--- MITgcm/doc/tag-index	2002/04/06 01:36:25	1.70
+++ MITgcm/doc/tag-index	2003/02/18 05:33:53	1.134
@@ -1,8 +1,513 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.70 2002/04/06 01:36:25 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.134 2003/02/18 05:33:53 dimitri Exp $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+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)
+
+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
+  - bug fixes carried over from ecco-branch
+    (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.
+  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
+
+checkpoint45b_post
+o cleaned exchange calls in cg2d
+o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
+o included CPP option SINGLE_LAYER_MODE in thermodynamics
+  to configure barotropic setup (Martin Losch)
+o moved some initialisations within bi,bj loop in dynamics
+  (TAF flow dependency)
+o in initialise_varia, moved call packages_init_variables
+  before convective_adjustment_init
+  (corresponding adjustment of TAF tape initialisation).
+o in calc_diffusivity/calc_viscosity extended domain to full overlap.
+
+checkpoint45a_post
+o compute Rho over the whole domain (extend iMin,jMin indices)
+o specific exchange for X-slice domain (case Ny=1)
 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
 o solve_for_pressure : set cg2d_x to zero where OBCS are applied