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revision 1.1403 by jmc, Tue Mar 29 02:36:05 2011 UTC revision 1.1552 by mlosch, Mon Dec 19 11:51:22 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_readparms.F: make ocean_emissivity*stefanBoltzmann the
8      default for SEAICE_emissivity, if useEXF; requires setting a wrong
9      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
10      backward compatiblity
11    o model/src: use sigmaR in calc_ivdc
12    
13    checkpoint63g (2011/12/16)
14    o pkg/seaice/seaice_growth.F:
15      fix heat conservation of the coupled ocean-seaice system.
16      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
17      solid vs liquid water treatment is resolved via QNET.
18    o pkg/seaice/seaice_growth.F:
19      add missing term for sublimation in saltFlux, which was breaking conservation.
20    o pkg/seaice/seaice_model.F:
21      Remove this patholigical case treatment in evolution branch,
22      where it is un-necessary and breaks conservation.
23      Update global_ocean.cs32x15/results accordingly for
24      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
25    o model/src:
26      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
27      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
28    o pkg/obcs:
29      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
30      tendency for temperature and salinity that is then applied to update
31      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
32      horizontal advection and diffusion contributions on the boundary (in
33      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
34      removing the mask in S/R timestep_tracer. The advantage of this approach is
35      that the updated tracer values include contributions from the surface
36      forcing and vertical diffusion.
37      This modification changes exp4.stevens because of vertical diffusion.
38    o model/src:
39      change non-curvilinear grid setting to also work with exch2 + blank tiles:
40      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
41        face dimensions.
42      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
43        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
44        and INI_SPHERICAL_POLAR_GRID.
45      change test-experiment global_ocean.90x40x15:
46      - split the domain in many more tiles (9x4 tiles of 10x10 each);
47      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
48      - update results of both test (std & dwnslp).
49    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
50       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
51    o model/src:
52      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
53        and fix initialisation when using sigma-coords.
54    o model/src:
55     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
56       to their current value at the beginning of forward_step.F": add a new run-time
57       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
58     - set doResetHFactors=T in the following test exp:
59        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
60        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
61        and tutorial_global_oce_in_p (nonLinFS in p)
62    o pkg/ecco
63      - added IES cost term
64    o verification/advect_xz
65      - scale down the depth by 1/100 (from 200 km to just 2.km)
66      - add secondary test using divergent flow, r-star and implicit vertical advection.
67      - add note (check_conserve_TS.txt) and matlab script to check global
68        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
69    o pkg/rbcs:
70      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
71    o pkg/obcs (Stevens BCs):
72      - fix various problems in the phase speed computations of the Stevens
73        boundary conditions:
74        - sign error for western and southern boundaries,
75        - time tendencies were underestimated by factor of dTracerLev and some just
76          zero (for multidim advection schemes) -> now estimate time tendencies
77          from difference between previous (n) time level and the one before (n-1);
78          this requires storing a field per tracer per boundary, also in the pickup
79          files.
80        - replace deltaTmom in cflMer/Zon computation with dTracerLev
81        - set default phase velocity to cflMer/Zon
82      - update verification experiment exp4.stevens
83    o pkg/generic_advdiff (implicit_r):
84      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
85        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
86      - fix implicit vertical diffusion or advection with NonLin FreeSurf
87        (was using current recip_hFacC instead of future recip_hFacC): set future
88        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
89        solver S/R ;
90      - fill diagnostics of vertical advective fluxes (computed from tendency)
91        when using implicit vert. advection;
92      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
93         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
94         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
95         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
96    o pkg/diagnostics:
97      - add diags for T & S tendency which goes through Adams-Bashforth.
98    
99    checkpoint63f (2011/11/30)
100    o pkg/obcs/obcs_calc_stevens.F:
101      - join some loops to reduce number of if-statements
102      - fix a bug in code for northern and southern boundaries.
103    o pkg/seaice/seaice_init_varia.F
104      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
105        caused zero ice-velocities for the B-grid code
106    o pkg/seaice/seaice_init_fixed.F
107      - fix a bug in the initialisation of the second metric terms
108        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
109      - this affects all seaice configurations with useCurviLinearGrid = .true.
110        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
111        = .true. (default)
112      - the only verification experiment affected is global_ocean.cs32x15:
113        icedyn, seaice, and seaice_dynmix (AD)
114    o pkg/thsice/thsice_diagnostics_state.F
115      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
116        not contain garbage that can lead to surprises in diagstats_calc.F
117    o model/src:
118      - move bi,bj loops inside INTEGR_CONTINUITY ;
119      - call INTEGR_CONTINUITY directly from forward_step.F
120        (previously called from momentum_correction_step.F)
121      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
122        forward_step.F and pkg/ecco/the_main_loop.F
123    o model/src/do_oceanic_phys.F:
124      - reset addMass to zero only if useICEFRONT ;
125      - separated k-loop for rhoInSitu calculation ;
126      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
127        and at constant T,S (= WdRHOdP);
128      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
129        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
130        transport of locally-referenced potential density);
131        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
132    o gluemnc:
133      - replace ncrcat with ncks when adding variables to *.glob.nc
134      - change the way variables without record dimensions are handled so that
135        files that have variables with and without record variables can be glued:
136        add a record dimension with a new unique name to be able to differentiate
137        between variable with and without a-prior record dimensions. Remove
138        this record dimension before adding the variable to the *.glob.nc file.
139        This procedure automatically works also for grid.*.nc files that do not
140        have any record dimension.
141    o verification/cpl_aim+ocn:
142      - generate new reference output on baudelaire (gfortran, mpich2) (previously
143        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
144    o pkg/obcs/obcs_calc_stevens.F:
145      - add code for northern and southern boundaries.
146      - reorder some loops to save some operations and so that drFBar can be scalar
147    o model/src:
148      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
149        truncation) and add diagnostics for Adams-Bashforth tendency increment.
150      - update test-exp. AD output:
151        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
152      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
153        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
154        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
155        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
156        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
157        tutorial_plume_on_slope.
158    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
159      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
160      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
161      does not even come with an F77 compiler anymore, this should not be
162      a limitation
163    
164    checkpoint63e (2011/11/06)
165    o pkg/seaice adjoint of LSR:
166      - substantially rework STORE dirs.
167      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
168        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
169        and only perform SOLV_MAX_FIXED adjoint iters.
170        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
171        always goes to same record, meaning that the last forward field will be
172        the one used in the adjoint - an approximation.
173      - now produces non-zero LSR-related gradients, and acceptable gradients for
174        An's zonal (x-z) test case (to be checked in)
175      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
176        (but these are screwed up by the thermodynamics in the first place);
177        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
178        output_adm.txt also reflects changes to seaice_lsr
179      - global_ocean.cs32x15:
180        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
181          (output_adm.seaice.txt was updated)
182        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
183          (output_adm.seaice_dynmix.txt)
184    o test-exp. exp4+stevens:
185      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
186    o pkg/seaice (lsr solver):
187      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
188        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
189      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
190      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
191        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
192      - compute (with new S/R) and print initial (+ free-driff sol. if available)
193        and final residual of linearised system.
194    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
195      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
196    o pkg/obcs: Stevens BCs (still only for east and west)
197      - fix Stevens BCs by using intermediate velocities of previous
198        time step as "baroclinic" contribution rather velocity of one grid cell
199        inside the boundaries; more consistent but makes the entire treatment
200        more complicated, requires new pickup files and two new S/Rs:
201        obcs_copy_uv_n and obcs_save_uv_n
202        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
203        (undefined by default)
204      - silently move computation of some grid factors into separate loops to
205        save some recomputations
206      - add a hack for non-linear free surface
207      - add a verification experiment to exp4 that tests this code
208    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
209    
210    checkpoint63d (2011/10/25)
211    o pkg/obcs + seaice-dynamics:
212      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
213        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
214        values (consistent with an implicit method).
215      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
216        return to older implementation (same results as before); note that none of
217        the "experimental" OBCS_SEAICE options are implemented in the new version.
218      - switch test exp. seaice_obcs to use new version (update output).
219    o pkg/seaice:
220      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
221      - add parenthesis in Water-Ice drag calculations (evp & lsr);
222      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
223        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
224      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
225        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
226    o pkg/layers:
227      - Include potential density as new coordinate (Thanks to David Munday)
228    o pkg/dic:
229      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
230        carbonate computation/output to CALC_PCO2_APPROX
231    o pkg/generic_advdiff
232      - make TAF generate code that vectorizes:
233        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
234    o model/src:
235      - improve vectorization also for adjoint code of
236        solve_tridiagonal and solve_pentadiagonal. As this requires up to
237        5 new 3D-fields, this code is only turned on for the combination of
238        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
239        for singular matrix check (only for TARGET_NEC_SX).
240      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
241        ALLOW_AUTODIFF. This flag now needs to be set outside of
242        solve_tri/pentadiagonal.F
243    o pkg/exf:
244      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
245        optional namelist EXF_NML_OBCS).
246      - add many debug-print (to trace down where pkg/cal error msg comes from)
247    o pkg/mom_vecinv/mom_vi_hdissip.F
248      - rearrange loops so that vectorization is improved and in particular
249        the adjoint routine vectorizes. The code is a little longer now, but I
250        think easier to read.
251        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
252    o pkg/seaice:
253      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
254    o pkg/exch2:
255      - alternative code (without tile x tile matrix) for cumulated (global) sum;
256        used as default; keep using matrix version in adjustment.cs-32x32x1.
257    o tools/build_options:
258      - after merging some MPI and/or multi-threads specific optfiles so that
259        the modified default optfile support both built (using genmake2 -mpi
260        for the MPI built, using genmake2 -omp for OpenMP built),
261        move now obsolete optfiles to tools/build_options/unsupported/
262       (add copy of email sent to support list in doc/optfiles_changes.txt)
263    
264    checkpoint63c (2011/09/28)
265    o pkg/ebm:
266      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
267        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
268    o pkg/seaice (SItracer pickup)
269    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
270      To be done:
271      - thorough testing of missing fields in S/R seaice_read_pickup
272      - thorough matching between generic tracers and specific fields used
273        (e.g. volume-weighted age, area-weighted age, salinity, ...)
274    o pkg/grdchk:
275      - all procs calculate and print finite-difference gradient (for testreport)
276      - change description output used by testreport;
277      - AD testing: also compare and report Finite-difference gradient;
278        => update all output_adm*.txt
279    o test exp. global_ocean_ebm:
280      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
281        and turn on exactConserve; update (fwd) output.
282    o pkg/seaice (LSR):
283      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
284      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
285        * identical results with non-CS topology (but save up to half of EXCH calls)
286        * no much changes in cs-32 verification tests since no ice at face edges
287         (differences due to convergence criteria, since nb of iterations changed)
288        * expect some differences on lat-lon-cap grid.
289        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
290    o pkg/exch2:
291      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
292        many tiles); until alternative coding is added, just add a stop.
293    o pkg/kpp:
294      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
295        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
296    o optfiles:
297      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
298        into corresponding standard one, which now support different build:
299        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
300      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
301    o pkg/obcs (seaice):
302      - add missing EXCH for uIce,vIce after applying OBCS;
303      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
304        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
305        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
306      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
307      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
308        and eedata.mth for MPI and mutlti-threaded testing.
309    o pkg/flt:
310      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
311      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
312      - fix pickup and trajectories + profiles output with multi-threads;
313      - add parameter to select group of fields to write along trajectory and
314        profile (default unchanged);
315      - only call PORT_RAND* function when flt_noise <> 0;
316      - add multi-threaded test for verification exp. flt_example.
