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revision 1.817 by mlosch, Tue May 15 14:34:44 2007 UTC revision 1.1161 by dfer, Thu Sep 24 20:32:36 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/aim/thsice:
8     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
9      (works as SST restoring)
10    o pkg/thsice:
11     -add specific parameter for salt restoring in slab mixed-layer
12       (by default equal to the temperature restoring)
13    
14    checkpoint61v
15    o pkg/kpp:
16     -add double diffusive contributions as a hack, turned off by default
17      for now, and the code can be excluded with a CPP-flag
18      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
19     -add a verification experiments to "vermix" to test this code
20    o pkg/mom_common:
21      Move computation of length scales to mom_init_fixed.F (avoid recomputation
22      at each time-steps*levels).
23    o pkg/layers:
24      Created a new package for computing volume fluxes in temperature or
25      [not yet implemented] density layers, e.g. for calculating residual
26      overturning circulations.
27    o pkg/diagnostics:
28      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
29    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
30    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
31      To avoid mixing type (RS/RL) of input/output array argument,
32      replace single mixed-type array with a pair from each type (RS/RL).
33    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
34      is now implemented for all pkgs (previously only done for the main pickup)
35    
36    checkpoint61u
37    o pkg/obcs:
38      - change OB?eta from _RS to _RL and put them into a separate commen block
39      - add code to read OB?eta from a file via obcs_prescribe_read: the code
40        compiles and does not destroy any other experiments, the data is read
41        properly, but the code is not tested in actual applications
42    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
43      create a meaningful unit attribute for the time coordinate variable
44    o pkg/ebm: add plenty of missing "_d 0" ;
45       update results of experiment global_ocean_ebm (fwd + adjoint tests)
46      Notes: several pieces of code only works for (very) specific set up
47       (domain size, lat range, etc ...); should be documented & stop if one
48       of those assumptions is not meet.
49    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
50       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
51          and offline_exf_seaice (seaicetd + adjoint).
52    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
53       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
54        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
55    o few changes to pass when compiling with strick checking of arguments
56       across S/R (allow to find few bugs in S/R calls).
57    o pkg/seaice:
58     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
59       2d-fields, for slightly better performance
60    
61    checkpoint61t
62    o pkg/seaice:
63     - remove unused variables in seaice_evp
64     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
65    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
66       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
67       each processor opens a different file (a fix from Matt).
68    o cg2d:
69       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
70       this reduces number of EXCH calls by 2 when using exch2.
71       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
72       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
73    o pkg/thsice:
74       add code for Near Infra-Red albedo (from Jeff)
75       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
76    o ini_model_io:
77       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
78       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
79       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
80    
81    checkpoint61s
82    o pkg/exch2 (exch2_rxN_cube*):
83       remove last BARRIER (no need to synchronise after getting data from shared
84       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
85    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
86      and generate new output (for the 2 tests) using default rotationPeriod.
87    o pkg/exch2:
88      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
89        (was already the case with AUTODIFF_EXCH2 defined)
90      - add bj in exch2 arrays and S/R.
91      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
92        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
93    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
94      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
95        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
96      - verification experiment natl_box.longstep
97    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
98      allow different versions of ifort (8 or 9) and different versions
99       of mpi (mpich or mpich2) to be used with the same optfile.
100      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
101       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
102    o pkg/seaice:
103      fix previous modif (3-level field removed) for old-pickup reading
104    
105    checkpoint61r
106    o pkg/seaice:
107     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
108      1. introduce fields for time step (N-1)
109      2. do not use levels 2 and 3 anymore (but keep them)
110      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
111         includes changes to pkg/thsice/thsice_get_velocity.F,
112         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
113         pkg/obcs/obcs_apply_uvice.F.
114     - completely remove code for leap-frog time stepping for second order
115       advection
116     - adjusted adjoint accordingly;
117       gradient checks have improved by an order of magnitude!
118    
119    checkpoint61q
120    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
121     - the boundary conditions along open boundaries are unclear, because the
122       associated masks are set to zero and are thus treated as closed when
123       applying the slip-boundary conditions.
124     - move initialisation of grid variables from seaice_init_varia to _fixed
125    o adding doc/diags_changes.txt
126    o model/src:
127      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
128       to avoid "_diags" naming if no relation to pkg/diagnostics.
129      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
130       file and only call PLOT_FIELD_XYZ if debugMode=T.
131      remove few PLOT_FIELD_XY calls outside initialisation.
132      remove few unnecessary BARRIER.
133    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
134      of salt_plume package in Southern Ocean
135    o pkg/thsice:
136     - fix hOceMxL in overlap (needed for sea-ice advection);
137       update output of experiment global_ocean.cs32x15.icedyn.
138    o pkg/seaice:
139     - make the (placeholder-)tracer IceAge a little more meaningful
140      by avoiding ridging of age due to convergent ice flow
141     - add diagnostics for surface temperature, atmospheric and oceanic
142       heat flux, and atmospheric and oceanic ice growth
143    
144    checkpoint61p
145    o eesupp (global_max & global_sum):
146     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
147     - remove starting & endding barrier (no longer needed)
148    o pkg/mdsio, writelocal:
149       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
150       (remove the STOP): uses shared buffer IO to store data from all threads
151       and then let master-thread write nThreads tiles.
152    o pkg/mdsio (read/write field):
153     - tiled IO done in 1 piece (all levels at a time);
154     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
155     - multi-threaded: allow to read/write local (non-shared) array
156       (was already working with singleCpuIO ; now works also without);
157       => no longer needs barrier call after reading a file (added inside
158       mds_read/write field).
159     - move barrier calls outside gather/scatter_2d to mds_read/write_field
160    o pkg/obcs/exf
161      - exf_getffieldrec.F: add a few ". _d 0" and
162                            add code to catch the case fldperiod = 0.  
163      - obcs_precribe_read.F: change if statements so that they match
164                              the variable type (_RL)
165      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
166        exf_iprec) as part of namelist EXF_NML_01
167    o pkg/mdsio:
168      - read/write tiled (local) files: read/write 1-level tile chunk at a time
169        (instead of segment of length sNx); expected to speed up tiled IO.
170    o pkg/exch2:
171      - take buffer copy from/to array out of S/R exch2_send/recv into new
172        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
173        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
174      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
175      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
176        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
177        including Topology header file (and common blocks).
178      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
179        remove 2nd exch call in exch2_s3d_rx (no longer needed).
180      - document S/R arg. list (+ update some comments)
181    o pkg/seaice:
182      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
183        temperature and humidity over sea ice based on climatological values.
184      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
185        of LSR (this change is expected to change the results slightly because now
186        it uses slightly difference moduli from the second last LSR solution, but
187        that is more consistent with the stress computations; this part of the code
188        is not tested in the verification experiments)
189      - fix diagnostics for flux of ice in case of B-grid
190      - turn strain rates eij and press into global fields within global
191        common block in SEAICE.h for more straighforward diagnostics
192      - fix diagnostics for principal stress components, press, zeta, eta
193        to give something meaning full
194    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
195      new output (all 4 tests) using default rotationPeriod.
196    o pkg KPP:
197      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
198      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
199        and normal grid from 1 to Nr)
200    o Fix computations of L4rdt in mom_calc_visc.F
201    o eesupp:
202      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
203      should be called before a "stop" if we know that all process are going
204      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
205    
206    checkpoint61o
207    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
208    o model/src/ini_curvilinear_grid.F:
209       compute angleSin/CosC when they are not read from a file
210    o pkg/seaice:
211       add pseudo time stepping for LSOR
212    o pkg/exch2:
213       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
214    o pkg/seaice:
215       Adding separate sea ice albedo, drag coefficients, and HO in Southern
216       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
217    o SingleCpuIO:
218       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
219    o pkg/seaice:
220       put exchanged variable in (local) common block for MPI+Multi-Threads
221       to work (necessary with exch1, and for now with exch2 too).
222    o verification: to get more experiments tested with mpi, mth and mpi+mth,
223      change tiling of:
224       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
225       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
226      update output of exp:
227       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
228       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
229      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
230                       (note: output.txt generated on faulks using only 1 tile)
231    o eesupp & mdsio (SingleCpuIO):
232     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
233       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
234       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
235     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
236     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
237       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
238    o pkg/exch2:
239     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
240       read parameter file "data.exch2" if it exists; otherwise try default regular
241       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
242     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
243       with new code (not to be used, just as a backup solution).
244     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
245       in utils/exch2/input.
246    
247    checkpoint61n
248    o eesupp & mdsio (SingleCpuIO):
249      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
250        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
251        receive real*4 array (instead of real*8) to read/write 32.bit files.
252        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
253         and remove new mapping S/R)
254    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
255      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
256        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
257        when using exch2. Add S/R to map global io-buffer to global model array.
258      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
259    
260    checkpoint61m
261    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
262      and add 3 other S/R for other types (R4,R8,RS).
263      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
264    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
265     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
266     - reduce number of macro definitions (keep only those which are used);
267       can always call directly the corrresponding S/R if needed.
268     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
269       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
270     Fixed wrong type of arg in:
271       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
272       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
273     To fix: global_sum of var in common block is wrong (multi-threaded) in:
274       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
275     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
276    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
277      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
278    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
279    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
280      edges are closed (zero depth); might happen with "blank tiles";
281      for now, disabled if using OBCS.
282    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
283      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
284    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
285      to reduce length of 1.D array print in STDOUT.
286    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
287      + use 48 tiles (16x8): this will allow to test "blank tiles".
288    o start to test MPI + multi-threaded (change testreport to skip tests
289      where number of tiles do not match).
290    o genmake2: add option "-omp" to turn on Open-MP ;
291      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
292    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
293      and keep the original tile numbering. Note: compatible with old
294      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
295    
296    checkpoint61l
297    o Overlaps had been forgotten in calculating ijk keys : fixed
298    o fix cyrus makedepend for gcc 4.4
299    o experiment fizhi-cs-aqualev20:
300      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
301      and generate new output. Note: new output is much closer to the old
302      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
303      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
304    o pkg/fizhi:
305     - change to avoid indices going deliberately over array-bounds
306     - remove unnecessary MPI stuff
307     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
308     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
309       does not go over array-bounds and therefore returns reliable output.
310     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
311       this S/R has 4 output arguments, which are used inside "get_alarm";
312       when it is called with the same variable "ndum" in place of several
313       output arguments, this produces weird side effect inside "get_alarm"
314      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
315       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
316       address) and produces error.
317    o tools/gemake2: (March 27-29 2009)
318      with option "-mpi": link *_mpi files from "MODS" dir (this is what
319      testreport does).
320    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
321    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
322       update lab_sea.lsr & lab_sea.salt_plume results
323    o pkg/seaice:
324      Major overhaul of the LSOR solver: change discretization from original
325      finite differences to finite volume. The old routine is still in the
326      file seaice_lsr.F and can be turned on with the CPP-flag
327      SEAICE_OLD_AND_BAD_DISCRETIZATION
328      Along with this change, the discretization of the strain rates is changed.
329      The same flag turns on the old discretization in seaice_calc_strainrates.F
330      All verification experiments with seaice are affected (except for
331      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
332      results by setting the above flag.
333      Further changes involve changes in defaults:
334      - ALLOW_FLOODING is defined and turned on by default
335      - SEAICEadvSnow = .true. is now the default
336      - SEAICEadvSalt = .true. is now the default
337      - SEAICEadvAge  = .true. is now the default
338      - SEAICE_clipVelocities  = .false. is now the default
339                                         (as per J. Zhang's recommendation)
340      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
341        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
342      - seaice_growth: replace computation of UG by a simple copy from wspeed
343    
344    checkpoint61k
345    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
346      seaice_lsr: fixed a few metric terms,
347                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
348                  add more debugging diagnostics
349      seaice_evp: removed superfluous many metric terms of FV discretization
350                  of stress divergence
351                  affects lab_sea, lab_sea.hb87
352      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
353                  of stress divergence for non-evp solver
354                  (this part is not tested anywhere)
355      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
356                  they were effectively only half slip
357                  affects lab_sea.hb87
358      updated all relevant verification experiments (except lab_sea//output_adm.txt
359        which was left over, but fails at level 7 & 6)
360    
361    checkpoint61j
362    o pkg/seaice: turn a few hard wired parameters into run time parameters
363    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
364      time in seconds as promised by the usints in seaice_monitor and exf_monitor
365    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
366      that are not cubed-sphere grids
367    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
368    o pkg/ctrl:
369      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
370    o non-hydrostatic (calc_gw.F):
371      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
372      update output of exp. global_ocean.cs32x15.viscA4
373    o remove backward compatibility for thetaMin,phiMin
374      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
375    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
376      interpolated wind field not only for curvilineargrid=.true., but also
377      for a rotated grid (rotateGrid=.true.)
378    o pkg/exf: add capability to bypass interpolation for runoff
379      by setting yet another CPP-flag
380    o eesupp/src, B-grid exchange:
381      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
382    o autodiff
383      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
384      allows to switch to single-prec common blocks;
385      corresponding switch occurs in tamc.h, integer isbyte
386      TAF store directivs "byte" and "kind" seem equivalent;
387      Most tamc.h have been updated correspondingly.
388    
389    checkpoint61i
390    o autodiff:
391      fix autodiff_sore/_restore indices for obcs
392      (spotted by I. Hoteit, M. Mazloff)
393    o pkg/autodiff, pkg/ctrl:
394      Add flag to reduce all tapelev I/O to single-prec.
395      In data.ctrl set
396        doSinglePrecTapelev = .TRUE.
397    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
398      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
399    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
400      real fresh water flux (not yet)
401    o pkg/mdsio & rw:
402     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
403     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
404    o pkg/flt:
405     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
406       init_fixed & ini_varia.
407     - clean-up & simplify linear interpolation S/R:
408       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
409     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
410     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
411     - add vert. coordinate & horiz. indices to output files.
412     - change vertical position in initial condition, from index to depth [m].
413     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
414       (easier to get to a curvilinear grid) ; delX,delY no longer used.
415    o pkg/ggl90: a few modifications:
416     - fix bottom boundary condition, and interpolation of KappaE
417       near top and bottom
418     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
419     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
420     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
421    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
422      (maintain temporary backward compatibility, until next checkpoint)
423    
424    checkpoint61h
425    o pkg/diagnostics with "periodic averaging diagnostics":
426      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
427    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
428    o pkg/obcs: fix loop ranges for balancing code
429    o pkg/flt:
430     - improve criteria for finding which tile owns a float.
431     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
432    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
433      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
434      with ocean biogeo)
435    o pkg/flt:
436     - do some cleaning and fix the restart ;
437     - add output.txt in flt_example/results to get this pkg tested.
438    o genmake2: add an EXTENDED_SRC option and flag.
439       for now, cannot be turned on on command line (only through genmake_local)
440    o pkg/mdsio: read/write vector:
441     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
442     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
443       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
444     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
445      (drop to 4 digits matching for grad). But this test does not look very
446      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
447    
448    checkpoint61g
449    o pkg/flt:
450      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
451       + make OPTIONS file more standard.
452      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
453      - fix _BYTESWAPIO CPP-Flag
454      - standard reading of file-parameter "data.flt"
455      - fix argument list of S/R FLT_RESTART
456      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
457    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
458    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
459      a still unfixed compiler/optimization bug
460    
461    checkpoint61f
462    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
463      update results of global_ocean.cs32x15.icedyn test.
464    o move getcon.F from model/src to pkg/fizhi.
465    o pkg/exf: add parameter for extrapolation of temp up to the surface
466       and option to prevent negative evap (in bulk_largeyeager04 only).
467    o Prather Advection scheme: fix tracer conservation for divergent flow
468      (e.g., when using NonLin Free-Surface).
469    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
470    o gmredi (Visbeck-variable-K):
471     - add more parameters to Visbeck-variable-K.
472     - use a 5 points average for dSigmaR in Visbeck-K calculation
473       (more "homogenous": same stencil and same weights as in dSigmaH)
474     - update output of ideal_2D_oce experiment.
