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revision 1.1361 by jmc, Wed Dec 29 16:41:28 2010 UTC revision 1.1507 by jmc, Wed Sep 28 13:39:54 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint63c (2011/09/28)
8    o pkg/ebm:
9      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
10        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
11    o pkg/seaice (SItracer pickup)
12    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
13      To be done:
14      - thorough testing of missing fields in S/R seaice_read_pickup
15      - thorough matching between generic tracers and specific fields used
16        (e.g. volume-weighted age, area-weighted age, salinity, ...)
17    o pkg/grdchk:
18      - all procs calculate and print finite-difference gradient (for testreport)
19      - change description output used by testreport;
20      - AD testing: also compare and report Finite-difference gradient;
21        => update all output_adm*.txt
22    o test exp. global_ocean_ebm:
23      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
24        and turn on exactConserve; update (fwd) output.
25    o pkg/seaice (LSR):
26      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
27      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
28        * identical results with non-CS topology (but save up to half of EXCH calls)
29        * no much changes in cs-32 verification tests since no ice at face edges
30         (differences due to convergence criteria, since nb of iterations changed)
31        * expect some differences on lat-lon-cap grid.
32        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
33    o pkg/exch2:
34      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
35        many tiles); until alternative coding is added, just add a stop.
36    o pkg/kpp:
37      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
38        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
39    o optfiles:
40      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
41        into corresponding standard one, which now support different build:
42        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
43      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
44    o pkg/obcs (seaice):
45      - add missing EXCH for uIce,vIce after applying OBCS;
46      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
47        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
48        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
49      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
50      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
51        and eedata.mth for MPI and mutlti-threaded testing.
52    o pkg/flt:
53      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
54      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
55      - fix pickup and trajectories + profiles output with multi-threads;
56      - add parameter to select group of fields to write along trajectory and
57        profile (default unchanged);
58      - only call PORT_RAND* function when flt_noise <> 0;
59      - add multi-threaded test for verification exp. flt_example.
60    o eesupp/src:
61      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
62      - USE_OMP_THREADING: check that number of threads (from eedata) matches
63        actual number (from env.var. setting).
64    o pkg/ebm:
65      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
66      - add multi-threaded test for verification exp. global_ocean_ebm
67    
68    checkpoint63b (2011/08/29)
69    o pkg/ebm:
70      - fix sign of runoff;
71      - update directly forcing fields (Qnet,EmPmR) to use standard
72        external_forcing_surf.F (remove ebm_forcing_surf.F);
73      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
74      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
75        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
76      - update global_ocean_ebm parameters file data and update output (fwd+ad).
77    o verification/matrix_example:
78      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
79        MPI and mutlti-threaded testing.
80    o pkg/matrix:
81      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
82      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
83      - fix for multi-threaded (remove DATA statement);
84      - use standard DIFFERENT_MULTIPLE function;
85      - add MATRIX_OPTIONS.h
86    o verification/matrix_example:
87       To allow to split the domain in several tiles, change the domain size
88        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
89        Western side) of land points.
90    o (*_)write_pickup:
91      - fix few bugs in mypackage_read/write_pickup.F
92      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
93        array of length 1 (was caught by compiler syntax-check).
94    o pkg/diagnostics (velocity potential solver):
95      - fix initialisation of main diagonal matrix (for overlap values)
96    o tools/build_options:
97      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
98        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
99      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
100        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
101        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
102        and use "-devel" testreport option for standard testing on baudelaire.
103    o pkg/grdchk:
104      - Assume that all gradient-check position are within the same tile
105        corresponding to global indices (iGloTile,jGloTile) and that
106        positions (i,j indices or nbeg) are local to this tile;
107      - set tile local-indices and proc. number according to tile global-indices;
108      - remove grdchkwhichproc from namelist (retired param);
109      - send adjoint gradient to all procs so that all procs print it to STDOUT;
110      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
111    o adding package bbl (Bottom Boundary Layer)
112      description in MITgcm/pkg/bbl/bbl_description.tex
113      example/test experiment in MITgcm_contrib/bbl
114    o adjoint verifications
115      - changed 5 experiments to multi-tiles
116        * global_ocean.90x40x15
117        * obcs_ctrl
118        * offline_exf_seaice
119        * tutorial_dic_adjoffline
120        * tutorial_tracer_adjsens
121        changed reference output for those that crossed tile boundaries
122        (changed choices of gradient check positions)
123      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
124      - temporary bug fix in grdchk_loc.F for obcs
125    o genmake2 & testreport
126      - add target "obj" (just for OBJFILES files) to Makefile;
127      - add option to specify FEXTRAFLAGS on command line.
