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revision 1.842 by jmc, Thu Jun 21 00:53:20 2007 UTC revision 1.1164 by mlosch, Wed Sep 30 16:03:49 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 ctrl
8     - make obcs as control parameter work also with useSingleCPUio
9     - replace a few sny and snx by Ny and Nx to be consistent with
10       ctrl_set_globfld_x/yz.F
11    o pkg seaice
12     - re-introduce global field frWtrAtm for the case of
13       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
14     - catch the case of an empty filename in seaice_cost_init_fixed.F
15    o pkg ecco:
16     - small bug fixes in the_main_loop
17      . fix order of monitor arguments
18      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
19      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
20        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
21     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
22       imbalance diagnostics for wmean_h/sflux = 0
23     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
24     - catch the case of empty filenames in ecco_cost_init_fixed.F
25       and ecco_readparms.F
26     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
27       to make this statement meaningfull in ecco_cost_weights.F
28    o pkg zonal_filt:
29      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
30      - when using rStar, filter uVel*hFacW instead of uVel
31       (tested without topography: fix a Pb of growing instability with NLFS)
32    o pkg/aim/thsice:
33     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
34      (works as SST restoring)
35    o pkg/thsice:
36     -add specific parameter for salt restoring in slab mixed-layer
37       (by default equal to the temperature restoring)
38    
39    checkpoint61v
40    o pkg/kpp:
41     -add double diffusive contributions as a hack, turned off by default
42      for now, and the code can be excluded with a CPP-flag
43      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
44     -add a verification experiments to "vermix" to test this code
45    o pkg/mom_common:
46      Move computation of length scales to mom_init_fixed.F (avoid recomputation
47      at each time-steps*levels).
48    o pkg/layers:
49      Created a new package for computing volume fluxes in temperature or
50      [not yet implemented] density layers, e.g. for calculating residual
51      overturning circulations.
52    o pkg/diagnostics:
53      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
54    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
55    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
56      To avoid mixing type (RS/RL) of input/output array argument,
57      replace single mixed-type array with a pair from each type (RS/RL).
58    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
59      is now implemented for all pkgs (previously only done for the main pickup)
60    
61    checkpoint61u
62    o pkg/obcs:
63      - change OB?eta from _RS to _RL and put them into a separate commen block
64      - add code to read OB?eta from a file via obcs_prescribe_read: the code
65        compiles and does not destroy any other experiments, the data is read
66        properly, but the code is not tested in actual applications
67    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
68      create a meaningful unit attribute for the time coordinate variable
69    o pkg/ebm: add plenty of missing "_d 0" ;
70       update results of experiment global_ocean_ebm (fwd + adjoint tests)
71      Notes: several pieces of code only works for (very) specific set up
72       (domain size, lat range, etc ...); should be documented & stop if one
73       of those assumptions is not meet.
74    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
75       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
76          and offline_exf_seaice (seaicetd + adjoint).
77    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
78       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
79        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
80    o few changes to pass when compiling with strick checking of arguments
81       across S/R (allow to find few bugs in S/R calls).
82    o pkg/seaice:
83     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
84       2d-fields, for slightly better performance
85    
86    checkpoint61t
87    o pkg/seaice:
88     - remove unused variables in seaice_evp
89     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
90    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
91       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
92       each processor opens a different file (a fix from Matt).
93    o cg2d:
94       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
95       this reduces number of EXCH calls by 2 when using exch2.
96       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
97       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
98    o pkg/thsice:
99       add code for Near Infra-Red albedo (from Jeff)
100       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
101    o ini_model_io:
102       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
103       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
104       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
105    
106    checkpoint61s
107    o pkg/exch2 (exch2_rxN_cube*):
108       remove last BARRIER (no need to synchronise after getting data from shared
109       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
110    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
111      and generate new output (for the 2 tests) using default rotationPeriod.
112    o pkg/exch2:
113      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
114        (was already the case with AUTODIFF_EXCH2 defined)
115      - add bj in exch2 arrays and S/R.
116      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
117        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
118    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
119      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
120        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
121      - verification experiment natl_box.longstep
122    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
123      allow different versions of ifort (8 or 9) and different versions
124       of mpi (mpich or mpich2) to be used with the same optfile.
125      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
126       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
127    o pkg/seaice:
128      fix previous modif (3-level field removed) for old-pickup reading
129    
130    checkpoint61r
131    o pkg/seaice:
132     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
133      1. introduce fields for time step (N-1)
134      2. do not use levels 2 and 3 anymore (but keep them)
135      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
136         includes changes to pkg/thsice/thsice_get_velocity.F,
137         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
138         pkg/obcs/obcs_apply_uvice.F.
139     - completely remove code for leap-frog time stepping for second order
140       advection
141     - adjusted adjoint accordingly;
142       gradient checks have improved by an order of magnitude!
143    
144    checkpoint61q
145    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
146     - the boundary conditions along open boundaries are unclear, because the
147       associated masks are set to zero and are thus treated as closed when
148       applying the slip-boundary conditions.
149     - move initialisation of grid variables from seaice_init_varia to _fixed
150    o adding doc/diags_changes.txt
151    o model/src:
152      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
153       to avoid "_diags" naming if no relation to pkg/diagnostics.
154      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
155       file and only call PLOT_FIELD_XYZ if debugMode=T.
156      remove few PLOT_FIELD_XY calls outside initialisation.
157      remove few unnecessary BARRIER.
158    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
159      of salt_plume package in Southern Ocean
160    o pkg/thsice:
161     - fix hOceMxL in overlap (needed for sea-ice advection);
162       update output of experiment global_ocean.cs32x15.icedyn.
163    o pkg/seaice:
164     - make the (placeholder-)tracer IceAge a little more meaningful
165      by avoiding ridging of age due to convergent ice flow
166     - add diagnostics for surface temperature, atmospheric and oceanic
167       heat flux, and atmospheric and oceanic ice growth
168    
169    checkpoint61p
170    o eesupp (global_max & global_sum):
171     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
172     - remove starting & endding barrier (no longer needed)
173    o pkg/mdsio, writelocal:
174       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
175       (remove the STOP): uses shared buffer IO to store data from all threads
176       and then let master-thread write nThreads tiles.
177    o pkg/mdsio (read/write field):
178     - tiled IO done in 1 piece (all levels at a time);
179     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
180     - multi-threaded: allow to read/write local (non-shared) array
181       (was already working with singleCpuIO ; now works also without);
182       => no longer needs barrier call after reading a file (added inside
183       mds_read/write field).
184     - move barrier calls outside gather/scatter_2d to mds_read/write_field
185    o pkg/obcs/exf
186      - exf_getffieldrec.F: add a few ". _d 0" and
187                            add code to catch the case fldperiod = 0.  
188      - obcs_precribe_read.F: change if statements so that they match
189                              the variable type (_RL)
190      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
191        exf_iprec) as part of namelist EXF_NML_01
192    o pkg/mdsio:
193      - read/write tiled (local) files: read/write 1-level tile chunk at a time
194        (instead of segment of length sNx); expected to speed up tiled IO.
195    o pkg/exch2:
196      - take buffer copy from/to array out of S/R exch2_send/recv into new
197        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
198        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
199      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
200      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
201        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
202        including Topology header file (and common blocks).
203      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
204        remove 2nd exch call in exch2_s3d_rx (no longer needed).
205      - document S/R arg. list (+ update some comments)
206    o pkg/seaice:
207      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
208        temperature and humidity over sea ice based on climatological values.
209      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
210        of LSR (this change is expected to change the results slightly because now
211        it uses slightly difference moduli from the second last LSR solution, but
212        that is more consistent with the stress computations; this part of the code
213        is not tested in the verification experiments)
214      - fix diagnostics for flux of ice in case of B-grid
215      - turn strain rates eij and press into global fields within global
216        common block in SEAICE.h for more straighforward diagnostics
217      - fix diagnostics for principal stress components, press, zeta, eta
218        to give something meaning full
219    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
220      new output (all 4 tests) using default rotationPeriod.
221    o pkg KPP:
222      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
223      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
224        and normal grid from 1 to Nr)
225    o Fix computations of L4rdt in mom_calc_visc.F
226    o eesupp:
227      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
228      should be called before a "stop" if we know that all process are going
229      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
230    
231    checkpoint61o
232    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
233    o model/src/ini_curvilinear_grid.F:
234       compute angleSin/CosC when they are not read from a file
235    o pkg/seaice:
236       add pseudo time stepping for LSOR
237    o pkg/exch2:
238       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
239    o pkg/seaice:
240       Adding separate sea ice albedo, drag coefficients, and HO in Southern
241       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
242    o SingleCpuIO:
243       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
244    o pkg/seaice:
245       put exchanged variable in (local) common block for MPI+Multi-Threads
246       to work (necessary with exch1, and for now with exch2 too).
247    o verification: to get more experiments tested with mpi, mth and mpi+mth,
248      change tiling of:
249       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
250       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
251      update output of exp:
252       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
253       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
254      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
255                       (note: output.txt generated on faulks using only 1 tile)
256    o eesupp & mdsio (SingleCpuIO):
257     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
258       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
259       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
260     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
261     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
262       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
263    o pkg/exch2:
264     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
265       read parameter file "data.exch2" if it exists; otherwise try default regular
266       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
267     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
268       with new code (not to be used, just as a backup solution).
269     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
270       in utils/exch2/input.
271    
272    checkpoint61n
273    o eesupp & mdsio (SingleCpuIO):
274      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
275        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
276        receive real*4 array (instead of real*8) to read/write 32.bit files.
277        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
278         and remove new mapping S/R)
279    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
280      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
281        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
282        when using exch2. Add S/R to map global io-buffer to global model array.
283      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
284    
285    checkpoint61m
286    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
287      and add 3 other S/R for other types (R4,R8,RS).
288      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
289    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
290     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
291     - reduce number of macro definitions (keep only those which are used);
292       can always call directly the corrresponding S/R if needed.
293     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
294       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
295     Fixed wrong type of arg in:
296       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
297       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
298     To fix: global_sum of var in common block is wrong (multi-threaded) in:
299       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
300     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
301    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
302      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
303    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
304    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
305      edges are closed (zero depth); might happen with "blank tiles";
306      for now, disabled if using OBCS.
307    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
308      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
309    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
310      to reduce length of 1.D array print in STDOUT.
311    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
312      + use 48 tiles (16x8): this will allow to test "blank tiles".
313    o start to test MPI + multi-threaded (change testreport to skip tests
314      where number of tiles do not match).
315    o genmake2: add option "-omp" to turn on Open-MP ;
316      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
317    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
318      and keep the original tile numbering. Note: compatible with old
319      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
320    
321    checkpoint61l
322    o Overlaps had been forgotten in calculating ijk keys : fixed
323    o fix cyrus makedepend for gcc 4.4
324    o experiment fizhi-cs-aqualev20:
325      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
326      and generate new output. Note: new output is much closer to the old
327      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
328      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
329    o pkg/fizhi:
330     - change to avoid indices going deliberately over array-bounds
331     - remove unnecessary MPI stuff
332     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
333     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
334       does not go over array-bounds and therefore returns reliable output.
335     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
336       this S/R has 4 output arguments, which are used inside "get_alarm";
337       when it is called with the same variable "ndum" in place of several
338       output arguments, this produces weird side effect inside "get_alarm"
339      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
340       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
341       address) and produces error.
342    o tools/gemake2: (March 27-29 2009)
343      with option "-mpi": link *_mpi files from "MODS" dir (this is what
344      testreport does).
345    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
346    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
347       update lab_sea.lsr & lab_sea.salt_plume results
348    o pkg/seaice:
349      Major overhaul of the LSOR solver: change discretization from original
350      finite differences to finite volume. The old routine is still in the
351      file seaice_lsr.F and can be turned on with the CPP-flag
352      SEAICE_OLD_AND_BAD_DISCRETIZATION
353      Along with this change, the discretization of the strain rates is changed.
354      The same flag turns on the old discretization in seaice_calc_strainrates.F
355      All verification experiments with seaice are affected (except for
356      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
357      results by setting the above flag.
358      Further changes involve changes in defaults:
359      - ALLOW_FLOODING is defined and turned on by default
360      - SEAICEadvSnow = .true. is now the default
361      - SEAICEadvSalt = .true. is now the default
362      - SEAICEadvAge  = .true. is now the default
363      - SEAICE_clipVelocities  = .false. is now the default
364                                         (as per J. Zhang's recommendation)
365      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
366        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
367      - seaice_growth: replace computation of UG by a simple copy from wspeed
368    
369    checkpoint61k
370    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
371      seaice_lsr: fixed a few metric terms,
372                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
373                  add more debugging diagnostics
374      seaice_evp: removed superfluous many metric terms of FV discretization
375                  of stress divergence
376                  affects lab_sea, lab_sea.hb87
377      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
378                  of stress divergence for non-evp solver
379                  (this part is not tested anywhere)
380      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
381                  they were effectively only half slip
382                  affects lab_sea.hb87
383      updated all relevant verification experiments (except lab_sea//output_adm.txt
384        which was left over, but fails at level 7 & 6)
385    
386    checkpoint61j
387    o pkg/seaice: turn a few hard wired parameters into run time parameters
388    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
389      time in seconds as promised by the usints in seaice_monitor and exf_monitor
390    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
391      that are not cubed-sphere grids
392    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
393    o pkg/ctrl:
394      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
395    o non-hydrostatic (calc_gw.F):
396      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
397      update output of exp. global_ocean.cs32x15.viscA4
398    o remove backward compatibility for thetaMin,phiMin
399      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
400    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
401      interpolated wind field not only for curvilineargrid=.true., but also
402      for a rotated grid (rotateGrid=.true.)
403    o pkg/exf: add capability to bypass interpolation for runoff
404      by setting yet another CPP-flag
405    o eesupp/src, B-grid exchange:
406      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
407    o autodiff
408      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
409      allows to switch to single-prec common blocks;
410      corresponding switch occurs in tamc.h, integer isbyte
411      TAF store directivs "byte" and "kind" seem equivalent;
412      Most tamc.h have been updated correspondingly.
413    
414    checkpoint61i
415    o autodiff:
416      fix autodiff_sore/_restore indices for obcs
417      (spotted by I. Hoteit, M. Mazloff)
418    o pkg/autodiff, pkg/ctrl:
419      Add flag to reduce all tapelev I/O to single-prec.
420      In data.ctrl set
421        doSinglePrecTapelev = .TRUE.
422    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
423      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
424    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
425      real fresh water flux (not yet)
426    o pkg/mdsio & rw:
427     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
428     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
429    o pkg/flt:
430     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
431       init_fixed & ini_varia.
432     - clean-up & simplify linear interpolation S/R:
433       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
434     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
435     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
436     - add vert. coordinate & horiz. indices to output files.
437     - change vertical position in initial condition, from index to depth [m].
438     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
439       (easier to get to a curvilinear grid) ; delX,delY no longer used.
440    o pkg/ggl90: a few modifications:
441     - fix bottom boundary condition, and interpolation of KappaE
442       near top and bottom
443     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
444     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
445     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
446    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
447      (maintain temporary backward compatibility, until next checkpoint)
448    
449    checkpoint61h
450    o pkg/diagnostics with "periodic averaging diagnostics":
451      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
452    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
453    o pkg/obcs: fix loop ranges for balancing code
454    o pkg/flt:
455     - improve criteria for finding which tile owns a float.
456     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
457    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
458      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
459      with ocean biogeo)
460    o pkg/flt:
461     - do some cleaning and fix the restart ;
462     - add output.txt in flt_example/results to get this pkg tested.
463    o genmake2: add an EXTENDED_SRC option and flag.
464       for now, cannot be turned on on command line (only through genmake_local)
465    o pkg/mdsio: read/write vector:
466     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
467     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
468       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
469     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
470      (drop to 4 digits matching for grad). But this test does not look very
471      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
472    
473    checkpoint61g
474    o pkg/flt:
475      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
476       + make OPTIONS file more standard.
477      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
478      - fix _BYTESWAPIO CPP-Flag
479      - standard reading of file-parameter "data.flt"
480      - fix argument list of S/R FLT_RESTART
481      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
482    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
483    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
484      a still unfixed compiler/optimization bug
485    
486    checkpoint61f
487    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
488      update results of global_ocean.cs32x15.icedyn test.
489    o move getcon.F from model/src to pkg/fizhi.
490    o pkg/exf: add parameter for extrapolation of temp up to the surface
491       and option to prevent negative evap (in bulk_largeyeager04 only).
492    o Prather Advection scheme: fix tracer conservation for divergent flow
493      (e.g., when using NonLin Free-Surface).
494    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
495    o gmredi (Visbeck-variable-K):
496     - add more parameters to Visbeck-variable-K.
497     - use a 5 points average for dSigmaR in Visbeck-K calculation
498       (more "homogenous": same stencil and same weights as in dSigmaH)
499     - update output of ideal_2D_oce experiment.
500    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
501      (#undef REAL4_IS_SLOW)
502     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
503       coordinate variable
504     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
505       (surface forcing fields), removes some of the functionality
506     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
507     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
508       probably not all: copy _RS surface flux fields to RL field before
509       calling DIAGNOSTICS_FILL
510     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
511       real*4 (CALL EXCH_*_RS) versions.
512     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
513       (generate new output).
514    
515    checkpoint61e
516    o gmredi (Visbeck-variable-K):
517      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
518      - change computation of Visbeck-K where Slope > Smax :        
519        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
520        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
521    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
522      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
523    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
524    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
525      does not become too large (to avoid precision problems in implicit-diffusion
526      solver); update ideal_2D_oce output.
527    o pkg ggl90:
528      - in ggl90_cal.F: compute only one set of visc/diff, used to
529        step forward TKE/T/S/momentum
530      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
531        have Prandlt =1)
532    o gmredi (fm07):
533      - add lower limit on Transition layer thickness + lower limit on 1/lambda
534      - allow to set few more params from data.gmredi
535    o pkg ggl90:
536          - add missing sqrt(2) factor in computation of mixing length
537            scale in ggl90_calc.F
538            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
539    
540    checkpoint61d
541    o adjoint modifs
542      - adapt to new field rhoInSitu
543      - allow to revert from StoreDynVars2D, StoreDynVars3D
544        to individual fields
545        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
546    o store 3-D (in-situ) density in commom block (DYNVARS.h)
547     - save 1 rho computation.
548     - no longer modify T & S inland when using down_slope pkg.
549    o gad_som : allow to switch to SOM advection for T & S without corresponding
550      pickup files (using new S/R: MDS_CHECK4FILE).
551    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
552      (for useSingleCpuIO to work in multi-threaded)
553    o pkg/shelfice:
554     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
555       with SHELFICEtopoFile in data.shelfice
556     - move code for reading ice shelf topography and modifying hFacC into separate
557       subroutines of the shelfice package
558     - separate initialisation of "fixed" and "variable" variables
559     - kTopC is not (yet) replaced by kSurfC, although this is possible
560    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
561    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
562      and rename:
563      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
564      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
565    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
566    
567    checkpoint61c
568    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
569      to add mass source/sink of fluid in the interior (3-D generalisation
570      of oceanic real-fresh water flux).
571    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
572    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
573    o new pkg: down_slope
574      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
575      - presently, modify T & S inland (dwnslp_calc_rho.F).
576        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
577      - implementation for ocean in P-coords not tested.
578      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
579    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
580      (to facilitate conversion of oceanic pkg to p-coordinate).
581    o change FIND_RHO to FIND_RHO_2D :
582      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
583    o new pkg: cheapaml
584    
585    checkpoint61b
586    o exch2:
587      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
588      - no longer depend on the order sequence (N,S,E,W).
589      - 3rd exchange no longer needed (tested with 24 tiles).
590      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
591      - exch_UV_A-grid readily available (but not yet tested).
592      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
593      (both are no longer needed) in exch_uv: no effect in forward run; but
594       get truncation error differences with adjoint exch.
595    o exch2:
596     - change index-bounds storage (moved from target to local tile,
597       more intuitive this way) ; rename/remove some variables.
598     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
599    
600    checkpoint61a
601    o exch2/matlab-topology-generator:
602      fix bug in index bounds for N-S internal exchange (hard to tell if this
603      had any effect on the solution).
604    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
605      is exceeded
606    o testreport: modify syntax of awk, so that it works also with
607      awk, and not only with nawk and gawk
608    
609    checkpoint61
610    o autodiff
611      Change default for TAF usage by removing argument '-nonew_arg'
612      This changes TAF subroutine argument list (ordering of active var.)
613      Omission of this flag leads to incompatibility w.r.t. TAMC
614      To restore TAMC-compatibility, need following modifs:
615      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
616      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
617      Tested TAF version is 1.9.22
618      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
619    
620    checkpoint60
621    --->>> This is the last checkpoint for which generating the adjoint
622    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
623    --->>> by default.
624    --->>> Future checkpoints will ommit this flag by default.
625    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
626    o pkg/grdchk: Add gradient check to etan0 perturbations.
627    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
628    o pkg/autodiff: more flexibility in zeroadj.
629      model/src: modifying do_oceanic_phys.F accordingly.
630    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
631    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
632      special setup of gmredi for which the adjoint is stable
633      enough for parameter optimization.
634    o bridging the gap between eddy stress and GM.
635      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
636          along with a change in CPP option (now ALLOW_EDDYPSI).
637      -> when using GM w/ GM_AdvForm:
638          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
639          is applied either in the tracer Eq. or in momentum Eq.
640          depending on data.gmredi (intro. GM_InMomAsStress).
641      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
642      The key modifications are in model/src/taueddy_external_forcing.F
643      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
644    
645    checkpoint59r
646    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
647      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
648      fix option to read coriolis(@ cell-corner) from files with CS-grid.
649    o pkg/mnc: add some attributes to standard 1D-coordinate variables
650    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
651      mass points, when using mnc for output
652      - add runtime parameter (missing_value, missing_value_int) to override
653        default (which is the value of getcon('UNDEF'))
654    o pkg/mnc: prepare mnc for the actual use of missing values with the
655      diagnostics package: small fix in mnc_cw_readwrite.template and more
656      initialisation of never used fields
657      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
658      versions
659    o pkg/thsice/thsice_ini_vars.F added default initial values so that
660      thermodynamics sea ice solver does not blow up when some initial fields
661      are missing.
662    o move from external_forcing_surf.F to ini_forcing.F
663      the p-coord. hack consisting in using pLoad to set phi0surf ;
664      update output of tutorial_global_oce_in_p (affected @ truncation level).
665    o Freshen up a bit hs94.1x64x5, notably:
666      remove rotationPeriod and tRef=5*0. (adjoint only), and add
667      exactConserv=.TRUE.
668    o pkg/generic_advdiff:
669      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
670      applies to files where Temperature & Salinity 2nd Order moments are used.
671    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
672      this uses a dynamically allocated internal state data structure
673      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
674      and requires a fortran 90 compiler
675    
676    checkpoint59q
677    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
678       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
679    o Refresh tutorial_global_oce_biogeo, notably:
680      - change bathymetry (put back seamounts in ACC, use hFacs)
681      - change EOS (POLY3 --> JMD95Z)
682      - use Bryan-Lewis vertical diffusivity
683      - use multidimensional advection
684      - remove old virtual virtual in dic pkg, now done through ptracer pkg
685      - change a couple of parameters in dic pkg
686    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
687    o pkg/obcs: change default to OBCSfixTopo = .true.,
688      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
689      - replace "debugMode" with "debugLevel .GE. debLevB"
690    o implementation of TAF directives for gchem,cfc,dic
691    o remove "exp5" (replaced by tutorial_deep_convection).
692    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
693      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
694      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
695      --> changes results in exp4, seaice_obcs
696    o tutorial_deep_convection :
697      update the set-up and increase resolution and domain size ; start
698      from pseudo initial conditions = output at t=120mn in order to see
699      something happening when running testreport.
700    o pkg/seaice: add os7mp as an advection scheme
701                  add check for advection schemes
702                  add a flag for restoring T and S underneath sea ice
703    o pkg/my82: add netcdf-support and diagnostics
704    o thsice pkg:
705      - Now hsMax limits snow height by turning it into ice following
706        flooding scheme (and now conserving energy)
707      - Slight rewriting of the formula in thsice_calc_thick.F
708      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
709      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
710    
711    checkpoint59p
712    o gchem / dic / cfc :
713      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
714      - add new parameter files: "data.dic" & "data.cfc" ;
715      - various re-arrangement in initialisation & header file ;
716      - fix tutorial_global_oce_biogeo for multi-threaded test.
