--- MITgcm/doc/tag-index	2013/02/08 07:56:45	1.1821
+++ MITgcm/doc/tag-index	2013/04/05 21:29:21	1.1851
@@ -1,16 +1,168 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1821 2013/02/08 07:56:45 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1851 2013/04/05 21:29:21 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o tools/genmake2:
+  - change default makedepend from the system default to tools/xmakedepend:
+    When no makedepend is specified, select tools/xmakedepend it the test pass,
+    otherwise select the system default (if exist and pass the test) or
+    try to build cyrus-makedepend ; stop if none of the 3 works.
+o pkg/exf & pkg/thsice:
+  - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
+    for energy content of Precip + RunOff & Evap. Assumes:
+   1) Rain has same temp as Air.
+   2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
+   3) Run-Off comes at the temp of surface water (with same Cp)
+   4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
+    put directly into Latent Heat flux & should use water-vapor heat capacity.
+   5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
+    with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
+o pkg/seaice: simplify the use of CPP flags in JFNK-related files
+    (compile when SEAICE_ALLOW_JFNK is defined)
+o pkg/thsice:
+  - fix oceanic flux diagnostics & timeave (left from new sequence of calls
+    implementation): move THSICE_AVE call after the advection (called directly
+    from thsice_do_advect.F).
+o verification/global_ocean.90x40x15 and OpenAD:
+  New experiment for OpenAD is identical to the one in input_ad except that
+    multiDimAdvection=.FALSE.,
+  There is still an issue with this.
+o pkg/thsice:
+  - account for ice velocity (ocean relative velocity) in turbulent heat flux
+    at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
+    and offline_exf_seaice (main test).
+
+checkpoint64f (2013/03/31)
+o verification/OpenAD:
+  - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
+o verification/isomip, pkg/shelfice and OpenAD:
+  - add OpenAD setup to this exp and make shelfice package work with OpenAD
+o verification/tutorial_global_oce_biogeo:
+  - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
+o verification/offline_exf_seaice:
+  - replace adjoint experiment (now similar to fwd input.thermo/ setup).
+o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
+  - add OpenAD setup to this exp and make ptracers package work with OpenAD
+o pkg/seaice/seaice_evp.F:
+   mask the asymmetric contribution of the ice-ocean stress (when
+   the turningAngle is non-zero) over open water to avoid stripes
+   in the EVP-solutions after many EVP-substeps. This does not change
+   the verification experiment (because turningAngle=0 in that experiment),
+   but will affect other EVP solutions with turningAngle.ne.0
+o verification, AD & TLM output:
+  - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
+    additions and multiplications which affect results at machine truncation
+    level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
+    lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
+    (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
+    digits of matching.
+o pkg/seaice:
+   modify lsr-algorithm so that it vectorizes AND converges by using a
+   "zebra" method: split vector loop into two with step size 2; this
+   solves a general convergence problem for the JFNK solver on a vector
+   computer. It has the potential to even improve convergence for
+   non-vector machines, but it does change the results so it is turned
+   off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
+   SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
+
+checkpoint64e (2013/03/05)
+o pkg/ecco and several verification experiments:
+   Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
+   from ecco package, and revert to unified routine in model/src/
+   Adjust verification experiments accordingly, especially gloal_oce_llc90
+   Should conclude long-standing work by Gael to reconsile the_main_loop with
+   ECCO and will enable OpenAD's revolve loop in ECCO setup.
+o pkg/generic_advdiff:
+  - implement compressible flow method for multi-dim advection (similar to
+    gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
+    TAF generates many recomputations) to use it; no yet coded with implicit
+    vertical advection.
+  - change experiment advect_cs (new output) and advect_xy (same output)
+    to test compressible flow multi-dim advection.
+o pkg/generic_advdiff:
+  - fix SOM advection for unusual cases (linear Free-Surf in r*, other
+    cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
+o pkg/seaice:
+  - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
+    bug affects two verification experiments (lab_sea and lab_sea.hb87),
+    recover old (wrong) results by setting noSlipFac = 2. in
+    seaice_calc_strainrates.F;
+  - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
+  - add runtime parameter SEAICE_JFNKepsilon for that finite difference
+    gradient in the Jacobian times vector operation (s/r seaice_jacvec)
+  - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
+o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
+  - new subroutines seaice_lsr_tridiagu/v
+  - introduce loop bounds i/jmin/max to be able to use a restricted
+    additive Schwarz method, but not used for now.
+  - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
+  - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
+o OpenAD support
+   Reorganize S/R call for overall time-stepping loop to facilitate
+   OpenAD revolve loop replacement
+   (new S/R main_do_loop.F)
+o model/src:
+  - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
+  - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
+    ADAMS_BASHFORTH2.
+o pkg/cheapaml:
+  - add new parameter (default=F, same as before) to disable full domain
+    (including land) periodicity in X & Y dir.
+  - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
+    prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
+    into single S/R CHEAPAML_TIMESTEP.
+
+checkpoint64d (2013/02/17)
+o pkg/monitor (angular momentum):
+  - do not add Eta contribution to the total AM if using rigid-lid;
+  - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
+  - horizontal discretisation: compute Zonal wind contribution separately for
+    each component (instead of from cell centered averaged) and use the 4
+    grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
+  - Check that AM is conserved with linear dynamics (momAdvection=F and linear
+    FreeSurf) if using vectorInvariant momentum.
+o model/src (horizontal grid):
+  - move initialisation of all horizontal grid arrays to null value
+    from specific horizontal grid S/R to main S/R INI_GRID;
+  - add 2 new arrays to project model C-grid velocity on to zonal direction
+    (similar to AngleCosC & -AngleSinC but at U and V point location) and
+    compute them in S/R CALC_GRID_ANGLES.
+o pkg/seaice: replace a hard coded parameter by a runtime parameter
+    SEAICE_JFNK_tolIter
+o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
+    preconditioner for JFNK (run LSR into the overlaps as far as possible,
+    i.e OLx/y-2, but overwrite the solution in the overlaps)
+  - extend loop range in seaice_calc_viscosity
+  - add new parameters SEAICE_OLx/y (default = OLx/y-2)
+  - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
+  - slightly modify loops in tridiagonal solver lsr-preconditioner
+  - by default remove the extra exchange in seaice_preconditioner with a
+    replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
+  - modify offline_exf_seaice so that old results without RAS are reproduced
+    for output.dyn_jfnk.txt
+  in seaice_fgmres.F (unrelated to RAS)
+  - add a cpp-flag option for a re-ordered mapping (potentially more
+    efficient), but because this changes the results, turn it off by
+    default
+  - replace the save statement by local common blocks
+o utils/matlab:
+  - fix tile-offset in rdmnc.m when output was produced using EXCH2.
+  - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
+    instead of local script "load_cs.m".
+o pkg/seaice:
+  - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
+    to the scalarProductMetric and the unrolling. By chance this does not
+    change the verification experiment, because of the particular domain
+    decomposition
 o pkg/diagnostics:
   - change default missing_value from UNSET_RL to -999.
 o pkg/layers: improve vectorization of layers_fluxcalc.F
-  - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu 
+  - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
     time spent in this routine by more than a factor of 3 on an NEC-SX8
   - step 2: replace search algorithm by a bisection algorithm found in
-    Press et al. Numerical Recipes in Fortran. This algorithm can be 
+    Press et al. Numerical Recipes in Fortran. This algorithm can be
     vectorized and finds the correct bin in approx. log2(Nlayers) steps.
     For now, use this algorithm only for TARGET_NEC_SX defined.
   - moved the search algorithm into a separate subroutine, that is kept