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revision 1.811 by mlosch, Wed May 9 14:32:05 2007 UTC revision 1.1147 by jmc, Wed Aug 5 22:58:06 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: add missing "_d 0" in HSNOW initialisation
8       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
9          and offline_exf_seaice (seaicetd + adjoint).
10    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
11       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
12        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
13    o few changes to pass when compiling with strick checking of arguments
14       across S/R (allow to find few bugs in S/R calls).
15    o pkg/seaice:
16     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
17       2d-fields, for slightly better performance
18    
19    checkpoint61t
20    o pkg/seaice:
21     - remove unused variables in seaice_evp
22     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
23    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
24       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
25       each processor opens a different file (a fix from Matt).
26    o cg2d:
27       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
28       this reduces number of EXCH calls by 2 when using exch2.
29       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
30       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
31    o pkg/thsice:
32       add code for Near Infra-Red albedo (from Jeff)
33       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
34    o ini_model_io:
35       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
36       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
37       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
38    
39    checkpoint61s
40    o pkg/exch2 (exch2_rxN_cube*):
41       remove last BARRIER (no need to synchronise after getting data from shared
42       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
43    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
44      and generate new output (for the 2 tests) using default rotationPeriod.
45    o pkg/exch2:
46      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
47        (was already the case with AUTODIFF_EXCH2 defined)
48      - add bj in exch2 arrays and S/R.
49      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
50        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
51    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
52      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
53        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
54      - verification experiment natl_box.longstep
55    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
56      allow different versions of ifort (8 or 9) and different versions
57       of mpi (mpich or mpich2) to be used with the same optfile.
58      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
59       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
60    o pkg/seaice:
61      fix previous modif (3-level field removed) for old-pickup reading
62    
63    checkpoint61r
64    o pkg/seaice:
65     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
66      1. introduce fields for time step (N-1)
67      2. do not use levels 2 and 3 anymore (but keep them)
68      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
69         includes changes to pkg/thsice/thsice_get_velocity.F,
70         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
71         pkg/obcs/obcs_apply_uvice.F.
72     - completely remove code for leap-frog time stepping for second order
73       advection
74     - adjusted adjoint accordingly;
75       gradient checks have improved by an order of magnitude!
76    
77    checkpoint61q
78    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
79     - the boundary conditions along open boundaries are unclear, because the
80       associated masks are set to zero and are thus treated as closed when
81       applying the slip-boundary conditions.
82     - move initialisation of grid variables from seaice_init_varia to _fixed
83    o adding doc/diags_changes.txt
84    o model/src:
85      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
86       to avoid "_diags" naming if no relation to pkg/diagnostics.
87      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
88       file and only call PLOT_FIELD_XYZ if debugMode=T.
89      remove few PLOT_FIELD_XY calls outside initialisation.
90      remove few unnecessary BARRIER.
91    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
92      of salt_plume package in Southern Ocean
93    o pkg/thsice:
94     - fix hOceMxL in overlap (needed for sea-ice advection);
95       update output of experiment global_ocean.cs32x15.icedyn.
96    o pkg/seaice:
97     - make the (placeholder-)tracer IceAge a little more meaningful
98      by avoiding ridging of age due to convergent ice flow
99     - add diagnostics for surface temperature, atmospheric and oceanic
100       heat flux, and atmospheric and oceanic ice growth
101    
102    checkpoint61p
103    o eesupp (global_max & global_sum):
104     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
105     - remove starting & endding barrier (no longer needed)
106    o pkg/mdsio, writelocal:
107       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
108       (remove the STOP): uses shared buffer IO to store data from all threads
109       and then let master-thread write nThreads tiles.
110    o pkg/mdsio (read/write field):
111     - tiled IO done in 1 piece (all levels at a time);
112     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
113     - multi-threaded: allow to read/write local (non-shared) array
114       (was already working with singleCpuIO ; now works also without);
115       => no longer needs barrier call after reading a file (added inside
116       mds_read/write field).
117     - move barrier calls outside gather/scatter_2d to mds_read/write_field
118    o pkg/obcs/exf
119      - exf_getffieldrec.F: add a few ". _d 0" and
120                            add code to catch the case fldperiod = 0.  
121      - obcs_precribe_read.F: change if statements so that they match
122                              the variable type (_RL)
123      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
124        exf_iprec) as part of namelist EXF_NML_01
125    o pkg/mdsio:
126      - read/write tiled (local) files: read/write 1-level tile chunk at a time
127        (instead of segment of length sNx); expected to speed up tiled IO.
128    o pkg/exch2:
129      - take buffer copy from/to array out of S/R exch2_send/recv into new
130        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
131        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
132      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
133      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
134        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
135        including Topology header file (and common blocks).
136      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
137        remove 2nd exch call in exch2_s3d_rx (no longer needed).
138      - document S/R arg. list (+ update some comments)
139    o pkg/seaice:
140      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
141        temperature and humidity over sea ice based on climatological values.
142      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
143        of LSR (this change is expected to change the results slightly because now
144        it uses slightly difference moduli from the second last LSR solution, but
145        that is more consistent with the stress computations; this part of the code
146        is not tested in the verification experiments)
147      - fix diagnostics for flux of ice in case of B-grid
148      - turn strain rates eij and press into global fields within global
149        common block in SEAICE.h for more straighforward diagnostics
150      - fix diagnostics for principal stress components, press, zeta, eta
151        to give something meaning full
152    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
153      new output (all 4 tests) using default rotationPeriod.
154    o pkg KPP:
155      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
156      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
157        and normal grid from 1 to Nr)
158    o Fix computations of L4rdt in mom_calc_visc.F
159    o eesupp:
160      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
161      should be called before a "stop" if we know that all process are going
162      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
163    
164    checkpoint61o
165    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
166    o model/src/ini_curvilinear_grid.F:
167       compute angleSin/CosC when they are not read from a file
168    o pkg/seaice:
169       add pseudo time stepping for LSOR
170    o pkg/exch2:
171       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
172    o pkg/seaice:
173       Adding separate sea ice albedo, drag coefficients, and HO in Southern
174       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
175    o SingleCpuIO:
176       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
177    o pkg/seaice:
178       put exchanged variable in (local) common block for MPI+Multi-Threads
179       to work (necessary with exch1, and for now with exch2 too).
180    o verification: to get more experiments tested with mpi, mth and mpi+mth,
181      change tiling of:
182       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
183       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
184      update output of exp:
185       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
186       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
187      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
188                       (note: output.txt generated on faulks using only 1 tile)
189    o eesupp & mdsio (SingleCpuIO):
190     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
191       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
192       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
193     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
194     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
195       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
196    o pkg/exch2:
197     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
198       read parameter file "data.exch2" if it exists; otherwise try default regular
199       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
200     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
201       with new code (not to be used, just as a backup solution).
202     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
203       in utils/exch2/input.
204    
205    checkpoint61n
206    o eesupp & mdsio (SingleCpuIO):
207      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
208        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
209        receive real*4 array (instead of real*8) to read/write 32.bit files.
210        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
211         and remove new mapping S/R)
212    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
213      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
214        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
215        when using exch2. Add S/R to map global io-buffer to global model array.
216      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
217    
218    checkpoint61m
219    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
220      and add 3 other S/R for other types (R4,R8,RS).
221      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
222    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
223     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
224     - reduce number of macro definitions (keep only those which are used);
225       can always call directly the corrresponding S/R if needed.
226     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
227       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
228     Fixed wrong type of arg in:
229       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
230       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
231     To fix: global_sum of var in common block is wrong (multi-threaded) in:
232       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
233     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
234    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
235      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
236    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
237    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
238      edges are closed (zero depth); might happen with "blank tiles";
239      for now, disabled if using OBCS.
240    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
241      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
242    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
243      to reduce length of 1.D array print in STDOUT.
244    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
245      + use 48 tiles (16x8): this will allow to test "blank tiles".
246    o start to test MPI + multi-threaded (change testreport to skip tests
247      where number of tiles do not match).
248    o genmake2: add option "-omp" to turn on Open-MP ;
249      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
250    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
251      and keep the original tile numbering. Note: compatible with old
252      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
253    
254    checkpoint61l
255    o Overlaps had been forgotten in calculating ijk keys : fixed
256    o fix cyrus makedepend for gcc 4.4
257    o experiment fizhi-cs-aqualev20:
258      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
259      and generate new output. Note: new output is much closer to the old
260      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
261      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
262    o pkg/fizhi:
263     - change to avoid indices going deliberately over array-bounds
264     - remove unnecessary MPI stuff
265     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
266     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
267       does not go over array-bounds and therefore returns reliable output.
268     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
269       this S/R has 4 output arguments, which are used inside "get_alarm";
270       when it is called with the same variable "ndum" in place of several
271       output arguments, this produces weird side effect inside "get_alarm"
272      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
273       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
274       address) and produces error.
275    o tools/gemake2: (March 27-29 2009)
276      with option "-mpi": link *_mpi files from "MODS" dir (this is what
277      testreport does).
278    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
279    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
280       update lab_sea.lsr & lab_sea.salt_plume results
281    o pkg/seaice:
282      Major overhaul of the LSOR solver: change discretization from original
283      finite differences to finite volume. The old routine is still in the
284      file seaice_lsr.F and can be turned on with the CPP-flag
285      SEAICE_OLD_AND_BAD_DISCRETIZATION
286      Along with this change, the discretization of the strain rates is changed.
287      The same flag turns on the old discretization in seaice_calc_strainrates.F
288      All verification experiments with seaice are affected (except for
289      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
290      results by setting the above flag.
291      Further changes involve changes in defaults:
292      - ALLOW_FLOODING is defined and turned on by default
293      - SEAICEadvSnow = .true. is now the default
294      - SEAICEadvSalt = .true. is now the default
295      - SEAICEadvAge  = .true. is now the default
296      - SEAICE_clipVelocities  = .false. is now the default
297                                         (as per J. Zhang's recommendation)
298      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
299        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
300      - seaice_growth: replace computation of UG by a simple copy from wspeed
301    
302    checkpoint61k
303    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
304      seaice_lsr: fixed a few metric terms,
305                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
306                  add more debugging diagnostics
307      seaice_evp: removed superfluous many metric terms of FV discretization
308                  of stress divergence
309                  affects lab_sea, lab_sea.hb87
310      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
311                  of stress divergence for non-evp solver
312                  (this part is not tested anywhere)
313      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
314                  they were effectively only half slip
315                  affects lab_sea.hb87
316      updated all relevant verification experiments (except lab_sea//output_adm.txt
317        which was left over, but fails at level 7 & 6)
318    
319    checkpoint61j
320    o pkg/seaice: turn a few hard wired parameters into run time parameters
321    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
322      time in seconds as promised by the usints in seaice_monitor and exf_monitor
323    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
324      that are not cubed-sphere grids
325    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
326    o pkg/ctrl:
327      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
328    o non-hydrostatic (calc_gw.F):
329      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
330      update output of exp. global_ocean.cs32x15.viscA4
331    o remove backward compatibility for thetaMin,phiMin
332      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
333    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
334      interpolated wind field not only for curvilineargrid=.true., but also
335      for a rotated grid (rotateGrid=.true.)
