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revision 1.989 by jmc, Fri May 9 21:51:26 2008 UTC revision 1.1149 by mlosch, Mon Aug 10 09:21:10 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 ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
8      create a meaningful unit attribute for the time coordinate variable
9    o pkg/ebm: add plenty of missing "_d 0" ;
10       update results of experiment global_ocean_ebm (fwd + adjoint tests)
11      Notes: several pieces of code only works for (very) specific set up
12       (domain size, lat range, etc ...); should be documented & stop if one
13       of those assumptions is not meet.
14    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
15       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
16          and offline_exf_seaice (seaicetd + adjoint).
17    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
18       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
19        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
20    o few changes to pass when compiling with strick checking of arguments
21       across S/R (allow to find few bugs in S/R calls).
22    o pkg/seaice:
23     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
24       2d-fields, for slightly better performance
25    
26    checkpoint61t
27    o pkg/seaice:
28     - remove unused variables in seaice_evp
29     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
30    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
31       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
32       each processor opens a different file (a fix from Matt).
33    o cg2d:
34       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
35       this reduces number of EXCH calls by 2 when using exch2.
36       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
37       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
38    o pkg/thsice:
39       add code for Near Infra-Red albedo (from Jeff)
40       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
41    o ini_model_io:
42       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
43       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
44       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
45    
46    checkpoint61s
47    o pkg/exch2 (exch2_rxN_cube*):
48       remove last BARRIER (no need to synchronise after getting data from shared
49       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
50    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
51      and generate new output (for the 2 tests) using default rotationPeriod.
52    o pkg/exch2:
53      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
54        (was already the case with AUTODIFF_EXCH2 defined)
55      - add bj in exch2 arrays and S/R.
56      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
57        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
58    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
59      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
60        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
61      - verification experiment natl_box.longstep
62    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
63      allow different versions of ifort (8 or 9) and different versions
64       of mpi (mpich or mpich2) to be used with the same optfile.
65      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
66       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
67    o pkg/seaice:
68      fix previous modif (3-level field removed) for old-pickup reading
69    
70    checkpoint61r
71    o pkg/seaice:
72     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
73      1. introduce fields for time step (N-1)
74      2. do not use levels 2 and 3 anymore (but keep them)
75      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
76         includes changes to pkg/thsice/thsice_get_velocity.F,
77         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
78         pkg/obcs/obcs_apply_uvice.F.
79     - completely remove code for leap-frog time stepping for second order
80       advection
81     - adjusted adjoint accordingly;
82       gradient checks have improved by an order of magnitude!
83    
84    checkpoint61q
85    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
86     - the boundary conditions along open boundaries are unclear, because the
87       associated masks are set to zero and are thus treated as closed when
88       applying the slip-boundary conditions.
89     - move initialisation of grid variables from seaice_init_varia to _fixed
90    o adding doc/diags_changes.txt
91    o model/src:
92      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
93       to avoid "_diags" naming if no relation to pkg/diagnostics.
94      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
95       file and only call PLOT_FIELD_XYZ if debugMode=T.
96      remove few PLOT_FIELD_XY calls outside initialisation.
97      remove few unnecessary BARRIER.
98    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
99      of salt_plume package in Southern Ocean
100    o pkg/thsice:
101     - fix hOceMxL in overlap (needed for sea-ice advection);
102       update output of experiment global_ocean.cs32x15.icedyn.
103    o pkg/seaice:
104     - make the (placeholder-)tracer IceAge a little more meaningful
105      by avoiding ridging of age due to convergent ice flow
106     - add diagnostics for surface temperature, atmospheric and oceanic
107       heat flux, and atmospheric and oceanic ice growth
108    
109    checkpoint61p
110    o eesupp (global_max & global_sum):
111     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
112     - remove starting & endding barrier (no longer needed)
113    o pkg/mdsio, writelocal:
114       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
115       (remove the STOP): uses shared buffer IO to store data from all threads
116       and then let master-thread write nThreads tiles.
117    o pkg/mdsio (read/write field):
118     - tiled IO done in 1 piece (all levels at a time);
119     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
120     - multi-threaded: allow to read/write local (non-shared) array
121       (was already working with singleCpuIO ; now works also without);
122       => no longer needs barrier call after reading a file (added inside
123       mds_read/write field).
