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revision 1.1407 by jmc, Thu Apr 14 22:23:58 2011 UTC revision 1.1565 by jmc, Fri Dec 30 16:54:46 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint63h (2011/12/30)
8    o pkg/offline:
9      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
10      - compute vertical velocity if not read from file (switch on exactConserv
11        & staggerTimeStep);
12      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
13    o verification:
14      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
15        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
16        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
17      - update output of exp. global_ocean.cs32x15.viscA4 after changing
18        grid-file angles (used here for coriolis-3d);
19      - remove (or gzip) few files not needed to run fizhi-cs experiments.
20    o pkg/exf (vertor interpolation):
21      - rotate vector component toward local grid-axis orientation using grid-angles
22        (stored in GRID.h) instead of locally computed rotation angle; keep old code
23        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
24    o pkg/seaice:
25      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
26        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
27    o pkg/PKG_OPTIONS.h files:
28      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
29        outside of the #ifdef ALLOW_THISPKG / #endif block.
30      - update verification/*/code/PKG_OPTIONS.h files.
31    o add a verification experiment (offline_exf_seaice/input.seaice) that test
32      the B-grid LSOR solver
33    o pkg/seaice: sort out emissivity and long wave radiation step 2:
34      - add emissivity for snow and ice as new run-time parameters
35        (unfortunately) that default to the corresponding exf values; this
36        changes results in most verification experiments so that for backward
37        compatibility these parameter have to be set explicitly to inconsistent
38        values (ugly);
39      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
40        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
41        until we agree how to handle this bug properly
42    o pkg/exf (interpolation):
43      - add a set of run-time param ({inputfield}_interpMethod), one for
44        each interpolated input field, to select the interpolation method
45        with a value of zero switching off the interpolation;
46      - print interpolation parameters to standard output;
47      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
48        (to use instead runoff_interpMethod=0 in data.exf).
49      - simplify default setting of interpolation parameters (for all fields,
50        set position to match model grid cell-center position, leading to trivial
51        interpolation in case of regular Lat-Lon grid) and fix for the case of
52        non-uniform delY.
53    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
54       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
55       this factor is absolutely required, because the lw exitance (= out-going
56       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
57       where the reflectivity rho = 1-emissivity for conservation reasons. Once
58       this is established, we can remove the CPP-Flag (if we want to).
59    o pkg/seaice:
60      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
61        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
62      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
63        what the name implies (and not emissivity*BoltzmannConstant), this means
64        the old default value of 5.5e-8 now means
65        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
66        S/R exf_readparms
67      - FV-discretization of the B-grid LSOR solver, turn on with
68        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
69        of the calling routine dynsolver, so that B and C-grid code look a
70        little more alike.
71      - fix index bugs in ostres.F (B-grid code)
72    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
73    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
74      default for SEAICE_emissivity, if useEXF; requires setting a wrong
75      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
76      backward compatiblity
77    o model/src: use sigmaR in calc_ivdc
78    
79    checkpoint63g (2011/12/16)
80    o pkg/seaice/seaice_growth.F:
81      fix heat conservation of the coupled ocean-seaice system.
82      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
83      solid vs liquid water treatment is resolved via QNET.
84    o pkg/seaice/seaice_growth.F:
85      add missing term for sublimation in saltFlux, which was breaking conservation.
86    o pkg/seaice/seaice_model.F:
87      Remove this patholigical case treatment in evolution branch,
88      where it is un-necessary and breaks conservation.
89      Update global_ocean.cs32x15/results accordingly for
90      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
91    o model/src:
92      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
93      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
94    o pkg/obcs:
95      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
96      tendency for temperature and salinity that is then applied to update
97      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
98      horizontal advection and diffusion contributions on the boundary (in
99      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
100      removing the mask in S/R timestep_tracer. The advantage of this approach is
101      that the updated tracer values include contributions from the surface
102      forcing and vertical diffusion.
103      This modification changes exp4.stevens because of vertical diffusion.
104    o model/src:
105      change non-curvilinear grid setting to also work with exch2 + blank tiles:
106      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
107        face dimensions.
108      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
109        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
110        and INI_SPHERICAL_POLAR_GRID.
111      change test-experiment global_ocean.90x40x15:
112      - split the domain in many more tiles (9x4 tiles of 10x10 each);
113      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
114      - update results of both test (std & dwnslp).
115    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
116       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
117    o model/src:
118      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
119        and fix initialisation when using sigma-coords.
120    o model/src:
121     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
122       to their current value at the beginning of forward_step.F": add a new run-time
123       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
124     - set doResetHFactors=T in the following test exp:
125        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
126        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
127        and tutorial_global_oce_in_p (nonLinFS in p)
128    o pkg/ecco
129      - added IES cost term
130    o verification/advect_xz
131      - scale down the depth by 1/100 (from 200 km to just 2.km)
132      - add secondary test using divergent flow, r-star and implicit vertical advection.
133      - add note (check_conserve_TS.txt) and matlab script to check global
134        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
135    o pkg/rbcs:
136      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
137    o pkg/obcs (Stevens BCs):
138      - fix various problems in the phase speed computations of the Stevens
139        boundary conditions:
140        - sign error for western and southern boundaries,
141        - time tendencies were underestimated by factor of dTracerLev and some just
142          zero (for multidim advection schemes) -> now estimate time tendencies
143          from difference between previous (n) time level and the one before (n-1);
144          this requires storing a field per tracer per boundary, also in the pickup
145          files.
146        - replace deltaTmom in cflMer/Zon computation with dTracerLev
147        - set default phase velocity to cflMer/Zon
148      - update verification experiment exp4.stevens
149    o pkg/generic_advdiff (implicit_r):
150      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
151        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
152      - fix implicit vertical diffusion or advection with NonLin FreeSurf
153        (was using current recip_hFacC instead of future recip_hFacC): set future
154        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
155        solver S/R ;
156      - fill diagnostics of vertical advective fluxes (computed from tendency)
157        when using implicit vert. advection;
158      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
159         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
160         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
161         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
162    o pkg/diagnostics:
163      - add diags for T & S tendency which goes through Adams-Bashforth.
164    
165    checkpoint63f (2011/11/30)
166    o pkg/obcs/obcs_calc_stevens.F:
167      - join some loops to reduce number of if-statements
168      - fix a bug in code for northern and southern boundaries.
169    o pkg/seaice/seaice_init_varia.F
170      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
171        caused zero ice-velocities for the B-grid code
172    o pkg/seaice/seaice_init_fixed.F
173      - fix a bug in the initialisation of the second metric terms
174        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
175      - this affects all seaice configurations with useCurviLinearGrid = .true.
176        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
177        = .true. (default)
178      - the only verification experiment affected is global_ocean.cs32x15:
179        icedyn, seaice, and seaice_dynmix (AD)
180    o pkg/thsice/thsice_diagnostics_state.F
181      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
182        not contain garbage that can lead to surprises in diagstats_calc.F
183    o model/src:
184      - move bi,bj loops inside INTEGR_CONTINUITY ;
185      - call INTEGR_CONTINUITY directly from forward_step.F
186        (previously called from momentum_correction_step.F)
187      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
188        forward_step.F and pkg/ecco/the_main_loop.F
189    o model/src/do_oceanic_phys.F:
190      - reset addMass to zero only if useICEFRONT ;
191      - separated k-loop for rhoInSitu calculation ;
192      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
193        and at constant T,S (= WdRHOdP);
194      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
195        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
196        transport of locally-referenced potential density);
197        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
198    o gluemnc:
199      - replace ncrcat with ncks when adding variables to *.glob.nc
200      - change the way variables without record dimensions are handled so that
201        files that have variables with and without record variables can be glued:
202        add a record dimension with a new unique name to be able to differentiate
203        between variable with and without a-prior record dimensions. Remove
204        this record dimension before adding the variable to the *.glob.nc file.
205        This procedure automatically works also for grid.*.nc files that do not
206        have any record dimension.
207    o verification/cpl_aim+ocn:
208      - generate new reference output on baudelaire (gfortran, mpich2) (previously
209        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
210    o pkg/obcs/obcs_calc_stevens.F:
211      - add code for northern and southern boundaries.
212      - reorder some loops to save some operations and so that drFBar can be scalar
213    o model/src:
214      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
215        truncation) and add diagnostics for Adams-Bashforth tendency increment.
216      - update test-exp. AD output:
217        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
218      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
219        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
220        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
221        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
222        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
223        tutorial_plume_on_slope.
224    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
225      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
226      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
227      does not even come with an F77 compiler anymore, this should not be
228      a limitation
229    
230    checkpoint63e (2011/11/06)
231    o pkg/seaice adjoint of LSR:
232      - substantially rework STORE dirs.
233      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
234        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
235        and only perform SOLV_MAX_FIXED adjoint iters.
236        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
237        always goes to same record, meaning that the last forward field will be
238        the one used in the adjoint - an approximation.
239      - now produces non-zero LSR-related gradients, and acceptable gradients for
240        An's zonal (x-z) test case (to be checked in)
241      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
242        (but these are screwed up by the thermodynamics in the first place);
243        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
244        output_adm.txt also reflects changes to seaice_lsr
245      - global_ocean.cs32x15:
246        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
247          (output_adm.seaice.txt was updated)
248        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
249          (output_adm.seaice_dynmix.txt)
250    o test-exp. exp4+stevens:
251      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
252    o pkg/seaice (lsr solver):
253      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
254        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
255      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
256      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
257        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
258      - compute (with new S/R) and print initial (+ free-driff sol. if available)
259        and final residual of linearised system.
260    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
261      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
262    o pkg/obcs: Stevens BCs (still only for east and west)
263      - fix Stevens BCs by using intermediate velocities of previous
264        time step as "baroclinic" contribution rather velocity of one grid cell
265        inside the boundaries; more consistent but makes the entire treatment
266        more complicated, requires new pickup files and two new S/Rs:
267        obcs_copy_uv_n and obcs_save_uv_n
268        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
269        (undefined by default)
270      - silently move computation of some grid factors into separate loops to
271        save some recomputations
272      - add a hack for non-linear free surface
273      - add a verification experiment to exp4 that tests this code
274    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
275    
276    checkpoint63d (2011/10/25)
277    o pkg/obcs + seaice-dynamics:
278      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
279        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
280        values (consistent with an implicit method).
281      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
282        return to older implementation (same results as before); note that none of
283        the "experimental" OBCS_SEAICE options are implemented in the new version.
284      - switch test exp. seaice_obcs to use new version (update output).
285    o pkg/seaice:
286      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
287      - add parenthesis in Water-Ice drag calculations (evp & lsr);
288      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
289        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
290      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
291        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
292    o pkg/layers:
293      - Include potential density as new coordinate (Thanks to David Munday)
294    o pkg/dic:
295      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
296        carbonate computation/output to CALC_PCO2_APPROX
297    o pkg/generic_advdiff
298      - make TAF generate code that vectorizes:
299        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
300    o model/src:
301      - improve vectorization also for adjoint code of
302        solve_tridiagonal and solve_pentadiagonal. As this requires up to
303        5 new 3D-fields, this code is only turned on for the combination of
304        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
305        for singular matrix check (only for TARGET_NEC_SX).
306      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
307        ALLOW_AUTODIFF. This flag now needs to be set outside of
308        solve_tri/pentadiagonal.F
309    o pkg/exf:
310      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
311        optional namelist EXF_NML_OBCS).
312      - add many debug-print (to trace down where pkg/cal error msg comes from)
313    o pkg/mom_vecinv/mom_vi_hdissip.F
314      - rearrange loops so that vectorization is improved and in particular
315        the adjoint routine vectorizes. The code is a little longer now, but I
316        think easier to read.
317        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
318    o pkg/seaice:
319      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
320    o pkg/exch2:
321      - alternative code (without tile x tile matrix) for cumulated (global) sum;
322        used as default; keep using matrix version in adjustment.cs-32x32x1.
323    o tools/build_options:
324      - after merging some MPI and/or multi-threads specific optfiles so that
325        the modified default optfile support both built (using genmake2 -mpi
326        for the MPI built, using genmake2 -omp for OpenMP built),
327        move now obsolete optfiles to tools/build_options/unsupported/
328       (add copy of email sent to support list in doc/optfiles_changes.txt)
329    
330    checkpoint63c (2011/09/28)
331    o pkg/ebm:
332      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
333        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
334    o pkg/seaice (SItracer pickup)
335    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
336      To be done:
337      - thorough testing of missing fields in S/R seaice_read_pickup
338      - thorough matching between generic tracers and specific fields used
339        (e.g. volume-weighted age, area-weighted age, salinity, ...)
340    o pkg/grdchk:
341      - all procs calculate and print finite-difference gradient (for testreport)
342      - change description output used by testreport;
343      - AD testing: also compare and report Finite-difference gradient;
344        => update all output_adm*.txt
345    o test exp. global_ocean_ebm:
346      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
347        and turn on exactConserve; update (fwd) output.
348    o pkg/seaice (LSR):
349      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
350      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
351        * identical results with non-CS topology (but save up to half of EXCH calls)
352        * no much changes in cs-32 verification tests since no ice at face edges
353         (differences due to convergence criteria, since nb of iterations changed)
354        * expect some differences on lat-lon-cap grid.
355        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
356    o pkg/exch2:
357      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
358        many tiles); until alternative coding is added, just add a stop.
359    o pkg/kpp:
360      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
361        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
362    o optfiles:
363      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
364        into corresponding standard one, which now support different build:
365        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
366      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
367    o pkg/obcs (seaice):
368      - add missing EXCH for uIce,vIce after applying OBCS;
369      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
370        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
371        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
372      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
373      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
374        and eedata.mth for MPI and mutlti-threaded testing.
375    o pkg/flt:
376      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
377      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
378      - fix pickup and trajectories + profiles output with multi-threads;
379      - add parameter to select group of fields to write along trajectory and
380        profile (default unchanged);
381      - only call PORT_RAND* function when flt_noise <> 0;
382      - add multi-threaded test for verification exp. flt_example.
383    o eesupp/src:
384      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
385      - USE_OMP_THREADING: check that number of threads (from eedata) matches
386        actual number (from env.var. setting).
387    o pkg/ebm:
388      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
389      - add multi-threaded test for verification exp. global_ocean_ebm
390    
391    checkpoint63b (2011/08/29)
392    o pkg/ebm:
393      - fix sign of runoff;
394      - update directly forcing fields (Qnet,EmPmR) to use standard
395        external_forcing_surf.F (remove ebm_forcing_surf.F);
396      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
397      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
398        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
399      - update global_ocean_ebm parameters file data and update output (fwd+ad).
400    o verification/matrix_example:
401      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
402        MPI and mutlti-threaded testing.
403    o pkg/matrix:
404      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
405      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
406      - fix for multi-threaded (remove DATA statement);
407      - use standard DIFFERENT_MULTIPLE function;
408      - add MATRIX_OPTIONS.h
409    o verification/matrix_example:
410       To allow to split the domain in several tiles, change the domain size
411        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
412        Western side) of land points.
413    o (*_)write_pickup:
414      - fix few bugs in mypackage_read/write_pickup.F
415      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
416        array of length 1 (was caught by compiler syntax-check).
417    o pkg/diagnostics (velocity potential solver):
418      - fix initialisation of main diagonal matrix (for overlap values)
419    o tools/build_options:
420      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
421        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
422      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
423        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
424        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
425        and use "-devel" testreport option for standard testing on baudelaire.
426    o pkg/grdchk:
427      - Assume that all gradient-check position are within the same tile
428        corresponding to global indices (iGloTile,jGloTile) and that
429        positions (i,j indices or nbeg) are local to this tile;
430      - set tile local-indices and proc. number according to tile global-indices;
431      - remove grdchkwhichproc from namelist (retired param);
432      - send adjoint gradient to all procs so that all procs print it to STDOUT;
433      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
434    o adding package bbl (Bottom Boundary Layer)
435      description in MITgcm/pkg/bbl/bbl_description.tex
436      example/test experiment in MITgcm_contrib/bbl
437    o adjoint verifications
438      - changed 5 experiments to multi-tiles
439        * global_ocean.90x40x15
440        * obcs_ctrl
441        * offline_exf_seaice
442        * tutorial_dic_adjoffline
443        * tutorial_tracer_adjsens
444        changed reference output for those that crossed tile boundaries
445        (changed choices of gradient check positions)
446      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
447      - temporary bug fix in grdchk_loc.F for obcs
448    o genmake2 & testreport
449      - add target "obj" (just for OBJFILES files) to Makefile;
450      - add option to specify FEXTRAFLAGS on command line.
451    o pkg/mypackage:
452      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
453    
454    checkpoint63a (2011/08/02)
455    o pkg/diagnostics (velocity potential):
456      - fix velocity-potential calculation when using OBCS: balance net inflow
457        at each level (new S/R OBCS_DIAG_BALANCE).
458      - fix some of the problems with OBCS in stream-function calculation.
459    o pkg/exf/exf_readparms.F
460      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
461        EXF_NML_OBCS) more consistent, so that you need not have these lists
462        in data.exf when they are not used.
463    o optim/optim_readdata.F:
464      - add some output about obcs variables that might help debugging
465      - add a check about nvarlength
466    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
467    o pkg/diagnostics (velocity potential):
468      - fix mask for OBCS (still problems in stream-function with OBCS);
469      - add specific parameter (default = main code CG2D params) for solver;
470      - in case of poor convergence, use solution corresponding to lowest residual.
471    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
472      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
473      and should be avoided where possible.
474    o model/src (rStar):
475      - include r* effect on reference-state (PhiRef) in totPhiHyd
476        (so that it's really the potential anomaly at the cell center);
477        affect solution only if z* with full pressure in EOS.
478      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
479        update output (because of z* in totPhiHyd and viscA4 changes);
480      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
481        @ constant r) until interpolation at constant r is implemented.
482    o pkg/diagnostics
483      - fix RCENTER diagnostics in case cell center is not at interface middle
484    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
485      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
486      that THETA and SALT are "conservative temperature" and "absolute
487      salinity"
488    o pkg/ctrl
489      - fix computation of endrec in s/r ctrl_init_rec
490      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
491    o pkg/seaice/seaice_growth.F
492      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
493        remove then obsolete STORE directives
494      - fix STORE directives for tice and tices, so that only the
495        appropriate part of the fields are stored (and not the entire
496        field); update global_ocean.cs32x15.seaice AD output.
497      - cosmetic changes: adjust CPP flags and indentation for better
498        legibilty
499    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
500      Chris Wilson)
501    o pkg/gmredi:
502       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
503       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
504    
505    checkpoint63  (2011/07/11)
506    o pkg/exch2:
507     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
508     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
509       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
510       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
511    o pkg/diagnostics:
512     - deal with pairs of post-processed diags which are computed together; in
513       particular, re-order list of diags within 1 file to save 2nd computation.
514     - add S/R to compute velocity stream-function (called after velocity-potential
515       calculation) from divergence free transport -> new diagnostics "PsiVEL".
516     - add parameter to select grid-point location where PsiVEL == 0.
517    o eesupp/src:
518       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
519       (specific S/R needed with exch2 topology - for now, just print an error msg)
520    o pkg/shelfice
521     - Implement friction velocity-dependent transfer coefficients following
522       Holland and Jenkins, JPO, 1999
523       Original code by M. Losch with small modifs.
524       Enable with CPP option SHI_ALLOW_GAMMAFRICT
525       and runtime flag SHELFICEuseGammaFrict
526    o verification lab_sea & global_ocean.cs32x15:
527     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
528       does not miss some dependencies (but is slower) and also works with many files
529       (default makedepend limitation for AD built).
530     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
531    o pkg/diagnostics:
532     - add run-time parameter "useMissingValue" (def=False) to fill land-point
533        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
534       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
535     - Extend the use of "missing_value" setting from data.diagnostics for the case
536       of counter-diagnostics (where fraction-weight is zero). This applies both to
537       MNC and MDS output files.
538    o pkg/seaice/seaice_growth.F:
539      - add 'a priori' cap of latent heat flux based on actual mass considerations
540        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
541        non-legacy seaice_solve4temp.
542      - add diagnostic of the residual sublimation freshwater flux (the freshwater
543        flux taken from the ocean if the total actual latent heat fluxes exceed
544        the maximum)
545      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
546       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
547      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
548       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
549      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
550      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
551    o verification 1D_ocean_ice_column:
552       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
553       update results
554    o pkg/diagnostics:
555     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
556       which are not filled-up but computed from other diags ; In this case, the mate
557       diag points to the primary (filled-up) diag to used for post processing.
558     - Update Velocity-potential computation using post-processed diag framework.
559     ==> Change the ordering of fields and time-periods in MDS output file
560       when using periodic averaging: now writes one time record with the full set
561       of fields for this time period, then the next time reccord (it used to be
562       one field with the full set of time records then the next field).
563         Note: this is now similar to NetCDF (MNC) output file. <==
564    
565    checkpoint62z (2011/06/21)
566    o adjoint monitor:
567     - Add adjoint monitor output for packages exf, seaice
568       and update relevant testreport output
569    o pkg/seaice:
570     - re-order diags inits so that they appear in order in available_diagnostics.log
571     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
572       area/heff/hsnow preceeding thermodynamic growth/melt.
573     - modified diag: SIdA; output actual effect, as the description states.
574     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
575     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
576       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
577        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
578     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
579     - added diagnostics for seaice generic tracers (SItr*).
580     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
581     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
582     I. Fenty: 18-Jun-2011:
583     Minor changes to seaice package:
584     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
585        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
586       - Differentiated "regularization variables" from "floor variables"
587        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
588        * hiceMin became SEAICE_hice_reg (old hiceMin)
589          (with _reg meaning regularization variable)
590       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
591        so as to ensure energy conservation when going between phases
592      - A22 was not used anywhere
593     2) Changed regularization procedure for heffActual and hsnowActual to ensure
594        well-boundedness and smooth adjoint in seaice_growth.F
595     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
596        because the old regularization always set heffActual >= 0.05 cm
597     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
598        on AREA when HEFF > 0.
599      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
600        requiring that DISABLE_AREA_FLOOR *not* be defined
601     Affected verifications:
602      - 1D_ocean_ice_column (output.txt output_adm.txt)
603      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
604    o pkg/diagnostics:
605      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
606      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
607        (was _RL, now integer) with option = 0 to retrieve all levels.
608      - add pieces of code to compute velocity potential at each level (new diagnostics
609        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
610        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
611      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
612        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
613        and in diagnostics_fract_fill.F (do not need a valid pointer for the
614        diagnostics counter-mate); check that definition of counter-diagnostic
615        includes a valid counter-mate (in diagnostics_set_levels.F).
616    o model/src (rStar):
617      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
618        affect solution only if z* with full pressure in EOS;
619        update output of test-exp global_ocean.90x40x15.
620    o pkg/seaice:
621      - introduce siEps=1e-5 parameter
622      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
623      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
624      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
625        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
626        as well as ice cover age and ridging index (attached to AREA).
627        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
628        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
629        Up to SItrMaxNum=3 tracers can be used simultaneously.
630    o pkg/salt_plume:
631      -introduce SPsalFRAC run time parameter that sets the fraction of the
632       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
633       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
634    o model debug options:
635      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
636        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
637      - Refine debug-msg printing selection (3 new levels):
638        debugMode  : controls printing of debug messages (sequence of S/R calls).
639        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
640         debLevZero =  0 ; /* level of disabled aux. msg printing */
641         debLevA =  1 ; /* level of minimum  aux. msg printing */
642         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
643         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
644         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
645         debLevE =  5 ; /* level of extensive debug printing */
646        New debugLevel default: with default debugMode value (=F),
647          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
648          and if debugMode=T, default debugLevel = 4 (debLevD).
649        Relation with previous settings:
650         debLevB (=2) corresponds to former debLevA (=1)
651         debLevD (=4) corresponds to former debLevB (=2)
652        Note:
653         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
654         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
655            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
656      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
657        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
658    o pkg/obcs:
659      - change OBCSfixTopo default from True to False (should not change the results);
660        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
661    o pkg/thsice:
662      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
663        2nd layer seaice sublimation (unlikely to happen)
664      - use Interior mask for OBCS in thsice_advection.F (similar to what is
665        done in gad_advection & seaice_advection).
