--- MITgcm/doc/tag-index	2003/10/23 04:41:40	1.193
+++ MITgcm/doc/tag-index	2006/03/30 20:59:21	1.643
@@ -1,9 +1,1538 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.193 2003/10/23 04:41:40 edhill Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.643 2006/03/30 20:59:21 jmc Exp $
+$Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
-untagged
+o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
+  and add those terms in Vector-Invariant formulation.
+o in ctrl pkg, if ALLOW_CAL, use monthly mean controls 
+  if the control period (xx_hfluxperiod etc) is 0
+o in profiles pkg, clean routines and fix details
+o in ecco pkg, reading ssh data: 
+  fix problem in case the model does not start at iter0=0
+o fix mnc-pickup/restart for ptracers
+o new package prifiles:
+  code to compute profile-based cost by Gael Forget
+  (modifs in ecco, ctrl, autodiff)
+o Benign bug fix in initialization (spotted by M. Mazloff) of
+  ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
+
+checkpoint58c_post
+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 
+  documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
+  SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only 
+  with SEAICE_CGRID defined.
+o move calendarDumps from "data" to "data.cal" and clean-up the code
+  with a simple call to pkg/cal S/R: CAL_TIME2WRITE
+o add useEXF & useCAL flags (for now, set in hard-coded way)
+o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
+  (were missing in NH mode, and wrong in quasihydrostatic mode).
+  waiting for Chris updated version of calc_gw to add those CALLs.
+o fix bug in quasihydrostatic S/R ;
+  add a test for this option: global_ocean.90x40x15.qshyd
+o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
+  (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
+o add on/off flag useOffLine for package OFFLINE
+o seaice: 
+  - modify advection so that it works also on the C-grid
+  - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes 
+    problem in multi-tile runs with C-grid
+  - add flags for clipping ice velocities and/or masking solver forcing
+  - fix drag (ocean on ice) formulation and a bug that caused noise in the
+    C-grid solver
+  - added a few comments to seaice_diffusion.F
+  - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
+    are now exclusive)
+  - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which 
+    required re-ordering the code a little:
+   + make DAIRN global variable (defined in SEAICE)
+   + 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
+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:
+  + shrink lookup tables by factor of ~4
+  + better error reporting when running out of lookup space
+  + able to handle longer path/file names (up to 500 chars)
+o adjoint:
+  - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
+  - TBD: "hidden" mom_vecinv recomp. in dynamics
+o change forcing_In_AB to affects both T,S forcing and Momentum forcing
+ (allow to differentiate between forcing components using new integer flags:
+  momForcingOutAB=1/0 & tracForcingOutAB=1/0)
+ and add new flag to put Dissipation tendency out of Adams-Bashforth.
+o ecco
+  - enable trend removal from SSH anomaly obs.
+o adjoint
+  - a fix for PmEpR when #undef EXACT_CONSERV
+  - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
+  - try to fix "hidden" recomp. in forward_step for NLFS
+    (NLFS seems broken sometimes after I checked it in)
+o seaice: 
+ - add c-grid version of the dynamic solver:
+   + three new routines that are the c-grid substitute lsr, dynsolver
+     and ostres
+   + put a few fields that were local to dynsolver into global common
+     blocks, so that I can move the computation of stresses etc into
+     seaice_lsr (saves coding but may break the adjoint).
+ - replace more hardwired parameters by runtime parameters
+ - add ice masks that mask the rhs of the implicit solvers where there
+   is no ice (commented out in seaice_dynsolver, because i am not sure
+   if this works properly), eventually this should replace the clipping
+   of ice velocities in seaice_dynsolver to +/-40cm/s.
+o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly 
+  include it only where its needed
+o move balancing of fluxes before the call of external_forcing_surf
+o seaice:
+  - correct units of turning angles (now they are really in degrees)
+  - move computation of GWATX/Y out of main routine into dynsolver
+  - initialize GWATX/Y in seaice_init
+o Apply mask on Fresh-Water flux (needed for SSH forcing).
+  update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) 
+o seaice: add runtime flags for turning angles (default to zero)
+o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean 
+  and trend from exf forcing and ctrl control adjustments
+o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
+  (since checkpoint57x_post)
+o change the default rotation period to 86164.s = the Earth rotation
+o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
+  and based on a reference stratification. Tested within hs94.cs-32x32x5.
+o seaice advection: add code for choosing between the default (2nd order
+  central differences) and multiDim advection schemes provided by
+  pkg/generic_advdiff
+o seaice:
+  - removed all references to SEAICE_GRID.h fields from 
+    dynsolver, advect, diffus, lsr, without changing the results of lab_sea
+    (cubed-sphere configuration will change a little)
+  - grid computations in seaice_init are obsolete now.
+  - cleaned up code a little so that is easier to read (hopefully).
+  - added new (better?) discretizations of default advection and diffusion
+    (turn on with SEAICEuseFluxForm)
+  - replace 1 in 3d global fields by kSurface in growth.F
+  
+checkpoint58a_post
+o seaice:
+  - bug fix in advect.F
+o shelfice: 
+  - separate shelfice load anomaly from pload (breaks with time 
+    dependent forcing), => introduce constant field shelficeLoadAnomaly.
+    Its default is 0., but it may be computed more cleverly from (unknown)
+    t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
+    done offline. A good approximation of the pressure load anomaly is
+    necessary to avoid large initial adjustment processes underneath 
+    deep-reaching shelfice.
+  - small fix in ISOMIP shelfice_thermodynamics
+  - add more sophisticated thermodynamics of Hellmer (1989), this is 
+    now the default
+  - give a few constants more intuitive names
+o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
+  if bulk formulae are used in long integration (especially EmPmR). Turn
+  on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
+  if balancePrintMean, the imbalance that is substracted is printed to
+  STDOUT.
+o fix bug (typo) in obcs_apply_eta.F
+o add a new package shelfice which enables us to model the circulation
+  underneath shelf-ice with draughts of hundreds of meters.
+ - works
+ - to do: + include improved thermodynamics
+          + check whether kSurfC (from model/inc/SURFACE.h) can be used
+            instead of new field kTopC
+          + can we use topoFile, Ro_surf and existing code in ini_depth.F 
+            instead of new field R_shelfIce and new code in ini_depth.F
+            and ini_mask_etc.F?
+          + adjust vertical mixing schemes?
+o seaice pkg: 
+ - add a cpp-flag to include a simple formula for a salinity dependent 
+   freezing point of sea water at the surface
+ - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
+   meridional stresses are now different (and hopefully correct)
+o AIM pkg: change threshold on large-scale condensation to conserve Heat.
+   update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
+   and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
+o pkg/diagnostics: add options and parameters for regional-statistics 
+   diagnostics ; define regions by reading a region-mask from a file 
+   (might add other options later)
+o pkg/bulk_force:
+ - add option and parameters to use AIM surface-flux formulae.
+ - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
+   others forcing fields (defined in PARM05, parameter file "data") are loaded 
+   from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
+ - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F 
+ - use the right EXCH call for uwind,vwind (to work on CS-grid).
+ - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
+   and parameters (note: calcWindStress replaces .NOT.readwindstress).
+ - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
+
+checkpoint58
+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 
+  (*.[fFhc] + Makefile) used for the build within the executable
+  - requested by CNH but off by default
+  - adds a paltry <9MB to the mitgcmuv executable in most cases
+  - only writes the output when useEMBEDSRC in eedata is true
+o clean up 3-dim. relaxation codes:
+  * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
+  * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
+  * Thanks to Tom Haine for testing!
+
+checkpoint57z_post
+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
+o fix a bug in ptracers_external_fields_load
+o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
+  affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
+o transfered surface NH pressure to eta field (if exactConserv).
+o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
+     and update lab_sea output.txt file.
+o completing 3-dim. relaxation code: additional term
+     1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
+  in S/R EXTERNAL_FORCING_T (file external_forcing.F)
+  * At compile time, in "EXF_OPTIONS.h" set
+      #define  ALLOW_CLIMTEMP_RELAXATION
+      #define  ALLOW_CLIMSALT_RELAXATION
+  * At runtime in "data", under &PARM03 set (e.g., units in seconds)
+      tauThetaClimRelax3Dim = 15552000.0,
+      tauSaltClimRelax3Dim  = 15552000.0,
+  * 3 cases:
+      1) Use a constant-in-time 3-dim. field
+      2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
+      3) Real-time relax. to time-evolving prescribed field
+o Adding Laplacian-type smoothness constraint on 
+  initial and boundary (forcing) controls (ic, bc)
+  * enable at compile-time via 
+    ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
+  * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
+  * Absolute scale somewhat unclear so far
+  * no area weighting was included since no other cost term does so far
+
+checkpoint57y_post
+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
+
+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)
+o add new offset feature to offline pkg (plus minor cleanup)
+o cfc fixes for final year of integration
+o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
+  be in GCHEM_OPTIONS).
+
+checkpoint57x_post
+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)
+  - allows the vast majority of our tests to work with gfortran
+o Non-Hydrostatic:
+ - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
+ - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
+o Allow to apply AB on T,S rather than on AB(gT,gS):
+ - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
+ - use the same arrays (gtNm,gsNm) to hold tracer field at previous
+   time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
+ - need a "clever" read_pickup to restart from the other AB formulation
+o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h 
+o remove some unused variables (reduces number of compiler warnings)
+o adjoint
+  * Disable useVariableViscosity for adjoint for time being
+    (there are a number of extensive recomputations)
+  * Initialize certain variables needed for adjoint
+
+checkpoint57w_post
+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.
+o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
+  using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
+o tracer advection scheme:
+  add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get 
+   those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, 
+   was not very convenient).
+  add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
+   (further tests needed for the implicit DST & Flux-Limiter schemes).
+o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
+  and sRef for convenience, handy, when you want to initialize
+  ptracers in a large domain with a constant non-zero value. Also,
+  untangle ptracers_init.F a little.
+
+checkpoint57v_post
+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
+  identical results for a few days of testing
+o add new parameter: sideDragFactor to enable half-slip-side BC
+  and change side-drag S/R to use viscosity from mom_calc_visc
+  (can switch back by setting sideDragFactor=0.); affects results at 
+  truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), 
+   global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
+o vorticity & strain are now computed without masking, to account for 
+  no-slip-side BC in variable viscosity calculation ; mask is applied
+  anyway later on, before computing advection/coriolis terms.
+o modify exp4 to test new obcs support for reading from external files
+  and for passive tracers
+o fix behavior of ptracers_monitor when monitor output is written to a 
+  netcdf-file; still not independent of monitor.F (writes in the same
+  file).
+o change default value of tRef (put a uniform, meaningful value for ocean 
+  & atmos) and initialize sRef (was missing, as Martin mentioned).
+o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity 
+  to be proportional to enstrophy dissipation length.  Thus,
+   viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
+  This is now consistent with Smagorinsky and with the manual.
+
+checkpoint57u_post
+o OBCS and PTRACERS: add open boundary support for passive tracers
+  - either use homogenous (pseudo) v.Neumann conditions or prescribe 
+    OB-values from file; this is not different from the way theta and salinity
+    are treated
+  - however, Orlanski-radiation conditions are not supported, and the model
+    will stop if you use pTracers and Orlanski at the same time. 
+  - beefed up the rountine obcs_external_fields_load: now only those open
+    boundary values are overwritten with values from files for which there 
+    are really files, otherwise the OB-fields remain untouched. This makes
+    it possible to use different OBs at different ends of the domain (as 
+    with EXF)
+o reduce number of exch calls in shap_filt (s2). 
+o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ 
+  truncation level) 4/5 MLAdjust test results (11&12 digits match).
+
+checkpoint57t_post
+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
+  test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
+o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
+  note that biharmonic viscosity + no-slip was not tested in any experiment.
+o fix bug in non-linear free-surf side-drag ; generate new output for
+  global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
+o make mnc honor the writeBinaryPrec flag for most kinds of output
+o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
+o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
+  error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
+o add brackets in multi-terms sum to get same truncation, independent of
+  the face number (manage to get exactly same value of gU,gV at the cs-edge)
+  affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
+o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
+  and viscA4Remax, which allow one to limit the minimum viscosity by specifying
+  a maximum grid-scale Reynolds number.  Also, changes all length calculations
+  in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
+  Suggested values of viscosity parameters found in mom_calc_visc. 
+  Many new viscosity diagnostics available.
+
+checkpoint57s_post
+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 
+  used simultaneously, and to be used in mom_vecinv and mom_fluxform. 
+  Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
+  and with Strain-Tension viscous term calculation (mom_hdissip.F).  
+  The Strain-Tension form is now called with useStrainTensonVisc=.true.
+  ViscAhStrain and viscAhTension are now retired.
+o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
+o In response to JMC's bug report, genmake2 now ignores any soft-links
+  that it finds in the *current* directory when searching for files.