124     - move barrier calls outside gather/scatter_2d to mds_read/write_field
125    o pkg/obcs/exf
126      - exf_getffieldrec.F: add a few ". _d 0" and
127                            add code to catch the case fldperiod = 0.  
128      - obcs_precribe_read.F: change if statements so that they match
129                              the variable type (_RL)
130      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
131        exf_iprec) as part of namelist EXF_NML_01
132    o pkg/mdsio:
133      - read/write tiled (local) files: read/write 1-level tile chunk at a time
134        (instead of segment of length sNx); expected to speed up tiled IO.
135    o pkg/exch2:
136      - take buffer copy from/to array out of S/R exch2_send/recv into new
137        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
138        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
139      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
140      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
141        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
142        including Topology header file (and common blocks).
143      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
144        remove 2nd exch call in exch2_s3d_rx (no longer needed).
145      - document S/R arg. list (+ update some comments)
146    o pkg/seaice:
147      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
148        temperature and humidity over sea ice based on climatological values.
149      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
150        of LSR (this change is expected to change the results slightly because now
151        it uses slightly difference moduli from the second last LSR solution, but
152        that is more consistent with the stress computations; this part of the code
153        is not tested in the verification experiments)
154      - fix diagnostics for flux of ice in case of B-grid
155      - turn strain rates eij and press into global fields within global
156        common block in SEAICE.h for more straighforward diagnostics
157      - fix diagnostics for principal stress components, press, zeta, eta
158        to give something meaning full
159    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
160      new output (all 4 tests) using default rotationPeriod.
161    o pkg KPP:
162      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
163      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
164        and normal grid from 1 to Nr)
165    o Fix computations of L4rdt in mom_calc_visc.F
166    o eesupp:
167      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
168      should be called before a "stop" if we know that all process are going
169      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
170    
171    checkpoint61o
172    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
173    o model/src/ini_curvilinear_grid.F:
174       compute angleSin/CosC when they are not read from a file
175    o pkg/seaice:
176       add pseudo time stepping for LSOR
177    o pkg/exch2:
178       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
179    o pkg/seaice:
180       Adding separate sea ice albedo, drag coefficients, and HO in Southern
181       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
182    o SingleCpuIO:
183       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
184    o pkg/seaice:
185       put exchanged variable in (local) common block for MPI+Multi-Threads
186       to work (necessary with exch1, and for now with exch2 too).
187    o verification: to get more experiments tested with mpi, mth and mpi+mth,
188      change tiling of:
189       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
190       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
191      update output of exp:
192       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
193       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
194      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
195                       (note: output.txt generated on faulks using only 1 tile)
196    o eesupp & mdsio (SingleCpuIO):
197     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
198       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
199       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
200     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
201     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
202       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
203    o pkg/exch2:
204     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
205       read parameter file "data.exch2" if it exists; otherwise try default regular
206       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
207     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
208       with new code (not to be used, just as a backup solution).
209     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
210       in utils/exch2/input.
211    
212    checkpoint61n
213    o eesupp & mdsio (SingleCpuIO):
214      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
215        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
216        receive real*4 array (instead of real*8) to read/write 32.bit files.
217        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
218         and remove new mapping S/R)
219    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
220      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
221        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
222        when using exch2. Add S/R to map global io-buffer to global model array.
223      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
224    
225    checkpoint61m
226    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
227      and add 3 other S/R for other types (R4,R8,RS).
228      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
229    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
230     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
231     - reduce number of macro definitions (keep only those which are used);
232       can always call directly the corrresponding S/R if needed.
233     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
234       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
235     Fixed wrong type of arg in:
236       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
237       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
238     To fix: global_sum of var in common block is wrong (multi-threaded) in:
239       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
240     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
241    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
242      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
243    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
244    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
245      edges are closed (zero depth); might happen with "blank tiles";
246      for now, disabled if using OBCS.
247    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
248      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
249    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
250      to reduce length of 1.D array print in STDOUT.
251    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
252      + use 48 tiles (16x8): this will allow to test "blank tiles".
253    o start to test MPI + multi-threaded (change testreport to skip tests
254      where number of tiles do not match).
