--- MITgcm/doc/tag-index	2007/05/30 09:27:05	1.824
+++ MITgcm/doc/tag-index	2010/04/13 15:05:12	1.1250
@@ -1,28 +1,1531 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.824 2007/05/30 09:27:05 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1250 2010/04/13 15:05:12 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/dic:
+  -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
+    (note: not presently tested in any forward verification exp.)
+   update tutorial_global_oce_biogeo AD output file.
+o pkg/exf:
+  - account for the variation of albedo as a function of zenith angle
+    by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
+o build_options:
+ - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
+o pkg/dic:
+  change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
+  - use binary pickup file for restart;
+  - initialise atmos-CO2 box from dic_pCO2 parameter;
+  - fix multi-threaded.
+o pkg/rbcs:
+ - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
+   change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
+ - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
+   and update output.txt
+o pkg/kpp:
+ - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
+ - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
+   (= ratio of KPP non-local (salt) flux relative to surface-flux) when
+   using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
+ - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
+   KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
+o pkg/offline:
+  fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
+  (bug was added in version 1.10 on 2007-08-23).
+o pkg/offline:
+  - no need to specify periodicExternalForcing, etc ... to use offline pack
+  - offline input files no longer just single prec --> parameter offlineLoadPrec
+o verification/lab_sea:
+  change AD test to multi-tile setup and update all 4 AD output.
+  NOTE: while cost function values remain very similar,
+  gradients are very different, although gradient checks are self-consistent
+  Should try to get to the bottom of this (cost function summation order?)
+o pkg/dic:
+  in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
+  a weakness of TAF that drops part of double precision in log10 derivative.
+  <= changes removed since problem has been fixed in current TAF version 1.9.71
+  update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
+o pkg/ecco:
+  add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
+  update all 4 lab_sea AD output.
+
+checkpoint62d (2010/03/22)
+o build_options:
+  remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
+o remove unbalanced quote (single or double) in commented line of source code
+  (may cause some warning with some preprocessor/makedepend versions).
+o pkg/seaice:
+  fix seaice_model.F for adjoint (gael) and update AD results of experiments
+   lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
+o testreport:
+  add option '-runonly' (short: '-ro') to just do the run part (without make).
+o eesupp: remove JAM communication code (obsolete).
+o add option to genmake2 & testreport to switch "_RS" type to "real*4"
+  (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return 
+  to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
+  (update also the output).
+
+checkpoint62c (2010/03/02)
+o tools/build_options :
+   move (some) old optfiles from build_options/ to build_options/unsupported/
+o model/src and pkg/exf
+   surface relaxation -- separating data and data.exf options
+   The point is to ensure that we specify the surface relaxation
+   either in data or in data.exf (but not half and half) and to 
+   avoid an accidental relaxation to 0 (which happened if a time 
+   scale was specified but the file name was left empty)
+o model/src model/inc and pkg/mom_common
+   ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
+   => addition to the viscosity field as computed by others schemes
+o tools/build_options: 
+  - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
+    but keep the former optfile for few weeks for smooth transition
+o pkg/ecco
+  - allow user defined cost function contributions
+	CPP: ALLOW_USERCOST_CONTRIBUTION
+	USAGE: compute contributions in cost_usercost_all.F
+  - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
+      the two options are complementary.
+o pkg/smooth
+  - migration from contrib to the main repository
+
+checkpoint62b (2010/01/26)
+o pkg/monitor:
+  - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop 
+    (in case someone forgot to update customized pieces of code)
+o nonHydrostatic:
+  - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
+  - add a simple 2-D experiment (short_surf_wave) to test it.
+o pkg/icefront:
+   adding the shell of, and the hooks to, a new package that
+   will model melting and freezing of vertical glacier ice fronts
+o momentum:
+  add diagnostics of momentum tendency from Hydrostatic pressure gradient
+   (without surf.pressure term: would need a 2nd filling since implicit term).
+o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
+  two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
+  cannot deal with the former
+o cleaning:
+  - remove all (except OpenAD) old TLM output from results_ad dirs.
+  - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
+  - comment out maskH definition (replaced by maskInC)
+o pkg/monitor:
+  - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
+    & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
+
+checkpoint62a (2010/01/15)
+o model/src:
+  - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
+o pkg/diagnostics:
+  - add optional level number diagnostics (i.e., level number to be define
+    explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
+  - strictly check for valid parser-code(10) ;
+  - check if adding diag to the list from the right place.
+o pkg/longstep:
+  - change parameters and fix tracer conservation with rstar/nonlinear free surface
+o diagnostics:
+ - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
+   S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
+o pkg/diagnostics:
+ - Add option for writing vertical integral (sum of selected levels) of an output
+    field instead of writing output field levels. Activate this option on a per
+    output-file basis, by setting the 2nd character of fileflag to 'I'.
+ - Add field-specific information relative to level integral in 3rd postion
+    of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
+    vertically (x level-thickness x hFac), "r"=same but without hFac.
+o do_the_model_io:
+  - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
+    in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
+    writing pickups and stopping.
+o pkg/diagnostics (for now, only with mdsio):
+  - write time information to meta file (and modify accordingly rdmds.m) :
+    time-averaged diagnostics output: write starting and ending time of the
+    time-averaging interval ; snap-shot diagnostics output remains unchanged;
+o pkg/timeave:
+  - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
+    always Nr), now assumed to be equal to number of levels of averaged field;
+    only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
+o pkg/sbo:
+  - fix ocean bottom pressure global-average & 2-D time-ave output (was
+    neither initialised nor filled).
+  - add starting iteration in suffix of global-average output file
+    (to avoid over-writing the file after a restart)
+  - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
+o time-average:
+  - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
+    (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
+     ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
+    this fix DIC_COST cumulative-time array (previously: bi,bj,k)
+  - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
+  - fix missing accumulation for pkg/opps.
+  - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
+     (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
+  - fix initialisation of time-ave vars and do only full time-step increment
+    (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
+o pkg/layers:
+  - use standard RW pkg S/R to write the output
+    and remove local write_fld version (which had a problem).
+  - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
+  - fix LAYERS_CALC argument list.
+o pkg/timeave:
+  - store cumulative-time in a simple tiled array (drop the level index)
+  - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
+o pkg/ocn,aim_compon_interf
+  - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
+
+checkpoint62  (2009/12/23)
+o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
+    (was not previously tested in any other exp.)
+o pkg/monitor:
+  - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
+    mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
+    (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
+  - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
+  - change del2 calculation.
+  - use interior masks (instead of maskH, <- to be remove).
+  - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
+o mask & obcs:
+  - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
+  - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
+    (called after packages_init_fixed)
+o pkg/obcs:
+  - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
+    Fixes bug in obcs+exf with nSx*nSy.GT.1
+  - fix multi-tile handling in obcs balance code
+o nonHydrostatic:
+  - Implement AB-3 for non-hydrostatic vertical momentum ;
+    (change ordering of var. stored in pickup file when using NH)
+  - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
+  - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
+    (in prep. for new NH free surface form).
+o pkg/obcs:
+  add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
+o model/src:
+  fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
+
+checkpoint61z (2009/12/01)
+o nonHydrostatic:
+  Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
+    a spurious source of energy in simple baroclinic adjusment test case.
+  Update all non-hydrostatic exp output.
+o model/src (3-d solver):
+  Change again 3-D solver free-surface RHS term when exactConserv=T:
+    simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
+    (which was not the case with previous formulation).
+  To recover previous version, just reset "oldFreeSurfTerm" to previous value.
+  Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
+o nonHydrostatic:
+  - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
+    for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
+  - change 3-D solver to work with r* (for now, only with linear free-surf.)
+  - add few debug diagnostics (cg3d_x, residual)
+o model/src:
+  fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
+    update output of exp. global_ocean.cs32x15.viscA4
+o update output of exp. global_ocean.cs32x15.icedyn after removing
+  #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
+o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
+o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output 
+  for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
+o model: add Christopher Wolfe's implemetation of the single reduction cg2d
+  (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
+  runtime flag useSRCGSolver. Modify verification experiment global_with_exf 
+  to test this code
+o pkg/cd_code:
+  Change defaut D-grid time-stepping to get the same for D-grid momentum as for
+   C-grid momentum. D-grid velocity used to be stepped forward in time with
+   Adams-Bashforth only on surface pressure term. Tests show that using AB on
+   D-grid coriolis term improves stability (as expected from CD-scheme paper).
+  To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
+  Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
+   lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
+   tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
+  Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
+       global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
+o pkg/obcs:
+ - fix bug in initialisation (broken since Oct 1rst modification)
+   for useOBCSprescribe without useEXF.
+
+checkpoint61y (2009/11/15)
+o pkg/seaice
+ - change (once again) the discretization for the evp solver: rather than
+   squaring the averages of strain rates, average the squares to give
+   a better approximation to VP behavior (in simple test); this breaks
+   verification experiments that use EVP (lab_sea and lab_sea.hb87)
+    --> update outputs
+o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
+  to improve vectorization of adjoint code on TARGET_NEC_SX
+o verification/vermix:
+  - change vermix to a more "classical" 1d column with high vertical 
+    resolution, seasonal heat flux forcing and constant wind forcing 
+    --> update outputs
+o pkg/seaice
+ - fix diagnostics of principal stress components for EVP
+ - add optional diagnostics of non-linear convergence for LSOR solver
+ - make maximum zeta a runtime parameter
+o model/src (3-d solver):
+  Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
+   which consisted in removing the Surf. Non-Hydrostatic pressure from the
+   whole column and adding it to Eta (inspired from Casualli, 1999):
+   Only affects 3-D solver initial guess and only if using ExactConserv,
+   but tests did show a degradation of solver convergence. For this reason,
+   decide to disable this piece of code.
+   to recover previous version, just set zeroPsNH = exactConserv (line 78).
+  Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
+o pkg/ggl90: 
+ - fix previous modif (unfortunatly has not been documented here).
+o pkg/seaice/autodiff:
+ - add CPP flag to include clipping of zeta in EVP code;
+   although clipping of zeta is not necessary for EVP and not recommended
+   it was done by default, now clipping is disabled by default
+ - modify computation and store zetaC/Z in seaice_evp for TAF
+ - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
+ - change seaice_calc_viscosities/strainrates for better
+   vectorization after AD by TAF
+ - rearrange common blocks in SEAICE.h once again for easier dumps of
+   adjoint output, adjust adcommon.h and g_common.h
+ - change flux form of default advection scheme for better vectorization
+   of adjoint code
+ - modify lab_sea/input.lsr to test the flux form of default advection 
+   scheme
+o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
+  transition in checkpoint61r)
+
+checkpoint61x (2009/10/19)
+o adjoint: adding two new verification experiments
+  * tutorial_global_biogeo: an online dic sensitivity experiment 
+    (work with G. Forget)
+  * tutorial_dic_adjoffline: an offline dic sensitivity experiment
+    (an update of the Dutkiewicz et al., 2006 paper)
+  Both use the same CO2FLUX cost function, but different controls
