--- MITgcm/doc/tag-index	2014/04/23 12:42:19	1.1980
+++ MITgcm/doc/tag-index	2014/07/15 23:07:57	1.2024
@@ -1,17 +1,232 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1980 2014/04/23 12:42:19 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.2024 2014/07/15 23:07:57 heimbach Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o OpenAD
+  - clean up code_oad/ directories somewhat by moving files
+    dontCompile, dontTransform, keepOriginal to OAD_support/
+o model/src:
+  - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
+    (not currently tested): add dissipation terms before NLFS rescaling of
+    tendencies (previously done after).
+o pkg/diagnostics:
+  - write stats-diags in ascii file with more digits (same as in monitor).
+o pkg/down_slope:
+  - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
+    NLFS (not tested), use new recip_hFac value in order to conserve tracer.
+o model/src:
+  - new file "apply_forcing.F" containing all the code previously in
+    external_forcing.F, but with new argument list: pass, as new argument,
+    the current level tendency array to update (instead of a direct update
+    of the common bloc array). Change the corresponding calls.
+  - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
+    EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
+o pkg/seaice/seaice_lsr, a little bit of clean up
+  - rearrange some code blocks, so that now all calculations for
+    setting up the right-hand-sides done within one single block
+    (I find that easier to read and understand)
+  - rearrange freedrift-code to reduce the number of ifdefs
+  - adjust some indentations and comments
+
+checkpoint64z (2014/07/10)
+o model/src and several pkgs:
+  - change argument list of all S/R called from external_forcing.F and
+    called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
+    to pass, as argument, the current level tendency array to update
+    (instead of a direct update of the common bloc array).
+  - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
+  - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
+o pkg/seaice/seaice_lsr.F
+  - always initialize local arrays in seaice_lsr_tridiagu/v
+  - add more local tapes to seaice_lsr_tridiagu/v
+  - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
+    keep it in bi/bj loop; this seems to be essential
+  - gradients are still wrong but only by 4-7 orders of magnitude
+    instead of 15 orders of magnitude, lab_sea improves a little
+o pkg/seaice
+  - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
+    generates unnecessary code in seaice_lsr_ad
+  - add more store directives in seaice_lsr to avoid unnecessary code
+    in seaice_lsr_ad
+  - exclude some residual computations in seaice_lsr when
+    ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
+    in seaice_lsr_ad
+  - add more storing, a new tape (model/src/the_main_loop.F) and
+    another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
+    and klockey should be checked by a specialist)
+  - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
+    and update lab_sea after previous changes in pkg/seaice below
+o pkg/autodiff:
+  - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
+    viscFacInAd : run time parameters allowing for adjoint switches
+    note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
+o pkg/ecco:
+  - introduce cost_gencost_boxmean.F that computes a box mean
+    temperature (for use in adjoint sensitivity studies).
+o model/src/set_defaults.F : initialize viscFacAdj to 1.
+o pkg/mom_common/mom_calc_visc.F:
+  - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
+o pkg/seaice/seaice_summary.F:
+  - statement for SEAICEadjMODE now in autodiff_readparms.F
+o pkg/seaice:
+  - remove some store directives and add new ones in an effort to get
+    finally rid off the recomputation warnings. This is successful
+    when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
+    defined (i.e. no extensive recomputation warnings left), but there
+    are still too many recomputations on the solver iteration level
+  - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
+  - move definition of MPSEUDOTIMESTEPS into TAMC-block in
+    SEAICE_SIZE.h
+  - add a store directive in S/R seaice_calc_viscosities
+o pkg/seaice (ITD code):
+  - fix definition of Hlimit for multi-threaded case
+  - use double precision arithmetic to compute Hlimit: this affects results;
+    update output of experiment seaice_itd.
+o replace content of verification/seaice_itd
+  - instead of a 1D column use the configuration of offline_exf_seaice
+    to test the ice thickness distribution code with ridging
+  - this is a first shot at this experiment
+  - change of some defaults of ridging parameters SEAICEhStar (from
+    100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
+    and lot of new comments.
+
+checkpoint64y (2014/06/20)
+o pkg/seaice/seaice_reg_ridge.F:
+  - modify the regularization of very small volumes of ice; only check
+    total volume HEFF, and do not apply correction to individual ice
+    classes because that leads to funny patterns in the heat and fw-fluxes
+    into the ocean. Adjust seaice_itd/results/output.txt
+  - replace nITD by SEAICE_multDim in loop-ranges
+o pkg/exf:
+  - add code to process the case field period = -12. with UV interpolation.
+  - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
+    into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
+o verification/global_with_exf:
+  - switch all fields period to -12. (was previously untested) in input/data.exf
+    (but keep secondary test ".yearly" unchanged); update the reference output.
+o pkg/cal:
+  - new calendar type "noLeapYear" for 365 days calendar without any leap year.
+o pkg/exf:
+  - new integer parameter "exf_debugLev" (default set to main model debugLevel)
+    to replace logical switch "exf_verbose"
+  - report in STDOUT when loading a new record (if exf_debugLev >= 3)
+o pkg/sbo:
+  - update from Katherine Quinn: evaluate mass directly from density and SSH
+    (budget using Finite Volume method) instead of from bottom pressure.
+  - allow testreport to collect few selected SBO output ; tested in exp.
+    global_ocean.90x40x15 (after updating the results, to include SBO output).
+  - fix some multi-threading issues (in output part).
+o model/src & most packages:
+  - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
+  - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
+    PACKAGES_UNUSED_MSG to print a weak warning when parameter file
+    "data.{pkg}" exist ; and leave the S/R (return) just after.
+  - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
+    + call LAND_READPARMS from packages_readparms.F
+o pkg/seaice:
+  - remove code that resets useThSice in S/R seaice_readparms and
+    replace it by a warning in S/R seaice_check
+  - remove parameter MULTDIM, replace with nITD and runtime
+    parameter SEAICE_multDim (still hard-wired to nITD if
+    SEAICE_ITD is defined)
+
+checkpoint64x (2014/05/24)
+o verification/lab_sea:
+  - update adjoint and TLM output following changes to pkg/salt_plume
+  - un-do the update after putting back local recip_Cp in few places.
+o pkg/salt_plume: modifications by An Nguyen:
+  - add capability to do brine rejection (salt-plume) as function of
+    volume+tracers (instead of only salinity tracer).
+  - conserve volume by exchanging volume from each kLev to above to
+    accommodate in-coming brine volume
+  - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
+  - switch KPP surf buoyancy due to brine forcing to 3-d
+    (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
+  - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
+  - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
+    in East/West Arctic.
+o pkg/sbo:
+  - incorporate modifications from Katherine Quinn to enable the use of sbo
+    pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
+    output for future testreport verification (unfinished).
+o pkg/atm_phys:
+  - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
+    skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
+    output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
+o pkg/seaice
+  seaice_calc_ice_strength.F: modify expression to avoid divisions
+    (affects truncation)
+  seaice_do_ridging.F: clean up the insectarium
+  - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
+  - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
+  - set closing/openingRate to zero where no extra iteration is need (3rd bug)
+  - add some debugging information and error messages (warnings)
+o model/src: modifications relatd to atmosphere p*:
+  - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
+  - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
+    of vertical profile tRef in geopotential background and anomaly.
+  - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
+    and pkg/atm_phys.
+  - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
+    fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
+o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
+o pkg/ptracers: compute ptracer source/sink due to linear free surface.
+    not used right now, but can be used in BGC packages to fix conservation.
+o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
+    other packages too.
+o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
+    SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
+o model/src:
+  - since we have several heat capacity (even in model/src), define "recip_Cp"
+    as local variable (no longer in common block) to avoid any confusion.
+  - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
+o pkg/exf:
+  - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
+    air density as function of air Temp, Humidity and atm pressure.
+
+checkpoint64w (2014/05/02)
+o verification:
+  - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
+    seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
+    code from seaice_growth.F & seaice_advdiff.F to new ridging routines
+    seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
+    (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
+o model/src: for atmosphere in p* coords:
+  - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
+  - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
+    but not yet activated.
+o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
+  - move computation of opnWtrFrac = 1-AREA to before computing ice strength
+  - this changes the results (but not for any verification experiment, because
+    none tests this), but avoids having an extra field in the restart files
+o pkg/seaice: remove global variable TICE (not needed)
+  - replace by TICES or local variable where necessary (cost_seaice_test,
+    seaice_diagnostics_state)
+  - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
+  - use specific read/write routines for reading and writing individual leves
+    of a multilevel field
+o pkg/ctrl & model/inc:
+  - move additional anomaly fields of control vars (related to options:
+     ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
+    from DYNVARS.h into new header file: CTRL_FIELDS.h
+o pkg/seaice: some small modifications to the ridging code
+  - make fw2ObyRidge a global variable and add the freshwater flux to
+    seaice_growth
+  - pass actual thickness from seaice_prepare_ridging, so that it is
+    computed only in one place and compute it in the same way as in
+    seaice_growth
+  - initialise more fields in seaice_do_ridging that where cause floating
+    point exceptions over land
 o pkg/seaice: preparations for ridging code and first real ridging code
-  - move most of "PART 1" of S/R seaice_growth into a new and separate 
+  - move most of "PART 1" of S/R seaice_growth into a new and separate
     S/R seaice_reg_ridge that will both regularize the state variable after
     advection call the actual ridging routine;
-  - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG, 
+  - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
     d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
   - remove ridging code from seaice_advdiff
-  - clean up remaining part 1 of seaice_growth in an attempt to make it 
+  - clean up remaining part 1 of seaice_growth in an attempt to make it
     more readable (this is probably subjective)
   - call seaice_itd_redist once in the initialisation phase to have the initial
     conditions in the correct category