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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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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); |
11 |
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- fix Min & Max for case where 1 thread has only empty tiles; |
12 |
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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/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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|
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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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|
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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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|
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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). |
78 |
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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; |
89 |
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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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|
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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); |
105 |
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- add options (parameter selectP_inEOS_Zc) to select which pressure to use |
106 |
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in EOS for height coordinate: enable to include NH Pressure or to use |
107 |
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more accurate pressure vertical profile; options not linked to EOS type |
108 |
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(as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type; |
109 |
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- start to implement variable gravity (along vertical): for now, only with |
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z-coords (not even z*). |
111 |
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- add Ideal Gas equation of state for height coordinate. |
112 |
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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. |
114 |
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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 |
118 |
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identically mimics the input file organization (e.g. record numbers in year |
119 |
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by year input files) besides the change in horizontal grid. |
120 |
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- add rotateStressOnAgrid run-time switch so that wind stress fields |
121 |
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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. |
124 |
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o model/src: |
125 |
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- rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since |
126 |
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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) |
128 |
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|
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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. |
132 |
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o model/src: |
133 |
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- fix vertical inter/extra-polation of density factor rhoFacF (for anelastic) |
134 |
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for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F. |
135 |
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Update output of exp. deep_anelastic (changes at truncation level). |
136 |
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o tools: |
137 |
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- add a hack in "remove_comments_sed" (used only with TAF) for recent |
138 |
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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. |
140 |
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o pkg/seaice: |
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- change the termination criterion so that maxits (SEAICElinearIterMax) |
142 |
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has an effect |
143 |
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- unify iteration parameters for implicit solvers (JFNK and Picard) |
144 |
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SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS |
145 |
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SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER |
146 |
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SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner |
147 |
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SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner |
148 |
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SEAICEnonLinTol replaces JFNKgamma_nonlin |
149 |
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- remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN |
150 |
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- add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and |
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use with SEAICEuseKrylov |
152 |
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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 |
154 |
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relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have |
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an effect. |
156 |
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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) |
159 |
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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), |
165 |
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- global_ocean.cs32x15.seaice (11 digits), |
166 |
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- seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update |
167 |
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- also update global_ocean.cs32x15 adjoint and tangent-linear results |
168 |
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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. |
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o pkg/dic: |
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- use the updated seaice fraction (from seaice pkgs) for DIC forcing |
177 |
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instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE |
178 |
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called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD); |
179 |
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- move also update with values from ATM-OCN Coupler in the same new S/R |
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(previously done in ocn_apply_import.F). |
181 |
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o tools/adjoint_options: |
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- specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default) |
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has been changed on Jan 14, 2016. |
184 |
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o pkg/ggl90: |
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- add alternative discretisation of vertical shear (off by default), to |
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compute the mean (@ grid-cell center) of vertical shear compon instead of |
187 |
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vertical shear of mean flow (@ grid-cell center). |
188 |
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- add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated |
189 |
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results on adjacent faces of cubed-sphere grids; this fix the restart. |
190 |
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o pkg/atm_compon_interf: |
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- skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just |
192 |
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pass last value, stored directly before export to CPL ; |
193 |
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Note: this affects results of Coupled set-up where OCN uses useImportSLP=T |
194 |
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- remove atmSLPr from pickup files (no longer needed for restart) |
195 |
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|
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checkpoint65s (2016/01/13) |
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o eesupp & genmake2: |
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- first check for Function ETIME and, if it fails, then check for subroutine |
199 |
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ETIME and consistent output; use the appropriate version in timers.F |
200 |
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o model/src: |
201 |
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- to check restart test, add option to apply EXCH to U,V earlier, just before |
202 |
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integr_continuity; turned off by default. |
203 |
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o pkg/dic: |
204 |
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- remove CPP option USE_ATMOSCO2 (not needed) |
205 |
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o tools/tst_2+2: |
206 |
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- try to ignore difference between +0 and -0 in binary file, causing test |
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to fail for no good reason. |
208 |
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o eesupp & genmake2: |
209 |
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- put back modif from Jinxuan Zhu - change etime fct call to S/R call - |
210 |
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but also check (in genmake2) that test runs and returns meaningful results. |
211 |
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o coupler pkgs: |
212 |
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Finish implementation of optionally-exchanged variable switches (started on |
213 |
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Nov 12) with addition of few more exchanged fields, including 2-way exchange |
214 |
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of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice |
215 |
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advection in OCN component; this requires sequential coupling. |
216 |
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coupler (pkg/atm_ocn_coupler): |
217 |
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- add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS |
218 |
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routines (useful for debug). |
219 |
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- only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume |
220 |
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flux, DIC fields) if corresponding switch is ON. |
221 |
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- add option to export RunOff to OCN (to use for DIC river input) |
222 |
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- add 2-way thSIce vars exchange; check for consistent cpl_sequential setting. |
223 |
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components (pkg/atm_ & ocn_compon_interf): |
224 |
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- to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around |
225 |
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optionally exchanged fields; add a check & stop in cpl_readparms.F. |
226 |
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ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2; |
227 |
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OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice. |
228 |
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- rename: fracIce -> sIceFrac_cpl (<- match coupler var name) |
229 |
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+ in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime. |
230 |
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- add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN. |
231 |
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- hold in common block coupler optionally-exchanged variable switch |
232 |
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and set default "useImportXXX" accordingly; + check & stop if inconsistent. |
233 |
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- add diagnostics for all imported fields from coupler (in both OCN & ATM); |
234 |
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this is intended to replace the OCN cplFldtave.* output files (not updated |
235 |
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to contain new additional exchanged fields). |
236 |
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o pkg/dic: |
237 |
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- fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code. |
238 |
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o pkg/thsice: |
239 |
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- when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading |
240 |
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and writing of thsice pickup files. |
241 |
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o pkg/atm_compon_interf: |
242 |
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- move all field individual export-call out of cpl_export_import_data.F |
243 |
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into new S/R ATM_EXPORT_FIELDS |
244 |
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o pkg/atm_compon_interf: |
245 |
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- store state variables (for now, only thSIce fields) just before beeing |
246 |
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exported (in cpl_export_import_data.F, like on ocean side) instead of from |
247 |
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atm_store_my_data.F like all exported fluxes. |
248 |
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- new version of pickup_cpl: write field names into meta file and read meta |
249 |
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file to find field postion in pickup. Also only write/read fields meeded for |
250 |
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restart (same logic as main pickup file ; also using pickupStrictlyMatch) |
251 |
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o pkg/dic: |
252 |
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- fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3. |
253 |
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o pkg/seaice: add new parameter SEAICEpressReplFac to choose between |
254 |
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pressure replacement method (=1., default) or original Hibler (1979) (=0.) |
255 |
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value can be from domain [0,1] to average between the two methods |
256 |
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o pkg/atm_phys: |
257 |
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- allow to provide 2-d map of albedo and mixed-layer depth from files (but |
258 |
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hold fixed in time). |
259 |
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|
260 |
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checkpoint65r (2015/12/21) |
261 |
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o pkg/seaice: |
262 |
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fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK |
263 |
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solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated |
264 |
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o pkg/seaice: |
265 |
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- fix a bug in computing areaS in (J-J -> J-1) that affects runs |
266 |
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when SEAICEscaleSurfStress=.TRUE., |
267 |
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- apply areaW and areaS in S/R seaice_calc_lhs |
268 |
|
o pkg/atm_phys: |
269 |
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- add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes |
270 |
|
(shortwave & longwave, net & downward) and diagnostics of temp. tendency |
271 |
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for individual contribution (convection, LSC cond, radiation) |
272 |
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- add Ruth Geen etal, GRL 2016, radiation options (see paper supp. |
273 |
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information); activated with: solar_exponent=0. and wv_exponent=-1. |
274 |
|
o pkg/ggl90: |
275 |
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- within IDEMIX add upper limit for horizontal group velocity to |
276 |
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avoid instability problems in the explicit horizontal diffusion term for |
277 |
|
long time steps or high resolution |
278 |
o pkg/diagnostics: |
o pkg/diagnostics: |
279 |
- simplify setting of local-array size in diagstats_output.F: uses "numLevels" |
- simplify setting of local-array size in diagstats_output.F: uses "numLevels" |
280 |
(from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels. |
(from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels. |
792 |
just copy level Nr value to level Nr+1. |
just copy level Nr value to level Nr+1. |
793 |
o doc: |
o doc: |
794 |
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
795 |
o pkg/streamice: |
o pkg/shelfice: |
796 |
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
797 |
SHELFICE.h: move array shelficemass to init_varia, initialise |
SHELFICE.h: move array shelficemass to init_varia, initialise |
798 |
from array shelficemassinit, which is set in init_fixed and |
from array shelficemassinit, which is set in init_fixed and |