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-revision 1.1111 by mlosch,
Fri May 29 14:52:48 2009 UTC
+revision 1.1221 by mlosch,
Tue Jan 19 14:25:53 2010 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ 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 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 pendant to 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
+d-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:
+. introduce fields for time step (N-1)
+. do not use levels 2 and 3 anymore (but keep them)
+. 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
-Line 17 
 o pkg/seaice:
+Line 450 
 o pkg/seaice:
      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
+ 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
-Line 64 
 o pkg/exch2:
+Line 501 
 o pkg/exch2:
   - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
     in utils/exch2/input.
- checkpoint61n
+ 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/
-Line 77 
 o pkg/mdsio: in preparation for topology
+Line 514 
 o pkg/mdsio: in preparation for topology
      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
+ 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.
-Line 113 
 o pkg/exch2 (+ utils/exch2): ignore blan
+Line 550 
 o pkg/exch2 (+ utils/exch2): ignore blan
    and keep the original tile numbering. Note: compatible with old
    W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
- checkpoint61l
+ 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:
-Line 161 
 o pkg/seaice:
+Line 598 
 o pkg/seaice:
      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
+ 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
-Line 178 
 o pkg/seaice: a few bug fixes mostly con
+Line 615 
 o pkg/seaice: a few bug fixes mostly con
    updated all relevant verification experiments (except lab_sea//output_adm.txt
      which was left over, but fails at level 7 & 6)
- checkpoint61j
+ 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
-Line 206 
 o autodiff
+Line 643 
 o autodiff
    TAF store directivs "byte" and "kind" seem equivalent;
    Most tamc.h have been updated correspondingly.
- checkpoint61i
+ checkpoint61i (2009/02/13)
  o autodiff:
    fix autodiff_sore/_restore indices for obcs
    (spotted by I. Hoteit, M. Mazloff)
-Line 241 
 o pkg/ggl90: a few modifications:
+Line 678 
 o pkg/ggl90: a few modifications:
  o rename thetaMin,phiMin -> xgOrigin,ygOrigin
    (maintain temporary backward compatibility, until next checkpoint)
- checkpoint61h
+ 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
-Line 265 
 o pkg/mdsio: read/write vector:
+Line 702 
 o pkg/mdsio: read/write vector:
    (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
+ checkpoint61g (2008/12/29)
  o pkg/flt:
    - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
     + make OPTIONS file more standard.
-Line 278 
 o pkg/obcs: fix a CPP-flag, bug reported
+Line 715 
 o pkg/obcs: fix a CPP-flag, bug reported
  o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
    a still unfixed compiler/optimization bug
- checkpoint61f
+ 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.
-Line 307 
 o fix CPP-flag REAL4_IS_SLOW, when _RS e
+Line 744 
 o fix CPP-flag REAL4_IS_SLOW, when _RS e
   - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
     (generate new output).
- checkpoint61e
+ 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 :
-Line 332 
 o pkg ggl90:
+Line 769 
 o pkg ggl90:
          scale in ggl90_calc.F
          (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
- checkpoint61d
+ checkpoint61d (2008/09/25)
  o adjoint modifs
    - adapt to new field rhoInSitu
    - allow to revert from StoreDynVars2D, StoreDynVars3D
-Line 359 
 o add initialisation of deepFac if using
+Line 796 
 o add initialisation of deepFac if using
    ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
  o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
- checkpoint61c
+ 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).
-Line 377 
 o change FIND_RHO to FIND_RHO_2D :
+Line 814 
 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
+ 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).
-Line 392 
 o exch2:
+Line 829 
 o exch2:
     more intuitive this way) ; rename/remove some variables.
   - change utils/exch2/matlab-topology-generator & code_mods accordingly.
- checkpoint61a
+ 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).
-Line 401 
 o pkg/mnc: small fix in mnc_handle_err:
+Line 838 
 o pkg/mnc: small fix in mnc_handle_err:
  o testreport: modify syntax of awk, so that it works also with
    awk, and not only with nawk and gawk
- checkpoint61
+ 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.)
-Line 412 
 o autodiff
+Line 849 
 o autodiff
    Tested TAF version is 1.9.22
    N.B.: exch2 hand-written adjoint code currently not TAMC compatible
- checkpoint60
+ 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.
-Line 437 
 o bridging the gap between eddy stress a
+Line 874 
 o bridging the gap between eddy stress a
    The key modifications are in model/src/taueddy_external_forcing.F
    pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
- checkpoint59r
+ 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.
-Line 468 
 o pkg/ptracers: add second-order moment
+Line 905 
 o pkg/ptracers: add second-order moment
    (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
    and requires a fortran 90 compiler
- checkpoint59q
+ 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:
-Line 503 
 o thsice pkg:
+Line 940 
 o thsice pkg:
    - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
    --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
- checkpoint59p
+ 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" ;
-Line 529 
 o in mom_calc_visc, fix average value of
+Line 966 
 o in mom_calc_visc, fix average value of
    bottom ; only used with variable horizontal viscosity and non-hydrostatic.
    also fix diagnostics VISCAHW & VISCA4W.
- checkpoint59o
+ 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
-Line 570 
 o pkg/ctrl:
+Line 1007 
 o pkg/ctrl:
      introducing a generic routine (ctrl_map_ini_gen.F).
    - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
- checkpoint59n
+ 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
-Line 624 
 o pkg/seaice: add a new flag SEAICEuseTE
+Line 1061 
 o pkg/seaice: add a new flag SEAICEuseTE
    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
+ 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
-Line 642 
 o pkg/obcs and pkg/seaice:
+Line 1079 
 o pkg/obcs and pkg/seaice:
  o pkg/salt_plume: added various options for salt plume depth
    criterion and for vertical distribution of the salt
- checkpoint59l
+ 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 )
-Line 664 
 o no longer write pickup from THE_MODEL_
+Line 1101 
 o no longer write pickup from THE_MODEL_
  o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
    or U/VICE from U/VWIND before computing U/VSTRESS
- checkpoint59k
+ 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):
-Line 686 
 o pkg/ptracers:
+Line 1123 
 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
+ 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).
-Line 729 
 o pkg/mdsio & pkg/rw:
+Line 1166 
 o pkg/mdsio & pkg/rw:
  o added open boundary conditions capability for seaice
      HSNOW, HSALT, UICE, and VICE
- checkpoint59i
+ checkpoint59i (2007/10/21)
  o adjoint:
    * fix multiDimAdvection adjoint
      (partial recomputation problem by TAF for fVerT(:,:,kDown)
-Line 770 
 o change units of EmPmR (inside the code
+Line 1207 
 o change units of EmPmR (inside the code
    Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
    Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
- checkpoint59h
+ checkpoint59h (2007/09/29)
  o pkg/exf:
    - improve vectorization by moving if-statement out of loops in
      exf_mapfields, exf_radiation
-Line 803 
 o pkg/thsice:
+Line 1240 
 o pkg/thsice:
  o testreport: change AD testing : check against results/output_adm.txt
    using same scripts as for forward test.
- checkpoint59g
+ 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")
-Line 848 
 o pkg/cd_code: add brackets in multiple
+Line 1285 
 o pkg/cd_code: add brackets in multiple
    global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
    ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
- checkpoint59f
+ 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)
-Line 879 
 o pkg/seaice
+Line 1316 
 o pkg/seaice
  o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
     output of global_ocean.cs32x15.thsice .
- checkpoint59e
+ 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).
-Line 909 
 o pkg/seaice:
+Line 1346 
 o pkg/seaice:
    * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
    * applied OBCS T/S mask to HEFFM sea ice mask
- checkpoint59d
+ 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)
-Line 955 
 o pkg/seaice:
+Line 1392 
 o pkg/seaice:
     It is turned off by default (=-1.), because it changes the results.
   - make it possible to read AREA from a file, too.
- checkpoint59c
+ 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:
-Line 988 
 o adjoint:
+Line 1425 
 o adjoint:
    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:
-Line 1059 
 o pkg/seaice
+Line 1496 
 o pkg/seaice
  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
-Line 1101 
 o pkg/seaice: fix bug in evp solver, whi
+Line 1538 
 o pkg/seaice: fix bug in evp solver, whi
  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
-Line 1127 
 o pkg/thsise
+Line 1564 
 o pkg/thsise
    - 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
-Line 1143 
 o ice dynamics (pkg/seaice) with thsice
+Line 1580 
 o ice dynamics (pkg/seaice) with thsice
         - 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).
-Line 1151 
 o IO option for global-file compact form
+Line 1588 
 o IO option for global-file compact form
    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).
