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revision 1.255 by heimbach, Wed Feb 18 22:34:52 2004 UTC revision 1.1187 by jmc, Wed Oct 28 17:54:44 2009 UTC
# Line 1  Line 1 
1  $Header$  $Header$
2    $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice/autodiff:
8     - add CPP flag to include clipping of zeta in EVP code;
9       although clipping of zeta is not necessary for EVP and not recommended
10       it was done by default, now clipping is disabled by default
11     - modify computation and store zetaC/Z in seaice_evp for TAF
12     - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
13     - change seaice_calc_viscosities/strainraties for better
14       vectorization after AD by TAF
15     - rearrange common blocks in SEAICE.h once again for easier dumps of
16       adjoint output, adjust adcommon.h and g_common.h
17     - change flux form of default advection scheme for better vectorization
18       of adjoint code
19     - modify lab_sea/input.lsr to test the flux form of default advection
20       scheme
21    o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
22      transition in checkpoint61r)
23    
24    checkpoint61x
25    o adjoint: adding two new verification experiments
26      * tutorial_global_biogeo: an online dic sensitivity experiment
27        (work with G. Forget)
28      * tutorial_dic_adjoffline: an offline dic sensitivity experiment
29        (an update of the Dutkiewicz et al., 2006 paper)
30      Both use the same CO2FLUX cost function, but different controls
31      Gradient checks look good, but some recomp. could still be traightened out
32      Should add xx_dic control variable to test at some point
33    o model/src:
34      add run-time parameters to check and/or mask initial Temp & Salt
35    o pkg/ptracers:
36      apply zonal filter (if used) to all passive tracers
37    
38    checkpoint61w
39    o adjoint:
40      * update and finish work on adjoint of dic package (G. Forget)
41      * start adjoint of offline package
42      * bug fix for cube-sphere TLM code (active_file_g.F)
43    o tutorial_global_oce_optim:
44      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
45      and add SIZE.h_mpi for MPI testing
46    o pkg autodiff
47     - fix bug in autodiff_restore
48     - make genmake2 remove comments and empty lines from ad_input_code.f in
49       order to reduce file size (new script file remove_comments_sed)
50    o allows to specify vertical profile of vertical viscosity (viscArNr)
51    o pkg autodiff
52      autodiff_ini_model_io: comment out writing of grid information to netcdf
53      files, because at this time the grid fields are a bunch of zeros
54      (this is analogous to ini_mnc_vars.F)
55    o pkg seaice/autodiff:
56     left-over from removing the 3-time-level fields:
57     - small rearrangement of common blocks (SEAICE.h)
58     - fix field declaration in order to get meaningful output in
59       adseaice.*.nc (adcommon.h)
60    o pkg obcs:
61     - go through NH code only if nonHydrostatic=T
62     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
63     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
64       => Update output of experiment seaice_obcs
65     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
66     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
67     - fix restart for useOBCSprescribe + useEXF
68    o pkg ctrl
69     - make obcs as control parameter work also with useSingleCPUio
70     - replace a few sny and snx by Ny and Nx to be consistent with
71       ctrl_set_globfld_x/yz.F
72    o pkg seaice
73     - re-introduce global field frWtrAtm for the case of
74       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
75     - catch the case of an empty filename in seaice_cost_init_fixed.F
76    o pkg ecco:
77     - small bug fixes in the_main_loop
78      . fix order of monitor arguments
79      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
80      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
81        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
82     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
83       imbalance diagnostics for wmean_h/sflux = 0
84     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
85     - catch the case of empty filenames in ecco_cost_init_fixed.F
86       and ecco_readparms.F
87     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
88       to make this statement meaningfull in ecco_cost_weights.F
89    o pkg zonal_filt:
90      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
91      - when using rStar, filter uVel*hFacW instead of uVel
92       (tested without topography: fix a Pb of growing instability with NLFS)
93    o pkg/aim/thsice:
94     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
95      (works as SST restoring)
96    o pkg/thsice:
97     -add specific parameter for salt restoring in slab mixed-layer
98       (by default equal to the temperature restoring)
99    
100    checkpoint61v
101    o pkg/kpp:
102     -add double diffusive contributions as a hack, turned off by default
103      for now, and the code can be excluded with a CPP-flag
104      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
105     -add a verification experiments to "vermix" to test this code
106    o pkg/mom_common:
107      Move computation of length scales to mom_init_fixed.F (avoid recomputation
108      at each time-steps*levels).
109    o pkg/layers:
110      Created a new package for computing volume fluxes in temperature or
111      [not yet implemented] density layers, e.g. for calculating residual
112      overturning circulations.
113    o pkg/diagnostics:
114      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
115    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
116    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
117      To avoid mixing type (RS/RL) of input/output array argument,
118      replace single mixed-type array with a pair from each type (RS/RL).
119    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
120      is now implemented for all pkgs (previously only done for the main pickup)
121    
122    checkpoint61u
123    o pkg/obcs:
124      - change OB?eta from _RS to _RL and put them into a separate commen block
125      - add code to read OB?eta from a file via obcs_prescribe_read: the code
126        compiles and does not destroy any other experiments, the data is read
127        properly, but the code is not tested in actual applications
128    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
129      create a meaningful unit attribute for the time coordinate variable
130    o pkg/ebm: add plenty of missing "_d 0" ;
131       update results of experiment global_ocean_ebm (fwd + adjoint tests)
132      Notes: several pieces of code only works for (very) specific set up
133       (domain size, lat range, etc ...); should be documented & stop if one
134       of those assumptions is not meet.
135    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
136       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
137          and offline_exf_seaice (seaicetd + adjoint).
138    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
139       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
140        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
141    o few changes to pass when compiling with strick checking of arguments
142       across S/R (allow to find few bugs in S/R calls).
143    o pkg/seaice:
144     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
145       2d-fields, for slightly better performance
146    
147    checkpoint61t
148    o pkg/seaice:
149     - remove unused variables in seaice_evp
150     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
151    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
152       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
153       each processor opens a different file (a fix from Matt).
154    o cg2d:
155       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
156       this reduces number of EXCH calls by 2 when using exch2.
157       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
158       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
159    o pkg/thsice:
160       add code for Near Infra-Red albedo (from Jeff)
161       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
162    o ini_model_io:
163       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
164       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
165       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
166    
167    checkpoint61s
168    o pkg/exch2 (exch2_rxN_cube*):
169       remove last BARRIER (no need to synchronise after getting data from shared
170       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
171    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
172      and generate new output (for the 2 tests) using default rotationPeriod.
173    o pkg/exch2:
174      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
175        (was already the case with AUTODIFF_EXCH2 defined)
176      - add bj in exch2 arrays and S/R.
177      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
178        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
179    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
180      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
181        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
182      - verification experiment natl_box.longstep
183    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
184      allow different versions of ifort (8 or 9) and different versions
185       of mpi (mpich or mpich2) to be used with the same optfile.
186      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
187       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
188    o pkg/seaice:
189      fix previous modif (3-level field removed) for old-pickup reading
190    
191    checkpoint61r
192    o pkg/seaice:
193     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
194      1. introduce fields for time step (N-1)
195      2. do not use levels 2 and 3 anymore (but keep them)
196      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
197         includes changes to pkg/thsice/thsice_get_velocity.F,
198         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
199         pkg/obcs/obcs_apply_uvice.F.
200     - completely remove code for leap-frog time stepping for second order
201       advection
202     - adjusted adjoint accordingly;
203       gradient checks have improved by an order of magnitude!
204    
205    checkpoint61q
206    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
207     - the boundary conditions along open boundaries are unclear, because the
208       associated masks are set to zero and are thus treated as closed when
209       applying the slip-boundary conditions.
210     - move initialisation of grid variables from seaice_init_varia to _fixed
211    o adding doc/diags_changes.txt
212    o model/src:
213      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
214       to avoid "_diags" naming if no relation to pkg/diagnostics.
215      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
216       file and only call PLOT_FIELD_XYZ if debugMode=T.
217      remove few PLOT_FIELD_XY calls outside initialisation.
218      remove few unnecessary BARRIER.
219    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
220      of salt_plume package in Southern Ocean
221    o pkg/thsice:
222     - fix hOceMxL in overlap (needed for sea-ice advection);
223       update output of experiment global_ocean.cs32x15.icedyn.
224    o pkg/seaice:
225     - make the (placeholder-)tracer IceAge a little more meaningful
226      by avoiding ridging of age due to convergent ice flow
227     - add diagnostics for surface temperature, atmospheric and oceanic
228       heat flux, and atmospheric and oceanic ice growth
229    
230    checkpoint61p
231    o eesupp (global_max & global_sum):
232     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
233     - remove starting & endding barrier (no longer needed)
234    o pkg/mdsio, writelocal:
235       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
236       (remove the STOP): uses shared buffer IO to store data from all threads
237       and then let master-thread write nThreads tiles.
238    o pkg/mdsio (read/write field):
239     - tiled IO done in 1 piece (all levels at a time);
240     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
241     - multi-threaded: allow to read/write local (non-shared) array
242       (was already working with singleCpuIO ; now works also without);
243       => no longer needs barrier call after reading a file (added inside
244       mds_read/write field).
245     - move barrier calls outside gather/scatter_2d to mds_read/write_field
246    o pkg/obcs/exf
247      - exf_getffieldrec.F: add a few ". _d 0" and
248                            add code to catch the case fldperiod = 0.  
249      - obcs_precribe_read.F: change if statements so that they match
250                              the variable type (_RL)
251      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
252        exf_iprec) as part of namelist EXF_NML_01
253    o pkg/mdsio:
254      - read/write tiled (local) files: read/write 1-level tile chunk at a time
255        (instead of segment of length sNx); expected to speed up tiled IO.
256    o pkg/exch2:
257      - take buffer copy from/to array out of S/R exch2_send/recv into new
258        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
259        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
260      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
261      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
262        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
263        including Topology header file (and common blocks).
264      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
265        remove 2nd exch call in exch2_s3d_rx (no longer needed).
266      - document S/R arg. list (+ update some comments)
267    o pkg/seaice:
268      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
269        temperature and humidity over sea ice based on climatological values.
270      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
271        of LSR (this change is expected to change the results slightly because now
272        it uses slightly difference moduli from the second last LSR solution, but
273        that is more consistent with the stress computations; this part of the code
274        is not tested in the verification experiments)
275      - fix diagnostics for flux of ice in case of B-grid
276      - turn strain rates eij and press into global fields within global
277        common block in SEAICE.h for more straighforward diagnostics
278      - fix diagnostics for principal stress components, press, zeta, eta
279        to give something meaning full
280    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
281      new output (all 4 tests) using default rotationPeriod.
282    o pkg KPP:
283      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
284      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
285        and normal grid from 1 to Nr)
286    o Fix computations of L4rdt in mom_calc_visc.F
287    o eesupp:
288      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
289      should be called before a "stop" if we know that all process are going
290      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
291    
292    checkpoint61o
293    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
294    o model/src/ini_curvilinear_grid.F:
295       compute angleSin/CosC when they are not read from a file
296    o pkg/seaice:
297       add pseudo time stepping for LSOR
298    o pkg/exch2:
299       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
300    o pkg/seaice:
301       Adding separate sea ice albedo, drag coefficients, and HO in Southern
302       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
303    o SingleCpuIO:
304       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
305    o pkg/seaice:
306       put exchanged variable in (local) common block for MPI+Multi-Threads
307       to work (necessary with exch1, and for now with exch2 too).
308    o verification: to get more experiments tested with mpi, mth and mpi+mth,
309      change tiling of:
310       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
311       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
312      update output of exp:
313       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
314       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
315      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
316                       (note: output.txt generated on faulks using only 1 tile)
317    o eesupp & mdsio (SingleCpuIO):
318     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
319       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
320       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
321     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
322     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
323       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
324    o pkg/exch2:
325     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
326       read parameter file "data.exch2" if it exists; otherwise try default regular
327       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
328     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
329       with new code (not to be used, just as a backup solution).
330     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
331       in utils/exch2/input.
332    
333    checkpoint61n
334    o eesupp & mdsio (SingleCpuIO):
335      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
336        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
337        receive real*4 array (instead of real*8) to read/write 32.bit files.
338        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
339         and remove new mapping S/R)
340    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
341      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
342        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
343        when using exch2. Add S/R to map global io-buffer to global model array.
344      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
345    
346    checkpoint61m
347    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
348      and add 3 other S/R for other types (R4,R8,RS).
349      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
350    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
351     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
352     - reduce number of macro definitions (keep only those which are used);
353       can always call directly the corrresponding S/R if needed.
354     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
355       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
356     Fixed wrong type of arg in:
357       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
358       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
359     To fix: global_sum of var in common block is wrong (multi-threaded) in:
360       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
361     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
362    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
363      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
364    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
365    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
366      edges are closed (zero depth); might happen with "blank tiles";
367      for now, disabled if using OBCS.
368    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
369      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
370    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
371      to reduce length of 1.D array print in STDOUT.
372    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
373      + use 48 tiles (16x8): this will allow to test "blank tiles".
374    o start to test MPI + multi-threaded (change testreport to skip tests
375      where number of tiles do not match).
376    o genmake2: add option "-omp" to turn on Open-MP ;
377      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
378    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
379      and keep the original tile numbering. Note: compatible with old
380      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
381    
382    checkpoint61l
383    o Overlaps had been forgotten in calculating ijk keys : fixed
384    o fix cyrus makedepend for gcc 4.4
385    o experiment fizhi-cs-aqualev20:
386      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
387      and generate new output. Note: new output is much closer to the old
388      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
389      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
390    o pkg/fizhi:
391     - change to avoid indices going deliberately over array-bounds
392     - remove unnecessary MPI stuff
393     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
394     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
395       does not go over array-bounds and therefore returns reliable output.
396     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
397       this S/R has 4 output arguments, which are used inside "get_alarm";
398       when it is called with the same variable "ndum" in place of several
399       output arguments, this produces weird side effect inside "get_alarm"
400      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
401       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
402       address) and produces error.
403    o tools/gemake2: (March 27-29 2009)
404      with option "-mpi": link *_mpi files from "MODS" dir (this is what
405      testreport does).
406    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
407    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
408       update lab_sea.lsr & lab_sea.salt_plume results
409    o pkg/seaice:
410      Major overhaul of the LSOR solver: change discretization from original
411      finite differences to finite volume. The old routine is still in the
412      file seaice_lsr.F and can be turned on with the CPP-flag
413      SEAICE_OLD_AND_BAD_DISCRETIZATION
414      Along with this change, the discretization of the strain rates is changed.
415      The same flag turns on the old discretization in seaice_calc_strainrates.F
416      All verification experiments with seaice are affected (except for
417      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
418      results by setting the above flag.
