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revision 1.1442 by gforget, Wed May 25 23:56:29 2011 UTC revision 1.1554 by mlosch, Mon Dec 19 16:33:53 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:
8      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
9        what the name implies (and not emissivity*BoltzmannConstant), this means
10        the old default value of 5.5e-8 now means
11        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
12        S/R exf_readparms
13      - FV-discretization of the B-grid LSOR solver, turn on with
14      SEAICE_LSRBNEW. This new solver also involves a slight re-organization
15      of the calling routine dynsolver, so that B and C-grid code look a
16      little more alike.
17    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
18    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
19      default for SEAICE_emissivity, if useEXF; requires setting a wrong
20      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
21      backward compatiblity
22    o model/src: use sigmaR in calc_ivdc
23    
24    checkpoint63g (2011/12/16)
25    o pkg/seaice/seaice_growth.F:
26      fix heat conservation of the coupled ocean-seaice system.
27      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
28      solid vs liquid water treatment is resolved via QNET.
29    o pkg/seaice/seaice_growth.F:
30      add missing term for sublimation in saltFlux, which was breaking conservation.
31    o pkg/seaice/seaice_model.F:
32      Remove this patholigical case treatment in evolution branch,
33      where it is un-necessary and breaks conservation.
34      Update global_ocean.cs32x15/results accordingly for
35      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
36    o model/src:
37      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
38      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
39    o pkg/obcs:
40      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
41      tendency for temperature and salinity that is then applied to update
42      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
43      horizontal advection and diffusion contributions on the boundary (in
44      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
45      removing the mask in S/R timestep_tracer. The advantage of this approach is
46      that the updated tracer values include contributions from the surface
47      forcing and vertical diffusion.
48      This modification changes exp4.stevens because of vertical diffusion.
49    o model/src:
50      change non-curvilinear grid setting to also work with exch2 + blank tiles:
51      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
52        face dimensions.
53      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
54        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
55        and INI_SPHERICAL_POLAR_GRID.
56      change test-experiment global_ocean.90x40x15:
57      - split the domain in many more tiles (9x4 tiles of 10x10 each);
58      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
59      - update results of both test (std & dwnslp).
60    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
61       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
62    o model/src:
63      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
64        and fix initialisation when using sigma-coords.
65    o model/src:
66     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
67       to their current value at the beginning of forward_step.F": add a new run-time
68       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
69     - set doResetHFactors=T in the following test exp:
70        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
71        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
72        and tutorial_global_oce_in_p (nonLinFS in p)
73    o pkg/ecco
74      - added IES cost term
75    o verification/advect_xz
76      - scale down the depth by 1/100 (from 200 km to just 2.km)
77      - add secondary test using divergent flow, r-star and implicit vertical advection.
78      - add note (check_conserve_TS.txt) and matlab script to check global
79        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
80    o pkg/rbcs:
81      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
82    o pkg/obcs (Stevens BCs):
83      - fix various problems in the phase speed computations of the Stevens
84        boundary conditions:
85        - sign error for western and southern boundaries,
86        - time tendencies were underestimated by factor of dTracerLev and some just
87          zero (for multidim advection schemes) -> now estimate time tendencies
88          from difference between previous (n) time level and the one before (n-1);
89          this requires storing a field per tracer per boundary, also in the pickup
90          files.
91        - replace deltaTmom in cflMer/Zon computation with dTracerLev
92        - set default phase velocity to cflMer/Zon
93      - update verification experiment exp4.stevens
94    o pkg/generic_advdiff (implicit_r):
95      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
96        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
97      - fix implicit vertical diffusion or advection with NonLin FreeSurf
98        (was using current recip_hFacC instead of future recip_hFacC): set future
99        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
100        solver S/R ;
101      - fill diagnostics of vertical advective fluxes (computed from tendency)
102        when using implicit vert. advection;
103      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
104         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
105         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
106         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
107    o pkg/diagnostics:
108      - add diags for T & S tendency which goes through Adams-Bashforth.
109    
110    checkpoint63f (2011/11/30)
111    o pkg/obcs/obcs_calc_stevens.F:
112      - join some loops to reduce number of if-statements
113      - fix a bug in code for northern and southern boundaries.
