--- MITgcm/doc/tag-index	2009/04/02 21:47:23	1.1084
+++ MITgcm/doc/tag-index	2009/05/29 14:52:48	1.1111
@@ -1,13 +1,125 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1084 2009/04/02 21:47:23 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1111 2009/05/29 14:52:48 mlosch Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/seaice: 
+  - 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 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".
+o start to test MPI + multi-threaded (change testreport to skip tests
+  where number of tiles do not match).
+o genmake2: add option "-omp" to turn on Open-MP ;
+  passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
+o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
+  and keep the original tile numbering. Note: compatible with old
+  W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
+
+checkpoint61l
+o Overlaps had been forgotten in calculating ijk keys : fixed
+o fix cyrus makedepend for gcc 4.4
 o experiment fizhi-cs-aqualev20:
   switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
-  and generate new output. Note: new output is much closer to the old 
-  one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from 
+  and generate new output. Note: new output is much closer to the old
+  one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
   the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
 o pkg/fizhi:
  - change to avoid indices going deliberately over array-bounds
@@ -22,6 +134,9 @@
   (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
@@ -37,9 +152,9 @@
   results by setting the above flag.
   Further changes involve changes in defaults:
   - ALLOW_FLOODING is defined and turned on by default
-  - SEAICE_advSnow = .true. is now the default
-  - SEAICE_advSalt = .true. is now the default
-  - SEAICE_advAge  = .true. is now the default
+  - SEAICEadvSnow = .true. is now the default
+  - SEAICEadvSalt = .true. is now the default
+  - SEAICEadvAge  = .true. is now the default
   - SEAICE_clipVelocities  = .false. is now the default 
                                      (as per J. Zhang's recommendation)
   - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE