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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 Freshen up a bit hs94.1x64x5, notably: |
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remove rotationPeriod and tRef=5*0. (adjoint only), and add exactConserv=.TRUE. |
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o pkg/generic_advdiff: |
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change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
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applies to files where Temperature & Salinity 2nd Order moments are used. |
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o pkg/ptracers: add second-order moment advection schemes (80 and 81); |
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this uses a dynamically allocated internal state data structure |
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(#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) |
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and requires a fortran 90 compiler |
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checkpoint59q |
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o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) |
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(from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) |
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o Refresh tutorial_global_oce_biogeo, notably: |
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- change bathymetry (put back seamounts in ACC, use hFacs) |
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- change EOS (POLY3 --> JMD95Z) |
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- use Bryan-Lewis vertical diffusivity |
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- use multidimensional advection |
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- remove old virtual virtual in dic pkg, now done through ptracer pkg |
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- change a couple of parameters in dic pkg |
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o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F |
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o pkg/obcs: change default to OBCSfixTopo = .true., |
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- set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result |
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- replace "debugMode" with "debugLevel .GE. debLevB" |
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o implementation of TAF directives for gchem,cfc,dic |
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o remove "exp5" (replaced by tutorial_deep_convection). |
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o pkg/obcs: add code to fix topography gradients normal to open boundaries; |
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this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; |
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the code can be turned on by setting OBCSfixTopo = .true. in data.obcs |
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--> changes results in exp4, seaice_obcs |
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o tutorial_deep_convection : |
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update the set-up and increase resolution and domain size ; start |
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from pseudo initial conditions = output at t=120mn in order to see |
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something happening when running testreport. |
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o pkg/seaice: add os7mp as an advection scheme |
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add check for advection schemes |
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add a flag for restoring T and S underneath sea ice |
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o pkg/my82: add netcdf-support and diagnostics |
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o thsice pkg: |
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- Now hsMax limits snow height by turning it into ice following |
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flooding scheme (and now conserving energy) |
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- Slight rewriting of the formula in thsice_calc_thick.F |
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- Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos |
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--> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice |
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checkpoint59p |
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o gchem / dic / cfc : |
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- add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); |
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- add new parameter files: "data.dic" & "data.cfc" ; |
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- various re-arrangement in initialisation & header file ; |
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- fix tutorial_global_oce_biogeo for multi-threaded test. |
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o pkg/dic: test for "pickup_dic" file when restarting ; |
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if no pickup-file, can restart with a re-initialised pH (same as it did |
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before) providing pickupStrictlyMatch is set to False. |
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o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP |
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+ fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP |
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o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2 |
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and staggerTimeStep is off (needed for stability of Internal-wave dynamics). |
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o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax, |
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& lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers |
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(note: not clear to me what lambdaTr1ClimRelax is still used for ...) |
| 68 |
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o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which |
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scheme to use for vorticty-term ; |
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- compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F |
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(with default selectVortScheme, return to original discretisation) |
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- remove weird combination (e.g.: upwindVorticity & highOrderVorticity) |
| 73 |
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o pkg/seaice: add a line to the summary to indicate grid type (B/C) |
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o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the |
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bottom ; only used with variable horizontal viscosity and non-hydrostatic. |
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also fix diagnostics VISCAHW & VISCA4W. |
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| 78 |
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checkpoint59o |
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o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). |
| 80 |
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o change the loop ordering in most gad_*_adv_x.F to improve vectorization: |
| 81 |
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move a few statemens out the main loop into separate loops |
| 82 |
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o pkg/shelfice: |
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- sort out freshwater flux; convert freshwater fluxes to mass fluxes |
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(kg/m^2/s), does not break tests, because in verification/isomip, |
| 85 |
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rhoConstFresh=rhoConst (by accident) |
| 86 |
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- rearrange computation of tLoc, sLoc, pLoc to make code more efficient |
| 87 |
