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-revision 1.158 by heimbach,
Fri May 23 18:24:17 2003 UTC
+revision 1.331 by jmc,
Sun Jul 18 01:57:02 2004 UTC
 Line 3 
 $Header$
      Notes on tags used in MITgcmUV
      ==============================
+ o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
+   this affects (truncation error) output.txt of test-exp:
+    global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
+ o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
+ o change Qnet to always be the net heat flux, (+upward).
+   affects (truncation error) output of natl_box exp.: updated
+ o define the max number of passive tracers in PTRACERS_SIZE.h
+ o start to test mnc routinely in exp0
+ o add sea-ice loading (sIceLoad) as a new forcing field.
+ checkpoint54b_post
+ o add testreport "-j JOBS" option for parallel builds (tested and pretty
+    impressive on Altix and Opteron systems)
+ o diagnostics can now write NetCDF files through the mnc package
+ o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
+ o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
+ o staggerTimeStep & NLFS: rescale T & S surface tendencies.
+   affects (truncation error) output of lab_sea & natl_box exp.: updated
+ o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
+ checkpoint54a_post
+ o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
+ o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
+ o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
+ o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
+   + internal_wave (shift in writing cg2d_ini_res)
+ checkpoint54a_pre
+ o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
+   - modified verification/lab_sea and natl_box_adjoint accordingly
+ checkpoint54
+ checkpoint53g_post
+ o prepare splitting of thermodynamics: store convect.counter in common block
+ o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
+   output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
+ o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
+ o new parameter "nShapS": allow to treat differently S from T (nShapT)
+ o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
+ o restore adjointability
+ checkpoint53f_post
+ o modifications that affect AIM experiment results (update output.txt):
+   - no advection of S at top interface Nr (pkg/generic_advdiff)
+   - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
+ o AIM pkg:
+   - include stability function into surf.Flux derivative relative to Tsurf
+   - calculate clear-sky radiation & surface temp. change (for diagnostics)
+ checkpoint53e_post
+ o merged cylindrical coord configuration
+ o added rotating_tank experiment
+ checkpoint53e_pre
+ checkpoint53d_post
+ o faulks upgraded: re-generate output.txt that have changed:
+    global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
+ o Added Bryan and Lewis, 1979, vertical diffusivity profile
+ o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
+ o added Sadourny discretization of Coriolis
+   - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
+   - re-enabled use of omega3 (useAbsVorticity)
+ o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
+   vector-invariant equations
+   - note: does *NOT* yet use same variable visc. for no-slip BC's.
+ o recoded the lateral boundary conditions for non-hydrostatic w, this time
+   hopefully without new bugs
+   - still to do: biharmonic friction for non-hydrostatic w
+ o bug fix for mom_*_sidedrag: rA -> rAs,rAw
+ o regenerated output for global_ocean_ebm (using -ieee)
+ o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
+   of mom_common/
+   - simple re-arrangement of instructions within computing loop
+ checkpoint53d_pre
+ checkpoint53c_post
+ o new version of coupler for AIM+thSIce and Ocean models
+  - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
+  - land: change Evaporation of snow
+  - aim with thSIce: fix bug in snow-precip.
+ o changes to calc_gw.F
+  - bug fix for w^2 term near the bottom boundary
+  - (hopefully) improve the lateral slip boundary condtions for use with
+     partial/looped cells
+   - because the bug fix changes two verification experiments anyway (exp5
+     and plume on slope), change the lateral boundary condition from half slip
+     to the value of no_slip_sides
+ o ebm package wasnt quite up to the parallel task. Fixed that.
+ o Adjoint of EBM package + verification
+   * TLM OK
+   * ADM not sufficient accuracy yet (needs further testing)
+ checkpoint53b_post
+ o Commiting new energy balance model to repository
+   * package is pkg/ebm
+   * verif. is verification/global_ocean_ebm
+   * references are in ebm_driver.F
+ C      * X. Wang, P. Stone and J. Marotzke, 1999:
+ C        Global thermohaline circulation. Part I:
+ C        Sensitivity to atmospheric moisture transport.
