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revision 1.1444 by jmc, Fri May 27 00:44:49 2011 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:  o pkg/seaice:
384    diffusion with centered advection scheme (diffus.F & advect.F):    diffusion with centered advection scheme (diffus.F & advect.F):
385    - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)    - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
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