--- MITgcm/doc/tag-index	2009/06/08 04:33:33	1.1118
+++ MITgcm/doc/tag-index	2009/11/30 20:32:11	1.1202
@@ -1,16 +1,317 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1118 2009/06/08 04:33:33 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1202 2009/11/30 20:32:11 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o nonHydrostatic:
+  Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
+    a spurious source of energy in simple baroclinic adjusment test case.
+  Update all non-hydrostatic exp output.
+o model/src (3-d solver):
+  Change again 3-D solver free-surface RHS term when exactConserv=T:
+    simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
+    (which was not the case with previous formulation).
+  To recover previous version, just reset "oldFreeSurfTerm" to previous value.
+  Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
+o nonHydrostatic:
+  - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
+    for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
+  - change 3-D solver to work with r* (for now, only with linear free-surf.)
+  - add few debug diagnostics (cg3d_x, residual)
+o model/src:
+  fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
+    update output of exp. global_ocean.cs32x15.viscA4
+o update output of exp. global_ocean.cs32x15.icedyn after removing
+  #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
+o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
+o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output 
+  for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
+o model: add Christopher Wolfe's implemetation of the single reduction cg2d
+  (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
+  runtime flag useSRCGSolver. Modify verification experiment global_with_exf 
+  to test this code
+o pkg/cd_code:
+  Change defaut D-grid time-stepping to get the same for D-grid momentum as for
+   C-grid momentum. D-grid velocity used to be stepped forward in time with
+   Adams-Bashforth only on surface pressure term. Tests show that using AB on
+   D-grid coriolis term improves stability (as expected from CD-scheme paper).
+  To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
+  Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
+   lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
+   tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
+  Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
+       lobal_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
+o pkg/obcs:
+ - fix bug in initialisation (broken since Oct 1rst modification)
+   for useOBCSprescribe without useEXF.
+
+checkpoint61y
+o pkg/seaice
+ - change (once again) the discretization for the evp solver: rather than
+   squaring the averages of strain rates, average the squares to give
+   a better approximation to VP behavior (in simple test); this breaks
+   verification experiments that use EVP (lab_sea and lab_sea.hb87)
+    --> update outputs
+o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
+  to improve vectorization of adjoint code on TARGET_NEC_SX
+o verification/vermix:
+  - change vermix to a more "classical" 1d column with high vertical 
+    resolution, seasonal heat flux forcing and constant wind forcing 
+    --> update outputs
+o pkg/seaice
+ - fix diagnostics of principal stress components for EVP
+ - add optional diagnostics of non-linear convergence for LSOR solver
+ - make maximum zeta a runtime parameter
+o model/src (3-d solver):
+  Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
+   which consisted in removing the Surf. Non-Hydrostatic pressure from the
+   whole column and adding it to Eta (inspired from Casualli, 1999):
+   Only affects 3-D solver initial guess and only if using ExactConserv,
+   but tests did show a degradation of solver convergence. For this reason,
+   decide to disable this piece of code.
+   to recover previous version, just set zeroPsNH = exactConserv (line 78).
+  Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
+o pkg/ggl90: 
+ - fix previous modif (unfortunatly has not been documented here).
+o pkg/seaice/autodiff:
+ - add CPP flag to include clipping of zeta in EVP code;
+   although clipping of zeta is not necessary for EVP and not recommended
+   it was done by default, now clipping is disabled by default
+ - modify computation and store zetaC/Z in seaice_evp for TAF
+ - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
+ - change seaice_calc_viscosities/strainrates for better
+   vectorization after AD by TAF
+ - rearrange common blocks in SEAICE.h once again for easier dumps of
+   adjoint output, adjust adcommon.h and g_common.h
+ - change flux form of default advection scheme for better vectorization
+   of adjoint code
+ - modify lab_sea/input.lsr to test the flux form of default advection 
+   scheme
+o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
+  transition in checkpoint61r)
+
+checkpoint61x
+o adjoint: adding two new verification experiments
+  * tutorial_global_biogeo: an online dic sensitivity experiment 
+    (work with G. Forget)
+  * tutorial_dic_adjoffline: an offline dic sensitivity experiment
+    (an update of the Dutkiewicz et al., 2006 paper)
+  Both use the same CO2FLUX cost function, but different controls
+  Gradient checks look good, but some recomp. could still be traightened out
+  Should add xx_dic control variable to test at some point
+o model/src:
+  add run-time parameters to check and/or mask initial Temp & Salt
+o pkg/ptracers:
+  apply zonal filter (if used) to all passive tracers
+
+checkpoint61w
+o adjoint:
+  * update and finish work on adjoint of dic package (G. Forget)
+  * start adjoint of offline package
+  * bug fix for cube-sphere TLM code (active_file_g.F)
+o tutorial_global_oce_optim:
+  now tested with 4 tiles (change data.grdchk and update output_adm.txt)
+  and add SIZE.h_mpi for MPI testing
+o pkg autodiff
+ - fix bug in autodiff_restore
+ - make genmake2 remove comments and empty lines from ad_input_code.f in 
+   order to reduce file size (new script file remove_comments_sed)
+o allows to specify vertical profile of vertical viscosity (viscArNr)
+o pkg autodiff
+  autodiff_ini_model_io: comment out writing of grid information to netcdf 
+  files, because at this time the grid fields are a bunch of zeros 
+  (this is analogous to ini_mnc_vars.F) 
+o pkg seaice/autodiff:
+ left-over from removing the 3-time-level fields: 
+ - small rearrangement of common blocks (SEAICE.h)
+ - fix field declaration in order to get meaningful output in 
+   adseaice.*.nc (adcommon.h) 
+o pkg obcs:
+ - go through NH code only if nonHydrostatic=T
+ - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
+ - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
+   => Update output of experiment seaice_obcs
+ - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
+ - fix NH+Orlanski restart (add wvel OBC value in pickup file)
+ - fix restart for useOBCSprescribe + useEXF
+o pkg ctrl
+ - make obcs as control parameter work also with useSingleCPUio
+ - replace a few sny and snx by Ny and Nx to be consistent with
+   ctrl_set_globfld_x/yz.F
+o pkg seaice
+ - re-introduce global field frWtrAtm for the case of 
+   ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
+ - catch the case of an empty filename in seaice_cost_init_fixed.F
+o pkg ecco:
+ - small bug fixes in the_main_loop
+  . fix order of monitor arguments
+  . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
+  . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
+    that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
+ - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the 
+   imbalance diagnostics for wmean_h/sflux = 0 
+ - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
+ - catch the case of empty filenames in ecco_cost_init_fixed.F 
+   and ecco_readparms.F
+ - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
+   to make this statement meaningfull in ecco_cost_weights.F
+o pkg zonal_filt:
+  - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
+  - when using rStar, filter uVel*hFacW instead of uVel
+   (tested without topography: fix a Pb of growing instability with NLFS)
+o pkg/aim/thsice:
+ -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
+  (works as SST restoring)
+o pkg/thsice:
+ -add specific parameter for salt restoring in slab mixed-layer
+   (by default equal to the temperature restoring)
+
+checkpoint61v
+o pkg/kpp:
+ -add double diffusive contributions as a hack, turned off by default 
+  for now, and the code can be excluded with a CPP-flag 
+  EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
+ -add a verification experiments to "vermix" to test this code
+o pkg/mom_common:
+  Move computation of length scales to mom_init_fixed.F (avoid recomputation
+  at each time-steps*levels).
+o pkg/layers:
+  Created a new package for computing volume fluxes in temperature or
+  [not yet implemented] density layers, e.g. for calculating residual
+  overturning circulations. 
+o pkg/diagnostics: 
+  implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
+o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
+o pkg/mdsio (& pkg/rw): rework high level S/R interface:
+  To avoid mixing type (RS/RL) of input/output array argument,
+  replace single mixed-type array with a pair from each type (RS/RL).
+o setting pickupSuff force to start from a pickup (even if nIter0=0): this
+  is now implemented for all pkgs (previously only done for the main pickup) 
+
+checkpoint61u
+o pkg/obcs:
+  - change OB?eta from _RS to _RL and put them into a separate commen block
+  - add code to read OB?eta from a file via obcs_prescribe_read: the code
+    compiles and does not destroy any other experiments, the data is read
+    properly, but the code is not tested in actual applications
+o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to 
+  create a meaningful unit attribute for the time coordinate variable 
+o pkg/ebm: add plenty of missing "_d 0" ;
+   update results of experiment global_ocean_ebm (fwd + adjoint tests) 
+  Notes: several pieces of code only works for (very) specific set up
+   (domain size, lat range, etc ...); should be documented & stop if one 
+   of those assumptions is not meet.
+o pkg/seaice: add missing "_d 0" in HSNOW initialisation
+   update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests) 
+      and offline_exf_seaice (seaicetd + adjoint).
+o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
+   update results of experiments: lab_sea (4 fwd tests + 3 adjoint), 
+    seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
+o few changes to pass when compiling with strick checking of arguments 
+   across S/R (allow to find few bugs in S/R calls).
+o pkg/seaice:
+ - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new 
+   2d-fields, for slightly better performance
+
+checkpoint61t
+o pkg/seaice: 
+ - remove unused variables in seaice_evp
+ - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
+o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
+   named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
+   each processor opens a different file (a fix from Matt).
+o cg2d:
+   use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
+   this reduces number of EXCH calls by 2 when using exch2.
+   For now, keep previous size array for gc2d_nsa.F to avoid Pb with store 
+   directives and missing simple EXCH (exch_s3d_rx) adjoint code.
+o pkg/thsice: 
+   add code for Near Infra-Red albedo (from Jeff)
+   (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
+o ini_model_io:
+   move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
+   MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
+   to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
+
+checkpoint61s
+o pkg/exch2 (exch2_rxN_cube*):
+   remove last BARRIER (no need to synchronise after getting data from shared
+   buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
+o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
+  and generate new output (for the 2 tests) using default rotationPeriod.
+o pkg/exch2:
+  - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
+    (was already the case with AUTODIFF_EXCH2 defined)
+  - add bj in exch2 arrays and S/R.
+  - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
+    MLAdjust to exch2 (identical results except with MPI -> truncation diff);
+o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
+  - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
+    GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
+  - verification experiment natl_box.longstep
+o build_options: ifort+mpi_aces optfile (following Constantinos advise):
+  allow different versions of ifort (8 or 9) and different versions
+   of mpi (mpich or mpich2) to be used with the same optfile.
+  requires to load a netcdf module and set MPI_INC_DIR (see comments inside
+   optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
+o pkg/seaice: 
+  fix previous modif (3-level field removed) for old-pickup reading 
+
+checkpoint61r
+o pkg/seaice: 
+ - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
+  1. introduce fields for time step (N-1)
+  2. do not use levels 2 and 3 anymore (but keep them)
+  3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This 
+     includes changes to pkg/thsice/thsice_get_velocity.F, 
+     model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
+     pkg/obcs/obcs_apply_uvice.F.
+ - completely remove code for leap-frog time stepping for second order
+   advection
+ - adjusted adjoint accordingly;
+   gradient checks have improved by an order of magnitude!
+ 
+checkpoint61q
+o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
+ - the boundary conditions along open boundaries are unclear, because the
+   associated masks are set to zero and are thus treated as closed when
+   applying the slip-boundary conditions.
+ - move initialisation of grid variables from seaice_init_varia to _fixed
+o adding doc/diags_changes.txt
+o model/src: 
+  do_the_model_io: rename few pkg S/R which are called from do_the_model_io, 
+   to avoid "_diags" naming if no relation to pkg/diagnostics.
+  ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF 
+   file and only call PLOT_FIELD_XYZ if debugMode=T.
+  remove few PLOT_FIELD_XY calls outside initialisation.
+  remove few unnecessary BARRIER.
+o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
+  of salt_plume package in Southern Ocean 
+o pkg/thsice: 
+ - fix hOceMxL in overlap (needed for sea-ice advection); 
+   update output of experiment global_ocean.cs32x15.icedyn.
+o pkg/seaice: 
+ - make the (placeholder-)tracer IceAge a little more meaningful
+  by avoiding ridging of age due to convergent ice flow
+ - add diagnostics for surface temperature, atmospheric and oceanic
+   heat flux, and atmospheric and oceanic ice growth
+
+checkpoint61p
+o eesupp (global_max & global_sum):
+ - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
+ - remove starting & endding barrier (no longer needed)
+o pkg/mdsio, writelocal:
+   works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
+   (remove the STOP): uses shared buffer IO to store data from all threads
+   and then let master-thread write nThreads tiles.
 o pkg/mdsio (read/write field):
  - tiled IO done in 1 piece (all levels at a time);
+ - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
  - multi-threaded: allow to read/write local (non-shared) array
    (was already working with singleCpuIO ; now works also without);
    => no longer needs barrier call after reading a file (added inside
-   mds_read/write field). 
- - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
+   mds_read/write field).
  - move barrier calls outside gather/scatter_2d to mds_read/write_field
 o pkg/obcs/exf
   - exf_getffieldrec.F: add a few ". _d 0" and