat content used to melt or grow ice
1065      * commented out cap of HICE: it helps keep ice thinner
1066      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
1067      * applied OBCS T/S mask to HEFFM sea ice mask
1068    
1069    checkpoint59d
1070    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
1071     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
1072     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
1073    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
1074     and change default value of parameter "GM_Small_Number";
1075     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
1076       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
1077       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
1078    o pkg/ecco: cost function when applying pkg/smooth to controls
1079    o pkg/ctrl: add forcingPrecond run time parameter
1080    o pkg/seaice:
1081     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
1082     - fix bug in metric terms of u-equation in LSR solver (implicit part),
1083       changes verification/lab_sea
1084     - rearrange implicit part of u-equation in LSR solver to make it easier to
1085       read, understand, and debug. This causes changes at the truncation level.
1086     - fix (serious) bug in the boundary conditions (sign error in the implicit
1087       part) of the LSR solver. Changes all LSR results.
1088     - fixed problem with HSNOW initialization to avoid thick snow when AREA
1089       is initilized with small values - does not change lab_sea results.
1090     - added HsnowFile initialization capability
1091    o pkg/smooth: addition to model/src and pkg/ctrl so allow
1092     initialization of pkg/smooth and application to control vector
1093    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
1094    o dependencies: pkg/profiles requires pkg/cal
1095    o pkg/profiles:
1096     - added option ALLOW_PROFILES_GENERICGRID
1097         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
1098         that interpolation information (grid points and coefficients) is provided
1099         within the netcdf input files.
1100         -> sample matlab scripts can be found in MITgcm_contrib/gael
1101         that allow you to prepare netcdf input files.
1102     - also modified: cleaner include statements, cleaner error print statements,
1103       cleaner stops when error, and more tests of the netcdf input files consistency.
1104    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
1105    o pkg/seaice:
1106     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
1107       requires a new routine: seaice_diagnostics_fill.F
1108     - make sure that seaice does not move if not forced (pressure replacement
1109       method, Hibler and Ip, 1995), changes results
1110     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
1111     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
1112       It is turned off by default (=-1.), because it changes the results.
1113     - make it possible to read AREA from a file, too.
1114    
1115    checkpoint59c
1116    o add S/R and diagnostics for oceanic mixed-layer depth
1117    o move GMRedi call after all vertical mixing schemes (including KPP)
1118    o pkg/thsice:
1119     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
1120      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
1121    o pkg/obcs:
1122     - bug fix for balance code
1123    o pkg/seaice:
1124      - allow values of SEAICE_elasticParm > 1
1125      - add new parameter SEAICE_evpTauRelax as an alternative
1126        to SEAICE_elasticParm
1127      - make lsr boundary conditions free slip (by default), changes result
1128      - add code for no slip boundary conditions for lsr
1129    - set minimum of zeta to zero (and not 4e8) (changes results)    - set minimum of zeta to zero (and not 4e8) (changes results)
1130      - add a cap on AREA after advecting AREA if seaice_growth is not called
1131  o change calculation of Visbeck K:  o change calculation of Visbeck K:
1132    - no longer depend on tapering scheme; instead, compute slope (limited    - no longer depend on tapering scheme; instead, compute slope (limited
1133      by GM_maxSlope). this is equivalent to what was comuted before with      by GM_maxSlope). this is equivalent to what was comuted before with
1134      clipping or linear tappering.      clipping or linear tappering.
1135    - fix vertical averaging (wrong by 1 level)    - fix vertical averaging (wrong by 1/2 level)
1136    - leave the old version (but will not be maintained) within    - leave the old version (but will not be maintained) within
1137      #ifdef OLD_VISBECK_CALC / #endif      #ifdef OLD_VISBECK_CALC / #endif
1138      - update output of exp. ideal_2D_oce
1139  o change error catch in calc_r_star to improve vectorization  o change error catch in calc_r_star to improve vectorization
1140  o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and  o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
1141    add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).    add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
1142    o adjoint:
1143      Re-organized adjoint checkpointing according to Matt Mazloff
1144      (but with modifs/completions/cleanups)
1145      Storing is now bundled into large arrays to optimized I/O
1146      (and second step in cleanup of the_main_loop)
1147    
1148  checkpoint59b  checkpoint59b
1149  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
# Line 73  o pkg/exf: some cleaning-up: Line 1197  o pkg/exf: some cleaning-up:
1197  o pkg/thsice:  o pkg/thsice:
1198   fix few little problems, in thsice_calc_thickn.F:   fix few little problems, in thsice_calc_thickn.F:
1199    - growth vertically (and not laterally) if iceFrac == iceMaskMax    - growth vertically (and not laterally) if iceFrac == iceMaskMax
1200    - melt laterally only if hIce < hThinIce (as the comments say)    - melt only laterally if hIce < hThinIce (as the comments say)
1201    and in thsice_extend.F:    and in thsice_extend.F:
1202    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
1203    - start to form ice as soon as the minimum ice-volume is reachable.    - start to form ice as soon as the minimum ice-volume is reachable.
# Line 110  o in FFIELDS.h: Line 1234  o in FFIELDS.h:
1234       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
1235  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
1236  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
1237      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
1238        are no longer updating the vertical diffusivity array
1239        (passed as argument) but are (re-) setting those arrays.
1240  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
1241    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
1242      cgrid-lsr and evp solver      cgrid-lsr and evp solver
# Line 1592  o add two new packages Line 2718  o add two new packages
2718    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2719    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2720      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2721      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2722  o add offline package  o add offline package
2723  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2724    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz
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