+  Gradient checks look good, but some recomp. could still be traightened out
+  Should add xx_dic control variable to test at some point
+o model/src:
+  add run-time parameters to check and/or mask initial Temp & Salt
+o pkg/ptracers:
+  apply zonal filter (if used) to all passive tracers
+
+checkpoint61w (2009/10/12)
+o adjoint:
+  * update and finish work on adjoint of dic package (G. Forget)
+  * start adjoint of offline package
+  * bug fix for cube-sphere TLM code (active_file_g.F)
+o tutorial_global_oce_optim:
+  now tested with 4 tiles (change data.grdchk and update output_adm.txt)
+  and add SIZE.h_mpi for MPI testing
+o pkg autodiff
+ - fix bug in autodiff_restore
+ - make genmake2 remove comments and empty lines from ad_input_code.f in 
+   order to reduce file size (new script file remove_comments_sed)
+o allows to specify vertical profile of vertical viscosity (viscArNr)
+o pkg autodiff
+  autodiff_ini_model_io: comment out writing of grid information to netcdf 
+  files, because at this time the grid fields are a bunch of zeros 
+  (this is analogous to ini_mnc_vars.F) 
+o pkg seaice/autodiff:
+ left-over from removing the 3-time-level fields: 
+ - small rearrangement of common blocks (SEAICE.h)
+ - fix field declaration in order to get meaningful output in 
+   adseaice.*.nc (adcommon.h) 
+o pkg obcs:
+ - go through NH code only if nonHydrostatic=T
+ - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
+ - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
+   => Update output of experiment seaice_obcs
+ - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
+ - fix NH+Orlanski restart (add wvel OBC value in pickup file)
+ - fix restart for useOBCSprescribe + useEXF
+o pkg ctrl
+ - make obcs as control parameter work also with useSingleCPUio
+ - replace a few sny and snx by Ny and Nx to be consistent with
+   ctrl_set_globfld_x/yz.F
+o pkg seaice
+ - re-introduce global field frWtrAtm for the case of 
+   ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
+ - catch the case of an empty filename in seaice_cost_init_fixed.F
+o pkg ecco:
+ - small bug fixes in the_main_loop
+  . fix order of monitor arguments
+  . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
+  . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
+    that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
+ - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the 
+   imbalance diagnostics for wmean_h/sflux = 0 
+ - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
+ - catch the case of empty filenames in ecco_cost_init_fixed.F 
+   and ecco_readparms.F
+ - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
+   to make this statement meaningfull in ecco_cost_weights.F
+o pkg zonal_filt:
+  - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
+  - when using rStar, filter uVel*hFacW instead of uVel
+   (tested without topography: fix a Pb of growing instability with NLFS)
+o pkg/aim/thsice:
+ -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
+  (works as SST restoring)
+o pkg/thsice:
+ -add specific parameter for salt restoring in slab mixed-layer
+   (by default equal to the temperature restoring)
+
+checkpoint61v (2009/09/21)
+o pkg/kpp:
+ -add double diffusive contributions as a hack, turned off by default 
+  for now, and the code can be excluded with a CPP-flag 
+  EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
+ -add a verification experiments to "vermix" to test this code
+o pkg/mom_common:
+  Move computation of length scales to mom_init_fixed.F (avoid recomputation
+  at each time-steps*levels).
+o pkg/layers:
+  Created a new package for computing volume fluxes in temperature or
+  [not yet implemented] density layers, e.g. for calculating residual
+  overturning circulations. 
+o pkg/diagnostics: 
+  implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
+o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
+o pkg/mdsio (& pkg/rw): rework high level S/R interface:
+  To avoid mixing type (RS/RL) of input/output array argument,
+  replace single mixed-type array with a pair from each type (RS/RL).
+o setting pickupSuff force to start from a pickup (even if nIter0=0): this
+  is now implemented for all pkgs (previously only done for the main pickup) 
+
+checkpoint61u (2009/08/25)
+o pkg/obcs:
+  - change OB?eta from _RS to _RL and put them into a separate commen block
+  - add code to read OB?eta from a file via obcs_prescribe_read: the code
+    compiles and does not destroy any other experiments, the data is read
+    properly, but the code is not tested in actual applications
+o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to 
+  create a meaningful unit attribute for the time coordinate variable 
+o pkg/ebm: add plenty of missing "_d 0" ;
+   update results of experiment global_ocean_ebm (fwd + adjoint tests) 
+  Notes: several pieces of code only works for (very) specific set up
+   (domain size, lat range, etc ...); should be documented & stop if one 
+   of those assumptions is not meet.
+o pkg/seaice: add missing "_d 0" in HSNOW initialisation
+   update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests) 
+      and offline_exf_seaice (seaicetd + adjoint).
+o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
+   update results of experiments: lab_sea (4 fwd tests + 3 adjoint), 
+    seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
+o few changes to pass when compiling with strick checking of arguments 
+   across S/R (allow to find few bugs in S/R calls).
+o pkg/seaice:
+ - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new 
+   2d-fields, for slightly better performance
+
+checkpoint61t (2009/07/22)
+o pkg/seaice: 
+ - remove unused variables in seaice_evp
+ - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
+o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
+   named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
+   each processor opens a different file (a fix from Matt).
+o cg2d:
+   use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
+   this reduces number of EXCH calls by 2 when using exch2.
+   For now, keep previous size array for gc2d_nsa.F to avoid Pb with store 
+   directives and missing simple EXCH (exch_s3d_rx) adjoint code.
+o pkg/thsice: 
+   add code for Near Infra-Red albedo (from Jeff)
+   (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
+o ini_model_io:
+   move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
+   MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
+   to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
+
+checkpoint61s (2009/06/30)
+o pkg/exch2 (exch2_rxN_cube*):
+   remove last BARRIER (no need to synchronise after getting data from shared
+   buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
+o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
+  and generate new output (for the 2 tests) using default rotationPeriod.
+o pkg/exch2:
+  - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
+    (was already the case with AUTODIFF_EXCH2 defined)
+  - add bj in exch2 arrays and S/R.
+  - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
+    MLAdjust to exch2 (identical results except with MPI -> truncation diff);
+o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
+  - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
+    GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
+  - verification experiment natl_box.longstep
+o build_options: ifort+mpi_aces optfile (following Constantinos advise):
+  allow different versions of ifort (8 or 9) and different versions
+   of mpi (mpich or mpich2) to be used with the same optfile.
+  requires to load a netcdf module and set MPI_INC_DIR (see comments inside
+   optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
+o pkg/seaice: 
+  fix previous modif (3-level field removed) for old-pickup reading 
+
+checkpoint61r (2009/06/25)
+o pkg/seaice: 
+ - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
+  1. introduce fields for time step (N-1)
+  2. do not use levels 2 and 3 anymore (but keep them)
+  3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This 
+     includes changes to pkg/thsice/thsice_get_velocity.F, 
+     model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
+     pkg/obcs/obcs_apply_uvice.F.
+ - completely remove code for leap-frog time stepping for second order
+   advection
+ - adjusted adjoint accordingly;
+   gradient checks have improved by an order of magnitude!
+ 
+checkpoint61q (2009/06/22)
+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 (2009/06/10)
+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 (2009/05/26)
+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 (2009/05/12)
+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 (2009/04/29)
+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 (2009/04/07)
+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 (2009/03/18)
+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 (2009/03/17)
+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 (2009/02/13)
+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 (2009/01/27)
+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 (2008/12/29)
+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 (2008/11/21)
+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 (2008/10/23)
+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 (2008/09/25)
+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 (2008/08/30)
+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 (2008/08/05)
+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 (2008/07/29)
+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 (2008/06/24)
+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 (2008/06/19)
+--->>> 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 (2008/05/29)
+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 (2008/05/06)
+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 (2008/04/10)
+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 (2008/03/07)
+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
+     COMM="$CC $CFLAGS -c genmake_tc_1.c"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_warnings 2>&1
+  to make genmake2 always see the value of CC as specified in the optfile.
+o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
+  - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
+  - modify verification advect_cs test to test SOM-advection on CS-grid.
+o pkg/ctrl:
+  - Rewrite of ctrl_map_ini_ecco.F, 
+    introducing a generic routine (ctrl_map_ini_gen.F).
+  - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
+
+checkpoint59n (2008/02/09)
+o pkg/diagnostics: for large number of diagnostics, store diagnostic mate 
+  number in dedicate array "hdiag":
+  - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
+    with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
+  - many small changes (integer format) for large number of diagnostics
+  - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
+    a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
+o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
+  usingSphericalGrid, this allows to define the rotated grid coordinates
+  via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
+  geographical coordinates according to the inverse of the rotation defined
+  by the Euler angles, so that Coriolis parameter and online-interpolation by 
+  exf works with the geographical coordinates on XC/YC/XG/YG.
+  Naturally, this feature does not work with all packages, so some 
+  combinations are prohibited in config_summary (flt, flt_zonal, ecco, 
+  profiles), because there the coordinates are assumed to be regular 
+  spherical grid coordinates. 
+o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
+  - introduce isopycnal diffusion coefficient control.
+o tools/adjoint_options: 
+  - additional control vector components.
+o pkg/mnc: have mnc create marginally meaning full coordinate variables
+  (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 
+o pkg/mypackage: 
+  - add example of read/write pickup for state-var ; 
+  - add entry points to the main code for state-vars diags & write-pickup.
+o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
+  transitions for useExfYearlyFields
+  - add new subroutine that determines the file to read from for 
+    use*YearlyFields = .TRUE. and .FALSE.
+  - add a verification experiment to global_with_exf that tests 
+    useExfYearlyFields with USE_EXF_INTERPOLATION defined
+o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in 
+  analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new 
+  subroutines (which could be generated from a template, because they are 
+  almost identical), for now they are included in obcs_prescribe_read.F for
+  simplicity
+o pkg/exf:
+  - add a little more diagnostic to exf_interp_read (in analogy to 
+    mds_read_field, can be turned off with debugLevel < debugLevA=1)
+  - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
+    ugly but fast by unrolling short inner loops, inserting a unroll=8 
+    directive in routine lagran, and splitting a loop and making do while the
+    outermost loop (the latter requires the intoduction of index arrays)
+o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
+o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
+  http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
+o verification/seaice_obcs: updated for restart test and latest options
+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 (2008/01/14)
+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 (2007/12/18)
+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 (2007/11/30)
+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 (2007/11/09)
+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 (2007/10/21)
+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 (2007/09/29)
+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 (2007/09/17)
+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 (2007/08/21)
+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 (2007/07/26)
+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 (2007/06/21)
+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 (2007/06/04)
+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_elaticParm > 1
-  - make lsr boundary conditions free slip (by default)
+  - 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 level)
+  - 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
+checkpoint59b (2007/05/16)
 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: 
@@ -74,7 +1577,7 @@
 o pkg/thsice:
  fix few little problems, in thsice_calc_thickn.F:
   - growth vertically (and not laterally) if iceFrac == iceMaskMax
-  - melt laterally only if hIce < hThinIce (as the comments say)
+  - 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.
@@ -93,7 +1596,7 @@
 o OpenAD
  - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
 
-checkpoint59a
+checkpoint59a (2007/05/01)
 o pkg/seaice: some parameter clarifications and a little bit of clean up
 o pkg/thsice: rename run-time parameters:
    himin       -> hIceMin
@@ -111,7 +1614,9 @@
      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
@@ -133,7 +1638,7 @@
 o pkg/kpp: add code to have mixing in shelf ice caverns
   - add myThid to all kpp routines (long overdue)
 
-checkpoint59
+checkpoint59 (2007/04/19)
 o pkg/exf: 
   - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
     ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
@@ -159,7 +1664,7 @@
   - 2nd set of modifs for thsice adjoint in conjunction with exf
 o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
 
-checkpoint58y_post
+checkpoint58y_post (2007/04/15)
 o Added capability for latitudinal dependence of Bryan and Lewis, 1979
   vertical diffusivity, similar to that in MOM4; turned on using
   #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
@@ -175,7 +1680,7 @@
        - better when using non-linear advection scheme (not yet fully tested)
        - can also be used in atmospheric set-up (for now, only the diffusion).
 
-checkpoint58x_post
+checkpoint58x_post (2007/04/04)
 o IO option for global-file compact format:
   - add options when generating topology (utils/exch2/matlab-topology-generator)
   - add I/O capability (pkg/mdsio).
@@ -183,7 +1688,7 @@
   for now long-line format not yet supported by pkg/mdsio (& exch2).
 o shelfice: add a few diagnostics
 
-checkpoint58w_post
+checkpoint58w_post (2007/03/13)
 o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
   rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
   (and replace horiVertRatio in NH code).
@@ -204,7 +1709,7 @@
 o move call to cal_readparms up to make calendar parameters/variable available
   to all packages
 
-checkpoint58v_post
+checkpoint58v_post (2007/02/08)
 o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
   useDynP_inEos_Zc tested.
 o pkg/exf: changes to properly interpolate/mask/scale initial fields
@@ -223,7 +1728,7 @@
  - use this scheme for temperature & salinity in 2 advection test exp.:
    advect_xy & advect_xz, respectively.
 
-checkpoint58u_post
+checkpoint58u_post (2007/01/12)
 o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
 o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
 o testreport: add option "-skipdir" to skip some test.
@@ -238,7 +1743,7 @@
 o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
 o pkg/thsice: fix reading mnc-pickups
 
-checkpoint58t_post
+checkpoint58t_post (2006/12/30)
 o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
 o pkg/mdsio:
  - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
@@ -281,7 +1786,7 @@
  - introduce a few local fields to avoid modifying external fields such
    as atemp, etc.
 
-checkpoint58s_post
+checkpoint58s_post (2006/12/11)
 o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
   changed exf_set_gen.F so that
     genperiod=0 means input file is one time-constant field and
@@ -315,7 +1820,7 @@
   as actual snow thickness.  It now refers everywhere to effective snow
   thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
 
-checkpoint58r_post
+checkpoint58r_post (2006/11/17)
 o modifications to pkg/seaice/growth.F, which change results of
   lab_sea experiment: fixes pertain to melting snow over open water, to
   masking EVAP under sea ice, and to using the correct AREA variable for
@@ -339,7 +1844,7 @@
 o ctrl: adding new control variables:
   lwflux, lwdown, evap, snowprecip, apressure, runoff
 
-checkpoint58q_post
+checkpoint58q_post (2006/10/20)
 o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
   1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
   high_res_cube configuration by 4% on Columbia.
@@ -350,7 +1855,7 @@
   single CPU io) so that TAF does not have to see EESUPPORT.h
 o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
 
-checkpoint58p_post
+checkpoint58p_post (2006/09/08)
 o obcs: stop if obcs is used with useCDscheme = .true.
 o shelfice: 
  - fix a sign error so that no slip at shelfice interface works
@@ -361,7 +1866,7 @@
 o added adjoint exch routined for all exch*3d* routines
   and updated flow directives
 
-checkpoint58o_post
+checkpoint58o_post (2006/08/28)
 o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
   remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
 o change controling S/R for writing pickup file (new S/R do_write_pickup)
@@ -375,7 +1880,7 @@
  - add a simple boundary layer scheme to reduce noise
  - fix the indexing in shelfice_u/v_drag so that there will be actually drag
 
-checkpoint58n_post
+checkpoint58n_post (2006/08/14)
 o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to 
    local variable (not in common block).
 o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. 
@@ -396,7 +1901,7 @@
   and stop cleanly when MAX_NO_THREADS is too small. 
 o add S/R BAR_CHECK to check multi-threaded barrier synchronization
 
-checkpoint58m_post
+checkpoint58m_post (2006/07/17)
 o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
    and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
@@ -422,7 +1927,7 @@
   update rotating_tank results, but not plume_on_slope (affected at 
   truncation level, 11 digits).
 
-checkpoint58l_post
+checkpoint58l_post (2006/07/12)
 o calc_gw: 
  - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
  - remove side-drag for now (need to fix it); update plume_on_slope results.
@@ -440,7 +1945,7 @@
 o pkg/rbcs
   * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
 
-checkpoint58k_post
+checkpoint58k_post (2006/07/06)
 o testreport:
  - always build in dir. "build" (if not there, mkdir build instead of building 
    & running in input)
@@ -473,7 +1978,7 @@
    advection subroutine (but still not used within DST advection S/R)
 o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
 
-checkpoint58j_post
+checkpoint58j_post (2006/06/15)
 o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
   from file (collects calls previously in FORWARD_STEP)
 o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
@@ -481,7 +1986,7 @@
 o genmake2
   replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
 
-checkpoint58i_post
+checkpoint58i_post (2006/06/14)
 o pkg/seaice: add parameter that allows to scale/turn off effect of seaice 
   on wind stress (SEAICEstressFactor defaults to 1.)
 o Total number of Timers is finite (<=40): comment out 2 non-essential one
@@ -495,7 +2000,7 @@
     non-EVP pickup files when using SEAICEuseEVP
   - fix sign error in diffusion in seaice_calc_rhs
 
-checkpoint58h_post
+checkpoint58h_post (2006/06/07)
 * Modifications for bottom topography control
   o replace hFacC by _hFacC at various places
   o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
@@ -505,7 +2010,7 @@
   o works for 5x5 box, doesnt work for global_ocean.90x40x15
 * Adding verification for 5x5 box (4-layer) bottom topography control
 
-checkpoint58g_post
+checkpoint58g_post (2006/06/07)
 o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
    used for mean seasonal cycle, mean diurnal cycle); add an example
    in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
@@ -521,7 +2026,7 @@
 o pkg/seaice
   - make (default) second order advection a bit less confusing?
 
-checkpoint58f_post
+checkpoint58f_post (2006/06/05)
 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice 
   to pkg/seaice): 
   - new routines thsice_map_exf and thsice_get_exf provide the interface
@@ -552,7 +2057,7 @@
 o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
   testreport accordingly
 
-checkpoint58e_post
+checkpoint58e_post (2006/05/17)
 o SEAICE_CGRID adjoint done
 o R_STAR adjoint implemented.
   * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
@@ -560,7 +2065,7 @@
 o Make pkg/profile fully independent of ecco,cost, etc. stuff
   to be able to use it in pure forward.
 
-checkpoint58d_post
+checkpoint58d_post (2006/04/21)
 o upgrade simple test-experiment to tutorial example:
  step.1: duplicate the experiment and (step.2) will remove the old copy.
   tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
@@ -600,7 +2105,7 @@
 o Benign bug fix in initialization (spotted by M. Mazloff) of
   ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
 
-checkpoint58c_post
+checkpoint58c_post (2006/03/23)
 o adjoint: finish NLFS adjoint and provide reference output in
   verification/global_ocean.90x40x15/results_ad_nlfs
 o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the 
@@ -634,7 +2139,7 @@
    + move computation of the viscosities eta and zeta into a new separate
      routine (because I need to recompute them in seaice_ocean_stress.F)
 
-checkpoint58b_post
+checkpoint58b_post (2006/03/13)
 o AIM+thSIce: fix sign of Short-Wave through the Ice ; 
   update output.txt of exp. aim.5l_cs.thSI
 o various mnc cleanups and improvements:
@@ -697,7 +2202,7 @@
     (turn on with SEAICEuseFluxForm)
   - replace 1 in 3d global fields by kSurface in growth.F
   
-checkpoint58a_post
+checkpoint58a_post (2006/02/13)
 o seaice:
   - bug fix in advect.F
 o shelfice: 
@@ -750,7 +2255,7 @@
    and parameters (note: calcWindStress replaces .NOT.readwindstress).
  - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
 
-checkpoint58
+checkpoint58 (2006/01/12)
 o add "--embed-source" option to genmake2 which, when the supporting 
   tools can be compiled (as determined by genmake2) will turn on the 
   embed_files package which then embeds the entire MITgcm source code 
@@ -763,7 +2268,7 @@
   * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
   * Thanks to Tom Haine for testing!
 
-checkpoint57z_post
+checkpoint57z_post (2005/12/31)
 o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
   affects output (@ truncation level) of exp. plume_on_slope ; updated.
 o fix the pickup behavior for obcs in combination with ptracers
@@ -794,13 +2299,13 @@
   * Absolute scale somewhat unclear so far
   * no area weighting was included since no other cost term does so far
 
-checkpoint57y_post
+checkpoint57y_post (2005/12/08)
 First step for a NLFS adjoint
 o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
 o new init. routines for calc_r_star, calc_surf_dr
 o still need to deal with ini_masks_etc
 o testreport seemed happy
-checkpoint57y_pre
+checkpoint57y_pre (2005/12/08)
 
 o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
 o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
@@ -809,7 +2314,7 @@
 o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
   be in GCHEM_OPTIONS).
 
-checkpoint57x_post
+checkpoint57x_post (2005/12/04)
 o fix testreport Pb in multiple test experiment.
 o cleanup our namelist syntax in verification:
   - make it more F95 standards compliant (some work still needed)
@@ -829,7 +2334,7 @@
     (there are a number of extensive recomputations)
   * Initialize certain variables needed for adjoint
 
-checkpoint57w_post
+checkpoint57w_post (2005/11/03)
 o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
              fix the singleCpuIO RS version of MDSWRITEFIELD
    and add a WARNING if using globalFiles=T with multi-processors.
@@ -846,7 +2351,7 @@
   ptracers in a large domain with a constant non-zero value. Also,
   untangle ptracers_init.F a little.
 
-checkpoint57v_post
+checkpoint57v_post (2005/10/13)
 o change dome exp. to use variable viscosity in side-drag terms.
 o remove all the files from the cfc_offline test since they are now
   incorporated into tutorial_cfc_offline which has been producing
@@ -887,7 +2392,7 @@
 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ 
   truncation level) 4/5 MLAdjust test results (11&12 digits match).
 
-checkpoint57t_post
+checkpoint57t_post (2005/10/03)
 o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
 o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
   same truncation, independent of the face number: affects affects several
@@ -910,7 +2415,7 @@
   Suggested values of viscosity parameters found in mom_calc_visc. 
   Many new viscosity diagnostics available.
 
