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-revision 1.53.4.32.2.2 by dimitri,
Tue Mar 11 18:20:38 2003 UTC
+revision 1.135 by jmc,
Tue Feb 18 19:19:56 2003 UTC
 Line 3 
 $Header$
      Notes on tags used in MITgcmUV
      ==============================
- Branch icebear
+ checkpoint48g_post
+ --- EOS:
+ o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
+   store total Potential in totPhyHyd for diagnostics & EOS.
-mar 03
+ o fix restart and overlap Pb when using Z-coord and EOS funct. of P
-  Branched off ecco_c44_e27
+ --- Pressure/geopotential gradient:
-  pkg/ctrl/ctrl_init.F
+ o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
-    Fix for determination of startrec and endrec.
+ o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
-  pkg/cal/cal_toseconds.F
+   ( changes results of global_ocean_pressure )
-    Fix for negative intervals shorter than 1 day.
+ o NLFS + z-coord.: add eta*Rho' contribution.
-  pkg/cost/cost_ice.F, cost.h, cost_readparms.F
+ o accurate phiHyd when using interface-W at the middle between 2 centers
-    Added costIceStart and costIceEnd.
+  ( changes results of ideal_2D_oce )
-  verification/natl_box_adjoint.
+ o includes r* 2nd term in potential gradient.
-    Updated test experiments
+ checkpoint48f_post
- ====================================================================
+ Merging from release1_p12:
+ o Modifications for using pkg/exf with pkg/seaice
+   - improved description of the various forcing configurations
+   - added basic radiation bulk formulae to pkg/exf
+   - units/sign fix for evap computation in exf_getffields.F
+   - updated verification/global_with_exf/results/output.txt
+ o Added pkg/sbo for computing IERS Special Bureau for the Oceans
+   (SBO) core products, including oceanic mass, center-of-mass,
+   angular, and bottom pressure (see pkg/sbo/README.sbo).
+ o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
+   to avoid negative values in shallow regions.
+   - updated verification/natl_box/results/output.txt
+   - updated verification/lab_sea/results/output.txt
+ o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
+ o Added useSingleCpuIO option (see PARAMS.h).
+ o Updated useSingleCpuIO option in mdsio_writefield.F to
+   work with multi-field files, e.g., for single-file pickup.
+ o pkg/seaice:
+   - bug fix in growth.F: QNET for no shortwave case
+   - added HeffFile for specifying initial sea-ice thickness
+   - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
+ o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
+   kpp_transport_t.F, forward_step.F, and the_main_loop.F
+ o pkg/seaice:
+   - adjoint-friendly modifications
+   - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
+ checkpoint48e_post
+ o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
+ o dynamics: change definition of computational domain & adapt mom_fluxform
+   accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
+ o following exp works with Olx=Oly=2 (and pass through checkbounds option):
+     adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
+     exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
+     global_ocean.90x40x15 global_with_exf global_ocean_pressure
+     inverted_barometer solid-body.cs-32x32x1
+   (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
+ checkpoint48d_post
+ o in preparation for r*:
+  a) use pre-computed gradient of hydrostatic potential:
+     changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
+  b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
+     => affects results of glob_oce_pressure (different truncation error)
+   update output.txt of ideal_2D_oce & global_ocean_pressure
+ checkpoint48d_pre
+ o in preparation for r*:
+   new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
+   pass the 2 comp. of the grad. as arguments to momentum S/R.
+   but for the moment, only used if it does not change the results.
+ o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
+ checkpoint48c_post
+ Modifications in treatment of initial flux forcing controls
+ to avoid extra storing of flux fields.
+ checkpoint48c_pre
+ o Added tidal_basin_2d experiment (currently 1D!)
+ o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
+ checkpoint48b_post
+ o r* coordinate added in #ifdef NONLIN_FRSURF block.
+  (modification to pressure gradient not yet implemented)
+ o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
+   (for U & V) that are used for vertical advection of momentum.
+ checkpoint48a_post
+ o In preparation for r*, use temp. array to compute vertical transport
+    in flux-form momentum pkg. => change results of few test-exp.
+   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)
- ecco_c44_e27
+ checkpoint47b_post
- o exf:
+ Merging from release1_p9:
-   - 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.
-   - 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
-   - cost_averagesfields.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)
-     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 bug fix plus modif for ubar, vbar in cost_averagesfields
- o cal: synchronized between MAIN and ecco-branch
- icebear4
- o Added cost_ice for sea-ice volume sensitivity experiment.
- 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
- o Removed spurious iikey and idkey
- o pkg/exf
-   - bug fix in treatment of downward radiation
  o pkg/seaice
-   - added initial sea-ice thickness parameter SEAICE_initialHEFF
+   - removed GOTO's and added taf directives
- o updated verification/natl_box_adjoint
+   - double precision constants to reduce the g77 (Linux)
+     to F77 (SGI) differences reported in release1_p8
- icebear2
+ o tools/genmake
- o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
+   - added SGI options
-   kpp_transport_t.F,and ecco_the_main_loop.F
+ o verification/testscript
- o adjoint-friendly modifications to pkg/seaice
+   - updated to that of checkpoint47a_post
- o added verification/lab_sea as per release1_p12_pre
+ o verification/global_ocean.90x40x15/input/eedata
+   - modified for SGI f77 compatibility
- ecco_c44_e26
+ o verification/lab_sea
- o Merging pkg/exf and pkg/seaice from cvs tag ecco_ice2
+   - added description of sea-ice model
- o exf: Modifications to correctly handle evap field for adjoint
+   - added missing matlab routines
- o grdchk:
+   - added test of thermodynamics parallelization
-   Added code to perform gradient checks for bulk formulae/atmos. state
-   (atemp, aqh, uwind, vwind).
+ checkpoint47a_post
-   NOTE:
+ o new pkg: aim_v23
-   This package is out of synch with c48 package.
+  = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
-   The latter also has the tangent linear gradient checks.
+    for now, keep the same surface forcing as before.
-   Need to be merged.
+  - Part-Cell implemented into AIM; check that Heat & Water are conserved
- o verification/natl_box_adjoint:
+  - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
-   * added new setup: code_bulk/, input_bulk, results_bulk
+  - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
-     (Experiment 2, described in README)
+ o add diagnostic of surface correction term in monitor output
-     uses bulk formulae and atmos. state as control instead of
-     air-sea fluxes.
+ o bulk_force and therm_seaice
-     Performs gradient checks for first 4 elements of atemp control.
+ - Two packages:  bulk_force (Bulk forcing)
-   * changed standard verification to perform
+   and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
-     gradient checks on first 4 elements on hflux control.
+ - Earlier integration from Stephaine Dutkiewicz
-   * gmredi switched off (will come after merge with c48).
+   and Patrick Heimbach.
+ - Two ifdef statements for compile time,
- ecco_c44_e25
+    ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
- o Merging some GM changes from main trunk (c47) to ecco-branch.
- o Updating verif. natl_box_adjoint with GMRedi.
+ checkpoint47
- o Adding setup with explicit differentiaton of pressure solver.
+ differentiable version of checkpoint46n_post
- o Bug fix: missing OBCS_OPTIONS.h for sponge layer code.
+ o bug fix in quasihydrostaticterms
- o (Re-?) Commiting old bug fixes in kpp to ecco-branch
+ o * "clean" adjoint code (in terms of extensive recomputations)
-   (kpp_calc.F, kpp_routines.F)
+     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 275 
 o this is the second part of changes nec
+Line 604 
 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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