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- add new S/R call (to CPL_IMPORT_CPLPARMS) after PACKAGES_BOOT and before PACKAGES_READPARMS to import coupling-exchange selectors from coupler;
- Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD: because ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
Merge OpenAD-specific code into main branch.
to refine CS-grid check, add logical flag: true if using Cubed-Sphere Exch with CS-corners inside the domain; create new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate globalArea and to set this new logical flag.
add many debug-print (to trace down where pkg/cal error msg comes from)
debugMode can now be used early on in initialisation process (read from parameter file "eedata" instead of previously from "data")
update comments (+ typo)
move MNC & MONITOR initialisation calls to INI_MODEL_IO
- add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) - move things around: ini_phiref.F --> set_ref_state.F (+ set anelastic factors) ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
move calls to packages_check & config_check after config_summary
clean-up multi-threaded problems (reported by debugger tcheck on ACES).
add few calls to BAR_CHECK to check multi-threading barrier synchronization
New S/R "SET_PARMS" (pieces of code from INI_PARMS): set parameters that might depend on the use of some pkgs; called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS NOTES: After leaving this S/R, parameters will not change anymore.
store geopotential profile (computed from tRef) at center & interface level in common block (note: for now, only available in atmospheric config)
call ini_model_io.F earlier
o make MNC variable initialization happen earlier
remove MINIMAL_TAVE_OUTPUT option.
use baseTime as time origin ; DIFF_BASE_MULTIPLE replaces DIFFERENT_MULTIPLE
Reduced output when CPP option MINIMAL_TAVE_OUTPUT is set to speed-up start-up time for large configurations.
update comments
o do package initialization earlier in the boot-up sequence - make MNC follow the package guidelines
o I am *sick* of moving these variables around. But Jean-Michel has all but threatened a hissy fit if they aren't removed from PARAMS.h. So now here they are *back* in MNC_PARAMS.h where they were just a few days ago.
o move useMNC and related runtime switches to PARAMS.h
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
Grid files were being written twice, the first time in the wrong place. Also fixed call tree in comments.
o remove the "Nphys"-related MNC grid type definitions from MNC
and place them in the fizhi package per the discussions
with AM and JMC
o the code compiles cleanly but has not been run
o the two files added to fizhi do not (yet) interact with any of the
other fizhi routines--no changes to existing fizhi code
o and Nrphys
Slight re-arrangment to satisfy JMC opinions on file names!
o ini_mnc_io.F has been split and replaced by
ini_model_io.F - responsible for setting units/flags for model-state i/o
write_grid.F - responsible for writing the grid variables to file
o the passing of flags to MDSIO has been moved from ini_parms to ini_model_io
o ini_depths and ini_masks_etc no longer do I/O which is now in write_grid
o in the MNC_CW_xxx_[R|W]_yyy calls, move the yyy=[R|D|I] part to
a string variable within the argument list so that the output
types are now run-time selectable
o fix a bug in the initialization order -- ini_mnc_io() must be called
after grid initialization
o per AJA & JMC request, re-write the MNC directory creation code: - directory names (strings) are passed, encoded using integers - everything is run-time optional with flags in "data.mnc" - tested and works but would benefit from some cleanup
o finish implementation of the separate unlimited-dim handling for the MNC_CW_*_R_* and MNC_CW_*_W_* functions
o move MNC init routines to initialise_fixed.F o flags in data.mnc for output of the pre-defined "grid types"
o edit all MNC subroutines so that myThid is the _last_ argument
o fix the calling sequence for MNC o add coordinates to the variables within the "state" file o reads still unfinished
o add MNC functionality to: - write all the per-tile grid information - mimic the functionality already in WRITE_STATE()
o fix indexing error in mnc_cw_readwrite.template o add function calls to initialise_fixed.F and write_state.F o add global attributes for w2/exch2
o getting closer to a usable MNC package through the "cw" layer: - numerous bug fixes - global attributes added - improved handling of the unlimited dimension - "cw" can handle variables with up to 7 dimensions - added list of pre-defined grid types
o working (though incomplete) version of the "wrapper":
- 149 pre-defined grids:
- all "meaningful" X,Y,Z,T combinations
- X,Y with or without halos
- Horiz: centered, U, V, and corner (vorticity) grids
- Vert: centered or interface
- just two function calls to write a variable using one of the
pre-defined grids
o tile numbering scheme for both cube and XY grids
o read, write, and append NetCDF files
o checks for (acceptable) re-definition of dims, grids, and vars
o numerous small bug fixes
o warning: the two mnc_model_* files are now broken/obsolete and
will soon be removed
o add hooks for MNC
o minor fixes to MNC error handling o remove unnecessary attribute(s) from grid definitions o write grid information
o demo generation of netCDF "grid file"
allow multi-components set-up with a coupler interface and using MPI. exchanges between component and coupler is done in forward_step
o add demo "call NETCDF_WRITEGRID( ... )"
call PACKAGES_CHECK after PACKAGES_INIT_FIXED : parameters that are set in GAD_INIT (called from PACKAGES_INIT_FIXED) are not compatible with some parameters and pkg options (e.g.: in GMREDI) therefore PACKAGES_CHECK needs to be called after.
o convert all the '#ifndef "EXCLUDE_MONITOR"'-isms to the now-standard
'#ifdef "ALLOW_MONITOR"' format as is done with all the other packages
- note that this also means removal of the monitor package from the
packages.conf list for the AD examples
o first check-in for the "branch-genmake2" merge
o verification suite as run on shelley (gcc 3.2.2):
Wed Oct 8 23:42:29 EDT 2003
T S U V
G D M c m s m s m s m s
E p a R g m m e . m m e . m m e . m m e .
N n k u 2 i a a d i a a d i a a d i a a d
2 d e n d n x n . n x n . n x n . n x n .
OPTFILE=NONE
Y Y Y Y 13 16 16 16 0 16 16 16 16 16 16 16 16 13 12 0 0 pass adjustment.128x64x1
Y Y Y Y 16 16 16 16 0 16 16 16 16 16 16 0 0 16 16 0 0 pass adjustment.cs-32x32x1
Y Y Y Y 16 16 16 16 0 16 16 16 16 16 16 22 0 16 16 22 0 pass adjust_nlfs.cs-32x32x1
Y Y Y Y -- 13 13 16 16 13 13 13 13 16 16 16 16 16 16 16 16 N/O advect_cs
Y Y Y Y -- 22 16 16 16 16 16 16 13 16 16 16 16 16 16 16 16 N/O advect_xy
Y Y Y Y -- 13 16 13 16 16 16 16 16 16 16 22 16 16 16 16 16 N/O advect_xz
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 pass aim.5l_cs
Y Y Y Y 14 16 16 16 16 16 16 16 16 13 16 16 16 16 16 13 16 pass aim.5l_Equatorial_Channel
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 13 16 16 13 13 16 pass aim.5l_LatLon
Y Y Y Y 13 16 16 16 16 16 16 16 16 16 13 12 13 13 16 13 16 pass exp0
Y Y Y Y 14 16 16 16 16 16 16 16 22 16 16 16 13 16 16 22 16 pass exp1
Y Y Y Y 13 13 16 13 16 16 16 16 16 13 13 16 16 13 13 13 13 pass exp2
Y Y Y Y 16 16 16 16 16 16 16 16 22 16 16 16 16 16 16 16 16 pass exp4
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 22 16 16 16 22 16 pass exp5
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 pass front_relax
Y Y Y Y 14 16 16 13 13 16 16 13 13 16 13 13 16 12 13 13 16 pass global_ocean.90x40x15
Y Y Y Y 10 16 16 13 13 16 13 16 16 13 13 13 13 16 16 13 16 FAIL global_ocean.cs32x15
Y Y Y Y 6 11 12 13 13 12 13 16 13 9 9 9 9 10 9 9 11 FAIL global_ocean_pressure
Y Y Y Y 14 16 16 13 16 16 16 13 13 13 13 13 16 12 16 13 16 pass global_with_exf
Y Y Y Y 14 16 16 16 16 16 16 16 16 11 13 22 13 16 16 9 16 pass hs94.128x64x5
Y Y Y Y 13 16 16 16 16 16 16 16 16 11 16 16 16 13 16 22 13 pass hs94.1x64x5
Y Y Y Y 14 16 16 16 16 16 16 16 16 13 16 13 13 16 16 22 13 pass hs94.cs-32x32x5
Y Y Y Y 10 10 16 13 13 16 16 16 22 16 13 13 13 13 13 22 13 FAIL ideal_2D_oce
Y Y Y Y 8 16 16 16 16 16 16 16 16 13 13 8 16 16 16 16 16 FAIL internal_wave
Y Y Y Y 14 16 16 16 16 16 16 16 16 13 13 22 13 13 13 22 16 pass inverted_barometer
Y Y Y Y 12 16 16 16 16 16 16 16 16 16 13 12 13 13 13 13 13 FAIL lab_sea
Y Y Y Y 11 16 16 16 16 16 16 16 13 13 13 12 13 16 13 12 13 FAIL natl_box
Y Y Y Y 16 16 16 16 16 16 16 16 22 16 16 16 16 16 16 16 16 pass plume_on_slope
Y Y Y Y 13 16 16 16 16 13 16 16 16 16 16 16 16 13 16 16 16 pass solid-body.cs-32x32x1
o included PACKAGES_CONFIG.h in all files where the ALLOW_${PKG_NAME}
defines are used
o added comments where IF ( use${PKG_NAME} ) statements will probably
be needed -- or need to be edited
Merging from c51
merging c49 and e27
move INI_LINEAR_PHSURF & INI_CORI calls after package initialization
call ZONAL_FILT_INIT only if useZONAL_FILT (avoid out-of-bounds index)
o Added new equation of state -> JMD95Z and JMD95P - EOS of Jackett and McDougall, 1995, JPO - moved all EOS parameters into EOS.h - new routines ini_eos.F, store_pressure.F o Added UNESCO EOS, but not recommended because it requires in-situ temperature (see JMD95) o Modified formatting for knudsen2.f in utils/knudsen2 and added unesco.f to be used with POLY3
Changes encapsulated by checkpoint43a-release1mods and chkpt44d_post
on the main trunk.
These are:
o added missing EXCLUDE_MONITOR flags
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
(incompatible typ in MIN/MAX expressions caused problems
on IBM SP3)
o in genmake added variable MAKEDEPEND
plus resetting for case SunOS
o added timer_stats.c routine for IBM SP3
o removed variables in dynamics
o real fresh water flux implemented with non-linear free-surface.
o few fix (mask in shap_s2, EmPmR in external_field_load,
USE_NATURAL_BCS in solve_for_P);
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
o merge of relevant stuff from the ecco-branch:
- genmake: removed $S64 overwrite for case SunOS
- pkg/exf: update and corrections for field swapping and obcs
- pkg/ecco: parameter lists for the_model_main, the_main_loop
harmonized between ECCO and MITgcm
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
updated checkpointing_lev... lists for obcs
- model/src: minor changes in forward_step, plot_field
added directive for divided adjoint in the_main_loop
- pkg/mdsio: added mdsio_gl_slice
o check parameters & config (chkpt44a_pre,post)
o OBC and NonLin_FrSurf.
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)
o update AIM experiments (NCEP input files)
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
o added some stuff for AD
These were merged with
cvs co -r release1 -P MITgcm
cd MITgcm
cvs update -kk
cvs update -j checkpoint43a-release1mods -j chkpt44d_post -d -P -kk
check parameters and modelf config.
Bringing comments up to data and formatting for document extraction.
compute Bo_surf(Po_ground,Tref) inside routine INI_LINEAR_PHISURF
Add to main branch of o CS atmos with AIM physics o Multi-threaded AIM physics for LatLon and CS tests o Tidied up monitor() output
Made sure each .F and .h file had the CVS keywords Header and Name at its start. Most had header but very few currently have Name, so lots of changes!
Merged changes from branch "branch-atmos-merge" into MAIN (checkpoint34) - substantial modifications to algorithm sequence (dynamics.F) - packaged OBCS, Shapiro filter, Zonal filter, Atmospheric Physics
Packaged OBCS (open boundary conditions) o source code now in pkg/obcs o controlled by namelist in data.obcs o includes Orlanski radiation condition (in same directory) o affects exp4 and internal_wave
Packaged zonal filter code: - Like the Shapiro code, this is quasi-packaged (it uses the main namelist to set it's 3 parameters) - FFTPACK is included in pkg/zonal_filt
Tentative implimentatin of OBCs.
Rearranged for packages routines; calls to packages_readparms initialise_fixed.F packages_init initialise_varia.F Tested for exp(0,2,4)
Introduced calls to package_init() and package_check() to begin process of packaging model.
Restructered the calling tree between THE_MODEL_MAIN()
and DYNAMICS(). Two calling levels have been inserted
to better split the "fixed" initialization phase from
the main time-loop for easier connectivity with the adjoint
infrastructure.
The calling tree now looks like:
the_model_main:
initialise_fixed()
the_main_loop()
the_main_loop:
initialise_varia()
do i=1,nIters
forward_step()
enddo
forward_step()
forward_step:
load_external_fields()
dynamics()
do_the_model_io()
solve_for_pressure()
do_gterm_blocking_exchanges()
write_checkpoint()
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