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switch reading of debugMode from S/R INI_PARMS (parameter file "data") to S/R EESET_PARMS (parameter file "eedata").
- fix startTime setting when baseTime<>0 & nIter0=0 are specified ; - initialise startTime & nIter0 with unlikely values: allows to set one from the other without ambiguity.
Add allowInteriorFreezing option to check for water below freezing point at depth and bring the negative heat anomaly to the surface level. Modified Files: doc/tag-index, model/inc/PARAMS.h, model/src/do_oceanic_phys.F, ini_parms.F, set_defaults.F, thermodynamics.F Added File: model/src/freeze_interior.F
add new param to scale curvilinear grid distance and area when using a different rSphere.
- call standard S/R OPEN_COPY_DATA_FILE (replace local copy to scratch file) - remove calls to S/R modeldata_example (out of date for very long)
initialise new parameter adTapeDir
remove "if debugLevel=2 => debugMode" to differentiate (again) between debugMode & debugLevel=2 (but keep "debugMode => debugLevel=2"): => allows to print solver convergence without all the sequence of call msgs.
- remove useConstantF, useBetaPlaneF, useSphereF and replace them with integer parameter "selectCoriMap" (=0,1,2). - add parameter "fPrime" for constant second Coriolis coeff (default=0).
first check-in of sigma (and hybrid-sigma) coordinate code
Adding parameters to specify temperature and salinity of addMass array separately from temp_EvPrRn and salt_EvPrRn
surface relaxation -- separating data and data.exf options
ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity => addition to the viscosity field as computed by others schemes
add parameter for Non-Hydrostatic free-surface option (in development)
explicit time-stepping for part of Non-Hydrostatic pressure gradient
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
epsAB_CD (CD-code AB parameter): default is set to abEps
add run-time parameters to check and mask initial T & S
- allow to specify a vertical profile of vertical viscosity - more accurate check of vertical profile setting
From Matt: each processor open different scratch files (for TARGET_BGL or TARGET_CRAYXT) as an alternative to opening status 'SCRATCH'.
remove backward compatibility for thetaMin,phiMin (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
rename thetaMin,phiMin -> xgOrigin,ygOrigin (temporary backward compatibility in ini_parms.F, until next checkpoint)
Add smoothing parameter for mixed-layer diagnostics
dRhoSmall (for mixed-layer diagnostics) now a run-time paramater
disentangle parameters: retire shelfIceFile in data/PARM05 and substitute with SHELFICEtopoFile in data.shelfice, update data files in verification experiment
initialisation and option setting for mass source/sink of fluid
add atm_Po to 1rst namelist.
Put eddyPsi back now that PARAMS is there!!!! :-)
Changing back Gaels mod - since they don't compile due to missing PARAMS.h mods
o bridging the gap between eddy stress and GM.
-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
along with a change in CPP option (now ALLOW_EDDYPSI).
-> when using GM w/ GM_AdvForm:
The total eddy streamfunction (Psi = eddyPsi + K x Slope)
is applied either in the tracer Eq. or in momentum Eq.
depending on data.gmredi (intro. GM_InMomAsStress).
-> ALLOW_EDDYPSI_CONTROL for estimation purpose.
The key modifications are in model/src/taueddy_external_forcing.F
pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
Added TARGET_CRAYXT for I/O from/to SCRATCH
remove from PARAMS.h: doTr1ClimRelax, tauTr1ClimRelax, lambdaTr1ClimRelax
clarify highOrderVorticity & upwindVorticity (now exclusive); mom_vi_u/v_coriolis_c4.F now also deal with upwindVorticity ;
fix previous check-in (put back SadournyCoriolis in namelist)
new parameter "selectVortScheme" to select which scheme to use for vorticty-term (in Vector Inv.); remove "SadournyCoriolis" flag.
add a flag writePickupAtEnd (default=true) to be able to suppress writing a pickup at the last timestep
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.
add "monitorSelect" to reduce number of monitored fields (default unchanged)
add new run-time parameter, "pickupStrictlyMatch": when reading pickup, check and stop if pickup-files do not stricly match; default=T.
move (and fix) extension of mdsioLocalDir (with Proc.# appended) from ini_parms.F to ini_model_io.F (better place)
there is still some old debug code controlled by debugMode flag: added
IF ( debugLevel .GE. debLevB ) debugMode = .TRUE.
which is needed until debugMode is completely replaced
finishing EmPmR unit changes: replace convertEmP2rUnit by mass2rUnit
Change EmPmR units: from m/s to kg/m2/s
use mass2rUnit & rUnit2mass as units conversion factor (for surface forcing) and remove horiVertRatio (& recip_horiVertRatio);
add temperaure criteria for Mixed-layer diagnostic
Modify mdsioLocalDir for MPI.
latitudinal dependence of Bryan and Lewis, 1979 fixed and reworked as per JM suggestions
o Added capability for latitudinal dependence of Bryan and Lewis, 1979 vertical diffusivity, similar to that in MOM4; vertical diffusivity is specified using diffKrBL79* diffKrBLEQ* and KbryanLewisLatTransition
Modified capability for 3D specification of background vertical diffusion
coefficient as per JM requests. 3D diffusion is now specified by
(i) #define ALLOW_3D_DIFFKR in CPP_OPTIONS.h and
(ii) specifying file diffKrFile in runtime "data" file that contains
the 3D vertical diffusivity coefficients.
o Added capability for 3D specification of vertical diffusion coefficient.
This is done by specifying files diffKr3dSfile and diffKr3dTfile that
contain the 3D vertical diffusivity coefficients.
Modified files: doc/tag-index model/inc/PARAMS.h
model/src/calc_3d_diffusivity.F, calc_diffusivity.F, ini_mixing.F,
ini_parms.F, and set_defaults.F
Added missing file verification/tutorial_global_oce_latlon/run/.cvsignore
usePickupBeforeC35 no longer supported ; remove this option.
initial check in: correction of tracer source/sink due to Linear Free surface
add "deepAtmosphere" flag
allow to read vertical arrays: tRef,sRef,delR & delRc from (binary) file ; + start adding anelastic-code parameters
add useSphereF, useBetaPlaneF and use3dCoriolis to namelist PARAM01 ; change default of useSphereF to T (if set to F => read Coriolis from files);
if deltaT=0 (unset), set it to deltaTClock (previously, when only deltaTClock was set >0, all deltaT were left unset (=0) and was getting NaNs)
Modifications for bottom topography control o replace hFacC by _hFacC at various places o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL o add non-self-adjoint cg2d_nsa o update autodiff support routines o re-initialise hfac after ctrl_depth_ini o works for 5x5 box, doesnt work for global_ocean.90x40x15
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)
remove "usingSphericalPolarMterms" that was not always initialized, and with no equivalent for other grids (e.g.: CylindricalGrid).
fix CylindricalGrid metricTerms (lost with set_parms check-in)
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.
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)
set 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 add hooks for new package shelfice, painless
Adding unfinished 3-dim relaxation code.
add new parameter (implicitIntGravWave) even if the code is not yet ready; (hard to maintain a different version of theses files during testing phase)
new parameter: doAB_onGtGs to (always) apply Adams.Bashforth on tracer tendencies (rather than on tracers <- coming soon).
new parameter: sideDragFactor to enable half-slip-side BC.
change default value of tRef (uniform, meaningfull value for ocean & atmos) and initialize sRef (was missing, as Martin mentioned).
add KEscheme selector.
Allow use of old scheme for viscous lengths with useAreaViscLength=.TRUE. Default: .FALSE.
Adding clean version of mom_calc_visc and viscAhRemax and viscA4Remax params.
put back viscAstrain & viscAtension in namelist01, but as retired parameters
Parameter and config_summary changes for mom_calc_visc.F
"dumpInitAndLast" replaces "nodumps" (& partly MINIMAL_TAVE_OUTPUT)
Add new flag in PARM03 namelist called nodumps - true to turn off all dumps, indep of freq
Changed SCRATCH files to named files to avoid mysterious runtime error on Blue Gene/L. Linux/PPC64 also complains at runtime but completes execution. Introduce TARGET_BGL to avoid scraping scratch files.
reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F (ini_parms.F is shorter ; allows later to read from netcdf files)
do not need to set implicitFreeSurface=F to use rigidLid.
although horizGridFile is for 2.D type input, better in namelist 4 than 5.
add "horizGridFile" for curvilinear-grid input file.
rkSign & usingPCoords replace -rkFac & groundAtK1 (<- removed)
add flag for momentum vertical advection (upwindShear)
Added run-time parameters nh_Am2 which scales the non-hydrostatic terms and changes internal scales (i.e. allows convection at different Rayleigh numbers).
added useConstantF to PARM01
add parameters for AB-3 ; remove readPickupWithTracer & writePickupWithTracer
Added flag useAnisotropicViscAGridMax to turn on and off (off by default) Alistair's latest length scale computation for horizontal viscosity. It is used only for maximum viscosity calculations. Alistair recommends a value of viscA*GridMax=.25
Make lambda[Theta,Salt]ClimRelax spatially varying.
add baseTime parameter = model base time (time origin)
Added Harmonic Smagorinsky Viscosity. May not work with strongly anisotropic grids.
Expanded Leith viscosity to follow Ahgridmin and Ahgridmax, and select between 'full' and approximate form. Also added leith-like viscosity that is proportional to grad(div.v_h).
Adding eddy stress controls a la Ferreira et al.
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.
Add flag(s) inAdExact to help D. grow seaice in the Sahara.
initialise useConstantF, useBetaPlaneF & useSphereF in set_defaults.F
added ability to set inner and outer rotating tank temperatures
add saltFlux(+File) forcing capability with periodicExternalForcing
debugMode & debugLevel: go back to what it was before. version 1.137 (ini_parms.F) & 1.77 (set_defaults.F)
hack to allow deblevelzero, until debugmode flag is removed
add horizontal bi-harmonic viscosity of vertical viscosity - used only in non-hydrostatic code - add a parameter viscA4W that defaults to viscA4 if unset, otherwise usefull if you want to use the Leith viscosity for horizontal velocity an biharmonic viscosity in the vertical.
depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
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
Allow case externForcingCycle = externForcingPeriod
remove some obsolete params.
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
add separated viscosity for Divergence and Vorticity
set flags: fluidIsAir, fluidIsWater, usingPCoords, usingZCoords according to buoyancyRelation
o remove all the *_ioinc flags and replace them with the single global outputTypesInclusive flag
allow to set a vertical profile of vertical diffusivity for T & S
o move *_ioinc variables
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 non-hydrostatic code:
- add new parameter viscAhW, replaces viscAh in calc_gw, defaults to
viscAh. Useful when viscAh=0 in non-hydrostatic simulations
o finish MNC_CW_ADD_VATTR_* cleanup and add 'IF (useMNC) THEN' around
all current sections of MNC code
- the following tests compiled & ran with these fixes:
exp0 global_ocean.90x40x15 aim.5l_cs dic_example hs94.cs-32x32x5
add a print before reading a namelist
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) (adjoint stuff still has some tr1 names, but all use ptracer arrays)
o fix name error: "monitor_mdsio" --> "monitor_stdio" - add "monitor_grid" output for ini_cori.F,ini_parms.F
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 make the mon_iotype setup in monitor the poster child for MNC/MDSIO flag handling
o add header info to both the NetCDF output and the model stdout - requested by Steph
change Qnet to always be the net heat flux, (+upward).
Only update cg2d preconditioner every "cg2dPreCondFreq" iter. (default=1)
re-write staggerTimeStep: change pickup file ; (flag usePickupBeforeC54 to start from old pickup)
T & S: separate Vert.Advec.Scheme from horizontal Advec.Scheme
merged cylindrical coord configuration and rotating_tank exp
Added new flag to fix aim.5l_cs - useJamartMomAdv distingiushes the non-linear terms from linear Coriolis when using Jamart wet points
Added vertical diffusivity profile (T/S) due to Bryan and Lewis, 1979. New parameters: diffKrBL79surf - surface diffusivity diffKrBL79deep - deep diffusivity diffKrBL79Ho - turning depth for arctan function diffKrBL79scl - depth scale for arctan function This diffusivity is added to all other diffusivities. The defaults are set so as to give zero diffusivity.
Added Sadourny discretization of Coriolis in V.I. mode - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h - re-enabled use of omega3 in mom_vecinv.F
Added variable viscosity for the vector invariant equations based on Leith, 1968, Phys. Fluids (10) 1409-1416 - the use of the variable viscosty in the no-slip boundary conditions has not been implemented (but should be) - new parameters viscC2leith and viscC4leith are non-dimensional - I decided to modulate the variable viscosuty with the same viscAhMax and viscA4max; ideally we should have another maximum based on dx^2/dt etc.
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
adding parameter adjDumpFreq
Added compile time flag to set namelist terminator __everywhere__ . This allows lf95 to work with appropriate optfile. Tested on faulks, but this could break on other compilers platforms.
Added new grid-dependent viscosity and biharmonic dissipation terms: o new parameters = viscAhGrid, viscAhMax, viscA4Grid and viscA4Max o new stuff in mom_vi_hdissip.F which is bound to break the adjoint!!!! This has been "verified" against old experiments **BUT** there is a known issue involving exch2 - results are dependent on using exch1 or exch2 and we don't know which is right (if either).
Header was lost; put it back.
add run-time parameters for implicit vertical advection.
use CartesianGrid as default only if no horizontal grid is specified
change convertEmP2rUnit to rhoConstFresh/rhoConst for ocean in Z. (unchanged for ocean-P) and change the default value of rhoConstFresh to rhoConst.
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"
delp,delz viscAz,viscAp ... are only local variables (and no longer in a common bloc).
* reverse gravitySign back to "logical" value: +1 when R increases downward * add a parameter to apply surface relaxation only in a latitude band
specific volume (atmospheric geopotential) includes water vapor effect
o introducing integer flag debugLevel o introducing pathname variable mdsioLocalDir for mdsio
New variable in PARM03: pickupSuff is a string that can be set to indicate the suffix on pickup files. This allows us to avoid renaming the temporary pickup files.
new flag "useCDscheme" (default=F);
deal with zero rotation when setting omega & rotationPeriod
set the Earth rotation either directly (omega) or from the rotation period
o fix restart and overlap Pb when using Z-coord and EOS funct. of P
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
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.
Added new routine quasihydrostaticterms() and flag "quasihydrostatic" which is false by default and enables QH mode. Exlcusive with nonhydrostatic flag.
Added new flag "useNHMTerms" which controls appearance of non-hydrostatic metric
terms:
- defaults to TRUE but is set to false when metricTerms is false.
This means no output is currently affected since N-H metric terms have
always been associated with spherical metric terms to date.
- note that N-H metric terms are both incomplete and disctetized incorrectly
and are not fixed as yet.
- turning off useNHMTerms affects these experiments
adjustment.128x64x1, aim.5l_Equatorial_Channel, exp1, exp2, global_ocean.90x40x1,
hs94.128x64x5, hs94.1x64x5, natl_box
which means they all have non-hydrostatic metric terms in them.
Removed second appearance of gravitySign in a namelist.
* update timeave pkg for wVel diagnostic ; put convertEmP2rUnit in PARAMS.h
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
and the dynamical equations are all divided by rhoConst
o introduced new parameter rhoConstFresh, a reference density of fresh
water, to remove the fresh water flux's dependence on rhoNil. The default
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
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.
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
Added pressure loading term and experiment based on Wunsch and Stammer (1997) o new field in FFIELDS.h, etc... o new cpp flag ATMOSPHERIC_LOADING o Changed hFacC to _hFacC in calc_phi_hyd.F o Added SHORTWAVE_HEATING to some files for consistency
Added new parameter: deltaTfreesurf Previously, the free-surface equation was intergrated forward synchronously with the momentum equations. It is more consistent to use the tracer time-step. This increases the number of iterations required but strengthens the damping. We *SHOULD* make the default time-step equal to the tracer time-step. However, we don't for backward compatibility. At some point in the future we need to change the default behaviour. It turns out that the reason for the "reduced stability" encountered in large-scale runs seems to be related to excess variability in the free surface which in turn happens when the waves aren't damped. Using a longer time-step fixes this.
Add new flags: * T,S forcing outside Adams-Bashforh * temp,salt Advection and Forcing (turn on/off) * for each tracer: internal flag for multiDimAdvection & A-B
o define cell Center vertical spacing and then put Interface at the middle
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.
add parameters to use real fresh water flux (replace USE_NATURALBCS option) with non-linear free-surface.
Added trap for retired parameters zonal_filt_lat appearing in "data". Parameter zonal_filt_lat is now set in namelist in file data.zonfilt
zonal_filt parameters are now in a specific data file (data.zonfilt)
Added new parm to PARM01
easier to find which NAMELIST causes problem when reading file "data".
Added energy conserving discretization for Coriolis term. o don't panic - the default is off so you can continue not conserving energy just like you always have... o new flag: useEnergyConservingCoriolis defaults to .F.
Bringing comments up to data and formatting for document extraction.
Added multi-dimensional form of advection o available only for single step schemes (ie. can't be used with ABII) o stable for max(cfl_u,cfl_v,cfl_w)<=1 (without cfl_u+cfl_v+cfl_w <=1) o selected using multiDimAdvection=.T. (default) o had to hack some existing routines to work on local arrays
Added tension/strain form of dissipation. * NOT working on cubed sphere.
Added method for dumping intermediate local arrays: mdsio_writetile - same as mdsio_writefield except works from inside bi,bj loop mdsio_writelocal - same as mdsio_writetile except works for local arrays write_local_r? - higher-level wrapper for mdsio_writelocal Controlled by diagFreq. Defaults to zero (ie. no dumps) Example given at end of mom_vecinv.F that dumps some local arrays.
Added run-time control of vector-invariant/flux-form momentum eqns.
Added run-time control of advection schemes.
- advection scheme determines method of forward integration.
- unfortunately, we have to use integers in "data" since ENUM_CENTERED_2ND
doesn't mean anything to fortran
- defaults are centered second
- output differs due to these mods! This is due to the g77 optimization.
I have tested that using -ffloat-store, these mods do not affect
the output so am confident about changes.
T S U V
C D M c m s m s m s m s
n p a R g m m e . m m e . m m e . m m e .
f n k u 2 i a a d i a a d i a a d i a a d
g d e n d n x n . n x n . n x n . n x n .
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 22 16 16 pass adjustment.128x64x1
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 pass adjustment.cs-32x32x1
Y Y N N -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- N/O aim.5l_Equatorial_Channel
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 pass aim.5l_LatLon
Y Y N N -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- N/O aim.5l_zon-ave
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 22 16 pass exp0
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 22 16 pass exp1
Y Y Y Y 13 16 16 16 16 16 16 16 13 16 13 13 13 13 13 13 16 pass exp2
Y Y Y Y 12 16 16 13 16 16 16 16 16 13 16 16 16 16 13 13 16 FAIL 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 16 16 16 16 16 16 16 16 16 16 16 22 16 16 16 11 16 pass hs94.128x64x5
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 22 16 pass hs94.1x64x5
Y Y Y Y 14 16 16 16 16 16 16 16 16 16 13 16 16 16 16 16 13 pass hs94.cs-32x32x5
Y Y Y Y 16 16 16 22 16 16 16 16 16 16 16 22 16 16 16 16 16 pass internal_wave
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 pass natl_box
Y Y Y Y 16 16 16 16 16 13 16 13 16 16 16 16 16 16 16 16 16 pass solid-body.cs-32x32x1
o Added grdchk package handling o Added passive tracer handling
add options related to Geopotential computation and Orography definition: read orography (in m) from file ; compute Bo_surf(P_ground); select the form of geopotential integration;
Changed default behaviour of monitorFreq.
Added a debugMode that uses same statistics stuff as monitor.F Can be disabled with -DEXCLUDE_DEBUGMODE. Turn on at run-time with debugMode=.true. Default is enabled but off.
Adding skeleton "monitor" routines. The default is to do it every time-step. monitorFreq=0 disables.
Merge from branch pre38: o essential mods for cubed sphere o debugged atmosphere, dynamcis + physics (aim) o new packages (mom_vecinv, mom_fluxform, ...)
See doc/tag-index and doc/notes_c37_adj.txt Preparation for stand-alone autodifferentiability.
Modifications and additions to enable automatic differentiation. Detailed info's in doc/notes_c37_adj.txt
remove "include CG2D.h" ; make the running flag "metricTerms" active
add 2 parameters to define a Crank-Nickelson barotropic time-stepping
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
Added surfQswfile to namelist (shortwave heating).
Removed all mention of KPP and GM/Redi parameters from ini_parms(). Initialization of these parameters is done by kpp_init() and gmredi_init().
Corrected specification of hFacMinDr. If hFacMinDp or hFacMinDz were used, it used to do something strange...
Added separate initialization routine for pSurf (otherwise known as cg2d_x). This allows easy initial value problem in free surface height (read from file in pSurfInitFile) and helps split up the initializations of "fixed" and "variable" arrays.
Various updates for OBCs and Non-hydrostatic routines. o OBCs now fits into time-stepping properly o div.G has been moved to solve_for_pressure()
Corrected interaction between OBCs and algorithm. The positioning of set_obcs() within the time-stepping sequence is crucial for stable open-boundaries. Forcing the boundaries with time-dependent flow previously led to horrible results...
Added IVDC (Implicit Vertical Diffusion Convection). Also facilitated a "convection counter" that is output through "diags".
Added a parameter "implicitViscosity" to separately control implicit viscosity and diffusion.
Added COS(latitude)^cosPower dependence to viscosity terms. New parameter "cosPower" defaults to 0.0 which removes latitudinal dependence.
Modifications/additions for KPP mixing scheme. Instigated by Dimitri.
Implemented new I/O package (mdsio.F). This package does parallel
I/O in much the same way as dfile.F used to except it uses "direct
access" rather than (f77) unformatted sequential access.
Problems with dfile.F package included:
o unnecessary memory use (each process had two global sized buffers)
o inability to read the files it had written without post-processing
o "tiled" files were tiled by process/thread rather than actual tiles
o created huge numbers of files with no alternatives
Features of the mdsio.F package:
o direct-access binary writes
o no excessive memory use
o ability to read/write from multiple record files
o "tiled" files are based on "WRAPPER" tiles so that the number
and content of files is independent of the number of threads
and/or processes
o option to create single "global" files rather than "tiled" files
o ability to read both "global" and "tiled" files
[Caveat: the tiling of files must match the model tiles]
o checkpoints now use a single file per model section
ie. one file for the hydrostatic model core, one file
for the non-hydrostatic extensions and one file for the C-D
extensions
o the mid-level I/O routines now is broken into more source files
read_write_fld.F supplies basic I/O routines with the same interface
as the original I/O package
read_write_rec.F supplies I/O routines which allow multiple records
write_state.F writes the model state
checkpoint.F supplies the read/write checkpoint routines
All the example input data has had to be modified to be direct-access.
Otherwise only routines that used I/O have been affected and not
all of those have been due to the continuity of arguments in
the read_write_fld.F routines.
What needs to be done? We have to create a suite of conversion
utilities for users with old-style data. Also supply the option
for using old-style I/O, not just for die-hards but for reading
data too extensive to be converted. And more...
Modifications for non-hydrostatic ability + updates for open-boundaries.
Fixed minor bug. writeBinaryPrec was not included in NAMELIST while writeStatePrec was included twice. You'd have thought the compiler would catch that...
o Added "natural BCs" as alternative to "virtual salt flux" o Re-difined precFloat32 and precFloat64 to be 32 and 64 so that their values can be meaningfuly set in the data file o Modified read_write.F to create an exception if readBinaryPrec is not set o Replaced CPP control of viscous BCs with run-time control o Tidied up input-data precision (ie. ini_depths cnh_dbg...) o ini_forcing.F now initialises *all* forcing arrays to zero o Definitively tested verification experiments 0,1,2 and 4 (3 is atmospheric set-up which is in a state of flux)
Added IMPLICIT NONE in a lot of subroutines. Also corrected the recip_Rhonil bug: we didn't set it in ini_parms.F
Implementation of Open Boundaries:
o new source code: ini_obcs.F set_obcs.F apply_obcs1.F apply_obcs2.F
OBCS.h
o modified code at a few points, key changes are in
dynamcis.F the_model_main.F and ini_cg2d.F
o documentation in OBCS.h and doc/OpenBound.*
Changes to allow for atmospheric integration builds of the code
Changes for TAMC compatability. Added exp0 a barotropic basin scale box example Modified exp1 and exp2 to correct SIZE.h for Nr and variable overlap width support.
Changes to support - g77 compilation under Linux - LR(1) form of 64-bit is D or E for constants - Modified adjoint of exch with adjoint variables acuumulated.
