--- MITgcm/doc/tag-index	2013/07/01 16:55:57	1.1889
+++ MITgcm/doc/tag-index	2013/10/22 21:14:03	1.1933
@@ -1,12 +1,240 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1889 2013/07/01 16:55:57 dimitri Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1933 2013/10/22 21:14:03 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o verification/isomip:
+  - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
+o tools/build_options:
+  - optfile linux_amd64_ifort11, fast (no ieee) case:
+    to get a working restart for all experiments, add "-fp-model source"
+    to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
+
+checkpoint64p (2013/10/20)
+o pkg/autodiff:
+  - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
+    criteria, return to simple (default) tape IO format.
+o pkg/mdsio (+ eesupp/src):
+  - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
+    previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
+  - fix globalFile and singleCpuIO options using simpler global mapping.
+  - new pairs of scatter/gather vector S/R (one for each type, generated from
+    template) corresponding to simpler global mapping.
+  - adread_write.F: switch to new S/R (but leave old calls commented) and write
+    to globalFile when parameter globalFiles is set to True.
+  - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
+o pkg/autodiff:
+  - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
+    with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
+    missing, just add a STOP if array type do not match.
+o pkg/exf:
+  - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
+     rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
+     and rename array obsSIce to exf_iceFraction.
+o tutorial_deep_convection:
+  - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
+    for now all in this exp. code dir.
+  - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
+    testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
+o eesupp/src:
+  - added SINGLE_DISK_IO option because reading of parameter files on
+    very large number of processors did not work with existing set-up
+
+checkpoint64o (2013/09/25)
+o pkg/atm_phys & atm_compon_interf:
+  - allows for coupling of gray-atmosphere (atm_phys) with ocean.
+o tools/build_options:
+  - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
+    & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
+    remove CPP setting (was identical to genmake2 default).
+o pkg/gmredi & model/src: Some updating and work done on the residual model.
+  - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
+  - fixed up the calculation of the eddy stress and how it is added to the
+    external forcing via taueddy_external_forcing.F
+  - at the moment, it is very experimental and only works with the variable eddy
+    diffusivity calculated in gmredi_k3d.F
+o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
+    lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
+o testreport (& tools/do_tst_2+2):
+  - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
+o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
+  - remove CPP='cpp -traditional -P' (this is genmake2 default)
+  - add switch (for big setups) to use 'medium' memory-model (but leave it
+    commented out for now). Note: needed with FC 19 to compile big setups.
+o pkg/atm_compon_interf:
+  - regroup per field origin (model & pkgs) the coupling storage routines
+     (which accumalate in time each coupling field)
+  - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
+    update accordingly + simplify aim_do_physics.F
+
+checkpoint64n (2013/08/26)
+o pkg/bbl:
+  - update formulation to reduce dispersion of tracer properties in bbl
+  - replaced horizontal and vertical transport parameters with velocities
+  - changes results for verification/global_with_exf.yearly
+o verification/halfpipe_streamice:
+  - change to matrix construction; update both Fwd & AD output.
+o verification/tutorial_tracer_adjsens:
+  - OpenAD test: switch to vector-invariant momentum since fluxform with
+    rStar causes problems with OpenAD; update output.
+o tools:
+  - genmake2: define a common prefix for all temp-file names ; move them
+    to local /tmp disk (but would be easy to move them back);
+  - xmakedepend: apply the same switch for temp-files.
+o pkg/offline:
+  - changes for use with rStar (NLFS): assume that we continue to provide
+    UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
+    output files) and apply r* scaling at each time-step (function of the time
+    varying Eta field); use normal pickup files (needed for restart with NLFS).
+o adjoint with OpenAD:
+  - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
+    package openad.  This package has to be compiled for all runs with OpenAD
+    instead of specifying code_oad_all as a modification directory.
+  - link the fortran templates from tools/OAD_support to the build directory
+    for preprocessing to avoid conflicts between different setups compiled
+    simultaneously and simplify cleanup.
+o pkg/exf:
+  - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
+    main model or other pkgs are exchanged in EXF_MAPFIELDS).
+o model/src:
+  - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
+    (similar to do_fields_blocking_exchanges.F).
+o tools/genmake2:
+  - remove TAF output src code just before calling staf (when not doing a fresh
+    built, will stop if things go wrong with staf).
+  - fix target "adobj" (left from TAF version-2 transition)
+o pkg/diagnostics:
+  - add a parameter to track the status of pkg/diagnostics activation;
+    this replace/extend the use of logical param "settingDiags" (to check
+    when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
+    New S/R to print error message and stop when pkgStatus is not right.
+  - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
+
+checkpoint64m (2013/08/13)
+o model/inc:
+  - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
+    8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
+o pkg/kpp & aim_v23:
+  - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
+o pkg/seaice:
+  - restore (last time on 2011/12/24) ability to compile pkg/seaice with
+    undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
+  - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
+o eesupp/src:
+  - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
+    in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
+o switch to TAF version-2:
+  - add flow directives to "freeze" naming convention for ad-routines that
+    are used in I/O routines of adjoint state and associated common blocks
+    that are used in adcommon.h (backward compatible with version-1)
+  - update all ad-optfiles (in tools/adjoint_options + few local to some
+    verification exp) to switch to latest TAF version (currently 2.5.5);
+    merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
+    out except for diva).
+  - the major change with TAF version-2 is that both the differentiated
+    routines and the forward routines (new) are returned as part of the TAF
+    output source code. Update genmake2 accordingly.
+  - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
+    with version-2 when compared to TLM or FWD gradient); other experiments
+    output show minor changes (machine truncation level); update the few AD &
+    TLM output with 12 matching digits only (some prior to version-2 switch).
+
+checkpoint64l (2013/08/05)
+o model/src:
+  - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
+  - main_do_loop.F: no longer includes additional (AUTODIFF) header files
+    when using TAF but only if using OpenAD.
+o pkg/mom_common+fluxform+vecinv:
+  - always set horiz. viscosity arrays to background value before calling
+    MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
+    only when using variable horiz. viscosity (useVariableVisc=T);
+  - simplify mom_vecinv.F (only 1 block for momViscosity).
+o pkg/mom_common: variable horiz. viscosity in NH code
+  - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
+    from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
+  - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
+    useBiharmonicVisc & useVariableVisc.
+  - fix old bug (already in 1rst implementation of variable horizontal viscosity
+    in calc_gw.F, version 1.27, 2006/06/20):
+    horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
+    even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
+  - change background horiz viscosity in vertical momentum (gW) to always be
+    viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
+    any type of variable viscosity, e.g., viscAh/4Grid)
+  - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
+    viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
+    horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
+    default viscAh,viscA4 is zero).
+o model/src:
+  - extend length of drC & recip_drC from Nr to Nr+1.
+o Divided Adjoint (DIVA) with MPI:
+  - genmake2: do not create local ./mpi_headers dir when no file to copy into.
+  - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
+    and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
+
+checkpoint64k (2013/07/23)
+o tools/OAD_support:
+  - avoid the need for file "oadtempflile" in insertTemplateDir.bash
+    and remove it from genmake2.
+o tools/build_options:
+  - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
+    MPI_HEADER_FILES list (let genmake2 find the missing headers)
+o verification/halfpipe_streamice:
+  - change to driving stress formulation; update both Fwd & AD output.
+o tools/genmake2 and Divided Adjoint with MPI:
+  - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
+  - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
+  - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
+    Makefile, which is set by genmake2, and check which mpi-headers are needed.
+    Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
+  - update target "CLEAN" (to also remove ./mpi_headers/ dir).
+o testreport:
+  - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
+    perform additional runs (number of additional runs is "add_DIVA_runs" taken
+    from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
+o verification/lab_sea (AD test):
+  - change to test Divided Adjoint Run in this set-up (both standard AD test
+    and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
+o pkg atm_ & ocn_compon_interf:
+  - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
+    staggerTimeStep implementation) and disable (retired) corresponding
+    parameter.
+o pkg/offline:
+  - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
+  - add S/R OFFLINE_CHECK to print offline parameter summary
+    and stop if loading a file that is not used;
+  - enable to calculate GMRedi tensor, KPP mixing and convective index
+    when the corresponding file(s) is/are not specified (but pkg is used).
+  - comment out resetting of monitorFreq (to endTime) since it still useful
+    for monitoring CFL numbers and checking offline fields.
+o OpenAD:
+  - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
+    smaller standard output) and generate new (smaller) output (on baudelaire
+    using gfortran with -ieee) for exp. tutorial_tracer_adjsens
+o model/src:
+  - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
+    (where external_forcing_adjust was called) and change list of arguments;
+  - merge external_forcing_adjust.F into external_forcing_surf.F
+  - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
+    which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
+    previously in file "balance_relax.F", now removed); remove corresponding
+    arrays in FFIELDS.h.
+  - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
+    a hack for getting back surfaceForcingS (loaded from file) when using
+    ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
+  - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
+    (was getting only 11 digits for AD-grad, due to different truncation
+     error in AD code).
+
+checkpoint64j (2013/07/04)
+o pkg/offline:
+  - to enable the use of other features with pkg offline (e.g., obcs),
+    also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
+  - comment out "allowFreezing" (now active) in 2 offline testing exp.
 o pkg/exf ALLOW_RUNOFTEMP
   - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
-  - added RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
+  - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
   - changes verification/global_ocean.cs32x15/results/output.seaice.txt
 o pkg/atm_phys:
   - allows to add some damping on uVel,vVel (strength only function of k).