475    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
476      (#undef REAL4_IS_SLOW)
477     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
478       coordinate variable
479     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
480       (surface forcing fields), removes some of the functionality
481     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
482     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
483       probably not all: copy _RS surface flux fields to RL field before
484       calling DIAGNOSTICS_FILL
485     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
486       real*4 (CALL EXCH_*_RS) versions.
487     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
488       (generate new output).
489    
490    checkpoint61e
491    o gmredi (Visbeck-variable-K):
492      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
493      - change computation of Visbeck-K where Slope > Smax :        
494        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
495        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
496    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
497      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
498    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
499    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
500      does not become too large (to avoid precision problems in implicit-diffusion
501      solver); update ideal_2D_oce output.
502    o pkg ggl90:
503      - in ggl90_cal.F: compute only one set of visc/diff, used to
504        step forward TKE/T/S/momentum
505      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
506        have Prandlt =1)
507    o gmredi (fm07):
508      - add lower limit on Transition layer thickness + lower limit on 1/lambda
509      - allow to set few more params from data.gmredi
510    o pkg ggl90:
511          - add missing sqrt(2) factor in computation of mixing length
512            scale in ggl90_calc.F
513            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
514    
515    checkpoint61d
516    o adjoint modifs
517      - adapt to new field rhoInSitu
518      - allow to revert from StoreDynVars2D, StoreDynVars3D
519        to individual fields
520        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
521    o store 3-D (in-situ) density in commom block (DYNVARS.h)
522     - save 1 rho computation.
523     - no longer modify T & S inland when using down_slope pkg.
524    o gad_som : allow to switch to SOM advection for T & S without corresponding
525      pickup files (using new S/R: MDS_CHECK4FILE).
526    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
527      (for useSingleCpuIO to work in multi-threaded)
528    o pkg/shelfice:
529     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
530       with SHELFICEtopoFile in data.shelfice
531     - move code for reading ice shelf topography and modifying hFacC into separate
532       subroutines of the shelfice package
533     - separate initialisation of "fixed" and "variable" variables
534     - kTopC is not (yet) replaced by kSurfC, although this is possible
535    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
536    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
537      and rename:
538      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
539      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
540    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
541    
542    checkpoint61c
543    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
544      to add mass source/sink of fluid in the interior (3-D generalisation
545      of oceanic real-fresh water flux).
546    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
547    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
548    o new pkg: down_slope
549      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
550      - presently, modify T & S inland (dwnslp_calc_rho.F).
551        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
552      - implementation for ocean in P-coords not tested.
553      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
554    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
555      (to facilitate conversion of oceanic pkg to p-coordinate).
556    o change FIND_RHO to FIND_RHO_2D :
557      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
558    o new pkg: cheapaml
559    
560    checkpoint61b
561    o exch2:
562      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
563      - no longer depend on the order sequence (N,S,E,W).
564      - 3rd exchange no longer needed (tested with 24 tiles).
565      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
566      - exch_UV_A-grid readily available (but not yet tested).
567      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
568      (both are no longer needed) in exch_uv: no effect in forward run; but
569       get truncation error differences with adjoint exch.
570    o exch2:
571     - change index-bounds storage (moved from target to local tile,
572       more intuitive this way) ; rename/remove some variables.
573     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
574    
575    checkpoint61a
576    o exch2/matlab-topology-generator:
577      fix bug in index bounds for N-S internal exchange (hard to tell if this
578      had any effect on the solution).
579    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
580      is exceeded
581    o testreport: modify syntax of awk, so that it works also with
582      awk, and not only with nawk and gawk
583    
584    checkpoint61
585    o autodiff
586      Change default for TAF usage by removing argument '-nonew_arg'
587      This changes TAF subroutine argument list (ordering of active var.)
588      Omission of this flag leads to incompatibility w.r.t. TAMC
589      To restore TAMC-compatibility, need following modifs:
590      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
591      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
592      Tested TAF version is 1.9.22
593      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
594    
595    checkpoint60
596    --->>> This is the last checkpoint for which generating the adjoint
597    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
598    --->>> by default.
599    --->>> Future checkpoints will ommit this flag by default.
600    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
601    o pkg/grdchk: Add gradient check to etan0 perturbations.
602    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
603    o pkg/autodiff: more flexibility in zeroadj.
604      model/src: modifying do_oceanic_phys.F accordingly.
605    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
606    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
607      special setup of gmredi for which the adjoint is stable
608      enough for parameter optimization.
609    o bridging the gap between eddy stress and GM.
610      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
611          along with a change in CPP option (now ALLOW_EDDYPSI).
612      -> when using GM w/ GM_AdvForm:
613          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
614          is applied either in the tracer Eq. or in momentum Eq.
615          depending on data.gmredi (intro. GM_InMomAsStress).
616      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
617      The key modifications are in model/src/taueddy_external_forcing.F
618      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
619    
620    checkpoint59r
621    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
622      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
623      fix option to read coriolis(@ cell-corner) from files with CS-grid.
624    o pkg/mnc: add some attributes to standard 1D-coordinate variables
625    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
626      mass points, when using mnc for output
627      - add runtime parameter (missing_value, missing_value_int) to override
628        default (which is the value of getcon('UNDEF'))
629    o pkg/mnc: prepare mnc for the actual use of missing values with the
630      diagnostics package: small fix in mnc_cw_readwrite.template and more
631      initialisation of never used fields
632      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
633      versions
634    o pkg/thsice/thsice_ini_vars.F added default initial values so that
635      thermodynamics sea ice solver does not blow up when some initial fields
636      are missing.
