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revision 1.1367 by mlosch, Wed Jan 19 13:52:14 2011 UTC revision 1.1529 by jmc, Mon Nov 7 22:28:38 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 model/src:
8      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
9        truncation) and add diagnostics for Adams-Bashforth tendency increment.
10      - update test-exp. AD output:
11        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
12      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
13        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
14        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
15        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
16        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
17        tutorial_plume_on_slope.
18    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
19      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
20      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
21      does not even come with an F77 compiler anymore, this should not be
22      a limitation
23    
24    checkpoint63e (2011/11/06)
25    o pkg/seaice adjoint of LSR:
26      - substantially rework STORE dirs.
27      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
28        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
29        and only perform SOLV_MAX_FIXED adjoint iters.
30        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
31        always goes to same record, meaning that the last forward field will be
32        the one used in the adjoint - an approximation.
33      - now produces non-zero LSR-related gradients, and acceptable gradients for
34        An's zonal (x-z) test case (to be checked in)
35      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
36        (but these are screwed up by the thermodynamics in the first place);
37        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
38        output_adm.txt also reflects changes to seaice_lsr
39      - global_ocean.cs32x15:
40        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
41          (output_adm.seaice.txt was updated)
42        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
43          (output_adm.seaice_dynmix.txt)
44    o test-exp. exp4+stevens:
45      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
46    o pkg/seaice (lsr solver):
47      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
48        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
49      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
50      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
51        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
52      - compute (with new S/R) and print initial (+ free-driff sol. if available)
53        and final residual of linearised system.
54    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
55      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
56    o pkg/obcs: Stevens BCs (still only for east and west)
57      - fix Stevens BCs by using intermediate velocities of previous
58        time step as "baroclinic" contribution rather velocity of one grid cell
59        inside the boundaries; more consistent but makes the entire treatment
60        more complicated, requires new pickup files and two new S/Rs:
61        obcs_copy_uv_n and obcs_save_uv_n
62        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
63        (undefined by default)
64      - silently move computation of some grid factors into separate loops to
65        save some recomputations
66      - add a hack for non-linear free surface
67      - add a verification experiment to exp4 that tests this code
68    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
69    
70    checkpoint63d (2011/10/25)
71    o pkg/obcs + seaice-dynamics:
72      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
73        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
74        values (consistent with an implicit method).
75      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
76        return to older implementation (same results as before); note that none of
77        the "experimental" OBCS_SEAICE options are implemented in the new version.
78      - switch test exp. seaice_obcs to use new version (update output).
79    o pkg/seaice:
80      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
81      - add parenthesis in Water-Ice drag calculations (evp & lsr);
82      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
83        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
84      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
85        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
86    o pkg/layers:
87      - Include potential density as new coordinate (Thanks to David Munday)
88    o pkg/dic:
89      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
90        carbonate computation/output to CALC_PCO2_APPROX
91    o pkg/generic_advdiff
92      - make TAF generate code that vectorizes:
93        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
94    o model/src:
95      - improve vectorization also for adjoint code of
96        solve_tridiagonal and solve_pentadiagonal. As this requires up to
97        5 new 3D-fields, this code is only turned on for the combination of
98        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
99        for singular matrix check (only for TARGET_NEC_SX).
100      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
101        ALLOW_AUTODIFF. This flag now needs to be set outside of
102        solve_tri/pentadiagonal.F
103    o pkg/exf:
104      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
105        optional namelist EXF_NML_OBCS).
106      - add many debug-print (to trace down where pkg/cal error msg comes from)
107    o pkg/mom_vecinv/mom_vi_hdissip.F
108      - rearrange loops so that vectorization is improved and in particular
109        the adjoint routine vectorizes. The code is a little longer now, but I
110        think easier to read.
111        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
112    o pkg/seaice:
113      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
114    o pkg/exch2:
115      - alternative code (without tile x tile matrix) for cumulated (global) sum;
116        used as default; keep using matrix version in adjustment.cs-32x32x1.
