--- MITgcm/doc/tag-index	2011/11/29 10:56:03	1.1537
+++ MITgcm/doc/tag-index	2012/01/01 01:25:54	1.1567
@@ -1,16 +1,185 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1537 2011/11/29 10:56:03 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1567 2012/01/01 01:25:54 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+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.
+o model/src:
+ - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
+   to their current value at the beginning of forward_step.F": add a new run-time
+   switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
+ - set doResetHFactors=T in the following test exp:
+    global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
+    global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
+    and tutorial_global_oce_in_p (nonLinFS in p)
+o pkg/ecco
+  - added IES cost term
+o verification/advect_xz
+  - scale down the depth by 1/100 (from 200 km to just 2.km)
+  - add secondary test using divergent flow, r-star and implicit vertical advection.
+  - add note (check_conserve_TS.txt) and matlab script to check global
+    conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
+o pkg/rbcs:
+  - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
+o pkg/obcs (Stevens BCs):
+  - fix various problems in the phase speed computations of the Stevens
+    boundary conditions:
+    - sign error for western and southern boundaries,
+    - time tendencies were underestimated by factor of dTracerLev and some just
+      zero (for multidim advection schemes) -> now estimate time tendencies
+      from difference between previous (n) time level and the one before (n-1);
+      this requires storing a field per tracer per boundary, also in the pickup
+      files.
+    - replace deltaTmom in cflMer/Zon computation with dTracerLev
+    - set default phase velocity to cflMer/Zon
+  - update verification experiment exp4.stevens
+o pkg/generic_advdiff (implicit_r):
+  - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
+    (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
+  - fix implicit vertical diffusion or advection with NonLin FreeSurf
+    (was using current recip_hFacC instead of future recip_hFacC): set future
+    recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
+    solver S/R ;
+  - fill diagnostics of vertical advective fluxes (computed from tendency)
+    when using implicit vert. advection;
+  - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
+     global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
+     tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
+     and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
+o pkg/diagnostics:
+  - add diags for T & S tendency which goes through Adams-Bashforth.
+
+checkpoint63f (2011/11/30)
 o pkg/obcs/obcs_calc_stevens.F:
+  - join some loops to reduce number of if-statements
   - fix a bug in code for northern and southern boundaries.
 o pkg/seaice/seaice_init_varia.F
-  - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and 
+  - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
     caused zero ice-velocities for the B-grid code
 o pkg/seaice/seaice_init_fixed.F
-  - fix a bug in the initialisation of the second metric terms 
+  - fix a bug in the initialisation of the second metric terms
     k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
   - this affects all seaice configurations with useCurviLinearGrid = .true.
     and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms