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revision 1.1407 by jmc, Thu Apr 14 22:23:58 2011 UTC revision 1.1553 by mlosch, Mon Dec 19 12:09:25 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/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
8    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
9      default for SEAICE_emissivity, if useEXF; requires setting a wrong
10      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
11      backward compatiblity
12    o model/src: use sigmaR in calc_ivdc
13    
14    checkpoint63g (2011/12/16)
15    o pkg/seaice/seaice_growth.F:
16      fix heat conservation of the coupled ocean-seaice system.
17      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
18      solid vs liquid water treatment is resolved via QNET.
19    o pkg/seaice/seaice_growth.F:
20      add missing term for sublimation in saltFlux, which was breaking conservation.
21    o pkg/seaice/seaice_model.F:
22      Remove this patholigical case treatment in evolution branch,
23      where it is un-necessary and breaks conservation.
24      Update global_ocean.cs32x15/results accordingly for
25      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
26    o model/src:
27      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
28      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
29    o pkg/obcs:
30      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
31      tendency for temperature and salinity that is then applied to update
32      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
33      horizontal advection and diffusion contributions on the boundary (in
34      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
35      removing the mask in S/R timestep_tracer. The advantage of this approach is
36      that the updated tracer values include contributions from the surface
37      forcing and vertical diffusion.
38      This modification changes exp4.stevens because of vertical diffusion.
39    o model/src:
40      change non-curvilinear grid setting to also work with exch2 + blank tiles:
41      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
42        face dimensions.
43      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
44        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
45        and INI_SPHERICAL_POLAR_GRID.
46      change test-experiment global_ocean.90x40x15:
47      - split the domain in many more tiles (9x4 tiles of 10x10 each);
48      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
49      - update results of both test (std & dwnslp).
50    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
51       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
52    o model/src:
53      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
54        and fix initialisation when using sigma-coords.
55    o model/src:
56     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
57       to their current value at the beginning of forward_step.F": add a new run-time
58       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
59     - set doResetHFactors=T in the following test exp:
60        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
61        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
62        and tutorial_global_oce_in_p (nonLinFS in p)
63    o pkg/ecco
64      - added IES cost term
65    o verification/advect_xz
66      - scale down the depth by 1/100 (from 200 km to just 2.km)
67      - add secondary test using divergent flow, r-star and implicit vertical advection.
68      - add note (check_conserve_TS.txt) and matlab script to check global
69        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
70    o pkg/rbcs:
71      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
72    o pkg/obcs (Stevens BCs):
73      - fix various problems in the phase speed computations of the Stevens
74        boundary conditions:
75        - sign error for western and southern boundaries,
76        - time tendencies were underestimated by factor of dTracerLev and some just
77          zero (for multidim advection schemes) -> now estimate time tendencies
78          from difference between previous (n) time level and the one before (n-1);
79          this requires storing a field per tracer per boundary, also in the pickup
80          files.
81        - replace deltaTmom in cflMer/Zon computation with dTracerLev
82        - set default phase velocity to cflMer/Zon
83      - update verification experiment exp4.stevens
84    o pkg/generic_advdiff (implicit_r):
85      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
86        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
87      - fix implicit vertical diffusion or advection with NonLin FreeSurf
88        (was using current recip_hFacC instead of future recip_hFacC): set future
89        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
90        solver S/R ;
91      - fill diagnostics of vertical advective fluxes (computed from tendency)
92        when using implicit vert. advection;
93      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
94         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
95         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
96         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
97    o pkg/diagnostics:
98      - add diags for T & S tendency which goes through Adams-Bashforth.
99    
100    checkpoint63f (2011/11/30)
101    o pkg/obcs/obcs_calc_stevens.F:
102      - join some loops to reduce number of if-statements
103      - fix a bug in code for northern and southern boundaries.
104    o pkg/seaice/seaice_init_varia.F
105      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
106        caused zero ice-velocities for the B-grid code
107    o pkg/seaice/seaice_init_fixed.F
108      - fix a bug in the initialisation of the second metric terms
109        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
110      - this affects all seaice configurations with useCurviLinearGrid = .true.
