--- MITgcm/doc/tag-index	2007/05/01 12:29:18	1.805
+++ MITgcm/doc/tag-index	2008/01/16 09:48:41	1.939
@@ -1,9 +1,449 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.805 2007/05/01 12:29:18 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.939 2008/01/16 09:48:41 mlosch Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
+  ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
+  for now this is only available for the C-grid code and also within
+  #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
+
+checkpoint59m
+o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
+  and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
+o gad_som : fix flux output (& diagnostics) to have same units as other   
+  advection scheme fluxes (was previously multiplied by deltaT).   
+o added verification/seaice_obcs both to test seaice open boundaries
+  and to provide an example matlab scrpt for generating them
+o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
+o pkg/salt_plume: clean up salt_plume_frac.F to
+  remove redundancy in PlumeMethod 1 and 4
+o pkg/kpp: added saltplume diagnostics
+o pkg/obcs and pkg/seaice:
+  - do not set uice and vice to zero when OB*icefile are unspecified
+  - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
+  - moved seaice tracer obcs after call to seaice_growth
+o pkg/salt_plume: added various options for salt plume depth
+  criterion and for vertical distribution of the salt
+
+checkpoint59l
+o pkg/ptracers: new version of ptracers pickup:
+  read meta file and write only fields which are needed to restart.
+  ( same logic as main pickup file ; also using pickupStrictlyMatch )
+o pkg/seaice:
+  - add timescale for melting due to warm mixed layer as a means of
+    setting SEAICE_availHeatFrac more conveniently
+  - add a CPP-flag/runtime parameter check for flooding algorithm
+  - reformulated availHeat in seaice_growth.F to be independent of AREA
+o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
+  unit changes
+o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
+o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
+  SX vector computer.
+o pkg/seaice:
+  - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
+    seaice forcing fields can now be read only through pkg/exf
+  - removed some unused halos
+o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
+o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
+  or U/VICE from U/VWIND before computing U/VSTRESS
+
+checkpoint59k
+o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
+  dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
+o fix un-initialised variable problem (in mom_vecinv & shap_filt):
+  all experiments pass when compile with un-initialised var. checking option.
+o added pkg/salt_plume
+o script to test restart (for now, in MITgcm_contrib/jmc_script)
+o pkg/seaice: new read/write pickup version. 
+  read meta file and write only fields which are needed to restart.
+  ( same logic as main pickup file ; also using pickupStrictlyMatch )
+o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
+o lab_sea.hb87: modify the domain & update output.hb87.txt :
+  lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
+  at j=1 & j=Ny+1 : this case is not treated correctly in the restart
+  process. Fixed here by closing the domain at the Northern boundary.
+o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
+o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
+  a set of consecutive levels in/from a 3-D array.
+o pkg/ptracers: 
+  use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
+  to-do: fix pkg/diagnostics when large number of diagnostics are defined.
+
+checkpoint59j
+o in pkgs: dic, obcs, offline, rbcs:
+  standard way to compute coeff. for time interpolation between 2 time reccords
+  which retains full precision (& make results less dependent on compiler).
+  update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
+o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
+  packages instead of reading ice cover and wind speed separately
+o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
+ (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
+  to allow to compile customized code before the update)
+o cleaning-up: 
+  - fix CPP instruction syntax in pkg/obcs
+  - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
+    add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
+  - fix some threads issue in IO parts.
+o pkg/dic:
+  - add tons of "_d 0" (--> much better testreports !)
+   and then update outputs of tutorial_global_oce_biogeo
+o pkg/mom_fluxform:
+  add a special version of momentum advection intended to conserve momentum
+  next to a bathymetry step or a coastline edge. (default = off = #undef)
+o new read/write pickup version:
+  - for now, only implemented for main (mdsio) pickup file.
+  - write out only what is needed to restart; merge pickup_nh , pickup_ph
+    and main pickup together.
+  - read meta file; read only what is needed to restart; stop if a field
+    is missing (if pickupStrictlyMatch=T, = the default) or try to restart
+    if it make sense (even if the restart is not perfect).
+  - if no meta file, assume that pickup to read corresponds exactly to
+    a pickup that would currently be written.
+  - read pickup written in the old format (until checkpoint59i) if it
+    recognizes an old meta file (no field-list).
+  - add a meta file in exp. which starts from a pickup: 2 cases:
+    a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
+     e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
+    b) a meta file describing the content of the associated pickup file
+     e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
+o pkg/mdsio & pkg/rw:
+  - new routine to read a meta file ; new set of routine to read
+    Multiple-fields file (with meta file).
+o added open boundary conditions capability for seaice
+    HSNOW, HSALT, UICE, and VICE
+
+checkpoint59i
+o adjoint:
+  * fix multiDimAdvection adjoint 
+    (partial recomputation problem by TAF for fVerT(:,:,kDown)
+    and comlev1 size definition (maxpass vs. max. number of tracers)
+  * verification/global_ocean.90x45x15 adjoint now tests
+    NLFS and multiDimAdvection using DST3 (=30)
+  * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
+o pkg/kpp: add "_d 0" to real constant (if missing); 
+  update output of exp: natl_box (10.digits); vermix (std, 7.digits)
+  and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
+o prepare for "clever pickup" implementation: add new header file "RESTART.h"
+  for internal parameters related to restart process (formerly from PARAMS.h)
+  and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
+o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
+  as argument. (only atm2d & obcs write_pickup have not yet been updated)
+o pkg/monitor:
+  - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
+  - fix mon_stats_rs (statistics over the full domain, even where field is zero)
+  - account for deep Atmosphere factor and density factor (anelastic)
+o added open boundary conditions capability for seaice HEFF and AREA
+o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
+  thermodynamics
+  - requires a little reorganization, which affects the testreport results 
+    of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
+    so that now the conservative form is tested
+  - add a few comments
+o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
+o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
+o add new diagnostics to seaice: advective, diffusive fluxes (only for
+  multidim-advection, for scheme 2 they are not filled) and transports, 
+  thermodynamic growth rates
+o change units of EmPmR (inside the code, + within coupling interface)
+  from m/s to kg/m2/s (mass flux) but leave input file unchanged.
+  Affects results @ truncation level (cg2d match) and update output of 
+   experiments: lab_sea(6), global_ocean.90x40x15(10),
+  global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
+  + adjoint results: global_ocean_ebm(11) and lab_sea (12).
+  Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
+  Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
+
+checkpoint59h
+o pkg/exf: 
+  - improve vectorization by moving if-statement out of loops in
+    exf_mapfields, exf_radiation
+  - exf_bulkformulae.F: introduce 2D fields and vectorize code
+o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
+o testreport: 
+  - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE 
+    monitor & update offline_exf_seaice exp. output.
+  - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
+o pkg/seaice:
+  - bug fix in the evp solver: boundary conditions were affected be
+    masking of zMax/zMin (changes results)
+  - minor bug fix in boundary conditions in seaice_calc_strainrates 
+    (changes results for no_slip)
+  - seaice_lsr.F: make interpolation of eta dependent on boundaries
+  - replace hardcoded lower limit for zeta (zMin) by runtime parameter
+  - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
+    stress formulation and no-slip boundary conditions
+o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
+  in gad_calc_rhs.F ; add few safety stops in initialisation phase.
+o pkg/seaice: a first HSALT time stepping equation has been checked in
+o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
+  in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
+  without requiring DO-IF statements
+o pkg/thsice:
+  use continuous power-law function for partition of energy between lateral
+  melting/freezing and thinning/thickening ; old code using step function
+  still available with #undef THSICE_FRACEN_POWERLAW
+  update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
+o testreport: change AD testing : check against results/output_adm.txt
+  using same scripts as for forward test.
+
+checkpoint59g
+o adjoint testing: in preparation for changing testreport:
+  - output format: cost and grad written on separated lines
+  - ad output results in directory "results" (instead of "results_ad")
+o pkg/seaice: adding ice salinity HSALT as a prognostic variable
+o pkg/seaice: changes for using pkg/seaice with pkg/obcs
+o pkg/ecco: allow user defined cost function contributions 
+o testreport:
+  Allow to choose (per experiment) the list of tested output variables
+   and the main variable (used to issue a pass/FAIL ) ;
+  - for now, done by adding the specific list in file: [exp]/input/tr_checklist
+  - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
+  Also modify printing of summary:
+   a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
+   b) echo the list of tested variables in the individual summary.txt of
+      each experiment.
+o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
+  threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
+  (but still depend on the tile decompostion of the domain).
+o pkg/seaice: change a discretization detail to make the B-grid code 
+  "more symmetric". This change is likely to remove all "ridges/leads" that 
+  where quasi-aligned with the grid in B-grid solutions. It may also be 
+  the solution to the stress coupling issues with the B-grid.
+o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
+  remove .cvsignore from input dir. (since testreport no longer run here).
+o pkg/thsice:
+ - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
+ - fix reshaping of sea-ice just after advection:
+   melt all the ice only if ice-volume is too small.
+ - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
+   prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
+ and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
+o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
+  tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
+o define mass2rUnit & rUnit2mass as units conversion factor, used for surface 
+  forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
+  (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
+  and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
+  of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
+  -> update output.txt
+o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
+ this affects truncation error: -> update output.txt of exp:
+  global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
+  ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
+
+checkpoint59f
+o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) 
+o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in 
+  a bounded range (in forward mode)
+o pkg/ecco, ctrl, autodiff and mom_common:
+ internal parameter controls, completements of implementations
+o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
+o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
+  (not seem any difference in testing results).
+o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains 
+   at face corners.
+o pkg/generic_advdiff: 
+ - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
+  loop range indices for computing vertical advection tendency
+  and do the calculation in the interior only (no overlap) ;
+  for now, only implemented for SOM advection (to save CPU time).
+ - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
+o exch2 adjoint
+  First set of changes:
+  - add exch2 hand-written adjoint templates
+  - exch2 hand-written no longer use TAF-flag 'nownew_arg'
+    This will require cleanup in pkg/autodiff/*.F
+    (changed routines currently kept separate in verif. code/)
+  - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
+    that used to hide exch2 or cubed-sphere specific code
+    (commented via 'cph-exch2')
+o pkg/seaice
+  - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
+o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update 
+   output of global_ocean.cs32x15.thsice .
+
+checkpoint59e
+o exch2: new S/R that only use the cube-tracer (center-position) exchange:
+  for B-grid vector (not yet tested) and C-grid vector (<- only used
+  when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
+o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
+  (#ifdef ALLOW_SALT_PLUME)
+o gather_2d/scatter_2d: removed halo regions
+o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
+  scheme and the corresponding test case (under front_relax dir). For now,
+  only available with Skew-flux form and not yet tested in realistic set-up.
+  adjoint: store directives updated, but gradient checks deteriorated,
+  so maybe GM/Redi adjoint is now broken.
+o seaice adjoint
+  * add AREA, HEFF, HSNOW as control variable
+    (should not change lab_sea results)
+  * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
+o pkg/seaice:
+  * added computation of saltFlux in seaice_growth;
+    For time being, sea ice salinity is assumed constant
+    contribution of snow flooding to freshening of sea ice is neglected.
+    SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
+    defaults to 0.0 in order to maintain backward compatibility.
+    Typical values for SEAICE_salinity are 4 to 10 g/kg.
+  * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
+  * added SEAICE_availHeatFrac, which specifies fraction of surface level
+    heat content used to melt or grow ice
+  * commented out cap of HICE: it helps keep ice thinner
+  * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
+  * applied OBCS T/S mask to HEFFM sea ice mask
+
+checkpoint59d
+o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
+ for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
+ (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
+o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
+ and change default value of parameter "GM_Small_Number";
+ update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
+   global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
+   tutorial_global_oce_biogeo, tutorial_global_oce_latlon
+o pkg/ecco: cost function when applying pkg/smooth to controls
+o pkg/ctrl: add forcingPrecond run time parameter
+o pkg/seaice:
+ - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
+ - fix bug in metric terms of u-equation in LSR solver (implicit part), 
+   changes verification/lab_sea
+ - rearrange implicit part of u-equation in LSR solver to make it easier to
+   read, understand, and debug. This causes changes at the truncation level.
+ - fix (serious) bug in the boundary conditions (sign error in the implicit 
+   part) of the LSR solver. Changes all LSR results.
+ - fixed problem with HSNOW initialization to avoid thick snow when AREA
+   is initilized with small values - does not change lab_sea results.
+ - added HsnowFile initialization capability
+o pkg/smooth: addition to model/src and pkg/ctrl so allow 
+ initialization of pkg/smooth and application to control vector
+o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
+o dependencies: pkg/profiles requires pkg/cal
+o pkg/profiles:
+ - added option ALLOW_PROFILES_GENERICGRID
+     -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
+     that interpolation information (grid points and coefficients) is provided 
+     within the netcdf input files.
+     -> sample matlab scripts can be found in MITgcm_contrib/gael
+     that allow you to prepare netcdf input files.
+ - also modified: cleaner include statements, cleaner error print statements, 
+   cleaner stops when error, and more tests of the netcdf input files consistency.
+o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
+o pkg/seaice:
+ - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
+   requires a new routine: seaice_diagnostics_fill.F
+ - make sure that seaice does not move if not forced (pressure replacement
+   method, Hibler and Ip, 1995), changes results
+ - and new damping criterion for EVP solver according to Hunke, JCP, 2001
+ - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). 
+   It is turned off by default (=-1.), because it changes the results.
+ - make it possible to read AREA from a file, too.
+
+checkpoint59c
+o add S/R and diagnostics for oceanic mixed-layer depth
+o move GMRedi call after all vertical mixing schemes (including KPP)
+o pkg/thsice: 
+ - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
+  (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
+o pkg/obcs:
+ - bug fix for balance code
+o pkg/seaice:
+  - allow values of SEAICE_elasticParm > 1
+  - add new parameter SEAICE_evpTauRelax as an alternative 
+    to SEAICE_elasticParm
+  - make lsr boundary conditions free slip (by default), changes result
+  - add code for no slip boundary conditions for lsr
+  - set minimum of zeta to zero (and not 4e8) (changes results)
+  - add a cap on AREA after advecting AREA if seaice_growth is not called
+o change calculation of Visbeck K:
+  - no longer depend on tapering scheme; instead, compute slope (limited 
+    by GM_maxSlope). this is equivalent to what was comuted before with
+    clipping or linear tappering.
+  - fix vertical averaging (wrong by 1/2 level)
+  - leave the old version (but will not be maintained) within
+    #ifdef OLD_VISBECK_CALC / #endif
+  - update output of exp. ideal_2D_oce
+o change error catch in calc_r_star to improve vectorization
+o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
+  add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
+o adjoint:
+  Re-organized adjoint checkpointing according to Matt Mazloff
+  (but with modifs/completions/cleanups)
+  Storing is now bundled into large arrays to optimized I/O
+  (and second step in cleanup of the_main_loop)
+
+checkpoint59b
+o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
+  - export/import (between ocean & coupler) fields needed for ocean DIC.
+o pkg/seaice: 
+  - get rid of three more exchanges seaice_calc_viscosities (required 
+    different loop boundaries in seaice_lsr and seaice_ocean_stress)
+  - bug fix in seaice_ocean_stress (update of lab_sea required)
+  - reduce loop boundaries to necessary minimum also in seaice_evp
+  - go back to the old way of computing deltaC/Z as the adjoint likes that 
+    better
+o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
+  passive tracer to an Age Tracer) + update output.txt
+o pkg/exf:
+  - implement A-grid / C-grid selection for wind-stress input files.
+  - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
+  for now, in exf_bulk_largeyeager04.F only :
+  - change implementation for case where windspeed + 2. components wind-stress
+    are read-in. AND use rhoConstFresh to convert evap.
+o pkg/seaice:
+  - use correct EXCH_UV for wind-forcing (on A-grid).
+  - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
+    SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
+o pkg/exf:
+  - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
+  EXF_INTERPOLATION: 
+  - merge global_with_exf/code version of exf_interp_read.F
+    to the main code ; 
+  - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when 
+    reading the file ; Important: This options needs to be defined to recover 
+    previous code.
+    otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
+  - no longer loose real*8 precision along the way when using exf_iprec=64.
+o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
+  - change discretisation of evp-solver in order to avoid another exchange
+    (changes lab_sea) and clean up a little
+  - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS) 
+    help the adjoint (this also changes the results slightly)
+  - add a few "_d 0" where they had been missing in seaice_evp.F
+  - cleaning up: remove unused seaice_calc_rhs.F
+o pkg/exf: some cleaning-up:
+  - change various "constants" into runtime parameters
+  - cleaned-up Large&Yeager04 routine which should eventually
+    replace exf_bulkformulae.F (changed names of S/R and CPP)
+    and merged various ALLOW_ATM_WIND options
+ only used with thsice pkg (in thsice_get_exf.F):
+  - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
+    which are used when useStabilityFct_overIce=TRUE (= the default)
+  - change default values of ice & snow emissivity and scale downward LW
+    by ice & snow emissivity.
+o pkg/thsice:
+ fix few little problems, in thsice_calc_thickn.F:
+  - growth vertically (and not laterally) if iceFrac == iceMaskMax
+  - melt only laterally if hIce < hThinIce (as the comments say)
+  and in thsice_extend.F:
+  - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
+  - start to form ice as soon as the minimum ice-volume is reachable.
+ update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice), 
+  and cpl_aim+ocn
+o pkg/kpp
+ - move computation of surface related input fields to KPP into a new
+   subroutine kpp_forcing_surf.F
+ - remove wrong (within bi,bj loops) EXCH calls.
+ - little cleaning (add argument myThid in last position, cvs header ...)
+ - for now, fix conservation problem by exchanging KPPviscAz (may not 
+   be the best fix)
+o pkg/seaice
+ - check for inconsistent evp parameter/cpp-flag combination
+ - remove leftover errIO flat for obsolete name list error handling
+o OpenAD
+ - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
+
 checkpoint59a
 o pkg/seaice: some parameter clarifications and a little bit of clean up
 o pkg/thsice: rename run-time parameters:
@@ -22,7 +462,9 @@
      ATMOSPHERIC_LOADING is #define).
 o pkg/kpp: replaced _KPP_RL with _RL
 o bug fixes for vertical diffusivity computations when both KPP and
-    3D diffusivity arrays are used.
+    3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
+    are no longer updating the vertical diffusivity array
+    (passed as argument) but are (re-) setting those arrays.
 o pkg/seaice: fix bug in evp solver, while doing that
   - change (improve?) discretization of stress computations for both
     cgrid-lsr and evp solver