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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 every instance of _END_MASTER() has been found and replaced with |
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_END_MASTER( myThid ) in order to satisfy certain picky Sun |
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preprocessors |
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o re-arrange diagnostics pkg initialisation: |
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- allow each package to extend the available diagnostics list |
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- add some checking and fix small problems (multi-threaded, ...) |
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- new S/R diagnostics_fill (replace fill_diagnostics): |
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look through the short list of active diag. (instead of the long list) |
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create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
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checkpoint57a_post |
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o this set of changes restores TAMC compatibility |
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tested for global_ocean.90x40x15 adjoint on trough |
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(what a pain) |
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checkpoint57a_pre |
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o some modifs in tools/build_options for sunos |
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o call ctrl_pack for ctrl at end for optimcycle=0 |
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checkpoint57 |
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o add horizontal bi-harmonic viscosity for vertical velocity |
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- new parameter viscA4W (defaults to viscA4) |
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- affects only non-hydrostatic code |
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- to be done: no-slip lateral boundary conditions |
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o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
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o implement Implicit Vertical advection for pTracers |
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o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
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(implemented also for implicit vertical diffusion & advection) |
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o OBCS: extend application of tracer open boundary conditions |
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to a strip beyond the boundary of width Olx/Oly |
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o add call monitor to TAF set of required calls (flow directives) |
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and include in natl_box_adjoint |
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o untangle a few ifdefs related to cost, ctrl, autodiff |
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untangel a few ALLOW_ECCO_OPTIMIZATION |
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o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
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(theta2, salt2 in ecco_cost_weights) |
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checkpoint56c_post |
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o OBCS as control variables |
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- update ctrl_ad_diff.list, obcs_ad_diff.list |
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- remove balance of obcs controls from default |
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- fix index bug nobcs in ctrl_init |
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- fix dummy fields filen in ctrl_pack |
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- add dummy weights for obcs |
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o lsopt: comment out fort.94 output |
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o optim: |
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- remove unnecessary header files |
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- adjusted namelists |
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- add xerbla.F to Makefile |
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o exf: |
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- multiple modifications of exf_check_range |
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- unit change in exf_init_runoff from [m/year] to [m/s] |
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o mdsio: |
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- i/o-vector change debugLevel from debLevA to debLevB |
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checkpoint56b_post |
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o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
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is called from DO_THE_MODEL_IO |
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- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
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- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
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- clean up PTRACERS_WRITE_TIMEAVE a little |
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o add another verification experiment that tests both the cfc-pkg and |
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the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
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reactive tendencies treated inline with regular timestepping |
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o testreport previously did a lousy job of comparing small numbers, so |
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we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
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implemented in the little c-progam tmp_cmpnum.c which is embedded in |
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testreport. |
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o ptracers_monitor: bug fix for MPI |
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checkpoint56a_post |
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o GCHEM: finish reorganizating the package |
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- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
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(introduces another 3D-array for each passive tracer, but only if |
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GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
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gchemTendency is not needed because the timestep is done separately) |
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- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
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- GCHEM is now---more or less cleanly---separate from PTRACERS |
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- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
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so clear to me how that should be done in a general way. |
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o CFC: improve formatting of output in CFC_ATMOS |
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o PTRACERS: |
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- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
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that ALL experiments with ptracers enable can be checked. This makes |
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GCHEM_MONITOR obsolete. |
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- include a runtime parameter PTRACERS_monitorFreq that defaults to |
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monitorFreq |
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- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
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o add PTRACERS (PTR0[1-5]) to testreport output |
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o exf_check_range: |
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* default changed to .TRUE. |
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* will check values for niter0 if debLevA, every timestep if debLevB |
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* STOP in exf_check_range if 'out of range' |
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* range chosen generous to allow for potential extema |
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TBD: a version with stricter range |
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permitted range would be runtime parameters |
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o GMredi: |
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- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
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- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
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- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
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o GCHEM: |
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- move call to GCHEM_FORCING_SEP, so that it is now called before |
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the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
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- introduced a useGCHEM runtime flag and applied it everywhere. |
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- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
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this flag is now only visible within GCHEM-pkg routines. |
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- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
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be replaced by a 3D array that is computed before thermodynamics; for |
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this, the tracer ID iTracer had to be included into the parameter list |
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of ptracers_forcing |
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- set up forward_step to call gchem_forcing, that will replace |
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gchem_forcing_int in ptracers_forcing |
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- cleaning up |
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o small cleaning of exch2: remove files that are also in eesupp/src |
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checkpoint56 |
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o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
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o mnc: cleanup "full" files--fixes out-of-memory problem |
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o ECCO-GODAE |
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* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
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* fully merged and updated from SIO code |
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windstress sign change affects |
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- exf_inscal_[u/v]stress |
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- sign of xx_tau[u/v] adjustments |
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- signs in cost_scat |
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* ctrl_get_gen: avoid update of tau[u/v] for first few days |
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* natl_box_adjoint updated and compressed |
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* 2-level checkpoint switch added |
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(tested in EXP. 1 of natl_box_adjoint) |
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* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
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o SVD |
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* first complete, non-hacked version for SVD calculations |
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* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
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performed via direct access files admtlm_vector.it???? |
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(via ctrl_[un]pack) |
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* optimcycle is used for ARPACK iteration counter |
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(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
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* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
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and add linear transforms where necessary |
