--- MITgcm/doc/tag-index	2008/10/25 20:49:22	1.1034
+++ MITgcm/doc/tag-index	2009/04/02 21:47:23	1.1084
@@ -1,9 +1,182 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1034 2008/10/25 20:49:22 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1084 2009/04/02 21:47:23 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o experiment fizhi-cs-aqualev20:
+  switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
+  and generate new output. Note: new output is much closer to the old 
+  one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from 
+  the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
+o pkg/fizhi:
+ - change to avoid indices going deliberately over array-bounds
+ - remove unnecessary MPI stuff
+ - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
+ - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
+   does not go over array-bounds and therefore returns reliable output.
+ - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
+   this S/R has 4 output arguments, which are used inside "get_alarm";
+   when it is called with the same variable "ndum" in place of several
+   output arguments, this produces weird side effect inside "get_alarm"
+  (e.g., datein=dates(n) is overwritten by timein=times(n) since both
+   datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
+   address) and produces error.
+o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
+o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
+   update lab_sea.lsr & lab_sea.salt_plume results
+o pkg/seaice: 
+  Major overhaul of the LSOR solver: change discretization from original
+  finite differences to finite volume. The old routine is still in the
+  file seaice_lsr.F and can be turned on with the CPP-flag
+  SEAICE_OLD_AND_BAD_DISCRETIZATION
+  Along with this change, the discretization of the strain rates is changed.
+  The same flag turns on the old discretization in seaice_calc_strainrates.F
+  All verification experiments with seaice are affected (except for 
+  seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
+  results by setting the above flag.
+  Further changes involve changes in defaults:
+  - ALLOW_FLOODING is defined and turned on by default
+  - SEAICE_advSnow = .true. is now the default
+  - SEAICE_advSalt = .true. is now the default
+  - SEAICE_advAge  = .true. is now the default
+  - SEAICE_clipVelocities  = .false. is now the default 
+                                     (as per J. Zhang's recommendation)
+  - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
+    is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
+  - seaice_growth: replace computation of UG by a simple copy from wspeed
+
+checkpoint61k
+o pkg/seaice: a few bug fixes mostly concerning the metric terms:
+  seaice_lsr: fixed a few metric terms,
+              affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
+              add more debugging diagnostics
+  seaice_evp: removed superfluous many metric terms of FV discretization
+              of stress divergence
+              affects lab_sea, lab_sea.hb87
+  seaice_ocean_stress: removed superfluous many metric terms of FV discretization
+              of stress divergence for non-evp solver 
+              (this part is not tested anywhere)
+  seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
+              they were effectively only half slip
+              affects lab_sea.hb87
+  updated all relevant verification experiments (except lab_sea//output_adm.txt
+    which was left over, but fails at level 7 & 6)
+
+checkpoint61j
+o pkg/seaice: turn a few hard wired parameters into run time parameters
+o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model 
+  time in seconds as promised by the usints in seaice_monitor and exf_monitor
+o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
+  that are not cubed-sphere grids
+o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
+o pkg/ctrl:
+  fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
+o non-hydrostatic (calc_gw.F):
+  fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
+  update output of exp. global_ocean.cs32x15.viscA4
+o remove backward compatibility for thetaMin,phiMin
+  (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
+o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the 
+  interpolated wind field not only for curvilineargrid=.true., but also 
+  for a rotated grid (rotateGrid=.true.)
+o pkg/exf: add capability to bypass interpolation for runoff
+  by setting yet another CPP-flag
+o eesupp/src, B-grid exchange:
+  add simple (6 tiles, non MPI) CS exch + standard interface S/R.
+o autodiff
+  new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
+  allows to switch to single-prec common blocks;
+  corresponding switch occurs in tamc.h, integer isbyte
+  TAF store directivs "byte" and "kind" seem equivalent;
+  Most tamc.h have been updated correspondingly.
+
+checkpoint61i
+o autodiff:
+  fix autodiff_sore/_restore indices for obcs
+  (spotted by I. Hoteit, M. Mazloff)
+o pkg/autodiff, pkg/ctrl:
+  Add flag to reduce all tapelev I/O to single-prec. 
+  In data.ctrl set
+    doSinglePrecTapelev = .TRUE.
+o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
+  check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
+o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for 
+  real fresh water flux (not yet)
+o pkg/mdsio & rw:
+ - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
+ - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
+o pkg/flt:
+ - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
+   init_fixed & ini_varia.
+ - clean-up & simplify linear interpolation S/R:
+   move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
+ - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
+ - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
+ - add vert. coordinate & horiz. indices to output files.
+ - change vertical position in initial condition, from index to depth [m].
+ - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
+   (easier to get to a curvilinear grid) ; delX,delY no longer used.
+o pkg/ggl90: a few modifications:
+ - fix bottom boundary condition, and interpolation of KappaE
+   near top and bottom
+ - use same set of viscosity/diffusivity for TKE/momnetum/tracer 
+ - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
+ - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
+o rename thetaMin,phiMin -> xgOrigin,ygOrigin
+  (maintain temporary backward compatibility, until next checkpoint)
+
+checkpoint61h
+o pkg/diagnostics with "periodic averaging diagnostics":
+  fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. 
+o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
+o pkg/obcs: fix loop ranges for balancing code
+o pkg/flt:
+ - improve criteria for finding which tile owns a float.
+ - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
+o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
+  aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
+  with ocean biogeo)
+o pkg/flt:
+ - do some cleaning and fix the restart ;
+ - add output.txt in flt_example/results to get this pkg tested.
+o genmake2: add an EXTENDED_SRC option and flag.
+   for now, cannot be turned on on command line (only through genmake_local)
+o pkg/mdsio: read/write vector:
+ - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
+ - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
+   & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
+ - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
+  (drop to 4 digits matching for grad). But this test does not look very
+  reliable (was already failling on eddy, fc5, at 6.digits). Update output.
+
+checkpoint61g
+o pkg/flt:
+  - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
+   + make OPTIONS file more standard.
+  - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
+  - fix _BYTESWAPIO CPP-Flag
+  - standard reading of file-parameter "data.flt"
+  - fix argument list of S/R FLT_RESTART
+  still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
+o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
+o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
+  a still unfixed compiler/optimization bug
+
+checkpoint61f
+o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; 
+  update results of global_ocean.cs32x15.icedyn test.
+o move getcon.F from model/src to pkg/fizhi.
+o pkg/exf: add parameter for extrapolation of temp up to the surface 
+   and option to prevent negative evap (in bulk_largeyeager04 only).
+o Prather Advection scheme: fix tracer conservation for divergent flow
+  (e.g., when using NonLin Free-Surface).
+o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
+o gmredi (Visbeck-variable-K):
+ - add more parameters to Visbeck-variable-K.
+ - use a 5 points average for dSigmaR in Visbeck-K calculation
+   (more "homogenous": same stencil and same weights as in dSigmaH)
+ - update output of ideal_2D_oce experiment.
 o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 
   (#undef REAL4_IS_SLOW)
  - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 
@@ -14,6 +187,10 @@
  - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but 
    probably not all: copy _RS surface flux fields to RL field before 
    calling DIAGNOSTICS_FILL
+ - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into 
+   real*4 (CALL EXCH_*_RS) versions.
+ - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
+   (generate new output).
 
 checkpoint61e
 o gmredi (Visbeck-variable-K):
@@ -2269,7 +2446,7 @@
   - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
   - these scheme operate in a similar manner as KPP (without ghat, of 
     course), however there is only one diffusivity that is used for both
-    temperature and salinity (and passive tracers)ç
+    temperature and salinity (and passive tracers)
 o add offline package
 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
   provided by Stephanie Dutkiewicz