666    o adjoint:
667      bug fix spotted by Gael Forget:
668      seaice_advection and thsice_advection still had
669      legacy CPP options to avoid CS corner updates for adjoint
670    o pkg/seaice:
671      => Change some of the defaults (2011/05/29):
672         - change SEAICEuseFluxForm default (from False to True)
673         - change DIFF1 default (from 0.004 m/s to 0. m/s)
674         And print warnings if DIFF1 is not set in data.seaice and centered
675          avection scheme is used without any diffusion.
676      also:
677      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
678      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
679      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
680        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
681        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
682      update results of test exp.:
683         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
684             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
685             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
686         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
687         seaice_obcs: output (SEAICEuseFluxForm=T)
688      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
689          for standard fwd & AD lab_sea tests (to keep the same output).
690    o pkg/seaice/seaice_growth.F:
691      - use Ian Fenty's capping formulas for actual ice
692      thickness thoughout EVOLUTION branch.
693      - put treatment pathological case #2) in CPP brackets
694      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
695      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
696    o pkg/seaice:
697      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
698      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
699      also pass fac as a param, which can be 1. (to update the tendency
700      field) or the time step (to update the field itself).
701      - seaice_advdiff.F: for multidim, call seaice_diffusion with
702      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
703      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
704      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
705      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
706    o pkg/seaice:
707      diffusion with centered advection scheme (diffus.F & advect.F):
708      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
709        to just compute the laplacian of input-field.
710      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
711      - fix flux-form version in diffus.F to conserve tracer.
712      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
713       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
714    
715    checkpoint62y (2011/05/26)
716    o pkg/seaice:
717     - seaice_growth.F : in EVOLUTION branch, always include
718       a_QSWbyATM_cover in qnet (as it should be).
719     - verification/global_ocean.cs32x15 : update results accordingly
720       (output.seaice.txt output_adm.seaice.txt).
721    o pkg/seaice + obcs:
722     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
723       equivalent of assuming no tracer gradient outside the OB region.
724       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
725     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
726       after changes above);
727     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
728       only at OB location (instead of over a band of OLx width).
729    o pkg/seaice:
730     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
731       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
732    o pkg/obcs:
733      - split header file "OBCS.h" into 4 separated files:
734        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
735       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
736         (contain no conditional statement which depends on OBCS options).
737      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
738        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
739    o ctrl, cost, grdchk & autodiff pkgs:
740      - make options file more standard (like other {PKG}_OPTIONS.h file but
741        with AD_CONFIG.h); clean-up some of the included header files.
742    o pkg/obcs:
743      - do not mask tracer when applying OB (tracer == 0 could generate problems)
744      - apply tracer OB values to tracer field only at OB location (instead of
745        over a band of OLx width)
746      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
747      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
748        obcs_apply_tloc.F & obcs_apply_sloc.F
749    o obcs in model/src:
750      - call OBCS_APPLY_W only if NonHydrostatic.
751      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
752      - reset dEtaHdt and wVel to zero outside OB interior region ;
753      - leave tracer unchanged outside OB interior region: This has no effect
754        on the solution but just to prevent unrealistic tracer value outside OB.
755      - zero out velocity outside OB interior region: This has no effect on
756        the solution but just to prevent unrealistic velocity outside OB.
757    o obcs and non-lin free-surf:
758       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
759       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
760       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
761       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
762       update results of test-exp. exp4(nlfs).
763    o exp4 (nlfs) test-exp:
764       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
765       with NonLin-FreeSurf); update output.nlfs.txt
766    o obcs and 2d/3d solver norm:
767       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
768       and outside OB interior region (will allow to place OB further inside the
769       domain). Depending on the domain, can affects cg2d-Norm (previous
770       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
771       and cg3d-Norm (previous Norm was computed before canceling OB terms),
772       e.g. in tutorial_plume_on_slope.
773      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
774    o pkg rbcs:
775      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
776      - add capability to apply relaxation to horizontal velocity uVel & vVel.
