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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
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|
| 7 |
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o pkg/ptracers: add Bruno Deremble's code to complete the linear surface |
| 8 |
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correction for tracer conservation |
| 9 |
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- enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE. |
| 10 |
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|
| 11 |
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checkpoint65y (2016/07/29) |
| 12 |
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o pkg/debug (stats): |
| 13 |
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- change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to |
| 14 |
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proc/thread mapping); |
| 15 |
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- fix Min & Max for case where 1 thread has only empty tiles; |
| 16 |
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- use RL variable to count number of wet grid points (with big domain, |
| 17 |
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can be too large to fit into integer*4). |
| 18 |
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o pkg/monitor: |
| 19 |
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- use RL variable to count number of wet grid points (but used only for del2) |
| 20 |
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- add new routine to compute Advective CFL within tracer time-stepping with |
| 21 |
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writing delayed until next monitor output. |
| 22 |
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o pkg/obcs: |
| 23 |
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- fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW) |
| 24 |
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o pkg/dic & seaice: |
| 25 |
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- fix compilation of ocean component for coupled atm+ocn model with |
| 26 |
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seaice dynamics & dic. |
| 27 |
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|
| 28 |
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checkpoint65x (2016/06/11) |
| 29 |
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o add a license text file in main MITgcm tree. |
| 30 |
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o added pkg/bling: |
| 31 |
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- intermediate complexity biogeochemical model |
| 32 |
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- see bling_description.txt for details |
| 33 |
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- verification experiment is global_oce_biogeo_bling (for now, in |
| 34 |
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Contrib/verification_other/); tested daily on baudelaire with gfortran. |
| 35 |
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- add entry point in pkg/gchem for new pkg "bling". |
| 36 |
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o pkg/seaice: fix tensile stength computation |
| 37 |
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- replace global field tensileStrength by tensileStrFac |
| 38 |
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- tensileStrFac can be computed once in S/R seaice_init_varia |
| 39 |
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- fortunately that does not affect any verification results |
| 40 |
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|
| 41 |
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checkpoint65w (2016/05/12) |
| 42 |
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o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles |
| 43 |
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with ECCO_CTRL_DEPRECATED defined |
| 44 |
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o verification/global_ocean.cs32x15: |
| 45 |
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- change secondary test "viscA4" to also test "selectP_inEOS_Zc=3" |
| 46 |
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with "selectNHfreeSurf=1". |
| 47 |
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o model/src (non-hydrostatic free-surface): |
| 48 |
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- More "natural" expression of NH free-surface term (case selectNHfreeSurf=1): |
| 49 |
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was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf. |
| 50 |
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- Calculate surface vertical velocity after 2-D solver adjustment (accounts |
| 51 |
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for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv |
| 52 |
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and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1. |
| 53 |
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This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux. |
| 54 |
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- Update output (changes at machine truncation level) of verification exp: |
| 55 |
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exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d), |
| 56 |
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short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d). |
| 57 |
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o pkg/seaice: ITD code |
| 58 |
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- fix picking up from a single category model by initialising |
| 59 |
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heff/area/hsnowITD = 0. in seaice_itd_pickup.F |
| 60 |
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- split a long warning message in seaice_check_pickup.F into two lines, |
| 61 |
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because NEC SX-ACE cannot deal with the long line. |
| 62 |
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o model/src: |
| 63 |
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- fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3) |
| 64 |
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o pkg/seaice: |
| 65 |
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- add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG |
| 66 |
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o pkg/seaice: |
| 67 |
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- add basal stress as parameterisation for grounding ice |
| 68 |
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following Lemieux et al. (2015) |
| 69 |
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- turn on by setting new parameter SEAICEbasalDragK2 to a value |
| 70 |
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larger than 0. Lemieux et al. (2015) recommend 15. |
| 71 |
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- The adjoint complains with extra recomputations so there is also a |
| 72 |
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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 |
| 74 |
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- compile the new code in lab_sea |
| 75 |
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o verification/halfpipe_streamice: |
| 76 |
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- update both TAF and OpenAD adm output (machine truncation differences) |
| 77 |
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|
| 78 |
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checkpoint65v (2016/04/08) |
| 79 |
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o verification/advect_xz: |
| 80 |
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- increase overlap size from 3 to 4 and add new secondary test for PQM |
| 81 |
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advection scheme (with mono & wino limiter). |
| 82 |
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- change main exp. to test PPM (with weno limiter) adv.scheme on Temp. |
| 83 |
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o model/src: |
| 84 |
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- new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently |
| 85 |
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added phi0Ref) to set vertical axis origin and phiRef origin; |
| 86 |
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keep Ro_SeaLevel for backward compatibility (with a warning). |
| 87 |
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According to coordinate and fluid type: |
| 88 |
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OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top) |
| 89 |
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ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom) |
| 90 |
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OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top) |
| 91 |
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ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom) |
| 92 |
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- remove Ro_SeaLevel from ATM experiment parameter files; |
| 93 |
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- in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the |
| 94 |
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complement; update output.txt (changes at machine truncation level). |
| 95 |
o pkg/seaice/seaice_evp.F |
o pkg/seaice/seaice_evp.F |
| 96 |
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- simplify computation of deltaZ and zetaZ to simple averaging following |
| 97 |
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Bouillon et al. (2013). This removes a lot of code, but also changes |
| 98 |
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verification experiment lab_sea.hb87 -> updated |
| 99 |
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|
| 100 |
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checkpoint65u (2016/03/14) |
| 101 |
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o pkg/generic_advdiff: |
| 102 |
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- from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52) |
| 103 |
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with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP); |
| 104 |
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Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for |
| 105 |
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testing and not for actual use. |
| 106 |
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o model/src: |
| 107 |
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- add parameter "phi0Ref" to specify reference [pressure/geo] potential at |