114    o pkg/seaice/seaice_init_varia.F
115      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
116        caused zero ice-velocities for the B-grid code
117    o pkg/seaice/seaice_init_fixed.F
118      - fix a bug in the initialisation of the second metric terms
119        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
120      - this affects all seaice configurations with useCurviLinearGrid = .true.
121        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
122        = .true. (default)
123      - the only verification experiment affected is global_ocean.cs32x15:
124        icedyn, seaice, and seaice_dynmix (AD)
125    o pkg/thsice/thsice_diagnostics_state.F
126      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
127        not contain garbage that can lead to surprises in diagstats_calc.F
128    o model/src:
129      - move bi,bj loops inside INTEGR_CONTINUITY ;
130      - call INTEGR_CONTINUITY directly from forward_step.F
131        (previously called from momentum_correction_step.F)
132      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
133        forward_step.F and pkg/ecco/the_main_loop.F
134    o model/src/do_oceanic_phys.F:
135      - reset addMass to zero only if useICEFRONT ;
136      - separated k-loop for rhoInSitu calculation ;
137      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
138        and at constant T,S (= WdRHOdP);
139      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
140        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
141        transport of locally-referenced potential density);
142        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
143    o gluemnc:
144      - replace ncrcat with ncks when adding variables to *.glob.nc
145      - change the way variables without record dimensions are handled so that
146        files that have variables with and without record variables can be glued:
147        add a record dimension with a new unique name to be able to differentiate
148        between variable with and without a-prior record dimensions. Remove
149        this record dimension before adding the variable to the *.glob.nc file.
150        This procedure automatically works also for grid.*.nc files that do not
151        have any record dimension.
152    o verification/cpl_aim+ocn:
153      - generate new reference output on baudelaire (gfortran, mpich2) (previously
154        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
155    o pkg/obcs/obcs_calc_stevens.F:
156      - add code for northern and southern boundaries.
157      - reorder some loops to save some operations and so that drFBar can be scalar
158    o model/src:
159      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
160        truncation) and add diagnostics for Adams-Bashforth tendency increment.
161      - update test-exp. AD output:
162        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
163      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
164        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
165        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
166        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
167        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
168        tutorial_plume_on_slope.
169    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
170      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
171      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
172      does not even come with an F77 compiler anymore, this should not be
173      a limitation
174    
175    checkpoint63e (2011/11/06)
176    o pkg/seaice adjoint of LSR:
177      - substantially rework STORE dirs.
178      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
179        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
180        and only perform SOLV_MAX_FIXED adjoint iters.
181        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
182        always goes to same record, meaning that the last forward field will be
183        the one used in the adjoint - an approximation.
184      - now produces non-zero LSR-related gradients, and acceptable gradients for
185        An's zonal (x-z) test case (to be checked in)
186      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
187        (but these are screwed up by the thermodynamics in the first place);
188        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
189        output_adm.txt also reflects changes to seaice_lsr
190      - global_ocean.cs32x15:
191        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
192          (output_adm.seaice.txt was updated)
193        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
194          (output_adm.seaice_dynmix.txt)
195    o test-exp. exp4+stevens:
196      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
197    o pkg/seaice (lsr solver):
198      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
199        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
200      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
201      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
202        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
203      - compute (with new S/R) and print initial (+ free-driff sol. if available)
204        and final residual of linearised system.
205    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
206      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
207    o pkg/obcs: Stevens BCs (still only for east and west)
208      - fix Stevens BCs by using intermediate velocities of previous
209        time step as "baroclinic" contribution rather velocity of one grid cell
210        inside the boundaries; more consistent but makes the entire treatment
211        more complicated, requires new pickup files and two new S/Rs:
212        obcs_copy_uv_n and obcs_save_uv_n
213        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
214        (undefined by default)
215      - silently move computation of some grid factors into separate loops to
216        save some recomputations
217      - add a hack for non-linear free surface
218      - add a verification experiment to exp4 that tests this code
219    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
220    
221    checkpoint63d (2011/10/25)
222    o pkg/obcs + seaice-dynamics:
223      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
224        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
225        values (consistent with an implicit method).
226      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
227        return to older implementation (same results as before); note that none of
228        the "experimental" OBCS_SEAICE options are implemented in the new version.
229      - switch test exp. seaice_obcs to use new version (update output).
230    o pkg/seaice:
231      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
232      - add parenthesis in Water-Ice drag calculations (evp & lsr);
233      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
234        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
235      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
236        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
237    o pkg/layers:
238      - Include potential density as new coordinate (Thanks to David Munday)
239    o pkg/dic:
240      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
241        carbonate computation/output to CALC_PCO2_APPROX
242    o pkg/generic_advdiff
243      - make TAF generate code that vectorizes:
244        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
245    o model/src:
246      - improve vectorization also for adjoint code of
247        solve_tridiagonal and solve_pentadiagonal. As this requires up to
248        5 new 3D-fields, this code is only turned on for the combination of
249        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
250        for singular matrix check (only for TARGET_NEC_SX).
251      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
252        ALLOW_AUTODIFF. This flag now needs to be set outside of
253        solve_tri/pentadiagonal.F
254    o pkg/exf:
255      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
256        optional namelist EXF_NML_OBCS).
257      - add many debug-print (to trace down where pkg/cal error msg comes from)
258    o pkg/mom_vecinv/mom_vi_hdissip.F
259      - rearrange loops so that vectorization is improved and in particular
260        the adjoint routine vectorizes. The code is a little longer now, but I
261        think easier to read.
262        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
263    o pkg/seaice:
264      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
265    o pkg/exch2:
266      - alternative code (without tile x tile matrix) for cumulated (global) sum;
267        used as default; keep using matrix version in adjustment.cs-32x32x1.
268    o tools/build_options:
269      - after merging some MPI and/or multi-threads specific optfiles so that
270        the modified default optfile support both built (using genmake2 -mpi
271        for the MPI built, using genmake2 -omp for OpenMP built),
272        move now obsolete optfiles to tools/build_options/unsupported/
273       (add copy of email sent to support list in doc/optfiles_changes.txt)
274    
275    checkpoint63c (2011/09/28)
276    o pkg/ebm:
277      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
278        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
279    o pkg/seaice (SItracer pickup)
280    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
281      To be done:
282      - thorough testing of missing fields in S/R seaice_read_pickup
283      - thorough matching between generic tracers and specific fields used
284        (e.g. volume-weighted age, area-weighted age, salinity, ...)
285    o pkg/grdchk:
286      - all procs calculate and print finite-difference gradient (for testreport)
287      - change description output used by testreport;
288      - AD testing: also compare and report Finite-difference gradient;
289        => update all output_adm*.txt
290    o test exp. global_ocean_ebm:
291      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
292        and turn on exactConserve; update (fwd) output.
293    o pkg/seaice (LSR):
294      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
295      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
296        * identical results with non-CS topology (but save up to half of EXCH calls)
297        * no much changes in cs-32 verification tests since no ice at face edges
298         (differences due to convergence criteria, since nb of iterations changed)
299        * expect some differences on lat-lon-cap grid.
300        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
301    o pkg/exch2:
302      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
303        many tiles); until alternative coding is added, just add a stop.
304    o pkg/kpp:
305      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
306        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
307    o optfiles:
308      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
309        into corresponding standard one, which now support different build:
310        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
311      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
312    o pkg/obcs (seaice):
313      - add missing EXCH for uIce,vIce after applying OBCS;
314      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
315        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
316        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
317      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
318      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
319        and eedata.mth for MPI and mutlti-threaded testing.
320    o pkg/flt:
321      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
322      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
323      - fix pickup and trajectories + profiles output with multi-threads;
324      - add parameter to select group of fields to write along trajectory and
325        profile (default unchanged);
326      - only call PORT_RAND* function when flt_noise <> 0;
327      - add multi-threaded test for verification exp. flt_example.
328    o eesupp/src:
329      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
330      - USE_OMP_THREADING: check that number of threads (from eedata) matches
331        actual number (from env.var. setting).
332    o pkg/ebm:
333      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
334      - add multi-threaded test for verification exp. global_ocean_ebm
335    
336    checkpoint63b (2011/08/29)
337    o pkg/ebm:
338      - fix sign of runoff;
339      - update directly forcing fields (Qnet,EmPmR) to use standard
340        external_forcing_surf.F (remove ebm_forcing_surf.F);
341      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
342      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
343        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
344      - update global_ocean_ebm parameters file data and update output (fwd+ad).