717    o pkg/dic: test for "pickup_dic" file when restarting ;
718      if no pickup-file, can restart with a re-initialised pH (same as it did
719      before) providing pickupStrictlyMatch is set to False.
720    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
721      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
722    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
723      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
724    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
725     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
726       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
727    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
728       scheme to use for vorticty-term ;
729     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
730       (with default selectVortScheme, return to original discretisation)
731     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
732    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
733    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
734      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
735      also fix diagnostics VISCAHW & VISCA4W.
736    
737    checkpoint59o
738    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
739    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
740      move a few statemens out the main loop into separate loops
741    o pkg/shelfice:
742      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
743        (kg/m^2/s), does not break tests, because in verification/isomip,
744        rhoConstFresh=rhoConst (by accident)
745      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
746      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
747        new file model/src/seawater.F, so that they are available for all pkgs.
748      - convert potential temperature into in-situ temperature. This changes the
749        isomip tests => update tests
750    o add a flag writePickupAtEnd (default=true) to be able to suppress
751      writing a pickup at the last timestep
752    o tools/mpack-1.6 :
753      - disable automake (not working) and autoconf (not needed).
754      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
755        also cleaner with much less compilation warnings.
756    o pkg/profiles:
757      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
758      (for "less than 32 characters name" compiler requirement)
759    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
760      conditions that have a different sampling frequency than S/T/U/V obcs
761    o pkg/diagnostics (stats-diags):
762      - fix global Min/Max in case 1 processor get only empty tiles
763    o genmake2: replace (4 times)
764         make genmake_tc_1.o >> genmake_warnings 2>&1
765      with
766         COMM="$CC $CFLAGS -c genmake_tc_1.c"
767         echo $COMM >> genmake_warnings
768         $COMM >> genmake_warnings 2>&1
769      to make genmake2 always see the value of CC as specified in the optfile.
770    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
771      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
772      - modify verification advect_cs test to test SOM-advection on CS-grid.
773    o pkg/ctrl:
774      - Rewrite of ctrl_map_ini_ecco.F,
775        introducing a generic routine (ctrl_map_ini_gen.F).
776      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
777    
778    checkpoint59n
779    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
780      number in dedicate array "hdiag":
781      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
782        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
783      - many small changes (integer format) for large number of diagnostics
784      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
785        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
786    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
787      usingSphericalGrid, this allows to define the rotated grid coordinates
788      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
789      geographical coordinates according to the inverse of the rotation defined
790      by the Euler angles, so that Coriolis parameter and online-interpolation by
791      exf works with the geographical coordinates on XC/YC/XG/YG.
792      Naturally, this feature does not work with all packages, so some
793      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
794      profiles), because there the coordinates are assumed to be regular
795      spherical grid coordinates.
796    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
797      - introduce isopycnal diffusion coefficient control.
798    o tools/adjoint_options:
799      - additional control vector components.
800    o pkg/mnc: have mnc create marginally meaning full coordinate variables
801      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
802    o pkg/mypackage:
803      - add example of read/write pickup for state-var ;
804      - add entry points to the main code for state-vars diags & write-pickup.
805    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
806      transitions for useExfYearlyFields
807      - add new subroutine that determines the file to read from for
808        use*YearlyFields = .TRUE. and .FALSE.
809      - add a verification experiment to global_with_exf that tests
810        useExfYearlyFields with USE_EXF_INTERPOLATION defined
811    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
812      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
813      subroutines (which could be generated from a template, because they are
814      almost identical), for now they are included in obcs_prescribe_read.F for
815      simplicity
816    o pkg/exf:
817      - add a little more diagnostic to exf_interp_read (in analogy to
818        mds_read_field, can be turned off with debugLevel < debugLevA=1)
819      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
820        ugly but fast by unrolling short inner loops, inserting a unroll=8
821        directive in routine lagran, and splitting a loop and making do while the
822        outermost loop (the latter requires the intoduction of index arrays)
823    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
824    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
825      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
826    o verification/seaice_obcs: updated for restart test and latest options
827    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
828      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
829      for now this is only available for the C-grid code and also within
830      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
831    
832    checkpoint59m
833    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
834      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
835    o gad_som : fix flux output (& diagnostics) to have same units as other  
836      advection scheme fluxes (was previously multiplied by deltaT).  
837    o added verification/seaice_obcs both to test seaice open boundaries
838      and to provide an example matlab scrpt for generating them
839    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
840    o pkg/salt_plume: clean up salt_plume_frac.F to
841      remove redundancy in PlumeMethod 1 and 4
842    o pkg/kpp: added saltplume diagnostics
843    o pkg/obcs and pkg/seaice:
844      - do not set uice and vice to zero when OB*icefile are unspecified
845      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
846      - moved seaice tracer obcs after call to seaice_growth
847    o pkg/salt_plume: added various options for salt plume depth
848      criterion and for vertical distribution of the salt
849    
850    checkpoint59l
851    o pkg/ptracers: new version of ptracers pickup:
852      read meta file and write only fields which are needed to restart.
