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revision 1.1435 by jmc, Wed May 18 02:21:49 2011 UTC revision 1.1524 by jmc, Fri Oct 28 19:44:35 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 test-exp. exp4+stevens:
8      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
9    o pkg/seaice (lsr solver):
10      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
11        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
12      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
13      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
14        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
15      - compute (with new S/R) and print initial (+ free-driff sol. if available)
16        and final residual of linearised system.
17    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
18      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
19    o pkg/obcs: Stevens BCs (still only for east and west)
20      - fix Stevens BCs by using intermediate velocities of previous
21        time step as "baroclinic" contribution rather velocity of one grid cell
22        inside the boundaries; more consistent but makes the entire treatment
23        more complicated, requires new pickup files and two new S/Rs:
24        obcs_copy_uv_n and obcs_save_uv_n
25        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
26        (undefined by default)
27      - silently move computation of some grid factors into separate loops to
28        save some recomputations
29      - add a hack for non-linear free surface
30      - add a verification experiment to exp4 that tests this code
31    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
32    
33    checkpoint63d (2011/10/25)
34    o pkg/obcs + seaice-dynamics:
35      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
36        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
37        values (consistent with an implicit method).
38      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
39        return to older implementation (same results as before); note that none of
40        the "experimental" OBCS_SEAICE options are implemented in the new version.
41      - switch test exp. seaice_obcs to use new version (update output).
42    o pkg/seaice:
43      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
44      - add parenthesis in Water-Ice drag calculations (evp & lsr);
45      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
46        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
47      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
48        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
49    o pkg/layers:
50      - Include potential density as new coordinate (Thanks to David Munday)
51    o pkg/dic:
52      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
53        carbonate computation/output to CALC_PCO2_APPROX
54    o pkg/generic_advdiff
55      - make TAF generate code that vectorizes:
56        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
57    o model/src:
58      - improve vectorization also for adjoint code of
59        solve_tridiagonal and solve_pentadiagonal. As this requires up to
60        5 new 3D-fields, this code is only turned on for the combination of
61        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
62        for singular matrix check (only for TARGET_NEC_SX).
63      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
64        ALLOW_AUTODIFF. This flag now needs to be set outside of
65        solve_tri/pentadiagonal.F
66    o pkg/exf:
67      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
68        optional namelist EXF_NML_OBCS).
69      - add many debug-print (to trace down where pkg/cal error msg comes from)
70    o pkg/mom_vecinv/mom_vi_hdissip.F
71      - rearrange loops so that vectorization is improved and in particular
72        the adjoint routine vectorizes. The code is a little longer now, but I
73        think easier to read.
74        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
75    o pkg/seaice:
76      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
77    o pkg/exch2:
78      - alternative code (without tile x tile matrix) for cumulated (global) sum;
79        used as default; keep using matrix version in adjustment.cs-32x32x1.
80    o tools/build_options:
81      - after merging some MPI and/or multi-threads specific optfiles so that
82        the modified default optfile support both built (using genmake2 -mpi
83        for the MPI built, using genmake2 -omp for OpenMP built),
84        move now obsolete optfiles to tools/build_options/unsupported/
85       (add copy of email sent to support list in doc/optfiles_changes.txt)
86    
87    checkpoint63c (2011/09/28)
88    o pkg/ebm:
89      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
90        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
91    o pkg/seaice (SItracer pickup)
92    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
93      To be done:
94      - thorough testing of missing fields in S/R seaice_read_pickup
95      - thorough matching between generic tracers and specific fields used
96        (e.g. volume-weighted age, area-weighted age, salinity, ...)
97    o pkg/grdchk:
98      - all procs calculate and print finite-difference gradient (for testreport)
99      - change description output used by testreport;
100      - AD testing: also compare and report Finite-difference gradient;
101        => update all output_adm*.txt
102    o test exp. global_ocean_ebm:
103      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
104        and turn on exactConserve; update (fwd) output.
105    o pkg/seaice (LSR):
106      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
107      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
108        * identical results with non-CS topology (but save up to half of EXCH calls)
109        * no much changes in cs-32 verification tests since no ice at face edges
110         (differences due to convergence criteria, since nb of iterations changed)
111        * expect some differences on lat-lon-cap grid.
112        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
113    o pkg/exch2:
114      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
115        many tiles); until alternative coding is added, just add a stop.
116    o pkg/kpp:
117      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
118        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
119    o optfiles:
120      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
121        into corresponding standard one, which now support different build:
122        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
123      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
124    o pkg/obcs (seaice):
125      - add missing EXCH for uIce,vIce after applying OBCS;
126      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
127        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
128        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
129      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
130      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
131        and eedata.mth for MPI and mutlti-threaded testing.
132    o pkg/flt:
133      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
134      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
135      - fix pickup and trajectories + profiles output with multi-threads;
136      - add parameter to select group of fields to write along trajectory and
137        profile (default unchanged);
138      - only call PORT_RAND* function when flt_noise <> 0;
139      - add multi-threaded test for verification exp. flt_example.
140    o eesupp/src:
141      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
142      - USE_OMP_THREADING: check that number of threads (from eedata) matches
143        actual number (from env.var. setting).
144    o pkg/ebm:
145      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
146      - add multi-threaded test for verification exp. global_ocean_ebm
147    
148    checkpoint63b (2011/08/29)
149    o pkg/ebm:
150      - fix sign of runoff;
151      - update directly forcing fields (Qnet,EmPmR) to use standard
152        external_forcing_surf.F (remove ebm_forcing_surf.F);
153      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
154      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
155        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
156      - update global_ocean_ebm parameters file data and update output (fwd+ad).
157    o verification/matrix_example:
158      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
159        MPI and mutlti-threaded testing.
160    o pkg/matrix:
161      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
162      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
163      - fix for multi-threaded (remove DATA statement);
164      - use standard DIFFERENT_MULTIPLE function;
165      - add MATRIX_OPTIONS.h
166    o verification/matrix_example:
167       To allow to split the domain in several tiles, change the domain size
168        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
169        Western side) of land points.
170    o (*_)write_pickup:
171      - fix few bugs in mypackage_read/write_pickup.F
172      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
173        array of length 1 (was caught by compiler syntax-check).
174    o pkg/diagnostics (velocity potential solver):
175      - fix initialisation of main diagonal matrix (for overlap values)
176    o tools/build_options:
177      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
178        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
179      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
180        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
181        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
182        and use "-devel" testreport option for standard testing on baudelaire.
183    o pkg/grdchk:
184      - Assume that all gradient-check position are within the same tile
185        corresponding to global indices (iGloTile,jGloTile) and that
186        positions (i,j indices or nbeg) are local to this tile;
187      - set tile local-indices and proc. number according to tile global-indices;
188      - remove grdchkwhichproc from namelist (retired param);
189      - send adjoint gradient to all procs so that all procs print it to STDOUT;
190      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
191    o adding package bbl (Bottom Boundary Layer)
192      description in MITgcm/pkg/bbl/bbl_description.tex
193      example/test experiment in MITgcm_contrib/bbl
194    o adjoint verifications
195      - changed 5 experiments to multi-tiles
196        * global_ocean.90x40x15
197        * obcs_ctrl
198        * offline_exf_seaice
199        * tutorial_dic_adjoffline
200        * tutorial_tracer_adjsens
201        changed reference output for those that crossed tile boundaries
202        (changed choices of gradient check positions)
203      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
204      - temporary bug fix in grdchk_loc.F for obcs
205    o genmake2 & testreport
206      - add target "obj" (just for OBJFILES files) to Makefile;
207      - add option to specify FEXTRAFLAGS on command line.
208    o pkg/mypackage:
209      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
210    
211    checkpoint63a (2011/08/02)
212    o pkg/diagnostics (velocity potential):
213      - fix velocity-potential calculation when using OBCS: balance net inflow
214        at each level (new S/R OBCS_DIAG_BALANCE).
215      - fix some of the problems with OBCS in stream-function calculation.
216    o pkg/exf/exf_readparms.F
217      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
218        EXF_NML_OBCS) more consistent, so that you need not have these lists
219        in data.exf when they are not used.
220    o optim/optim_readdata.F:
221      - add some output about obcs variables that might help debugging
222      - add a check about nvarlength
223    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
224    o pkg/diagnostics (velocity potential):
225      - fix mask for OBCS (still problems in stream-function with OBCS);
226      - add specific parameter (default = main code CG2D params) for solver;
227      - in case of poor convergence, use solution corresponding to lowest residual.
228    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
229      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
230      and should be avoided where possible.
231    o model/src (rStar):
232      - include r* effect on reference-state (PhiRef) in totPhiHyd
233        (so that it's really the potential anomaly at the cell center);
234        affect solution only if z* with full pressure in EOS.
235      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
236        update output (because of z* in totPhiHyd and viscA4 changes);
237      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
238        @ constant r) until interpolation at constant r is implemented.
239    o pkg/diagnostics
240      - fix RCENTER diagnostics in case cell center is not at interface middle
241    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
242      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
243      that THETA and SALT are "conservative temperature" and "absolute
244      salinity"
245    o pkg/ctrl
246      - fix computation of endrec in s/r ctrl_init_rec
247      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
248    o pkg/seaice/seaice_growth.F
249      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
250        remove then obsolete STORE directives
251      - fix STORE directives for tice and tices, so that only the
252        appropriate part of the fields are stored (and not the entire
253        field); update global_ocean.cs32x15.seaice AD output.
254      - cosmetic changes: adjust CPP flags and indentation for better
255        legibilty
256    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
257      Chris Wilson)
258    o pkg/gmredi:
259       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
260       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
261    
262    checkpoint63  (2011/07/11)
263    o pkg/exch2:
264     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
265     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
266       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
267       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
268    o pkg/diagnostics:
269     - deal with pairs of post-processed diags which are computed together; in
270       particular, re-order list of diags within 1 file to save 2nd computation.
271     - add S/R to compute velocity stream-function (called after velocity-potential
272       calculation) from divergence free transport -> new diagnostics "PsiVEL".
273     - add parameter to select grid-point location where PsiVEL == 0.
274    o eesupp/src:
275       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
276       (specific S/R needed with exch2 topology - for now, just print an error msg)
277    o pkg/shelfice
278     - Implement friction velocity-dependent transfer coefficients following
279       Holland and Jenkins, JPO, 1999
280       Original code by M. Losch with small modifs.
281       Enable with CPP option SHI_ALLOW_GAMMAFRICT
282       and runtime flag SHELFICEuseGammaFrict
283    o verification lab_sea & global_ocean.cs32x15:
284     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
285       does not miss some dependencies (but is slower) and also works with many files
286       (default makedepend limitation for AD built).
287     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
288    o pkg/diagnostics:
289     - add run-time parameter "useMissingValue" (def=False) to fill land-point
290        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
291       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
292     - Extend the use of "missing_value" setting from data.diagnostics for the case
293       of counter-diagnostics (where fraction-weight is zero). This applies both to
294       MNC and MDS output files.
295    o pkg/seaice/seaice_growth.F:
296      - add 'a priori' cap of latent heat flux based on actual mass considerations
297        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
298        non-legacy seaice_solve4temp.
299      - add diagnostic of the residual sublimation freshwater flux (the freshwater
300        flux taken from the ocean if the total actual latent heat fluxes exceed
301        the maximum)
302      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
303       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
304      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
305       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
306      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
307      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
308    o verification 1D_ocean_ice_column:
309       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
310       update results
311    o pkg/diagnostics:
312     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
313       which are not filled-up but computed from other diags ; In this case, the mate
314       diag points to the primary (filled-up) diag to used for post processing.
315     - Update Velocity-potential computation using post-processed diag framework.
316     ==> Change the ordering of fields and time-periods in MDS output file
317       when using periodic averaging: now writes one time record with the full set
318       of fields for this time period, then the next time reccord (it used to be
319       one field with the full set of time records then the next field).
320         Note: this is now similar to NetCDF (MNC) output file. <==
321    
322    checkpoint62z (2011/06/21)
323    o adjoint monitor:
324     - Add adjoint monitor output for packages exf, seaice
325       and update relevant testreport output
326    o pkg/seaice:
327     - re-order diags inits so that they appear in order in available_diagnostics.log
328     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
329       area/heff/hsnow preceeding thermodynamic growth/melt.
330     - modified diag: SIdA; output actual effect, as the description states.
331     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
332     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
333       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
334        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
335     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
336     - added diagnostics for seaice generic tracers (SItr*).
337     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
338     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
339     I. Fenty: 18-Jun-2011:
340     Minor changes to seaice package:
341     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
342        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
343       - Differentiated "regularization variables" from "floor variables"
344        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
345        * hiceMin became SEAICE_hice_reg (old hiceMin)
346          (with _reg meaning regularization variable)
347       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
348        so as to ensure energy conservation when going between phases
349      - A22 was not used anywhere
350     2) Changed regularization procedure for heffActual and hsnowActual to ensure
351        well-boundedness and smooth adjoint in seaice_growth.F
352     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
353        because the old regularization always set heffActual >= 0.05 cm
354     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
355        on AREA when HEFF > 0.
356      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
357        requiring that DISABLE_AREA_FLOOR *not* be defined
358     Affected verifications:
359      - 1D_ocean_ice_column (output.txt output_adm.txt)
360      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
361    o pkg/diagnostics:
362      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
363      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
364        (was _RL, now integer) with option = 0 to retrieve all levels.
365      - add pieces of code to compute velocity potential at each level (new diagnostics
366        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
367        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
368      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
369        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
370        and in diagnostics_fract_fill.F (do not need a valid pointer for the
371        diagnostics counter-mate); check that definition of counter-diagnostic
372        includes a valid counter-mate (in diagnostics_set_levels.F).
373    o model/src (rStar):
374      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
375        affect solution only if z* with full pressure in EOS;
376        update output of test-exp global_ocean.90x40x15.
377    o pkg/seaice:
378      - introduce siEps=1e-5 parameter
379      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
380      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
381      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
382        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
383        as well as ice cover age and ridging index (attached to AREA).
384        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
385        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
386        Up to SItrMaxNum=3 tracers can be used simultaneously.
387    o pkg/salt_plume:
388      -introduce SPsalFRAC run time parameter that sets the fraction of the
389       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
390       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
391    o model debug options:
392      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
393        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
394      - Refine debug-msg printing selection (3 new levels):
395        debugMode  : controls printing of debug messages (sequence of S/R calls).
396        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
397         debLevZero =  0 ; /* level of disabled aux. msg printing */
398         debLevA =  1 ; /* level of minimum  aux. msg printing */
399         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
400         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
401         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
402         debLevE =  5 ; /* level of extensive debug printing */
403        New debugLevel default: with default debugMode value (=F),
404          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
405          and if debugMode=T, default debugLevel = 4 (debLevD).
406        Relation with previous settings:
407         debLevB (=2) corresponds to former debLevA (=1)
408         debLevD (=4) corresponds to former debLevB (=2)
409        Note:
410         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
411         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
412            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
413      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
414        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
415    o pkg/obcs:
416      - change OBCSfixTopo default from True to False (should not change the results);
417        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
418    o pkg/thsice:
419      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
420        2nd layer seaice sublimation (unlikely to happen)
421      - use Interior mask for OBCS in thsice_advection.F (similar to what is
422        done in gad_advection & seaice_advection).
423    o adjoint:
424      bug fix spotted by Gael Forget:
425      seaice_advection and thsice_advection still had
426      legacy CPP options to avoid CS corner updates for adjoint
427    o pkg/seaice:
428      => Change some of the defaults (2011/05/29):
429         - change SEAICEuseFluxForm default (from False to True)
430         - change DIFF1 default (from 0.004 m/s to 0. m/s)
431         And print warnings if DIFF1 is not set in data.seaice and centered
432          avection scheme is used without any diffusion.
433      also:
434      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
435      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
436      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
437        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
438        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
439      update results of test exp.:
440         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
441             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
442             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
443         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
444         seaice_obcs: output (SEAICEuseFluxForm=T)
445      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
446          for standard fwd & AD lab_sea tests (to keep the same output).
447    o pkg/seaice/seaice_growth.F:
448      - use Ian Fenty's capping formulas for actual ice
449      thickness thoughout EVOLUTION branch.
450      - put treatment pathological case #2) in CPP brackets
451      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
452      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
453    o pkg/seaice:
454      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
455      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
456      also pass fac as a param, which can be 1. (to update the tendency
457      field) or the time step (to update the field itself).
458      - seaice_advdiff.F: for multidim, call seaice_diffusion with
459      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
460      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
461      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
462      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
463    o pkg/seaice:
464      diffusion with centered advection scheme (diffus.F & advect.F):
465      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
466        to just compute the laplacian of input-field.
467      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
468      - fix flux-form version in diffus.F to conserve tracer.
469      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
470       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
471    
472    checkpoint62y (2011/05/26)
473    o pkg/seaice:
474     - seaice_growth.F : in EVOLUTION branch, always include
475       a_QSWbyATM_cover in qnet (as it should be).
476     - verification/global_ocean.cs32x15 : update results accordingly
477       (output.seaice.txt output_adm.seaice.txt).
478    o pkg/seaice + obcs:
479     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
480       equivalent of assuming no tracer gradient outside the OB region.
481       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
482     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
483       after changes above);
484     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
485       only at OB location (instead of over a band of OLx width).
486    o pkg/seaice:
487     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
488       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
489    o pkg/obcs:
490      - split header file "OBCS.h" into 4 separated files:
491        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
492       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
493         (contain no conditional statement which depends on OBCS options).
494      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
495        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
496    o ctrl, cost, grdchk & autodiff pkgs:
497      - make options file more standard (like other {PKG}_OPTIONS.h file but
498        with AD_CONFIG.h); clean-up some of the included header files.
499    o pkg/obcs:
500      - do not mask tracer when applying OB (tracer == 0 could generate problems)
501      - apply tracer OB values to tracer field only at OB location (instead of
502        over a band of OLx width)
503      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
504      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
505        obcs_apply_tloc.F & obcs_apply_sloc.F
506    o obcs in model/src:
507      - call OBCS_APPLY_W only if NonHydrostatic.
508      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
509      - reset dEtaHdt and wVel to zero outside OB interior region ;
510      - leave tracer unchanged outside OB interior region: This has no effect
511        on the solution but just to prevent unrealistic tracer value outside OB.
512      - zero out velocity outside OB interior region: This has no effect on
513        the solution but just to prevent unrealistic velocity outside OB.
514    o obcs and non-lin free-surf:
515       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
516       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
517       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
518       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
519       update results of test-exp. exp4(nlfs).
520    o exp4 (nlfs) test-exp:
521       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
522       with NonLin-FreeSurf); update output.nlfs.txt
523  o obcs and 2d/3d solver norm:  o obcs and 2d/3d solver norm:
524     use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB     use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
525     and outside OB interior region (will allow to place OB further inside the     and outside OB interior region (will allow to place OB further inside the
526     domain). Depending on the domain, can affects cg2d-Norm (previous     domain). Depending on the domain, can affects cg2d-Norm (previous
527     cancelation outside OB was only partial), e.g. in exp4 & obcs_ctrl,     cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
528     and cg3d-Norm (previous Norm was computed before canceling OB terms),     and cg3d-Norm (previous Norm was computed before canceling OB terms),
529     e.g. in tutorial_plume_on_slope.     e.g. in tutorial_plume_on_slope.
530    - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.    - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
# Line 20  o pkg/shelfice/shelfice_init_fixed.F Line 536  o pkg/shelfice/shelfice_init_fixed.F
536    fix CPP-flag combinations    fix CPP-flag combinations
537  o pkg/seaice: Merge iceage code of Pierre Rampal  o pkg/seaice: Merge iceage code of Pierre Rampal
538    * update/change/correct ice age calculations    * update/change/correct ice age calculations
539    * add age updates for pathological cases    * add age updates for pathological cases
540    Probably needs more testing...    Probably needs more testing...
541    
542  checkpoint62x (2011/05/13)  checkpoint62x (2011/05/13)
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