| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
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|
| 7 |
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o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
| 8 |
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for B-grid vector (not yet tested) and C-grid vector (<- only used |
| 9 |
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when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). |
| 10 |
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o starting implementation of Duffy et al. (GRL 1999) salt plume scheme |
| 11 |
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(#ifdef ALLOW_SALT_PLUME) |
| 12 |
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o gather_2d/scatter_2d: removed halo regions |
| 13 |
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o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
| 14 |
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scheme and the corresponding test case (under front_relax dir). For now, |
| 15 |
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only available with Skew-flux form and not yet tested in realistic set-up. |
| 16 |
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adjoint: store directives updated, but gradient checks deteriorated, |
| 17 |
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so maybe GM/Redi adjoint is now broken. |
| 18 |
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o seaice adjoint |
| 19 |
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* add AREA, HEFF, HSNOW as control variable |
| 20 |
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(should not change lab_sea results) |
| 21 |
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* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
| 22 |
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o pkg/seaice: |
| 23 |
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* added computation of saltFlux in seaice_growth; |
| 24 |
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For time being, sea ice salinity is assumed constant |
| 25 |
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contribution of snow flooding to freshening of sea ice is neglected. |
| 26 |
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SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
| 27 |
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defaults to 0.0 in order to maintain backward compatibility. |
| 28 |
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Typical values for SEAICE_salinity are 4 to 10 g/kg. |
| 29 |
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* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
| 30 |
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* added SEAICE_availHeatFrac, which specifies fraction of surface level |
| 31 |
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heat content used to melt or grow ice |
| 32 |
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* commented out cap of HICE: it helps keep ice thinner |
| 33 |
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* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
| 34 |
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* applied OBCS T/S mask to HEFFM sea ice mask |
| 35 |
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|
| 36 |
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checkpoint59d |
| 37 |
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o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
| 38 |
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for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
| 39 |
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(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
| 40 |
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o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
| 41 |
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and change default value of parameter "GM_Small_Number"; |
| 42 |
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update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
| 43 |
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global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
| 44 |
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tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
| 45 |
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o pkg/ecco: cost function when applying pkg/smooth to controls |
| 46 |
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o pkg/ctrl: add forcingPrecond run time parameter |
| 47 |
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o pkg/seaice: |
| 48 |
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- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
| 49 |
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- fix bug in metric terms of u-equation in LSR solver (implicit part), |
| 50 |
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changes verification/lab_sea |
| 51 |
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- rearrange implicit part of u-equation in LSR solver to make it easier to |
| 52 |
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read, understand, and debug. This causes changes at the truncation level. |
| 53 |
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- fix (serious) bug in the boundary conditions (sign error in the implicit |
| 54 |
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part) of the LSR solver. Changes all LSR results. |
| 55 |
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- fixed problem with HSNOW initialization to avoid thick snow when AREA |
| 56 |
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is initilized with small values - does not change lab_sea results. |
| 57 |
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- added HsnowFile initialization capability |
| 58 |
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o pkg/smooth: addition to model/src and pkg/ctrl so allow |
| 59 |
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initialization of pkg/smooth and application to control vector |
| 60 |
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o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
| 61 |
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o dependencies: pkg/profiles requires pkg/cal |
| 62 |
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o pkg/profiles: |
| 63 |
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- added option ALLOW_PROFILES_GENERICGRID |
| 64 |
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-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
| 65 |
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that interpolation information (grid points and coefficients) is provided |
| 66 |
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within the netcdf input files. |
| 67 |
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-> sample matlab scripts can be found in MITgcm_contrib/gael |
| 68 |
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that allow you to prepare netcdf input files. |
| 69 |
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- also modified: cleaner include statements, cleaner error print statements, |
| 70 |
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cleaner stops when error, and more tests of the netcdf input files consistency. |
| 71 |
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o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
| 72 |
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o pkg/seaice: |
| 73 |
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- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
| 74 |
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requires a new routine: seaice_diagnostics_fill.F |
| 75 |
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- make sure that seaice does not move if not forced (pressure replacement |
| 76 |
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method, Hibler and Ip, 1995), changes results |
| 77 |
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- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
| 78 |
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- SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). |
| 79 |
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It is turned off by default (=-1.), because it changes the results. |
| 80 |
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- make it possible to read AREA from a file, too. |
| 81 |
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|
| 82 |
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checkpoint59c |
| 83 |
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o add S/R and diagnostics for oceanic mixed-layer depth |
| 84 |
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o move GMRedi call after all vertical mixing schemes (including KPP) |
| 85 |
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o pkg/thsice: |
| 86 |
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- ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs |
| 87 |
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(melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice |
| 88 |
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o pkg/obcs: |
| 89 |
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- bug fix for balance code |
| 90 |
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o pkg/seaice: |
| 91 |
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- allow values of SEAICE_elasticParm > 1 |
| 92 |
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- add new parameter SEAICE_evpTauRelax as an alternative |
| 93 |
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to SEAICE_elasticParm |
| 94 |
|
- make lsr boundary conditions free slip (by default), changes result |
| 95 |
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- add code for no slip boundary conditions for lsr |
| 96 |
|
- set minimum of zeta to zero (and not 4e8) (changes results) |
| 97 |
|
- add a cap on AREA after advecting AREA if seaice_growth is not called |
| 98 |
|
o change calculation of Visbeck K: |
| 99 |
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- no longer depend on tapering scheme; instead, compute slope (limited |
| 100 |
|
by GM_maxSlope). this is equivalent to what was comuted before with |
| 101 |
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clipping or linear tappering. |
| 102 |
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- fix vertical averaging (wrong by 1/2 level) |
| 103 |
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- leave the old version (but will not be maintained) within |
| 104 |
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#ifdef OLD_VISBECK_CALC / #endif |
| 105 |
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- update output of exp. ideal_2D_oce |
| 106 |
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o change error catch in calc_r_star to improve vectorization |
| 107 |
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o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
| 108 |
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add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
| 109 |
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o adjoint: |
| 110 |
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Re-organized adjoint checkpointing according to Matt Mazloff |
| 111 |
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(but with modifs/completions/cleanups) |
| 112 |
|
Storing is now bundled into large arrays to optimized I/O |
| 113 |
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(and second step in cleanup of the_main_loop) |
| 114 |
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|
| 115 |
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checkpoint59b |
| 116 |
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o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
| 117 |
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- export/import (between ocean & coupler) fields needed for ocean DIC. |
| 118 |
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o pkg/seaice: |
| 119 |
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- get rid of three more exchanges seaice_calc_viscosities (required |
| 120 |
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different loop boundaries in seaice_lsr and seaice_ocean_stress) |
| 121 |
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- bug fix in seaice_ocean_stress (update of lab_sea required) |
| 122 |
|
- reduce loop boundaries to necessary minimum also in seaice_evp |
| 123 |
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- go back to the old way of computing deltaC/Z as the adjoint likes that |
| 124 |
|
better |
| 125 |
|
o Refresh of tutorial_global_oce_latlon (includes changing salinity-like |
| 126 |
|
passive tracer to an Age Tracer) + update output.txt |
| 127 |
|
o pkg/exf: |
| 128 |
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- implement A-grid / C-grid selection for wind-stress input files. |
| 129 |
|
- clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) |
| 130 |
|
for now, in exf_bulk_largeyeager04.F only : |
| 131 |
|
- change implementation for case where windspeed + 2. components wind-stress |
| 132 |
|
are read-in. AND use rhoConstFresh to convert evap. |
| 133 |
|
o pkg/seaice: |
| 134 |
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- use correct EXCH_UV for wind-forcing (on A-grid). |
| 135 |
|
- change SEAICE_OPTIONS.h to limit the number of option combinations (regarding |
| 136 |
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SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops. |
| 137 |
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o pkg/exf: |
| 138 |
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- default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC) |
| 139 |
|
EXF_INTERPOLATION: |
| 140 |
|
- merge global_with_exf/code version of exf_interp_read.F |
| 141 |
|
to the main code ; |
| 142 |
|
- Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when |
| 143 |
|
reading the file ; Important: This options needs to be defined to recover |
| 144 |
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previous code. |
| 145 |
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otherwise, use fixed size array to read in (size=exf_interp_bufferSize). |
| 146 |
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- no longer loose real*8 precision along the way when using exf_iprec=64. |
| 147 |
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o pkg/seaice: rearrangement of common blocks (really needs more cleaning up) |
| 148 |
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- change discretisation of evp-solver in order to avoid another exchange |
| 149 |
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(changes lab_sea) and clean up a little |
| 150 |
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- replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS) |
| 151 |
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help the adjoint (this also changes the results slightly) |
| 152 |
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- add a few "_d 0" where they had been missing in seaice_evp.F |
| 153 |
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- cleaning up: remove unused seaice_calc_rhs.F |
| 154 |
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o pkg/exf: some cleaning-up: |
| 155 |
|
- change various "constants" into runtime parameters |
| 156 |
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- cleaned-up Large&Yeager04 routine which should eventually |
| 157 |
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replace exf_bulkformulae.F (changed names of S/R and CPP) |
| 158 |
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and merged various ALLOW_ATM_WIND options |
| 159 |
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only used with thsice pkg (in thsice_get_exf.F): |
| 160 |
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- implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04) |
| 161 |
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which are used when useStabilityFct_overIce=TRUE (= the default) |
| 162 |
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- change default values of ice & snow emissivity and scale downward LW |
| 163 |
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by ice & snow emissivity. |
| 164 |
|
o pkg/thsice: |
| 165 |
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fix few little problems, in thsice_calc_thickn.F: |
| 166 |
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- growth vertically (and not laterally) if iceFrac == iceMaskMax |
| 167 |
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- melt only laterally if hIce < hThinIce (as the comments say) |
| 168 |
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and in thsice_extend.F: |
| 169 |
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- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
| 170 |
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- start to form ice as soon as the minimum ice-volume is reachable. |
| 171 |
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update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice), |
| 172 |
|
and cpl_aim+ocn |
| 173 |
|
o pkg/kpp |
| 174 |
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- move computation of surface related input fields to KPP into a new |
| 175 |
|
subroutine kpp_forcing_surf.F |
| 176 |
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- remove wrong (within bi,bj loops) EXCH calls. |
| 177 |
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- little cleaning (add argument myThid in last position, cvs header ...) |
| 178 |
|
- for now, fix conservation problem by exchanging KPPviscAz (may not |
| 179 |
|
be the best fix) |
| 180 |
|
o pkg/seaice |
| 181 |
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- check for inconsistent evp parameter/cpp-flag combination |
| 182 |
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- remove leftover errIO flat for obsolete name list error handling |
| 183 |
|
o OpenAD |
| 184 |
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- changed verification/OpenAD to full baroclinic setup (including GM/Redi) |
| 185 |
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|
| 186 |
|
checkpoint59a |
| 187 |
|
o pkg/seaice: some parameter clarifications and a little bit of clean up |
| 188 |
|
o pkg/thsice: rename run-time parameters: |
| 189 |
|
himin -> hIceMin |
| 190 |
|
himin0 -> hThinIce |
| 191 |
|
hihig -> hThickIce |
| 192 |
|
i0 -> i0swFrac |
| 193 |
|
transCoef -> bMeltCoef |
| 194 |
|
frac_energy -> fracMelting |
| 195 |
|
add new parameters: hNewIceMax, fracFreezing, dhSnowLin |
| 196 |
|
with default values (for now) that do not change the results. |
| 197 |
|
remove old version of thsice vars advection in pkg/seaice. |
| 198 |
|
o in FFIELDS.h: |
| 199 |
|
- replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD |
| 200 |
|
- make pLoad & sIceLoad always available (but still only used if |
| 201 |
|
ATMOSPHERIC_LOADING is #define). |
| 202 |
|
o pkg/kpp: replaced _KPP_RL with _RL |
| 203 |
|
o bug fixes for vertical diffusivity computations when both KPP and |
| 204 |
|
3D diffusivity arrays are used. |
| 205 |
|
o pkg/seaice: fix bug in evp solver, while doing that |
| 206 |
|
- change (improve?) discretization of stress computations for both |
| 207 |
|
cgrid-lsr and evp solver |
| 208 |
|
- add a new routine to compute strain rates |
| 209 |
|
- the above changes lab_sea results |
| 210 |
|
- add no slip conditions for evp solver (off by default), lsr-version |
| 211 |
|
may follow |
| 212 |
|
- fix exchange for shear at Z-points (does not change lab_sea) |
| 213 |
|
- retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp |
| 214 |
|
(to force the user to pick a time step since there is not "safe" way |
| 215 |
|
of choosing it) |
| 216 |
|
- add principal stress diagnostics |
| 217 |
|
- rearrange fields for evp a little to avoid having to call a: too many |
| 218 |
|
exchanges and b: exchanges for stress trensor components which we do |
| 219 |
|
not have. |
| 220 |
|
- modify Hibler+Bryan (1987) stress coupling so that it reuses information |
| 221 |
|
of evp, complete rewrite for lsr case (latter is does not yet work |
| 222 |
|
in all cases) |
| 223 |
|
o pkg/kpp: add code to have mixing in shelf ice caverns |
| 224 |
|
- add myThid to all kpp routines (long overdue) |
| 225 |
|
|
| 226 |
|
checkpoint59 |
| 227 |
|
o pkg/exf: |
| 228 |
|
- fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND & |
| 229 |
|
ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid |
| 230 |
|
- move exf header files from lower_case.h to UPPER_CASE.h ; |
| 231 |
|
add missing cvs Header & Name |
| 232 |
|
- add adjoint routines and flow dirs for newly used exch_uv_agrid routines |
| 233 |
|
- add namelist param. selectStressGridPosition, exf_monFreq |
| 234 |
|
- retire many _CLIM routines, and remove data.exf_clim |
| 235 |
|
+ params moved to data.exf |
| 236 |
|
+ climsst, climsss now handled by exf_set_gen, i.e. |
| 237 |
|
climss?period=0 refers to constant field, |
| 238 |
|
climss?period=-12 to monthly forcing |
| 239 |
|
- split up namelists in data.exf |
| 240 |
|
o pkg/seaice: |
| 241 |
|
- remove seaice_exch and seaice_exch_uv |
| 242 |
|
- remove superfluous exchange of theta |
| 243 |
|
- add myThid to seaice_budget_ocean/ice |
| 244 |
|
- add new interface for atmospheric wind forcing (C-grid only) |
| 245 |
|
+ new routine |
| 246 |
|
+ two new field (taux, tauy for stress over ice) |
| 247 |
|
+ removed one global field (DAIRN) for C-grid case only |
| 248 |
|
o pkg/thsise |
| 249 |
|
- 2nd set of modifs for thsice adjoint in conjunction with exf |
| 250 |
|
o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.) |
| 251 |
|
|
| 252 |
|
checkpoint58y_post |
| 253 |
|
o Added capability for latitudinal dependence of Bryan and Lewis, 1979 |
| 254 |
|
vertical diffusivity, similar to that in MOM4; turned on using |
| 255 |
|
#define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using |
| 256 |
|
diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file. |
| 257 |
|
o Added capability for 3D specification of background vertical diffusion |
| 258 |
|
coefficient. This is done by (i) #define ALLOW_3D_DIFFKR |
| 259 |
|
in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime |
| 260 |
|
"data" file that contains the 3D vertical diffusivity coefficients. |
| 261 |
|
o ice dynamics (pkg/seaice) with thsice thermodynamics: |
| 262 |
|
- add code within pkg thsice to advect & diffuse sea-ice fields |
| 263 |
|
similar to (and will replace) what has been added in seaice_advdiff.F, |
| 264 |
|
but: - conserving Mass, Heat & Salt. |
| 265 |
|
- better when using non-linear advection scheme (not yet fully tested) |
| 266 |
|
- can also be used in atmospheric set-up (for now, only the diffusion). |
| 267 |
|
|
| 268 |
|
checkpoint58x_post |
| 269 |
|
o IO option for global-file compact format: |
| 270 |
|
- add options when generating topology (utils/exch2/matlab-topology-generator) |
| 271 |
|
- add I/O capability (pkg/mdsio). |
| 272 |
|
- adapt utils/matlab/rdmds.m to read this format. |
| 273 |
|
for now long-line format not yet supported by pkg/mdsio (& exch2). |
| 274 |
|
o shelfice: add a few diagnostics |
| 275 |
|
|
| 276 |
|
checkpoint58w_post |
| 277 |
|
o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: |
| 278 |
|
rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref |
| 279 |
|
(and replace horiVertRatio in NH code). |
| 280 |
|
Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) |
| 281 |
|
and tutorial_plume_on_slope (sensitive to truncation) |
| 282 |
|
o seaice: if ALLOW_ATM_WIND is undefined use wind stress |
| 283 |
|
directly to drive seaice model (C-grid only) |
| 284 |
|
o exf: when input wind-stress (#undef ALLOW_ATM_WIND): |
| 285 |
|
- reintroduce computation of wind from stress, |
| 286 |
|
- compute tau (in exf_bulkformulae.F) from windstress averaged to |
| 287 |
|
mass points to avoid tau = 0 |
| 288 |
|
- fix serious bug: (1/3) in Fortran is not the same as (1./3.) |
| 289 |
|
o rdmnc.m: make it work with "global" files created with gluemnc |
| 290 |
|
o rdmnc.m : some improvements in dealing with singleton dimension |
| 291 |
|
(tested on all testreport mnc output files). |
| 292 |
|
o genmake2: disable pkg/profiles if netcdf test fails. |
| 293 |
|
o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output. |
| 294 |
|
o move call to cal_readparms up to make calendar parameters/variable available |
| 295 |
|
to all packages |
| 296 |
|
|
| 297 |
|
checkpoint58v_post |
| 298 |
|
o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get |
| 299 |
|
useDynP_inEos_Zc tested. |
| 300 |
|
o pkg/exf: changes to properly interpolate/mask/scale initial fields |
| 301 |
|
o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields |
| 302 |
|
and portions thereof. See read_cs.txt for description and examples. |
| 303 |
|
o utils/matlab/cs_grid/bk_line: to compute transport through passages, |
| 304 |
|
add a script (grt_circ_bkl.m) to generate broken-line between 2 points, |
| 305 |
|
following the great-circle arc between those 2 points. |
| 306 |
|
o trap un-initialized variable with pathscale compiler on weddell.mit.edu |
| 307 |
|
(thanks to Constantinos): fix few problems and get (almost) all exp to pass. |
| 308 |
|
o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in |
| 309 |
|
- enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) |
| 310 |
|
- used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81) |
| 311 |
|
- still needs work (not working with some options ; efficiency to improve) |
| 312 |
|
and serious testing. |
| 313 |
|
- use this scheme for temperature & salinity in 2 advection test exp.: |
| 314 |
|
advect_xy & advect_xz, respectively. |
| 315 |
|
|
| 316 |
|
checkpoint58u_post |
| 317 |
|
o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. |
| 318 |
o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. |
o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. |
| 319 |
o testreport: add option "-skipdir" to skip some test. |
o testreport: add option "-skipdir" to skip some test. |
| 320 |
o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent |
o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent |
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