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-revision 1.53.4.56 by heimbach,
Mon Aug 18 10:33:41 2003 UTC
+revision 1.395 by mlosch,
Mon Nov 29 20:30:52 2004 UTC
 Line 3 
 $Header$
      Notes on tags used in MITgcmUV
      ==============================
- ecco_c51_e34f
+ o testreport previously did a lousy job of comparing small numbers, so
- o added case gfdl-sgi-o3k to genmake
+   we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
- o added genmake option -arpack and provided default lib dir
+   implemented in the little c-progam tmp_cmpnum.c which is embedded in
- o exf_mapfields:
+   testreport.
-   Interpolate ustress,vstress computed via exf bulk formulae
+ o ptracers_monitor: bug fix for MPI
-   to W/S points. Assume
-   on input: uwind,vwind on C-points
+ checkpoint56a_post
-   on output: ustress[C],vstress[C] -> fu[W],fv[S]
+ o GCHEM: finish reorganizating the package
- o Very prelim. preparations for forward dump&restart
+   - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
-   during adjoint calculation.
+     (introduces another 3D-array for each passive tracer, but only if
+     GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
- ecco_C51_e34e
+     gchemTendency is not needed because the timestep is done separately)
- o bug fix in cost_drifter
+   - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
- o updating timeave package in ecco-branch to c51
+   - GCHEM is now---more or less cleanly---separate from PTRACERS
+   - to bo done: handling of surfaceForcingPtr that is needed for KPP not
- ecco_c51_e34d
+     so clear to me how that should be done in a general way.
+ o CFC: improve formatting of output in CFC_ATMOS
+ o PTRACERS:
+   - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
+     that ALL experiments with ptracers enable can be checked. This makes
+     GCHEM_MONITOR obsolete.
+   - include a runtime parameter PTRACERS_monitorFreq that defaults to
+     monitorFreq
+   - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
+ o add PTRACERS (PTR0[1-5]) to testreport output
+ o exf_check_range:
+   * default changed to .TRUE.
+   * will check values for niter0 if debLevA, every timestep if debLevB
+   * STOP in exf_check_range if 'out of range'
+   * range chosen generous to allow for potential extema
+   TBD: a version with stricter range
+        permitted range would be runtime parameters
+ o GMredi:
+   - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
+   - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
+   - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
+ o GCHEM:
+   - move call to GCHEM_FORCING_SEP, so that it is now called before
+     the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
+   - introduced a useGCHEM runtime flag and applied it everywhere.
+   - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
+     this flag is now only visible within GCHEM-pkg routines.
+   - moved gchem_forcing_int temporarily into ptracers_forcing, this will
+     be replaced by a 3D array that is computed before thermodynamics; for
+     this, the tracer ID iTracer had to be included into the parameter list
+     of ptracers_forcing
+   - set up forward_step to call gchem_forcing, that will replace
+     gchem_forcing_int in ptracers_forcing
+   - cleaning up
+ o small cleaning of exch2: remove files that are also in eesupp/src
+ checkpoint56
+ o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
+ o mnc: cleanup "full" files--fixes out-of-memory problem
+ o ECCO-GODAE
+   * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
+   * fully merged and updated from SIO code
+     windstress sign change affects
+     - exf_inscal_[u/v]stress
+     - sign of xx_tau[u/v] adjustments
+     - signs in cost_scat
+   * ctrl_get_gen: avoid update of tau[u/v] for first few days
+   * natl_box_adjoint updated and compressed
+   * 2-level checkpoint switch added
+     (tested in EXP. 1 of natl_box_adjoint)
+   * new switch doInitXX to avoid init. of xx_... in optimcycle=0
+ o SVD
+   * first complete, non-hacked version for SVD calculations
+   * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
+     performed via direct access files admtlm_vector.it????
+     (via ctrl_[un]pack)
+   * optimcycle is used for ARPACK iteration counter
+     (note: adxx_... is iterated, rather than xx_...; latter is constant!)
+   * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
+     and add linear transforms where necessary
+   * controls are initial/final SST, SSS (can be extended; need to check
+     ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
+ o mdsio: filename info to both stderr, stdout
+ o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
+   from sign change
+ checkpoint55j_post
+ o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
+   affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
+ o add consistent build directories and .cvsignore files to verification
+ o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
+ o make all subroutines 30 or less characters in length for certain older
+   compilers to work (a thorough search only turns up two routines in
+   pkg/ptracers)
+ o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
+   affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
+ checkpoint55i_post
+ o change arrays for total vertical diffusivity (2.D if explicit,
+.D if implicit) ; each ptracer uses its own background value.
+ o added mnc/NetCDF output capability to ocn_compon_interf
+   - added bits to verification/cpl_aim+ocn so that it can run on
+     ITRDA and other clusters without the mpirun "-wd" option
+ o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
+   configuration
+ o give MNC the ability to create additional files rather than
+   exceeding a specified file size limit "MNC_MAX_FILESIZE"
+   - the default is just less than 2GB which is a practical limit
+     on many systems
+ o Compute the non-local term using either KPP vertical diffusivity (=default)
+    or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
+ checkpoint55h_post
+ o add verification test "vermix"
+ o remove all the *_ioinc flags and replace with the single global
+   outputTypesInclusive flag
+ o allow to set a vertical profile of vertical diffusivity for T & S
+ o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
+ o useMNC moved from data.mnc to data.pkg
+ checkpoint55g_post
+ o Renaming carbon AD experiments to comply with testreport conventions
+ o Updating adjoint of Held-Suarez hs94.1x64x5
+ o Fixing directives for non-ECCO forward_step, after ECCO directives
+   have been fixed to avoid recomp. of do_oceanic_phys
+   Works well for global_ocean.90x40x15,
+   but recomp. issue remains for carbon
+ o Updating adjoint output for natl_box_adjoint after
+   pkg/ecco has been modified (see taga c55d_post)
+ checkpoint55f_post
+ o rename to timeave_init_fixed
+ checkpoint55e_post
+ o some delicate re-shuffle of store directives to avoid one
+   extra call of do_oceanic_physics
+   affects ecco_the_main_loop.F, do_oceanic_physics.F
+   checkpoint_lev1_directives.h
+ o NB: this may break global_ocean adjoint temporarily,
+   but it is clear how to fix it. Will do later, need this now.
+ checkpoint55d_post
+ o ECCO specific cost function terms (up-to-date with 1x1 runs)
+ o ecco_cost_weights is modified to 1x1 runs
+ o modifs to allow observations to be read in as
+   single file or yearly files
+ o enable to read exf forcing fields as either
+   single file or yearly files (flag useExfYearlyFields)
+ checkpoint55d_pre
+ o switch between 2-level and 3-level checkpointing
+ o add ability of MNC to write local and "partial" (eg. 2D slices where
+   the full 3D field is never actually stored) arrays to NetCDF files
+   with the correct (that is, the complete multi-dimensional) set of
+   array indicies
+   - used in mom_vecinv() to write the diagFreq output
+   - tested (demonstrated) in verification/aim.5l_cs
+ o further mnc-ification
+   - add verification/lab_sea to the list with mnc setups
+   - fix undefined mnc v-names in cd_code
+   - add kpp to mnc output (both snapshot and timeave)
+ o non-hydrostatic code
+   - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
+     in calc_gw.F
+   - defaults to viscAh
+   - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
+     friction or Leith) in non-hydrostatic mode, as long as there is
+     no biharmonic friction and/or Leigth or equivalent for vertical velocity.
+ o pkg/cost
+   extend simple cost functions to treat time mean quantities
+   (T,U,V) via cost_accumulate_state from cost_tile
+ o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
+     be 2 times larger than the minimum size the advection scheme requires.
+     now get a perfect conservation of salt in advect_cs test-exp (updated)
+ o GGL90 (Gaspar's TKE mixed layer)
+   - add horizontal diffusion of TKE, requires exchanges in
+     do_fields_blocking_exchanges, horizontal diffusivity is zero by
+     default. In OPA there is no horizontal diffusion of TKE but the
+     mixing coefficients are computed from a horizontal average of TKE of
+points or so. I think that diffusion has a little more physical
+     justification.
+   - clean up ggl90_calc in the hope of reducing memory usage (this hope
+     was in vain)
+   - mask tke-variable in ggl90_init
+ o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
+ o fix biharmonic diffusion on CS-grid.
+ o more obcs stuff
+   - added obcs_external_fields_load as an alternative to the EXF-pkg option
+     for reading boundary values. This routine is called from
+     obcs_prescribe_read
+   - updated obcs_check
+   - changed sponge layer relaxation parameter units for days to seconds
+   - turned off sponge layer by default
+   - changed argument list of OBCS_CALC to myTime+deltaTclock
+   - fixed about 35 bugs in obcs_external_fields_load
+ checkpoint55c_post
+ o obcs stuff
+   - new runtime flags useOBCSprescribe, useOBCSbalance
+   - re-arranged obcs_calc
+   - moved exf_getobcs to obcs_prescibe_read
+     obcs_prescibe_read is called after ORLANSKI stuff
+     and independent of it (executable can contain all).
+   - updated obcs_check
+   - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
+     These may be necessary only if tangential velocities are
+     prescribed at OB, not sure, needs testing.
+ o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
+   which simplifies the calls and passes the ifc check-bounds test
+ checkpoint55b_post
+ o add a 2D scalar, Z location, exchange_2 routine.
+ o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
+   to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
+   affects advect_cs results (for the wrong reason): update output.txt
+ o use a more standard discretization for biharmonic viscosity ;
+  (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
+   affects results of dome set-up: update output.txt
+ o fix gad_advection.F (CubedSphere part), back to version 1.23
+ o fix bug in mom_vi_del2uv.F (CubedSphere part).
+ checkpoint55a_post
+ o merged code to
+   * prescribe/read time-dependent open boundaries
+     (works in conjunction with exf, cal)
+   * sponge layer code for open boundaries
+   * each boundary N/S/E/W now has its own CPP option
+     (healthy for the adjoint)
+ checkpoint55
+ o up-to-date adjoint of previous breaks
+   - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
+   - global_ocean_ebm: adjoint still needs fix (TLM ok)
+   - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
+   - carbon: * remove tr1-related adjoint verification
+             * add ptracer as control variable
+ o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
+   (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
+ checkpoint54f_post
+ o in verification/carbin/ remove experiment related to
+   ALLOW_PASSIVE_TRACER (array tr1 etc)
+   code_ad/ input_ad/ results_ad
+ 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)�
+ 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
+   - 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
- o bug fixes for 3d packing and I/O of sliced (xz/yz) fields
-   to increase I/O performance.
- ecco_c51_e34c
+ checkpoint51c_post
  o introducing integer flag debugLevel
    - debLevZero: suppress all output
    - debLevA: standard
-Line 37 
 o introducing integer flag debugLevel
+Line 920 
 o introducing integer flag debugLevel
  o introducing pathname variable mdsioLocalDir for mdsio
    that can be specified at runtime
    (relevant for cluster I/O to local disk)
+ `
- ecco_c51_e34b
+ >>>checkpoint51b_post
- o Modifications of obcs
+ adjoint of ptracers
-   - bug fixes in cost package
+ o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
-   - bug fixes in grdchk package
+ o extended state in checkpoint_lev?, etc.
- o new parameter maxKPPhbl in KPP
+ o alternative ctrl/cost with tr1 or ptracer
- o added input for obcs verification
+ o new comlev1_bibj_ptracers
+ o new ptracers.flow
- ecco_c51_e34a
+ o made ptracers_forcing same as external_forcing_s
- o Modifications to pkg/seaice, verification/lab_sea, and
+ o added verification for adjoint with ptracers
-   verification/natl_box_adjoint for testing sea-ice adjoint code.
+   - adm. grdchk fail so far
+   - tlm. grdchk OK
- ecco_c51_e34
+   - checked tapelev/comlev recomputations: OK
- o merging c51 into ecco-branch
+ <<<checkpoint51b_pre
- ecco_c50_e33a
+ checkpoint51a_post
- o first step in c51 merge
+ o added code for biogeochemistry package
-   - redundant update in model/src/
+   - new pkgs: dic, gchem
-   - merge back's in autodiff, ctrl, kpp, seaice
+   - new subroutine in ptracers
+ o modify code for biogeo packages
- ecco_c50_e33
+   - in model/src and pkg/ptracers
- o minor changes to pkg/seaice pkg/cost/cost_ice.F
-   and verification/natl_box_adjoint/README
+ checkpoint51
- o Modif's to enable tangent linear run in ECCO environment
+ o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
-   including time-dependent forcing
+   - autodiff, ctrl, exf, grdchk, seaice
-   * main problem is missing call mdsreadfield out of exf_set_gen
+   kept separate packages
-     (i.e. computation of trajectory in TLM mode)
+   - cost, ecco, obcs
-   * incorrect g_active_write_...
+ o updating verification/internal_wave, verification/lab_sea
-   * (re-) init of bar files and g_bar files
+   (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
- o Reverted back to 3-dim. tbar, sbar for SST, SSS bar files.
- o MERGES:
+ checkpoint50i_post
-   * obcs/ ctrl/ G. Gebbie code
+ o Preparing next differentiable checkpoint and sync
-     (major changes in ctrl handling, volume flux balancing etc.)
+   of MAIN vs. ecco-branch
-   * cost/ ctrl/ A. Koehl code
+   - 1st step: this one is differentiable
-     - new cost contributions (new data types)
+   - 2nd step: next(! not this) checkpoint will have updated packages
-     - efficient pack/unpack for time-dependent 2-d fields
+               from ecco-branch)
- o replaced mutiple ctrl_get... by single generic ctrl_get_gen.F
-   (except obcs)
+ 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/
+   ctrl/ cost/ ecco/ in packages_... routines
- o extended grdchk to enable obcs gradient checks
- o some generalizations for easier TLM <-> ADM switches
+ checkpoint50g_post
- o added configuration example for parallel divided adjoint
+ o merged with release1_p17 (pkg/seaice and verification/lab_sea)
-   (see verification/natl_box_adjoint/code_diva_mpi/README )
- o started verification exp. for obcs control
-   (still needs checking)
- ecco_c50_e32
- o Patrick's adjoint-model storage directives for pkg/seaice
- o merged with checkpoint50g_post (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
- o Modifications for adjoint of SEAICE_ALLOW_DYNAMICS
-   - extended state in checkpoint_lev...
-   - in lsr.F, replaced GO TO by fixed loop index (also avoid DO WHILE)
-   - YEAH: in lsr.F, (first) successful use of CADJ LOOP = ITERATION
-   - avoid stoing in S/R budget for now
-   - in dynsolver.F, avoid NPSEUDO loop for adjoint
-   - new comlev1_lsr in the_main_loop
- o Small modif's in lsopt/, optim/ to ease compilation
-   New script to run optim (lsopt)
- ecco_c50_e31
+ 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
- o New cost function: Tini-Tfin to do model spinup optimization.
+   - updated adjoint/makefile and relevant verif. accordingly
- o Started new verification exp for Tini-Tfin optimization.
- ecco_c50_e30
+ 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
- o Merging from release1_p13 and from icebear5
-   - bug fix for pkg/seaice dynamic solver
-   - Added SEAICE_initialHEFF to pkg/seaice
-   - Additional options for pkg/cost/cost_ice.F
-   - Updates to verification/natl_box_adjoint
-   - pkg/ctrl/ctrl_init.F
-     Fix for determination of startrec and endrec.
-   - pkg/cal/cal_toseconds.F
-     Fix for negative intervals shorter than 1 day.
- ecco_c50_e29
- 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.
- ecco_c50_e28
- o major merge:
-   ecco-branch merged with checkpoint50
-   gmredi now available, grdchk, DIVA up-to-date for MPI
-   However, two outstanding problems:
-   - kpp adjoint is broken, needs fixing!
-   - a few minor modif's in handling of CPP option
-     ALLOW_TANGENTLINEAR_RUN in conjunction with
-     ALLOW_ECCO_OPTIMIZATION are necessary to enable
-     TLM runs with ECCO setup
- ecco_c44_e27
+ 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.
-Line 154 
 o exf:
+Line 1064 
 o exf:
        fldsecs  = int(fldsecs/fldperiod)*fldperiod
        fldcount = int(fldsecs/fldperiod) + 1
      and were modified.
-   - added repeatPeriod (from MAIN branch)
- o grdchk: updated and merged
-   - has both ADM and TLM checks
-   - works for single- and multi-proc.
-   - output cleaned
-   - worked successfully for parallel DIVA
-   Needed one update in EEPARAMS.h and updates in ctrl package
-   More modif's may be necessary for ECCO code to support TLM.
  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
-   - cost_init.F
+   - the_main_loop.F
-   - cost_averagesfields.F
+   - the_model_main.F
-   - ecco_the_main_loop.F
-   - ecco_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)
-Line 185 
 o DIVA:
+Line 1085 
 o DIVA:
    The current changes apply to TAF-1.4.26.
    TAF has one remaining bug, requiring one manual change
    (see MITgcm manual).
- o bug fix plus modif for ubar, vbar in cost_averagesfields
  o cal: synchronized between MAIN and ecco-branch
- icebear4
+ checkpoint48i_post
- o Added cost_ice for sea-ice volume sensitivity experiment.
+ 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
- o Reduced derivative singularities in pkg/seaice.
- o Updated verification/natl_box_adjoint
- icebear3
+ checkpoint48g_post
- o Removed spurious iikey and idkey
+ --- EOS:
- o pkg/exf
+ o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
-   - bug fix in treatment of downward radiation
+   store total Potential in totPhyHyd for diagnostics & EOS.
- o pkg/seaice
+ o fix restart and overlap Pb when using Z-coord and EOS funct. of P
-   - added initial sea-ice thickness parameter SEAICE_initialHEFF
+ --- Pressure/geopotential gradient:
- o updated verification/natl_box_adjoint
+ 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
- icebear2
+   ( 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,and ecco_the_main_loop.F
+   kpp_transport_t.F, forward_step.F, and the_main_loop.F
- o adjoint-friendly modifications to pkg/seaice
+ o pkg/seaice:
- o added verification/lab_sea as per release1_p12_pre
+   - adjoint-friendly modifications
+   - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
- ecco_c44_e26
- o Merging pkg/exf and pkg/seaice from cvs tag ecco_ice2
+ checkpoint48e_post
- o exf: Modifications to correctly handle evap field for adjoint
+ o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
- o grdchk:
+ o dynamics: change definition of computational domain & adapt mom_fluxform
-   Added code to perform gradient checks for bulk formulae/atmos. state
+   accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
-   (atemp, aqh, uwind, vwind).
+ o following exp works with Olx=Oly=2 (and pass through checkbounds option):
-   NOTE:
+     adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
-   This package is out of synch with c48 package.
+     exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
-   The latter also has the tangent linear gradient checks.
+     global_ocean.90x40x15 global_with_exf global_ocean_pressure
-   Need to be merged.
+     inverted_barometer solid-body.cs-32x32x1
- o verification/natl_box_adjoint:
+   (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
-   * added new setup: code_bulk/, input_bulk, results_bulk
-     (Experiment 2, described in README)
+ checkpoint48d_post
-     uses bulk formulae and atmos. state as control instead of
+ o in preparation for r*:
-     air-sea fluxes.
+  a) use pre-computed gradient of hydrostatic potential:
-     Performs gradient checks for first 4 elements of atemp control.
+     changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
-   * changed standard verification to perform
+  b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
-     gradient checks on first 4 elements on hflux control.
+     => affects results of glob_oce_pressure (different truncation error)
-   * gmredi switched off (will come after merge with c48).
+   update output.txt of ideal_2D_oce & global_ocean_pressure
- ecco_c44_e25
+ checkpoint48d_pre
- o Merging some GM changes from main trunk (c47) to ecco-branch.
+ o in preparation for r*:
- o Updating verif. natl_box_adjoint with GMRedi.
+   new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
- o Adding setup with explicit differentiaton of pressure solver.
+   pass the 2 comp. of the grad. as arguments to momentum S/R.
- o Bug fix: missing OBCS_OPTIONS.h for sponge layer code.
+   but for the moment, only used if it does not change the results.
- o (Re-?) Commiting old bug fixes in kpp to ecco-branch
+ o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
-   (kpp_calc.F, kpp_routines.F)
+ 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.
+   Update output of: exp4, exp5, front_relax, global_ocean_pressure,
+                     lab_sea, natl_box & plume_on_slope
+ checkpoint48
+ o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
+ checkpoint47j_post
+ o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
+ o moved adexch from forward_step to addummy_in_stepping
+ o added exch in ctrl_map_...
+ o aveFreq.=0. at end of cost_final to avoid overwrite in
+   reverse checkpointing loop
+ o Yet more changes in gmredi:
+   * adgmredi_calc_tensor
+     avoiding all recomputation of gmredi_slope_limit
+   * adgmredi_x/y/rtransport
+     added flag for excessive storing to avoid recomp. of
+     u/v/rtans, dTdx/y/z
+     -> this is not really necessary and very memory-consuming
+   * adgmredi_slope_psi:
+     consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
+   * gmredi_slope_limit
+     re-activated full calculation of taperfct for case 'ac02'
+ o updating verification/ adjoints of carbon, global_ocean.90x40x15
+ checkpoint47i_post
+ o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
+ o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
+   default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
+ o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
+ o gmredi: fix few bugs.
+ checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
+ This will be a good checkpoint to plug into the ecco-branch.
+ o few modif.'s to get latest version adjointed
+   (mainly kick out code in ini_linear_phisurf)
+ o modif's to run adjoint with exactConserv
+ o case GM_BOLUS_ADVEC should be cleaned
+   S/R gmredi_slope_psi should be cleaned
+ o verification/carbon now has exactConserv=.TRUE.
+ checkpoint47g_post
+ o time-average AIM output: becomes independent from statvars time-average
+   (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
+ o After TAF bug fix:
+   Tested adjoint of gmredi package.
+   Tests were done with checkpoint47 rather than with latest
+   checkpoint47f_post since the latter is broken for the adjoint
+   verification/carbon/ contains both ADM and TLM gradient checks.
+ Here they are, before they get changed/lost/stolen.
+ Mostly modif.'s to fix numerical sensitivities.
+ Gradient checks OK for
+ - GM_taper_scheme:
+   * clipping
+   * ac02
+   * linear
+   * glw91
+   * dm95
+   * ldd97
+ - GMREDI_OPTIONS:
+   * GM_VISBECK_VARIABLE_K
+   * GM_NON_UNITY_DIAGONAL
+   * GM_EXTRA_DIAGONAL
+   * GM_BOLUS_ADVEC
+ in conjunction with data.gmredi parameters to be checked in
+ in a few minutes under verification/carbon/code/
+ checkpoint47f_post
+ Merging from release1_p10:
+ o modifications for using pkg/exf with pkg/seaice
+   - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
+     and SEAICE_EXTERNAL_FLUXES
+   - pkg/exf CPP options EXF_READ_EVAP and
+     EXF_NO_BULK_COMPUTATIONS
+   - usage examples are Experiments 8 and 9 in
+     verification/lab_sea/README
+   - verification/lab_sea default experiment now uses
+     pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
+ checkpoint47e_post
+ o created a tag prior to creating a branch
+ checkpoint47d_post
+ o fixed bug in the oceanic pressure coordinates code: vertical viscosity
+   at the bottom boundary had an erroneous half slip boundary condition
+ o added bottom drag and no slip boundary condition capabilities to
+   oceanic pressure coordinates code
+ o added new verification experiment global_ocean_pressure, this experiment is
+   also described in the tutorial section of the manual
+ checkpoint47d_pre
+ checkpoint47c_post
+ o Added a verification experiment for a global cubed-sphere ocean run
+   -  verification/global_ocean.cubed32x32x30
+   -  uses pkg/therm_seaice and pkg/bulk_forcing
+ o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
+ o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
+   when using P-coordinate; only implemented for atmospheric config.
+ o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
+   NOTES: requires option NONLIN_FRSURF to be "#define".
+ o update advect_xz/results/output.txt (left from checkpoint44g_post)
+ checkpoint47b_post
+ Merging from release1_p9:
+ o pkg/seaice
+   - removed GOTO's and added taf directives
+   - double precision constants to reduce the g77 (Linux)
+     to F77 (SGI) differences reported in release1_p8
+ o tools/genmake
+   - added SGI options
+ o verification/testscript
+   - updated to that of checkpoint47a_post
+ o verification/global_ocean.90x40x15/input/eedata
+   - modified for SGI f77 compatibility
+ o verification/lab_sea
+   - added description of sea-ice model
+   - added missing matlab routines
+   - added test of thermodynamics parallelization
+ checkpoint47a_post
+ o new pkg: aim_v23
+  = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
+    for now, keep the same surface forcing as before.
+  - Part-Cell implemented into AIM; check that Heat & Water are conserved
+  - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
+  - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
+ o add diagnostic of surface correction term in monitor output
+ o bulk_force and therm_seaice
+ - Two packages:  bulk_force (Bulk forcing)
+   and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
+ - Earlier integration from Stephaine Dutkiewicz
+   and Patrick Heimbach.
+ - Two ifdef statements for compile time,
+    ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
+ checkpoint47
+ differentiable version of checkpoint46n_post
+ o bug fix in quasihydrostaticterms
+ o * "clean" adjoint code (in terms of extensive recomputations)
+     can now be obtained for all GMREDI options (i.e. for
+     - GM_VISBECK_VARIABLE_K
+     - GM_NON_UNITY_DIAGONAL
+     - GM_EXTRA_DIAGONAL
+     - GM_BOLUS_ADVEC )
+   * However, wrong gradient check problem remains unsolved.
+   * New CPP options have been introduced for different
+     tapering schemes
+ o external_fields_load now part of differentiation list
+ o pressure needs multiple storing;
+   would be nice to have store_pressure at beginning or
+   end of forward_step, e.g. by having phiHyd global (5-dim.)
+   (NB: pressure is needed for certain cases in find_rho,
+   which is also invoked through convective_adjustment).
+ o recomputations in find_rho for cases
+  'JMD95'/'UNESCO' or 'MDJWF' are OK.
+ o #define ATMOSPHERIC_LOADING should be differentiable
+ o ini_forcing shifted to begining of initialise_varia
+ o Incorporating QNVS line search routines into MITgcm
+   (this is separate code, and therefore not under pkg)
+   lsopt/, optim/
+ o Updated verification/carbon/
+   - #define GM_VISBECK_VARIABLE_K
+   - GM_taper_scheme    = 'ldd97'
+ checkpoint46n_post
+ Merging from release1_p8:
+ o verification/natl_box:
+   updating new external_fields_load routine
+ o New package: pkg/seaice
+   Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
+   The sea-ice code is based on Hibler (1979-1980).
+   Two sea-ice dynamic solvers, ADI and LSR, are included.
+   In addition to computing prognostic sea-ice variables and diagnosing
+   the forcing/external data fields that drive the ocean model,
+   SEAICE_MODEL also sets theta to the freezing point under sea-ice.
+   The implied surface heat flux is then stored in variable
+   surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
+   kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
+   non-local transport term.  Because this call precedes model
+   thermodynamics, temperature under sea-ice may not be "exactly" at
+   the freezing point by the time theta is dumped or time-averaged.
+   N.B.: fairly large differences in accuracy occur across
+         different platforms/compilers; comparison between
+         g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
+         generated output gives:
+    T           S           U           V
+   C D M    c        m  s        m  s        m  s        m  s
+   n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
+   f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
+   g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
+   Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
+ o GAD:
+   - generated new common blocks to account for call of
+     same gad routines with differing traceridentities
+     (needed to modify tracerIdentity indices in GAD.h)
+   - generated separate common blocks for case useCubedSphereExchange
+     (Department of Futurology)
+   - parameter lists to gmredi_?transport: added tracerIdentity
+   - added new key indices to tamc.h
+ o external_fields_load:
+   - added this routine to TAF list
+   - needed to make some common blocks global and additional storing
+     along the same lines as exf package (checkpoint_lev?_directives.h)
  o exf:
    updated external forcing package
-   - cleaned old exfa stuff
+   - bug fixes carried over from ecco-branch
-   - bug fixes
      (missing OBCS_OPTIONS.h in two routines)
    - enable easy to use "no forcing".
    - added exf I/O for atmospheric loading
    - added exf I/O for runoff data
    - transfered scaling between exf <-> MITgcm to exf namelist
+ o Adding new verification experiment global_with_exf.
- ecco_c44_e24
+   This verification experiment is almost identical to the
+   global_ocean.90x40x15 experiment, except that it uses
+   the exf (and cal) package instead of the
+   external_fields_load routine (cf README file).
+ checkpoint46m_post
+ o modified testscript to return -- when there are no lines of "%MON" output
+ o added new flag "quasiHydrostatic" for QH mode
+   and new routine quasihydrostaticterms()
+ o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
+   New routine: mom_u_coriolis_nh()
+ o fixed sign of non-hydrostatic metric terms in u and v equations.
+   Depend on correct sign of gravitySign.
+ o added work.pc* to .cvsignore in aim directories using ifc
+ o introduced flag for controllin non-hydrostatic metric terms
+ o removed gravitySign from PARM04
+ o switched to g77/ifc from pgf77 in aim experiments
+ checkpoint46l_post
+ o made convective adjustment work with pressure coordinates:
+  - changed the direction of k-loop in convective_adjustment.F for the
+    case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
+  - adjusted the reference pressure k-index in convective_adjustment.F
+  - adjusted the convection condition in convect.F (in analogy to
+    calc_ivdc.F)
+  - convective_adjustment no longer computes anything on the halos
+  - removed the warnings about negative salinity from find_rho.F and
+    find_alpha.F; instead the new routine look_for_neg_salinity, called
+    at the beginning of find_rho, find_alpha, and find_beta, does a
+    check of the entire slice, if CPP-option
+    CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
+ checkpoint46l_pre
+ checkpoint46k_post
+ o fixed the verification/global_ocean.90x40x15 experiment:
+  - new bathymetry (the world according to A., JMC, and M.)
+  - new initial fields and forcing fields (*.bin files)
+  - new POLY3.COEFFS (for the next release one should switch to a full
+    equation of state: JMD95P or MDJWF)
+  - fixed several errors and redundancies in the data file
+  - experiment uses looped cells
+  - added matlab directory with diagnostic scripts for plotting of output
+ o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
+  - read AIM physics parameters from a file (data.aimphys)
+  - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
+ checkpoint46j_post
+ o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
+ o move wVel computation at the end of the time step, in S/R integr_continuity
+ o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
+ o update timeave pkg for wVel diagnostic.
