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revision 1.1321 by dimitri, Wed Oct 27 05:48:33 2010 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:
524       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
526       domain). Depending on the domain, can affects cg2d-Norm (previous
527       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
528       and cg3d-Norm (previous Norm was computed before canceling OB terms),
529       e.g. in tutorial_plume_on_slope.
530      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
531    o pkg rbcs:
532      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
533      - add capability to apply relaxation to horizontal velocity uVel & vVel.
534    o pkg/grdchk: add gradient check for control variable xx_shifwflx
535    o pkg/shelfice/shelfice_init_fixed.F
536      fix CPP-flag combinations
537    o pkg/seaice: Merge iceage code of Pierre Rampal
538      * update/change/correct ice age calculations
539      * add age updates for pathological cases
540      Probably needs more testing...
541    
542    checkpoint62x (2011/05/13)
543    o pkg/mom_vecinv:
544       high-order vorticity scheme: use interior masks (maskInW & S)
545       to zero-out (outside OB) gradient of vorticity.
546    o verification exp.:
547       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
548       hs94.128x64x5 and seaice_obcs ; update results.
549    o pkg/obcs:
550      fix bug in OBeta for YZ sections in obcs_exf_load.F
551    o pkg/ctrl, pkg/shelfice, and optim:
552      - add new control variable xx_shifwflx (fresh water flux underneath ice
553        shelves). This is almost as tedious as obcs-ctrl, because the
554        variables needs its own mask.
555      - add a cost function term that penalizes the deviation of xx_shifwflx
556        from the first guess (zero) in analogy to other control variables
557    o pkg/shelfice:
558      - start basic adjoint
559    o pkg/ctrl:
560      - remove extra 2D field "for good measure" when initializing in
561        ctrl_set_globfld_[xy/xz/yz].F
562      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
563      - improve error messages in ctrl_set_unpack_*
564    o OBC implementation in momentum:
565       use interior masks (maskInC,W & S) in momentum S/R:
566       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
567       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
568       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
569       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
570       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
571        (and also with Leith/Smagorinsky harmonic-viscosity).
572       Update output of experiment dome and exp4 (+nlfs).
573    o exp4 test-exp:
574      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
575        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
576        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
577        time-varying OB at Western-side for wVel (NonHyd); update output.
578      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
579        and biharmonic-viscosity ; also use prescribed time varying OB.
580    o pkg/obcs:
581      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
582    o model/src:
583      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
584      - initialise startTime & nIter0 with unlikely values: allows to set one
585        from the other without ambiguity.
586    o seaice_obcs test-exp.:
587      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
588    o pkg/obcs:
589      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
590        no longer needed with maskInC,W,S in pkg/generic_advdiff.
591    o pkg/seaice:
592      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
593        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
594      - fixed bug in the initialization of sea ice salinity variable HSALT
595        in seaice_init_varia.F  (removed dependence on ICE2WATR)
596    o fizhi-cs test exp.:
597       switch reference output convention for these 2 non-standard test-exp,
598        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
599          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
600       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
601    o model/inc:
602      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
603        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
604    o pkg/seaice:
605      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
606    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
607      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
608        and initial HSALT
609    
610    checkpoint62w (2011/04/26)
611    o pkg/mom_fluxform:
612      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
613      - use parameter "sideDragFactor" in no-slip BC side-drag part.
614      - update output of exp. global_ocean.90x40x15
615    o pkg/mom_vecinv:
616      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
617    o update seaice exp.:
618      use more consistent parameter values (remove "backward compatability only":
619       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
620      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
621       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
622    o update test-exp global_ocean.90x40x15:
623      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
624      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
625      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
626      o turn on zStar & viscA4 in standard set-up (dir input/)
627        and update output files: output.txt & output.dwnslp.txt
628    o new AD-test experiment: obcs_ctrl
629      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
630    o pkg/dic:
631      fix two bugs in handling water vapour pressure in carbonate chemistry
632      and air-sea fluxes. Found by Val Bennington and Galen McKinley
633      (add DIC Option = WATERVAP_BUG to recover old results)
634      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
635    o adding allowInteriorFreezing option to check for water below freezing point
636      at depth and bring the negative heat anomaly to the surface level
637    o pkgs _fields_load:
638      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
639      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
640        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
641        rbcs to get interpolation weights and time reccord number.
642      - fix multi-threading in aim_fields_load.F
643      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
644    o external_fields_load:
645      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
646       interpolation weights) to use in a periodic time-series ; do not divide by
647       time-step to convert to integer:
648       - this fixes case where externForcingPeriod is not multiple of time-step
649          (Thanks to Christopher L. Wolfe)
650       - this fixes case where externForcingPeriod is an odd multiple of time-step
651         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
652      store index of time-record which is currently loaded:
653       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
654       - needed for the adjoint but not yet used because of extensive recomputations;
655         (to be fixed soon)
656    
657    checkpoint62v (2011/04/02)
658    o verification/1D_ocean_ice_column added to test Ian Fenty's
659      pkg/seaice_growth.F modifications for improving sea ice code differentiability
660    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
661      (new velocity statistics after changing maskInW & maskInS definition)
662    o pkg/generic_advdiff with OBCS:
663      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
664      equivalent to assumption of no tracer gradient outside the OB region.
665      This will affect the results if using obcs+biharmonic diffusion.
666      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
667    o pkg/obcs:
668      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
669      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
670      in Interior region. No impact on solution but affects Velocity monitor stats.
671    o pkg/ptracers (adjoint)
672      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
673      tape file for each tracer
674    o model/inc/src and pkg/autodiff: add parameters that allow to turn
675      of parts of the adjoint code at run time. For now, there are only
676      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
677      parameters are set in data.pkg.
678      This is the lazy coward's version of doing this, but still useful for
679      debugging. In order to do it right, everything needs to be moved to
680      pkg/autodiff.
681    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
682      the end; this fixes the adjoint balancing code for open boundaries.
683    o pkg/ctrl:
684      - change behavior of xx_${varname}period to be analogous to exf-conventions:
685        xx_${varname}period =   0.,  means time-independent control part
686        xx_${varname}period = -12., means one-year-periodic monthly control part
687      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
688        clean up ctrl_init a little, remove unused variables
689      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
690      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
691    
692    checkpoint62u (2011/03/15)
693    o model/src:
694      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
695        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
696      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
697        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
698    o pkg/ctrl/obcs/ecco:
699      - remove obsolete, unused, and partially broken code:
700        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
701        ALLOW_CTRL_OBCS_BALANCE
702      - put a stop statement into ecco/cost_obcsvol.F, but also add
703        cost_obcsvol to ecco_ad_diff.list
704    o pkg/ecco: fix counting cost function contributions for obcs (code
705      by Matt M.) and diffkr for diagnostics
706    o pkg/ecco, pkg/ctrl, pkg/grdchk:
707      add cost penalty terms for initial uvel, vvel, eta controls
708      and I/O for prior error files
709    o pkg/mdsio:
710       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
711       (new argument) to check for tiled file in mdsioLocalDir : this fix the
712       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
713    o pkg/ctrl:
714     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
715       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
716       unused and superfluous variables
717     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
718    o pkg/ecco
719     - enable adjoint of Stevens OB
720    o pkg/ctrl/ecco/grdchk:
721      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
722        Fortunately, we do not have any tests for the numerous cpp-flagged
723        option of "obcs as control parameters" so we will never know
724        if this is an improvement (but at least now things compile).
725      - remove an obsolete initialization from ecco_cost_init_barfiles.F
726      - fix some problems within never used ifdefs to make the code compile
727    o pkg/obcs:
728     - Refine Interior mask definition to work with more complex OB (e.g.
729       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
730       read in Interior mask from file. Check if Interior mask is consistent
731       with OB list of indices.
732    o pkg/seaice
733     - beginning code for a seaice tracer package,
734       but currently only used for seaice age: SEAICE_AGE
735       SEAICE_num = 4
736       iTracer = 1: area-weighted ice age
737               = 2: volume-weighted ice age
738               = 3, 4: template for one-year vs. multi-year ice
739       data.seaice has new namelist SEAICE_PARM03 for arrays related to
740       SEAICE_num
741    
742    checkpoint62t (2011/03/05)
743    o pkg/obcs:
744     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
745       then normal component. This ensures that the normal component is set
746       correctly even when it conficts with tangential setting from an other OB.
747       Affects results of test-experiment seaice_obcs: update the output.txt
748    o pkg/obcs:
749     - add code to monitor statistics of dynamical fields at OB.
750     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
751       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
752       - change default: balance the Net inflow through all OB (instead of balancing
753         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
754     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
755       to match Nortern OB inflow (OBCS_balanceFacN=0).
756    o pkg/seaice:
757     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
758    o pkg/seaice (seaice_growth v 1.113):
759     - reverting seaice_growth to v 1.111 in order to have code with exact bit
760       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
761       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
762       runtime flag SEAICEareaFormula is kept but is inactive
763    o model/src:
764     - add new param to scale curvilinear grid distance and area when using
765       a different sphere radius from the grid-files.
766     - test/check multi-threads EXCH applied to local variable (cg2d_x)
767    o adjoint:
768     - enable adjoint of Stevens OB
769     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
770       (a bit delicate because of potentially modified adj. common block structure;
771       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
772    
773    checkpoint62s (2011/02/15)
774    o pkg/seaice (seaice_growth v 1.112):
775     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
776       computing the ice cover tendency from effective thickness tendencies. Include
777       Ian Fenty's formula.
778     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
779       SEAICEareaFormula.
780     - simplify notations for the various d_HEFF/d_AREA terms.
781    o pkg/gmredi:
782     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
783       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
784       add a verification test-run (front_relax.bvp) to test GM_useBVP.
785    o pkg/seaice (seaice_growth v 1.111):
786     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
787     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
788       also melt ice.
789    o pkg/seaice:
790     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
791     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
792    o pkg/cheapaml:
793     - from Nico Wienders: New version of this package.
794    o pkg/flt:
795     - add CPP options to prevent floats to re-enter the opposite side of
796       a periodic domain (default: keep periodicity)
797    o pkg/gmredi:
798     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
799       (needed for multi-dim advection).
800     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
801    o model/src:
802     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
803    o tutorial_tracer_adjsens
804     - extend to NLFS and replace maskC by hFacC
805       (change reference output accordingly)
806    
807    checkpoint62r (2011/01/24)
808    o testreport:
809     - add option -deloutp (-do) to remove output file after successful run
810     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
811       extract exact list of procs from this file ; adjust COMMAND by
812       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
813    o pkg/ecco: replace old ineffective way of penalizing deviations from
814      first guess (of obcs) with code by Matt Mazloff
815    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
816      exf/cal
817      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
818        and handle case of obcs?period == 0
819        Not affected by these changes: There is still an inconsistency in
820        the computation of start/endrec for the obcs variables for ALLOW_CAL
821        defined (see comment by Menemenlis, 7-Mar-2003)
822      - make S/R ctrl_get_gen_rec return something meaningful even if
823        ALLOW_CAL is not defined
824      - ctrl_getobcs?: simplify code so that it does not need to use
825                       S/R exf_swapfields
826    o testreport:
827       allow to test MPI with different number of processors for each experiment:
828       create file "SIZE.h.mpi" in each build dir.
829       Note: update of "-command" argument not yet implemented.
830    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
831      alleviate the need for additional 3D tapes when using
832      the non-inear free surface in the adjoint. This is done
833      by adding an 'update' of hfacc etc. to their current
834      value at the beginning of forward_step.F.
835    o pkg/seaice
836      seaice_lsr: move stress-divergence computations out of outer pseudo-
837      timestepping loop
838    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
839      up, so that the calls of the ctrl_* subroutines are really at the end
840      of the routine.
841    o pkg/gmredi:
842      allow to specify a 2-D horizontal map and a 1-D vertical profil
843      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
844    o pkg/seaice:
845      move lsr iterations from seaice_dynsolver to seaice_lsr.
846    o pkg/seaice:
847      reduce memory footprint of seaice mutldim advection tapes,
848      by using a 2D tape independent of the generic_advdiff ones,
849      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
850    
851    checkpoint62q (2010/12/29)
852    o model/src:
853      - check horizontal grid-spacing for unset or zero/negative values.
