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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 vorticity & strain are now computed without masking, to account for |
| 8 |
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no-slip-side BC in variable viscosity calculation ; mask is applied |
| 9 |
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anyway later on, before computing advection/coriolis terms. |
| 10 |
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o modify exp4 to test new obcs support reading from external files |
| 11 |
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and for passive tracers |
| 12 |
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o fix behavior of ptracers_monitor when monitor output is written to a |
| 13 |
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netcdf-file; still not independent of monitor.F (writes in the same |
| 14 |
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file). |
| 15 |
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o change default value of tRef (put a uniform, meaningful value for ocean |
| 16 |
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& atmos) and initialize sRef (was missing, as Martin mentioned). |
| 17 |
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o Redefine viscC?Leith*. Change the coefficients of Leith viscosity |
| 18 |
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to be proportional to enstrophy dissipation length. Thus, |
| 19 |
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viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) |
| 20 |
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This is now consistent with Smagorinsky and with the manual. |
| 21 |
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|
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checkpoint57u_post |
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o OBCS and PTRACERS: add open boundary support for passive tracers |
| 24 |
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- either use homogenous (pseudo) v.Neumann conditions or prescribe |
| 25 |
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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 |
| 28 |
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will stop if you use pTracers and Orlanski at the same time. |
| 29 |
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- beefed up the rountine obcs_external_fields_load: now only those open |
| 30 |
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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) |
| 34 |
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o reduce number of exch calls in shap_filt (s2). |
| 35 |
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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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| 38 |
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checkpoint57t_post |
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o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
| 40 |
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o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
| 41 |
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same truncation, independent of the face number: affects affects several |
| 42 |
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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. |
| 45 |
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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. |
| 47 |
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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 |
| 49 |
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o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
| 50 |
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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 |
| 52 |
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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. |
| 58 |
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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. |
| 66 |
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Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
| 67 |
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and with Strain-Tension viscous term calculation (mom_hdissip.F). |
| 68 |
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The Strain-Tension form is now called with useStrainTensonVisc=.true. |
| 69 |
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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 |
| 76 |
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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 |
| 79 |
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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 |
| 81 |
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- output can now be grouped so that all files within a group |
| 82 |
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change the ITER portion of their names in lock-step together |
| 83 |
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- can now read ("global") PER-FACE (in addition to PER-TILE) files |
| 84 |
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and works with both EXCH1 and EXCH2 (but needs more testing) |
| 85 |
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- writing works for all verification test cases w/ g77 on Linux |
| 86 |
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|
| 87 |
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checkpoint57r_post |
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o make MNC variable initialization happen earlier |
| 89 |
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o add diagnostics for (almost) each term of the momentum Eq. |
| 90 |
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o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
| 91 |
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o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
| 92 |
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o remove MINIMAL_TAVE_OUTPUT option ; |
| 93 |
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add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
| 94 |
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o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
| 95 |
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allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
| 96 |
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o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
| 97 |
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o add time-dependent SST, SSS control |
| 98 |
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o cost terms in ecco/ modularized (new cost_generic.F) |
| 99 |
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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) |
| 103 |
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* gradient check in Exp. 6a of natl_box_adjoint/ |
| 104 |
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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) |
| 109 |
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o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
| 110 |
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- bug was reported by Jean-Michel and Ian Fenty |
| 111 |
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o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
| 112 |
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update exp. cpl_aim+ocn output. |
| 113 |
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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 |
| 115 |
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to be able to limit tapelev size |
| 116 |
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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 |
| 120 |
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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) |
| 128 |
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o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
| 129 |
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o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
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(was already the case for dissipation with mom_vecinv, |
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and also the case for grad.PhiHyd when staggered-timeStep) |
| 132 |
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This will allow to put dissipation out-off the AB time-stepping. |
| 133 |
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Unfortunately, affects truncation error. Update output of exp. that "fails" |
| 134 |
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(cg2d matching number) and leave the others for later: front_relax(10), |
| 135 |
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global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
| 136 |
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matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
| 137 |
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| 138 |
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checkpoint57o_post |
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o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
| 140 |
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(2) its ready to be documented during the 20050801 DocFest |
| 141 |
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o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
| 142 |
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for ideal_2D_oce and lab_sea on linux_ia32_g77 |
| 143 |
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o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
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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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| 147 |
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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 |
| 150 |
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o Replacing 10 forcing penalty cost routines by 1 generic. |
| 151 |
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o Implementing partitioning in time-mean and variable adjustment |
| 152 |
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for atmos. state. |
| 153 |
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o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
| 154 |
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o in natl_box_adjoint: |
| 155 |
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* updated exp 1 to 10 |
| 156 |
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(but does not have time-mean vs. variable split results yet) |
| 157 |
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o updated global1x1/*_seaice_adj/ |
| 158 |
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to incorporate latest changes |
| 159 |
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o enable useSingleCpuIO for mdsio vector routines |
| 160 |
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(applies in particular to tapelev I/O) |
| 161 |
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o removed inefficient K-loop in all active_file*control*.F |
| 162 |
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| 163 |
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checkpoint57m_post |
| 164 |
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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). |
| 166 |
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o pkg/exch2: filling of face-corner halo regions is optional |
| 167 |
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(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
| 168 |
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|
| 169 |
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checkpoint57l_post |
| 170 |
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tag before updating tutorials (pre-release-2) |
| 171 |
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o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
| 172 |
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for output and interpolation of input fields onto model grid) |
| 173 |
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o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
| 174 |
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Affects results of exp. rotating_tank ; update output.txt. |
| 175 |
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o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
| 176 |
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and taking the square quantity and/or using a fraction-weight field. |
| 177 |
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o fix aim_diagnostics_init.F mate numbers. |
| 178 |
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o add mnc output capability to diagnostics/diagstat and update |
| 179 |
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our cvsignore files for the ACSII output generated |
| 180 |
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|
| 181 |
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checkpoint57k_post |
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o lab_sea now uses diagnostics package and provides a suite of |
| 183 |
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new EXF diagnostics output. |
| 184 |
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|
| 185 |
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checkpoint57j_post |
| 186 |
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o exf |
| 187 |
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* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
| 188 |
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Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
| 189 |
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terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
| 190 |
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* extended diagnostics output |
| 191 |
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- now includes all EXF variables |
| 192 |
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- hs, hl moved to common block |
| 193 |
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- separate S/R for diagnostics, called after ctrl vector is added |
| 194 |
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- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
| 195 |
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- EXFqnet contains true Qnet (i.e. includes qsw) |
| 196 |
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* updated verif. lab_sea, global_with_exf |
| 197 |
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* Rearranging hflux (exf_mapfields -> exf_getforcing) |
| 198 |
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to ensure that diagnostics sees a true EXFqnet |
| 199 |
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o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
| 200 |
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o diagnostics pkg: change pointers so that 1 diagnostic can be used |
| 201 |
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several times with different frequencies. |
| 202 |
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o mnc-ify the thsice package as requested by Daniel Enderton |
| 203 |
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- the monitor--MNC output needs work |
| 204 |
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- many attributes need to be added (most are currently blank) |
| 205 |
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o mnc-ify theaim_v23 package as requested by Daniel Enderton |
| 206 |
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- many attributes need to be added (most are currently blank) |
| 207 |
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o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
| 208 |
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o add Sadourny like discretization to the 4th.O vorticity advection scheme |
| 209 |
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o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
| 210 |
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update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
| 211 |
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fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
| 212 |
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o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
| 213 |
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(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
| 214 |
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|
| 215 |
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checkpoint57i_post |
| 216 |
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o Diagnostics package was changed: diagnostic allocation is now deactivated |
| 217 |
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by setting an empty file name in the namelist (used to be by setting 0 frequency) |
| 218 |
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o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
| 219 |
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add 1rst Order upwind vertical Shear. |
| 220 |
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o add a quick fix for A/B checkpointing in OFFLINE mode |
| 221 |
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o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
| 222 |
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end-run around the C/Fortran linking horror in eesup/src/timers.F |
| 223 |
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o added pkg/runclock: allows user to terminate run based on wall clock |
| 224 |
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o added non-hydrostatic scaling parameter: nh_am2 |
| 225 |
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o pkg/my82: futile attempt to make results compiler-independent by adding |
| 226 |
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some "_d 0", etc. no effect. |
| 227 |
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o for mnc output, fill the 'T' coordinate var with myTime and create a |
| 228 |
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separate 'iter' variable for iteration count |
| 229 |
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o pkg/diagnostics: |
| 230 |
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add new capability: output of Global/Regional & per-level statistics ; |
| 231 |
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tested against monitor output (including land & thSIce) on various exp. |
| 232 |
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o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
| 233 |
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|
| 234 |
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checkpoint57h_done |
| 235 |
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tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
| 236 |
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data.diagnostics, data.gchem, data.ptracers) is done. |
| 237 |
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|
| 238 |
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o pkg/diagnostics: prepare for Global/Regional statistics. |
| 239 |
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add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
| 240 |
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o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
| 241 |
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and rename it: DIFFERENT_MULTIPLE |
| 242 |
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|
| 243 |
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checkpoint57h_post |
| 244 |
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o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
| 245 |
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o pkg/diagnostics: change output frequency, now in seconds (instead |
| 246 |
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of Nb of iterations). This requires to change data.diagnostics. |
| 247 |
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checkpoint57h_pre |
| 248 |
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|
| 249 |
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o in mnc, let the user create the output dir if both mnc_outdir_date |
| 250 |
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and mnc_outdir_num are false |
| 251 |
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o add fflags() to pkg/diagnostics which allows one to specify, on a |
| 252 |
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per-file basis, the file precision [default behavior is unchanged] |
| 253 |
|
o added diagnostics to pkg/kpp, including computation of mixed layer |
| 254 |
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depth based on a temperature/density criterion |
| 255 |
|
o updated verification/natl_box to test the new pkg/kpp diagnostics |
| 256 |
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
| 257 |
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
| 258 |
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
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