--- MITgcm/doc/tag-index	2009/04/21 16:48:31	1.1089
+++ MITgcm/doc/tag-index	2009/06/24 20:28:21	1.1131
@@ -1,10 +1,188 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1089 2009/04/21 16:48:31 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1131 2009/06/24 20:28:21 heimbach Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
-o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D) 
+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):
+  - move mapping to global io-buffer inside gather_2d/scater_2d: this save
+    memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
+    receive real*4 array (instead of real*8) to read/write 32.bit files.
+    (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
+     and remove new mapping S/R)
+o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
+  - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
+    xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
+    when using exch2. Add S/R to map global io-buffer to global model array.
+  - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
+
+checkpoint61m
+o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
+  and add 3 other S/R for other types (R4,R8,RS).
+  Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
+o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
+ - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
+ - reduce number of macro definitions (keep only those which are used);
+   can always call directly the corrresponding S/R if needed.
+ - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
+   _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
+ Fixed wrong type of arg in:
+   atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
+   ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
+ To fix: global_sum of var in common block is wrong (multi-threaded) in:
+   dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
+ To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
+o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
+  "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
+o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
+o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
+  edges are closed (zero depth); might happen with "blank tiles";
+  for now, disabled if using OBCS.
+o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
+  link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
+o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
   to reduce length of 1.D array print in STDOUT.
 o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
   + use 48 tiles (16x8): this will allow to test "blank tiles".
@@ -37,6 +215,9 @@
   (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 tools/gemake2: (March 27-29 2009)
+  with option "-mpi": link *_mpi files from "MODS" dir (this is what 
+  testreport does).
 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