853      ( same logic as main pickup file ; also using pickupStrictlyMatch )
854    o pkg/seaice:
855      - add timescale for melting due to warm mixed layer as a means of
856        setting SEAICE_availHeatFrac more conveniently
857      - add a CPP-flag/runtime parameter check for flooding algorithm
858      - reformulated availHeat in seaice_growth.F to be independent of AREA
859    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
860      unit changes
861    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
862    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
863      SX vector computer.
864    o pkg/seaice:
865      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
866        seaice forcing fields can now be read only through pkg/exf
867      - removed some unused halos
868    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
869    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
870      or U/VICE from U/VWIND before computing U/VSTRESS
871    
872    checkpoint59k
873    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
874      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
875    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
876      all experiments pass when compile with un-initialised var. checking option.
877    o added pkg/salt_plume
878    o script to test restart (for now, in MITgcm_contrib/jmc_script)
879    o pkg/seaice: new read/write pickup version.
880      read meta file and write only fields which are needed to restart.
881      ( same logic as main pickup file ; also using pickupStrictlyMatch )
882    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
883    o lab_sea.hb87: modify the domain & update output.hb87.txt :
884      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
885      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
886      process. Fixed here by closing the domain at the Northern boundary.
887    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
888    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
889      a set of consecutive levels in/from a 3-D array.
890    o pkg/ptracers:
891      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
892      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
893    
894    checkpoint59j
895    o in pkgs: dic, obcs, offline, rbcs:
896      standard way to compute coeff. for time interpolation between 2 time reccords
897      which retains full precision (& make results less dependent on compiler).
898      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
899    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
900      packages instead of reading ice cover and wind speed separately
901    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
902     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
903      to allow to compile customized code before the update)
904    o cleaning-up:
905      - fix CPP instruction syntax in pkg/obcs
906      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
907        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
908      - fix some threads issue in IO parts.
909    o pkg/dic:
910      - add tons of "_d 0" (--> much better testreports !)
911       and then update outputs of tutorial_global_oce_biogeo
912    o pkg/mom_fluxform:
913      add a special version of momentum advection intended to conserve momentum
914      next to a bathymetry step or a coastline edge. (default = off = #undef)
915    o new read/write pickup version:
916      - for now, only implemented for main (mdsio) pickup file.
917      - write out only what is needed to restart; merge pickup_nh , pickup_ph
918        and main pickup together.
919      - read meta file; read only what is needed to restart; stop if a field
920        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
921        if it make sense (even if the restart is not perfect).
922      - if no meta file, assume that pickup to read corresponds exactly to
923        a pickup that would currently be written.
924      - read pickup written in the old format (until checkpoint59i) if it
925        recognizes an old meta file (no field-list).
926      - add a meta file in exp. which starts from a pickup: 2 cases:
927        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
928         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
929        b) a meta file describing the content of the associated pickup file
930         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
931    o pkg/mdsio & pkg/rw:
932      - new routine to read a meta file ; new set of routine to read
933        Multiple-fields file (with meta file).
934    o added open boundary conditions capability for seaice
935        HSNOW, HSALT, UICE, and VICE
936    
937    checkpoint59i
938    o adjoint:
939      * fix multiDimAdvection adjoint
940        (partial recomputation problem by TAF for fVerT(:,:,kDown)
941        and comlev1 size definition (maxpass vs. max. number of tracers)
942      * verification/global_ocean.90x45x15 adjoint now tests
943        NLFS and multiDimAdvection using DST3 (=30)
944      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
945    o pkg/kpp: add "_d 0" to real constant (if missing);
946      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
947      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
948    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
949      for internal parameters related to restart process (formerly from PARAMS.h)
950      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
951    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
952      as argument. (only atm2d & obcs write_pickup have not yet been updated)
953    o pkg/monitor:
954      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
955      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
956      - account for deep Atmosphere factor and density factor (anelastic)
957    o added open boundary conditions capability for seaice HEFF and AREA
958    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
959      thermodynamics
960      - requires a little reorganization, which affects the testreport results
961        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
962        so that now the conservative form is tested
963      - add a few comments
964    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
965    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
966    o add new diagnostics to seaice: advective, diffusive fluxes (only for
967      multidim-advection, for scheme 2 they are not filled) and transports,
968      thermodynamic growth rates
969    o change units of EmPmR (inside the code, + within coupling interface)
970      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
971      Affects results @ truncation level (cg2d match) and update output of
972       experiments: lab_sea(6), global_ocean.90x40x15(10),
973      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
974      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
975      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
976      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
977    
978    checkpoint59h
979    o pkg/exf:
980      - improve vectorization by moving if-statement out of loops in
981        exf_mapfields, exf_radiation
982      - exf_bulkformulae.F: introduce 2D fields and vectorize code
983    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
984    o testreport:
985      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
986        monitor & update offline_exf_seaice exp. output.