777    o pkg/grdchk: add gradient check for control variable xx_shifwflx
778    o pkg/shelfice/shelfice_init_fixed.F
779      fix CPP-flag combinations
780    o pkg/seaice: Merge iceage code of Pierre Rampal
781      * update/change/correct ice age calculations
782      * add age updates for pathological cases
783      Probably needs more testing...
784    
785    checkpoint62x (2011/05/13)
786    o pkg/mom_vecinv:
787       high-order vorticity scheme: use interior masks (maskInW & S)
788       to zero-out (outside OB) gradient of vorticity.
789    o verification exp.:
790       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
791       hs94.128x64x5 and seaice_obcs ; update results.
792    o pkg/obcs:
793      fix bug in OBeta for YZ sections in obcs_exf_load.F
794    o pkg/ctrl, pkg/shelfice, and optim:
795      - add new control variable xx_shifwflx (fresh water flux underneath ice
796        shelves). This is almost as tedious as obcs-ctrl, because the
797        variables needs its own mask.
798      - add a cost function term that penalizes the deviation of xx_shifwflx
799        from the first guess (zero) in analogy to other control variables
800    o pkg/shelfice:
801      - start basic adjoint
802    o pkg/ctrl:
803      - remove extra 2D field "for good measure" when initializing in
804        ctrl_set_globfld_[xy/xz/yz].F
805      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
806      - improve error messages in ctrl_set_unpack_*
807    o OBC implementation in momentum:
808       use interior masks (maskInC,W & S) in momentum S/R:
809       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
810       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
811       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
812       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
813       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
814        (and also with Leith/Smagorinsky harmonic-viscosity).
815       Update output of experiment dome and exp4 (+nlfs).
816    o exp4 test-exp:
817      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
818        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
819        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
820        time-varying OB at Western-side for wVel (NonHyd); update output.
821      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
822        and biharmonic-viscosity ; also use prescribed time varying OB.
823    o pkg/obcs:
824      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
825    o model/src:
826      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
827      - initialise startTime & nIter0 with unlikely values: allows to set one
828        from the other without ambiguity.
829    o seaice_obcs test-exp.:
830      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
831    o pkg/obcs:
832      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
833        no longer needed with maskInC,W,S in pkg/generic_advdiff.
834    o pkg/seaice:
835      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
836        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
837      - fixed bug in the initialization of sea ice salinity variable HSALT
838        in seaice_init_varia.F  (removed dependence on ICE2WATR)
839    o fizhi-cs test exp.:
840       switch reference output convention for these 2 non-standard test-exp,
841        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
842          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
843       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
844    o model/inc:
845      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
846        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
847    o pkg/seaice:
848      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
849    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
850      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
851        and initial HSALT
852    
853    checkpoint62w (2011/04/26)
854    o pkg/mom_fluxform:
855      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
856      - use parameter "sideDragFactor" in no-slip BC side-drag part.
857      - update output of exp. global_ocean.90x40x15
858    o pkg/mom_vecinv:
859      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
860    o update seaice exp.:
861      use more consistent parameter values (remove "backward compatability only":
862       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
863      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
864       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
865    o update test-exp global_ocean.90x40x15:
866      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
867      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
868      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
869      o turn on zStar & viscA4 in standard set-up (dir input/)
870        and update output files: output.txt & output.dwnslp.txt
871    o new AD-test experiment: obcs_ctrl
872      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
873    o pkg/dic:
874      fix two bugs in handling water vapour pressure in carbonate chemistry
875      and air-sea fluxes. Found by Val Bennington and Galen McKinley
876      (add DIC Option = WATERVAP_BUG to recover old results)
877      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
878    o adding allowInteriorFreezing option to check for water below freezing point
879      at depth and bring the negative heat anomaly to the surface level
880    o pkgs _fields_load:
881      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
882      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
883        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
884        rbcs to get interpolation weights and time reccord number.
885      - fix multi-threading in aim_fields_load.F
886      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
887  o external_fields_load:  o external_fields_load:
888    new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear    new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
889     interpolation weights) to use in a periodic time-series ; do not divide by     interpolation weights) to use in a periodic time-series ; do not divide by
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