637    o move from external_forcing_surf.F to ini_forcing.F
638      the p-coord. hack consisting in using pLoad to set phi0surf ;
639      update output of tutorial_global_oce_in_p (affected @ truncation level).
640    o Freshen up a bit hs94.1x64x5, notably:
641      remove rotationPeriod and tRef=5*0. (adjoint only), and add
642      exactConserv=.TRUE.
643    o pkg/generic_advdiff:
644      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
645      applies to files where Temperature & Salinity 2nd Order moments are used.
646    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
647      this uses a dynamically allocated internal state data structure
648      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
649      and requires a fortran 90 compiler
650    
651    checkpoint59q
652    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
653       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
654    o Refresh tutorial_global_oce_biogeo, notably:
655      - change bathymetry (put back seamounts in ACC, use hFacs)
656      - change EOS (POLY3 --> JMD95Z)
657      - use Bryan-Lewis vertical diffusivity
658      - use multidimensional advection
659      - remove old virtual virtual in dic pkg, now done through ptracer pkg
660      - change a couple of parameters in dic pkg
661    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
662    o pkg/obcs: change default to OBCSfixTopo = .true.,
663      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
664      - replace "debugMode" with "debugLevel .GE. debLevB"
665    o implementation of TAF directives for gchem,cfc,dic
666    o remove "exp5" (replaced by tutorial_deep_convection).
667    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
668      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
669      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
670      --> changes results in exp4, seaice_obcs
671    o tutorial_deep_convection :
672      update the set-up and increase resolution and domain size ; start
673      from pseudo initial conditions = output at t=120mn in order to see
674      something happening when running testreport.
675    o pkg/seaice: add os7mp as an advection scheme
676                  add check for advection schemes
677                  add a flag for restoring T and S underneath sea ice
678    o pkg/my82: add netcdf-support and diagnostics
679    o thsice pkg:
680      - Now hsMax limits snow height by turning it into ice following
681        flooding scheme (and now conserving energy)
682      - Slight rewriting of the formula in thsice_calc_thick.F
683      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
684      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
685    
686    checkpoint59p
687    o gchem / dic / cfc :
688      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
689      - add new parameter files: "data.dic" & "data.cfc" ;
690      - various re-arrangement in initialisation & header file ;
691      - fix tutorial_global_oce_biogeo for multi-threaded test.
692    o pkg/dic: test for "pickup_dic" file when restarting ;
693      if no pickup-file, can restart with a re-initialised pH (same as it did
694      before) providing pickupStrictlyMatch is set to False.
695    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
696      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
697    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
698      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
699    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
700     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
701       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
702    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
703       scheme to use for vorticty-term ;
704     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
705       (with default selectVortScheme, return to original discretisation)
706     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
707    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
708    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
709      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
710      also fix diagnostics VISCAHW & VISCA4W.
711    
712    checkpoint59o
713    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
714    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
715      move a few statemens out the main loop into separate loops
716    o pkg/shelfice:
717      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
718        (kg/m^2/s), does not break tests, because in verification/isomip,
719        rhoConstFresh=rhoConst (by accident)
720      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
721      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
722        new file model/src/seawater.F, so that they are available for all pkgs.
723      - convert potential temperature into in-situ temperature. This changes the
724        isomip tests => update tests
725    o add a flag writePickupAtEnd (default=true) to be able to suppress
726      writing a pickup at the last timestep
727    o tools/mpack-1.6 :
728      - disable automake (not working) and autoconf (not needed).
729      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
730        also cleaner with much less compilation warnings.
731    o pkg/profiles:
732      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
733      (for "less than 32 characters name" compiler requirement)
734    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
735      conditions that have a different sampling frequency than S/T/U/V obcs
736    o pkg/diagnostics (stats-diags):
737      - fix global Min/Max in case 1 processor get only empty tiles
738    o genmake2: replace (4 times)
739         make genmake_tc_1.o >> genmake_warnings 2>&1
740      with
741         COMM="$CC $CFLAGS -c genmake_tc_1.c"
742         echo $COMM >> genmake_warnings
743         $COMM >> genmake_warnings 2>&1
744      to make genmake2 always see the value of CC as specified in the optfile.
745    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
746      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
747      - modify verification advect_cs test to test SOM-advection on CS-grid.
748    o pkg/ctrl:
749      - Rewrite of ctrl_map_ini_ecco.F,
750        introducing a generic routine (ctrl_map_ini_gen.F).
751      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
752    
753    checkpoint59n
754    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
755      number in dedicate array "hdiag":
756      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
757        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
758      - many small changes (integer format) for large number of diagnostics
759      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
760        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
761    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
762      usingSphericalGrid, this allows to define the rotated grid coordinates
763      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
764      geographical coordinates according to the inverse of the rotation defined
765      by the Euler angles, so that Coriolis parameter and online-interpolation by
766      exf works with the geographical coordinates on XC/YC/XG/YG.
767      Naturally, this feature does not work with all packages, so some
768      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
769      profiles), because there the coordinates are assumed to be regular
770      spherical grid coordinates.
771    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
772      - introduce isopycnal diffusion coefficient control.
773    o tools/adjoint_options:
774      - additional control vector components.
775    o pkg/mnc: have mnc create marginally meaning full coordinate variables
776      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
777    o pkg/mypackage:
778      - add example of read/write pickup for state-var ;
779      - add entry points to the main code for state-vars diags & write-pickup.
780    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
781      transitions for useExfYearlyFields
782      - add new subroutine that determines the file to read from for
783        use*YearlyFields = .TRUE. and .FALSE.