419      Further changes involve changes in defaults:
420      - ALLOW_FLOODING is defined and turned on by default
421      - SEAICEadvSnow = .true. is now the default
422      - SEAICEadvSalt = .true. is now the default
423      - SEAICEadvAge  = .true. is now the default
424      - SEAICE_clipVelocities  = .false. is now the default
425                                         (as per J. Zhang's recommendation)
426      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
427        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
428      - seaice_growth: replace computation of UG by a simple copy from wspeed
429    
430    checkpoint61k
431    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
432      seaice_lsr: fixed a few metric terms,
433                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
434                  add more debugging diagnostics
435      seaice_evp: removed superfluous many metric terms of FV discretization
436                  of stress divergence
437                  affects lab_sea, lab_sea.hb87
438      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
439                  of stress divergence for non-evp solver
440                  (this part is not tested anywhere)
441      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
442                  they were effectively only half slip
443                  affects lab_sea.hb87
444      updated all relevant verification experiments (except lab_sea//output_adm.txt
445        which was left over, but fails at level 7 & 6)
446    
447    checkpoint61j
448    o pkg/seaice: turn a few hard wired parameters into run time parameters
449    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
450      time in seconds as promised by the usints in seaice_monitor and exf_monitor
451    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
452      that are not cubed-sphere grids
453    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
454    o pkg/ctrl:
455      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
456    o non-hydrostatic (calc_gw.F):
457      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
458      update output of exp. global_ocean.cs32x15.viscA4
459    o remove backward compatibility for thetaMin,phiMin
460      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
461    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
462      interpolated wind field not only for curvilineargrid=.true., but also
463      for a rotated grid (rotateGrid=.true.)
464    o pkg/exf: add capability to bypass interpolation for runoff
465      by setting yet another CPP-flag
466    o eesupp/src, B-grid exchange:
467      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
468    o autodiff
469      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
470      allows to switch to single-prec common blocks;
471      corresponding switch occurs in tamc.h, integer isbyte
472      TAF store directivs "byte" and "kind" seem equivalent;
473      Most tamc.h have been updated correspondingly.
474    
475    checkpoint61i
476    o autodiff:
477      fix autodiff_sore/_restore indices for obcs
478      (spotted by I. Hoteit, M. Mazloff)
479    o pkg/autodiff, pkg/ctrl:
480      Add flag to reduce all tapelev I/O to single-prec.
481      In data.ctrl set
482        doSinglePrecTapelev = .TRUE.
483    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
484      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
485    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
486      real fresh water flux (not yet)
487    o pkg/mdsio & rw:
488     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
489     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
490    o pkg/flt:
491     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
492       init_fixed & ini_varia.
493     - clean-up & simplify linear interpolation S/R:
494       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
495     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
496     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
497     - add vert. coordinate & horiz. indices to output files.
498     - change vertical position in initial condition, from index to depth [m].
499     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
500       (easier to get to a curvilinear grid) ; delX,delY no longer used.
501    o pkg/ggl90: a few modifications:
502     - fix bottom boundary condition, and interpolation of KappaE
503       near top and bottom
504     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
505     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
506     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
507    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
508      (maintain temporary backward compatibility, until next checkpoint)
509    
510    checkpoint61h
511    o pkg/diagnostics with "periodic averaging diagnostics":
512      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
513    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
514    o pkg/obcs: fix loop ranges for balancing code
515    o pkg/flt:
516     - improve criteria for finding which tile owns a float.
517     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
518    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
519      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
520      with ocean biogeo)
521    o pkg/flt:
522     - do some cleaning and fix the restart ;
523     - add output.txt in flt_example/results to get this pkg tested.
524    o genmake2: add an EXTENDED_SRC option and flag.
525       for now, cannot be turned on on command line (only through genmake_local)
526    o pkg/mdsio: read/write vector:
527     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
528     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
529       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
530     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
531      (drop to 4 digits matching for grad). But this test does not look very
532      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
533    
534    checkpoint61g
535    o pkg/flt:
536      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
537       + make OPTIONS file more standard.
538      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
539      - fix _BYTESWAPIO CPP-Flag
540      - standard reading of file-parameter "data.flt"
541      - fix argument list of S/R FLT_RESTART
542      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
543    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
544    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
545      a still unfixed compiler/optimization bug
546    
547    checkpoint61f
548    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
549      update results of global_ocean.cs32x15.icedyn test.
550    o move getcon.F from model/src to pkg/fizhi.
551    o pkg/exf: add parameter for extrapolation of temp up to the surface
552       and option to prevent negative evap (in bulk_largeyeager04 only).
553    o Prather Advection scheme: fix tracer conservation for divergent flow
554      (e.g., when using NonLin Free-Surface).
555    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
556    o gmredi (Visbeck-variable-K):
557     - add more parameters to Visbeck-variable-K.
558     - use a 5 points average for dSigmaR in Visbeck-K calculation
559       (more "homogenous": same stencil and same weights as in dSigmaH)
560     - update output of ideal_2D_oce experiment.
561    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
562      (#undef REAL4_IS_SLOW)
563     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
564       coordinate variable
565     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
566       (surface forcing fields), removes some of the functionality
567     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
568     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
569       probably not all: copy _RS surface flux fields to RL field before
570       calling DIAGNOSTICS_FILL
571     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
572       real*4 (CALL EXCH_*_RS) versions.
573     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
574       (generate new output).
575    
576    checkpoint61e
577    o gmredi (Visbeck-variable-K):
578      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
579      - change computation of Visbeck-K where Slope > Smax :        
580        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
581        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
582    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
583      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
584    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
585    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
586      does not become too large (to avoid precision problems in implicit-diffusion
587      solver); update ideal_2D_oce output.
588    o pkg ggl90:
589      - in ggl90_cal.F: compute only one set of visc/diff, used to
590        step forward TKE/T/S/momentum
591      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
592        have Prandlt =1)
593    o gmredi (fm07):
594      - add lower limit on Transition layer thickness + lower limit on 1/lambda
595      - allow to set few more params from data.gmredi
596    o pkg ggl90:
597          - add missing sqrt(2) factor in computation of mixing length
598            scale in ggl90_calc.F
599            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
600    
601    checkpoint61d
602    o adjoint modifs
603      - adapt to new field rhoInSitu
604      - allow to revert from StoreDynVars2D, StoreDynVars3D
605        to individual fields
606        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
607    o store 3-D (in-situ) density in commom block (DYNVARS.h)
608     - save 1 rho computation.
609     - no longer modify T & S inland when using down_slope pkg.
610    o gad_som : allow to switch to SOM advection for T & S without corresponding
611      pickup files (using new S/R: MDS_CHECK4FILE).
612    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
613      (for useSingleCpuIO to work in multi-threaded)
614    o pkg/shelfice:
615     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
616       with SHELFICEtopoFile in data.shelfice
617     - move code for reading ice shelf topography and modifying hFacC into separate
618       subroutines of the shelfice package
619     - separate initialisation of "fixed" and "variable" variables
620     - kTopC is not (yet) replaced by kSurfC, although this is possible
621    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
622    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
623      and rename:
624      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
625      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
626    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
627    
628    checkpoint61c
629    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
630      to add mass source/sink of fluid in the interior (3-D generalisation
631      of oceanic real-fresh water flux).
632    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
633    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
634    o new pkg: down_slope
635      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
636      - presently, modify T & S inland (dwnslp_calc_rho.F).
637        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
638      - implementation for ocean in P-coords not tested.
639      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
640    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
641      (to facilitate conversion of oceanic pkg to p-coordinate).
642    o change FIND_RHO to FIND_RHO_2D :
643      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
644    o new pkg: cheapaml
645    
646    checkpoint61b
647    o exch2:
648      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
649      - no longer depend on the order sequence (N,S,E,W).
650      - 3rd exchange no longer needed (tested with 24 tiles).
651      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
652      - exch_UV_A-grid readily available (but not yet tested).
653      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
654      (both are no longer needed) in exch_uv: no effect in forward run; but
655       get truncation error differences with adjoint exch.
656    o exch2:
657     - change index-bounds storage (moved from target to local tile,
658       more intuitive this way) ; rename/remove some variables.
659     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
660    
661    checkpoint61a
662    o exch2/matlab-topology-generator:
663      fix bug in index bounds for N-S internal exchange (hard to tell if this
664      had any effect on the solution).
665    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
666      is exceeded
667    o testreport: modify syntax of awk, so that it works also with
668      awk, and not only with nawk and gawk
669    
670    checkpoint61
671    o autodiff
672      Change default for TAF usage by removing argument '-nonew_arg'
673      This changes TAF subroutine argument list (ordering of active var.)
674      Omission of this flag leads to incompatibility w.r.t. TAMC
675      To restore TAMC-compatibility, need following modifs:
676      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
677      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
678      Tested TAF version is 1.9.22
679      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
680    
681    checkpoint60
682    --->>> This is the last checkpoint for which generating the adjoint
683    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
684    --->>> by default.
685    --->>> Future checkpoints will ommit this flag by default.
686    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
687    o pkg/grdchk: Add gradient check to etan0 perturbations.
688    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
689    o pkg/autodiff: more flexibility in zeroadj.
690      model/src: modifying do_oceanic_phys.F accordingly.
691    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
692    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
693      special setup of gmredi for which the adjoint is stable
694      enough for parameter optimization.
695    o bridging the gap between eddy stress and GM.
696      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
697          along with a change in CPP option (now ALLOW_EDDYPSI).
698      -> when using GM w/ GM_AdvForm:
699          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
700          is applied either in the tracer Eq. or in momentum Eq.
701          depending on data.gmredi (intro. GM_InMomAsStress).
702      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
703      The key modifications are in model/src/taueddy_external_forcing.F
704      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
705    
706    checkpoint59r
707    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
708      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
709      fix option to read coriolis(@ cell-corner) from files with CS-grid.
710    o pkg/mnc: add some attributes to standard 1D-coordinate variables
711    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
712      mass points, when using mnc for output
713      - add runtime parameter (missing_value, missing_value_int) to override
714        default (which is the value of getcon('UNDEF'))
715    o pkg/mnc: prepare mnc for the actual use of missing values with the
716      diagnostics package: small fix in mnc_cw_readwrite.template and more
717      initialisation of never used fields
718      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
719      versions
720    o pkg/thsice/thsice_ini_vars.F added default initial values so that
721      thermodynamics sea ice solver does not blow up when some initial fields
722      are missing.
723    o move from external_forcing_surf.F to ini_forcing.F
724      the p-coord. hack consisting in using pLoad to set phi0surf ;
725      update output of tutorial_global_oce_in_p (affected @ truncation level).
726    o Freshen up a bit hs94.1x64x5, notably:
727      remove rotationPeriod and tRef=5*0. (adjoint only), and add
728      exactConserv=.TRUE.
729    o pkg/generic_advdiff:
730      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
731      applies to files where Temperature & Salinity 2nd Order moments are used.
732    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
733      this uses a dynamically allocated internal state data structure
734      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
735      and requires a fortran 90 compiler
736    
737    checkpoint59q
738    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
739       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
740    o Refresh tutorial_global_oce_biogeo, notably:
741      - change bathymetry (put back seamounts in ACC, use hFacs)
742      - change EOS (POLY3 --> JMD95Z)
743      - use Bryan-Lewis vertical diffusivity
744      - use multidimensional advection
745      - remove old virtual virtual in dic pkg, now done through ptracer pkg
746      - change a couple of parameters in dic pkg
747    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
748    o pkg/obcs: change default to OBCSfixTopo = .true.,
749      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
750      - replace "debugMode" with "debugLevel .GE. debLevB"
751    o implementation of TAF directives for gchem,cfc,dic
752    o remove "exp5" (replaced by tutorial_deep_convection).
753    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
754      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
755      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
756      --> changes results in exp4, seaice_obcs
757    o tutorial_deep_convection :
758      update the set-up and increase resolution and domain size ; start
759      from pseudo initial conditions = output at t=120mn in order to see
760      something happening when running testreport.
761    o pkg/seaice: add os7mp as an advection scheme
762                  add check for advection schemes
763                  add a flag for restoring T and S underneath sea ice
764    o pkg/my82: add netcdf-support and diagnostics
765    o thsice pkg:
766      - Now hsMax limits snow height by turning it into ice following
767        flooding scheme (and now conserving energy)
768      - Slight rewriting of the formula in thsice_calc_thick.F
769      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
770      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
771    
772    checkpoint59p
773    o gchem / dic / cfc :
774      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
775      - add new parameter files: "data.dic" & "data.cfc" ;
776      - various re-arrangement in initialisation & header file ;
777      - fix tutorial_global_oce_biogeo for multi-threaded test.
778    o pkg/dic: test for "pickup_dic" file when restarting ;
779      if no pickup-file, can restart with a re-initialised pH (same as it did
780      before) providing pickupStrictlyMatch is set to False.
781    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
782      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
783    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
784      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
785    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
786     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
787       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
788    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
789       scheme to use for vorticty-term ;
790     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
791       (with default selectVortScheme, return to original discretisation)
792     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
793    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
794    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
795      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
796      also fix diagnostics VISCAHW & VISCA4W.
797    
798    checkpoint59o
799    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
800    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
801      move a few statemens out the main loop into separate loops
802    o pkg/shelfice:
803      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
804        (kg/m^2/s), does not break tests, because in verification/isomip,
805        rhoConstFresh=rhoConst (by accident)
806      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
807      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
808        new file model/src/seawater.F, so that they are available for all pkgs.
809      - convert potential temperature into in-situ temperature. This changes the
810        isomip tests => update tests
811    o add a flag writePickupAtEnd (default=true) to be able to suppress
812      writing a pickup at the last timestep
813    o tools/mpack-1.6 :
814      - disable automake (not working) and autoconf (not needed).
815      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
816        also cleaner with much less compilation warnings.
817    o pkg/profiles:
818      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
819      (for "less than 32 characters name" compiler requirement)
820    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
821      conditions that have a different sampling frequency than S/T/U/V obcs
822    o pkg/diagnostics (stats-diags):
823      - fix global Min/Max in case 1 processor get only empty tiles
824    o genmake2: replace (4 times)
825         make genmake_tc_1.o >> genmake_warnings 2>&1
826      with
827         COMM="$CC $CFLAGS -c genmake_tc_1.c"
828         echo $COMM >> genmake_warnings
829         $COMM >> genmake_warnings 2>&1
830      to make genmake2 always see the value of CC as specified in the optfile.
831    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
832      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
833      - modify verification advect_cs test to test SOM-advection on CS-grid.
834    o pkg/ctrl:
835      - Rewrite of ctrl_map_ini_ecco.F,
836        introducing a generic routine (ctrl_map_ini_gen.F).
837      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
838    
839    checkpoint59n
840    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
841      number in dedicate array "hdiag":
842      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
843        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
844      - many small changes (integer format) for large number of diagnostics
845      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
846        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
847    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
848      usingSphericalGrid, this allows to define the rotated grid coordinates
849      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
850      geographical coordinates according to the inverse of the rotation defined
851      by the Euler angles, so that Coriolis parameter and online-interpolation by
852      exf works with the geographical coordinates on XC/YC/XG/YG.
853      Naturally, this feature does not work with all packages, so some
854      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
855      profiles), because there the coordinates are assumed to be regular
856      spherical grid coordinates.
857    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
858      - introduce isopycnal diffusion coefficient control.
859    o tools/adjoint_options:
860      - additional control vector components.
861    o pkg/mnc: have mnc create marginally meaning full coordinate variables
862      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
863    o pkg/mypackage:
864      - add example of read/write pickup for state-var ;
865      - add entry points to the main code for state-vars diags & write-pickup.
866    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
867      transitions for useExfYearlyFields
868      - add new subroutine that determines the file to read from for
869        use*YearlyFields = .TRUE. and .FALSE.
870      - add a verification experiment to global_with_exf that tests
871        useExfYearlyFields with USE_EXF_INTERPOLATION defined
872    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
873      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
874      subroutines (which could be generated from a template, because they are
875      almost identical), for now they are included in obcs_prescribe_read.F for
876      simplicity
877    o pkg/exf:
878      - add a little more diagnostic to exf_interp_read (in analogy to
879        mds_read_field, can be turned off with debugLevel < debugLevA=1)
880      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
881        ugly but fast by unrolling short inner loops, inserting a unroll=8
882        directive in routine lagran, and splitting a loop and making do while the
883        outermost loop (the latter requires the intoduction of index arrays)
884    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
885    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
886      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
887    o verification/seaice_obcs: updated for restart test and latest options
888    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
889      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
890      for now this is only available for the C-grid code and also within
891      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
892    
893    checkpoint59m
894    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
895      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
896    o gad_som : fix flux output (& diagnostics) to have same units as other  
897      advection scheme fluxes (was previously multiplied by deltaT).  
898    o added verification/seaice_obcs both to test seaice open boundaries
899      and to provide an example matlab scrpt for generating them
900    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
901    o pkg/salt_plume: clean up salt_plume_frac.F to
902      remove redundancy in PlumeMethod 1 and 4
903    o pkg/kpp: added saltplume diagnostics
904    o pkg/obcs and pkg/seaice:
905      - do not set uice and vice to zero when OB*icefile are unspecified
906      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
907      - moved seaice tracer obcs after call to seaice_growth
908    o pkg/salt_plume: added various options for salt plume depth
909      criterion and for vertical distribution of the salt
910    
911    checkpoint59l
912    o pkg/ptracers: new version of ptracers pickup:
913      read meta file and write only fields which are needed to restart.
914      ( same logic as main pickup file ; also using pickupStrictlyMatch )
915    o pkg/seaice:
916      - add timescale for melting due to warm mixed layer as a means of
917        setting SEAICE_availHeatFrac more conveniently
918      - add a CPP-flag/runtime parameter check for flooding algorithm
919      - reformulated availHeat in seaice_growth.F to be independent of AREA
920    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
921      unit changes
922    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
923    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
924      SX vector computer.
925    o pkg/seaice:
926      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
927        seaice forcing fields can now be read only through pkg/exf
928      - removed some unused halos
929    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
930    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
931      or U/VICE from U/VWIND before computing U/VSTRESS
932    
933    checkpoint59k
934    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
935      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
936    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
937      all experiments pass when compile with un-initialised var. checking option.
938    o added pkg/salt_plume
939    o script to test restart (for now, in MITgcm_contrib/jmc_script)
940    o pkg/seaice: new read/write pickup version.
941      read meta file and write only fields which are needed to restart.
942      ( same logic as main pickup file ; also using pickupStrictlyMatch )
943    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
944    o lab_sea.hb87: modify the domain & update output.hb87.txt :
945      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
946      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
947      process. Fixed here by closing the domain at the Northern boundary.
948    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
949    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
950      a set of consecutive levels in/from a 3-D array.
951    o pkg/ptracers:
952      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
953      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
954    
955    checkpoint59j
956    o in pkgs: dic, obcs, offline, rbcs:
957      standard way to compute coeff. for time interpolation between 2 time reccords
958      which retains full precision (& make results less dependent on compiler).
959      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
960    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
961      packages instead of reading ice cover and wind speed separately
962    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
963     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
964      to allow to compile customized code before the update)
965    o cleaning-up:
966      - fix CPP instruction syntax in pkg/obcs
967      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
968        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
969      - fix some threads issue in IO parts.
970    o pkg/dic:
971      - add tons of "_d 0" (--> much better testreports !)
972       and then update outputs of tutorial_global_oce_biogeo
973    o pkg/mom_fluxform:
974      add a special version of momentum advection intended to conserve momentum
975      next to a bathymetry step or a coastline edge. (default = off = #undef)
976    o new read/write pickup version:
977      - for now, only implemented for main (mdsio) pickup file.
978      - write out only what is needed to restart; merge pickup_nh , pickup_ph
979        and main pickup together.
980      - read meta file; read only what is needed to restart; stop if a field
981        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
982        if it make sense (even if the restart is not perfect).
983      - if no meta file, assume that pickup to read corresponds exactly to
984        a pickup that would currently be written.
985      - read pickup written in the old format (until checkpoint59i) if it
986        recognizes an old meta file (no field-list).
987      - add a meta file in exp. which starts from a pickup: 2 cases:
988        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
989         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
990        b) a meta file describing the content of the associated pickup file
991         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
992    o pkg/mdsio & pkg/rw:
993      - new routine to read a meta file ; new set of routine to read
994        Multiple-fields file (with meta file).
995    o added open boundary conditions capability for seaice
996        HSNOW, HSALT, UICE, and VICE
997    
998    checkpoint59i
999    o adjoint:
1000      * fix multiDimAdvection adjoint
1001        (partial recomputation problem by TAF for fVerT(:,:,kDown)
1002        and comlev1 size definition (maxpass vs. max. number of tracers)
1003      * verification/global_ocean.90x45x15 adjoint now tests
1004        NLFS and multiDimAdvection using DST3 (=30)
1005      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
1006    o pkg/kpp: add "_d 0" to real constant (if missing);
1007      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
1008      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
1009    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
1010      for internal parameters related to restart process (formerly from PARAMS.h)
1011      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
1012    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
1013      as argument. (only atm2d & obcs write_pickup have not yet been updated)
1014    o pkg/monitor:
1015      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
1016      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
1017      - account for deep Atmosphere factor and density factor (anelastic)
1018    o added open boundary conditions capability for seaice HEFF and AREA
1019    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
1020      thermodynamics
1021      - requires a little reorganization, which affects the testreport results
1022        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
1023        so that now the conservative form is tested
1024      - add a few comments
1025    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
1026    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
1027    o add new diagnostics to seaice: advective, diffusive fluxes (only for
1028      multidim-advection, for scheme 2 they are not filled) and transports,
1029      thermodynamic growth rates
1030    o change units of EmPmR (inside the code, + within coupling interface)
1031      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
1032      Affects results @ truncation level (cg2d match) and update output of
1033       experiments: lab_sea(6), global_ocean.90x40x15(10),
1034      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
1035      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
1036      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
1037      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
1038    
1039    checkpoint59h
1040    o pkg/exf:
1041      - improve vectorization by moving if-statement out of loops in
1042        exf_mapfields, exf_radiation
1043      - exf_bulkformulae.F: introduce 2D fields and vectorize code
1044    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
1045    o testreport:
1046      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
1047        monitor & update offline_exf_seaice exp. output.
1048      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
1049    o pkg/seaice:
1050      - bug fix in the evp solver: boundary conditions were affected be
1051        masking of zMax/zMin (changes results)
1052      - minor bug fix in boundary conditions in seaice_calc_strainrates
1053        (changes results for no_slip)
1054      - seaice_lsr.F: make interpolation of eta dependent on boundaries
1055      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
1056      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
1057        stress formulation and no-slip boundary conditions
1058    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
1059      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
1060    o pkg/seaice: a first HSALT time stepping equation has been checked in
1061    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
1062      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
1063      without requiring DO-IF statements
1064    o pkg/thsice:
1065      use continuous power-law function for partition of energy between lateral
1066      melting/freezing and thinning/thickening ; old code using step function
1067      still available with #undef THSICE_FRACEN_POWERLAW
1068      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
1069    o testreport: change AD testing : check against results/output_adm.txt
1070      using same scripts as for forward test.
1071    
1072    checkpoint59g
1073    o adjoint testing: in preparation for changing testreport:
1074      - output format: cost and grad written on separated lines
1075      - ad output results in directory "results" (instead of "results_ad")
1076    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
1077    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
1078    o pkg/ecco: allow user defined cost function contributions
1079    o testreport:
1080      Allow to choose (per experiment) the list of tested output variables
1081       and the main variable (used to issue a pass/FAIL ) ;
1082      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
1083      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
1084      Also modify printing of summary:
1085       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
1086       b) echo the list of tested variables in the individual summary.txt of
1087          each experiment.
1088    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
1089      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
1090      (but still depend on the tile decompostion of the domain).
1091    o pkg/seaice: change a discretization detail to make the B-grid code
1092      "more symmetric". This change is likely to remove all "ridges/leads" that
1093      where quasi-aligned with the grid in B-grid solutions. It may also be
1094      the solution to the stress coupling issues with the B-grid.
1095    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
1096      remove .cvsignore from input dir. (since testreport no longer run here).
1097    o pkg/thsice:
1098     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
1099     - fix reshaping of sea-ice just after advection:
1100       melt all the ice only if ice-volume is too small.
1101     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
1102       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
1103     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
1104    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
1105      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
1106    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
1107      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
1108      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
1109      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
1110      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
1111      -> update output.txt
1112    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
1113     this affects truncation error: -> update output.txt of exp:
1114      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
1115      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
1116    
1117    checkpoint59f
1118    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
1119    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
1120      a bounded range (in forward mode)
1121    o pkg/ecco, ctrl, autodiff and mom_common:
1122     internal parameter controls, completements of implementations
1123    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
1124    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
1125      (not seem any difference in testing results).
1126    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
1127       at face corners.
1128    o pkg/generic_advdiff:
1129     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
1130      loop range indices for computing vertical advection tendency
1131      and do the calculation in the interior only (no overlap) ;
1132      for now, only implemented for SOM advection (to save CPU time).
1133     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
1134    o exch2 adjoint
1135      First set of changes:
1136      - add exch2 hand-written adjoint templates
1137      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
1138        This will require cleanup in pkg/autodiff/*.F
1139        (changed routines currently kept separate in verif. code/)
1140      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
1141        that used to hide exch2 or cubed-sphere specific code
1142        (commented via 'cph-exch2')
1143    o pkg/seaice
1144      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
1145    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
1146       output of global_ocean.cs32x15.thsice .
1147    
1148    checkpoint59e
1149    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
1150      for B-grid vector (not yet tested) and C-grid vector (<- only used
1151      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
1152    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
1153      (#ifdef ALLOW_SALT_PLUME)
1154    o gather_2d/scatter_2d: removed halo regions
1155    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
1156      scheme and the corresponding test case (under front_relax dir). For now,
1157      only available with Skew-flux form and not yet tested in realistic set-up.
1158      adjoint: store directives updated, but gradient checks deteriorated,
1159      so maybe GM/Redi adjoint is now broken.
1160    o seaice adjoint
1161      * add AREA, HEFF, HSNOW as control variable
1162        (should not change lab_sea results)
1163      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
1164    o pkg/seaice:
1165      * added computation of saltFlux in seaice_growth;
1166        For time being, sea ice salinity is assumed constant
1167        contribution of snow flooding to freshening of sea ice is neglected.
1168        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
1169        defaults to 0.0 in order to maintain backward compatibility.
1170        Typical values for SEAICE_salinity are 4 to 10 g/kg.
1171      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
1172      * added SEAICE_availHeatFrac, which specifies fraction of surface level
1173        heat content used to melt or grow ice
1174      * commented out cap of HICE: it helps keep ice thinner
1175      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
1176      * applied OBCS T/S mask to HEFFM sea ice mask
1177    
1178    checkpoint59d
1179    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
1180     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
1181     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
1182    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
1183     and change default value of parameter "GM_Small_Number";
1184     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
1185       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
1186       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
1187    o pkg/ecco: cost function when applying pkg/smooth to controls
1188    o pkg/ctrl: add forcingPrecond run time parameter
1189    o pkg/seaice:
1190     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
1191     - fix bug in metric terms of u-equation in LSR solver (implicit part),
1192       changes verification/lab_sea
1193     - rearrange implicit part of u-equation in LSR solver to make it easier to
1194       read, understand, and debug. This causes changes at the truncation level.
1195     - fix (serious) bug in the boundary conditions (sign error in the implicit
1196       part) of the LSR solver. Changes all LSR results.
1197     - fixed problem with HSNOW initialization to avoid thick snow when AREA
1198       is initilized with small values - does not change lab_sea results.
1199     - added HsnowFile initialization capability
1200    o pkg/smooth: addition to model/src and pkg/ctrl so allow
1201     initialization of pkg/smooth and application to control vector
1202    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
1203    o dependencies: pkg/profiles requires pkg/cal
1204    o pkg/profiles:
1205     - added option ALLOW_PROFILES_GENERICGRID
1206         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
1207         that interpolation information (grid points and coefficients) is provided
1208         within the netcdf input files.
1209         -> sample matlab scripts can be found in MITgcm_contrib/gael
1210         that allow you to prepare netcdf input files.
1211     - also modified: cleaner include statements, cleaner error print statements,
1212       cleaner stops when error, and more tests of the netcdf input files consistency.
1213    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
1214    o pkg/seaice:
1215     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
1216       requires a new routine: seaice_diagnostics_fill.F
1217     - make sure that seaice does not move if not forced (pressure replacement
1218       method, Hibler and Ip, 1995), changes results
1219     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
1220     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
1221       It is turned off by default (=-1.), because it changes the results.
1222     - make it possible to read AREA from a file, too.
1223    
1224    checkpoint59c
1225    o add S/R and diagnostics for oceanic mixed-layer depth
1226    o move GMRedi call after all vertical mixing schemes (including KPP)
1227    o pkg/thsice:
1228     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
1229      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
1230    o pkg/obcs:
1231     - bug fix for balance code
1232    o pkg/seaice:
1233      - allow values of SEAICE_elasticParm > 1
1234      - add new parameter SEAICE_evpTauRelax as an alternative
1235        to SEAICE_elasticParm
1236      - make lsr boundary conditions free slip (by default), changes result
1237      - add code for no slip boundary conditions for lsr
1238      - set minimum of zeta to zero (and not 4e8) (changes results)
1239      - add a cap on AREA after advecting AREA if seaice_growth is not called
1240    o change calculation of Visbeck K:
1241      - no longer depend on tapering scheme; instead, compute slope (limited
1242        by GM_maxSlope). this is equivalent to what was comuted before with
1243        clipping or linear tappering.
1244      - fix vertical averaging (wrong by 1/2 level)
1245      - leave the old version (but will not be maintained) within
1246        #ifdef OLD_VISBECK_CALC / #endif
1247      - update output of exp. ideal_2D_oce
1248    o change error catch in calc_r_star to improve vectorization
1249    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
1250      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
1251    o adjoint:
1252      Re-organized adjoint checkpointing according to Matt Mazloff
1253      (but with modifs/completions/cleanups)
1254      Storing is now bundled into large arrays to optimized I/O
1255      (and second step in cleanup of the_main_loop)
1256    
1257    checkpoint59b
1258    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
1259      - export/import (between ocean & coupler) fields needed for ocean DIC.
1260    o pkg/seaice:
1261      - get rid of three more exchanges seaice_calc_viscosities (required
1262        different loop boundaries in seaice_lsr and seaice_ocean_stress)
1263      - bug fix in seaice_ocean_stress (update of lab_sea required)
1264      - reduce loop boundaries to necessary minimum also in seaice_evp
1265      - go back to the old way of computing deltaC/Z as the adjoint likes that
1266        better
1267    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
1268      passive tracer to an Age Tracer) + update output.txt
1269    o pkg/exf:
1270      - implement A-grid / C-grid selection for wind-stress input files.
1271      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
1272      for now, in exf_bulk_largeyeager04.F only :
1273      - change implementation for case where windspeed + 2. components wind-stress
1274        are read-in. AND use rhoConstFresh to convert evap.
1275    o pkg/seaice:
1276      - use correct EXCH_UV for wind-forcing (on A-grid).
1277      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
1278        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
1279    o pkg/exf:
1280      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
1281      EXF_INTERPOLATION:
1282      - merge global_with_exf/code version of exf_interp_read.F
1283        to the main code ;
1284      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
1285        reading the file ; Important: This options needs to be defined to recover
1286        previous code.
1287        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
1288      - no longer loose real*8 precision along the way when using exf_iprec=64.
1289    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
1290      - change discretisation of evp-solver in order to avoid another exchange
1291        (changes lab_sea) and clean up a little
1292      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
1293        help the adjoint (this also changes the results slightly)
1294      - add a few "_d 0" where they had been missing in seaice_evp.F
1295      - cleaning up: remove unused seaice_calc_rhs.F
1296    o pkg/exf: some cleaning-up:
1297      - change various "constants" into runtime parameters
1298      - cleaned-up Large&Yeager04 routine which should eventually
1299        replace exf_bulkformulae.F (changed names of S/R and CPP)
1300        and merged various ALLOW_ATM_WIND options
1301     only used with thsice pkg (in thsice_get_exf.F):
1302      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
1303        which are used when useStabilityFct_overIce=TRUE (= the default)
1304      - change default values of ice & snow emissivity and scale downward LW
1305        by ice & snow emissivity.
1306    o pkg/thsice:
1307     fix few little problems, in thsice_calc_thickn.F:
1308      - growth vertically (and not laterally) if iceFrac == iceMaskMax
1309      - melt only laterally if hIce < hThinIce (as the comments say)
1310      and in thsice_extend.F:
1311      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
1312      - start to form ice as soon as the minimum ice-volume is reachable.
1313     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
1314      and cpl_aim+ocn
1315    o pkg/kpp
1316     - move computation of surface related input fields to KPP into a new
1317       subroutine kpp_forcing_surf.F
1318     - remove wrong (within bi,bj loops) EXCH calls.
1319     - little cleaning (add argument myThid in last position, cvs header ...)
1320     - for now, fix conservation problem by exchanging KPPviscAz (may not
1321       be the best fix)
1322    o pkg/seaice
1323     - check for inconsistent evp parameter/cpp-flag combination
1324     - remove leftover errIO flat for obsolete name list error handling
1325    o OpenAD
1326     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
1327    
1328    checkpoint59a
1329    o pkg/seaice: some parameter clarifications and a little bit of clean up
1330    o pkg/thsice: rename run-time parameters:
1331       himin       -> hIceMin
1332       himin0      -> hThinIce
1333       hihig       -> hThickIce
1334       i0          -> i0swFrac
1335       transCoef   -> bMeltCoef
1336       frac_energy -> fracMelting
1337      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
1338       with default values (for now) that do not change the results.
1339      remove old version of thsice vars advection in pkg/seaice.
1340    o in FFIELDS.h:
1341      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
1342      - make pLoad & sIceLoad always available (but still only used if
1343         ATMOSPHERIC_LOADING is #define).
1344    o pkg/kpp: replaced _KPP_RL with _RL
1345    o bug fixes for vertical diffusivity computations when both KPP and
1346        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
1347        are no longer updating the vertical diffusivity array
1348        (passed as argument) but are (re-) setting those arrays.
1349    o pkg/seaice: fix bug in evp solver, while doing that
1350      - change (improve?) discretization of stress computations for both
1351        cgrid-lsr and evp solver
1352      - add a new routine to compute strain rates
1353      - the above changes lab_sea results
1354      - add no slip conditions for evp solver (off by default), lsr-version
1355        may follow
1356      - fix exchange for shear at Z-points (does not change lab_sea)
1357      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
1358        (to force the user to pick a time step since there is not "safe" way
1359        of choosing it)
1360      - add principal stress diagnostics
1361      - rearrange fields for evp a little to avoid having to call a: too many
1362        exchanges and b: exchanges for stress trensor components which we do
1363        not have.
1364      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
1365        of evp, complete rewrite for lsr case (latter is does not yet work
1366        in all cases)
1367    o pkg/kpp: add code to have mixing in shelf ice caverns
1368      - add myThid to all kpp routines (long overdue)
1369    
1370    checkpoint59
1371    o pkg/exf:
1372      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
1373        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
1374      - move exf header files from lower_case.h to UPPER_CASE.h ;
1375        add missing cvs Header & Name
1376      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
1377      - add namelist param. selectStressGridPosition, exf_monFreq
1378      - retire many _CLIM routines, and remove data.exf_clim
1379        + params moved to data.exf
1380        + climsst, climsss now handled by exf_set_gen, i.e.
1381          climss?period=0 refers to constant field,
1382          climss?period=-12 to monthly forcing
1383      - split up namelists in data.exf
1384    o pkg/seaice:
1385      - remove seaice_exch and seaice_exch_uv
1386      - remove superfluous exchange of theta
1387      - add myThid to seaice_budget_ocean/ice
1388      - add new interface for atmospheric wind forcing (C-grid only)
1389        + new routine
1390        + two new field (taux, tauy for stress over ice)
1391        + removed one global field (DAIRN) for C-grid case only
1392    o pkg/thsise
1393      - 2nd set of modifs for thsice adjoint in conjunction with exf
1394    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
1395    
1396    checkpoint58y_post
1397    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
1398      vertical diffusivity, similar to that in MOM4; turned on using
1399      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
1400      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
1401    o Added capability for 3D specification of background vertical diffusion
1402      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
1403      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
1404      "data" file that contains the 3D vertical diffusivity coefficients.
1405    o ice dynamics (pkg/seaice) with thsice thermodynamics:
1406      - add code within pkg thsice to advect & diffuse sea-ice fields
1407      similar to (and will replace) what has been added in  seaice_advdiff.F,
1408      but: - conserving Mass, Heat & Salt.
1409           - better when using non-linear advection scheme (not yet fully tested)
1410           - can also be used in atmospheric set-up (for now, only the diffusion).
1411    
1412    checkpoint58x_post
1413    o IO option for global-file compact format:
1414      - add options when generating topology (utils/exch2/matlab-topology-generator)
1415      - add I/O capability (pkg/mdsio).
1416      - adapt utils/matlab/rdmds.m to read this format.
1417      for now long-line format not yet supported by pkg/mdsio (& exch2).
1418    o shelfice: add a few diagnostics
1419    
1420    checkpoint58w_post
1421    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
1422      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
1423      (and replace horiVertRatio in NH code).
1424      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
1425                         and tutorial_plume_on_slope (sensitive to truncation)
1426    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
1427      directly to drive seaice model (C-grid only)
1428    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
1429     - reintroduce computation of wind from stress,
1430     - compute tau (in exf_bulkformulae.F) from windstress averaged to
1431       mass points to avoid tau = 0
1432     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
1433    o rdmnc.m: make it work with "global" files created with gluemnc
1434    o rdmnc.m : some improvements in dealing with singleton dimension
1435      (tested on all testreport mnc output files).
1436    o genmake2: disable pkg/profiles if netcdf test fails.
1437    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
1438    o move call to cal_readparms up to make calendar parameters/variable available
1439      to all packages
1440    
1441    checkpoint58v_post
1442    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
1443      useDynP_inEos_Zc tested.
1444    o pkg/exf: changes to properly interpolate/mask/scale initial fields
1445    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
1446      and portions thereof.  See read_cs.txt for description and examples.
1447    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
1448      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
1449      following the great-circle arc between those 2 points.
1450    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
1451      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
1452    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
1453     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
1454     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
1455     - still needs work (not working with some options ; efficiency to improve)
1456       and serious testing.
1457     - use this scheme for temperature & salinity in 2 advection test exp.:
1458       advect_xy & advect_xz, respectively.
1459    
1460    checkpoint58u_post
1461    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
1462    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
1463    o testreport: add option "-skipdir" to skip some test.
1464    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
1465      momentum calculation.
1466    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
1467    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
1468      remove checkpoint.F and the_correction_step.F (no longer used);
1469      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
1470    o add option (linFSConserveTr) to correct for tracer source/sink due to
1471      Linear Free surface
1472    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
1473    o pkg/thsice: fix reading mnc-pickups
1474    
1475    checkpoint58t_post
1476    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
1477    o pkg/mdsio:
1478     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
1479       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
1480       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
1481     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
1482     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
1483       either MDS_READ_FIELD or MDS_WRITE_FIELD )
1484     - new S/R (to replace MDSWRITEMETA), which allows to write more
1485       informations (variable names, time ...) to meta files.
1486     - modify rdmds.m to give back the meta file content.
1487    o pkg/diagnostics: change vertical interpolation to be safer, and more
1488       flexible (define p-levels to interpolate to in data.diagnostics);
1489      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
1490       diagnostic pointer.
1491    o pkg/seaice: more cleaning up of seaice_growth, added many comments
1492    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
1493    o fix multi-category seaice:
1494     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
1495       SEAICE_MULTICATEGORY
1496     - fix short wave heat flux
1497    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
1498       and allow to use EVP solver. Change forward lab_sea: test both EVP
1499       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
1500    o Initial check-in of lab_sea adjoint
1501      (very similar to natl_box_adjoint/code_seaice)
1502      * used C-grid and EVP solver
1503      * used KPP, GM/Redi
1504      * uses inAdExact=.TRUE.
1505      * gradient checks fail for both ADM and TLM
1506        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
1507        f.d. gradients actually seem more problematic than ADM, TLM gradients;
1508        issue is related to forward mismatch between g77 an ifort
1509    o pkg/seaice: overhaul of thermodynamics
1510     - growth.F and groatb.F are replaced by new routine seaice_growth.F
1511     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
1512     - move a few global fields out of SEAICE.h into seaice_growth.F and
1513       make them 2D (FICE/QNETO/ ...)
1514     - remove FO (it is the same as QNETO)
1515     - introduce a few local fields to avoid modifying external fields such
1516       as atemp, etc.
1517    
1518    checkpoint58s_post
1519    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
1520      changed exf_set_gen.F so that
1521        genperiod=0 means input file is one time-constant field and
1522        genperiod=-12 means input file contains 12 monthly means
1523    o CG2D: use pre-computed solver main-diagonal (stored in common block);
1524      this affects truncation error ; generate new output file for exp. which
1525      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
1526        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
1527        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
1528        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
1529        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
1530        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
1531    o start implementation of deep-atmosphere and anelastic formulation
1532    o verification: remove 2nd copy of input files and use script "prepare_run"
1533      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
1534    o mom_common/vecinv/fluxform: fix a few initialisation isssues
1535    o profiles: fix for multithreaded case
1536    
1537    o diagnostics: rename few diags:
1538      s/'PRESSURE'/'RCENTER '/g
1539      s/'TICE    '/'oceFreez'/g
1540      s/'TAUX    '/'oceTAUX '/g
1541      s/'TAUY    '/'oceTAUY '/g
1542      s/'SWFLUX  '/'oceQsw  '/g
1543      s/DIFx/DFxE/g
1544      s/DIFy/DFyE/g
1545      and add few ocean-forcing diagnostics:
1546      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
1547    o modifications to pkg/seaice/growth.F and budget.F, which change results of
1548      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
1549      as actual snow thickness.  It now refers everywhere to effective snow
1550      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
1551    
1552    checkpoint58r_post
1553    o modifications to pkg/seaice/growth.F, which change results of
1554      lab_sea experiment: fixes pertain to melting snow over open water, to
1555      masking EVAP under sea ice, and to using the correct AREA variable for
1556      computations of EVAP, PRECIP, HSNOW, and GHEFF
1557    o add ability to read bathy, salt, and theta using MNC (off by def)
1558    o add flooding algorithm and advection of HSNOW for pkg/seaice;
1559      both are turned off by default and do no change any results
1560    o seaice advection with pkg/thsice: a step toward the use of non-linear
1561      advection scheme, but #ifdef or commented out for now (requires more EXCH).
1562    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
1563      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
1564      in natl_box (affects results @ truncation level: update output.txt)
1565    o multi-threading and IO:
1566      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
1567      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
1568        (needed to work with SingleCpuIO): tested in all verif. exp.
1569    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
1570      affects the results (but none of the verification test uses this scheme).
1571    o Adding some pkg/diagnostics capability to pkg/seaice
1572      (will certainly be subject to changes)
1573    o ctrl: adding new control variables:
1574      lwflux, lwdown, evap, snowprecip, apressure, runoff
1575    
1576    checkpoint58q_post
1577    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
1578      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
1579      high_res_cube configuration by 4% on Columbia.
1580    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
1581      add (in global_with_exf/code) a version of EXF_INTERP_READ without
1582      dynamical allocation (seems to work in multi-threaded).
1583    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
1584      single CPU io) so that TAF does not have to see EESUPPORT.h
1585    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
1586    
1587    checkpoint58p_post
1588    o obcs: stop if obcs is used with useCDscheme = .true.
1589    o shelfice:
1590     - fix a sign error so that no slip at shelfice interface works
1591     - remove stop for combination non-hydrostatic code and shelfice. That does
1592       not mean, that the results are correct, but at least they are numerically
1593       stable
1594    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
1595    o added adjoint exch routined for all exch*3d* routines
1596      and updated flow directives
1597    
1598    checkpoint58o_post
1599    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
1600      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
1601    o change controling S/R for writing pickup file (new S/R do_write_pickup)
1602      and clean-up reading/writing of pickup files.
1603    o fix local version of read/write pickup (NH part) in rotating_tank/code
1604    o simplify EXCH interface:
1605     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
1606     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
1607    o added the regrid package
1608    o shelfice:
1609     - add a simple boundary layer scheme to reduce noise
1610     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
1611    
1612    checkpoint58n_post
1613    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
1614       local variable (not in common block).
1615    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
1616      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
1617      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
1618        to work with SingleCpuIO.
1619    o add "_d 0" to real constant of pkg/cfc subroutines ;
1620       update exp. cfc_exemple & tutorial_cfc_offline output files.
1621    o multi-threading and IO:
1622      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
1623        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
1624      - barrier before and after reading.
1625      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
1626      - avoid using MDS_WRITELOCAL for LAND pkg output.
1627      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
1628        common-block variables ; Allows multi-threading with master-thread IO.
1629    o change default MAX_NO_THREADS from 32 to 4 ;
1630      and stop cleanly when MAX_NO_THREADS is too small.
1631    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
1632    
1633    checkpoint58m_post
1634    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
1635       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
1636    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
1637       keep global_ocean.90x40x15 (for AD testing) with former secondary test
1638       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
1639    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
1640        add MITgcm_tutorials (= code + all the tutorials)
1641    o ecco, option to compute cost for total ssh (mean+anom)
1642    o consistent with addition of ptracer and ssh in pkg/profiles
1643    o profiles: adding ptracer and ssh
1644    o testreport: change multi-test output-file name
1645      (from output.txt.{name} to output.{name}.txt)
1646    o profiles: now ok for mutli-tiles case
1647    o seaice: add 4 parameters for different advection schemes for area,
1648      (effective) seaice thickness, enthalphy, and snow height. Their default
1649      is the standard parameter SEAICEadvScheme
1650    o calc_gw:
1651     - add cosFacU in zonal viscous flux (harmonic.visc.).
1652     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
1653       of tutorial_plume_on_slope.
1654    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
1655    o calc_gw: true flux-form, account for horizontal grid spacing.
1656      update rotating_tank results, but not plume_on_slope (affected at
1657      truncation level, 11 digits).
1658    
1659    checkpoint58l_post
1660    o calc_gw:
1661     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
1662     - remove side-drag for now (need to fix it); update plume_on_slope results.
1663     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
1664    o commit code to make SST/SSS weights spatially variable
1665      (based on either variable in-situ or variable initial T/S weights)
1666    o pkg/ecco:
1667      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
1668        now based on horizontally varying weights wthetaLev, wsaltLev
1669      * cost_averagesflags now returns year indices in addition to day, month
1670      * sflux balance is performed on annual basis
1671        (sflxumm, sfluxmm2, bal_sfluxmm)
1672      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
1673        including separate counting and multipliers
1674    o pkg/rbcs
1675      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
1676    
1677    checkpoint58k_post
1678    o testreport:
1679     - always build in dir. "build" (if not there, mkdir build instead of building
1680       & running in input)
1681     - run in dir run (if it exists), in build otherwise.
1682     - call prepare_run (if input/prepare_run exists)
1683     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
1684    o pkg/exf modifications to interpolation and rotation routines for more
1685       reasonable treatment of North Pole singularity: for tracers North Pole
1686       value is set to northernmost zonal-mean value, for zonal velocity it is
1687       set to zero, and for meridional velocity it is set to northernmost value.
1688    o pkg/exf/exf_check_range.F
1689     - add tile index to diagnostics and move stop statement to the very
1690       end of the routine.
1691    o pkg/diagnostics: (diagnostics_main_init.F)
1692      define title of isomorphic variables according to the current config.
1693    o pkg/thsice with pkg/seaice dynamics:
1694    - fix domain of computation (interior only, required for exf) and do exchanges
1695    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
1696    o towards a standard way of dealing with multi-threading in MONITOR
1697      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
1698    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
1699       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
1700    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
1701    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
1702    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
1703       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
1704    o tracer advection:
1705     - clean-up and simplify calc_common_factors.F
1706     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
1707       advection subroutine (but still not used within DST advection S/R)
1708    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
1709    
1710    checkpoint58j_post
1711    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
1712      from file (collects calls previously in FORWARD_STEP)
1713    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
1714    o adjoint store dir. adjusted accordingly
1715    o genmake2
1716      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
1717    
1718    checkpoint58i_post
1719    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
1720      on wind stress (SEAICEstressFactor defaults to 1.)
1721    o Total number of Timers is finite (<=40): comment out 2 non-essential one
1722      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
1723    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
1724      on CS-grid: no longer loosing mass.
1725    o exf & curvilinear-grid: no longer modify longitude xC & xG.
1726    o pkg/ggl90: fix sloppy output and fix a bug
1727    o pkg/seaice: added SEAICEuseEVPpickup parameter
1728      - Set to false in order to start EVP solver with
1729        non-EVP pickup files when using SEAICEuseEVP
1730      - fix sign error in diffusion in seaice_calc_rhs
1731    
1732    checkpoint58h_post
1733    * Modifications for bottom topography control
1734      o replace hFacC by _hFacC at various places
1735      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
1736      o add non-self-adjoint cg2d_nsa
1737      o update autodiff support routines
1738      o re-initialise hfac after ctrl_depth_ini
1739      o works for 5x5 box, doesnt work for global_ocean.90x40x15
1740    * Adding verification for 5x5 box (4-layer) bottom topography control
1741    
1742    checkpoint58g_post
1743    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
1744       used for mean seasonal cycle, mean diurnal cycle); add an example
1745       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
1746    o pkg/ggl90:
1747      - add parameter (minimum surface kinetic energy)
1748      - fix bug (avoiding division by zero)
1749    o couple pkg/thsice to pkg/seaice:
1750      - modify advection in seaice to accomodate new scalar fields to be advected
1751      - only muliDimAdection scheme work with seaice/thsice
1752      - mapping of thsice-variables to seaice-variables, back and forth
1753      - does not break the verification experiments, but does not give the
1754        desired results either
1755    o pkg/seaice
1756      - make (default) second order advection a bit less confusing?
1757    
1758    checkpoint58f_post
1759    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
1760      to pkg/seaice):
1761      - new routines thsice_map_exf and thsice_get_exf provide the interface
1762      - add an additional formal parameter to thsice_solve4temp
1763    o pkg/exf:
1764      - add new fields wspeed, snowprecip (to be able to couple to thsice)
1765      - correct Stefan-Boltzmann constant
1766      - new parameter for longwave surface emittance
1767      - separate some stuff from exf_bulkformulae into new routines  
1768        exf_radiation, exf_wind
1769      - add new parameters and constants: longwave emissivity for ocean, ice
1770        and snow, evaporation parameters over ice
1771      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
1772        either wind from stress or stress from wind
1773    o pkg/thSIce:
1774    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
1775    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
1776       and THSICE_CALC_THICKN
1777    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
1778    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
1779      to make debugging easier.
1780    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
1781    o pkg/bulk_force:
1782      - clean-up comments and parameters ;
1783      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
1784    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
1785      generate new output for test-experiment: aim.5l_cs.thSI
1786    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
1787      testreport accordingly
1788    
1789    checkpoint58e_post
1790    o SEAICE_CGRID adjoint done
1791    o R_STAR adjoint implemented.
1792      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
1793      * need to sort out init. of h0facc, etc.
1794    o Make pkg/profile fully independent of ecco,cost, etc. stuff
1795      to be able to use it in pure forward.
1796    
1797    checkpoint58d_post
1798    o upgrade simple test-experiment to tutorial example:
1799     step.1: duplicate the experiment and (step.2) will remove the old copy.
1800      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
1801      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
1802      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
1803      tutorial_global_oce_biogeo    <- copy of dic_example
1804      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
1805      tutorial_plume_on_slope       <- copy of plume_on_slope
1806      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
1807      tutorial_global_oce_optim     <- empty for now (David ?)
1808      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
1809     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
1810    o correct a sign problem in cost_scat.F
1811    o obcs and ptracers: fix boundary conditions for advections schemes
1812      with larger stencil
1813    o thsice adjoint: start
1814    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
1815      completeness
1816    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
1817      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
1818    o ptracers adjoint:
1819      * avoid extensive recomputatations
1820      * fix missing re-init. of gptr (missed by TAF)
1821    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
1822      me to turn off the excessive output to STDOUT that this package produces
1823    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
1824      and add those terms in Vector-Invariant formulation.
1825    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
1826      if the control period (xx_hfluxperiod etc) is 0
1827    o in profiles pkg, clean routines and fix details
1828    o in ecco pkg, reading ssh data:
1829      fix problem in case the model does not start at iter0=0
1830    o fix mnc-pickup/restart for ptracers
1831    o new package prifiles:
1832      code to compute profile-based cost by Gael Forget
1833      (modifs in ecco, ctrl, autodiff)
1834    o Benign bug fix in initialization (spotted by M. Mazloff) of
1835      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
1836    
1837    checkpoint58c_post
1838    o adjoint: finish NLFS adjoint and provide reference output in
1839      verification/global_ocean.90x40x15/results_ad_nlfs
1840    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
1841      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
1842      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
1843      with SEAICE_CGRID defined.
1844    o move calendarDumps from "data" to "data.cal" and clean-up the code
1845      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
1846    o add useEXF & useCAL flags (for now, set in hard-coded way)
1847    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
1848      (were missing in NH mode, and wrong in quasihydrostatic mode).
1849      waiting for Chris updated version of calc_gw to add those CALLs.
1850    o fix bug in quasihydrostatic S/R ;
1851      add a test for this option: global_ocean.90x40x15.qshyd
1852    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
1853      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
1854    o add on/off flag useOffLine for package OFFLINE
1855    o seaice:
1856      - modify advection so that it works also on the C-grid
1857      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
1858        problem in multi-tile runs with C-grid
1859      - add flags for clipping ice velocities and/or masking solver forcing
1860      - fix drag (ocean on ice) formulation and a bug that caused noise in the
1861        C-grid solver
1862      - added a few comments to seaice_diffusion.F
1863      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
1864        are now exclusive)
1865      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
1866        required re-ordering the code a little:
1867       + make DAIRN global variable (defined in SEAICE)
1868       + move computation of the viscosities eta and zeta into a new separate
1869         routine (because I need to recompute them in seaice_ocean_stress.F)
1870    
1871    checkpoint58b_post
1872    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
1873      update output.txt of exp. aim.5l_cs.thSI
1874    o various mnc cleanups and improvements:
1875      + shrink lookup tables by factor of ~4
1876      + better error reporting when running out of lookup space
1877      + able to handle longer path/file names (up to 500 chars)
1878    o adjoint:
1879      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
1880      - TBD: "hidden" mom_vecinv recomp. in dynamics
1881    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
1882     (allow to differentiate between forcing components using new integer flags:
1883      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
1884     and add new flag to put Dissipation tendency out of Adams-Bashforth.
1885    o ecco
1886      - enable trend removal from SSH anomaly obs.
1887    o adjoint
1888      - a fix for PmEpR when #undef EXACT_CONSERV
1889      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
1890      - try to fix "hidden" recomp. in forward_step for NLFS
1891        (NLFS seems broken sometimes after I checked it in)
1892    o seaice:
1893     - add c-grid version of the dynamic solver:
1894       + three new routines that are the c-grid substitute lsr, dynsolver
1895         and ostres
1896       + put a few fields that were local to dynsolver into global common
1897         blocks, so that I can move the computation of stresses etc into
1898         seaice_lsr (saves coding but may break the adjoint).
1899     - replace more hardwired parameters by runtime parameters
1900     - add ice masks that mask the rhs of the implicit solvers where there
1901       is no ice (commented out in seaice_dynsolver, because i am not sure
1902       if this works properly), eventually this should replace the clipping
1903       of ice velocities in seaice_dynsolver to +/-40cm/s.
1904    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
1905      include it only where its needed
1906    o move balancing of fluxes before the call of external_forcing_surf
1907    o seaice:
1908      - correct units of turning angles (now they are really in degrees)
1909      - move computation of GWATX/Y out of main routine into dynsolver
1910      - initialize GWATX/Y in seaice_init
1911    o Apply mask on Fresh-Water flux (needed for SSH forcing).
1912      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
1913    o seaice: add runtime flags for turning angles (default to zero)
1914    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
1915      and trend from exf forcing and ctrl control adjustments
1916    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
1917      (since checkpoint57x_post)
1918    o change the default rotation period to 86164.s = the Earth rotation
1919    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
1920      and based on a reference stratification. Tested within hs94.cs-32x32x5.
1921    o seaice advection: add code for choosing between the default (2nd order
1922      central differences) and multiDim advection schemes provided by
1923      pkg/generic_advdiff
1924    o seaice:
1925      - removed all references to SEAICE_GRID.h fields from
1926        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
1927        (cubed-sphere configuration will change a little)
1928      - grid computations in seaice_init are obsolete now.
1929      - cleaned up code a little so that is easier to read (hopefully).
1930      - added new (better?) discretizations of default advection and diffusion
1931        (turn on with SEAICEuseFluxForm)
1932      - replace 1 in 3d global fields by kSurface in growth.F
1933      
1934    checkpoint58a_post
1935    o seaice:
1936      - bug fix in advect.F
1937    o shelfice:
1938      - separate shelfice load anomaly from pload (breaks with time
1939        dependent forcing), => introduce constant field shelficeLoadAnomaly.
1940        Its default is 0., but it may be computed more cleverly from (unknown)
1941        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
1942        done offline. A good approximation of the pressure load anomaly is
1943        necessary to avoid large initial adjustment processes underneath
1944        deep-reaching shelfice.
1945      - small fix in ISOMIP shelfice_thermodynamics
1946      - add more sophisticated thermodynamics of Hellmer (1989), this is
1947        now the default
1948      - give a few constants more intuitive names
1949    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
1950      if bulk formulae are used in long integration (especially EmPmR). Turn
1951      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
1952      if balancePrintMean, the imbalance that is substracted is printed to
1953      STDOUT.
1954    o fix bug (typo) in obcs_apply_eta.F
1955    o add a new package shelfice which enables us to model the circulation
1956      underneath shelf-ice with draughts of hundreds of meters.
1957     - works
1958     - to do: + include improved thermodynamics
1959              + check whether kSurfC (from model/inc/SURFACE.h) can be used
1960                instead of new field kTopC
1961              + can we use topoFile, Ro_surf and existing code in ini_depth.F
1962                instead of new field R_shelfIce and new code in ini_depth.F
1963                and ini_mask_etc.F?
1964              + adjust vertical mixing schemes?
1965    o seaice pkg:
1966     - add a cpp-flag to include a simple formula for a salinity dependent
1967       freezing point of sea water at the surface
1968     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
1969       meridional stresses are now different (and hopefully correct)
1970    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
1971       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
1972       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
1973    o pkg/diagnostics: add options and parameters for regional-statistics
1974       diagnostics ; define regions by reading a region-mask from a file
1975       (might add other options later)
1976    o pkg/bulk_force:
1977     - add option and parameters to use AIM surface-flux formulae.
1978     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
1979       others forcing fields (defined in PARM05, parameter file "data") are loaded
1980       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
1981     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
1982     - use the right EXCH call for uwind,vwind (to work on CS-grid).
1983     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
1984       and parameters (note: calcWindStress replaces .NOT.readwindstress).
1985     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
1986    
1987    checkpoint58
1988    o add "--embed-source" option to genmake2 which, when the supporting
1989      tools can be compiled (as determined by genmake2) will turn on the
1990      embed_files package which then embeds the entire MITgcm source code
1991      (*.[fFhc] + Makefile) used for the build within the executable
1992      - requested by CNH but off by default
1993      - adds a paltry <9MB to the mitgcmuv executable in most cases
1994      - only writes the output when useEMBEDSRC in eedata is true
1995    o clean up 3-dim. relaxation codes:
1996      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
1997      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
1998      * Thanks to Tom Haine for testing!
1999    
2000    checkpoint57z_post
2001    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
2002      affects output (@ truncation level) of exp. plume_on_slope ; updated.
2003    o fix the pickup behavior for obcs in combination with ptracers
2004    o fix a bug in ptracers_external_fields_load
2005    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
2006      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
2007    o transfered surface NH pressure to eta field (if exactConserv).
2008    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
2009         and update lab_sea output.txt file.
2010    o completing 3-dim. relaxation code: additional term
2011         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
2012      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
2013      * At compile time, in "EXF_OPTIONS.h" set
2014          #define  ALLOW_CLIMTEMP_RELAXATION
2015          #define  ALLOW_CLIMSALT_RELAXATION
2016      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
2017          tauThetaClimRelax3Dim = 15552000.0,
2018          tauSaltClimRelax3Dim  = 15552000.0,
2019      * 3 cases:
2020          1) Use a constant-in-time 3-dim. field
2021          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
2022          3) Real-time relax. to time-evolving prescribed field
2023    o Adding Laplacian-type smoothness constraint on
2024      initial and boundary (forcing) controls (ic, bc)
2025      * enable at compile-time via
2026        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
2027      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
2028      * Absolute scale somewhat unclear so far
2029      * no area weighting was included since no other cost term does so far
2030    
2031    checkpoint57y_post
2032    First step for a NLFS adjoint
2033    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
2034    o new init. routines for calc_r_star, calc_surf_dr
2035    o still need to deal with ini_masks_etc
2036    o testreport seemed happy
2037    checkpoint57y_pre
2038    
2039    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
2040    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
2041    o add new offset feature to offline pkg (plus minor cleanup)
2042    o cfc fixes for final year of integration
2043    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
2044      be in GCHEM_OPTIONS).
2045    
2046    checkpoint57x_post
2047    o fix testreport Pb in multiple test experiment.
2048    o cleanup our namelist syntax in verification:
2049      - make it more F95 standards compliant (some work still needed)
2050      - allows the vast majority of our tests to work with gfortran
2051    o Non-Hydrostatic:
2052     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
2053     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
2054    o Allow to apply AB on T,S rather than on AB(gT,gS):
2055     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
2056     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
2057       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
2058     - need a "clever" read_pickup to restart from the other AB formulation
2059    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
2060    o remove some unused variables (reduces number of compiler warnings)
2061    o adjoint
2062      * Disable useVariableViscosity for adjoint for time being
2063        (there are a number of extensive recomputations)
2064      * Initialize certain variables needed for adjoint
2065    
2066    checkpoint57w_post
2067    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
2068                 fix the singleCpuIO RS version of MDSWRITEFIELD
2069       and add a WARNING if using globalFiles=T with multi-processors.
2070    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
2071      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
2072    o tracer advection scheme:
2073      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
2074       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
2075       was not very convenient).
2076      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
2077       (further tests needed for the implicit DST & Flux-Limiter schemes).
2078    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
2079      and sRef for convenience, handy, when you want to initialize
2080      ptracers in a large domain with a constant non-zero value. Also,
2081      untangle ptracers_init.F a little.
2082    
2083    checkpoint57v_post
2084    o change dome exp. to use variable viscosity in side-drag terms.
2085    o remove all the files from the cfc_offline test since they are now
2086      incorporated into tutorial_cfc_offline which has been producing
2087      identical results for a few days of testing
2088    o add new parameter: sideDragFactor to enable half-slip-side BC
2089      and change side-drag S/R to use viscosity from mom_calc_visc
2090      (can switch back by setting sideDragFactor=0.); affects results at
2091      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
2092       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
2093    o vorticity & strain are now computed without masking, to account for
2094      no-slip-side BC in variable viscosity calculation ; mask is applied
2095      anyway later on, before computing advection/coriolis terms.
2096    o modify exp4 to test new obcs support for reading from external files
2097      and for passive tracers
2098    o fix behavior of ptracers_monitor when monitor output is written to a
2099      netcdf-file; still not independent of monitor.F (writes in the same
2100      file).
2101    o change default value of tRef (put a uniform, meaningful value for ocean
2102      & atmos) and initialize sRef (was missing, as Martin mentioned).
2103    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
2104      to be proportional to enstrophy dissipation length.  Thus,
2105       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
2106      This is now consistent with Smagorinsky and with the manual.
2107    
2108    checkpoint57u_post
2109    o OBCS and PTRACERS: add open boundary support for passive tracers
2110      - either use homogenous (pseudo) v.Neumann conditions or prescribe
2111        OB-values from file; this is not different from the way theta and salinity
2112        are treated
2113      - however, Orlanski-radiation conditions are not supported, and the model
2114        will stop if you use pTracers and Orlanski at the same time.
2115      - beefed up the rountine obcs_external_fields_load: now only those open
2116        boundary values are overwritten with values from files for which there
2117        are really files, otherwise the OB-fields remain untouched. This makes
2118        it possible to use different OBs at different ends of the domain (as
2119        with EXF)
2120    o reduce number of exch calls in shap_filt (s2).
2121    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
2122      truncation level) 4/5 MLAdjust test results (11&12 digits match).
2123    
2124    checkpoint57t_post
2125    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
2126    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
2127      same truncation, independent of the face number: affects affects several
2128      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
2129    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
2130      note that biharmonic viscosity + no-slip was not tested in any experiment.
2131    o fix bug in non-linear free-surf side-drag ; generate new output for
2132      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
2133    o make mnc honor the writeBinaryPrec flag for most kinds of output
2134    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
2135    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
2136      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
2137    o add brackets in multi-terms sum to get same truncation, independent of
2138      the face number (manage to get exactly same value of gU,gV at the cs-edge)
2139      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
2140    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
2141      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
2142      a maximum grid-scale Reynolds number.  Also, changes all length calculations
2143      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
2144      Suggested values of viscosity parameters found in mom_calc_visc.
2145      Many new viscosity diagnostics available.
2146    
2147    checkpoint57s_post
2148    o Add clearing-house for viscosity calculations, mom_calc_visc and
2149      correct numerous bugs in LeithD and Smagorinsky discretizations.  
2150      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
2151      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
2152      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
2153      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
2154      The Strain-Tension form is now called with useStrainTensonVisc=.true.
2155      ViscAhStrain and viscAhTension are now retired.
2156    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
2157    o In response to JMC's bug report, genmake2 now ignores any soft-links
2158      that it finds in the *current* directory when searching for files.
2159      Soft-links found in any other source directories will still work as
2160      they did before.
2161    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
2162      a C routine to unlimit the stack size
2163    o mnc-ify pkg/aim snapshot vars
2164    o mnc-ify pkg/land as requested by Daniel
2165    o various changes to mnc including:
2166      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
2167      - output can now be grouped so that all files within a group
2168          change the ITER portion of their names in lock-step together
2169      - can now read ("global") PER-FACE (in addition to PER-TILE) files
2170          and works with both EXCH1 and EXCH2 (but needs more testing)
2171      - writing works for all verification test cases w/ g77 on Linux
2172    
2173    checkpoint57r_post
2174    o make MNC variable initialization happen earlier
2175    o add diagnostics for (almost) each term of the momentum Eq.
2176    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
2177    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
2178    o remove MINIMAL_TAVE_OUTPUT option ;
2179      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
2180    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
2181      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
2182    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
2183    o add time-dependent SST, SSS control
2184    o cost terms in ecco/ modularized (new cost_generic.F)
2185    o cost_averages routines are modularized (new cost_averagesgeneric.F)
2186    o new infrastructure for seaice model vs. obs misfits in seaice/
2187      * driver from the_main_loop.F is seaice_cost_driver.F
2188      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
2189      * gradient check in Exp. 6a of natl_box_adjoint/
2190    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
2191      (see README file)
2192    
2193    checkpoint57q_post
2194    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
2195    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
2196      - bug was reported by Jean-Michel and Ian Fenty
2197    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
2198      update exp. cpl_aim+ocn output.
2199    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
2200      Needed for high-res. runs with large global files
2201      to be able to limit tapelev size
2202    o Changed some tests for adjoint:
2203      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
2204      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
2205      * global_ocean.90x40x15/ back to default 3-level checkpointing
2206    o Modifications to enable scripted COMMON to MODULE conversion
2207      * verification/OpenAD/code/ has necessary scripts and description;
2208      * converts, compiles and runs successfully;
2209    
2210    checkpoint57p_post
2211    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
2212    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
2213      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
2214    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
2215    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
2216      (was already the case for dissipation with mom_vecinv,
2217       and also the case for grad.PhiHyd when staggered-timeStep)
2218      This will allow to put dissipation out-off the AB time-stepping.
2219     Unfortunately, affects truncation error. Update output of exp. that "fails"
2220      (cg2d matching number) and leave the others for later: front_relax(10),
2221      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
2222      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
2223    
2224    checkpoint57o_post
2225    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
2226      (2) its ready to be documented during the 20050801 DocFest
2227    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
2228      for ideal_2D_oce and lab_sea on linux_ia32_g77
2229    o set to #undef CTRL_SET_OLD_MAXCVARS_30
2230      in global1x1_tot/code_seaice_adj to access indices 32, 33
2231      (worth another tag)
2232    
2233    checkpoint57n_post
2234    o adding precip control xx_precip 32
2235    o adding swflux control xx_swflux 33
2236    o Replacing 10 forcing penalty cost routines by 1 generic.
2237    o Implementing partitioning in time-mean and variable adjustment
2238      for atmos. state.
2239    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
2240    o in natl_box_adjoint:
2241      * updated exp 1 to 10
2242        (but does not have time-mean vs. variable split results yet)
2243    o updated global1x1/*_seaice_adj/
2244      to incorporate latest changes
2245    o enable useSingleCpuIO for mdsio vector routines
2246      (applies in particular to tapelev I/O)
2247    o removed inefficient K-loop in all active_file*control*.F
2248    
2249    checkpoint57m_post
2250    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
2251      and advect_cs (use EXCH-2 and standard cs-32 grid files).
2252    o pkg/exch2: filling of face-corner halo regions is optional
2253      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
2254    
2255    checkpoint57l_post
2256     tag before updating tutorials (pre-release-2)
2257    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
2258       for output and interpolation of input fields onto model grid)
2259    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
2260       Affects results of exp. rotating_tank ; update output.txt.
2261    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
2262          and taking the square quantity and/or using a fraction-weight field.
2263    o fix aim_diagnostics_init.F mate numbers.
2264    o add mnc output capability to diagnostics/diagstat and update
2265      our cvsignore files for the ACSII output generated
2266    
2267    checkpoint57k_post
2268    o lab_sea now uses diagnostics package and provides a suite of
2269      new EXF diagnostics output.
2270    
2271    checkpoint57j_post
2272    o exf
2273      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
2274        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
2275        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
2276      * extended diagnostics output
2277        - now includes all EXF variables
2278        - hs, hl moved to common block
2279        - separate S/R for diagnostics, called after ctrl vector is added
2280        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
2281        - EXFqnet contains true Qnet (i.e. includes qsw)
2282      * updated verif. lab_sea, global_with_exf
2283      * Rearranging hflux (exf_mapfields -> exf_getforcing)
2284        to ensure that diagnostics sees a true EXFqnet
2285    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
2286    o diagnostics pkg: change pointers so that 1 diagnostic can be used
2287      several times with different frequencies.
2288    o mnc-ify the thsice package as requested by Daniel Enderton
2289      - the monitor--MNC output needs work
2290      - many attributes need to be added (most are currently blank)
2291    o mnc-ify theaim_v23 package as requested by Daniel Enderton
2292      - many attributes need to be added (most are currently blank)
2293    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
2294    o add Sadourny like discretization to the 4th.O vorticity advection scheme
2295    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
2296      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
2297         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
2298    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
2299     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
2300    
2301    checkpoint57i_post
2302    o Diagnostics package was changed: diagnostic allocation is now deactivated
2303      by setting an empty file name in the namelist (used to be by setting 0 frequency)
2304    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
2305      add 1rst Order upwind vertical Shear.
2306    o add a quick fix for A/B checkpointing in OFFLINE mode
2307    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
2308      end-run around the C/Fortran linking horror in eesup/src/timers.F
2309    o added pkg/runclock: allows user to terminate run based on wall clock
2310    o added non-hydrostatic scaling parameter: nh_am2
2311    o pkg/my82: futile attempt to make results compiler-independent by adding
2312      some "_d 0", etc. no effect.
2313    o for mnc output, fill the 'T' coordinate var with myTime and create a
2314      separate 'iter' variable for iteration count
2315    o pkg/diagnostics:
2316      add new capability: output of Global/Regional & per-level statistics ;
2317      tested against monitor output (including land & thSIce) on various exp.
2318    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
2319    
2320    checkpoint57h_done
2321      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
2322      data.diagnostics, data.gchem, data.ptracers) is done.
2323    
2324    o pkg/diagnostics: prepare for Global/Regional statistics.
2325      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
2326    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
2327      and rename it: DIFFERENT_MULTIPLE
2328    
2329    checkpoint57h_post
2330    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
2331    o pkg/diagnostics: change output frequency, now in seconds (instead
2332      of Nb of iterations). This requires to change data.diagnostics.
2333    checkpoint57h_pre
2334    
2335    o in mnc, let the user create the output dir if both mnc_outdir_date
2336      and mnc_outdir_num are false
2337    o add fflags() to pkg/diagnostics which allows one to specify, on a
2338      per-file basis, the file precision [default behavior is unchanged]
2339    o added diagnostics to pkg/kpp, including computation of mixed layer
2340      depth based on a temperature/density criterion
2341    o updated verification/natl_box to test the new pkg/kpp diagnostics
2342    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
2343    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
2344    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
2345      not mnc -- this mistake was found by JMC and is now corrected
2346    
2347    checkpoint57g_post
2348    o add Adams-Bashforth 3rd Order time stepping:
2349      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
2350      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
2351    checkpoint57g_pre
2352    
2353    o make lambda[Theta,Salt]ClimRelax spatially varying
2354      (default remains spatially uniform constant based on tau)
2355    o added new control variables
2356      * init. uVel, vVel, etanN
2357      * lambda[Theta,Salt]ClimRelax
2358    o separate masks used for ctrl_pack/unpack 'from write_grid' output
2359      (suggested by G. Forget)
2360    
2361    checkpoint57f_post
2362    o add parameter "baseTime" = model base time = time at iteration zero
2363      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
2364      account for baseTime shift
2365    o move Coriolis arrays from PARAMS.h to GRID.h
2366    checkpoint57f_pre
2367    
2368    o mnc-ifying the seaice package
2369    o introduced an alternative length scale calculation for use in the limiting
2370      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
2371    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
2372    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
2373      as well as grad(vort3).  Made it compatible with both approximate form
2374      for the cubed sphere and full form of these gradients.  Added flag
2375      useFullLeith to select between approximate and full form.  
