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-revision 1.1926 by dimitri,
Sat Sep 28 19:09:38 2013 UTC
+revision 1.1977 by atn,
Mon Apr  7 18:41:13 2014 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ o pkg/ecco:
+   - add runtime parameters mdt[start,end]date[1,2]
+   - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
+ o pkg/seaice:
+   - make deltaC a global variable, so that it can be used in ridging code
+   - first step towards ridging: introduce new routines that compute
+     ice strength based on ridging parameters
+ o pkg/salt_plume + pkg/seaice/seaice_growth.F
+   - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
+     AREA exceeds a threshold (code contributed by I.Fenty in 2011)
+ o verification/hs94.1x64x5:
+   - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
+   - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
+ o autodiff:
+   - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
+     and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
+     For now, only in pkgs used in verification/hs94.1x64x5.
+   - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
+     which are specific to TAF/TAMC).
+   - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
+     since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
+     is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
+   - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
+     building mitgcmuv_ad (make adAll).
+ o pkg/ecco:
+   - cost_gencost_seaicev4.F:
+      reformulate proxy cost as function of sst and local param SEAICE_freeze
+      change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
+   - add stop statement if old names siv4-[sst,vol] are used
+   - add snapshots + cost reports for atmospheric longwave
+   - remove factor 0.1 in front of wtau[u,v]
+   - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
+      ALLOW_TMI_SST_COST_CONTRIBUTION
+ o pkg/atm_phys:
+   - add some diagnostics for Short-wave and for convection S/R.
+ o pkg/seaice/seaice_growth:
+   - fix a bug in the lateral melt parameterization for SEAICE_ITD
+     in seaice_growth; tempFrz needs to be computed inside the i/j-loop
+   - rearrange loop order for better vector code in the same code block
+   - rewrite the floeDiameter formula to have fewer divisions
+   -  (miraculously) none of this changes the results of seaice_itd
+ o pkg/smooth:
+   - move param smooth2Ddiffnbt to pkg/ecco
+ o pkg/salt_plume:
+   - salt_plume_frac.F:
+      clean up local param names
+      reformulate (1-frac) to frac; original 1-frac was based on swfrac code
+ o pkg/rw:
+   - add RS version of S/R READ_MFLDS_LEV.
+ o pkg/streamice:
+   - fix the restart test by writing/reading pickup_streamice files.
+ o pkg/seaice:
+   - refine checks for jfnk-related parameters
+   - comment out if statement with SEAICEuseIMEX parameter as long as there
+     is no IMEX code to avoid confusion and surprises
+ checkpoint64u (2014/03/07)
+ o verification/MLAdjust:
+   - rename secondary test suffix:
+.leith  -> A4FlxF  + switch to flux-form & add side-drag
+.leithD -> AhFlxF  + switch to flux-form
+.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
+.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
+ o pkg/mom_vecinv:
+   - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
+     to be before mom_calc_visc.F)
+   - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
+   - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
+     this is simpler for the adjoint and for diagnostics.
+ o model/src + pkg/momentum:
+   - add input files for  2-D additional Western and Southern cell-edge wall
+      (e.g., to add "thin-wall" where it is =1).
+   - fix sideDrag option for thin-walls with Non-Lin Free-Surf
+     using 2nd hFacZ that is computed from initial (fix domain) hFac
+   - known limitations of thin wall implementation: not yet coded for sigma
+     coords; not working with CD-scheme neither.
+ o pkg/seaice:
+   - rename recently introduced parameters from (wrong name) AB to
+     BDF (backward difference time discretisation)
+   - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
+ o tools/adjoint_options:
+   - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
+ checkpoint64t (2014/02/01)
+ o pkg/ecco
+   - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
+     runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
+   - replace hard-coded record number and period which only work for monthly
+     with read-in runtime param that works for other periods (month,day,year)
+ o pkg/thsice
+   - corrected store directive fixes thsice adjoint gradient checks
+ o genmake2 & testreport:
+   - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
+     in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
+     Update testreport accordingly. No need to set "export OPENAD=true"
+     in adjoint_options/adjoint_oad anymore (will be removed later).
+ o pkg/shelfice:
+   - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
+     only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
+     so that surface forcing applies to k=kSurf if using pkg/shelfice.
+ o pkg/ctrl, pkg/grdchk, pkg/ecco:
+   - Changes to make GENARR more modular (i.e. invisible if not used)
+ o model/src/temp_integrate.F and salt_integrate.F
+   - re-include store directives that were removed on Dec 27th.
+ o model/src/external_forcing_surf.F
+   - add storage directives for EmPmR and PmEpR to avoid recomputation of
+     seaice_model in the adjoint that is problematic when seaice_model is
+     turned off in the adjoint. The resolved issue dated back to July when
+     EXTERNAL_FORCING_SURF call was moved.
+     Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
+ o pkg/exf/exf_check.F
+   - fix a small bug again (originally found by Wentao Liu, now found again)
+   - streamline error output
+ o pkg/streamice and aim_v23:
+   - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
+     Apple's /usr/bin/cpp knows what to do:
+     Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
+     Target: x86_64-apple-darwin13.0.0
+ checkpoint64s (2014/01/05)
+ 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_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 added SINGLE_DISK_IO option because reading of parameter files on
-   very large number of processors did not work with existing set-up
  o pkg/atm_phys & atm_compon_interf:
    - allows for coupling of gray-atmosphere (atm_phys) with ocean.
  o tools/build_options:

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