+  Soft-links found in any other source directories will still work as
+  they did before.
+o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls 
+  a C routine to unlimit the stack size
+o mnc-ify pkg/aim snapshot vars
+o mnc-ify pkg/land as requested by Daniel
+o various changes to mnc including:
+  - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
+  - output can now be grouped so that all files within a group 
+      change the ITER portion of their names in lock-step together
+  - can now read ("global") PER-FACE (in addition to PER-TILE) files
+      and works with both EXCH1 and EXCH2 (but needs more testing)
+  - writing works for all verification test cases w/ g77 on Linux
+
+checkpoint57r_post
+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.
+o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
+o remove MINIMAL_TAVE_OUTPUT option ; 
+  add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
+o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
+  allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
+o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
+o add time-dependent SST, SSS control
+o cost terms in ecco/ modularized (new cost_generic.F)
+o cost_averages routines are modularized (new cost_averagesgeneric.F)
+o new infrastructure for seaice model vs. obs misfits in seaice/
+  * driver from the_main_loop.F is seaice_cost_driver.F
+  * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
+  * gradient check in Exp. 6a of natl_box_adjoint/
+o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
+  (see README file)
+
+checkpoint57q_post
+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
+o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
+  update exp. cpl_aim+ocn output. 
+o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
+  Needed for high-res. runs with large global files 
+  to be able to limit tapelev size
+o Changed some tests for adjoint:
+  * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
+  * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
+  * global_ocean.90x40x15/ back to default 3-level checkpointing
+o Modifications to enable scripted COMMON to MODULE conversion
+  * verification/OpenAD/code/ has necessary scripts and description;
+  * converts, compiles and runs successfully;
+
+checkpoint57p_post
+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)
+o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
+o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
+  (was already the case for dissipation with mom_vecinv,
+   and also the case for grad.PhiHyd when staggered-timeStep)
+  This will allow to put dissipation out-off the AB time-stepping.
+ Unfortunately, affects truncation error. Update output of exp. that "fails"
+  (cg2d matching number) and leave the others for later: front_relax(10),
+  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
+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 
+  for ideal_2D_oce and lab_sea on linux_ia32_g77
+o set to #undef CTRL_SET_OLD_MAXCVARS_30
+  in global1x1_tot/code_seaice_adj to access indices 32, 33
+  (worth another tag)
+
+checkpoint57n_post
+o adding precip control xx_precip 32
+o adding swflux control xx_swflux 33
+o Replacing 10 forcing penalty cost routines by 1 generic.
+o Implementing partitioning in time-mean and variable adjustment
+  for atmos. state.
+o Time-mean constant error is now read in data.ecco (instead of hard-coded)
+o in natl_box_adjoint:
+  * updated exp 1 to 10 
+    (but does not have time-mean vs. variable split results yet)
+o updated global1x1/*_seaice_adj/
+  to incorporate latest changes
+o enable useSingleCpuIO for mdsio vector routines
+  (applies in particular to tapelev I/O)
+o removed inefficient K-loop in all active_file*control*.F
+
+checkpoint57m_post
+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
+ 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)
+o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
+   Affects results of exp. rotating_tank ; update output.txt.
+o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
+      and taking the square quantity and/or using a fraction-weight field.
+o fix aim_diagnostics_init.F mate numbers.
+o add mnc output capability to diagnostics/diagstat and update
+  our cvsignore files for the ACSII output generated
+
+checkpoint57k_post
+o lab_sea now uses diagnostics package and provides a suite of
+  new EXF diagnostics output.
+
+checkpoint57j_post
+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);
+    terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
+  * extended diagnostics output
+    - now includes all EXF variables
+    - hs, hl moved to common block
+    - separate S/R for diagnostics, called after ctrl vector is added
+    - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
+    - EXFqnet contains true Qnet (i.e. includes qsw)
+  * updated verif. lab_sea, global_with_exf
+  * Rearranging hflux (exf_mapfields -> exf_getforcing)
+    to ensure that diagnostics sees a true EXFqnet
+o add matlab scripts for CS-grid vectors (in utils/cs_grid)
+o diagnostics pkg: change pointers so that 1 diagnostic can be used
+  several times with different frequencies.
+o mnc-ify the thsice package as requested by Daniel Enderton
+  - the monitor--MNC output needs work
+  - many attributes need to be added (most are currently blank)
+o mnc-ify theaim_v23 package as requested by Daniel Enderton
+  - many attributes need to be added (most are currently blank)
+o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
+o add Sadourny like discretization to the 4th.O vorticity advection scheme
+o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. 
+  update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
+     fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
+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
+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 ;
+  add 1rst Order upwind vertical Shear.
+o add a quick fix for A/B checkpointing in OFFLINE mode
+o add IGNORE_TIME define and -ignore_time option to genmake2 as an
+  end-run around the C/Fortran linking horror in eesup/src/timers.F
+o added pkg/runclock: allows user to terminate run based on wall clock
+o added non-hydrostatic scaling parameter: nh_am2
+o pkg/my82: futile attempt to make results compiler-independent by adding
+  some "_d 0", etc. no effect.
+o for mnc output, fill the 'T' coordinate var with myTime and create a 
+  separate 'iter' variable for iteration count
+o pkg/diagnostics: 
+  add new capability: output of Global/Regional & per-level statistics ;
+  tested against monitor output (including land & thSIce) on various exp.
+o make seaice-pkg I/O type flags (MNC/MDS) more standard.
+
+checkpoint57h_done
+  tag after changing user customized files (DIAGNOSTICS_SIZE.h, 
+  data.diagnostics, data.gchem, data.ptracers) is done.
+
+o pkg/diagnostics: prepare for Global/Regional statistics. 
+  add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h 
+o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
+  and rename it: DIFFERENT_MULTIPLE
+
+checkpoint57h_post
+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
+
+o in mnc, let the user create the output dir if both mnc_outdir_date
+  and mnc_outdir_num are false
+o add fflags() to pkg/diagnostics which allows one to specify, on a
+  per-file basis, the file precision [default behavior is unchanged]
+o added diagnostics to pkg/kpp, including computation of mixed layer
+  depth based on a temperature/density criterion
+o updated verification/natl_box to test the new pkg/kpp diagnostics
+o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
+o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
+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
+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
+
+o make lambda[Theta,Salt]ClimRelax spatially varying
+  (default remains spatially uniform constant based on tau)
+o added new control variables
+  * init. uVel, vVel, etanN
+  * lambda[Theta,Salt]ClimRelax
+o separate masks used for ctrl_pack/unpack 'from write_grid' output
+  (suggested by G. Forget)
+
+checkpoint57f_post
+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
+
+o mnc-ifying the seaice package
+o introduced an alternative length scale calculation for use in the limiting
+  maximum viscosity (off by default, see mom_vi_hdissip.F for details)
+o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
+o added modified Leith scheme with viscosity proportional to grad(Hdiv) 
+  as well as grad(vort3).  Made it compatible with both approximate form
+  for the cubed sphere and full form of these gradients.  Added flag
+  useFullLeith to select between approximate and full form.  
+o add "d0" in getcon.F to reduce differences between compilers/platforms
+  update output.txt of exp. fizhi-gridalt-hs
+o change port_rand funtion to allow to set the seed.
+o fix obscure MNC bug involving conversion between reals and integers
+  - it caused no problems with certain (eg. gcc, ifc) compilers but the 
+    new version is now more standards-compliant
+o adjoint-related modifications
+  * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
+  * 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
+o Adding eddy stress controls a la Ferreira et al.
+checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
+
+o fizhi pkg: fix AtoC and CtoA when called with same input & output array
+  update output.txt of exp. fizhi-gridalt-hs
+o add more "Z" dimensions and associated coordinate vars to MNC
+o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
+o parameter calendarDumps: when set, approximate months (30-31 days) and years
+  (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
+  KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
+  months and years.  Requires pkg/cal.
+o diagnostics: add pickup functionality
+  - off by default for backwards compatibility
+  - current version only uses MDSIO -- MNC will be added
+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
+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
+o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
+o make genmake2 more portable by using ".$FS" instead of ".f" for more
+  of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
+o add coordinate variables to the MNC output from the diagnostics package
+o change MNC-flags default value: true when useMNC=TRUE
+o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
+  the ability (off by default) to read the grid information using MNC 
+o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
+o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
+o do snap-shot diagnostics at the middle of the time-interval (instead of 
+  at the end).
+o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
+  new test for AIM with thSIce + slab-ocean
+o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
+o move state variable diagnostics to the beginning of the time step ;
+  (note: still needs some work specially for snap-shot diagnostics)
+  duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
+
+checkpoint57c_post
+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
+
+o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
+  update output.txt of exp. global_ocean.90x40x15
+o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer 
+  results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
+o add saltFlux(+File) forcing capability with periodicExternalForcing
+o allow to use pkg diagnostics for GM-Redi & ThSIce output
+o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
+o improvements for the MNC output from DIAGNOSTICS:
+  - correct handling of the unlimitied dimension
+  - all dims now have associated coordinate variables
+  - variables located at U, V, and Corner ("Z") points are now written
+    with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that 
+    *all* data points are output
+o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
+o added pkg/seaice/seaice_monitor.F
+o mdsio_readfield.F can now read files visible only to master MPI process.
+o pkg/seaice: some test code for ice-modified ocean stress
+o exf_getffields interpolation defaults to bilinear for all scalar forcing
+  fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
+  spurious negative numbers for precipitation and humidity.  Will cause
+  some small numerical differences for integrations using pkg/exf/exf_interp.F.
+o pkg/ctrl/
+  * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
+    May be enabled via doPackDiag
+  *  introduce z-scaling of 
+     + gradient (doZscalePack) and 
+     + control (doZscaleUnpack)
+o pkg/mdsio/
+  * 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
+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 
+  general, EXCH2 grids are only aligned to a "local" coordinate system
+o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
+o Implement instantaneous output within pkg diagnostics:
+  setting a negative frequency in data.diagnostics produces
+ "snap-shot" output (as opposed to time-average if freq > 0)
+o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
+  NOTE: change ptracer diagnostics name: use 2 characters to work with 
+        more than 9 tracers. Add also diagnostics of advect & diffus flux.
+o more CF compliance: convert all MNC 'iter' variables to 'T' so that it 
+  becomes the coordinate variable for the 'T' dimension
+o add CF-style coordinate variables to MNC
+  - just a first cut:  numbers are meaningless on the cubesphere and 
+    missing along the T axis but otherwise it works!
+o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
+o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
+o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
+  this is based directly on what the model compute, so that the content of
+  each diagnostics might be affected by switching options (e.g., implicitDiffusion)
+o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
+o clean up build options files for SunOS, in particular 
+  - remove -traditional from xmakedepend
+  - change -xarch=v9 to -xarch=native for f77
+  - restore use of make (not gmake)
+  - add CC=gcc if using g77
+o changes per discussion of AM, JMC, & EH3 today:
+  - move redundant "grid" variables out of "state" -- in preparation of 
+    creating proper CF-style coordinate variables and in recognition 
+    that any/all grid variables can be easily copied (eg. w/NCO) from 
+    the grid files into any of the other NetCDF files
+  - *always* output grid variables with MDSIO (this will eventually be 
+    changed)
+  - output MNC grid file if useMNC is true
+o every instance of _END_MASTER() has been found and replaced with 
+  _END_MASTER( myThid ) in order to satisfy certain picky Sun 
+  preprocessors
+o re-arrange diagnostics pkg initialisation:
+ - allow each package to extend the available diagnostics list
+ - add some checking and fix small problems (multi-threaded, ...)
+ - new S/R diagnostics_fill (replace fill_diagnostics):
+   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
+o this set of changes restores TAMC compatibility
+  tested for global_ocean.90x40x15 adjoint on trough
+  (what a pain)
+
+checkpoint57a_pre
+o some modifs in tools/build_options for sunos
+o call ctrl_pack for ctrl at end for optimcycle=0
+
+checkpoint57
+o add horizontal bi-harmonic viscosity for vertical velocity
+  - new parameter viscA4W (defaults to viscA4)
+  - affects only non-hydrostatic code
+  - to be done: no-slip lateral boundary conditions
+o switch back to "sflux = sflux - runoff" in exf_getforcing.F
+o implement Implicit Vertical advection for pTracers
+o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
+  (implemented also for implicit vertical diffusion & advection)
+o OBCS: extend application of tracer open boundary conditions
+  to a strip beyond the boundary of width Olx/Oly
+o add call monitor to TAF set of required calls (flow directives)
+  and include in natl_box_adjoint
+o untangle a few ifdefs related to cost, ctrl, autodiff
+  untangel a few ALLOW_ECCO_OPTIMIZATION
+o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
+  (theta2, salt2 in ecco_cost_weights)
+
+checkpoint56c_post
+o OBCS as control variables
+  - update ctrl_ad_diff.list, obcs_ad_diff.list
+  - remove balance of obcs controls from default
+  - fix index bug nobcs in ctrl_init
+  - fix dummy fields filen in ctrl_pack
+  - add dummy weights for obcs
+o lsopt: comment out fort.94 output
+o optim: 
+  - remove unnecessary header files
+  - adjusted namelists
+  - add xerbla.F to Makefile
+o exf: 
+  - multiple modifications of exf_check_range
+  - unit change in exf_init_runoff from [m/year] to [m/s]
+o mdsio:
+  - i/o-vector change debugLevel from debLevA to debLevB
+
+checkpoint56b_post
+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
+  - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
+  - clean up PTRACERS_WRITE_TIMEAVE a little
+o add another verification experiment that tests both the cfc-pkg and
+  the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with 
+  reactive tendencies treated inline with regular timestepping
+o testreport previously did a lousy job of comparing small numbers, so
+  we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
+  implemented in the little c-progam tmp_cmpnum.c which is embedded in
+  testreport. 