111        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
112        = .true. (default)
113      - the only verification experiment affected is global_ocean.cs32x15:
114        icedyn, seaice, and seaice_dynmix (AD)
115    o pkg/thsice/thsice_diagnostics_state.F
116      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
117        not contain garbage that can lead to surprises in diagstats_calc.F
118    o model/src:
119      - move bi,bj loops inside INTEGR_CONTINUITY ;
120      - call INTEGR_CONTINUITY directly from forward_step.F
121        (previously called from momentum_correction_step.F)
122      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
123        forward_step.F and pkg/ecco/the_main_loop.F
124    o model/src/do_oceanic_phys.F:
125      - reset addMass to zero only if useICEFRONT ;
126      - separated k-loop for rhoInSitu calculation ;
127      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
128        and at constant T,S (= WdRHOdP);
129      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
130        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
131        transport of locally-referenced potential density);
132        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
133    o gluemnc:
134      - replace ncrcat with ncks when adding variables to *.glob.nc
135      - change the way variables without record dimensions are handled so that
136        files that have variables with and without record variables can be glued:
137        add a record dimension with a new unique name to be able to differentiate
138        between variable with and without a-prior record dimensions. Remove
139        this record dimension before adding the variable to the *.glob.nc file.
140        This procedure automatically works also for grid.*.nc files that do not
141        have any record dimension.
142    o verification/cpl_aim+ocn:
143      - generate new reference output on baudelaire (gfortran, mpich2) (previously
144        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
145    o pkg/obcs/obcs_calc_stevens.F:
146      - add code for northern and southern boundaries.
147      - reorder some loops to save some operations and so that drFBar can be scalar
148    o model/src:
149      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
150        truncation) and add diagnostics for Adams-Bashforth tendency increment.
151      - update test-exp. AD output:
152        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
153      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
154        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
155        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
156        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
157        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
158        tutorial_plume_on_slope.
159    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
160      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
161      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
162      does not even come with an F77 compiler anymore, this should not be
163      a limitation
164    
165    checkpoint63e (2011/11/06)
166    o pkg/seaice adjoint of LSR:
167      - substantially rework STORE dirs.
168      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
169        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
170        and only perform SOLV_MAX_FIXED adjoint iters.
171        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
172        always goes to same record, meaning that the last forward field will be
173        the one used in the adjoint - an approximation.
174      - now produces non-zero LSR-related gradients, and acceptable gradients for
175        An's zonal (x-z) test case (to be checked in)
176      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
177        (but these are screwed up by the thermodynamics in the first place);
178        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
179        output_adm.txt also reflects changes to seaice_lsr
180      - global_ocean.cs32x15:
181        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
182          (output_adm.seaice.txt was updated)
183        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
184          (output_adm.seaice_dynmix.txt)
185    o test-exp. exp4+stevens:
186      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
187    o pkg/seaice (lsr solver):
188      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
189        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
190      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
191      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
192        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
193      - compute (with new S/R) and print initial (+ free-driff sol. if available)
194        and final residual of linearised system.
195    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
196      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
197    o pkg/obcs: Stevens BCs (still only for east and west)
198      - fix Stevens BCs by using intermediate velocities of previous
199        time step as "baroclinic" contribution rather velocity of one grid cell
200        inside the boundaries; more consistent but makes the entire treatment
201        more complicated, requires new pickup files and two new S/Rs:
202        obcs_copy_uv_n and obcs_save_uv_n
203        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
204        (undefined by default)
205      - silently move computation of some grid factors into separate loops to
206        save some recomputations
207      - add a hack for non-linear free surface
208      - add a verification experiment to exp4 that tests this code
209    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
210    
211    checkpoint63d (2011/10/25)
212    o pkg/obcs + seaice-dynamics:
213      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
214        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
215        values (consistent with an implicit method).
216      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
217        return to older implementation (same results as before); note that none of
218        the "experimental" OBCS_SEAICE options are implemented in the new version.
219      - switch test exp. seaice_obcs to use new version (update output).
220    o pkg/seaice:
221      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
222      - add parenthesis in Water-Ice drag calculations (evp & lsr);
223      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
224        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
225      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
226        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
227    o pkg/layers:
228      - Include potential density as new coordinate (Thanks to David Munday)
229    o pkg/dic:
230      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
231        carbonate computation/output to CALC_PCO2_APPROX
232    o pkg/generic_advdiff
233      - make TAF generate code that vectorizes:
234        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
235    o model/src:
236      - improve vectorization also for adjoint code of
237        solve_tridiagonal and solve_pentadiagonal. As this requires up to
238        5 new 3D-fields, this code is only turned on for the combination of
239        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
240        for singular matrix check (only for TARGET_NEC_SX).
