--- MITgcm/doc/tag-index	2008/02/25 20:59:01	1.961
+++ MITgcm/doc/tag-index	2008/11/26 15:27:02	1.1045
@@ -1,11 +1,283 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.961 2008/02/25 20:59:01 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1045 2008/11/26 15:27:02 mlosch Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+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 
+   coordinate variable
+ - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables 
+   (surface forcing fields), removes some of the functionality
+ - model/src/write_grid.F: write _RS variables as RS-netcdf variables 
+ - 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):
+  - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
+  - change computation of Visbeck-K where Slope > Smax :        
+    now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
+    previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
+o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
+  to be the same as with Z-coord. (i.e., m/s & no-units respectively).
+o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
+o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
+  does not become too large (to avoid precision problems in implicit-diffusion
+  solver); update ideal_2D_oce output.
+o pkg ggl90:
+  - in ggl90_cal.F: compute only one set of visc/diff, used to
+    step forward TKE/T/S/momentum
+  - default value of GGL90viscMax/GGL90diffMax larger and equal (to
+    have Prandlt =1)
+o gmredi (fm07):
+  - add lower limit on Transition layer thickness + lower limit on 1/lambda
+  - allow to set few more params from data.gmredi
+o pkg ggl90:
+      - add missing sqrt(2) factor in computation of mixing length 
+        scale in ggl90_calc.F
+        (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
+
+checkpoint61d
+o adjoint modifs
+  - adapt to new field rhoInSitu
+  - allow to revert from StoreDynVars2D, StoreDynVars3D
+    to individual fields
+    (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
+o store 3-D (in-situ) density in commom block (DYNVARS.h)
+ - save 1 rho computation.
+ - no longer modify T & S inland when using down_slope pkg.
+o gad_som : allow to switch to SOM advection for T & S without corresponding 
+  pickup files (using new S/R: MDS_CHECK4FILE).
+o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
+  (for useSingleCpuIO to work in multi-threaded)
+o pkg/shelfice:
+ - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
+   with SHELFICEtopoFile in data.shelfice
+ - move code for reading ice shelf topography and modifying hFacC into separate
+   subroutines of the shelfice package
+ - separate initialisation of "fixed" and "variable" variables
+ - kTopC is not (yet) replaced by kSurfC, although this is possible
+o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
+o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
+  and rename:
+  ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
+  ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
+o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
+
+checkpoint61c
+o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" 
+  to add mass source/sink of fluid in the interior (3-D generalisation 
+  of oceanic real-fresh water flux).
+o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
+o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
+o new pkg: down_slope
+  density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
+  - presently, modify T & S inland (dwnslp_calc_rho.F).
+    can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
+  - implementation for ocean in P-coords not tested.
+  - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
+o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
+  (to facilitate conversion of oceanic pkg to p-coordinate).
+o change FIND_RHO to FIND_RHO_2D : 
+  pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
+o new pkg: cheapaml
+
+checkpoint61b
+o exch2: 
+  change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
+  - no longer depend on the order sequence (N,S,E,W).
+  - 3rd exchange no longer needed (tested with 24 tiles).
+  - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
+  - exch_UV_A-grid readily available (but not yet tested).
+  comment out 3rd exch call and remove copy of V to U at SE & NE face-corners 
+  (both are no longer needed) in exch_uv: no effect in forward run; but 
+   get truncation error differences with adjoint exch.
+o exch2: 
+ - change index-bounds storage (moved from target to local tile,
+   more intuitive this way) ; rename/remove some variables.
+ - change utils/exch2/matlab-topology-generator & code_mods accordingly.
+
+checkpoint61a
+o exch2/matlab-topology-generator: 
+  fix bug in index bounds for N-S internal exchange (hard to tell if this
+  had any effect on the solution).
+o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
+  is exceeded
+o testreport: modify syntax of awk, so that it works also with 
+  awk, and not only with nawk and gawk
+
+checkpoint61
+o autodiff
+  Change default for TAF usage by removing argument '-nonew_arg'
+  This changes TAF subroutine argument list (ordering of active var.)
+  Omission of this flag leads to incompatibility w.r.t. TAMC
+  To restore TAMC-compatibility, need following modifs:
+  * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
+  * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
+  Tested TAF version is 1.9.22
+  N.B.: exch2 hand-written adjoint code currently not TAMC compatible
+
+checkpoint60
+--->>> This is the last checkpoint for which generating the adjoint
+--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
+--->>> by default.
+--->>> Future checkpoints will ommit this flag by default.
+o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
+o pkg/grdchk: Add gradient check to etan0 perturbations.
+o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). 
+o pkg/autodiff: more flexibility in zeroadj. 
+  model/src: modifying do_oceanic_phys.F accordingly. 
+o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
+o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
+  special setup of gmredi for which the adjoint is stable 
+  enough for parameter optimization.
+o bridging the gap between eddy stress and GM.
+  -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
+      along with a change in CPP option (now ALLOW_EDDYPSI).
+  -> when using GM w/ GM_AdvForm: 
+      The total eddy streamfunction (Psi = eddyPsi + K x Slope)
+      is applied either in the tracer Eq. or in momentum Eq.
+      depending on data.gmredi (intro. GM_InMomAsStress).
+  -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
+  The key modifications are in model/src/taueddy_external_forcing.F
+  pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
+
+checkpoint59r
+o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
+  from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
+  fix option to read coriolis(@ cell-corner) from files with CS-grid.
+o pkg/mnc: add some attributes to standard 1D-coordinate variables
+o pkg/diagnostics: enforce missing_value attribute for scalar variables at
+  mass points, when using mnc for output
+  - add runtime parameter (missing_value, missing_value_int) to override 
+    default (which is the value of getcon('UNDEF'))
+o pkg/mnc: prepare mnc for the actual use of missing values with the
+  diagnostics package: small fix in mnc_cw_readwrite.template and more
+  initialisation of never used fields
+  - replace mnc_common.h and mnc_id_header.h with corresponding upper case
+  versions
+o pkg/thsice/thsice_ini_vars.F added default initial values so that 
+  thermodynamics sea ice solver does not blow up when some initial fields 
+  are missing.
+o move from external_forcing_surf.F to ini_forcing.F
+  the p-coord. hack consisting in using pLoad to set phi0surf ;
+  update output of tutorial_global_oce_in_p (affected @ truncation level).
+o Freshen up a bit hs94.1x64x5, notably: 
+  remove rotationPeriod and tRef=5*0. (adjoint only), and add 
+  exactConserv=.TRUE.
+o pkg/generic_advdiff:
+  change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
+  applies to files where Temperature & Salinity 2nd Order moments are used.
+o pkg/ptracers: add second-order moment advection schemes (80 and 81);
+  this uses a dynamically allocated internal state data structure
+  (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) 
+  and requires a fortran 90 compiler
+
+checkpoint59q
+o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
+   (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
+o Refresh tutorial_global_oce_biogeo, notably:
+  - change bathymetry (put back seamounts in ACC, use hFacs)
+  - change EOS (POLY3 --> JMD95Z)
+  - use Bryan-Lewis vertical diffusivity
+  - use multidimensional advection
+  - remove old virtual virtual in dic pkg, now done through ptracer pkg
+  - change a couple of parameters in dic pkg
+o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
+o pkg/obcs: change default to OBCSfixTopo = .true., 
+  - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
+  - replace "debugMode" with "debugLevel .GE. debLevB"
+o implementation of TAF directives for gchem,cfc,dic 
+o remove "exp5" (replaced by tutorial_deep_convection).
+o pkg/obcs: add code to fix topography gradients normal to open boundaries;
+  this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
+  the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
+  --> changes results in exp4, seaice_obcs
+o tutorial_deep_convection :
+  update the set-up and increase resolution and domain size ; start
+  from pseudo initial conditions = output at t=120mn in order to see
+  something happening when running testreport.
+o pkg/seaice: add os7mp as an advection scheme
+              add check for advection schemes
+              add a flag for restoring T and S underneath sea ice
+o pkg/my82: add netcdf-support and diagnostics 
+o thsice pkg:
+  - Now hsMax limits snow height by turning it into ice following
+    flooding scheme (and now conserving energy)
+  - Slight rewriting of the formula in thsice_calc_thick.F
+  - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
+  --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice 
+
+checkpoint59p
+o gchem / dic / cfc :
+  - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
+  - add new parameter files: "data.dic" & "data.cfc" ;
+  - various re-arrangement in initialisation & header file ;
+  - fix tutorial_global_oce_biogeo for multi-threaded test.
+o pkg/dic: test for "pickup_dic" file when restarting ;
+  if no pickup-file, can restart with a re-initialised pH (same as it did
+  before) providing pickupStrictlyMatch is set to False.
+o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
+  + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
+o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
+  and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
+o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
+ & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
+   (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
+o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
+   scheme to use for vorticty-term ;
+ - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F 
+   (with default selectVortScheme, return to original discretisation)
+ - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
+o pkg/seaice: add a line to the summary to indicate grid type (B/C)
+o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
+  bottom ; only used with variable horizontal viscosity and non-hydrostatic.
+  also fix diagnostics VISCAHW & VISCA4W.
+
+checkpoint59o
+o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
+o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
+  move a few statemens out the main loop into separate loops
+o pkg/shelfice: 
+  - sort out freshwater flux; convert freshwater fluxes to mass fluxes 
+    (kg/m^2/s), does not break tests, because in verification/isomip,
+    rhoConstFresh=rhoConst (by accident)
+  - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
+  - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
+    new file model/src/seawater.F, so that they are available for all pkgs.
+  - convert potential temperature into in-situ temperature. This changes the
+    isomip tests => update tests
 o add a flag writePickupAtEnd (default=true) to be able to suppress 
   writing a pickup at the last timestep
+o tools/mpack-1.6 : 
+  - disable automake (not working) and autoconf (not needed).
+  - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
+    also cleaner with much less compilation warnings.
 o pkg/profiles: 
   rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
   (for "less than 32 characters name" compiler requirement)