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revision 1.1462 by jmc, Wed Jun 22 19:17:36 2011 UTC revision 1.1497 by jmc, Mon Aug 29 17:23:24 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint63b (2011/08/29)
8    o pkg/ebm:
9      - fix sign of runoff;
10      - update directly forcing fields (Qnet,EmPmR) to use standard
11        external_forcing_surf.F (remove ebm_forcing_surf.F);
12      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
13      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
14        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
15      - update global_ocean_ebm parameters file data and update output (fwd+ad).
16    o verification/matrix_example:
17      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
18        MPI and mutlti-threaded testing.
19    o pkg/matrix:
20      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
21      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
22      - fix for multi-threaded (remove DATA statement);
23      - use standard DIFFERENT_MULTIPLE function;
24      - add MATRIX_OPTIONS.h
25    o verification/matrix_example:
26       To allow to split the domain in several tiles, change the domain size
27        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
28        Western side) of land points.
29    o (*_)write_pickup:
30      - fix few bugs in mypackage_read/write_pickup.F
31      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
32        array of length 1 (was caught by compiler syntax-check).
33    o pkg/diagnostics (velocity potential solver):
34      - fix initialisation of main diagonal matrix (for overlap values)
35    o tools/build_options:
36      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
37        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
38      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
39        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
40        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
41        and use "-devel" testreport option for standard testing on baudelaire.
42    o pkg/grdchk:
43      - Assume that all gradient-check position are within the same tile
44        corresponding to global indices (iGloTile,jGloTile) and that
45        positions (i,j indices or nbeg) are local to this tile;
46      - set tile local-indices and proc. number according to tile global-indices;
47      - remove grdchkwhichproc from namelist (retired param);
48      - send adjoint gradient to all procs so that all procs print it to STDOUT;
49      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
50    o adding package bbl (Bottom Boundary Layer)
51      description in MITgcm/pkg/bbl/bbl_description.tex
52      example/test experiment in MITgcm_contrib/bbl
53    o adjoint verifications
54      - changed 5 experiments to multi-tiles
55        * global_ocean.90x40x15
56        * obcs_ctrl
57        * offline_exf_seaice
58        * tutorial_dic_adjoffline
59        * tutorial_tracer_adjsens
60        changed reference output for those that crossed tile boundaries
61        (changed choices of gradient check positions)
62      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
63      - temporary bug fix in grdchk_loc.F for obcs
64    o genmake2 & testreport
65      - add target "obj" (just for OBJFILES files) to Makefile;
66      - add option to specify FEXTRAFLAGS on command line.
67    o pkg/mypackage:
68      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
69    
70    checkpoint63a (2011/08/02)
71    o pkg/diagnostics (velocity potential):
72      - fix velocity-potential calculation when using OBCS: balance net inflow
73        at each level (new S/R OBCS_DIAG_BALANCE).
74      - fix some of the problems with OBCS in stream-function calculation.
75    o pkg/exf/exf_readparms.F
76      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
77        EXF_NML_OBCS) more consistent, so that you need not have these lists
78        in data.exf when they are not used.
79    o optim/optim_readdata.F:
80      - add some output about obcs variables that might help debugging
81      - add a check about nvarlength
82    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
83    o pkg/diagnostics (velocity potential):
84      - fix mask for OBCS (still problems in stream-function with OBCS);
85      - add specific parameter (default = main code CG2D params) for solver;
86      - in case of poor convergence, use solution corresponding to lowest residual.
87    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
88      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
89      and should be avoided where possible.
90    o model/src (rStar):
91      - include r* effect on reference-state (PhiRef) in totPhiHyd
92        (so that it's really the potential anomaly at the cell center);
93        affect solution only if z* with full pressure in EOS.
94      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
95        update output (because of z* in totPhiHyd and viscA4 changes);
96      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
97        @ constant r) until interpolation at constant r is implemented.
98    o pkg/diagnostics
99      - fix RCENTER diagnostics in case cell center is not at interface middle
100    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
101      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
102      that THETA and SALT are "conservative temperature" and "absolute
103      salinity"
104    o pkg/ctrl
105      - fix computation of endrec in s/r ctrl_init_rec
106      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
107    o pkg/seaice/seaice_growth.F
108      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
109        remove then obsolete STORE directives
110      - fix STORE directives for tice and tices, so that only the
111        appropriate part of the fields are stored (and not the entire
112        field); update global_ocean.cs32x15.seaice AD output.
113      - cosmetic changes: adjust CPP flags and indentation for better
114        legibilty
115    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
116      Chris Wilson)
117    o pkg/gmredi:
118       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
119       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
120    
121    checkpoint63  (2011/07/11)
122    o pkg/exch2:
123     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
124     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
125       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
126       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
127    o pkg/diagnostics:
128     - deal with pairs of post-processed diags which are computed together; in
129       particular, re-order list of diags within 1 file to save 2nd computation.
130     - add S/R to compute velocity stream-function (called after velocity-potential
131       calculation) from divergence free transport -> new diagnostics "PsiVEL".
132     - add parameter to select grid-point location where PsiVEL == 0.
133    o eesupp/src:
134       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
135       (specific S/R needed with exch2 topology - for now, just print an error msg)
136    o pkg/shelfice
137     - Implement friction velocity-dependent transfer coefficients following
138       Holland and Jenkins, JPO, 1999
139       Original code by M. Losch with small modifs.
140       Enable with CPP option SHI_ALLOW_GAMMAFRICT
141       and runtime flag SHELFICEuseGammaFrict
142    o verification lab_sea & global_ocean.cs32x15:
143     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
144       does not miss some dependencies (but is slower) and also works with many files
145       (default makedepend limitation for AD built).
146     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
147    o pkg/diagnostics:
148     - add run-time parameter "useMissingValue" (def=False) to fill land-point
149        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
150       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
151     - Extend the use of "missing_value" setting from data.diagnostics for the case
152       of counter-diagnostics (where fraction-weight is zero). This applies both to
153       MNC and MDS output files.
154    o pkg/seaice/seaice_growth.F:
155      - add 'a priori' cap of latent heat flux based on actual mass considerations
156        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
157        non-legacy seaice_solve4temp.
158      - add diagnostic of the residual sublimation freshwater flux (the freshwater
159        flux taken from the ocean if the total actual latent heat fluxes exceed
160        the maximum)
161      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
162       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
163      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
164       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
165      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
166      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
167    o verification 1D_ocean_ice_column:
168       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
169       update results
170  o pkg/diagnostics:  o pkg/diagnostics:
171   - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')   - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
172     which are not filled-up but computed from other diags ; In this case, the mate     which are not filled-up but computed from other diags ; In this case, the mate
173     diag points to the primary (filled-up) diag to used for post processing.     diag points to the primary (filled-up) diag to used for post processing.
174   - Update Velocity-potential computation using post-processed diag framework.   - Update Velocity-potential computation using post-processed diag framework.
175   Change the ordering of fields and time-periods in MDS output file   ==> Change the ordering of fields and time-periods in MDS output file
176     when using periodic averaging: now writes one time record with the full set     when using periodic averaging: now writes one time record with the full set
177     of fields for this time period, then the next time reccord (it used to be     of fields for this time period, then the next time reccord (it used to be
178     one field with the full set of time records then the next field).     one field with the full set of time records then the next field).
179     Note: this is now similar to NetCDF (MNC) output file.       Note: this is now similar to NetCDF (MNC) output file. <==
180    
181  checkpoint62z (2011/06/21)  checkpoint62z (2011/06/21)
182  o adjoint monitor:  o adjoint monitor:
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