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fix a comment
- add missing useAUTODIFF and useSMOOTH switches.
- packages_boot.F :
- add useCTRL, useECCO to run time parameters list.
- default is true if ALLOW_AUTODIFF, false otherwise.
- IF (useECCO) useCAL = .TRUE.
- IF (useGrdchk) useCTRL = .TRUE.
- do_oceanic_phys.F, packages_check.F, packages_init_fixed.F,
packages_init_variables.F, the_main_loop.F : add useECCO switch
- forward_step.F, load_fields_driver.F, packages_check.F, packages_init_fixed.F,
packages_init_variables.F, the_model_main.F : add useCTRL switch
- initialise_varia.F : add ALLOW_CTRL bracket
document calling sequence
- add new pkg "kl10" for mixing due to internal wave breaking ( http://www.sciencedirect.com/science/article/pii/S1463500310000144 )
more standard LAND pkg interface: - call LAND_READPARMS from packages_readparms.F - add a call to LAND_CHECK in packages_check.F - rename LAND_INITIALISE to LAND_INIT_FIXED
add S/R OFFLINE_CHECK to print offline parameter summary and stop if loading a file that is not used;
add call to ATM_PHYS_CHECK
- add entry point for new pkg "atm_phys" (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008). - re-order sequence of calls within packages_readparms.F, packages_init_fixed.F and packages_write_pickup.F (but skip packages_init_variables.F because of TAF issues).
- add run-time switch usePROFILES.
allow to set useCAL in data.pkg
move pkg/ptracers summary and setup check into separated S/R.
- avoid multiple print to the same file (STDOUT) if multi-threads - call ALL_PROC_DIE before stopping
check if pkg/frazil is compiled before using it
Breaking three rules (at least): 1. No check-ins Friday after 5:30pm 2. No check-ins after two beers 3. Forgot the third one
o adding package bbl (Bottom Boundary Layer) description in MITgcm/pkg/bbl/bbl_description.tex example/test experiment in MITgcm_contrib/bbl
remove hack that I put 5 month ago (changing printDomain)
move call to S/R EXF_CHECK from exf_readparms.F to packages_check.F
A hack to prevent a 2nd printing of domain fields with default debugLevel.
move call to GAD_CHECK after other ${pkg}_check S/R calls
since it's now checking overlap minimum size.
add hooks for new packages OASIS, the package will follow (hooks exclude the seaice pkg for now)
stop if useEBM, useCheapAML, useFizhi, useGridAlt, useEMBED_FILES, is true but corresponding pacakge has not been compiled
Adding the shell of, and the hooks to, a new package that will be used to model melting and freezing of vertical glacier ice fronts: Modified Files: doc/tag-index model/inc/PARAMS.h model/src/do_oceanic_phys.F model/src/external_forcing.F model/src/packages_boot.F model/src/packages_check.F model/src/packages_init_fixed.F model/src/packages_init_variables.F model/src/packages_readparms.F Added Files: pkg/icefront/ICEFRONT.h pkg/icefront/ICEFRONT_OPTIONS.h pkg/icefront/icefront_check.F pkg/icefront/icefront_description.tex pkg/icefront/icefront_diagnostics_init.F pkg/icefront/icefront_init_fixed.F pkg/icefront/icefront_init_varia.F pkg/icefront/icefront_readparms.F pkg/icefront/icefront_tendency_apply.F pkg/icefront/icefront_thermodynamics.F
incorporate modif from Contrib/nesting_sannino/code_nest_merged
Added calls to layers package
Update.
new pkg "down_slope".
print a message to std-output (since calling order has changed)
added check, readparms, and more diagnostice to pkg/salt_plume also changed package flag from useSaltPlume to useSALT_PLUME
S/R PACKAGES_ERROR_MSG replaces PACKAGES_CHECK_ERROR : - add 1 argument (used in larger Nb of cases) and update the error message
First set of modifs for TAF-ing thsice.
move checking for un-compiled pkg, from CONFIG_CHECK to PACKAGES_CHECK.
2nd-Order Moment Advection Scheme (Prather, 1986): first check-in - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
add hooks for atm2d package
add the regrid package hooks
Adding template package MYPACKAGE to serve as reference. Does nothing.
Add runtime flag useGRDCHK.
add on/off flag for package OFFLINE
o add hooks for new package shelfice, painless
remove unused variables (reduces number of compiler warning)
use standard PACKAGE_CHECK_ERROR call for pkg MATRIX.
Add more checks for jpl ;o)
New package for controlling termination of the model based on the wall clock:
This is handy for those of us who keep losing 5000 cpuhours because the model
took 5 minutes longer than it did the day before.
To use:
In package.conf, add runclock
In data.pkg, add useRunClock=.TRUE.
Add data.runclock to read
&RUNCLOCK
RC_maxtime_hr=2,
RC_maxtime_mi=30,
RC_maxtime_sc=0,
&
The package also write the delta Wall Clock between each model step.
Who can explain a 30% slow down after 60 iterations? Who even knew about it?