317    o eesupp/src:
318      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
319      - USE_OMP_THREADING: check that number of threads (from eedata) matches
320        actual number (from env.var. setting).
321    o pkg/ebm:
322      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
323      - add multi-threaded test for verification exp. global_ocean_ebm
324    
325    checkpoint63b (2011/08/29)
326    o pkg/ebm:
327      - fix sign of runoff;
328      - update directly forcing fields (Qnet,EmPmR) to use standard
329        external_forcing_surf.F (remove ebm_forcing_surf.F);
330      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
331      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
332        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
333      - update global_ocean_ebm parameters file data and update output (fwd+ad).
334    o verification/matrix_example:
335      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
336        MPI and mutlti-threaded testing.
337    o pkg/matrix:
338      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
339      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
340      - fix for multi-threaded (remove DATA statement);
341      - use standard DIFFERENT_MULTIPLE function;
342      - add MATRIX_OPTIONS.h
343    o verification/matrix_example:
344       To allow to split the domain in several tiles, change the domain size
345        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
346        Western side) of land points.
347    o (*_)write_pickup:
348      - fix few bugs in mypackage_read/write_pickup.F
349      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
350        array of length 1 (was caught by compiler syntax-check).
351    o pkg/diagnostics (velocity potential solver):
352      - fix initialisation of main diagonal matrix (for overlap values)
353    o tools/build_options:
354      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
355        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
356      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
357        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
358        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
359        and use "-devel" testreport option for standard testing on baudelaire.
360    o pkg/grdchk:
361      - Assume that all gradient-check position are within the same tile
362        corresponding to global indices (iGloTile,jGloTile) and that
363        positions (i,j indices or nbeg) are local to this tile;
364      - set tile local-indices and proc. number according to tile global-indices;
365      - remove grdchkwhichproc from namelist (retired param);
366      - send adjoint gradient to all procs so that all procs print it to STDOUT;
367      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
368    o adding package bbl (Bottom Boundary Layer)
369      description in MITgcm/pkg/bbl/bbl_description.tex
370      example/test experiment in MITgcm_contrib/bbl
371    o adjoint verifications
372      - changed 5 experiments to multi-tiles
373        * global_ocean.90x40x15
374        * obcs_ctrl
375        * offline_exf_seaice
376        * tutorial_dic_adjoffline
377        * tutorial_tracer_adjsens
378        changed reference output for those that crossed tile boundaries
379        (changed choices of gradient check positions)
380      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
381      - temporary bug fix in grdchk_loc.F for obcs
382    o genmake2 & testreport
383      - add target "obj" (just for OBJFILES files) to Makefile;
384      - add option to specify FEXTRAFLAGS on command line.
385    o pkg/mypackage:
386      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
387    
388    checkpoint63a (2011/08/02)
389    o pkg/diagnostics (velocity potential):
390      - fix velocity-potential calculation when using OBCS: balance net inflow
391        at each level (new S/R OBCS_DIAG_BALANCE).
392      - fix some of the problems with OBCS in stream-function calculation.
393    o pkg/exf/exf_readparms.F
394      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
395        EXF_NML_OBCS) more consistent, so that you need not have these lists
396        in data.exf when they are not used.
397    o optim/optim_readdata.F:
398      - add some output about obcs variables that might help debugging
399      - add a check about nvarlength
400    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
401    o pkg/diagnostics (velocity potential):
402      - fix mask for OBCS (still problems in stream-function with OBCS);
403      - add specific parameter (default = main code CG2D params) for solver;
404      - in case of poor convergence, use solution corresponding to lowest residual.
405    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
406      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
407      and should be avoided where possible.
408    o model/src (rStar):
409      - include r* effect on reference-state (PhiRef) in totPhiHyd
410        (so that it's really the potential anomaly at the cell center);
411        affect solution only if z* with full pressure in EOS.
412      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
413        update output (because of z* in totPhiHyd and viscA4 changes);
414      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
415        @ constant r) until interpolation at constant r is implemented.