336    o pkg/exf: add capability to bypass interpolation for runoff
337      by setting yet another CPP-flag
338    o eesupp/src, B-grid exchange:
339      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
340    o autodiff
341      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
342      allows to switch to single-prec common blocks;
343      corresponding switch occurs in tamc.h, integer isbyte
344      TAF store directivs "byte" and "kind" seem equivalent;
345      Most tamc.h have been updated correspondingly.
346    
347    checkpoint61i
348    o autodiff:
349      fix autodiff_sore/_restore indices for obcs
350      (spotted by I. Hoteit, M. Mazloff)
351    o pkg/autodiff, pkg/ctrl:
352      Add flag to reduce all tapelev I/O to single-prec.
353      In data.ctrl set
354        doSinglePrecTapelev = .TRUE.
355    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
356      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
357    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
358      real fresh water flux (not yet)
359    o pkg/mdsio & rw:
360     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
361     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
362    o pkg/flt:
363     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
364       init_fixed & ini_varia.
365     - clean-up & simplify linear interpolation S/R:
366       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
367     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
368     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
369     - add vert. coordinate & horiz. indices to output files.
370     - change vertical position in initial condition, from index to depth [m].
371     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
372       (easier to get to a curvilinear grid) ; delX,delY no longer used.
373    o pkg/ggl90: a few modifications:
374     - fix bottom boundary condition, and interpolation of KappaE
375       near top and bottom
376     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
377     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
378     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
379    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
380      (maintain temporary backward compatibility, until next checkpoint)
381    
382    checkpoint61h
383    o pkg/diagnostics with "periodic averaging diagnostics":
384      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
385    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
386    o pkg/obcs: fix loop ranges for balancing code
387    o pkg/flt:
388     - improve criteria for finding which tile owns a float.
389     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
390    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
391      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
392      with ocean biogeo)
393    o pkg/flt:
394     - do some cleaning and fix the restart ;
395     - add output.txt in flt_example/results to get this pkg tested.
396    o genmake2: add an EXTENDED_SRC option and flag.
397       for now, cannot be turned on on command line (only through genmake_local)
398    o pkg/mdsio: read/write vector:
399     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
400     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
401       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
402     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
403      (drop to 4 digits matching for grad). But this test does not look very
404      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
405    
406    checkpoint61g
407    o pkg/flt:
408      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
409       + make OPTIONS file more standard.
410      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
411      - fix _BYTESWAPIO CPP-Flag
412      - standard reading of file-parameter "data.flt"
413      - fix argument list of S/R FLT_RESTART
414      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
415    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
416    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
417      a still unfixed compiler/optimization bug
418    
419    checkpoint61f
420    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
421      update results of global_ocean.cs32x15.icedyn test.
422    o move getcon.F from model/src to pkg/fizhi.
423    o pkg/exf: add parameter for extrapolation of temp up to the surface
424       and option to prevent negative evap (in bulk_largeyeager04 only).
425    o Prather Advection scheme: fix tracer conservation for divergent flow
426      (e.g., when using NonLin Free-Surface).
427    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
428    o gmredi (Visbeck-variable-K):
429     - add more parameters to Visbeck-variable-K.
430     - use a 5 points average for dSigmaR in Visbeck-K calculation
431       (more "homogenous": same stencil and same weights as in dSigmaH)
432     - update output of ideal_2D_oce experiment.
433    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
434      (#undef REAL4_IS_SLOW)
435     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
436       coordinate variable
437     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
438       (surface forcing fields), removes some of the functionality
439     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
440     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
441       probably not all: copy _RS surface flux fields to RL field before
442       calling DIAGNOSTICS_FILL
443     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
444       real*4 (CALL EXCH_*_RS) versions.
445     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
446       (generate new output).
447    
448    checkpoint61e
449    o gmredi (Visbeck-variable-K):
450      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
451      - change computation of Visbeck-K where Slope > Smax :        
452        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
453        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
454    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
455      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
456    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
457    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
458      does not become too large (to avoid precision problems in implicit-diffusion
459      solver); update ideal_2D_oce output.
460    o pkg ggl90:
461      - in ggl90_cal.F: compute only one set of visc/diff, used to
462        step forward TKE/T/S/momentum
463      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
464        have Prandlt =1)
465    o gmredi (fm07):
466      - add lower limit on Transition layer thickness + lower limit on 1/lambda
467      - allow to set few more params from data.gmredi
468    o pkg ggl90:
469          - add missing sqrt(2) factor in computation of mixing length
470            scale in ggl90_calc.F
471            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
472    
473    checkpoint61d
474    o adjoint modifs
475      - adapt to new field rhoInSitu
476      - allow to revert from StoreDynVars2D, StoreDynVars3D
477        to individual fields
478        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
479    o store 3-D (in-situ) density in commom block (DYNVARS.h)
480     - save 1 rho computation.
481     - no longer modify T & S inland when using down_slope pkg.
482    o gad_som : allow to switch to SOM advection for T & S without corresponding
483      pickup files (using new S/R: MDS_CHECK4FILE).
