--- MITgcm/doc/tag-index	2011/12/09 01:01:11	1.1546
+++ MITgcm/doc/tag-index	2012/01/16 23:53:58	1.1574
@@ -1,9 +1,177 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1546 2011/12/09 01:01:11 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1574 2012/01/16 23:53:58 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/exf and seaice exp:
+  - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
+    so that switching off area & heff advection flags does not affect results.
+  - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
+  - keep seaice_obcs unchanged (using #undef EXF_LWDOWN_WITH_EMISSIVITY)
+    and, using pkg/exf default emissivities, update results of fwd verification
+    experiments: 1D_ocean_ice_column, global_ocean.cs32x15.seaice, lab_sea (x4)
+    and offline_exf_seaice (x3).
+o pkg/seaice:
+  - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
+    remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
+  - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
+    but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
+    not multi-dim advection;
+  - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
+    SHORTWAVE_HEATING #undef.
+o optim: make Makefile more robust (?)
+o pkg/obcs:
+  * fix treatment of obcs_read_pickup for TAF
+o pkg/shelfice:
+  * add missing initialisation of num_shifwflx
+  * new adjoint verification exp. for isomip
+  * change Prandtl and Schmidt numbers from generic formulations
+    (in terms of model diffus. and visc.) to separate runtime
+    parameters, with Holland and Jenkins (1999) default values.
+o pkg/exf (interpolation):
+  - extended input field (2 rows) near the N & S poles:
+    * fill in with the symetric value (when even Nb of data in longitude)
+    * add average value at the poles only for scalar quantities ; for vector
+      component interpolation, skip the averaging and keep duplicated values,
+      unless the 2 components have same location (uvInterp=T) in which case
+      interpolate the 2 components together using S/R EXF_INTERP_UV.
+  - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
+    together: this allows to account properly for local orientation when
+    averaging at N & S pole.
+  - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
+    exf-interpolation near N & S poles. Undef by default.
+  - add debug check/print on 1rst iter if debugLevel >=2.
+o pkg/exf:
+  - change masking flags definition (no longer "parameter"), put them in
+    common block and set them in S/R EXF_INIT_FIXED.
+  - change recognized masking flag from s,u,v to c,w,s since the mask
+    to use (maskC,W,S) depends on position on model grid and has little to
+    do with scalar/vector difference; fix masking if using P-coordinates.
+  - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
+    and update results of exp. global_with_exf (x2).
+  - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
+o pkg/obcs
+  - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
+o pkg/exf (interpolation):
+  - assume periodicity in X only if input field cover full longitude range.
+  - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
+    and should vectorise).
+  - fix input lat of the 2 added row (in case we provide N.pole data).
+
+checkpoint63h (2011/12/30)
+o pkg/seaice:
+  - change declaration of UVM from _RL to _RS in order to get B-grid
+    uIce,vIce monitor when _RS = real*4
+o pkg/offline:
+  - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
+  - compute vertical velocity if not read from file (switch on exactConserv
+    & staggerTimeStep);
+  - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
+o verification:
+  - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
+    with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
+    fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
+  - update output of exp. global_ocean.cs32x15.viscA4 after changing
+    grid-file angles (used here for coriolis-3d);
+  - remove (or gzip) few files not needed to run fizhi-cs experiments.
+o pkg/exf (vector interpolation):
+  - rotate vector component toward local grid-axis orientation using grid-angles
+    (stored in GRID.h) instead of locally computed rotation angle; keep old code
+    available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
+o pkg/seaice:
+  - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
+    undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
+o pkg/PKG_OPTIONS.h files:
+  - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
+    outside of the #ifdef ALLOW_THISPKG / #endif block.
+  - update verification/*/code/PKG_OPTIONS.h files.
+o add a verification experiment (offline_exf_seaice/input.seaice) that test
+  the B-grid LSOR solver
+o pkg/seaice: sort out emissivity and long wave radiation step 2:
+  - add emissivity for snow and ice as new run-time parameters
+    (unfortunately) that default to the corresponding exf values; this
+    changes results in most verification experiments so that for backward
+    compatibility these parameter have to be set explicitly to inconsistent
+    values (ugly);
+  - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
+    emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
+    until we agree how to handle this bug properly
+o pkg/exf (interpolation):
+  - add a set of run-time param ({inputfield}_interpMethod), one for
+    each interpolated input field, to select the interpolation method
+    with a value of zero switching off the interpolation;
+  - print interpolation parameters to standard output;
+  - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
+    (to use instead runoff_interpMethod=0 in data.exf).
+  - simplify default setting of interpolation parameters (for all fields,
+    set position to match model grid cell-center position, leading to trivial
+    interpolation in case of regular Lat-Lon grid) and fix for the case of
+    non-uniform delY.
+o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
+   within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
+   this factor is absolutely required, because the lw exitance (= out-going
+   long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
+   where the reflectivity rho = 1-emissivity for conservation reasons. Once
+   this is established, we can remove the CPP-Flag (if we want to).
+o pkg/seaice:
+  - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
+    ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
+  - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
+    what the name implies (and not emissivity*BoltzmannConstant), this means
+    the old default value of 5.5e-8 now means
+    5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
+    S/R exf_readparms
+  - FV-discretization of the B-grid LSOR solver, turn on with
+    SEAICE_LSRBNEW. This new solver also involves a slight re-organization
+    of the calling routine dynsolver, so that B and C-grid code look a
+    little more alike.
+  - fix index bugs in ostres.F (B-grid code)
+o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
+o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
+  default for SEAICE_emissivity, if useEXF; requires setting a wrong
+  parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
+  backward compatiblity
+o model/src: use sigmaR in calc_ivdc
+
+checkpoint63g (2011/12/16)
+o pkg/seaice/seaice_growth.F:
+  fix heat conservation of the coupled ocean-seaice system.
+  when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
+  solid vs liquid water treatment is resolved via QNET.
+o pkg/seaice/seaice_growth.F:
+  add missing term for sublimation in saltFlux, which was breaking conservation.
+o pkg/seaice/seaice_model.F:
+  Remove this patholigical case treatment in evolution branch,
+  where it is un-necessary and breaks conservation.
+  Update global_ocean.cs32x15/results accordingly for
+  output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
+o model/src:
+  useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
+  external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
+o pkg/obcs:
+  modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
+  tendency for temperature and salinity that is then applied to update
+  theta and salt in S/R obcs_apply_ts; this requires proper masking of all
+  horizontal advection and diffusion contributions on the boundary (in
+  S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
+  removing the mask in S/R timestep_tracer. The advantage of this approach is
+  that the updated tracer values include contributions from the surface
+  forcing and vertical diffusion.
+  This modification changes exp4.stevens because of vertical diffusion.
+o model/src:
+  change non-curvilinear grid setting to also work with exch2 + blank tiles:
+  - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
+    face dimensions.
+  - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
+    as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
+    and INI_SPHERICAL_POLAR_GRID.
+  change test-experiment global_ocean.90x40x15:
+  - split the domain in many more tiles (9x4 tiles of 10x10 each);
+  - switch to exch2 and remove 1 blank-tile (but only for MPI test).
+  - update results of both test (std & dwnslp).
+o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
+   tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
 o model/src:
   - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
     and fix initialisation when using sigma-coords.