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-revision 1.223 by jmc,
Sun Dec 14 23:30:13 2003 UTC
+revision 1.437 by jmc,
Thu Jan 27 14:11:44 2005 UTC
 Line 3 
 $Header$
      Notes on tags used in MITgcmUV
      ==============================
+ checkpoint57c_pre
+ o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
+   update output.txt of exp. global_ocean.90x40x15
+ o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
+   results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
+ o add saltFlux(+File) forcing capability with periodicExternalForcing
+ o allow to use pkg diagnostics for GM-Redi & ThSIce output
+ o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
+ o improvements for the MNC output from DIAGNOSTICS:
+   - correct handling of the unlimitied dimension
+   - all dims now have associated coordinate variables
+   - variables located at U, V, and Corner ("Z") points are now written
+     with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
+     *all* data points are output
+ o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
+ o added pkg/seaice/seaice_monitor.F
+ o mdsio_readfield.F can now read files visible only to master MPI process.
+ o pkg/seaice: some test code for ice-modified ocean stress
+ o exf_getffields interpolation defaults to bilinear for all scalar forcing
+   fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
+   spurious negative numbers for precipitation and humidity.  Will cause
+   some small numerical differences for integrations using pkg/exf/exf_interp.F.
+ o pkg/ctrl/
+   * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
+     May be enabled via doPackDiag
+   *  introduce z-scaling of
+      + gradient (doZscalePack) and
+      + control (doZscaleUnpack)
+ o pkg/mdsio/
+   * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
+   * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
+ checkpoint57b_post
+ o simplify options in diagnostics_fill arguments (remove weird combinations)
+ o fix MNC coordinate variables so that they now contain per-face index
+   values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
+   general, EXCH2 grids are only aligned to a "local" coordinate system
+ o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
+ o Implement instantaneous output within pkg diagnostics:
+   setting a negative frequency in data.diagnostics produces
+  "snap-shot" output (as opposed to time-average if freq > 0)
+ o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
+   NOTE: change ptracer diagnostics name: use 2 characters to work with
+         more than 9 tracers. Add also diagnostics of advect & diffus flux.
+ o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
+   becomes the coordinate variable for the 'T' dimension
+ o add CF-style coordinate variables to MNC
+   - just a first cut:  numbers are meaningless on the cubesphere and
+     missing along the T axis but otherwise it works!
+ o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
+ o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
+ o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
+   this is based directly on what the model compute, so that the content of
+   each diagnostics might be affected by switching options (e.g., implicitDiffusion)
+ o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
+ o clean up build options files for SunOS, in particular
+   - remove -traditional from xmakedepend
+   - change -xarch=v9 to -xarch=native for f77
+   - restore use of make (not gmake)
+   - add CC=gcc if using g77
+ o changes per discussion of AM, JMC, & EH3 today:
+   - move redundant "grid" variables out of "state" -- in preparation of
+     creating proper CF-style coordinate variables and in recognition
+     that any/all grid variables can be easily copied (eg. w/NCO) from
+     the grid files into any of the other NetCDF files
+   - *always* output grid variables with MDSIO (this will eventually be
+     changed)
+   - output MNC grid file if useMNC is true
+ o every instance of _END_MASTER() has been found and replaced with
+   _END_MASTER( myThid ) in order to satisfy certain picky Sun
+   preprocessors
+ o re-arrange diagnostics pkg initialisation:
+  - allow each package to extend the available diagnostics list
+  - add some checking and fix small problems (multi-threaded, ...)
+  - new S/R diagnostics_fill (replace fill_diagnostics):
+    look through the short list of active diag. (instead of the long list)
+    create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
+ checkpoint57a_post
+ o this set of changes restores TAMC compatibility
+   tested for global_ocean.90x40x15 adjoint on trough
+   (what a pain)
+ checkpoint57a_pre
+ o some modifs in tools/build_options for sunos
+ o call ctrl_pack for ctrl at end for optimcycle=0
+ checkpoint57
+ o add horizontal bi-harmonic viscosity for vertical velocity
+   - new parameter viscA4W (defaults to viscA4)
+   - affects only non-hydrostatic code
+   - to be done: no-slip lateral boundary conditions
+ o switch back to "sflux = sflux - runoff" in exf_getforcing.F
+ o implement Implicit Vertical advection for pTracers
+ o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
+   (implemented also for implicit vertical diffusion & advection)
+ o OBCS: extend application of tracer open boundary conditions
+   to a strip beyond the boundary of width Olx/Oly
+ o add call monitor to TAF set of required calls (flow directives)
+   and include in natl_box_adjoint
+ o untangle a few ifdefs related to cost, ctrl, autodiff
+   untangel a few ALLOW_ECCO_OPTIMIZATION
+ o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
+   (theta2, salt2 in ecco_cost_weights)
+ checkpoint56c_post
+ o OBCS as control variables
+   - update ctrl_ad_diff.list, obcs_ad_diff.list
+   - remove balance of obcs controls from default
+   - fix index bug nobcs in ctrl_init
+   - fix dummy fields filen in ctrl_pack
+   - add dummy weights for obcs
+ o lsopt: comment out fort.94 output
+ o optim:
+   - remove unnecessary header files
+   - adjusted namelists
+   - add xerbla.F to Makefile
+ o exf:
+   - multiple modifications of exf_check_range
+   - unit change in exf_init_runoff from [m/year] to [m/s]
+ o mdsio:
+   - i/o-vector change debugLevel from debLevA to debLevB
+ checkpoint56b_post
+ o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
+   is called from DO_THE_MODEL_IO
+   - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
+   - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
+   - clean up PTRACERS_WRITE_TIMEAVE a little
+ o add another verification experiment that tests both the cfc-pkg and
+   the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
+   reactive tendencies treated inline with regular timestepping
+ o testreport previously did a lousy job of comparing small numbers, so
+   we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
+   implemented in the little c-progam tmp_cmpnum.c which is embedded in
+   testreport.
+ o ptracers_monitor: bug fix for MPI
+ checkpoint56a_post
+ o GCHEM: finish reorganizating the package
+   - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
+     (introduces another 3D-array for each passive tracer, but only if
+     GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
+     gchemTendency is not needed because the timestep is done separately)
+   - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
+   - GCHEM is now---more or less cleanly---separate from PTRACERS
+   - to bo done: handling of surfaceForcingPtr that is needed for KPP not
+     so clear to me how that should be done in a general way.
+ o CFC: improve formatting of output in CFC_ATMOS
+ o PTRACERS:
+   - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
+     that ALL experiments with ptracers enable can be checked. This makes
+     GCHEM_MONITOR obsolete.
+   - include a runtime parameter PTRACERS_monitorFreq that defaults to
+     monitorFreq
+   - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
+ o add PTRACERS (PTR0[1-5]) to testreport output
+ o exf_check_range:
+   * default changed to .TRUE.
+   * will check values for niter0 if debLevA, every timestep if debLevB
+   * STOP in exf_check_range if 'out of range'
+   * range chosen generous to allow for potential extema
+   TBD: a version with stricter range
+        permitted range would be runtime parameters
+ o GMredi:
+   - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
+   - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
+   - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
+ o GCHEM:
+   - move call to GCHEM_FORCING_SEP, so that it is now called before
+     the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
+   - introduced a useGCHEM runtime flag and applied it everywhere.
+   - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
+     this flag is now only visible within GCHEM-pkg routines.
+   - moved gchem_forcing_int temporarily into ptracers_forcing, this will
+     be replaced by a 3D array that is computed before thermodynamics; for
+     this, the tracer ID iTracer had to be included into the parameter list
+     of ptracers_forcing
+   - set up forward_step to call gchem_forcing, that will replace
+     gchem_forcing_int in ptracers_forcing
+   - cleaning up
+ o small cleaning of exch2: remove files that are also in eesupp/src
+ checkpoint56
+ o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
+ o mnc: cleanup "full" files--fixes out-of-memory problem
+ o ECCO-GODAE
+   * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
+   * fully merged and updated from SIO code
+     windstress sign change affects
+     - exf_inscal_[u/v]stress
+     - sign of xx_tau[u/v] adjustments
+     - signs in cost_scat
+   * ctrl_get_gen: avoid update of tau[u/v] for first few days
+   * natl_box_adjoint updated and compressed
+   * 2-level checkpoint switch added
+     (tested in EXP. 1 of natl_box_adjoint)
+   * new switch doInitXX to avoid init. of xx_... in optimcycle=0
+ o SVD
+   * first complete, non-hacked version for SVD calculations
+   * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
+     performed via direct access files admtlm_vector.it????
+     (via ctrl_[un]pack)
+   * optimcycle is used for ARPACK iteration counter
+     (note: adxx_... is iterated, rather than xx_...; latter is constant!)
+   * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
+     and add linear transforms where necessary
+   * controls are initial/final SST, SSS (can be extended; need to check
+     ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
+ o mdsio: filename info to both stderr, stdout
+ o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
+   from sign change
+ checkpoint55j_post
+ o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
+   affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
+ o add consistent build directories and .cvsignore files to verification
+ o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
+ o make all subroutines 30 or less characters in length for certain older
+   compilers to work (a thorough search only turns up two routines in
+   pkg/ptracers)
+ o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
+   affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
+ checkpoint55i_post
+ o change arrays for total vertical diffusivity (2.D if explicit,
+.D if implicit) ; each ptracer uses its own background value.
+ o added mnc/NetCDF output capability to ocn_compon_interf
+   - added bits to verification/cpl_aim+ocn so that it can run on
+     ITRDA and other clusters without the mpirun "-wd" option
+ o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
+   configuration
+ o give MNC the ability to create additional files rather than
+   exceeding a specified file size limit "MNC_MAX_FILESIZE"
+   - the default is just less than 2GB which is a practical limit
+     on many systems
+ o Compute the non-local term using either KPP vertical diffusivity (=default)
+    or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
+ checkpoint55h_post
+ o add verification test "vermix"
+ o remove all the *_ioinc flags and replace with the single global
+   outputTypesInclusive flag
+ o allow to set a vertical profile of vertical diffusivity for T & S
+ o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
+ o useMNC moved from data.mnc to data.pkg
+ checkpoint55g_post
+ o Renaming carbon AD experiments to comply with testreport conventions
+ o Updating adjoint of Held-Suarez hs94.1x64x5
+ o Fixing directives for non-ECCO forward_step, after ECCO directives
+   have been fixed to avoid recomp. of do_oceanic_phys
+   Works well for global_ocean.90x40x15,
+   but recomp. issue remains for carbon
+ o Updating adjoint output for natl_box_adjoint after
+   pkg/ecco has been modified (see taga c55d_post)
+ checkpoint55f_post
+ o rename to timeave_init_fixed
+ checkpoint55e_post
+ o some delicate re-shuffle of store directives to avoid one
+   extra call of do_oceanic_physics
+   affects ecco_the_main_loop.F, do_oceanic_physics.F
+   checkpoint_lev1_directives.h
+ o NB: this may break global_ocean adjoint temporarily,
+   but it is clear how to fix it. Will do later, need this now.
+ checkpoint55d_post
+ o ECCO specific cost function terms (up-to-date with 1x1 runs)
+ o ecco_cost_weights is modified to 1x1 runs
+ o modifs to allow observations to be read in as
+   single file or yearly files
+ o enable to read exf forcing fields as either
+   single file or yearly files (flag useExfYearlyFields)
+ checkpoint55d_pre
+ o switch between 2-level and 3-level checkpointing
+ o add ability of MNC to write local and "partial" (eg. 2D slices where
+   the full 3D field is never actually stored) arrays to NetCDF files
+   with the correct (that is, the complete multi-dimensional) set of
+   array indicies
+   - used in mom_vecinv() to write the diagFreq output
+   - tested (demonstrated) in verification/aim.5l_cs
+ o further mnc-ification
+   - add verification/lab_sea to the list with mnc setups
+   - fix undefined mnc v-names in cd_code
+   - add kpp to mnc output (both snapshot and timeave)
+ o non-hydrostatic code
+   - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
+     in calc_gw.F
+   - defaults to viscAh
+   - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
+     friction or Leith) in non-hydrostatic mode, as long as there is
+     no biharmonic friction and/or Leigth or equivalent for vertical velocity.
+ o pkg/cost
+   extend simple cost functions to treat time mean quantities
+   (T,U,V) via cost_accumulate_state from cost_tile
+ o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
+     be 2 times larger than the minimum size the advection scheme requires.
+     now get a perfect conservation of salt in advect_cs test-exp (updated)
+ o GGL90 (Gaspar's TKE mixed layer)
+   - add horizontal diffusion of TKE, requires exchanges in
+     do_fields_blocking_exchanges, horizontal diffusivity is zero by
+     default. In OPA there is no horizontal diffusion of TKE but the
+     mixing coefficients are computed from a horizontal average of TKE of
+points or so. I think that diffusion has a little more physical
+     justification.
+   - clean up ggl90_calc in the hope of reducing memory usage (this hope
+     was in vain)
+   - mask tke-variable in ggl90_init
+ o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
+ o fix biharmonic diffusion on CS-grid.
+ o more obcs stuff
+   - added obcs_external_fields_load as an alternative to the EXF-pkg option
+     for reading boundary values. This routine is called from
+     obcs_prescribe_read
+   - updated obcs_check
+   - changed sponge layer relaxation parameter units for days to seconds
+   - turned off sponge layer by default
+   - changed argument list of OBCS_CALC to myTime+deltaTclock
+   - fixed about 35 bugs in obcs_external_fields_load
+ checkpoint55c_post
+ o obcs stuff
+   - new runtime flags useOBCSprescribe, useOBCSbalance
+   - re-arranged obcs_calc
+   - moved exf_getobcs to obcs_prescibe_read
+     obcs_prescibe_read is called after ORLANSKI stuff
+     and independent of it (executable can contain all).
+   - updated obcs_check
+   - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
+     These may be necessary only if tangential velocities are
+     prescribed at OB, not sure, needs testing.
+ o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
+   which simplifies the calls and passes the ifc check-bounds test
+ checkpoint55b_post
+ o add a 2D scalar, Z location, exchange_2 routine.
+ o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
+   to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
+   affects advect_cs results (for the wrong reason): update output.txt
+ o use a more standard discretization for biharmonic viscosity ;
+  (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
+   affects results of dome set-up: update output.txt
+ o fix gad_advection.F (CubedSphere part), back to version 1.23
+ o fix bug in mom_vi_del2uv.F (CubedSphere part).