+ C        J. Climate 12(1), 71-82
+ C      * X. Wang, P. Stone and J. Marotzke, 1999:
+ C        Global thermohaline circulation. Part II:
+ C        Sensitivity with interactive transport.
+ C        J. Climate 12(1), 83-91
+ C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
+ C        Destabilization of the thermohaline circulation
+ C        by atmospheric eddy transports.
+ C        J. Climate 7(12), 1870-1882
+ o Will need long integration testing.
+ checkpoint53b_pre
+ o created pkg/mom_common in preparation for variable viscosity code
+ o renamed and split ini_mnc_io
+ o pkg/land: only liquid water can diffuse or run-off
+ o AIM using land: soil wetness availability account for snow
+ o added printMapIncludesZeros to EEPARMS namelist
+ checkpoint53a_post
+ o restore TAMC compatiility for exf_constants.h
+   (no usage of _d in .h)
+ o Additional storing in KPP in an attempt to fix
+   TAMC problem with adjoint of KPP code.
+   (no success...)
+   Identical code works fine with TAF.
+ o Fixed verification/natl_box_adjoint experiments.
+   Initial conditions for Experiments 4 and 5 are now
+   set to "SEAICE_initialHEFF=0", which is more reasonable,
+   and hence gives results closer to that of Experiment 2.
+   Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
+ checkpoint53
+ o stable checkpoint with up to date adjoint
+   TLM tests only run for 1st grdchk at the moment. Its unclear if
+   this is a code problem or a problem with resetting code for g_
+   variables that is being autogenerated wrong.
+   Otherwise:
+    o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
+    o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
+      are both still in chaos following their security messes.
+ checkpoint52n_post
+ o various build (mostly genmake2) changes including:
+   - ability to build/run more easily within Cygwin and MacOS X
+   - more complicated Makefiles with a stronger dependence on Gnu Make
+ o pkg/seaice modifications
+   - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
+     of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
+     and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
+   - changed proxy for geostrophic velocity and updated
+     verification/lab_sea/results/* accordingly
+   - removed ADI dynamic solver from pkg/seaice
+   - replaced all occurrences of 1/CSTICE or 1/CSUICE
+     they caused a segmentation fault under certain circumstances
+   - removed unused field WATR
+ o bug fix in exf-package:
+   -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
+      now reflect that.
+ o small fixes in the cal-package:
+   - set reference date to first of January for the 'model'-calendar
+   - failing of cal_CheckDate in cal_FullDate now actually results in a
+     warning
+ o small modifications in exf-package to increase flexibility:
+   - change climtempfreeze from a constant to a runtime parameter that
+     is specified in data.exf_clim (default = -1.9)
+   - introduce runtime parameter windstressmax (default = 2.0) that is
+     specified in data.exf
+ o fix in pkg/thsice:
+   - update Evap (Tsf changes) to be consistent with Latent heat flux
+   - maintain snow precipitation unchanged (even if Tsf >=0).
+  both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
+ checkpoint52m_post
+ o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
+   this does not change any of the results, because myIter=0 in swfrac always
+   lead to jwtype=2 (the default anyway), but the call makes little sense
+   as a default
+ o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
+ o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
+   atmospheric model (AIM) to use it ; add a "slab ocean" component.
+ o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
+ o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
+ o extending useSingleCpuIO option to work with new exch2 I/O format
+   - old-style, missing-tile I/O is still accessible by defining CPP
+     option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
+ o monitor package can write to NetCDF files and/or STDOUT
+ o fix re-definition bug in MNC_GRID_INIT_ALL()
+ o doc/api_reference added
+   - a framework for building an API Reference Manual using all
+     the "protex" comments embedded in the code
+   - see pkg/generic_advdiff, pkg/mnc for examples
+ o MNC:
+   - make myThid the last argument for all subroutines
+   - new default for the grid files: NO halos
+   - add useMNC and other run-time flags
+   - separate per-file-group handling of the unlimited dimension
+   - early initialization of MNC w/ flags read at the eeboot stage
+     and lookup tables set in initialize_fixed
+   - write all MNC output to a freshly-created directory
+ o thermodynamics sea-ice (thsice) is now tested with testreport.