128    o pkg/mypackage:
129      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
130    
131    checkpoint63a (2011/08/02)
132    o pkg/diagnostics (velocity potential):
133      - fix velocity-potential calculation when using OBCS: balance net inflow
134        at each level (new S/R OBCS_DIAG_BALANCE).
135      - fix some of the problems with OBCS in stream-function calculation.
136    o pkg/exf/exf_readparms.F
137      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
138        EXF_NML_OBCS) more consistent, so that you need not have these lists
139        in data.exf when they are not used.
140    o optim/optim_readdata.F:
141      - add some output about obcs variables that might help debugging
142      - add a check about nvarlength
143    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
144    o pkg/diagnostics (velocity potential):
145      - fix mask for OBCS (still problems in stream-function with OBCS);
146      - add specific parameter (default = main code CG2D params) for solver;
147      - in case of poor convergence, use solution corresponding to lowest residual.
148    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
149      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
150      and should be avoided where possible.
151    o model/src (rStar):
152      - include r* effect on reference-state (PhiRef) in totPhiHyd
153        (so that it's really the potential anomaly at the cell center);
154        affect solution only if z* with full pressure in EOS.
155      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
156        update output (because of z* in totPhiHyd and viscA4 changes);
157      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
158        @ constant r) until interpolation at constant r is implemented.
159    o pkg/diagnostics
160      - fix RCENTER diagnostics in case cell center is not at interface middle
161    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
162      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
163      that THETA and SALT are "conservative temperature" and "absolute
164      salinity"
165    o pkg/ctrl
166      - fix computation of endrec in s/r ctrl_init_rec
167      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
168    o pkg/seaice/seaice_growth.F
169      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
170        remove then obsolete STORE directives
171      - fix STORE directives for tice and tices, so that only the
172        appropriate part of the fields are stored (and not the entire
173        field); update global_ocean.cs32x15.seaice AD output.
174      - cosmetic changes: adjust CPP flags and indentation for better
175        legibilty
176    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
177      Chris Wilson)
178    o pkg/gmredi:
179       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
180       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
181    
182    checkpoint63  (2011/07/11)
183    o pkg/exch2:
184     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
185     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
186       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
187       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
188    o pkg/diagnostics:
189     - deal with pairs of post-processed diags which are computed together; in
190       particular, re-order list of diags within 1 file to save 2nd computation.
191     - add S/R to compute velocity stream-function (called after velocity-potential
192       calculation) from divergence free transport -> new diagnostics "PsiVEL".
193     - add parameter to select grid-point location where PsiVEL == 0.
194    o eesupp/src:
195       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
196       (specific S/R needed with exch2 topology - for now, just print an error msg)
197    o pkg/shelfice
198     - Implement friction velocity-dependent transfer coefficients following
199       Holland and Jenkins, JPO, 1999
200       Original code by M. Losch with small modifs.
201       Enable with CPP option SHI_ALLOW_GAMMAFRICT
202       and runtime flag SHELFICEuseGammaFrict
203    o verification lab_sea & global_ocean.cs32x15:
204     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
205       does not miss some dependencies (but is slower) and also works with many files
206       (default makedepend limitation for AD built).
207     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
208    o pkg/diagnostics:
209     - add run-time parameter "useMissingValue" (def=False) to fill land-point
210        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
211       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
212     - Extend the use of "missing_value" setting from data.diagnostics for the case
213       of counter-diagnostics (where fraction-weight is zero). This applies both to
214       MNC and MDS output files.
215    o pkg/seaice/seaice_growth.F:
216      - add 'a priori' cap of latent heat flux based on actual mass considerations
217        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
218        non-legacy seaice_solve4temp.
219      - add diagnostic of the residual sublimation freshwater flux (the freshwater
220        flux taken from the ocean if the total actual latent heat fluxes exceed
221        the maximum)
222      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
223       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
224      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
225       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
226      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
227      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
228    o verification 1D_ocean_ice_column:
229       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
230       update results
231    o pkg/diagnostics:
232     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
233       which are not filled-up but computed from other diags ; In this case, the mate
234       diag points to the primary (filled-up) diag to used for post processing.
235     - Update Velocity-potential computation using post-processed diag framework.
236     ==> Change the ordering of fields and time-periods in MDS output file
237       when using periodic averaging: now writes one time record with the full set
238       of fields for this time period, then the next time reccord (it used to be
239       one field with the full set of time records then the next field).
240         Note: this is now similar to NetCDF (MNC) output file. <==
241    
242    checkpoint62z (2011/06/21)
243    o adjoint monitor:
244     - Add adjoint monitor output for packages exf, seaice
245       and update relevant testreport output
246    o pkg/seaice:
247     - re-order diags inits so that they appear in order in available_diagnostics.log
248     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
249       area/heff/hsnow preceeding thermodynamic growth/melt.
250     - modified diag: SIdA; output actual effect, as the description states.
251     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
252     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
253       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
254        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
255     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
256     - added diagnostics for seaice generic tracers (SItr*).
257     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
258     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
259     I. Fenty: 18-Jun-2011:
260     Minor changes to seaice package:
261     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
262        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
263       - Differentiated "regularization variables" from "floor variables"
264        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
265        * hiceMin became SEAICE_hice_reg (old hiceMin)
266          (with _reg meaning regularization variable)
267       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
268        so as to ensure energy conservation when going between phases
269      - A22 was not used anywhere
270     2) Changed regularization procedure for heffActual and hsnowActual to ensure
271        well-boundedness and smooth adjoint in seaice_growth.F
272     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
273        because the old regularization always set heffActual >= 0.05 cm
274     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
275        on AREA when HEFF > 0.
276      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
277        requiring that DISABLE_AREA_FLOOR *not* be defined
278     Affected verifications:
279      - 1D_ocean_ice_column (output.txt output_adm.txt)
280      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
281    o pkg/diagnostics:
282      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
283      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
284        (was _RL, now integer) with option = 0 to retrieve all levels.
285      - add pieces of code to compute velocity potential at each level (new diagnostics
286        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
287        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
288      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
289        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
290        and in diagnostics_fract_fill.F (do not need a valid pointer for the
291        diagnostics counter-mate); check that definition of counter-diagnostic
292        includes a valid counter-mate (in diagnostics_set_levels.F).
293    o model/src (rStar):
294      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
295        affect solution only if z* with full pressure in EOS;
296        update output of test-exp global_ocean.90x40x15.
297    o pkg/seaice:
298      - introduce siEps=1e-5 parameter
299      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
300      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
301      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
302        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
303        as well as ice cover age and ridging index (attached to AREA).
304        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
305        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
306        Up to SItrMaxNum=3 tracers can be used simultaneously.
307    o pkg/salt_plume:
308      -introduce SPsalFRAC run time parameter that sets the fraction of the
309       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
310       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
311    o model debug options:
312      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
313        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
314      - Refine debug-msg printing selection (3 new levels):
315        debugMode  : controls printing of debug messages (sequence of S/R calls).
316        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
317         debLevZero =  0 ; /* level of disabled aux. msg printing */
318         debLevA =  1 ; /* level of minimum  aux. msg printing */
319         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
320         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
321         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
322         debLevE =  5 ; /* level of extensive debug printing */
323        New debugLevel default: with default debugMode value (=F),
324          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
325          and if debugMode=T, default debugLevel = 4 (debLevD).