+ checkpoint55a_post
+ o merged code to
+   * prescribe/read time-dependent open boundaries
+     (works in conjunction with exf, cal)
+   * sponge layer code for open boundaries
+   * each boundary N/S/E/W now has its own CPP option
+     (healthy for the adjoint)
+ checkpoint55
+ o up-to-date adjoint of previous breaks
+   - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
+   - global_ocean_ebm: adjoint still needs fix (TLM ok)
+   - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
+   - carbon: * remove tr1-related adjoint verification
+             * add ptracer as control variable
+ o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
+   (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
+ checkpoint54f_post
+ o in verification/carbin/ remove experiment related to
+   ALLOW_PASSIVE_TRACER (array tr1 etc)
+   code_ad/ input_ad/ results_ad
+ o add two new packages
+   - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
+     + subject to optimization (memory)
+   - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
+     + subject to reordering (many GOTOs in the original code)
+     + so far opps is called for every (i,j) point, and then operates in
+       the vertical; one may want to reorder the scheme in order operate in
+       horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
+       fields)
+ o overhaul of IO so that we now have flags for MDSIO and/or MNC
+   - all verification tests compile and run with linux_ia32_g77
+   - defaults are compatible with current input files--nothing
+     should change if you were not previously using MNC
+   - MNC output has been added in numerous places (eg. timeave)
+     but there are still a few writes not yet do-able with MNC
+     (this is in progress)
+   - flags now allow for either/or/both use of MDSIO and MNC and
+     documentation will soon follow
+   - numerous small formatting cleanups for ProTeX
+ o add version info (via BUILD_INFO.h) to MNC and stdout
+ checkpoint54e_post
+ o add two new packages
+   - pp81 (Packanowski and Philander, 1981), Richardson number and
+     stratification dependent mixing
+   - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
+   - these scheme operate in a similar manner as KPP (without ghat, of
+     course), however there is only one diffusivity that is used for both
+     temperature and salinity (and passive tracers)�
+ o add offline package
+ o add "verification/dic_example" which contains a dic-gchem-ptracer setup
+   provided by Stephanie Dutkiewicz
+ o genmake2: add ability to search for C compilers and cleanup test output
+   - fixes recent SX-6 problems and should help with others (eg. HP-UX)
+ checkpoint54d_post
+ o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
+ o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
+   leading to additional shift by 5 days each year of integration
+    (i.e. leading to considerable offset over the years)
+ o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
+ o start with no AB and no initial filtering (staggerTimeStep):
+   change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
+ o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
+   (external loading & cpl import/export stay in forward_step.F)
+ o update coupling interface to work with new staggerTimeStep
+ o change MDSIO ptracers_pickup.
+ o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
+ o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
+ o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
+ checkpoint54c_post
+ o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
+   this affects (truncation error) output.txt of test-exp:
+    global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
+ o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
+ o change Qnet to always be the net heat flux, (+upward).
+   affects (truncation error) output of natl_box exp.: updated
+ o define the max number of passive tracers in PTRACERS_SIZE.h
+ o start to test mnc routinely in exp0
+ o add sea-ice loading (sIceLoad) as a new forcing field.
+ checkpoint54b_post
+ o add testreport "-j JOBS" option for parallel builds (tested and pretty
+    impressive on Altix and Opteron systems)
+ o diagnostics can now write NetCDF files through the mnc package
+ o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
+ o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
+ o staggerTimeStep & NLFS: rescale T & S surface tendencies.
+   affects (truncation error) output of lab_sea & natl_box exp.: updated
+ o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
+ checkpoint54a_post
+ o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
+ o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
+ o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
+ o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
+   + internal_wave (shift in writing cg2d_ini_res)
+ checkpoint54a_pre
+ o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
+   - modified verification/lab_sea and natl_box_adjoint accordingly
+ checkpoint54
+ checkpoint53g_post
+ o prepare splitting of thermodynamics: store convect.counter in common block
+ o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
+   output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
+ o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
+ o new parameter "nShapS": allow to treat differently S from T (nShapT)
+ o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
+ o restore adjointability
+ checkpoint53f_post
+ o modifications that affect AIM experiment results (update output.txt):
+   - no advection of S at top interface Nr (pkg/generic_advdiff)
+   - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
+ o AIM pkg:
+   - include stability function into surf.Flux derivative relative to Tsurf
+   - calculate clear-sky radiation & surface temp. change (for diagnostics)
+ checkpoint53e_post
+ o merged cylindrical coord configuration
+ o added rotating_tank experiment
+ checkpoint53e_pre
+ checkpoint53d_post
+ o faulks upgraded: re-generate output.txt that have changed:
+    global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
+ o Added Bryan and Lewis, 1979, vertical diffusivity profile
+ o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
+ o added Sadourny discretization of Coriolis
+   - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
+   - re-enabled use of omega3 (useAbsVorticity)
+ o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
+   vector-invariant equations
+   - note: does *NOT* yet use same variable visc. for no-slip BC's.
+ o recoded the lateral boundary conditions for non-hydrostatic w, this time
+   hopefully without new bugs
+   - still to do: biharmonic friction for non-hydrostatic w
+ o bug fix for mom_*_sidedrag: rA -> rAs,rAw
+ o regenerated output for global_ocean_ebm (using -ieee)
+ o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
+   of mom_common/
+   - simple re-arrangement of instructions within computing loop
+ checkpoint53d_pre
+ checkpoint53c_post
+ o new version of coupler for AIM+thSIce and Ocean models
+  - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
+  - land: change Evaporation of snow
+  - aim with thSIce: fix bug in snow-precip.
+ o changes to calc_gw.F
+  - bug fix for w^2 term near the bottom boundary
+  - (hopefully) improve the lateral slip boundary condtions for use with
+     partial/looped cells
+   - because the bug fix changes two verification experiments anyway (exp5
+     and plume on slope), change the lateral boundary condition from half slip
+     to the value of no_slip_sides
+ o ebm package wasnt quite up to the parallel task. Fixed that.
+ o Adjoint of EBM package + verification
+   * TLM OK
+   * ADM not sufficient accuracy yet (needs further testing)
+ checkpoint53b_post
+ o Commiting new energy balance model to repository
+   * package is pkg/ebm
+   * verif. is verification/global_ocean_ebm
+   * references are in ebm_driver.F
+ C      * X. Wang, P. Stone and J. Marotzke, 1999:
+ C        Global thermohaline circulation. Part I:
+ C        Sensitivity to atmospheric moisture transport.
+ C        J. Climate 12(1), 71-82
+ C      * X. Wang, P. Stone and J. Marotzke, 1999:
+ C        Global thermohaline circulation. Part II:
+ C        Sensitivity with interactive transport.
+ C        J. Climate 12(1), 83-91
+ C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
+ C        Destabilization of the thermohaline circulation
+ C        by atmospheric eddy transports.
+ C        J. Climate 7(12), 1870-1882
+ o Will need long integration testing.
+ checkpoint53b_pre
+ o created pkg/mom_common in preparation for variable viscosity code
+ o renamed and split ini_mnc_io
+ o pkg/land: only liquid water can diffuse or run-off
+ o AIM using land: soil wetness availability account for snow
+ o added printMapIncludesZeros to EEPARMS namelist
+ checkpoint53a_post
+ o restore TAMC compatiility for exf_constants.h
+   (no usage of _d in .h)
+ o Additional storing in KPP in an attempt to fix
+   TAMC problem with adjoint of KPP code.
+   (no success...)
+   Identical code works fine with TAF.
+ o Fixed verification/natl_box_adjoint experiments.
+   Initial conditions for Experiments 4 and 5 are now
+   set to "SEAICE_initialHEFF=0", which is more reasonable,
+   and hence gives results closer to that of Experiment 2.
+   Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
+ checkpoint53
+ o stable checkpoint with up to date adjoint
+   TLM tests only run for 1st grdchk at the moment. Its unclear if
+   this is a code problem or a problem with resetting code for g_
+   variables that is being autogenerated wrong.
+   Otherwise:
+    o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
+    o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
+      are both still in chaos following their security messes.
+ checkpoint52n_post
+ o various build (mostly genmake2) changes including:
+   - ability to build/run more easily within Cygwin and MacOS X
+   - more complicated Makefiles with a stronger dependence on Gnu Make
+ o pkg/seaice modifications
+   - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
+     of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
+     and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
+   - changed proxy for geostrophic velocity and updated
+     verification/lab_sea/results/* accordingly
+   - removed ADI dynamic solver from pkg/seaice
+   - replaced all occurrences of 1/CSTICE or 1/CSUICE
+     they caused a segmentation fault under certain circumstances
+   - removed unused field WATR
+ o bug fix in exf-package:
+   -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
+      now reflect that.
+ o small fixes in the cal-package:
+   - set reference date to first of January for the 'model'-calendar
+   - failing of cal_CheckDate in cal_FullDate now actually results in a
+     warning
+ o small modifications in exf-package to increase flexibility:
+   - change climtempfreeze from a constant to a runtime parameter that
+     is specified in data.exf_clim (default = -1.9)
+   - introduce runtime parameter windstressmax (default = 2.0) that is
+     specified in data.exf
+ o fix in pkg/thsice:
+   - update Evap (Tsf changes) to be consistent with Latent heat flux
+   - maintain snow precipitation unchanged (even if Tsf >=0).
+  both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
+ checkpoint52m_post
+ o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
+   this does not change any of the results, because myIter=0 in swfrac always
+   lead to jwtype=2 (the default anyway), but the call makes little sense
+   as a default
+ o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
+ o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
+   atmospheric model (AIM) to use it ; add a "slab ocean" component.
+ o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
+ o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
+ o extending useSingleCpuIO option to work with new exch2 I/O format
+   - old-style, missing-tile I/O is still accessible by defining CPP
+     option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
+ o monitor package can write to NetCDF files and/or STDOUT
+ o fix re-definition bug in MNC_GRID_INIT_ALL()
+ o doc/api_reference added
+   - a framework for building an API Reference Manual using all
+     the "protex" comments embedded in the code
+   - see pkg/generic_advdiff, pkg/mnc for examples
+ o MNC:
+   - make myThid the last argument for all subroutines
+   - new default for the grid files: NO halos
+   - add useMNC and other run-time flags
+   - separate per-file-group handling of the unlimited dimension
+   - early initialization of MNC w/ flags read at the eeboot stage
+     and lookup tables set in initialize_fixed
+   - write all MNC output to a freshly-created directory
+ o thermodynamics sea-ice (thsice) is now tested with testreport.
+ o test exp. advect_cs: use the standard cs32 grid ; update output.
+ o Added functionality to grdchk:
+   pick global i,j,k position (or nearest wet) where to perform check.
+ checkpoint52l_post
+ o new land formulation:
+   a) use ground enthalpy as prognostic variable to ensure exact
+      energy conservation.
+   b) account for water temperature and for latent heat of freezing
+      in all processes (rain, run-off, ground storage)
+   c) compute surface and ground temperature implicitly.
+ o aim_v23 modification for new land model:
+   a) Treat separately land / ocean / sea-ice surface fluxes
+      to allow implicit computation of land & sea-ice surface temp.
+   b) add snow precipitation.
+ checkpoint52l_pre
+ o fix problem (when 1 tile is empty) in min/max monitor.
+ o fix bug in timeAve (u,vZetatave in common block)
+ o no restoring terms under ice for pkg/seaice
+ o moved SEAICE_DO_DIAGS to S/R do_the_model_io
+ o bug fix for pkg/seaice pickups
+ o change MNC call locations and add coordinate attributes
+ o mask vorticity at the corner ; affects global_ocean.cs output
+ o fix ini_curvilinear_grid ; test CS experiments with mpi
+ o aim.5l_cs: modify sea-ice fraction input file ; update output
+ o exf: Adding simple range check routine for exf fields after read
+ checkpoint52k_post
+ o removed top-level directory "diags"
+   - we migrated these functions to pkg/timeave a long time ago
+ o fixed bug introduced in pkg/monitor
+ o accuracy ctrlprec = 32 insuffient for gradient checks using
+   averaged fields (I/O via cost_averages)
+   -> use ctrl.h in active_file*.F to control I/O precision.
+ o paramter list of CALL ADTHE_MAIN_LOOP
+ o added initial do_the_model_io to ecco
+ o set all ...Freq to zero after cost_final
+   taveFreq, dumpFreq, pChkptFreq
+ o MAIN and ECCO differentiability restored
+ checkpoint52j_post
+ o fix nchklev in tamc.h for global_ocean...
+ o Bringing flow and store directives up-to-date
+ o Really weird thing!
+   call do_the_model_io from the_main_loop with parameters
+   starttime, niter0, instead of mytime, myiter, screws up the adjoint:
+   TAF places a faulty re-call of initialise_varia
+   after cost_final call which should not be there!
+ checkpoint52j_pre
+ o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
+   error messages
+ o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
+ o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
+   debug output
+ o modfied mdsio_writefield.F to handle non-global files under exch2
+ o update AIM Cubed-Sphere exp (aim.5l_cs):
+   use land, p*, and Franco.M forcing fields with fractional land-sea mask.
+ o update AIM Equatorial Channel exp:
+   use standard aim_v23 pkg and change the SST fields to be more realistic.
+ o globalFile now works with exch2
+ o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
+   mon_vort3.F to make exch2 friendly with >1 tile per cube face
+ o limit timeave output for hi-res integrations
+ checkpoint52i_post
+ o removed CPP_EEOPTIONS.h from verification/*/code
+ o updated the tiling for global_ocean_pressure
+ checkpoint52i_pre
+ o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
+   the old pkg/aim).
+ checkpoint52h_pre
+ o shortened offending lines in exch2_send_rx?.template
+ o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
+ o genmake2: add build & execute test for NetCDF code
+ o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
+   old grid files, moved CPP_EEMACROS.h to pkg/exch2
+ o added useSingleCPUIO flag to monitor.F and mon_out.F
+ o added temporary hack for sea-ice dynamics on the cube:
+   metric terms are ignored and it is assumed that
+   there is no sea-ice on cube faces 1, 2, 4, and 5.
+ checkpoint52f_post
+ o added exch2 cube routines to pkg/exch2
+ o modified hs94.cs-32x32x5 to use it
+ o added new grid files to hs94.cs-32x32x5
+ checkpoint52f_pre
+ checkpoint52e_post
+ o first attempt to solve vertical advection (momemtum & T,S) Implicitly
+   for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
+ o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
+   to work with implicit vertical advection and AB ;
+ o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
+ o update output (gad_calc_rhs.F changes affect truncation error) of exp:
+  front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
+ checkpoint52e_pre
+ o fix bug in impldiff when Nr=1 or Nr=2.
+ o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
+ o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
+ o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
+   ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
+ o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
+ o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
+ o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
+ checkpoint52d_post
+ o re-tiled many expts to allow comparison in multi-processor mode
+   - updated output accordingly
+   - changed hs94.128x64x5 to use intial T from file rather than use the
+     random number generator
+ o add infrastructure in model routines for fizhi and gridalt packages
  o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
  o changes to permit hi-res, cubed-sphere, configuration
    - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
-Line 17 
 o changes to permit hi-res, cubed-sphere
+Line 757 
 o changes to permit hi-res, cubed-sphere
  o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
     but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
     to conform to the common rule.
+ o check-in the first version of the coupler + interfaces for multi-components
+    set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
+    - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
+    - atmosphere: use pkg aim_v23 ; no sea-ice for now.
+    - ocean and atmos. share the same horizontal grid (no interpolation).
+    - exchanges between component and coupler is done in forward_step
+ o new verification experiment, cpl_aim+ocn:
+    coupled ocean - AIM atmosphere on cs32 grid.
  checkpoint52d_pre
  o surface flux time-av diagnostic modified for NLFS & RealFreshWater

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