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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/dic: |
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- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
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gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
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in gchem_forcing_sep.F |
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o pkg/autodiff & obcs: |
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- add storage of current OB values for U & V (was already done for T & S). |
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checkpoint65c (2014/08/30) |
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o pkg/dic: |
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- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
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and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
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AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
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o verification: |
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- new experiment testing OBCS and DIC pkgs, using params & output from |
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tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
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passage: take OBCS from the last year of a 2 yrs simulation and initial |
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conditions from t=1.yr while keeping the same forcing. |
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o model/src: |
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- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
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(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
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o pkg/diagnostics (Stats-Diags): |
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- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
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a) refine region where stats are computed, excluding where arrhFac=0 ; |
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b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
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c) extend regional stats over the region edges (for U or V pt location). |
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o pkg/gchem: |
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- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
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pkg/dic is currently changing/updating ptracers values beyond the OB). |
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o verification (hs94): |
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- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
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bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
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hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
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apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
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o pkg/ptracers: |
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- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
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switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
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- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
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with AB-2 code (so that it get tested). |
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o model/src: |
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- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
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with AB-2 code (previously only available with AB-3 code). |
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Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
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to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
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there, by calling CYCLE_AB_TRACER). |
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o pkg/generic_advdiff: |
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- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
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GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
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+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
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S/R temp/salt/ptracers_integrate.F |
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o model/src & pkg/ptracers: |
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- remove common block variables gT,gS (in DYNVARS.h), except when |
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USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
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- remove common block variable gPtr. |
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o model/src & pkgs: |
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- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
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ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
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IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
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GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
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+ change accordingly all calling S/R. |
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- use local temperature/salinity/ptracer tendency array (without bi,bj) |
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in S/R temp/salt/ptracers_integrate.F |
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o pkg/seaice: |
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- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
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to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
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- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
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in seaice_lsr |
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- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
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in s/r seaice_lsr_calc_coeffs |
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o pkg/mdsio: |
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- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
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(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
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too long (e.g., > MAX_LEN_FNAM/2 ) |
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checkpoint65b (2014/08/12) |
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o pkg/matrix: |
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- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
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o model/src: |
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- fix initialisation of geothermalFile; compile geothermal-flux code in |
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natl_box verification experiment. |
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o model/src & pkg/down_slope: |
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- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
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- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
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field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
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results at machine truncation level: update output of experiments |
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global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
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o pkg/diagnostics (Stats-Diags): |
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- do not cumulate the full volume when DIAGNOSTICS_FILL is |
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called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
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This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
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times (but Min,Max and StD are still wrong). |
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o model/src: |
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- add geothermal flux forcing: read in ini_forcing.F as time-constant |
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field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
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o model/src: |
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- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
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_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
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arrays are already updated while adjustments (filters, conv.adjustment) are |
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still applied later, in S/R TRACERS_CORRECTION_STEP. |
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o model/src: |
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- store in common bloc array "rhoInSitu" the virtual potential temperature |
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anomaly that is used to compute geopotential: this make the atmos code |
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more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
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o pkg/seaice/seaice_lsr.F |
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- rename integer variable ilcall to ipass (that's what it is called |
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in the residual diagnostics |
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- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
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default) for improved non-linear convergence of the first few steps |
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- adjust a few comments and add new ones to explain some of the store |
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directives |
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o pkg/generic_advdiff (& ptracers): |
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- re-work the code to check for valid advection scheme and for minimum |
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size of overlap (now stored in local common bloc in gad_advscheme.F) |
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o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
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- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
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- add an auxilliary variable "bet" and fix store directives and keys in |
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seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
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less exact gradients in my tests); but there are still |
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recomputation warning (although gradients are sort of OK), when |
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SEAICE_LSR_VECTORIZE is not defined, so this flag and |
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SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
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- update verification experiments lab_sea. |
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- change some comments in S/R seaice_calc_viscosities |
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o model/src: |
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- if staggerTimeStep=T, always apply exchange to velocity field in |
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do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
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(independent of using multi-dim advection or not); no effect on FWD run |
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but affects AD results (at machine truncation level): update output of |
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experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
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and isomip (oad: 12.d). |
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o pkg/generic_advdiff: |
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- stop if doAB_onGtGs is set to FALSE but ignored |
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- refine warning related to stability of tracer time-stepping |
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regarding internal wave dynamics. |
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- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
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on staggerTimeStep & implicitIntGravWave (will now get a warning |
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if potentially unstable). |
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o pkg/kl10: |
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- add new pkg "kl10" for mixing due to internal wave breaking, from |
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http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
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(contribution from Jody Klymak), tested in verification experiment |
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verification/internal_wave/input.kl10/ |
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o isomip experiment: |
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- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
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(input.htd) and update the output. |
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o cd_code experiments: |
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- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
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#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
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global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
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update the corresponding output. |
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o pkg/seaice: |
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- reduce the number of include files and store directives in |
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S/R seaice_lsr_tridiagu/v |
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- change the order of loops in one case in S/R seaice_lsr_tridiagv |
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(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
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get rid off one store directive (a TAF bug?) |
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- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
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S/R seaice_lsr_tridiagv to change the loop range for consistency |
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- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
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- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
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S/R seaice_lsr_tridiagu/v (requires update of |
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offline_exf_seaice/input.dyn_jfnk) |
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|
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checkpoint65a (2014/07/27) |
checkpoint65a (2014/07/27) |
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o model/src: |
o model/src: |
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- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
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- collect T & S forcing tendency into local 2-D array (passed as argument to |
- collect T & S forcing tendency into local 2-D array (passed as argument to |
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apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
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affects results at machine truncation level (e.g., ocean: if using |
affects results at machine truncation level (e.g., ocean: if using |
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SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0) |
SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
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moist correction due to vertical advection). |
correction due to vertical advection). |
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- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
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global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
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seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |