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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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checkpoint57y_pre |
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o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
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o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) |
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o add new offset feature to offline pkg (plus minor cleanup) |
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o cfc fixes for final year of integration |
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o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should |
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be in GCHEM_OPTIONS). |
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checkpoint57x_post |
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o fix testreport Pb in multiple test experiment. |
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o cleanup our namelist syntax in verification: |
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- make it more F95 standards compliant (some work still needed) |
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- allows the vast majority of our tests to work with gfortran |
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o Non-Hydrostatic: |
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- put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h |
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- fix exchange calls for CS-grid using the new EXCH_S3D_RL. |
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o Allow to apply AB on T,S rather than on AB(gT,gS): |
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- implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 |
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- use the same arrays (gtNm,gsNm) to hold tracer field at previous |
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time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). |
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- need a "clever" read_pickup to restart from the other AB formulation |
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o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h |
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o remove some unused variables (reduces number of compiler warnings) |
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o adjoint |
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* Disable useVariableViscosity for adjoint for time being |
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(there are a number of extensive recomputations) |
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* Initialize certain variables needed for adjoint |
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checkpoint57w_post |
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o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names |
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fix the singleCpuIO RS version of MDSWRITEFIELD |
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and add a WARNING if using globalFiles=T with multi-processors. |
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o write grid-file(s) in only one format (MDS or MNC): default=MNC (if |
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using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc |
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o tracer advection scheme: |
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add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get |
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those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, |
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was not very convenient). |
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add implicit version for DST-3 & DST3_Flux_Limit vertical advection; |
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(further tests needed for the implicit DST & Flux-Limiter schemes). |
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o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef |
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and sRef for convenience, handy, when you want to initialize |
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ptracers in a large domain with a constant non-zero value. Also, |
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untangle ptracers_init.F a little. |
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checkpoint57v_post |
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o change dome exp. to use variable viscosity in side-drag terms. |
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o remove all the files from the cfc_offline test since they are now |
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incorporated into tutorial_cfc_offline which has been producing |
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identical results for a few days of testing |
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o add new parameter: sideDragFactor to enable half-slip-side BC |
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and change side-drag S/R to use viscosity from mom_calc_visc |
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(can switch back by setting sideDragFactor=0.); affects results at |
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truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), |
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global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). |
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o vorticity & strain are now computed without masking, to account for |
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no-slip-side BC in variable viscosity calculation ; mask is applied |
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anyway later on, before computing advection/coriolis terms. |
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o modify exp4 to test new obcs support for reading from external files |
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and for passive tracers |
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o fix behavior of ptracers_monitor when monitor output is written to a |
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netcdf-file; still not independent of monitor.F (writes in the same |
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file). |
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o change default value of tRef (put a uniform, meaningful value for ocean |
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& atmos) and initialize sRef (was missing, as Martin mentioned). |
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o Redefine viscC?Leith*. Change the coefficients of Leith viscosity |
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to be proportional to enstrophy dissipation length. Thus, |
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viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) |
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This is now consistent with Smagorinsky and with the manual. |
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checkpoint57u_post |
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o OBCS and PTRACERS: add open boundary support for passive tracers |
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- either use homogenous (pseudo) v.Neumann conditions or prescribe |
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OB-values from file; this is not different from the way theta and salinity |
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are treated |
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- however, Orlanski-radiation conditions are not supported, and the model |
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will stop if you use pTracers and Orlanski at the same time. |
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- beefed up the rountine obcs_external_fields_load: now only those open |
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boundary values are overwritten with values from files for which there |
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are really files, otherwise the OB-fields remain untouched. This makes |
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it possible to use different OBs at different ends of the domain (as |
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with EXF) |
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o reduce number of exch calls in shap_filt (s2). |
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o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ |
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truncation level) 4/5 MLAdjust test results (11&12 digits match). |
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checkpoint57t_post |
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o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
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o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
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same truncation, independent of the face number: affects affects several |
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test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). |
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o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); |
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note that biharmonic viscosity + no-slip was not tested in any experiment. |
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o fix bug in non-linear free-surf side-drag ; generate new output for |
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global_ocean.cs32x15(+.thsice) & global_ocean_pressure. |
| 103 |
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o make mnc honor the writeBinaryPrec flag for most kinds of output |
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o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
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o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
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error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
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o add brackets in multi-terms sum to get same truncation, independent of |
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the face number (manage to get exactly same value of gU,gV at the cs-edge) |
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affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
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o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
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and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
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a maximum grid-scale Reynolds number. Also, changes all length calculations |
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in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
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Suggested values of viscosity parameters found in mom_calc_visc. |
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Many new viscosity diagnostics available. |
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checkpoint57s_post |
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o Add clearing-house for viscosity calculations, mom_calc_visc and |
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correct numerous bugs in LeithD and Smagorinsky discretizations. |
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mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
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used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
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Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
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and with Strain-Tension viscous term calculation (mom_hdissip.F). |
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The Strain-Tension form is now called with useStrainTensonVisc=.true. |
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ViscAhStrain and viscAhTension are now retired. |
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o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
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o In response to JMC's bug report, genmake2 now ignores any soft-links |
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that it finds in the *current* directory when searching for files. |
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Soft-links found in any other source directories will still work as |
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they did before. |
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o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
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a C routine to unlimit the stack size |
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o mnc-ify pkg/aim snapshot vars |
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o mnc-ify pkg/land as requested by Daniel |
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o various changes to mnc including: |
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- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
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- output can now be grouped so that all files within a group |
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change the ITER portion of their names in lock-step together |
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- can now read ("global") PER-FACE (in addition to PER-TILE) files |
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and works with both EXCH1 and EXCH2 (but needs more testing) |
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- writing works for all verification test cases w/ g77 on Linux |
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checkpoint57r_post |
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o make MNC variable initialization happen earlier |
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o add diagnostics for (almost) each term of the momentum Eq. |
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o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
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o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
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o remove MINIMAL_TAVE_OUTPUT option ; |
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add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
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o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
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allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
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o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
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o add time-dependent SST, SSS control |
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o cost terms in ecco/ modularized (new cost_generic.F) |
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o cost_averages routines are modularized (new cost_averagesgeneric.F) |
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o new infrastructure for seaice model vs. obs misfits in seaice/ |
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* driver from the_main_loop.F is seaice_cost_driver.F |
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* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
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* gradient check in Exp. 6a of natl_box_adjoint/ |
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o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
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(see README file) |
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checkpoint57q_post |
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o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
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o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
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- bug was reported by Jean-Michel and Ian Fenty |
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o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
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update exp. cpl_aim+ocn output. |
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o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
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Needed for high-res. runs with large global files |
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to be able to limit tapelev size |
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o Changed some tests for adjoint: |
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* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
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* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
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* global_ocean.90x40x15/ back to default 3-level checkpointing |
| 176 |
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o Modifications to enable scripted COMMON to MODULE conversion |
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* verification/OpenAD/code/ has necessary scripts and description; |
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* converts, compiles and runs successfully; |
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checkpoint57p_post |
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o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
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o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
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(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
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o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
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o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
| 186 |
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(was already the case for dissipation with mom_vecinv, |
| 187 |
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and also the case for grad.PhiHyd when staggered-timeStep) |
| 188 |
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This will allow to put dissipation out-off the AB time-stepping. |
| 189 |
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Unfortunately, affects truncation error. Update output of exp. that "fails" |
| 190 |
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(cg2d matching number) and leave the others for later: front_relax(10), |
| 191 |
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global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
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matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
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checkpoint57o_post |
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o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
| 196 |
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(2) its ready to be documented during the 20050801 DocFest |
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o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
| 198 |
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for ideal_2D_oce and lab_sea on linux_ia32_g77 |
| 199 |
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o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
| 200 |
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in global1x1_tot/code_seaice_adj to access indices 32, 33 |
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(worth another tag) |
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checkpoint57n_post |
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o adding precip control xx_precip 32 |
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o adding swflux control xx_swflux 33 |
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o Replacing 10 forcing penalty cost routines by 1 generic. |
| 207 |
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o Implementing partitioning in time-mean and variable adjustment |
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for atmos. state. |
| 209 |
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o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
| 210 |
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o in natl_box_adjoint: |
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* updated exp 1 to 10 |
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(but does not have time-mean vs. variable split results yet) |
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o updated global1x1/*_seaice_adj/ |
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to incorporate latest changes |
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o enable useSingleCpuIO for mdsio vector routines |
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(applies in particular to tapelev I/O) |
| 217 |
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o removed inefficient K-loop in all active_file*control*.F |
| 218 |
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checkpoint57m_post |
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o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
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and advect_cs (use EXCH-2 and standard cs-32 grid files). |
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o pkg/exch2: filling of face-corner halo regions is optional |
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(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
| 224 |
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|
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checkpoint57l_post |
| 226 |
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tag before updating tutorials (pre-release-2) |
| 227 |
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o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
| 228 |
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for output and interpolation of input fields onto model grid) |
| 229 |
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o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
| 230 |
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Affects results of exp. rotating_tank ; update output.txt. |
| 231 |
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o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
| 232 |
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and taking the square quantity and/or using a fraction-weight field. |
| 233 |
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o fix aim_diagnostics_init.F mate numbers. |
| 234 |
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o add mnc output capability to diagnostics/diagstat and update |
| 235 |
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our cvsignore files for the ACSII output generated |
| 236 |
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|
| 237 |
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checkpoint57k_post |
| 238 |
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o lab_sea now uses diagnostics package and provides a suite of |
| 239 |
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new EXF diagnostics output. |
| 240 |
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|
| 241 |
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checkpoint57j_post |
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o exf |
| 243 |
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* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
| 244 |
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Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
| 245 |
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terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
| 246 |
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* extended diagnostics output |
| 247 |
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- now includes all EXF variables |
| 248 |
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- hs, hl moved to common block |
| 249 |
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- separate S/R for diagnostics, called after ctrl vector is added |
| 250 |
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- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
| 251 |
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- EXFqnet contains true Qnet (i.e. includes qsw) |
| 252 |
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* updated verif. lab_sea, global_with_exf |
| 253 |
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* Rearranging hflux (exf_mapfields -> exf_getforcing) |
| 254 |
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to ensure that diagnostics sees a true EXFqnet |
| 255 |
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
| 256 |
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
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several times with different frequencies. |
several times with different frequencies. |
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