+ checkpoint46j_pre
+ checkpoint46i_post
+ o Clean up AIM package (and keep the results unchanged):
+   include CPP_OPTION and use IMPLICT NONE in all routines ;
+   declare all the variables _RL ; use _d 0 for all numerical constants.
+   use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
+ checkpoint46h_post
+ o cleaned up the use of rhoNil and rhoConst.
+   - rhoNil should only appear in the LINEAR equation of state, everywhere
+     else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
+     and the dynamical equations are all divided by rhoConst
+ o introduced new parameter rhoConstFresh, a reference density of fresh
+   water, to remove the fresh water flux's dependence on rhoNil. The default
+   value is 999.8 kg/m^3
+ o cleanup up external_forcing.F and external_forcing_surf.F
+   - can now be used by both OCEANIC and OCEANICP
+ checkpoint46h_pre
+  Added code to convert surface volume flux (fresh water) into
+  a mass flux when using P coordinates in the ocean (OCEANICP).
+  Note: It assumes you have set rho0=rhoConst=density of fresh water.
+ checkpoint46g_post
+ o Include a new diagnostic variable phiHydLow for the ocean model
+   - in z-coordinates, it is the bottom pressure anomaly
+   - in p-coordinates, it is the sea surface elevation
+   - in both cases, these variable have global drift, reflecting the mass
+     drift in z-coordinates and the volume drift in p-coordinates
+   - included time averaging for phiHydLow, be aware of the drift!
+ o depth-dependent computation of Bo_surf for pressure coordinates
+   in the ocean (buoyancyRelation='OCEANICP')
+   - requires a new routine (FIND_RHO_SCALAR) to compute density with only
+     Theta, Salinity, and Pressure in the parameter list. This routine is
+     presently contained in find_rho.F. This routine does not give the
+     correct density for 'POLY3', which would be a z-dependent reference
+     density.
+ o cleaned up find_rho
+   - removed obsolete 'eqn' from the parameter list.
+ o added two new verification experiments: gop and goz
+   (4x4 degree global ocean, 15 layers in pressure and height coordinates)
+ checkpoint46g_pre
+ checkpoint46f_post
+ o Enable tangent linear (forward mode) gradient checks:
+   - extended active file handling to g_... files
+   - added TANGENT_SIMULATION to theSimulationMode
+   - extended grdchk package accordingly
+ o added tangent linear setup in verification/carbon/code_ftl
+ o added adjoint setup in verification/front_relax/code_ad
+ checkpoint46e_post
+ o Added new equation of state -> MDJWF
+   - EOS of McDougall et al., 2002, JAOT, submitted
+   - caveat: the equation of state is only valid for a smaller (more
+     realistic?) range of values than JMD95P/Z and UNESCO
+   - added masks to the calculation of pressure in store_pressure
+   - added more check values for density in check_eos (ini_eos.F), some of
+     the old check values are out of the range of the MDJWF-eos, so don't
+     expect perfect matches for those
+ checkpoint46e_pre
+ checkpoint46d_post
+ o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
+   'OCEANICP', also initialised field pressure correctly in ini_eos in the
+   case of pressure coordinates. eosType='JMD95Z' in
+   combination with buoyancyRelation='OCEANICP' now causes an error.
+ o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
+   in find_alpha/beta.
+ checkpoint46d_pre
+ o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
+   so that JMD95Z and JMD95P give approptiate static stability in find_rho.
+ checkpoint46c_post
+ o Changes necessary for ocean in p-coordinates
+  -  Added new buoyancy relation = 'OCEANICP'
+  -  Added new parameters = gravitySign (this used to be contained inside
+     the factor dRdZ which I added when we first switched to R coordinates).
+  X GM/Redi is not compatible (yet)
+  X bottom drag and no-slip need to be debugged.
+ checkpoint46c_pre
+ checkpoint46b_post
+ o Added new equation of state -> JMD95Z and JMD95P
+   - EOS of Jackett and McDougall, 1995, JAOT
+   - moved all EOS parameters into EOS.h
+   - new routines ini_eos.F, store_pressure.F
+ o Added UNESCO EOS, but not recommended because it requires
+   in-situ temperature (see JMD95)
+ o Modified formatting for knudsen2.f in utils/knudsen2 and added
+   unesco.f to be used with POLY3
+ checkpoint46b_pre
+ checkpoint46a_post
+ o Added (atmospheric) pressure loading
+   - new field in FFIELDS.h, etc...
+   - new cpp flag ATMOSPHERIC_LOADING
+ o Changed hFacC to _hFacC in calc_phi_hyd.F
+ o Added SHORTWAVE_HEATING to some files for consistency
+ checkpoint46a_pre
+ checkpoint46
+ further merges from release1_p5
+ o new ctrl package
+   - adopted from ECCO environment to enable optimization
+   - added Eliassen Palm fluxes to controls
+ o added Eliassen Palm flux controls to gradient check package
+ o cost package
+   - Compatible with new ctrl package
+   - added Eliassen Palm cost hooks
+   - modif's of existing cost functions
+ o Adjoint-related bug fixes in kpp:
+   - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
+   - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
+ o autodiff package
+   - flow directives:
+     + new for S/R do_the_model_io
+     + enhanced for S/R checkpoint
+     + new gmredi.flow
+   - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
+     disable adcommon.h/g_common.h by default.
+   - fixed problem for adjoint of global_max
+ o modified verification/carbon/
+ o New setup for adjoint of global_ocean
+ o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
+ o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
+ o incorporated hooks for sponge layer code (external_forcing.F)
+ checkpoint45d_post
+ o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
+ o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
+   (affects plume_on_slope "cg2d" output)
+ o add new parameter deltaTfreesurf for free-surface time stepping
+ o exchange gT,gS when using staggerTimeStep & GM & Oly<4
+ o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
+ o change phiMin in exp1 (to agree with documentation)
+ o add new flags:
+  - T,S forcing inside/outside Adams-Bashforth
+  - turn off temp,salt advection and/or forcing
+  - for each tracer, define internal flag for multiDimAdvection & A-B
+ o monitor: change definition of KE to check conservation of Energy
+ checkpoint45c_post
+ o Removed f90 comments ("!")
+ o Modified initialisations to enable exf package for MITgcm
+   (without invoking ECCO_PACKAGE).
  o modifications to gradient check package (Martin Losch)
    - enable centered differences
    - modified format of standard output
- o bug fix for nwettile contents
-   so far assumed global sum  in first entry (1,1,k),
+ checkpoint45b_post
-   needed for global control vector
+ o cleaned exchange calls in cg2d
-   -> introduced new variable nwet[c/w/s]global(nr)
+ o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
- o shifts of calls to cal/exf package to be accessible
+ o included CPP option SINGLE_LAYER_MODE in thermodynamics
-   in MITgcm stand-alone
+   to configure barotropic setup (Martin Losch)
- o shifted packages_init_variables before convective_adjustment_ini
+ o moved some initialisations within bi,bj loop in dynamics
-   (corresponding update of TAF tape initialisation).
+   (TAF flow dependency)
- o removed auxiliary field in impldiff
+ o in initialise_varia, moved call packages_init_variables
-   (caused numerical differences for GMRedi cases)
+   before convective_adjustment_init
- o updated obcs control part (G. Gebbie)
+   (corresponding adjustment of TAF tape initialisation).
- o removed some f90 comments ("!")
+ o in calc_diffusivity/calc_viscosity extended domain to full overlap.
- o Bug fixes and updates in cost package
-  * cost_final: correct multiplier mult_tauv, mult_sflux
+ checkpoint45a_post
-  * cost_hyd: added call cost_ssh
+ o compute Rho over the whole domain (extend iMin,jMin indices)
-  * cost_init_barfiles.F: replaced arrays by tmpfld's
+ o specific exchange for X-slice domain (case Ny=1)
-  * cost_readtopexmean.F: ersmask -> tpmeanmask
+ o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
-  * cost_weights.F: corrected wtheta[2], wsalt[2]
+ o solve_for_pressure : set cg2d_x to zero where OBCS are applied
- o cleaned exchanges in cg2d.F
+ checkpoint44h_post = checkpoint45
- ecco_c44_e23
+ o Fix to restore differentiability:
- merged patches between release1_p1 and release1_p2:
+   place at which packages_init_variables is called in
- o fixed array boundary problem for adjoint
+   initialise_varia is crucial for reverse control flow.
-   (related to partial recomputation within subroutine
+ o modifications in GMRedi to enable stable adjoint
-   related to dynamics -> calc_viscosity -> mom_...
+   (corresponding modif's in thermodynamics, dynamics)
- o fixed recomputation in thermodynamics
+ o added missing hook for sponge layer code in external_forcing
- o prepare (but not complete) recomputation problem in impldiff
+ o modified test cost functions
- o fixed problem for adjoint of global_max
+ o storing in gad_advection (plus removal of write(0,*)!
- o switched off sponge layer code in external_forcing
+ o missing headers TR1.h added in convective_adjustment routines
- Bug fix in ctrl_mask_set_yz (spotted by G. Gebbie)
+ o errorMessageUnit set non-equal zero in eeboot
+   (conflict on some platforms, e.g. IBM SP3)
- ecco_c44_e22
+ o modified carbon verif.
- o Finally, the merges with the Scripps cost function terms:
-   Various additions, modifications, quality checks.
+ checkpoint44h_pre
- o Plus: Included switch ALLOW_AUTODIFF_MONITOR to handle
+ o vertical grid option: allow to put the Interface at the middle between
-   monitoring of adjoint state.
+cell-centers ; replace delZ in pkg/kpp by drF.
- o Plus: removed comm_stats, ini_communication_patterns from diff. list
+ o GM Advective form: Tracers are advected using the residual transport (=
-   (no more need to "keep" MPI headers for adjoint generation)
+   Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
- o Plus: exf changes:
-   o added run-off routine
+ checkpoint44g_post
-   o additional storing needed for ustress,vstess
+ o fix surface correction term in multiDimAdvection (affects plume_on_slope
-     because of state-dependent quality check
+   results) ; ifdef missing in thermodynamics.F
-   o added missing initialisations
- o Plus: genmake with MAKEDEPEND variable was still missing in ecco-branch
+ checkpoint44f_pre,checkpoint44f_post
- NB: - verification/natl_box_adjoint/ 240 steps run
+ o added PTRACERS package
-       * looks ok under Linux (twain.lcs.mit.edu)
+   This allows an arbitrary number of passive tracers to be integrated
-       * looks ok on MIT SUN's (fjord.mit.edu)
+   forward simultaneously with the dynamicaly model.
-       * NaN in reverse mode on Scripps SUN's at iter=214
+   + Implemented so far:
-       * NaN in reverse mode on IBM SP3 (BlueHorizon) at iter=204
+     - basic forward algorithm (time-stepping, advection, diffusion, convection)
-     - 1 year forward int. global 2x2 deg. produces similar cost functions
+     - I/O and checkpointing
-       * all cost terms of new code are slightly smaller (0.5 to 3%).
+     - GM/Redi  *but*  using the GM/Redi coefficient of Salt
+   + Not implemented so far:
- ecco_c44_e21
+     - KPP
- o reversed order of ctrl/cost initialisation
+     - OBCS
- o gmredi_slope_psi.F: Inconsistent types in MIN/MAX expressions
+   + No specific example supplied (yet) but global_ocean.90x40x15 has the
- o modified to enable ctrl field swapping
+     necessary data.ptracer file. Simply use -enable=ptracers and uncomment
- o bug fix for global sum of ncvarlength in ctrl_init
+     line in data.pkg.
- o no more call to ctrl_unpack from ctrl_init
+   + This package is disabled by default since it increases storage.
- o no more write of ctrl vector in ctrl_pack
-   however, init. of control vector from ctrl_unpack
- o various bug fixes & consistent nobcs handling in
+ o testscript: added -cleanup option
-   ctrl_pack/unpack routines (by G. Gebbie)
+ o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
- o optim package: Added obcs control part for lsopt I/O
+              b) enable to filter 2D fields.
-   (by G. Gebbie)
- o missing call to obcs_diags
+ checkpoint44e_pre,post
- o moved calls in packages_init_fixed to packages_readparms
+ o re-wrote convective adjustment to use pre-calculated weights
-   because some quantities are needed earlier.
+   Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
+   Adds:    model/src/convective_weights.F, convectively_mixtracer.F
- ecco_c44_e20
+   Original calls to convect() still in place.
- o before major merges from the Scripps setup
-   here are two small updates:
+ chkpt44d_pre,post
-   - field swapping for surface flux controls enabled
+ o added missing EXCLUDE_MONITOR flags
-     (remains t.b.d. for atmos. state plus obcs)
+ o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
-   - bug fix in active_file.F for xz-/yz- routines
+   (incompatible typ in MIN/MAX expressions caused problems
-   - added missing xz-/yz- routines to active_file_ad.F
+   on IBM SP3)
+ o in genmake added variable MAKEDEPEND
- ecco_c44_e19
+   plus resetting for case SunOS
- o merged necessary patches:
+ o added timer_stats.c routine for IBM SP3
-   - AD-related changes for GMRedi
+ o removed variables in dynamics
-   - fixes i KPP (delZ -> drF)
+ !!! I forgot to create tag chkpt44d_pre !!!
-   - hook to OBCS songe layer code in external_forcing
+ !!! But chkpt44d_pre = chkpt44c_post    !!!
-   - errorMessageUnit non-zero in eeboot.F
-   - included GMREDI, EXACT_CONSERV to natl_box_adjoint verif.
+ o real fresh water flux implemented with non-linear free-surface.
- ecco_c44_e18
+ chkpt44c_pre,post
- o sponge layer code for obcs was missing
+ o few fix (mask in shap_s2, EmPmR in external_field_load,
-   - added hook in external_forcing.F
+   USE_NATURAL_BCS in solve_for_P);
-   - added storing for TAF
+ o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
- o new routine cost_init_barfiles to initialise
-   adjoint fields adtbar, adsbar, adpsbar
+ checkpoint44b_pre/_post
-   (needed in conjunction with corrected ladinit for active I/O)
+ o merge of relevant stuff from the ecco-branch:
- o cleaned up and corrected order in packages_readparms, ecco_readparms
- o corrected and simplified weights for obcs controls
-   - weight fields simplified
-   - bug fix in ctrl_pack
-   - no more write of control vector in ctrl_pack
- o i/j index bug fixes in cost_ssh_mean
- ecco_c44_e17
- o bug fixes in cost package
-   * wrong identifier for active I/O of monthly mean psbar
-     (cost_averagesfields, cost_ssh) xx_psbar_dummy
-   * cleaned all identifier for active I/O of monthly fields
-   * wrong ladinit in various cost routines
- o merge with interval (chkpt44c_post - chkpt44d_post)
-   * added missing EXCLUDE_MONITOR flags
-   * changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
-     (incompatible typ in MIN/MAX expressions caused problems
-     on IBM SP3)
-   * in genmake added variable MAKEDEPEND
-     plus resetting for case SunOS
-     added timer_stats.c routine for IBM SP3
-   * removed variables in dynamics
- ecco_c44_e16
- o new ECCO checkpoint, the first since ecco_c43_e15
-   which is branched from MITgcm.
-   All changes were merged in between (see ecco-branch-mod? tags).
- o last changes:
-   * assuming path for TAF and TAMC are known (e.g. in $path)
-   * genmake:
-     - added tools/xmakedepend to circumvene shortcoming of
-       SUN's makedepend (size too small)
-     - invoking ../tools/xmakedepend instead of makedepend
-     - changed compiler flags for case SunOS
- ecco-branch-mod5
- o mod's to reproduce open boundary run
- o enable field swapping for OB's and climatology
- o update store directives for OB control
- o added option ALLOW_OBCS_PRESCRIBE
- o call of getobcs now out of obcs_calc (param. list modified)
- ecco-branch-mod4
- o this is the second part of changes necessary to reconcile
-   the natl_box_adjoint verification (with and without grdchk).
-   >>>!!! CHANGES BETWEEN THE TAGS ecco-branch-mod3 !!!<<<
-   >>>!!!                      AND ecco-branch-mod4 !!!<<<
-   >>>!!! SHOULD BE MERGED INTO THE MAIN TRUNK      !!!<<<
    - genmake: removed $S64 overwrite for case SunOS
    - pkg/exf: update and corrections for field swapping and obcs
    - pkg/ecco: parameter lists for the_model_main, the_main_loop
-Line 395 
 o this is the second part of changes nec
+Line 1712 
 o this is the second part of changes nec
    - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
                    updated checkpointing_lev... lists for obcs
    - model/src: minor changes in forward_step, plot_field
+                added directive for divided adjoint in the_main_loop
    - pkg/mdsio: added mdsio_gl_slice
- ecco-branch-mod3
+ o check parameters & config (chkpt44a_pre,post)
- o this is the first part of changes necessary to reconcile
+ o OBC and NonLin_FrSurf.
-   natl_box_adjoint verification (with and without grdchk).
-   This set of changes is relevant for ECCO only.
-   The next set/tag of changes (ecco-branch-mod4)
-   should be merged into the main trunk.
-   - update some options
-   - parameter lists of ecco_the_model_main and ecco_the_main_loop
-     differed from those of the MITgcm counterparts.
- ecco-branch-mod2
- o update ecco-branch-mod1 to checkpoint44
- o exclude from updates:
-   - verification/
-   - adjoint/
-   - pkg/cost
-   - pkg/ctrl
-   - pkg/ecco
-   - pkg/obcs
-   - model/src/the_model_main.F
-   - model/src/the_main_loop.F
  checkpoint44
- o apply Shapiro filter on T&S before calc_PhiHyd (stagger time stepping)
  o fix bug in mom_vi_del2uv
+ o select when filters are applied ; add options to zonal_filter (data.zonfilt)
+ o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
+ o update AIM experiments (NCEP input files)
+ o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
  o added some stuff for AD
- ecco-branch-mod1
- o based on c43
- o replaced packages cost, ctrl, ecco, obcs
- o removed MITgcm verif.'s, added ECCO verif.'s
- o added lsopt, optim for line search optimization.
  checkpoint43
  o added two new advection tests
  o added global 4x4 degree ocean test

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