Consistent isomorphism changes
Consistent isomorphism chages
Consistent isomorphism changes
Consistent isomorphism changes
Consistent isomorphism changes
Consistent isomorphism changes
Consistent isomorphism changes
Isomorphism consistency changes
Added close of I/O unit that was missing
Changed Z co-ordinate and lopping code: o Z now increases upwards (ie. for the ocean, z<0) This needed changes only in ini_vertical_grid() where zC and zFace are calculated and in ini_masks_etc() where hFacC is calculated using IF's (eg. IF H(i,j,bi,bj).LT.zFace(K) ...). o The lopping code needed a correction to the hydrostatic pressure calculation. o Two new parameters control the lopping: hFacMin - is the lower limit for water fraction in a cell hFacMinDz - is the lower limit for water thickness in lopped cells Both default to 0 so that pure lopping is the default. To force full cells, using continuous bathymetry, set hFacMin=1
Added diagnostics for KapGM. Added GMmaxval to limit values of KapGM when using the Ri # formula.
Changed the #include at the top from CPP_EEOPTIONS.h to CPP_OPTIONS.h This ought to be done through-out (?) but was necessary in at least the_model_main.F, dynamics.F, ini_parms.F because of the new macro ALLOW_DIAGNOSTICS.
The time-averaging diagnostics has been modified to include averages of "intermediate" quantities that exist only on a tile. We currently only time-average K13, K23 and wVel but these should be usable as a template for other diagnostics. We have now split off these routines into a separate module called diags/. Use of these routines is enabled by the CPP flag ALLOW_DIAGNOSTICS set in model/inc/CPP_OPTIONS.h
Added time-averaging (written by Elodie K.). Controlled by parameter taveFreq. taveFreq=0 turns it off.
Introduced time-dependant forcing, loaded and interpolated in load_external_fields.F in a subroutine load_interpolate_forcing(). Control is by one logical and two real variables in PARAMS.h: periodicExternalForcing, externForcingCycle and externForcingPeriod. The code in load_external_fields.F is "customized" so needs to be edited for non-global type runs. We'll tidy it up later.
Fairly coplete 4 degree global intercomparison setup. Includes changes to make convective adjustment and hydrostatic pressure correct as well as IO for climatological datasets
Chages to make default setup correct for 4 degreee global comparison
Added code to bring "salt" up-to-date with "theta". One caveat is that implicit diffusion of salt is done with the diffusivity of theta. We'll sort this out later. In explicit mode, diffKzS is used.
Changes to support topography, hydrography and forcing from files
Merge of GM Redi and spherical polar and inplicit diffusion and CD. Everything for a global run is now included, however, still some discrepancies with GM Redi.
Various corrections: o implicitDiffusion was missing from PARAMS.h (obviously forgot to commit) o maskUp in calc_common_fact() is now correct o find_rho() now has the proper "referencing" for "LINEAR" eos-mode [also affected a call from dynamics()]
Implemented implicit vertical diffusion (tracers only). Involved introducing a "total" diffusivity array (local 3D) calculated by calc_diffusivity(). Made some small changes to time-stepping algorithm. Switched on by setting implicitZdiffusion. (note: *Not* fully tested with topography. But when switched off this does produce identical results)
Changes to: o read in coefficients for POLY3 EOS. o find_rho() polynomial evaluation has been factorized. o additional density field needed in calc_iso_slopes() with non-linear EOS. This EOS must use the appropriate version of KNUDSEN to generate the coefficients file (POLY3.COEFFS). C7 and C8 were back to front in all previous versions of the model (compare01).
Added flags for turning off momentum equation and/or temperature equation
Added extra IO features - runtime on/off flags - more reporting of configuration
Added changes to support implicit free-surface. - included gBaro a "barotropic" gravity that can be set differently to the g.rhoprime gravity. - discovered and fixed coding error in dynamics loop. Per tile temporaries that needed correct initial values were not being reset for each tile.
Added support for binary IO of model fields for restart and/or postprocessing
GM/Redi parameterization. calc_isoslopes() calculates components of Redi tensor. calc_gt() then uses these components in a modified vertical tracer flux. AJA
Further changes to reporting of model configuration on standard output
Improvements to I/O and feedback info.
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Further $Id to $Header conversions
Initial revision
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