-Line 1172 
 o cpl_aim+ocn exp.: use consistent rhoCo
+Line 1609 
 o cpl_aim+ocn exp.: use consistent rhoCo
  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
-Line 1191 
 o 2nd-Order Moment Advection Scheme (Pra
+Line 1628 
 o 2nd-Order Moment Advection Scheme (Pra
   - 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.
-Line 1206 
 o add option (linFSConserveTr) to correc
+Line 1643 
 o add option (linFSConserveTr) to correc
  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
-Line 1249 
 o pkg/seaice: overhaul of thermodynamics
+Line 1686 
 o pkg/seaice: overhaul of thermodynamics
   - 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
-Line 1283 
 o modifications to pkg/seaice/growth.F a
+Line 1720 
 o modifications to pkg/seaice/growth.F a
    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
-Line 1307 
 o Adding some pkg/diagnostics capability
+Line 1744 
 o Adding some pkg/diagnostics capability
  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
 /6-deg Southern Ocean configuration by 8% on IBM Datastar and
    high_res_cube configuration by 4% on Columbia.
-Line 1318 
 o new function "MASTER_CPU_IO" (=T if ma
+Line 1755 
 o new function "MASTER_CPU_IO" (=T if ma
    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
-Line 1329 
 o diagnoctics: modify UVELPHI and VVELPH
+Line 1766 
 o diagnoctics: modify UVELPHI and VVELPH
  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)
-Line 1343 
 o shelfice:
+Line 1780 
 o shelfice:
   - 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.
-Line 1364 
 o change default MAX_NO_THREADS from 32
+Line 1801 
 o change default MAX_NO_THREADS from 32
    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.
-Line 1390 
 o calc_gw: true flux-form, account for h
+Line 1827 
 o calc_gw: true flux-form, account for h
    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.
-Line 1408 
 o pkg/ecco:
+Line 1845 
 o pkg/ecco:
  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)
-Line 1441 
 o tracer advection:
+Line 1878 
 o tracer advection:
     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
-Line 1449 
 o adjoint store dir. adjusted accordingl
+Line 1886 
 o adjoint store dir. adjusted accordingl
  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
-Line 1463 
 o pkg/seaice: added SEAICEuseEVPpickup p
+Line 1900 
 o pkg/seaice: added SEAICEuseEVPpickup p
      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
-Line 1473 
 checkpoint58h_post
+Line 1910 
 checkpoint58h_post
    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
-Line 1489 
 o couple pkg/thsice to pkg/seaice:
+Line 1926 
 o couple pkg/thsice to pkg/seaice:
  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
-Line 1520 
 o fix bug in aim+thsice albedo: snow & i
+Line 1957 
 o fix bug in aim+thsice albedo: snow & i
  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/ )
-Line 1528 
 o R_STAR adjoint implemented.
+Line 1965 
 o R_STAR adjoint implemented.
  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)
-Line 1568 
 o new package prifiles:
+Line 2005 
 o new package prifiles:
  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
-Line 1602 
 o seaice:
+Line 2039 
 o 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
+ 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:
-Line 1665 
 o seaice:
+Line 2102 
 o seaice:
      (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:
-Line 1718 
 o pkg/bulk_force:
+Line 2155 
 o pkg/bulk_force:
     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
-Line 1731 
 o clean up 3-dim. relaxation codes:
+Line 2168 
 o clean up 3-dim. relaxation codes:
    * 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
-Line 1762 
 o Adding Laplacian-type smoothness const
+Line 2199 
 o Adding Laplacian-type smoothness const
    * 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)
-Line 1777 
 o cfc fixes for final year of integratio
+Line 2214 
 o cfc fixes for final year of integratio
  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)
-Line 1797 
 o adjoint
+Line 2234 
 o adjoint
      (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.
-Line 1814 
 o PTRACERS: added namelist parameter PTR
+Line 2251 
 o PTRACERS: added namelist parameter PTR
    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
-Line 1855 
 o reduce number of exch calls in shap_fi
+Line 2292 
 o reduce number of exch calls in shap_fi
  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
-Line 1878 
 o Clean, new version of mom_calc_visc.
+Line 2315 
 o Clean, new version of mom_calc_visc.
    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
-Line 1904 
 o various changes to mnc including:
+Line 2341 
 o various changes to mnc including:
        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.
-Line 1924 
 o new infrastructure for seaice model vs
+Line 2361 
 o new infrastructure for seaice model vs
  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
-Line 1941 
 o Modifications to enable scripted COMMO
+Line 2378 
 o Modifications to enable scripted COMMO
    * 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)
-Line 1955 
 o Dissipation & phiHyd gradient are alwa
+Line 2392 
 o Dissipation & phiHyd gradient are alwa
    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
-Line 1964 
 o set to #undef CTRL_SET_OLD_MAXCVARS_30
+Line 2401 
 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
+ 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.
-Line 1980 
 o enable useSingleCpuIO for mdsio vector
+Line 2417 
 o enable useSingleCpuIO for mdsio vector
    (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)
-Line 1998 
 o fix aim_diagnostics_init.F mate number
+Line 2435 
 o fix aim_diagnostics_init.F mate number
  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);
-Line 2032 
 o fix bug in rStar code (calc_r_star.F)
+Line 2469 
 o fix bug in rStar code (calc_r_star.F)
  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 ;
-Line 2051 
 o pkg/diagnostics:
+Line 2488 
 o pkg/diagnostics:
    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.
-Line 2060 
 o pkg/diagnostics: prepare for Global/Re
+Line 2497 
 o pkg/diagnostics: prepare for Global/Re
  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
-Line 2078 
 o test AB-3 code with 4th.Order advectio
+Line 2515 
 o test AB-3 code with 4th.Order advectio
  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)
-Line 2092 
 o added new control variables
+Line 2529 
 o added new control variables
  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
-Line 2118 
 o adjoint-related modifications
+Line 2555 
 o adjoint-related modifications
    * 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)
-Line 2136 
 o diagnostics: add pickup functionality
+Line 2573 
 o diagnostics: add pickup functionality
  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
-Line 2158 
 o move state variable diagnostics to the
+Line 2595 
 o move state variable diagnostics to the
    (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
-Line 2194 
 o pkg/mdsio/
+Line 2631 
 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
+ 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
-Line 2240 
 o re-arrange diagnostics pkg initialisat
+Line 2677 
 o re-arrange diagnostics pkg initialisat
     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
-Line 2267 
 o untangle a few ifdefs related to cost,
+Line 2704 
 o untangle a few ifdefs related to cost,
  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
-Line 2285 
 o exf:
+Line 2722 
 o exf:
  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
-Line 2300 
 o testreport previously did a lousy job
+Line 2737 
 o testreport previously did a lousy job
    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
-Line 2345 
 o GCHEM:
+Line 2782 
 o GCHEM:
    - 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
-Line 2375 
 o mdsio: filename info to both stderr, s
+Line 2812 
 o mdsio: filename info to both stderr, s
  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
-Line 2386 
 o make all subroutines 30 or less charac
+Line 2823 
 o make all subroutines 30 or less charac
  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,
 .D if implicit) ; each ptracer uses its own background value.
  o added mnc/NetCDF output capability to ocn_compon_interf
-Line 2401 
 o give MNC the ability to create additio
+Line 2838 
 o give MNC the ability to create additio
  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
-Line 2409 
 o allow to set a vertical profile of ver
+Line 2846 
 o allow to set a vertical profile of ver
  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
-Line 2419 
 o Fixing directives for non-ECCO forward
+Line 2856 
 o Fixing directives for non-ECCO forward
  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
-Line 2430 
 o some delicate re-shuffle of store dire
+Line 2867 
 o some delicate re-shuffle of store dire
  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
-Line 2485 
 o more obcs stuff
+Line 2922 
 o more obcs stuff
    - 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
-Line 2499 
 o obcs stuff
+Line 2936 
 o obcs stuff
  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)]
-Line 2510 
 o use a more standard discretization for
+Line 2947 
 o use a more standard discretization for
  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)
-Line 2518 
 o merged code to
+Line 2955 
 o merged code to
    * 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)
-Line 2528 
 o up-to-date adjoint of previous breaks
+Line 2965 
 o up-to-date adjoint of previous breaks
  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
-Line 2554 
 o overhaul of IO so that we now have fla
+Line 2991 
 o overhaul of IO so that we now have fla
    - 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
-Line 2568 
 o add "verification/dic_example" which c
+Line 3005 
 o add "verification/dic_example" which c
  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
-Line 2584 
 o fix a bug in Flux deriv. vs Ts (pkg/ai
+Line 3021 
 o fix a bug in Flux deriv. vs Ts (pkg/ai
  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
-Line 2595 
 o define the max number of passive trace
+Line 3032 
 o define the max number of passive trace
  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
-Line 2605 
 o staggerTimeStep & NLFS: rescale T & S
+Line 3042 
 o staggerTimeStep & NLFS: rescale T & S
    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
+ checkpoint54 (2004/07/02)
- checkpoint53g_post
+ 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
-Line 2626 
 o new parameter "nShapS": allow to treat
+Line 3063 
 o new parameter "nShapS": allow to treat
  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)
-Line 2639 
 o merged cylindrical coord configuration
+Line 3076 
 o merged cylindrical coord configuration
  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
-Line 2658 
 o regenerated output for global_ocean_eb
+Line 3095 
 o regenerated output for global_ocean_eb
  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
-Line 2677 
 o Adjoint of EBM package + verification
+Line 3114 
 o Adjoint of EBM package + verification
    * 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
-Line 2695 
 C        Destabilization of the thermoha
+Line 3132 
 C        Destabilization of the thermoha
  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
-Line 2703 
 o pkg/land: only liquid water can diffus
+Line 3140 
 o pkg/land: only liquid water can diffus
  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
-Line 2716 
 o Fixed verification/natl_box_adjoint ex
+Line 3153 
 o Fixed verification/natl_box_adjoint ex
    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_
-Line 2726 
 o stable checkpoint with up to date adjo
+Line 3163 
 o stable checkpoint with up to date adjo
     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
-Line 2757 
 o fix in pkg/thsice:
+Line 3194 
 o fix in pkg/thsice:
    - 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
-Line 2789 
 o test exp. advect_cs: use the standard
+Line 3226 
 o test exp. advect_cs: use the standard
  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.
-Line 2800 
 o aim_v23 modification for new land mode
+Line 3237 
 o aim_v23 modification for new land mode
    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)
-Line 2813 
 o fix ini_curvilinear_grid ; test CS exp
+Line 3250 
 o fix ini_curvilinear_grid ; test CS exp
  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
-Line 2826 
 o set all ...Freq to zero after cost_fin
+Line 3263 
 o set all ...Freq to zero after cost_fin
    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!
-Line 2834 
 o Really weird thing!
+Line 3271 
 o Really weird thing!
    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
-Line 2851 
 o merged mom_vi_calc_relvort3.F, mom_vi_
+Line 3288 
 o merged mom_vi_calc_relvort3.F, mom_vi_
    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
-Line 2870 
 o added temporary hack for sea-ice dynam
+Line 3307 
 o added temporary hack for sea-ice dynam
    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)
-Line 2884 
 o step.1 : rewrite (as in MultiDimAdvec)
+Line 3321 
 o step.1 : rewrite (as in MultiDimAdvec)
  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
-Line 2895 
 o added exf_offset_atemp for Celsius to
+Line 3332 
 o added exf_offset_atemp for Celsius to
  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
-Line 2924 
 o check-in the first version of the coup
+Line 3361 
 o check-in the first version of the coup
  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
-Line 2942 
 o Removed all CPP options for cal packag
+Line 3379 
 o Removed all CPP options for cal packag
  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;
-Line 2950 
 o new version: "thsice" of thermodynamic
+Line 3387 
 o new version: "thsice" of thermodynamic
   - 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)
-Line 2960 
 o missing PTRACERS headers in some routi
+Line 3397 
 o missing PTRACERS headers in some routi
  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
-Line 2975 
 o fix problem with ECCO-related divided
+Line 3412 
 o fix problem with ECCO-related divided
    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
-Line 2996 
 o top level routines the_main_loop, forw
+Line 3433 
 o top level routines the_main_loop, forw
    (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'
-Line 3008 
 o pkg/grdchk
+Line 3445 
 o pkg/grdchk
    - 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
-Line 3029 
 o ctrl package totally restructured
+Line 3466 
 o ctrl package totally restructured
    - 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
-Line 3044 
 o create initial cd_code package
+Line 3481 
 o create initial cd_code package
  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/
-Line 3065 
 o Correcting initialisations for fVerU,
+Line 3502 
 o Correcting initialisations for fVerU,
  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
-Line 3073 
 o added the [#include "AD_CONFIG.h"] sta
+Line 3510 
 o added the [#include "AD_CONFIG.h"] sta
   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
-Line 3082 
 o modifications to make FREEZE flux visi
+Line 3519 
 o modifications to make FREEZE flux visi
       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:
-Line 3090 
 o added [#include "AD_CONFIG.h"] to all
+Line 3527 
 o added [#include "AD_CONFIG.h"] to all
    - 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
-Line 3123 
 o added an include barrier to the defaul
+Line 3560 
 o added an include barrier to the defaul
    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
-Line 3137 
 o Moving pkg-specific flow directives to
+Line 3574 
 o Moving pkg-specific flow directives to
         - 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
-Line 3155 
 o modify gchem pkg to be more versatile
+Line 3592 
 o modify gchem pkg to be more versatile
  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
-Line 3163 
 o update AD-related stuff
+Line 3600 
 o update AD-related stuff
  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
-Line 3180 
 o Bug fix to pkg/ptracers, pkg/generic_a
+Line 3617 
 o Bug fix to pkg/ptracers, pkg/generic_a
      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.
-Line 3190 
 o atmospheric geopotential: - include wa
+Line 3627 
 o atmospheric geopotential: - include wa
  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)
-Line 3203 
 o Use cluster local disks for purely loc
+Line 3640 
 o Use cluster local disks for purely loc
    - 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
-Line 3226 
 o added verification for adjoint with pt
+Line 3663 
 o added verification for adjoint with pt
    - 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
-Line 3241 
 o merged improved packages from ecco-bra
+Line 3678 
 o merged improved packages from ecco-bra
  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
-Line 3257 
 o New variable in PARM03 for more flexib
+Line 3694 
 o New variable in PARM03 for more flexib
  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
-Line 3271 
 o exf totally restructured
+Line 3708 
 o exf totally restructured
    - 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
-Line 3281 
 checkpoint50f_pre
+Line 3718 
 checkpoint50f_pre
   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
-Line 3320 
 o new flag "useCDscheme" (default=F); re
+Line 3757 
 o new flag "useCDscheme" (default=F); re
  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
-Line 3340 
 checkpoint50
+Line 3777 
 checkpoint50
  - 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
-Line 3378 
 o DIVA:
+Line 3815 
 o DIVA:
    (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).
-Line 3396 
 o Modif. for DIVA:
+Line 3833 
 o Modif. for DIVA:
    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.
-Line 3416 
 o accurate phiHyd when using interface-W
+Line 3853 
 o accurate phiHyd when using interface-W
   ( 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
-Line 3444 
 o pkg/seaice:
+Line 3881 
 o pkg/seaice:
    - 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.
-Line 3455 
 o following exp works with Olx=Oly=2 (an
+Line 3892 
 o following exp works with Olx=Oly=2 (an
      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
-Line 3463 
 o in preparation for r*:
+Line 3900 
 o in preparation for r*:
      => 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_...
-Line 3512 
 o Yet more changes in gmredi:
+Line 3949 
 o Yet more changes in gmredi:
      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)
-Line 3528 
 o case GM_BOLUS_ADVEC should be cleaned
+Line 3965 
 o case GM_BOLUS_ADVEC should be cleaned
    S/R gmredi_slope_psi should be cleaned
  o verification/carbon now has exactConserv=.TRUE.
- checkpoint47g_post
+ 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:
-Line 3554 
 Gradient checks OK for
+Line 3991 
 Gradient checks OK for
  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
-Line 3566 
 o modifications for using pkg/exf with p
+Line 4003 
 o modifications for using pkg/exf with p
    - 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
-Line 3590 
 o OCEANICP & realFreshWater: include P-E
+Line 4027 
 o OCEANICP & realFreshWater: include P-E
    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
-Line 3607 
 o verification/lab_sea
+Line 4044 
 o verification/lab_sea
    - 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.
-Line 3624 
 o bulk_force and therm_seaice
+Line 4061 
 o bulk_force and therm_seaice
  - 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)
-Line 3653 
 o Updated verification/carbon/
+Line 4090 
 o Updated verification/carbon/
    - #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
-Line 3707 
 o Adding new verification experiment glo
+Line 4144 
 o Adding new verification experiment glo
    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()
-Line 3720 
 o introduced flag for controllin non-hyd
+Line 4157 
 o introduced flag for controllin non-hyd
  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)
-Line 3733 
 o made convective adjustment work with p
+Line 4170 
 o made convective adjustment work with p
     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)
-Line 3749 
 o S/R aim_initialise.F replace S/R aim_i
+Line 4186 
 o S/R aim_initialise.F replace S/R aim_i
   - 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
-Line 3772 
 o introduced new parameter rhoConstFresh
+Line 4209 
 o introduced new parameter rhoConstFresh
    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
-Line 3796 
 o cleaned up find_rho
+Line 4233 
 o cleaned up find_rho
    - removed obsolete 'eqn' from the parameter list.
  o added two new verification experiments: gop and goz
    (4x4 degree global ocean, 15 layers in pressure and height coordinates)
- checkpoint46g_pre
+ 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
-Line 3806 
 o Enable tangent linear (forward mode) g
+Line 4243 
 o Enable tangent linear (forward mode) g
  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
-Line 3815 
 o Added new equation of state -> MDJWF
+Line 4252 
 o Added new equation of state -> MDJWF
    - 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
-Line 3847 
 o Added UNESCO EOS, but not recommended
+Line 4284 
 o Added UNESCO EOS, but not recommended
    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
-Line 3884 
 o added hooks for Eliassen Palm fluxes (
+Line 4321 
 o added hooks for Eliassen Palm fluxes (
  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)
-Line 3898 
 o add new flags:
+Line 4335 
 o add new flags:
   - 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).
-Line 3906 
 o modifications to gradient check packag
+Line 4343 
 o modifications to gradient check packag
    - 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
-Line 3918 
 o in initialise_varia, moved call packag
+Line 4355 
 o in initialise_varia, moved call packag
    (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
-Line 3938 
 o errorMessageUnit set non-equal zero in
+Line 4375 
 o errorMessageUnit set non-equal zero in
    (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
 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
-Line 4009 
 o merge of relevant stuff from the ecco-
+Line 4446 
 o merge of relevant stuff from the ecco-
  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)
-Line 4017 
 o update AIM experiments (NCEP input fil
+Line 4454 
 o update AIM experiments (NCEP input fil
  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)
-Line 4035 
 o Modified store directives for split of
+Line 4472 
 o Modified store directives for split of
    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
-Line 4048 
 o more mods for non-linear free-surface
+Line 4485 
 o more mods for non-linear free-surface
  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
-Line 4058 
 o changes to commenting of arguments for
+Line 4495 
 o changes to commenting of arguments for
  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
-Line 4077 
 o TAMC-related update to cope with mom_f
+Line 4514 
 o TAMC-related update to cope with mom_f
    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
-Line 4092 
 o corresponding split of calc_diffusivit
+Line 4529 
 o corresponding split of calc_diffusivit
  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
-Line 4106 
 o added new expt "solid-body.cs-32x32x1"
+Line 4543 
 o added new expt "solid-body.cs-32x32x1"
    + 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,
-Line 4114 
 o extended iMin,jMin range for calc_comm
+Line 4551 
 o extended iMin,jMin range for calc_comm
  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
-Line 4139 
 checkpoint39
+Line 4576 
 checkpoint39
           (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
-Line 4147 
 checkpoint38
+Line 4584 
 checkpoint38
     (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)
-Line 4164 
 checkpoint37
+Line 4601 
 checkpoint37
   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).
-Line 4187 
 checkpoint34
+Line 4624 
 checkpoint34
   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:
-Line 4205 
 checkpoint33
+Line 4642 
 checkpoint33
       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
-Line 4216 
 checkpoint32
+Line 4653 
 checkpoint32
   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
-Line 4233 
 checkpoint31
+Line 4670 
 checkpoint31
     - 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/
-Line 4242 
 checkpoint30
+Line 4679 
 checkpoint30
   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_...
-Line 4258 
 checkpoint28
+Line 4695 
 checkpoint28
     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()
-Line 4266 
 checkpoint27
+Line 4703 
 checkpoint27
   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
-Line 4276 
 checkpoint26
+Line 4713 
 checkpoint26
     (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
-Line 4287 
 checkpoint25
+Line 4724 
 checkpoint25
      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.
-Line 4320 
 checkpoint19
+Line 4757 
 checkpoint19
   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.
-Line 4339 
 checkpoint16
+Line 4776 
 checkpoint16
     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? )
-Line 4348 
 checkpoint15
+Line 4785 
 checkpoint15
     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
-Line 4367 
 branch-point-rdot
+Line 4804 
 branch-point-rdot
   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
-Line 4397 
 checkpoint7-4degree-ref
+Line 4834 
 checkpoint7-4degree-ref
   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.
-Line 4405 
 checkpoint7
+Line 4842 
 checkpoint7
   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

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