117    o tools/build_options:
118      - after merging some MPI and/or multi-threads specific optfiles so that
119        the modified default optfile support both built (using genmake2 -mpi
120        for the MPI built, using genmake2 -omp for OpenMP built),
121        move now obsolete optfiles to tools/build_options/unsupported/
122       (add copy of email sent to support list in doc/optfiles_changes.txt)
123    
124    checkpoint63c (2011/09/28)
125    o pkg/ebm:
126      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
127        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
128    o pkg/seaice (SItracer pickup)
129    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
130      To be done:
131      - thorough testing of missing fields in S/R seaice_read_pickup
132      - thorough matching between generic tracers and specific fields used
133        (e.g. volume-weighted age, area-weighted age, salinity, ...)
134    o pkg/grdchk:
135      - all procs calculate and print finite-difference gradient (for testreport)
136      - change description output used by testreport;
137      - AD testing: also compare and report Finite-difference gradient;
138        => update all output_adm*.txt
139    o test exp. global_ocean_ebm:
140      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
141        and turn on exactConserve; update (fwd) output.
142    o pkg/seaice (LSR):
143      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
144      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
145        * identical results with non-CS topology (but save up to half of EXCH calls)
146        * no much changes in cs-32 verification tests since no ice at face edges
147         (differences due to convergence criteria, since nb of iterations changed)
148        * expect some differences on lat-lon-cap grid.
149        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
150    o pkg/exch2:
151      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
152        many tiles); until alternative coding is added, just add a stop.
153    o pkg/kpp:
154      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
155        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
156    o optfiles:
157      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
158        into corresponding standard one, which now support different build:
159        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
160      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
161    o pkg/obcs (seaice):
162      - add missing EXCH for uIce,vIce after applying OBCS;
163      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
164        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
165        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
166      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
167      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
168        and eedata.mth for MPI and mutlti-threaded testing.
169    o pkg/flt:
170      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
171      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
172      - fix pickup and trajectories + profiles output with multi-threads;
173      - add parameter to select group of fields to write along trajectory and
174        profile (default unchanged);
175      - only call PORT_RAND* function when flt_noise <> 0;
176      - add multi-threaded test for verification exp. flt_example.
177    o eesupp/src:
178      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
179      - USE_OMP_THREADING: check that number of threads (from eedata) matches
180        actual number (from env.var. setting).
181    o pkg/ebm:
182      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
183      - add multi-threaded test for verification exp. global_ocean_ebm
184    
185    checkpoint63b (2011/08/29)
186    o pkg/ebm:
187      - fix sign of runoff;
188      - update directly forcing fields (Qnet,EmPmR) to use standard
189        external_forcing_surf.F (remove ebm_forcing_surf.F);
190      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
191      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
192        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
193      - update global_ocean_ebm parameters file data and update output (fwd+ad).
194    o verification/matrix_example:
195      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
196        MPI and mutlti-threaded testing.
197    o pkg/matrix:
198      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
199      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
200      - fix for multi-threaded (remove DATA statement);
201      - use standard DIFFERENT_MULTIPLE function;
202      - add MATRIX_OPTIONS.h
203    o verification/matrix_example:
204       To allow to split the domain in several tiles, change the domain size
205        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
206        Western side) of land points.
207    o (*_)write_pickup:
208      - fix few bugs in mypackage_read/write_pickup.F
209      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
210        array of length 1 (was caught by compiler syntax-check).
211    o pkg/diagnostics (velocity potential solver):
212      - fix initialisation of main diagonal matrix (for overlap values)
213    o tools/build_options:
214      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
215        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
216      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
217        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
218        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
219        and use "-devel" testreport option for standard testing on baudelaire.
220    o pkg/grdchk:
221      - Assume that all gradient-check position are within the same tile
222        corresponding to global indices (iGloTile,jGloTile) and that
223        positions (i,j indices or nbeg) are local to this tile;
224      - set tile local-indices and proc. number according to tile global-indices;
225      - remove grdchkwhichproc from namelist (retired param);
226      - send adjoint gradient to all procs so that all procs print it to STDOUT;
227      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
228    o adding package bbl (Bottom Boundary Layer)
229      description in MITgcm/pkg/bbl/bbl_description.tex
230      example/test experiment in MITgcm_contrib/bbl
231    o adjoint verifications
232      - changed 5 experiments to multi-tiles
233        * global_ocean.90x40x15
234        * obcs_ctrl
235        * offline_exf_seaice
236        * tutorial_dic_adjoffline
237        * tutorial_tracer_adjsens
238        changed reference output for those that crossed tile boundaries
239        (changed choices of gradient check positions)
240      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
241      - temporary bug fix in grdchk_loc.F for obcs
242    o genmake2 & testreport
243      - add target "obj" (just for OBJFILES files) to Makefile;
244      - add option to specify FEXTRAFLAGS on command line.
245    o pkg/mypackage:
246      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
247    
248    checkpoint63a (2011/08/02)
249    o pkg/diagnostics (velocity potential):
250      - fix velocity-potential calculation when using OBCS: balance net inflow
251        at each level (new S/R OBCS_DIAG_BALANCE).
252      - fix some of the problems with OBCS in stream-function calculation.
253    o pkg/exf/exf_readparms.F
254      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
255        EXF_NML_OBCS) more consistent, so that you need not have these lists
256        in data.exf when they are not used.
257    o optim/optim_readdata.F:
258      - add some output about obcs variables that might help debugging
259      - add a check about nvarlength
260    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
261    o pkg/diagnostics (velocity potential):
262      - fix mask for OBCS (still problems in stream-function with OBCS);
263      - add specific parameter (default = main code CG2D params) for solver;
264      - in case of poor convergence, use solution corresponding to lowest residual.
265    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
266      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
267      and should be avoided where possible.
268    o model/src (rStar):
269      - include r* effect on reference-state (PhiRef) in totPhiHyd
270        (so that it's really the potential anomaly at the cell center);
271        affect solution only if z* with full pressure in EOS.
272      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
273        update output (because of z* in totPhiHyd and viscA4 changes);
274      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
275        @ constant r) until interpolation at constant r is implemented.
276    o pkg/diagnostics
277      - fix RCENTER diagnostics in case cell center is not at interface middle
278    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
279      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
280      that THETA and SALT are "conservative temperature" and "absolute
281      salinity"
282    o pkg/ctrl
283      - fix computation of endrec in s/r ctrl_init_rec
284      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
285    o pkg/seaice/seaice_growth.F
286      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
287        remove then obsolete STORE directives
288      - fix STORE directives for tice and tices, so that only the
289        appropriate part of the fields are stored (and not the entire
290        field); update global_ocean.cs32x15.seaice AD output.
291      - cosmetic changes: adjust CPP flags and indentation for better
292        legibilty
293    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
294      Chris Wilson)
295    o pkg/gmredi:
296       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
297       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
298    
299    checkpoint63  (2011/07/11)
300    o pkg/exch2:
301     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
302     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
303       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
304       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
305    o pkg/diagnostics:
306     - deal with pairs of post-processed diags which are computed together; in
307       particular, re-order list of diags within 1 file to save 2nd computation.
308     - add S/R to compute velocity stream-function (called after velocity-potential
309       calculation) from divergence free transport -> new diagnostics "PsiVEL".
310     - add parameter to select grid-point location where PsiVEL == 0.
311    o eesupp/src:
312       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
313       (specific S/R needed with exch2 topology - for now, just print an error msg)
314    o pkg/shelfice
315     - Implement friction velocity-dependent transfer coefficients following
316       Holland and Jenkins, JPO, 1999
317       Original code by M. Losch with small modifs.
318       Enable with CPP option SHI_ALLOW_GAMMAFRICT
319       and runtime flag SHELFICEuseGammaFrict
320    o verification lab_sea & global_ocean.cs32x15:
321     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
322       does not miss some dependencies (but is slower) and also works with many files
323       (default makedepend limitation for AD built).
324     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
325    o pkg/diagnostics:
326     - add run-time parameter "useMissingValue" (def=False) to fill land-point
327        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
328       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
329     - Extend the use of "missing_value" setting from data.diagnostics for the case
330       of counter-diagnostics (where fraction-weight is zero). This applies both to
331       MNC and MDS output files.
332    o pkg/seaice/seaice_growth.F:
333      - add 'a priori' cap of latent heat flux based on actual mass considerations
334        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
335        non-legacy seaice_solve4temp.
336      - add diagnostic of the residual sublimation freshwater flux (the freshwater
337        flux taken from the ocean if the total actual latent heat fluxes exceed
338        the maximum)
339      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
340       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
341      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
342       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
343      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
344      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
345    o verification 1D_ocean_ice_column:
346       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
347       update results
348    o pkg/diagnostics:
349     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
350       which are not filled-up but computed from other diags ; In this case, the mate
351       diag points to the primary (filled-up) diag to used for post processing.
352     - Update Velocity-potential computation using post-processed diag framework.
353     ==> Change the ordering of fields and time-periods in MDS output file
354       when using periodic averaging: now writes one time record with the full set
355       of fields for this time period, then the next time reccord (it used to be
356       one field with the full set of time records then the next field).
357         Note: this is now similar to NetCDF (MNC) output file. <==
358    
359    checkpoint62z (2011/06/21)
360    o adjoint monitor:
361     - Add adjoint monitor output for packages exf, seaice
362       and update relevant testreport output
363    o pkg/seaice:
364     - re-order diags inits so that they appear in order in available_diagnostics.log
365     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
366       area/heff/hsnow preceeding thermodynamic growth/melt.
367     - modified diag: SIdA; output actual effect, as the description states.
368     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
369     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
370       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
371        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
372     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
373     - added diagnostics for seaice generic tracers (SItr*).
374     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
375     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
376     I. Fenty: 18-Jun-2011:
377     Minor changes to seaice package:
378     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
379        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
380       - Differentiated "regularization variables" from "floor variables"
381        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
382        * hiceMin became SEAICE_hice_reg (old hiceMin)
383          (with _reg meaning regularization variable)
384       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
385        so as to ensure energy conservation when going between phases
386      - A22 was not used anywhere
387     2) Changed regularization procedure for heffActual and hsnowActual to ensure
388        well-boundedness and smooth adjoint in seaice_growth.F
389     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
390        because the old regularization always set heffActual >= 0.05 cm
391     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
392        on AREA when HEFF > 0.
393      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
394        requiring that DISABLE_AREA_FLOOR *not* be defined
395     Affected verifications:
396      - 1D_ocean_ice_column (output.txt output_adm.txt)
397      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
398    o pkg/diagnostics:
399      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
400      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
401        (was _RL, now integer) with option = 0 to retrieve all levels.
402      - add pieces of code to compute velocity potential at each level (new diagnostics
403        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
404        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
405      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
406        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
407        and in diagnostics_fract_fill.F (do not need a valid pointer for the
408        diagnostics counter-mate); check that definition of counter-diagnostic
409        includes a valid counter-mate (in diagnostics_set_levels.F).
410    o model/src (rStar):
411      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
412        affect solution only if z* with full pressure in EOS;
413        update output of test-exp global_ocean.90x40x15.
414    o pkg/seaice:
415      - introduce siEps=1e-5 parameter
416      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
417      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
418      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
419        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
420        as well as ice cover age and ridging index (attached to AREA).
421        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
422        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
423        Up to SItrMaxNum=3 tracers can be used simultaneously.
424    o pkg/salt_plume:
425      -introduce SPsalFRAC run time parameter that sets the fraction of the
426       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
427       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
428    o model debug options:
429      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
430        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
431      - Refine debug-msg printing selection (3 new levels):
432        debugMode  : controls printing of debug messages (sequence of S/R calls).
433        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
434         debLevZero =  0 ; /* level of disabled aux. msg printing */
435         debLevA =  1 ; /* level of minimum  aux. msg printing */
436         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
437         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
438         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
439         debLevE =  5 ; /* level of extensive debug printing */
440        New debugLevel default: with default debugMode value (=F),
441          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
442          and if debugMode=T, default debugLevel = 4 (debLevD).
443        Relation with previous settings:
444         debLevB (=2) corresponds to former debLevA (=1)
445         debLevD (=4) corresponds to former debLevB (=2)
446        Note:
447         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
448         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
449            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
450      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
451        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
452    o pkg/obcs:
453      - change OBCSfixTopo default from True to False (should not change the results);
454        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
455    o pkg/thsice:
456      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
457        2nd layer seaice sublimation (unlikely to happen)
458      - use Interior mask for OBCS in thsice_advection.F (similar to what is
459        done in gad_advection & seaice_advection).
460    o adjoint:
461      bug fix spotted by Gael Forget:
462      seaice_advection and thsice_advection still had
463      legacy CPP options to avoid CS corner updates for adjoint
464    o pkg/seaice:
465      => Change some of the defaults (2011/05/29):
466         - change SEAICEuseFluxForm default (from False to True)
467         - change DIFF1 default (from 0.004 m/s to 0. m/s)
468         And print warnings if DIFF1 is not set in data.seaice and centered
469          avection scheme is used without any diffusion.
470      also:
471      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
472      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
473      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
474        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
475        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
476      update results of test exp.:
477         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
478             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
479             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
480         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
481         seaice_obcs: output (SEAICEuseFluxForm=T)
482      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
483          for standard fwd & AD lab_sea tests (to keep the same output).
484    o pkg/seaice/seaice_growth.F:
485      - use Ian Fenty's capping formulas for actual ice
486      thickness thoughout EVOLUTION branch.
487      - put treatment pathological case #2) in CPP brackets
488      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
489      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
490    o pkg/seaice:
491      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
492      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
493      also pass fac as a param, which can be 1. (to update the tendency
494      field) or the time step (to update the field itself).
495      - seaice_advdiff.F: for multidim, call seaice_diffusion with
496      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
497      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
498      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
499      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
500    o pkg/seaice:
501      diffusion with centered advection scheme (diffus.F & advect.F):
502      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
503        to just compute the laplacian of input-field.
504      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
505      - fix flux-form version in diffus.F to conserve tracer.
506      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
507       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
508    
509    checkpoint62y (2011/05/26)
510    o pkg/seaice:
511     - seaice_growth.F : in EVOLUTION branch, always include
512       a_QSWbyATM_cover in qnet (as it should be).
513     - verification/global_ocean.cs32x15 : update results accordingly
514       (output.seaice.txt output_adm.seaice.txt).
515    o pkg/seaice + obcs:
516     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
517       equivalent of assuming no tracer gradient outside the OB region.
518       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
519     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
520       after changes above);
521     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
522       only at OB location (instead of over a band of OLx width).
523    o pkg/seaice:
524     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
525       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
526    o pkg/obcs:
527      - split header file "OBCS.h" into 4 separated files:
528        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
529       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
530         (contain no conditional statement which depends on OBCS options).
531      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
532        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
533    o ctrl, cost, grdchk & autodiff pkgs:
534      - make options file more standard (like other {PKG}_OPTIONS.h file but
535        with AD_CONFIG.h); clean-up some of the included header files.
536    o pkg/obcs:
537      - do not mask tracer when applying OB (tracer == 0 could generate problems)
538      - apply tracer OB values to tracer field only at OB location (instead of
539        over a band of OLx width)
540      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
541      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
542        obcs_apply_tloc.F & obcs_apply_sloc.F
543    o obcs in model/src:
544      - call OBCS_APPLY_W only if NonHydrostatic.
545      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
546      - reset dEtaHdt and wVel to zero outside OB interior region ;
547      - leave tracer unchanged outside OB interior region: This has no effect
548        on the solution but just to prevent unrealistic tracer value outside OB.
549      - zero out velocity outside OB interior region: This has no effect on
550        the solution but just to prevent unrealistic velocity outside OB.
551    o obcs and non-lin free-surf:
552       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
553       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
554       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
555       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
556       update results of test-exp. exp4(nlfs).
557    o exp4 (nlfs) test-exp:
558       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
559       with NonLin-FreeSurf); update output.nlfs.txt
560    o obcs and 2d/3d solver norm:
561       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
562       and outside OB interior region (will allow to place OB further inside the
563       domain). Depending on the domain, can affects cg2d-Norm (previous
564       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
565       and cg3d-Norm (previous Norm was computed before canceling OB terms),
566       e.g. in tutorial_plume_on_slope.
567      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
568    o pkg rbcs:
569      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
570      - add capability to apply relaxation to horizontal velocity uVel & vVel.
571    o pkg/grdchk: add gradient check for control variable xx_shifwflx
572    o pkg/shelfice/shelfice_init_fixed.F
573      fix CPP-flag combinations
574    o pkg/seaice: Merge iceage code of Pierre Rampal
575      * update/change/correct ice age calculations
576      * add age updates for pathological cases
577      Probably needs more testing...
578    
579    checkpoint62x (2011/05/13)
580    o pkg/mom_vecinv:
581       high-order vorticity scheme: use interior masks (maskInW & S)
582       to zero-out (outside OB) gradient of vorticity.
583    o verification exp.:
584       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
585       hs94.128x64x5 and seaice_obcs ; update results.
586    o pkg/obcs:
587      fix bug in OBeta for YZ sections in obcs_exf_load.F
588    o pkg/ctrl, pkg/shelfice, and optim:
589      - add new control variable xx_shifwflx (fresh water flux underneath ice
590        shelves). This is almost as tedious as obcs-ctrl, because the
591        variables needs its own mask.
592      - add a cost function term that penalizes the deviation of xx_shifwflx
593        from the first guess (zero) in analogy to other control variables
594    o pkg/shelfice:
595      - start basic adjoint
596    o pkg/ctrl:
597      - remove extra 2D field "for good measure" when initializing in
598        ctrl_set_globfld_[xy/xz/yz].F
599      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
600      - improve error messages in ctrl_set_unpack_*
601    o OBC implementation in momentum:
602       use interior masks (maskInC,W & S) in momentum S/R:
603       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
604       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
605       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
606       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
607       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
608        (and also with Leith/Smagorinsky harmonic-viscosity).
609       Update output of experiment dome and exp4 (+nlfs).
610    o exp4 test-exp:
611      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
612        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
613        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
614        time-varying OB at Western-side for wVel (NonHyd); update output.
615      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
616        and biharmonic-viscosity ; also use prescribed time varying OB.
617    o pkg/obcs:
618      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
619    o model/src:
620      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
621      - initialise startTime & nIter0 with unlikely values: allows to set one
622        from the other without ambiguity.
623    o seaice_obcs test-exp.:
624      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
625    o pkg/obcs:
626      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
627        no longer needed with maskInC,W,S in pkg/generic_advdiff.
628    o pkg/seaice:
629      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
630        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
631      - fixed bug in the initialization of sea ice salinity variable HSALT
632        in seaice_init_varia.F  (removed dependence on ICE2WATR)
633    o fizhi-cs test exp.:
634       switch reference output convention for these 2 non-standard test-exp,
635        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
636          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
637       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
638    o model/inc:
639      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
640        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
641    o pkg/seaice:
642      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
643    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
644      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
645        and initial HSALT
646    
647    checkpoint62w (2011/04/26)
648    o pkg/mom_fluxform:
649      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
650      - use parameter "sideDragFactor" in no-slip BC side-drag part.
651      - update output of exp. global_ocean.90x40x15
652    o pkg/mom_vecinv:
653      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
654    o update seaice exp.:
655      use more consistent parameter values (remove "backward compatability only":
656       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
657      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
658       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
659    o update test-exp global_ocean.90x40x15:
660      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
661      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
662      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
663      o turn on zStar & viscA4 in standard set-up (dir input/)
664        and update output files: output.txt & output.dwnslp.txt
665    o new AD-test experiment: obcs_ctrl
666      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
667    o pkg/dic:
668      fix two bugs in handling water vapour pressure in carbonate chemistry
669      and air-sea fluxes. Found by Val Bennington and Galen McKinley
670      (add DIC Option = WATERVAP_BUG to recover old results)
671      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
672    o adding allowInteriorFreezing option to check for water below freezing point
673      at depth and bring the negative heat anomaly to the surface level
674    o pkgs _fields_load:
675      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
676      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
677        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
678        rbcs to get interpolation weights and time reccord number.
679      - fix multi-threading in aim_fields_load.F
680      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
681    o external_fields_load:
682      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
683       interpolation weights) to use in a periodic time-series ; do not divide by
684       time-step to convert to integer:
685       - this fixes case where externForcingPeriod is not multiple of time-step
686          (Thanks to Christopher L. Wolfe)
687       - this fixes case where externForcingPeriod is an odd multiple of time-step
688         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
689      store index of time-record which is currently loaded:
690       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
691       - needed for the adjoint but not yet used because of extensive recomputations;
692         (to be fixed soon)
693    
694    checkpoint62v (2011/04/02)
695    o verification/1D_ocean_ice_column added to test Ian Fenty's
696      pkg/seaice_growth.F modifications for improving sea ice code differentiability
697    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
698      (new velocity statistics after changing maskInW & maskInS definition)
699    o pkg/generic_advdiff with OBCS:
700      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
701      equivalent to assumption of no tracer gradient outside the OB region.
702      This will affect the results if using obcs+biharmonic diffusion.
703      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
704    o pkg/obcs:
705      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
706      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
707      in Interior region. No impact on solution but affects Velocity monitor stats.
708    o pkg/ptracers (adjoint)
709      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
710      tape file for each tracer
711    o model/inc/src and pkg/autodiff: add parameters that allow to turn
712      of parts of the adjoint code at run time. For now, there are only
713      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
714      parameters are set in data.pkg.
715      This is the lazy coward's version of doing this, but still useful for
716      debugging. In order to do it right, everything needs to be moved to
717      pkg/autodiff.
718    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
719      the end; this fixes the adjoint balancing code for open boundaries.
720    o pkg/ctrl:
721      - change behavior of xx_${varname}period to be analogous to exf-conventions:
722        xx_${varname}period =   0.,  means time-independent control part
723        xx_${varname}period = -12., means one-year-periodic monthly control part
724      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
725        clean up ctrl_init a little, remove unused variables
726      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
727      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
728    
729    checkpoint62u (2011/03/15)
730    o model/src:
731      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
732        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
733      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
734        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
735    o pkg/ctrl/obcs/ecco:
736      - remove obsolete, unused, and partially broken code:
737        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
738        ALLOW_CTRL_OBCS_BALANCE
739      - put a stop statement into ecco/cost_obcsvol.F, but also add
740        cost_obcsvol to ecco_ad_diff.list
741    o pkg/ecco: fix counting cost function contributions for obcs (code
742      by Matt M.) and diffkr for diagnostics
743    o pkg/ecco, pkg/ctrl, pkg/grdchk:
744      add cost penalty terms for initial uvel, vvel, eta controls
745      and I/O for prior error files
746    o pkg/mdsio:
747       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
748       (new argument) to check for tiled file in mdsioLocalDir : this fix the
749       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
750    o pkg/ctrl:
751     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
752       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
753       unused and superfluous variables
754     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
755    o pkg/ecco
756     - enable adjoint of Stevens OB
757    o pkg/ctrl/ecco/grdchk:
758      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
759        Fortunately, we do not have any tests for the numerous cpp-flagged
760        option of "obcs as control parameters" so we will never know
761        if this is an improvement (but at least now things compile).
762      - remove an obsolete initialization from ecco_cost_init_barfiles.F
763      - fix some problems within never used ifdefs to make the code compile
764    o pkg/obcs:
765     - Refine Interior mask definition to work with more complex OB (e.g.
766       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
767       read in Interior mask from file. Check if Interior mask is consistent
768       with OB list of indices.
769    o pkg/seaice
770     - beginning code for a seaice tracer package,
771       but currently only used for seaice age: SEAICE_AGE
772       SEAICE_num = 4
773       iTracer = 1: area-weighted ice age
774               = 2: volume-weighted ice age
775               = 3, 4: template for one-year vs. multi-year ice
776       data.seaice has new namelist SEAICE_PARM03 for arrays related to
777       SEAICE_num
778    
779    checkpoint62t (2011/03/05)
780    o pkg/obcs:
781     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
782       then normal component. This ensures that the normal component is set
783       correctly even when it conficts with tangential setting from an other OB.
784       Affects results of test-experiment seaice_obcs: update the output.txt
785    o pkg/obcs:
786     - add code to monitor statistics of dynamical fields at OB.
787     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
788       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
789       - change default: balance the Net inflow through all OB (instead of balancing
790         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
791     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
792       to match Nortern OB inflow (OBCS_balanceFacN=0).
793    o pkg/seaice:
794     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
795    o pkg/seaice (seaice_growth v 1.113):
796     - reverting seaice_growth to v 1.111 in order to have code with exact bit
797       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
798       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
799       runtime flag SEAICEareaFormula is kept but is inactive
800    o model/src:
801     - add new param to scale curvilinear grid distance and area when using
802       a different sphere radius from the grid-files.
803     - test/check multi-threads EXCH applied to local variable (cg2d_x)
804    o adjoint:
805     - enable adjoint of Stevens OB
806     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
807       (a bit delicate because of potentially modified adj. common block structure;
808       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
809    
810    checkpoint62s (2011/02/15)
811    o pkg/seaice (seaice_growth v 1.112):
812     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
813       computing the ice cover tendency from effective thickness tendencies. Include
814       Ian Fenty's formula.
815     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
816       SEAICEareaFormula.
817     - simplify notations for the various d_HEFF/d_AREA terms.
818    o pkg/gmredi:
819     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
820       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
821       add a verification test-run (front_relax.bvp) to test GM_useBVP.
822    o pkg/seaice (seaice_growth v 1.111):
823     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
824     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
825       also melt ice.
826    o pkg/seaice:
827     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
828     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
829    o pkg/cheapaml:
830     - from Nico Wienders: New version of this package.
831    o pkg/flt:
832     - add CPP options to prevent floats to re-enter the opposite side of
833       a periodic domain (default: keep periodicity)
834    o pkg/gmredi:
835     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
836       (needed for multi-dim advection).
837     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
838    o model/src:
839     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
840    o tutorial_tracer_adjsens
841     - extend to NLFS and replace maskC by hFacC
842       (change reference output accordingly)
843    
844    checkpoint62r (2011/01/24)
845    o testreport:
846     - add option -deloutp (-do) to remove output file after successful run
847     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
848       extract exact list of procs from this file ; adjust COMMAND by
849       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
850  o pkg/ecco: replace old ineffective way of penalizing deviations from  o pkg/ecco: replace old ineffective way of penalizing deviations from
851    first guess (of obcs) with code by Matt Mazloff    first guess (of obcs) with code by Matt Mazloff
852  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
853    exf/cal    exf/cal
854    - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl    - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
855      and handle case of obcs?period == 0      and handle case of obcs?period == 0
856      Not affected by these changes: There is still an inconsistency in      Not affected by these changes: There is still an inconsistency in
857      the computation of start/endrec for the obcs variables for ALLOW_CAL      the computation of start/endrec for the obcs variables for ALLOW_CAL
858      defined (see comment by Menemenlis, 7-Mar-2003)      defined (see comment by Menemenlis, 7-Mar-2003)
859    - make S/R ctrl_get_gen_rec return something meaningful even if    - make S/R ctrl_get_gen_rec return something meaningful even if
860      ALLOW_CAL is not defined      ALLOW_CAL is not defined
861    - ctrl_getobcs?: simplify code so that it does not need to use    - ctrl_getobcs?: simplify code so that it does not need to use
862                     S/R exf_swapfields                     S/R exf_swapfields
863  o testreport:  o testreport:
864     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 867  o testreport:
867  o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:  o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
868    alleviate the need for additional 3D tapes when using    alleviate the need for additional 3D tapes when using
869    the non-inear free surface in the adjoint. This is done    the non-inear free surface in the adjoint. This is done
870    by adding an 'update' of hfacc etc. to their current    by adding an 'update' of hfacc etc. to their current
871    value at the beginning of forward_step.F.    value at the beginning of forward_step.F.
872  o pkg/seaice  o pkg/seaice
873    seaice_lsr: move stress-divergence computations out of outer pseudo-    seaice_lsr: move stress-divergence computations out of outer pseudo-
874    timestepping loop    timestepping loop
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