update_history

    Update history and content of "MITgcm/verification_other"
    =================================================================

checkpoint69c (2024/12/06) synchronised with main MITgcm code.
checkpoint69b (2024/10/31) synchronised with main MITgcm code.
checkpoint69a (2024/09/09) synchronised with main MITgcm code.
checkpoint68z (2024/07/27) synchronised with main MITgcm code.
checkpoint68y (2024/06/05) synchronised with main MITgcm code.
checkpoint68x (2024/04/30) synchronised with main MITgcm code.
  - add PJ Tuckman idealized, cs32, coupled Ocean - Atmosphere set-up
    using simplified gray atmospheric physics with swamp over continent

checkpoint68w (2024/03/05) synchronised with main MITgcm code.
  - post PR #796: update all data.grdchk by setting "grdchkvarname" instead
    of "grdchkvarindex".
  - update seaice parameters for global_oce_llc90.ecmwf secondary test.
  - in exp. "global_ocean.gm_k3d", add new secondary test for GEOMETRIC
    parameterization of Kappa GM, initially added by @mjlosch in PR #674.
  - add David Ferreira idealized, cs24, coupled Ocean - Atmosphere set-up
    using AIM simplified atmospheric physics with interactive CO2 feedback.

checkpoint68v (2024/02/03) synchronised with main MITgcm code.
  - post PR #800 (pkg/shelfice kTopC): update customized source code for
    experiment "shelfice_remeshing"

checkpoint68u (2023/12/10) synchronised with main MITgcm code.
checkpoint68t (2023/10/28) synchronised with main MITgcm code.
  - post PR #769: after fixing bug in GM_ExtraDiag setting, update ref. output
    of the 2 exp. that use Bates-K3d (previous wrong results as ExtraDiag=F).
  - post PR #768: change #include "ctrl_dummy.h" to "CTRL_DUMMY.h" in 1 file.
  - post PR #767: change #include "ctrl.h" to "CTRL.h" in 1 customized src file.

checkpoint68s (2023/09/11) synchronised with main MITgcm code.
  - update seaice and AD related CPP-headers files in exp. offline_cheapaml,
    global_oce_cs32 & global_oce_llc90 (all in code/ dir).

checkpoint68r (2023/08/02) synchronised with main MITgcm code.
  - post PR #749: remove parameter "nobcs" from SIZE.h (now in CTRL_OBCS.h).

checkpoint68q (2023/06/29) synchronised with main MITgcm code.
  - post PR #714: update both Fwd & Ad ref output for cs32 & llc90 tests that
    uses pkg/ggl90 (i.e., all except the 2 AD tests llc90 primary + core2 ).

checkpoint68p (2023/05/07) synchronised with main MITgcm code.
checkpoint68o (2023/03/13) synchronised with main MITgcm code.
  - post PR #689: update and clean-up exp. global_oce_cs32 & global_oce_llc90
    local CPP header files ; also, for llc90, replace few parameter files from
    input_ad & input_ad.ecco_v4 with sym-link from prepare_run.
  - add comments in "data.ecco" from (llc90) input.ecco_v4/ on how to try to
    use S/R cost_gencost_bpv4.

checkpoint68n (2023/02/08) synchronised with main MITgcm code.
checkpoint68m (2022/12/05) synchronised with main MITgcm code.
  - post PR #650: update local "tamc.h" as done in verification/*/code_ad/

checkpoint68l (2022/10/26) synchronised with main MITgcm code.
checkpoint68k (2022/08/17) synchronised with main MITgcm code.
  - remove both parameters "useSmoothCorrel2D/3D" from data.ctrl and options
    ALLOW_SMOOTH_CORREL2D/3D from CTRL_OPTIONS.h in experiments: glogal_oce_cs32
    and global_oce_llc90 (not doing anything outside ECCO_CTRL_DEPRECATED code).
  - post PR #637: define new CPP options GM_INPUT_K3D_GM & GM_INPUT_K3D_REDI
    (in GMREDI_OPTIONS.h) to use ALLOW_KAPGM_CONTROL & ALLOW_KAPREDI_CONTROL

checkpoint68j (2022/06/28) synchronised with main MITgcm code.
  - post PR #611: due to single prec tapes (isbyte=4), switching to local tapes
    in gad_advection.F affects AD-grad of ecco_v4 exp. (6 matching digits left)
    and AD monitor (in all 4 llc90 + 2 cs32 exp); update all 4 llc90 output_adm
    reference output.

checkpoint68i (2022/04/27) synchronised with main MITgcm code.
  - post PR #587 & #609: cleaning/updating some parameter files

checkpoint68h (2022/03/22) synchronised with main MITgcm code.
  - post PR #560 (extra_diags): update cs32 (primary) output_adm.txt

checkpoint68g (2022/02/19) synchronised with main MITgcm code.
  - following main code PR #576, rename GM_K3D to GM_BATES(_K3D).

checkpoint68f (2022/01/14) synchronised with main MITgcm code.
checkpoint68e (2021/12/10) synchronised with main MITgcm code.
checkpoint68d (2021/11/05) synchronised with main MITgcm code.
checkpoint68c (2021/10/02) synchronised with main MITgcm code.
checkpoint68b (2021/08/24) synchronised with main MITgcm code.
  - post PR #507: Turn on "sterGloH" output in global_oce_cs32 "data.ecco".
  - post PR #502 (improve_remove_mean): update 3 llc90 output_adm (all except
    ecco_v4) since FWD results & FWD Grad change at machine truncation level.

checkpoint68a (2021/07/16) synchronised with main MITgcm code.
  - define ALLOW_DIFFKR_CONTROL in experiment global_oce_cs32 & llc90:
    with generic-control and ALLOW_3D_DIFFKR, diffKr was available as a control
    without ALLOW_DIFFKR_CONTROL defined (not well documented); this was dropped
    in https://github.com/MITgcm/MITgcm/pull/447 (ctrl_map_ini_genarr.F) and is
    put back here ; results unchanged (ctrl "xx_diffkr" only set in FWD tests).
  - post PR #471 (pkg/ctrl cleanup): update few local source code, mainly for
    experiment global_oce_cs32 & llc90.

checkpoint67z (2021/06/12) synchronised with main MITgcm code.
  - post PR #445 (ctrl & shelfice): update customized source code for experiment
     shelfice_remeshing
  - post PR #446 (store directives): update all 6 output_adm (oce_cs32 & llc90);
    since these 2 experiments use real*4 storage (isbyte=4), get changes (for
    all 6) in AD-monitor and in AD-grad for oce_cs32 primary test.

checkpoint67y (2021/05/05) synchronised with main MITgcm code.
  - post PR #456 (fix shelfice pLoc): update shelfice_remeshing alternative
    "vrm" output (output_vrm.txt).
  - AD experiments global_oce_cs32 & llc90: Reduce adjMonitorFreq to get few
    AD-Monitor output while running these short tests (e.g., with testreport);
    update all 2+4 reference output_adm from these 2 eperiments.

checkpoint67x (2021/04/12) synchronised with main MITgcm code.
  - post PR #449 (fix TICES storage): update ADM output of exp global_oce_llc90,
    ecco_v4 test only.
  - post PR #438: update 2 ADM output from exp.: global_oce_llc90.
    Fixing missing re-initialisation of recip_hFac change gradient-check of
    ecco_v4 & ecmwf AD tests. Update reference output (from engaging, gfortran).
  - post PR #433: update FWD output of exp.: global_ocean.gm_k3d & .gm_res since
    both use quasiHydrostatic=T (-> affects results @ machine trunc. level).

checkpoint67w (2021/03/06) synchronised with main MITgcm code.
  - add MOC sensitivity cost in experiment global_oce_cs32/input_ad.sens/ and
    generate new ADM output, now from villon.mit.edu (previously from engaging)

checkpoint67v (2021/02/03) synchronised with main MITgcm code.
  - global_oce_llc90 experiment:
   1) clean/simplify parameter files location:
    * move un-used (in any FWD or AD exp) param files from input/ into
      input/unused/
    * param files which are not used in any FWD exp (but only used in some AD
      exp): move them from input/ to input_ad/
    * simplify "prepare_run" from 4 FWD input dir by removing it's own dir.
    * Ajoint input dir: since local "prepare_run" is no longer linking all files
      from corresponding FWD input dir, make a copy of few needed files.
   2) Bring back the use of viscFacInAd:
      before PR #384, the effect of viscFacAdj, was ignored. Bring it back by
      defining the (new) corresponding CPP option: AUTODIFF_ALLOW_VISCFACADJ
      (in AUTODIFF_OPTIONS.h), uncomment viscFacInAd setting in data.autodiff
      and update all 4 AD reference outputs (since viscFacInAd=2 is now active).
  - global_oce_llc90 Adjoint experiment: comment out "viscFacInAd=2." in
    data.autodiff since it was previously inactive until PR #384 code fix
    but would now require to define AUTODIFF_ALLOW_VISCFACADJ to be used.
  - update output of experiment "shelfice_remeshing" following changes in
    solve_pentadiagonal.F (-> affects results @ machine trunc. level), PR #410.

checkpoint67u (2020/12/30) synchronised with main MITgcm code.
  - update FWD output of experiment "global_oce_llc90" following changes in
    seaice_lsr.F (-> affects results @ machine trunc. level), PR #369.
  - update some AD output of experiments "global_oce_cs32" & "global_oce_llc90"
    following fix for self-adjoint cg2d with nonlinFreeSurf > 1 (PR #392).

checkpoint67t (2020/11/30) synchronised with main MITgcm code.
checkpoint67s (2020/07/31) synchronised with main MITgcm code.
  - cleaning experiment "packages.conf":
    1) add a 1 line description at the top ;
    2) use similar ordering of pkgs in packages.conf, same as for main
      MITgcm/verification (see doc/tag-index) ;
    3) remove few unused pkgs (timeave, mnc).

checkpoint67r (2020/06/04) synchronised with main MITgcm code.
checkpoint67q (2020/03/19) synchronised with main MITgcm code.
  - Remove completely "global_oce_biogeo_bling" experiment since it has been
    moved to main MITgcm repository, in verification, on Dec 7, 2019 (PR #307).

checkpoint67p (2020/02/12) synchronised with main MITgcm code.
  - Update code of experiment "shelice_remeshing" after main MITgcm PR #124
    ( https://github.com/MITgcm/MITgcm/pull/124 ) was merged in on Dec 17, 2019.

checkpoint67o (2019/12/23) synchronised with main MITgcm code.
  - update results of experiment "shelice_remeshing" following pkg/shelfice
    changes from PR #311 (Shelfice implicit drag).
  - move here, in dir "shelice_remeshing", the original shelfice_remeshing
    experiment from PR #124 "Branch Remeshing" of main MITgcm repos,
    with suffix "_vrm" (for: Vertical ReMeshing).
  - update results of experiment "offline_cheapaml" following pkg/cheapaml
    changes from PR #254

checkpoint67n (2019/11/26) synchronised with main MITgcm code.
  - clean-up adjoint code dir of experiment global_oce_biogeo_bling
  - new output (generated on new ref. machine "villon") for the 2 GM-K3D
    experiments: global_ocean.gm_k3d & gm_res

checkpoint67m (2019/10/16) synchronised with main MITgcm code.
  - update output of exp. global_oce_llc90 (all 4 FWD and 2 ADM)
    after merging PR #219 on Aug 15.

checkpoint67l (2019/08/29) synchronised with main MITgcm code.
  - update output of exp. shelfice_remeshing after merging PR #219 on Aug 15.
  - add (TAF) Adjoint set-up to experiment global_oce_biogeo_bling

checkpoint67k (2019/07/19) synchronised with main MITgcm code.
2019/06/19:
  - new experiment "atm_strato" (from Matt Kasoar) with enough resolution
    in stratosphere to test stratospheric ozone absorption.

checkpoint67j (2019/06/18) synchronised with main MITgcm code.
  - update output of experiment global_oce_biogeo_bling (new version of
    pkg/bling from PR #243)

checkpoint67i (2019/05/08) synchronised with main MITgcm code.
  - update global_oce_cs32 & global_oce_llc90 customized code following
    PR #96 modifications in mom_calc_visc.F

checkpoint67h (2019/03/21) synchronised with main MITgcm code.
checkpoint67g (2019/01/03) synchronised with main MITgcm code.
checkpoint67f (2018/11/23) synchronised with main MITgcm code.

  - update results of experiment atm_gray (secondary test, ape) after
    changing/fixing dependence on water-vapor in wv_exponent=-1 case.

checkpoint67e (2018/10/16) synchronised with main MITgcm code.

2018/10/10: verification_other development moved to GitHub and
            CVS repos made read-only

  - update (on Sep 12) remaining "data.seaice" from global_oce_cs32
    & global_oce_llc90 experiments.

checkpoint67d (2018/09/04) synchronised with main MITgcm code.
  - update "data.seaice" from offline_cheapaml/input.dyn by putting back
    old seaice parameter default (see PR 116. merged on Aug 25, 2018)
  Remain to update: all data.seaice from global_oce_cs32 & global_oce_llc90
  - update SIZE.h comments

checkpoint67b (2018/05/05) synchronised with main MITgcm code.
checkpoint67a (2018/03/11) synchronised with main MITgcm code.

checkpoint66o (2018/01/30) synchronised with final CVS tag of main MITgcm code.
checkpoint66n (2018/01/18) synchronised with main MITgcm code.
checkpoint66m (2017/12/12) synchronised with main MITgcm code.
checkpoint66l (2017/10/24) synchronised with main MITgcm code.
checkpoint66k (2017/09/20) synchronised with main MITgcm code.
  - update results of experiment global_oce_biogeo_bling (changes in
    pkg/bling on 17/09/02, see doc/tag-index).
checkpoint66j (2017/08/15) synchronised with main MITgcm code.
  - update results of experiments: atm_gray & cpl_gray+ocn after changing
    the way atm-phys momentum tendencies are applied to C-grid dynamics.

checkpoint66i (2017/07/18) synchronised with main MITgcm code.
  - experiment "offline_cheapaml": change to use directly the wind
    (instead of relative wind) and update output
checkpoint66h (2017/06/02) synchronised with main MITgcm code.
checkpoint66g (2017/04/24) synchronised with main MITgcm code.
checkpoint66f (2017/04/06) synchronised with main MITgcm code.
checkpoint66e (2017/03/14) synchronised with main MITgcm code.
checkpoint66d (2017/02/13) synchronised with main MITgcm code.
checkpoint66c (2017/01/19) synchronised with main MITgcm code.
checkpoint66b (2016/12/01) synchronised with main MITgcm code.
checkpoint66a (2016/10/18) synchronised with main MITgcm code.

  - after adding parenthesis in main diagonal calculation of implicit vertical
    diffusion matrix (impldiff.F & gad_implicit_r.F), update output of exp.:
    global_ocean.gm_k3d, shelfice_remeshing, global_oce_cs32, global_oce_llc90
    and cpl_gray+ocn.

checkpoint65z (2016/09/28) synchronised with main MITgcm code.
checkpoint65y (2016/07/29) synchronised with main MITgcm code.

2016/07/07:
  - moved old input/code for shelfice_remeshing to MITgcm_contrib/dgoldber/CPL1
  - now shelfice_remeshing only tests vertical remeshing

2016/06/29:
  - add exp. "global_oce_cs32" to daily  gfortran+mpi test on baudelaire
  - add exp. "global_oce_biogeo_bling" to ifort daily test on baudelaire

checkpoint65x (2016/06/11) synchronised with main MITgcm code.

2016/05/19-27:
  - new pkg "bling" added and tested (daily) with verification experiment
    global_oce_biogeo_bling (see MITgcm_contrib/bling/README.txt)

checkpoint65w (2016/05/12) synchronised with main MITgcm code.
checkpoint65v (2016/04/08) synchronised with main MITgcm code.

2016/04/05: remove Ro_SeaLevel from ATM experiment parameter files;

checkpoint65u (2016/03/14) synchronised with main MITgcm code.

2016/03/01:
  - exp. shelfice_remeshing tested every night (gfortran & ifort)

checkpoint65s (2016/01/13) synchronised with main MITgcm code.
checkpoint65r (2015/12/21) synchronised with main MITgcm code.

2015/12/13:
  - atm_gray: add secondary testing set-up using fixed SST (APE)
    and improved radiation code from Ruth Geen.
2015/12/11:
  - add experiment "shelfice_remeshing" (Dan & Jim)

checkpoint65q (2015/11/18) synchronised with main MITgcm code.

2015/11/12:
  - update cpl_gray+ocn/share-code (ATMIDS.h & OCNIDS.h) and coupler parameter
    file (in input_cpl) following coupling pkg changes.
2015/11/04:
  - switch from #define GLOBAL_SUM_SEND_RECV to #define GLOBAL_SUM_ORDER_TILES
    (i.e., the new default) experiments atm_gray (3 code dir),
    global_ocean.gm_k3d & global_ocean.gm_res ; change cpl_gray+ocn (code_atm
    & ocn) to also use the new default (#define GLOBAL_SUM_ORDER_TILES).

checkpoint65p (2015/10/23) synchronised with main MITgcm code.

2015/10/23:
  - fix cpl_gray+ocn: specify an existing SST file (in data.atm_phys) since
    old one was been removed on Jan 22, 2015

checkpoint65n (2015/07/29) synchronised with main MITgcm code.
checkpoint65m (2015/06/15) synchronised with main MITgcm code.
checkpoint65j (2015/02/25) synchronised with main MITgcm code.

2015/02/22:
  - update global_ocean.gm_k3d & global_ocean.gm_res output after fixing
    pkg/gmredi related code.

checkpoint65i (2015/01/23) synchronised with main MITgcm code.

2015/01/22:
  - update atm_gray/input set-up: start from a 1.yr run pickup file (run with
    atmPhys_stepSST=F) using closer to present new SST file: SST_symEx3.bin ;
    and then switch on atmPhys_stepSST=True and use Qflux file: Qflux_w90.bin
2015/01/21:
  - update output of experiments atm_gray & cpl_gray+ocean after fixing
    bug in frictional heating in S/R ATM_PHYS_TENDENCY_APPLY_V.
2015/01/14:
  - add a test case using ALLOW_EDDYPSI + gmredi K3D scheme (from Michael Bates)
    similar to global_ocean.90x40x15 & tutorial_global_oce_latlon experiments;

checkpoint65h (2014/12/17) synchronised with main MITgcm code.
checkpoint65f (2014/10/13) synchronised with main MITgcm code.

2014/10/06:
  - update cpl_gray+ocn set-up: switch on saisonal insolation and add two
    thin-walls in the ocean from North pole down to 34.S (Double-Drake config);
    also adjust diagnostics to get climatological seasonal output.

checkpoint65e (2014/09/28) synchronised with main MITgcm code.
checkpoint65c (2014/08/30) synchronised with main MITgcm code.
checkpoint65a (2014/07/27) synchronised with main MITgcm code.
checkpoint65  (2014/07/18) synchronised with main MITgcm code.
checkpoint64z (2014/07/10) synchronised with main MITgcm code.
checkpoint64x (2014/05/24) synchronised with main MITgcm code.

2014/05/23:
  - add experiment global_oce_biogeo_bling (see MITgcm_contrib/bling/README.txt)

2014/05/21:
atm_gray & cpl_gray+ocn: change convection parameters:
    switch on "do_virtual" and "do_shallower" (recommended by Paul O'Gorman)
    but keep default RH threshold (=0.8)
    Update output of cpl_gray+ocn (no need to update atm_gray output,
    too short cold start run).
global_ocean.gm_k3d: Update output after fixing minor bugs relating to
    finding the +eigenvalues/vectors (in gmredi_calc_eigs.F & gmredi_k3d.F):
    was getting only 3 matching digits for cg2d.
    New output generated on baudelaire using gfortran and "-devel" option.
    Added to bi-weekly ifort+MPI test on acesgrid.

2014/05/11:
  - update atm_gray & cpl_gray+ocn output after changes in atmospheric p*:
    + Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
    + use constant reference Pot.Temp (thetaConst) instead of tRef
    + Acount for true p* correction in theta <-> T conversion in pkg/atm_phys

2014/05/07:
  - add a test case for gmredi K3D scheme (set up from Michael Bates)
    similar to global_ocean.90x40x15 & tutorial_global_oce_latlon experiments;
    daily test on acesgrid (using gfortran with MPI).

checkpoint64w (2014/05/02) synchronised with main MITgcm code.
checkpoint64v (2014/04/11) synchronised with main MITgcm code.
checkpoint64r (2013/12/08) synchronised with main MITgcm code.
checkpoint64p (2013/10/20) synchronised with main MITgcm code.

2013/09/25:
  - add simple atm-gray + ocean coupled cs-32 aquaplanet setup
    in dir=cpl_gray+ocn; for now, no land, no seaice.

checkpoint64o (2013/09/25) synchronised with main MITgcm code.
checkpoint64m (2013/08/13) synchronised with main MITgcm code.
checkpoint64k (2013/07/23) synchronised with main MITgcm code.

2013/07/07:
  - add a 3rd atm_gray set-up, CS-32 with 26 levels and evolving SST

checkpoint64i (2013/06/18) synchronised with main MITgcm code.

2013/06/12:
  - add the 2 working set-up (atm_gray & offline_cheapaml) to one acesgrid
    daily test (using gfortran with MPI & mth and testing also the restart)

2013/06/10:
  - add secondary test (offline_cheapaml/input.dyn/) using seaice-dynamics
    and convergent wind to produce precip.

checkpoint64h (2013/05/26)
  - add this file and make synchronised tag with main MITgcm code.

2013/05/22:
  - add simple experiment "offline_cheapaml" (cartesian-coordinate zonally
    periodic channel, similar to offline_exf_seaice/input.thsice)
    using cheapAML pkg without ocean time-stepping (offline) but with seaice.

2013/05/08:
  - update atm_gray experiments to use new pkg "atm_phys" (instead of mypackage)

2012/09/11:
  - add code (for now, using "mypackage") and 2 example experiments
    using gray atmospheric physics in dir "atm_gray"; see atm_gray/README.

2012/02/04:
  - Create dir "verification_other" in Contrib area (MITgcm_contrib) for
    additional - not automatically tested - experiments, some might or
    might not be up to date with the main MITgcm code.
  - Move from MITgcm/verification to Contrib/verification_other
    the following un-tested set-up:
      global1x1_tot/
      global2x2_tot/
      lab_sea/code_ad_seaice_ocean/
             input_ad_seaice_ocean/
              code_ad_seaice_only/
             input_ad_seaice_only/
      natl_box_adjoint/
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