--- MITgcm/doc/tag-index	2012/01/16 23:53:58	1.1574
+++ MITgcm/doc/tag-index	2012/04/02 04:34:07	1.1641
@@ -1,17 +1,359 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1574 2012/01/16 23:53:58 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1641 2012/04/02 04:34:07 dimitri Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/bbl:
+  - modification so it can work with z*
+  - replace deltaT with dTtracerLev(k) for asynchronous time stepping
+  - global_with_exf/input.yearly verification; changes output.yearly.txt
+o eesupp/src:
+  - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
+    writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
+  - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
+    # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
+  - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
+  - when using MPI, always set usingMPI=T ; set default accordingly and stop
+    if not consistent.
+  - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
+    argument is zero (in case called within single-thread section).
+o pkg/fizhi:
+    clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
+    in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
+o pkg/exch2:
+  - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
+    activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
+  - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
+    but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
+    with bad ones coming from a not-yet-updated halo.
+    This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
+o pkg/frazil:
+    move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
+    http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
+o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
+o verification/lab_sea
+  * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
+  * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
+  * nTimeSteps 3 -> 4
+  * changed reference output accordingly
+o pkg/ctrl:
+  * fix ctrl_get_gen for xx_sst, xx_sss
+o pkg/fizhi:
+  - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
+    update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
+  - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
+    fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
+    clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
+o pkg/gmredi:
+  - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
+o pkg/fizhi:
+  - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
+    (old)aces open64 tuv test.
+o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
+o pkg/mom_vecinv:
+  - fix 1 loop range in mom_vecinv.F to be like all the other loops which
+    set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
+    with non-lin free-surf).
+o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
+  in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
+  some compilers (gfortran 4.6.0 on MacOS)
+o momentum:
+  - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
+    & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
+    fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
+
+checkpoint63k (2012/03/17)
+o model/src:
+   - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
+     flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
+   - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
+     (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
+o model/src: solve_*diagonal.F
+   - replace division with multiplication by inverse (similar to original version)
+     update output of AD exp. global_ocean.90x40x15.
+   - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
+     to enable the use of the vectorized & differentiable solve_tridiagonal.F
+   - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
+     vertical advection (to get solve_tridiagonal tested in AD mode).
+o pkg/seaice: ECCO-CLIVAR merge:
+  1. seaice AREA relaxation
+     * CPP option: SEAICE_ALLOW_AREA_RELAXATION
+     * runtime flag: SEAICE_tauAreaObsRelax
+  2. modified global mean cost imbalance code: CPP option
+      ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
+o another iteration on solve_*diagonal.F
+   Make choices independent of AUTODIFF
+   Default will be the adjoinable vectorized version.
+   Alternative choices are:
+   * non-adjoinable original version with low memory footprint:
+     #define SOLVE_DIAGONAL_LOWMEMORY
+   * still adjoinable but does not vectorize (k as inner-most loop):
+     #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
+o testreport
+ - add option to use a home made wrapper around "make"
+ - remove MITGCM_IEEE env. variable (no longer active)
+o pkg/shelfice
+ - improve computation of friction velocity for velocity dependent
+   exchange coefficients: include velocities into SHELFICEBoundaryLayer
+   block to average velocities vertically
+ - add TAF store directives for SHI_ALLOW_GAMMAFRICT
+o Modify diagonal solvers, now three versions (upon request):
+  #ifndef SOLVE_DIAGONAL_AUTODIFF
+    1. default version (dating back a while ago)
+  #else /* def SOLVE_DIAGONAL_AUTODIFF */
+  # ifdef SOLVE_DIAGONAL_KINNER
+    2. adjoinable version with k-innermost loop (G. Forget)
+  # else
+    3. adjoinable vectorized version of 2.
+  # endif
+  #endif /* SOLVE_DIAGONAL_AUTODIFF */
+  All flags are currently set within routines, but could/should be moved to CPP-options.
+  Array bounds for 1. are as before, for 2.,3. cover the entire domain
+  (could be changed for 1. too).
+o verification/lab_sea (fwd):
+  - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
+    use 7 categories (except hb87), new solve4temp params (except salt_plume),
+    constant salinity (=4) or variable salinity (salt_plume) done through
+    SItracer.
+o pkg/seaice:
+  - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
+  - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
+     SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
+    from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
+    SEAICE_freeze got retired) but already better than previously with
+    SEAICE_freeze=123456.7 deg.C;
+  - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
+    (safer multi-threaded setting); always set SEAICEuseEVP;
+  - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
+    SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
+    stop if multiple specifications for the same coeff; make sure default
+    SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
+o pkg/obcs:
+  - allow to switch to upwind 1rst order advection scheme for the advective
+    flux computation at the open-boundary; disabled for adjoint built.
+o pkg/ptracers:
+  - rename PTRACERS_RESTART.h -> PTRACERS_START.h
+  - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
+  - add parameter to decide when to start a tracer; use internal flag to
+    know which tracer to step-forward; switch this internal flag at the top
+    of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
+    for adjoint built.
+o pkg/seaice:
+  - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
+  - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
+  - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
+o pkg/ecco:
+  - fix writing of output file DiagnosCost_ClimSalt/Theta
+    and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
+o pkg/seaice:
+  - add missing initialisation of COR_ICE array in dynsolver.F
+  - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
+    compiled either way, and is tested in all exps (multidim was only tested
+    in lab_sea ad before).
+  - cosmetic change to prepare for future addition of ITD. no change to results.
+    no defaults change.
+  - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
+  - by lack of adequate verification experiments, I further used custom versions
+    of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
+    should be correct.
+  - avoid recomputations in ad.
+o array initialisation in adjoint mode:
+  1) pkg/mom_common/mom_calc_ke.F:
+    add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
+    The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
+    part this initialisation is gone, resulting in Floating Point Exception
+    (caught by open64 compiler with debug option).
+  2) model/src/convective_weights.F
+    set output convectCount over the full array range (instead of doing
+    an update): this fix a similar issue when called within recomputation (adjoint)
+    which could by-pass the initialisation (normally done in the caller S/R).
+o pkg/seaice:
+  - final version of turbulent flux params, as agreed at MIT ice meet:
+       SEAICE_mcPheePiston (default is ~ 0.000875)
+       SEAICE_mcPheeTaper (default is 0.)
+       SEAICE_frazilFrac (defualt is 1.)
+       SEAICE_mcPheeStepFunc (default is false)
+  - changes results at trunction error level
+  - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
+o added pkg/frazil:
+  - see frazil_description.tex for details
+  - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
+o pkg/shelfice/shelfice_thermodynamics.F
+  - fix exponents for velocity dependent exchange coefficients: change
+    from 2/3(=0) to 0.66666666666666667
+  - move computation of velocity dependent exchange coefficients into
+    separate loop, so that it applies to both thermodynamics
+  - move some divisions by constants out of loops
+
+checkpoint63j (2012/02/16)
+o pkg/seaice:
+  - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
+  - SItracer:  added run time params, and allow coupling to ocn salinity.
+o pkg/seaice: remove (almost) all divisions by constants within loops
+  in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
+  results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
+  those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
+  output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
+o pkg/seaice :
+  - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
+    = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
+  - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
+  - add permanent SItflux diag that corresponds to TFLUX but includes
+    ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
+  - allow activation/testing of a fix for suspected missing term in
+    ocn-ice heat budget (to be confirmed). To test this, you want to
+    undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
+    SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
+  - no change in results, fwd or ad.
+o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
+  - switch to variable freezing point.
+       Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
+  - bug fix : the sublimation term that was missing is now activated.
+       Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
+  - bug fix : flooding sign term for SIsal0.NE.0.
+       Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
+o pkg/seaice:
+  - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
+    is now the default, and the old default constant freezing point is recovered
+    with SEAICE_tempFrz0    = -1.96,
+         SEAICE_dTempFrz_dS = 0.,
+  - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
+  - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
+  - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
+    activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
+  - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
+    was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
+  - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
+    seaice_growth r149 for legacy branch (no results change).
+  - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
+    from I. Fenty).
+  - results did not change except for global_ocean.cs32x15, mostly due to the
+    switch to variable freezing point (see above item for detail).
+o pkg/thsice:
+  - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
+    seawater freezing in thsice_calc_thickn (not used).
+o pkg/seaice: turbulent flux term specification via run time params.
+  - replace CPP switches with run time switches to facilitate testing
+  - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
+                   GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
+  - added runtime parameter : SEAICEturbFluxFormula
+  - move Mcphee constants to SEAICE_PARAMS.h
+  - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
+             SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
+             remove seaice_summary call (moved to seaice_init_fixed)
+  - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
+    SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
+  - seaice_summary.F : add missing report of read turbulent flux term set up
+                       and SITRACER.
+  - seaice_check.F : check range; inform and stop if retired CPPs are used
+                     (incl. SEAICE_AGE).
+  - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
+         CPP switch, same computation as before for the different options.
+  - change results at the truncation level.
+o pkg/seaice:
+  - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
+    useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
+    SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
+  - update verification/*/input*/data.seaice:
+    to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
+    code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
+    and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
+    set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
+o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
+  - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
+    algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
+    difference in results only due to machine truncation.
+  - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
+    MaykutPolySatVap; keep MIN_LWDOWN.
+  - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
+  - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
+    + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
+o pkg/salt_plume:
+  - isolate saltPlumeFlux array exch into a specific S/R called from
+    do_oceanic_phys.F
+  - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
+o verification:
+  - move untested set-up to MITgcm_contrib/verification_other.
+o pkg/seaice:
+  - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
+o pkg/seaice:
+  - seaice_solve4temp.F (keeping results unchanged):
+    * add 2 future run-time params to select which saturation vapor pressure
+      formula is used and how post-iteration fluxes are set.
+      Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
+    * New piece of code (not used) to update surf. atmos. heat flux F_ia using
+      the linearized expression to stay consistent with tsurf finding.
+  - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
+    can be < 0.
+o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
+  - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
+    conductive heat flux F_c , and add it explicitly when updating tsurf as
+    solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
+    so that now F_ia has a consistent meaning through the entire routine.
+    This causes differences at truncation level: update output of fwd exp.
+    global_ocean.cs32x15.seaice.
+o pkg/seaice:
+  - lots of editing/cleaning in seaice_solve4temp.F + better documentation
+    of arrays, sign/direction of fluxes; no effect on results.
+  - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
+    in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
+    note: this should have been done before changing celsius2K default.
+  - to keep results unchanged, add back old value of celsius2K in verification
+    exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
+  - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
+    SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
+    value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
+    freezing temp is consistent with value in seaice_growth.F ; this causes
+    differences at machine truncation level: update lab_sea AD output (3/4).
+o pkg/seaice:
+  - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
+    and climsst/sss even when using seaice (to prevent calculation that might
+    use SST on land); does not affect any verification exp.
+  - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
+    of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
+o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
+  over land (non-legacy code)
+o vectorize salt_plume package:
+  - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
+  - this code computes plumebk everywhere (also over land), thus requires
+    code to avoid divisions by zero and catch the case of kLev=Nr.
+  - efficiency of salt_plume_frac is still sub-optimal
+o tools (genmake2):
+  - fix makefile NAME specification (option: -makefile NAME) by adding
+    "-f $MAKEFILE" in few places where it was missing including makedepend
+    command (contribution from Paul).
+
+checkpoint63i (2012/01/24)
+o model/src:
+  - add factorized versions of some EOS code to find_rho.F,
+    define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
+o model/src:
+  - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
+  - change default celsius2K from 273.16 to 273.15
+  - to keep results unchanged, add back old value of celsius2K in verification
+    exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
+     global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
+o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
+  to make TAF generate vectorizable code
+o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
+   Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
+   have flags that do this more efficiently.
+o pkg/diagnostics/diagstats_calc.F
+  - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
+o pkg/obcs (with exch2):
+  - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
+    and remove code (in obcs_readparms.F) which was based on EXCH of indices
+    (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
 o pkg/exf and seaice exp:
   - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
     so that switching off area & heff advection flags does not affect results.
   - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
-  - keep seaice_obcs unchanged (using #undef EXF_LWDOWN_WITH_EMISSIVITY)
-    and, using pkg/exf default emissivities, update results of fwd verification
-    experiments: 1D_ocean_ice_column, global_ocean.cs32x15.seaice, lab_sea (x4)
-    and offline_exf_seaice (x3).
+  - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
+    EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
+    results of verification experiments: 1D_ocean_ice_column(fwd),
+    global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
+    and offline_exf_seaice (all 4).
 o pkg/seaice:
   - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
     remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.