| 4 |
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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o pkg/seaice: |
| 8 |
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Major overhaul of the LSOR solver: change discretization from original |
| 9 |
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finite differences to finite volume. The old routine is still in the |
| 10 |
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file seaice_lsr.F and can be turned on with the CPP-flag |
| 11 |
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SEAICE_OLD_AND_BAD_DISCRETIZATION |
| 12 |
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Along with this change, the discretization of the strain rates is changed. |
| 13 |
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The same flag turns on the old discretization in seaice_calc_strainrates.F |
| 14 |
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All verification experiments with seaice are affected (except for |
| 15 |
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seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old |
| 16 |
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results by setting the above flag. |
| 17 |
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Further changes involve changes in defaults: |
| 18 |
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- ALLOW_FLOODING is defined and turned on by default |
| 19 |
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- SEAICE_advSnow = .true. is now the default |
| 20 |
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- SEAICE_advSalt = .true. is now the default |
| 21 |
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- SEAICE_advAge = .true. is now the default |
| 22 |
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- B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE |
| 23 |
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is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS |
| 24 |
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- seaice_growth: replace computation of UG by a simple copy from wspeed |
| 25 |
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|
| 26 |
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checkpoint61k |
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o pkg/seaice: a few bug fixes mostly concerning the metric terms: |
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seaice_lsr: fixed a few metric terms, |
| 29 |
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affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs |
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add more debugging diagnostics |
| 31 |
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seaice_evp: removed superfluous many metric terms of FV discretization |
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of stress divergence |
| 33 |
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affects lab_sea, lab_sea.hb87 |
| 34 |
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seaice_ocean_stress: removed superfluous many metric terms of FV discretization |
| 35 |
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of stress divergence for non-evp solver |
| 36 |
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(this part is not tested anywhere) |
| 37 |
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seaice_calc_strainrates: fixed a bug in no-slip boundary conditions, |
| 38 |
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they were effectively only half slip |
| 39 |
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affects lab_sea.hb87 |
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updated all relevant verification experiments |
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|
| 42 |
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checkpoint61j |
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o pkg/seaice: turn a few hard wired parameters into run time parameters |
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o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model |
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time in seconds as promised by the usints in seaice_monitor and exf_monitor |
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o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids |
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that are not cubed-sphere grids |
| 48 |
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o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR |
| 49 |
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o pkg/ctrl: |
| 50 |
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fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low) |
| 51 |
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o non-hydrostatic (calc_gw.F): |
| 52 |
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fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec |
| 53 |
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update output of exp. global_ocean.cs32x15.viscA4 |
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o remove backward compatibility for thetaMin,phiMin |
| 55 |
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(replaced by xgOrigin,ygOrigin on Jan 27, 2009) |
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o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the |
| 57 |
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interpolated wind field not only for curvilineargrid=.true., but also |
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for a rotated grid (rotateGrid=.true.) |
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o pkg/exf: add capability to bypass interpolation for runoff |
| 60 |
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by setting yet another CPP-flag |
| 61 |
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o eesupp/src, B-grid exchange: |
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add simple (6 tiles, non MPI) CS exch + standard interface S/R. |
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o autodiff |
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new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV |
| 65 |
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allows to switch to single-prec common blocks; |
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corresponding switch occurs in tamc.h, integer isbyte |
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TAF store directivs "byte" and "kind" seem equivalent; |
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Most tamc.h have been updated correspondingly. |
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|
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checkpoint61i |
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o autodiff: |
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fix autodiff_sore/_restore indices for obcs |
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(spotted by I. Hoteit, M. Mazloff) |
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o pkg/autodiff, pkg/ctrl: |
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Add flag to reduce all tapelev I/O to single-prec. |
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In data.ctrl set |
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doSinglePrecTapelev = .TRUE. |
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o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2: |
| 79 |
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check in hack for SX8 compiler (for dxV, dyU); remove it afterwards. |
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o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for |
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real fresh water flux (not yet) |
| 82 |
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o pkg/mdsio & rw: |
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- add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta) |
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- add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX. |
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o pkg/flt: |
| 86 |
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- replace FLT_INIT by 3-steps standard initialization S/R: readparms, |
| 87 |
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init_fixed & ini_varia. |
| 88 |
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- clean-up & simplify linear interpolation S/R: |
| 89 |
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move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid. |
| 90 |
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- fix some indices (mainly vertical index) ; add IMPLICIT NONE. |
| 91 |
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- more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R. |
| 92 |
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- add vert. coordinate & horiz. indices to output files. |
| 93 |
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- change vertical position in initial condition, from index to depth [m]. |
| 94 |
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- store horizontal (decimal) indices i,j in common block (instead of coord. x,y) |
| 95 |
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(easier to get to a curvilinear grid) ; delX,delY no longer used. |
| 96 |
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o pkg/ggl90: a few modifications: |
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- fix bottom boundary condition, and interpolation of KappaE |
| 98 |
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near top and bottom |
| 99 |
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- use same set of viscosity/diffusivity for TKE/momnetum/tracer |
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- add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH) |
| 101 |
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- add a few options for mixing-length upper limit (--> mxlMaxFlag) |
| 102 |
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o rename thetaMin,phiMin -> xgOrigin,ygOrigin |
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(maintain temporary backward compatibility, until next checkpoint) |
| 104 |
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|
| 105 |
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checkpoint61h |
| 106 |
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o pkg/diagnostics with "periodic averaging diagnostics": |
| 107 |
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fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. |
| 108 |
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o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82 |
| 109 |
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o pkg/obcs: fix loop ranges for balancing code |
| 110 |
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o pkg/flt: |
| 111 |
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- improve criteria for finding which tile owns a float. |
| 112 |
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- fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case. |
| 113 |
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o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg |
| 114 |
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aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling |
| 115 |
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with ocean biogeo) |
| 116 |
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o pkg/flt: |
| 117 |
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- do some cleaning and fix the restart ; |
| 118 |
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- add output.txt in flt_example/results to get this pkg tested. |
| 119 |
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o genmake2: add an EXTENDED_SRC option and flag. |
| 120 |
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for now, cannot be turned on on command line (only through genmake_local) |
| 121 |
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o pkg/mdsio: read/write vector: |
| 122 |
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- singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS |
| 123 |
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- singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR |
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& MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. |
| 125 |
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- affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) |
| 126 |
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(drop to 4 digits matching for grad). But this test does not look very |
| 127 |
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reliable (was already failling on eddy, fc5, at 6.digits). Update output. |
| 128 |
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|
| 129 |
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checkpoint61g |
| 130 |
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o pkg/flt: |
| 131 |
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- move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) |
| 132 |
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+ make OPTIONS file more standard. |
| 133 |
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- rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) |
| 134 |
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- fix _BYTESWAPIO CPP-Flag |
| 135 |
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- standard reading of file-parameter "data.flt" |
| 136 |
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- fix argument list of S/R FLT_RESTART |
| 137 |
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still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F |
| 138 |
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o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell |
| 139 |
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o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to |
| 140 |
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a still unfixed compiler/optimization bug |
| 141 |
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|
| 142 |
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checkpoint61f |
| 143 |
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o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; |
| 144 |
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update results of global_ocean.cs32x15.icedyn test. |
| 145 |
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o move getcon.F from model/src to pkg/fizhi. |
| 146 |
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o pkg/exf: add parameter for extrapolation of temp up to the surface |
| 147 |
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and option to prevent negative evap (in bulk_largeyeager04 only). |
| 148 |
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o Prather Advection scheme: fix tracer conservation for divergent flow |
| 149 |
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(e.g., when using NonLin Free-Surface). |
| 150 |
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o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead |
| 151 |
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o gmredi (Visbeck-variable-K): |
| 152 |
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- add more parameters to Visbeck-variable-K. |
| 153 |
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- use a 5 points average for dSigmaR in Visbeck-K calculation |
| 154 |
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(more "homogenous": same stencil and same weights as in dSigmaH) |
| 155 |
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- update output of ideal_2D_oce experiment. |
| 156 |
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o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 |
| 157 |
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(#undef REAL4_IS_SLOW) |
| 158 |
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- pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 |
| 159 |
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coordinate variable |
| 160 |
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- pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables |
| 161 |
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(surface forcing fields), removes some of the functionality |
| 162 |
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- model/src/write_grid.F: write _RS variables as RS-netcdf variables |
| 163 |
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- model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but |
| 164 |
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probably not all: copy _RS surface flux fields to RL field before |
| 165 |
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calling DIAGNOSTICS_FILL |
| 166 |
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- model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into |
| 167 |
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real*4 (CALL EXCH_*_RS) versions. |
| 168 |
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- tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 |
| 169 |
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(generate new output). |
| 170 |
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|
| 171 |
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checkpoint61e |
| 172 |
|
o gmredi (Visbeck-variable-K): |
| 173 |
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- fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h |
| 174 |
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- change computation of Visbeck-K where Slope > Smax : |
| 175 |
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now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct) |
| 176 |
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previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output. |
| 177 |
|
o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic |
| 178 |
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to be the same as with Z-coord. (i.e., m/s & no-units respectively). |
| 179 |
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o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc) |
| 180 |
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o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz |
| 181 |
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does not become too large (to avoid precision problems in implicit-diffusion |
| 182 |
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solver); update ideal_2D_oce output. |
| 183 |
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o pkg ggl90: |
| 184 |
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- in ggl90_cal.F: compute only one set of visc/diff, used to |
| 185 |
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step forward TKE/T/S/momentum |
| 186 |
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- default value of GGL90viscMax/GGL90diffMax larger and equal (to |
| 187 |
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have Prandlt =1) |
| 188 |
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o gmredi (fm07): |
| 189 |
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- add lower limit on Transition layer thickness + lower limit on 1/lambda |
| 190 |
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- allow to set few more params from data.gmredi |
| 191 |
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o pkg ggl90: |
| 192 |
|
- add missing sqrt(2) factor in computation of mixing length |
| 193 |
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scale in ggl90_calc.F |
| 194 |
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(see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) |
| 195 |
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|
| 196 |
|
checkpoint61d |
| 197 |
|
o adjoint modifs |
| 198 |
|
- adapt to new field rhoInSitu |
| 199 |
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- allow to revert from StoreDynVars2D, StoreDynVars3D |
| 200 |
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to individual fields |
| 201 |
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(switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) |
| 202 |
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o store 3-D (in-situ) density in commom block (DYNVARS.h) |
| 203 |
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- save 1 rho computation. |
| 204 |
|
- no longer modify T & S inland when using down_slope pkg. |
| 205 |
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o gad_som : allow to switch to SOM advection for T & S without corresponding |
| 206 |
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pickup files (using new S/R: MDS_CHECK4FILE). |
| 207 |
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o keep removing _BEGIN/_END_MASTER between MDSIO S/R call |
| 208 |
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(for useSingleCpuIO to work in multi-threaded) |
| 209 |
|
o pkg/shelfice: |
| 210 |
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- disentangle parameters: retire shelfIceFile in data/PARM05 and substitute |
| 211 |
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with SHELFICEtopoFile in data.shelfice |
| 212 |
|
- move code for reading ice shelf topography and modifying hFacC into separate |
| 213 |
|
subroutines of the shelfice package |
| 214 |
|
- separate initialisation of "fixed" and "variable" variables |
| 215 |
|
- kTopC is not (yet) replaced by kSurfC, although this is possible |
| 216 |
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o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
| 217 |
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o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
| 218 |
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and rename: |
| 219 |
|
ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
| 220 |
|
ini_reference_state.F --> load_ref_files.F (- set anelastic factors) |
| 221 |
|
o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) |
| 222 |
|
|
| 223 |
|
checkpoint61c |
| 224 |
|
o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" |
| 225 |
|
to add mass source/sink of fluid in the interior (3-D generalisation |
| 226 |
|
of oceanic real-fresh water flux). |
| 227 |
|
o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) |
| 228 |
|
o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) |
| 229 |
|
o new pkg: down_slope |
| 230 |
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density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). |
| 231 |
|
- presently, modify T & S inland (dwnslp_calc_rho.F). |
| 232 |
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can be avoided if rho was stored in common bloc and used in calc_phi_hyd. |
| 233 |
|
- implementation for ocean in P-coords not tested. |
| 234 |
|
- add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. |
| 235 |
|
o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) |
| 236 |
|
(to facilitate conversion of oceanic pkg to p-coordinate). |
| 237 |
|
o change FIND_RHO to FIND_RHO_2D : |
| 238 |
|
pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. |
| 239 |
|
o new pkg: cheapaml |
| 240 |
|
|
| 241 |
|
checkpoint61b |
| 242 |
|
o exch2: |
| 243 |
|
change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) |
| 244 |
|
- no longer depend on the order sequence (N,S,E,W). |
| 245 |
|
- 3rd exchange no longer needed (tested with 24 tiles). |
| 246 |
|
- same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) |
| 247 |
|
- exch_UV_A-grid readily available (but not yet tested). |
| 248 |
|
comment out 3rd exch call and remove copy of V to U at SE & NE face-corners |
| 249 |
|
(both are no longer needed) in exch_uv: no effect in forward run; but |
| 250 |
|
get truncation error differences with adjoint exch. |
| 251 |
|
o exch2: |
| 252 |
|
- change index-bounds storage (moved from target to local tile, |
| 253 |
|
more intuitive this way) ; rename/remove some variables. |
| 254 |
|
- change utils/exch2/matlab-topology-generator & code_mods accordingly. |
| 255 |
|
|
| 256 |
|
checkpoint61a |
| 257 |
|
o exch2/matlab-topology-generator: |
| 258 |
|
fix bug in index bounds for N-S internal exchange (hard to tell if this |
| 259 |
|
had any effect on the solution). |
| 260 |
|
o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf |
| 261 |
|
is exceeded |
| 262 |
|
o testreport: modify syntax of awk, so that it works also with |
| 263 |
|
awk, and not only with nawk and gawk |
| 264 |
|
|
| 265 |
|
checkpoint61 |
| 266 |
|
o autodiff |
| 267 |
|
Change default for TAF usage by removing argument '-nonew_arg' |
| 268 |
|
This changes TAF subroutine argument list (ordering of active var.) |
| 269 |
|
Omission of this flag leads to incompatibility w.r.t. TAMC |
| 270 |
|
To restore TAMC-compatibility, need following modifs: |
| 271 |
|
* use adoptfile tools/adjoint_options/adjoint_tamc_compatibility |
| 272 |
|
* use CPP option #define AUTODIFF_TAMC_COMPATIBILITY |
| 273 |
|
Tested TAF version is 1.9.22 |
| 274 |
|
N.B.: exch2 hand-written adjoint code currently not TAMC compatible |
| 275 |
|
|
| 276 |
|
checkpoint60 |
| 277 |
|
--->>> This is the last checkpoint for which generating the adjoint |
| 278 |
|
--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" |
| 279 |
|
--->>> by default. |
| 280 |
|
--->>> Future checkpoints will ommit this flag by default. |
| 281 |
|
o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. |
| 282 |
|
o pkg/grdchk: Add gradient check to etan0 perturbations. |
| 283 |
|
o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). |
| 284 |
|
o pkg/autodiff: more flexibility in zeroadj. |
| 285 |
|
model/src: modifying do_oceanic_phys.F accordingly. |
| 286 |
|
o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. |
| 287 |
|
o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option |
| 288 |
|
special setup of gmredi for which the adjoint is stable |
| 289 |
|
enough for parameter optimization. |
| 290 |
|
o bridging the gap between eddy stress and GM. |
| 291 |
|
-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) |
| 292 |
|
along with a change in CPP option (now ALLOW_EDDYPSI). |
| 293 |
|
-> when using GM w/ GM_AdvForm: |
| 294 |
|
The total eddy streamfunction (Psi = eddyPsi + K x Slope) |
| 295 |
|
is applied either in the tracer Eq. or in momentum Eq. |
| 296 |
|
depending on data.gmredi (intro. GM_InMomAsStress). |
| 297 |
|
-> ALLOW_EDDYPSI_CONTROL for estimation purpose. |
| 298 |
|
The key modifications are in model/src/taueddy_external_forcing.F |
| 299 |
|
pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F |
| 300 |
|
|
| 301 |
|
checkpoint59r |
| 302 |
|
o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array |
| 303 |
|
from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); |
| 304 |
|
fix option to read coriolis(@ cell-corner) from files with CS-grid. |
| 305 |
|
o pkg/mnc: add some attributes to standard 1D-coordinate variables |
| 306 |
|
o pkg/diagnostics: enforce missing_value attribute for scalar variables at |
| 307 |
|
mass points, when using mnc for output |
| 308 |
|
- add runtime parameter (missing_value, missing_value_int) to override |
| 309 |
|
default (which is the value of getcon('UNDEF')) |
| 310 |
|
o pkg/mnc: prepare mnc for the actual use of missing values with the |
| 311 |
|
diagnostics package: small fix in mnc_cw_readwrite.template and more |
| 312 |
|
initialisation of never used fields |
| 313 |
|
- replace mnc_common.h and mnc_id_header.h with corresponding upper case |
| 314 |
|
versions |
| 315 |
|
o pkg/thsice/thsice_ini_vars.F added default initial values so that |
| 316 |
|
thermodynamics sea ice solver does not blow up when some initial fields |
| 317 |
|
are missing. |
| 318 |
|
o move from external_forcing_surf.F to ini_forcing.F |
| 319 |
|
the p-coord. hack consisting in using pLoad to set phi0surf ; |
| 320 |
|
update output of tutorial_global_oce_in_p (affected @ truncation level). |
| 321 |
o Freshen up a bit hs94.1x64x5, notably: |
o Freshen up a bit hs94.1x64x5, notably: |
| 322 |
remove rotationPeriod and tRef=5*0. (adjoint only), and add exactConserv=.TRUE. |
remove rotationPeriod and tRef=5*0. (adjoint only), and add |
| 323 |
|
exactConserv=.TRUE. |
| 324 |
o pkg/generic_advdiff: |
o pkg/generic_advdiff: |
| 325 |
change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
| 326 |
applies to files where Temperature & Salinity 2nd Order moments are used. |
applies to files where Temperature & Salinity 2nd Order moments are used. |
| 2422 |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
| 2423 |
- these scheme operate in a similar manner as KPP (without ghat, of |
- these scheme operate in a similar manner as KPP (without ghat, of |
| 2424 |
course), however there is only one diffusivity that is used for both |
course), however there is only one diffusivity that is used for both |
| 2425 |
temperature and salinity (and passive tracers)ç |
temperature and salinity (and passive tracers) |
| 2426 |
o add offline package |
o add offline package |
| 2427 |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
| 2428 |
provided by Stephanie Dutkiewicz |
provided by Stephanie Dutkiewicz |
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