Now you can find out lots of dark secrets about the EM EYE TEE GEE SEE EM...
re-arrange diagnostics pkg initialization: allow each package to extend the available diagnostics list
More untangling.
GCHEM: introduced a useGCHEM runtime flag
switch btw. 2-level and 3-level checkpointing
o prepare addition of new packages GGL90 and OPPS - new parameters useGGL90 and useOPPS - include call to the new routines at the (hopefully) right places
o add calls for two new packages
- pp81 (Packanowski and Philander, 1981), Richardson number and
stratification dependent mixing
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
use the new thermodynamic Sea-Ice pkg: thSIce
o updated and tested version of the cd_code package o almost all of the cd_code functionality has been moved into the package but some cleanups (read/write checkpoints) remain
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
o bug fix in find_alpha.F for MDJWF:
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
change rho -> rho-rhoConst
- replace call find_rho to find_rhonum
o added the [#include "AD_CONFIG.h"] statement to all files that need it for adjoint/tl #defines o re-worked the build logic in genmake2 to support AD_CONFIG.h o removed tools/genmake since it no longer works
stop if trying to use pkg BULK_FORCE or THERM_SEAICE that are not compiled
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
o somewhat cleaned package initialisation sequence for ctrl/ cost/ ecco/
Preparing next round of sync MAIN vs. ecco-branch and adjoint of next checkpoint. o somewhat cleaned package initialisation sequence for ctrl/ cost/ ecco/
add new package "land" ; move CALL AIM_INITIALISE from packages_readparms.F to packages_init_fixed.F
release1_p14 o Added interpolation routine pkg/exf/new_interp.F for on-the-fly interpolation. Enable with USE_EXF_INTERPOLATION and specify input grids in data.exf o Added direct pressure solver pkg/solver. See pkg/solver/README.directSolver for instructions.
merging c49 and e27
Merging from release1_p12: o Modifications for using pkg/exf with pkg/seaice - improved description of the various forcing configurations - added basic radiation bulk formulae to pkg/exf - units/sign fix for evap computation in exf_getffields.F - updated verification/global_with_exf/results/output.txt o Added pkg/sbo for computing IERS Special Bureau for the Oceans (SBO) core products, including oceanic mass, center-of-mass, angular, and bottom pressure (see pkg/sbo/README.sbo). o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F to avoid negative values in shallow regions. - updated verification/natl_box/results/output.txt - updated verification/lab_sea/results/output.txt o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F o Added useSingleCpuIO option (see PARAMS.h). o Updated useSingleCpuIO option in mdsio_writefield.F to work with multi-field files, e.g., for single-file pickup. o pkg/seaice: - bug fix in growth.F: QNET for no shortwave case - added HeffFile for specifying initial sea-ice thickness - changed SEAICE_EXTERNAL_FLUXES wind stress implementation o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, kpp_transport_t.F, forward_step.F, and the_main_loop.F o pkg/seaice: - adjoint-friendly modifications - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
o Merging pkg/exf and pkg/seaice from cvs tag ecco_ice2
02/12/03 Added pkg/seaice and modified pkg/exf as per release1_p12_pre
o added pkg/sbo for computing IERS Special Bureau for the Oceans (SBO) core products, including oceanic mass, center-of-mass, angular, and bottom pressure. Modified Files: doc/tag-index model/inc/CPP_OPTIONS.h model/inc/PARAMS.h model/src/do_the_model_io.F model/src/packages_boot.F model/src/packages_check.F model/src/packages_readparms.F model/src/the_model_main.F
Merging from release1_p8 branch: Adding package parameters and hooks for new seaice package.
o Adding package parameters and hooks to MITgcm for new seaice package. o Adjusting KPP package for use with seaice package.
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
Added PTRACERS package
This allows an arbitrary number of passive tracers to be integrated
forward simultaneously with the dynamicaly model.
+ Implemented so far:
- basic forward algorithm (time-stepping, advection, diffusion, convection)
- I/O and checkpointing
- GM/Redi *but* using the GM/Redi coefficient of Salt
+ Not implemented so far:
- KPP
- OBCS
+ No specific example supplied (yet) but global_ocean.90x40x15 has the
necessary data.ptracer file. Simply use -enable=ptracers and uncomment
line in data.pkg. PTRACER01 then reproduces Salt exactly.
+ This package is disabled by default since it increases storage.
check parameters and modelf config.
Bringing comments up to data and formatting for document extraction.
Added package "flt". o pkg/flt o verification/flt_example o visualization of trajectories supplied o works but output not available to testscript
AIM (Atmosphere Intermediate Physics) define as a standard package
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
Tidying up comments and heads in package_NNN routines
Rescaling of forcing fields done immediately after reading fields.
Bug fix (CVS header).
Removed flag kppPackageIsOn.
Package structure rearranged to comply with standard. Includes useKPP, useGMRedi. Tested for exp(0,2,4).
Two routines to configure and check depenances between packages. The details of how this should work is still in flux.
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