255    o genmake2: add option "-omp" to turn on Open-MP ;
256      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
257    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
258      and keep the original tile numbering. Note: compatible with old
259      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
260    
261    checkpoint61l
262    o Overlaps had been forgotten in calculating ijk keys : fixed
263    o fix cyrus makedepend for gcc 4.4
264    o experiment fizhi-cs-aqualev20:
265      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
266      and generate new output. Note: new output is much closer to the old
267      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
268      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
269    o pkg/fizhi:
270     - change to avoid indices going deliberately over array-bounds
271     - remove unnecessary MPI stuff
272     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
273     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
274       does not go over array-bounds and therefore returns reliable output.
275     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
276       this S/R has 4 output arguments, which are used inside "get_alarm";
277       when it is called with the same variable "ndum" in place of several
278       output arguments, this produces weird side effect inside "get_alarm"
279      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
280       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
281       address) and produces error.
282    o tools/gemake2: (March 27-29 2009)
283      with option "-mpi": link *_mpi files from "MODS" dir (this is what
284      testreport does).
285    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
286    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
287       update lab_sea.lsr & lab_sea.salt_plume results
288    o pkg/seaice:
289      Major overhaul of the LSOR solver: change discretization from original
290      finite differences to finite volume. The old routine is still in the
291      file seaice_lsr.F and can be turned on with the CPP-flag
292      SEAICE_OLD_AND_BAD_DISCRETIZATION
293      Along with this change, the discretization of the strain rates is changed.
294      The same flag turns on the old discretization in seaice_calc_strainrates.F
295      All verification experiments with seaice are affected (except for
296      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
297      results by setting the above flag.
298      Further changes involve changes in defaults:
299      - ALLOW_FLOODING is defined and turned on by default
300      - SEAICEadvSnow = .true. is now the default
301      - SEAICEadvSalt = .true. is now the default
302      - SEAICEadvAge  = .true. is now the default
303      - SEAICE_clipVelocities  = .false. is now the default
304                                         (as per J. Zhang's recommendation)
305      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
306        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
307      - seaice_growth: replace computation of UG by a simple copy from wspeed
308    
309    checkpoint61k
310    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
311      seaice_lsr: fixed a few metric terms,
312                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
313                  add more debugging diagnostics
314      seaice_evp: removed superfluous many metric terms of FV discretization
315                  of stress divergence
316                  affects lab_sea, lab_sea.hb87
317      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
318                  of stress divergence for non-evp solver
319                  (this part is not tested anywhere)
320      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
321                  they were effectively only half slip
322                  affects lab_sea.hb87
323      updated all relevant verification experiments (except lab_sea//output_adm.txt
324        which was left over, but fails at level 7 & 6)
325    
326    checkpoint61j
327    o pkg/seaice: turn a few hard wired parameters into run time parameters
328    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
329      time in seconds as promised by the usints in seaice_monitor and exf_monitor
330    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
331      that are not cubed-sphere grids
332    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
333    o pkg/ctrl:
334      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
335    o non-hydrostatic (calc_gw.F):
336      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
337      update output of exp. global_ocean.cs32x15.viscA4
338    o remove backward compatibility for thetaMin,phiMin
339      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
340    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
341      interpolated wind field not only for curvilineargrid=.true., but also
342      for a rotated grid (rotateGrid=.true.)
343    o pkg/exf: add capability to bypass interpolation for runoff
344      by setting yet another CPP-flag
345    o eesupp/src, B-grid exchange:
346      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
347    o autodiff
348      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
349      allows to switch to single-prec common blocks;
350      corresponding switch occurs in tamc.h, integer isbyte
351      TAF store directivs "byte" and "kind" seem equivalent;
352      Most tamc.h have been updated correspondingly.
353    
354    checkpoint61i
355    o autodiff:
356      fix autodiff_sore/_restore indices for obcs
357      (spotted by I. Hoteit, M. Mazloff)
358    o pkg/autodiff, pkg/ctrl:
359      Add flag to reduce all tapelev I/O to single-prec.
360      In data.ctrl set
361        doSinglePrecTapelev = .TRUE.
362    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
363      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
364    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
365      real fresh water flux (not yet)
366    o pkg/mdsio & rw:
367     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
368     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
369    o pkg/flt:
370     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
371       init_fixed & ini_varia.
372     - clean-up & simplify linear interpolation S/R:
373       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
374     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
375     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
376     - add vert. coordinate & horiz. indices to output files.
377     - change vertical position in initial condition, from index to depth [m].
378     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
379       (easier to get to a curvilinear grid) ; delX,delY no longer used.
380    o pkg/ggl90: a few modifications:
381     - fix bottom boundary condition, and interpolation of KappaE
382       near top and bottom
383     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
384     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
385     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
386    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
387      (maintain temporary backward compatibility, until next checkpoint)
388    
389    checkpoint61h
390    o pkg/diagnostics with "periodic averaging diagnostics":
391      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
392    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
393    o pkg/obcs: fix loop ranges for balancing code
394    o pkg/flt:
395     - improve criteria for finding which tile owns a float.
396     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
397    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
398      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
399      with ocean biogeo)
400    o pkg/flt:
401     - do some cleaning and fix the restart ;
402     - add output.txt in flt_example/results to get this pkg tested.
403    o genmake2: add an EXTENDED_SRC option and flag.
404       for now, cannot be turned on on command line (only through genmake_local)
405    o pkg/mdsio: read/write vector:
406     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
407     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
408       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
409     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
410      (drop to 4 digits matching for grad). But this test does not look very
411      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
412    
413    checkpoint61g
414    o pkg/flt:
415      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
416       + make OPTIONS file more standard.
417      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
418      - fix _BYTESWAPIO CPP-Flag
419      - standard reading of file-parameter "data.flt"
420      - fix argument list of S/R FLT_RESTART
421      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
422    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
423    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
424      a still unfixed compiler/optimization bug
425    
426    checkpoint61f
427    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
428      update results of global_ocean.cs32x15.icedyn test.
429    o move getcon.F from model/src to pkg/fizhi.
430    o pkg/exf: add parameter for extrapolation of temp up to the surface
431       and option to prevent negative evap (in bulk_largeyeager04 only).
432    o Prather Advection scheme: fix tracer conservation for divergent flow
433      (e.g., when using NonLin Free-Surface).
434    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
435    o gmredi (Visbeck-variable-K):
436     - add more parameters to Visbeck-variable-K.
437     - use a 5 points average for dSigmaR in Visbeck-K calculation
438       (more "homogenous": same stencil and same weights as in dSigmaH)
439     - update output of ideal_2D_oce experiment.
440    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
441      (#undef REAL4_IS_SLOW)
442     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
443       coordinate variable
444     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
445       (surface forcing fields), removes some of the functionality
446     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
447     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
448       probably not all: copy _RS surface flux fields to RL field before
449       calling DIAGNOSTICS_FILL
450     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
451       real*4 (CALL EXCH_*_RS) versions.
452     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
453       (generate new output).
454    
455    checkpoint61e
456    o gmredi (Visbeck-variable-K):
457      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
458      - change computation of Visbeck-K where Slope > Smax :        
459        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
460        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
461    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
462      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
463    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
464    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
465      does not become too large (to avoid precision problems in implicit-diffusion
466      solver); update ideal_2D_oce output.
467    o pkg ggl90:
468      - in ggl90_cal.F: compute only one set of visc/diff, used to
469        step forward TKE/T/S/momentum
470      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
471        have Prandlt =1)
472    o gmredi (fm07):
473      - add lower limit on Transition layer thickness + lower limit on 1/lambda
474      - allow to set few more params from data.gmredi
475    o pkg ggl90:
476          - add missing sqrt(2) factor in computation of mixing length
477            scale in ggl90_calc.F
478            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
479    
480    checkpoint61d
481    o adjoint modifs
482      - adapt to new field rhoInSitu
483      - allow to revert from StoreDynVars2D, StoreDynVars3D
484        to individual fields
485        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
486    o store 3-D (in-situ) density in commom block (DYNVARS.h)
487     - save 1 rho computation.
488     - no longer modify T & S inland when using down_slope pkg.
489    o gad_som : allow to switch to SOM advection for T & S without corresponding
490      pickup files (using new S/R: MDS_CHECK4FILE).
491    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
492      (for useSingleCpuIO to work in multi-threaded)
493    o pkg/shelfice:
494     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
495       with SHELFICEtopoFile in data.shelfice
496     - move code for reading ice shelf topography and modifying hFacC into separate
497       subroutines of the shelfice package
498     - separate initialisation of "fixed" and "variable" variables
499     - kTopC is not (yet) replaced by kSurfC, although this is possible
500    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
501    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
502      and rename:
503      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
504      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
505    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
506    
507    checkpoint61c
508    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
509      to add mass source/sink of fluid in the interior (3-D generalisation
510      of oceanic real-fresh water flux).
511    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
512    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
513    o new pkg: down_slope
514      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
515      - presently, modify T & S inland (dwnslp_calc_rho.F).
516        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
517      - implementation for ocean in P-coords not tested.
518      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
519    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
520      (to facilitate conversion of oceanic pkg to p-coordinate).
521    o change FIND_RHO to FIND_RHO_2D :
522      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
523    o new pkg: cheapaml
524    
525    checkpoint61b
526    o exch2:
527      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
528      - no longer depend on the order sequence (N,S,E,W).
529      - 3rd exchange no longer needed (tested with 24 tiles).
530      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
531      - exch_UV_A-grid readily available (but not yet tested).
532      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
533      (both are no longer needed) in exch_uv: no effect in forward run; but
534       get truncation error differences with adjoint exch.
535    o exch2:
536     - change index-bounds storage (moved from target to local tile,
537       more intuitive this way) ; rename/remove some variables.
538     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
539    
540    checkpoint61a
541    o exch2/matlab-topology-generator:
542      fix bug in index bounds for N-S internal exchange (hard to tell if this
543      had any effect on the solution).
544    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
545      is exceeded
546    o testreport: modify syntax of awk, so that it works also with
547      awk, and not only with nawk and gawk
548    
549    checkpoint61
550    o autodiff
551      Change default for TAF usage by removing argument '-nonew_arg'
552      This changes TAF subroutine argument list (ordering of active var.)
553      Omission of this flag leads to incompatibility w.r.t. TAMC
554      To restore TAMC-compatibility, need following modifs:
555      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
556      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
557      Tested TAF version is 1.9.22
558      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
559    
560    checkpoint60
561    --->>> This is the last checkpoint for which generating the adjoint
562    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
563    --->>> by default.
564    --->>> Future checkpoints will ommit this flag by default.
565    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
566    o pkg/grdchk: Add gradient check to etan0 perturbations.
567    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
568    o pkg/autodiff: more flexibility in zeroadj.
569      model/src: modifying do_oceanic_phys.F accordingly.
570    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
571    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
572      special setup of gmredi for which the adjoint is stable
573      enough for parameter optimization.
574    o bridging the gap between eddy stress and GM.
575      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
576          along with a change in CPP option (now ALLOW_EDDYPSI).
577      -> when using GM w/ GM_AdvForm:
578          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
579          is applied either in the tracer Eq. or in momentum Eq.
580          depending on data.gmredi (intro. GM_InMomAsStress).
581      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
582      The key modifications are in model/src/taueddy_external_forcing.F
583      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
584    
585    checkpoint59r
586    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
587      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
588      fix option to read coriolis(@ cell-corner) from files with CS-grid.
589    o pkg/mnc: add some attributes to standard 1D-coordinate variables
590    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
591      mass points, when using mnc for output
592      - add runtime parameter (missing_value, missing_value_int) to override
593        default (which is the value of getcon('UNDEF'))
594    o pkg/mnc: prepare mnc for the actual use of missing values with the
595      diagnostics package: small fix in mnc_cw_readwrite.template and more
596      initialisation of never used fields
597      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
598      versions
599    o pkg/thsice/thsice_ini_vars.F added default initial values so that
600      thermodynamics sea ice solver does not blow up when some initial fields
601      are missing.
602    o move from external_forcing_surf.F to ini_forcing.F
603      the p-coord. hack consisting in using pLoad to set phi0surf ;
604      update output of tutorial_global_oce_in_p (affected @ truncation level).
605    o Freshen up a bit hs94.1x64x5, notably:
606      remove rotationPeriod and tRef=5*0. (adjoint only), and add
607      exactConserv=.TRUE.
608  o pkg/generic_advdiff:  o pkg/generic_advdiff:
609    change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only    change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
610    applies to files where Temperature & Salinity 2nd Order moments are used.    applies to files where Temperature & Salinity 2nd Order moments are used.
# Line 2105  o add two new packages Line 2706  o add two new packages
2706    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2707    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2708      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2709      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2710  o add offline package  o add offline package
2711  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2712    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz

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