345    o verification/matrix_example:
346      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
347        MPI and mutlti-threaded testing.
348    o pkg/matrix:
349      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
350      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
351      - fix for multi-threaded (remove DATA statement);
352      - use standard DIFFERENT_MULTIPLE function;
353      - add MATRIX_OPTIONS.h
354    o verification/matrix_example:
355       To allow to split the domain in several tiles, change the domain size
356        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
357        Western side) of land points.
358    o (*_)write_pickup:
359      - fix few bugs in mypackage_read/write_pickup.F
360      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
361        array of length 1 (was caught by compiler syntax-check).
362    o pkg/diagnostics (velocity potential solver):
363      - fix initialisation of main diagonal matrix (for overlap values)
364    o tools/build_options:
365      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
366        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
367      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
368        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
369        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
370        and use "-devel" testreport option for standard testing on baudelaire.
371    o pkg/grdchk:
372      - Assume that all gradient-check position are within the same tile
373        corresponding to global indices (iGloTile,jGloTile) and that
374        positions (i,j indices or nbeg) are local to this tile;
375      - set tile local-indices and proc. number according to tile global-indices;
376      - remove grdchkwhichproc from namelist (retired param);
377      - send adjoint gradient to all procs so that all procs print it to STDOUT;
378      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
379    o adding package bbl (Bottom Boundary Layer)
380      description in MITgcm/pkg/bbl/bbl_description.tex
381      example/test experiment in MITgcm_contrib/bbl
382    o adjoint verifications
383      - changed 5 experiments to multi-tiles
384        * global_ocean.90x40x15
385        * obcs_ctrl
386        * offline_exf_seaice
387        * tutorial_dic_adjoffline
388        * tutorial_tracer_adjsens
389        changed reference output for those that crossed tile boundaries
390        (changed choices of gradient check positions)
391      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
392      - temporary bug fix in grdchk_loc.F for obcs
393    o genmake2 & testreport
394      - add target "obj" (just for OBJFILES files) to Makefile;
395      - add option to specify FEXTRAFLAGS on command line.
396    o pkg/mypackage:
397      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
398    
399    checkpoint63a (2011/08/02)
400    o pkg/diagnostics (velocity potential):
401      - fix velocity-potential calculation when using OBCS: balance net inflow
402        at each level (new S/R OBCS_DIAG_BALANCE).
403      - fix some of the problems with OBCS in stream-function calculation.
404    o pkg/exf/exf_readparms.F
405      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
406        EXF_NML_OBCS) more consistent, so that you need not have these lists
407        in data.exf when they are not used.
408    o optim/optim_readdata.F:
409      - add some output about obcs variables that might help debugging
410      - add a check about nvarlength
411    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
412    o pkg/diagnostics (velocity potential):
413      - fix mask for OBCS (still problems in stream-function with OBCS);
414      - add specific parameter (default = main code CG2D params) for solver;
415      - in case of poor convergence, use solution corresponding to lowest residual.
416    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
417      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
418      and should be avoided where possible.
419    o model/src (rStar):
420      - include r* effect on reference-state (PhiRef) in totPhiHyd
421        (so that it's really the potential anomaly at the cell center);
422        affect solution only if z* with full pressure in EOS.
423      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
424        update output (because of z* in totPhiHyd and viscA4 changes);
425      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
426        @ constant r) until interpolation at constant r is implemented.
427    o pkg/diagnostics
428      - fix RCENTER diagnostics in case cell center is not at interface middle
429    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
430      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
431      that THETA and SALT are "conservative temperature" and "absolute
432      salinity"
433    o pkg/ctrl
434      - fix computation of endrec in s/r ctrl_init_rec
435      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
436    o pkg/seaice/seaice_growth.F
437      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
438        remove then obsolete STORE directives
439      - fix STORE directives for tice and tices, so that only the
440        appropriate part of the fields are stored (and not the entire
441        field); update global_ocean.cs32x15.seaice AD output.
