--- MITgcm/doc/tag-index	2013/07/25 01:12:45	1.1901
+++ MITgcm/doc/tag-index	2014/01/03 17:28:19	1.1953
@@ -1,9 +1,328 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1901 2013/07/25 01:12:45 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1953 2014/01/03 17:28:19 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o tools/adjoint_options:
+  - switch to fastopt.net TAF server (instead of default fastopt.de) for
+    AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
+o model/src:
+  - remove some unnecessary TAF storage directives in forward_step.F and
+    in dynamics.F (note: not always removed by TAF, e.g., double storage
+    of kappaRU,kappaRV in former version of dynamics.F).
+o model/src & pkg/ptracers:
+  - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
+    salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
+    and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
+  - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
+  - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
+  - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
+o useSingleCpuInput separates single-CPU input from single-CPU output;
+    for now only implemented for in exf_interp_read.F
+o verification/advect_xy:
+  - fix missing EXCH call in local version of ini_salt.F and update output.
+o momentum diagnostics:
+  - fix which deltaT is used in Total-Tendency diagnostics.
+  - fix typo in diagnostics for momentum tendency from AB.
+o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
+    SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
+
+checkpoint64r (2013/12/08)
+o verification/*/results:
+  - Update reference output of experiments that were passing with just 13 digits
+     (make it easier to detect future changes in results)
+o model/src & pkg/ptracers:
+  - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
+    inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
+    to inside ptracers_integrate.F ; remove ptracers_advection.F
+o coupling interface pkgs:
+    [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
+  - change the config check to test the agreement of Ocean Depth
+    with ATM land/sea mask (instead of ATM orography);
+  - send to coupler the number of coupler time-steps to do for this run:
+    this allows to check for consistency and don't need anymore to be
+    specified in parameter file "data";
+  in coupler:
+  - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
+  - improve report to log-file of config setting (pass log-file unit to few S/R)
+o pkg/compon_communic:
+  - add coupling send/receive for non-tiled integer vector;
+  - add S/R to check and stop if any proc has an error (similar to
+    eesupp/src/stop_if_error.F but single thread and across Comm_World).
+o pkg/exch2:
+  - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
+    through list of all tiles my proc owns.
+o model/src:
+  - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
+    from rTrans) to simplify dependencies (no need to store rTrans anymore in
+    calling S/R); this affects AD results at machine truncation level:
+    update AD-output (TAF) of experiments: 1D_ocean_ice_column,
+    bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
+o tools/build_options:
+  - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
+o coupling interface pkgs:
+    [compon_communic, atm_compon_interf & ocn_compon_interf]
+  - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
+    to each S/R that needs it; remove un-used variables.
+  - change component tile registration (cpl_register.F in both compon_interf
+    and mitcomponent_tile_register.F) to pass the full list of tiles
+    information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
+  - with pkg/exch2: adopt the same convention used for I/O to define mapping
+    towards coupler global array (unless W2_useE2ioLayOut=F):
+     a) can now use different tiling between atm & ocn comp.
+     b) no needs to modify the run-Off map when changing tiling (was needed
+        even if using the same tiling between atm & ocn).
+     c) will allow to run with blank-tiles in 1 component (e.g., for ocean
+        full land tiles); not yet tested.
+  - check for valid mapping from comp. tile to coupler global array
+  - improve report of tile registration results to log file.
+o pkg/exch2:
+  - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
+    tile-registration (CPL_REGISTER);
+  - activate (un-comment) definition and setting of "W2_tileIndex" list to
+    store the local bi,bj indices of each tile;
+  - also print bi,bj in local report to log file;
+  - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
+    Jun 2009 modif of pkg/exch2).
+o testing on baudelaire:
+  - run 2 tests at a time: no significant slow down (since enough cpu) and
+    get the full set of test done earlier
+  - switch the ifort test to "-devel" ; run the OpenAD test everyday.
+o model/src/thermodynamics.F and routines called from it:
+  - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
+    gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
+    velocity (outp) by adding bolus velocity.
+  - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
+    mass transport from velocity + lateral grid cell area
+  - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
+  - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
+ in thermodynamics.F
+  - remove k from thermodynamics.F and move it to temp_integrate.F
+    salt_integrate.F and ptracers_integrate.F (now done inside the tracer
+    loop).
+  - compute locally (in thermodynamics.F) 3-D velocity field that is used to
+    advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
+    PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
+    GAD_IMPLICIT_R and PTRACERS_IMPLICIT
+  - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
+    global_ocean.90x40x15, tutorial_global_oce_biogeo and
+    tutorial_tracer_adjsens (+ TLM output).
+o tools/OAD_support and (verification/*/) code_oad:
+  - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
+    module conversion ; remove unneeded CPP_EEOPTIONS.h.
+  - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
+    version (closer to model/inc/CPP_OPTIONS.h).
+o model/src:
+  - remove parameter "useOldFreezing" from PARAMS.h and push it to the
+    retired list of parameters (routine FREEZE has been replace by surface
+    freezing (10.yrs ago) and by pkg/frazil (interior freezing).
+o pkg/gmredi:
+  - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
+    velocity (same scheme but affects machine truncation) for GM_AdvForm.
+  - update output of FWD experiments: front_relax.bvp,
+    global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
+
+checkpoint64q (2013/11/17)
+o verification:
+  - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
+    tutorial_global_oce_biogeo and global_ocean.90x40x15.
+  - generate new output (growth & melt) for seaice_itd experiment after
+    updating the input pickup_seaice files (previously wrong).
+o pkg/cost:
+  - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
+    (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
+    o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL
+      cannot be applied to var in common block).
+    o allows to get results independent of tile-per-proc setting (if using
+      slower GLOBAL_SUM_SEND_RECV option).
+  - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
+    thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
+    forward gradients: update output).
+  - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
+    S/R and, for most exp., also comment out GLOBAL_SUM_R8.
+o pkg/mom_common:
+  - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
+    code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
+    viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
+    ensure that all field value that are used are set.
+o tutorial_deep_convection (smag3d):
+  - add missing scaling in mom_calc_smag_3d.F;
+  - set smag3D_coeff in input.smag3d such that results do not change.
+o pkg/dic:
+  - change dic_cost.F to compute cost on each tile first and then apply
+    GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
+    tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
+  - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
+o eesupp/src & pkg/mdsio:
+  - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
+    (from pkg/mdsio) since they are no longer used for tape IO.
+  - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
+    (+ keep a copy in pkg/atm_ocn_coupler).
+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