484    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
485      (for useSingleCpuIO to work in multi-threaded)
486    o pkg/shelfice:
487     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
488       with SHELFICEtopoFile in data.shelfice
489     - move code for reading ice shelf topography and modifying hFacC into separate
490       subroutines of the shelfice package
491     - separate initialisation of "fixed" and "variable" variables
492     - kTopC is not (yet) replaced by kSurfC, although this is possible
493    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
494    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
495      and rename:
496      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
497      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
498    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
499    
500    checkpoint61c
501    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
502      to add mass source/sink of fluid in the interior (3-D generalisation
503      of oceanic real-fresh water flux).
504    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
505    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
506    o new pkg: down_slope
507      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
508      - presently, modify T & S inland (dwnslp_calc_rho.F).
509        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
510      - implementation for ocean in P-coords not tested.
511      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
512    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
513      (to facilitate conversion of oceanic pkg to p-coordinate).
514    o change FIND_RHO to FIND_RHO_2D :
515      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
516    o new pkg: cheapaml
517    
518    checkpoint61b
519    o exch2:
520      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
521      - no longer depend on the order sequence (N,S,E,W).
522      - 3rd exchange no longer needed (tested with 24 tiles).
523      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
524      - exch_UV_A-grid readily available (but not yet tested).
525      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
526      (both are no longer needed) in exch_uv: no effect in forward run; but
527       get truncation error differences with adjoint exch.
528    o exch2:
529     - change index-bounds storage (moved from target to local tile,
530       more intuitive this way) ; rename/remove some variables.
531     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
532    
533    checkpoint61a
534    o exch2/matlab-topology-generator:
535      fix bug in index bounds for N-S internal exchange (hard to tell if this
536      had any effect on the solution).
537    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
538      is exceeded
539    o testreport: modify syntax of awk, so that it works also with
540      awk, and not only with nawk and gawk
541    
542    checkpoint61
543    o autodiff
544      Change default for TAF usage by removing argument '-nonew_arg'
545      This changes TAF subroutine argument list (ordering of active var.)
546      Omission of this flag leads to incompatibility w.r.t. TAMC
547      To restore TAMC-compatibility, need following modifs:
548      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
549      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
550      Tested TAF version is 1.9.22
551      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
552    
553    checkpoint60
554    --->>> This is the last checkpoint for which generating the adjoint
555    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
556    --->>> by default.
557    --->>> Future checkpoints will ommit this flag by default.
558    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
559    o pkg/grdchk: Add gradient check to etan0 perturbations.
560    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
561    o pkg/autodiff: more flexibility in zeroadj.
562      model/src: modifying do_oceanic_phys.F accordingly.
563    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
564    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
565      special setup of gmredi for which the adjoint is stable
566      enough for parameter optimization.
567    o bridging the gap between eddy stress and GM.
568      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
569          along with a change in CPP option (now ALLOW_EDDYPSI).
570      -> when using GM w/ GM_AdvForm:
571          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
572          is applied either in the tracer Eq. or in momentum Eq.
573          depending on data.gmredi (intro. GM_InMomAsStress).
574      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
575      The key modifications are in model/src/taueddy_external_forcing.F
576      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
577    
578    checkpoint59r
579    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
580      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
581      fix option to read coriolis(@ cell-corner) from files with CS-grid.
582    o pkg/mnc: add some attributes to standard 1D-coordinate variables
583    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
584      mass points, when using mnc for output
585      - add runtime parameter (missing_value, missing_value_int) to override
586        default (which is the value of getcon('UNDEF'))
587    o pkg/mnc: prepare mnc for the actual use of missing values with the
588      diagnostics package: small fix in mnc_cw_readwrite.template and more
589      initialisation of never used fields
590      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
591      versions
592    o pkg/thsice/thsice_ini_vars.F added default initial values so that
593      thermodynamics sea ice solver does not blow up when some initial fields
594      are missing.
595    o move from external_forcing_surf.F to ini_forcing.F
596      the p-coord. hack consisting in using pLoad to set phi0surf ;
597      update output of tutorial_global_oce_in_p (affected @ truncation level).
598    o Freshen up a bit hs94.1x64x5, notably:
599      remove rotationPeriod and tRef=5*0. (adjoint only), and add
600      exactConserv=.TRUE.
601    o pkg/generic_advdiff:
602      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
603      applies to files where Temperature & Salinity 2nd Order moments are used.
604    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
605      this uses a dynamically allocated internal state data structure
606      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
607      and requires a fortran 90 compiler
608    
609    checkpoint59q
610    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
611       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
612    o Refresh tutorial_global_oce_biogeo, notably:
613      - change bathymetry (put back seamounts in ACC, use hFacs)
614      - change EOS (POLY3 --> JMD95Z)
615      - use Bryan-Lewis vertical diffusivity
616      - use multidimensional advection
617      - remove old virtual virtual in dic pkg, now done through ptracer pkg
618      - change a couple of parameters in dic pkg
619    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
620    o pkg/obcs: change default to OBCSfixTopo = .true.,
621      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
622      - replace "debugMode" with "debugLevel .GE. debLevB"
623    o implementation of TAF directives for gchem,cfc,dic
624    o remove "exp5" (replaced by tutorial_deep_convection).
625    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
626      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
627      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
628      --> changes results in exp4, seaice_obcs
629    o tutorial_deep_convection :
630      update the set-up and increase resolution and domain size ; start
631      from pseudo initial conditions = output at t=120mn in order to see
632      something happening when running testreport.