+o ptracers_monitor: bug fix for MPI
+
+checkpoint56a_post
+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
+    GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
+    gchemTendency is not needed because the timestep is done separately)
+  - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
+  - GCHEM is now---more or less cleanly---separate from PTRACERS
+  - to bo done: handling of surfaceForcingPtr that is needed for KPP not
+    so clear to me how that should be done in a general way.
+o CFC: improve formatting of output in CFC_ATMOS
+o PTRACERS:
+  - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
+    that ALL experiments with ptracers enable can be checked. This makes
+    GCHEM_MONITOR obsolete.
+  - include a runtime parameter PTRACERS_monitorFreq that defaults to
+    monitorFreq
+  - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true 
+o add PTRACERS (PTR0[1-5]) to testreport output
+o exf_check_range:
+  * default changed to .TRUE.
+  * will check values for niter0 if debLevA, every timestep if debLevB
+  * STOP in exf_check_range if 'out of range'
+  * range chosen generous to allow for potential extema
+  TBD: a version with stricter range
+       permitted range would be runtime parameters
+o GMredi:
+  - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
+  - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
+  - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
+o GCHEM: 
+  - move call to GCHEM_FORCING_SEP, so that it is now called before
+    the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
+  - introduced a useGCHEM runtime flag and applied it everywhere. 
+  - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
+    this flag is now only visible within GCHEM-pkg routines.
+  - moved gchem_forcing_int temporarily into ptracers_forcing, this will
+    be replaced by a 3D array that is computed before thermodynamics; for 
+    this, the tracer ID iTracer had to be included into the parameter list
+    of ptracers_forcing
+  - set up forward_step to call gchem_forcing, that will replace 
+    gchem_forcing_int in ptracers_forcing
+  - cleaning up
+o small cleaning of exch2: remove files that are also in eesupp/src
+
+checkpoint56
+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
+  * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
+  * fully merged and updated from SIO code
+    windstress sign change affects
+    - exf_inscal_[u/v]stress
+    - sign of xx_tau[u/v] adjustments
+    - signs in cost_scat
+  * ctrl_get_gen: avoid update of tau[u/v] for first few days
+  * natl_box_adjoint updated and compressed
+  * 2-level checkpoint switch added
+    (tested in EXP. 1 of natl_box_adjoint)
+  * new switch doInitXX to avoid init. of xx_... in optimcycle=0
+o SVD
+  * first complete, non-hacked version for SVD calculations
+  * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
+    performed via direct access files admtlm_vector.it????
+    (via ctrl_[un]pack)
+  * optimcycle is used for ARPACK iteration counter
+    (note: adxx_... is iterated, rather than xx_...; latter is constant!)
+  * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
+    and add linear transforms where necessary 
+  * controls are initial/final SST, SSS (can be extended; need to check
+    ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
+o mdsio: filename info to both stderr, stdout
+o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
+  from sign change 
+
+checkpoint55j_post
+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
+o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
+o make all subroutines 30 or less characters in length for certain older 
+  compilers to work (a thorough search only turns up two routines in 
+  pkg/ptracers)
+o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; 
+  affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
+
+checkpoint55i_post
+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
+  - added bits to verification/cpl_aim+ocn so that it can run on 
+    ITRDA and other clusters without the mpirun "-wd" option
+o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
+  configuration 
+o give MNC the ability to create additional files rather than 
+  exceeding a specified file size limit "MNC_MAX_FILESIZE" 
+  - the default is just less than 2GB which is a practical limit 
+    on many systems
+o Compute the non-local term using either KPP vertical diffusivity (=default) 
+   or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
+
+checkpoint55h_post
+o add verification test "vermix"
+o remove all the *_ioinc flags and replace with the single global
+  outputTypesInclusive flag
+o allow to set a vertical profile of vertical diffusivity for T & S
+o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
+o useMNC moved from data.mnc to data.pkg
+
+checkpoint55g_post
+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
+  have been fixed to avoid recomp. of do_oceanic_phys
+  Works well for global_ocean.90x40x15,
+  but recomp. issue remains for carbon
+o Updating adjoint output for natl_box_adjoint after 
+  pkg/ecco has been modified (see taga c55d_post)
+
+checkpoint55f_post
+o rename to timeave_init_fixed
+
+checkpoint55e_post
+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
+  checkpoint_lev1_directives.h
+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
+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
+
+o switch between 2-level and 3-level checkpointing
+o add ability of MNC to write local and "partial" (eg. 2D slices where 
+  the full 3D field is never actually stored) arrays to NetCDF files
+  with the correct (that is, the complete multi-dimensional) set of 
+  array indicies
+  - used in mom_vecinv() to write the diagFreq output
+  - tested (demonstrated) in verification/aim.5l_cs
+o further mnc-ification
+  - add verification/lab_sea to the list with mnc setups
+  - fix undefined mnc v-names in cd_code
+  - add kpp to mnc output (both snapshot and timeave)
+o non-hydrostatic code
+  - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
+    in calc_gw.F
+  - defaults to viscAh
+  - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
+    friction or Leith) in non-hydrostatic mode, as long as there is 
+    no biharmonic friction and/or Leigth or equivalent for vertical velocity.
+o pkg/cost
+  extend simple cost functions to treat time mean quantities
+  (T,U,V) via cost_accumulate_state from cost_tile
+o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
+    be 2 times larger than the minimum size the advection scheme requires.
