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revision 1.1367 by mlosch, Wed Jan 19 13:52:14 2011 UTC revision 1.1502 by jmc, Wed Sep 21 16:29:49 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/exch2:
8      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
9        many tiles); until alternative coding is added, just add a stop.
10    o pkg/kpp:
11      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
12        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
13    o optfiles:
14      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
15        into corresponding standard one, which now support different build:
16        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
17      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
18    o pkg/obcs (seaice):
19      - add missing EXCH for uIce,vIce after applying OBCS;
20      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
21        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
22        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
23      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
24      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
25        and eedata.mth for MPI and mutlti-threaded testing.
26    o pkg/flt:
27      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
28      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
29      - fix pickup and trajectories + profiles output with multi-threads;
30      - add parameter to select group of fields to write along trajectory and
31        profile (default unchanged);
32      - only call PORT_RAND* function when flt_noise <> 0;
33      - add multi-threaded test for verification exp. flt_example.
34    o eesupp/src:
35      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
36      - USE_OMP_THREADING: check that number of threads (from eedata) matches
37        actual number (from env.var. setting).
38    o pkg/ebm:
39      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
40      - add multi-threaded test for verification exp. global_ocean_ebm
41    
42    checkpoint63b (2011/08/29)
43    o pkg/ebm:
44      - fix sign of runoff;
45      - update directly forcing fields (Qnet,EmPmR) to use standard
46        external_forcing_surf.F (remove ebm_forcing_surf.F);
47      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
48      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
49        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
50      - update global_ocean_ebm parameters file data and update output (fwd+ad).
51    o verification/matrix_example:
52      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
53        MPI and mutlti-threaded testing.
54    o pkg/matrix:
55      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
56      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
57      - fix for multi-threaded (remove DATA statement);
58      - use standard DIFFERENT_MULTIPLE function;
59      - add MATRIX_OPTIONS.h
60    o verification/matrix_example:
61       To allow to split the domain in several tiles, change the domain size
62        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
63        Western side) of land points.
64    o (*_)write_pickup:
65      - fix few bugs in mypackage_read/write_pickup.F
66      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
67        array of length 1 (was caught by compiler syntax-check).
68    o pkg/diagnostics (velocity potential solver):
69      - fix initialisation of main diagonal matrix (for overlap values)
70    o tools/build_options:
71      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
72        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
73      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
74        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
75        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
76        and use "-devel" testreport option for standard testing on baudelaire.
77    o pkg/grdchk:
78      - Assume that all gradient-check position are within the same tile
79        corresponding to global indices (iGloTile,jGloTile) and that
80        positions (i,j indices or nbeg) are local to this tile;
81      - set tile local-indices and proc. number according to tile global-indices;
82      - remove grdchkwhichproc from namelist (retired param);
83      - send adjoint gradient to all procs so that all procs print it to STDOUT;
84      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
85    o adding package bbl (Bottom Boundary Layer)
86      description in MITgcm/pkg/bbl/bbl_description.tex
87      example/test experiment in MITgcm_contrib/bbl
88    o adjoint verifications
89      - changed 5 experiments to multi-tiles
90        * global_ocean.90x40x15
91        * obcs_ctrl
92        * offline_exf_seaice
93        * tutorial_dic_adjoffline
94        * tutorial_tracer_adjsens
95        changed reference output for those that crossed tile boundaries
96        (changed choices of gradient check positions)
97      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
98      - temporary bug fix in grdchk_loc.F for obcs
99    o genmake2 & testreport
100      - add target "obj" (just for OBJFILES files) to Makefile;
101      - add option to specify FEXTRAFLAGS on command line.
102    o pkg/mypackage:
103      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
104    
105    checkpoint63a (2011/08/02)
106    o pkg/diagnostics (velocity potential):
107      - fix velocity-potential calculation when using OBCS: balance net inflow
108        at each level (new S/R OBCS_DIAG_BALANCE).
109      - fix some of the problems with OBCS in stream-function calculation.
110    o pkg/exf/exf_readparms.F
111      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
112        EXF_NML_OBCS) more consistent, so that you need not have these lists
113        in data.exf when they are not used.
114    o optim/optim_readdata.F:
115      - add some output about obcs variables that might help debugging
116      - add a check about nvarlength
117    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
118    o pkg/diagnostics (velocity potential):
119      - fix mask for OBCS (still problems in stream-function with OBCS);
120      - add specific parameter (default = main code CG2D params) for solver;
121      - in case of poor convergence, use solution corresponding to lowest residual.
122    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
123      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
124      and should be avoided where possible.
125    o model/src (rStar):
126      - include r* effect on reference-state (PhiRef) in totPhiHyd
127        (so that it's really the potential anomaly at the cell center);
128        affect solution only if z* with full pressure in EOS.
129      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
130        update output (because of z* in totPhiHyd and viscA4 changes);
131      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
132        @ constant r) until interpolation at constant r is implemented.
133    o pkg/diagnostics
134      - fix RCENTER diagnostics in case cell center is not at interface middle
135    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
136      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
137      that THETA and SALT are "conservative temperature" and "absolute
138      salinity"
139    o pkg/ctrl
140      - fix computation of endrec in s/r ctrl_init_rec
141      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
142    o pkg/seaice/seaice_growth.F
143      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
144        remove then obsolete STORE directives
145      - fix STORE directives for tice and tices, so that only the
146        appropriate part of the fields are stored (and not the entire
147        field); update global_ocean.cs32x15.seaice AD output.
148      - cosmetic changes: adjust CPP flags and indentation for better
149        legibilty
150    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
151      Chris Wilson)
152    o pkg/gmredi:
153       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
154       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
155    
156    checkpoint63  (2011/07/11)
157    o pkg/exch2:
158     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
159     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
160       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
161       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
162    o pkg/diagnostics:
163     - deal with pairs of post-processed diags which are computed together; in
164       particular, re-order list of diags within 1 file to save 2nd computation.
165     - add S/R to compute velocity stream-function (called after velocity-potential
166       calculation) from divergence free transport -> new diagnostics "PsiVEL".
167     - add parameter to select grid-point location where PsiVEL == 0.
168    o eesupp/src:
169       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
170       (specific S/R needed with exch2 topology - for now, just print an error msg)
171    o pkg/shelfice
172     - Implement friction velocity-dependent transfer coefficients following
173       Holland and Jenkins, JPO, 1999
174       Original code by M. Losch with small modifs.
175       Enable with CPP option SHI_ALLOW_GAMMAFRICT
176       and runtime flag SHELFICEuseGammaFrict
177    o verification lab_sea & global_ocean.cs32x15:
178     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
179       does not miss some dependencies (but is slower) and also works with many files
180       (default makedepend limitation for AD built).
181     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
182    o pkg/diagnostics:
183     - add run-time parameter "useMissingValue" (def=False) to fill land-point
184        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
185       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
186     - Extend the use of "missing_value" setting from data.diagnostics for the case
187       of counter-diagnostics (where fraction-weight is zero). This applies both to
188       MNC and MDS output files.
189    o pkg/seaice/seaice_growth.F:
190      - add 'a priori' cap of latent heat flux based on actual mass considerations
191        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
192        non-legacy seaice_solve4temp.
193      - add diagnostic of the residual sublimation freshwater flux (the freshwater
194        flux taken from the ocean if the total actual latent heat fluxes exceed
195        the maximum)
196      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
197       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
198      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
199       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
200      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
201      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
202    o verification 1D_ocean_ice_column:
203       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
204       update results
205    o pkg/diagnostics:
206     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
207       which are not filled-up but computed from other diags ; In this case, the mate
208       diag points to the primary (filled-up) diag to used for post processing.
209     - Update Velocity-potential computation using post-processed diag framework.
210     ==> Change the ordering of fields and time-periods in MDS output file
211       when using periodic averaging: now writes one time record with the full set
212       of fields for this time period, then the next time reccord (it used to be
213       one field with the full set of time records then the next field).
214         Note: this is now similar to NetCDF (MNC) output file. <==
215    
216    checkpoint62z (2011/06/21)
217    o adjoint monitor:
218     - Add adjoint monitor output for packages exf, seaice
219       and update relevant testreport output
220    o pkg/seaice:
221     - re-order diags inits so that they appear in order in available_diagnostics.log
222     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
223       area/heff/hsnow preceeding thermodynamic growth/melt.
224     - modified diag: SIdA; output actual effect, as the description states.
225     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
226     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
227       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
228        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
229     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
230     - added diagnostics for seaice generic tracers (SItr*).
231     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
232     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
233     I. Fenty: 18-Jun-2011:
234     Minor changes to seaice package:
235     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
236        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
237       - Differentiated "regularization variables" from "floor variables"
238        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
239        * hiceMin became SEAICE_hice_reg (old hiceMin)
240          (with _reg meaning regularization variable)
241       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
242        so as to ensure energy conservation when going between phases
243      - A22 was not used anywhere
244     2) Changed regularization procedure for heffActual and hsnowActual to ensure
245        well-boundedness and smooth adjoint in seaice_growth.F
246     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
247        because the old regularization always set heffActual >= 0.05 cm
248     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
249        on AREA when HEFF > 0.
250      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
251        requiring that DISABLE_AREA_FLOOR *not* be defined
252     Affected verifications:
253      - 1D_ocean_ice_column (output.txt output_adm.txt)
254      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
255    o pkg/diagnostics:
256      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
257      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
258        (was _RL, now integer) with option = 0 to retrieve all levels.
259      - add pieces of code to compute velocity potential at each level (new diagnostics
260        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
261        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
262      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
263        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
264        and in diagnostics_fract_fill.F (do not need a valid pointer for the
265        diagnostics counter-mate); check that definition of counter-diagnostic
266        includes a valid counter-mate (in diagnostics_set_levels.F).
267    o model/src (rStar):
268      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
269        affect solution only if z* with full pressure in EOS;
270        update output of test-exp global_ocean.90x40x15.
271    o pkg/seaice:
272      - introduce siEps=1e-5 parameter
273      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
274      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
275      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
276        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
277        as well as ice cover age and ridging index (attached to AREA).
278        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
279        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
280        Up to SItrMaxNum=3 tracers can be used simultaneously.
281    o pkg/salt_plume:
282      -introduce SPsalFRAC run time parameter that sets the fraction of the
283       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
284       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
285    o model debug options:
286      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
287        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
288      - Refine debug-msg printing selection (3 new levels):
289        debugMode  : controls printing of debug messages (sequence of S/R calls).
290        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
291         debLevZero =  0 ; /* level of disabled aux. msg printing */
292         debLevA =  1 ; /* level of minimum  aux. msg printing */
293         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
294         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
295         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
296         debLevE =  5 ; /* level of extensive debug printing */
297        New debugLevel default: with default debugMode value (=F),
298          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
299          and if debugMode=T, default debugLevel = 4 (debLevD).
300        Relation with previous settings:
301         debLevB (=2) corresponds to former debLevA (=1)
302         debLevD (=4) corresponds to former debLevB (=2)
303        Note:
304         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
305         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
306            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
307      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
308        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
309    o pkg/obcs:
310      - change OBCSfixTopo default from True to False (should not change the results);
311        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
312    o pkg/thsice:
313      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
314        2nd layer seaice sublimation (unlikely to happen)
315      - use Interior mask for OBCS in thsice_advection.F (similar to what is
316        done in gad_advection & seaice_advection).
317    o adjoint:
318      bug fix spotted by Gael Forget:
319      seaice_advection and thsice_advection still had
320      legacy CPP options to avoid CS corner updates for adjoint
321    o pkg/seaice:
322      => Change some of the defaults (2011/05/29):
323         - change SEAICEuseFluxForm default (from False to True)
324         - change DIFF1 default (from 0.004 m/s to 0. m/s)
325         And print warnings if DIFF1 is not set in data.seaice and centered
326          avection scheme is used without any diffusion.
327      also:
328      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
329      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
330      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
331        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
332        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
333      update results of test exp.:
334         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
335             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
336             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
337         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
338         seaice_obcs: output (SEAICEuseFluxForm=T)
339      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
340          for standard fwd & AD lab_sea tests (to keep the same output).
341    o pkg/seaice/seaice_growth.F:
342      - use Ian Fenty's capping formulas for actual ice
343      thickness thoughout EVOLUTION branch.
344      - put treatment pathological case #2) in CPP brackets
345      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
346      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
347    o pkg/seaice:
348      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
349      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
350      also pass fac as a param, which can be 1. (to update the tendency
351      field) or the time step (to update the field itself).
352      - seaice_advdiff.F: for multidim, call seaice_diffusion with
353      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
354      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
355      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
356      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
357    o pkg/seaice:
358      diffusion with centered advection scheme (diffus.F & advect.F):
359      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
360        to just compute the laplacian of input-field.
361      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
362      - fix flux-form version in diffus.F to conserve tracer.
363      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
364       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
365    
366    checkpoint62y (2011/05/26)
367    o pkg/seaice:
368     - seaice_growth.F : in EVOLUTION branch, always include
369       a_QSWbyATM_cover in qnet (as it should be).
370     - verification/global_ocean.cs32x15 : update results accordingly
371       (output.seaice.txt output_adm.seaice.txt).
372    o pkg/seaice + obcs:
373     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
374       equivalent of assuming no tracer gradient outside the OB region.
375       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
376     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
377       after changes above);
378     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
379       only at OB location (instead of over a band of OLx width).
380    o pkg/seaice:
381     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
382       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
383    o pkg/obcs:
384      - split header file "OBCS.h" into 4 separated files:
385        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
386       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
387         (contain no conditional statement which depends on OBCS options).
388      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
389        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
390    o ctrl, cost, grdchk & autodiff pkgs:
391      - make options file more standard (like other {PKG}_OPTIONS.h file but
392        with AD_CONFIG.h); clean-up some of the included header files.
393    o pkg/obcs:
394      - do not mask tracer when applying OB (tracer == 0 could generate problems)
395      - apply tracer OB values to tracer field only at OB location (instead of
396        over a band of OLx width)
397      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
398      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
399        obcs_apply_tloc.F & obcs_apply_sloc.F
400    o obcs in model/src:
401      - call OBCS_APPLY_W only if NonHydrostatic.
402      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
403      - reset dEtaHdt and wVel to zero outside OB interior region ;
404      - leave tracer unchanged outside OB interior region: This has no effect
405        on the solution but just to prevent unrealistic tracer value outside OB.
406      - zero out velocity outside OB interior region: This has no effect on
407        the solution but just to prevent unrealistic velocity outside OB.
408    o obcs and non-lin free-surf:
409       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
410       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
411       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
412       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
413       update results of test-exp. exp4(nlfs).
414    o exp4 (nlfs) test-exp:
415       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
416       with NonLin-FreeSurf); update output.nlfs.txt
417    o obcs and 2d/3d solver norm:
418       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
419       and outside OB interior region (will allow to place OB further inside the
420       domain). Depending on the domain, can affects cg2d-Norm (previous
421       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
422       and cg3d-Norm (previous Norm was computed before canceling OB terms),
423       e.g. in tutorial_plume_on_slope.
424      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
425    o pkg rbcs:
426      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
427      - add capability to apply relaxation to horizontal velocity uVel & vVel.
428    o pkg/grdchk: add gradient check for control variable xx_shifwflx
429    o pkg/shelfice/shelfice_init_fixed.F
430      fix CPP-flag combinations
431    o pkg/seaice: Merge iceage code of Pierre Rampal
432      * update/change/correct ice age calculations
433      * add age updates for pathological cases
434      Probably needs more testing...
435    
436    checkpoint62x (2011/05/13)
437    o pkg/mom_vecinv:
438       high-order vorticity scheme: use interior masks (maskInW & S)
439       to zero-out (outside OB) gradient of vorticity.
440    o verification exp.:
441       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
442       hs94.128x64x5 and seaice_obcs ; update results.
443    o pkg/obcs:
444      fix bug in OBeta for YZ sections in obcs_exf_load.F
445    o pkg/ctrl, pkg/shelfice, and optim:
446      - add new control variable xx_shifwflx (fresh water flux underneath ice
447        shelves). This is almost as tedious as obcs-ctrl, because the
448        variables needs its own mask.
449      - add a cost function term that penalizes the deviation of xx_shifwflx
450        from the first guess (zero) in analogy to other control variables
451    o pkg/shelfice:
452      - start basic adjoint
453    o pkg/ctrl:
454      - remove extra 2D field "for good measure" when initializing in
455        ctrl_set_globfld_[xy/xz/yz].F
456      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
457      - improve error messages in ctrl_set_unpack_*
458    o OBC implementation in momentum:
459       use interior masks (maskInC,W & S) in momentum S/R:
460       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
461       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
462       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
463       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
464       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
465        (and also with Leith/Smagorinsky harmonic-viscosity).
466       Update output of experiment dome and exp4 (+nlfs).
467    o exp4 test-exp:
468      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
469        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
470        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
471        time-varying OB at Western-side for wVel (NonHyd); update output.
472      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
473        and biharmonic-viscosity ; also use prescribed time varying OB.
474    o pkg/obcs:
475      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
476    o model/src:
477      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
478      - initialise startTime & nIter0 with unlikely values: allows to set one
479        from the other without ambiguity.
480    o seaice_obcs test-exp.:
481      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
482    o pkg/obcs:
483      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
484        no longer needed with maskInC,W,S in pkg/generic_advdiff.
485    o pkg/seaice:
486      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
487        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
488      - fixed bug in the initialization of sea ice salinity variable HSALT
489        in seaice_init_varia.F  (removed dependence on ICE2WATR)
490    o fizhi-cs test exp.:
491       switch reference output convention for these 2 non-standard test-exp,
492        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
493          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
494       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
495    o model/inc:
496      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
497        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
498    o pkg/seaice:
499      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
500    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
501      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
502        and initial HSALT
503    
504    checkpoint62w (2011/04/26)
505    o pkg/mom_fluxform:
506      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
507      - use parameter "sideDragFactor" in no-slip BC side-drag part.
508      - update output of exp. global_ocean.90x40x15
509    o pkg/mom_vecinv:
510      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
511    o update seaice exp.:
512      use more consistent parameter values (remove "backward compatability only":
513       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
514      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
515       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
516    o update test-exp global_ocean.90x40x15:
517      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
518      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
519      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
520      o turn on zStar & viscA4 in standard set-up (dir input/)
521        and update output files: output.txt & output.dwnslp.txt
522    o new AD-test experiment: obcs_ctrl
523      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
524    o pkg/dic:
525      fix two bugs in handling water vapour pressure in carbonate chemistry
526      and air-sea fluxes. Found by Val Bennington and Galen McKinley
527      (add DIC Option = WATERVAP_BUG to recover old results)
528      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
529    o adding allowInteriorFreezing option to check for water below freezing point
530      at depth and bring the negative heat anomaly to the surface level
531    o pkgs _fields_load:
532      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
533      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
534        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
535        rbcs to get interpolation weights and time reccord number.
536      - fix multi-threading in aim_fields_load.F
537      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
538    o external_fields_load:
539      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
540       interpolation weights) to use in a periodic time-series ; do not divide by
541       time-step to convert to integer:
542       - this fixes case where externForcingPeriod is not multiple of time-step
543          (Thanks to Christopher L. Wolfe)
544       - this fixes case where externForcingPeriod is an odd multiple of time-step
545         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
546      store index of time-record which is currently loaded:
547       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
548       - needed for the adjoint but not yet used because of extensive recomputations;
549         (to be fixed soon)
550    
551    checkpoint62v (2011/04/02)
552    o verification/1D_ocean_ice_column added to test Ian Fenty's
553      pkg/seaice_growth.F modifications for improving sea ice code differentiability
554    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
555      (new velocity statistics after changing maskInW & maskInS definition)
556    o pkg/generic_advdiff with OBCS:
557      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
558      equivalent to assumption of no tracer gradient outside the OB region.
559      This will affect the results if using obcs+biharmonic diffusion.
560      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
561    o pkg/obcs:
562      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
563      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
564      in Interior region. No impact on solution but affects Velocity monitor stats.
565    o pkg/ptracers (adjoint)
566      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
567      tape file for each tracer
568    o model/inc/src and pkg/autodiff: add parameters that allow to turn
569      of parts of the adjoint code at run time. For now, there are only
570      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
571      parameters are set in data.pkg.
572      This is the lazy coward's version of doing this, but still useful for
573      debugging. In order to do it right, everything needs to be moved to
574      pkg/autodiff.
575    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
576      the end; this fixes the adjoint balancing code for open boundaries.
577    o pkg/ctrl:
578      - change behavior of xx_${varname}period to be analogous to exf-conventions:
579        xx_${varname}period =   0.,  means time-independent control part
580        xx_${varname}period = -12., means one-year-periodic monthly control part
581      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
582        clean up ctrl_init a little, remove unused variables
583      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
584      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
585    
586    checkpoint62u (2011/03/15)
587    o model/src:
588      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
589        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
590      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
591        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
592    o pkg/ctrl/obcs/ecco:
593      - remove obsolete, unused, and partially broken code:
594        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
595        ALLOW_CTRL_OBCS_BALANCE
596      - put a stop statement into ecco/cost_obcsvol.F, but also add
597        cost_obcsvol to ecco_ad_diff.list
598    o pkg/ecco: fix counting cost function contributions for obcs (code
599      by Matt M.) and diffkr for diagnostics
600    o pkg/ecco, pkg/ctrl, pkg/grdchk:
601      add cost penalty terms for initial uvel, vvel, eta controls
602      and I/O for prior error files
603    o pkg/mdsio:
604       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
605       (new argument) to check for tiled file in mdsioLocalDir : this fix the
606       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
607    o pkg/ctrl:
608     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
609       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
610       unused and superfluous variables
611     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
612    o pkg/ecco
613     - enable adjoint of Stevens OB
614    o pkg/ctrl/ecco/grdchk:
615      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
616        Fortunately, we do not have any tests for the numerous cpp-flagged
617        option of "obcs as control parameters" so we will never know
618        if this is an improvement (but at least now things compile).
619      - remove an obsolete initialization from ecco_cost_init_barfiles.F
620      - fix some problems within never used ifdefs to make the code compile
621    o pkg/obcs:
622     - Refine Interior mask definition to work with more complex OB (e.g.
623       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
624       read in Interior mask from file. Check if Interior mask is consistent
625       with OB list of indices.
626    o pkg/seaice
627     - beginning code for a seaice tracer package,
628       but currently only used for seaice age: SEAICE_AGE
629       SEAICE_num = 4
630       iTracer = 1: area-weighted ice age
631               = 2: volume-weighted ice age
632               = 3, 4: template for one-year vs. multi-year ice
633       data.seaice has new namelist SEAICE_PARM03 for arrays related to
634       SEAICE_num
635    
636    checkpoint62t (2011/03/05)
637    o pkg/obcs:
638     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
639       then normal component. This ensures that the normal component is set
640       correctly even when it conficts with tangential setting from an other OB.
641       Affects results of test-experiment seaice_obcs: update the output.txt
642    o pkg/obcs:
643     - add code to monitor statistics of dynamical fields at OB.
644     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
645       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
646       - change default: balance the Net inflow through all OB (instead of balancing
647         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
648     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
649       to match Nortern OB inflow (OBCS_balanceFacN=0).
650    o pkg/seaice:
651     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
652    o pkg/seaice (seaice_growth v 1.113):
653     - reverting seaice_growth to v 1.111 in order to have code with exact bit
654       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
655       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
656       runtime flag SEAICEareaFormula is kept but is inactive
657    o model/src:
658     - add new param to scale curvilinear grid distance and area when using
659       a different sphere radius from the grid-files.
660     - test/check multi-threads EXCH applied to local variable (cg2d_x)
661    o adjoint:
662     - enable adjoint of Stevens OB
663     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
664       (a bit delicate because of potentially modified adj. common block structure;
665       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
666    
667    checkpoint62s (2011/02/15)
668    o pkg/seaice (seaice_growth v 1.112):
669     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
670       computing the ice cover tendency from effective thickness tendencies. Include
671       Ian Fenty's formula.
672     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
673       SEAICEareaFormula.
674     - simplify notations for the various d_HEFF/d_AREA terms.
675    o pkg/gmredi:
676     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
677       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
678       add a verification test-run (front_relax.bvp) to test GM_useBVP.
679    o pkg/seaice (seaice_growth v 1.111):
680     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
681     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
682       also melt ice.
683    o pkg/seaice:
684     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
685     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
686    o pkg/cheapaml:
687     - from Nico Wienders: New version of this package.
688    o pkg/flt:
689     - add CPP options to prevent floats to re-enter the opposite side of
690       a periodic domain (default: keep periodicity)
691    o pkg/gmredi:
692     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
693       (needed for multi-dim advection).
694     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
695    o model/src:
696     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
697    o tutorial_tracer_adjsens
698     - extend to NLFS and replace maskC by hFacC
699       (change reference output accordingly)
700    
701    checkpoint62r (2011/01/24)
702    o testreport:
703     - add option -deloutp (-do) to remove output file after successful run
704     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
705       extract exact list of procs from this file ; adjust COMMAND by
706       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
707  o pkg/ecco: replace old ineffective way of penalizing deviations from  o pkg/ecco: replace old ineffective way of penalizing deviations from
708    first guess (of obcs) with code by Matt Mazloff    first guess (of obcs) with code by Matt Mazloff
709  o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without  o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
710    exf/cal    exf/cal
711    - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl    - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
712      and handle case of obcs?period == 0      and handle case of obcs?period == 0
713      Not affected by these changes: There is still an inconsistency in      Not affected by these changes: There is still an inconsistency in
714      the computation of start/endrec for the obcs variables for ALLOW_CAL      the computation of start/endrec for the obcs variables for ALLOW_CAL
715      defined (see comment by Menemenlis, 7-Mar-2003)      defined (see comment by Menemenlis, 7-Mar-2003)
716    - make S/R ctrl_get_gen_rec return something meaningful even if    - make S/R ctrl_get_gen_rec return something meaningful even if
717      ALLOW_CAL is not defined      ALLOW_CAL is not defined
718    - ctrl_getobcs?: simplify code so that it does not need to use    - ctrl_getobcs?: simplify code so that it does not need to use
719                     S/R exf_swapfields                     S/R exf_swapfields
720  o testreport:  o testreport:
721     allow to test MPI with different number of processors for each experiment:     allow to test MPI with different number of processors for each experiment:
# Line 24  o testreport: Line 724  o testreport:
724  o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:  o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
725    alleviate the need for additional 3D tapes when using    alleviate the need for additional 3D tapes when using
726    the non-inear free surface in the adjoint. This is done    the non-inear free surface in the adjoint. This is done
727    by adding an 'update' of hfacc etc. to their current    by adding an 'update' of hfacc etc. to their current
728    value at the beginning of forward_step.F.    value at the beginning of forward_step.F.
729  o pkg/seaice  o pkg/seaice
730    seaice_lsr: move stress-divergence computations out of outer pseudo-    seaice_lsr: move stress-divergence computations out of outer pseudo-
731    timestepping loop    timestepping loop
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