442      - cosmetic changes: adjust CPP flags and indentation for better
443        legibilty
444    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
445      Chris Wilson)
446    o pkg/gmredi:
447       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
448       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
449    
450    checkpoint63  (2011/07/11)
451    o pkg/exch2:
452     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
453     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
454       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
455       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
456    o pkg/diagnostics:
457     - deal with pairs of post-processed diags which are computed together; in
458       particular, re-order list of diags within 1 file to save 2nd computation.
459     - add S/R to compute velocity stream-function (called after velocity-potential
460       calculation) from divergence free transport -> new diagnostics "PsiVEL".
461     - add parameter to select grid-point location where PsiVEL == 0.
462    o eesupp/src:
463       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
464       (specific S/R needed with exch2 topology - for now, just print an error msg)
465    o pkg/shelfice
466     - Implement friction velocity-dependent transfer coefficients following
467       Holland and Jenkins, JPO, 1999
468       Original code by M. Losch with small modifs.
469       Enable with CPP option SHI_ALLOW_GAMMAFRICT
470       and runtime flag SHELFICEuseGammaFrict
471    o verification lab_sea & global_ocean.cs32x15:
472     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
473       does not miss some dependencies (but is slower) and also works with many files
474       (default makedepend limitation for AD built).
475     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
476    o pkg/diagnostics:
477     - add run-time parameter "useMissingValue" (def=False) to fill land-point
478        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
479       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
480     - Extend the use of "missing_value" setting from data.diagnostics for the case
481       of counter-diagnostics (where fraction-weight is zero). This applies both to
482       MNC and MDS output files.
483    o pkg/seaice/seaice_growth.F:
484      - add 'a priori' cap of latent heat flux based on actual mass considerations
485        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
486        non-legacy seaice_solve4temp.
487      - add diagnostic of the residual sublimation freshwater flux (the freshwater
488        flux taken from the ocean if the total actual latent heat fluxes exceed
489        the maximum)
490      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
491       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
492      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
493       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
494      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
495      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
496    o verification 1D_ocean_ice_column:
497       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
498       update results
499    o pkg/diagnostics:
500     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
501       which are not filled-up but computed from other diags ; In this case, the mate
502       diag points to the primary (filled-up) diag to used for post processing.
503     - Update Velocity-potential computation using post-processed diag framework.
504     ==> Change the ordering of fields and time-periods in MDS output file
505       when using periodic averaging: now writes one time record with the full set
506       of fields for this time period, then the next time reccord (it used to be
507       one field with the full set of time records then the next field).
508         Note: this is now similar to NetCDF (MNC) output file. <==
509    
510    checkpoint62z (2011/06/21)
511    o adjoint monitor:
512     - Add adjoint monitor output for packages exf, seaice
513       and update relevant testreport output
514    o pkg/seaice:
515     - re-order diags inits so that they appear in order in available_diagnostics.log
516     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
517       area/heff/hsnow preceeding thermodynamic growth/melt.
518     - modified diag: SIdA; output actual effect, as the description states.
519     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
520     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
521       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
522        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
523     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
524     - added diagnostics for seaice generic tracers (SItr*).
525     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
526     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
527     I. Fenty: 18-Jun-2011:
528     Minor changes to seaice package:
529     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
530        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
531       - Differentiated "regularization variables" from "floor variables"
532        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
533        * hiceMin became SEAICE_hice_reg (old hiceMin)
534          (with _reg meaning regularization variable)
535       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
536        so as to ensure energy conservation when going between phases
537      - A22 was not used anywhere
538     2) Changed regularization procedure for heffActual and hsnowActual to ensure
539        well-boundedness and smooth adjoint in seaice_growth.F
540     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
541        because the old regularization always set heffActual >= 0.05 cm
542     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
543        on AREA when HEFF > 0.
544      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
545        requiring that DISABLE_AREA_FLOOR *not* be defined
546     Affected verifications:
547      - 1D_ocean_ice_column (output.txt output_adm.txt)
548      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
549    o pkg/diagnostics:
550      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
551      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
552        (was _RL, now integer) with option = 0 to retrieve all levels.
