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-revision 1.1876 by jmc,
Tue Jun 11 02:52:42 2013 UTC
+revision 1.2002 by jmc,
Wed May 28 23:14:38 2014 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ 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 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
+     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,
+     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
+     more readable (this is probably subjective)
+   - call seaice_itd_redist once in the initialisation phase to have the initial
+     conditions in the correct category
+   - finally: add new ridging routine for ITD code
+ checkpoint64v (2014/04/11)
+ 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
+   - add diagnostic for HSNOWITD
+   - add opnWtrFrac as a global variable (required for ridging scheme)
+ 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 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
+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
+     and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
+ checkpoint64k (2013/07/23)
+ o tools/OAD_support:
+   - avoid the need for file "oadtempflile" in insertTemplateDir.bash
+     and remove it from genmake2.
+ o tools/build_options:
+   - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
+     MPI_HEADER_FILES list (let genmake2 find the missing headers)
+ o verification/halfpipe_streamice:
+   - change to driving stress formulation; update both Fwd & AD output.
+ o tools/genmake2 and Divided Adjoint with MPI:
+   - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
+   - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
+   - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
+     Makefile, which is set by genmake2, and check which mpi-headers are needed.
+     Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
+   - update target "CLEAN" (to also remove ./mpi_headers/ dir).
+ o testreport:
+   - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
+     perform additional runs (number of additional runs is "add_DIVA_runs" taken
+     from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
+ o verification/lab_sea (AD test):
+   - change to test Divided Adjoint Run in this set-up (both standard AD test
+     and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
+ o pkg atm_ & ocn_compon_interf:
+   - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
+     staggerTimeStep implementation) and disable (retired) corresponding
+     parameter.
+ o pkg/offline:
+   - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
+   - add S/R OFFLINE_CHECK to print offline parameter summary
+     and stop if loading a file that is not used;
+   - enable to calculate GMRedi tensor, KPP mixing and convective index
+     when the corresponding file(s) is/are not specified (but pkg is used).
+   - comment out resetting of monitorFreq (to endTime) since it still useful
+     for monitoring CFL numbers and checking offline fields.
+ o OpenAD:
+   - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
+     smaller standard output) and generate new (smaller) output (on baudelaire
+     using gfortran with -ieee) for exp. tutorial_tracer_adjsens
+ o model/src:
+   - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
+     (where external_forcing_adjust was called) and change list of arguments;
+   - merge external_forcing_adjust.F into external_forcing_surf.F
+   - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
+     which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
+     previously in file "balance_relax.F", now removed); remove corresponding
+     arrays in FFIELDS.h.
+   - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
+     a hack for getting back surfaceForcingS (loaded from file) when using
+     ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
+   - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
+     (was getting only 11 digits for AD-grad, due to different truncation
+      error in AD code).
+ checkpoint64j (2013/07/04)
+ o pkg/offline:
+   - to enable the use of other features with pkg offline (e.g., obcs),
+     also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
+   - comment out "allowFreezing" (now active) in 2 offline testing exp.
+ o pkg/exf ALLOW_RUNOFTEMP
+   - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
+   - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
+   - changes verification/global_ocean.cs32x15/results/output.seaice.txt
+ o pkg/atm_phys:
+   - allows to add some damping on uVel,vVel (strength only function of k).
+ o verification, ad-tests:
+   - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
+     global_ocean_ebm and offline_exf_seaice.thsice.
+ o verification/halfpipe_streamice:
+   - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
+     flux input boundary conditions to be ignored; a fix for this bug changed
+     verification results for forward test.
+   - add adjoint test.
+ o pkg/ptracers:
+   - allow to restart without SOM pickup (resetting SOM to zero).
+ o pkg/gmredi:
+   - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
+   - It uses mixing length theory and suppression by steering level effects to
+     calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
+     to JPO, for more details).
+   - It also uses the diffusivity to calculate an eddy induced streamfunction
+     based on a PV closure (rather than a buoyancy closure as in GM).
+   - New files added to pkg/gmredi:
+     gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
+       induced overturning streamfunction (called from gmredi_calc_tensor)
+     gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
+       for use in gmredi_k3d
+     gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
+       the eddy diffusivity
+ checkpoint64i (2013/06/18)
+ o pkg/cheapaml:
+   - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
+     that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
+     with pkg/cheapaml.
+ o utils/python: add subpackage for cubed sphere function, first example is
+     simple cs.pcol to plot 2D fields on a map
+ o pkg/streamice:
+   - This is a new package in MITgcm, which solves dynamic equations for ice
+      sheets and ice streams
+   - At the moment it is independent of atmosphere/ocean dynamics, or any
+     other physical packages in MITgcm, even ShelfIce (although it is anticipat-
+     ed that this will change)
+   - There is a new verification exercise that tests it, halfpipe_streamice,
+     evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
+     rectangular embayment
+   - halfpipe_streamice is forward-only for now, will have TAF test soon
+   - for questions, email dgoldber@mit.edu
  o pkg/thsice:
    - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
      of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
-Line 21 
 o pkg/cfc:
+Line 690 
 o pkg/cfc:
      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
    - new routine to print summary of CFC params and check for consistency.
+ o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
+   similar to thsice_advdiff.
+   Note that for the B-grid case the routine parameters uc/vc are overwritten.
  o pkg/cfc:
    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.

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