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revision 1.1442 by gforget, Wed May 25 23:56:29 2011 UTC revision 1.1557 by jmc, Wed Dec 21 17:31:53 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/exf (interpolation):
8      - add a set of run-time param ({inputfield}_interpMethod), one for
9        each interpolated input field, to select the interpolation method
10        with a value of zero switching off the interpolation;
11      - print interpolation parameters to standard output;
12      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
13        (to use instead runoff_interpMethod=0 in data.exf).
14    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
15       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
16       this factor is absolutely required, because the lw exitance (= out-going
17       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
18       where the reflectivity rho = 1-emissivity for conservation reasons. Once
19       this is established, we can remove the CPP-Flag (if we want to).
20  o pkg/seaice:  o pkg/seaice:
21   - seaice_growth.F : in EVOLUTION branch, always include    - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
22        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
23      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
24        what the name implies (and not emissivity*BoltzmannConstant), this means
25        the old default value of 5.5e-8 now means
26        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
27        S/R exf_readparms
28      - FV-discretization of the B-grid LSOR solver, turn on with
29        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
30        of the calling routine dynsolver, so that B and C-grid code look a
31        little more alike.
32      - fix index bugs in ostres.F (B-grid code)
33    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
34    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
35      default for SEAICE_emissivity, if useEXF; requires setting a wrong
36      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
37      backward compatiblity
38    o model/src: use sigmaR in calc_ivdc
39    
40    checkpoint63g (2011/12/16)
41    o pkg/seaice/seaice_growth.F:
42      fix heat conservation of the coupled ocean-seaice system.
43      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
44      solid vs liquid water treatment is resolved via QNET.
45    o pkg/seaice/seaice_growth.F:
46      add missing term for sublimation in saltFlux, which was breaking conservation.
47    o pkg/seaice/seaice_model.F:
48      Remove this patholigical case treatment in evolution branch,
49      where it is un-necessary and breaks conservation.
50      Update global_ocean.cs32x15/results accordingly for
51      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
52    o model/src:
53      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
54      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
55    o pkg/obcs:
56      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
57      tendency for temperature and salinity that is then applied to update
58      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
59      horizontal advection and diffusion contributions on the boundary (in
60      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
61      removing the mask in S/R timestep_tracer. The advantage of this approach is
62      that the updated tracer values include contributions from the surface
63      forcing and vertical diffusion.
64      This modification changes exp4.stevens because of vertical diffusion.
65    o model/src:
66      change non-curvilinear grid setting to also work with exch2 + blank tiles:
67      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
68        face dimensions.
69      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
70        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
71        and INI_SPHERICAL_POLAR_GRID.
72      change test-experiment global_ocean.90x40x15:
73      - split the domain in many more tiles (9x4 tiles of 10x10 each);
74      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
75      - update results of both test (std & dwnslp).
76    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
77       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
78    o model/src:
79      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
80        and fix initialisation when using sigma-coords.
81    o model/src:
82     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
83       to their current value at the beginning of forward_step.F": add a new run-time
84       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
85     - set doResetHFactors=T in the following test exp:
86        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
87        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
88        and tutorial_global_oce_in_p (nonLinFS in p)
89    o pkg/ecco
90      - added IES cost term
91    o verification/advect_xz
92      - scale down the depth by 1/100 (from 200 km to just 2.km)
93      - add secondary test using divergent flow, r-star and implicit vertical advection.
94      - add note (check_conserve_TS.txt) and matlab script to check global
95        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
96    o pkg/rbcs:
97      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
98    o pkg/obcs (Stevens BCs):
99      - fix various problems in the phase speed computations of the Stevens
100        boundary conditions:
101        - sign error for western and southern boundaries,
102        - time tendencies were underestimated by factor of dTracerLev and some just
103          zero (for multidim advection schemes) -> now estimate time tendencies
104          from difference between previous (n) time level and the one before (n-1);
105          this requires storing a field per tracer per boundary, also in the pickup
106          files.
107        - replace deltaTmom in cflMer/Zon computation with dTracerLev
108        - set default phase velocity to cflMer/Zon
109      - update verification experiment exp4.stevens
110    o pkg/generic_advdiff (implicit_r):
111      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
112        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
113      - fix implicit vertical diffusion or advection with NonLin FreeSurf
114        (was using current recip_hFacC instead of future recip_hFacC): set future
115        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
116        solver S/R ;
117      - fill diagnostics of vertical advective fluxes (computed from tendency)
118        when using implicit vert. advection;
119      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
120         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
121         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
122         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
123    o pkg/diagnostics:
124      - add diags for T & S tendency which goes through Adams-Bashforth.
125    
126    checkpoint63f (2011/11/30)
127    o pkg/obcs/obcs_calc_stevens.F:
128      - join some loops to reduce number of if-statements
129      - fix a bug in code for northern and southern boundaries.
130    o pkg/seaice/seaice_init_varia.F
131      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
132        caused zero ice-velocities for the B-grid code
133    o pkg/seaice/seaice_init_fixed.F
134      - fix a bug in the initialisation of the second metric terms
135        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
136      - this affects all seaice configurations with useCurviLinearGrid = .true.
137        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
138        = .true. (default)
139      - the only verification experiment affected is global_ocean.cs32x15:
140        icedyn, seaice, and seaice_dynmix (AD)
141    o pkg/thsice/thsice_diagnostics_state.F
142      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
143        not contain garbage that can lead to surprises in diagstats_calc.F
144    o model/src:
145      - move bi,bj loops inside INTEGR_CONTINUITY ;
146      - call INTEGR_CONTINUITY directly from forward_step.F
147        (previously called from momentum_correction_step.F)
148      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
149        forward_step.F and pkg/ecco/the_main_loop.F
150    o model/src/do_oceanic_phys.F:
151      - reset addMass to zero only if useICEFRONT ;
152      - separated k-loop for rhoInSitu calculation ;
153      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
154        and at constant T,S (= WdRHOdP);
155      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
156        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
157        transport of locally-referenced potential density);
158        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
159    o gluemnc:
160      - replace ncrcat with ncks when adding variables to *.glob.nc
161      - change the way variables without record dimensions are handled so that
162        files that have variables with and without record variables can be glued:
163        add a record dimension with a new unique name to be able to differentiate
164        between variable with and without a-prior record dimensions. Remove
165        this record dimension before adding the variable to the *.glob.nc file.
166        This procedure automatically works also for grid.*.nc files that do not
167        have any record dimension.
168    o verification/cpl_aim+ocn:
169      - generate new reference output on baudelaire (gfortran, mpich2) (previously
170        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
171    o pkg/obcs/obcs_calc_stevens.F:
172      - add code for northern and southern boundaries.
173      - reorder some loops to save some operations and so that drFBar can be scalar
174    o model/src:
175      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
176        truncation) and add diagnostics for Adams-Bashforth tendency increment.
177      - update test-exp. AD output:
178        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
179      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
180        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
181        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
182        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
183        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
184        tutorial_plume_on_slope.
185    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
186      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
187      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
188      does not even come with an F77 compiler anymore, this should not be
189      a limitation
190    
191    checkpoint63e (2011/11/06)
192    o pkg/seaice adjoint of LSR:
193      - substantially rework STORE dirs.
194      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
195        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
196        and only perform SOLV_MAX_FIXED adjoint iters.
197        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
198        always goes to same record, meaning that the last forward field will be
199        the one used in the adjoint - an approximation.
200      - now produces non-zero LSR-related gradients, and acceptable gradients for
201        An's zonal (x-z) test case (to be checked in)
202      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
203        (but these are screwed up by the thermodynamics in the first place);
204        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
205        output_adm.txt also reflects changes to seaice_lsr
206      - global_ocean.cs32x15:
207        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
208          (output_adm.seaice.txt was updated)
209        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
210          (output_adm.seaice_dynmix.txt)
211    o test-exp. exp4+stevens:
212      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
213    o pkg/seaice (lsr solver):
214      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
215        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
216      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
217      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
218        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
219      - compute (with new S/R) and print initial (+ free-driff sol. if available)
220        and final residual of linearised system.
221    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
222      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
223    o pkg/obcs: Stevens BCs (still only for east and west)
224      - fix Stevens BCs by using intermediate velocities of previous
225        time step as "baroclinic" contribution rather velocity of one grid cell
226        inside the boundaries; more consistent but makes the entire treatment
227        more complicated, requires new pickup files and two new S/Rs:
228        obcs_copy_uv_n and obcs_save_uv_n
229        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
230        (undefined by default)
231      - silently move computation of some grid factors into separate loops to
232        save some recomputations
233      - add a hack for non-linear free surface
234      - add a verification experiment to exp4 that tests this code
235    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
236    
237    checkpoint63d (2011/10/25)
238    o pkg/obcs + seaice-dynamics:
239      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
240        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
241        values (consistent with an implicit method).
242      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
243        return to older implementation (same results as before); note that none of
244        the "experimental" OBCS_SEAICE options are implemented in the new version.
245      - switch test exp. seaice_obcs to use new version (update output).
246    o pkg/seaice:
247      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
248      - add parenthesis in Water-Ice drag calculations (evp & lsr);
249      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
250        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
251      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
252        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
253    o pkg/layers:
254      - Include potential density as new coordinate (Thanks to David Munday)
255    o pkg/dic:
256      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
257        carbonate computation/output to CALC_PCO2_APPROX
258    o pkg/generic_advdiff
259      - make TAF generate code that vectorizes:
260        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
261    o model/src:
262      - improve vectorization also for adjoint code of
263        solve_tridiagonal and solve_pentadiagonal. As this requires up to
264        5 new 3D-fields, this code is only turned on for the combination of
265        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
266        for singular matrix check (only for TARGET_NEC_SX).
267      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
268        ALLOW_AUTODIFF. This flag now needs to be set outside of
269        solve_tri/pentadiagonal.F
270    o pkg/exf:
271      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
272        optional namelist EXF_NML_OBCS).
273      - add many debug-print (to trace down where pkg/cal error msg comes from)
274    o pkg/mom_vecinv/mom_vi_hdissip.F
275      - rearrange loops so that vectorization is improved and in particular
276        the adjoint routine vectorizes. The code is a little longer now, but I
277        think easier to read.
278        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
279    o pkg/seaice:
280      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
281    o pkg/exch2:
282      - alternative code (without tile x tile matrix) for cumulated (global) sum;
283        used as default; keep using matrix version in adjustment.cs-32x32x1.
284    o tools/build_options:
285      - after merging some MPI and/or multi-threads specific optfiles so that
286        the modified default optfile support both built (using genmake2 -mpi
287        for the MPI built, using genmake2 -omp for OpenMP built),
288        move now obsolete optfiles to tools/build_options/unsupported/
289       (add copy of email sent to support list in doc/optfiles_changes.txt)
290    
291    checkpoint63c (2011/09/28)
292    o pkg/ebm:
293      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
294        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
295    o pkg/seaice (SItracer pickup)
296    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
297      To be done:
298      - thorough testing of missing fields in S/R seaice_read_pickup
299      - thorough matching between generic tracers and specific fields used
300        (e.g. volume-weighted age, area-weighted age, salinity, ...)
301    o pkg/grdchk:
302      - all procs calculate and print finite-difference gradient (for testreport)
303      - change description output used by testreport;
304      - AD testing: also compare and report Finite-difference gradient;
305        => update all output_adm*.txt
306    o test exp. global_ocean_ebm:
307      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
308        and turn on exactConserve; update (fwd) output.
309    o pkg/seaice (LSR):
310      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
311      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
312        * identical results with non-CS topology (but save up to half of EXCH calls)
313        * no much changes in cs-32 verification tests since no ice at face edges
314         (differences due to convergence criteria, since nb of iterations changed)
315        * expect some differences on lat-lon-cap grid.
316        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
317    o pkg/exch2:
318      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
319        many tiles); until alternative coding is added, just add a stop.
320    o pkg/kpp:
321      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
322        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
323    o optfiles:
324      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
325        into corresponding standard one, which now support different build:
326        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
327      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
328    o pkg/obcs (seaice):
329      - add missing EXCH for uIce,vIce after applying OBCS;
330      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
331        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
332        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
333      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
334      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
335        and eedata.mth for MPI and mutlti-threaded testing.
336    o pkg/flt:
337      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
338      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
339      - fix pickup and trajectories + profiles output with multi-threads;
340      - add parameter to select group of fields to write along trajectory and
341        profile (default unchanged);
342      - only call PORT_RAND* function when flt_noise <> 0;
343      - add multi-threaded test for verification exp. flt_example.
344    o eesupp/src:
345      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
346      - USE_OMP_THREADING: check that number of threads (from eedata) matches
347        actual number (from env.var. setting).
348    o pkg/ebm:
349      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
350      - add multi-threaded test for verification exp. global_ocean_ebm
351    
352    checkpoint63b (2011/08/29)
353    o pkg/ebm:
354      - fix sign of runoff;
355      - update directly forcing fields (Qnet,EmPmR) to use standard
356        external_forcing_surf.F (remove ebm_forcing_surf.F);
357      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
358      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
359        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
360      - update global_ocean_ebm parameters file data and update output (fwd+ad).
361    o verification/matrix_example:
362      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
363        MPI and mutlti-threaded testing.
364    o pkg/matrix:
365      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
366      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
367      - fix for multi-threaded (remove DATA statement);
368      - use standard DIFFERENT_MULTIPLE function;
369      - add MATRIX_OPTIONS.h
370    o verification/matrix_example:
371       To allow to split the domain in several tiles, change the domain size
372        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
373        Western side) of land points.
374    o (*_)write_pickup:
375      - fix few bugs in mypackage_read/write_pickup.F
376      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
377        array of length 1 (was caught by compiler syntax-check).
378    o pkg/diagnostics (velocity potential solver):
379      - fix initialisation of main diagonal matrix (for overlap values)
380    o tools/build_options:
381      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
382        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
383      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
384        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
385        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
386        and use "-devel" testreport option for standard testing on baudelaire.
387    o pkg/grdchk:
388      - Assume that all gradient-check position are within the same tile
389        corresponding to global indices (iGloTile,jGloTile) and that
390        positions (i,j indices or nbeg) are local to this tile;
391      - set tile local-indices and proc. number according to tile global-indices;
392      - remove grdchkwhichproc from namelist (retired param);
393      - send adjoint gradient to all procs so that all procs print it to STDOUT;
394      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
395    o adding package bbl (Bottom Boundary Layer)
396      description in MITgcm/pkg/bbl/bbl_description.tex
397      example/test experiment in MITgcm_contrib/bbl
398    o adjoint verifications
399      - changed 5 experiments to multi-tiles
400        * global_ocean.90x40x15
401        * obcs_ctrl
402        * offline_exf_seaice
403        * tutorial_dic_adjoffline
404        * tutorial_tracer_adjsens
405        changed reference output for those that crossed tile boundaries
406        (changed choices of gradient check positions)
407      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
408      - temporary bug fix in grdchk_loc.F for obcs
409    o genmake2 & testreport
410      - add target "obj" (just for OBJFILES files) to Makefile;
411      - add option to specify FEXTRAFLAGS on command line.
412    o pkg/mypackage:
413      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
414    
415    checkpoint63a (2011/08/02)
416    o pkg/diagnostics (velocity potential):
417      - fix velocity-potential calculation when using OBCS: balance net inflow
418        at each level (new S/R OBCS_DIAG_BALANCE).
419      - fix some of the problems with OBCS in stream-function calculation.
420    o pkg/exf/exf_readparms.F
421      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
422        EXF_NML_OBCS) more consistent, so that you need not have these lists
423        in data.exf when they are not used.
424    o optim/optim_readdata.F:
425      - add some output about obcs variables that might help debugging
426      - add a check about nvarlength
427    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
428    o pkg/diagnostics (velocity potential):
429      - fix mask for OBCS (still problems in stream-function with OBCS);
430      - add specific parameter (default = main code CG2D params) for solver;
431      - in case of poor convergence, use solution corresponding to lowest residual.
432    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
433      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
434      and should be avoided where possible.
435    o model/src (rStar):
436      - include r* effect on reference-state (PhiRef) in totPhiHyd
437        (so that it's really the potential anomaly at the cell center);
438        affect solution only if z* with full pressure in EOS.
439      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
440        update output (because of z* in totPhiHyd and viscA4 changes);
441      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
442        @ constant r) until interpolation at constant r is implemented.
443    o pkg/diagnostics
444      - fix RCENTER diagnostics in case cell center is not at interface middle
445    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
446      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
447      that THETA and SALT are "conservative temperature" and "absolute
448      salinity"
449    o pkg/ctrl
450      - fix computation of endrec in s/r ctrl_init_rec
451      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
452    o pkg/seaice/seaice_growth.F
453      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
454        remove then obsolete STORE directives
455      - fix STORE directives for tice and tices, so that only the
456        appropriate part of the fields are stored (and not the entire
457        field); update global_ocean.cs32x15.seaice AD output.
458      - cosmetic changes: adjust CPP flags and indentation for better
459        legibilty
460    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
461      Chris Wilson)
462    o pkg/gmredi:
463       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
464       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
465    
466    checkpoint63  (2011/07/11)
467    o pkg/exch2:
468     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
469     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
470       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
471       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
472    o pkg/diagnostics:
473     - deal with pairs of post-processed diags which are computed together; in
474       particular, re-order list of diags within 1 file to save 2nd computation.
475     - add S/R to compute velocity stream-function (called after velocity-potential
476       calculation) from divergence free transport -> new diagnostics "PsiVEL".
477     - add parameter to select grid-point location where PsiVEL == 0.
478    o eesupp/src:
479       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
480       (specific S/R needed with exch2 topology - for now, just print an error msg)
481    o pkg/shelfice
482     - Implement friction velocity-dependent transfer coefficients following
483       Holland and Jenkins, JPO, 1999
484       Original code by M. Losch with small modifs.
485       Enable with CPP option SHI_ALLOW_GAMMAFRICT
486       and runtime flag SHELFICEuseGammaFrict
487    o verification lab_sea & global_ocean.cs32x15:
488     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
489       does not miss some dependencies (but is slower) and also works with many files
490       (default makedepend limitation for AD built).
491     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
492    o pkg/diagnostics:
493     - add run-time parameter "useMissingValue" (def=False) to fill land-point
494        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
495       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
496     - Extend the use of "missing_value" setting from data.diagnostics for the case
497       of counter-diagnostics (where fraction-weight is zero). This applies both to
498       MNC and MDS output files.
499    o pkg/seaice/seaice_growth.F:
500      - add 'a priori' cap of latent heat flux based on actual mass considerations
501        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
502        non-legacy seaice_solve4temp.
503      - add diagnostic of the residual sublimation freshwater flux (the freshwater
504        flux taken from the ocean if the total actual latent heat fluxes exceed
505        the maximum)
506      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
507       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
508      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
509       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
510      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
511      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
512    o verification 1D_ocean_ice_column:
513       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
514       update results
515    o pkg/diagnostics:
516     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
517       which are not filled-up but computed from other diags ; In this case, the mate
518       diag points to the primary (filled-up) diag to used for post processing.
519     - Update Velocity-potential computation using post-processed diag framework.
520     ==> Change the ordering of fields and time-periods in MDS output file
521       when using periodic averaging: now writes one time record with the full set
522       of fields for this time period, then the next time reccord (it used to be
523       one field with the full set of time records then the next field).
524         Note: this is now similar to NetCDF (MNC) output file. <==
525    
526    checkpoint62z (2011/06/21)
527    o adjoint monitor:
528     - Add adjoint monitor output for packages exf, seaice
529       and update relevant testreport output
530    o pkg/seaice:
531     - re-order diags inits so that they appear in order in available_diagnostics.log
532     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
533       area/heff/hsnow preceeding thermodynamic growth/melt.
534     - modified diag: SIdA; output actual effect, as the description states.
535     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
536     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
537       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
538        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
539     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
540     - added diagnostics for seaice generic tracers (SItr*).
541     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
542     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
543     I. Fenty: 18-Jun-2011:
544     Minor changes to seaice package:
545     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
546        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
547       - Differentiated "regularization variables" from "floor variables"
548        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
549        * hiceMin became SEAICE_hice_reg (old hiceMin)
550          (with _reg meaning regularization variable)
551       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
552        so as to ensure energy conservation when going between phases
553      - A22 was not used anywhere
554     2) Changed regularization procedure for heffActual and hsnowActual to ensure
555        well-boundedness and smooth adjoint in seaice_growth.F
556     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
557        because the old regularization always set heffActual >= 0.05 cm
558     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
559        on AREA when HEFF > 0.
560      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
561        requiring that DISABLE_AREA_FLOOR *not* be defined
562     Affected verifications:
563      - 1D_ocean_ice_column (output.txt output_adm.txt)
564      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
565    o pkg/diagnostics:
566      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
567      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
568        (was _RL, now integer) with option = 0 to retrieve all levels.
569      - add pieces of code to compute velocity potential at each level (new diagnostics
570        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
571        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
572      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
573        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
574        and in diagnostics_fract_fill.F (do not need a valid pointer for the
575        diagnostics counter-mate); check that definition of counter-diagnostic
576        includes a valid counter-mate (in diagnostics_set_levels.F).
577    o model/src (rStar):
578      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
579        affect solution only if z* with full pressure in EOS;
580        update output of test-exp global_ocean.90x40x15.
581    o pkg/seaice:
582      - introduce siEps=1e-5 parameter
583      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
584      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
585      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
586        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
587        as well as ice cover age and ridging index (attached to AREA).
588        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
589        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
590        Up to SItrMaxNum=3 tracers can be used simultaneously.
591    o pkg/salt_plume:
592      -introduce SPsalFRAC run time parameter that sets the fraction of the
593       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
594       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
595    o model debug options:
596      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
597        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
598      - Refine debug-msg printing selection (3 new levels):
599        debugMode  : controls printing of debug messages (sequence of S/R calls).
600        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
601         debLevZero =  0 ; /* level of disabled aux. msg printing */
602         debLevA =  1 ; /* level of minimum  aux. msg printing */
603         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
604         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
605         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
606         debLevE =  5 ; /* level of extensive debug printing */
607        New debugLevel default: with default debugMode value (=F),
608          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
609          and if debugMode=T, default debugLevel = 4 (debLevD).
610        Relation with previous settings:
611         debLevB (=2) corresponds to former debLevA (=1)
612         debLevD (=4) corresponds to former debLevB (=2)
613        Note:
614         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
615         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
616            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
617      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
618        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
619    o pkg/obcs:
620      - change OBCSfixTopo default from True to False (should not change the results);
621        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
622    o pkg/thsice:
623      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
624        2nd layer seaice sublimation (unlikely to happen)
625      - use Interior mask for OBCS in thsice_advection.F (similar to what is
626        done in gad_advection & seaice_advection).
627    o adjoint:
628      bug fix spotted by Gael Forget:
629      seaice_advection and thsice_advection still had
630      legacy CPP options to avoid CS corner updates for adjoint
631    o pkg/seaice:
632      => Change some of the defaults (2011/05/29):
633         - change SEAICEuseFluxForm default (from False to True)
634         - change DIFF1 default (from 0.004 m/s to 0. m/s)
635         And print warnings if DIFF1 is not set in data.seaice and centered
636          avection scheme is used without any diffusion.
637      also:
638      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
639      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
640      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
641        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
642        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
643      update results of test exp.:
644         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
645             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
646             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
647         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
648         seaice_obcs: output (SEAICEuseFluxForm=T)
649      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
650          for standard fwd & AD lab_sea tests (to keep the same output).
651    o pkg/seaice/seaice_growth.F:
652      - use Ian Fenty's capping formulas for actual ice
653      thickness thoughout EVOLUTION branch.
654      - put treatment pathological case #2) in CPP brackets
655      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
656      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
657    o pkg/seaice:
658      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
659      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
660      also pass fac as a param, which can be 1. (to update the tendency
661      field) or the time step (to update the field itself).
662      - seaice_advdiff.F: for multidim, call seaice_diffusion with
663      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
664      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
665      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
666      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
667    o pkg/seaice:
668      diffusion with centered advection scheme (diffus.F & advect.F):
669      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
670        to just compute the laplacian of input-field.
671      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
672      - fix flux-form version in diffus.F to conserve tracer.
673      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
674       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
675    
676    checkpoint62y (2011/05/26)
677    o pkg/seaice:
678     - seaice_growth.F : in EVOLUTION branch, always include
679     a_QSWbyATM_cover in qnet (as it should be).     a_QSWbyATM_cover in qnet (as it should be).
680   - verification/global_ocean.cs32x15 : update results accordingly   - verification/global_ocean.cs32x15 : update results accordingly
681     (output.seaice.txt output_adm.seaice.txt).     (output.seaice.txt output_adm.seaice.txt).
682  o pkg/seaice + obcs:  o pkg/seaice + obcs:
683   - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:   - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
684     equivalent of assuming no tracer gradient outside the OB region.     equivalent of assuming no tracer gradient outside the OB region.
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