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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 improvements for the MNC output from DIAGNOSTICS: |
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- correct handling of the unlimitied dimension |
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- all dims now have associated coordinate variables |
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- variables located at U, V, and Corner ("Z") points are now written |
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with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
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*all* data points are output |
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o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
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o added pkg/seaice/seaice_monitor.F |
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o mdsio_readfield.F can now read files visible only to master MPI process. |
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o pkg/seaice: some test code for ice-modified ocean stress |
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o exf_getffields interpolation defaults to bilinear for all scalar forcing |
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fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
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spurious negative numbers for precipitation and humidity. Will cause |
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some small numerical differences for integrations using pkg/exf/exf_interp.F. |
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checkpoint57b_post |
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o simplify options in diagnostics_fill arguments (remove weird combinations) |
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o fix MNC coordinate variables so that they now contain per-face index |
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values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
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general, EXCH2 grids are only aligned to a "local" coordinate system |
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o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
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o Implement instantaneous output within pkg diagnostics: |
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setting a negative frequency in data.diagnostics produces |
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"snap-shot" output (as opposed to time-average if freq > 0) |
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o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
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NOTE: change ptracer diagnostics name: use 2 characters to work with |
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more than 9 tracers. Add also diagnostics of advect & diffus flux. |
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o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
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becomes the coordinate variable for the 'T' dimension |
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o add CF-style coordinate variables to MNC |
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- just a first cut: numbers are meaningless on the cubesphere and |
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missing along the T axis but otherwise it works! |
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o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
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o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
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o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
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this is based directly on what the model compute, so that the content of |
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each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
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o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
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o clean up build options files for SunOS, in particular |
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- remove -traditional from xmakedepend |
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- change -xarch=v9 to -xarch=native for f77 |
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- restore use of make (not gmake) |
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- add CC=gcc if using g77 |
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o changes per discussion of AM, JMC, & EH3 today: |
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- move redundant "grid" variables out of "state" -- in preparation of |
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creating proper CF-style coordinate variables and in recognition |
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that any/all grid variables can be easily copied (eg. w/NCO) from |
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the grid files into any of the other NetCDF files |
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- *always* output grid variables with MDSIO (this will eventually be |
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changed) |
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- output MNC grid file if useMNC is true |
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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 |
| 180 |
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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 |
| 196 |
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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 |
| 198 |
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o mdsio: filename info to both stderr, stdout |
| 199 |
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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. |
| 204 |
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affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 205 |
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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 |
| 207 |
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o make all subroutines 30 or less characters in length for certain older |
| 208 |
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compilers to work (a thorough search only turns up two routines in |
| 209 |
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pkg/ptracers) |
| 210 |
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o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
| 211 |
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affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 212 |
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checkpoint55i_post |
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o change arrays for total vertical diffusivity (2.D if explicit, |
| 215 |
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3.D if implicit) ; each ptracer uses its own background value. |
| 216 |
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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 |
| 218 |
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ITRDA and other clusters without the mpirun "-wd" option |
| 219 |
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o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
| 220 |
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configuration |
| 221 |
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o give MNC the ability to create additional files rather than |
| 222 |
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exceeding a specified file size limit "MNC_MAX_FILESIZE" |
| 223 |
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- the default is just less than 2GB which is a practical limit |
| 224 |
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on many systems |
| 225 |
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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" |
| 230 |
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o remove all the *_ioinc flags and replace with the single global |
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outputTypesInclusive flag |
| 232 |
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o allow to set a vertical profile of vertical diffusivity for T & S |
| 233 |
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o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
| 234 |
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o useMNC moved from data.mnc to data.pkg |
| 235 |
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|
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checkpoint55g_post |
| 237 |
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o Renaming carbon AD experiments to comply with testreport conventions |
| 238 |
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o Updating adjoint of Held-Suarez hs94.1x64x5 |
| 239 |
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o Fixing directives for non-ECCO forward_step, after ECCO directives |
| 240 |
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have been fixed to avoid recomp. of do_oceanic_phys |
| 241 |
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Works well for global_ocean.90x40x15, |
| 242 |
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but recomp. issue remains for carbon |
| 243 |
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o Updating adjoint output for natl_box_adjoint after |
| 244 |
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pkg/ecco has been modified (see taga c55d_post) |
| 245 |
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|
| 246 |
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checkpoint55f_post |
| 247 |
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o rename to timeave_init_fixed |
| 248 |
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|
| 249 |
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checkpoint55e_post |
| 250 |
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o some delicate re-shuffle of store directives to avoid one |
| 251 |
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extra call of do_oceanic_physics |
| 252 |
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affects ecco_the_main_loop.F, do_oceanic_physics.F |
| 253 |
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checkpoint_lev1_directives.h |
| 254 |
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o NB: this may break global_ocean adjoint temporarily, |
| 255 |
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but it is clear how to fix it. Will do later, need this now. |
| 256 |
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|
| 257 |
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checkpoint55d_post |
| 258 |
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o ECCO specific cost function terms (up-to-date with 1x1 runs) |
| 259 |
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o ecco_cost_weights is modified to 1x1 runs |
| 260 |
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o modifs to allow observations to be read in as |
| 261 |
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single file or yearly files |
| 262 |
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o enable to read exf forcing fields as either |
| 263 |
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single file or yearly files (flag useExfYearlyFields) |
| 264 |
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checkpoint55d_pre |
| 265 |
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|
| 266 |
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o switch between 2-level and 3-level checkpointing |
| 267 |
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o add ability of MNC to write local and "partial" (eg. 2D slices where |
| 268 |
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the full 3D field is never actually stored) arrays to NetCDF files |
| 269 |
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with the correct (that is, the complete multi-dimensional) set of |
| 270 |
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array indicies |
| 271 |
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- used in mom_vecinv() to write the diagFreq output |
| 272 |
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- tested (demonstrated) in verification/aim.5l_cs |
| 273 |
o further mnc-ification |
o further mnc-ification |
| 274 |
- add verification/lab_sea to the list with mnc setups |
- add verification/lab_sea to the list with mnc setups |
| 275 |
- fix undefined mnc v-names in cd_code |
- fix undefined mnc v-names in cd_code |
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