553      - add pieces of code to compute velocity potential at each level (new diagnostics
554        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
555        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
556      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
557        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
558        and in diagnostics_fract_fill.F (do not need a valid pointer for the
559        diagnostics counter-mate); check that definition of counter-diagnostic
560        includes a valid counter-mate (in diagnostics_set_levels.F).
561    o model/src (rStar):
562      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
563        affect solution only if z* with full pressure in EOS;
564        update output of test-exp global_ocean.90x40x15.
565    o pkg/seaice:
566      - introduce siEps=1e-5 parameter
567      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
568      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
569      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
570        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
571        as well as ice cover age and ridging index (attached to AREA).
572        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
573        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
574        Up to SItrMaxNum=3 tracers can be used simultaneously.
575    o pkg/salt_plume:
576      -introduce SPsalFRAC run time parameter that sets the fraction of the
577       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
578       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
579    o model debug options:
580      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
581        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
582      - Refine debug-msg printing selection (3 new levels):
583        debugMode  : controls printing of debug messages (sequence of S/R calls).
584        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
585         debLevZero =  0 ; /* level of disabled aux. msg printing */
586         debLevA =  1 ; /* level of minimum  aux. msg printing */
587         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
588         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
589         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
590         debLevE =  5 ; /* level of extensive debug printing */
591        New debugLevel default: with default debugMode value (=F),
592          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
593          and if debugMode=T, default debugLevel = 4 (debLevD).
594        Relation with previous settings:
595         debLevB (=2) corresponds to former debLevA (=1)
596         debLevD (=4) corresponds to former debLevB (=2)
597        Note:
598         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
599         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
600            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
601      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
602        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
603    o pkg/obcs:
604      - change OBCSfixTopo default from True to False (should not change the results);
605        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
606    o pkg/thsice:
607      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
608        2nd layer seaice sublimation (unlikely to happen)
609      - use Interior mask for OBCS in thsice_advection.F (similar to what is
610        done in gad_advection & seaice_advection).
611    o adjoint:
612      bug fix spotted by Gael Forget:
613      seaice_advection and thsice_advection still had
614      legacy CPP options to avoid CS corner updates for adjoint
615    o pkg/seaice:
616      => Change some of the defaults (2011/05/29):
617         - change SEAICEuseFluxForm default (from False to True)
618         - change DIFF1 default (from 0.004 m/s to 0. m/s)
619         And print warnings if DIFF1 is not set in data.seaice and centered
620          avection scheme is used without any diffusion.
621      also:
622      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
623      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
624      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
625        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
626        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
627      update results of test exp.:
628         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
629             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
630             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
631         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
632         seaice_obcs: output (SEAICEuseFluxForm=T)
633      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
634          for standard fwd & AD lab_sea tests (to keep the same output).
635    o pkg/seaice/seaice_growth.F:
636      - use Ian Fenty's capping formulas for actual ice
637      thickness thoughout EVOLUTION branch.
638      - put treatment pathological case #2) in CPP brackets
639      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
640      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
641    o pkg/seaice:
642      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
643      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
644      also pass fac as a param, which can be 1. (to update the tendency
645      field) or the time step (to update the field itself).
646      - seaice_advdiff.F: for multidim, call seaice_diffusion with
647      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
648      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
649      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
650      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
651    o pkg/seaice:
652      diffusion with centered advection scheme (diffus.F & advect.F):
653      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
654        to just compute the laplacian of input-field.
655      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
656      - fix flux-form version in diffus.F to conserve tracer.
657      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
658       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
659    
660    checkpoint62y (2011/05/26)
661  o pkg/seaice:  o pkg/seaice:
662   - seaice_growth.F : in EVOLUTION branch, always include   - seaice_growth.F : in EVOLUTION branch, always include
663     a_QSWbyATM_cover in qnet (as it should be).     a_QSWbyATM_cover in qnet (as it should be).
664   - verification/global_ocean.cs32x15 : update results accordingly   - verification/global_ocean.cs32x15 : update results accordingly
665     (output.seaice.txt output_adm.seaice.txt).     (output.seaice.txt output_adm.seaice.txt).
666  o pkg/seaice + obcs:  o pkg/seaice + obcs:
667   - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:   - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
668     equivalent of assuming no tracer gradient outside the OB region.     equivalent of assuming no tracer gradient outside the OB region.
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