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revision 1.1367 by mlosch, Wed Jan 19 13:52:14 2011 UTC revision 1.1532 by mlosch, Thu Nov 10 14:26:41 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o gluemnc:
8      - replace ncrcat with ncks when adding variables to *.glob.nc
9      - change the way variables without record dimensions are handled so that
10        files that have variables with and without record variables can be glued:
11        add a record dimension with a new unique name to be able to differentiate
12        between variable with and without a-prior record dimensions. Remove
13        this record dimension before adding the variable to the *.glob.nc file.
14        This procedure automatically works also for grid.*.nc files that do not
15        have any record dimension.
16    o verification/cpl_aim+ocn:
17      - generate new reference output on baudelaire (gfortran, mpich2) (previously
18        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
19    o pkg/obcs/obcs_calc_stevens.F:
20      - add code for northern and southern boundaries.
21      - reorder some loops to save some operations and so that drFBar can be scalar
22    o model/src:
23      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
24        truncation) and add diagnostics for Adams-Bashforth tendency increment.
25      - update test-exp. AD output:
26        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
27      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
28        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
29        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
30        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
31        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
32        tutorial_plume_on_slope.
33    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
34      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
35      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
36      does not even come with an F77 compiler anymore, this should not be
37      a limitation
38    
39    checkpoint63e (2011/11/06)
40    o pkg/seaice adjoint of LSR:
41      - substantially rework STORE dirs.
42      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
43        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
44        and only perform SOLV_MAX_FIXED adjoint iters.
45        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
46        always goes to same record, meaning that the last forward field will be
47        the one used in the adjoint - an approximation.
48      - now produces non-zero LSR-related gradients, and acceptable gradients for
49        An's zonal (x-z) test case (to be checked in)
50      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
51        (but these are screwed up by the thermodynamics in the first place);
52        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
53        output_adm.txt also reflects changes to seaice_lsr
54      - global_ocean.cs32x15:
55        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
56          (output_adm.seaice.txt was updated)
57        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
58          (output_adm.seaice_dynmix.txt)
59    o test-exp. exp4+stevens:
60      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
61    o pkg/seaice (lsr solver):
62      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
63        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
64      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
65      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
66        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
67      - compute (with new S/R) and print initial (+ free-driff sol. if available)
68        and final residual of linearised system.
69    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
70      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
71    o pkg/obcs: Stevens BCs (still only for east and west)
72      - fix Stevens BCs by using intermediate velocities of previous
73        time step as "baroclinic" contribution rather velocity of one grid cell
74        inside the boundaries; more consistent but makes the entire treatment
75        more complicated, requires new pickup files and two new S/Rs:
76        obcs_copy_uv_n and obcs_save_uv_n
77        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
78        (undefined by default)
79      - silently move computation of some grid factors into separate loops to
80        save some recomputations
81      - add a hack for non-linear free surface
82      - add a verification experiment to exp4 that tests this code
83    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
84    
85    checkpoint63d (2011/10/25)
86    o pkg/obcs + seaice-dynamics:
87      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
88        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
89        values (consistent with an implicit method).
90      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
91        return to older implementation (same results as before); note that none of
92        the "experimental" OBCS_SEAICE options are implemented in the new version.
93      - switch test exp. seaice_obcs to use new version (update output).
94    o pkg/seaice:
95      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
96      - add parenthesis in Water-Ice drag calculations (evp & lsr);
97      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
98        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
99      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
100        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
101    o pkg/layers:
102      - Include potential density as new coordinate (Thanks to David Munday)
103    o pkg/dic:
104      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
105        carbonate computation/output to CALC_PCO2_APPROX
106    o pkg/generic_advdiff
107      - make TAF generate code that vectorizes:
108        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
109    o model/src:
110      - improve vectorization also for adjoint code of
111        solve_tridiagonal and solve_pentadiagonal. As this requires up to
112        5 new 3D-fields, this code is only turned on for the combination of
113        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
114        for singular matrix check (only for TARGET_NEC_SX).
115      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
116        ALLOW_AUTODIFF. This flag now needs to be set outside of
117        solve_tri/pentadiagonal.F
118    o pkg/exf:
119      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
120        optional namelist EXF_NML_OBCS).
121      - add many debug-print (to trace down where pkg/cal error msg comes from)
122    o pkg/mom_vecinv/mom_vi_hdissip.F
123      - rearrange loops so that vectorization is improved and in particular
124        the adjoint routine vectorizes. The code is a little longer now, but I
125        think easier to read.
126        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
127    o pkg/seaice:
128      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
129    o pkg/exch2:
130      - alternative code (without tile x tile matrix) for cumulated (global) sum;
131        used as default; keep using matrix version in adjustment.cs-32x32x1.
132    o tools/build_options:
133      - after merging some MPI and/or multi-threads specific optfiles so that
134        the modified default optfile support both built (using genmake2 -mpi
135        for the MPI built, using genmake2 -omp for OpenMP built),
136        move now obsolete optfiles to tools/build_options/unsupported/
137       (add copy of email sent to support list in doc/optfiles_changes.txt)
138    
139    checkpoint63c (2011/09/28)
140    o pkg/ebm:
141      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
142        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
143    o pkg/seaice (SItracer pickup)
144    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
145      To be done:
146      - thorough testing of missing fields in S/R seaice_read_pickup
147      - thorough matching between generic tracers and specific fields used
148        (e.g. volume-weighted age, area-weighted age, salinity, ...)
149    o pkg/grdchk:
150      - all procs calculate and print finite-difference gradient (for testreport)
151      - change description output used by testreport;
152      - AD testing: also compare and report Finite-difference gradient;
153        => update all output_adm*.txt
154    o test exp. global_ocean_ebm:
155      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
156        and turn on exactConserve; update (fwd) output.
157    o pkg/seaice (LSR):
158      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
159      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
160        * identical results with non-CS topology (but save up to half of EXCH calls)
161        * no much changes in cs-32 verification tests since no ice at face edges
162         (differences due to convergence criteria, since nb of iterations changed)
163        * expect some differences on lat-lon-cap grid.
164        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
165    o pkg/exch2:
166      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
167        many tiles); until alternative coding is added, just add a stop.
168    o pkg/kpp:
169      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
170        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
171    o optfiles:
172      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
173        into corresponding standard one, which now support different build:
174        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
175      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
176    o pkg/obcs (seaice):
177      - add missing EXCH for uIce,vIce after applying OBCS;
178      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
179        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
180        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
181      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
182      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
183        and eedata.mth for MPI and mutlti-threaded testing.
184    o pkg/flt:
185      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
186      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
187      - fix pickup and trajectories + profiles output with multi-threads;
188      - add parameter to select group of fields to write along trajectory and
189        profile (default unchanged);
190      - only call PORT_RAND* function when flt_noise <> 0;
191      - add multi-threaded test for verification exp. flt_example.
192    o eesupp/src:
193      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
194      - USE_OMP_THREADING: check that number of threads (from eedata) matches
195        actual number (from env.var. setting).
196    o pkg/ebm:
197      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
198      - add multi-threaded test for verification exp. global_ocean_ebm
199    
200    checkpoint63b (2011/08/29)
201    o pkg/ebm:
202      - fix sign of runoff;
203      - update directly forcing fields (Qnet,EmPmR) to use standard
204        external_forcing_surf.F (remove ebm_forcing_surf.F);
205      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
206      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
207        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
208      - update global_ocean_ebm parameters file data and update output (fwd+ad).
209    o verification/matrix_example:
210      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
211        MPI and mutlti-threaded testing.
212    o pkg/matrix:
213      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
214      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
215      - fix for multi-threaded (remove DATA statement);
216      - use standard DIFFERENT_MULTIPLE function;
217      - add MATRIX_OPTIONS.h
218    o verification/matrix_example:
219       To allow to split the domain in several tiles, change the domain size
220        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
221        Western side) of land points.
222    o (*_)write_pickup:
223      - fix few bugs in mypackage_read/write_pickup.F
224      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
225        array of length 1 (was caught by compiler syntax-check).
226    o pkg/diagnostics (velocity potential solver):
227      - fix initialisation of main diagonal matrix (for overlap values)
228    o tools/build_options:
229      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
230        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
231      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
232        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
233        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
234        and use "-devel" testreport option for standard testing on baudelaire.
235    o pkg/grdchk:
236      - Assume that all gradient-check position are within the same tile
237        corresponding to global indices (iGloTile,jGloTile) and that
238        positions (i,j indices or nbeg) are local to this tile;
239      - set tile local-indices and proc. number according to tile global-indices;
240      - remove grdchkwhichproc from namelist (retired param);
241      - send adjoint gradient to all procs so that all procs print it to STDOUT;
242      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
243    o adding package bbl (Bottom Boundary Layer)
244      description in MITgcm/pkg/bbl/bbl_description.tex
245      example/test experiment in MITgcm_contrib/bbl
246    o adjoint verifications
247      - changed 5 experiments to multi-tiles
248        * global_ocean.90x40x15
249        * obcs_ctrl
250        * offline_exf_seaice
251        * tutorial_dic_adjoffline
252        * tutorial_tracer_adjsens
253        changed reference output for those that crossed tile boundaries
254        (changed choices of gradient check positions)
255      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
256      - temporary bug fix in grdchk_loc.F for obcs
257    o genmake2 & testreport
258      - add target "obj" (just for OBJFILES files) to Makefile;
259      - add option to specify FEXTRAFLAGS on command line.
260    o pkg/mypackage:
261      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
262    
263    checkpoint63a (2011/08/02)
264    o pkg/diagnostics (velocity potential):
265      - fix velocity-potential calculation when using OBCS: balance net inflow
266        at each level (new S/R OBCS_DIAG_BALANCE).
267      - fix some of the problems with OBCS in stream-function calculation.
268    o pkg/exf/exf_readparms.F
269      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
270        EXF_NML_OBCS) more consistent, so that you need not have these lists
271        in data.exf when they are not used.
272    o optim/optim_readdata.F:
273      - add some output about obcs variables that might help debugging
274      - add a check about nvarlength
275    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
276    o pkg/diagnostics (velocity potential):
277      - fix mask for OBCS (still problems in stream-function with OBCS);
278      - add specific parameter (default = main code CG2D params) for solver;
279      - in case of poor convergence, use solution corresponding to lowest residual.
280    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
281      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
282      and should be avoided where possible.
283    o model/src (rStar):
284      - include r* effect on reference-state (PhiRef) in totPhiHyd
285        (so that it's really the potential anomaly at the cell center);
286        affect solution only if z* with full pressure in EOS.
287      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
288        update output (because of z* in totPhiHyd and viscA4 changes);
289      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
290        @ constant r) until interpolation at constant r is implemented.
291    o pkg/diagnostics
292      - fix RCENTER diagnostics in case cell center is not at interface middle
293    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
294      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
295      that THETA and SALT are "conservative temperature" and "absolute
296      salinity"
297    o pkg/ctrl
298      - fix computation of endrec in s/r ctrl_init_rec
299      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
300    o pkg/seaice/seaice_growth.F
301      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
302        remove then obsolete STORE directives
303      - fix STORE directives for tice and tices, so that only the
304        appropriate part of the fields are stored (and not the entire
305        field); update global_ocean.cs32x15.seaice AD output.
306      - cosmetic changes: adjust CPP flags and indentation for better
307        legibilty
308    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
309      Chris Wilson)
310    o pkg/gmredi:
311       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
312       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
313    
314    checkpoint63  (2011/07/11)
315    o pkg/exch2:
316     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
317     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
318       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
319       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
320    o pkg/diagnostics:
321     - deal with pairs of post-processed diags which are computed together; in
322       particular, re-order list of diags within 1 file to save 2nd computation.
323     - add S/R to compute velocity stream-function (called after velocity-potential
324       calculation) from divergence free transport -> new diagnostics "PsiVEL".
325     - add parameter to select grid-point location where PsiVEL == 0.
326    o eesupp/src:
327       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
328       (specific S/R needed with exch2 topology - for now, just print an error msg)
329    o pkg/shelfice
330     - Implement friction velocity-dependent transfer coefficients following
331       Holland and Jenkins, JPO, 1999
332       Original code by M. Losch with small modifs.
333       Enable with CPP option SHI_ALLOW_GAMMAFRICT
334       and runtime flag SHELFICEuseGammaFrict
335    o verification lab_sea & global_ocean.cs32x15:
336     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
337       does not miss some dependencies (but is slower) and also works with many files
338       (default makedepend limitation for AD built).
339     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
340    o pkg/diagnostics:
341     - add run-time parameter "useMissingValue" (def=False) to fill land-point
342        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
343       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
344     - Extend the use of "missing_value" setting from data.diagnostics for the case
345       of counter-diagnostics (where fraction-weight is zero). This applies both to
346       MNC and MDS output files.
347    o pkg/seaice/seaice_growth.F:
348      - add 'a priori' cap of latent heat flux based on actual mass considerations
349        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
350        non-legacy seaice_solve4temp.
351      - add diagnostic of the residual sublimation freshwater flux (the freshwater
352        flux taken from the ocean if the total actual latent heat fluxes exceed
353        the maximum)
354      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
355       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
356      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
357       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
358      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
359      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
360    o verification 1D_ocean_ice_column:
361       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
362       update results
363    o pkg/diagnostics:
364     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
365       which are not filled-up but computed from other diags ; In this case, the mate
366       diag points to the primary (filled-up) diag to used for post processing.
367     - Update Velocity-potential computation using post-processed diag framework.
368     ==> Change the ordering of fields and time-periods in MDS output file
369       when using periodic averaging: now writes one time record with the full set
370       of fields for this time period, then the next time reccord (it used to be
371       one field with the full set of time records then the next field).
372         Note: this is now similar to NetCDF (MNC) output file. <==
373    
374    checkpoint62z (2011/06/21)
375    o adjoint monitor:
376     - Add adjoint monitor output for packages exf, seaice
377       and update relevant testreport output
378    o pkg/seaice:
379     - re-order diags inits so that they appear in order in available_diagnostics.log
380     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
381       area/heff/hsnow preceeding thermodynamic growth/melt.
382     - modified diag: SIdA; output actual effect, as the description states.
383     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
384     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
385       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
386        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
387     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
388     - added diagnostics for seaice generic tracers (SItr*).
389     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
390     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
391     I. Fenty: 18-Jun-2011:
392     Minor changes to seaice package:
393     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
394        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
395       - Differentiated "regularization variables" from "floor variables"
396        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
397        * hiceMin became SEAICE_hice_reg (old hiceMin)
398          (with _reg meaning regularization variable)
399       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
400        so as to ensure energy conservation when going between phases
401      - A22 was not used anywhere
402     2) Changed regularization procedure for heffActual and hsnowActual to ensure
403        well-boundedness and smooth adjoint in seaice_growth.F
404     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
405        because the old regularization always set heffActual >= 0.05 cm
406     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
407        on AREA when HEFF > 0.
408      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
409        requiring that DISABLE_AREA_FLOOR *not* be defined
410     Affected verifications:
411      - 1D_ocean_ice_column (output.txt output_adm.txt)
412      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
413    o pkg/diagnostics:
414      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
415      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
416        (was _RL, now integer) with option = 0 to retrieve all levels.
417      - add pieces of code to compute velocity potential at each level (new diagnostics
418        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
419        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
420      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
421        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
422        and in diagnostics_fract_fill.F (do not need a valid pointer for the
423        diagnostics counter-mate); check that definition of counter-diagnostic
424        includes a valid counter-mate (in diagnostics_set_levels.F).
425    o model/src (rStar):
426      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
427        affect solution only if z* with full pressure in EOS;
428        update output of test-exp global_ocean.90x40x15.
429    o pkg/seaice:
430      - introduce siEps=1e-5 parameter
431      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
432      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
433      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
434        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
435        as well as ice cover age and ridging index (attached to AREA).
436        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
437        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
438        Up to SItrMaxNum=3 tracers can be used simultaneously.
439    o pkg/salt_plume:
440      -introduce SPsalFRAC run time parameter that sets the fraction of the
441       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
442       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
443    o model debug options:
444      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
445        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
446      - Refine debug-msg printing selection (3 new levels):
447        debugMode  : controls printing of debug messages (sequence of S/R calls).
448        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
449         debLevZero =  0 ; /* level of disabled aux. msg printing */
450         debLevA =  1 ; /* level of minimum  aux. msg printing */
451         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
452         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
453         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
454         debLevE =  5 ; /* level of extensive debug printing */
455        New debugLevel default: with default debugMode value (=F),
456          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
457          and if debugMode=T, default debugLevel = 4 (debLevD).