+ o test exp. advect_cs: use the standard cs32 grid ; update output.
+ o Added functionality to grdchk:
+   pick global i,j,k position (or nearest wet) where to perform check.
+ checkpoint52l_post
+ o new land formulation:
+   a) use ground enthalpy as prognostic variable to ensure exact
+      energy conservation.
+   b) account for water temperature and for latent heat of freezing
+      in all processes (rain, run-off, ground storage)
+   c) compute surface and ground temperature implicitly.
+ o aim_v23 modification for new land model:
+   a) Treat separately land / ocean / sea-ice surface fluxes
+      to allow implicit computation of land & sea-ice surface temp.
+   b) add snow precipitation.
+ checkpoint52l_pre
+ o fix problem (when 1 tile is empty) in min/max monitor.
+ o fix bug in timeAve (u,vZetatave in common block)
+ o no restoring terms under ice for pkg/seaice
+ o moved SEAICE_DO_DIAGS to S/R do_the_model_io
+ o bug fix for pkg/seaice pickups
+ o change MNC call locations and add coordinate attributes
+ o mask vorticity at the corner ; affects global_ocean.cs output
+ o fix ini_curvilinear_grid ; test CS experiments with mpi
+ o aim.5l_cs: modify sea-ice fraction input file ; update output
+ o exf: Adding simple range check routine for exf fields after read
+ checkpoint52k_post
+ o removed top-level directory "diags"
+   - we migrated these functions to pkg/timeave a long time ago
+ o fixed bug introduced in pkg/monitor
+ o accuracy ctrlprec = 32 insuffient for gradient checks using
+   averaged fields (I/O via cost_averages)
+   -> use ctrl.h in active_file*.F to control I/O precision.
+ o paramter list of CALL ADTHE_MAIN_LOOP
+ o added initial do_the_model_io to ecco
+ o set all ...Freq to zero after cost_final
+   taveFreq, dumpFreq, pChkptFreq
+ o MAIN and ECCO differentiability restored
+ checkpoint52j_post
+ o fix nchklev in tamc.h for global_ocean...
+ o Bringing flow and store directives up-to-date
+ o Really weird thing!
+   call do_the_model_io from the_main_loop with parameters
+   starttime, niter0, instead of mytime, myiter, screws up the adjoint:
+   TAF places a faulty re-call of initialise_varia
+   after cost_final call which should not be there!
+ checkpoint52j_pre
+ o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
+   error messages
+ o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
+ o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
+   debug output
+ o modfied mdsio_writefield.F to handle non-global files under exch2
+ o update AIM Cubed-Sphere exp (aim.5l_cs):
+   use land, p*, and Franco.M forcing fields with fractional land-sea mask.
+ o update AIM Equatorial Channel exp:
+   use standard aim_v23 pkg and change the SST fields to be more realistic.
+ o globalFile now works with exch2
+ o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
+   mon_vort3.F to make exch2 friendly with >1 tile per cube face
+ o limit timeave output for hi-res integrations
+ checkpoint52i_post
+ o removed CPP_EEOPTIONS.h from verification/*/code
+ o updated the tiling for global_ocean_pressure
+ checkpoint52i_pre
+ o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
+   the old pkg/aim).
+ checkpoint52h_pre
+ o shortened offending lines in exch2_send_rx?.template
+ o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
+ o genmake2: add build & execute test for NetCDF code
+ o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
+   old grid files, moved CPP_EEMACROS.h to pkg/exch2
+ o added useSingleCPUIO flag to monitor.F and mon_out.F
+ o added temporary hack for sea-ice dynamics on the cube:
+   metric terms are ignored and it is assumed that
+   there is no sea-ice on cube faces 1, 2, 4, and 5.
