--- MITgcm/doc/tag-index	2003/01/24 17:55:25	1.123
+++ MITgcm/doc/tag-index	2004/04/05 06:05:07	1.273
@@ -1,8 +1,722 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.123 2003/01/24 17:55:25 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.273 2004/04/05 06:05:07 edhill Exp $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+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
+    1) its important to initially zero the entire field including 
+       the "halo" region
+    2) 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)
+ o added missing .cvsignores and made uniform across expts
+ o changed configuration of tidal_basin_2d expt
+ o added pkg/debug functions for tracing code in fatal crashes
+ o tidied pkg/monitor to use MONITOR_OPTIONS.h
+ o new fn in pkg/monitor to stop model if solution grows too big
+ o removed lots of single quotes from comments
+
+checkpoint50e_post
+o make KPP work with PTRACERS
+ - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
+   nearly a copy of kpp_transport_s
+ - there is no analogue to SurfaceTendencyS, so I have to use 
+   gPtr(of the surface layer) instead
+o add a new platform SunFire+mpi (SunFire 15000) to genmake
+checkpoint50e_pre
+
+checkpoint50d_post
+o change kpp output from multiple-record state files to single-record state 
+  files analogous to write_state.F
+o reduce the output frequency of cg3d-related stuff to the monitor frequency, 
+  analogous to the cg2d-related output. 
+o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, 
+  so that writing to internal file fn (with length 512) fails.
+checkpoint50d_pre
+
+checkpoint50c_post
+o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
+o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
+o add time-average diagnostic of U*V and vertical diffusive flux for theta.
+o bug fixed in convective adjustment diagnostic (multi-tile set-up).
+o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
+
+checkpoint50c_pre
+Merging from release1_p13:
+o bug fix for pkg/seaice dynamic solver
+o Added SEAICE_initialHEFF to pkg/seaice
+
+checkpoint50b_post
+o store u*,v* in gU,V instead of in guNm1,gvNm1
+o in order to put the momForcing out of the Adams-Bashforth:
+  move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
+  to timestep.F
+o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
+o re-generate output for highly sensitive test-exp:
+   global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
+
+checkpoint50b_pre
+o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
+o corrected CPP option mismatch in exf_Bulk... functions for case 
+  #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
+
+checkpoint50a_post
+o Bug fix for merging between c50 and KPP.
+  ikey was passed from thermodynamics to kpp_calc via
+  common block rather than being recomputed in kpp_calc,
+  in contradiction with new key itdkey.
+  New key ikppkey created, and tamc.h headers updated.
+
+checkpoint50
+- 2nd step of merge with ecco-branch:
+  merge changes in ecco-branch back into main trunk
+- bug fix in find_alpha
+- more storing in gmredi_calc_tensor.F, kpp_routines.F
+- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
+- merged some sliced AD support routines
+
+checkpoint49
+merged from ecco-branch:
+o exf:
+  - Enable initialisation of forcing fields to constant 
+    (runtime) values.
+  - in exf_getffields.F
+    Reduce i-/j-loop to interior domain, discarding overlaps.
+    That also fixes wrong TAF-key computations for key_1, key_2
+    with bulf formulae.
+  - exf_init.F modify #ifdef for exf_init_evap
+  - exf_getffieldrec.F, ctrl_getrec.F
+    The following INT-usages are not safe:
+      fldsecs  = int(fldsecs/fldperiod)*fldperiod
+      fldcount = int(fldsecs/fldperiod) + 1
+    and were modified.
+o autodiff: checkpoint_lev...
+  - updated storing for bulk formulae (some arrays were missing)
+  - added state for seaice package
+  - synchronized with main branch
+o DIVA:
+  Modif.s in
+  - the_main_loop.F
+  - the_model_main.F
+  and added cost_final_restore.F cost_final_store.F
+  o With these changes, it is possible to fully separate
+    the first forward run to compute the cost function (mdthe_main_loop)
+    and adjoint runs over individual DIVA intervals (adthe_main_loop)
+    into separate model executions.
+    This enables better tuning of DIVA to given queue sizes.
+  o Loss of cost function value in consecutive DIVA runs is
+    fixed by storing to 'costfinal' file.
+  o Appropriate call of ctrl_unpack/_pack,grdchk_main at 
+    beginning/end of adjoint integration is accounted for.
+  The current changes apply to TAF-1.4.26.
+  TAF has one remaining bug, requiring one manual change
+  (see MITgcm manual).
+o cal: synchronized between MAIN and ecco-branch
+
+checkpoint48i_post
+o Changes to restore differentiability of code w.r.t. previous tag
+  (mostly adding new routines to make list and replacing
+  pressure by totPhiHyd).
+o Updated and merged grdchk package
+  - has both ADM and TLM checks
+  - works for single- and multi-proc.
+  - output cleaned
+  - worked successfully for parallel DIVA
+o genmake:
+  - Adding -platform=SP4
+  - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
+o Modif. for DIVA:
+  ctrl_unpack should not be called in intermediate DIVA interval.
+  (similar thing would apply for active files such as
+  tbar, sbar, psbar, which should not be reinitialised;
+  only relevant for ecco-branch)
+
+checkpoint48h_post
+o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
+o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
+o Added SEAICE_initialHEFF to pkg/seaice
+o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
+
+checkpoint48g_post
+--- EOS:
+o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
+  store total Potential in totPhyHyd for diagnostics & EOS.
+o fix restart and overlap Pb when using Z-coord and EOS funct. of P
+--- Pressure/geopotential gradient:
+o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
+o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
+  ( changes results of global_ocean_pressure )
+o NLFS + z-coord.: add eta*Rho' contribution.
+o accurate phiHyd when using interface-W at the middle between 2 centers
+ ( changes results of ideal_2D_oce )
+o includes r* 2nd term in potential gradient.
+
+checkpoint48f_post
+Merging from release1_p12:
+o Modifications for using pkg/exf with pkg/seaice
+  - improved description of the various forcing configurations
+  - added basic radiation bulk formulae to pkg/exf
+  - units/sign fix for evap computation in exf_getffields.F
+  - updated verification/global_with_exf/results/output.txt
+o Added pkg/sbo for computing IERS Special Bureau for the Oceans
+  (SBO) core products, including oceanic mass, center-of-mass,
+  angular, and bottom pressure (see pkg/sbo/README.sbo).
+o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
+  to avoid negative values in shallow regions.
+  - updated verification/natl_box/results/output.txt
+  - updated verification/lab_sea/results/output.txt
+o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
+o Added useSingleCpuIO option (see PARAMS.h).
+o Updated useSingleCpuIO option in mdsio_writefield.F to
+  work with multi-field files, e.g., for single-file pickup.
+o pkg/seaice:
+  - bug fix in growth.F: QNET for no shortwave case
+  - added HeffFile for specifying initial sea-ice thickness
+  - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
+o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
+  kpp_transport_t.F, forward_step.F, and the_main_loop.F
+o pkg/seaice:
+  - adjoint-friendly modifications
+  - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
+
+checkpoint48e_post
+o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
+o dynamics: change definition of computational domain & adapt mom_fluxform
+  accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. 
+o following exp works with Olx=Oly=2 (and pass through checkbounds option):
+    adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
+    exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
+    global_ocean.90x40x15 global_with_exf global_ocean_pressure 
+    inverted_barometer solid-body.cs-32x32x1
+  (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
+
+checkpoint48d_post
+o in preparation for r*:
+ a) use pre-computed gradient of hydrostatic potential:
+    changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
+ b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
+    => affects results of glob_oce_pressure (different truncation error)  
+  update output.txt of ideal_2D_oce & global_ocean_pressure
+
+checkpoint48d_pre
+o in preparation for r*:
+  new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
+  pass the 2 comp. of the grad. as arguments to momentum S/R.
+  but for the moment, only used if it does not change the results. 
+o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
+
+checkpoint48c_post
+Modifications in treatment of initial flux forcing controls
+to avoid extra storing of flux fields.
+
+checkpoint48c_pre
+o Added tidal_basin_2d experiment (currently 1D!)
+o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) 
+
+checkpoint48b_post
+o r* coordinate added in #ifdef NONLIN_FRSURF block.
+ (modification to pressure gradient not yet implemented)
+o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
+  (for U & V) that are used for vertical advection of momentum.
+
 checkpoint48a_post
 o In preparation for r*, use temp. array to compute vertical transport
    in flux-form momentum pkg. => change results of few test-exp.