--- MITgcm/doc/tag-index	2008/02/13 07:43:39	1.957
+++ MITgcm/doc/tag-index	2009/06/22 15:33:02	1.1128
@@ -1,9 +1,628 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.957 2008/02/13 07:43:39 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1128 2009/06/22 15:33:02 mlosch Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+checkpoint61q
+o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
+ - the boundary conditions along open boundaries are unclear, because the
+   associated masks are set to zero and are thus treated as closed when
+   applying the slip-boundary conditions.
+ - move initialisation of grid variables from seaice_init_varia to _fixed
+o adding doc/diags_changes.txt
+o model/src: 
+  do_the_model_io: rename few pkg S/R which are called from do_the_model_io, 
+   to avoid "_diags" naming if no relation to pkg/diagnostics.
+  ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF 
+   file and only call PLOT_FIELD_XYZ if debugMode=T.
+  remove few PLOT_FIELD_XY calls outside initialisation.
+  remove few unnecessary BARRIER.
+o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
+  of salt_plume package in Southern Ocean 
+o pkg/thsice: 
+ - fix hOceMxL in overlap (needed for sea-ice advection); 
+   update output of experiment global_ocean.cs32x15.icedyn.
+o pkg/seaice: 
+ - make the (placeholder-)tracer IceAge a little more meaningful
+  by avoiding ridging of age due to convergent ice flow
+ - add diagnostics for surface temperature, atmospheric and oceanic
+   heat flux, and atmospheric and oceanic ice growth
+
+checkpoint61p
+o eesupp (global_max & global_sum):
+ - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
+ - remove starting & endding barrier (no longer needed)
+o pkg/mdsio, writelocal:
+   works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
+   (remove the STOP): uses shared buffer IO to store data from all threads
+   and then let master-thread write nThreads tiles.
+o pkg/mdsio (read/write field):
+ - tiled IO done in 1 piece (all levels at a time);
+ - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
+ - multi-threaded: allow to read/write local (non-shared) array
+   (was already working with singleCpuIO ; now works also without);
+   => no longer needs barrier call after reading a file (added inside
+   mds_read/write field).
+ - move barrier calls outside gather/scatter_2d to mds_read/write_field
+o pkg/obcs/exf
+  - exf_getffieldrec.F: add a few ". _d 0" and 
+                        add code to catch the case fldperiod = 0.  
+  - obcs_precribe_read.F: change if statements so that they match 
+                          the variable type (_RL)
+  - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to 
+    exf_iprec) as part of namelist EXF_NML_01
+o pkg/mdsio:
+  - read/write tiled (local) files: read/write 1-level tile chunk at a time
+    (instead of segment of length sNx); expected to speed up tiled IO.
+o pkg/exch2:
+  - take buffer copy from/to array out of S/R exch2_send/recv into new
+    S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
+    (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
+  - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
+  - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
+    (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
+    including Topology header file (and common blocks).
+  - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
+    remove 2nd exch call in exch2_s3d_rx (no longer needed).
+  - document S/R arg. list (+ update some comments)
+o pkg/seaice:
+  - added SEAICE_CLIM_AIR code, which permits modulation of surface air
+    temperature and humidity over sea ice based on climatological values.
+  - clean up computation of Hibler+Bryan (1987) stress coupling for the case
+    of LSR (this change is expected to change the results slightly because now 
+    it uses slightly difference moduli from the second last LSR solution, but
+    that is more consistent with the stress computations; this part of the code 
+    is not tested in the verification experiments)
+  - fix diagnostics for flux of ice in case of B-grid
+  - turn strain rates eij and press into global fields within global 
+    common block in SEAICE.h for more straighforward diagnostics
+  - fix diagnostics for principal stress components, press, zeta, eta
+    to give something meaning full
+o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
+  new output (all 4 tests) using default rotationPeriod.
+o pkg KPP:
+  - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
+  - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
+    and normal grid from 1 to Nr)
+o Fix computations of L4rdt in mom_calc_visc.F
+o eesupp:
+  new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
+  should be called before a "stop" if we know that all process are going
+  to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
+
+checkpoint61o
+o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
+o model/src/ini_curvilinear_grid.F:
+   compute angleSin/CosC when they are not read from a file
+o pkg/seaice:
+   add pseudo time stepping for LSOR
+o pkg/exch2:
+   temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
+o pkg/seaice:
+   Adding separate sea ice albedo, drag coefficients, and HO in Southern
+   Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
+o SingleCpuIO:
+   fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
+o pkg/seaice:
+   put exchanged variable in (local) common block for MPI+Multi-Threads
+   to work (necessary with exch1, and for now with exch2 too).
+o verification: to get more experiments tested with mpi, mth and mpi+mth,
+  change tiling of:
+   aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
+   hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
+  update output of exp:
+   exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
+   tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
+  + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
+                   (note: output.txt generated on faulks using only 1 tile)
+o eesupp & mdsio (SingleCpuIO):
+ - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
+   parameter "W2_useE2ioLayOut" (read from file "data.exch2").
+   Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
+ - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
+ - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
+   gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
+o pkg/exch2:
+ - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
+   read parameter file "data.exch2" if it exists; otherwise try default regular
+   cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
+ - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
+   with new code (not to be used, just as a backup solution).
+ - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2" 
+   in utils/exch2/input.
+
+checkpoint61n
+o eesupp & mdsio (SingleCpuIO):
+  - move mapping to global io-buffer inside gather_2d/scater_2d: this save
+    memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
+    receive real*4 array (instead of real*8) to read/write 32.bit files.
+    (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
+     and remove new mapping S/R)
+o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
+  - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
+    xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
+    when using exch2. Add S/R to map global io-buffer to global model array.
+  - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
+
+checkpoint61m
+o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
+  and add 3 other S/R for other types (R4,R8,RS).
+  Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
+o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
+ - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
+ - reduce number of macro definitions (keep only those which are used);
+   can always call directly the corrresponding S/R if needed.
+ - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
+   _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
+ Fixed wrong type of arg in:
+   atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
+   ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
+ To fix: global_sum of var in common block is wrong (multi-threaded) in:
+   dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
+ To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
+o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
+  "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
+o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
+o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
+  edges are closed (zero depth); might happen with "blank tiles";
+  for now, disabled if using OBCS.
+o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
+  link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
+o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
+  to reduce length of 1.D array print in STDOUT.
+o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
+  + use 48 tiles (16x8): this will allow to test "blank tiles".
+o start to test MPI + multi-threaded (change testreport to skip tests
+  where number of tiles do not match).
+o genmake2: add option "-omp" to turn on Open-MP ;
+  passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
+o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
+  and keep the original tile numbering. Note: compatible with old
+  W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
+
+checkpoint61l
+o Overlaps had been forgotten in calculating ijk keys : fixed
+o fix cyrus makedepend for gcc 4.4
+o experiment fizhi-cs-aqualev20:
+  switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
+  and generate new output. Note: new output is much closer to the old
+  one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
+  the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
+o pkg/fizhi:
+ - change to avoid indices going deliberately over array-bounds
+ - remove unnecessary MPI stuff
+ - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
+ - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
+   does not go over array-bounds and therefore returns reliable output.
+ - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
+   this S/R has 4 output arguments, which are used inside "get_alarm";
+   when it is called with the same variable "ndum" in place of several
+   output arguments, this produces weird side effect inside "get_alarm"
+  (e.g., datein=dates(n) is overwritten by timein=times(n) since both
+   datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
+   address) and produces error.
+o tools/gemake2: (March 27-29 2009)
+  with option "-mpi": link *_mpi files from "MODS" dir (this is what 
+  testreport does).
+o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
+o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
+   update lab_sea.lsr & lab_sea.salt_plume results
+o pkg/seaice: 
+  Major overhaul of the LSOR solver: change discretization from original
+  finite differences to finite volume. The old routine is still in the
+  file seaice_lsr.F and can be turned on with the CPP-flag
+  SEAICE_OLD_AND_BAD_DISCRETIZATION
+  Along with this change, the discretization of the strain rates is changed.
+  The same flag turns on the old discretization in seaice_calc_strainrates.F
+  All verification experiments with seaice are affected (except for 
+  seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
+  results by setting the above flag.
+  Further changes involve changes in defaults:
+  - ALLOW_FLOODING is defined and turned on by default
+  - SEAICEadvSnow = .true. is now the default
+  - SEAICEadvSalt = .true. is now the default
+  - SEAICEadvAge  = .true. is now the default
+  - SEAICE_clipVelocities  = .false. is now the default 
+                                     (as per J. Zhang's recommendation)
+  - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
+    is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
+  - seaice_growth: replace computation of UG by a simple copy from wspeed
+
+checkpoint61k
+o pkg/seaice: a few bug fixes mostly concerning the metric terms:
+  seaice_lsr: fixed a few metric terms,
+              affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
+              add more debugging diagnostics
+  seaice_evp: removed superfluous many metric terms of FV discretization
+              of stress divergence
+              affects lab_sea, lab_sea.hb87
+  seaice_ocean_stress: removed superfluous many metric terms of FV discretization
+              of stress divergence for non-evp solver 
+              (this part is not tested anywhere)
+  seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
+              they were effectively only half slip
+              affects lab_sea.hb87
+  updated all relevant verification experiments (except lab_sea//output_adm.txt
+    which was left over, but fails at level 7 & 6)
+
+checkpoint61j
+o pkg/seaice: turn a few hard wired parameters into run time parameters
+o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model 
+  time in seconds as promised by the usints in seaice_monitor and exf_monitor
+o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
+  that are not cubed-sphere grids
+o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
+o pkg/ctrl:
+  fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
+o non-hydrostatic (calc_gw.F):
+  fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
+  update output of exp. global_ocean.cs32x15.viscA4
+o remove backward compatibility for thetaMin,phiMin
+  (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
+o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the 
+  interpolated wind field not only for curvilineargrid=.true., but also 
+  for a rotated grid (rotateGrid=.true.)
+o pkg/exf: add capability to bypass interpolation for runoff
+  by setting yet another CPP-flag
+o eesupp/src, B-grid exchange:
+  add simple (6 tiles, non MPI) CS exch + standard interface S/R.
+o autodiff
+  new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
+  allows to switch to single-prec common blocks;
+  corresponding switch occurs in tamc.h, integer isbyte
+  TAF store directivs "byte" and "kind" seem equivalent;
+  Most tamc.h have been updated correspondingly.
+
+checkpoint61i
+o autodiff:
+  fix autodiff_sore/_restore indices for obcs
+  (spotted by I. Hoteit, M. Mazloff)
+o pkg/autodiff, pkg/ctrl:
+  Add flag to reduce all tapelev I/O to single-prec. 
+  In data.ctrl set
+    doSinglePrecTapelev = .TRUE.
+o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
+  check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
+o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for 
+  real fresh water flux (not yet)
+o pkg/mdsio & rw:
+ - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
+ - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
+o pkg/flt:
+ - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
+   init_fixed & ini_varia.
+ - clean-up & simplify linear interpolation S/R:
+   move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
+ - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
+ - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
+ - add vert. coordinate & horiz. indices to output files.
+ - change vertical position in initial condition, from index to depth [m].
+ - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
+   (easier to get to a curvilinear grid) ; delX,delY no longer used.
+o pkg/ggl90: a few modifications:
+ - fix bottom boundary condition, and interpolation of KappaE
+   near top and bottom
+ - use same set of viscosity/diffusivity for TKE/momnetum/tracer 
+ - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
+ - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
+o rename thetaMin,phiMin -> xgOrigin,ygOrigin
+  (maintain temporary backward compatibility, until next checkpoint)
+
+checkpoint61h
+o pkg/diagnostics with "periodic averaging diagnostics":
+  fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. 
+o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
+o pkg/obcs: fix loop ranges for balancing code
+o pkg/flt:
+ - improve criteria for finding which tile owns a float.
+ - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
+o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
+  aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
+  with ocean biogeo)
+o pkg/flt:
+ - do some cleaning and fix the restart ;
+ - add output.txt in flt_example/results to get this pkg tested.
+o genmake2: add an EXTENDED_SRC option and flag.
+   for now, cannot be turned on on command line (only through genmake_local)
+o pkg/mdsio: read/write vector:
+ - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
+ - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
+   & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
+ - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
+  (drop to 4 digits matching for grad). But this test does not look very
+  reliable (was already failling on eddy, fc5, at 6.digits). Update output.
+
+checkpoint61g
+o pkg/flt:
+  - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
+   + make OPTIONS file more standard.
+  - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
+  - fix _BYTESWAPIO CPP-Flag
+  - standard reading of file-parameter "data.flt"
+  - fix argument list of S/R FLT_RESTART
+  still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
+o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
+o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
+  a still unfixed compiler/optimization bug
+
+checkpoint61f
+o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; 
+  update results of global_ocean.cs32x15.icedyn test.
+o move getcon.F from model/src to pkg/fizhi.
+o pkg/exf: add parameter for extrapolation of temp up to the surface 
+   and option to prevent negative evap (in bulk_largeyeager04 only).
+o Prather Advection scheme: fix tracer conservation for divergent flow
+  (e.g., when using NonLin Free-Surface).
+o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
+o gmredi (Visbeck-variable-K):
+ - add more parameters to Visbeck-variable-K.
+ - use a 5 points average for dSigmaR in Visbeck-K calculation
+   (more "homogenous": same stencil and same weights as in dSigmaH)
+ - update output of ideal_2D_oce experiment.
+o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 
+  (#undef REAL4_IS_SLOW)
+ - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 
+   coordinate variable
+ - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables 
+   (surface forcing fields), removes some of the functionality
+ - model/src/write_grid.F: write _RS variables as RS-netcdf variables 
+ - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but 
+   probably not all: copy _RS surface flux fields to RL field before 
+   calling DIAGNOSTICS_FILL
+ - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into 
+   real*4 (CALL EXCH_*_RS) versions.
+ - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
+   (generate new output).
+
+checkpoint61e
+o gmredi (Visbeck-variable-K):
+  - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
+  - change computation of Visbeck-K where Slope > Smax :        
+    now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
+    previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
+o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
+  to be the same as with Z-coord. (i.e., m/s & no-units respectively).
+o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
+o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
+  does not become too large (to avoid precision problems in implicit-diffusion
+  solver); update ideal_2D_oce output.
+o pkg ggl90:
+  - in ggl90_cal.F: compute only one set of visc/diff, used to
+    step forward TKE/T/S/momentum
+  - default value of GGL90viscMax/GGL90diffMax larger and equal (to
+    have Prandlt =1)
+o gmredi (fm07):
+  - add lower limit on Transition layer thickness + lower limit on 1/lambda
+  - allow to set few more params from data.gmredi
+o pkg ggl90:
+      - add missing sqrt(2) factor in computation of mixing length 
+        scale in ggl90_calc.F
+        (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
+
+checkpoint61d
+o adjoint modifs
+  - adapt to new field rhoInSitu
+  - allow to revert from StoreDynVars2D, StoreDynVars3D
+    to individual fields
+    (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
+o store 3-D (in-situ) density in commom block (DYNVARS.h)
+ - save 1 rho computation.
+ - no longer modify T & S inland when using down_slope pkg.
+o gad_som : allow to switch to SOM advection for T & S without corresponding 
+  pickup files (using new S/R: MDS_CHECK4FILE).
+o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
+  (for useSingleCpuIO to work in multi-threaded)
+o pkg/shelfice:
+ - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
+   with SHELFICEtopoFile in data.shelfice
+ - move code for reading ice shelf topography and modifying hFacC into separate
+   subroutines of the shelfice package
+ - separate initialisation of "fixed" and "variable" variables
+ - kTopC is not (yet) replaced by kSurfC, although this is possible
+o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
+o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
+  and rename:
+  ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
+  ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
+o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
+
+checkpoint61c
+o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" 
+  to add mass source/sink of fluid in the interior (3-D generalisation 
+  of oceanic real-fresh water flux).
+o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
+o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
+o new pkg: down_slope
+  density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
+  - presently, modify T & S inland (dwnslp_calc_rho.F).
+    can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
+  - implementation for ocean in P-coords not tested.
+  - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
+o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
+  (to facilitate conversion of oceanic pkg to p-coordinate).
+o change FIND_RHO to FIND_RHO_2D : 
+  pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
+o new pkg: cheapaml
+
+checkpoint61b
+o exch2: 
+  change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
+  - no longer depend on the order sequence (N,S,E,W).
+  - 3rd exchange no longer needed (tested with 24 tiles).
+  - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
+  - exch_UV_A-grid readily available (but not yet tested).
+  comment out 3rd exch call and remove copy of V to U at SE & NE face-corners 
+  (both are no longer needed) in exch_uv: no effect in forward run; but 
+   get truncation error differences with adjoint exch.
+o exch2: 
+ - change index-bounds storage (moved from target to local tile,
+   more intuitive this way) ; rename/remove some variables.
+ - change utils/exch2/matlab-topology-generator & code_mods accordingly.
+
+checkpoint61a
+o exch2/matlab-topology-generator: 
+  fix bug in index bounds for N-S internal exchange (hard to tell if this
+  had any effect on the solution).
+o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
+  is exceeded
+o testreport: modify syntax of awk, so that it works also with 
+  awk, and not only with nawk and gawk
+
+checkpoint61
+o autodiff
+  Change default for TAF usage by removing argument '-nonew_arg'
+  This changes TAF subroutine argument list (ordering of active var.)
+  Omission of this flag leads to incompatibility w.r.t. TAMC
+  To restore TAMC-compatibility, need following modifs:
+  * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
+  * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
+  Tested TAF version is 1.9.22
+  N.B.: exch2 hand-written adjoint code currently not TAMC compatible
+
+checkpoint60
+--->>> This is the last checkpoint for which generating the adjoint
+--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
+--->>> by default.
+--->>> Future checkpoints will ommit this flag by default.
+o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
+o pkg/grdchk: Add gradient check to etan0 perturbations.
+o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). 
+o pkg/autodiff: more flexibility in zeroadj. 
+  model/src: modifying do_oceanic_phys.F accordingly. 
+o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
+o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
+  special setup of gmredi for which the adjoint is stable 
+  enough for parameter optimization.
+o bridging the gap between eddy stress and GM.
+  -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
+      along with a change in CPP option (now ALLOW_EDDYPSI).
+  -> when using GM w/ GM_AdvForm: 
+      The total eddy streamfunction (Psi = eddyPsi + K x Slope)
+      is applied either in the tracer Eq. or in momentum Eq.
+      depending on data.gmredi (intro. GM_InMomAsStress).
+  -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
+  The key modifications are in model/src/taueddy_external_forcing.F
+  pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
+
+checkpoint59r
+o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
+  from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
+  fix option to read coriolis(@ cell-corner) from files with CS-grid.
+o pkg/mnc: add some attributes to standard 1D-coordinate variables
+o pkg/diagnostics: enforce missing_value attribute for scalar variables at
+  mass points, when using mnc for output
+  - add runtime parameter (missing_value, missing_value_int) to override 
+    default (which is the value of getcon('UNDEF'))
+o pkg/mnc: prepare mnc for the actual use of missing values with the
+  diagnostics package: small fix in mnc_cw_readwrite.template and more
+  initialisation of never used fields
+  - replace mnc_common.h and mnc_id_header.h with corresponding upper case
+  versions
+o pkg/thsice/thsice_ini_vars.F added default initial values so that 
+  thermodynamics sea ice solver does not blow up when some initial fields 
+  are missing.
+o move from external_forcing_surf.F to ini_forcing.F
+  the p-coord. hack consisting in using pLoad to set phi0surf ;
+  update output of tutorial_global_oce_in_p (affected @ truncation level).
+o Freshen up a bit hs94.1x64x5, notably: 
+  remove rotationPeriod and tRef=5*0. (adjoint only), and add 
+  exactConserv=.TRUE.
+o pkg/generic_advdiff:
+  change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
+  applies to files where Temperature & Salinity 2nd Order moments are used.
+o pkg/ptracers: add second-order moment advection schemes (80 and 81);
+  this uses a dynamically allocated internal state data structure
+  (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) 
+  and requires a fortran 90 compiler
+
+checkpoint59q
+o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
+   (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
+o Refresh tutorial_global_oce_biogeo, notably:
+  - change bathymetry (put back seamounts in ACC, use hFacs)
+  - change EOS (POLY3 --> JMD95Z)
+  - use Bryan-Lewis vertical diffusivity
+  - use multidimensional advection
+  - remove old virtual virtual in dic pkg, now done through ptracer pkg
+  - change a couple of parameters in dic pkg
+o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
+o pkg/obcs: change default to OBCSfixTopo = .true., 
+  - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
+  - replace "debugMode" with "debugLevel .GE. debLevB"
+o implementation of TAF directives for gchem,cfc,dic 
+o remove "exp5" (replaced by tutorial_deep_convection).
+o pkg/obcs: add code to fix topography gradients normal to open boundaries;
+  this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
+  the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
+  --> changes results in exp4, seaice_obcs
+o tutorial_deep_convection :
+  update the set-up and increase resolution and domain size ; start
+  from pseudo initial conditions = output at t=120mn in order to see
+  something happening when running testreport.
+o pkg/seaice: add os7mp as an advection scheme
+              add check for advection schemes
+              add a flag for restoring T and S underneath sea ice
+o pkg/my82: add netcdf-support and diagnostics 
+o thsice pkg:
+  - Now hsMax limits snow height by turning it into ice following
+    flooding scheme (and now conserving energy)
+  - Slight rewriting of the formula in thsice_calc_thick.F
+  - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
+  --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice 
+
+checkpoint59p
+o gchem / dic / cfc :
+  - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
+  - add new parameter files: "data.dic" & "data.cfc" ;
+  - various re-arrangement in initialisation & header file ;
+  - fix tutorial_global_oce_biogeo for multi-threaded test.
+o pkg/dic: test for "pickup_dic" file when restarting ;
+  if no pickup-file, can restart with a re-initialised pH (same as it did
+  before) providing pickupStrictlyMatch is set to False.
+o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
+  + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
+o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
+  and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
+o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
+ & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
+   (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
+o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
+   scheme to use for vorticty-term ;
+ - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F 
+   (with default selectVortScheme, return to original discretisation)
+ - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
+o pkg/seaice: add a line to the summary to indicate grid type (B/C)
+o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
+  bottom ; only used with variable horizontal viscosity and non-hydrostatic.
+  also fix diagnostics VISCAHW & VISCA4W.
+
+checkpoint59o
+o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
+o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
+  move a few statemens out the main loop into separate loops
+o pkg/shelfice: 
+  - sort out freshwater flux; convert freshwater fluxes to mass fluxes 
+    (kg/m^2/s), does not break tests, because in verification/isomip,
+    rhoConstFresh=rhoConst (by accident)
+  - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
+  - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
+    new file model/src/seawater.F, so that they are available for all pkgs.
+  - convert potential temperature into in-situ temperature. This changes the
+    isomip tests => update tests
+o add a flag writePickupAtEnd (default=true) to be able to suppress 
+  writing a pickup at the last timestep
+o tools/mpack-1.6 : 
+  - disable automake (not working) and autoconf (not needed).
+  - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
+    also cleaner with much less compilation warnings.
+o pkg/profiles: 
+  rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
+  (for "less than 32 characters name" compiler requirement)
+o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
+  conditions that have a different sampling frequency than S/T/U/V obcs
+o pkg/diagnostics (stats-diags): 
+  - fix global Min/Max in case 1 processor get only empty tiles
 o genmake2: replace (4 times)
      make genmake_tc_1.o >> genmake_warnings 2>&1
   with
@@ -2010,7 +2629,7 @@
   - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
   - these scheme operate in a similar manner as KPP (without ghat, of 
     course), however there is only one diffusivity that is used for both
-    temperature and salinity (and passive tracers)ç
+    temperature and salinity (and passive tracers)
 o add offline package
 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
   provided by Stephanie Dutkiewicz