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new options 1) to account for true vertical distance (including hFac)
in vertical viscous flux and diffusive flux ;
2) to increase vertical mixing near surface and/or bottom where partial
cell is too thin ;
add run-time param to allow to turn off tidal forcing.
add new parameter "selectImplicitDrag" for implicit treatment of bottom drag
add a STOP if trying to run nonHydrostatic with any implicit factor = 0
rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since it's also used with pkg/atm_phys) and add few more parameters (but still inactive, src code yet to come)
allow to use Vector-Invariant form in deep atmos and anelastic formulation
improve report of error/warning associated with CD-scheme
remove the stop for addFrictionHeating with not synchronous time-stepping
add run-time parameters to select bottom-drag options
stop if trying to use geothermalFile with corresponding code not compiled
stop if staggerTimeStep and implicitIntGravWave
- Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage which are specific to TAF/TAMC).
check size of overlap for the unlikely case useSmag3D & useCDscheme
add some check & stop in case pressure is not computed.
add run-time parameters for isotropic 3-D Smagorinsky (Smag3D)
add a warning if select_rStar=2 with nonlinFreeSurf <> 4 (not consistent to account for the slope of the coordinate when ignoring the variations of level-thickness in PhiHyd calculation)
add run-time parameter to select CG2D solver minimum-residual solution (in case of a poor convergence)
- allow to read-in time-constant addMass field from file (addMassFile); - add support to account for frictional heating (run-time switch & CPP option).
- add warning if usingCurvilinearGrid and momAdvection in flux-form (missing metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form. - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if useCDscheme and useCubedSphereExchange).
remove commented out stop (implicitDiffusion & ALLOW_DEPTH_CONTROL)
stop if select_rStar > 0 and Linear FreeSurf (nonlinFreeSurf =< 0)
- introduce ALLOW_BALANCE_RELAX which allow the removal of the global mean of relaxation terms by setting balanceThetaClimRelax and balanceSaltClimRelax - disable balanceEmPmR and balanceQnet in the case when useSeaice. This case is now treated appropriately in seaice_growth.F - do_oceanic_physics.F : include EXF_OPTIONS.h to avoid recomputations in the ALLOW_ECCO_EVOLUTION case.
packages_boot.F switch usePROFILES to fals if netcdf is missing (preliminary fix) config_check.F rotateGrid vs profiles is now tested in profiles_init_fixed
- add run-time switch usePROFILES.
Re-enable a config.
disable Overlap-size checking if disconnect tiles
collect the errors and stop cleanly at the end by calling ALL_PROC_DIE
- add a check for OLx>sNx and OLy>sNy, only allowed with EXCH1 and if Nx=1 or Ny=1
disable implicitDiffusion when compiling with ALLOW_DEPTH_CONTROL
stop if trying to use OBCS with ALLOW_DEPTH_CONTROL
- check for valid value of "selectCoriMap" parameter.
first check-in of sigma (and hybrid-sigma) coordinate code
Adjoint related modifications -- allowing the use of implicit vertical advection in adjoint model.
avoid unbalanced quote (single or double) in commented line
update non-hydrostatic related parameter checking ; add warning if using implicitViscosity & non-hydrostatic.
forgot to include output of new parameter useSRCGSolver and a test
Allow CD-scheme on cubed-sphere topology for now (testing) assuming that cube corners are on land
- stop if trying to use 1 seaice pkg with allowFreezing=T - some limitations of AddFluid option.
print a message to std-output (since calling order has changed)
set flags for Dynamically Active Tracers
clarify highOrderVorticity & upwindVorticity (now exclusive); mom_vi_u/v_coriolis_c4.F now also deal with upwindVorticity ;
add the computation of the cos/sin(angle between model north and geographical north). I put the new routine into rotate_spherical_polar_grid.F, and so far the only place where it is called is from ini_spherical_polar_grid.F. But I guess it could also be called elsewhere (whenever AngleCosN and AngleSinN are not read or incorrect[=0]).
add a STOP if use3dcoriolis is used together with rotateGrid (non-zero Euler angles) until I have implemented the computation of angleCosC and angleSinC, thanks to JMC for spotting this.
add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For usingSphericalGrid, this allows to define the rotated grid coordinates via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the geographical coordinates according to the inverse of the rotation defined by the Euler angles, so that Coriolis parameter and online-interpolation by exf works with the geographical coordinates on XC/YC/XG/YG. The three Euler angles PhiEuler, ThetaEuler, and PsiEuler define the rotation about the original z-axis (of an sphere centered cartesian grid), the new x-axis, and the new z-axis, respectively. Naturally, this feature does not work with all packages, so the some combinations are prohibited in config_summary (flt, flt_zonal, ecco, profiles), because there the coordinates are assumed to be regular spherical grid coordinates.
If diffKrFile is set, then we should make sure the corresponing code is being compiled.
move checking for un-compiled pkg, from CONFIG_CHECK to PACKAGES_CHECK.
initial check in: correction of tracer source/sink due to Linear Free surface
deep-Atmosphere & Anelastic limitations (implementation not finished)
Pass the variable viscosities on to calc_gw.
remove warning after fixing highOrderVorticity on CS-grid.
downgraded to a warning: 'CONFIG_CHECK: highOrderVorticity Scheme does not work on CubedSphere grid'
stop when mom_fluxform/mom_vecinv are not compiled but monStepping=T
move calendarDumps from "data" to "data.cal" and clean-up the code with a simple call to pkg/cal S/R: CAL_TIME2WRITE (the former piece of code started to spread over newly checked-in S/R) add useEXF & useCAL flags (for now, set in hard-coded way)
change forcing_In_AB to affects both T,S forcing and Momentum forcing (allow to differentiate between forcing components using new integer flags: momForcingOutAB=1/0 & tracForcingOutAB=1/0) and add new flag to put Dissipation tendency out of Adams-Bashforth.
move tauThetaClimRelax3Dim & tauSaltClimRelax3Dim from common block to "retired parameter" list (in ini_parms.F)
add internal parameter "use3Dsolver"
o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful if bulk formulae are used in long integration (especially EmPmR). Turn on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01 if balancePrintMean, the imbalance that is substracted is printed to STDOUT.
o Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec o Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) o Thanks to Tom Haine for testing!
Fixed stdout format bug for tauCD
stop if using Leith viscosity with divergence part and Olx,Oly < 3
STOP when trying to use highOrderVorticity scheme on CS-grid: Pb in defining the 4 vorticity points stencil next to a face corner.
re-STOP.
Suppressed STOP for #undef ALLOW_GENERIC_ADVDIFF because: You CAN run a seaice-only (or bulk formula-only) config. without using generic_advdiff.
o fix Samar's sloppiness: all code needs to be <73 characters long
Added configuration check for pkg/matrix
add parameters for AB-3 ; remove readPickupWithTracer & writePickupWithTracer
use baseTime as time origin ; DIFF_BASE_MULTIPLE replaces DIFFERENT_MULTIPLE
o parameter calendarDumps: when set, approximate months (30-31 days) and years (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar months and years. Requires pkg/cal.
implement Implicit Vertical advection for pTracers
depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
update: size of overlap when using biharmonic viscosity
o do package initialization earlier in the boot-up sequence - make MNC follow the package guidelines
consistent with recent modifications of the code (post c54)
Double check that CD scheme is not turned inconsistent with configuration.
add run-time parameters for implicit vertical advection.
additional changes for FREEZE: - new S/R FREEZE_SURFACE only apllied to surface level. - add run-time parameter "useOldFreezing" to use the old version "FREEZE"
o add a "cd_code" package and update all the verification tests so that they use the new package instead of "INCLUDE_CD_CODE"
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
new flag "useCDscheme" (default=F);
merging c49 and e27
dynamics: change definition of computational domain & adapt mom_fluxform accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
can use OBC pkg with r* Coordinate (Orlanski Rad. BC not yet implemented)
improve checking compatible options with r*
first step in r* implementation: add param "select_rStar"
* allows a more accurate definition of Ro_Surf (selectFindRoSurf=1) when using P-coordinate; only implemented for atmospheric config.
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
add parameters to use real fresh water flux (replace USE_NATURALBCS option) with non-linear free-surface.
updated according to recent development (OBC+NLFS).
check parameters and modelf config.
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