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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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| 7 |
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checkpoint59g |
| 8 |
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o adjoint testing: in preparation for changing testreport: |
| 9 |
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- output format: cost and grad written on separated lines |
| 10 |
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- ad output results in directory "results" (instead of "results_ad") |
| 11 |
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o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
| 12 |
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o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
| 13 |
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o pkg/ecco: allow user defined cost function contributions |
| 14 |
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o testreport: |
| 15 |
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Allow to choose (per experiment) the list of tested output variables |
| 16 |
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and the main variable (used to issue a pass/FAIL ) ; |
| 17 |
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- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
| 18 |
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- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
| 19 |
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Also modify printing of summary: |
| 20 |
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a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
| 21 |
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b) echo the list of tested variables in the individual summary.txt of |
| 22 |
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each experiment. |
| 23 |
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o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
| 24 |
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threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
| 25 |
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(but still depend on the tile decompostion of the domain). |
| 26 |
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o pkg/seaice: change a discretization detail to make the B-grid code |
| 27 |
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"more symmetric". This change is likely to remove all "ridges/leads" that |
| 28 |
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where quasi-aligned with the grid in B-grid solutions. It may also be |
| 29 |
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the solution to the stress coupling issues with the B-grid. |
| 30 |
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o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
| 31 |
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remove .cvsignore from input dir. (since testreport no longer run here). |
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o pkg/thsice: |
| 33 |
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- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
| 34 |
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- fix reshaping of sea-ice just after advection: |
| 35 |
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melt all the ice only if ice-volume is too small. |
| 36 |
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- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
| 37 |
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prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
| 38 |
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and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
| 39 |
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o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
| 40 |
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tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
| 41 |
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o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
| 42 |
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forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
| 43 |
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(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
| 44 |
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and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
| 45 |
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of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
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-> update output.txt |
| 47 |
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o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
| 48 |
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this affects truncation error: -> update output.txt of exp: |
| 49 |
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global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
| 50 |
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ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
| 51 |
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|
| 52 |
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checkpoint59f |
| 53 |
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o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
| 54 |
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o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
| 55 |
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a bounded range (in forward mode) |
| 56 |
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o pkg/ecco, ctrl, autodiff and mom_common: |
| 57 |
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internal parameter controls, completements of implementations |
| 58 |
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o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
| 59 |
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o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
| 60 |
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(not seem any difference in testing results). |
| 61 |
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o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
| 62 |
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at face corners. |
| 63 |
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o pkg/generic_advdiff: |
| 64 |
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- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