416    o pkg/diagnostics
417      - fix RCENTER diagnostics in case cell center is not at interface middle
418    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
419      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
420      that THETA and SALT are "conservative temperature" and "absolute
421      salinity"
422    o pkg/ctrl
423      - fix computation of endrec in s/r ctrl_init_rec
424      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
425    o pkg/seaice/seaice_growth.F
426      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
427        remove then obsolete STORE directives
428      - fix STORE directives for tice and tices, so that only the
429        appropriate part of the fields are stored (and not the entire
430        field); update global_ocean.cs32x15.seaice AD output.
431      - cosmetic changes: adjust CPP flags and indentation for better
432        legibilty
433    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
434      Chris Wilson)
435    o pkg/gmredi:
436       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
437       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
438    
439    checkpoint63  (2011/07/11)
440    o pkg/exch2:
441     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
442     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
443       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
444       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
445    o pkg/diagnostics:
446     - deal with pairs of post-processed diags which are computed together; in
447       particular, re-order list of diags within 1 file to save 2nd computation.
448     - add S/R to compute velocity stream-function (called after velocity-potential
449       calculation) from divergence free transport -> new diagnostics "PsiVEL".
450     - add parameter to select grid-point location where PsiVEL == 0.
451    o eesupp/src:
452       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
453       (specific S/R needed with exch2 topology - for now, just print an error msg)
454    o pkg/shelfice
455     - Implement friction velocity-dependent transfer coefficients following
456       Holland and Jenkins, JPO, 1999
457       Original code by M. Losch with small modifs.
458       Enable with CPP option SHI_ALLOW_GAMMAFRICT
459       and runtime flag SHELFICEuseGammaFrict
460    o verification lab_sea & global_ocean.cs32x15:
461     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
462       does not miss some dependencies (but is slower) and also works with many files
463       (default makedepend limitation for AD built).
464     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
465    o pkg/diagnostics:
466     - add run-time parameter "useMissingValue" (def=False) to fill land-point
467        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
468       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
469     - Extend the use of "missing_value" setting from data.diagnostics for the case
470       of counter-diagnostics (where fraction-weight is zero). This applies both to
471       MNC and MDS output files.
472    o pkg/seaice/seaice_growth.F:
473      - add 'a priori' cap of latent heat flux based on actual mass considerations
474        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
475        non-legacy seaice_solve4temp.
476      - add diagnostic of the residual sublimation freshwater flux (the freshwater
477        flux taken from the ocean if the total actual latent heat fluxes exceed
478        the maximum)
479      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
480       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
481      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
482       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
483      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
484      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
485    o verification 1D_ocean_ice_column:
486       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
487       update results
488    o pkg/diagnostics:
489     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
490       which are not filled-up but computed from other diags ; In this case, the mate
491       diag points to the primary (filled-up) diag to used for post processing.
492     - Update Velocity-potential computation using post-processed diag framework.
493     ==> Change the ordering of fields and time-periods in MDS output file
494       when using periodic averaging: now writes one time record with the full set
495       of fields for this time period, then the next time reccord (it used to be
496       one field with the full set of time records then the next field).
497         Note: this is now similar to NetCDF (MNC) output file. <==
498    
499    checkpoint62z (2011/06/21)
500    o adjoint monitor:
501     - Add adjoint monitor output for packages exf, seaice
502       and update relevant testreport output
503    o pkg/seaice:
504     - re-order diags inits so that they appear in order in available_diagnostics.log
505     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
506       area/heff/hsnow preceeding thermodynamic growth/melt.
507     - modified diag: SIdA; output actual effect, as the description states.
508     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
509     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
510       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
511        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
512     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
513     - added diagnostics for seaice generic tracers (SItr*).
