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-revision 1.53.2.27 by dimitri,
Fri Feb 14 16:37:34 2003 UTC
+revision 1.192 by dimitri,
Wed Oct 22 16:35:47 2003 UTC
 Line 3 
 $Header$
      Notes on tags used in MITgcmUV
      ==============================
- release1_p12_pre
+ untagged
- o Updated useSingleCpuIO option in mdsio_writefield.F to
+ o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
-   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
-   - adjoint-friendly modifications
- release1_p11
+ 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
-Line 27 
 o Lower bound for viscosity/diffusivity
+Line 348 
 o Lower bound for viscosity/diffusivity
    - 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.
+   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/
- release1_p10
+ 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
-Line 39 
 o modifications for using pkg/exf with p
+Line 482 
 o modifications for using pkg/exf with p
    - verification/lab_sea default experiment now uses
      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
- release1_p9
+ 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)
-Line 55 
 o verification/lab_sea
+Line 523 
 o verification/lab_sea
    - added missing matlab routines
    - added test of thermodynamics parallelization
- release1_p8
+ 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
-Line 82 
 o New package: pkg/seaice
+Line 597 
 o New package: pkg/seaice
    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
- release1_p7
  o GAD:
    - generated new common blocks to account for call of
      same gad routines with differing traceridentities
-Line 110 
 o Adding new verification experiment glo
+Line 623 
 o Adding new verification experiment glo
    the exf (and cal) package instead of the
    external_fields_load routine (cf README file).
- release1_p6
+ 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)
+    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
- release1_p5
+ o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
- o import recent fix from MAIN branch:
+  - read AIM physics parameters from a file (data.aimphys)
-   - use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
+  - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
-   - change phiMin in exp1 (to agree with documentation)
-  from checkpoint45 to checkpoint45a_post:
+ checkpoint46j_post
-   - specific exchange for X-slice domain (case Ny=1)
+ o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
-   - argument futureIter of S/R obcs_calc missing in
+ o move wVel computation at the end of the time step, in S/R integr_continuity
-     exp4 & internal_wave /code
+ o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
-   - solve_for_pressure : set cg2d_x to zero where OBCS are applied
+ o update timeave pkg for wVel diagnostic.
-  from checkpoint44f_post to checkpoint44g_post:
+ checkpoint46j_pre
-   - fix surface correction term in multiDimAdvection
-     (affects plume_on_slope results
+ checkpoint46i_post
- o bug fix in packages_readparms (missing ALLOW_CALENDAR)
+ o Clean up AIM package (and keep the results unchanged):
- o bug fix in CG2D.h (correct array size for LETS_MAKE_JAM
+   include CPP_OPTION and use IMPLICT NONE in all routines ;
- o Adjoint-related bug fixes in kpp:
+   declare all the variables _RL ; use _d 0 for all numerical constants.
-   - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
+   use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
-   - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
- o added Eliassen-Palm flux hooks (dynamics,ini_fields)
+ checkpoint46h_post
- o removed unused TAF keys iikey, idkey (dynamics,thermodynamics)
+ o cleaned up the use of rhoNil and rhoConst.
- o flow directives:
+   - rhoNil should only appear in the LINEAR equation of state, everywhere
-   - new for S/R do_the_model_io
+     else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
-   - enhanced for S/R checkpoint
+     and the dynamical equations are all divided by rhoConst
- o added Eliassen Palm flux controls to gradient check package
+ 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
-   - adjusted global_ocean.90x40x15/ and carbon/ accordingly
+ 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
- release1_p4
+ checkpoint45c_post
  o Removed f90 comments ("!")
  o Modified initialisations to enable exf package for MITgcm
    (without invoking ECCO_PACKAGE).
-Line 156 
 o modifications to gradient check packag
+Line 822 
 o modifications to gradient check packag
    - enable centered differences
    - modified format of standard output
- release1_p3
+ checkpoint45b_post
- o added tangent linear setup to verification/carbon/
+ o cleaned exchange calls in cg2d
- o added adjoint sensitivity setup to verification/global_ocean...
+ o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
- o moved packages_init_variables before convective_adjustment
+ o included CPP option SINGLE_LAYER_MODE in thermodynamics
- o output of verif. which use GMRedi brought up-to-date with
+   to configure barotropic setup (Martin Losch)
-   MAIN trunk (those were re-created after changes in GMRedi)
+ o moved some initialisations within bi,bj loop in dynamics
- o included CPP option SINGLE_LAYER_MODE
+   (TAF flow dependency)
-   to configure barotropic setup (Martin Losch).
+ o in initialise_varia, moved call packages_init_variables
- o Removed auxiliary variable in impldiff
+   before convective_adjustment_init
-   (caused numerical differences with MAIN trunk routine).
+   (corresponding adjustment of TAF tape initialisation).
- o Introduced CPP option ALLOW_AUTODIFF_MONITOR to
+ o in calc_diffusivity/calc_viscosity extended domain to full overlap.
-   disable adcommon.h/g_common.h by default.
- o Cleaned exchange calls in cg2d.
+ checkpoint45a_post
+ o compute Rho over the whole domain (extend iMin,jMin indices)
- release1_p2
+ o specific exchange for X-slice domain (case Ny=1)
- o fixed array boundary problem for adjoint
+ o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
-   (related to partial recomputation within subroutine
+ o solve_for_pressure : set cg2d_x to zero where OBCS are applied
-   related to dynamics -> calc_viscosity -> mom_...
- o fixed recomputation in thermodynamics
+ checkpoint44h_post = checkpoint45
- o prepare (but not complete) recomputation problem in impldiff
+ o Fix to restore differentiability:
- o fixed problem for adjoint of global_max
+   place at which packages_init_variables is called in
- o switched off sponge layer code in external_forcing
+   initialise_varia is crucial for reverse control flow.
+ o modifications in GMRedi to enable stable adjoint
- release1_p1
+   (corresponding modif's in thermodynamics, dynamics)
- o merged necessary patches:
+ o added missing hook for sponge layer code in external_forcing
-   - AD-related changes for GMRedi
+ o modified test cost functions
-   - fixes i KPP (delZ -> drF)
+ o storing in gad_advection (plus removal of write(0,*)!
-   - hook to OBCS songe layer code in external_forcing
+ o missing headers TR1.h added in convective_adjustment routines
-   - errorMessageUnit non-zero in eeboot.F
+ o errorMessageUnit set non-equal zero in eeboot
-   - modified test cost function and carbon verif.
+   (conflict on some platforms, e.g. IBM SP3)
+ o modified carbon verif.
- release1_chkpt44d_post = chkpt44d_post
+ checkpoint44h_pre
+ o vertical grid option: allow to put the Interface at the middle between
+cell-centers ; replace delZ in pkg/kpp by drF.
+ o GM Advective form: Tracers are advected using the residual transport (=
+   Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
+ checkpoint44g_post
+ o fix surface correction term in multiDimAdvection (affects plume_on_slope
+   results) ; ifdef missing in thermodynamics.F
+ checkpoint44f_pre,checkpoint44f_post
+ o added PTRACERS package
+   This allows an arbitrary number of passive tracers to be integrated
+   forward simultaneously with the dynamicaly model.
+   + Implemented so far:
+     - basic forward algorithm (time-stepping, advection, diffusion, convection)
+     - I/O and checkpointing
+     - GM/Redi  *but*  using the GM/Redi coefficient of Salt
+   + Not implemented so far:
+     - KPP
+     - OBCS
+   + No specific example supplied (yet) but global_ocean.90x40x15 has the
+     necessary data.ptracer file. Simply use -enable=ptracers and uncomment
+     line in data.pkg.
+   + This package is disabled by default since it increases storage.
+ o testscript: added -cleanup option
+ o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
+              b) enable to filter 2D fields.
+ checkpoint44e_pre,post
+ o re-wrote convective adjustment to use pre-calculated weights
+   Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
+   Adds:    model/src/convective_weights.F, convectively_mixtracer.F
+   Original calls to convect() still in place.
  chkpt44d_pre,post
  o added missing EXCLUDE_MONITOR flags
-Line 198 
 o in genmake added variable MAKEDEPEND
+Line 900 
 o in genmake added variable MAKEDEPEND
    plus resetting for case SunOS
  o added timer_stats.c routine for IBM SP3
  o removed variables in dynamics
+ !!! I forgot to create tag chkpt44d_pre !!!
+ !!! But chkpt44d_pre = chkpt44c_post    !!!
  o real fresh water flux implemented with non-linear free-surface.

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