458        Relation with previous settings:
459         debLevB (=2) corresponds to former debLevA (=1)
460         debLevD (=4) corresponds to former debLevB (=2)
461        Note:
462         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
463         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
464            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
465      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
466        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
467    o pkg/obcs:
468      - change OBCSfixTopo default from True to False (should not change the results);
469        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
470    o pkg/thsice:
471      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
472        2nd layer seaice sublimation (unlikely to happen)
473      - use Interior mask for OBCS in thsice_advection.F (similar to what is
474        done in gad_advection & seaice_advection).
475    o adjoint:
476      bug fix spotted by Gael Forget:
477      seaice_advection and thsice_advection still had
478      legacy CPP options to avoid CS corner updates for adjoint
479    o pkg/seaice:
480      => Change some of the defaults (2011/05/29):
481         - change SEAICEuseFluxForm default (from False to True)
482         - change DIFF1 default (from 0.004 m/s to 0. m/s)
483         And print warnings if DIFF1 is not set in data.seaice and centered
484          avection scheme is used without any diffusion.
485      also:
486      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
487      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
488      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
489        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
490        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
491      update results of test exp.:
492         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
493             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
494             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
495         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
496         seaice_obcs: output (SEAICEuseFluxForm=T)
497      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
498          for standard fwd & AD lab_sea tests (to keep the same output).
499    o pkg/seaice/seaice_growth.F:
500      - use Ian Fenty's capping formulas for actual ice
501      thickness thoughout EVOLUTION branch.
502      - put treatment pathological case #2) in CPP brackets
503      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
504      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
505    o pkg/seaice:
506      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
507      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
508      also pass fac as a param, which can be 1. (to update the tendency
509      field) or the time step (to update the field itself).
510      - seaice_advdiff.F: for multidim, call seaice_diffusion with
511      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
512      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
513      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
514      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
515    o pkg/seaice:
516      diffusion with centered advection scheme (diffus.F & advect.F):
517      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
518        to just compute the laplacian of input-field.
519      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
520      - fix flux-form version in diffus.F to conserve tracer.
521      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
522       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
523    
524    checkpoint62y (2011/05/26)
525    o pkg/seaice:
526     - seaice_growth.F : in EVOLUTION branch, always include
527       a_QSWbyATM_cover in qnet (as it should be).
528     - verification/global_ocean.cs32x15 : update results accordingly
529       (output.seaice.txt output_adm.seaice.txt).
530    o pkg/seaice + obcs:
531     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
532       equivalent of assuming no tracer gradient outside the OB region.
533       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
534     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
535       after changes above);
536     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
537       only at OB location (instead of over a band of OLx width).
538    o pkg/seaice:
539     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
540       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
541    o pkg/obcs:
542      - split header file "OBCS.h" into 4 separated files:
543        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
544       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
545         (contain no conditional statement which depends on OBCS options).
546      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
547        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
548    o ctrl, cost, grdchk & autodiff pkgs:
549      - make options file more standard (like other {PKG}_OPTIONS.h file but
550        with AD_CONFIG.h); clean-up some of the included header files.
551    o pkg/obcs:
552      - do not mask tracer when applying OB (tracer == 0 could generate problems)
553      - apply tracer OB values to tracer field only at OB location (instead of
554        over a band of OLx width)
555      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
556      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
557        obcs_apply_tloc.F & obcs_apply_sloc.F
558    o obcs in model/src:
559      - call OBCS_APPLY_W only if NonHydrostatic.
560      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
561      - reset dEtaHdt and wVel to zero outside OB interior region ;
562      - leave tracer unchanged outside OB interior region: This has no effect
563        on the solution but just to prevent unrealistic tracer value outside OB.
564      - zero out velocity outside OB interior region: This has no effect on
565        the solution but just to prevent unrealistic velocity outside OB.
566    o obcs and non-lin free-surf:
567       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
568       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
569       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
570       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
571       update results of test-exp. exp4(nlfs).
572    o exp4 (nlfs) test-exp:
573       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
574       with NonLin-FreeSurf); update output.nlfs.txt
575    o obcs and 2d/3d solver norm:
576       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
577       and outside OB interior region (will allow to place OB further inside the
578       domain). Depending on the domain, can affects cg2d-Norm (previous
579       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
580       and cg3d-Norm (previous Norm was computed before canceling OB terms),
581       e.g. in tutorial_plume_on_slope.
582      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
583    o pkg rbcs:
584      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
585      - add capability to apply relaxation to horizontal velocity uVel & vVel.
586    o pkg/grdchk: add gradient check for control variable xx_shifwflx
587    o pkg/shelfice/shelfice_init_fixed.F
588      fix CPP-flag combinations
589    o pkg/seaice: Merge iceage code of Pierre Rampal
590      * update/change/correct ice age calculations
591      * add age updates for pathological cases
592      Probably needs more testing...
593    
594    checkpoint62x (2011/05/13)
595    o pkg/mom_vecinv:
596       high-order vorticity scheme: use interior masks (maskInW & S)
597       to zero-out (outside OB) gradient of vorticity.
598    o verification exp.:
599       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
600       hs94.128x64x5 and seaice_obcs ; update results.
601    o pkg/obcs:
602      fix bug in OBeta for YZ sections in obcs_exf_load.F
603    o pkg/ctrl, pkg/shelfice, and optim:
604      - add new control variable xx_shifwflx (fresh water flux underneath ice
605        shelves). This is almost as tedious as obcs-ctrl, because the
606        variables needs its own mask.
607      - add a cost function term that penalizes the deviation of xx_shifwflx
608        from the first guess (zero) in analogy to other control variables
609    o pkg/shelfice:
610      - start basic adjoint
611    o pkg/ctrl:
612      - remove extra 2D field "for good measure" when initializing in
613        ctrl_set_globfld_[xy/xz/yz].F
614      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
615      - improve error messages in ctrl_set_unpack_*
616    o OBC implementation in momentum:
617       use interior masks (maskInC,W & S) in momentum S/R:
618       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
619       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
620       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
621       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
622       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
623        (and also with Leith/Smagorinsky harmonic-viscosity).
624       Update output of experiment dome and exp4 (+nlfs).
625    o exp4 test-exp:
626      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
627        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
628        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
629        time-varying OB at Western-side for wVel (NonHyd); update output.
630      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
631        and biharmonic-viscosity ; also use prescribed time varying OB.
632    o pkg/obcs:
633      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
634    o model/src:
635      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
636      - initialise startTime & nIter0 with unlikely values: allows to set one
637        from the other without ambiguity.
638    o seaice_obcs test-exp.:
639      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
640    o pkg/obcs:
641      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
642        no longer needed with maskInC,W,S in pkg/generic_advdiff.
643    o pkg/seaice:
644      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
645        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
646      - fixed bug in the initialization of sea ice salinity variable HSALT
647        in seaice_init_varia.F  (removed dependence on ICE2WATR)
648    o fizhi-cs test exp.:
649       switch reference output convention for these 2 non-standard test-exp,
650        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
651          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
652       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
653    o model/inc:
654      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
655        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
656    o pkg/seaice:
657      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
658    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
659      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
660        and initial HSALT
661    
662    checkpoint62w (2011/04/26)
663    o pkg/mom_fluxform:
664      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
665      - use parameter "sideDragFactor" in no-slip BC side-drag part.
666      - update output of exp. global_ocean.90x40x15
667    o pkg/mom_vecinv:
668      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
669    o update seaice exp.:
670      use more consistent parameter values (remove "backward compatability only":
671       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
672      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
673       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
674    o update test-exp global_ocean.90x40x15:
675      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
676      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
677      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
678      o turn on zStar & viscA4 in standard set-up (dir input/)
679        and update output files: output.txt & output.dwnslp.txt
680    o new AD-test experiment: obcs_ctrl
681      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
682    o pkg/dic:
683      fix two bugs in handling water vapour pressure in carbonate chemistry
684      and air-sea fluxes. Found by Val Bennington and Galen McKinley
685      (add DIC Option = WATERVAP_BUG to recover old results)
686      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
687    o adding allowInteriorFreezing option to check for water below freezing point
688      at depth and bring the negative heat anomaly to the surface level
689    o pkgs _fields_load:
690      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
691      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
692        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
693        rbcs to get interpolation weights and time reccord number.
694      - fix multi-threading in aim_fields_load.F
695      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
696    o external_fields_load:
697      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
698       interpolation weights) to use in a periodic time-series ; do not divide by
699       time-step to convert to integer:
700       - this fixes case where externForcingPeriod is not multiple of time-step
701          (Thanks to Christopher L. Wolfe)
702       - this fixes case where externForcingPeriod is an odd multiple of time-step
703         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
704      store index of time-record which is currently loaded:
705       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
706       - needed for the adjoint but not yet used because of extensive recomputations;
707         (to be fixed soon)
708    
709    checkpoint62v (2011/04/02)
710    o verification/1D_ocean_ice_column added to test Ian Fenty's
711      pkg/seaice_growth.F modifications for improving sea ice code differentiability
712    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
713      (new velocity statistics after changing maskInW & maskInS definition)
714    o pkg/generic_advdiff with OBCS:
715      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
716      equivalent to assumption of no tracer gradient outside the OB region.
717      This will affect the results if using obcs+biharmonic diffusion.
718      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
719    o pkg/obcs:
720      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
721      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
722      in Interior region. No impact on solution but affects Velocity monitor stats.
723    o pkg/ptracers (adjoint)
724      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
725      tape file for each tracer
726    o model/inc/src and pkg/autodiff: add parameters that allow to turn
727      of parts of the adjoint code at run time. For now, there are only
728      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
729      parameters are set in data.pkg.
730      This is the lazy coward's version of doing this, but still useful for
731      debugging. In order to do it right, everything needs to be moved to
732      pkg/autodiff.
733    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
734      the end; this fixes the adjoint balancing code for open boundaries.
735    o pkg/ctrl:
736      - change behavior of xx_${varname}period to be analogous to exf-conventions:
737        xx_${varname}period =   0.,  means time-independent control part
738        xx_${varname}period = -12., means one-year-periodic monthly control part
739      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
740        clean up ctrl_init a little, remove unused variables
741      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
742      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
743    
744    checkpoint62u (2011/03/15)
745    o model/src:
746      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
747        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
748      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
749        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
750    o pkg/ctrl/obcs/ecco:
751      - remove obsolete, unused, and partially broken code:
752        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
753        ALLOW_CTRL_OBCS_BALANCE
754      - put a stop statement into ecco/cost_obcsvol.F, but also add
755        cost_obcsvol to ecco_ad_diff.list
756    o pkg/ecco: fix counting cost function contributions for obcs (code
757      by Matt M.) and diffkr for diagnostics
758    o pkg/ecco, pkg/ctrl, pkg/grdchk:
759      add cost penalty terms for initial uvel, vvel, eta controls
760      and I/O for prior error files
761    o pkg/mdsio:
762       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
763       (new argument) to check for tiled file in mdsioLocalDir : this fix the
764       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
765    o pkg/ctrl:
766     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
767       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
768       unused and superfluous variables
769     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
770    o pkg/ecco
771     - enable adjoint of Stevens OB
772    o pkg/ctrl/ecco/grdchk:
773      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
774        Fortunately, we do not have any tests for the numerous cpp-flagged
775        option of "obcs as control parameters" so we will never know
776        if this is an improvement (but at least now things compile).
777      - remove an obsolete initialization from ecco_cost_init_barfiles.F
778      - fix some problems within never used ifdefs to make the code compile
779    o pkg/obcs:
780     - Refine Interior mask definition to work with more complex OB (e.g.
781       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
782       read in Interior mask from file. Check if Interior mask is consistent
783       with OB list of indices.
784    o pkg/seaice
785     - beginning code for a seaice tracer package,
786       but currently only used for seaice age: SEAICE_AGE
787       SEAICE_num = 4
788       iTracer = 1: area-weighted ice age
789               = 2: volume-weighted ice age
790               = 3, 4: template for one-year vs. multi-year ice
791       data.seaice has new namelist SEAICE_PARM03 for arrays related to
792       SEAICE_num
793    
794    checkpoint62t (2011/03/05)
795    o pkg/obcs:
796     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
797       then normal component. This ensures that the normal component is set
798       correctly even when it conficts with tangential setting from an other OB.
799       Affects results of test-experiment seaice_obcs: update the output.txt
800    o pkg/obcs:
801     - add code to monitor statistics of dynamical fields at OB.
802     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
803       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
804       - change default: balance the Net inflow through all OB (instead of balancing
805         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
806     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
807       to match Nortern OB inflow (OBCS_balanceFacN=0).
808    o pkg/seaice:
809     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
810    o pkg/seaice (seaice_growth v 1.113):
811     - reverting seaice_growth to v 1.111 in order to have code with exact bit
812       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
813       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
814       runtime flag SEAICEareaFormula is kept but is inactive
815    o model/src:
816     - add new param to scale curvilinear grid distance and area when using
817       a different sphere radius from the grid-files.
818     - test/check multi-threads EXCH applied to local variable (cg2d_x)
819    o adjoint:
820     - enable adjoint of Stevens OB
821     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
822       (a bit delicate because of potentially modified adj. common block structure;
823       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
824    
825    checkpoint62s (2011/02/15)
826    o pkg/seaice (seaice_growth v 1.112):
827     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
828       computing the ice cover tendency from effective thickness tendencies. Include
829       Ian Fenty's formula.
830     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
831       SEAICEareaFormula.
832     - simplify notations for the various d_HEFF/d_AREA terms.
833    o pkg/gmredi:
834     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
835       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
836       add a verification test-run (front_relax.bvp) to test GM_useBVP.
837    o pkg/seaice (seaice_growth v 1.111):
838     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
839     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
840       also melt ice.
841    o pkg/seaice:
842     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
843     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
844    o pkg/cheapaml:
845     - from Nico Wienders: New version of this package.
846    o pkg/flt:
847     - add CPP options to prevent floats to re-enter the opposite side of
848       a periodic domain (default: keep periodicity)
849    o pkg/gmredi:
850     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
851       (needed for multi-dim advection).
852     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
853    o model/src:
854     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
855    o tutorial_tracer_adjsens
856     - extend to NLFS and replace maskC by hFacC
857       (change reference output accordingly)
858    
859    checkpoint62r (2011/01/24)
860    o testreport:
861     - add option -deloutp (-do) to remove output file after successful run
862     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
863       extract exact list of procs from this file ; adjust COMMAND by
864       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
865  o pkg/ecco: replace old ineffective way of penalizing deviations from  o pkg/ecco: replace old ineffective way of penalizing deviations from
866    first guess (of obcs) with code by Matt Mazloff    first guess (of obcs) with code by Matt Mazloff
867  o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without  o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
868    exf/cal    exf/cal
869    - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl    - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
870      and handle case of obcs?period == 0      and handle case of obcs?period == 0
871      Not affected by these changes: There is still an inconsistency in      Not affected by these changes: There is still an inconsistency in
872      the computation of start/endrec for the obcs variables for ALLOW_CAL      the computation of start/endrec for the obcs variables for ALLOW_CAL
873      defined (see comment by Menemenlis, 7-Mar-2003)      defined (see comment by Menemenlis, 7-Mar-2003)
874    - make S/R ctrl_get_gen_rec return something meaningful even if    - make S/R ctrl_get_gen_rec return something meaningful even if
875      ALLOW_CAL is not defined      ALLOW_CAL is not defined
876    - ctrl_getobcs?: simplify code so that it does not need to use    - ctrl_getobcs?: simplify code so that it does not need to use
877                     S/R exf_swapfields                     S/R exf_swapfields
878  o testreport:  o testreport:
879     allow to test MPI with different number of processors for each experiment:     allow to test MPI with different number of processors for each experiment:
# Line 24  o testreport: Line 882  o testreport:
882  o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:  o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
883    alleviate the need for additional 3D tapes when using    alleviate the need for additional 3D tapes when using
884    the non-inear free surface in the adjoint. This is done    the non-inear free surface in the adjoint. This is done
885    by adding an 'update' of hfacc etc. to their current    by adding an 'update' of hfacc etc. to their current
886    value at the beginning of forward_step.F.    value at the beginning of forward_step.F.
887  o pkg/seaice  o pkg/seaice
888    seaice_lsr: move stress-divergence computations out of outer pseudo-    seaice_lsr: move stress-divergence computations out of outer pseudo-
889    timestepping loop    timestepping loop
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