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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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checkpoint59h |
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o pkg/exf: |
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- improve vectorization by moving if-statement out of loops in |
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exf_mapfields, exf_radiation |
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- exf_bulkformulae.F: introduce 2D fields and vectorize code |
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o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package |
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o testreport: |
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- allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE |
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monitor & update offline_exf_seaice exp. output. |
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- AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) |
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o pkg/seaice: |
o pkg/seaice: |
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- bug fix in the evp solver: boundary conditions were affected be |
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masking of zMax/zMin (changes results) |
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- minor bug fix in boundary conditions in seaice_calc_strainrates |
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(changes results for no_slip) |
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- seaice_lsr.F: make interpolation of eta dependent on boundaries |
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- replace hardcoded lower limit for zeta (zMin) by runtime parameter |
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- add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean |
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stress formulation and no-slip boundary conditions |
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o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP |
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in gad_calc_rhs.F ; add few safety stops in initialisation phase. |
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o pkg/seaice: a first HSALT time stepping equation has been checked in |
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o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV |
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in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem |
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without requiring DO-IF statements |
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o pkg/thsice: |
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use continuous power-law function for partition of energy between lateral |
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melting/freezing and thinning/thickening ; old code using step function |
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still available with #undef THSICE_FRACEN_POWERLAW |
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update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice |
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o testreport: change AD testing : check against results/output_adm.txt |
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using same scripts as for forward test. |
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checkpoint59g |
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o adjoint testing: in preparation for changing testreport: |
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- output format: cost and grad written on separated lines |
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- ad output results in directory "results" (instead of "results_ad") |
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o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
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o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
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o pkg/ecco: allow user defined cost function contributions |
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o testreport: |
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Allow to choose (per experiment) the list of tested output variables |
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and the main variable (used to issue a pass/FAIL ) ; |
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- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
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- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
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Also modify printing of summary: |
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a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
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b) echo the list of tested variables in the individual summary.txt of |
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each experiment. |
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o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
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threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
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(but still depend on the tile decompostion of the domain). |
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o pkg/seaice: change a discretization detail to make the B-grid code |
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"more symmetric". This change is likely to remove all "ridges/leads" that |
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where quasi-aligned with the grid in B-grid solutions. It may also be |
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the solution to the stress coupling issues with the B-grid. |
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o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
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remove .cvsignore from input dir. (since testreport no longer run here). |
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o pkg/thsice: |
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- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
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- fix reshaping of sea-ice just after advection: |
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melt all the ice only if ice-volume is too small. |
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- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
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prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
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and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
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o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
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tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
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o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
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forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
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(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
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and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
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of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
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-> update output.txt |
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o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
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this affects truncation error: -> update output.txt of exp: |
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global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
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ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
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checkpoint59f |
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o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
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o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
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a bounded range (in forward mode) |
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o pkg/ecco, ctrl, autodiff and mom_common: |
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internal parameter controls, completements of implementations |
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o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
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o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
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(not seem any difference in testing results). |
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o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
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at face corners. |
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o pkg/generic_advdiff: |
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- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
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loop range indices for computing vertical advection tendency |
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and do the calculation in the interior only (no overlap) ; |
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for now, only implemented for SOM advection (to save CPU time). |
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- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
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o exch2 adjoint |
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First set of changes: |
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- add exch2 hand-written adjoint templates |
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- exch2 hand-written no longer use TAF-flag 'nownew_arg' |
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This will require cleanup in pkg/autodiff/*.F |
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(changed routines currently kept separate in verif. code/) |
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- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
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that used to hide exch2 or cubed-sphere specific code |
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(commented via 'cph-exch2') |
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o pkg/seaice |
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- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
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o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
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output of global_ocean.cs32x15.thsice . |
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checkpoint59e |
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o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
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for B-grid vector (not yet tested) and C-grid vector (<- only used |
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when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). |
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o starting implementation of Duffy et al. (GRL 1999) salt plume scheme |
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(#ifdef ALLOW_SALT_PLUME) |
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o gather_2d/scatter_2d: removed halo regions |
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o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
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scheme and the corresponding test case (under front_relax dir). For now, |
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only available with Skew-flux form and not yet tested in realistic set-up. |
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adjoint: store directives updated, but gradient checks deteriorated, |
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so maybe GM/Redi adjoint is now broken. |
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o seaice adjoint |
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* add AREA, HEFF, HSNOW as control variable |
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(should not change lab_sea results) |
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* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
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o pkg/seaice: |
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* added computation of saltFlux in seaice_growth; |
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For time being, sea ice salinity is assumed constant |
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contribution of snow flooding to freshening of sea ice is neglected. |
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SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
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defaults to 0.0 in order to maintain backward compatibility. |
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Typical values for SEAICE_salinity are 4 to 10 g/kg. |
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* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
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* added SEAICE_availHeatFrac, which specifies fraction of surface level |
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heat content used to melt or grow ice |
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* commented out cap of HICE: it helps keep ice thinner |
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* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
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* applied OBCS T/S mask to HEFFM sea ice mask |
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checkpoint59d |
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o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
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for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
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(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
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o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
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and change default value of parameter "GM_Small_Number"; |
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update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
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global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
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tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
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o pkg/ecco: cost function when applying pkg/smooth to controls |
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o pkg/ctrl: add forcingPrecond run time parameter |
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o pkg/seaice: |
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- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
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- fix bug in metric terms of u-equation in LSR solver (implicit part), |
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changes verification/lab_sea |
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- rearrange implicit part of u-equation in LSR solver to make it easier to |
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read, understand, and debug. This causes changes at the truncation level. |
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- fix (serious) bug in the boundary conditions (sign error in the implicit |
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part) of the LSR solver. Changes all LSR results. |
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- fixed problem with HSNOW initialization to avoid thick snow when AREA |
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is initilized with small values - does not change lab_sea results. |
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- added HsnowFile initialization capability |
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o pkg/smooth: addition to model/src and pkg/ctrl so allow |
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initialization of pkg/smooth and application to control vector |
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o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
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o dependencies: pkg/profiles requires pkg/cal |
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o pkg/profiles: |
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- added option ALLOW_PROFILES_GENERICGRID |
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-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
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that interpolation information (grid points and coefficients) is provided |
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within the netcdf input files. |
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-> sample matlab scripts can be found in MITgcm_contrib/gael |
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that allow you to prepare netcdf input files. |
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- also modified: cleaner include statements, cleaner error print statements, |
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cleaner stops when error, and more tests of the netcdf input files consistency. |
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o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
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o pkg/seaice: |
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- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
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requires a new routine: seaice_diagnostics_fill.F |
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- make sure that seaice does not move if not forced (pressure replacement |
- make sure that seaice does not move if not forced (pressure replacement |
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method, Hibler and Ip, 1995), changes results |
method, Hibler and Ip, 1995), changes results |
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- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
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ATMOSPHERIC_LOADING is #define). |
ATMOSPHERIC_LOADING is #define). |
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o pkg/kpp: replaced _KPP_RL with _RL |
o pkg/kpp: replaced _KPP_RL with _RL |
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o bug fixes for vertical diffusivity computations when both KPP and |
o bug fixes for vertical diffusivity computations when both KPP and |
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3D diffusivity arrays are used. |
3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F |
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are no longer updating the vertical diffusivity array |
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(passed as argument) but are (re-) setting those arrays. |
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o pkg/seaice: fix bug in evp solver, while doing that |
o pkg/seaice: fix bug in evp solver, while doing that |
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- change (improve?) discretization of stress computations for both |
- change (improve?) discretization of stress computations for both |
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cgrid-lsr and evp solver |
cgrid-lsr and evp solver |
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