-checkpoint57s_post
+checkpoint57s_post (2005/09/20)
 o Add clearing-house for viscosity calculations, mom_calc_visc and 
   correct numerous bugs in LeithD and Smagorinsky discretizations.  
   mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be 
@@ -936,7 +2441,7 @@
       and works with both EXCH1 and EXCH2 (but needs more testing)
   - writing works for all verification test cases w/ g77 on Linux
 
-checkpoint57r_post
+checkpoint57r_post (2005/09/07)
 o make MNC variable initialization happen earlier
 o add diagnostics for (almost) each term of the momentum Eq.
 o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
@@ -956,7 +2461,7 @@
 o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
   (see README file)
 
-checkpoint57q_post
+checkpoint57q_post (2005/08/19)
 o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
 o fix annoying months-old bug in mnc/mdsio output for seaice pkg
   - bug was reported by Jean-Michel and Ian Fenty
@@ -973,7 +2478,7 @@
   * verification/OpenAD/code/ has necessary scripts and description;
   * converts, compiles and runs successfully;
 
-checkpoint57p_post
+checkpoint57p_post (2005/08/01)
 o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
 o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
   (already the case for some pkgs, including recent MNC_init, e.g. thsice)
@@ -987,7 +2492,7 @@
   global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
   matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
 
-checkpoint57o_post
+checkpoint57o_post (2005/07/30)
 o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and 
   (2) its ready to be documented during the 20050801 DocFest
 o MNC-ify the gmredi package -- tested and works w/ and w/o mnc 
@@ -996,7 +2501,7 @@
   in global1x1_tot/code_seaice_adj to access indices 32, 33
   (worth another tag)
 
-checkpoint57n_post
+checkpoint57n_post (2005/07/29)
 o adding precip control xx_precip 32
 o adding swflux control xx_swflux 33
 o Replacing 10 forcing penalty cost routines by 1 generic.
@@ -1012,13 +2517,13 @@
   (applies in particular to tapelev I/O)
 o removed inefficient K-loop in all active_file*control*.F
 
-checkpoint57m_post
+checkpoint57m_post (2005/07/28)
 o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
   and advect_cs (use EXCH-2 and standard cs-32 grid files).
 o pkg/exch2: filling of face-corner halo regions is optional 
   (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
 
-checkpoint57l_post
+checkpoint57l_post (2005/07/14)
  tag before updating tutorials (pre-release-2) 
 o add cos & sin of grid-direction orientation angle (curvilinear grid only,
    for output and interpolation of input fields onto model grid)
@@ -1030,11 +2535,11 @@
 o add mnc output capability to diagnostics/diagstat and update
   our cvsignore files for the ACSII output generated
 
-checkpoint57k_post
+checkpoint57k_post (2005/07/02)
 o lab_sea now uses diagnostics package and provides a suite of
   new EXF diagnostics output.
 
-checkpoint57j_post
+checkpoint57j_post (2005/06/30)
 o exf
   * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
     Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
@@ -1064,7 +2569,7 @@
 o fix few little things to avoid floating error with -ftrapuv (ifort v9)
  (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
 
-checkpoint57i_post
+checkpoint57i_post (2005/06/19)
 o Diagnostics package was changed: diagnostic allocation is now deactivated
   by setting an empty file name in the namelist (used to be by setting 0 frequency)
 o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
@@ -1083,7 +2588,7 @@
   tested against monitor output (including land & thSIce) on various exp.
 o make seaice-pkg I/O type flags (MNC/MDS) more standard.
 
-checkpoint57h_done
+checkpoint57h_done (2005/05/19)
   tag after changing user customized files (DIAGNOSTICS_SIZE.h, 
   data.diagnostics, data.gchem, data.ptracers) is done.
 
@@ -1092,11 +2597,11 @@
 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
   and rename it: DIFFERENT_MULTIPLE
 
-checkpoint57h_post
+checkpoint57h_post (2005/05/14)
 o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
 o pkg/diagnostics: change output frequency, now in seconds (instead
   of Nb of iterations). This requires to change data.diagnostics.
-checkpoint57h_pre
+checkpoint57h_pre (2005/05/12)
 
 o in mnc, let the user create the output dir if both mnc_outdir_date
   and mnc_outdir_num are false
@@ -1110,11 +2615,11 @@
 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
   not mnc -- this mistake was found by JMC and is now corrected
 
-checkpoint57g_post
+checkpoint57g_post (2005/04/15)
 o add Adams-Bashforth 3rd Order time stepping:
   - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
   - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
-checkpoint57g_pre
+checkpoint57g_pre (2005/04/15)
 
 o make lambda[Theta,Salt]ClimRelax spatially varying
   (default remains spatially uniform constant based on tau)
@@ -1124,12 +2629,12 @@
 o separate masks used for ctrl_pack/unpack 'from write_grid' output
   (suggested by G. Forget)
 
-checkpoint57f_post
+checkpoint57f_post (2005/04/06)
 o add parameter "baseTime" = model base time = time at iteration zero
   new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to 
   account for baseTime shift
 o move Coriolis arrays from PARAMS.h to GRID.h
-checkpoint57f_pre
+checkpoint57f_pre (2005/04/06)
 
 o mnc-ifying the seaice package
 o introduced an alternative length scale calculation for use in the limiting
@@ -1150,7 +2655,7 @@
   * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
   * mom_vi_hdissip: to be able to use Leith scheme in adjoint
 
-checkpoint57e_post
+checkpoint57e_post (2005/02/28)
 o Adding eddy stress controls a la Ferreira et al.
 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
 
@@ -1168,7 +2673,7 @@
 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
 
-checkpoint57d_post
+checkpoint57d_post (2005/02/11)
 o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
 o modify verification/ideal_2D_oce so that it tests the creation of mnc 
   output from the diagnostics package
@@ -1190,10 +2695,10 @@
   (note: still needs some work specially for snap-shot diagnostics)
   duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
 
-checkpoint57c_post
+checkpoint57c_post (2005/01/27)
 o Change testing option (-ieee) to get closer agreement between g77 & ifort
 o generate new output.txt files on faulks with g77 & the new -ieee option
-checkpoint57c_pre
+checkpoint57c_pre (2005/01/27)
 
 o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
   update output.txt of exp. global_ocean.90x40x15
@@ -1226,7 +2731,7 @@
   * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
   * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
 
-checkpoint57b_post
+checkpoint57b_post (2004/12/20)
 o simplify options in diagnostics_fill arguments (remove weird combinations)
 o fix MNC coordinate variables so that they now contain per-face index
   values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in 
@@ -1272,16 +2777,16 @@
    look through the short list of active diag. (instead of the long list)
    create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
 
-checkpoint57a_post
+checkpoint57a_post (2004/12/10)
 o this set of changes restores TAMC compatibility
   tested for global_ocean.90x40x15 adjoint on trough
   (what a pain)
 
-checkpoint57a_pre
+checkpoint57a_pre (2004/12/10)
 o some modifs in tools/build_options for sunos
 o call ctrl_pack for ctrl at end for optimcycle=0
 
-checkpoint57
+checkpoint57 (2004/12/09)
 o add horizontal bi-harmonic viscosity for vertical velocity
   - new parameter viscA4W (defaults to viscA4)
   - affects only non-hydrostatic code
@@ -1299,7 +2804,7 @@
 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
   (theta2, salt2 in ecco_cost_weights)
 
-checkpoint56c_post
+checkpoint56c_post (2004/12/03)
 o OBCS as control variables
   - update ctrl_ad_diff.list, obcs_ad_diff.list
   - remove balance of obcs controls from default
@@ -1317,7 +2822,7 @@
 o mdsio:
   - i/o-vector change debugLevel from debLevA to debLevB
 
-checkpoint56b_post
+checkpoint56b_post (2004/12/01)
 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
   is called from DO_THE_MODEL_IO
   - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
@@ -1332,7 +2837,7 @@
   testreport. 
 o ptracers_monitor: bug fix for MPI
 
-checkpoint56a_post
+checkpoint56a_post (2004/11/28)
 o GCHEM: finish reorganizating the package
   - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency 
     (introduces another 3D-array for each passive tracer, but only if
@@ -1377,7 +2882,7 @@
   - cleaning up
 o small cleaning of exch2: remove files that are also in eesupp/src
 
-checkpoint56
+checkpoint56 (2004/11/17)
 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
 o mnc: cleanup "full" files--fixes out-of-memory problem
 o ECCO-GODAE
@@ -1407,7 +2912,7 @@
 o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
   from sign change 
 
-checkpoint55j_post
+checkpoint55j_post (2004/11/10)
 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
   affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
 o add consistent build directories and .cvsignore files to verification
@@ -1418,7 +2923,7 @@
 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; 
   affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
 
-checkpoint55i_post
+checkpoint55i_post (2004/10/28)
 o change arrays for total vertical diffusivity (2.D if explicit,
   3.D if implicit) ; each ptracer uses its own background value.
 o added mnc/NetCDF output capability to ocn_compon_interf
@@ -1433,7 +2938,7 @@
 o Compute the non-local term using either KPP vertical diffusivity (=default) 
    or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
 
-checkpoint55h_post
+checkpoint55h_post (2004/10/20)
 o add verification test "vermix"
 o remove all the *_ioinc flags and replace with the single global
   outputTypesInclusive flag
@@ -1441,7 +2946,7 @@
 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
 o useMNC moved from data.mnc to data.pkg
 
-checkpoint55g_post
+checkpoint55g_post (2004/10/14)
 o Renaming carbon AD experiments to comply with testreport conventions
 o Updating adjoint of Held-Suarez hs94.1x64x5
 o Fixing directives for non-ECCO forward_step, after ECCO directives
@@ -1451,10 +2956,10 @@
 o Updating adjoint output for natl_box_adjoint after 
   pkg/ecco has been modified (see taga c55d_post)
 
-checkpoint55f_post
+checkpoint55f_post (2004/10/13)
 o rename to timeave_init_fixed
 
-checkpoint55e_post
+checkpoint55e_post (2004/10/13)
 o some delicate re-shuffle of store directives to avoid one
   extra call of do_oceanic_physics
   affects ecco_the_main_loop.F, do_oceanic_physics.F
@@ -1462,14 +2967,14 @@
 o NB: this may break global_ocean adjoint temporarily,
   but it is clear how to fix it. Will do later, need this now.
 
-checkpoint55d_post
+checkpoint55d_post (2004/10/11)
 o ECCO specific cost function terms (up-to-date with 1x1 runs)
 o ecco_cost_weights is modified to 1x1 runs
 o modifs to allow observations to be read in as
   single file or yearly files
 o enable to read exf forcing fields as either
   single file or yearly files (flag useExfYearlyFields)
-checkpoint55d_pre
+checkpoint55d_pre (2004/10/08)
 
 o switch between 2-level and 3-level checkpointing
 o add ability of MNC to write local and "partial" (eg. 2D slices where 
@@ -1517,7 +3022,7 @@
   - changed argument list of OBCS_CALC to myTime+deltaTclock
   - fixed about 35 bugs in obcs_external_fields_load
 
-checkpoint55c_post
+checkpoint55c_post (2004/09/23)
 o obcs stuff
   - new runtime flags useOBCSprescribe, useOBCSbalance
   - re-arranged obcs_calc
@@ -1531,7 +3036,7 @@
 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
   which simplifies the calls and passes the ifc check-bounds test
 
-checkpoint55b_post
+checkpoint55b_post (2004/09/22)
 o add a 2D scalar, Z location, exchange_2 routine.
 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
   to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
@@ -1542,7 +3047,7 @@
 o fix gad_advection.F (CubedSphere part), back to version 1.23
 o fix bug in mom_vi_del2uv.F (CubedSphere part).
 