854      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
855    o pkg/flt:
856      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
857      - precision of input and output files set according to readBinaryPrec
858        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
859      - initial float position from tiled file was not converted to index space
860        (looks like a bug): fixed to make it similar to initial pos. global file.
861    o global_ocean.cs32x15:
862       change SIZE.h of AD set-up to get same tiling as with MPI.
863       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
864    o model/src:
865       add flag to control printing of domain fields (bathymetry, hFac ...) in
866       ini_mask_etc (call to plot_fieds_xy*).
867    o pkg/thsice:
868       if useEXF, some forcing fields are not valid in overlap: fixed by computing
869       over the interior only + apply EXCH at the end (like with SEAICE advection).
870    o pkg/mdsio:
871      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
872        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
873      - change barrier call for safe multi-threads access to 3-D shared buffer.
874      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
875      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
876        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
877    o pkg/flt:
878      - add fourth-order Runge-Kutta integration
879      - add basic exch2 support (only 1 facet supported so far!)
880    o pkg/mdsio+rw:
881      new S/R to read local (or tile independent) vector (read counterpart of
882       mds_writevec_loc, and front-end write_glvec_rl/rs).
883    o global_ocean.cs32x15: additional input_ad.seaice experiment
884        that uses pkg/seaice rather than pkg/thsice.
885        (using multidim advection for seaice)
886    o towards more F95 syntax for array specification in namelist:
887      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
888        of all verification experiments.
889           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
890          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
891      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
892    o global_ocean.cs32x15: additional input.seaice experiment
893        that uses pkg/seaice rather than pkg/thsice.
894    
895    checkpoint62p (2010/12/17)
896    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
897        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
898    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
899        allow for use of multim. advection in seaice adjoint.
900    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
901      - first attempt to close budgets by taking into account the freshwater
902        flux implied by the sublimation of snow and ice. So far only the
903        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
904        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
905    o eesupp/src:
906      new S/R with new option (NML_EXTENDED_F77) to change array specification
907      from F95 standard to commonly accepted extended F77 form.
908      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
909      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
910      for less tolerant f77 compiler (e.g., pgf77, g77).
911    o globalFiles:
912      commented out in parameter file "data" since it's not safe with MPI
913      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
914      in this case); no longer commented out in restart test (tst_2+2).
915    o add adTapeDir to specify a special directory where adjoint tapes are
916      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
917      and cannot be used together with mdsioLocalDir.
918    o nesting pkgs:
919      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
920      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
921      - add parameter files + utils dir + output from short run on beagle.
922    o pkg/seaice:
923        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
924    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
925      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
926    
927    checkpoint62o (2010/11/25)
928    o pkg/exf:
929      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
930    o pkg/seaice:
931      - seaice_ocean_stress: split a loop for better vectorization of the
932        adjoint code
933      - seaice_growth.F: fix bug in conservation of freshwater connected to
934        capping of heff, put contribution into d_HEFFbyNEG
935      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
936        by something more sensible (parameters that are what their name implies)
937      - change some defaults, so that by default exf-parameters are used for
938        things like rhoAir, cpAir,latent/sensible heat parameters, in order
939        to reproduce the old results, many data.seaice now contain funny values
940        for cpAir and latent heat of sublimation
941    o packages_readparms.F: move exf_readparms up in line so that
942        exf-parameters are visible for other packages (e.g. seaice)
943    o debugMode & debugLevel=2:
944      - differentiate between debugMode & debugLevel=2:
945        debugMode: controls printing of debug messages (sequence of S/R calls).
946        debugLevel: controls printing of algorithm intermediate results and stats.
947      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
948        => allows to print debug-stats without all sequence of call messages.
949      - switch control of debug print from debugLevel to debugMode in many S/R.
950    o pkg/obcs (obcs-sponge):
951        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
952        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
953    o pkg/generic_advdiff:
954      - record overlap minimum size for each advection scheme;
955      - refine criteria on overlap minimum size;
956      - check and stop (in gad_check) if overlap size is too small.