326        Relation with previous settings:
327         debLevB (=2) corresponds to former debLevA (=1)
328         debLevD (=4) corresponds to former debLevB (=2)
329        Note:
330         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
331         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
332            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
333      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
334        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
335    o pkg/obcs:
336      - change OBCSfixTopo default from True to False (should not change the results);
337        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
338    o pkg/thsice:
339      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
340        2nd layer seaice sublimation (unlikely to happen)
341      - use Interior mask for OBCS in thsice_advection.F (similar to what is
342        done in gad_advection & seaice_advection).
343    o adjoint:
344      bug fix spotted by Gael Forget:
345      seaice_advection and thsice_advection still had
346      legacy CPP options to avoid CS corner updates for adjoint
347    o pkg/seaice:
348      => Change some of the defaults (2011/05/29):
349         - change SEAICEuseFluxForm default (from False to True)
350         - change DIFF1 default (from 0.004 m/s to 0. m/s)
351         And print warnings if DIFF1 is not set in data.seaice and centered
352          avection scheme is used without any diffusion.
353      also:
354      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
355      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
356      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
357        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
358        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
359      update results of test exp.:
360         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
361             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
362             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
363         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
364         seaice_obcs: output (SEAICEuseFluxForm=T)
365      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
366          for standard fwd & AD lab_sea tests (to keep the same output).
367    o pkg/seaice/seaice_growth.F:
368      - use Ian Fenty's capping formulas for actual ice
369      thickness thoughout EVOLUTION branch.
370      - put treatment pathological case #2) in CPP brackets
371      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
372      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
373    o pkg/seaice:
374      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
375      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
376      also pass fac as a param, which can be 1. (to update the tendency
377      field) or the time step (to update the field itself).
378      - seaice_advdiff.F: for multidim, call seaice_diffusion with
379      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
380      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
381      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
382      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
383    o pkg/seaice:
384      diffusion with centered advection scheme (diffus.F & advect.F):
385      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
386        to just compute the laplacian of input-field.
387      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
388      - fix flux-form version in diffus.F to conserve tracer.
389      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
390       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
391    
392    checkpoint62y (2011/05/26)
393    o pkg/seaice:
394     - seaice_growth.F : in EVOLUTION branch, always include
395       a_QSWbyATM_cover in qnet (as it should be).
396     - verification/global_ocean.cs32x15 : update results accordingly
397       (output.seaice.txt output_adm.seaice.txt).
398    o pkg/seaice + obcs:
399     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
400       equivalent of assuming no tracer gradient outside the OB region.
401       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
402     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
403       after changes above);
404     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
405       only at OB location (instead of over a band of OLx width).
406    o pkg/seaice:
407     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
408       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
409    o pkg/obcs:
410      - split header file "OBCS.h" into 4 separated files:
411        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
412       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
413         (contain no conditional statement which depends on OBCS options).
414      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
415        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
416    o ctrl, cost, grdchk & autodiff pkgs:
417      - make options file more standard (like other {PKG}_OPTIONS.h file but
418        with AD_CONFIG.h); clean-up some of the included header files.
419    o pkg/obcs:
420      - do not mask tracer when applying OB (tracer == 0 could generate problems)
421      - apply tracer OB values to tracer field only at OB location (instead of
422        over a band of OLx width)
423      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
424      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
425        obcs_apply_tloc.F & obcs_apply_sloc.F
426    o obcs in model/src:
427      - call OBCS_APPLY_W only if NonHydrostatic.
428      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
429      - reset dEtaHdt and wVel to zero outside OB interior region ;
430      - leave tracer unchanged outside OB interior region: This has no effect
431        on the solution but just to prevent unrealistic tracer value outside OB.
432      - zero out velocity outside OB interior region: This has no effect on
433        the solution but just to prevent unrealistic velocity outside OB.
434    o obcs and non-lin free-surf:
435       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
436       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
437       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
438       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
439       update results of test-exp. exp4(nlfs).
440    o exp4 (nlfs) test-exp:
441       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
442       with NonLin-FreeSurf); update output.nlfs.txt
443    o obcs and 2d/3d solver norm:
444       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
445       and outside OB interior region (will allow to place OB further inside the
446       domain). Depending on the domain, can affects cg2d-Norm (previous
447       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
448       and cg3d-Norm (previous Norm was computed before canceling OB terms),
449       e.g. in tutorial_plume_on_slope.
450      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
451    o pkg rbcs:
452      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
453      - add capability to apply relaxation to horizontal velocity uVel & vVel.
454    o pkg/grdchk: add gradient check for control variable xx_shifwflx
455    o pkg/shelfice/shelfice_init_fixed.F
456      fix CPP-flag combinations
457    o pkg/seaice: Merge iceage code of Pierre Rampal
458      * update/change/correct ice age calculations
459      * add age updates for pathological cases
460      Probably needs more testing...
461    
462    checkpoint62x (2011/05/13)
463    o pkg/mom_vecinv:
464       high-order vorticity scheme: use interior masks (maskInW & S)
465       to zero-out (outside OB) gradient of vorticity.
466    o verification exp.:
467       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
468       hs94.128x64x5 and seaice_obcs ; update results.
469    o pkg/obcs:
470      fix bug in OBeta for YZ sections in obcs_exf_load.F
471    o pkg/ctrl, pkg/shelfice, and optim:
472      - add new control variable xx_shifwflx (fresh water flux underneath ice
473        shelves). This is almost as tedious as obcs-ctrl, because the
474        variables needs its own mask.
475      - add a cost function term that penalizes the deviation of xx_shifwflx
476        from the first guess (zero) in analogy to other control variables
477    o pkg/shelfice:
478      - start basic adjoint
479    o pkg/ctrl:
480      - remove extra 2D field "for good measure" when initializing in
481        ctrl_set_globfld_[xy/xz/yz].F
482      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
483      - improve error messages in ctrl_set_unpack_*
484    o OBC implementation in momentum:
485       use interior masks (maskInC,W & S) in momentum S/R:
486       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
487       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
488       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
489       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
490       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
491        (and also with Leith/Smagorinsky harmonic-viscosity).
492       Update output of experiment dome and exp4 (+nlfs).
493    o exp4 test-exp:
494      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
495        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
496        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
497        time-varying OB at Western-side for wVel (NonHyd); update output.
498      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
499        and biharmonic-viscosity ; also use prescribed time varying OB.
500    o pkg/obcs:
501      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
502    o model/src:
503      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
504      - initialise startTime & nIter0 with unlikely values: allows to set one
505        from the other without ambiguity.
506    o seaice_obcs test-exp.:
507      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
508    o pkg/obcs:
509      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
510        no longer needed with maskInC,W,S in pkg/generic_advdiff.
511    o pkg/seaice:
512      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
513        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
514      - fixed bug in the initialization of sea ice salinity variable HSALT
515        in seaice_init_varia.F  (removed dependence on ICE2WATR)
516    o fizhi-cs test exp.:
517       switch reference output convention for these 2 non-standard test-exp,
518        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
519          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
520       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
521    o model/inc:
522      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
523        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
524    o pkg/seaice:
525      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
526    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
527      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
528        and initial HSALT
529    
530    checkpoint62w (2011/04/26)
531    o pkg/mom_fluxform:
532      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
533      - use parameter "sideDragFactor" in no-slip BC side-drag part.
534      - update output of exp. global_ocean.90x40x15
535    o pkg/mom_vecinv:
536      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
537    o update seaice exp.:
538      use more consistent parameter values (remove "backward compatability only":
539       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
540      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
541       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
542    o update test-exp global_ocean.90x40x15:
543      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
544      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
545      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
546      o turn on zStar & viscA4 in standard set-up (dir input/)
547        and update output files: output.txt & output.dwnslp.txt
548    o new AD-test experiment: obcs_ctrl
549      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
550    o pkg/dic:
551      fix two bugs in handling water vapour pressure in carbonate chemistry
552      and air-sea fluxes. Found by Val Bennington and Galen McKinley
553      (add DIC Option = WATERVAP_BUG to recover old results)
554      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
555    o adding allowInteriorFreezing option to check for water below freezing point
556      at depth and bring the negative heat anomaly to the surface level
557    o pkgs _fields_load:
558      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
559      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
560        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
561        rbcs to get interpolation weights and time reccord number.
562      - fix multi-threading in aim_fields_load.F
563      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
564    o external_fields_load:
565      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
566       interpolation weights) to use in a periodic time-series ; do not divide by
567       time-step to convert to integer:
568       - this fixes case where externForcingPeriod is not multiple of time-step
569          (Thanks to Christopher L. Wolfe)
570       - this fixes case where externForcingPeriod is an odd multiple of time-step
571         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
572      store index of time-record which is currently loaded:
573       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
574       - needed for the adjoint but not yet used because of extensive recomputations;
575         (to be fixed soon)
576    
577    checkpoint62v (2011/04/02)
578    o verification/1D_ocean_ice_column added to test Ian Fenty's
579      pkg/seaice_growth.F modifications for improving sea ice code differentiability
580    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
581      (new velocity statistics after changing maskInW & maskInS definition)
582    o pkg/generic_advdiff with OBCS:
583      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
584      equivalent to assumption of no tracer gradient outside the OB region.
585      This will affect the results if using obcs+biharmonic diffusion.
586      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
587    o pkg/obcs:
588      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
589      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
590      in Interior region. No impact on solution but affects Velocity monitor stats.
591    o pkg/ptracers (adjoint)
592      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
593      tape file for each tracer
594    o model/inc/src and pkg/autodiff: add parameters that allow to turn
595      of parts of the adjoint code at run time. For now, there are only
596      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
597      parameters are set in data.pkg.
598      This is the lazy coward's version of doing this, but still useful for
599      debugging. In order to do it right, everything needs to be moved to
600      pkg/autodiff.
601    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
602      the end; this fixes the adjoint balancing code for open boundaries.
603    o pkg/ctrl:
604      - change behavior of xx_${varname}period to be analogous to exf-conventions:
605        xx_${varname}period =   0.,  means time-independent control part
606        xx_${varname}period = -12., means one-year-periodic monthly control part
607      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
608        clean up ctrl_init a little, remove unused variables
609      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
610      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
611    
612    checkpoint62u (2011/03/15)
613    o model/src:
614      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
615        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
616      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
617        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
618    o pkg/ctrl/obcs/ecco:
619      - remove obsolete, unused, and partially broken code:
620        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
621        ALLOW_CTRL_OBCS_BALANCE
622      - put a stop statement into ecco/cost_obcsvol.F, but also add
623        cost_obcsvol to ecco_ad_diff.list
624    o pkg/ecco: fix counting cost function contributions for obcs (code
625      by Matt M.) and diffkr for diagnostics
626    o pkg/ecco, pkg/ctrl, pkg/grdchk:
627      add cost penalty terms for initial uvel, vvel, eta controls
628      and I/O for prior error files
629    o pkg/mdsio:
630       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
631       (new argument) to check for tiled file in mdsioLocalDir : this fix the
632       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
633    o pkg/ctrl:
634     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
635       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
636       unused and superfluous variables
637     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
638    o pkg/ecco
639     - enable adjoint of Stevens OB
640    o pkg/ctrl/ecco/grdchk:
641      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
642        Fortunately, we do not have any tests for the numerous cpp-flagged
643        option of "obcs as control parameters" so we will never know
644        if this is an improvement (but at least now things compile).
645      - remove an obsolete initialization from ecco_cost_init_barfiles.F
646      - fix some problems within never used ifdefs to make the code compile
647    o pkg/obcs:
648     - Refine Interior mask definition to work with more complex OB (e.g.
649       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
650       read in Interior mask from file. Check if Interior mask is consistent
651       with OB list of indices.
652    o pkg/seaice
653     - beginning code for a seaice tracer package,
654       but currently only used for seaice age: SEAICE_AGE
655       SEAICE_num = 4
656       iTracer = 1: area-weighted ice age
657               = 2: volume-weighted ice age
658               = 3, 4: template for one-year vs. multi-year ice
659       data.seaice has new namelist SEAICE_PARM03 for arrays related to
660       SEAICE_num
661    
662    checkpoint62t (2011/03/05)
663    o pkg/obcs:
664     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
665       then normal component. This ensures that the normal component is set
666       correctly even when it conficts with tangential setting from an other OB.
