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revision 1.1401 by mlosch, Fri Mar 18 10:50:53 2011 UTC revision 1.1504 by heimbach, Mon Sep 26 18:24:26 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/seaice (SItracer pickup)
8    of parts of the adjoint code at run time. For now, there are only  * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
9    useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These    To be done:
10    parameters are set in data.pkg.    - thorough testing of missing fields in S/R seaice_read_pickup
11    This is the lazy coward's version of doing this, but still useful for    - thorough matching between generic tracers and specific fields used
12    debugging. In order to do it right, everything needs to be moved to      (e.g. volume-weighted age, area-weighted age, salinity, ...)
13    o pkg/seaice (LSR):
14      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
15      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
16        * identical results with non-CS topology (but save up to half of EXCH calls)
17        * no much changes in cs-32 verification tests since no ice at face edges
18         (differences due to convergence criteria, since nb of iterations changed)
19        * expect some differences on lat-lon-cap grid.
20        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
21    o pkg/exch2:
22      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
23        many tiles); until alternative coding is added, just add a stop.
24    o pkg/kpp:
25      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
26        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
27    o optfiles:
28      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
29        into corresponding standard one, which now support different build:
30        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
31      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
32    o pkg/obcs (seaice):
33      - add missing EXCH for uIce,vIce after applying OBCS;
34      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
35        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
36        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
37      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
38      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
39        and eedata.mth for MPI and mutlti-threaded testing.
40    o pkg/flt:
41      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
42      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
43      - fix pickup and trajectories + profiles output with multi-threads;
44      - add parameter to select group of fields to write along trajectory and
45        profile (default unchanged);
46      - only call PORT_RAND* function when flt_noise <> 0;
47      - add multi-threaded test for verification exp. flt_example.
48    o eesupp/src:
49      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
50      - USE_OMP_THREADING: check that number of threads (from eedata) matches
51        actual number (from env.var. setting).
52    o pkg/ebm:
53      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
54      - add multi-threaded test for verification exp. global_ocean_ebm
55    
56    checkpoint63b (2011/08/29)
57    o pkg/ebm:
58      - fix sign of runoff;
59      - update directly forcing fields (Qnet,EmPmR) to use standard
60        external_forcing_surf.F (remove ebm_forcing_surf.F);
61      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
62      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
63        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
64      - update global_ocean_ebm parameters file data and update output (fwd+ad).
65    o verification/matrix_example:
66      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
67        MPI and mutlti-threaded testing.
68    o pkg/matrix:
69      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
70      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
71      - fix for multi-threaded (remove DATA statement);
72      - use standard DIFFERENT_MULTIPLE function;
73      - add MATRIX_OPTIONS.h
74    o verification/matrix_example:
75       To allow to split the domain in several tiles, change the domain size
76        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
77        Western side) of land points.
78    o (*_)write_pickup:
79      - fix few bugs in mypackage_read/write_pickup.F
80      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
81        array of length 1 (was caught by compiler syntax-check).
82    o pkg/diagnostics (velocity potential solver):
83      - fix initialisation of main diagonal matrix (for overlap values)
84    o tools/build_options:
85      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
86        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
87      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
88        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
89        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
90        and use "-devel" testreport option for standard testing on baudelaire.
91    o pkg/grdchk:
92      - Assume that all gradient-check position are within the same tile
93        corresponding to global indices (iGloTile,jGloTile) and that
94        positions (i,j indices or nbeg) are local to this tile;
95      - set tile local-indices and proc. number according to tile global-indices;
96      - remove grdchkwhichproc from namelist (retired param);
97      - send adjoint gradient to all procs so that all procs print it to STDOUT;
98      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
99    o adding package bbl (Bottom Boundary Layer)
100      description in MITgcm/pkg/bbl/bbl_description.tex
101      example/test experiment in MITgcm_contrib/bbl
102    o adjoint verifications
103      - changed 5 experiments to multi-tiles
104        * global_ocean.90x40x15
105        * obcs_ctrl
106        * offline_exf_seaice
107        * tutorial_dic_adjoffline
108        * tutorial_tracer_adjsens
109        changed reference output for those that crossed tile boundaries
110        (changed choices of gradient check positions)
111      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
112      - temporary bug fix in grdchk_loc.F for obcs
113    o genmake2 & testreport
114      - add target "obj" (just for OBJFILES files) to Makefile;
115      - add option to specify FEXTRAFLAGS on command line.
116    o pkg/mypackage:
117      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
118    
119    checkpoint63a (2011/08/02)
120    o pkg/diagnostics (velocity potential):
121      - fix velocity-potential calculation when using OBCS: balance net inflow
122        at each level (new S/R OBCS_DIAG_BALANCE).
123      - fix some of the problems with OBCS in stream-function calculation.
124    o pkg/exf/exf_readparms.F
125      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
126        EXF_NML_OBCS) more consistent, so that you need not have these lists
127        in data.exf when they are not used.
128    o optim/optim_readdata.F:
129      - add some output about obcs variables that might help debugging
130      - add a check about nvarlength
131    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
132    o pkg/diagnostics (velocity potential):
133      - fix mask for OBCS (still problems in stream-function with OBCS);
134      - add specific parameter (default = main code CG2D params) for solver;
135      - in case of poor convergence, use solution corresponding to lowest residual.
136    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
137      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
138      and should be avoided where possible.
139    o model/src (rStar):
140      - include r* effect on reference-state (PhiRef) in totPhiHyd
141        (so that it's really the potential anomaly at the cell center);
142        affect solution only if z* with full pressure in EOS.
143      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
144        update output (because of z* in totPhiHyd and viscA4 changes);
145      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
146        @ constant r) until interpolation at constant r is implemented.
147    o pkg/diagnostics
148      - fix RCENTER diagnostics in case cell center is not at interface middle
149    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
150      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
151      that THETA and SALT are "conservative temperature" and "absolute
152      salinity"
153    o pkg/ctrl
154      - fix computation of endrec in s/r ctrl_init_rec
155      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
156    o pkg/seaice/seaice_growth.F
157      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
158        remove then obsolete STORE directives
159      - fix STORE directives for tice and tices, so that only the
160        appropriate part of the fields are stored (and not the entire
161        field); update global_ocean.cs32x15.seaice AD output.
162      - cosmetic changes: adjust CPP flags and indentation for better
163        legibilty
164    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
165      Chris Wilson)
166    o pkg/gmredi:
167       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
168       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
169    
170    checkpoint63  (2011/07/11)
171    o pkg/exch2:
172     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
173     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
174       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
175       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
176    o pkg/diagnostics:
177     - deal with pairs of post-processed diags which are computed together; in
178       particular, re-order list of diags within 1 file to save 2nd computation.
179     - add S/R to compute velocity stream-function (called after velocity-potential
180       calculation) from divergence free transport -> new diagnostics "PsiVEL".
181     - add parameter to select grid-point location where PsiVEL == 0.
182    o eesupp/src:
183       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
184       (specific S/R needed with exch2 topology - for now, just print an error msg)
185    o pkg/shelfice
186     - Implement friction velocity-dependent transfer coefficients following
187       Holland and Jenkins, JPO, 1999
188       Original code by M. Losch with small modifs.
189       Enable with CPP option SHI_ALLOW_GAMMAFRICT
190       and runtime flag SHELFICEuseGammaFrict
191    o verification lab_sea & global_ocean.cs32x15:
192     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
193       does not miss some dependencies (but is slower) and also works with many files
194       (default makedepend limitation for AD built).
195     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
196    o pkg/diagnostics:
197     - add run-time parameter "useMissingValue" (def=False) to fill land-point
198        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
199       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
200     - Extend the use of "missing_value" setting from data.diagnostics for the case
201       of counter-diagnostics (where fraction-weight is zero). This applies both to
202       MNC and MDS output files.
203    o pkg/seaice/seaice_growth.F:
204      - add 'a priori' cap of latent heat flux based on actual mass considerations
205        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
206        non-legacy seaice_solve4temp.
207      - add diagnostic of the residual sublimation freshwater flux (the freshwater
208        flux taken from the ocean if the total actual latent heat fluxes exceed
209        the maximum)
210      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
211       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
212      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
213       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
214      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
215      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
216    o verification 1D_ocean_ice_column:
217       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
218       update results
219    o pkg/diagnostics:
220     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
221       which are not filled-up but computed from other diags ; In this case, the mate
222       diag points to the primary (filled-up) diag to used for post processing.
223     - Update Velocity-potential computation using post-processed diag framework.
224     ==> Change the ordering of fields and time-periods in MDS output file
225       when using periodic averaging: now writes one time record with the full set
226       of fields for this time period, then the next time reccord (it used to be
227       one field with the full set of time records then the next field).
