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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/exf: |
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- replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter |
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"exf_output_interp" (in namelist: EXF_NML_04); change output file name |
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(add suffix "_out" instead of a prefix); keep same record number as in |
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input file but always write record 1 first (to avoid a STOP in I/O S/R). |
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Change output file content by writing interpolated field before applying |
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land-sea mask (helpful for debug). |
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- 2 compon. vector interpolation with rotation: apply scaling factor on |
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each compon. (Eastward and Northward) just before rotation. |
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o pkg/bling: |
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- Cleaned package. Removed not needed code and comments. |
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- adjoint example now works |
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(MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad) |
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o pkg/ptracers: |
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- add Bruno Deremble's code to complete the linear surface correction |
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for tracer conservation; |
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- enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE. |
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checkpoint65y (2016/07/29) |
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o pkg/debug (stats): |
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- change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to |
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proc/thread mapping); |
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- fix Min & Max for case where 1 thread has only empty tiles; |
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- use RL variable to count number of wet grid points (with big domain, |
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can be too large to fit into integer*4). |
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o pkg/monitor: |
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- use RL variable to count number of wet grid points (but used only for del2) |
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- add new routine to compute Advective CFL within tracer time-stepping with |
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writing delayed until next monitor output. |
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o pkg/obcs: |
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- fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW) |
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o pkg/cal: |
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- calandar-dump: treat case myTime < timePhase in the same way as in |
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eesupp/src/diff_phase_multiple.F (when not using calandar-dump). |
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o pkg/dic & seaice: |
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- fix compilation of ocean component for coupled atm+ocn model with |
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seaice dynamics & dic. |
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checkpoint65x (2016/06/11) |
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o add a license text file in main MITgcm tree. |
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o added pkg/bling: |
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- intermediate complexity biogeochemical model |
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- see bling_description.txt for details |
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- verification experiment is global_oce_biogeo_bling (for now, in |
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Contrib/verification_other/); tested daily on baudelaire with gfortran. |
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- add entry point in pkg/gchem for new pkg "bling". |
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o pkg/seaice: fix tensile stength computation |
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- replace global field tensileStrength by tensileStrFac |
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- tensileStrFac can be computed once in S/R seaice_init_varia |
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- fortunately that does not affect any verification results |
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checkpoint65w (2016/05/12) |
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o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles |
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with ECCO_CTRL_DEPRECATED defined |
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o verification/global_ocean.cs32x15: |
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- change secondary test "viscA4" to also test "selectP_inEOS_Zc=3" |
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with "selectNHfreeSurf=1". |
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o model/src (non-hydrostatic free-surface): |
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- More "natural" expression of NH free-surface term (case selectNHfreeSurf=1): |
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was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf. |
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- Calculate surface vertical velocity after 2-D solver adjustment (accounts |
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for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv |
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and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1. |
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This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux. |
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- Update output (changes at machine truncation level) of verification exp: |
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exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d), |
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short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d). |
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o pkg/seaice: ITD code |
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- fix picking up from a single category model by initialising |
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heff/area/hsnowITD = 0. in seaice_itd_pickup.F |
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- split a long warning message in seaice_check_pickup.F into two lines, |
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because NEC SX-ACE cannot deal with the long line. |
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o model/src: |
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- fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3) |
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o pkg/seaice: |
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- add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG |
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o pkg/seaice: |
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- add basal stress as parameterisation for grounding ice |
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following Lemieux et al. (2015) |
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- turn on by setting new parameter SEAICEbasalDragK2 to a value |
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larger than 0. Lemieux et al. (2015) recommend 15. |
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- The adjoint complains with extra recomputations so there is also a |
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new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in |
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order to postpone the problem |
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- compile the new code in lab_sea |
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o verification/halfpipe_streamice: |
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- update both TAF and OpenAD adm output (machine truncation differences) |
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checkpoint65v (2016/04/08) |
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o verification/advect_xz: |
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- increase overlap size from 3 to 4 and add new secondary test for PQM |
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advection scheme (with mono & wino limiter). |
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- change main exp. to test PPM (with weno limiter) adv.scheme on Temp. |
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o model/src: |
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- new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently |
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added phi0Ref) to set vertical axis origin and phiRef origin; |
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keep Ro_SeaLevel for backward compatibility (with a warning). |
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According to coordinate and fluid type: |
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OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top) |
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ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom) |
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OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top) |
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ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom) |
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- remove Ro_SeaLevel from ATM experiment parameter files; |
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- in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the |
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complement; update output.txt (changes at machine truncation level). |
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o pkg/seaice/seaice_evp.F |
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- simplify computation of deltaZ and zetaZ to simple averaging following |
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Bouillon et al. (2013). This removes a lot of code, but also changes |
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verification experiment lab_sea.hb87 -> updated |
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checkpoint65u (2016/03/14) |
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o pkg/generic_advdiff: |
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- from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52) |
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with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP); |
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Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for |
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testing and not for actual use. |
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o model/src: |
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- add parameter "phi0Ref" to specify reference [pressure/geo] potential at |
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origin r = rF(1); |
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- add options (parameter selectP_inEOS_Zc) to select which pressure to use |
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in EOS for height coordinate: enable to include NH Pressure or to use |
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more accurate pressure vertical profile; options not linked to EOS type |
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(as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type; |
| 130 |
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- start to implement variable gravity (along vertical): for now, only with |
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z-coords (not even z*). |
| 132 |
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- add Ideal Gas equation of state for height coordinate. |
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- update OpenAD output (affected at machine truncation level) of exp: |
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global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo. |
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o pkg/exf: |
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- add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result |
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of exf interpolation (before any rescaling, rotation or interpolation |
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to velocity point) for each field that gets loaded from file. This option |
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identically mimics the input file organization (e.g. record numbers in year |
| 140 |
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by year input files) besides the change in horizontal grid. |
| 141 |
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- add rotateStressOnAgrid run-time switch so that wind stress fields |
| 142 |
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can be provided on the A-grid in zonal/meridional direction and |
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rotated on the fly. This only applies to the case when the exf |
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interpolation is off and rotateStressOnAgrid is false by default. |
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o model/src: |
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- rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since |
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it's also used with pkg/atm_phys) and add few more parameters (but still |
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inactive, src code yet to come) |
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checkpoint65t (2016/02/10) |
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o pkg/atm_phys: |
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- from Ruth Geen: add optical depth dependence on CO2 concentration. |
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o model/src: |
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- fix vertical inter/extra-polation of density factor rhoFacF (for anelastic) |
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for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F. |
| 156 |
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Update output of exp. deep_anelastic (changes at truncation level). |
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o tools: |
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- add a hack in "remove_comments_sed" (used only with TAF) for recent |
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version of OpenMPI (shipped with FC.23): comment out the new header |
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file "mpif-sizeof.h" which causes problems to TAF. |
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o pkg/seaice: |
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- change the termination criterion so that maxits (SEAICElinearIterMax) |
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has an effect |
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- unify iteration parameters for implicit solvers (JFNK and Picard) |
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SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS |
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SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER |
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SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner |
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SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner |
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SEAICEnonLinTol replaces JFNKgamma_nonlin |
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- remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN |
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- add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and |
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use with SEAICEuseKrylov |
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o pkg/seaice/seaice_lsr.F |
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fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only |
| 175 |
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relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have |
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an effect. |
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o pkg/seaice: add two new parameters |
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- SEAICEuseLSR to simplify the logic in seaice_dynsolver (this |
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parameter is not in any namelist) |
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- SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as |
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a preconditioner for the non-linear Newton iteration of the JFNK |
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solver |
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o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT, |
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affects some experiments at truncation level: |
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- global_ocean.cs32x15.icedyn (11 digits), |
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- global_ocean.cs32x15.seaice (11 digits), |
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- seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update |
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- also update global_ocean.cs32x15 adjoint and tangent-linear results |
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o pkg/salt_plume & pkg/thsice: |
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- for coupled set-up with pkg/thsice in ATM and pkg/salt_plume in OCN, |
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connect salt_plume flux to ATM-OCN coupling pkgs interface: |
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a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for |
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export to coupler interface) even without compiling pkg/salt_plume ; |
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b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field |
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(saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH. |
| 196 |
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o pkg/dic: |
| 197 |
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- use the updated seaice fraction (from seaice pkgs) for DIC forcing |
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instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE |
| 199 |
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called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD); |
| 200 |
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- move also update with values from ATM-OCN Coupler in the same new S/R |
| 201 |
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(previously done in ocn_apply_import.F). |
| 202 |
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o tools/adjoint_options: |
| 203 |
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- specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default) |
| 204 |
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has been changed on Jan 14, 2016. |
| 205 |
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o pkg/ggl90: |
| 206 |
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- add alternative discretisation of vertical shear (off by default), to |
| 207 |
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compute the mean (@ grid-cell center) of vertical shear compon instead of |
| 208 |
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vertical shear of mean flow (@ grid-cell center). |
| 209 |
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- add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated |
| 210 |
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results on adjacent faces of cubed-sphere grids; this fix the restart. |
| 211 |
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o pkg/atm_compon_interf: |
| 212 |
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- skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just |
| 213 |
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pass last value, stored directly before export to CPL ; |
| 214 |
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Note: this affects results of Coupled set-up where OCN uses useImportSLP=T |
| 215 |
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- remove atmSLPr from pickup files (no longer needed for restart) |
| 216 |
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|
| 217 |
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checkpoint65s (2016/01/13) |
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o eesupp & genmake2: |
| 219 |
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- first check for Function ETIME and, if it fails, then check for subroutine |
| 220 |
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ETIME and consistent output; use the appropriate version in timers.F |
| 221 |
o model/src: |
o model/src: |
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- to check restart test, add option to apply EXCH to U,V earlier, just before |
- to check restart test, add option to apply EXCH to U,V earlier, just before |
| 223 |
integr_continuity; turned off by default. |
integr_continuity; turned off by default. |
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- add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes |
- add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes |
| 291 |
(shortwave & longwave, net & downward) and diagnostics of temp. tendency |
(shortwave & longwave, net & downward) and diagnostics of temp. tendency |
| 292 |
for individual contribution (convection, LSC cond, radiation) |
for individual contribution (convection, LSC cond, radiation) |
| 293 |
- add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp. |
- add Ruth Geen etal, GRL 2016, radiation options (see paper supp. |
| 294 |
information); activated with: solar_exponent=0. and wv_exponent=-1. |
information); activated with: solar_exponent=0. and wv_exponent=-1. |
| 295 |
o pkg/ggl90: |
o pkg/ggl90: |
| 296 |
- within IDEMIX add upper limit for horizontal group velocity to |
- within IDEMIX add upper limit for horizontal group velocity to |
| 813 |
just copy level Nr value to level Nr+1. |
just copy level Nr value to level Nr+1. |
| 814 |
o doc: |
o doc: |
| 815 |
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
| 816 |
o pkg/streamice: |
o pkg/shelfice: |
| 817 |
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
| 818 |
SHELFICE.h: move array shelficemass to init_varia, initialise |
SHELFICE.h: move array shelficemass to init_varia, initialise |
| 819 |
from array shelficemassinit, which is set in init_fixed and |
from array shelficemassinit, which is set in init_fixed and |
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