| 65 |
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loop range indices for computing vertical advection tendency |
| 66 |
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and do the calculation in the interior only (no overlap) ; |
| 67 |
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for now, only implemented for SOM advection (to save CPU time). |
| 68 |
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- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
| 69 |
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o exch2 adjoint |
| 70 |
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First set of changes: |
| 71 |
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- add exch2 hand-written adjoint templates |
| 72 |
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- exch2 hand-written no longer use TAF-flag 'nownew_arg' |
| 73 |
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This will require cleanup in pkg/autodiff/*.F |
| 74 |
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(changed routines currently kept separate in verif. code/) |
| 75 |
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- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
| 76 |
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that used to hide exch2 or cubed-sphere specific code |
| 77 |
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(commented via 'cph-exch2') |
| 78 |
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o pkg/seaice |
| 79 |
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- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
| 80 |
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o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
| 81 |
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output of global_ocean.cs32x15.thsice . |
| 82 |
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|
| 83 |
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checkpoint59e |
| 84 |
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o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
| 85 |
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for B-grid vector (not yet tested) and C-grid vector (<- only used |
| 86 |
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when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). |
| 87 |
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o starting implementation of Duffy et al. (GRL 1999) salt plume scheme |
| 88 |
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(#ifdef ALLOW_SALT_PLUME) |
| 89 |
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o gather_2d/scatter_2d: removed halo regions |
| 90 |
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o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
| 91 |
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scheme and the corresponding test case (under front_relax dir). For now, |
| 92 |
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only available with Skew-flux form and not yet tested in realistic set-up. |
| 93 |
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adjoint: store directives updated, but gradient checks deteriorated, |
| 94 |
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so maybe GM/Redi adjoint is now broken. |
| 95 |
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o seaice adjoint |
| 96 |
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* add AREA, HEFF, HSNOW as control variable |
| 97 |
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(should not change lab_sea results) |
| 98 |
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* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
| 99 |
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o pkg/seaice: |
| 100 |
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* added computation of saltFlux in seaice_growth; |
| 101 |
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For time being, sea ice salinity is assumed constant |
| 102 |
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contribution of snow flooding to freshening of sea ice is neglected. |
| 103 |
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SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
| 104 |
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defaults to 0.0 in order to maintain backward compatibility. |
| 105 |
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Typical values for SEAICE_salinity are 4 to 10 g/kg. |
| 106 |
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* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
| 107 |
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* added SEAICE_availHeatFrac, which specifies fraction of surface level |
| 108 |
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heat content used to melt or grow ice |
| 109 |
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* commented out cap of HICE: it helps keep ice thinner |
| 110 |
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* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
| 111 |
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* applied OBCS T/S mask to HEFFM sea ice mask |
| 112 |
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|
| 113 |
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checkpoint59d |
| 114 |
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o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
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for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
| 116 |
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(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
| 117 |
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o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
| 118 |
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and change default value of parameter "GM_Small_Number"; |
| 119 |
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update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
| 120 |
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global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
| 121 |
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tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
| 122 |
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o pkg/ecco: cost function when applying pkg/smooth to controls |
| 123 |
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o pkg/ctrl: add forcingPrecond run time parameter |
| 124 |
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o pkg/seaice: |