228         Note: this is now similar to NetCDF (MNC) output file. <==
229    
230    checkpoint62z (2011/06/21)
231    o adjoint monitor:
232     - Add adjoint monitor output for packages exf, seaice
233       and update relevant testreport output
234    o pkg/seaice:
235     - re-order diags inits so that they appear in order in available_diagnostics.log
236     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
237       area/heff/hsnow preceeding thermodynamic growth/melt.
238     - modified diag: SIdA; output actual effect, as the description states.
239     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
240     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
241       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
242        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
243     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
244     - added diagnostics for seaice generic tracers (SItr*).
245     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
246     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
247     I. Fenty: 18-Jun-2011:
248     Minor changes to seaice package:
249     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
250        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
251       - Differentiated "regularization variables" from "floor variables"
252        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
253        * hiceMin became SEAICE_hice_reg (old hiceMin)
254          (with _reg meaning regularization variable)
255       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
256        so as to ensure energy conservation when going between phases
257      - A22 was not used anywhere
258     2) Changed regularization procedure for heffActual and hsnowActual to ensure
259        well-boundedness and smooth adjoint in seaice_growth.F
260     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
261        because the old regularization always set heffActual >= 0.05 cm
262     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
263        on AREA when HEFF > 0.
264      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
265        requiring that DISABLE_AREA_FLOOR *not* be defined
266     Affected verifications:
267      - 1D_ocean_ice_column (output.txt output_adm.txt)
268      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
269    o pkg/diagnostics:
270      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
271      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
272        (was _RL, now integer) with option = 0 to retrieve all levels.
273      - add pieces of code to compute velocity potential at each level (new diagnostics
274        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
275        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
276      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
277        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
278        and in diagnostics_fract_fill.F (do not need a valid pointer for the
279        diagnostics counter-mate); check that definition of counter-diagnostic
280        includes a valid counter-mate (in diagnostics_set_levels.F).
281    o model/src (rStar):
282      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
283        affect solution only if z* with full pressure in EOS;
284        update output of test-exp global_ocean.90x40x15.
285    o pkg/seaice:
286      - introduce siEps=1e-5 parameter
287      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
288      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
289      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
290        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
291        as well as ice cover age and ridging index (attached to AREA).
292        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
293        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
294        Up to SItrMaxNum=3 tracers can be used simultaneously.
295    o pkg/salt_plume:
296      -introduce SPsalFRAC run time parameter that sets the fraction of the
297       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
298       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
299    o model debug options:
300      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
301        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
302      - Refine debug-msg printing selection (3 new levels):
303        debugMode  : controls printing of debug messages (sequence of S/R calls).
304        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
305         debLevZero =  0 ; /* level of disabled aux. msg printing */
306         debLevA =  1 ; /* level of minimum  aux. msg printing */
307         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
308         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
309         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
310         debLevE =  5 ; /* level of extensive debug printing */
311        New debugLevel default: with default debugMode value (=F),
312          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
313          and if debugMode=T, default debugLevel = 4 (debLevD).
314        Relation with previous settings:
315         debLevB (=2) corresponds to former debLevA (=1)
316         debLevD (=4) corresponds to former debLevB (=2)
317        Note:
318         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
319         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
320            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
321      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
322        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
323    o pkg/obcs:
324      - change OBCSfixTopo default from True to False (should not change the results);
325        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
326    o pkg/thsice:
327      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
328        2nd layer seaice sublimation (unlikely to happen)
329      - use Interior mask for OBCS in thsice_advection.F (similar to what is
330        done in gad_advection & seaice_advection).
331    o adjoint:
332      bug fix spotted by Gael Forget:
333      seaice_advection and thsice_advection still had
334      legacy CPP options to avoid CS corner updates for adjoint
335    o pkg/seaice:
336      => Change some of the defaults (2011/05/29):
337         - change SEAICEuseFluxForm default (from False to True)
338         - change DIFF1 default (from 0.004 m/s to 0. m/s)
339         And print warnings if DIFF1 is not set in data.seaice and centered
340          avection scheme is used without any diffusion.
341      also:
342      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
343      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
344      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
345        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
346        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
347      update results of test exp.:
348         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
349             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
350             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
351         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
352         seaice_obcs: output (SEAICEuseFluxForm=T)
353      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
354          for standard fwd & AD lab_sea tests (to keep the same output).
355    o pkg/seaice/seaice_growth.F:
356      - use Ian Fenty's capping formulas for actual ice
357      thickness thoughout EVOLUTION branch.
358      - put treatment pathological case #2) in CPP brackets
359      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
360      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
361    o pkg/seaice:
362      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
363      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
364      also pass fac as a param, which can be 1. (to update the tendency
365      field) or the time step (to update the field itself).
366      - seaice_advdiff.F: for multidim, call seaice_diffusion with
367      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
368      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
369      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
370      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
371    o pkg/seaice:
372      diffusion with centered advection scheme (diffus.F & advect.F):
373      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
374        to just compute the laplacian of input-field.
375      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
376      - fix flux-form version in diffus.F to conserve tracer.
377      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
378       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
379    
380    checkpoint62y (2011/05/26)
381    o pkg/seaice:
382     - seaice_growth.F : in EVOLUTION branch, always include
383       a_QSWbyATM_cover in qnet (as it should be).
384     - verification/global_ocean.cs32x15 : update results accordingly
385       (output.seaice.txt output_adm.seaice.txt).
386    o pkg/seaice + obcs:
387     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
388       equivalent of assuming no tracer gradient outside the OB region.
389       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
390     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
391       after changes above);
392     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
393       only at OB location (instead of over a band of OLx width).
394    o pkg/seaice:
395     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
396       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
397    o pkg/obcs:
398      - split header file "OBCS.h" into 4 separated files:
399        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
400       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
401         (contain no conditional statement which depends on OBCS options).
402      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
403        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
404    o ctrl, cost, grdchk & autodiff pkgs:
405      - make options file more standard (like other {PKG}_OPTIONS.h file but
406        with AD_CONFIG.h); clean-up some of the included header files.
407    o pkg/obcs:
408      - do not mask tracer when applying OB (tracer == 0 could generate problems)
409      - apply tracer OB values to tracer field only at OB location (instead of
410        over a band of OLx width)
411      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
412      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
413        obcs_apply_tloc.F & obcs_apply_sloc.F
414    o obcs in model/src:
415      - call OBCS_APPLY_W only if NonHydrostatic.
416      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
417      - reset dEtaHdt and wVel to zero outside OB interior region ;
418      - leave tracer unchanged outside OB interior region: This has no effect
419        on the solution but just to prevent unrealistic tracer value outside OB.
420      - zero out velocity outside OB interior region: This has no effect on
421        the solution but just to prevent unrealistic velocity outside OB.
422    o obcs and non-lin free-surf:
423       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
424       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
425       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
426       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
427       update results of test-exp. exp4(nlfs).
428    o exp4 (nlfs) test-exp:
429       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
430       with NonLin-FreeSurf); update output.nlfs.txt
431    o obcs and 2d/3d solver norm:
432       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
433       and outside OB interior region (will allow to place OB further inside the
434       domain). Depending on the domain, can affects cg2d-Norm (previous
435       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
436       and cg3d-Norm (previous Norm was computed before canceling OB terms),
437       e.g. in tutorial_plume_on_slope.
438      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
439    o pkg rbcs:
440      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
441      - add capability to apply relaxation to horizontal velocity uVel & vVel.
442    o pkg/grdchk: add gradient check for control variable xx_shifwflx
443    o pkg/shelfice/shelfice_init_fixed.F
444      fix CPP-flag combinations
445    o pkg/seaice: Merge iceage code of Pierre Rampal
446      * update/change/correct ice age calculations
447      * add age updates for pathological cases
448      Probably needs more testing...
449    
450    checkpoint62x (2011/05/13)
451    o pkg/mom_vecinv:
452       high-order vorticity scheme: use interior masks (maskInW & S)
453       to zero-out (outside OB) gradient of vorticity.
454    o verification exp.:
455       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
456       hs94.128x64x5 and seaice_obcs ; update results.
457    o pkg/obcs:
458      fix bug in OBeta for YZ sections in obcs_exf_load.F
459    o pkg/ctrl, pkg/shelfice, and optim:
460      - add new control variable xx_shifwflx (fresh water flux underneath ice
461        shelves). This is almost as tedious as obcs-ctrl, because the
462        variables needs its own mask.
463      - add a cost function term that penalizes the deviation of xx_shifwflx
464        from the first guess (zero) in analogy to other control variables
465    o pkg/shelfice:
466      - start basic adjoint
467    o pkg/ctrl:
468      - remove extra 2D field "for good measure" when initializing in
469        ctrl_set_globfld_[xy/xz/yz].F
470      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
471      - improve error messages in ctrl_set_unpack_*
472    o OBC implementation in momentum:
473       use interior masks (maskInC,W & S) in momentum S/R:
474       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
475       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
476       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
477       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
478       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
479        (and also with Leith/Smagorinsky harmonic-viscosity).
480       Update output of experiment dome and exp4 (+nlfs).
481    o exp4 test-exp:
482      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
483        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
484        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
485        time-varying OB at Western-side for wVel (NonHyd); update output.
486      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
487        and biharmonic-viscosity ; also use prescribed time varying OB.
488    o pkg/obcs:
489      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
490    o model/src:
491      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
492      - initialise startTime & nIter0 with unlikely values: allows to set one
493        from the other without ambiguity.
494    o seaice_obcs test-exp.:
495      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
496    o pkg/obcs:
497      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
498        no longer needed with maskInC,W,S in pkg/generic_advdiff.
499    o pkg/seaice:
500      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
501        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
502      - fixed bug in the initialization of sea ice salinity variable HSALT
503        in seaice_init_varia.F  (removed dependence on ICE2WATR)
504    o fizhi-cs test exp.:
505       switch reference output convention for these 2 non-standard test-exp,
506        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
507          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
508       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
509    o model/inc:
510      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
511        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
512    o pkg/seaice:
513      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
514    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
515      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
516        and initial HSALT
517    
518    checkpoint62w (2011/04/26)
519    o pkg/mom_fluxform:
520      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
521      - use parameter "sideDragFactor" in no-slip BC side-drag part.
522      - update output of exp. global_ocean.90x40x15
523    o pkg/mom_vecinv:
524      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
525    o update seaice exp.:
526      use more consistent parameter values (remove "backward compatability only":
527       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
528      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
529       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
530    o update test-exp global_ocean.90x40x15:
531      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
532      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
533      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
534      o turn on zStar & viscA4 in standard set-up (dir input/)
535        and update output files: output.txt & output.dwnslp.txt
536    o new AD-test experiment: obcs_ctrl
537      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
538    o pkg/dic:
539      fix two bugs in handling water vapour pressure in carbonate chemistry
540      and air-sea fluxes. Found by Val Bennington and Galen McKinley
541      (add DIC Option = WATERVAP_BUG to recover old results)
542      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
543    o adding allowInteriorFreezing option to check for water below freezing point
544      at depth and bring the negative heat anomaly to the surface level
545    o pkgs _fields_load:
546      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
547      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
548        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
549        rbcs to get interpolation weights and time reccord number.
550      - fix multi-threading in aim_fields_load.F
551      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
552    o external_fields_load:
553      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
554       interpolation weights) to use in a periodic time-series ; do not divide by
555       time-step to convert to integer:
556       - this fixes case where externForcingPeriod is not multiple of time-step
557          (Thanks to Christopher L. Wolfe)
558       - this fixes case where externForcingPeriod is an odd multiple of time-step
559         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
560      store index of time-record which is currently loaded:
561       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
562       - needed for the adjoint but not yet used because of extensive recomputations;
563         (to be fixed soon)
564    
565    checkpoint62v (2011/04/02)
566    o verification/1D_ocean_ice_column added to test Ian Fenty's
567      pkg/seaice_growth.F modifications for improving sea ice code differentiability
568    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
569      (new velocity statistics after changing maskInW & maskInS definition)
570    o pkg/generic_advdiff with OBCS:
571      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
572      equivalent to assumption of no tracer gradient outside the OB region.
573      This will affect the results if using obcs+biharmonic diffusion.
574      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
575    o pkg/obcs:
576      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
577      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
578      in Interior region. No impact on solution but affects Velocity monitor stats.
579    o pkg/ptracers (adjoint)
580      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
581      tape file for each tracer
582    o model/inc/src and pkg/autodiff: add parameters that allow to turn
583      of parts of the adjoint code at run time. For now, there are only
584      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
585      parameters are set in data.pkg.
586      This is the lazy coward's version of doing this, but still useful for
587      debugging. In order to do it right, everything needs to be moved to
588    pkg/autodiff.    pkg/autodiff.
589  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
590    the end; this fixes the adjoint balancing code for open boundaries.    the end; this fixes the adjoint balancing code for open boundaries.
591  o pkg/ctrl:  o pkg/ctrl:
592    - change behavior of xx_${varname}period to be analogous to exf-conventions:    - change behavior of xx_${varname}period to be analogous to exf-conventions:
593      xx_${varname}period =   0.,  means time-independent control part      xx_${varname}period =   0.,  means time-independent control part
594      xx_${varname}period = -12., means one-year-periodic monthly control part      xx_${varname}period = -12., means one-year-periodic monthly control part
595    - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to    - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
596      clean up ctrl_init a little, remove unused variables      clean up ctrl_init a little, remove unused variables
597    - 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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