--- MITgcm/doc/tag-index 2005/08/24 23:36:01 1.536 +++ MITgcm/doc/tag-index 2005/12/04 22:14:06 1.583 @@ -1,14 +1,155 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.536 2005/08/24 23:36:01 jmc Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.583 2005/12/04 22:14:06 jmc Exp $ $Name: $ Notes on tags used in MITgcmUV ============================== +checkpoint57x_post +o fix testreport Pb in multiple test experiment. +o cleanup our namelist syntax in verification: + - make it more F95 standards compliant (some work still needed) + - allows the vast majority of our tests to work with gfortran +o Non-Hydrostatic: + - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h + - fix exchange calls for CS-grid using the new EXCH_S3D_RL. +o Allow to apply AB on T,S rather than on AB(gT,gS): + - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 + - use the same arrays (gtNm,gsNm) to hold tracer field at previous + time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). + - need a "clever" read_pickup to restart from the other AB formulation +o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h +o remove some unused variables (reduces number of compiler warnings) +o adjoint + * Disable useVariableViscosity for adjoint for time being + (there are a number of extensive recomputations) + * Initialize certain variables needed for adjoint + +checkpoint57w_post +o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names + fix the singleCpuIO RS version of MDSWRITEFIELD + and add a WARNING if using globalFiles=T with multi-processors. +o write grid-file(s) in only one format (MDS or MNC): default=MNC (if + using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc +o tracer advection scheme: + add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get + those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, + was not very convenient). + add implicit version for DST-3 & DST3_Flux_Limit vertical advection; + (further tests needed for the implicit DST & Flux-Limiter schemes). +o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef + and sRef for convenience, handy, when you want to initialize + ptracers in a large domain with a constant non-zero value. Also, + untangle ptracers_init.F a little. + +checkpoint57v_post +o change dome exp. to use variable viscosity in side-drag terms. +o remove all the files from the cfc_offline test since they are now + incorporated into tutorial_cfc_offline which has been producing + identical results for a few days of testing +o add new parameter: sideDragFactor to enable half-slip-side BC + and change side-drag S/R to use viscosity from mom_calc_visc + (can switch back by setting sideDragFactor=0.); affects results at + truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), + global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). +o vorticity & strain are now computed without masking, to account for + no-slip-side BC in variable viscosity calculation ; mask is applied + anyway later on, before computing advection/coriolis terms. +o modify exp4 to test new obcs support for reading from external files + and for passive tracers +o fix behavior of ptracers_monitor when monitor output is written to a + netcdf-file; still not independent of monitor.F (writes in the same + file). +o change default value of tRef (put a uniform, meaningful value for ocean + & atmos) and initialize sRef (was missing, as Martin mentioned). +o Redefine viscC?Leith*. Change the coefficients of Leith viscosity + to be proportional to enstrophy dissipation length. Thus, + viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) + This is now consistent with Smagorinsky and with the manual. + +checkpoint57u_post +o OBCS and PTRACERS: add open boundary support for passive tracers + - either use homogenous (pseudo) v.Neumann conditions or prescribe + OB-values from file; this is not different from the way theta and salinity + are treated + - however, Orlanski-radiation conditions are not supported, and the model + will stop if you use pTracers and Orlanski at the same time. + - beefed up the rountine obcs_external_fields_load: now only those open + boundary values are overwritten with values from files for which there + are really files, otherwise the OB-fields remain untouched. This makes + it possible to use different OBs at different ends of the domain (as + with EXF) +o reduce number of exch calls in shap_filt (s2). +o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ + truncation level) 4/5 MLAdjust test results (11&12 digits match). + +checkpoint57t_post +o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 +o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get + same truncation, independent of the face number: affects affects several + test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). +o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); + note that biharmonic viscosity + no-slip was not tested in any experiment. +o fix bug in non-linear free-surf side-drag ; generate new output for + global_ocean.cs32x15(+.thsice) & global_ocean_pressure. +o make mnc honor the writeBinaryPrec flag for most kinds of output +o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum +o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation + error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). +o add brackets in multi-terms sum to get same truncation, independent of + the face number (manage to get exactly same value of gU,gV at the cs-edge) + affects several test. exp. Update global_ocean.cs32x15 (+.thsice). +o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax + and viscA4Remax, which allow one to limit the minimum viscosity by specifying + a maximum grid-scale Reynolds number. Also, changes all length calculations + in the case of grid anisotropy to geometric mean of dx**2 and dy**2. + Suggested values of viscosity parameters found in mom_calc_visc. + Many new viscosity diagnostics available. + +checkpoint57s_post +o Add clearing-house for viscosity calculations, mom_calc_visc and + correct numerous bugs in LeithD and Smagorinsky discretizations. + mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be + used simultaneously, and to be used in mom_vecinv and mom_fluxform. + Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) + and with Strain-Tension viscous term calculation (mom_hdissip.F). + The Strain-Tension form is now called with useStrainTensonVisc=.true. + ViscAhStrain and viscAhTension are now retired. +o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". +o In response to JMC's bug report, genmake2 now ignores any soft-links + that it finds in the *current* directory when searching for files. + Soft-links found in any other source directories will still work as + they did before. +o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls + a C routine to unlimit the stack size +o mnc-ify pkg/aim snapshot vars +o mnc-ify pkg/land as requested by Daniel +o various changes to mnc including: + - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format + - output can now be grouped so that all files within a group + change the ITER portion of their names in lock-step together + - can now read ("global") PER-FACE (in addition to PER-TILE) files + and works with both EXCH1 and EXCH2 (but needs more testing) + - writing works for all verification test cases w/ g77 on Linux + +checkpoint57r_post +o make MNC variable initialization happen earlier +o add diagnostics for (almost) each term of the momentum Eq. +o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) o remove MINIMAL_TAVE_OUTPUT option ; add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) +o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) +o add time-dependent SST, SSS control +o cost terms in ecco/ modularized (new cost_generic.F) +o cost_averages routines are modularized (new cost_averagesgeneric.F) +o new infrastructure for seaice model vs. obs misfits in seaice/ + * driver from the_main_loop.F is seaice_cost_driver.F + * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) + * gradient check in Exp. 6a of natl_box_adjoint/ +o natl_box_adjoint input_seaice for Lab. Sea now available online via wget + (see README file) checkpoint57q_post o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)