--- MITgcm/doc/tag-index	2007/09/27 14:42:59	1.883
+++ MITgcm/doc/tag-index	2008/02/13 07:43:39	1.957
@@ -1,10 +1,229 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.883 2007/09/27 14:42:59 dimitri Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.957 2008/02/13 07:43:39 mlosch Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
-o pkg/exf: improve vectorization by moving if-statement out of loops
+o genmake2: replace (4 times)
+     make genmake_tc_1.o >> genmake_warnings 2>&1
+  with
+     COMM="$CC $CFLAGS -c genmake_tc_1.c"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_warnings 2>&1
+  to make genmake2 always see the value of CC as specified in the optfile.
+o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
+  - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
+  - modify verification advect_cs test to test SOM-advection on CS-grid.
+o pkg/ctrl:
+  - Rewrite of ctrl_map_ini_ecco.F, 
+    introducing a generic routine (ctrl_map_ini_gen.F).
+  - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
+
+checkpoint59n
+o pkg/diagnostics: for large number of diagnostics, store diagnostic mate 
+  number in dedicate array "hdiag":
+  - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
+    with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
+  - many small changes (integer format) for large number of diagnostics
+  - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
+    a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
+o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
+  usingSphericalGrid, this allows to define the rotated grid coordinates
+  via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
+  geographical coordinates according to the inverse of the rotation defined
+  by the Euler angles, so that Coriolis parameter and online-interpolation by 
+  exf works with the geographical coordinates on XC/YC/XG/YG.
+  Naturally, this feature does not work with all packages, so some 
+  combinations are prohibited in config_summary (flt, flt_zonal, ecco, 
+  profiles), because there the coordinates are assumed to be regular 
+  spherical grid coordinates. 
+o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
+  - introduce isopycnal diffusion coefficient control.
+o tools/adjoint_options: 
+  - additional control vector components.
+o pkg/mnc: have mnc create marginally meaning full coordinate variables
+  (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 
+o pkg/mypackage: 
+  - add example of read/write pickup for state-var ; 
+  - add entry points to the main code for state-vars diags & write-pickup.
+o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
+  transitions for useExfYearlyFields
+  - add new subroutine that determines the file to read from for 
+    use*YearlyFields = .TRUE. and .FALSE.
+  - add a verification experiment to global_with_exf that tests 
+    useExfYearlyFields with USE_EXF_INTERPOLATION defined
+o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in 
+  analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new 
+  subroutines (which could be generated from a template, because they are 
+  almost identical), for now they are included in obcs_prescribe_read.F for
+  simplicity
+o pkg/exf:
+  - add a little more diagnostic to exf_interp_read (in analogy to 
+    mds_read_field, can be turned off with debugLevel < debugLevA=1)
+  - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
+    ugly but fast by unrolling short inner loops, inserting a unroll=8 
+    directive in routine lagran, and splitting a loop and making do while the
+    outermost loop (the latter requires the intoduction of index arrays)
+o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
+o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
+  http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
+o verification/seaice_obcs: updated for restart test and latest options
+o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
+  ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
+  for now this is only available for the C-grid code and also within
+  #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
+
+checkpoint59m
+o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
+  and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
+o gad_som : fix flux output (& diagnostics) to have same units as other   
+  advection scheme fluxes (was previously multiplied by deltaT).   
+o added verification/seaice_obcs both to test seaice open boundaries
+  and to provide an example matlab scrpt for generating them
+o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
+o pkg/salt_plume: clean up salt_plume_frac.F to
+  remove redundancy in PlumeMethod 1 and 4
+o pkg/kpp: added saltplume diagnostics
+o pkg/obcs and pkg/seaice:
+  - do not set uice and vice to zero when OB*icefile are unspecified
+  - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
+  - moved seaice tracer obcs after call to seaice_growth
+o pkg/salt_plume: added various options for salt plume depth
+  criterion and for vertical distribution of the salt
+
+checkpoint59l
+o pkg/ptracers: new version of ptracers pickup:
+  read meta file and write only fields which are needed to restart.
+  ( same logic as main pickup file ; also using pickupStrictlyMatch )
+o pkg/seaice:
+  - add timescale for melting due to warm mixed layer as a means of
+    setting SEAICE_availHeatFrac more conveniently
+  - add a CPP-flag/runtime parameter check for flooding algorithm
+  - reformulated availHeat in seaice_growth.F to be independent of AREA
+o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
+  unit changes
+o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
+o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
+  SX vector computer.
+o pkg/seaice:
+  - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
+    seaice forcing fields can now be read only through pkg/exf
+  - removed some unused halos
+o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
+o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
+  or U/VICE from U/VWIND before computing U/VSTRESS
+
+checkpoint59k
+o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
+  dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
+o fix un-initialised variable problem (in mom_vecinv & shap_filt):
+  all experiments pass when compile with un-initialised var. checking option.
+o added pkg/salt_plume
+o script to test restart (for now, in MITgcm_contrib/jmc_script)
+o pkg/seaice: new read/write pickup version. 
+  read meta file and write only fields which are needed to restart.
+  ( same logic as main pickup file ; also using pickupStrictlyMatch )
+o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
+o lab_sea.hb87: modify the domain & update output.hb87.txt :
+  lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
+  at j=1 & j=Ny+1 : this case is not treated correctly in the restart
+  process. Fixed here by closing the domain at the Northern boundary.
+o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
+o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
+  a set of consecutive levels in/from a 3-D array.
+o pkg/ptracers: 
+  use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
+  to-do: fix pkg/diagnostics when large number of diagnostics are defined.
+
+checkpoint59j
+o in pkgs: dic, obcs, offline, rbcs:
+  standard way to compute coeff. for time interpolation between 2 time reccords
+  which retains full precision (& make results less dependent on compiler).
+  update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
+o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
+  packages instead of reading ice cover and wind speed separately
+o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
+ (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
+  to allow to compile customized code before the update)
+o cleaning-up: 
+  - fix CPP instruction syntax in pkg/obcs
+  - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
+    add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
+  - fix some threads issue in IO parts.
+o pkg/dic:
+  - add tons of "_d 0" (--> much better testreports !)
+   and then update outputs of tutorial_global_oce_biogeo
+o pkg/mom_fluxform:
+  add a special version of momentum advection intended to conserve momentum
+  next to a bathymetry step or a coastline edge. (default = off = #undef)
+o new read/write pickup version:
+  - for now, only implemented for main (mdsio) pickup file.
+  - write out only what is needed to restart; merge pickup_nh , pickup_ph
+    and main pickup together.
+  - read meta file; read only what is needed to restart; stop if a field
+    is missing (if pickupStrictlyMatch=T, = the default) or try to restart
+    if it make sense (even if the restart is not perfect).
+  - if no meta file, assume that pickup to read corresponds exactly to
+    a pickup that would currently be written.
+  - read pickup written in the old format (until checkpoint59i) if it
+    recognizes an old meta file (no field-list).
+  - add a meta file in exp. which starts from a pickup: 2 cases:
+    a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
+     e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
+    b) a meta file describing the content of the associated pickup file
+     e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
+o pkg/mdsio & pkg/rw:
+  - new routine to read a meta file ; new set of routine to read
+    Multiple-fields file (with meta file).
+o added open boundary conditions capability for seaice
+    HSNOW, HSALT, UICE, and VICE
+
+checkpoint59i
+o adjoint:
+  * fix multiDimAdvection adjoint 
+    (partial recomputation problem by TAF for fVerT(:,:,kDown)
+    and comlev1 size definition (maxpass vs. max. number of tracers)
+  * verification/global_ocean.90x45x15 adjoint now tests
+    NLFS and multiDimAdvection using DST3 (=30)
+  * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
+o pkg/kpp: add "_d 0" to real constant (if missing); 
+  update output of exp: natl_box (10.digits); vermix (std, 7.digits)
+  and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
+o prepare for "clever pickup" implementation: add new header file "RESTART.h"
+  for internal parameters related to restart process (formerly from PARAMS.h)
+  and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
+o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
+  as argument. (only atm2d & obcs write_pickup have not yet been updated)
+o pkg/monitor:
+  - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
+  - fix mon_stats_rs (statistics over the full domain, even where field is zero)
+  - account for deep Atmosphere factor and density factor (anelastic)
+o added open boundary conditions capability for seaice HEFF and AREA
+o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
+  thermodynamics
+  - requires a little reorganization, which affects the testreport results 
+    of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
+    so that now the conservative form is tested
+  - add a few comments
+o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
+o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
+o add new diagnostics to seaice: advective, diffusive fluxes (only for
+  multidim-advection, for scheme 2 they are not filled) and transports, 
+  thermodynamic growth rates
+o change units of EmPmR (inside the code, + within coupling interface)
+  from m/s to kg/m2/s (mass flux) but leave input file unchanged.
+  Affects results @ truncation level (cg2d match) and update output of 
+   experiments: lab_sea(6), global_ocean.90x40x15(10),
+  global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
+  + adjoint results: global_ocean_ebm(11) and lab_sea (12).
+  Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
+  Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
+
+checkpoint59h
+o pkg/exf: 
+  - improve vectorization by moving if-statement out of loops in
+    exf_mapfields, exf_radiation
+  - exf_bulkformulae.F: introduce 2D fields and vectorize code
 o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
 o testreport: 
   - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE