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revision 1.1396 by mlosch, Mon Mar 14 17:35:43 2011 UTC revision 1.1543 by mmazloff, Tue Dec 6 04:19:24 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 pkg/ctrl/obcs/ecco:  o pkg/ecco
8      - added IES cost term
9    o verification/advect_xz
10      - scale down the depth by 1/100 (from 200 km to just 2.km)
11      - add secondary test using divergent flow, r-star and implicit vertical advection.
12    o pkg/rbcs:
13      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
14    o pkg/obcs (Stevens BCs):
15      - fix various problems in the phase speed computations of the Stevens
16        boundary conditions:
17        - sign error for western and southern boundaries,
18        - time tendencies were underestimated by factor of dTracerLev and some just
19          zero (for multidim advection schemes) -> now estimate time tendencies
20          from difference between previous (n) time level and the one before (n-1);
21          this requires storing a field per tracer per boundary, also in the pickup
22          files.
23        - replace deltaTmom in cflMer/Zon computation with dTracerLev
24        - set default phase velocity to cflMer/Zon
25      - update verification experiment exp4.stevens
26    o pkg/generic_advdiff (implicit_r):
27      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
28        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
29      - fix implicit vertical diffusion or advection with NonLin FreeSurf
30        (was using current recip_hFacC instead of future recip_hFacC): set future
31        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
32        solver S/R ;
33      - fill diagnostics of vertical advective fluxes (computed from tendency)
34        when using implicit vert. advection;
35      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
36         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
37         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
38         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
39    o pkg/diagnostics:
40      - add diags for T & S tendency which goes through Adams-Bashforth.
41    
42    checkpoint63f (2011/11/30)
43    o pkg/obcs/obcs_calc_stevens.F:
44      - join some loops to reduce number of if-statements
45      - fix a bug in code for northern and southern boundaries.
46    o pkg/seaice/seaice_init_varia.F
47      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
48        caused zero ice-velocities for the B-grid code
49    o pkg/seaice/seaice_init_fixed.F
50      - fix a bug in the initialisation of the second metric terms
51        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
52      - this affects all seaice configurations with useCurviLinearGrid = .true.
53        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
54        = .true. (default)
55      - the only verification experiment affected is global_ocean.cs32x15:
56        icedyn, seaice, and seaice_dynmix (AD)
57    o pkg/thsice/thsice_diagnostics_state.F
58      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
59        not contain garbage that can lead to surprises in diagstats_calc.F
60    o model/src:
61      - move bi,bj loops inside INTEGR_CONTINUITY ;
62      - call INTEGR_CONTINUITY directly from forward_step.F
63        (previously called from momentum_correction_step.F)
64      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
65        forward_step.F and pkg/ecco/the_main_loop.F
66    o model/src/do_oceanic_phys.F:
67      - reset addMass to zero only if useICEFRONT ;
68      - separated k-loop for rhoInSitu calculation ;
69      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
70        and at constant T,S (= WdRHOdP);
71      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
72        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
73        transport of locally-referenced potential density);
74        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
75    o gluemnc:
76      - replace ncrcat with ncks when adding variables to *.glob.nc
77      - change the way variables without record dimensions are handled so that
78        files that have variables with and without record variables can be glued:
79        add a record dimension with a new unique name to be able to differentiate
80        between variable with and without a-prior record dimensions. Remove
81        this record dimension before adding the variable to the *.glob.nc file.
82        This procedure automatically works also for grid.*.nc files that do not
83        have any record dimension.
84    o verification/cpl_aim+ocn:
85      - generate new reference output on baudelaire (gfortran, mpich2) (previously
86        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
87    o pkg/obcs/obcs_calc_stevens.F:
88      - add code for northern and southern boundaries.
89      - reorder some loops to save some operations and so that drFBar can be scalar
90    o model/src:
91      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
92        truncation) and add diagnostics for Adams-Bashforth tendency increment.
93      - update test-exp. AD output:
94        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
95      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
96        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
97        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
98        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
99        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
100        tutorial_plume_on_slope.
101    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
102      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
103      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
104      does not even come with an F77 compiler anymore, this should not be
105      a limitation
106    
107    checkpoint63e (2011/11/06)
108    o pkg/seaice adjoint of LSR:
109      - substantially rework STORE dirs.
110      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
111        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
112        and only perform SOLV_MAX_FIXED adjoint iters.
113        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
114        always goes to same record, meaning that the last forward field will be
115        the one used in the adjoint - an approximation.
116      - now produces non-zero LSR-related gradients, and acceptable gradients for
117        An's zonal (x-z) test case (to be checked in)
118      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
119        (but these are screwed up by the thermodynamics in the first place);
120        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
121        output_adm.txt also reflects changes to seaice_lsr
122      - global_ocean.cs32x15:
123        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
124          (output_adm.seaice.txt was updated)
125        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
126          (output_adm.seaice_dynmix.txt)
127    o test-exp. exp4+stevens:
128      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
129    o pkg/seaice (lsr solver):
130      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
131        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
132      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
133      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
134        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
135      - compute (with new S/R) and print initial (+ free-driff sol. if available)
136        and final residual of linearised system.
137    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
138      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
139    o pkg/obcs: Stevens BCs (still only for east and west)
140      - fix Stevens BCs by using intermediate velocities of previous
141        time step as "baroclinic" contribution rather velocity of one grid cell
142        inside the boundaries; more consistent but makes the entire treatment
143        more complicated, requires new pickup files and two new S/Rs:
144        obcs_copy_uv_n and obcs_save_uv_n
145        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
146        (undefined by default)
147      - silently move computation of some grid factors into separate loops to
148        save some recomputations
149      - add a hack for non-linear free surface
150      - add a verification experiment to exp4 that tests this code
151    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
152    
153    checkpoint63d (2011/10/25)
154    o pkg/obcs + seaice-dynamics:
155      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
156        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
157        values (consistent with an implicit method).
158      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
159        return to older implementation (same results as before); note that none of
160        the "experimental" OBCS_SEAICE options are implemented in the new version.
161      - switch test exp. seaice_obcs to use new version (update output).
162    o pkg/seaice:
163      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
164      - add parenthesis in Water-Ice drag calculations (evp & lsr);
165      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
166        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
167      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
168        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
169    o pkg/layers:
170      - Include potential density as new coordinate (Thanks to David Munday)
171    o pkg/dic:
172      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
173        carbonate computation/output to CALC_PCO2_APPROX
174    o pkg/generic_advdiff
175      - make TAF generate code that vectorizes:
176        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
177    o model/src:
178      - improve vectorization also for adjoint code of
179        solve_tridiagonal and solve_pentadiagonal. As this requires up to
180        5 new 3D-fields, this code is only turned on for the combination of
181        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
182        for singular matrix check (only for TARGET_NEC_SX).
183      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
184        ALLOW_AUTODIFF. This flag now needs to be set outside of
185        solve_tri/pentadiagonal.F
186    o pkg/exf:
187      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
188        optional namelist EXF_NML_OBCS).
189      - add many debug-print (to trace down where pkg/cal error msg comes from)
190    o pkg/mom_vecinv/mom_vi_hdissip.F
191      - rearrange loops so that vectorization is improved and in particular
192        the adjoint routine vectorizes. The code is a little longer now, but I
193        think easier to read.
194        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
195    o pkg/seaice:
196      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
197    o pkg/exch2:
198      - alternative code (without tile x tile matrix) for cumulated (global) sum;
199        used as default; keep using matrix version in adjustment.cs-32x32x1.
200    o tools/build_options:
201      - after merging some MPI and/or multi-threads specific optfiles so that
202        the modified default optfile support both built (using genmake2 -mpi
203        for the MPI built, using genmake2 -omp for OpenMP built),
204        move now obsolete optfiles to tools/build_options/unsupported/
205       (add copy of email sent to support list in doc/optfiles_changes.txt)
206    
207    checkpoint63c (2011/09/28)
208    o pkg/ebm:
209      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
210        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
211    o pkg/seaice (SItracer pickup)
212    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
213      To be done:
214      - thorough testing of missing fields in S/R seaice_read_pickup
215      - thorough matching between generic tracers and specific fields used
216        (e.g. volume-weighted age, area-weighted age, salinity, ...)
217    o pkg/grdchk:
218      - all procs calculate and print finite-difference gradient (for testreport)
219      - change description output used by testreport;
220      - AD testing: also compare and report Finite-difference gradient;
221        => update all output_adm*.txt
222    o test exp. global_ocean_ebm:
223      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
224        and turn on exactConserve; update (fwd) output.
225    o pkg/seaice (LSR):
226      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
227      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
228        * identical results with non-CS topology (but save up to half of EXCH calls)
229        * no much changes in cs-32 verification tests since no ice at face edges
230         (differences due to convergence criteria, since nb of iterations changed)
231        * expect some differences on lat-lon-cap grid.
232        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
233    o pkg/exch2:
234      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
235        many tiles); until alternative coding is added, just add a stop.
236    o pkg/kpp:
237      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
238        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
239    o optfiles:
240      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
241        into corresponding standard one, which now support different build:
242        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
243      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
244    o pkg/obcs (seaice):
245      - add missing EXCH for uIce,vIce after applying OBCS;
246      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
247        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
248        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
249      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
250      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
251        and eedata.mth for MPI and mutlti-threaded testing.
252    o pkg/flt:
253      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
254      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
255      - fix pickup and trajectories + profiles output with multi-threads;
256      - add parameter to select group of fields to write along trajectory and
257        profile (default unchanged);
258      - only call PORT_RAND* function when flt_noise <> 0;
259      - add multi-threaded test for verification exp. flt_example.
260    o eesupp/src:
261      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
262      - USE_OMP_THREADING: check that number of threads (from eedata) matches
263        actual number (from env.var. setting).
264    o pkg/ebm:
265      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
266      - add multi-threaded test for verification exp. global_ocean_ebm
267    
268    checkpoint63b (2011/08/29)
269    o pkg/ebm:
270      - fix sign of runoff;
271      - update directly forcing fields (Qnet,EmPmR) to use standard
272        external_forcing_surf.F (remove ebm_forcing_surf.F);
273      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
274      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
275        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
276      - update global_ocean_ebm parameters file data and update output (fwd+ad).
277    o verification/matrix_example:
278      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
279        MPI and mutlti-threaded testing.
280    o pkg/matrix:
281      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
282      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
283      - fix for multi-threaded (remove DATA statement);
284      - use standard DIFFERENT_MULTIPLE function;
285      - add MATRIX_OPTIONS.h
286    o verification/matrix_example:
287       To allow to split the domain in several tiles, change the domain size
288        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
289        Western side) of land points.
290    o (*_)write_pickup:
291      - fix few bugs in mypackage_read/write_pickup.F
292      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
293        array of length 1 (was caught by compiler syntax-check).
294    o pkg/diagnostics (velocity potential solver):
295      - fix initialisation of main diagonal matrix (for overlap values)
296    o tools/build_options:
297      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
298        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
299      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
300        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
301        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
302        and use "-devel" testreport option for standard testing on baudelaire.
303    o pkg/grdchk:
304      - Assume that all gradient-check position are within the same tile
305        corresponding to global indices (iGloTile,jGloTile) and that
306        positions (i,j indices or nbeg) are local to this tile;
307      - set tile local-indices and proc. number according to tile global-indices;
308      - remove grdchkwhichproc from namelist (retired param);
309      - send adjoint gradient to all procs so that all procs print it to STDOUT;
310      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
311    o adding package bbl (Bottom Boundary Layer)
312      description in MITgcm/pkg/bbl/bbl_description.tex
313      example/test experiment in MITgcm_contrib/bbl
314    o adjoint verifications
315      - changed 5 experiments to multi-tiles
316        * global_ocean.90x40x15
317        * obcs_ctrl
318        * offline_exf_seaice
319        * tutorial_dic_adjoffline
320        * tutorial_tracer_adjsens
321        changed reference output for those that crossed tile boundaries
322        (changed choices of gradient check positions)
323      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
324      - temporary bug fix in grdchk_loc.F for obcs
325    o genmake2 & testreport
326      - add target "obj" (just for OBJFILES files) to Makefile;
327      - add option to specify FEXTRAFLAGS on command line.
328    o pkg/mypackage:
329      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
330    
331    checkpoint63a (2011/08/02)
332    o pkg/diagnostics (velocity potential):
333      - fix velocity-potential calculation when using OBCS: balance net inflow
334        at each level (new S/R OBCS_DIAG_BALANCE).
335      - fix some of the problems with OBCS in stream-function calculation.
336    o pkg/exf/exf_readparms.F
337      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
338        EXF_NML_OBCS) more consistent, so that you need not have these lists
339        in data.exf when they are not used.
340    o optim/optim_readdata.F:
341      - add some output about obcs variables that might help debugging
342      - add a check about nvarlength
343    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
344    o pkg/diagnostics (velocity potential):
345      - fix mask for OBCS (still problems in stream-function with OBCS);
346      - add specific parameter (default = main code CG2D params) for solver;
347      - in case of poor convergence, use solution corresponding to lowest residual.
348    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
349      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
350      and should be avoided where possible.
351    o model/src (rStar):
352      - include r* effect on reference-state (PhiRef) in totPhiHyd
353        (so that it's really the potential anomaly at the cell center);
354        affect solution only if z* with full pressure in EOS.
355      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
356        update output (because of z* in totPhiHyd and viscA4 changes);
357      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
358        @ constant r) until interpolation at constant r is implemented.
359    o pkg/diagnostics
360      - fix RCENTER diagnostics in case cell center is not at interface middle
361    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
362      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
363      that THETA and SALT are "conservative temperature" and "absolute
364      salinity"
365    o pkg/ctrl
366      - fix computation of endrec in s/r ctrl_init_rec
367      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
368    o pkg/seaice/seaice_growth.F
369      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
370        remove then obsolete STORE directives
371      - fix STORE directives for tice and tices, so that only the
372        appropriate part of the fields are stored (and not the entire
373        field); update global_ocean.cs32x15.seaice AD output.
374      - cosmetic changes: adjust CPP flags and indentation for better
375        legibilty
376    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
377      Chris Wilson)
378    o pkg/gmredi:
379       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
380       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
381    
382    checkpoint63  (2011/07/11)
383    o pkg/exch2:
384     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
385     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
386       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
387       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
388    o pkg/diagnostics:
389     - deal with pairs of post-processed diags which are computed together; in
390       particular, re-order list of diags within 1 file to save 2nd computation.
391     - add S/R to compute velocity stream-function (called after velocity-potential
392       calculation) from divergence free transport -> new diagnostics "PsiVEL".
393     - add parameter to select grid-point location where PsiVEL == 0.
394    o eesupp/src:
395       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
396       (specific S/R needed with exch2 topology - for now, just print an error msg)
397    o pkg/shelfice
398     - Implement friction velocity-dependent transfer coefficients following
399       Holland and Jenkins, JPO, 1999
400       Original code by M. Losch with small modifs.
401       Enable with CPP option SHI_ALLOW_GAMMAFRICT
402       and runtime flag SHELFICEuseGammaFrict
403    o verification lab_sea & global_ocean.cs32x15:
404     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
405       does not miss some dependencies (but is slower) and also works with many files
406       (default makedepend limitation for AD built).
407     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
408    o pkg/diagnostics:
409     - add run-time parameter "useMissingValue" (def=False) to fill land-point
410        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
411       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
412     - Extend the use of "missing_value" setting from data.diagnostics for the case
413       of counter-diagnostics (where fraction-weight is zero). This applies both to
414       MNC and MDS output files.
415    o pkg/seaice/seaice_growth.F:
416      - add 'a priori' cap of latent heat flux based on actual mass considerations
417        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
418        non-legacy seaice_solve4temp.
419      - add diagnostic of the residual sublimation freshwater flux (the freshwater
420        flux taken from the ocean if the total actual latent heat fluxes exceed
421        the maximum)
422      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
423       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
424      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
425       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
426      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
427      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
428    o verification 1D_ocean_ice_column:
429       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
430       update results
431    o pkg/diagnostics:
432     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
433       which are not filled-up but computed from other diags ; In this case, the mate
434       diag points to the primary (filled-up) diag to used for post processing.
435     - Update Velocity-potential computation using post-processed diag framework.
436     ==> Change the ordering of fields and time-periods in MDS output file
437       when using periodic averaging: now writes one time record with the full set
438       of fields for this time period, then the next time reccord (it used to be
439       one field with the full set of time records then the next field).
440         Note: this is now similar to NetCDF (MNC) output file. <==
441    
442    checkpoint62z (2011/06/21)
443    o adjoint monitor:
444     - Add adjoint monitor output for packages exf, seaice
445       and update relevant testreport output
446    o pkg/seaice:
447     - re-order diags inits so that they appear in order in available_diagnostics.log
448     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
449       area/heff/hsnow preceeding thermodynamic growth/melt.
450     - modified diag: SIdA; output actual effect, as the description states.
451     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
452     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
453       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
454        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
455     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
456     - added diagnostics for seaice generic tracers (SItr*).
457     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
458     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
459     I. Fenty: 18-Jun-2011:
460     Minor changes to seaice package:
461     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
462        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
463       - Differentiated "regularization variables" from "floor variables"
464        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
465        * hiceMin became SEAICE_hice_reg (old hiceMin)
466          (with _reg meaning regularization variable)
467       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
468        so as to ensure energy conservation when going between phases
469      - A22 was not used anywhere
470     2) Changed regularization procedure for heffActual and hsnowActual to ensure
471        well-boundedness and smooth adjoint in seaice_growth.F
472     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
473        because the old regularization always set heffActual >= 0.05 cm
474     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
475        on AREA when HEFF > 0.
476      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
477        requiring that DISABLE_AREA_FLOOR *not* be defined
478     Affected verifications:
479      - 1D_ocean_ice_column (output.txt output_adm.txt)
480      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
481    o pkg/diagnostics:
482      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
483      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
484        (was _RL, now integer) with option = 0 to retrieve all levels.
485      - add pieces of code to compute velocity potential at each level (new diagnostics
486        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
487        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
488      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
489        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
490        and in diagnostics_fract_fill.F (do not need a valid pointer for the
491        diagnostics counter-mate); check that definition of counter-diagnostic
492        includes a valid counter-mate (in diagnostics_set_levels.F).
493    o model/src (rStar):
494      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
495        affect solution only if z* with full pressure in EOS;
496        update output of test-exp global_ocean.90x40x15.
497    o pkg/seaice:
498      - introduce siEps=1e-5 parameter
499      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
500      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
501      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
502        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
503        as well as ice cover age and ridging index (attached to AREA).
504        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
505        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
506        Up to SItrMaxNum=3 tracers can be used simultaneously.
507    o pkg/salt_plume:
508      -introduce SPsalFRAC run time parameter that sets the fraction of the
509       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
510       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
511    o model debug options:
512      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
513        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
514      - Refine debug-msg printing selection (3 new levels):
515        debugMode  : controls printing of debug messages (sequence of S/R calls).
516        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
517         debLevZero =  0 ; /* level of disabled aux. msg printing */
518         debLevA =  1 ; /* level of minimum  aux. msg printing */
519         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
520         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
521         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
522         debLevE =  5 ; /* level of extensive debug printing */
523        New debugLevel default: with default debugMode value (=F),
524          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
525          and if debugMode=T, default debugLevel = 4 (debLevD).
526        Relation with previous settings:
527         debLevB (=2) corresponds to former debLevA (=1)
528         debLevD (=4) corresponds to former debLevB (=2)
529        Note:
530         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
531         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
532            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
533      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
534        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
535    o pkg/obcs:
536      - change OBCSfixTopo default from True to False (should not change the results);
537        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
538    o pkg/thsice:
539      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
540        2nd layer seaice sublimation (unlikely to happen)
541      - use Interior mask for OBCS in thsice_advection.F (similar to what is
542        done in gad_advection & seaice_advection).
543    o adjoint:
544      bug fix spotted by Gael Forget:
545      seaice_advection and thsice_advection still had
546      legacy CPP options to avoid CS corner updates for adjoint
547    o pkg/seaice:
548      => Change some of the defaults (2011/05/29):
549         - change SEAICEuseFluxForm default (from False to True)
550         - change DIFF1 default (from 0.004 m/s to 0. m/s)
551         And print warnings if DIFF1 is not set in data.seaice and centered
552          avection scheme is used without any diffusion.
553      also:
554      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
555      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
556      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
557        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
558        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
559      update results of test exp.:
560         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
561             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
562             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
563         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
564         seaice_obcs: output (SEAICEuseFluxForm=T)
565      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
566          for standard fwd & AD lab_sea tests (to keep the same output).
567    o pkg/seaice/seaice_growth.F:
568      - use Ian Fenty's capping formulas for actual ice
569      thickness thoughout EVOLUTION branch.
570      - put treatment pathological case #2) in CPP brackets
571      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
572      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
573    o pkg/seaice:
574      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
575      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
576      also pass fac as a param, which can be 1. (to update the tendency
577      field) or the time step (to update the field itself).
578      - seaice_advdiff.F: for multidim, call seaice_diffusion with
579      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
580      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
581      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
582      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
583    o pkg/seaice:
584      diffusion with centered advection scheme (diffus.F & advect.F):
585      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
586        to just compute the laplacian of input-field.
587      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
588      - fix flux-form version in diffus.F to conserve tracer.
589      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
590       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
591    
592    checkpoint62y (2011/05/26)
593    o pkg/seaice:
594     - seaice_growth.F : in EVOLUTION branch, always include
595       a_QSWbyATM_cover in qnet (as it should be).
596     - verification/global_ocean.cs32x15 : update results accordingly
597       (output.seaice.txt output_adm.seaice.txt).
598    o pkg/seaice + obcs:
599     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
600       equivalent of assuming no tracer gradient outside the OB region.
601       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
602     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
603       after changes above);
604     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
605       only at OB location (instead of over a band of OLx width).
606    o pkg/seaice:
607     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
608       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
609    o pkg/obcs:
610      - split header file "OBCS.h" into 4 separated files:
611        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
612       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
613         (contain no conditional statement which depends on OBCS options).
614      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
615        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
616    o ctrl, cost, grdchk & autodiff pkgs:
617      - make options file more standard (like other {PKG}_OPTIONS.h file but
618        with AD_CONFIG.h); clean-up some of the included header files.
619    o pkg/obcs:
620      - do not mask tracer when applying OB (tracer == 0 could generate problems)
621      - apply tracer OB values to tracer field only at OB location (instead of
622        over a band of OLx width)
623      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
624      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
625        obcs_apply_tloc.F & obcs_apply_sloc.F
626    o obcs in model/src:
627      - call OBCS_APPLY_W only if NonHydrostatic.
628      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
629      - reset dEtaHdt and wVel to zero outside OB interior region ;
630      - leave tracer unchanged outside OB interior region: This has no effect
631        on the solution but just to prevent unrealistic tracer value outside OB.
632      - zero out velocity outside OB interior region: This has no effect on
633        the solution but just to prevent unrealistic velocity outside OB.
634    o obcs and non-lin free-surf:
635       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
636       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
637       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
638       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
639       update results of test-exp. exp4(nlfs).
640    o exp4 (nlfs) test-exp:
641       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
642       with NonLin-FreeSurf); update output.nlfs.txt
643    o obcs and 2d/3d solver norm:
644       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
645       and outside OB interior region (will allow to place OB further inside the
646       domain). Depending on the domain, can affects cg2d-Norm (previous
647       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
648       and cg3d-Norm (previous Norm was computed before canceling OB terms),
649       e.g. in tutorial_plume_on_slope.
650      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
651    o pkg rbcs:
652      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
653      - add capability to apply relaxation to horizontal velocity uVel & vVel.
654    o pkg/grdchk: add gradient check for control variable xx_shifwflx
655    o pkg/shelfice/shelfice_init_fixed.F
656      fix CPP-flag combinations
657    o pkg/seaice: Merge iceage code of Pierre Rampal
658      * update/change/correct ice age calculations
659      * add age updates for pathological cases
660      Probably needs more testing...
661    
662    checkpoint62x (2011/05/13)
663    o pkg/mom_vecinv:
664       high-order vorticity scheme: use interior masks (maskInW & S)
665       to zero-out (outside OB) gradient of vorticity.
666    o verification exp.:
667       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
668       hs94.128x64x5 and seaice_obcs ; update results.
669    o pkg/obcs:
670      fix bug in OBeta for YZ sections in obcs_exf_load.F
671    o pkg/ctrl, pkg/shelfice, and optim:
672      - add new control variable xx_shifwflx (fresh water flux underneath ice
673        shelves). This is almost as tedious as obcs-ctrl, because the
674        variables needs its own mask.
675      - add a cost function term that penalizes the deviation of xx_shifwflx
676        from the first guess (zero) in analogy to other control variables
677    o pkg/shelfice:
678      - start basic adjoint
679    o pkg/ctrl:
680      - remove extra 2D field "for good measure" when initializing in
681        ctrl_set_globfld_[xy/xz/yz].F
682      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
683      - improve error messages in ctrl_set_unpack_*
684    o OBC implementation in momentum:
685       use interior masks (maskInC,W & S) in momentum S/R:
686       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
687       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
688       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
689       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
690       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
691        (and also with Leith/Smagorinsky harmonic-viscosity).
692       Update output of experiment dome and exp4 (+nlfs).
693    o exp4 test-exp:
694      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
695        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
696        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
697        time-varying OB at Western-side for wVel (NonHyd); update output.
698      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
699        and biharmonic-viscosity ; also use prescribed time varying OB.
700    o pkg/obcs:
701      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
702    o model/src:
703      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
704      - initialise startTime & nIter0 with unlikely values: allows to set one
705        from the other without ambiguity.
706    o seaice_obcs test-exp.:
707      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
708    o pkg/obcs:
709      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
710        no longer needed with maskInC,W,S in pkg/generic_advdiff.
711    o pkg/seaice:
712      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
713        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
714      - fixed bug in the initialization of sea ice salinity variable HSALT
715        in seaice_init_varia.F  (removed dependence on ICE2WATR)
716    o fizhi-cs test exp.:
717       switch reference output convention for these 2 non-standard test-exp,
718        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
719          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
720       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
721    o model/inc:
722      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
723        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
724    o pkg/seaice:
725      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
726    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
727      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
728        and initial HSALT
729    
730    checkpoint62w (2011/04/26)
731    o pkg/mom_fluxform:
732      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
733      - use parameter "sideDragFactor" in no-slip BC side-drag part.
734      - update output of exp. global_ocean.90x40x15
735    o pkg/mom_vecinv:
736      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
737    o update seaice exp.:
738      use more consistent parameter values (remove "backward compatability only":
739       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
740      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
741       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
742    o update test-exp global_ocean.90x40x15:
743      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
744      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
745      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
746      o turn on zStar & viscA4 in standard set-up (dir input/)
747        and update output files: output.txt & output.dwnslp.txt
748    o new AD-test experiment: obcs_ctrl
749      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
750    o pkg/dic:
751      fix two bugs in handling water vapour pressure in carbonate chemistry
752      and air-sea fluxes. Found by Val Bennington and Galen McKinley
753      (add DIC Option = WATERVAP_BUG to recover old results)
754      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
755    o adding allowInteriorFreezing option to check for water below freezing point
756      at depth and bring the negative heat anomaly to the surface level
757    o pkgs _fields_load:
758      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
759      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
760        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
761        rbcs to get interpolation weights and time reccord number.
762      - fix multi-threading in aim_fields_load.F
763      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
764    o external_fields_load:
765      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
766       interpolation weights) to use in a periodic time-series ; do not divide by
767       time-step to convert to integer:
768       - this fixes case where externForcingPeriod is not multiple of time-step
769          (Thanks to Christopher L. Wolfe)
770       - this fixes case where externForcingPeriod is an odd multiple of time-step
771         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
772      store index of time-record which is currently loaded:
773       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
774       - needed for the adjoint but not yet used because of extensive recomputations;
775         (to be fixed soon)
776    
777    checkpoint62v (2011/04/02)
778    o verification/1D_ocean_ice_column added to test Ian Fenty's
779      pkg/seaice_growth.F modifications for improving sea ice code differentiability
780    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
781      (new velocity statistics after changing maskInW & maskInS definition)
782    o pkg/generic_advdiff with OBCS:
783      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
784      equivalent to assumption of no tracer gradient outside the OB region.
785      This will affect the results if using obcs+biharmonic diffusion.
786      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
787    o pkg/obcs:
788      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
789      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
790      in Interior region. No impact on solution but affects Velocity monitor stats.
791    o pkg/ptracers (adjoint)
792      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
793      tape file for each tracer
794    o model/inc/src and pkg/autodiff: add parameters that allow to turn
795      of parts of the adjoint code at run time. For now, there are only
796      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
797      parameters are set in data.pkg.
798      This is the lazy coward's version of doing this, but still useful for
799      debugging. In order to do it right, everything needs to be moved to
800      pkg/autodiff.
801    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
802      the end; this fixes the adjoint balancing code for open boundaries.
803    o pkg/ctrl:
804      - change behavior of xx_${varname}period to be analogous to exf-conventions:
805        xx_${varname}period =   0.,  means time-independent control part
806        xx_${varname}period = -12., means one-year-periodic monthly control part
807      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
808        clean up ctrl_init a little, remove unused variables
809      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
810      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
811    
812    checkpoint62u (2011/03/15)
813    o model/src:
814      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
815        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
816      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
817        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
818    o pkg/ctrl/obcs/ecco:
819    - remove obsolete, unused, and partially broken code:    - remove obsolete, unused, and partially broken code:
820      ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within      ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
821      ALLOW_CTRL_OBCS_BALANCE      ALLOW_CTRL_OBCS_BALANCE
822    - put a stop statement into ecco/cost_obcsvol.F, but also add    - put a stop statement into ecco/cost_obcsvol.F, but also add
823      cost_obcsvol to ecco_ad_diff.list      cost_obcsvol to ecco_ad_diff.list
824  o pkg/ecco: fix counting cost function contributions for obcs (code  o pkg/ecco: fix counting cost function contributions for obcs (code
825    by Matt M.) and diffkr for diagnostics    by Matt M.) and diffkr for diagnostics
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