--- MITgcm/doc/tag-index	2005/09/11 04:37:01	1.545
+++ MITgcm/doc/tag-index	2005/11/03 17:34:32	1.576
@@ -1,9 +1,105 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.545 2005/09/11 04:37:01 edhill Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.576 2005/11/03 17:34:32 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
+             fix the singleCpuIO RS version of MDSWRITEFIELD
+   and add a WARNING if using globalFiles=T with multi-processors.
+o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
+  using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
+o tracer advection scheme:
+  add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get 
+   those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, 
+   was not very convenient).
+  add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
+   (further tests needed for the implicit DST & Flux-Limiter schemes).
+o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
+  and sRef for convenience, handy, when you want to initialize
+  ptracers in a large domain with a constant non-zero value. Also,
+  untangle ptracers_init.F a little.
+
+checkpoint57v_post
+o change dome exp. to use variable viscosity in side-drag terms.
+o remove all the files from the cfc_offline test since they are now
+  incorporated into tutorial_cfc_offline which has been producing
+  identical results for a few days of testing
+o add new parameter: sideDragFactor to enable half-slip-side BC
+  and change side-drag S/R to use viscosity from mom_calc_visc
+  (can switch back by setting sideDragFactor=0.); affects results at 
+  truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), 
+   global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
+o vorticity & strain are now computed without masking, to account for 
+  no-slip-side BC in variable viscosity calculation ; mask is applied
+  anyway later on, before computing advection/coriolis terms.
+o modify exp4 to test new obcs support for reading from external files
+  and for passive tracers
+o fix behavior of ptracers_monitor when monitor output is written to a 
+  netcdf-file; still not independent of monitor.F (writes in the same
+  file).
+o change default value of tRef (put a uniform, meaningful value for ocean 
+  & atmos) and initialize sRef (was missing, as Martin mentioned).
+o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity 
+  to be proportional to enstrophy dissipation length.  Thus,
+   viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
+  This is now consistent with Smagorinsky and with the manual.
+
+checkpoint57u_post
+o OBCS and PTRACERS: add open boundary support for passive tracers
+  - either use homogenous (pseudo) v.Neumann conditions or prescribe 
+    OB-values from file; this is not different from the way theta and salinity
+    are treated
+  - however, Orlanski-radiation conditions are not supported, and the model
+    will stop if you use pTracers and Orlanski at the same time. 
+  - beefed up the rountine obcs_external_fields_load: now only those open
+    boundary values are overwritten with values from files for which there 
+    are really files, otherwise the OB-fields remain untouched. This makes
+    it possible to use different OBs at different ends of the domain (as 
+    with EXF)
+o reduce number of exch calls in shap_filt (s2). 
+o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ 
+  truncation level) 4/5 MLAdjust test results (11&12 digits match).
+
+checkpoint57t_post
+o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
+o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
+  same truncation, independent of the face number: affects affects several
+  test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
+o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
+  note that biharmonic viscosity + no-slip was not tested in any experiment.
+o fix bug in non-linear free-surf side-drag ; generate new output for
+  global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
+o make mnc honor the writeBinaryPrec flag for most kinds of output
+o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
+o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
+  error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
+o add brackets in multi-terms sum to get same truncation, independent of
+  the face number (manage to get exactly same value of gU,gV at the cs-edge)
+  affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
+o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
+  and viscA4Remax, which allow one to limit the minimum viscosity by specifying
+  a maximum grid-scale Reynolds number.  Also, changes all length calculations
+  in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
+  Suggested values of viscosity parameters found in mom_calc_visc. 
+  Many new viscosity diagnostics available.
+
+checkpoint57s_post
+o Add clearing-house for viscosity calculations, mom_calc_visc and 
+  correct numerous bugs in LeithD and Smagorinsky discretizations.  
+  mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be 
+  used simultaneously, and to be used in mom_vecinv and mom_fluxform. 
+  Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
+  and with Strain-Tension viscous term calculation (mom_hdissip.F).  
+  The Strain-Tension form is now called with useStrainTensonVisc=.true.
+  ViscAhStrain and viscAhTension are now retired.
+o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
+o In response to JMC's bug report, genmake2 now ignores any soft-links
+  that it finds in the *current* directory when searching for files.
+  Soft-links found in any other source directories will still work as
+  they did before.
+o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls 
+  a C routine to unlimit the stack size
 o mnc-ify pkg/aim snapshot vars
 o mnc-ify pkg/land as requested by Daniel
 o various changes to mnc including: