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revision 1.1401 by mlosch, Fri Mar 18 10:50:53 2011 UTC revision 1.1509 by jmc, Mon Oct 3 12:48:20 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 model/inc/scr and pkg/autodiff: add parameters that allow to turn  o pkg/exch2:
8    of parts of the adjoint code at run time. For now, there are only    - alternative code (without tile x tile matrix) for cumulated (global) sum;
9    useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These      used as default; keep using matrix version in adjustment.cs-32x32x1.
10    parameters are set in data.pkg.  o tools/build_options:
11    This is the lazy coward's version of doing this, but still useful for    - after merging some MPI and/or multi-threads specific optfiles so that
12    debugging. In order to do it right, everything needs to be moved to      the modified default optfile support both built (using genmake2 -mpi
13        for the MPI built, using genmake2 -omp for OpenMP built),
14        move now obsolete optfiles to tools/build_options/unsupported/
15       (add copy of email sent to support list in doc/optfiles_changes.txt)
16    
17    checkpoint63c (2011/09/28)
18    o pkg/ebm:
19      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
20        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
21    o pkg/seaice (SItracer pickup)
22    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
23      To be done:
24      - thorough testing of missing fields in S/R seaice_read_pickup
25      - thorough matching between generic tracers and specific fields used
26        (e.g. volume-weighted age, area-weighted age, salinity, ...)
27    o pkg/grdchk:
28      - all procs calculate and print finite-difference gradient (for testreport)
29      - change description output used by testreport;
30      - AD testing: also compare and report Finite-difference gradient;
31        => update all output_adm*.txt
32    o test exp. global_ocean_ebm:
33      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
34        and turn on exactConserve; update (fwd) output.
35    o pkg/seaice (LSR):
36      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
37      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
38        * identical results with non-CS topology (but save up to half of EXCH calls)
39        * no much changes in cs-32 verification tests since no ice at face edges
40         (differences due to convergence criteria, since nb of iterations changed)
41        * expect some differences on lat-lon-cap grid.
42        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
43    o pkg/exch2:
44      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
45        many tiles); until alternative coding is added, just add a stop.
46    o pkg/kpp:
47      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
48        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
49    o optfiles:
50      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
51        into corresponding standard one, which now support different build:
52        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
53      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
54    o pkg/obcs (seaice):
55      - add missing EXCH for uIce,vIce after applying OBCS;
56      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
57        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
58        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
59      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
60      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
61        and eedata.mth for MPI and mutlti-threaded testing.
62    o pkg/flt:
63      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
64      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
65      - fix pickup and trajectories + profiles output with multi-threads;
66      - add parameter to select group of fields to write along trajectory and
67        profile (default unchanged);
68      - only call PORT_RAND* function when flt_noise <> 0;
69      - add multi-threaded test for verification exp. flt_example.
70    o eesupp/src:
71      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
72      - USE_OMP_THREADING: check that number of threads (from eedata) matches
73        actual number (from env.var. setting).
74    o pkg/ebm:
75      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
76      - add multi-threaded test for verification exp. global_ocean_ebm
77    
78    checkpoint63b (2011/08/29)
79    o pkg/ebm:
80      - fix sign of runoff;
81      - update directly forcing fields (Qnet,EmPmR) to use standard
82        external_forcing_surf.F (remove ebm_forcing_surf.F);
83      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
84      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
85        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
86      - update global_ocean_ebm parameters file data and update output (fwd+ad).
87    o verification/matrix_example:
88      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
89        MPI and mutlti-threaded testing.
90    o pkg/matrix:
91      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
92      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
93      - fix for multi-threaded (remove DATA statement);
94      - use standard DIFFERENT_MULTIPLE function;
95      - add MATRIX_OPTIONS.h
96    o verification/matrix_example:
97       To allow to split the domain in several tiles, change the domain size
98        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
99        Western side) of land points.
100    o (*_)write_pickup:
101      - fix few bugs in mypackage_read/write_pickup.F
102      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
103        array of length 1 (was caught by compiler syntax-check).
104    o pkg/diagnostics (velocity potential solver):
105      - fix initialisation of main diagonal matrix (for overlap values)
106    o tools/build_options:
107      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
108        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
109      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
110        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
111        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
112        and use "-devel" testreport option for standard testing on baudelaire.
113    o pkg/grdchk:
114      - Assume that all gradient-check position are within the same tile
115        corresponding to global indices (iGloTile,jGloTile) and that
116        positions (i,j indices or nbeg) are local to this tile;
117      - set tile local-indices and proc. number according to tile global-indices;
118      - remove grdchkwhichproc from namelist (retired param);
119      - send adjoint gradient to all procs so that all procs print it to STDOUT;
120      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
121    o adding package bbl (Bottom Boundary Layer)
122      description in MITgcm/pkg/bbl/bbl_description.tex
123      example/test experiment in MITgcm_contrib/bbl
124    o adjoint verifications
125      - changed 5 experiments to multi-tiles
126        * global_ocean.90x40x15
127        * obcs_ctrl
128        * offline_exf_seaice
129        * tutorial_dic_adjoffline
130        * tutorial_tracer_adjsens
131        changed reference output for those that crossed tile boundaries
132        (changed choices of gradient check positions)
133      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
134      - temporary bug fix in grdchk_loc.F for obcs
135    o genmake2 & testreport
136      - add target "obj" (just for OBJFILES files) to Makefile;
137      - add option to specify FEXTRAFLAGS on command line.
138    o pkg/mypackage:
139      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
140    
141    checkpoint63a (2011/08/02)
142    o pkg/diagnostics (velocity potential):
143      - fix velocity-potential calculation when using OBCS: balance net inflow
144        at each level (new S/R OBCS_DIAG_BALANCE).
145      - fix some of the problems with OBCS in stream-function calculation.
146    o pkg/exf/exf_readparms.F
147      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
148        EXF_NML_OBCS) more consistent, so that you need not have these lists
149        in data.exf when they are not used.
150    o optim/optim_readdata.F:
151      - add some output about obcs variables that might help debugging
152      - add a check about nvarlength
153    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
154    o pkg/diagnostics (velocity potential):
155      - fix mask for OBCS (still problems in stream-function with OBCS);
156      - add specific parameter (default = main code CG2D params) for solver;
157      - in case of poor convergence, use solution corresponding to lowest residual.
158    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
159      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
160      and should be avoided where possible.
161    o model/src (rStar):
162      - include r* effect on reference-state (PhiRef) in totPhiHyd
163        (so that it's really the potential anomaly at the cell center);
164        affect solution only if z* with full pressure in EOS.
165      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
166        update output (because of z* in totPhiHyd and viscA4 changes);
167      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
168        @ constant r) until interpolation at constant r is implemented.
169    o pkg/diagnostics
170      - fix RCENTER diagnostics in case cell center is not at interface middle
171    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
172      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
173      that THETA and SALT are "conservative temperature" and "absolute
174      salinity"
175    o pkg/ctrl
176      - fix computation of endrec in s/r ctrl_init_rec
177      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
178    o pkg/seaice/seaice_growth.F
179      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
180        remove then obsolete STORE directives
181      - fix STORE directives for tice and tices, so that only the
182        appropriate part of the fields are stored (and not the entire
183        field); update global_ocean.cs32x15.seaice AD output.
184      - cosmetic changes: adjust CPP flags and indentation for better
185        legibilty
186    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
187      Chris Wilson)
188    o pkg/gmredi:
189       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
190       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
191    
192    checkpoint63  (2011/07/11)
193    o pkg/exch2:
194     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
195     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
196       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
197       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
198    o pkg/diagnostics:
199     - deal with pairs of post-processed diags which are computed together; in
200       particular, re-order list of diags within 1 file to save 2nd computation.
201     - add S/R to compute velocity stream-function (called after velocity-potential
202       calculation) from divergence free transport -> new diagnostics "PsiVEL".
203     - add parameter to select grid-point location where PsiVEL == 0.
204    o eesupp/src:
205       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
206       (specific S/R needed with exch2 topology - for now, just print an error msg)
207    o pkg/shelfice
208     - Implement friction velocity-dependent transfer coefficients following
209       Holland and Jenkins, JPO, 1999
210       Original code by M. Losch with small modifs.
211       Enable with CPP option SHI_ALLOW_GAMMAFRICT
212       and runtime flag SHELFICEuseGammaFrict
213    o verification lab_sea & global_ocean.cs32x15:
214     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
215       does not miss some dependencies (but is slower) and also works with many files
216       (default makedepend limitation for AD built).
217     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
218    o pkg/diagnostics:
219     - add run-time parameter "useMissingValue" (def=False) to fill land-point
220        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
221       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
222     - Extend the use of "missing_value" setting from data.diagnostics for the case
223       of counter-diagnostics (where fraction-weight is zero). This applies both to
224       MNC and MDS output files.
225    o pkg/seaice/seaice_growth.F:
226      - add 'a priori' cap of latent heat flux based on actual mass considerations
227        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
228        non-legacy seaice_solve4temp.
229      - add diagnostic of the residual sublimation freshwater flux (the freshwater
230        flux taken from the ocean if the total actual latent heat fluxes exceed
231        the maximum)
232      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
233       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
234      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
235       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
236      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
237      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
238    o verification 1D_ocean_ice_column:
239       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
240       update results
241    o pkg/diagnostics:
242     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
243       which are not filled-up but computed from other diags ; In this case, the mate
244       diag points to the primary (filled-up) diag to used for post processing.
245     - Update Velocity-potential computation using post-processed diag framework.
246     ==> Change the ordering of fields and time-periods in MDS output file
247       when using periodic averaging: now writes one time record with the full set
248       of fields for this time period, then the next time reccord (it used to be
249       one field with the full set of time records then the next field).
250         Note: this is now similar to NetCDF (MNC) output file. <==
251    
252    checkpoint62z (2011/06/21)
253    o adjoint monitor:
254     - Add adjoint monitor output for packages exf, seaice
255       and update relevant testreport output
256    o pkg/seaice:
257     - re-order diags inits so that they appear in order in available_diagnostics.log
258     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
259       area/heff/hsnow preceeding thermodynamic growth/melt.
260     - modified diag: SIdA; output actual effect, as the description states.
261     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
262     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
263       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
264        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
265     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
266     - added diagnostics for seaice generic tracers (SItr*).
267     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
268     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
269     I. Fenty: 18-Jun-2011:
270     Minor changes to seaice package:
271     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
272        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
273       - Differentiated "regularization variables" from "floor variables"
274        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
275        * hiceMin became SEAICE_hice_reg (old hiceMin)
276          (with _reg meaning regularization variable)
277       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
278        so as to ensure energy conservation when going between phases
279      - A22 was not used anywhere
280     2) Changed regularization procedure for heffActual and hsnowActual to ensure
281        well-boundedness and smooth adjoint in seaice_growth.F
282     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
283        because the old regularization always set heffActual >= 0.05 cm
284     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
285        on AREA when HEFF > 0.
286      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
287        requiring that DISABLE_AREA_FLOOR *not* be defined
288     Affected verifications:
289      - 1D_ocean_ice_column (output.txt output_adm.txt)
290      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
291    o pkg/diagnostics:
292      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
293      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
294        (was _RL, now integer) with option = 0 to retrieve all levels.
295      - add pieces of code to compute velocity potential at each level (new diagnostics
296        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
297        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
298      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
299        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
300        and in diagnostics_fract_fill.F (do not need a valid pointer for the
301        diagnostics counter-mate); check that definition of counter-diagnostic
302        includes a valid counter-mate (in diagnostics_set_levels.F).
303    o model/src (rStar):
304      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
305        affect solution only if z* with full pressure in EOS;
306        update output of test-exp global_ocean.90x40x15.
307    o pkg/seaice:
308      - introduce siEps=1e-5 parameter
309      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
310      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
311      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
312        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
313        as well as ice cover age and ridging index (attached to AREA).
314        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
315        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
316        Up to SItrMaxNum=3 tracers can be used simultaneously.
317    o pkg/salt_plume:
318      -introduce SPsalFRAC run time parameter that sets the fraction of the
319       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
320       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
321    o model debug options:
322      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
323        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
324      - Refine debug-msg printing selection (3 new levels):
325        debugMode  : controls printing of debug messages (sequence of S/R calls).
326        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
327         debLevZero =  0 ; /* level of disabled aux. msg printing */
328         debLevA =  1 ; /* level of minimum  aux. msg printing */
329         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
330         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
331         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
332         debLevE =  5 ; /* level of extensive debug printing */
333        New debugLevel default: with default debugMode value (=F),
334          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
335          and if debugMode=T, default debugLevel = 4 (debLevD).
336        Relation with previous settings:
337         debLevB (=2) corresponds to former debLevA (=1)
338         debLevD (=4) corresponds to former debLevB (=2)
339        Note:
340         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
341         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
342            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
343      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
344        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
345    o pkg/obcs:
346      - change OBCSfixTopo default from True to False (should not change the results);
347        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
348    o pkg/thsice:
349      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
350        2nd layer seaice sublimation (unlikely to happen)
351      - use Interior mask for OBCS in thsice_advection.F (similar to what is
352        done in gad_advection & seaice_advection).
353    o adjoint:
354      bug fix spotted by Gael Forget:
355      seaice_advection and thsice_advection still had
356      legacy CPP options to avoid CS corner updates for adjoint
357    o pkg/seaice:
358      => Change some of the defaults (2011/05/29):
359         - change SEAICEuseFluxForm default (from False to True)
360         - change DIFF1 default (from 0.004 m/s to 0. m/s)
361         And print warnings if DIFF1 is not set in data.seaice and centered
362          avection scheme is used without any diffusion.
363      also:
364      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
365      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
366      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
367        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
368        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
369      update results of test exp.:
370         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
371             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
372             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
373         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
374         seaice_obcs: output (SEAICEuseFluxForm=T)
375      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
376          for standard fwd & AD lab_sea tests (to keep the same output).
377    o pkg/seaice/seaice_growth.F:
378      - use Ian Fenty's capping formulas for actual ice
379      thickness thoughout EVOLUTION branch.
380      - put treatment pathological case #2) in CPP brackets
381      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
382      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
383    o pkg/seaice:
384      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
385      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
386      also pass fac as a param, which can be 1. (to update the tendency
387      field) or the time step (to update the field itself).
388      - seaice_advdiff.F: for multidim, call seaice_diffusion with
389      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
390      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
391      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
392      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
393    o pkg/seaice:
394      diffusion with centered advection scheme (diffus.F & advect.F):
395      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
396        to just compute the laplacian of input-field.
397      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
398      - fix flux-form version in diffus.F to conserve tracer.
399      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
400       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
401    
402    checkpoint62y (2011/05/26)
403    o pkg/seaice:
404     - seaice_growth.F : in EVOLUTION branch, always include
405       a_QSWbyATM_cover in qnet (as it should be).
406     - verification/global_ocean.cs32x15 : update results accordingly
407       (output.seaice.txt output_adm.seaice.txt).
408    o pkg/seaice + obcs:
409     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
410       equivalent of assuming no tracer gradient outside the OB region.
411       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
412     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
413       after changes above);
414     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
415       only at OB location (instead of over a band of OLx width).
416    o pkg/seaice:
417     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
418       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
419    o pkg/obcs:
420      - split header file "OBCS.h" into 4 separated files:
421        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
422       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
423         (contain no conditional statement which depends on OBCS options).
424      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
425        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
426    o ctrl, cost, grdchk & autodiff pkgs:
427      - make options file more standard (like other {PKG}_OPTIONS.h file but
428        with AD_CONFIG.h); clean-up some of the included header files.
429    o pkg/obcs:
430      - do not mask tracer when applying OB (tracer == 0 could generate problems)
431      - apply tracer OB values to tracer field only at OB location (instead of
432        over a band of OLx width)
433      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
434      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
435        obcs_apply_tloc.F & obcs_apply_sloc.F
436    o obcs in model/src:
437      - call OBCS_APPLY_W only if NonHydrostatic.
438      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
439      - reset dEtaHdt and wVel to zero outside OB interior region ;
440      - leave tracer unchanged outside OB interior region: This has no effect
441        on the solution but just to prevent unrealistic tracer value outside OB.
442      - zero out velocity outside OB interior region: This has no effect on
443        the solution but just to prevent unrealistic velocity outside OB.
444    o obcs and non-lin free-surf:
445       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
446       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
447       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
448       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
449       update results of test-exp. exp4(nlfs).
450    o exp4 (nlfs) test-exp:
451       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
452       with NonLin-FreeSurf); update output.nlfs.txt
453    o obcs and 2d/3d solver norm:
454       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
455       and outside OB interior region (will allow to place OB further inside the
456       domain). Depending on the domain, can affects cg2d-Norm (previous
457       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
458       and cg3d-Norm (previous Norm was computed before canceling OB terms),
459       e.g. in tutorial_plume_on_slope.
460      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
461    o pkg rbcs:
462      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
463      - add capability to apply relaxation to horizontal velocity uVel & vVel.
464    o pkg/grdchk: add gradient check for control variable xx_shifwflx
465    o pkg/shelfice/shelfice_init_fixed.F
466      fix CPP-flag combinations
467    o pkg/seaice: Merge iceage code of Pierre Rampal
468      * update/change/correct ice age calculations
469      * add age updates for pathological cases
470      Probably needs more testing...
471    
472    checkpoint62x (2011/05/13)
473    o pkg/mom_vecinv:
474       high-order vorticity scheme: use interior masks (maskInW & S)
475       to zero-out (outside OB) gradient of vorticity.
476    o verification exp.:
477       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
478       hs94.128x64x5 and seaice_obcs ; update results.
479    o pkg/obcs:
480      fix bug in OBeta for YZ sections in obcs_exf_load.F
481    o pkg/ctrl, pkg/shelfice, and optim:
482      - add new control variable xx_shifwflx (fresh water flux underneath ice
483        shelves). This is almost as tedious as obcs-ctrl, because the
484        variables needs its own mask.
485      - add a cost function term that penalizes the deviation of xx_shifwflx
486        from the first guess (zero) in analogy to other control variables
487    o pkg/shelfice:
488      - start basic adjoint
489    o pkg/ctrl:
490      - remove extra 2D field "for good measure" when initializing in
491        ctrl_set_globfld_[xy/xz/yz].F
492      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
493      - improve error messages in ctrl_set_unpack_*
494    o OBC implementation in momentum:
495       use interior masks (maskInC,W & S) in momentum S/R:
496       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
497       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
498       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
499       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
500       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
501        (and also with Leith/Smagorinsky harmonic-viscosity).
502       Update output of experiment dome and exp4 (+nlfs).
503    o exp4 test-exp:
504      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
505        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
506        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
507        time-varying OB at Western-side for wVel (NonHyd); update output.
508      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
509        and biharmonic-viscosity ; also use prescribed time varying OB.
510    o pkg/obcs:
511      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
512    o model/src:
513      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
514      - initialise startTime & nIter0 with unlikely values: allows to set one
515        from the other without ambiguity.
516    o seaice_obcs test-exp.:
517      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
518    o pkg/obcs:
519      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
520        no longer needed with maskInC,W,S in pkg/generic_advdiff.
521    o pkg/seaice:
522      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
523        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
524      - fixed bug in the initialization of sea ice salinity variable HSALT
525        in seaice_init_varia.F  (removed dependence on ICE2WATR)
526    o fizhi-cs test exp.:
527       switch reference output convention for these 2 non-standard test-exp,
528        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
529          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
530       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
531    o model/inc:
532      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
533        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
534    o pkg/seaice:
535      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
536    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
537      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
538        and initial HSALT
539    
540    checkpoint62w (2011/04/26)
541    o pkg/mom_fluxform:
542      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
543      - use parameter "sideDragFactor" in no-slip BC side-drag part.
544      - update output of exp. global_ocean.90x40x15
545    o pkg/mom_vecinv:
546      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
547    o update seaice exp.:
548      use more consistent parameter values (remove "backward compatability only":
549       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
550      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
551       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
552    o update test-exp global_ocean.90x40x15:
553      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
554      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
555      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
556      o turn on zStar & viscA4 in standard set-up (dir input/)
557        and update output files: output.txt & output.dwnslp.txt
558    o new AD-test experiment: obcs_ctrl
559      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
560    o pkg/dic:
561      fix two bugs in handling water vapour pressure in carbonate chemistry
562      and air-sea fluxes. Found by Val Bennington and Galen McKinley
563      (add DIC Option = WATERVAP_BUG to recover old results)
564      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
565    o adding allowInteriorFreezing option to check for water below freezing point
566      at depth and bring the negative heat anomaly to the surface level
567    o pkgs _fields_load:
568      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
569      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
570        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
571        rbcs to get interpolation weights and time reccord number.
572      - fix multi-threading in aim_fields_load.F
573      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
574    o external_fields_load:
575      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
576       interpolation weights) to use in a periodic time-series ; do not divide by
577       time-step to convert to integer:
578       - this fixes case where externForcingPeriod is not multiple of time-step
579          (Thanks to Christopher L. Wolfe)
580       - this fixes case where externForcingPeriod is an odd multiple of time-step
581         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
582      store index of time-record which is currently loaded:
583       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
584       - needed for the adjoint but not yet used because of extensive recomputations;
585         (to be fixed soon)
586    
587    checkpoint62v (2011/04/02)
588    o verification/1D_ocean_ice_column added to test Ian Fenty's
589      pkg/seaice_growth.F modifications for improving sea ice code differentiability
590    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
591      (new velocity statistics after changing maskInW & maskInS definition)
592    o pkg/generic_advdiff with OBCS:
593      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
594      equivalent to assumption of no tracer gradient outside the OB region.
595      This will affect the results if using obcs+biharmonic diffusion.
596      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
597    o pkg/obcs:
598      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
599      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
600      in Interior region. No impact on solution but affects Velocity monitor stats.
601    o pkg/ptracers (adjoint)
602      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
603      tape file for each tracer
604    o model/inc/src and pkg/autodiff: add parameters that allow to turn
605      of parts of the adjoint code at run time. For now, there are only
606      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
607      parameters are set in data.pkg.
608      This is the lazy coward's version of doing this, but still useful for
609      debugging. In order to do it right, everything needs to be moved to
610    pkg/autodiff.    pkg/autodiff.
611  o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at  o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
612    the end; this fixes the adjoint balancing code for open boundaries.    the end; this fixes the adjoint balancing code for open boundaries.
613  o pkg/ctrl:  o pkg/ctrl:
614    - change behavior of xx_${varname}period to be analogous to exf-conventions:    - change behavior of xx_${varname}period to be analogous to exf-conventions:
615      xx_${varname}period =   0.,  means time-independent control part      xx_${varname}period =   0.,  means time-independent control part
616      xx_${varname}period = -12., means one-year-periodic monthly control part      xx_${varname}period = -12., means one-year-periodic monthly control part
617    - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to    - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
618      clean up ctrl_init a little, remove unused variables      clean up ctrl_init a little, remove unused variables
619    - ctrl_init: fixed the handling of the start/endrec for obcs-variables    - ctrl_init: fixed the handling of the start/endrec for obcs-variables
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