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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/seaice: |
| 8 |
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- remove seaice_exch and seaice_exch_uv |
| 9 |
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- remove superfluous exchange of theta |
| 10 |
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- add myThid to seaice_budget_ocean/ice |
| 11 |
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| 12 |
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checkpoint58y_post |
| 13 |
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o Added capability for latitudinal dependence of Bryan and Lewis, 1979 |
| 14 |
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vertical diffusivity, similar to that in MOM4; turned on using |
| 15 |
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#define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using |
| 16 |
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diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file. |
| 17 |
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o Added capability for 3D specification of background vertical diffusion |
| 18 |
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coefficient. This is done by (i) #define ALLOW_3D_DIFFKR |
| 19 |
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in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime |
| 20 |
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"data" file that contains the 3D vertical diffusivity coefficients. |
| 21 |
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o ice dynamics (pkg/seaice) with thsice thermodynamics: |
| 22 |
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- add code within pkg thsice to advect & diffuse sea-ice fields |
| 23 |
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similar to (and will replace) what has been added in seaice_advdiff.F, |
| 24 |
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but: - conserving Mass, Heat & Salt. |
| 25 |
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- better when using non-linear advection scheme (not yet fully tested) |
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- can also be used in atmospheric set-up (for now, only the diffusion). |
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| 28 |
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checkpoint58x_post |
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o IO option for global-file compact format: |
| 30 |
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- add options when generating topology (utils/exch2/matlab-topology-generator) |
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- add I/O capability (pkg/mdsio). |
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- adapt utils/matlab/rdmds.m to read this format. |
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for now long-line format not yet supported by pkg/mdsio (& exch2). |
| 34 |
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o shelfice: add a few diagnostics |
| 35 |
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| 36 |
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checkpoint58w_post |
| 37 |
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o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: |
| 38 |
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rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref |
| 39 |
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(and replace horiVertRatio in NH code). |
| 40 |
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Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) |
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and tutorial_plume_on_slope (sensitive to truncation) |
| 42 |
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o seaice: if ALLOW_ATM_WIND is undefined use wind stress |
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directly to drive seaice model (C-grid only) |
| 44 |
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o exf: when input wind-stress (#undef ALLOW_ATM_WIND): |
| 45 |
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- reintroduce computation of wind from stress, |
| 46 |
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- compute tau (in exf_bulkformulae.F) from windstress averaged to |
| 47 |
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mass points to avoid tau = 0 |
| 48 |
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- fix serious bug: (1/3) in Fortran is not the same as (1./3.) |
| 49 |
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o rdmnc.m: make it work with "global" files created with gluemnc |
| 50 |
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o rdmnc.m : some improvements in dealing with singleton dimension |
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(tested on all testreport mnc output files). |
| 52 |
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o genmake2: disable pkg/profiles if netcdf test fails. |
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o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output. |
| 54 |
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o move call to cal_readparms up to make calendar parameters/variable available |
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to all packages |
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|
| 57 |
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checkpoint58v_post |
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o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get |
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useDynP_inEos_Zc tested. |
| 60 |
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o pkg/exf: changes to properly interpolate/mask/scale initial fields |
| 61 |
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o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields |
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and portions thereof. See read_cs.txt for description and examples. |
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o utils/matlab/cs_grid/bk_line: to compute transport through passages, |
| 64 |
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add a script (grt_circ_bkl.m) to generate broken-line between 2 points, |
| 65 |
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following the great-circle arc between those 2 points. |
| 66 |
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o trap un-initialized variable with pathscale compiler on weddell.mit.edu |
| 67 |
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(thanks to Constantinos): fix few problems and get (almost) all exp to pass. |
| 68 |
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o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in |
| 69 |
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- enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) |
| 70 |
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- used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81) |
| 71 |
