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revision 1.1009 by jmc, Mon Jul 28 21:23:29 2008 UTC revision 1.1178 by jmc, Thu Oct 15 01:23:59 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 model/src:
8      add run-time parameters to check and/or mask initial Temp & Salt
9    o pkg/ptracers:
10      apply zonal filter (if used) to all passive tracers
11    
12    checkpoint61w
13    o adjoint:
14      * update and finish work on adjoint of dic package (G. Forget)
15      * start adjoint of offline package
16      * bug fix for cube-sphere TLM code (active_file_g.F)
17    o tutorial_global_oce_optim:
18      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
19      and add SIZE.h_mpi for MPI testing
20    o pkg autodiff
21     - fix bug in autodiff_restore
22     - make genmake2 remove comments and empty lines from ad_input_code.f in
23       order to reduce file size (new script file remove_comments_sed)
24    o allows to specify vertical profile of vertical viscosity (viscArNr)
25    o pkg autodiff
26      autodiff_ini_model_io: comment out writing of grid information to netcdf
27      files, because at this time the grid fields are a bunch of zeros
28      (this is analogous to ini_mnc_vars.F)
29    o pkg seaice/autodiff:
30     left-over from removing the 3-time-level fields:
31     - small rearrangement of common blocks (SEAICE.h)
32     - fix field declaration in order to get meaningful output in
33       adseaice.*.nc (adcommon.h)
34    o pkg obcs:
35     - go through NH code only if nonHydrostatic=T
36     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
37     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
38       => Update output of experiment seaice_obcs
39     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
40     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
41     - fix restart for useOBCSprescribe + useEXF
42    o pkg ctrl
43     - make obcs as control parameter work also with useSingleCPUio
44     - replace a few sny and snx by Ny and Nx to be consistent with
45       ctrl_set_globfld_x/yz.F
46    o pkg seaice
47     - re-introduce global field frWtrAtm for the case of
48       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
49     - catch the case of an empty filename in seaice_cost_init_fixed.F
50    o pkg ecco:
51     - small bug fixes in the_main_loop
52      . fix order of monitor arguments
53      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
54      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
55        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
56     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
57       imbalance diagnostics for wmean_h/sflux = 0
58     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
59     - catch the case of empty filenames in ecco_cost_init_fixed.F
60       and ecco_readparms.F
61     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
62       to make this statement meaningfull in ecco_cost_weights.F
63    o pkg zonal_filt:
64      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
65      - when using rStar, filter uVel*hFacW instead of uVel
66       (tested without topography: fix a Pb of growing instability with NLFS)
67    o pkg/aim/thsice:
68     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
69      (works as SST restoring)
70    o pkg/thsice:
71     -add specific parameter for salt restoring in slab mixed-layer
72       (by default equal to the temperature restoring)
73    
74    checkpoint61v
75    o pkg/kpp:
76     -add double diffusive contributions as a hack, turned off by default
77      for now, and the code can be excluded with a CPP-flag
78      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
79     -add a verification experiments to "vermix" to test this code
80    o pkg/mom_common:
81      Move computation of length scales to mom_init_fixed.F (avoid recomputation
82      at each time-steps*levels).
83    o pkg/layers:
84      Created a new package for computing volume fluxes in temperature or
85      [not yet implemented] density layers, e.g. for calculating residual
86      overturning circulations.
87    o pkg/diagnostics:
88      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
89    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
90    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
91      To avoid mixing type (RS/RL) of input/output array argument,
92      replace single mixed-type array with a pair from each type (RS/RL).
93    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
94      is now implemented for all pkgs (previously only done for the main pickup)
95    
96    checkpoint61u
97    o pkg/obcs:
98      - change OB?eta from _RS to _RL and put them into a separate commen block
99      - add code to read OB?eta from a file via obcs_prescribe_read: the code
100        compiles and does not destroy any other experiments, the data is read
101        properly, but the code is not tested in actual applications
102    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
103      create a meaningful unit attribute for the time coordinate variable
104    o pkg/ebm: add plenty of missing "_d 0" ;
105       update results of experiment global_ocean_ebm (fwd + adjoint tests)
106      Notes: several pieces of code only works for (very) specific set up
107       (domain size, lat range, etc ...); should be documented & stop if one
108       of those assumptions is not meet.
109    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
110       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
111          and offline_exf_seaice (seaicetd + adjoint).
112    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
113       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
114        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
115    o few changes to pass when compiling with strick checking of arguments
116       across S/R (allow to find few bugs in S/R calls).
