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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 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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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 ; |
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(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
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affects results of dome set-up: update output.txt |
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o fix gad_advection.F (CubedSphere part), back to version 1.23 |
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o fix bug in mom_vi_del2uv.F (CubedSphere part). |
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checkpoint55a_post |
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o merged code to |
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* prescribe/read time-dependent open boundaries |
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(works in conjunction with exf, cal) |
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* sponge layer code for open boundaries |
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* each boundary N/S/E/W now has its own CPP option |
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(healthy for the adjoint) |
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checkpoint55 |
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o up-to-date adjoint of previous breaks |
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- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
| 187 |
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- global_ocean_ebm: adjoint still needs fix (TLM ok) |
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- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
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- carbon: * remove tr1-related adjoint verification |
| 190 |
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* add ptracer as control variable |
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o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
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(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
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checkpoint54f_post |
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o in verification/carbin/ remove experiment related to |
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ALLOW_PASSIVE_TRACER (array tr1 etc) |
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code_ad/ input_ad/ results_ad |
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o add two new packages |
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- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
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+ subject to optimization (memory) |
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- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
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+ subject to reordering (many GOTOs in the original code) |
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+ so far opps is called for every (i,j) point, and then operates in |
| 205 |
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the vertical; one may want to reorder the scheme in order operate in |
| 206 |
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horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
| 207 |
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fields) |
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o overhaul of IO so that we now have flags for MDSIO and/or MNC |
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- all verification tests compile and run with linux_ia32_g77 |
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- defaults are compatible with current input files--nothing |
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should change if you were not previously using MNC |
| 212 |
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- MNC output has been added in numerous places (eg. timeave) |
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but there are still a few writes not yet do-able with MNC |
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(this is in progress) |
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- flags now allow for either/or/both use of MDSIO and MNC and |
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documentation will soon follow |
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- numerous small formatting cleanups for ProTeX |
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o add version info (via BUILD_INFO.h) to MNC and stdout |
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checkpoint54e_post |
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o add two new packages |
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- pp81 (Packanowski and Philander, 1981), Richardson number and |
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stratification dependent mixing |
| 224 |
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- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
| 225 |
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- these scheme operate in a similar manner as KPP (without ghat, of |
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course), however there is only one diffusivity that is used for both |
| 227 |
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temperature and salinity (and passive tracers)ç |
| 228 |
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o add offline package |
| 229 |
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o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
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provided by Stephanie Dutkiewicz |
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o genmake2: add ability to search for C compilers and cleanup test output |
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- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
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checkpoint54d_post |
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o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
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o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
| 237 |
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leading to additional shift by 5 days each year of integration |
| 238 |
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(i.e. leading to considerable offset over the years) |
| 239 |
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o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
| 240 |
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o start with no AB and no initial filtering (staggerTimeStep): |
| 241 |
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change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
| 242 |
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o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
| 243 |
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(external loading & cpl import/export stay in forward_step.F) |
| 244 |
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o update coupling interface to work with new staggerTimeStep |
| 245 |
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o change MDSIO ptracers_pickup. |
| 246 |
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o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
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o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
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o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
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checkpoint54c_post |
checkpoint54c_post |
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o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
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