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- still needs work (not working with some options ; efficiency to improve) |
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and serious testing. |
| 73 |
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- use this scheme for temperature & salinity in 2 advection test exp.: |
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advect_xy & advect_xz, respectively. |
| 75 |
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|
| 76 |
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checkpoint58u_post |
| 77 |
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o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. |
| 78 |
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o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. |
| 79 |
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o testreport: add option "-skipdir" to skip some test. |
| 80 |
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o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent |
| 81 |
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momentum calculation. |
| 82 |
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o gad_advection: fix vertAdvecScheme (if different from advectionScheme) |
| 83 |
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o some cleaning: usePickupBeforeC35 no longer supported ; remove this option. |
| 84 |
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remove checkpoint.F and the_correction_step.F (no longer used); |
| 85 |
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do the k loop inside CYCLE_TRACER (supposed to be more efficient). |
| 86 |
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o add option (linFSConserveTr) to correct for tracer source/sink due to |
| 87 |
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Linear Free surface |
| 88 |
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o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine |
| 89 |
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o pkg/thsice: fix reading mnc-pickups |
| 90 |
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| 91 |
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checkpoint58t_post |
| 92 |
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o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) |
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o pkg/mdsio: |
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- clean-up mdsio_readfield.F & mdsio_writefield_new.F and |
| 95 |
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move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & |
| 96 |
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mdsio_write_field.F (S/R MDS_WRITE_FIELD); |
| 97 |
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- fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD |
| 98 |
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- collect old S/R in one file: mdsio_rw_field.F (now just a call to |
| 99 |
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either MDS_READ_FIELD or MDS_WRITE_FIELD ) |
| 100 |
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- new S/R (to replace MDSWRITEMETA), which allows to write more |
| 101 |
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informations (variable names, time ...) to meta files. |
| 102 |
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- modify rdmds.m to give back the meta file content. |
| 103 |
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o pkg/diagnostics: change vertical interpolation to be safer, and more |
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flexible (define p-levels to interpolate to in data.diagnostics); |
| 105 |
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add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right |
| 106 |
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diagnostic pointer. |
| 107 |
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o pkg/seaice: more cleaning up of seaice_growth, added many comments |
| 108 |
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o pkg/exf: put runoff0 and runoff1 into the appropriate common block |
| 109 |
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o fix multi-category seaice: |
| 110 |
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- change cpp flag SEAICE_MULTILEVEL to more meaningful name: |
| 111 |
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SEAICE_MULTICATEGORY |
| 112 |
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- fix short wave heat flux |
| 113 |
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o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics |
| 114 |
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and allow to use EVP solver. Change forward lab_sea: test both EVP |
| 115 |
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solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) |
| 116 |
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o Initial check-in of lab_sea adjoint |
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(very similar to natl_box_adjoint/code_seaice) |
| 118 |
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* used C-grid and EVP solver |
| 119 |
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* used KPP, GM/Redi |
| 120 |
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* uses inAdExact=.TRUE. |
| 121 |
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* gradient checks fail for both ADM and TLM |
| 122 |
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due to sensitive snow melt code in seaice_grwoth (look for "JZ") |
| 123 |
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f.d. gradients actually seem more problematic than ADM, TLM gradients; |
| 124 |
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issue is related to forward mismatch between g77 an ifort |
| 125 |
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o pkg/seaice: overhaul of thermodynamics |
| 126 |
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- growth.F and groatb.F are replaced by new routine seaice_growth.F |
| 127 |
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- budget.F is replaced by two new routines seaice_budget_ocean/ice.F |
| 128 |
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- move a few global fields out of SEAICE.h into seaice_growth.F and |
| 129 |
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make them 2D (FICE/QNETO/ ...) |
| 130 |
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- remove FO (it is the same as QNETO) |
| 131 |
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- introduce a few local fields to avoid modifying external fields such |
| 132 |
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as atemp, etc. |
| 133 |
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| 134 |
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checkpoint58s_post |
| 135 |
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o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F |
| 136 |
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changed exf_set_gen.F so that |
| 137 |
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genperiod=0 means input file is one time-constant field and |
| 138 |
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genperiod=-12 means input file contains 12 monthly means |
| 139 |
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o CG2D: use pre-computed solver main-diagonal (stored in common block); |
| 140 |
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this affects truncation error ; generate new output file for exp. which |
| 141 |
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fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), |
| 142 |
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global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), |
| 143 |
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ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), |
| 144 |
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MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), |
| 145 |
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tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), |
| 146 |
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vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) |
| 147 |
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o start implementation of deep-atmosphere and anelastic formulation |
| 148 |
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o verification: remove 2nd copy of input files and use script "prepare_run" |
| 149 |
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to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) |
| 150 |
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o mom_common/vecinv/fluxform: fix a few initialisation isssues |
| 151 |
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o profiles: fix for multithreaded case |
| 152 |
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| 153 |
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o diagnostics: rename few diags: |
| 154 |
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s/'PRESSURE'/'RCENTER '/g |
| 155 |
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s/'TICE '/'oceFreez'/g |
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s/'TAUX '/'oceTAUX '/g |
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s/'TAUY '/'oceTAUY '/g |
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s/'SWFLUX '/'oceQsw '/g |
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s/DIFx/DFxE/g |
| 160 |
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s/DIFy/DFyE/g |
| 161 |
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and add few ocean-forcing diagnostics: |
| 162 |
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atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS |
| 163 |
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o modifications to pkg/seaice/growth.F and budget.F, which change results of |
| 164 |
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lab_sea experiment: HSNOW was sometimes treated as effective and sometimes |
| 165 |
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as actual snow thickness. It now refers everywhere to effective snow |
| 166 |
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thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. |
| 167 |
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|
| 168 |
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checkpoint58r_post |
| 169 |
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o modifications to pkg/seaice/growth.F, which change results of |
| 170 |
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lab_sea experiment: fixes pertain to melting snow over open water, to |
| 171 |
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masking EVAP under sea ice, and to using the correct AREA variable for |
| 172 |
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computations of EVAP, PRECIP, HSNOW, and GHEFF |
| 173 |
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o add ability to read bathy, salt, and theta using MNC (off by def) |
| 174 |
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o add flooding algorithm and advection of HSNOW for pkg/seaice; |
| 175 |
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both are turned off by default and do no change any results |
| 176 |
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o seaice advection with pkg/thsice: a step toward the use of non-linear |
| 177 |
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advection scheme, but #ifdef or commented out for now (requires more EXCH). |
| 178 |
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o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens |
| 179 |
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(identical results) and the standard version of EXTERNAL_FIELDS_LOAD |
| 180 |
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in natl_box (affects results @ truncation level: update output.txt) |
| 181 |
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o multi-threading and IO: |
| 182 |
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- replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. |
| 183 |
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- remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls |
| 184 |
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(needed to work with SingleCpuIO): tested in all verif. exp. |
| 185 |
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o GAD: use simpler DST3 formulation as default (old version left within #ifdef) |
| 186 |
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affects the results (but none of the verification test uses this scheme). |
| 187 |
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o Adding some pkg/diagnostics capability to pkg/seaice |
| 188 |
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(will certainly be subject to changes) |
| 189 |
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o ctrl: adding new control variables: |
| 190 |
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lwflux, lwdown, evap, snowprecip, apressure, runoff |
| 191 |
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|
| 192 |
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checkpoint58q_post |
| 193 |
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o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up |
| 194 |
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1/6-deg Southern Ocean configuration by 8% on IBM Datastar and |
| 195 |
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high_res_cube configuration by 4% on Columbia. |
| 196 |
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o clean-up multi-threaded problems (reported by debugger tcheck on ACES); |
| 197 |
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add (in global_with_exf/code) a version of EXF_INTERP_READ without |
| 198 |
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dynamical allocation (seems to work in multi-threaded). |
| 199 |
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o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using |
| 200 |
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single CPU io) so that TAF does not have to see EESUPPORT.h |
| 201 |
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o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
| 202 |
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|
| 203 |
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checkpoint58p_post |
| 204 |
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o obcs: stop if obcs is used with useCDscheme = .true. |
| 205 |
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o shelfice: |
| 206 |
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- fix a sign error so that no slip at shelfice interface works |
| 207 |
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- remove stop for combination non-hydrostatic code and shelfice. That does |
| 208 |
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not mean, that the results are correct, but at least they are numerically |
| 209 |
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stable |
| 210 |
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o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) |
| 211 |
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o added adjoint exch routined for all exch*3d* routines |
| 212 |
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and updated flow directives |
| 213 |
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|
| 214 |
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checkpoint58o_post |
| 215 |
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o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; |
| 216 |
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remove old subroutines (_XY_ & _XYZ_); update the adjoint version. |
| 217 |
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o change controling S/R for writing pickup file (new S/R do_write_pickup) |
| 218 |
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and clean-up reading/writing of pickup files. |
| 219 |
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o fix local version of read/write pickup (NH part) in rotating_tank/code |
| 220 |
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o simplify EXCH interface: |
| 221 |
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- change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) |
| 222 |
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- not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version |
| 223 |
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o added the regrid package |
| 224 |
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o shelfice: |
| 225 |
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- add a simple boundary layer scheme to reduce noise |
| 226 |
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- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
| 227 |
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|
| 228 |
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checkpoint58n_post |
| 229 |
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o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
| 230 |
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local variable (not in common block). |
| 231 |
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o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
| 232 |
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- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
| 233 |
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- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
| 234 |
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to work with SingleCpuIO. |
| 235 |
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o add "_d 0" to real constant of pkg/cfc subroutines ; |
| 236 |
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update exp. cfc_exemple & tutorial_cfc_offline output files. |
| 237 |
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o multi-threading and IO: |
| 238 |
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- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
| 239 |
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(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
| 240 |
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- barrier before and after reading. |
| 241 |
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- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
| 242 |
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- avoid using MDS_WRITELOCAL for LAND pkg output. |
| 243 |
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- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
| 244 |
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common-block variables ; Allows multi-threading with master-thread IO. |
| 245 |
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o change default MAX_NO_THREADS from 32 to 4 ; |
| 246 |
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and stop cleanly when MAX_NO_THREADS is too small. |
| 247 |
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o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
| 248 |
|
|
| 249 |
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checkpoint58m_post |
| 250 |
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o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
| 251 |
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and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
| 252 |
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o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
| 253 |
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keep global_ocean.90x40x15 (for AD testing) with former secondary test |
| 254 |
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(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
| 255 |
|
o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
| 256 |
|
add MITgcm_tutorials (= code + all the tutorials) |
| 257 |
o ecco, option to compute cost for total ssh (mean+anom) |
o ecco, option to compute cost for total ssh (mean+anom) |
| 258 |
o consistent with addition of ptracer and ssh in pkg/profiles |
o consistent with addition of ptracer and ssh in pkg/profiles |
| 259 |
o profiles: adding ptracer and ssh |
o profiles: adding ptracer and ssh |
| 260 |
o testreport: change multi-test output-file name |
o testreport: change multi-test output-file name |
| 261 |
(from output.txt.{name} to output.{name}.txt) |
(from output.txt.{name} to output.{name}.txt) |
| 262 |
o profiles: now ok for mutli-threaded case |
o profiles: now ok for mutli-tiles case |
| 263 |
o seaice: add 4 parameters for different advection schemes for area, |
o seaice: add 4 parameters for different advection schemes for area, |
| 264 |
(effective) seaice thickness, enthalphy, and snow height. Their default |
(effective) seaice thickness, enthalphy, and snow height. Their default |
| 265 |
is the standard parameter SEAICEadvScheme |
is the standard parameter SEAICEadvScheme |
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