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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o pkg ggl90: |
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- in ggl90_cal.F: compute only one set of visc/diff, used to |
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step forward TKE/T/S/momentum |
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- default value of GGL90viscMax/GGL90diffMax larger and equal (to |
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have Prandlt =1) |
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o gmredi(fm07): |
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- add lower limit on Transition layer thickness D + lower limit on D/lambda |
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- allow to set few more params from data.gmredi |
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o pkg ggl90: |
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- add missing sqrt(2) factor in computation of mixing length |
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scale in ggl90_calc.F |
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(see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) |
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checkpoint61d |
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o adjoint modifs |
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- adapt to new field rhoInSitu |
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- allow to revert from StoreDynVars2D, StoreDynVars3D |
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to individual fields |
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(switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) |
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o store 3-D (in-situ) density in commom block (DYNVARS.h) |
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- save 1 rho computation. |
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- no longer modify T & S inland when using down_slope pkg. |
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o gad_som : allow to switch to SOM advection for T & S without corresponding |
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pickup files (using new S/R: MDS_CHECK4FILE). |
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o keep removing _BEGIN/_END_MASTER between MDSIO S/R call |
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(for useSingleCpuIO to work in multi-threaded) |
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o pkg/shelfice: |
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- disentangle parameters: retire shelfIceFile in data/PARM05 and substitute |
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with SHELFICEtopoFile in data.shelfice |
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- move code for reading ice shelf topography and modifying hFacC into separate |
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subroutines of the shelfice package |
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- separate initialisation of "fixed" and "variable" variables |
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- kTopC is not (yet) replaced by kSurfC, although this is possible |
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o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
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o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
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and rename: |
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ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
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ini_reference_state.F --> load_ref_files.F (- set anelastic factors) |
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o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) |
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checkpoint61c |
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o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" |
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to add mass source/sink of fluid in the interior (3-D generalisation |
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of oceanic real-fresh water flux). |
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o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) |
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o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) |
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o new pkg: down_slope |
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density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). |
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- presently, modify T & S inland (dwnslp_calc_rho.F). |
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can be avoided if rho was stored in common bloc and used in calc_phi_hyd. |
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- implementation for ocean in P-coords not tested. |
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- add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. |
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o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) |
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(to facilitate conversion of oceanic pkg to p-coordinate). |
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o change FIND_RHO to FIND_RHO_2D : |
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pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. |
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o new pkg: cheapaml |
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checkpoint61b |
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o exch2: |
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change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) |
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- no longer depend on the order sequence (N,S,E,W). |
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- 3rd exchange no longer needed (tested with 24 tiles). |
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- same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) |
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- exch_UV_A-grid readily available (but not yet tested). |
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comment out 3rd exch call and remove copy of V to U at SE & NE face-corners |
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(both are no longer needed) in exch_uv: no effect in forward run; but |
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get truncation error differences with adjoint exch. |
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o exch2: |
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- change index-bounds storage (moved from target to local tile, |
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more intuitive this way) ; rename/remove some variables. |
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- change utils/exch2/matlab-topology-generator & code_mods accordingly. |
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checkpoint61a |
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o exch2/matlab-topology-generator: |
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fix bug in index bounds for N-S internal exchange (hard to tell if this |
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had any effect on the solution). |
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o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf |
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is exceeded |
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o testreport: modify syntax of awk, so that it works also with |
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awk, and not only with nawk and gawk |
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checkpoint61 |
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o autodiff |
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Change default for TAF usage by removing argument '-nonew_arg' |
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This changes TAF subroutine argument list (ordering of active var.) |
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Omission of this flag leads to incompatibility w.r.t. TAMC |
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To restore TAMC-compatibility, need following modifs: |
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* use adoptfile tools/adjoint_options/adjoint_tamc_compatibility |
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* use CPP option #define AUTODIFF_TAMC_COMPATIBILITY |
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Tested TAF version is 1.9.22 |
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N.B.: exch2 hand-written adjoint code currently not TAMC compatible |
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checkpoint60 |
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--->>> This is the last checkpoint for which generating the adjoint |
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--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" |
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--->>> by default. |
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--->>> Future checkpoints will ommit this flag by default. |
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o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. |
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o pkg/grdchk: Add gradient check to etan0 perturbations. |
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o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). |
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o pkg/autodiff: more flexibility in zeroadj. |
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model/src: modifying do_oceanic_phys.F accordingly. |
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o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. |
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o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option |
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special setup of gmredi for which the adjoint is stable |
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enough for parameter optimization. |
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o bridging the gap between eddy stress and GM. |
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-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) |
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along with a change in CPP option (now ALLOW_EDDYPSI). |
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-> when using GM w/ GM_AdvForm: |
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The total eddy streamfunction (Psi = eddyPsi + K x Slope) |
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is applied either in the tracer Eq. or in momentum Eq. |
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depending on data.gmredi (intro. GM_InMomAsStress). |
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-> ALLOW_EDDYPSI_CONTROL for estimation purpose. |
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The key modifications are in model/src/taueddy_external_forcing.F |
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pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F |
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checkpoint59r |
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o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array |
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from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); |
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fix option to read coriolis(@ cell-corner) from files with CS-grid. |
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o pkg/mnc: add some attributes to standard 1D-coordinate variables |
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o pkg/diagnostics: enforce missing_value attribute for scalar variables at |
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mass points, when using mnc for output |
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- add runtime parameter (missing_value, missing_value_int) to override |
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default (which is the value of getcon('UNDEF')) |
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o pkg/mnc: prepare mnc for the actual use of missing values with the |
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diagnostics package: small fix in mnc_cw_readwrite.template and more |
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initialisation of never used fields |
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- replace mnc_common.h and mnc_id_header.h with corresponding upper case |
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versions |
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o pkg/thsice/thsice_ini_vars.F added default initial values so that |
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thermodynamics sea ice solver does not blow up when some initial fields |
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are missing. |
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o move from external_forcing_surf.F to ini_forcing.F |
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the p-coord. hack consisting in using pLoad to set phi0surf ; |
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update output of tutorial_global_oce_in_p (affected @ truncation level). |
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o Freshen up a bit hs94.1x64x5, notably: |
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remove rotationPeriod and tRef=5*0. (adjoint only), and add |
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exactConserv=.TRUE. |
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o pkg/generic_advdiff: |
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change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
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applies to files where Temperature & Salinity 2nd Order moments are used. |
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o pkg/ptracers: add second-order moment advection schemes (80 and 81); |
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this uses a dynamically allocated internal state data structure |
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(#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) |
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and requires a fortran 90 compiler |
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checkpoint59q |
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o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) |
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(from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) |
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o Refresh tutorial_global_oce_biogeo, notably: |
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- change bathymetry (put back seamounts in ACC, use hFacs) |
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- change EOS (POLY3 --> JMD95Z) |
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- use Bryan-Lewis vertical diffusivity |
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- use multidimensional advection |
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- remove old virtual virtual in dic pkg, now done through ptracer pkg |
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- change a couple of parameters in dic pkg |
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o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F |
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o pkg/obcs: change default to OBCSfixTopo = .true., |
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- set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result |
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- replace "debugMode" with "debugLevel .GE. debLevB" |
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o implementation of TAF directives for gchem,cfc,dic |
o implementation of TAF directives for gchem,cfc,dic |
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o remove "exp5" (replaced by tutorial_deep_convection). |
o remove "exp5" (replaced by tutorial_deep_convection). |
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o pkg/obcs: add code to fix topography gradients normal to open boundaries; |
o pkg/obcs: add code to fix topography gradients normal to open boundaries; |
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this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; |
this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; |
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the code can be turned on by setting OBCSfixTopo = .true. in data.obcs |
the code can be turned on by setting OBCSfixTopo = .true. in data.obcs |
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--> changes results in dome, exp4, internal_wave, seaice_obcs, and |
--> changes results in exp4, seaice_obcs |
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tutorial_plume_on_slope. |
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o tutorial_deep_convection : |
o tutorial_deep_convection : |
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update the set-up and increase resolution and domain size ; start |
update the set-up and increase resolution and domain size ; start |
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from pseudo initial conditions = output at t=120mn in order to see |
from pseudo initial conditions = output at t=120mn in order to see |
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