667       Affects results of test-experiment seaice_obcs: update the output.txt
668    o pkg/obcs:
669     - add code to monitor statistics of dynamical fields at OB.
670     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
671       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
672       - change default: balance the Net inflow through all OB (instead of balancing
673         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
674     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
675       to match Nortern OB inflow (OBCS_balanceFacN=0).
676    o pkg/seaice:
677     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
678    o pkg/seaice (seaice_growth v 1.113):
679     - reverting seaice_growth to v 1.111 in order to have code with exact bit
680       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
681       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
682       runtime flag SEAICEareaFormula is kept but is inactive
683    o model/src:
684     - add new param to scale curvilinear grid distance and area when using
685       a different sphere radius from the grid-files.
686     - test/check multi-threads EXCH applied to local variable (cg2d_x)
687    o adjoint:
688     - enable adjoint of Stevens OB
689     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
690       (a bit delicate because of potentially modified adj. common block structure;
691       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
692    
693    checkpoint62s (2011/02/15)
694    o pkg/seaice (seaice_growth v 1.112):
695     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
696       computing the ice cover tendency from effective thickness tendencies. Include
697       Ian Fenty's formula.
698     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
699       SEAICEareaFormula.
700     - simplify notations for the various d_HEFF/d_AREA terms.
701    o pkg/gmredi:
702     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
703       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
704       add a verification test-run (front_relax.bvp) to test GM_useBVP.
705    o pkg/seaice (seaice_growth v 1.111):
706     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
707     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
708       also melt ice.
709    o pkg/seaice:
710     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
711     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
712    o pkg/cheapaml:
713     - from Nico Wienders: New version of this package.
714    o pkg/flt:
715     - add CPP options to prevent floats to re-enter the opposite side of
716       a periodic domain (default: keep periodicity)
717    o pkg/gmredi:
718     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
719       (needed for multi-dim advection).
720     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
721    o model/src:
722     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
723    o tutorial_tracer_adjsens
724     - extend to NLFS and replace maskC by hFacC
725       (change reference output accordingly)
726    
727    checkpoint62r (2011/01/24)
728    o testreport:
729     - add option -deloutp (-do) to remove output file after successful run
730     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
731       extract exact list of procs from this file ; adjust COMMAND by
732       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
733    o pkg/ecco: replace old ineffective way of penalizing deviations from
734      first guess (of obcs) with code by Matt Mazloff
735    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
736      exf/cal
737      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
738        and handle case of obcs?period == 0
739        Not affected by these changes: There is still an inconsistency in
740        the computation of start/endrec for the obcs variables for ALLOW_CAL
741        defined (see comment by Menemenlis, 7-Mar-2003)
742      - make S/R ctrl_get_gen_rec return something meaningful even if
743        ALLOW_CAL is not defined
744      - ctrl_getobcs?: simplify code so that it does not need to use
745                       S/R exf_swapfields
746    o testreport:
747       allow to test MPI with different number of processors for each experiment:
748       create file "SIZE.h.mpi" in each build dir.
749       Note: update of "-command" argument not yet implemented.
750    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
751      alleviate the need for additional 3D tapes when using
752      the non-inear free surface in the adjoint. This is done
753      by adding an 'update' of hfacc etc. to their current
754      value at the beginning of forward_step.F.
755    o pkg/seaice
756      seaice_lsr: move stress-divergence computations out of outer pseudo-
757      timestepping loop
758    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
759      up, so that the calls of the ctrl_* subroutines are really at the end
760      of the routine.
761    o pkg/gmredi:
762      allow to specify a 2-D horizontal map and a 1-D vertical profil
763      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
764    o pkg/seaice:
765      move lsr iterations from seaice_dynsolver to seaice_lsr.
766    o pkg/seaice:
767      reduce memory footprint of seaice mutldim advection tapes,
768      by using a 2D tape independent of the generic_advdiff ones,
769      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
770    
771  checkpoint62q (2010/12/29)  checkpoint62q (2010/12/29)
772  o model/src:  o model/src:
773    - check horizontal grid-spacing for unset or zero/negative values.    - check horizontal grid-spacing for unset or zero/negative values.
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