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-revision 1.194 by dimitri,
Thu Oct 23 07:14:48 2003 UTC
+revision 1.344 by mlosch,
Thu Sep 16 12:40:37 2004 UTC
 Line 3 
 $Header$
      Notes on tags used in MITgcmUV
      ==============================
+ o add two new packages
+   - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
+     + subject to optimization (memory)
+   - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
+     + subject to reordering (many GOTOs in the original code)
+     + so far opps is called for every (i,j) point, and then operates in
+       the vertical; one may want to reorder the scheme in order operate in
+       horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
+       fields)
+ o overhaul of IO so that we now have flags for MDSIO and/or MNC
+   - all verification tests compile and run with linux_ia32_g77
+   - defaults are compatible with current input files--nothing
+     should change if you were not previously using MNC
+   - MNC output has been added in numerous places (eg. timeave)
+     but there are still a few writes not yet do-able with MNC
+     (this is in progress)
+   - flags now allow for either/or/both use of MDSIO and MNC and
+     documentation will soon follow
+   - numerous small formatting cleanups for ProTeX
+ o add version info (via BUILD_INFO.h) to MNC and stdout
+ checkpoint54e_post
+ o add two new packages
+   - pp81 (Packanowski and Philander, 1981), Richardson number and
+     stratification dependent mixing
+   - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
+   - these scheme operate in a similar manner as KPP (without ghat, of
+     course), however there is only one diffusivity that is used for both
+     temperature and salinity (and passive tracers)į
+ o add offline package
+ o add "verification/dic_example" which contains a dic-gchem-ptracer setup
+   provided by Stephanie Dutkiewicz
+ o genmake2: add ability to search for C compilers and cleanup test output
+   - fixes recent SX-6 problems and should help with others (eg. HP-UX)
+ checkpoint54d_post
+ o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
+ o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
+   leading to additional shift by 5 days each year of integration
+    (i.e. leading to considerable offset over the years)
+ o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
+ o start with no AB and no initial filtering (staggerTimeStep):
+   change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
+ o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
+   (external loading & cpl import/export stay in forward_step.F)
+ o update coupling interface to work with new staggerTimeStep
+ o change MDSIO ptracers_pickup.
+ o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
+ o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
+ o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
+ checkpoint54c_post
+ 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

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