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revision 1.1462 by jmc, Wed Jun 22 19:17:36 2011 UTC revision 1.1498 by jmc, Mon Aug 29 19:46:22 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/ebm:
8      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
9      - add multi-threaded test for verification exp. global_ocean_ebm
10    
11    checkpoint63b (2011/08/29)
12    o pkg/ebm:
13      - fix sign of runoff;
14      - update directly forcing fields (Qnet,EmPmR) to use standard
15        external_forcing_surf.F (remove ebm_forcing_surf.F);
16      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
17      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
18        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
19      - update global_ocean_ebm parameters file data and update output (fwd+ad).
20    o verification/matrix_example:
21      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
22        MPI and mutlti-threaded testing.
23    o pkg/matrix:
24      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
25      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
26      - fix for multi-threaded (remove DATA statement);
27      - use standard DIFFERENT_MULTIPLE function;
28      - add MATRIX_OPTIONS.h
29    o verification/matrix_example:
30       To allow to split the domain in several tiles, change the domain size
31        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
32        Western side) of land points.
33    o (*_)write_pickup:
34      - fix few bugs in mypackage_read/write_pickup.F
35      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
36        array of length 1 (was caught by compiler syntax-check).
37    o pkg/diagnostics (velocity potential solver):
38      - fix initialisation of main diagonal matrix (for overlap values)
39    o tools/build_options:
40      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
41        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
42      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
43        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
44        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
45        and use "-devel" testreport option for standard testing on baudelaire.
46    o pkg/grdchk:
47      - Assume that all gradient-check position are within the same tile
48        corresponding to global indices (iGloTile,jGloTile) and that
49        positions (i,j indices or nbeg) are local to this tile;
50      - set tile local-indices and proc. number according to tile global-indices;
51      - remove grdchkwhichproc from namelist (retired param);
52      - send adjoint gradient to all procs so that all procs print it to STDOUT;
53      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
54    o adding package bbl (Bottom Boundary Layer)
55      description in MITgcm/pkg/bbl/bbl_description.tex
56      example/test experiment in MITgcm_contrib/bbl
57    o adjoint verifications
58      - changed 5 experiments to multi-tiles
59        * global_ocean.90x40x15
60        * obcs_ctrl
61        * offline_exf_seaice
62        * tutorial_dic_adjoffline
63        * tutorial_tracer_adjsens
64        changed reference output for those that crossed tile boundaries
65        (changed choices of gradient check positions)
66      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
67      - temporary bug fix in grdchk_loc.F for obcs
68    o genmake2 & testreport
69      - add target "obj" (just for OBJFILES files) to Makefile;
70      - add option to specify FEXTRAFLAGS on command line.
71    o pkg/mypackage:
72      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
73    
74    checkpoint63a (2011/08/02)
75    o pkg/diagnostics (velocity potential):
76      - fix velocity-potential calculation when using OBCS: balance net inflow
77        at each level (new S/R OBCS_DIAG_BALANCE).
78      - fix some of the problems with OBCS in stream-function calculation.
79    o pkg/exf/exf_readparms.F
80      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
81        EXF_NML_OBCS) more consistent, so that you need not have these lists
82        in data.exf when they are not used.
83    o optim/optim_readdata.F:
84      - add some output about obcs variables that might help debugging
85      - add a check about nvarlength
86    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
87    o pkg/diagnostics (velocity potential):
88      - fix mask for OBCS (still problems in stream-function with OBCS);
89      - add specific parameter (default = main code CG2D params) for solver;
90      - in case of poor convergence, use solution corresponding to lowest residual.
91    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
92      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
93      and should be avoided where possible.
94    o model/src (rStar):
95      - include r* effect on reference-state (PhiRef) in totPhiHyd
96        (so that it's really the potential anomaly at the cell center);
97        affect solution only if z* with full pressure in EOS.
98      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
99        update output (because of z* in totPhiHyd and viscA4 changes);
100      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
101        @ constant r) until interpolation at constant r is implemented.
102    o pkg/diagnostics
103      - fix RCENTER diagnostics in case cell center is not at interface middle
104    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
105      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
106      that THETA and SALT are "conservative temperature" and "absolute
107      salinity"
108    o pkg/ctrl
109      - fix computation of endrec in s/r ctrl_init_rec
110      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
111    o pkg/seaice/seaice_growth.F
112      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
113        remove then obsolete STORE directives
114      - fix STORE directives for tice and tices, so that only the
115        appropriate part of the fields are stored (and not the entire
116        field); update global_ocean.cs32x15.seaice AD output.
117      - cosmetic changes: adjust CPP flags and indentation for better
118        legibilty
119    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
120      Chris Wilson)
121    o pkg/gmredi:
122       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
123       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
124    
125    checkpoint63  (2011/07/11)
126    o pkg/exch2:
127     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
128     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
129       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
130       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
131    o pkg/diagnostics:
132     - deal with pairs of post-processed diags which are computed together; in
133       particular, re-order list of diags within 1 file to save 2nd computation.
134     - add S/R to compute velocity stream-function (called after velocity-potential
135       calculation) from divergence free transport -> new diagnostics "PsiVEL".
136     - add parameter to select grid-point location where PsiVEL == 0.
137    o eesupp/src:
138       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
139       (specific S/R needed with exch2 topology - for now, just print an error msg)
140    o pkg/shelfice
141     - Implement friction velocity-dependent transfer coefficients following
142       Holland and Jenkins, JPO, 1999
143       Original code by M. Losch with small modifs.
144       Enable with CPP option SHI_ALLOW_GAMMAFRICT
145       and runtime flag SHELFICEuseGammaFrict
146    o verification lab_sea & global_ocean.cs32x15:
147     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
148       does not miss some dependencies (but is slower) and also works with many files
149       (default makedepend limitation for AD built).
150     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
151    o pkg/diagnostics:
152     - add run-time parameter "useMissingValue" (def=False) to fill land-point
153        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
154       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
155     - Extend the use of "missing_value" setting from data.diagnostics for the case
156       of counter-diagnostics (where fraction-weight is zero). This applies both to
157       MNC and MDS output files.
158    o pkg/seaice/seaice_growth.F:
159      - add 'a priori' cap of latent heat flux based on actual mass considerations
160        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
161        non-legacy seaice_solve4temp.
162      - add diagnostic of the residual sublimation freshwater flux (the freshwater
163        flux taken from the ocean if the total actual latent heat fluxes exceed
164        the maximum)
165      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
166       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
167      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
168       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
169      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
170      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
171    o verification 1D_ocean_ice_column:
172       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
173       update results
174  o pkg/diagnostics:  o pkg/diagnostics:
175   - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')   - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
176     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
177     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.
178   - Update Velocity-potential computation using post-processed diag framework.   - Update Velocity-potential computation using post-processed diag framework.
179   Change the ordering of fields and time-periods in MDS output file   ==> Change the ordering of fields and time-periods in MDS output file
180     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
181     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
182     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).
183     Note: this is now similar to NetCDF (MNC) output file.       Note: this is now similar to NetCDF (MNC) output file. <==
184    
185  checkpoint62z (2011/06/21)  checkpoint62z (2011/06/21)
186  o adjoint monitor:  o adjoint monitor:
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