957    o pkg/obcs:
958      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
959        once, in ptracers_implicit.F)
960      - with seaice: remove test on empty file name in obcs_apply_seaice (always
961        apply OB values when tile has OB)
962    o model/src, coriolis setting:
963      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
964        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
965        files (selectCoriMap=3) with any grid.
966      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
967    o pkg/seaice/seaice_growth.F:
968        a few cosmetic changes that reduce the number of lines of code
969    o pkg/obcs: add boundary conditions following Stevens (1990)
970      - the code follows old MOM/NAOSIM code
971      - so far it is only implemented for the eastern and western boundaries
972        and NOT for pTracers
973    o pkg/rbcs:
974      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
975        beginning of the first rbcs forcing period.
976      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
977        offline package, i.e., one file per time, labeled by iteration number;
978        deltaTrbcs sets the timestep with which the data was generated;
979        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
980      - rbcsForcingCycle=0 makes forcing non-cyclic.
981      - make arithmetic safe for negative times and odd forcing periods.
982    
983    checkpoint62n (2010/11/09)
984    o pkg/seaice:
985        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
986    o pkg/obcs:
987       New S/R to copy tracer value from the OB location to narrow band region
988        (width = same as overlap) beyond the OB: preserve OB value (needed for
989        high-order scheme) which were overwritten by EXCH call if in overlap
990        region. Applied to theta, salt, ptracer and advected seaice variables.
991       With seaice: use maskInC in similar way as in gad_advection.F,
992        in seaice_advection.F and advect.F.
993       Update output of experiment seaice_obcs and change exp4 to test OBCS with
994        4th order Adv.Scheme. for pasive salt and ptracer.
995    o tools/genmake2:
996      - when looking for an optfile (not specified), only search for Fortran compiler
997        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
998      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
999        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
1000      - set default for CPP to "cpp -traditional -P" (was the case without specifying
1001        an optfile, but otherwise default was just "cpp".
1002      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
1003      - when "CC" is not set in the optfile, look for possible C compiler
1004        (instead of just setting CC=cc)
1005      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
1006        => add a ".F" to ".o" rule for source files with no "#include" (such as
1007           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
1008      - move gfortran before g77 in list of possible Fortran compiler (consistent
1009        with reference compiler switch from g77 to gfortran)
1010    o pkg/seaice:
1011      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
1012        seaice_check that stops the model, when the CPP flag is used.
1013      o seaice_growth.F: make capping of ice volume conserving by returning the
1014        capped ice as freshwater to EmPmR. This does not change the verification
1015        experiments but will change runs where the capping is acutally active
1016    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
1017      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
1018         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
1019         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
1020    o tools/genmake2:
1021      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
1022      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
1023      - clean previous genmake log files before anything else.
1024      - change Makefile to remove testreport log files (*.tr_log) and genmake log
1025        files only with "CLEAN" target (instead of "Clean");
1026    o pkg/generic_advdiff:
1027      Change OBCS in multiDim advection (gad_advection.F):
1028       Use maskInC to prevent intermediate update of tracer-field in OB regions,
1029       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
1030       which were applying future time-step OB values.
1031      This way, all explicit calculations use current-time-step OB values
1032       (simpler and more consistent).
1033      Affects results when set-up uses time-varying OBC and multi-dim advection;
1034       update output of experiment seaice_obcs.
1035    o pkg/seaice:
1036      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
1037       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
1038         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
1039      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
1040       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
1041       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
1042    o pkg aim (2010/10/26):
1043      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
1044        formulation with obliquity, eccentricity, ... as run-time parameters,
1045      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
1046        upward shortwave radition at the surface (all-sky and clear-sky).
1047  o pkg/obcs:  o pkg/obcs:
1048    - writing sections with globalFiles=T does not work: switch to tiled-files    - writing sections with globalFiles=T does not work: switch to tiled-files
1049      when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).      when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
# Line 420  o tools/build_options: Line 1460  o tools/build_options:
1460      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1461  o pkg/ecco  o pkg/ecco
1462    - allow user defined cost function contributions    - allow user defined cost function contributions
1463          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1464          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1465    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1466        the two options are complementary.        the two options are complementary.
1467  o pkg/smooth  o pkg/smooth
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