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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 adjoint: |
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* update and finish work on adjoint of dic package (G. Forget) |
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* start adjoint of offline package |
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* bug fix for cube-sphere TLM code (active_file_g.F) |
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o tutorial_global_oce_optim: |
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now tested with 4 tiles (change data.grdchk and update output_adm.txt) |
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and add SIZE.h_mpi for MPI testing |
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o pkg autodiff |
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- fix bug in autodiff_restore |
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- make genmake2 remove comments and empty lines from ad_input_code.f in |
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order to reduce file size (new script file remove_comments_sed) |
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o allows to specify vertical profile of vertical viscosity (viscArNr) |
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o pkg autodiff |
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autodiff_ini_model_io: comment out writing of grid information to netcdf |
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files, because at this time the grid fields are a bunch of zeros |
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(this is analogous to ini_mnc_vars.F) |
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o pkg seaice/autodiff: |
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left-over from removing the 3-time-level fields: |
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- small rearrangement of common blocks (SEAICE.h) |
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- fix field declaration in order to get meaningful output in |
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adseaice.*.nc (adcommon.h) |
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o pkg obcs: |
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- go through NH code only if nonHydrostatic=T |
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- fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart) |
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- move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields |
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=> Update output of experiment seaice_obcs |
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- useOBCSbalance: code is wrong with multi-tile / proc: add a stop. |
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- fix NH+Orlanski restart (add wvel OBC value in pickup file) |
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- fix restart for useOBCSprescribe + useEXF |
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o pkg ctrl |
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- make obcs as control parameter work also with useSingleCPUio |
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- replace a few sny and snx by Ny and Nx to be consistent with |
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ctrl_set_globfld_x/yz.F |
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o pkg seaice |
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- re-introduce global field frWtrAtm for the case of |
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ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F) |
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- catch the case of an empty filename in seaice_cost_init_fixed.F |
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o pkg ecco: |
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- small bug fixes in the_main_loop |
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. fix order of monitor arguments |
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. change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY |
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. move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so |
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that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF |
| 50 |
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- replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the |
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imbalance diagnostics for wmean_h/sflux = 0 |
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- add actual values to f_obcsn/s/w/e in ecco_cost_final.F |
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- catch the case of empty filenames in ecco_cost_init_fixed.F |
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and ecco_readparms.F |
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- fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta) |
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to make this statement meaningfull in ecco_cost_weights.F |
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o pkg zonal_filt: |
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- change ZONAL_FILTER S/R interface (allows to filter 2-D fields) |
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- when using rStar, filter uVel*hFacW instead of uVel |
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(tested without topography: fix a Pb of growing instability with NLFS) |
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o pkg/aim/thsice: |
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-Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F |
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(works as SST restoring) |
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o pkg/thsice: |
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-add specific parameter for salt restoring in slab mixed-layer |
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(by default equal to the temperature restoring) |
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checkpoint61v |
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o pkg/kpp: |
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-add double diffusive contributions as a hack, turned off by default |
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for now, and the code can be excluded with a CPP-flag |
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EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX |
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-add a verification experiments to "vermix" to test this code |
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o pkg/mom_common: |
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Move computation of length scales to mom_init_fixed.F (avoid recomputation |
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at each time-steps*levels). |
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o pkg/layers: |
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Created a new package for computing volume fluxes in temperature or |
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[not yet implemented] density layers, e.g. for calculating residual |
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overturning circulations. |
| 81 |
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o pkg/diagnostics: |
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implement a RS type version for the set of DIAGNOSTICS-FILL subroutines |
| 83 |
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o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option) |
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o pkg/mdsio (& pkg/rw): rework high level S/R interface: |
| 85 |
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To avoid mixing type (RS/RL) of input/output array argument, |
| 86 |
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replace single mixed-type array with a pair from each type (RS/RL). |
| 87 |
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o setting pickupSuff force to start from a pickup (even if nIter0=0): this |
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is now implemented for all pkgs (previously only done for the main pickup) |
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checkpoint61u |
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o pkg/obcs: |
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- change OB?eta from _RS to _RL and put them into a separate commen block |
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- add code to read OB?eta from a file via obcs_prescribe_read: the code |
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compiles and does not destroy any other experiments, the data is read |
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properly, but the code is not tested in actual applications |
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o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to |
| 97 |
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create a meaningful unit attribute for the time coordinate variable |
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o pkg/ebm: add plenty of missing "_d 0" ; |
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update results of experiment global_ocean_ebm (fwd + adjoint tests) |
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Notes: several pieces of code only works for (very) specific set up |
| 101 |
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(domain size, lat range, etc ...); should be documented & stop if one |
| 102 |
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of those assumptions is not meet. |
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o pkg/seaice: add missing "_d 0" in HSNOW initialisation |
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update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests) |
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and offline_exf_seaice (seaicetd + adjoint). |
| 106 |
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o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC): |
| 107 |
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update results of experiments: lab_sea (4 fwd tests + 3 adjoint), |
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seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2). |
| 109 |
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o few changes to pass when compiling with strick checking of arguments |
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across S/R (allow to find few bugs in S/R calls). |
| 111 |
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o pkg/seaice: |
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- seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new |
| 113 |
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2d-fields, for slightly better performance |
| 114 |
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| 115 |
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checkpoint61t |
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o pkg/seaice: |
o pkg/seaice: |
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- completely remove code for leap-frog time stepping for second order |
- remove unused variables in seaice_evp |
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advection |
- reduce number of SQRT in seaice_evp and seaice_calc_viscosities |
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- clean up the 3-time levels of UICE,VICE,HEFF,AREA: |
o eeset_parms.F, open_copy_data_file.F & ini_parms.F: |
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1. introduce fields for time step (N-1) |
named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT): |
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2. do not use levels 2 and 3 anymore (but keep them for now) |
each processor opens a different file (a fix from Matt). |
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o cg2d: |
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use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F : |
| 124 |
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this reduces number of EXCH calls by 2 when using exch2. |
| 125 |
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For now, keep previous size array for gc2d_nsa.F to avoid Pb with store |
| 126 |
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directives and missing simple EXCH (exch_s3d_rx) adjoint code. |
| 127 |
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o pkg/thsice: |
| 128 |
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add code for Near Infra-Red albedo (from Jeff) |
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(turned on with run-time flag: thSIce_calc_albNIR, in data.ice). |
| 130 |
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o ini_model_io: |
| 131 |
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move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F |
| 132 |
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MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F |
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to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice. |
| 134 |
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|
| 135 |
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checkpoint61s |
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o pkg/exch2 (exch2_rxN_cube*): |
| 137 |
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remove last BARRIER (no need to synchronise after getting data from shared |
| 138 |
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buffer (get) as long as any change to buffer (put,recv) is between BARRIER) |
| 139 |
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o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH |
| 140 |
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and generate new output (for the 2 tests) using default rotationPeriod. |
| 141 |
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o pkg/exch2: |
| 142 |
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- always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F |
| 143 |
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(was already the case with AUTODIFF_EXCH2 defined) |
| 144 |
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- add bj in exch2 arrays and S/R. |
| 145 |
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- can now use pkg/exch2 for regular (non CS) set-up; switch test experiment |
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MLAdjust to exch2 (identical results except with MPI -> truncation diff); |
| 147 |
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o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep |
| 148 |
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- adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY |
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GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT |
| 150 |
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- verification experiment natl_box.longstep |
| 151 |
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o build_options: ifort+mpi_aces optfile (following Constantinos advise): |
| 152 |
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allow different versions of ifort (8 or 9) and different versions |
| 153 |
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of mpi (mpich or mpich2) to be used with the same optfile. |
| 154 |
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requires to load a netcdf module and set MPI_INC_DIR (see comments inside |
| 155 |
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optfile). Change testing scripts (example_scripts/ACESgrid) accordingly. |
| 156 |
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o pkg/seaice: |
| 157 |
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fix previous modif (3-level field removed) for old-pickup reading |
| 158 |
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|
| 159 |
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checkpoint61r |
| 160 |
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o pkg/seaice: |
| 161 |
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- clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps: |
| 162 |
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1. introduce fields for time step (N-1) |
| 163 |
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2. do not use levels 2 and 3 anymore (but keep them) |
| 164 |
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3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This |
| 165 |
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includes changes to pkg/thsice/thsice_get_velocity.F, |
| 166 |
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model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and |
| 167 |
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pkg/obcs/obcs_apply_uvice.F. |
| 168 |
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- completely remove code for leap-frog time stepping for second order |
| 169 |
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advection |
| 170 |
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- adjusted adjoint accordingly; |
| 171 |
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gradient checks have improved by an order of magnitude! |
| 172 |
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|
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checkpoint61q |
checkpoint61q |
| 174 |
o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver |
o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver |
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- the boundary conditions along open boundaries are unclear, because the |
- the boundary conditions along open boundaries are unclear, because the |
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