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- move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into |
| 88 |
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new file model/src/seawater.F, so that they are available for all pkgs. |
| 89 |
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- convert potential temperature into in-situ temperature. This changes the |
| 90 |
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isomip tests => update tests |
| 91 |
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o add a flag writePickupAtEnd (default=true) to be able to suppress |
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writing a pickup at the last timestep |
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o tools/mpack-1.6 : |
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- disable automake (not working) and autoconf (not needed). |
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- update to version 1.6.4 which fix MD5 code on some 64 bits platforms |
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also cleaner with much less compilation warnings. |
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o pkg/profiles: |
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rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg |
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(for "less than 32 characters name" compiler requirement) |
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o pkg/obcs and pkg/exf: added capability to specify seaice open boundary |
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conditions that have a different sampling frequency than S/T/U/V obcs |
| 102 |
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o pkg/diagnostics (stats-diags): |
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- fix global Min/Max in case 1 processor get only empty tiles |
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o genmake2: replace (4 times) |
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make genmake_tc_1.o >> genmake_warnings 2>&1 |
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with |
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COMM="$CC $CFLAGS -c genmake_tc_1.c" |
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echo $COMM >> genmake_warnings |
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$COMM >> genmake_warnings 2>&1 |
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to make genmake2 always see the value of CC as specified in the optfile. |
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o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid. |
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- add diagnostics for 1srt & 2nd Order moments and sub-grid variance. |
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- modify verification advect_cs test to test SOM-advection on CS-grid. |
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o pkg/ctrl: |
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- Rewrite of ctrl_map_ini_ecco.F, |
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introducing a generic routine (ctrl_map_ini_gen.F). |
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- Modification of ctrl_bound/adctrl_bound handling control vector bounds. |
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checkpoint59n |
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o pkg/diagnostics: for large number of diagnostics, store diagnostic mate |
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number in dedicate array "hdiag": |
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- new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST |
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with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST. |
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- many small changes (integer format) for large number of diagnostics |
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- start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with |
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a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23. |
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o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For |
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usingSphericalGrid, this allows to define the rotated grid coordinates |
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via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the |
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geographical coordinates according to the inverse of the rotation defined |
| 131 |
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by the Euler angles, so that Coriolis parameter and online-interpolation by |
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exf works with the geographical coordinates on XC/YC/XG/YG. |
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Naturally, this feature does not work with all packages, so some |
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combinations are prohibited in config_summary (flt, flt_zonal, ecco, |
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profiles), because there the coordinates are assumed to be regular |
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spherical grid coordinates. |
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o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc: |
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- introduce isopycnal diffusion coefficient control. |
| 139 |
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o tools/adjoint_options: |
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- additional control vector components. |
| 141 |
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o pkg/mnc: have mnc create marginally meaning full coordinate variables |
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(that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 |
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o pkg/mypackage: |
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- add example of read/write pickup for state-var ; |
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- add entry points to the main code for state-vars diags & write-pickup. |
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o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year |
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transitions for useExfYearlyFields |
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- add new subroutine that determines the file to read from for |
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use*YearlyFields = .TRUE. and .FALSE. |
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- add a verification experiment to global_with_exf that tests |
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useExfYearlyFields with USE_EXF_INTERPOLATION defined |
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o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in |
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analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new |
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subroutines (which could be generated from a template, because they are |
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almost identical), for now they are included in obcs_prescribe_read.F for |
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simplicity |
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o pkg/exf: |
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- add a little more diagnostic to exf_interp_read (in analogy to |
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mds_read_field, can be turned off with debugLevel < debugLevA=1) |
| 160 |
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- improve vectorizability of exf_interp for TARGET_NEC_SX, makes code |
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ugly but fast by unrolling short inner loops, inserting a unroll=8 |
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directive in routine lagran, and splitting a loop and making do while the |
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outermost loop (the latter requires the intoduction of index arrays) |
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o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice |
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o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver |
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http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html |
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o verification/seaice_obcs: updated for restart test and latest options |
| 168 |
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o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different |
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ice rheology (so-called truncated ellipse, that gets rid of tensile stress); |
| 170 |
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for now this is only available for the C-grid code and also within |
| 171 |
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#ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code |
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checkpoint59m |
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o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) |
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and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature |
| 176 |
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o gad_som : fix flux output (& diagnostics) to have same units as other |
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advection scheme fluxes (was previously multiplied by deltaT). |
| 178 |
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o added verification/seaice_obcs both to test seaice open boundaries |
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and to provide an example matlab scrpt for generating them |
| 180 |
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o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume |
| 181 |
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o pkg/salt_plume: clean up salt_plume_frac.F to |
| 182 |
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remove redundancy in PlumeMethod 1 and 4 |
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o pkg/kpp: added saltplume diagnostics |
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o pkg/obcs and pkg/seaice: |
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- do not set uice and vice to zero when OB*icefile are unspecified |
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- OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default |
| 187 |
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- moved seaice tracer obcs after call to seaice_growth |
| 188 |
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o pkg/salt_plume: added various options for salt plume depth |
| 189 |
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criterion and for vertical distribution of the salt |
| 190 |
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checkpoint59l |
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o pkg/ptracers: new version of ptracers pickup: |
| 193 |
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read meta file and write only fields which are needed to restart. |
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( same logic as main pickup file ; also using pickupStrictlyMatch ) |
| 195 |
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o pkg/seaice: |
| 196 |
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- add timescale for melting due to warm mixed layer as a means of |
| 197 |
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setting SEAICE_availHeatFrac more conveniently |
| 198 |
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- add a CPP-flag/runtime parameter check for flooding algorithm |
| 199 |
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- reformulated availHeat in seaice_growth.F to be independent of AREA |
| 200 |
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o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent |
| 201 |
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unit changes |
| 202 |
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o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint |
| 203 |
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o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC |
| 204 |
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SX vector computer. |
| 205 |
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o pkg/seaice: |
| 206 |
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- removed SEAICE_FFIELDS.h and seaice_get_forcing.F |
| 207 |
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seaice forcing fields can now be read only through pkg/exf |
| 208 |
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- removed some unused halos |
| 209 |
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o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP |
| 210 |
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o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL |
| 211 |
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or U/VICE from U/VWIND before computing U/VSTRESS |
| 212 |
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| 213 |
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checkpoint59k |
| 214 |
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o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between |
| 215 |
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dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. |
| 216 |
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o fix un-initialised variable problem (in mom_vecinv & shap_filt): |
| 217 |
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all experiments pass when compile with un-initialised var. checking option. |
| 218 |
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o added pkg/salt_plume |
| 219 |
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o script to test restart (for now, in MITgcm_contrib/jmc_script) |
| 220 |
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o pkg/seaice: new read/write pickup version. |
| 221 |
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read meta file and write only fields which are needed to restart. |
| 222 |
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( same logic as main pickup file ; also using pickupStrictlyMatch ) |
| 223 |
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o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) |
| 224 |
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o lab_sea.hb87: modify the domain & update output.hb87.txt : |
| 225 |
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lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 |
| 226 |
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at j=1 & j=Ny+1 : this case is not treated correctly in the restart |
| 227 |
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process. Fixed here by closing the domain at the Northern boundary. |
| 228 |
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o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. |
| 229 |
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o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing |
| 230 |
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a set of consecutive levels in/from a 3-D array. |
| 231 |
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o pkg/ptracers: |
| 232 |
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use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). |
| 233 |
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to-do: fix pkg/diagnostics when large number of diagnostics are defined. |
| 234 |
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| 235 |
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checkpoint59j |
| 236 |
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o in pkgs: dic, obcs, offline, rbcs: |
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standard way to compute coeff. for time interpolation between 2 time reccords |
| 238 |
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which retains full precision (& make results less dependent on compiler). |
| 239 |
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update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. |
| 240 |
o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those |
o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those |
| 241 |
packages instead of reading ice cover and wind speed separately |
packages instead of reading ice cover and wind speed separately |
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o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h |
o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h |
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