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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o pkg/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. |
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o pkg/diagnostics: |
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implement a RS type version for the set of DIAGNOSTICS-FILL subroutines |
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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: |
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To avoid mixing type (RS/RL) of input/output array argument, |
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replace single mixed-type array with a pair from each type (RS/RL). |
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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 |
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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 |
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(domain size, lat range, etc ...); should be documented & stop if one |
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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). |
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o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC): |
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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). |
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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). |
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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 |
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2d-fields, for slightly better performance |
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checkpoint61t |
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o pkg/seaice: |
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- remove unused variables in seaice_evp |
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- reduce number of SQRT in seaice_evp and seaice_calc_viscosities |
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o eeset_parms.F, open_copy_data_file.F & ini_parms.F: |
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named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT): |
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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 : |
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this reduces number of EXCH calls by 2 when using exch2. |
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For now, keep previous size array for gc2d_nsa.F to avoid Pb with store |
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directives and missing simple EXCH (exch_s3d_rx) adjoint code. |
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o pkg/thsice: |
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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). |
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o ini_model_io: |
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move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F |
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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. |
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checkpoint61s |
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o pkg/exch2 (exch2_rxN_cube*): |
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remove last BARRIER (no need to synchronise after getting data from shared |
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buffer (get) as long as any change to buffer (put,recv) is between BARRIER) |
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o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH |
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and generate new output (for the 2 tests) using default rotationPeriod. |
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o pkg/exch2: |
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- always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F |
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(was already the case with AUTODIFF_EXCH2 defined) |
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- add bj in exch2 arrays and S/R. |
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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); |
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o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep |
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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 |
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- verification experiment natl_box.longstep |
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o build_options: ifort+mpi_aces optfile (following Constantinos advise): |
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allow different versions of ifort (8 or 9) and different versions |
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of mpi (mpich or mpich2) to be used with the same optfile. |
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requires to load a netcdf module and set MPI_INC_DIR (see comments inside |
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optfile). Change testing scripts (example_scripts/ACESgrid) accordingly. |
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o pkg/seaice: |
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fix previous modif (3-level field removed) for old-pickup reading |
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checkpoint61r |
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o pkg/seaice: |
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- clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps: |
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1. introduce fields for time step (N-1) |
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2. do not use levels 2 and 3 anymore (but keep them) |
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3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This |
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includes changes to pkg/thsice/thsice_get_velocity.F, |
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model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and |
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pkg/obcs/obcs_apply_uvice.F. |
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- completely remove code for leap-frog time stepping for second order |
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advection |
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- adjusted adjoint accordingly; |
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gradient checks have improved by an order of magnitude! |
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checkpoint61q |
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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 |
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associated masks are set to zero and are thus treated as closed when |
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applying the slip-boundary conditions. |
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- move initialisation of grid variables from seaice_init_varia to _fixed |
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o adding doc/diags_changes.txt |
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o model/src: |
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do_the_model_io: rename few pkg S/R which are called from do_the_model_io, |
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to avoid "_diags" naming if no relation to pkg/diagnostics. |
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ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF |
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file and only call PLOT_FIELD_XYZ if debugMode=T. |
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remove few PLOT_FIELD_XY calls outside initialisation. |
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remove few unnecessary BARRIER. |
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o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling |
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of salt_plume package in Southern Ocean |
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o pkg/thsice: |
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- fix hOceMxL in overlap (needed for sea-ice advection); |
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update output of experiment global_ocean.cs32x15.icedyn. |
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o pkg/seaice: |
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- make the (placeholder-)tracer IceAge a little more meaningful |
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by avoiding ridging of age due to convergent ice flow |
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- add diagnostics for surface temperature, atmospheric and oceanic |
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heat flux, and atmospheric and oceanic ice growth |
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checkpoint61p |
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o eesupp (global_max & global_sum): |
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- add one more element to buffer (start at index 0) for GL_MAX/SUM output; |
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- remove starting & endding barrier (no longer needed) |
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o pkg/mdsio, writelocal: |
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works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined |
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(remove the STOP): uses shared buffer IO to store data from all threads |
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and then let master-thread write nThreads tiles. |
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o pkg/mdsio (read/write field): |
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- tiled IO done in 1 piece (all levels at a time); |
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- new header file "MDSIO_BUFF_3D.h" with 3-D buffers. |
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- multi-threaded: allow to read/write local (non-shared) array |
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(was already working with singleCpuIO ; now works also without); |
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=> no longer needs barrier call after reading a file (added inside |
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mds_read/write field). |
| 159 |
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- move barrier calls outside gather/scatter_2d to mds_read/write_field |
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o pkg/obcs/exf |
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- exf_getffieldrec.F: add a few ". _d 0" and |
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add code to catch the case fldperiod = 0. |
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- obcs_precribe_read.F: change if statements so that they match |
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the variable type (_RL) |
| 165 |
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- add a separate exf_iprec_obcs to exf_set_obcs (by default equal to |
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exf_iprec) as part of namelist EXF_NML_01 |
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o pkg/mdsio: |
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- read/write tiled (local) files: read/write 1-level tile chunk at a time |
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(instead of segment of length sNx); expected to speed up tiled IO. |
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o pkg/exch2: |
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- take buffer copy from/to array out of S/R exch2_send/recv into new |
| 172 |
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S/R exch2_put/get ; Exch of local variable now works with MPI+MTH |
| 173 |
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(tested by removing commom block statement in SOLVE_FOR_PRESSURE.h). |
| 174 |
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- ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get) |
| 175 |
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- simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds |
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(which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by |
| 177 |
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including Topology header file (and common blocks). |
| 178 |
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- implement EXCH_IGNORE_CORNERS in scalar exchange (rx1); |
| 179 |
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remove 2nd exch call in exch2_s3d_rx (no longer needed). |
| 180 |
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- document S/R arg. list (+ update some comments) |
| 181 |
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o pkg/seaice: |
| 182 |
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- added SEAICE_CLIM_AIR code, which permits modulation of surface air |
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temperature and humidity over sea ice based on climatological values. |
| 184 |
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- clean up computation of Hibler+Bryan (1987) stress coupling for the case |
| 185 |
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of LSR (this change is expected to change the results slightly because now |
| 186 |
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it uses slightly difference moduli from the second last LSR solution, but |
| 187 |
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that is more consistent with the stress computations; this part of the code |
| 188 |
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is not tested in the verification experiments) |
| 189 |
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- fix diagnostics for flux of ice in case of B-grid |
| 190 |
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- turn strain rates eij and press into global fields within global |
| 191 |
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common block in SEAICE.h for more straighforward diagnostics |
| 192 |
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- fix diagnostics for principal stress components, press, zeta, eta |
| 193 |
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to give something meaning full |
| 194 |
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o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate |
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new output (all 4 tests) using default rotationPeriod. |
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o pkg KPP: |
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- add flag (LimitHblStable) to avoid limiting BL depth under stable conditions |
| 198 |
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- fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1 |
| 199 |
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and normal grid from 1 to Nr) |
| 200 |
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o Fix computations of L4rdt in mom_calc_visc.F |
| 201 |
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o eesupp: |
| 202 |
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new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg): |
| 203 |
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should be called before a "stop" if we know that all process are going |
| 204 |
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to stop; if one Proc does call this S/R, will hang in MPI_FINALISE. |
| 205 |
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|
| 206 |
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checkpoint61o |
| 207 |
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o pkg/exch2: change check_depths to issue just a warning (instead of error+stop) |
| 208 |
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o model/src/ini_curvilinear_grid.F: |
| 209 |
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compute angleSin/CosC when they are not read from a file |
| 210 |
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o pkg/seaice: |
| 211 |
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add pseudo time stepping for LSOR |
| 212 |
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o pkg/exch2: |
| 213 |
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temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW |
| 214 |
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o pkg/seaice: |
| 215 |
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Adding separate sea ice albedo, drag coefficients, and HO in Southern |
| 216 |
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Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h |
| 217 |
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o SingleCpuIO: |
| 218 |
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fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used. |
| 219 |
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o pkg/seaice: |
| 220 |
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put exchanged variable in (local) common block for MPI+Multi-Threads |
| 221 |
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to work (necessary with exch1, and for now with exch2 too). |
| 222 |
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o verification: to get more experiments tested with mpi, mth and mpi+mth, |
| 223 |
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change tiling of: |
| 224 |
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aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15, |
| 225 |
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hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope |
| 226 |
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update output of exp: |
| 227 |
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exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5), |
| 228 |
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tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod) |
| 229 |
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+ ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU |
| 230 |
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(note: output.txt generated on faulks using only 1 tile) |
| 231 |
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o eesupp & mdsio (SingleCpuIO): |
| 232 |
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- remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time |
| 233 |
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parameter "W2_useE2ioLayOut" (read from file "data.exch2"). |
| 234 |
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Note: was not effective for globalFile & useSingleCpuIO=F; now fixed. |
| 235 |
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- move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc). |
| 236 |
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- fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same |
| 237 |
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gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array). |
| 238 |
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o pkg/exch2: |
| 239 |
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- new code to set-up W2-Exch2 topology (replace matlab-topology-generator): |
| 240 |
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read parameter file "data.exch2" if it exists; otherwise try default regular |
| 241 |
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cube without blank-tile; new header file "W2_EXCH2_SIZE.h"; |
| 242 |
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- update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible |
| 243 |
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with new code (not to be used, just as a backup solution). |
| 244 |
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- add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2" |
| 245 |
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in utils/exch2/input. |
| 246 |
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|
| 247 |
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checkpoint61n |
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o eesupp & mdsio (SingleCpuIO): |
o eesupp & mdsio (SingleCpuIO): |
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- move mapping to global io-buffer inside gather_2d/scater_2d: this save |
- move mapping to global io-buffer inside gather_2d/scater_2d: this save |
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memory (1 less 2D global RL array); skip 1 buffer copy; and only send/ |
memory (1 less 2D global RL array); skip 1 buffer copy; and only send/ |
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