633    o pkg/seaice: add os7mp as an advection scheme
634                  add check for advection schemes
635                  add a flag for restoring T and S underneath sea ice
636    o pkg/my82: add netcdf-support and diagnostics
637    o thsice pkg:
638      - Now hsMax limits snow height by turning it into ice following
639        flooding scheme (and now conserving energy)
640      - Slight rewriting of the formula in thsice_calc_thick.F
641      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
642      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
643    
644    checkpoint59p
645    o gchem / dic / cfc :
646      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
647      - add new parameter files: "data.dic" & "data.cfc" ;
648      - various re-arrangement in initialisation & header file ;
649      - fix tutorial_global_oce_biogeo for multi-threaded test.
650    o pkg/dic: test for "pickup_dic" file when restarting ;
651      if no pickup-file, can restart with a re-initialised pH (same as it did
652      before) providing pickupStrictlyMatch is set to False.
653    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
654      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
655    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
656      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
657    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
658     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
659       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
660    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
661       scheme to use for vorticty-term ;
662     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
663       (with default selectVortScheme, return to original discretisation)
664     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
665    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
666    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
667      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
668      also fix diagnostics VISCAHW & VISCA4W.
669    
670    checkpoint59o
671    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
672    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
673      move a few statemens out the main loop into separate loops
674    o pkg/shelfice:
675      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
676        (kg/m^2/s), does not break tests, because in verification/isomip,
677        rhoConstFresh=rhoConst (by accident)
678      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
679      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
680        new file model/src/seawater.F, so that they are available for all pkgs.
681      - convert potential temperature into in-situ temperature. This changes the
682        isomip tests => update tests
683    o add a flag writePickupAtEnd (default=true) to be able to suppress
684      writing a pickup at the last timestep
685    o tools/mpack-1.6 :
686      - disable automake (not working) and autoconf (not needed).
687      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
688        also cleaner with much less compilation warnings.
689    o pkg/profiles:
690      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
691      (for "less than 32 characters name" compiler requirement)
692    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
693      conditions that have a different sampling frequency than S/T/U/V obcs
694    o pkg/diagnostics (stats-diags):
695      - fix global Min/Max in case 1 processor get only empty tiles
696    o genmake2: replace (4 times)
697         make genmake_tc_1.o >> genmake_warnings 2>&1
698      with
699         COMM="$CC $CFLAGS -c genmake_tc_1.c"
700         echo $COMM >> genmake_warnings
701         $COMM >> genmake_warnings 2>&1
702      to make genmake2 always see the value of CC as specified in the optfile.
703    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
704      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
705      - modify verification advect_cs test to test SOM-advection on CS-grid.
706    o pkg/ctrl:
707      - Rewrite of ctrl_map_ini_ecco.F,
708        introducing a generic routine (ctrl_map_ini_gen.F).
709      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
710    
711    checkpoint59n
712    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
713      number in dedicate array "hdiag":
714      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
715        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
716      - many small changes (integer format) for large number of diagnostics
717      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
718        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
719    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
720      usingSphericalGrid, this allows to define the rotated grid coordinates
721      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
722      geographical coordinates according to the inverse of the rotation defined
723      by the Euler angles, so that Coriolis parameter and online-interpolation by
724      exf works with the geographical coordinates on XC/YC/XG/YG.
725      Naturally, this feature does not work with all packages, so some
726      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
727      profiles), because there the coordinates are assumed to be regular
728      spherical grid coordinates.
729    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
730      - introduce isopycnal diffusion coefficient control.
731    o tools/adjoint_options:
732      - additional control vector components.
733    o pkg/mnc: have mnc create marginally meaning full coordinate variables
734      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
735    o pkg/mypackage:
736      - add example of read/write pickup for state-var ;
737      - add entry points to the main code for state-vars diags & write-pickup.
738    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
739      transitions for useExfYearlyFields
740      - add new subroutine that determines the file to read from for
741        use*YearlyFields = .TRUE. and .FALSE.
742      - add a verification experiment to global_with_exf that tests
743        useExfYearlyFields with USE_EXF_INTERPOLATION defined
744    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
745      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
746      subroutines (which could be generated from a template, because they are
747      almost identical), for now they are included in obcs_prescribe_read.F for
748      simplicity
749    o pkg/exf:
750      - add a little more diagnostic to exf_interp_read (in analogy to
751        mds_read_field, can be turned off with debugLevel < debugLevA=1)
752      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
753        ugly but fast by unrolling short inner loops, inserting a unroll=8
754        directive in routine lagran, and splitting a loop and making do while the
755        outermost loop (the latter requires the intoduction of index arrays)
756    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
757    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
758      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
759    o verification/seaice_obcs: updated for restart test and latest options
760    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
761      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
762      for now this is only available for the C-grid code and also within
763      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
764    
765    checkpoint59m
766    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
767      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
768    o gad_som : fix flux output (& diagnostics) to have same units as other  
769      advection scheme fluxes (was previously multiplied by deltaT).  
770    o added verification/seaice_obcs both to test seaice open boundaries
771      and to provide an example matlab scrpt for generating them
772    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
773    o pkg/salt_plume: clean up salt_plume_frac.F to
774      remove redundancy in PlumeMethod 1 and 4
775    o pkg/kpp: added saltplume diagnostics
776    o pkg/obcs and pkg/seaice:
777      - do not set uice and vice to zero when OB*icefile are unspecified
778      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
779      - moved seaice tracer obcs after call to seaice_growth
780    o pkg/salt_plume: added various options for salt plume depth
781      criterion and for vertical distribution of the salt
782    
783    checkpoint59l
784    o pkg/ptracers: new version of ptracers pickup:
785      read meta file and write only fields which are needed to restart.
786      ( same logic as main pickup file ; also using pickupStrictlyMatch )
787    o pkg/seaice:
788      - add timescale for melting due to warm mixed layer as a means of
789        setting SEAICE_availHeatFrac more conveniently
790      - add a CPP-flag/runtime parameter check for flooding algorithm
791      - reformulated availHeat in seaice_growth.F to be independent of AREA
792    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
793      unit changes
794    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
795    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
796      SX vector computer.
797    o pkg/seaice:
798      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
799        seaice forcing fields can now be read only through pkg/exf
800      - removed some unused halos
801    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
802    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
803      or U/VICE from U/VWIND before computing U/VSTRESS
804    
805    checkpoint59k
806    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
807      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
808    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
809      all experiments pass when compile with un-initialised var. checking option.
810    o added pkg/salt_plume
811    o script to test restart (for now, in MITgcm_contrib/jmc_script)
812    o pkg/seaice: new read/write pickup version.
813      read meta file and write only fields which are needed to restart.
814      ( same logic as main pickup file ; also using pickupStrictlyMatch )
815    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
816    o lab_sea.hb87: modify the domain & update output.hb87.txt :
817      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
818      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
819      process. Fixed here by closing the domain at the Northern boundary.
820    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
821    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
822      a set of consecutive levels in/from a 3-D array.
823    o pkg/ptracers:
824      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
825      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
826    
827    checkpoint59j
828    o in pkgs: dic, obcs, offline, rbcs:
829      standard way to compute coeff. for time interpolation between 2 time reccords
830      which retains full precision (& make results less dependent on compiler).
831      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
832    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
833      packages instead of reading ice cover and wind speed separately
834    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
835     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
836      to allow to compile customized code before the update)
837    o cleaning-up:
838      - fix CPP instruction syntax in pkg/obcs
839      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
840        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
841      - fix some threads issue in IO parts.
842    o pkg/dic:
843      - add tons of "_d 0" (--> much better testreports !)
844       and then update outputs of tutorial_global_oce_biogeo
845    o pkg/mom_fluxform:
846      add a special version of momentum advection intended to conserve momentum
847      next to a bathymetry step or a coastline edge. (default = off = #undef)
848    o new read/write pickup version:
849      - for now, only implemented for main (mdsio) pickup file.
850      - write out only what is needed to restart; merge pickup_nh , pickup_ph
851        and main pickup together.
852      - read meta file; read only what is needed to restart; stop if a field
853        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
854        if it make sense (even if the restart is not perfect).
855      - if no meta file, assume that pickup to read corresponds exactly to
856        a pickup that would currently be written.
857      - read pickup written in the old format (until checkpoint59i) if it
858        recognizes an old meta file (no field-list).
859      - add a meta file in exp. which starts from a pickup: 2 cases:
860        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
861         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
862        b) a meta file describing the content of the associated pickup file
863         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
864    o pkg/mdsio & pkg/rw:
865      - new routine to read a meta file ; new set of routine to read
866        Multiple-fields file (with meta file).
867    o added open boundary conditions capability for seaice
868        HSNOW, HSALT, UICE, and VICE
869    
870    checkpoint59i
871    o adjoint:
872      * fix multiDimAdvection adjoint
873        (partial recomputation problem by TAF for fVerT(:,:,kDown)
874        and comlev1 size definition (maxpass vs. max. number of tracers)
875      * verification/global_ocean.90x45x15 adjoint now tests
876        NLFS and multiDimAdvection using DST3 (=30)
877      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
878    o pkg/kpp: add "_d 0" to real constant (if missing);
879      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
880      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
881    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
882      for internal parameters related to restart process (formerly from PARAMS.h)
883      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
884    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
885      as argument. (only atm2d & obcs write_pickup have not yet been updated)
886    o pkg/monitor:
887      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
888      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
889      - account for deep Atmosphere factor and density factor (anelastic)
890    o added open boundary conditions capability for seaice HEFF and AREA
891    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
892      thermodynamics
893      - requires a little reorganization, which affects the testreport results
894        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
895        so that now the conservative form is tested
896      - add a few comments
897    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
898    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
899    o add new diagnostics to seaice: advective, diffusive fluxes (only for
900      multidim-advection, for scheme 2 they are not filled) and transports,
901      thermodynamic growth rates
902    o change units of EmPmR (inside the code, + within coupling interface)
903      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
904      Affects results @ truncation level (cg2d match) and update output of
905       experiments: lab_sea(6), global_ocean.90x40x15(10),
906      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
907      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
908      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
909      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
910    
911    checkpoint59h
912    o pkg/exf:
913      - improve vectorization by moving if-statement out of loops in
914        exf_mapfields, exf_radiation
915      - exf_bulkformulae.F: introduce 2D fields and vectorize code
916    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
917    o testreport:
918      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
919        monitor & update offline_exf_seaice exp. output.
920      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
921    o pkg/seaice:
922      - bug fix in the evp solver: boundary conditions were affected be
923        masking of zMax/zMin (changes results)
924      - minor bug fix in boundary conditions in seaice_calc_strainrates
925        (changes results for no_slip)
926      - seaice_lsr.F: make interpolation of eta dependent on boundaries
927      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
928      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
929        stress formulation and no-slip boundary conditions
930    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
931      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
932    o pkg/seaice: a first HSALT time stepping equation has been checked in
933    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
934      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
935      without requiring DO-IF statements
936    o pkg/thsice:
937      use continuous power-law function for partition of energy between lateral
938      melting/freezing and thinning/thickening ; old code using step function
939      still available with #undef THSICE_FRACEN_POWERLAW
940      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
941    o testreport: change AD testing : check against results/output_adm.txt
942      using same scripts as for forward test.
943    
944    checkpoint59g
945    o adjoint testing: in preparation for changing testreport:
946      - output format: cost and grad written on separated lines
947      - ad output results in directory "results" (instead of "results_ad")
948    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
949    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
950    o pkg/ecco: allow user defined cost function contributions
951    o testreport:
952      Allow to choose (per experiment) the list of tested output variables
953       and the main variable (used to issue a pass/FAIL ) ;
954      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
955      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
956      Also modify printing of summary:
957       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
958       b) echo the list of tested variables in the individual summary.txt of
959          each experiment.
960    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
961      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
962      (but still depend on the tile decompostion of the domain).
963    o pkg/seaice: change a discretization detail to make the B-grid code
964      "more symmetric". This change is likely to remove all "ridges/leads" that
965      where quasi-aligned with the grid in B-grid solutions. It may also be
966      the solution to the stress coupling issues with the B-grid.
967    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
968      remove .cvsignore from input dir. (since testreport no longer run here).
969    o pkg/thsice:
970     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
971     - fix reshaping of sea-ice just after advection:
972       melt all the ice only if ice-volume is too small.
973     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
974       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
975     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
976    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
977      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
978    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
979      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
980      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
981      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
982      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
983      -> update output.txt
984    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
985     this affects truncation error: -> update output.txt of exp:
986      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
987      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
988    
989    checkpoint59f
990    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
991    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
992      a bounded range (in forward mode)
993    o pkg/ecco, ctrl, autodiff and mom_common:
994     internal parameter controls, completements of implementations
995    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
996    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
997      (not seem any difference in testing results).
998    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
999       at face corners.
1000    o pkg/generic_advdiff:
1001     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
1002      loop range indices for computing vertical advection tendency
1003      and do the calculation in the interior only (no overlap) ;
1004      for now, only implemented for SOM advection (to save CPU time).
1005     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
1006    o exch2 adjoint
1007      First set of changes:
1008      - add exch2 hand-written adjoint templates
1009      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
1010        This will require cleanup in pkg/autodiff/*.F
1011        (changed routines currently kept separate in verif. code/)
1012      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
1013        that used to hide exch2 or cubed-sphere specific code
1014        (commented via 'cph-exch2')
1015    o pkg/seaice
1016      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
1017    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
1018       output of global_ocean.cs32x15.thsice .
1019    
1020    checkpoint59e
1021    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
1022      for B-grid vector (not yet tested) and C-grid vector (<- only used
1023      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
1024    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
1025      (#ifdef ALLOW_SALT_PLUME)
1026    o gather_2d/scatter_2d: removed halo regions
1027    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
1028      scheme and the corresponding test case (under front_relax dir). For now,
1029      only available with Skew-flux form and not yet tested in realistic set-up.
1030      adjoint: store directives updated, but gradient checks deteriorated,
1031      so maybe GM/Redi adjoint is now broken.
1032    o seaice adjoint
1033      * add AREA, HEFF, HSNOW as control variable
1034        (should not change lab_sea results)
1035      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
1036    o pkg/seaice:
1037      * added computation of saltFlux in seaice_growth;
1038        For time being, sea ice salinity is assumed constant
1039        contribution of snow flooding to freshening of sea ice is neglected.
1040        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
1041        defaults to 0.0 in order to maintain backward compatibility.
1042        Typical values for SEAICE_salinity are 4 to 10 g/kg.
1043      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
1044      * added SEAICE_availHeatFrac, which specifies fraction of surface level
1045        heat content used to melt or grow ice
1046      * commented out cap of HICE: it helps keep ice thinner
1047      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
1048      * applied OBCS T/S mask to HEFFM sea ice mask
1049    
1050    checkpoint59d
1051    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
1052     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
1053     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
1054    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
1055     and change default value of parameter "GM_Small_Number";
1056     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
1057       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
1058       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
1059    o pkg/ecco: cost function when applying pkg/smooth to controls
1060    o pkg/ctrl: add forcingPrecond run time parameter
1061    o pkg/seaice:
1062     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
1063     - fix bug in metric terms of u-equation in LSR solver (implicit part),
1064       changes verification/lab_sea
1065     - rearrange implicit part of u-equation in LSR solver to make it easier to
1066       read, understand, and debug. This causes changes at the truncation level.
1067     - fix (serious) bug in the boundary conditions (sign error in the implicit
1068       part) of the LSR solver. Changes all LSR results.
1069     - fixed problem with HSNOW initialization to avoid thick snow when AREA
1070       is initilized with small values - does not change lab_sea results.
1071     - added HsnowFile initialization capability
1072    o pkg/smooth: addition to model/src and pkg/ctrl so allow
1073     initialization of pkg/smooth and application to control vector
1074    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
1075    o dependencies: pkg/profiles requires pkg/cal
1076    o pkg/profiles:
1077     - added option ALLOW_PROFILES_GENERICGRID
1078         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
1079         that interpolation information (grid points and coefficients) is provided
1080         within the netcdf input files.
1081         -> sample matlab scripts can be found in MITgcm_contrib/gael
1082         that allow you to prepare netcdf input files.
1083     - also modified: cleaner include statements, cleaner error print statements,
1084       cleaner stops when error, and more tests of the netcdf input files consistency.
1085    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
1086    o pkg/seaice:
1087     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
1088       requires a new routine: seaice_diagnostics_fill.F
1089     - make sure that seaice does not move if not forced (pressure replacement
1090       method, Hibler and Ip, 1995), changes results
1091     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
1092     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
1093       It is turned off by default (=-1.), because it changes the results.
1094     - make it possible to read AREA from a file, too.