+ checkpoint52f_post
+ o added exch2 cube routines to pkg/exch2
+ o modified hs94.cs-32x32x5 to use it
+ o added new grid files to hs94.cs-32x32x5
+ checkpoint52f_pre
+ checkpoint52e_post
+ o first attempt to solve vertical advection (momemtum & T,S) Implicitly
+   for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
+ o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
+   to work with implicit vertical advection and AB ;
+ o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
+ o update output (gad_calc_rhs.F changes affect truncation error) of exp:
+  front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
+ checkpoint52e_pre
+ o fix bug in impldiff when Nr=1 or Nr=2.
+ o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
+ o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
+ o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
+   ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
+ o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
+ o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
+ o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
+ checkpoint52d_post
+ o re-tiled many expts to allow comparison in multi-processor mode
+   - updated output accordingly
+   - changed hs94.128x64x5 to use intial T from file rather than use the
+     random number generator
+ o add infrastructure in model routines for fizhi and gridalt packages
+ o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
+ o changes to permit hi-res, cubed-sphere, configuration
+   - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
+   - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
+   - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
+     of surface winds for the cube
+   (A verification experiment, based on global_ocean.cs32x15, but with
+    pkg/seaice turned on and with on-the-fly interpolation from the NCEP
+    Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
+    complete with example surface forcing files and matlab scripts to look
+    at the output and compare it with that of global_ocean.cs32x15.)
+ o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
+    but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
+    to conform to the common rule.
+ o check-in the first version of the coupler + interfaces for multi-components
+    set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
+    - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
+    - atmosphere: use pkg aim_v23 ; no sea-ice for now.
+    - ocean and atmos. share the same horizontal grid (no interpolation).
+    - exchanges between component and coupler is done in forward_step
+ o new verification experiment, cpl_aim+ocn:
+    coupled ocean - AIM atmosphere on cs32 grid.
+ checkpoint52d_pre
+ o surface flux time-av diagnostic modified for NLFS & RealFreshWater
+ o add call to AIM pendant S/R in external_forcing & external_fields_load.F
+ checkpoint52c_post
+ o Fixing OPTIONS files for use of exf:
+   - ALLOW_ECCO not needed
+   - ECCO_CPPOPTIONS.h should not be included from
+     EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
+     as has been the case in the past
+   - All cal/exf related options are currently set in
+     single header file. Should remain so until we
+     agree on a consistent new policy.
+ o Removed all CPP options for cal package.
+   cal has no more CPP options.
+ o modified STOREs in GAD_ADVECTION
+ o corrected key comp. for passkey
+ checkpoint52b_post
+ o new version: "thsice" of thermodynamic sea-ice pkg:
+  - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
+  - modify fluxes but do not change theta directly;
+  - light cleaning of bulk_force pkg (still needed with thsice).
+  - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
+    + output_thsice.txt to test thsice & bulk_force pkgs.
+ o put back grid & coriolis monitor output.
+ checkpoint52b_pre
+ o call "do_the_model_io" at the beginning (=> dump initial state)
+ o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
+ o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
+   (need info on NUMBER_OF_PTRACERS)
+ o missing PTRACERS headers in some routines
+ o default tamc.h in pkg/autodiff supposed to crash
+   to ensure proper customization
+ checkpoint52a_post
+ o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
+   - moved surfaceTendencyTice from pkg/seaice to main code
+   - subroutine FREEZE_SURFACE now limits only surface temperature
+     and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
+     => new output.txt for global_ocean.cs32x15 & global_with_exf
+   - keep the old version of FREEZE for backward compatibility;
+     global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
+   - corresponding modifs for TAF directives
+ o added surface flux output variables to TIMEAVE_STATVARS
+ o time-averaged output for pkg/ptracers
+ o fix problem with ECCO-related divided adjoint
+   snapshot file was missing some ad-variables,
+   but no warning issued by TAF
+ checkpoint52a_pre
+ o some bug fixes for #undef REAL4_IS_SLOW
+ checkpoint52 = ecco_c52_e35
+ o after testing adjoints of checkpoint51u_post
+ checkpoint51u_post
+ o this is the post-merge tag of the ecco-branch
+   (needs another clean checkout and re-testing)
+ o various natl_box_adjoint configs and results
+   but no input fields
+ o obcs adjoint not yet merged!
+ o adding ECCO global 1x1 and 2x2 degree configs
+ o updated/extended some store directives for seaice
+ o pkg/ecco now containes ecco-specific part of cost function
+ o top level routines the_main_loop, forward_step
+   supersede those in model/src/
+   previous input data.cost now in data.ecco
+   (new namelist ecco_cost_nml)
+ o in ctrl/ cleaned some cross-dependencies and updated CPP options
+ checkpoint51t_post
+ o this is the pre-merge tag of the ecco-branch
+ checkpoint51s_post
+ o cleanup: removed various obsolete #define-s
+ o pkg/grdchk
+   - renamed 'ph-grd 3' to 'grad-res'
+   - merged from ecco-branch
+     (remaining bug fixes for obcs gradient checks)
+   - additional high-precision output for testreport
+     (grep for 'precision_grdchk_result')
+ checkpoint51r_post
+ o cleaned up or removed CPP_OPTIONS.h files
+ o updated results for some of the tests to reflect the new
+   optfiles (-ieee: -O0 instead of -O3)
+ checkpoint51q_post
+ o cd_code:
+   - moved cd_scheme.F -> cd_code_scheme.F
+   - separate read_checkpoint from cd_code_ini_vars.F
+   - separated cd_code part from write_checkpoint
+   - updated AD_SOURCE, generated .flow
+   - added CD_CODE_VARS.h to the_main_loop
+   - Moving cd_code specific store dir.s to pkg/cd_code
+ o ctrl package totally restructured
+   - pack/unpack now optional and decoupled from
+     xx_/adxx_ I/O
+   - ctrl_pack/unpack cleaned
+     (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
+   - confined inclusion of AD_CONFIG.h to where necessary.
+ o genmake2: changed AD dependencies from SRCFILES to AD_FILES
+ checkpoint51p_post
+ o create initial cd_code package
+   - WARNING: the initialization of fields within packages
+     is broken because INI_FIELDS (where READ_CHECKPOINT is
+     called) is called *before* PACKAGES_INIT_VARIABLES.
+     This seems to be backwards since
+) its important to initially zero the entire field including
+        the "halo" region
+) zeroing needs to be done *before* reading pickup info
+        and the pickup call might or might not happen in any
+        particular run
+   - this needs an overhaul for R2
+ o cleanup verification/*/code/GMREDI_OPTIONS.h
+ o cleanup testreport
+ checkpoint51o_post
+ o bringing AD-related verif's up to date with genmake2
+   - carbon/
+   - global_ocean.90x40x15/
+   - hs.94.1x64x5/
+   - (front_relax/ )
+ o (more) consistent directory structure for AD-related verif.'s
+ o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
+ o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
+ o bug fix in find_alpha.F for MDJWF:
+   - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
+     change rho -> rho-rhoConst
+   - replace call find_rho to find_rhonum
+ o initialisation of rFlx extended to full array (required by TAF)
+   and shifted to thermodynamics
+ o removed PTRACERS.h in ptracers routine
+ o added surfacetendencyPtr to S/R parameter list pracers_forcing
+ o Correcting initialisations for fVerU, fVerV.
+ o helping TAF to recognize dependency on kUp for
+   fVerU, fVerV
+ o Replacing delZ by delR in pkg/ctrl/
+ checkpoint51o_pre
+ o undid all of cp51 pending some cleanups and discussion
+ o added the [#include "AD_CONFIG.h"] statement to all files that need
+    it for adjoint/tl #defines
+  o re-worked the build logic in genmake2 to support AD_CONFIG.h
+  o removed tools/genmake since it no longer works
+ checkpoint51n_post
+ o modifications to make FREEZE flux visible to pkg/kpp
+   - moved surfaceTendencyTice from pkg/seaice to main code
+   - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
+   - subroutine FREEZE now limits only surface temperature
+     (this means new output.txt for global_ocean.90x40x15,
+      global_ocean.cs32x15, and global_with_exf)
+ o added surface flux output variables to TIMEAVE_STATVARS
+ checkpoint51n_pre
+ o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
+ o added [#include "AD_CONFIG.h"] to all files that use the following
+   defines:
+   - ALLOW_ADJOINT_RUN
+   - ALLOW_TANGENTLINEAR_RUN
+   - ALLOW_ECCO_OPTIMIZATION
+ checkpoint51m_post
+ o incorporating changes to get TAMC/TAF working in genmake2
+   - added new TAMC/TAF targets to the Makefile
+   - various cleanups related to package handling
+   - these changes should have no impact on the forward model
+ checkpoint51l_post
+ o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
+  - faster algorithm for cal_addtime.F
+  - higher precision arithmetic, where needed
+  - pkg/exf *startdate variables changed from calendar date to
+    model integration time
+ checkpoint51l_pre
+ o add salt flux to forcing fields (used when salty sea-ice forms or melts)
+ o enable to apply restoring on S & T only in a latitude band.
+ o update output (external_forcing_surf modif. change truncation errors)
+    global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
+ checkpoint51k_post
+ o change default to: useNHMTerms=.FALSE.
+  - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
+    adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
+  - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
+     exp1, ideal_2D_oce
+  - change data file of oceanic exp (leave the results unchanged for now)
+    exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
+ o set gravitySign automatically according to the vertical coordinate used
+   (and change sign: back to "logical" value: +1 when R increases downward)
+ o added an include barrier to the default CPP_OPTIONS.h and
+   removed the #include "PACKAGES_CONFIG.h" from it
+ o fix a bug in mom_fluxform (from chk51j_post)
+ checkpoint51j_post
+ o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
+ o adjusted some flow directives (dynamics, thermodynamics)
+ o added cubed-sphere case to test cost function
+ o heckpoint_lev?_directives.h now include
+   pkg-specific directives, whenever those are enabled.
+ o Moving pkg-specific flow directives to corresponding pkg
+   Moving pkg-specific differentiation list to corresponding pkg
+   Moving pkg-specific checkpoint-lev storing to corresponding pkg
+   ---> conventions are
+        - pkg_ad.flow
+        - pkg_ad_diff.list
+        - pkg_ad_check_lev?_dir.h
+ checkpoint51i_post
+ o merge of the branch-genmake2
+   - knowingly breaks the older genmake
+   - automatic generation of all ALLOW_${PKG_NAME} defines
+   - new testreport supersedes older testscript
+ o large number of package inclusion and header cleanups
+ checkpoint51i_pre
+ o new output for adjoin of global ocean vector invariant
+ o fix for checkpoint of thermodynamic seaice and bulk_force
+ o Steph gchem various cleanups
+ checkpoint 51h_pre
+ o fixed some single quotes
+ o modify gchem pkg to be more versatile
+ o modifications to clean up dic pkg
+ o add pkg/cfc
+ checkpoint51g_post
+ o provide links for ARPACK and ADM*TLM
+ o start removing verification/vero/
+ o update AD-related stuff
+   (in particular some IF-statements in model/src/ routines)
+ o adding to verification/global_ocean.90x40x15/ adjoint of
+   vector invariant setup
+ checkpoint51f_post
+ o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
+ o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
+   of tracer Green's fucntions for ocean inversion project.
+ checkpoint51f_pre
+ o Added on-the-fly spatial interpolation capability
+     "USE_EXF_INTERPOLATION" to pkg/exf.
+   - This is a temporary Cartesian-grid hack until
+     the super-duper ESMF coupler becomes available.
+   - See verification/global_with_exf/README for usage example.
+   - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
+     flags and modified pkg/seaice accordingly.
+ o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
+     and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
+     non-local transport term.
+ checkpoint51e_post
+ o pkg/mom_vecinv:
+   - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
+   - add time-ave diagnostic of vorticity advection.
+ o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
+ o atmospheric geopotential: - include water vapor effect;
+                             - use p^kappa in p* scaling.
+ o land pkg: read initial state from files.
+ o AIM : add stratospheric drag in the upper level
+ checkpoint51d_post
+ o change function ILNBLNK (=> last non-blank char.) to return zero
+   (instead of the string length) when the string. char is empty
+ o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
+ o modif's to restore TAMC compatibility
+   - avoid "_d" constructs in PARAMETER declarations
+   - avoid interrupting lines by comment lines
+ o Use cluster local disks for purely local I/O
+   vs. globally visible disks needed for ctrl stuff
+   (merged from ecco-branch)
+   - new active_file_loc... and mdsio_..._loc routines
+   - affected packages: autodiff, ctrl, grdchk, mdsio
+ checkpoint51c_post
+ o introducing integer flag debugLevel
+   - debLevZero: suppress all output
+   - debLevA: standard
+   - debLevB: equivalent to current debugMode=.TRUE.
+ o introducing pathname variable mdsioLocalDir for mdsio
+   that can be specified at runtime
+   (relevant for cluster I/O to local disk)
+ `
+ >>>checkpoint51b_post
+ adjoint of ptracers
+ o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
+ o extended state in checkpoint_lev?, etc.
+ o alternative ctrl/cost with tr1 or ptracer
+ o new comlev1_bibj_ptracers
+ o new ptracers.flow
+ o made ptracers_forcing same as external_forcing_s
+ o added verification for adjoint with ptracers
+   - adm. grdchk fail so far
+   - tlm. grdchk OK
+   - checked tapelev/comlev recomputations: OK
+ <<<checkpoint51b_pre
+ checkpoint51a_post
+ o added code for biogeochemistry package
+   - new pkgs: dic, gchem
+   - new subroutine in ptracers
+ o modify code for biogeo packages
+   - in model/src and pkg/ptracers
+ checkpoint51
+ o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
+   - autodiff, ctrl, exf, grdchk, seaice
+   kept separate packages
+   - cost, ecco, obcs
+ o updating verification/internal_wave, verification/lab_sea
+   (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
+ checkpoint50i_post
+ o Preparing next differentiable checkpoint and sync
+   of MAIN vs. ecco-branch
+   - 1st step: this one is differentiable
+   - 2nd step: next(! not this) checkpoint will have updated packages
+               from ecco-branch)
+ checkpoint50h_post
+ o new package "land": provide surface BC for AIM.
+ o pkg/ptracers: apply exchange to all tracers after reading a pickup.
+ o AIM: use true log-P extrapolation for near surface temp (= as in
+     F.Molteni paper) ; update aim.5l_cs output.
+ o New variable in PARM03 for more flexible pickups
+ o somewhat cleaned package initialisation sequence for
+   ctrl/ cost/ ecco/ in packages_... routines
+ checkpoint50g_post
+ o merged with release1_p17 (pkg/seaice and verification/lab_sea)
+   - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
+   - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
+     made the default because of faster convergence than ADI
+ checkpoint50f_post
+ o exf totally restructured
+   - replaced all exf_set_ routines by one generic exf_set_gen.F
+     and made sure it's still differentiable
+   - split exf_getffields.F into new exf_bulkformulae.F
+   - exf_inscal_/exf_outscal_ suffixes consistent with field names
+   - updated adjoint/makefile and relevant verif. accordingly
  checkpoint50f_pre
   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
        + change Evap over land. (update aim.5l_cs output)

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