987      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
988    o pkg/seaice:
989      - bug fix in the evp solver: boundary conditions were affected be
990        masking of zMax/zMin (changes results)
991      - minor bug fix in boundary conditions in seaice_calc_strainrates
992        (changes results for no_slip)
993      - seaice_lsr.F: make interpolation of eta dependent on boundaries
994      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
995      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
996        stress formulation and no-slip boundary conditions
997    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
998      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
999    o pkg/seaice: a first HSALT time stepping equation has been checked in
1000    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
1001      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
1002      without requiring DO-IF statements
1003    o pkg/thsice:
1004      use continuous power-law function for partition of energy between lateral
1005      melting/freezing and thinning/thickening ; old code using step function
1006      still available with #undef THSICE_FRACEN_POWERLAW
1007      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
1008    o testreport: change AD testing : check against results/output_adm.txt
1009      using same scripts as for forward test.
1010    
1011    checkpoint59g
1012    o adjoint testing: in preparation for changing testreport:
1013      - output format: cost and grad written on separated lines
1014      - ad output results in directory "results" (instead of "results_ad")
1015    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
1016    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
1017    o pkg/ecco: allow user defined cost function contributions
1018    o testreport:
1019      Allow to choose (per experiment) the list of tested output variables
1020       and the main variable (used to issue a pass/FAIL ) ;
1021      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
1022      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
1023      Also modify printing of summary:
1024       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
1025       b) echo the list of tested variables in the individual summary.txt of
1026          each experiment.
1027    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
1028      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
1029      (but still depend on the tile decompostion of the domain).
1030    o pkg/seaice: change a discretization detail to make the B-grid code
1031      "more symmetric". This change is likely to remove all "ridges/leads" that
1032      where quasi-aligned with the grid in B-grid solutions. It may also be
1033      the solution to the stress coupling issues with the B-grid.
1034    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
1035      remove .cvsignore from input dir. (since testreport no longer run here).
1036    o pkg/thsice:
1037     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
1038     - fix reshaping of sea-ice just after advection:
1039       melt all the ice only if ice-volume is too small.
1040     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
1041       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
1042     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
1043    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
1044      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
1045    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
1046      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
1047      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
1048      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
1049      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
1050      -> update output.txt
1051    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
1052     this affects truncation error: -> update output.txt of exp:
1053      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
1054      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
1055    
1056    checkpoint59f
1057    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
1058    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
1059      a bounded range (in forward mode)
1060    o pkg/ecco, ctrl, autodiff and mom_common:
1061     internal parameter controls, completements of implementations
1062    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
1063    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
1064      (not seem any difference in testing results).
1065    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
1066       at face corners.
1067    o pkg/generic_advdiff:
1068     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
1069      loop range indices for computing vertical advection tendency
1070      and do the calculation in the interior only (no overlap) ;
1071      for now, only implemented for SOM advection (to save CPU time).
1072     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
1073    o exch2 adjoint
1074      First set of changes:
1075      - add exch2 hand-written adjoint templates
1076      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
1077        This will require cleanup in pkg/autodiff/*.F
1078        (changed routines currently kept separate in verif. code/)
1079      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
1080        that used to hide exch2 or cubed-sphere specific code
1081        (commented via 'cph-exch2')
1082    o pkg/seaice
1083      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
1084    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
1085       output of global_ocean.cs32x15.thsice .
1086    
1087    checkpoint59e
1088    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
1089      for B-grid vector (not yet tested) and C-grid vector (<- only used
1090      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
1091    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
1092      (#ifdef ALLOW_SALT_PLUME)
1093    o gather_2d/scatter_2d: removed halo regions
1094    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
1095      scheme and the corresponding test case (under front_relax dir). For now,
1096      only available with Skew-flux form and not yet tested in realistic set-up.
1097      adjoint: store directives updated, but gradient checks deteriorated,
1098      so maybe GM/Redi adjoint is now broken.
1099    o seaice adjoint
1100      * add AREA, HEFF, HSNOW as control variable
1101        (should not change lab_sea results)
1102      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
1103    o pkg/seaice:
1104      * added computation of saltFlux in seaice_growth;
1105        For time being, sea ice salinity is assumed constant
1106        contribution of snow flooding to freshening of sea ice is neglected.
1107        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
1108        defaults to 0.0 in order to maintain backward compatibility.
1109        Typical values for SEAICE_salinity are 4 to 10 g/kg.
1110      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
1111      * added SEAICE_availHeatFrac, which specifies fraction of surface level
1112        heat content used to melt or grow ice
1113      * commented out cap of HICE: it helps keep ice thinner
1114      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
1115      * applied OBCS T/S mask to HEFFM sea ice mask
1116    
1117    checkpoint59d
1118  o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array  o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
1119   for {PKG} state variables, and called from DO_STATEVARS_DIAGS.   for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
1120   (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)   (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
# Line 171  o in FFIELDS.h: Line 1282  o in FFIELDS.h:
1282       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
1283  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
1284  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
1285      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
1286        are no longer updating the vertical diffusivity array
1287        (passed as argument) but are (re-) setting those arrays.
1288  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
1289    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
1290      cgrid-lsr and evp solver      cgrid-lsr and evp solver
# Line 1653  o add two new packages Line 2766  o add two new packages
2766    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2767    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2768      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2769      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2770  o add offline package  o add offline package
2771  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2772    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz

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