784      - add a verification experiment to global_with_exf that tests
785        useExfYearlyFields with USE_EXF_INTERPOLATION defined
786    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
787      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
788      subroutines (which could be generated from a template, because they are
789      almost identical), for now they are included in obcs_prescribe_read.F for
790      simplicity
791    o pkg/exf:
792      - add a little more diagnostic to exf_interp_read (in analogy to
793        mds_read_field, can be turned off with debugLevel < debugLevA=1)
794      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
795        ugly but fast by unrolling short inner loops, inserting a unroll=8
796        directive in routine lagran, and splitting a loop and making do while the
797        outermost loop (the latter requires the intoduction of index arrays)
798    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
799    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
800      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
801    o verification/seaice_obcs: updated for restart test and latest options
802    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
803      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
804      for now this is only available for the C-grid code and also within
805      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
806    
807    checkpoint59m
808    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
809      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
810    o gad_som : fix flux output (& diagnostics) to have same units as other  
811      advection scheme fluxes (was previously multiplied by deltaT).  
812    o added verification/seaice_obcs both to test seaice open boundaries
813      and to provide an example matlab scrpt for generating them
814    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
815    o pkg/salt_plume: clean up salt_plume_frac.F to
816      remove redundancy in PlumeMethod 1 and 4
817    o pkg/kpp: added saltplume diagnostics
818    o pkg/obcs and pkg/seaice:
819      - do not set uice and vice to zero when OB*icefile are unspecified
820      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
821      - moved seaice tracer obcs after call to seaice_growth
822    o pkg/salt_plume: added various options for salt plume depth
823      criterion and for vertical distribution of the salt
824    
825    checkpoint59l
826    o pkg/ptracers: new version of ptracers pickup:
827      read meta file and write only fields which are needed to restart.
828      ( same logic as main pickup file ; also using pickupStrictlyMatch )
829    o pkg/seaice:
830      - add timescale for melting due to warm mixed layer as a means of
831        setting SEAICE_availHeatFrac more conveniently
832      - add a CPP-flag/runtime parameter check for flooding algorithm
833      - reformulated availHeat in seaice_growth.F to be independent of AREA
834    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
835      unit changes
836    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
837    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
838      SX vector computer.
839    o pkg/seaice:
840      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
841        seaice forcing fields can now be read only through pkg/exf
842      - removed some unused halos
843    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
844    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
845      or U/VICE from U/VWIND before computing U/VSTRESS
846    
847    checkpoint59k
848    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
849      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
850    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
851      all experiments pass when compile with un-initialised var. checking option.
852    o added pkg/salt_plume
853    o script to test restart (for now, in MITgcm_contrib/jmc_script)
854    o pkg/seaice: new read/write pickup version.
855      read meta file and write only fields which are needed to restart.
856      ( same logic as main pickup file ; also using pickupStrictlyMatch )
857    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
858    o lab_sea.hb87: modify the domain & update output.hb87.txt :
859      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
860      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
861      process. Fixed here by closing the domain at the Northern boundary.
862    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
863    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
864      a set of consecutive levels in/from a 3-D array.
865    o pkg/ptracers:
866      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
867      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
868    
869    checkpoint59j
870    o in pkgs: dic, obcs, offline, rbcs:
871      standard way to compute coeff. for time interpolation between 2 time reccords
872      which retains full precision (& make results less dependent on compiler).
873      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
874    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
875      packages instead of reading ice cover and wind speed separately
876    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
877     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
878      to allow to compile customized code before the update)
879    o cleaning-up:
880      - fix CPP instruction syntax in pkg/obcs
881      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
882        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
883      - fix some threads issue in IO parts.
884    o pkg/dic:
885      - add tons of "_d 0" (--> much better testreports !)
886       and then update outputs of tutorial_global_oce_biogeo
887    o pkg/mom_fluxform:
888      add a special version of momentum advection intended to conserve momentum
889      next to a bathymetry step or a coastline edge. (default = off = #undef)
890    o new read/write pickup version:
891      - for now, only implemented for main (mdsio) pickup file.
892      - write out only what is needed to restart; merge pickup_nh , pickup_ph
893        and main pickup together.
894      - read meta file; read only what is needed to restart; stop if a field
895        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
896        if it make sense (even if the restart is not perfect).
897      - if no meta file, assume that pickup to read corresponds exactly to
898        a pickup that would currently be written.
899      - read pickup written in the old format (until checkpoint59i) if it
900        recognizes an old meta file (no field-list).
901      - add a meta file in exp. which starts from a pickup: 2 cases:
902        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
903         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
904        b) a meta file describing the content of the associated pickup file
905         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
906    o pkg/mdsio & pkg/rw:
907      - new routine to read a meta file ; new set of routine to read
908        Multiple-fields file (with meta file).
909    o added open boundary conditions capability for seaice
910        HSNOW, HSALT, UICE, and VICE
911    
912    checkpoint59i
913    o adjoint:
914      * fix multiDimAdvection adjoint
915        (partial recomputation problem by TAF for fVerT(:,:,kDown)
916        and comlev1 size definition (maxpass vs. max. number of tracers)
917      * verification/global_ocean.90x45x15 adjoint now tests
918        NLFS and multiDimAdvection using DST3 (=30)
919      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
920    o pkg/kpp: add "_d 0" to real constant (if missing);
921      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
922      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
923    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
924      for internal parameters related to restart process (formerly from PARAMS.h)
925      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
926    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
927      as argument. (only atm2d & obcs write_pickup have not yet been updated)
928    o pkg/monitor:
929      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
930      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
931      - account for deep Atmosphere factor and density factor (anelastic)
932    o added open boundary conditions capability for seaice HEFF and AREA
933    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
934      thermodynamics
935      - requires a little reorganization, which affects the testreport results
936        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
937        so that now the conservative form is tested
938      - add a few comments
939    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
940    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
941    o add new diagnostics to seaice: advective, diffusive fluxes (only for
942      multidim-advection, for scheme 2 they are not filled) and transports,
943      thermodynamic growth rates
944    o change units of EmPmR (inside the code, + within coupling interface)
945      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
946      Affects results @ truncation level (cg2d match) and update output of
947       experiments: lab_sea(6), global_ocean.90x40x15(10),
948      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
949      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
950      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
951      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
952    
953    checkpoint59h
954    o pkg/exf:
955      - improve vectorization by moving if-statement out of loops in
956        exf_mapfields, exf_radiation
957      - exf_bulkformulae.F: introduce 2D fields and vectorize code
958    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
959    o testreport:
960      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
961        monitor & update offline_exf_seaice exp. output.
962      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
963    o pkg/seaice:
964      - bug fix in the evp solver: boundary conditions were affected be
965        masking of zMax/zMin (changes results)
966      - minor bug fix in boundary conditions in seaice_calc_strainrates
967        (changes results for no_slip)
968      - seaice_lsr.F: make interpolation of eta dependent on boundaries
969      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
970      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
971        stress formulation and no-slip boundary conditions
972    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
973      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
974    o pkg/seaice: a first HSALT time stepping equation has been checked in
975    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
976      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
977      without requiring DO-IF statements
978    o pkg/thsice:
979      use continuous power-law function for partition of energy between lateral
980      melting/freezing and thinning/thickening ; old code using step function
981      still available with #undef THSICE_FRACEN_POWERLAW
982      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
983    o testreport: change AD testing : check against results/output_adm.txt
984      using same scripts as for forward test.
985    
986    checkpoint59g
987    o adjoint testing: in preparation for changing testreport:
988      - output format: cost and grad written on separated lines
989      - ad output results in directory "results" (instead of "results_ad")
990    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
991    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
992    o pkg/ecco: allow user defined cost function contributions
993    o testreport:
994      Allow to choose (per experiment) the list of tested output variables
995       and the main variable (used to issue a pass/FAIL ) ;
996      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
997      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
998      Also modify printing of summary:
999       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
1000       b) echo the list of tested variables in the individual summary.txt of
1001          each experiment.
1002    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
1003      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
1004      (but still depend on the tile decompostion of the domain).
1005    o pkg/seaice: change a discretization detail to make the B-grid code
1006      "more symmetric". This change is likely to remove all "ridges/leads" that
1007      where quasi-aligned with the grid in B-grid solutions. It may also be
1008      the solution to the stress coupling issues with the B-grid.
1009    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
1010      remove .cvsignore from input dir. (since testreport no longer run here).
1011    o pkg/thsice:
1012     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
1013     - fix reshaping of sea-ice just after advection:
1014       melt all the ice only if ice-volume is too small.
1015     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
1016       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
1017     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
1018    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
1019      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
1020    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
1021      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
1022      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
1023      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
1024      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
1025      -> update output.txt
1026    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
1027     this affects truncation error: -> update output.txt of exp:
1028      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
1029      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
1030    
1031    checkpoint59f
1032    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
1033    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
1034      a bounded range (in forward mode)
1035    o pkg/ecco, ctrl, autodiff and mom_common:
1036     internal parameter controls, completements of implementations
1037    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
1038    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
1039      (not seem any difference in testing results).
1040    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
1041       at face corners.
1042    o pkg/generic_advdiff:
1043     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
1044      loop range indices for computing vertical advection tendency
1045      and do the calculation in the interior only (no overlap) ;
1046      for now, only implemented for SOM advection (to save CPU time).
1047     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
1048    o exch2 adjoint
1049      First set of changes:
1050      - add exch2 hand-written adjoint templates
1051      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
1052        This will require cleanup in pkg/autodiff/*.F
1053        (changed routines currently kept separate in verif. code/)
1054      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
1055        that used to hide exch2 or cubed-sphere specific code
1056        (commented via 'cph-exch2')
1057    o pkg/seaice
1058      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
1059    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
1060       output of global_ocean.cs32x15.thsice .
1061    
1062    checkpoint59e
1063    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
1064      for B-grid vector (not yet tested) and C-grid vector (<- only used
1065      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
1066    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
1067      (#ifdef ALLOW_SALT_PLUME)
1068    o gather_2d/scatter_2d: removed halo regions
1069    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
1070      scheme and the corresponding test case (under front_relax dir). For now,
1071      only available with Skew-flux form and not yet tested in realistic set-up.
1072      adjoint: store directives updated, but gradient checks deteriorated,
1073      so maybe GM/Redi adjoint is now broken.
1074    o seaice adjoint
1075      * add AREA, HEFF, HSNOW as control variable
1076        (should not change lab_sea results)
1077      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
1078    o pkg/seaice:
1079      * added computation of saltFlux in seaice_growth;
1080        For time being, sea ice salinity is assumed constant
1081        contribution of snow flooding to freshening of sea ice is neglected.
1082        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
1083        defaults to 0.0 in order to maintain backward compatibility.