2376    o add "d0" in getcon.F to reduce differences between compilers/platforms
2377      update output.txt of exp. fizhi-gridalt-hs
2378    o change port_rand funtion to allow to set the seed.
2379    o fix obscure MNC bug involving conversion between reals and integers
2380      - it caused no problems with certain (eg. gcc, ifc) compilers but the
2381        new version is now more standards-compliant
2382    o adjoint-related modifications
2383      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
2384      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
2385      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
2386    
2387    checkpoint57e_post
2388    o Adding eddy stress controls a la Ferreira et al.
2389    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
2390    
2391    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
2392      update output.txt of exp. fizhi-gridalt-hs
2393    o add more "Z" dimensions and associated coordinate vars to MNC
2394    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
2395    o parameter calendarDumps: when set, approximate months (30-31 days) and years
2396      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
2397      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
2398      months and years.  Requires pkg/cal.
2399    o diagnostics: add pickup functionality
2400      - off by default for backwards compatibility
2401      - current version only uses MDSIO -- MNC will be added
2402    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
2403    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
2404    
2405    checkpoint57d_post
2406    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
2407    o modify verification/ideal_2D_oce so that it tests the creation of mnc
2408      output from the diagnostics package
2409    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
2410    o make genmake2 more portable by using ".$FS" instead of ".f" for more
2411      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
2412    o add coordinate variables to the MNC output from the diagnostics package
2413    o change MNC-flags default value: true when useMNC=TRUE
2414    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
2415      the ability (off by default) to read the grid information using MNC
2416    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
2417    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
2418    o do snap-shot diagnostics at the middle of the time-interval (instead of
2419      at the end).
2420    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
2421      new test for AIM with thSIce + slab-ocean
2422    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
2423    o move state variable diagnostics to the beginning of the time step ;
2424      (note: still needs some work specially for snap-shot diagnostics)
2425      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
2426    
2427    checkpoint57c_post
2428    o Change testing option (-ieee) to get closer agreement between g77 & ifort
2429    o generate new output.txt files on faulks with g77 & the new -ieee option
2430    checkpoint57c_pre
2431    
2432    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
2433      update output.txt of exp. global_ocean.90x40x15
2434    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
2435      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
2436    o add saltFlux(+File) forcing capability with periodicExternalForcing
2437    o allow to use pkg diagnostics for GM-Redi & ThSIce output
2438    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
2439    o improvements for the MNC output from DIAGNOSTICS:
2440      - correct handling of the unlimitied dimension
2441      - all dims now have associated coordinate variables
2442      - variables located at U, V, and Corner ("Z") points are now written
2443        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
2444        *all* data points are output
2445    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
2446    o added pkg/seaice/seaice_monitor.F
2447    o mdsio_readfield.F can now read files visible only to master MPI process.
2448    o pkg/seaice: some test code for ice-modified ocean stress
2449    o exf_getffields interpolation defaults to bilinear for all scalar forcing
2450      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
2451      spurious negative numbers for precipitation and humidity.  Will cause
2452      some small numerical differences for integrations using pkg/exf/exf_interp.F.
2453    o pkg/ctrl/
2454      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
2455        May be enabled via doPackDiag
2456      *  introduce z-scaling of
2457         + gradient (doZscalePack) and
2458         + control (doZscaleUnpack)
2459    o pkg/mdsio/
2460      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
2461      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
2462    
2463    checkpoint57b_post
2464    o simplify options in diagnostics_fill arguments (remove weird combinations)
2465    o fix MNC coordinate variables so that they now contain per-face index
2466      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
2467      general, EXCH2 grids are only aligned to a "local" coordinate system
2468    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
2469    o Implement instantaneous output within pkg diagnostics:
2470      setting a negative frequency in data.diagnostics produces
2471     "snap-shot" output (as opposed to time-average if freq > 0)
2472    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
2473      NOTE: change ptracer diagnostics name: use 2 characters to work with
2474            more than 9 tracers. Add also diagnostics of advect & diffus flux.
2475    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
2476      becomes the coordinate variable for the 'T' dimension
2477    o add CF-style coordinate variables to MNC
2478      - just a first cut:  numbers are meaningless on the cubesphere and
2479        missing along the T axis but otherwise it works!
2480    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
2481    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
2482    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
2483      this is based directly on what the model compute, so that the content of
2484      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
2485    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
2486    o clean up build options files for SunOS, in particular
2487      - remove -traditional from xmakedepend
2488      - change -xarch=v9 to -xarch=native for f77
2489      - restore use of make (not gmake)
2490      - add CC=gcc if using g77
2491    o changes per discussion of AM, JMC, & EH3 today:
2492      - move redundant "grid" variables out of "state" -- in preparation of
2493        creating proper CF-style coordinate variables and in recognition
2494        that any/all grid variables can be easily copied (eg. w/NCO) from
2495        the grid files into any of the other NetCDF files
2496      - *always* output grid variables with MDSIO (this will eventually be
2497        changed)
2498      - output MNC grid file if useMNC is true
2499    o every instance of _END_MASTER() has been found and replaced with
2500      _END_MASTER( myThid ) in order to satisfy certain picky Sun
2501      preprocessors
2502    o re-arrange diagnostics pkg initialisation:
2503     - allow each package to extend the available diagnostics list
2504     - add some checking and fix small problems (multi-threaded, ...)
2505     - new S/R diagnostics_fill (replace fill_diagnostics):
2506       look through the short list of active diag. (instead of the long list)
2507       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
2508    
2509    checkpoint57a_post
2510    o this set of changes restores TAMC compatibility
2511      tested for global_ocean.90x40x15 adjoint on trough
2512      (what a pain)
2513    
2514    checkpoint57a_pre
2515    o some modifs in tools/build_options for sunos
2516    o call ctrl_pack for ctrl at end for optimcycle=0
2517    
2518    checkpoint57
2519    o add horizontal bi-harmonic viscosity for vertical velocity
2520      - new parameter viscA4W (defaults to viscA4)
2521      - affects only non-hydrostatic code
2522      - to be done: no-slip lateral boundary conditions
2523    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
2524    o implement Implicit Vertical advection for pTracers
2525    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
2526      (implemented also for implicit vertical diffusion & advection)
2527    o OBCS: extend application of tracer open boundary conditions
2528      to a strip beyond the boundary of width Olx/Oly
2529    o add call monitor to TAF set of required calls (flow directives)
2530      and include in natl_box_adjoint
2531    o untangle a few ifdefs related to cost, ctrl, autodiff
2532      untangel a few ALLOW_ECCO_OPTIMIZATION
2533    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
2534      (theta2, salt2 in ecco_cost_weights)
2535    
2536    checkpoint56c_post
2537    o OBCS as control variables
2538      - update ctrl_ad_diff.list, obcs_ad_diff.list
2539      - remove balance of obcs controls from default
2540      - fix index bug nobcs in ctrl_init
2541      - fix dummy fields filen in ctrl_pack
2542      - add dummy weights for obcs
2543    o lsopt: comment out fort.94 output
2544    o optim:
2545      - remove unnecessary header files
2546      - adjusted namelists
2547      - add xerbla.F to Makefile
2548    o exf:
2549      - multiple modifications of exf_check_range
2550      - unit change in exf_init_runoff from [m/year] to [m/s]
2551    o mdsio:
2552      - i/o-vector change debugLevel from debLevA to debLevB
2553    
2554    checkpoint56b_post
2555    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
2556      is called from DO_THE_MODEL_IO
2557      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
2558      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
2559      - clean up PTRACERS_WRITE_TIMEAVE a little
2560    o add another verification experiment that tests both the cfc-pkg and
2561      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
2562      reactive tendencies treated inline with regular timestepping
2563    o testreport previously did a lousy job of comparing small numbers, so
2564      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
2565      implemented in the little c-progam tmp_cmpnum.c which is embedded in
2566      testreport.
2567    o ptracers_monitor: bug fix for MPI
2568    
2569    checkpoint56a_post
2570    o GCHEM: finish reorganizating the package
2571      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
2572        (introduces another 3D-array for each passive tracer, but only if
2573        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
2574        gchemTendency is not needed because the timestep is done separately)
2575      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
2576      - GCHEM is now---more or less cleanly---separate from PTRACERS
2577      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
2578        so clear to me how that should be done in a general way.
2579    o CFC: improve formatting of output in CFC_ATMOS
2580    o PTRACERS:
2581      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
2582        that ALL experiments with ptracers enable can be checked. This makes
2583        GCHEM_MONITOR obsolete.
2584      - include a runtime parameter PTRACERS_monitorFreq that defaults to
2585        monitorFreq
2586      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
2587    o add PTRACERS (PTR0[1-5]) to testreport output
2588    o exf_check_range:
2589      * default changed to .TRUE.
2590      * will check values for niter0 if debLevA, every timestep if debLevB
2591      * STOP in exf_check_range if 'out of range'
2592      * range chosen generous to allow for potential extema
2593      TBD: a version with stricter range
2594           permitted range would be runtime parameters
2595    o GMredi:
2596      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
2597      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
2598      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
2599    o GCHEM:
2600      - move call to GCHEM_FORCING_SEP, so that it is now called before
2601        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
2602      - introduced a useGCHEM runtime flag and applied it everywhere.
2603      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
2604        this flag is now only visible within GCHEM-pkg routines.
2605      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
2606        be replaced by a 3D array that is computed before thermodynamics; for
2607        this, the tracer ID iTracer had to be included into the parameter list
2608        of ptracers_forcing
2609      - set up forward_step to call gchem_forcing, that will replace
2610        gchem_forcing_int in ptracers_forcing
2611      - cleaning up
2612    o small cleaning of exch2: remove files that are also in eesupp/src
2613    
2614    checkpoint56
2615    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
2616    o mnc: cleanup "full" files--fixes out-of-memory problem
2617    o ECCO-GODAE
2618      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
2619      * fully merged and updated from SIO code
2620        windstress sign change affects
2621        - exf_inscal_[u/v]stress
2622        - sign of xx_tau[u/v] adjustments
2623        - signs in cost_scat
2624      * ctrl_get_gen: avoid update of tau[u/v] for first few days
2625      * natl_box_adjoint updated and compressed
2626      * 2-level checkpoint switch added
2627        (tested in EXP. 1 of natl_box_adjoint)
2628      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
2629    o SVD
2630      * first complete, non-hacked version for SVD calculations
2631      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
2632        performed via direct access files admtlm_vector.it????
2633        (via ctrl_[un]pack)
2634      * optimcycle is used for ARPACK iteration counter
2635        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
2636      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
2637        and add linear transforms where necessary
2638      * controls are initial/final SST, SSS (can be extended; need to check
2639        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
2640    o mdsio: filename info to both stderr, stdout
2641    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
2642      from sign change
2643    
2644    checkpoint55j_post
2645    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
2646      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
2647    o add consistent build directories and .cvsignore files to verification
2648    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
2649    o make all subroutines 30 or less characters in length for certain older
2650      compilers to work (a thorough search only turns up two routines in
2651      pkg/ptracers)
2652    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
2653      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
2654    
2655    checkpoint55i_post
2656    o change arrays for total vertical diffusivity (2.D if explicit,
2657      3.D if implicit) ; each ptracer uses its own background value.
2658    o added mnc/NetCDF output capability to ocn_compon_interf
2659      - added bits to verification/cpl_aim+ocn so that it can run on
2660        ITRDA and other clusters without the mpirun "-wd" option
2661    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
2662      configuration
2663    o give MNC the ability to create additional files rather than
2664      exceeding a specified file size limit "MNC_MAX_FILESIZE"
2665      - the default is just less than 2GB which is a practical limit
2666        on many systems
2667    o Compute the non-local term using either KPP vertical diffusivity (=default)
2668       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
2669    
2670    checkpoint55h_post
2671    o add verification test "vermix"
2672    o remove all the *_ioinc flags and replace with the single global
2673      outputTypesInclusive flag
2674    o allow to set a vertical profile of vertical diffusivity for T & S
2675    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
2676    o useMNC moved from data.mnc to data.pkg
2677    
2678    checkpoint55g_post
2679    o Renaming carbon AD experiments to comply with testreport conventions
2680    o Updating adjoint of Held-Suarez hs94.1x64x5
2681    o Fixing directives for non-ECCO forward_step, after ECCO directives
2682      have been fixed to avoid recomp. of do_oceanic_phys
2683      Works well for global_ocean.90x40x15,
2684      but recomp. issue remains for carbon
2685    o Updating adjoint output for natl_box_adjoint after
2686      pkg/ecco has been modified (see taga c55d_post)
2687    
2688    checkpoint55f_post
2689    o rename to timeave_init_fixed
2690    
2691    checkpoint55e_post
2692    o some delicate re-shuffle of store directives to avoid one
2693      extra call of do_oceanic_physics
2694      affects ecco_the_main_loop.F, do_oceanic_physics.F
2695      checkpoint_lev1_directives.h
2696    o NB: this may break global_ocean adjoint temporarily,
2697      but it is clear how to fix it. Will do later, need this now.
2698    
2699    checkpoint55d_post
2700    o ECCO specific cost function terms (up-to-date with 1x1 runs)
2701    o ecco_cost_weights is modified to 1x1 runs
2702    o modifs to allow observations to be read in as
2703      single file or yearly files
2704    o enable to read exf forcing fields as either
2705      single file or yearly files (flag useExfYearlyFields)
2706    checkpoint55d_pre
2707    
2708    o switch between 2-level and 3-level checkpointing
2709    o add ability of MNC to write local and "partial" (eg. 2D slices where
2710      the full 3D field is never actually stored) arrays to NetCDF files
2711      with the correct (that is, the complete multi-dimensional) set of
2712      array indicies
2713      - used in mom_vecinv() to write the diagFreq output
2714      - tested (demonstrated) in verification/aim.5l_cs
2715    o further mnc-ification
2716      - add verification/lab_sea to the list with mnc setups
2717      - fix undefined mnc v-names in cd_code
2718      - add kpp to mnc output (both snapshot and timeave)
2719    o non-hydrostatic code
2720      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
2721        in calc_gw.F
2722      - defaults to viscAh
2723      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
2724        friction or Leith) in non-hydrostatic mode, as long as there is
2725        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
2726    o pkg/cost
2727      extend simple cost functions to treat time mean quantities
2728      (T,U,V) via cost_accumulate_state from cost_tile
2729    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
2730        be 2 times larger than the minimum size the advection scheme requires.
2731        now get a perfect conservation of salt in advect_cs test-exp (updated)
2732    o GGL90 (Gaspar's TKE mixed layer)
2733      - add horizontal diffusion of TKE, requires exchanges in
2734        do_fields_blocking_exchanges, horizontal diffusivity is zero by
2735        default. In OPA there is no horizontal diffusion of TKE but the
2736        mixing coefficients are computed from a horizontal average of TKE of
2737        6 points or so. I think that diffusion has a little more physical
2738        justification.
2739      - clean up ggl90_calc in the hope of reducing memory usage (this hope
2740        was in vain)
2741      - mask tke-variable in ggl90_init
2742    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
2743    o fix biharmonic diffusion on CS-grid.
2744    o more obcs stuff
2745      - added obcs_external_fields_load as an alternative to the EXF-pkg option
2746        for reading boundary values. This routine is called from
2747        obcs_prescribe_read
2748      - updated obcs_check
2749      - changed sponge layer relaxation parameter units for days to seconds
2750      - turned off sponge layer by default
2751      - changed argument list of OBCS_CALC to myTime+deltaTclock
2752      - fixed about 35 bugs in obcs_external_fields_load
2753    
2754    checkpoint55c_post
2755    o obcs stuff
2756      - new runtime flags useOBCSprescribe, useOBCSbalance
2757      - re-arranged obcs_calc
2758      - moved exf_getobcs to obcs_prescibe_read
2759        obcs_prescibe_read is called after ORLANSKI stuff
2760        and independent of it (executable can contain all).
2761      - updated obcs_check
2762      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
2763        These may be necessary only if tangential velocities are
2764        prescribed at OB, not sure, needs testing.
2765    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
2766      which simplifies the calls and passes the ifc check-bounds test
2767    
2768    checkpoint55b_post
2769    o add a 2D scalar, Z location, exchange_2 routine.
2770    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
2771      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
2772      affects advect_cs results (for the wrong reason): update output.txt
2773    o use a more standard discretization for biharmonic viscosity ;
2774     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
2775      affects results of dome set-up: update output.txt
2776    o fix gad_advection.F (CubedSphere part), back to version 1.23
2777    o fix bug in mom_vi_del2uv.F (CubedSphere part).
2778    
2779    checkpoint55a_post
2780    o merged code to
2781      * prescribe/read time-dependent open boundaries
2782        (works in conjunction with exf, cal)
2783      * sponge layer code for open boundaries
2784      * each boundary N/S/E/W now has its own CPP option
2785        (healthy for the adjoint)
2786    
2787    checkpoint55
2788    o up-to-date adjoint of previous breaks
2789      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
2790      - global_ocean_ebm: adjoint still needs fix (TLM ok)
2791      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
2792      - carbon: * remove tr1-related adjoint verification
2793                * add ptracer as control variable
2794    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
2795      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
2796    
2797    checkpoint54f_post
2798    o in verification/carbin/ remove experiment related to
2799      ALLOW_PASSIVE_TRACER (array tr1 etc)
2800      code_ad/ input_ad/ results_ad
2801    
2802    o add two new packages
2803      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
2804        + subject to optimization (memory)
2805      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
2806        + subject to reordering (many GOTOs in the original code)
2807        + so far opps is called for every (i,j) point, and then operates in
2808          the vertical; one may want to reorder the scheme in order operate in
2809          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
2810          fields)
2811    o overhaul of IO so that we now have flags for MDSIO and/or MNC
2812      - all verification tests compile and run with linux_ia32_g77
2813      - defaults are compatible with current input files--nothing
2814        should change if you were not previously using MNC
2815      - MNC output has been added in numerous places (eg. timeave)
2816        but there are still a few writes not yet do-able with MNC
2817        (this is in progress)
2818      - flags now allow for either/or/both use of MDSIO and MNC and
2819        documentation will soon follow
2820      - numerous small formatting cleanups for ProTeX
2821    o add version info (via BUILD_INFO.h) to MNC and stdout
2822    
2823    checkpoint54e_post
2824    o add two new packages
2825      - pp81 (Packanowski and Philander, 1981), Richardson number and
2826        stratification dependent mixing
2827      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2828      - these scheme operate in a similar manner as KPP (without ghat, of
2829        course), however there is only one diffusivity that is used for both
2830        temperature and salinity (and passive tracers)
2831    o add offline package
2832    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2833      provided by Stephanie Dutkiewicz
2834    o genmake2: add ability to search for C compilers and cleanup test output
2835      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
2836    
2837    checkpoint54d_post
2838    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
2839    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
2840      leading to additional shift by 5 days each year of integration
2841       (i.e. leading to considerable offset over the years)
2842    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
2843    o start with no AB and no initial filtering (staggerTimeStep):
2844      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
2845    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
2846      (external loading & cpl import/export stay in forward_step.F)
2847    o update coupling interface to work with new staggerTimeStep
2848    o change MDSIO ptracers_pickup.
2849    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
2850    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
2851    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
2852    
2853    checkpoint54c_post
2854    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
2855      this affects (truncation error) output.txt of test-exp:
2856       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
2857    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
2858    o change Qnet to always be the net heat flux, (+upward).
2859      affects (truncation error) output of natl_box exp.: updated
2860    o define the max number of passive tracers in PTRACERS_SIZE.h
2861    o start to test mnc routinely in exp0
2862    o add sea-ice loading (sIceLoad) as a new forcing field.
2863    
2864    checkpoint54b_post
2865    o add testreport "-j JOBS" option for parallel builds (tested and pretty
2866       impressive on Altix and Opteron systems)
2867    o diagnostics can now write NetCDF files through the mnc package
2868    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
2869    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
2870    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
2871      affects (truncation error) output of lab_sea & natl_box exp.: updated
2872    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
2873    
2874    checkpoint54a_post
2875    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
2876    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
2877    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
2878    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
2879      + internal_wave (shift in writing cg2d_ini_res)
2880    checkpoint54a_pre
2881    
2882    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
2883      - modified verification/lab_sea and natl_box_adjoint accordingly
2884    
2885    checkpoint54
2886    checkpoint53g_post
2887    o prepare splitting of thermodynamics: store convect.counter in common block
2888    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
2889      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
2890    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
2891    o new parameter "nShapS": allow to treat differently S from T (nShapT)
2892    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
2893    o restore adjointability
2894    
2895    checkpoint53f_post
2896    o modifications that affect AIM experiment results (update output.txt):
2897      - no advection of S at top interface Nr (pkg/generic_advdiff)
2898      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
2899    o AIM pkg:
2900      - include stability function into surf.Flux derivative relative to Tsurf
2901      - calculate clear-sky radiation & surface temp. change (for diagnostics)
2902    
2903    checkpoint53e_post
2904    o merged cylindrical coord configuration
2905    o added rotating_tank experiment
2906    checkpoint53e_pre
2907    
2908    checkpoint53d_post
2909    o faulks upgraded: re-generate output.txt that have changed:
2910       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
2911    o Added Bryan and Lewis, 1979, vertical diffusivity profile
2912    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
2913    o added Sadourny discretization of Coriolis
2914      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
2915      - re-enabled use of omega3 (useAbsVorticity)
2916    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
2917      vector-invariant equations
2918      - note: does *NOT* yet use same variable visc. for no-slip BC's.
2919    o recoded the lateral boundary conditions for non-hydrostatic w, this time
2920      hopefully without new bugs
2921      - still to do: biharmonic friction for non-hydrostatic w
2922    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
2923    o regenerated output for global_ocean_ebm (using -ieee)
2924    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
2925      of mom_common/
2926      - simple re-arrangement of instructions within computing loop
2927    checkpoint53d_pre
2928    
2929    checkpoint53c_post
2930    o new version of coupler for AIM+thSIce and Ocean models
2931     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
2932     - land: change Evaporation of snow
2933     - aim with thSIce: fix bug in snow-precip.
2934    o changes to calc_gw.F
2935     - bug fix for w^2 term near the bottom boundary
2936     - (hopefully) improve the lateral slip boundary condtions for use with
2937        partial/looped cells
2938      - because the bug fix changes two verification experiments anyway (exp5
2939        and plume on slope), change the lateral boundary condition from half slip
2940        to the value of no_slip_sides
2941    o ebm package wasnt quite up to the parallel task. Fixed that.
2942    o Adjoint of EBM package + verification
2943      * TLM OK
2944      * ADM not sufficient accuracy yet (needs further testing)
2945    
2946    checkpoint53b_post
2947    o Commiting new energy balance model to repository
2948      * package is pkg/ebm
2949      * verif. is verification/global_ocean_ebm
2950      * references are in ebm_driver.F
2951    C      * X. Wang, P. Stone and J. Marotzke, 1999:
2952    C        Global thermohaline circulation. Part I:
2953    C        Sensitivity to atmospheric moisture transport.
2954    C        J. Climate 12(1), 71-82
2955    C      * X. Wang, P. Stone and J. Marotzke, 1999:
2956    C        Global thermohaline circulation. Part II:
2957    C        Sensitivity with interactive transport.
2958    C        J. Climate 12(1), 83-91
2959    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
2960    C        Destabilization of the thermohaline circulation
2961    C        by atmospheric eddy transports.
2962    C        J. Climate 7(12), 1870-1882
2963    o Will need long integration testing.
2964    checkpoint53b_pre
2965    
2966    o created pkg/mom_common in preparation for variable viscosity code
2967    o renamed and split ini_mnc_io
2968    o pkg/land: only liquid water can diffuse or run-off
2969    o AIM using land: soil wetness availability account for snow
2970    o added printMapIncludesZeros to EEPARMS namelist
2971    
2972    checkpoint53a_post
2973    o restore TAMC compatiility for exf_constants.h
2974      (no usage of _d in .h)
2975    o Additional storing in KPP in an attempt to fix
2976      TAMC problem with adjoint of KPP code.
2977      (no success...)
2978      Identical code works fine with TAF.
2979    o Fixed verification/natl_box_adjoint experiments.
2980      Initial conditions for Experiments 4 and 5 are now
2981      set to "SEAICE_initialHEFF=0", which is more reasonable,
2982      and hence gives results closer to that of Experiment 2.
2983      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
2984    
2985    checkpoint53
2986    o stable checkpoint with up to date adjoint
2987      TLM tests only run for 1st grdchk at the moment. Its unclear if
2988      this is a code problem or a problem with resetting code for g_
2989      variables that is being autogenerated wrong.
2990      Otherwise:
2991       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
2992       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
2993         are both still in chaos following their security messes.
2994    
2995    checkpoint52n_post
2996    o various build (mostly genmake2) changes including:
2997      - ability to build/run more easily within Cygwin and MacOS X
2998      - more complicated Makefiles with a stronger dependence on Gnu Make
2999    o pkg/seaice modifications
3000      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
3001        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
3002        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
3003      - changed proxy for geostrophic velocity and updated
3004        verification/lab_sea/results/* accordingly
3005      - removed ADI dynamic solver from pkg/seaice
3006      - replaced all occurrences of 1/CSTICE or 1/CSUICE
3007        they caused a segmentation fault under certain circumstances
3008      - removed unused field WATR
3009    o bug fix in exf-package:
3010      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
3011         now reflect that.
3012    o small fixes in the cal-package:
3013      - set reference date to first of January for the 'model'-calendar
3014      - failing of cal_CheckDate in cal_FullDate now actually results in a
3015        warning
3016    o small modifications in exf-package to increase flexibility:
3017      - change climtempfreeze from a constant to a runtime parameter that
3018        is specified in data.exf_clim (default = -1.9)
3019      - introduce runtime parameter windstressmax (default = 2.0) that is
3020        specified in data.exf
3021    o fix in pkg/thsice:
3022      - update Evap (Tsf changes) to be consistent with Latent heat flux
3023      - maintain snow precipitation unchanged (even if Tsf >=0).
3024     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
3025    
3026    checkpoint52m_post
3027    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
3028      this does not change any of the results, because myIter=0 in swfrac always
3029      lead to jwtype=2 (the default anyway), but the call makes little sense
3030      as a default
3031    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
3032    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
3033      atmospheric model (AIM) to use it ; add a "slab ocean" component.
3034    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
3035    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
3036    o extending useSingleCpuIO option to work with new exch2 I/O format
3037      - old-style, missing-tile I/O is still accessible by defining CPP
3038        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
3039    o monitor package can write to NetCDF files and/or STDOUT
3040    o fix re-definition bug in MNC_GRID_INIT_ALL()
3041    o doc/api_reference added
3042      - a framework for building an API Reference Manual using all
3043        the "protex" comments embedded in the code
3044      - see pkg/generic_advdiff, pkg/mnc for examples
3045    o MNC:
3046      - make myThid the last argument for all subroutines
3047      - new default for the grid files: NO halos
3048      - add useMNC and other run-time flags
3049      - separate per-file-group handling of the unlimited dimension
3050      - early initialization of MNC w/ flags read at the eeboot stage
3051        and lookup tables set in initialize_fixed
3052      - write all MNC output to a freshly-created directory
3053    o thermodynamics sea-ice (thsice) is now tested with testreport.
3054    o test exp. advect_cs: use the standard cs32 grid ; update output.
3055    o Added functionality to grdchk:
3056      pick global i,j,k position (or nearest wet) where to perform check.
3057    
3058    checkpoint52l_post
3059    o new land formulation:
3060      a) use ground enthalpy as prognostic variable to ensure exact
3061         energy conservation.
3062      b) account for water temperature and for latent heat of freezing
3063         in all processes (rain, run-off, ground storage)
3064      c) compute surface and ground temperature implicitly.
3065    o aim_v23 modification for new land model:
3066      a) Treat separately land / ocean / sea-ice surface fluxes
3067         to allow implicit computation of land & sea-ice surface temp.
3068      b) add snow precipitation.
3069    checkpoint52l_pre
3070    
3071    o fix problem (when 1 tile is empty) in min/max monitor.
3072    o fix bug in timeAve (u,vZetatave in common block)
3073    o no restoring terms under ice for pkg/seaice
3074    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
3075    o bug fix for pkg/seaice pickups
3076    o change MNC call locations and add coordinate attributes
3077    o mask vorticity at the corner ; affects global_ocean.cs output
3078    o fix ini_curvilinear_grid ; test CS experiments with mpi
3079    o aim.5l_cs: modify sea-ice fraction input file ; update output
3080    o exf: Adding simple range check routine for exf fields after read
3081    
3082    checkpoint52k_post
3083    o removed top-level directory "diags"
3084      - we migrated these functions to pkg/timeave a long time ago
3085    o fixed bug introduced in pkg/monitor
3086    o accuracy ctrlprec = 32 insuffient for gradient checks using
3087      averaged fields (I/O via cost_averages)
3088      -> use ctrl.h in active_file*.F to control I/O precision.
3089    o paramter list of CALL ADTHE_MAIN_LOOP
3090    o added initial do_the_model_io to ecco
3091    o set all ...Freq to zero after cost_final
3092      taveFreq, dumpFreq, pChkptFreq
3093    o MAIN and ECCO differentiability restored
3094    
3095  checkpoint52j_post  checkpoint52j_post
3096  o fix nchklev in tamc.h for global_ocean...  o fix nchklev in tamc.h for global_ocean...
3097  o Bringing flow and store directives up-to-date  o Bringing flow and store directives up-to-date

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