1095    
1096    checkpoint59c
1097    o add S/R and diagnostics for oceanic mixed-layer depth
1098    o move GMRedi call after all vertical mixing schemes (including KPP)
1099    o pkg/thsice:
1100     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
1101      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
1102    o pkg/obcs:
1103     - bug fix for balance code
1104    o pkg/seaice:
1105      - allow values of SEAICE_elasticParm > 1
1106      - add new parameter SEAICE_evpTauRelax as an alternative
1107        to SEAICE_elasticParm
1108      - make lsr boundary conditions free slip (by default), changes result
1109      - add code for no slip boundary conditions for lsr
1110      - set minimum of zeta to zero (and not 4e8) (changes results)
1111      - add a cap on AREA after advecting AREA if seaice_growth is not called
1112    o change calculation of Visbeck K:
1113      - no longer depend on tapering scheme; instead, compute slope (limited
1114        by GM_maxSlope). this is equivalent to what was comuted before with
1115        clipping or linear tappering.
1116      - fix vertical averaging (wrong by 1/2 level)
1117      - leave the old version (but will not be maintained) within
1118        #ifdef OLD_VISBECK_CALC / #endif
1119      - update output of exp. ideal_2D_oce
1120    o change error catch in calc_r_star to improve vectorization
1121    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
1122      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
1123    o adjoint:
1124      Re-organized adjoint checkpointing according to Matt Mazloff
1125      (but with modifs/completions/cleanups)
1126      Storing is now bundled into large arrays to optimized I/O
1127      (and second step in cleanup of the_main_loop)
1128    
1129    checkpoint59b
1130    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
1131      - export/import (between ocean & coupler) fields needed for ocean DIC.
1132    o pkg/seaice:
1133      - get rid of three more exchanges seaice_calc_viscosities (required
1134        different loop boundaries in seaice_lsr and seaice_ocean_stress)
1135      - bug fix in seaice_ocean_stress (update of lab_sea required)
1136      - reduce loop boundaries to necessary minimum also in seaice_evp
1137      - go back to the old way of computing deltaC/Z as the adjoint likes that
1138        better
1139    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
1140      passive tracer to an Age Tracer) + update output.txt
1141    o pkg/exf:
1142      - implement A-grid / C-grid selection for wind-stress input files.
1143      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
1144      for now, in exf_bulk_largeyeager04.F only :
1145      - change implementation for case where windspeed + 2. components wind-stress
1146        are read-in. AND use rhoConstFresh to convert evap.
1147    o pkg/seaice:
1148      - use correct EXCH_UV for wind-forcing (on A-grid).
1149      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
1150        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
1151    o pkg/exf:
1152      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
1153      EXF_INTERPOLATION:
1154      - merge global_with_exf/code version of exf_interp_read.F
1155        to the main code ;
1156      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
1157        reading the file ; Important: This options needs to be defined to recover
1158        previous code.
1159        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
1160      - no longer loose real*8 precision along the way when using exf_iprec=64.
1161  o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)  o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
1162      - change discretisation of evp-solver in order to avoid another exchange
1163        (changes lab_sea) and clean up a little
1164      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
1165        help the adjoint (this also changes the results slightly)
1166      - add a few "_d 0" where they had been missing in seaice_evp.F
1167      - cleaning up: remove unused seaice_calc_rhs.F
1168  o pkg/exf: some cleaning-up:  o pkg/exf: some cleaning-up:
1169    - change various "constants" into runtime parameters    - change various "constants" into runtime parameters
1170    - cleaned-up Large&Yeager04 routine which should eventually    - cleaned-up Large&Yeager04 routine which should eventually
# Line 18  o pkg/exf: some cleaning-up: Line 1178  o pkg/exf: some cleaning-up:
1178  o pkg/thsice:  o pkg/thsice:
1179   fix few little problems, in thsice_calc_thickn.F:   fix few little problems, in thsice_calc_thickn.F:
1180    - growth vertically (and not laterally) if iceFrac == iceMaskMax    - growth vertically (and not laterally) if iceFrac == iceMaskMax
1181    - melt laterally only if hIce < hThinIce (as the comments say)    - melt only laterally if hIce < hThinIce (as the comments say)
1182    and in thsice_extend.F:    and in thsice_extend.F:
1183    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
1184    - 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 34  o pkg/kpp Line 1194  o pkg/kpp
1194  o pkg/seaice  o pkg/seaice
1195   - check for inconsistent evp parameter/cpp-flag combination   - check for inconsistent evp parameter/cpp-flag combination
1196   - remove leftover errIO flat for obsolete name list error handling   - remove leftover errIO flat for obsolete name list error handling
1197    o OpenAD
1198     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
1199    
1200  checkpoint59a  checkpoint59a
1201  o pkg/seaice: some parameter clarifications and a little bit of clean up  o pkg/seaice: some parameter clarifications and a little bit of clean up
# Line 53  o in FFIELDS.h: Line 1215  o in FFIELDS.h:
1215       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
1216  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
1217  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
1218      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
1219        are no longer updating the vertical diffusivity array
1220        (passed as argument) but are (re-) setting those arrays.
1221  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
1222    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
1223      cgrid-lsr and evp solver      cgrid-lsr and evp solver
# Line 1535  o add two new packages Line 2699  o add two new packages
2699    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2700    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2701      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2702      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2703  o add offline package  o add offline package
2704  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2705    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz
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