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* controls are initial/final SST, SSS (can be extended; need to check |
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ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
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o mdsio: filename info to both stderr, stdout |
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o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
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from sign change |
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checkpoint55j_post |
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o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
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affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
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o add consistent build directories and .cvsignore files to verification |
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o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
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o make all subroutines 30 or less characters in length for certain older |
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compilers to work (a thorough search only turns up two routines in |
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pkg/ptracers) |
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o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
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affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
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checkpoint55i_post |
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o change arrays for total vertical diffusivity (2.D if explicit, |
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3.D if implicit) ; each ptracer uses its own background value. |
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o added mnc/NetCDF output capability to ocn_compon_interf |
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- added bits to verification/cpl_aim+ocn so that it can run on |
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ITRDA and other clusters without the mpirun "-wd" option |
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o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
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configuration |
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o give MNC the ability to create additional files rather than |
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exceeding a specified file size limit "MNC_MAX_FILESIZE" |
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- the default is just less than 2GB which is a practical limit |
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on many systems |
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o Compute the non-local term using either KPP vertical diffusivity (=default) |
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or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
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checkpoint55h_post |
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o add verification test "vermix" |
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o remove all the *_ioinc flags and replace with the single global |
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outputTypesInclusive flag |
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o allow to set a vertical profile of vertical diffusivity for T & S |
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o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
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o useMNC moved from data.mnc to data.pkg |
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checkpoint55g_post |
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o Renaming carbon AD experiments to comply with testreport conventions |
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o Updating adjoint of Held-Suarez hs94.1x64x5 |
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o Fixing directives for non-ECCO forward_step, after ECCO directives |
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have been fixed to avoid recomp. of do_oceanic_phys |
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Works well for global_ocean.90x40x15, |
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but recomp. issue remains for carbon |
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o Updating adjoint output for natl_box_adjoint after |
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pkg/ecco has been modified (see taga c55d_post) |
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checkpoint55f_post |
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o rename to timeave_init_fixed |
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checkpoint55e_post |
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o some delicate re-shuffle of store directives to avoid one |
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extra call of do_oceanic_physics |
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affects ecco_the_main_loop.F, do_oceanic_physics.F |
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checkpoint_lev1_directives.h |
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o NB: this may break global_ocean adjoint temporarily, |
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but it is clear how to fix it. Will do later, need this now. |
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checkpoint55d_post |
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o ECCO specific cost function terms (up-to-date with 1x1 runs) |
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o ecco_cost_weights is modified to 1x1 runs |
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o modifs to allow observations to be read in as |
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single file or yearly files |
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o enable to read exf forcing fields as either |
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single file or yearly files (flag useExfYearlyFields) |
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checkpoint55d_pre |
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o switch between 2-level and 3-level checkpointing |
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o add ability of MNC to write local and "partial" (eg. 2D slices where |
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the full 3D field is never actually stored) arrays to NetCDF files |
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with the correct (that is, the complete multi-dimensional) set of |
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array indicies |
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- used in mom_vecinv() to write the diagFreq output |
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- tested (demonstrated) in verification/aim.5l_cs |
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o further mnc-ification |
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- add verification/lab_sea to the list with mnc setups |
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- fix undefined mnc v-names in cd_code |
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- add kpp to mnc output (both snapshot and timeave) |
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o non-hydrostatic code |
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- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
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in calc_gw.F |
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- defaults to viscAh |
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- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
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friction or Leith) in non-hydrostatic mode, as long as there is |
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no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
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o pkg/cost |
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extend simple cost functions to treat time mean quantities |
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(T,U,V) via cost_accumulate_state from cost_tile |
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o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
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be 2 times larger than the minimum size the advection scheme requires. |
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now get a perfect conservation of salt in advect_cs test-exp (updated) |
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o GGL90 (Gaspar's TKE mixed layer) |
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- add horizontal diffusion of TKE, requires exchanges in |
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do_fields_blocking_exchanges, horizontal diffusivity is zero by |
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default. In OPA there is no horizontal diffusion of TKE but the |
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mixing coefficients are computed from a horizontal average of TKE of |
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6 points or so. I think that diffusion has a little more physical |
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justification. |
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- clean up ggl90_calc in the hope of reducing memory usage (this hope |
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was in vain) |
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- mask tke-variable in ggl90_init |
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o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
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o fix biharmonic diffusion on CS-grid. |
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o more obcs stuff |
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- added obcs_external_fields_load as an alternative to the EXF-pkg option |
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for reading boundary values. This routine is called from |
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obcs_prescribe_read |
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- updated obcs_check |
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- changed sponge layer relaxation parameter units for days to seconds |
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- turned off sponge layer by default |
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- changed argument list of OBCS_CALC to myTime+deltaTclock |
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- fixed about 35 bugs in obcs_external_fields_load |
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checkpoint55c_post |
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o obcs stuff |
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- new runtime flags useOBCSprescribe, useOBCSbalance |
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- re-arranged obcs_calc |
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- moved exf_getobcs to obcs_prescibe_read |
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obcs_prescibe_read is called after ORLANSKI stuff |
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and independent of it (executable can contain all). |
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- updated obcs_check |
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- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
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These may be necessary only if tangential velocities are |
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prescribed at OB, not sure, needs testing. |
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o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
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which simplifies the calls and passes the ifc check-bounds test |
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checkpoint55b_post |
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o add a 2D scalar, Z location, exchange_2 routine. |
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o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
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to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
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affects advect_cs results (for the wrong reason): update output.txt |
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o use a more standard discretization for biharmonic viscosity ; |
o use a more standard discretization for biharmonic viscosity ; |
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(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
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affects results of dome set-up: update output.txt |
affects results of dome set-up: update output.txt |
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