-checkpoint55a_post
+checkpoint55a_post (2004/09/20)
 o merged code to 
   * prescribe/read time-dependent open boundaries
     (works in conjunction with exf, cal)
@@ -1550,7 +3055,7 @@
   * each boundary N/S/E/W now has its own CPP option
     (healthy for the adjoint)
 
-checkpoint55
+checkpoint55 (2004/09/17)
 o up-to-date adjoint of previous breaks
   - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
   - global_ocean_ebm: adjoint still needs fix (TLM ok)
@@ -1560,7 +3065,7 @@
 o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
   (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
 
-checkpoint54f_post
+checkpoint54f_post (2004/09/16)
 o in verification/carbin/ remove experiment related to
   ALLOW_PASSIVE_TRACER (array tr1 etc)
   code_ad/ input_ad/ results_ad
@@ -1586,21 +3091,21 @@
   - numerous small formatting cleanups for ProTeX
 o add version info (via BUILD_INFO.h) to MNC and stdout
 
-checkpoint54e_post
+checkpoint54e_post (2004/09/02)
 o add two new packages
   - pp81 (Packanowski and Philander, 1981), Richardson number and 
     stratification dependent mixing
   - 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
 o genmake2: add ability to search for C compilers and cleanup test output
   - fixes recent SX-6 problems and should help with others (eg. HP-UX)
 
-checkpoint54d_post
+checkpoint54d_post (2004/07/27)
 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, 
   leading to additional shift by 5 days each year of integration
@@ -1616,7 +3121,7 @@
 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
 
-checkpoint54c_post
+checkpoint54c_post (2004/07/18)
 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
   this affects (truncation error) output.txt of test-exp:
    global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
@@ -1627,7 +3132,7 @@
 o start to test mnc routinely in exp0
 o add sea-ice loading (sIceLoad) as a new forcing field.
 
-checkpoint54b_post
+checkpoint54b_post (2004/07/08)
 o add testreport "-j JOBS" option for parallel builds (tested and pretty 
    impressive on Altix and Opteron systems)
 o diagnostics can now write NetCDF files through the mnc package
@@ -1637,19 +3142,19 @@
   affects (truncation error) output of lab_sea & natl_box exp.: updated
 o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
 
-checkpoint54a_post
+checkpoint54a_post (2004/07/06)
 o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
 o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
 o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
 o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
   + internal_wave (shift in writing cg2d_ini_res)
-checkpoint54a_pre
+checkpoint54a_pre (2004/07/05)
 
 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
   - modified verification/lab_sea and natl_box_adjoint accordingly
 
-checkpoint54
-checkpoint53g_post
+checkpoint54 (2004/07/02)
+checkpoint53g_post (2004/07/02)
 o prepare splitting of thermodynamics: store convect.counter in common block
 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
   output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
@@ -1658,7 +3163,7 @@
 o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
 o restore adjointability
 
-checkpoint53f_post
+checkpoint53f_post (2004/06/25)
 o modifications that affect AIM experiment results (update output.txt):
   - no advection of S at top interface Nr (pkg/generic_advdiff) 
   - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
@@ -1671,7 +3176,7 @@
 o added rotating_tank experiment
 checkpoint53e_pre
 
-checkpoint53d_post
+checkpoint53d_post (2004/06/14)
 o faulks upgraded: re-generate output.txt that have changed:
    global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
 o Added Bryan and Lewis, 1979, vertical diffusivity profile
@@ -1690,9 +3195,9 @@
 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
   of mom_common/
   - simple re-arrangement of instructions within computing loop
-checkpoint53d_pre
+checkpoint53d_pre (2004/05/21)
 
-checkpoint53c_post
+checkpoint53c_post (2004/05/21)
 o new version of coupler for AIM+thSIce and Ocean models
  - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
  - land: change Evaporation of snow
@@ -1709,7 +3214,7 @@
   * TLM OK
   * ADM not sufficient accuracy yet (needs further testing)
 
-checkpoint53b_post
+checkpoint53b_post (2004/05/14)
 o Commiting new energy balance model to repository
   * package is pkg/ebm
   * verif. is verification/global_ocean_ebm
@@ -1727,7 +3232,7 @@
 C        by atmospheric eddy transports.
 C        J. Climate 7(12), 1870-1882
 o Will need long integration testing.
-checkpoint53b_pre
+checkpoint53b_pre (2004/05/14)
 
 o created pkg/mom_common in preparation for variable viscosity code
 o renamed and split ini_mnc_io
@@ -1735,7 +3240,7 @@
 o AIM using land: soil wetness availability account for snow
 o added printMapIncludesZeros to EEPARMS namelist
 
-checkpoint53a_post
+checkpoint53a_post (2004/05/11)
 o restore TAMC compatiility for exf_constants.h
   (no usage of _d in .h)
 o Additional storing in KPP in an attempt to fix
@@ -1748,7 +3253,7 @@
   and hence gives results closer to that of Experiment 2.
   Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
 
-checkpoint53
+checkpoint53 (2004/05/06)
 o stable checkpoint with up to date adjoint
   TLM tests only run for 1st grdchk at the moment. Its unclear if
   this is a code problem or a problem with resetting code for g_
@@ -1758,7 +3263,7 @@
    o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) 
      are both still in chaos following their security messes.
 
-checkpoint52n_post
+checkpoint52n_post (2004/05/06)
 o various build (mostly genmake2) changes including:
   - ability to build/run more easily within Cygwin and MacOS X
   - more complicated Makefiles with a stronger dependence on Gnu Make
@@ -1789,7 +3294,7 @@
   - maintain snow precipitation unchanged (even if Tsf >=0).
  both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
 
-checkpoint52m_post
+checkpoint52m_post (2004/04/18)
 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
   this does not change any of the results, because myIter=0 in swfrac always
   lead to jwtype=2 (the default anyway), but the call makes little sense
@@ -1821,7 +3326,7 @@
 o Added functionality to grdchk:
   pick global i,j,k position (or nearest wet) where to perform check.
 
-checkpoint52l_post
+checkpoint52l_post (2004/03/11)
 o new land formulation:
   a) use ground enthalpy as prognostic variable to ensure exact
      energy conservation.
@@ -1832,7 +3337,7 @@
   a) Treat separately land / ocean / sea-ice surface fluxes
      to allow implicit computation of land & sea-ice surface temp.
   b) add snow precipitation.
-checkpoint52l_pre
+checkpoint52l_pre (2004/03/11)
 
 o fix problem (when 1 tile is empty) in min/max monitor.
 o fix bug in timeAve (u,vZetatave in common block) 
@@ -1845,7 +3350,7 @@
 o aim.5l_cs: modify sea-ice fraction input file ; update output
 o exf: Adding simple range check routine for exf fields after read
 
-checkpoint52k_post
+checkpoint52k_post (2004/02/23)
 o removed top-level directory "diags"
   - we migrated these functions to pkg/timeave a long time ago
 o fixed bug introduced in pkg/monitor
@@ -1858,7 +3363,7 @@
   taveFreq, dumpFreq, pChkptFreq
 o MAIN and ECCO differentiability restored
 
-checkpoint52j_post
+checkpoint52j_post (2004/02/18)
 o fix nchklev in tamc.h for global_ocean...
 o Bringing flow and store directives up-to-date
 o Really weird thing!
@@ -1866,7 +3371,7 @@
   starttime, niter0, instead of mytime, myiter, screws up the adjoint: 
   TAF places a faulty re-call of initialise_varia
   after cost_final call which should not be there!
-checkpoint52j_pre
+checkpoint52j_pre (2004/02/03)
 
 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
   error messages
@@ -1883,15 +3388,15 @@
   mon_vort3.F to make exch2 friendly with >1 tile per cube face
 o limit timeave output for hi-res integrations
 
-checkpoint52i_post
+checkpoint52i_post (2004/01/21)
 o removed CPP_EEOPTIONS.h from verification/*/code
 o updated the tiling for global_ocean_pressure
-checkpoint52i_pre
+checkpoint52i_pre (2004/01/20)
 
 o update aim.5l_LatLon using the standard aim_v23 pkg (instead of 
   the old pkg/aim).
 
-checkpoint52h_pre
+checkpoint52h_pre (2004/01/20)
 o shortened offending lines in exch2_send_rx?.template
 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
 o genmake2: add build & execute test for NetCDF code
@@ -1902,13 +3407,13 @@
   metric terms are ignored and it is assumed that
   there is no sea-ice on cube faces 1, 2, 4, and 5.
 
-checkpoint52f_post
+checkpoint52f_post (2004/01/09)
 o added exch2 cube routines to pkg/exch2
 o modified hs94.cs-32x32x5 to use it
 o added new grid files to hs94.cs-32x32x5
-checkpoint52f_pre
+checkpoint52f_pre (2004/01/07)
 
-checkpoint52e_post
+checkpoint52e_post (2004/01/07)
 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
   for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
@@ -1916,7 +3421,7 @@
 o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
 o update output (gad_calc_rhs.F changes affect truncation error) of exp:
  front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
-checkpoint52e_pre
+checkpoint52e_pre (2004/01/02)
 
 o fix bug in impldiff when Nr=1 or Nr=2.
 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
@@ -1927,7 +3432,7 @@
 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
 o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
 
-checkpoint52d_post
+checkpoint52d_post (2003/12/16)
 o re-tiled many expts to allow comparison in multi-processor mode
   - updated output accordingly
   - changed hs94.128x64x5 to use intial T from file rather than use the
@@ -1956,11 +3461,11 @@
 o new verification experiment, cpl_aim+ocn: 
    coupled ocean - AIM atmosphere on cs32 grid. 
 
-checkpoint52d_pre
+checkpoint52d_pre (2003/12/06)
 o surface flux time-av diagnostic modified for NLFS & RealFreshWater 
 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
 
-checkpoint52c_post
+checkpoint52c_post (2003/11/25)
 o Fixing OPTIONS files for use of exf:
   - ALLOW_ECCO not needed
   - ECCO_CPPOPTIONS.h should not be included from
@@ -1974,7 +3479,7 @@
 o modified STOREs in GAD_ADVECTION
 o corrected key comp. for passkey
 
-checkpoint52b_post
+checkpoint52b_post (2003/11/23)
 o new version: "thsice" of thermodynamic sea-ice pkg:
  - only 1 call from "forward_step"; conserve energy, fresh-water & salt. 
  - modify fluxes but do not change theta directly;
@@ -1982,7 +3487,7 @@
  - add forcing fields + data files in global_ocean.cs32x15/inp_thsice 
    + output_thsice.txt to test thsice & bulk_force pkgs.
 o put back grid & coriolis monitor output.
-checkpoint52b_pre
+checkpoint52b_pre (2003/11/23)
 
 o call "do_the_model_io" at the beginning (=> dump initial state) 
 o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
@@ -1992,7 +3497,7 @@
 o default tamc.h in pkg/autodiff supposed to crash
   to ensure proper customization
 
-checkpoint52a_post
+checkpoint52a_post (2003/11/17)
 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
   - moved surfaceTendencyTice from pkg/seaice to main code
   - subroutine FREEZE_SURFACE now limits only surface temperature
@@ -2007,13 +3512,13 @@
   snapshot file was missing some ad-variables,
   but no warning issued by TAF
 
-checkpoint52a_pre
+checkpoint52a_pre (2003/11/12)
 o some bug fixes for #undef REAL4_IS_SLOW
 
 checkpoint52 = ecco_c52_e35
 o after testing adjoints of checkpoint51u_post
 
-checkpoint51u_post
+checkpoint51u_post (2003/11/06)
 o this is the post-merge tag of the ecco-branch
   (needs another clean checkout and re-testing)
 o various natl_box_adjoint configs and results
@@ -2028,10 +3533,10 @@
   (new namelist ecco_cost_nml)
 o in ctrl/ cleaned some cross-dependencies and updated CPP options
 
-checkpoint51t_post
+checkpoint51t_post (2003/11/04)
 o this is the pre-merge tag of the ecco-branch
 
-checkpoint51s_post
+checkpoint51s_post (2003/11/04)
 o cleanup: removed various obsolete #define-s
 o pkg/grdchk
   - renamed 'ph-grd 3' to 'grad-res'
@@ -2040,12 +3545,12 @@
   - additional high-precision output for testreport
     (grep for 'precision_grdchk_result')
 
-checkpoint51r_post
+checkpoint51r_post (2003/11/03)
 o cleaned up or removed CPP_OPTIONS.h files
 o updated results for some of the tests to reflect the new
   optfiles (-ieee: -O0 instead of -O3)
 
-checkpoint51q_post
+checkpoint51q_post (2003/10/30)
 o cd_code:
   - moved cd_scheme.F -> cd_code_scheme.F
   - separate read_checkpoint from cd_code_ini_vars.F
@@ -2061,7 +3566,7 @@
   - confined inclusion of AD_CONFIG.h to where necessary.
 o genmake2: changed AD dependencies from SRCFILES to AD_FILES
 
-checkpoint51p_post
+checkpoint51p_post (2003/10/30)
 o create initial cd_code package
   - WARNING: the initialization of fields within packages
     is broken because INI_FIELDS (where READ_CHECKPOINT is
@@ -2076,7 +3581,7 @@
 o cleanup verification/*/code/GMREDI_OPTIONS.h
 o cleanup testreport
 
-checkpoint51o_post
+checkpoint51o_post (2003/10/27)
 o bringing AD-related verif's up to date with genmake2
   - carbon/
   - global_ocean.90x40x15/
@@ -2097,7 +3602,7 @@
 o helping TAF to recognize dependency on kUp for
   fVerU, fVerV
 o Replacing delZ by delR in pkg/ctrl/
-checkpoint51o_pre
+checkpoint51o_pre (2003/10/24)
 
 o undid all of cp51 pending some cleanups and discussion
 o added the [#include "AD_CONFIG.h"] statement to all files that need 
@@ -2105,7 +3610,7 @@
  o re-worked the build logic in genmake2 to support AD_CONFIG.h
  o removed tools/genmake since it no longer works
 
-checkpoint51n_post
+checkpoint51n_post (2003/10/23)
 o modifications to make FREEZE flux visible to pkg/kpp
   - moved surfaceTendencyTice from pkg/seaice to main code
   - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
@@ -2114,7 +3619,7 @@
      global_ocean.cs32x15, and global_with_exf)
 o added surface flux output variables to TIMEAVE_STATVARS
 
-checkpoint51n_pre
+checkpoint51n_pre (2003/10/23)
 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
 o added [#include "AD_CONFIG.h"] to all files that use the following
   defines:
@@ -2122,26 +3627,26 @@
   - ALLOW_TANGENTLINEAR_RUN
   - ALLOW_ECCO_OPTIMIZATION
 
-checkpoint51m_post
+checkpoint51m_post (2003/10/21)
 o incorporating changes to get TAMC/TAF working in genmake2
   - added new TAMC/TAF targets to the Makefile
   - various cleanups related to package handling
   - these changes should have no impact on the forward model
 
-checkpoint51l_post
+checkpoint51l_post (2003/10/20)
 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
  - faster algorithm for cal_addtime.F
  - higher precision arithmetic, where needed
  - pkg/exf *startdate variables changed from calendar date to
    model integration time
 
-checkpoint51l_pre
+checkpoint51l_pre (2003/10/17)
 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
 o enable to apply restoring on S & T only in a latitude band.
 o update output (external_forcing_surf modif. change truncation errors)
    global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
 
-checkpoint51k_post
+checkpoint51k_post (2003/10/16)
 o change default to: useNHMTerms=.FALSE.
  - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
    adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
@@ -2155,7 +3660,7 @@
   removed the #include "PACKAGES_CONFIG.h" from it
 o fix a bug in mom_fluxform (from chk51j_post)
 
-checkpoint51j_post
+checkpoint51j_post (2003/10/10)
 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
 o adjusted some flow directives (dynamics, thermodynamics)
 o added cubed-sphere case to test cost function
@@ -2169,13 +3674,13 @@
        - pkg_ad_diff.list
        - pkg_ad_check_lev?_dir.h
 
-checkpoint51i_post
+checkpoint51i_post (2003/10/09)
 o merge of the branch-genmake2
   - knowingly breaks the older genmake
   - automatic generation of all ALLOW_${PKG_NAME} defines
   - new testreport supersedes older testscript
 o large number of package inclusion and header cleanups
-checkpoint51i_pre
+checkpoint51i_pre (2003/10/08)
 
 o new output for adjoin of global ocean vector invariant
 o fix for checkpoint of thermodynamic seaice and bulk_force
@@ -2187,7 +3692,7 @@
 o modifications to clean up dic pkg
 o add pkg/cfc
 
-checkpoint51g_post
+checkpoint51g_post (2003/10/02)
 o provide links for ARPACK and ADM*TLM
 o start removing verification/vero/
 o update AD-related stuff
@@ -2195,12 +3700,12 @@
 o adding to verification/global_ocean.90x40x15/ adjoint of
   vector invariant setup
 
-checkpoint51f_post
+checkpoint51f_post (2003/10/02)
 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
   of tracer Green's fucntions for ocean inversion project.
 
-checkpoint51f_pre
+checkpoint51f_pre (2003/08/07)
 o Added on-the-fly spatial interpolation capability
     "USE_EXF_INTERPOLATION" to pkg/exf.
   - This is a temporary Cartesian-grid hack until
@@ -2212,7 +3717,7 @@
     and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
     non-local transport term.
 
-checkpoint51e_post
+checkpoint51e_post (2003/08/03)
 o pkg/mom_vecinv: 
   - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
   - add time-ave diagnostic of vorticity advection.
@@ -2222,7 +3727,7 @@
 o land pkg: read initial state from files.
 o AIM : add stratospheric drag in the upper level
 
-checkpoint51d_post
+checkpoint51d_post (2003/07/18)
 o change function ILNBLNK (=> last non-blank char.) to return zero
   (instead of the string length) when the string. char is empty
 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
@@ -2235,7 +3740,7 @@
   - new active_file_loc... and mdsio_..._loc routines
   - affected packages: autodiff, ctrl, grdchk, mdsio
 
-checkpoint51c_post
+checkpoint51c_post (2003/07/08)
 o introducing integer flag debugLevel
   - debLevZero: suppress all output
   - debLevA: standard
@@ -2258,14 +3763,14 @@
   - checked tapelev/comlev recomputations: OK
 <<<checkpoint51b_pre
 
-checkpoint51a_post
+checkpoint51a_post (2003/06/25)
 o added code for biogeochemistry package
   - new pkgs: dic, gchem
   - new subroutine in ptracers
 o modify code for biogeo packages
   - in model/src and pkg/ptracers
 
-checkpoint51
+checkpoint51 (2003/06/24)
 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
   - autodiff, ctrl, exf, grdchk, seaice
   kept separate packages
@@ -2273,14 +3778,14 @@
 o updating verification/internal_wave, verification/lab_sea
   (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
 
-checkpoint50i_post
+checkpoint50i_post (2003/06/23)
 o Preparing next differentiable checkpoint and sync
   of MAIN vs. ecco-branch
   - 1st step: this one is differentiable
   - 2nd step: next(! not this) checkpoint will have updated packages 
               from ecco-branch)
 
-checkpoint50h_post
+checkpoint50h_post (2003/06/20)
 o new package "land": provide surface BC for AIM.
 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
 o AIM: use true log-P extrapolation for near surface temp (= as in 
@@ -2289,13 +3794,13 @@
 o somewhat cleaned package initialisation sequence for
   ctrl/ cost/ ecco/ in packages_... routines
 
-checkpoint50g_post
+checkpoint50g_post (2003/05/23)
 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
   - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
   - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
     made the default because of faster convergence than ADI
 
-checkpoint50f_post
+checkpoint50f_post (2003/05/23)
 o exf totally restructured
   - replaced all exf_set_ routines by one generic exf_set_gen.F
     and made sure it's still differentiable
@@ -2303,7 +3808,7 @@
   - exf_inscal_/exf_outscal_ suffixes consistent with field names
   - updated adjoint/makefile and relevant verif. accordingly
 
-checkpoint50f_pre
+checkpoint50f_pre (2003/05/23)
  o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
       + change Evap over land. (update aim.5l_cs output)
  o added missing .cvsignores and made uniform across expts
@@ -2313,37 +3818,37 @@
  o new fn in pkg/monitor to stop model if solution grows too big
  o removed lots of single quotes from comments
 
-checkpoint50e_post
+checkpoint50e_post (2003/05/14)
 o make KPP work with PTRACERS
  - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
    nearly a copy of kpp_transport_s
  - there is no analogue to SurfaceTendencyS, so I have to use 
    gPtr(of the surface layer) instead
 o add a new platform SunFire+mpi (SunFire 15000) to genmake
-checkpoint50e_pre
+checkpoint50e_pre (2003/05/13)
 
-checkpoint50d_post
+checkpoint50d_post (2003/05/13)
 o change kpp output from multiple-record state files to single-record state 
   files analogous to write_state.F
 o reduce the output frequency of cg3d-related stuff to the monitor frequency, 
   analogous to the cg2d-related output. 
 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, 
   so that writing to internal file fn (with length 512) fails.
-checkpoint50d_pre
+checkpoint50d_pre (2003/05/12)
 
-checkpoint50c_post
+checkpoint50c_post (2003/05/12)
 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
 
-checkpoint50c_pre
+checkpoint50c_pre (2003/04/30)
 Merging from release1_p13:
 o bug fix for pkg/seaice dynamic solver
 o Added SEAICE_initialHEFF to pkg/seaice
 
-checkpoint50b_post
+checkpoint50b_post (2003/04/17)
 o store u*,v* in gU,V instead of in guNm1,gvNm1
 o in order to put the momForcing out of the Adams-Bashforth:
   move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
@@ -2352,19 +3857,19 @@
 o re-generate output for highly sensitive test-exp:
    global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
 
-checkpoint50b_pre
+checkpoint50b_pre (2003/04/17)
 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
 o corrected CPP option mismatch in exf_Bulk... functions for case 
   #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
 
-checkpoint50a_post
+checkpoint50a_post (2003/03/21)
 o Bug fix for merging between c50 and KPP.
   ikey was passed from thermodynamics to kpp_calc via
   common block rather than being recomputed in kpp_calc,
   in contradiction with new key itdkey.
   New key ikppkey created, and tamc.h headers updated.
 
-checkpoint50
+checkpoint50 (2003/03/08)
 - 2nd step of merge with ecco-branch:
   merge changes in ecco-branch back into main trunk
 - bug fix in find_alpha
@@ -2372,7 +3877,7 @@
 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
 - merged some sliced AD support routines
 
-checkpoint49
+checkpoint49 (2003/03/06)
 merged from ecco-branch:
 o exf:
   - Enable initialisation of forcing fields to constant 
@@ -2410,7 +3915,7 @@
   (see MITgcm manual).
 o cal: synchronized between MAIN and ecco-branch
 
-checkpoint48i_post
+checkpoint48i_post (2003/03/05)
 o Changes to restore differentiability of code w.r.t. previous tag
   (mostly adding new routines to make list and replacing
   pressure by totPhiHyd).
@@ -2428,13 +3933,13 @@
   tbar, sbar, psbar, which should not be reinitialised;
   only relevant for ecco-branch)
 
-checkpoint48h_post
+checkpoint48h_post (2003/02/28)
 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
 o Added SEAICE_initialHEFF to pkg/seaice
 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
 
-checkpoint48g_post
+checkpoint48g_post (2003/02/18)
 --- EOS:
 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
   store total Potential in totPhyHyd for diagnostics & EOS.
@@ -2448,7 +3953,7 @@
  ( changes results of ideal_2D_oce )
 o includes r* 2nd term in potential gradient.
 
-checkpoint48f_post
+checkpoint48f_post (2003/02/18)
 Merging from release1_p12:
 o Modifications for using pkg/exf with pkg/seaice
   - improved description of the various forcing configurations
@@ -2476,7 +3981,7 @@
   - adjoint-friendly modifications
   - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
 
-checkpoint48e_post
+checkpoint48e_post (2003/02/12)
 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. 
@@ -2487,7 +3992,7 @@
     inverted_barometer solid-body.cs-32x32x1
   (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
 
-checkpoint48d_post
+checkpoint48d_post (2003/02/09)
 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
@@ -2495,37 +4000,37 @@
     => affects results of glob_oce_pressure (different truncation error)  
   update output.txt of ideal_2D_oce & global_ocean_pressure
 
-checkpoint48d_pre
+checkpoint48d_pre (2003/02/08)
 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
+checkpoint48c_post (2003/02/06)
 Modifications in treatment of initial flux forcing controls
 to avoid extra storing of flux fields.
 
-checkpoint48c_pre
+checkpoint48c_pre (2003/01/21)
 o Added tidal_basin_2d experiment (currently 1D!)
 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) 
 
-checkpoint48b_post
+checkpoint48b_post (2003/01/27)
 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
+checkpoint48a_post (2003/01/24)
 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
+checkpoint48 (2003/01/23)
 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
 
-checkpoint47j_post
+checkpoint47j_post (2003/01/21)
 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_...
@@ -2544,7 +4049,7 @@
     re-activated full calculation of taperfct for case 'ac02'
 o updating verification/ adjoints of carbon, global_ocean.90x40x15
 
-checkpoint47i_post
+checkpoint47i_post (2003/01/13)
 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)
@@ -2560,7 +4065,7 @@
   S/R gmredi_slope_psi should be cleaned
 o verification/carbon now has exactConserv=.TRUE.
 
-checkpoint47g_post
+checkpoint47g_post (2003/01/10)
 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:
@@ -2586,7 +4091,7 @@
 in conjunction with data.gmredi parameters to be checked in
 in a few minutes under verification/carbon/code/
 
-checkpoint47f_post
+checkpoint47f_post (2002/12/28)
 Merging from release1_p10:
 o modifications for using pkg/exf with pkg/seaice
   - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
@@ -2598,19 +4103,19 @@
   - verification/lab_sea default experiment now uses
     pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
 
-checkpoint47e_post
+checkpoint47e_post (2002/12/27)
 o created a tag prior to creating a branch
 
-checkpoint47d_post
+checkpoint47d_post (2002/12/16)
 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
+checkpoint47d_pre (2002/12/16)
 
-checkpoint47c_post
+checkpoint47c_post (2002/12/16)
 o Added a verification experiment for a global cubed-sphere ocean run
   -  verification/global_ocean.cubed32x32x30
   -  uses pkg/therm_seaice and pkg/bulk_forcing
@@ -2622,7 +4127,7 @@
   NOTES: requires option NONLIN_FRSURF to be "#define".
 o update advect_xz/results/output.txt (left from checkpoint44g_post)
 
-checkpoint47b_post
+checkpoint47b_post (2002/12/05)
 Merging from release1_p9:
 o pkg/seaice
   - removed GOTO's and added taf directives
@@ -2639,7 +4144,7 @@
   - added missing matlab routines
   - added test of thermodynamics parallelization
 
-checkpoint47a_post
+checkpoint47a_post (2002/11/23)
 o new pkg: aim_v23 
  = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. 
    for now, keep the same surface forcing as before.
@@ -2656,7 +4161,7 @@
 - Two ifdef statements for compile time,
    ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
 
-checkpoint47
+checkpoint47 (2002/11/15)
 differentiable version of checkpoint46n_post
 o bug fix in quasihydrostaticterms
 o * "clean" adjoint code (in terms of extensive recomputations)
@@ -2685,7 +4190,7 @@
   - #define GM_VISBECK_VARIABLE_K
   - GM_taper_scheme    = 'ldd97'    
 
-checkpoint46n_post
+checkpoint46n_post (2002/11/12)
 Merging from release1_p8:
 o verification/natl_box:
   updating new external_fields_load routine
@@ -2739,7 +4244,7 @@
   the exf (and cal) package instead of the
   external_fields_load routine (cf README file).
 
-checkpoint46m_post
+checkpoint46m_post (2002/11/07)
 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()
@@ -2752,7 +4257,7 @@
 o removed gravitySign from PARM04
 o switched to g77/ifc from pgf77 in aim experiments
 
-checkpoint46l_post
+checkpoint46l_post (2002/11/01)
 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)
@@ -2765,9 +4270,9 @@
    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
+checkpoint46l_pre (2002/10/23)
 
-checkpoint46k_post
+checkpoint46k_post (2002/10/23)
 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)
@@ -2781,20 +4286,20 @@
  - read AIM physics parameters from a file (data.aimphys)
  - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
 
-checkpoint46j_post
+checkpoint46j_post (2002/10/07)
 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
+checkpoint46j_pre (2002/09/27)
 
-checkpoint46i_post
+checkpoint46i_post (2002/09/25)
 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
+checkpoint46h_post (2002/09/25)
 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
@@ -2804,13 +4309,13 @@
   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
+checkpoint46h_pre (2002/09/18)
 
  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
+checkpoint46g_post (2002/09/18)
 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
@@ -2828,9 +4333,9 @@
   - 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
+checkpoint46g_pre (2002/09/16)
 
-checkpoint46f_post
+checkpoint46f_post (2002/09/16)
 o Enable tangent linear (forward mode) gradient checks:
   - extended active file handling to g_... files
   - added TANGENT_SIMULATION to theSimulationMode
@@ -2838,7 +4343,7 @@
 o added tangent linear setup in verification/carbon/code_ftl
 o added adjoint setup in verification/front_relax/code_ad
 
-checkpoint46e_post
+checkpoint46e_post (2002/09/05)
 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
@@ -2847,30 +4352,30 @@
   - 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
+checkpoint46e_pre (2002/08/19)
 
-checkpoint46d_post
+checkpoint46d_post (2002/08/19)
 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
+checkpoint46d_pre (2002/08/15)
 
 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
+checkpoint46c_post (2002/08/15)
 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
+checkpoint46c_pre (2002/08/07)
 
-checkpoint46b_post
+checkpoint46b_post (2002/08/07)
 o Added new equation of state -> JMD95Z and JMD95P
   - EOS of Jackett and McDougall, 1995, JAOT
   - moved all EOS parameters into EOS.h
@@ -2879,17 +4384,17 @@
   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
+checkpoint46b_pre (2002/07/31)
 
-checkpoint46a_post
+checkpoint46a_post (2002/07/31)
 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
+checkpoint46a_pre (2002/07/13)
 
-checkpoint46
+checkpoint46 (2002/07/13)
 further merges from release1_p5
 o new ctrl package
   - adopted from ECCO environment to enable optimization
@@ -2916,7 +4421,7 @@
 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
 o incorporated hooks for sponge layer code (external_forcing.F)
 
-checkpoint45d_post
+checkpoint45d_post (2002/07/12)
 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)
@@ -2930,7 +4435,7 @@
  - for each tracer, define internal flag for multiDimAdvection & A-B
 o monitor: change definition of KE to check conservation of Energy
 
-checkpoint45c_post
+checkpoint45c_post (2002/05/30)
 o Removed f90 comments ("!")
 o Modified initialisations to enable exf package for MITgcm
   (without invoking ECCO_PACKAGE).
@@ -2938,7 +4443,7 @@
   - enable centered differences
   - modified format of standard output
 
-checkpoint45b_post
+checkpoint45b_post (2002/05/30)
 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
@@ -2950,7 +4455,7 @@
   (corresponding adjustment of TAF tape initialisation).
 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
 
-checkpoint45a_post
+checkpoint45a_post (2002/05/01)
 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
@@ -2970,13 +4475,13 @@
   (conflict on some platforms, e.g. IBM SP3)
 o modified carbon verif.
 
-checkpoint44h_pre
+checkpoint44h_pre (2002/03/14)
 o vertical grid option: allow to put the Interface at the middle between
   2 cell-centers ; replace delZ in pkg/kpp by drF.
 o GM Advective form: Tracers are advected using the residual transport (=
   Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
 
-checkpoint44g_post
+checkpoint44g_post (2002/03/05)
 o fix surface correction term in multiDimAdvection (affects plume_on_slope 
   results) ; ifdef missing in thermodynamics.F
 
@@ -3041,7 +4546,7 @@
 o check parameters & config (chkpt44a_pre,post)
 o OBC and NonLin_FrSurf.
 
-checkpoint44
+checkpoint44 (2002/01/18)
 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)
@@ -3049,13 +4554,13 @@
 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
 o added some stuff for AD
 
-checkpoint43
+checkpoint43 (2001/09/28)
 o added two new advection tests
 o added global 4x4 degree ocean test
 o added test of H&S94 with free surface on cube
 o some final mods for gradient check, adjoint,...
 
-checkpoint42
+checkpoint42 (2001/09/27)
   Fixed AD-related problems:
 o Store directives up-to-date with re-arranged Adams-Bashforth
   (mainly thermodynamics.F)
@@ -3067,11 +4572,11 @@
   for the case ALLOW_KPP
 o Cleaned argument list for timestep_tracer.F
 
-checkpoint41
+checkpoint41 (2001/09/27)
 o re-formatted/added comments in prologues of key subroutines
   to work with protex
 
-checkpoint40
+checkpoint40 (2001/09/27)
 o moved calc_gs, calc_gt and calc_tr1 back to model/src
 o added FLT (floats) package from Arne along with demo. experiment
 o re-arranged Adams-Bashforth scheme for tracers to allow easier
@@ -3080,7 +4585,7 @@
 o modified multi-dim method to work on cube
 o bug fix in KPP (from DM)
 
-checkpoint40pre9
+checkpoint40pre9 (2001/09/27)
 o added DST advection schemes
 o fix MPI bug on SGI's
 o modifications for non-linear free-surface
@@ -3090,7 +4595,7 @@
 o added/updated many matlab scripts
 o added multi-dimensional advection method for tracers
   
-checkpoint40pre8
+checkpoint40pre8 (2001/09/05)
 o new package rw/
   Added method for dumping intermediate local arrays:
   mdsio_writetile - same as mdsio_writefield except works from inside
@@ -3109,14 +4614,14 @@
   currently nothing implemented to switch this storing off
   in case fluxform is used since no CPP flag available).
 
-checkpoint40pre7
+checkpoint40pre7 (2001/08/14)
 o bug fix in dynamics.F
   calc_viscosity called before k=1,Nr loop.
 o added some #ifdef's ALLOW_PASSIVE_TRACER
 o cleaned initialisations in ctrl_map_ini
   related to TAF
 
-checkpoint40pre6
+checkpoint40pre6 (2001/08/13)
 o split dynamics into thermodynamics & dynamics
 o corresponding split of calc_diffusivity into
   calc_diffusivity, calc_viscosity
@@ -3124,7 +4629,7 @@
 o Added diffkr, kapgm to control variables
 o bug fix in gmredi_slope_limit for ldd97
 
-checkpoint40pre5
+checkpoint40pre5 (2001/07/31)
 o proper initialization of Adams-Bashforth time stepping
   + uses forward step for very first step of model (iter=0)
 o re-generated *all* output since almost all output is modified by this
@@ -3138,7 +4643,7 @@
   + this uses an alternative form of ini_curvilinear_grid.F which
     is not necessarily any better than the current one...
 
-checkpoint40pre4
+checkpoint40pre4 (2001/07/30)
 o added re-initialisations of utrans,vtrans,rtrans in
   calc_common_factors which are crucial for TAF.
 o extended iMin,jMin range for calc_common_factors,
@@ -3146,18 +4651,18 @@
 o added option ALLOW_PASSIVE_TRACER
 o a few minor updates and fixes
 
-checkpoint40pre3
+checkpoint40pre3 (2001/07/13)
 o created calc_gtr1.F for gad package
 o split the_main_loop and re-introduced forward_step
 o some recomputations of nIter0 for TAMC
 
-checkpoint40pre2
+checkpoint40pre2 (2001/07/13)
 o Updated to latest branch of AJA, JMC
 o Added gradient check package
 o Added routines for passive tracer handling
 o Added carbon sequestration sensitivity experiment
 
-checkpoint39
+checkpoint39 (2001/05/14)
  o Modifications and fixes to support TAMC
    (mainly missing or wrong directives)
  o Corrected common blocks when fooling TAMC to produce adjoint I/O
@@ -3171,7 +4676,7 @@
          (NB: this is not the full ECCO environment)
  o disabled some packages by default in genmake
 
-checkpoint38
+checkpoint38 (2001/04/10)
  o see notes_c37_adj.txt
  o corrected wrong layer index in external_forcing_t
  o replaced the_main_loop/forward_step by the_main_loop
@@ -3179,7 +4684,7 @@
    (replaced criteria for initial/final state)
  o added runtime flag for pre-C35 pickups: usePickupBeforeC35
 
-checkpoint37
+checkpoint37 (2001/03/13)
  o mdsio.F routine split and packaged in pkg/mdsio
    (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
     used unless genmake -disable=mdsio)
@@ -3196,19 +4701,19 @@
  o Non-Hydrostatic pickup file Pb fixed.
  o bug with Rigid-lid version (since c35) fixed.  
 
-checkpoint36
+checkpoint36 (2001/02/20)
  o implement Crank-Nickelson barotropic time-stepping
  o recover Time-Average diagnostics
  o fix Pb in checkpoint (PR#19) 
  o AIM become a standard package ; clean unused CPP_kees
 
-checkpoint35
+checkpoint35 (2001/02/08)
  o subtantial rewrite of dynamics.f
  o allows staggered time-stepping
  o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
  o added bottom drag (linear + quadratic)
 
-checkpoint34
+checkpoint34 (2001/01/30)
  o Modified exchange routines for correct reverse simulation.
  o Added verification output to comply with bug fix in impldiff.F
    as of c33 (exp2, natl_box).
@@ -3219,7 +4724,7 @@
  o Added routine GLOBAL_SUM_INT to global_sum.F
  o Added mdsio_gl.F for ECCO purposes.
 
-checkpoint33
+checkpoint33 (2000/11/30)
  o Fixed bug in lower BC in impldiff.F
  o Fixed confusion about units of forcing arrays in FFIELDS.h
    namely Fu,Fv,Qnet,Qsw,EmPmR:
@@ -3237,7 +4742,7 @@
      possibly use them.
  o Corrected genmake to delete a temporary file during configuration
 
-checkpoint32
+checkpoint32 (2000/11/13)
  o Scaling of forcing fields moved from external_forcing.F to
    external_fields_scale.F, called directly after loading fields.
  o Surface relaxation terms added to surface tendency fields in
@@ -3248,7 +4753,7 @@
  o Modifications and bug fixes in KPP package.
  o Verification experiment for KPP added (verification/nat_box/)
 
-checkpoint31
+checkpoint31 (2000/09/11)
  o Packages interface brought in line with defined standard
    -> new routines packages_...F
    -> changes in initialise_fixed.F, initialise_varia.F
@@ -3265,7 +4770,7 @@
    - not yet tested for GMRedi.
    - not yet tested for KPP.
 
-checkpoint30
+checkpoint30 (2000/07/13)
  o Updates for OBCs
  o New experiment for test OBCs (internal_wave)
  o New output.txt in verification/exp4/results/
@@ -3274,10 +4779,10 @@
  o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
    and entry for T90 in genmake
 
-checkpoint29
+checkpoint29 (2000/06/21)
  o packaged KPP and GM/Redi
 
-checkpoint28
+checkpoint28 (2000/06/09)
  o Corrected initialization of hFacMin for difference vertical coordinates
  o Modified calculation of partial cell thickness to more robust algorithm
  o config_summary.F: replaced write_1D_... by write_0D_...
@@ -3290,7 +4795,7 @@
    included store directives and tape key computations required for TAMC.
  o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
 
-checkpoint27
+checkpoint27 (2000/04/10)
  o fixed calc_isoslopes() to so that cancellation of terms in tensor
    formulation works properly with variable resolution.
  o restructured the calling tree between the_model_main() and dynamics()
@@ -3298,7 +4803,7 @@
  o introduced initialization file pSurfInitFile for free surface (cg2d_x)
    in new routine ini_psurf()
 
-checkpoint26
+checkpoint26 (2000/04/05)
  o moved some #ifdef in optional routines to encompass everything
    except the argument declarations. This was using up some memory.
  o fixed macros like _ADT to work with both versions of Linux cpp
@@ -3308,7 +4813,7 @@
    (macros are now in eesupp/inc/CPP_EEMACROS.h)
  o patch for 2 processor JAM mode
 
-checkpoint25
+checkpoint25 (2000/03/15)
  o updates for OBCs and NH
  o dramatically reduced memory usage
  o added "JAM" routines for use on Artic network
@@ -3319,32 +4824,32 @@
     an explicit free-surface option)
  o initial state input files for U and V
 
-checkpoint24
+checkpoint24 (1999/08/02)
  o Removed some spurious "REAL"s
  o Updated KPP to latest version from JPL
  o Added a COS(latitude) in horizontal viscosity
 
-checkpoint23
+checkpoint23 (1999/05/26)
  o Added del^4 diffusion for salt and temperature
  o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
 
-checkpoint22
+checkpoint22 (1999/05/18)
  o Made many small changes: implicit none, format(i5), etc...
  o Introduced KPP mixing scheme (compiles and runs but *not* tested)
 
-checkpoint21
+checkpoint21 (1999/05/18)
  o Introduced new I/O package that supports direct-access records (mdsio.F)
  o Split-up mid-level I/O routines
  o Updated input data for experiments 0,1,2,4 and 5
  o Finally removed the genmake.* scripts (everyone seems happy with genmake)
 
-checkpoint20
+checkpoint20 (1999/03/22)
  o Tidied up open-boundaries some more
  o Added non-hydrostatic code
  o Fixed some input data
  o Modified MPI start-up to work in "coupled" context.
 
-checkpoint19
+checkpoint19 (1998/12/15)
  o Tidied up directory structure for verification experiments.
  o Added new code for open boundaries.
  o Corrected advective terms near boundaries.
@@ -3352,18 +4857,18 @@
  o Implemented free-slip/no-slip BCs and del^4 dissipation.
  o Split default parameters out of ini_parms.F into set_defaults.F.
 
-checkpoint18
+checkpoint18 (1998/11/30)
  o Further changes for optional code generation with 
    CPP - ugh!
 
-checkpoint17
+checkpoint17 (1998/11/03)
  o Beginning to incorporating modularity
    for supporting atmos. and ocean configs.
  o Small changes for TAMC complinace
  o New ultra simple test case. Barotropic box
    configuration "exp0".
 
-checkpoint16
+checkpoint16 (1998/10/28)
  o Minor changes to exchange routines to support 
    accumulation in reverse mode. Adjoint of an
    assignment is an addition.
@@ -3371,7 +4876,7 @@
    syntax) and by g77 under Linux ( 72 character
    limit ).
 
-checkpoint15
+checkpoint15 (1998/09/29)
  Rewrote exchange routines to allow
  o General tile <-> tile connectivity.
  o TAMC reverse mode flag ( is this really needed? )
@@ -3380,11 +4885,11 @@
    shmput/shmget, VIA, SYSV shmem and every other cool 
    communication method.
 
-checkpoint14
+checkpoint14 (1998/09/09)
  Consistent isomorphism chages made. These allow dynamical core
  to support both pressure and meters as a vertical coordinate.
 
-checkpoint13
+checkpoint13 (1998/07/17)
  Release which corrects global_max problem and a couple
  of KGM time-averaging diagnostic errors. Also contains
  a double-gyre experiment setup as well as the baseline
@@ -3399,27 +4904,27 @@
  I don't want to commit the rDot to the main-trunk until
  we've actually tested it...
 
-checkpoint12
+checkpoint12 (1998/07/08)
  Tidy up and added generic genmake script (formerly
  configure script). 
  Released to testers.
 
-checkpoint11
+checkpoint11 (1998/07/02)
  Re-arranged initialise() and introduced ini_vertical_grid()
  and ini_masks_etc().
 
-checkpoint10
+checkpoint10 (1998/07/01)
  Introduced the configure script.
  Separated out the diags package.
  Added template for writing time-averages of tile/intermediate quantities.
  Updated SIZE.h in exp2 and made the data big-endian.
 
-checkpoint9
+checkpoint9 (1998/06/22)
  MPI fix. Filename changes (meta/data). salbin*y stuff.
  General tidy-up.
  SST.bin SSS.bin added to verification/exp2
 
-checkpoint8
+checkpoint8 (1998/06/22)
  Inludes time-dependant forcing and time-averaging.
  Works at 4x4 and 2.8125x2.8125 global
 
@@ -3429,7 +4934,7 @@
  model etc.. 
  Configured for verification/exp2 - 4 degree global, two process.
 
-checkpoint7
+checkpoint7 (1998/06/15)
  Created by cnh
  Simple 4 degree global simulation 
  configuration.
@@ -3437,27 +4942,27 @@
  hydrography, bathymetry etc
  Does not include Heat Flux and E-P
 
-checkpoint6
+checkpoint6 (1998/06/08)
  Created by cnh
  merged checkpoint5 with CD and 
  spherical polar code. 
  Still some problems with GM Redi
  abd full topography.
 
-checkpoint5
+checkpoint5 (1998/06/08)
  Created by AJA
  contains updates to GM Redi
  and reordered timestepping loop
  for Implicit Diffusion.
 
-checkpoint4
+checkpoint4 (1998/05/30)
  Created by cnh
  Contains memory saving macros ( _rdxc etc..) for when
  grid variations are limited.
  Contains polynomial coeffs for EOS and knudsen program
  for generation.
 
-checkpoint3
+checkpoint3 (1998/05/26)
  Created by cnh
  Added extra flags for runtime options
  Added this file