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revision 1.1445 by gforget, Fri May 27 23:28:39 2011 UTC revision 1.1494 by jmc, Thu Aug 25 22:47:03 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 verification/matrix_example:
8       To allow to split the domain in several tiles, change the domain size
9        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
10        Western side) of land points.
11    o (*_)write_pickup:
12      - fix few bugs in mypackage_read/write_pickup.F
13      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
14        array of length 1 (was caught by compiler syntax-check).
15    o pkg/diagnostics (velocity potential solver):
16      - fix initialisation of main diagonal matrix (for overlap values)
17    o tools/build_options:
18      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
19        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
20      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
21        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
22        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
23        and use "-devel" testreport option for standard testing on baudelaire.
24    o pkg/grdchk:
25      - Assume that all gradient-check position are within the same tile
26        corresponding to global indices (iGloTile,jGloTile) and that
27        positions (i,j indices or nbeg) are local to this tile;
28      - set tile local-indices and proc. number according to tile global-indices;
29      - remove grdchkwhichproc from namelist (retired param);
30      - send adjoint gradient to all procs so that all procs print it to STDOUT;
31      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
32    o adding package bbl (Bottom Boundary Layer)
33      description in MITgcm/pkg/bbl/bbl_description.tex
34      example/test experiment in MITgcm_contrib/bbl
35    o adjoint verifications
36      - changed 5 experiments to multi-tiles
37        * global_ocean.90x40x15
38        * obcs_ctrl
39        * offline_exf_seaice
40        * tutorial_dic_adjoffline
41        * tutorial_tracer_adjsens
42        changed reference output for those that crossed tile boundaries
43        (changed choices of gradient check positions)
44      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
45      - temporary bug fix in grdchk_loc.F for obcs
46    o genmake2 & testreport
47      - add target "obj" (just for OBJFILES files) to Makefile;
48      - add option to specify FEXTRAFLAGS on command line.
49    o pkg/mypackage:
50      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
51    
52    checkpoint63a (2011/08/02)
53    o pkg/diagnostics (velocity potential):
54      - fix velocity-potential calculation when using OBCS: balance net inflow
55        at each level (new S/R OBCS_DIAG_BALANCE).
56      - fix some of the problems with OBCS in stream-function calculation.
57    o pkg/exf/exf_readparms.F
58      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
59        EXF_NML_OBCS) more consistent, so that you need not have these lists
60        in data.exf when they are not used.
61    o optim/optim_readdata.F:
62      - add some output about obcs variables that might help debugging
63      - add a check about nvarlength
64    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
65    o pkg/diagnostics (velocity potential):
66      - fix mask for OBCS (still problems in stream-function with OBCS);
67      - add specific parameter (default = main code CG2D params) for solver;
68      - in case of poor convergence, use solution corresponding to lowest residual.
69    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
70      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
71      and should be avoided where possible.
72    o model/src (rStar):
73      - include r* effect on reference-state (PhiRef) in totPhiHyd
74        (so that it's really the potential anomaly at the cell center);
75        affect solution only if z* with full pressure in EOS.
76      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
77        update output (because of z* in totPhiHyd and viscA4 changes);
78      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
79        @ constant r) until interpolation at constant r is implemented.
80    o pkg/diagnostics
81      - fix RCENTER diagnostics in case cell center is not at interface middle
82    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
83      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
84      that THETA and SALT are "conservative temperature" and "absolute
85      salinity"
86    o pkg/ctrl
87      - fix computation of endrec in s/r ctrl_init_rec
88      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
89    o pkg/seaice/seaice_growth.F
90      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
91        remove then obsolete STORE directives
92      - fix STORE directives for tice and tices, so that only the
93        appropriate part of the fields are stored (and not the entire
94        field); update global_ocean.cs32x15.seaice AD output.
95      - cosmetic changes: adjust CPP flags and indentation for better
96        legibilty
97    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
98      Chris Wilson)
99    o pkg/gmredi:
100       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
101       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
102    
103    checkpoint63  (2011/07/11)
104    o pkg/exch2:
105     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
106     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
107       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
108       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
109    o pkg/diagnostics:
110     - deal with pairs of post-processed diags which are computed together; in
111       particular, re-order list of diags within 1 file to save 2nd computation.
112     - add S/R to compute velocity stream-function (called after velocity-potential
113       calculation) from divergence free transport -> new diagnostics "PsiVEL".
114     - add parameter to select grid-point location where PsiVEL == 0.
115    o eesupp/src:
116       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
117       (specific S/R needed with exch2 topology - for now, just print an error msg)
118    o pkg/shelfice
119     - Implement friction velocity-dependent transfer coefficients following
120       Holland and Jenkins, JPO, 1999
121       Original code by M. Losch with small modifs.
122       Enable with CPP option SHI_ALLOW_GAMMAFRICT
123       and runtime flag SHELFICEuseGammaFrict
124    o verification lab_sea & global_ocean.cs32x15:
125     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
126       does not miss some dependencies (but is slower) and also works with many files
127       (default makedepend limitation for AD built).
128     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
129    o pkg/diagnostics:
130     - add run-time parameter "useMissingValue" (def=False) to fill land-point
131        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
132       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
133     - Extend the use of "missing_value" setting from data.diagnostics for the case
134       of counter-diagnostics (where fraction-weight is zero). This applies both to
135       MNC and MDS output files.
136    o pkg/seaice/seaice_growth.F:
137      - add 'a priori' cap of latent heat flux based on actual mass considerations
138        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
139        non-legacy seaice_solve4temp.
140      - add diagnostic of the residual sublimation freshwater flux (the freshwater
141        flux taken from the ocean if the total actual latent heat fluxes exceed
142        the maximum)
143      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
144       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
145      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
146       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
147      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
148      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
149    o verification 1D_ocean_ice_column:
150       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
151       update results
152    o pkg/diagnostics:
153     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
154       which are not filled-up but computed from other diags ; In this case, the mate
155       diag points to the primary (filled-up) diag to used for post processing.
156     - Update Velocity-potential computation using post-processed diag framework.
157     ==> Change the ordering of fields and time-periods in MDS output file
158       when using periodic averaging: now writes one time record with the full set
159       of fields for this time period, then the next time reccord (it used to be
160       one field with the full set of time records then the next field).
161         Note: this is now similar to NetCDF (MNC) output file. <==
162    
163    checkpoint62z (2011/06/21)
164    o adjoint monitor:
165     - Add adjoint monitor output for packages exf, seaice
166       and update relevant testreport output
167    o pkg/seaice:
168     - re-order diags inits so that they appear in order in available_diagnostics.log
169     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
170       area/heff/hsnow preceeding thermodynamic growth/melt.
171     - modified diag: SIdA; output actual effect, as the description states.
172     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
173     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
174       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
175        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
176     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
177     - added diagnostics for seaice generic tracers (SItr*).
178     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
179     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
180     I. Fenty: 18-Jun-2011:
181     Minor changes to seaice package:
182     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
183        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
184       - Differentiated "regularization variables" from "floor variables"
185        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
186        * hiceMin became SEAICE_hice_reg (old hiceMin)
187          (with _reg meaning regularization variable)
188       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
189        so as to ensure energy conservation when going between phases
190      - A22 was not used anywhere
191     2) Changed regularization procedure for heffActual and hsnowActual to ensure
192        well-boundedness and smooth adjoint in seaice_growth.F
193     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
194        because the old regularization always set heffActual >= 0.05 cm
195     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
196        on AREA when HEFF > 0.
197      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
198        requiring that DISABLE_AREA_FLOOR *not* be defined
199     Affected verifications:
200      - 1D_ocean_ice_column (output.txt output_adm.txt)
201      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
202    o pkg/diagnostics:
203      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
204      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
205        (was _RL, now integer) with option = 0 to retrieve all levels.
206      - add pieces of code to compute velocity potential at each level (new diagnostics
207        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
208        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
209      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
210        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
211        and in diagnostics_fract_fill.F (do not need a valid pointer for the
212        diagnostics counter-mate); check that definition of counter-diagnostic
213        includes a valid counter-mate (in diagnostics_set_levels.F).
214    o model/src (rStar):
215      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
216        affect solution only if z* with full pressure in EOS;
217        update output of test-exp global_ocean.90x40x15.
218    o pkg/seaice:
219      - introduce siEps=1e-5 parameter
220      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
221      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
222      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
223        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
224        as well as ice cover age and ridging index (attached to AREA).
225        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
226        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
227        Up to SItrMaxNum=3 tracers can be used simultaneously.
228    o pkg/salt_plume:
229      -introduce SPsalFRAC run time parameter that sets the fraction of the
230       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
231       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
232    o model debug options:
233      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
234        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
235      - Refine debug-msg printing selection (3 new levels):
236        debugMode  : controls printing of debug messages (sequence of S/R calls).
237        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
238         debLevZero =  0 ; /* level of disabled aux. msg printing */
239         debLevA =  1 ; /* level of minimum  aux. msg printing */
240         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
241         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
242         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
243         debLevE =  5 ; /* level of extensive debug printing */
244        New debugLevel default: with default debugMode value (=F),
245          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
246          and if debugMode=T, default debugLevel = 4 (debLevD).
247        Relation with previous settings:
248         debLevB (=2) corresponds to former debLevA (=1)
249         debLevD (=4) corresponds to former debLevB (=2)
250        Note:
251         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
252         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
253            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
254      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
255        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
256    o pkg/obcs:
257      - change OBCSfixTopo default from True to False (should not change the results);
258        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
259    o pkg/thsice:
260      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
261        2nd layer seaice sublimation (unlikely to happen)
262      - use Interior mask for OBCS in thsice_advection.F (similar to what is
263        done in gad_advection & seaice_advection).
264    o adjoint:
265      bug fix spotted by Gael Forget:
266      seaice_advection and thsice_advection still had
267      legacy CPP options to avoid CS corner updates for adjoint
268    o pkg/seaice:
269      => Change some of the defaults (2011/05/29):
270         - change SEAICEuseFluxForm default (from False to True)
271         - change DIFF1 default (from 0.004 m/s to 0. m/s)
272         And print warnings if DIFF1 is not set in data.seaice and centered
273          avection scheme is used without any diffusion.
274      also:
275      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
276      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
277      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
278        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
279        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
280      update results of test exp.:
281         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
282             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
283             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
284         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
285         seaice_obcs: output (SEAICEuseFluxForm=T)
286      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
287          for standard fwd & AD lab_sea tests (to keep the same output).
288  o pkg/seaice/seaice_growth.F:  o pkg/seaice/seaice_growth.F:
289    - use Ian Fenty's capping formulas for actual ice    - use Ian Fenty's capping formulas for actual ice
290    thickness thoughout EVOLUTION branch.    thickness thoughout EVOLUTION branch.
291    - put treatment pathological case #2) in CPP brackets    - put treatment pathological case #2) in CPP brackets
292    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
293    - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
294  o pkg/seaice:  o pkg/seaice:
295    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
296    pass the Laplacian diffusivity (in m/s2) diffKh as a parameter;    pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
297    also pass fac as a param, which can be 1. (to update the tendency    also pass fac as a param, which can be 1. (to update the tendency
298    field) or the time step (to update the field itself).    field) or the time step (to update the field itself).
299    - seaice_advdiff.F: for multidim, call seaice_diffusion with    - seaice_advdiff.F: for multidim, call seaice_diffusion with
300    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
301    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
302    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
303    hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.    hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
   - note: if any of SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.  
   is specified to be >0, then DIFF1 is set to 0.  
304  o pkg/seaice:  o pkg/seaice:
305    diffusion with centered advection scheme (diffus.F & advect.F):    diffusion with centered advection scheme (diffus.F & advect.F):
306    - 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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