| 125 |
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- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
| 126 |
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- fix bug in metric terms of u-equation in LSR solver (implicit part), |
| 127 |
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changes verification/lab_sea |
| 128 |
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- rearrange implicit part of u-equation in LSR solver to make it easier to |
| 129 |
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read, understand, and debug. This causes changes at the truncation level. |
| 130 |
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- fix (serious) bug in the boundary conditions (sign error in the implicit |
| 131 |
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part) of the LSR solver. Changes all LSR results. |
| 132 |
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- fixed problem with HSNOW initialization to avoid thick snow when AREA |
| 133 |
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is initilized with small values - does not change lab_sea results. |
| 134 |
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- added HsnowFile initialization capability |
| 135 |
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o pkg/smooth: addition to model/src and pkg/ctrl so allow |
| 136 |
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initialization of pkg/smooth and application to control vector |
| 137 |
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o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
| 138 |
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o dependencies: pkg/profiles requires pkg/cal |
| 139 |
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o pkg/profiles: |
| 140 |
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- added option ALLOW_PROFILES_GENERICGRID |
| 141 |
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-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
| 142 |
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that interpolation information (grid points and coefficients) is provided |
| 143 |
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within the netcdf input files. |
| 144 |
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-> sample matlab scripts can be found in MITgcm_contrib/gael |
| 145 |
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that allow you to prepare netcdf input files. |
| 146 |
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- also modified: cleaner include statements, cleaner error print statements, |
| 147 |
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cleaner stops when error, and more tests of the netcdf input files consistency. |
| 148 |
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o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
| 149 |
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o pkg/seaice: |
| 150 |
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- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
| 151 |
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requires a new routine: seaice_diagnostics_fill.F |
| 152 |
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- make sure that seaice does not move if not forced (pressure replacement |
| 153 |
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method, Hibler and Ip, 1995), changes results |
| 154 |
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- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
| 155 |
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- SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). |
| 156 |
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It is turned off by default (=-1.), because it changes the results. |
| 157 |
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- make it possible to read AREA from a file, too. |
| 158 |
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|
| 159 |
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checkpoint59c |
| 160 |
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o add S/R and diagnostics for oceanic mixed-layer depth |
| 161 |
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o move GMRedi call after all vertical mixing schemes (including KPP) |
| 162 |
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o pkg/thsice: |
| 163 |
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- ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs |
| 164 |
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(melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice |
| 165 |
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o pkg/obcs: |
| 166 |
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- bug fix for balance code |
| 167 |
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o pkg/seaice: |
| 168 |
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- allow values of SEAICE_elasticParm > 1 |
| 169 |
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- add new parameter SEAICE_evpTauRelax as an alternative |
| 170 |
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to SEAICE_elasticParm |
| 171 |
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- make lsr boundary conditions free slip (by default), changes result |
| 172 |
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- add code for no slip boundary conditions for lsr |
| 173 |
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- set minimum of zeta to zero (and not 4e8) (changes results) |
| 174 |
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- add a cap on AREA after advecting AREA if seaice_growth is not called |
| 175 |
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o change calculation of Visbeck K: |
| 176 |
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- no longer depend on tapering scheme; instead, compute slope (limited |
| 177 |
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by GM_maxSlope). this is equivalent to what was comuted before with |
| 178 |
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clipping or linear tappering. |
| 179 |
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- fix vertical averaging (wrong by 1/2 level) |
| 180 |
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- leave the old version (but will not be maintained) within |
| 181 |
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#ifdef OLD_VISBECK_CALC / #endif |
| 182 |
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- update output of exp. ideal_2D_oce |
| 183 |
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o change error catch in calc_r_star to improve vectorization |
| 184 |
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o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
| 185 |
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add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
| 186 |
|
o adjoint: |
| 187 |
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Re-organized adjoint checkpointing according to Matt Mazloff |
| 188 |
|
(but with modifs/completions/cleanups) |
| 189 |
|
Storing is now bundled into large arrays to optimized I/O |
| 190 |
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(and second step in cleanup of the_main_loop) |
| 191 |
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|
| 192 |
|
checkpoint59b |
| 193 |
|
o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
| 194 |
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- export/import (between ocean & coupler) fields needed for ocean DIC. |
| 195 |
|
o pkg/seaice: |
| 196 |
|
- get rid of three more exchanges seaice_calc_viscosities (required |
| 197 |
|
different loop boundaries in seaice_lsr and seaice_ocean_stress) |
| 198 |
|
- bug fix in seaice_ocean_stress (update of lab_sea required) |
| 199 |
|
- reduce loop boundaries to necessary minimum also in seaice_evp |
| 200 |
|
- go back to the old way of computing deltaC/Z as the adjoint likes that |
| 201 |
|
better |
| 202 |
|
o Refresh of tutorial_global_oce_latlon (includes changing salinity-like |
| 203 |
|
passive tracer to an Age Tracer) + update output.txt |
| 204 |
|
o pkg/exf: |
| 205 |
|
- implement A-grid / C-grid selection for wind-stress input files. |
| 206 |
|
- clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) |
| 207 |
|
for now, in exf_bulk_largeyeager04.F only : |
| 208 |
|
- change implementation for case where windspeed + 2. components wind-stress |
| 209 |
|
are read-in. AND use rhoConstFresh to convert evap. |
| 210 |
|
o pkg/seaice: |
| 211 |
|
- use correct EXCH_UV for wind-forcing (on A-grid). |
| 212 |
|
- change SEAICE_OPTIONS.h to limit the number of option combinations (regarding |
| 213 |
|
SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops. |
| 214 |
|
o pkg/exf: |
| 215 |
|
- default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC) |
| 216 |
|
EXF_INTERPOLATION: |
| 217 |
|
- merge global_with_exf/code version of exf_interp_read.F |
| 218 |
|
to the main code ; |
| 219 |
|
- Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when |
| 220 |
|
reading the file ; Important: This options needs to be defined to recover |
| 221 |
|
previous code. |
| 222 |
|
otherwise, use fixed size array to read in (size=exf_interp_bufferSize). |
| 223 |
|
- no longer loose real*8 precision along the way when using exf_iprec=64. |
| 224 |
|
o pkg/seaice: rearrangement of common blocks (really needs more cleaning up) |
| 225 |
|
- change discretisation of evp-solver in order to avoid another exchange |
| 226 |
|
(changes lab_sea) and clean up a little |
| 227 |
|
- replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS) |
| 228 |
|
help the adjoint (this also changes the results slightly) |
| 229 |
|
- add a few "_d 0" where they had been missing in seaice_evp.F |
| 230 |
|
- cleaning up: remove unused seaice_calc_rhs.F |
| 231 |
|
o pkg/exf: some cleaning-up: |
| 232 |
|
- change various "constants" into runtime parameters |
| 233 |
|
- cleaned-up Large&Yeager04 routine which should eventually |
| 234 |
|
replace exf_bulkformulae.F (changed names of S/R and CPP) |
| 235 |
|
and merged various ALLOW_ATM_WIND options |
| 236 |
|
only used with thsice pkg (in thsice_get_exf.F): |
| 237 |
|
- implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04) |
| 238 |
|
which are used when useStabilityFct_overIce=TRUE (= the default) |
| 239 |
|
- change default values of ice & snow emissivity and scale downward LW |
| 240 |
|
by ice & snow emissivity. |
| 241 |
|
o pkg/thsice: |
| 242 |
|
fix few little problems, in thsice_calc_thickn.F: |
| 243 |
|
- growth vertically (and not laterally) if iceFrac == iceMaskMax |
| 244 |
|
- melt only laterally if hIce < hThinIce (as the comments say) |
| 245 |
|
and in thsice_extend.F: |
| 246 |
|
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
| 247 |
|
- start to form ice as soon as the minimum ice-volume is reachable. |
| 248 |
|
update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice), |
| 249 |
|
and cpl_aim+ocn |
| 250 |
|
o pkg/kpp |
| 251 |
|
- move computation of surface related input fields to KPP into a new |
| 252 |
|
subroutine kpp_forcing_surf.F |
| 253 |
|
- remove wrong (within bi,bj loops) EXCH calls. |
| 254 |
|
- little cleaning (add argument myThid in last position, cvs header ...) |
| 255 |
|
- for now, fix conservation problem by exchanging KPPviscAz (may not |
| 256 |
|
be the best fix) |
| 257 |
|
o pkg/seaice |
| 258 |
|
- check for inconsistent evp parameter/cpp-flag combination |
| 259 |
|
- remove leftover errIO flat for obsolete name list error handling |
| 260 |
|
o OpenAD |
| 261 |
|
- changed verification/OpenAD to full baroclinic setup (including GM/Redi) |
| 262 |
|
|
| 263 |
|
checkpoint59a |
| 264 |
|
o pkg/seaice: some parameter clarifications and a little bit of clean up |
| 265 |
|
o pkg/thsice: rename run-time parameters: |
| 266 |
|
himin -> hIceMin |
| 267 |
|
himin0 -> hThinIce |
| 268 |
|
hihig -> hThickIce |
| 269 |
|
i0 -> i0swFrac |
| 270 |
|
transCoef -> bMeltCoef |
| 271 |
|
frac_energy -> fracMelting |
| 272 |
|
add new parameters: hNewIceMax, fracFreezing, dhSnowLin |
| 273 |
|
with default values (for now) that do not change the results. |
| 274 |
|
remove old version of thsice vars advection in pkg/seaice. |
| 275 |
o in FFIELDS.h: |
o in FFIELDS.h: |
| 276 |
- replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD |
- replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD |
| 277 |
- make pLoad & sIceLoad always available (but still only used if |
- make pLoad & sIceLoad always available (but still only used if |
| 298 |
of evp, complete rewrite for lsr case (latter is does not yet work |
of evp, complete rewrite for lsr case (latter is does not yet work |
| 299 |
in all cases) |
in all cases) |
| 300 |
o pkg/kpp: add code to have mixing in shelf ice caverns |
o pkg/kpp: add code to have mixing in shelf ice caverns |
| 301 |
|
- add myThid to all kpp routines (long overdue) |
| 302 |
|
|
| 303 |
checkpoint59 |
checkpoint59 |
| 304 |
o pkg/exf: |
o pkg/exf: |
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