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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/seaice: |
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Major overhaul of the LSOR solver: change discretization from original |
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finite differences to finite volume. The old routine is still in the |
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file seaice_lsr.F and can be turned on with the CPP-flag |
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SEAICE_OLD_AND_BAD_DISCRETIZATION |
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Along with this change, the discretization of the strain rates is changed. |
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The same flag turns on the old discretization in seaice_calc_strainrates.F |
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All verification experiments with seaice are affected (except for |
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seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old |
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results by setting the above flag. |
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Further changes involve changes in defaults: |
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- ALLOW_FLOODING is defined and turned on by default |
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- SEAICE_advSnow = .true. is now the default |
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- B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE |
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is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS |
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- seaice_growth: replace computation of UG by a simple copy from wspeed |
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|
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checkpoint61k |
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o pkg/seaice: a few bug fixes mostly concerning the metric terms: |
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seaice_lsr: fixed a few metric terms, |
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affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs |
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add more debugging diagnostics |
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seaice_evp: removed superfluous many metric terms of FV discretization |
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of stress divergence |
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affects lab_sea, lab_sea.hb87 |
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seaice_ocean_stress: removed superfluous many metric terms of FV discretization |
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of stress divergence for non-evp solver |
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(this part is not tested anywhere) |
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seaice_calc_strainrates: fixed a bug in no-slip boundary conditions, |
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they were effectively only half slip |
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affects lab_sea.hb87 |
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updated all relevant verification experiments |
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checkpoint61j |
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o pkg/seaice: turn a few hard wired parameters into run time parameters |
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o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model |
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time in seconds as promised by the usints in seaice_monitor and exf_monitor |
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o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids |
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that are not cubed-sphere grids |
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o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR |
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o pkg/ctrl: |
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fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low) |
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o non-hydrostatic (calc_gw.F): |
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fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec |
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update output of exp. global_ocean.cs32x15.viscA4 |
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o remove backward compatibility for thetaMin,phiMin |
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(replaced by xgOrigin,ygOrigin on Jan 27, 2009) |
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o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the |
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interpolated wind field not only for curvilineargrid=.true., but also |
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for a rotated grid (rotateGrid=.true.) |
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o pkg/exf: add capability to bypass interpolation for runoff |
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by setting yet another CPP-flag |
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o eesupp/src, B-grid exchange: |
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add simple (6 tiles, non MPI) CS exch + standard interface S/R. |
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o autodiff |
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new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV |
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allows to switch to single-prec common blocks; |
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corresponding switch occurs in tamc.h, integer isbyte |
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TAF store directivs "byte" and "kind" seem equivalent; |
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Most tamc.h have been updated correspondingly. |
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checkpoint61i |
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o autodiff: |
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fix autodiff_sore/_restore indices for obcs |
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(spotted by I. Hoteit, M. Mazloff) |
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o pkg/autodiff, pkg/ctrl: |
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Add flag to reduce all tapelev I/O to single-prec. |
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In data.ctrl set |
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doSinglePrecTapelev = .TRUE. |
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o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2: |
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check in hack for SX8 compiler (for dxV, dyU); remove it afterwards. |
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o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for |
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real fresh water flux (not yet) |
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o pkg/mdsio & rw: |
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- add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta) |
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- add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX. |
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o pkg/flt: |
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- replace FLT_INIT by 3-steps standard initialization S/R: readparms, |
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init_fixed & ini_varia. |
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- clean-up & simplify linear interpolation S/R: |
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move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid. |
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- fix some indices (mainly vertical index) ; add IMPLICIT NONE. |
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- more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R. |
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- add vert. coordinate & horiz. indices to output files. |
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- change vertical position in initial condition, from index to depth [m]. |
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- store horizontal (decimal) indices i,j in common block (instead of coord. x,y) |
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(easier to get to a curvilinear grid) ; delX,delY no longer used. |
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o pkg/ggl90: a few modifications: |
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- fix bottom boundary condition, and interpolation of KappaE |
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near top and bottom |
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- use same set of viscosity/diffusivity for TKE/momnetum/tracer |
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- add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH) |
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- add a few options for mixing-length upper limit (--> mxlMaxFlag) |
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o rename thetaMin,phiMin -> xgOrigin,ygOrigin |
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(maintain temporary backward compatibility, until next checkpoint) |
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checkpoint61h |
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o pkg/diagnostics with "periodic averaging diagnostics": |
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fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. |
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o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82 |
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o pkg/obcs: fix loop ranges for balancing code |
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o pkg/flt: |
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- improve criteria for finding which tile owns a float. |
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- fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case. |
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o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg |
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aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling |
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with ocean biogeo) |
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o pkg/flt: |
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- do some cleaning and fix the restart ; |
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- add output.txt in flt_example/results to get this pkg tested. |
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o genmake2: add an EXTENDED_SRC option and flag. |
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for now, cannot be turned on on command line (only through genmake_local) |
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o pkg/mdsio: read/write vector: |
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- singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS |
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- singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR |
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& MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. |
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- affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) |
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(drop to 4 digits matching for grad). But this test does not look very |
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reliable (was already failling on eddy, fc5, at 6.digits). Update output. |
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checkpoint61g |
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o pkg/flt: |
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- move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) |
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+ make OPTIONS file more standard. |
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- rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) |
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- fix _BYTESWAPIO CPP-Flag |
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- standard reading of file-parameter "data.flt" |
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- fix argument list of S/R FLT_RESTART |
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still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F |
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o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell |
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o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to |
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a still unfixed compiler/optimization bug |
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|
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checkpoint61f |
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o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; |
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update results of global_ocean.cs32x15.icedyn test. |
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o move getcon.F from model/src to pkg/fizhi. |
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o pkg/exf: add parameter for extrapolation of temp up to the surface |
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and option to prevent negative evap (in bulk_largeyeager04 only). |
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o Prather Advection scheme: fix tracer conservation for divergent flow |
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(e.g., when using NonLin Free-Surface). |
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o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead |
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o gmredi (Visbeck-variable-K): |
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- add more parameters to Visbeck-variable-K. |
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- use a 5 points average for dSigmaR in Visbeck-K calculation |
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(more "homogenous": same stencil and same weights as in dSigmaH) |
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- update output of ideal_2D_oce experiment. |
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o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 |
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(#undef REAL4_IS_SLOW) |
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- pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 |
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coordinate variable |
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- pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables |
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(surface forcing fields), removes some of the functionality |
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- model/src/write_grid.F: write _RS variables as RS-netcdf variables |
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- model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but |
| 162 |
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probably not all: copy _RS surface flux fields to RL field before |
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calling DIAGNOSTICS_FILL |
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- model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into |
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real*4 (CALL EXCH_*_RS) versions. |
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- tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 |
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(generate new output). |
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|
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checkpoint61e |
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o gmredi (Visbeck-variable-K): |
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- fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h |
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- change computation of Visbeck-K where Slope > Smax : |
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now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct) |
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previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output. |
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o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic |
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to be the same as with Z-coord. (i.e., m/s & no-units respectively). |
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o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc) |
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o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz |
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does not become too large (to avoid precision problems in implicit-diffusion |
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solver); update ideal_2D_oce output. |
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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 |
| 185 |
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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 + lower limit on 1/lambda |
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- allow to set few more params from data.gmredi |
| 189 |
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o pkg ggl90: |
| 190 |
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- add missing sqrt(2) factor in computation of mixing length |
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scale in ggl90_calc.F |
| 192 |
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(see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) |
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|
| 194 |
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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 |
| 198 |
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to individual fields |
| 199 |
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(switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) |
| 200 |
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o store 3-D (in-situ) density in commom block (DYNVARS.h) |
| 201 |
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- save 1 rho computation. |
| 202 |
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- no longer modify T & S inland when using down_slope pkg. |
| 203 |
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o gad_som : allow to switch to SOM advection for T & S without corresponding |
| 204 |
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pickup files (using new S/R: MDS_CHECK4FILE). |
| 205 |
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o keep removing _BEGIN/_END_MASTER between MDSIO S/R call |
| 206 |
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(for useSingleCpuIO to work in multi-threaded) |
| 207 |
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o pkg/shelfice: |
| 208 |
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- disentangle parameters: retire shelfIceFile in data/PARM05 and substitute |
| 209 |
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with SHELFICEtopoFile in data.shelfice |
| 210 |
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- move code for reading ice shelf topography and modifying hFacC into separate |
| 211 |
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subroutines of the shelfice package |
| 212 |
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- separate initialisation of "fixed" and "variable" variables |
| 213 |
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- kTopC is not (yet) replaced by kSurfC, although this is possible |
| 214 |
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o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
| 215 |
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o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
| 216 |
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and rename: |
| 217 |
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ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
| 218 |
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ini_reference_state.F --> load_ref_files.F (- set anelastic factors) |
| 219 |
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o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) |
| 220 |
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|
| 221 |
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checkpoint61c |
| 222 |
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o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" |
| 223 |
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to add mass source/sink of fluid in the interior (3-D generalisation |
| 224 |
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of oceanic real-fresh water flux). |
| 225 |
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o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) |
| 226 |
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o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) |
| 227 |
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o new pkg: down_slope |
| 228 |
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density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). |
| 229 |
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- presently, modify T & S inland (dwnslp_calc_rho.F). |
| 230 |
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can be avoided if rho was stored in common bloc and used in calc_phi_hyd. |
| 231 |
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- implementation for ocean in P-coords not tested. |
| 232 |
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- add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. |
| 233 |
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o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) |
| 234 |
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(to facilitate conversion of oceanic pkg to p-coordinate). |
| 235 |
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o change FIND_RHO to FIND_RHO_2D : |
| 236 |
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pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. |
| 237 |
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o new pkg: cheapaml |
| 238 |
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|
| 239 |
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checkpoint61b |
| 240 |
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o exch2: |
| 241 |
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change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) |
| 242 |
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- no longer depend on the order sequence (N,S,E,W). |
| 243 |
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- 3rd exchange no longer needed (tested with 24 tiles). |
| 244 |
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- same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) |
| 245 |
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- exch_UV_A-grid readily available (but not yet tested). |
| 246 |
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comment out 3rd exch call and remove copy of V to U at SE & NE face-corners |
| 247 |
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(both are no longer needed) in exch_uv: no effect in forward run; but |
| 248 |
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get truncation error differences with adjoint exch. |
| 249 |
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o exch2: |
| 250 |
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- change index-bounds storage (moved from target to local tile, |
| 251 |
|
more intuitive this way) ; rename/remove some variables. |
| 252 |
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- change utils/exch2/matlab-topology-generator & code_mods accordingly. |
| 253 |
|
|
| 254 |
|
checkpoint61a |
| 255 |
o exch2/matlab-topology-generator: |
o exch2/matlab-topology-generator: |
| 256 |
fix bug in index bounds for N-S internal exchange (hard to tell if this |
fix bug in index bounds for N-S internal exchange (hard to tell if this |
| 257 |
had any effect on the solution). |
had any effect on the solution). |
| 2420 |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
| 2421 |
- these scheme operate in a similar manner as KPP (without ghat, of |
- these scheme operate in a similar manner as KPP (without ghat, of |
| 2422 |
course), however there is only one diffusivity that is used for both |
course), however there is only one diffusivity that is used for both |
| 2423 |
temperature and salinity (and passive tracers)ç |
temperature and salinity (and passive tracers) |
| 2424 |
o add offline package |
o add offline package |
| 2425 |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
| 2426 |
provided by Stephanie Dutkiewicz |
provided by Stephanie Dutkiewicz |
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