| 108 |
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origin r = rF(1); |
| 109 |
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- add options (parameter selectP_inEOS_Zc) to select which pressure to use |
| 110 |
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in EOS for height coordinate: enable to include NH Pressure or to use |
| 111 |
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more accurate pressure vertical profile; options not linked to EOS type |
| 112 |
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(as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type; |
| 113 |
|
- start to implement variable gravity (along vertical): for now, only with |
| 114 |
|
z-coords (not even z*). |
| 115 |
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- add Ideal Gas equation of state for height coordinate. |
| 116 |
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- update OpenAD output (affected at machine truncation level) of exp: |
| 117 |
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global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo. |
| 118 |
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o pkg/exf: |
| 119 |
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- add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result |
| 120 |
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of exf interpolation (before any rescaling, rotation or interpolation |
| 121 |
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to velocity point) for each field that gets loaded from file. This option |
| 122 |
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identically mimics the input file organization (e.g. record numbers in year |
| 123 |
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by year input files) besides the change in horizontal grid. |
| 124 |
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- add rotateStressOnAgrid run-time switch so that wind stress fields |
| 125 |
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can be provided on the A-grid in zonal/meridional direction and |
| 126 |
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rotated on the fly. This only applies to the case when the exf |
| 127 |
|
interpolation is off and rotateStressOnAgrid is false by default. |
| 128 |
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o model/src: |
| 129 |
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- rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since |
| 130 |
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it's also used with pkg/atm_phys) and add few more parameters (but still |
| 131 |
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inactive, src code yet to come) |
| 132 |
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|
| 133 |
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checkpoint65t (2016/02/10) |
| 134 |
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o pkg/atm_phys: |
| 135 |
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- from Ruth Geen: add optical depth dependence on CO2 concentration. |
| 136 |
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o model/src: |
| 137 |
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- fix vertical inter/extra-polation of density factor rhoFacF (for anelastic) |
| 138 |
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for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F. |
| 139 |
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Update output of exp. deep_anelastic (changes at truncation level). |
| 140 |
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o tools: |
| 141 |
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- add a hack in "remove_comments_sed" (used only with TAF) for recent |
| 142 |
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version of OpenMPI (shipped with FC.23): comment out the new header |
| 143 |
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file "mpif-sizeof.h" which causes problems to TAF. |
| 144 |
|
o pkg/seaice: |
| 145 |
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- change the termination criterion so that maxits (SEAICElinearIterMax) |
| 146 |
|
has an effect |
| 147 |
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- unify iteration parameters for implicit solvers (JFNK and Picard) |
| 148 |
|
SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS |
| 149 |
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SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER |
| 150 |
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SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner |
| 151 |
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SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner |
| 152 |
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SEAICEnonLinTol replaces JFNKgamma_nonlin |
| 153 |
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- remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN |
| 154 |
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- add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and |
| 155 |
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use with SEAICEuseKrylov |
| 156 |
|
o pkg/seaice/seaice_lsr.F |
| 157 |
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fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only |
| 158 |
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relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have |
| 159 |
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an effect. |
| 160 |
|
o pkg/seaice: add two new parameters |
| 161 |
|
- SEAICEuseLSR to simplify the logic in seaice_dynsolver (this |
| 162 |
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parameter is not in any namelist) |
| 163 |
|
- SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as |
| 164 |
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a preconditioner for the non-linear Newton iteration of the JFNK |
| 165 |
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solver |
| 166 |
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o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT, |
| 167 |
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affects some experiments at truncation level: |
| 168 |
|
- global_ocean.cs32x15.icedyn (11 digits), |
| 169 |
|
- global_ocean.cs32x15.seaice (11 digits), |
| 170 |
|
- seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update |
| 171 |
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- also update global_ocean.cs32x15 adjoint and tangent-linear results |
| 172 |
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o pkg/salt_plume & pkg/thsice: |
| 173 |
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- for coupled set-up with pkg/thsice in ATM and pkg/salt_plume in OCN, |
| 174 |
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connect salt_plume flux to ATM-OCN coupling pkgs interface: |
| 175 |
|
a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for |
| 176 |
|
export to coupler interface) even without compiling pkg/salt_plume ; |
| 177 |
|
b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field |
| 178 |
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(saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH. |
| 179 |
|
o pkg/dic: |
| 180 |
|
- use the updated seaice fraction (from seaice pkgs) for DIC forcing |
| 181 |
|
instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE |
| 182 |
|
called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD); |
| 183 |
|
- move also update with values from ATM-OCN Coupler in the same new S/R |
| 184 |
|
(previously done in ocn_apply_import.F). |
| 185 |
|
o tools/adjoint_options: |
| 186 |
|
- specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default) |
| 187 |
|
has been changed on Jan 14, 2016. |
| 188 |
|
o pkg/ggl90: |
| 189 |
|
- add alternative discretisation of vertical shear (off by default), to |
| 190 |
|
compute the mean (@ grid-cell center) of vertical shear compon instead of |
| 191 |
|
vertical shear of mean flow (@ grid-cell center). |
| 192 |
|
- add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated |
| 193 |
|
results on adjacent faces of cubed-sphere grids; this fix the restart. |
| 194 |
|
o pkg/atm_compon_interf: |
| 195 |
|
- skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just |
| 196 |
|
pass last value, stored directly before export to CPL ; |
| 197 |
|
Note: this affects results of Coupled set-up where OCN uses useImportSLP=T |
| 198 |
|
- remove atmSLPr from pickup files (no longer needed for restart) |
| 199 |
|
|
| 200 |
|
checkpoint65s (2016/01/13) |
| 201 |
|
o eesupp & genmake2: |
| 202 |
|
- first check for Function ETIME and, if it fails, then check for subroutine |
| 203 |
|
ETIME and consistent output; use the appropriate version in timers.F |
| 204 |
|
o model/src: |
| 205 |
|
- to check restart test, add option to apply EXCH to U,V earlier, just before |
| 206 |
|
integr_continuity; turned off by default. |
| 207 |
|
o pkg/dic: |
| 208 |
|
- remove CPP option USE_ATMOSCO2 (not needed) |
| 209 |
|
o tools/tst_2+2: |
| 210 |
|
- try to ignore difference between +0 and -0 in binary file, causing test |
| 211 |
|
to fail for no good reason. |
| 212 |
|
o eesupp & genmake2: |
| 213 |
|
- put back modif from Jinxuan Zhu - change etime fct call to S/R call - |
| 214 |
|
but also check (in genmake2) that test runs and returns meaningful results. |
| 215 |
|
o coupler pkgs: |
| 216 |
|
Finish implementation of optionally-exchanged variable switches (started on |
| 217 |
|
Nov 12) with addition of few more exchanged fields, including 2-way exchange |
| 218 |
|
of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice |
| 219 |
|
advection in OCN component; this requires sequential coupling. |
| 220 |
|
coupler (pkg/atm_ocn_coupler): |
| 221 |
|
- add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS |
| 222 |
|
routines (useful for debug). |
| 223 |
|
- only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume |
| 224 |
|
flux, DIC fields) if corresponding switch is ON. |
| 225 |
|
- add option to export RunOff to OCN (to use for DIC river input) |
| 226 |
|
- add 2-way thSIce vars exchange; check for consistent cpl_sequential setting. |
| 227 |
|
components (pkg/atm_ & ocn_compon_interf): |
| 228 |
|
- to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around |
| 229 |
|
optionally exchanged fields; add a check & stop in cpl_readparms.F. |
| 230 |
|
ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2; |
| 231 |
|
OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice. |
| 232 |
|
- rename: fracIce -> sIceFrac_cpl (<- match coupler var name) |
| 233 |
|
+ in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime. |
| 234 |
|
- add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN. |
| 235 |
|
- hold in common block coupler optionally-exchanged variable switch |
| 236 |
|
and set default "useImportXXX" accordingly; + check & stop if inconsistent. |
| 237 |
|
- add diagnostics for all imported fields from coupler (in both OCN & ATM); |
| 238 |
|
this is intended to replace the OCN cplFldtave.* output files (not updated |
| 239 |
|
to contain new additional exchanged fields). |
| 240 |
|
o pkg/dic: |
| 241 |
|
- fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code. |
| 242 |
|
o pkg/thsice: |
| 243 |
|
- when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading |
| 244 |
|
and writing of thsice pickup files. |
| 245 |
|
o pkg/atm_compon_interf: |
| 246 |
|
- move all field individual export-call out of cpl_export_import_data.F |
| 247 |
|
into new S/R ATM_EXPORT_FIELDS |
| 248 |
|
o pkg/atm_compon_interf: |
| 249 |
|
- store state variables (for now, only thSIce fields) just before beeing |
| 250 |
|
exported (in cpl_export_import_data.F, like on ocean side) instead of from |
| 251 |
|
atm_store_my_data.F like all exported fluxes. |
| 252 |
|
- new version of pickup_cpl: write field names into meta file and read meta |
| 253 |
|
file to find field postion in pickup. Also only write/read fields meeded for |
| 254 |
|
restart (same logic as main pickup file ; also using pickupStrictlyMatch) |
| 255 |
|
o pkg/dic: |
| 256 |
|
- fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3. |
| 257 |
|
o pkg/seaice: add new parameter SEAICEpressReplFac to choose between |
| 258 |
|
pressure replacement method (=1., default) or original Hibler (1979) (=0.) |
| 259 |
|
value can be from domain [0,1] to average between the two methods |
| 260 |
|
o pkg/atm_phys: |
| 261 |
|
- allow to provide 2-d map of albedo and mixed-layer depth from files (but |
| 262 |
|
hold fixed in time). |
| 263 |
|
|
| 264 |
|
checkpoint65r (2015/12/21) |
| 265 |
|
o pkg/seaice: |
| 266 |
|
fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK |
| 267 |
|
solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated |
| 268 |
|
o pkg/seaice: |
| 269 |
|
- fix a bug in computing areaS in (J-J -> J-1) that affects runs |
| 270 |
|
when SEAICEscaleSurfStress=.TRUE., |
| 271 |
|
- apply areaW and areaS in S/R seaice_calc_lhs |
| 272 |
|
o pkg/atm_phys: |
| 273 |
|
- add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes |
| 274 |
|
(shortwave & longwave, net & downward) and diagnostics of temp. tendency |
| 275 |
|
for individual contribution (convection, LSC cond, radiation) |
| 276 |
|
- add Ruth Geen etal, GRL 2016, radiation options (see paper supp. |
| 277 |
|
information); activated with: solar_exponent=0. and wv_exponent=-1. |
| 278 |
|
o pkg/ggl90: |
| 279 |
|
- within IDEMIX add upper limit for horizontal group velocity to |
| 280 |
|
avoid instability problems in the explicit horizontal diffusion term for |
| 281 |
|
long time steps or high resolution |
| 282 |
|
o pkg/diagnostics: |
| 283 |
|
- simplify setting of local-array size in diagstats_output.F: uses "numLevels" |
| 284 |
|
(from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels. |
| 285 |
|
o testreport: |
| 286 |
|
- remove "-v" (verbose option) in default mpirun command. |
| 287 |
|
o pkg/seaice/seaice_growth: |
| 288 |
|
- catch potential division by zero in ITD code, does not change |
| 289 |
|
verification results |
| 290 |
|
o pkg/ecco: |
| 291 |
|
- retire old codes to the Attic. The calls to retired functions are |
| 292 |
|
left in a commented form in case they ever need to be re-activated. |
| 293 |
|
- ecco_check.F: issue warning if any old CPP option is |
| 294 |
|
defined that corresponds to retired codes -- then stop. |
| 295 |
|
o pkg/atm_compon_interf: |
| 296 |
|
- change seaice fraction (use for OCN dic surf.flux) stored and sent to |
| 297 |
|
coupler: use last time-step value instead of average over cplSendFrq_iter |
| 298 |
|
time-step, similar to what is done for seaIceMass. |
| 299 |
|
This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up. |
| 300 |
|
o eesupp & genmake2: |
| 301 |
|
- from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME); |
| 302 |
|
<= remove until a fix is found for some ifort version on ia32 machine. |
| 303 |
|
o pkg/seaice/seaice_evp: |
| 304 |
|
- refine residual computation |
| 305 |
|
|
| 306 |
|
checkpoint65q (2015/11/18) |
| 307 |
|
o pkg/seaice/seaice_evp: |
| 308 |
- fix residual computations so that they no longer affect the actual |
- fix residual computations so that they no longer affect the actual |
| 309 |
simulation code |
simulation code |
| 310 |
|
- fix seaice_readparams to be able to actually set new parameters |
| 311 |
|
SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little |
| 312 |
o model/src: |
o model/src: |
| 313 |
- fix wrong truncation (single prec) from "FLOAT" function in expressions |
- fix wrong truncation (single prec) from "FLOAT" function in expressions |
| 314 |
like: deltaT*FLOAT(myIter) when myIter is large: |
like: deltaT*FLOAT(myIter) when myIter is large: |
| 796 |
just copy level Nr value to level Nr+1. |
just copy level Nr value to level Nr+1. |
| 797 |
o doc: |
o doc: |
| 798 |
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
| 799 |
o pkg/streamice: |
o pkg/shelfice: |
| 800 |
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
| 801 |
SHELFICE.h: move array shelficemass to init_varia, initialise |
SHELFICE.h: move array shelficemass to init_varia, initialise |
| 802 |
from array shelficemassinit, which is set in init_fixed and |
from array shelficemassinit, which is set in init_fixed and |
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