117    o pkg/seaice:
118     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
119       2d-fields, for slightly better performance
120    
121    checkpoint61t
122    o pkg/seaice:
123     - remove unused variables in seaice_evp
124     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
125    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
126       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
127       each processor opens a different file (a fix from Matt).
128    o cg2d:
129       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
130       this reduces number of EXCH calls by 2 when using exch2.
131       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
132       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
133    o pkg/thsice:
134       add code for Near Infra-Red albedo (from Jeff)
135       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
136    o ini_model_io:
137       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
138       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
139       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
140    
141    checkpoint61s
142    o pkg/exch2 (exch2_rxN_cube*):
143       remove last BARRIER (no need to synchronise after getting data from shared
144       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
145    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
146      and generate new output (for the 2 tests) using default rotationPeriod.
147    o pkg/exch2:
148      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
149        (was already the case with AUTODIFF_EXCH2 defined)
150      - add bj in exch2 arrays and S/R.
151      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
152        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
153    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
154      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
155        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
156      - verification experiment natl_box.longstep
157    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
158      allow different versions of ifort (8 or 9) and different versions
159       of mpi (mpich or mpich2) to be used with the same optfile.
160      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
161       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
162    o pkg/seaice:
163      fix previous modif (3-level field removed) for old-pickup reading
164    
165    checkpoint61r
166    o pkg/seaice:
167     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
168      1. introduce fields for time step (N-1)
169      2. do not use levels 2 and 3 anymore (but keep them)
170      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
171         includes changes to pkg/thsice/thsice_get_velocity.F,
172         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
173         pkg/obcs/obcs_apply_uvice.F.
174     - completely remove code for leap-frog time stepping for second order
175       advection
176     - adjusted adjoint accordingly;
177       gradient checks have improved by an order of magnitude!
178    
179    checkpoint61q
180    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
181     - the boundary conditions along open boundaries are unclear, because the
182       associated masks are set to zero and are thus treated as closed when
183       applying the slip-boundary conditions.
184     - move initialisation of grid variables from seaice_init_varia to _fixed
185    o adding doc/diags_changes.txt
186    o model/src:
187      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
188       to avoid "_diags" naming if no relation to pkg/diagnostics.
189      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
190       file and only call PLOT_FIELD_XYZ if debugMode=T.
191      remove few PLOT_FIELD_XY calls outside initialisation.
192      remove few unnecessary BARRIER.
193    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
194      of salt_plume package in Southern Ocean
195    o pkg/thsice:
196     - fix hOceMxL in overlap (needed for sea-ice advection);
197       update output of experiment global_ocean.cs32x15.icedyn.
198    o pkg/seaice:
199     - make the (placeholder-)tracer IceAge a little more meaningful
200      by avoiding ridging of age due to convergent ice flow
201     - add diagnostics for surface temperature, atmospheric and oceanic
202       heat flux, and atmospheric and oceanic ice growth
203    
204    checkpoint61p
205    o eesupp (global_max & global_sum):
206     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
207     - remove starting & endding barrier (no longer needed)
208    o pkg/mdsio, writelocal:
209       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
210       (remove the STOP): uses shared buffer IO to store data from all threads
211       and then let master-thread write nThreads tiles.
212    o pkg/mdsio (read/write field):
213     - tiled IO done in 1 piece (all levels at a time);
214     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
215     - multi-threaded: allow to read/write local (non-shared) array
216       (was already working with singleCpuIO ; now works also without);
217       => no longer needs barrier call after reading a file (added inside
218       mds_read/write field).
219     - move barrier calls outside gather/scatter_2d to mds_read/write_field
220    o pkg/obcs/exf
221      - exf_getffieldrec.F: add a few ". _d 0" and
222                            add code to catch the case fldperiod = 0.  
223      - obcs_precribe_read.F: change if statements so that they match
224                              the variable type (_RL)
225      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
226        exf_iprec) as part of namelist EXF_NML_01
227    o pkg/mdsio:
228      - read/write tiled (local) files: read/write 1-level tile chunk at a time
229        (instead of segment of length sNx); expected to speed up tiled IO.
230    o pkg/exch2:
231      - take buffer copy from/to array out of S/R exch2_send/recv into new
232        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
233        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
234      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
235      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
236        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
237        including Topology header file (and common blocks).
238      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
239        remove 2nd exch call in exch2_s3d_rx (no longer needed).
240      - document S/R arg. list (+ update some comments)
241    o pkg/seaice:
242      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
243        temperature and humidity over sea ice based on climatological values.
244      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
245        of LSR (this change is expected to change the results slightly because now
246        it uses slightly difference moduli from the second last LSR solution, but
247        that is more consistent with the stress computations; this part of the code
248        is not tested in the verification experiments)
249      - fix diagnostics for flux of ice in case of B-grid
250      - turn strain rates eij and press into global fields within global
251        common block in SEAICE.h for more straighforward diagnostics
252      - fix diagnostics for principal stress components, press, zeta, eta
253        to give something meaning full
254    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
255      new output (all 4 tests) using default rotationPeriod.
256    o pkg KPP:
257      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
258      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
259        and normal grid from 1 to Nr)
260    o Fix computations of L4rdt in mom_calc_visc.F
261    o eesupp:
262      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
263      should be called before a "stop" if we know that all process are going
264      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
265    
266    checkpoint61o
267    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
268    o model/src/ini_curvilinear_grid.F:
269       compute angleSin/CosC when they are not read from a file
270    o pkg/seaice:
271       add pseudo time stepping for LSOR
272    o pkg/exch2:
273       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
274    o pkg/seaice:
275       Adding separate sea ice albedo, drag coefficients, and HO in Southern
276       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
277    o SingleCpuIO:
278       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
279    o pkg/seaice:
280       put exchanged variable in (local) common block for MPI+Multi-Threads
281       to work (necessary with exch1, and for now with exch2 too).
282    o verification: to get more experiments tested with mpi, mth and mpi+mth,
283      change tiling of:
284       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
285       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
286      update output of exp:
287       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
288       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
289      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
290                       (note: output.txt generated on faulks using only 1 tile)
291    o eesupp & mdsio (SingleCpuIO):
292     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
293       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
294       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
295     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
296     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
297       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
298    o pkg/exch2:
299     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
300       read parameter file "data.exch2" if it exists; otherwise try default regular
301       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
302     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
303       with new code (not to be used, just as a backup solution).
304     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
305       in utils/exch2/input.
306    
307    checkpoint61n
308    o eesupp & mdsio (SingleCpuIO):
309      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
310        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
311        receive real*4 array (instead of real*8) to read/write 32.bit files.
312        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
313         and remove new mapping S/R)
314    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
315      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
316        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
317        when using exch2. Add S/R to map global io-buffer to global model array.
318      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
319    
320    checkpoint61m
321    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
322      and add 3 other S/R for other types (R4,R8,RS).
323      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
324    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
325     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
326     - reduce number of macro definitions (keep only those which are used);
327       can always call directly the corrresponding S/R if needed.
328     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
329       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
330     Fixed wrong type of arg in:
331       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
332       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
333     To fix: global_sum of var in common block is wrong (multi-threaded) in:
334       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
335     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
336    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
337      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
338    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
339    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
340      edges are closed (zero depth); might happen with "blank tiles";
341      for now, disabled if using OBCS.
342    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
343      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
344    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
345      to reduce length of 1.D array print in STDOUT.
346    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
347      + use 48 tiles (16x8): this will allow to test "blank tiles".
348    o start to test MPI + multi-threaded (change testreport to skip tests
349      where number of tiles do not match).
350    o genmake2: add option "-omp" to turn on Open-MP ;
351      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
352    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
353      and keep the original tile numbering. Note: compatible with old
354      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
355    
356    checkpoint61l
357    o Overlaps had been forgotten in calculating ijk keys : fixed
358    o fix cyrus makedepend for gcc 4.4
359    o experiment fizhi-cs-aqualev20:
360      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
361      and generate new output. Note: new output is much closer to the old
362      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
363      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
364    o pkg/fizhi:
365     - change to avoid indices going deliberately over array-bounds
366     - remove unnecessary MPI stuff
367     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
368     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
369       does not go over array-bounds and therefore returns reliable output.
370     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
371       this S/R has 4 output arguments, which are used inside "get_alarm";
372       when it is called with the same variable "ndum" in place of several
373       output arguments, this produces weird side effect inside "get_alarm"
374      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
375       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
376       address) and produces error.
377    o tools/gemake2: (March 27-29 2009)
378      with option "-mpi": link *_mpi files from "MODS" dir (this is what
379      testreport does).
380    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
381    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
382       update lab_sea.lsr & lab_sea.salt_plume results
383    o pkg/seaice:
384      Major overhaul of the LSOR solver: change discretization from original
385      finite differences to finite volume. The old routine is still in the
386      file seaice_lsr.F and can be turned on with the CPP-flag
387      SEAICE_OLD_AND_BAD_DISCRETIZATION
388      Along with this change, the discretization of the strain rates is changed.
389      The same flag turns on the old discretization in seaice_calc_strainrates.F
390      All verification experiments with seaice are affected (except for
391      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
392      results by setting the above flag.
393      Further changes involve changes in defaults:
394      - ALLOW_FLOODING is defined and turned on by default
395      - SEAICEadvSnow = .true. is now the default
396      - SEAICEadvSalt = .true. is now the default
397      - SEAICEadvAge  = .true. is now the default
398      - SEAICE_clipVelocities  = .false. is now the default
399                                         (as per J. Zhang's recommendation)
400      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
401        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
402      - seaice_growth: replace computation of UG by a simple copy from wspeed
403    
404    checkpoint61k
405    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
406      seaice_lsr: fixed a few metric terms,
407                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
408                  add more debugging diagnostics
409      seaice_evp: removed superfluous many metric terms of FV discretization
410                  of stress divergence
411                  affects lab_sea, lab_sea.hb87
412      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
413                  of stress divergence for non-evp solver
414                  (this part is not tested anywhere)
415      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
416                  they were effectively only half slip
417                  affects lab_sea.hb87
418      updated all relevant verification experiments (except lab_sea//output_adm.txt
419        which was left over, but fails at level 7 & 6)
420    
421    checkpoint61j
422    o pkg/seaice: turn a few hard wired parameters into run time parameters
423    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
424      time in seconds as promised by the usints in seaice_monitor and exf_monitor
425    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
426      that are not cubed-sphere grids
427    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
428    o pkg/ctrl:
429      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
430    o non-hydrostatic (calc_gw.F):
431      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
432      update output of exp. global_ocean.cs32x15.viscA4
433    o remove backward compatibility for thetaMin,phiMin
434      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
435    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
436      interpolated wind field not only for curvilineargrid=.true., but also
437      for a rotated grid (rotateGrid=.true.)
438    o pkg/exf: add capability to bypass interpolation for runoff
439      by setting yet another CPP-flag
440    o eesupp/src, B-grid exchange:
441      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
442    o autodiff
443      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
444      allows to switch to single-prec common blocks;
445      corresponding switch occurs in tamc.h, integer isbyte
446      TAF store directivs "byte" and "kind" seem equivalent;
447      Most tamc.h have been updated correspondingly.
448    
449    checkpoint61i
450    o autodiff:
451      fix autodiff_sore/_restore indices for obcs
452      (spotted by I. Hoteit, M. Mazloff)
453    o pkg/autodiff, pkg/ctrl:
454      Add flag to reduce all tapelev I/O to single-prec.
455      In data.ctrl set
456        doSinglePrecTapelev = .TRUE.
457    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
458      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
459    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
460      real fresh water flux (not yet)
461    o pkg/mdsio & rw:
462     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
463     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
464    o pkg/flt:
465     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
466       init_fixed & ini_varia.
467     - clean-up & simplify linear interpolation S/R:
468       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
469     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
470     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
471     - add vert. coordinate & horiz. indices to output files.
472     - change vertical position in initial condition, from index to depth [m].
473     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
474       (easier to get to a curvilinear grid) ; delX,delY no longer used.
475    o pkg/ggl90: a few modifications:
476     - fix bottom boundary condition, and interpolation of KappaE
477       near top and bottom
478     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
479     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
480     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
481    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
482      (maintain temporary backward compatibility, until next checkpoint)
483    
484    checkpoint61h
485    o pkg/diagnostics with "periodic averaging diagnostics":
486      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
487    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
488    o pkg/obcs: fix loop ranges for balancing code
489    o pkg/flt:
490     - improve criteria for finding which tile owns a float.
491     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
492    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
493      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
494      with ocean biogeo)
495    o pkg/flt:
496     - do some cleaning and fix the restart ;
497     - add output.txt in flt_example/results to get this pkg tested.
498    o genmake2: add an EXTENDED_SRC option and flag.
499       for now, cannot be turned on on command line (only through genmake_local)
500    o pkg/mdsio: read/write vector:
501     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
502     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
503       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
504     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
505      (drop to 4 digits matching for grad). But this test does not look very
506      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
507    
508    checkpoint61g
509    o pkg/flt:
510      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
511       + make OPTIONS file more standard.
512      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
513      - fix _BYTESWAPIO CPP-Flag
514      - standard reading of file-parameter "data.flt"
515      - fix argument list of S/R FLT_RESTART
516      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
517    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
518    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
519      a still unfixed compiler/optimization bug
520    
521    checkpoint61f
522    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
523      update results of global_ocean.cs32x15.icedyn test.
524    o move getcon.F from model/src to pkg/fizhi.
525    o pkg/exf: add parameter for extrapolation of temp up to the surface
526       and option to prevent negative evap (in bulk_largeyeager04 only).
527    o Prather Advection scheme: fix tracer conservation for divergent flow
528      (e.g., when using NonLin Free-Surface).
529    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
530    o gmredi (Visbeck-variable-K):
531     - add more parameters to Visbeck-variable-K.
532     - use a 5 points average for dSigmaR in Visbeck-K calculation
533       (more "homogenous": same stencil and same weights as in dSigmaH)
534     - update output of ideal_2D_oce experiment.
535    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
536      (#undef REAL4_IS_SLOW)
537     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
538       coordinate variable
539     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
540       (surface forcing fields), removes some of the functionality
541     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
542     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
543       probably not all: copy _RS surface flux fields to RL field before
544       calling DIAGNOSTICS_FILL
545     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
546       real*4 (CALL EXCH_*_RS) versions.
547     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
548       (generate new output).
549    
550    checkpoint61e
551    o gmredi (Visbeck-variable-K):
552      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
553      - change computation of Visbeck-K where Slope > Smax :        
554        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
555        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
556    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
557      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
558    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
559    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
560      does not become too large (to avoid precision problems in implicit-diffusion
561      solver); update ideal_2D_oce output.
562    o pkg ggl90:
563      - in ggl90_cal.F: compute only one set of visc/diff, used to
564        step forward TKE/T/S/momentum
565      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
566        have Prandlt =1)
567    o gmredi (fm07):
568      - add lower limit on Transition layer thickness + lower limit on 1/lambda
569      - allow to set few more params from data.gmredi
570    o pkg ggl90:
571          - add missing sqrt(2) factor in computation of mixing length
572            scale in ggl90_calc.F
573            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
574    
575    checkpoint61d
576    o adjoint modifs
577      - adapt to new field rhoInSitu
578      - allow to revert from StoreDynVars2D, StoreDynVars3D
579        to individual fields
580        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
581    o store 3-D (in-situ) density in commom block (DYNVARS.h)
582     - save 1 rho computation.
583     - no longer modify T & S inland when using down_slope pkg.
584    o gad_som : allow to switch to SOM advection for T & S without corresponding
585      pickup files (using new S/R: MDS_CHECK4FILE).
586    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
587      (for useSingleCpuIO to work in multi-threaded)
588    o pkg/shelfice:
589     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
590       with SHELFICEtopoFile in data.shelfice
591     - move code for reading ice shelf topography and modifying hFacC into separate
592       subroutines of the shelfice package
593     - separate initialisation of "fixed" and "variable" variables
594     - kTopC is not (yet) replaced by kSurfC, although this is possible
595    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
596    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
597      and rename:
598      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
599      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
600    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
601    
602    checkpoint61c
603    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
604      to add mass source/sink of fluid in the interior (3-D generalisation
605      of oceanic real-fresh water flux).
606    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
607    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
608    o new pkg: down_slope
609      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
610      - presently, modify T & S inland (dwnslp_calc_rho.F).
611        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
612      - implementation for ocean in P-coords not tested.
613      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
614    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
615      (to facilitate conversion of oceanic pkg to p-coordinate).
616    o change FIND_RHO to FIND_RHO_2D :
617      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
618    o new pkg: cheapaml
619    
620    checkpoint61b
621    o exch2:
622      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
623      - no longer depend on the order sequence (N,S,E,W).
624      - 3rd exchange no longer needed (tested with 24 tiles).
625      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
626      - exch_UV_A-grid readily available (but not yet tested).
627      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
628      (both are no longer needed) in exch_uv: no effect in forward run; but
629       get truncation error differences with adjoint exch.
630    o exch2:
631     - change index-bounds storage (moved from target to local tile,
632       more intuitive this way) ; rename/remove some variables.
633     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
634    
635    checkpoint61a
636  o exch2/matlab-topology-generator:  o exch2/matlab-topology-generator:
637    fix bug in index bounds for N-S internal exchange (hard to tell if this    fix bug in index bounds for N-S internal exchange (hard to tell if this
638    had any effect on the solution).    had any effect on the solution).
# Line 2172  o add two new packages Line 2801  o add two new packages
2801    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2802    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2803      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2804      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2805  o add offline package  o add offline package
2806  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2807    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz

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