1084        Typical values for SEAICE_salinity are 4 to 10 g/kg.
1085      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
1086      * added SEAICE_availHeatFrac, which specifies fraction of surface level
1087        heat content used to melt or grow ice
1088      * commented out cap of HICE: it helps keep ice thinner
1089      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
1090      * applied OBCS T/S mask to HEFFM sea ice mask
1091    
1092    checkpoint59d
1093    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
1094     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
1095     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
1096    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
1097     and change default value of parameter "GM_Small_Number";
1098     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
1099       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
1100       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
1101    o pkg/ecco: cost function when applying pkg/smooth to controls
1102    o pkg/ctrl: add forcingPrecond run time parameter
1103    o pkg/seaice:
1104     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
1105     - fix bug in metric terms of u-equation in LSR solver (implicit part),
1106       changes verification/lab_sea
1107     - rearrange implicit part of u-equation in LSR solver to make it easier to
1108       read, understand, and debug. This causes changes at the truncation level.
1109     - fix (serious) bug in the boundary conditions (sign error in the implicit
1110       part) of the LSR solver. Changes all LSR results.
1111     - fixed problem with HSNOW initialization to avoid thick snow when AREA
1112       is initilized with small values - does not change lab_sea results.
1113     - added HsnowFile initialization capability
1114    o pkg/smooth: addition to model/src and pkg/ctrl so allow
1115     initialization of pkg/smooth and application to control vector
1116    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
1117    o dependencies: pkg/profiles requires pkg/cal
1118    o pkg/profiles:
1119     - added option ALLOW_PROFILES_GENERICGRID
1120         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
1121         that interpolation information (grid points and coefficients) is provided
1122         within the netcdf input files.
1123         -> sample matlab scripts can be found in MITgcm_contrib/gael
1124         that allow you to prepare netcdf input files.
1125     - also modified: cleaner include statements, cleaner error print statements,
1126       cleaner stops when error, and more tests of the netcdf input files consistency.
1127    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
1128    o pkg/seaice:
1129     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
1130       requires a new routine: seaice_diagnostics_fill.F
1131     - make sure that seaice does not move if not forced (pressure replacement
1132       method, Hibler and Ip, 1995), changes results
1133     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
1134     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
1135       It is turned off by default (=-1.), because it changes the results.
1136     - make it possible to read AREA from a file, too.
1137    
1138    checkpoint59c
1139    o add S/R and diagnostics for oceanic mixed-layer depth
1140    o move GMRedi call after all vertical mixing schemes (including KPP)
1141    o pkg/thsice:
1142     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
1143      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
1144    o pkg/obcs:
1145     - bug fix for balance code
1146    o pkg/seaice:
1147      - allow values of SEAICE_elasticParm > 1
1148      - add new parameter SEAICE_evpTauRelax as an alternative
1149        to SEAICE_elasticParm
1150      - make lsr boundary conditions free slip (by default), changes result
1151      - add code for no slip boundary conditions for lsr
1152      - set minimum of zeta to zero (and not 4e8) (changes results)
1153      - add a cap on AREA after advecting AREA if seaice_growth is not called
1154    o change calculation of Visbeck K:
1155      - no longer depend on tapering scheme; instead, compute slope (limited
1156        by GM_maxSlope). this is equivalent to what was comuted before with
1157        clipping or linear tappering.
1158      - fix vertical averaging (wrong by 1/2 level)
1159      - leave the old version (but will not be maintained) within
1160        #ifdef OLD_VISBECK_CALC / #endif
1161      - update output of exp. ideal_2D_oce
1162    o change error catch in calc_r_star to improve vectorization
1163    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
1164      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
1165    o adjoint:
1166      Re-organized adjoint checkpointing according to Matt Mazloff
1167      (but with modifs/completions/cleanups)
1168      Storing is now bundled into large arrays to optimized I/O
1169      (and second step in cleanup of the_main_loop)
1170    
1171    checkpoint59b
1172    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
1173      - export/import (between ocean & coupler) fields needed for ocean DIC.
1174  o pkg/seaice:  o pkg/seaice:
1175    - get rid of three more exchanges seaice_calc_viscosities (required    - get rid of three more exchanges seaice_calc_viscosities (required
1176      different loop boundaries in seaice_lsr and seaice_ocean_stress)      different loop boundaries in seaice_lsr and seaice_ocean_stress)
# Line 53  o pkg/exf: some cleaning-up: Line 1220  o pkg/exf: some cleaning-up:
1220  o pkg/thsice:  o pkg/thsice:
1221   fix few little problems, in thsice_calc_thickn.F:   fix few little problems, in thsice_calc_thickn.F:
1222    - growth vertically (and not laterally) if iceFrac == iceMaskMax    - growth vertically (and not laterally) if iceFrac == iceMaskMax
1223    - melt laterally only if hIce < hThinIce (as the comments say)    - melt only laterally if hIce < hThinIce (as the comments say)
1224    and in thsice_extend.F:    and in thsice_extend.F:
1225    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
1226    - 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 90  o in FFIELDS.h: Line 1257  o in FFIELDS.h:
1257       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
1258  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
1259  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
1260      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
1261        are no longer updating the vertical diffusivity array
1262        (passed as argument) but are (re-) setting those arrays.
1263  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
1264    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
1265      cgrid-lsr and evp solver      cgrid-lsr and evp solver
# Line 1572  o add two new packages Line 2741  o add two new packages
2741    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2742    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2743      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2744      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2745  o add offline package  o add offline package
2746  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2747    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz
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