241      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
242        ALLOW_AUTODIFF. This flag now needs to be set outside of
243        solve_tri/pentadiagonal.F
244    o pkg/exf:
245      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
246        optional namelist EXF_NML_OBCS).
247      - add many debug-print (to trace down where pkg/cal error msg comes from)
248    o pkg/mom_vecinv/mom_vi_hdissip.F
249      - rearrange loops so that vectorization is improved and in particular
250        the adjoint routine vectorizes. The code is a little longer now, but I
251        think easier to read.
252        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
253    o pkg/seaice:
254      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
255    o pkg/exch2:
256      - alternative code (without tile x tile matrix) for cumulated (global) sum;
257        used as default; keep using matrix version in adjustment.cs-32x32x1.
258    o tools/build_options:
259      - after merging some MPI and/or multi-threads specific optfiles so that
260        the modified default optfile support both built (using genmake2 -mpi
261        for the MPI built, using genmake2 -omp for OpenMP built),
262        move now obsolete optfiles to tools/build_options/unsupported/
263       (add copy of email sent to support list in doc/optfiles_changes.txt)
264    
265    checkpoint63c (2011/09/28)
266    o pkg/ebm:
267      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
268        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
269    o pkg/seaice (SItracer pickup)
270    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
271      To be done:
272      - thorough testing of missing fields in S/R seaice_read_pickup
273      - thorough matching between generic tracers and specific fields used
274        (e.g. volume-weighted age, area-weighted age, salinity, ...)
275    o pkg/grdchk:
276      - all procs calculate and print finite-difference gradient (for testreport)
277      - change description output used by testreport;
278      - AD testing: also compare and report Finite-difference gradient;
279        => update all output_adm*.txt
280    o test exp. global_ocean_ebm:
281      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
282        and turn on exactConserve; update (fwd) output.
283    o pkg/seaice (LSR):
284      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
285      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
286        * identical results with non-CS topology (but save up to half of EXCH calls)
287        * no much changes in cs-32 verification tests since no ice at face edges
288         (differences due to convergence criteria, since nb of iterations changed)
289        * expect some differences on lat-lon-cap grid.
290        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
291    o pkg/exch2:
292      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
293        many tiles); until alternative coding is added, just add a stop.
294    o pkg/kpp:
295      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
296        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
297    o optfiles:
298      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
299        into corresponding standard one, which now support different build:
300        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
301      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
302    o pkg/obcs (seaice):
303      - add missing EXCH for uIce,vIce after applying OBCS;
304      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
305        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
306        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
307      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
308      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
309        and eedata.mth for MPI and mutlti-threaded testing.
310    o pkg/flt:
311      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
312      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
313      - fix pickup and trajectories + profiles output with multi-threads;
314      - add parameter to select group of fields to write along trajectory and
315        profile (default unchanged);
316      - only call PORT_RAND* function when flt_noise <> 0;
317      - add multi-threaded test for verification exp. flt_example.
318    o eesupp/src:
319      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
320      - USE_OMP_THREADING: check that number of threads (from eedata) matches
321        actual number (from env.var. setting).
322    o pkg/ebm:
323      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
324      - add multi-threaded test for verification exp. global_ocean_ebm
325    
326    checkpoint63b (2011/08/29)
327    o pkg/ebm:
328      - fix sign of runoff;
329      - update directly forcing fields (Qnet,EmPmR) to use standard
330        external_forcing_surf.F (remove ebm_forcing_surf.F);
331      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
332      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
333        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
334      - update global_ocean_ebm parameters file data and update output (fwd+ad).
335    o verification/matrix_example:
336      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
337        MPI and mutlti-threaded testing.
338    o pkg/matrix:
339      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
340      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
341      - fix for multi-threaded (remove DATA statement);
342      - use standard DIFFERENT_MULTIPLE function;
343      - add MATRIX_OPTIONS.h
344    o verification/matrix_example:
345       To allow to split the domain in several tiles, change the domain size
346        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
347        Western side) of land points.
348    o (*_)write_pickup:
349      - fix few bugs in mypackage_read/write_pickup.F
350      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
351        array of length 1 (was caught by compiler syntax-check).
352    o pkg/diagnostics (velocity potential solver):
353      - fix initialisation of main diagonal matrix (for overlap values)
354    o tools/build_options:
355      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
356        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
357      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
358        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
359        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
360        and use "-devel" testreport option for standard testing on baudelaire.
361    o pkg/grdchk:
362      - Assume that all gradient-check position are within the same tile
363        corresponding to global indices (iGloTile,jGloTile) and that
364        positions (i,j indices or nbeg) are local to this tile;
365      - set tile local-indices and proc. number according to tile global-indices;
366      - remove grdchkwhichproc from namelist (retired param);
367      - send adjoint gradient to all procs so that all procs print it to STDOUT;
368      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
369    o adding package bbl (Bottom Boundary Layer)
370      description in MITgcm/pkg/bbl/bbl_description.tex
371      example/test experiment in MITgcm_contrib/bbl
372    o adjoint verifications
373      - changed 5 experiments to multi-tiles
374        * global_ocean.90x40x15
375        * obcs_ctrl
376        * offline_exf_seaice
377        * tutorial_dic_adjoffline
378        * tutorial_tracer_adjsens
379        changed reference output for those that crossed tile boundaries
380        (changed choices of gradient check positions)
381      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
382      - temporary bug fix in grdchk_loc.F for obcs
383    o genmake2 & testreport
384      - add target "obj" (just for OBJFILES files) to Makefile;
385      - add option to specify FEXTRAFLAGS on command line.
386    o pkg/mypackage:
387      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
388    
389    checkpoint63a (2011/08/02)
390    o pkg/diagnostics (velocity potential):
391      - fix velocity-potential calculation when using OBCS: balance net inflow
392        at each level (new S/R OBCS_DIAG_BALANCE).
393      - fix some of the problems with OBCS in stream-function calculation.
394    o pkg/exf/exf_readparms.F
395      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
396        EXF_NML_OBCS) more consistent, so that you need not have these lists
397        in data.exf when they are not used.
398    o optim/optim_readdata.F:
399      - add some output about obcs variables that might help debugging
400      - add a check about nvarlength
401    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
402    o pkg/diagnostics (velocity potential):
403      - fix mask for OBCS (still problems in stream-function with OBCS);
404      - add specific parameter (default = main code CG2D params) for solver;
405      - in case of poor convergence, use solution corresponding to lowest residual.
406    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
407      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
408      and should be avoided where possible.
409    o model/src (rStar):
410      - include r* effect on reference-state (PhiRef) in totPhiHyd
411        (so that it's really the potential anomaly at the cell center);
412        affect solution only if z* with full pressure in EOS.
413      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
414        update output (because of z* in totPhiHyd and viscA4 changes);
415      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
416        @ constant r) until interpolation at constant r is implemented.
417    o pkg/diagnostics
418      - fix RCENTER diagnostics in case cell center is not at interface middle
419    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
420      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
421      that THETA and SALT are "conservative temperature" and "absolute
422      salinity"
423    o pkg/ctrl
424      - fix computation of endrec in s/r ctrl_init_rec
425      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
426    o pkg/seaice/seaice_growth.F
427      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
428        remove then obsolete STORE directives
429      - fix STORE directives for tice and tices, so that only the
430        appropriate part of the fields are stored (and not the entire
431        field); update global_ocean.cs32x15.seaice AD output.
432      - cosmetic changes: adjust CPP flags and indentation for better
433        legibilty
434    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
435      Chris Wilson)
436    o pkg/gmredi:
437       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
438       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
439    
440    checkpoint63  (2011/07/11)
441    o pkg/exch2:
442     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
443     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
444       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
445       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
446    o pkg/diagnostics:
447     - deal with pairs of post-processed diags which are computed together; in
448       particular, re-order list of diags within 1 file to save 2nd computation.
449     - add S/R to compute velocity stream-function (called after velocity-potential
450       calculation) from divergence free transport -> new diagnostics "PsiVEL".
451     - add parameter to select grid-point location where PsiVEL == 0.
452    o eesupp/src:
453       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
454       (specific S/R needed with exch2 topology - for now, just print an error msg)
455    o pkg/shelfice
456     - Implement friction velocity-dependent transfer coefficients following
457       Holland and Jenkins, JPO, 1999
458       Original code by M. Losch with small modifs.
459       Enable with CPP option SHI_ALLOW_GAMMAFRICT
460       and runtime flag SHELFICEuseGammaFrict
461    o verification lab_sea & global_ocean.cs32x15:
462     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
463       does not miss some dependencies (but is slower) and also works with many files
464       (default makedepend limitation for AD built).
465     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
466    o pkg/diagnostics:
467     - add run-time parameter "useMissingValue" (def=False) to fill land-point
468        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
469       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
470     - Extend the use of "missing_value" setting from data.diagnostics for the case
471       of counter-diagnostics (where fraction-weight is zero). This applies both to
472       MNC and MDS output files.
473    o pkg/seaice/seaice_growth.F:
474      - add 'a priori' cap of latent heat flux based on actual mass considerations
475        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
476        non-legacy seaice_solve4temp.
477      - add diagnostic of the residual sublimation freshwater flux (the freshwater
478        flux taken from the ocean if the total actual latent heat fluxes exceed
479        the maximum)
480      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
481       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
482      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
483       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
484      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
485      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
486    o verification 1D_ocean_ice_column:
487       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
488       update results
489    o pkg/diagnostics:
490     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
491       which are not filled-up but computed from other diags ; In this case, the mate
492       diag points to the primary (filled-up) diag to used for post processing.
493     - Update Velocity-potential computation using post-processed diag framework.
494     ==> Change the ordering of fields and time-periods in MDS output file
495       when using periodic averaging: now writes one time record with the full set
496       of fields for this time period, then the next time reccord (it used to be
497       one field with the full set of time records then the next field).
498         Note: this is now similar to NetCDF (MNC) output file. <==
499    
500    checkpoint62z (2011/06/21)
501    o adjoint monitor:
502     - Add adjoint monitor output for packages exf, seaice
503       and update relevant testreport output
504    o pkg/seaice:
505     - re-order diags inits so that they appear in order in available_diagnostics.log
506     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
507       area/heff/hsnow preceeding thermodynamic growth/melt.
508     - modified diag: SIdA; output actual effect, as the description states.
509     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
510     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
511       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
512        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
513     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
514     - added diagnostics for seaice generic tracers (SItr*).
515     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
516     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
517     I. Fenty: 18-Jun-2011:
518     Minor changes to seaice package:
519     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
520        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
521       - Differentiated "regularization variables" from "floor variables"
522        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
523        * hiceMin became SEAICE_hice_reg (old hiceMin)
524          (with _reg meaning regularization variable)
525       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
526        so as to ensure energy conservation when going between phases
527      - A22 was not used anywhere
528     2) Changed regularization procedure for heffActual and hsnowActual to ensure
529        well-boundedness and smooth adjoint in seaice_growth.F
530     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
531        because the old regularization always set heffActual >= 0.05 cm
532     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
533        on AREA when HEFF > 0.
534      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
535        requiring that DISABLE_AREA_FLOOR *not* be defined
536     Affected verifications:
537      - 1D_ocean_ice_column (output.txt output_adm.txt)
538      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
539    o pkg/diagnostics:
540      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
541      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
542        (was _RL, now integer) with option = 0 to retrieve all levels.
543      - add pieces of code to compute velocity potential at each level (new diagnostics
544        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
545        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
546      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
547        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
548        and in diagnostics_fract_fill.F (do not need a valid pointer for the
549        diagnostics counter-mate); check that definition of counter-diagnostic
550        includes a valid counter-mate (in diagnostics_set_levels.F).
551    o model/src (rStar):
552      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
553        affect solution only if z* with full pressure in EOS;
554        update output of test-exp global_ocean.90x40x15.
555    o pkg/seaice:
556      - introduce siEps=1e-5 parameter
557      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
558      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
559      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
560        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
561        as well as ice cover age and ridging index (attached to AREA).
562        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
563        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
564        Up to SItrMaxNum=3 tracers can be used simultaneously.
565    o pkg/salt_plume:
566      -introduce SPsalFRAC run time parameter that sets the fraction of the
567       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
568       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
569    o model debug options:
570      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
571        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
572      - Refine debug-msg printing selection (3 new levels):
573        debugMode  : controls printing of debug messages (sequence of S/R calls).
574        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
575         debLevZero =  0 ; /* level of disabled aux. msg printing */
576         debLevA =  1 ; /* level of minimum  aux. msg printing */
577         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
578         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
579         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
580         debLevE =  5 ; /* level of extensive debug printing */
581        New debugLevel default: with default debugMode value (=F),
582          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
583          and if debugMode=T, default debugLevel = 4 (debLevD).