514     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
515     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
516     I. Fenty: 18-Jun-2011:
517     Minor changes to seaice package:
518     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
519        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
520       - Differentiated "regularization variables" from "floor variables"
521        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
522        * hiceMin became SEAICE_hice_reg (old hiceMin)
523          (with _reg meaning regularization variable)
524       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
525        so as to ensure energy conservation when going between phases
526      - A22 was not used anywhere
527     2) Changed regularization procedure for heffActual and hsnowActual to ensure
528        well-boundedness and smooth adjoint in seaice_growth.F
529     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
530        because the old regularization always set heffActual >= 0.05 cm
531     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
532        on AREA when HEFF > 0.
533      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
534        requiring that DISABLE_AREA_FLOOR *not* be defined
535     Affected verifications:
536      - 1D_ocean_ice_column (output.txt output_adm.txt)
537      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
538    o pkg/diagnostics:
539      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
540      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
541        (was _RL, now integer) with option = 0 to retrieve all levels.
542      - add pieces of code to compute velocity potential at each level (new diagnostics
543        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
544        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
545      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
546        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
547        and in diagnostics_fract_fill.F (do not need a valid pointer for the
548        diagnostics counter-mate); check that definition of counter-diagnostic
549        includes a valid counter-mate (in diagnostics_set_levels.F).
550    o model/src (rStar):
551      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
552        affect solution only if z* with full pressure in EOS;
553        update output of test-exp global_ocean.90x40x15.
554    o pkg/seaice:
555      - introduce siEps=1e-5 parameter
556      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
557      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
558      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
559        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
560        as well as ice cover age and ridging index (attached to AREA).
561        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
562        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
563        Up to SItrMaxNum=3 tracers can be used simultaneously.
564    o pkg/salt_plume:
565      -introduce SPsalFRAC run time parameter that sets the fraction of the
566       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
567       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
568    o model debug options:
569      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
570        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
571      - Refine debug-msg printing selection (3 new levels):
572        debugMode  : controls printing of debug messages (sequence of S/R calls).
573        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
574         debLevZero =  0 ; /* level of disabled aux. msg printing */
575         debLevA =  1 ; /* level of minimum  aux. msg printing */
576         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
577         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
578         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
579         debLevE =  5 ; /* level of extensive debug printing */
580        New debugLevel default: with default debugMode value (=F),
581          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
582          and if debugMode=T, default debugLevel = 4 (debLevD).
583        Relation with previous settings:
584         debLevB (=2) corresponds to former debLevA (=1)
585         debLevD (=4) corresponds to former debLevB (=2)
586        Note:
587         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
588         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
589            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
590      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
591        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
592    o pkg/obcs:
593      - change OBCSfixTopo default from True to False (should not change the results);
594        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
595    o pkg/thsice:
596      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
597        2nd layer seaice sublimation (unlikely to happen)
598      - use Interior mask for OBCS in thsice_advection.F (similar to what is
599        done in gad_advection & seaice_advection).
600    o adjoint:
601      bug fix spotted by Gael Forget:
602      seaice_advection and thsice_advection still had
603      legacy CPP options to avoid CS corner updates for adjoint
604    o pkg/seaice:
605      => Change some of the defaults (2011/05/29):
606         - change SEAICEuseFluxForm default (from False to True)
607         - change DIFF1 default (from 0.004 m/s to 0. m/s)
608         And print warnings if DIFF1 is not set in data.seaice and centered
609          avection scheme is used without any diffusion.
610      also:
611      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
612      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
613      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
614        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
615        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
616      update results of test exp.:
617         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
618             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
619             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
620         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
621         seaice_obcs: output (SEAICEuseFluxForm=T)
622      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
623          for standard fwd & AD lab_sea tests (to keep the same output).
624    o pkg/seaice/seaice_growth.F:
625      - use Ian Fenty's capping formulas for actual ice
626      thickness thoughout EVOLUTION branch.
627      - put treatment pathological case #2) in CPP brackets
628      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
629      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
630    o pkg/seaice:
631      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
632      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
633      also pass fac as a param, which can be 1. (to update the tendency
634      field) or the time step (to update the field itself).
635      - seaice_advdiff.F: for multidim, call seaice_diffusion with
636      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
637      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
638      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
639      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
640    o pkg/seaice:
641      diffusion with centered advection scheme (diffus.F & advect.F):
642      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
643        to just compute the laplacian of input-field.
644      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
645      - fix flux-form version in diffus.F to conserve tracer.
646      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
647       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
648    
649    checkpoint62y (2011/05/26)
650    o pkg/seaice:
651     - seaice_growth.F : in EVOLUTION branch, always include
652       a_QSWbyATM_cover in qnet (as it should be).
653     - verification/global_ocean.cs32x15 : update results accordingly
654       (output.seaice.txt output_adm.seaice.txt).
655    o pkg/seaice + obcs:
656     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
657       equivalent of assuming no tracer gradient outside the OB region.
658       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
659     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
660       after changes above);
661     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
662       only at OB location (instead of over a band of OLx width).
663    o pkg/seaice:
664     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
665       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
666    o pkg/obcs:
667      - split header file "OBCS.h" into 4 separated files:
668        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
669       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
670         (contain no conditional statement which depends on OBCS options).
671      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
672        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
673    o ctrl, cost, grdchk & autodiff pkgs:
674      - make options file more standard (like other {PKG}_OPTIONS.h file but
675        with AD_CONFIG.h); clean-up some of the included header files.
676    o pkg/obcs:
677      - do not mask tracer when applying OB (tracer == 0 could generate problems)
678      - apply tracer OB values to tracer field only at OB location (instead of
679        over a band of OLx width)
680      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
681      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
682        obcs_apply_tloc.F & obcs_apply_sloc.F
683    o obcs in model/src:
684      - call OBCS_APPLY_W only if NonHydrostatic.
685      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
686      - reset dEtaHdt and wVel to zero outside OB interior region ;
687      - leave tracer unchanged outside OB interior region: This has no effect
688        on the solution but just to prevent unrealistic tracer value outside OB.
689      - zero out velocity outside OB interior region: This has no effect on
690        the solution but just to prevent unrealistic velocity outside OB.
691    o obcs and non-lin free-surf:
692       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
693       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
694       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
695       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
696       update results of test-exp. exp4(nlfs).
697    o exp4 (nlfs) test-exp:
698       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
699       with NonLin-FreeSurf); update output.nlfs.txt
700    o obcs and 2d/3d solver norm:
701       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
702       and outside OB interior region (will allow to place OB further inside the
703       domain). Depending on the domain, can affects cg2d-Norm (previous
704       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
705       and cg3d-Norm (previous Norm was computed before canceling OB terms),
706       e.g. in tutorial_plume_on_slope.
707      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
708    o pkg rbcs:
709      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
710      - add capability to apply relaxation to horizontal velocity uVel & vVel.
711    o pkg/grdchk: add gradient check for control variable xx_shifwflx
712    o pkg/shelfice/shelfice_init_fixed.F
713      fix CPP-flag combinations
714    o pkg/seaice: Merge iceage code of Pierre Rampal
715      * update/change/correct ice age calculations
716      * add age updates for pathological cases
717      Probably needs more testing...
718    
719    checkpoint62x (2011/05/13)
720    o pkg/mom_vecinv:
721       high-order vorticity scheme: use interior masks (maskInW & S)
722       to zero-out (outside OB) gradient of vorticity.
723    o verification exp.:
724       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
725       hs94.128x64x5 and seaice_obcs ; update results.
726    o pkg/obcs:
727      fix bug in OBeta for YZ sections in obcs_exf_load.F
728    o pkg/ctrl, pkg/shelfice, and optim:
729      - add new control variable xx_shifwflx (fresh water flux underneath ice
730        shelves). This is almost as tedious as obcs-ctrl, because the
731        variables needs its own mask.
732      - add a cost function term that penalizes the deviation of xx_shifwflx
733        from the first guess (zero) in analogy to other control variables
734    o pkg/shelfice:
735      - start basic adjoint
736    o pkg/ctrl:
737      - remove extra 2D field "for good measure" when initializing in
738        ctrl_set_globfld_[xy/xz/yz].F
739      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
740      - improve error messages in ctrl_set_unpack_*
741    o OBC implementation in momentum:
742       use interior masks (maskInC,W & S) in momentum S/R:
743       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
744       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
745       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
746       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
747       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
748        (and also with Leith/Smagorinsky harmonic-viscosity).
749       Update output of experiment dome and exp4 (+nlfs).
750    o exp4 test-exp:
751      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
752        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
753        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
754        time-varying OB at Western-side for wVel (NonHyd); update output.
755      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
756        and biharmonic-viscosity ; also use prescribed time varying OB.
757    o pkg/obcs:
758      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
759    o model/src:
760      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
761      - initialise startTime & nIter0 with unlikely values: allows to set one
762        from the other without ambiguity.
763    o seaice_obcs test-exp.:
764      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
765    o pkg/obcs:
766      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
767        no longer needed with maskInC,W,S in pkg/generic_advdiff.
768    o pkg/seaice:
769      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
770        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
771      - fixed bug in the initialization of sea ice salinity variable HSALT
772        in seaice_init_varia.F  (removed dependence on ICE2WATR)
773    o fizhi-cs test exp.:
774       switch reference output convention for these 2 non-standard test-exp,
775        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
776          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
777       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
778    o model/inc:
779      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
780        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
781    o pkg/seaice:
782      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
783    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
784      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
785        and initial HSALT
786    
787    checkpoint62w (2011/04/26)
788    o pkg/mom_fluxform:
789      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
790      - use parameter "sideDragFactor" in no-slip BC side-drag part.
791      - update output of exp. global_ocean.90x40x15
792    o pkg/mom_vecinv:
793      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
794    o update seaice exp.:
795      use more consistent parameter values (remove "backward compatability only":
796       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
797      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
798       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
799    o update test-exp global_ocean.90x40x15:
800      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
801      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
802      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
803      o turn on zStar & viscA4 in standard set-up (dir input/)
804        and update output files: output.txt & output.dwnslp.txt
805    o new AD-test experiment: obcs_ctrl
806      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
807    o pkg/dic:
808      fix two bugs in handling water vapour pressure in carbonate chemistry
809      and air-sea fluxes. Found by Val Bennington and Galen McKinley
810      (add DIC Option = WATERVAP_BUG to recover old results)
811      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
812    o adding allowInteriorFreezing option to check for water below freezing point
813      at depth and bring the negative heat anomaly to the surface level
814    o pkgs _fields_load:
815      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
816      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
817        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
818        rbcs to get interpolation weights and time reccord number.
819      - fix multi-threading in aim_fields_load.F
820      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
821    o external_fields_load:
822      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
823       interpolation weights) to use in a periodic time-series ; do not divide by
824       time-step to convert to integer:
825       - this fixes case where externForcingPeriod is not multiple of time-step
826          (Thanks to Christopher L. Wolfe)
827       - this fixes case where externForcingPeriod is an odd multiple of time-step
828         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
829      store index of time-record which is currently loaded:
830       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
831       - needed for the adjoint but not yet used because of extensive recomputations;
832         (to be fixed soon)
833    
834    checkpoint62v (2011/04/02)
835    o verification/1D_ocean_ice_column added to test Ian Fenty's
836      pkg/seaice_growth.F modifications for improving sea ice code differentiability
837    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
838      (new velocity statistics after changing maskInW & maskInS definition)
839    o pkg/generic_advdiff with OBCS:
840      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
841      equivalent to assumption of no tracer gradient outside the OB region.
842      This will affect the results if using obcs+biharmonic diffusion.
843      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
844  o pkg/obcs:  o pkg/obcs:
845    change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)    change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
846    (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still    (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
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