--- MITgcm/doc/tag-index	2009/05/13 21:35:21	1.1097
+++ MITgcm/doc/tag-index	2009/08/10 09:21:10	1.1149
@@ -1,15 +1,213 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1097 2009/05/13 21:35:21 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1149 2009/08/10 09:21:10 mlosch Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+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).
+ - 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 
+                        add code to catch the case fldperiod = 0.  
+  - obcs_precribe_read.F: change if statements so that they match 
+                          the variable type (_RL)
+  - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to 
+    exf_iprec) as part of namelist EXF_NML_01
+o pkg/mdsio:
+  - read/write tiled (local) files: read/write 1-level tile chunk at a time
+    (instead of segment of length sNx); expected to speed up tiled IO.
+o pkg/exch2:
+  - take buffer copy from/to array out of S/R exch2_send/recv into new
+    S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
+    (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
+  - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
+  - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
+    (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
+    including Topology header file (and common blocks).
+  - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
+    remove 2nd exch call in exch2_s3d_rx (no longer needed).
+  - document S/R arg. list (+ update some comments)
+o pkg/seaice:
+  - added SEAICE_CLIM_AIR code, which permits modulation of surface air
+    temperature and humidity over sea ice based on climatological values.
+  - clean up computation of Hibler+Bryan (1987) stress coupling for the case
+    of LSR (this change is expected to change the results slightly because now 
+    it uses slightly difference moduli from the second last LSR solution, but
+    that is more consistent with the stress computations; this part of the code 
+    is not tested in the verification experiments)
+  - fix diagnostics for flux of ice in case of B-grid
+  - turn strain rates eij and press into global fields within global 
+    common block in SEAICE.h for more straighforward diagnostics
+  - fix diagnostics for principal stress components, press, zeta, eta
+    to give something meaning full
+o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
+  new output (all 4 tests) using default rotationPeriod.
+o pkg KPP:
+  - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
+  - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
+    and normal grid from 1 to Nr)
+o Fix computations of L4rdt in mom_calc_visc.F
+o eesupp:
+  new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
+  should be called before a "stop" if we know that all process are going
+  to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
+
+checkpoint61o
+o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
+o model/src/ini_curvilinear_grid.F:
+   compute angleSin/CosC when they are not read from a file
+o pkg/seaice:
+   add pseudo time stepping for LSOR
+o pkg/exch2:
+   temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
+o pkg/seaice:
+   Adding separate sea ice albedo, drag coefficients, and HO in Southern
+   Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
+o SingleCpuIO:
+   fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
+o pkg/seaice:
+   put exchanged variable in (local) common block for MPI+Multi-Threads
+   to work (necessary with exch1, and for now with exch2 too).
+o verification: to get more experiments tested with mpi, mth and mpi+mth,
+  change tiling of:
+   aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
+   hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
+  update output of exp:
+   exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
+   tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
+  + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
+                   (note: output.txt generated on faulks using only 1 tile)
+o eesupp & mdsio (SingleCpuIO):
+ - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
+   parameter "W2_useE2ioLayOut" (read from file "data.exch2").
+   Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
+ - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
+ - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
+   gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
 o pkg/exch2:
  - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
    read parameter file "data.exch2" if it exists; otherwise try default regular
    cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
  - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
    with new code (not to be used, just as a backup solution).
+ - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2" 
+   in utils/exch2/input.
 
 checkpoint61n
 o eesupp & mdsio (SingleCpuIO):