584        Relation with previous settings:
585         debLevB (=2) corresponds to former debLevA (=1)
586         debLevD (=4) corresponds to former debLevB (=2)
587        Note:
588         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
589         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
590            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
591      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
592        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
593    o pkg/obcs:
594      - change OBCSfixTopo default from True to False (should not change the results);
595        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
596    o pkg/thsice:
597      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
598        2nd layer seaice sublimation (unlikely to happen)
599      - use Interior mask for OBCS in thsice_advection.F (similar to what is
600        done in gad_advection & seaice_advection).
601    o adjoint:
602      bug fix spotted by Gael Forget:
603      seaice_advection and thsice_advection still had
604      legacy CPP options to avoid CS corner updates for adjoint
605    o pkg/seaice:
606      => Change some of the defaults (2011/05/29):
607         - change SEAICEuseFluxForm default (from False to True)
608         - change DIFF1 default (from 0.004 m/s to 0. m/s)
609         And print warnings if DIFF1 is not set in data.seaice and centered
610          avection scheme is used without any diffusion.
611      also:
612      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
613      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
614      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
615        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
616        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
617      update results of test exp.:
618         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
619             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
620             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
621         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
622         seaice_obcs: output (SEAICEuseFluxForm=T)
623      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
624          for standard fwd & AD lab_sea tests (to keep the same output).
625    o pkg/seaice/seaice_growth.F:
626      - use Ian Fenty's capping formulas for actual ice
627      thickness thoughout EVOLUTION branch.
628      - put treatment pathological case #2) in CPP brackets
629      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
630      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
631    o pkg/seaice:
632      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
633      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
634      also pass fac as a param, which can be 1. (to update the tendency
635      field) or the time step (to update the field itself).
636      - seaice_advdiff.F: for multidim, call seaice_diffusion with
637      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
638      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
639      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
640      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
641    o pkg/seaice:
642      diffusion with centered advection scheme (diffus.F & advect.F):
643      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
644        to just compute the laplacian of input-field.
645      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
646      - fix flux-form version in diffus.F to conserve tracer.
647      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
648       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
649    
650    checkpoint62y (2011/05/26)
651    o pkg/seaice:
652     - seaice_growth.F : in EVOLUTION branch, always include
653       a_QSWbyATM_cover in qnet (as it should be).
654     - verification/global_ocean.cs32x15 : update results accordingly
655       (output.seaice.txt output_adm.seaice.txt).
656    o pkg/seaice + obcs:
657     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
658       equivalent of assuming no tracer gradient outside the OB region.
659       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
660     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
661       after changes above);
662     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
663       only at OB location (instead of over a band of OLx width).
664    o pkg/seaice:
665     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
666       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
667    o pkg/obcs:
668      - split header file "OBCS.h" into 4 separated files:
669        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
670       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
671         (contain no conditional statement which depends on OBCS options).
672      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
673        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
674    o ctrl, cost, grdchk & autodiff pkgs:
675      - make options file more standard (like other {PKG}_OPTIONS.h file but
676        with AD_CONFIG.h); clean-up some of the included header files.
677    o pkg/obcs:
678      - do not mask tracer when applying OB (tracer == 0 could generate problems)
679      - apply tracer OB values to tracer field only at OB location (instead of
680        over a band of OLx width)
681      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
682      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
683        obcs_apply_tloc.F & obcs_apply_sloc.F
684    o obcs in model/src:
685      - call OBCS_APPLY_W only if NonHydrostatic.
686      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
687      - reset dEtaHdt and wVel to zero outside OB interior region ;
688      - leave tracer unchanged outside OB interior region: This has no effect
689        on the solution but just to prevent unrealistic tracer value outside OB.
690      - zero out velocity outside OB interior region: This has no effect on
691        the solution but just to prevent unrealistic velocity outside OB.
692    o obcs and non-lin free-surf:
693       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
694       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
695       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
696       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
697       update results of test-exp. exp4(nlfs).
698    o exp4 (nlfs) test-exp:
699       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
700       with NonLin-FreeSurf); update output.nlfs.txt
701    o obcs and 2d/3d solver norm:
702       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
703       and outside OB interior region (will allow to place OB further inside the
704       domain). Depending on the domain, can affects cg2d-Norm (previous
705       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
706       and cg3d-Norm (previous Norm was computed before canceling OB terms),
707       e.g. in tutorial_plume_on_slope.
708      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
709    o pkg rbcs:
710      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
711      - add capability to apply relaxation to horizontal velocity uVel & vVel.
712    o pkg/grdchk: add gradient check for control variable xx_shifwflx
713    o pkg/shelfice/shelfice_init_fixed.F
714      fix CPP-flag combinations
715    o pkg/seaice: Merge iceage code of Pierre Rampal
716      * update/change/correct ice age calculations
717      * add age updates for pathological cases
718      Probably needs more testing...
719    
720    checkpoint62x (2011/05/13)
721    o pkg/mom_vecinv:
722       high-order vorticity scheme: use interior masks (maskInW & S)
723       to zero-out (outside OB) gradient of vorticity.
724    o verification exp.:
725       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
726       hs94.128x64x5 and seaice_obcs ; update results.
727    o pkg/obcs:
728      fix bug in OBeta for YZ sections in obcs_exf_load.F
729    o pkg/ctrl, pkg/shelfice, and optim:
730      - add new control variable xx_shifwflx (fresh water flux underneath ice
731        shelves). This is almost as tedious as obcs-ctrl, because the
732        variables needs its own mask.
733      - add a cost function term that penalizes the deviation of xx_shifwflx
734        from the first guess (zero) in analogy to other control variables
735    o pkg/shelfice:
736      - start basic adjoint
737    o pkg/ctrl:
738      - remove extra 2D field "for good measure" when initializing in
739        ctrl_set_globfld_[xy/xz/yz].F
740      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
741      - improve error messages in ctrl_set_unpack_*
742    o OBC implementation in momentum:
743       use interior masks (maskInC,W & S) in momentum S/R:
744       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
745       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
746       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
747       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
748       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
749        (and also with Leith/Smagorinsky harmonic-viscosity).
750       Update output of experiment dome and exp4 (+nlfs).
751    o exp4 test-exp:
752      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
753        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
754        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
755        time-varying OB at Western-side for wVel (NonHyd); update output.
756      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
757        and biharmonic-viscosity ; also use prescribed time varying OB.
758    o pkg/obcs:
759      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
760    o model/src:
761      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
762      - initialise startTime & nIter0 with unlikely values: allows to set one
763        from the other without ambiguity.
764    o seaice_obcs test-exp.:
765      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
766    o pkg/obcs:
767      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
768        no longer needed with maskInC,W,S in pkg/generic_advdiff.
769    o pkg/seaice:
770      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
771        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
772      - fixed bug in the initialization of sea ice salinity variable HSALT
773        in seaice_init_varia.F  (removed dependence on ICE2WATR)
774    o fizhi-cs test exp.:
775       switch reference output convention for these 2 non-standard test-exp,
776        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
777          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
778       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
779    o model/inc:
780      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
781        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
782    o pkg/seaice:
783      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
784    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
785      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
786        and initial HSALT
787    
788    checkpoint62w (2011/04/26)
789    o pkg/mom_fluxform:
790      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
791      - use parameter "sideDragFactor" in no-slip BC side-drag part.
792      - update output of exp. global_ocean.90x40x15
793    o pkg/mom_vecinv:
794      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
795    o update seaice exp.:
796      use more consistent parameter values (remove "backward compatability only":
797       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
798      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
799       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
800    o update test-exp global_ocean.90x40x15:
801      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
802      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
803      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
804      o turn on zStar & viscA4 in standard set-up (dir input/)
805        and update output files: output.txt & output.dwnslp.txt
806    o new AD-test experiment: obcs_ctrl
807      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
808    o pkg/dic:
809      fix two bugs in handling water vapour pressure in carbonate chemistry
810      and air-sea fluxes. Found by Val Bennington and Galen McKinley
811      (add DIC Option = WATERVAP_BUG to recover old results)
812      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
813    o adding allowInteriorFreezing option to check for water below freezing point
814      at depth and bring the negative heat anomaly to the surface level
815    o pkgs _fields_load:
816      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
817      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
818        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
819        rbcs to get interpolation weights and time reccord number.
820      - fix multi-threading in aim_fields_load.F
821      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
822  o external_fields_load:  o external_fields_load:
823    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
824     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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