+    now get a perfect conservation of salt in advect_cs test-exp (updated)
+o GGL90 (Gaspar's TKE mixed layer)
+  - add horizontal diffusion of TKE, requires exchanges in 
+    do_fields_blocking_exchanges, horizontal diffusivity is zero by 
+    default. In OPA there is no horizontal diffusion of TKE but the 
+    mixing coefficients are computed from a horizontal average of TKE of
+    6 points or so. I think that diffusion has a little more physical
+    justification.
+  - clean up ggl90_calc in the hope of reducing memory usage (this hope 
+    was in vain)
+  - mask tke-variable in ggl90_init
+o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
+o fix biharmonic diffusion on CS-grid.
+o more obcs stuff
+  - added obcs_external_fields_load as an alternative to the EXF-pkg option
+    for reading boundary values. This routine is called from 
+    obcs_prescribe_read
+  - updated obcs_check
+  - changed sponge layer relaxation parameter units for days to seconds
+  - turned off sponge layer by default
+  - changed argument list of OBCS_CALC to myTime+deltaTclock
+  - fixed about 35 bugs in obcs_external_fields_load
+
+checkpoint55c_post
+o obcs stuff
+  - new runtime flags useOBCSprescribe, useOBCSbalance
+  - re-arranged obcs_calc
+  - moved exf_getobcs to obcs_prescibe_read
+    obcs_prescibe_read is called after ORLANSKI stuff
+    and independent of it (executable can contain all).
+  - updated obcs_check
+  - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
+    These may be necessary only if tangential velocities are
+    prescribed at OB, not sure, needs testing.
+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
+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)]
+  affects advect_cs results (for the wrong reason): update output.txt
+o use a more standard discretization for biharmonic viscosity ; 
+ (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
+  affects results of dome set-up: update output.txt 
+o fix gad_advection.F (CubedSphere part), back to version 1.23
+o fix bug in mom_vi_del2uv.F (CubedSphere part).
+
+checkpoint55a_post
+o merged code to 
+  * prescribe/read time-dependent open boundaries
+    (works in conjunction with exf, cal)
+  * sponge layer code for open boundaries
+  * each boundary N/S/E/W now has its own CPP option
+    (healthy for the adjoint)
+
+checkpoint55
+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)
+  - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
+  - carbon: * remove tr1-related adjoint verification
+            * add ptracer as control variable
+o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
+  (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
+
+checkpoint54f_post
+o in verification/carbin/ remove experiment related to
+  ALLOW_PASSIVE_TRACER (array tr1 etc)
+  code_ad/ input_ad/ results_ad
+
+o add two new packages
+  - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
+    + subject to optimization (memory)
+  - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
+    + subject to reordering (many GOTOs in the original code)
+    + so far opps is called for every (i,j) point, and then operates in
+      the vertical; one may want to reorder the scheme in order operate in
+      horizontal slabs at the cost of (a lot of) memory, at least ten new 3D 
+      fields)
+o overhaul of IO so that we now have flags for MDSIO and/or MNC
+  - all verification tests compile and run with linux_ia32_g77
+  - defaults are compatible with current input files--nothing 
+    should change if you were not previously using MNC
+  - MNC output has been added in numerous places (eg. timeave)
+    but there are still a few writes not yet do-able with MNC
+    (this is in progress)
+  - flags now allow for either/or/both use of MDSIO and MNC and 
+    documentation will soon follow
+  - numerous small formatting cleanups for ProTeX
+o add version info (via BUILD_INFO.h) to MNC and stdout
+
+checkpoint54e_post
+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
+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
+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
+   (i.e. leading to considerable offset over the years)
+o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
+o start with no AB and no initial filtering (staggerTimeStep):
+  change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
+o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
+  (external loading & cpl import/export stay in forward_step.F)
+o update coupling interface to work with new staggerTimeStep
+o change MDSIO ptracers_pickup.
+o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
+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
+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
+o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
+o change Qnet to always be the net heat flux, (+upward).
+  affects (truncation error) output of natl_box exp.: updated
+o define the max number of passive tracers in PTRACERS_SIZE.h
+o start to test mnc routinely in exp0
+o add sea-ice loading (sIceLoad) as a new forcing field.
+
+checkpoint54b_post
+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
+o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
+o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added 
+o staggerTimeStep & NLFS: rescale T & S surface tendencies.
+  affects (truncation error) output of lab_sea & natl_box exp.: updated
+o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
+
+checkpoint54a_post
+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
+
+o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
+  - modified verification/lab_sea and natl_box_adjoint accordingly
+
+checkpoint54
+checkpoint53g_post
+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
+o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
+o new parameter "nShapS": allow to treat differently S from T (nShapT)
+o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
+o restore adjointability
+
+checkpoint53f_post
+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)
+o AIM pkg:
+  - include stability function into surf.Flux derivative relative to Tsurf
+  - calculate clear-sky radiation & surface temp. change (for diagnostics)
+ 
+checkpoint53e_post
+o merged cylindrical coord configuration
+o added rotating_tank experiment
+checkpoint53e_pre
+
+checkpoint53d_post
+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
+o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. 
+o added Sadourny discretization of Coriolis
+  - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
+  - re-enabled use of omega3 (useAbsVorticity)
+o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
+  vector-invariant equations
+  - note: does *NOT* yet use same variable visc. for no-slip BC's.
+o recoded the lateral boundary conditions for non-hydrostatic w, this time
+  hopefully without new bugs
+  - still to do: biharmonic friction for non-hydrostatic w
+o bug fix for mom_*_sidedrag: rA -> rAs,rAw
+o regenerated output for global_ocean_ebm (using -ieee)
+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
+
+checkpoint53c_post
+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
+ - aim with thSIce: fix bug in snow-precip.
+o changes to calc_gw.F
+ - bug fix for w^2 term near the bottom boundary
+ - (hopefully) improve the lateral slip boundary condtions for use with
+    partial/looped cells
+  - because the bug fix changes two verification experiments anyway (exp5
+    and plume on slope), change the lateral boundary condition from half slip
+    to the value of no_slip_sides
+o ebm package wasnt quite up to the parallel task. Fixed that.
+o Adjoint of EBM package + verification
+  * TLM OK
+  * ADM not sufficient accuracy yet (needs further testing)
+
+checkpoint53b_post
+o Commiting new energy balance model to repository
+  * package is pkg/ebm
+  * verif. is verification/global_ocean_ebm
+  * references are in ebm_driver.F
+C      * X. Wang, P. Stone and J. Marotzke, 1999:
+C        Global thermohaline circulation. Part I:
+C        Sensitivity to atmospheric moisture transport.
+C        J. Climate 12(1), 71-82
+C      * X. Wang, P. Stone and J. Marotzke, 1999:
+C        Global thermohaline circulation. Part II:
+C        Sensitivity with interactive transport.
+C        J. Climate 12(1), 83-91
+C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
+C        Destabilization of the thermohaline circulation
+C        by atmospheric eddy transports.
+C        J. Climate 7(12), 1870-1882
+o Will need long integration testing.
+checkpoint53b_pre
+
+o created pkg/mom_common in preparation for variable viscosity code
+o renamed and split ini_mnc_io
+o pkg/land: only liquid water can diffuse or run-off
+o AIM using land: soil wetness availability account for snow
+o added printMapIncludesZeros to EEPARMS namelist
+
+checkpoint53a_post
+o restore TAMC compatiility for exf_constants.h
+  (no usage of _d in .h)
+o Additional storing in KPP in an attempt to fix
+  TAMC problem with adjoint of KPP code.
+  (no success...)
+  Identical code works fine with TAF.
+o Fixed verification/natl_box_adjoint experiments.
+  Initial conditions for Experiments 4 and 5 are now
+  set to "SEAICE_initialHEFF=0", which is more reasonable,
+  and hence gives results closer to that of Experiment 2.
+  Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
+
+checkpoint53
+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_
+  variables that is being autogenerated wrong.
+  Otherwise:
+   o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. 
+   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
+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
+o pkg/seaice modifications
+  - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
+    of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
+    and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
+  - changed proxy for geostrophic velocity and updated 
+    verification/lab_sea/results/* accordingly
+  - removed ADI dynamic solver from pkg/seaice
+  - replaced all occurrences of 1/CSTICE or 1/CSUICE
+    they caused a segmentation fault under certain circumstances
+  - removed unused field WATR
+o bug fix in exf-package:
+  -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
+     now reflect that.
+o small fixes in the cal-package:
+  - set reference date to first of January for the 'model'-calendar
+  - failing of cal_CheckDate in cal_FullDate now actually results in a
+    warning
+o small modifications in exf-package to increase flexibility:
+  - change climtempfreeze from a constant to a runtime parameter that
+    is specified in data.exf_clim (default = -1.9)
+  - introduce runtime parameter windstressmax (default = 2.0) that is
+    specified in data.exf
+o fix in pkg/thsice:
+  - update Evap (Tsf changes) to be consistent with Latent heat flux
+  - maintain snow precipitation unchanged (even if Tsf >=0).
+ both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
+
+checkpoint52m_post
+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
+  as a default
+o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
+o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
+  atmospheric model (AIM) to use it ; add a "slab ocean" component.
+o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
+o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
+o extending useSingleCpuIO option to work with new exch2 I/O format
+  - old-style, missing-tile I/O is still accessible by defining CPP
+    option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
+o monitor package can write to NetCDF files and/or STDOUT
+o fix re-definition bug in MNC_GRID_INIT_ALL()
+o doc/api_reference added
+  - a framework for building an API Reference Manual using all
+    the "protex" comments embedded in the code
+  - see pkg/generic_advdiff, pkg/mnc for examples
+o MNC:
+  - make myThid the last argument for all subroutines
+  - new default for the grid files: NO halos
+  - add useMNC and other run-time flags
+  - separate per-file-group handling of the unlimited dimension
+  - early initialization of MNC w/ flags read at the eeboot stage 
+    and lookup tables set in initialize_fixed
+  - write all MNC output to a freshly-created directory
+o thermodynamics sea-ice (thsice) is now tested with testreport.
+o test exp. advect_cs: use the standard cs32 grid ; update output.
+o Added functionality to grdchk:
+  pick global i,j,k position (or nearest wet) where to perform check.
+
+checkpoint52l_post
+o new land formulation:
+  a) use ground enthalpy as prognostic variable to ensure exact
+     energy conservation.
+  b) account for water temperature and for latent heat of freezing
+     in all processes (rain, run-off, ground storage)
+  c) compute surface and ground temperature implicitly.
+o aim_v23 modification for new land model:
+  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
+
+o fix problem (when 1 tile is empty) in min/max monitor.
+o fix bug in timeAve (u,vZetatave in common block) 
+o no restoring terms under ice for pkg/seaice
+o moved SEAICE_DO_DIAGS to S/R do_the_model_io
+o bug fix for pkg/seaice pickups
+o change MNC call locations and add coordinate attributes
+o mask vorticity at the corner ; affects global_ocean.cs output
+o fix ini_curvilinear_grid ; test CS experiments with mpi
+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
+o removed top-level directory "diags"
+  - we migrated these functions to pkg/timeave a long time ago
+o fixed bug introduced in pkg/monitor
+o accuracy ctrlprec = 32 insuffient for gradient checks using
+  averaged fields (I/O via cost_averages)
+  -> use ctrl.h in active_file*.F to control I/O precision.
+o paramter list of CALL ADTHE_MAIN_LOOP
+o added initial do_the_model_io to ecco
+o set all ...Freq to zero after cost_final
+  taveFreq, dumpFreq, pChkptFreq
+o MAIN and ECCO differentiability restored
+
+checkpoint52j_post
+o fix nchklev in tamc.h for global_ocean...
+o Bringing flow and store directives up-to-date
+o Really weird thing!
+  call do_the_model_io from the_main_loop with parameters
+  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
+
+o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
+  error messages
+o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
+o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
+  debug output
+o modfied mdsio_writefield.F to handle non-global files under exch2
+o update AIM Cubed-Sphere exp (aim.5l_cs):
+  use land, p*, and Franco.M forcing fields with fractional land-sea mask.
+o update AIM Equatorial Channel exp:
+  use standard aim_v23 pkg and change the SST fields to be more realistic.
+o globalFile now works with exch2
+o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and 
+  mon_vort3.F to make exch2 friendly with >1 tile per cube face
+o limit timeave output for hi-res integrations
+
+checkpoint52i_post
+o removed CPP_EEOPTIONS.h from verification/*/code
+o updated the tiling for global_ocean_pressure
+checkpoint52i_pre
+
+o update aim.5l_LatLon using the standard aim_v23 pkg (instead of 
+  the old pkg/aim).
+
+checkpoint52h_pre
+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
+o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
+  old grid files, moved CPP_EEMACROS.h to pkg/exch2
+o added useSingleCPUIO flag to monitor.F and mon_out.F
+o added temporary hack for sea-ice dynamics on the cube:
+  metric terms are ignored and it is assumed that
+  there is no sea-ice on cube faces 1, 2, 4, and 5.
+
+checkpoint52f_post
+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
+
+checkpoint52e_post
+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)
+  to work with implicit vertical advection and AB ;
+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
+
+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
+o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
+o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
+  ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
+o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
+o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
+o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
+
+checkpoint52d_post
+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
+    random number generator
+o add infrastructure in model routines for fizhi and gridalt packages
+o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
+o changes to permit hi-res, cubed-sphere, configuration
+  - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
+  - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
+  - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
+    of surface winds for the cube
+  (A verification experiment, based on global_ocean.cs32x15, but with
+   pkg/seaice turned on and with on-the-fly interpolation from the NCEP
+   Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
+   complete with example surface forcing files and matlab scripts to look
+   at the output and compare it with that of global_ocean.cs32x15.)
+o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
+   but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
+   to conform to the common rule.
+o check-in the first version of the coupler + interfaces for multi-components 
+   set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
+   - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
+   - atmosphere: use pkg aim_v23 ; no sea-ice for now. 
+   - ocean and atmos. share the same horizontal grid (no interpolation).
+   - exchanges between component and coupler is done in forward_step
+o new verification experiment, cpl_aim+ocn: 
+   coupled ocean - AIM atmosphere on cs32 grid. 
+
+checkpoint52d_pre
+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
+o Fixing OPTIONS files for use of exf:
+  - ALLOW_ECCO not needed
+  - ECCO_CPPOPTIONS.h should not be included from
+    EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
+    as has been the case in the past
+  - All cal/exf related options are currently set in
+    single header file. Should remain so until we
+    agree on a consistent new policy.
+o Removed all CPP options for cal package.
+  cal has no more CPP options.
+o modified STOREs in GAD_ADVECTION
+o corrected key comp. for passkey
+
+checkpoint52b_post
+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;
+ - light cleaning of bulk_force pkg (still needed with thsice).
+ - 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
+
+o call "do_the_model_io" at the beginning (=> dump initial state) 
+o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
+o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
+  (need info on NUMBER_OF_PTRACERS)
+o missing PTRACERS headers in some routines
+o default tamc.h in pkg/autodiff supposed to crash
+  to ensure proper customization
+
+checkpoint52a_post
+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
+    and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
+    => new output.txt for global_ocean.cs32x15 & global_with_exf
+  - keep the old version of FREEZE for backward compatibility;
+    global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
+  - corresponding modifs for TAF directives
+o added surface flux output variables to TIMEAVE_STATVARS
+o time-averaged output for pkg/ptracers
+o fix problem with ECCO-related divided adjoint
+  snapshot file was missing some ad-variables,
+  but no warning issued by TAF
+
+checkpoint52a_pre
+o some bug fixes for #undef REAL4_IS_SLOW
+
+checkpoint52 = ecco_c52_e35
+o after testing adjoints of checkpoint51u_post
+
+checkpoint51u_post
+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
+  but no input fields
+o obcs adjoint not yet merged!
+o adding ECCO global 1x1 and 2x2 degree configs
+o updated/extended some store directives for seaice
+o pkg/ecco now containes ecco-specific part of cost function
+o top level routines the_main_loop, forward_step
+  supersede those in model/src/
+  previous input data.cost now in data.ecco
+  (new namelist ecco_cost_nml)
+o in ctrl/ cleaned some cross-dependencies and updated CPP options
+
+checkpoint51t_post
+o this is the pre-merge tag of the ecco-branch
+
+checkpoint51s_post
+o cleanup: removed various obsolete #define-s
+o pkg/grdchk
+  - renamed 'ph-grd 3' to 'grad-res'
+  - merged from ecco-branch 
+    (remaining bug fixes for obcs gradient checks)
+  - additional high-precision output for testreport
+    (grep for 'precision_grdchk_result')
+
+checkpoint51r_post
+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
+o cd_code:
+  - moved cd_scheme.F -> cd_code_scheme.F
+  - separate read_checkpoint from cd_code_ini_vars.F
+  - separated cd_code part from write_checkpoint
+  - updated AD_SOURCE, generated .flow
+  - added CD_CODE_VARS.h to the_main_loop
+  - Moving cd_code specific store dir.s to pkg/cd_code
+o ctrl package totally restructured
+  - pack/unpack now optional and decoupled from
+    xx_/adxx_ I/O
+  - ctrl_pack/unpack cleaned
+    (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
+  - confined inclusion of AD_CONFIG.h to where necessary.
+o genmake2: changed AD dependencies from SRCFILES to AD_FILES
+
+checkpoint51p_post
+o create initial cd_code package
+  - WARNING: the initialization of fields within packages
+    is broken because INI_FIELDS (where READ_CHECKPOINT is
+    called) is called *before* PACKAGES_INIT_VARIABLES.
+    This seems to be backwards since
+    1) its important to initially zero the entire field including 
+       the "halo" region
+    2) zeroing needs to be done *before* reading pickup info
+       and the pickup call might or might not happen in any 
+       particular run
+  - this needs an overhaul for R2
+o cleanup verification/*/code/GMREDI_OPTIONS.h
+o cleanup testreport
+
+checkpoint51o_post
+o bringing AD-related verif's up to date with genmake2
+  - carbon/
+  - global_ocean.90x40x15/
+  - hs.94.1x64x5/
+  - (front_relax/ )
+o (more) consistent directory structure for AD-related verif.'s
+o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
+o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
+o bug fix in find_alpha.F for MDJWF:
+  - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
+    change rho -> rho-rhoConst
+  - replace call find_rho to find_rhonum
+o initialisation of rFlx extended to full array (required by TAF)
+  and shifted to thermodynamics
+o removed PTRACERS.h in ptracers routine
+o added surfacetendencyPtr to S/R parameter list pracers_forcing
+o Correcting initialisations for fVerU, fVerV.
+o helping TAF to recognize dependency on kUp for
+  fVerU, fVerV
+o Replacing delZ by delR in pkg/ctrl/
+checkpoint51o_pre
+
+o undid all of cp51 pending some cleanups and discussion
+o added the [#include "AD_CONFIG.h"] statement to all files that need 
+   it for adjoint/tl #defines
+ o re-worked the build logic in genmake2 to support AD_CONFIG.h
+ o removed tools/genmake since it no longer works
+
+checkpoint51n_post
+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
+  - subroutine FREEZE now limits only surface temperature
+    (this means new output.txt for global_ocean.90x40x15,
+     global_ocean.cs32x15, and global_with_exf)
+o added surface flux output variables to TIMEAVE_STATVARS
+
+checkpoint51n_pre
 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: