--- MITgcm/doc/tag-index 2004/11/21 22:22:31 1.390 +++ MITgcm/doc/tag-index 2005/05/19 16:26:36 1.488 @@ -1,8 +1,284 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.390 2004/11/21 22:22:31 jmc Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.488 2005/05/19 16:26:36 jmc Exp $ +$Name: $ Notes on tags used in MITgcmUV ============================== +checkpoint57h_done + tag after changing user customized files (DIAGNOSTICS_SIZE.h, + data.diagnostics, data.gchem, data.ptracers) is done. + +o pkg/diagnostics: prepare for Global/Regional statistics. + add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h +o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE + and rename it: DIFFERENT_MULTIPLE + +checkpoint57h_post +o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers +o pkg/diagnostics: change output frequency, now in seconds (instead + of Nb of iterations). This requires to change data.diagnostics. +checkpoint57h_pre + +o in mnc, let the user create the output dir if both mnc_outdir_date + and mnc_outdir_num are false +o add fflags() to pkg/diagnostics which allows one to specify, on a + per-file basis, the file precision [default behavior is unchanged] +o added diagnostics to pkg/kpp, including computation of mixed layer + depth based on a temperature/density criterion +o updated verification/natl_box to test the new pkg/kpp diagnostics +o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) +o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) +o fix mnc flags in pkg/seaice so that they are "owned" by seaice, + not mnc -- this mistake was found by JMC and is now corrected + +checkpoint57g_post +o add Adams-Bashforth 3rd Order time stepping: + - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) + - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... +checkpoint57g_pre + +o make lambda[Theta,Salt]ClimRelax spatially varying + (default remains spatially uniform constant based on tau) +o added new control variables + * init. uVel, vVel, etanN + * lambda[Theta,Salt]ClimRelax +o separate masks used for ctrl_pack/unpack 'from write_grid' output + (suggested by G. Forget) + +checkpoint57f_post +o add parameter "baseTime" = model base time = time at iteration zero + new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to + account for baseTime shift +o move Coriolis arrays from PARAMS.h to GRID.h +checkpoint57f_pre + +o mnc-ifying the seaice package +o introduced an alternative length scale calculation for use in the limiting + maximum viscosity (off by default, see mom_vi_hdissip.F for details) +o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S +o added modified Leith scheme with viscosity proportional to grad(Hdiv) + as well as grad(vort3). Made it compatible with both approximate form + for the cubed sphere and full form of these gradients. Added flag + useFullLeith to select between approximate and full form. +o add "d0" in getcon.F to reduce differences between compilers/platforms + update output.txt of exp. fizhi-gridalt-hs +o change port_rand funtion to allow to set the seed. +o fix obscure MNC bug involving conversion between reals and integers + - it caused no problems with certain (eg. gcc, ifc) compilers but the + new version is now more standards-compliant +o adjoint-related modifications + * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint + * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 + * mom_vi_hdissip: to be able to use Leith scheme in adjoint + +checkpoint57e_post +o Adding eddy stress controls a la Ferreira et al. +checkpoint57e_pre (actually was tagged: eckpoint57e_pre) + +o fizhi pkg: fix AtoC and CtoA when called with same input & output array + update output.txt of exp. fizhi-gridalt-hs +o add more "Z" dimensions and associated coordinate vars to MNC +o pkg/exf: added twoDigitYear capability for option useExfYearlyFields +o parameter calendarDumps: when set, approximate months (30-31 days) and years + (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, + KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar + months and years. Requires pkg/cal. +o diagnostics: add pickup functionality + - off by default for backwards compatibility + - current version only uses MDSIO -- MNC will be added +o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. +o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) + +checkpoint57d_post +o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing +o modify verification/ideal_2D_oce so that it tests the creation of mnc + output from the diagnostics package +o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up +o make genmake2 more portable by using ".$FS" instead of ".f" for more + of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) +o add coordinate variables to the MNC output from the diagnostics package +o change MNC-flags default value: true when useMNC=TRUE +o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F + the ability (off by default) to read the grid information using MNC +o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt +o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging +o do snap-shot diagnostics at the middle of the time-interval (instead of + at the end). +o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add + new test for AIM with thSIce + slab-ocean +o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) +o move state variable diagnostics to the beginning of the time step ; + (note: still needs some work specially for snap-shot diagnostics) + duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z + +checkpoint57c_post +o Change testing option (-ieee) to get closer agreement between g77 & ifort +o generate new output.txt files on faulks with g77 & the new -ieee option +checkpoint57c_pre + +o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); + update output.txt of exp. global_ocean.90x40x15 +o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer + results; update global_ocean_pressure & global_ocean.cs32x15 output.txt +o add saltFlux(+File) forcing capability with periodicExternalForcing +o allow to use pkg diagnostics for GM-Redi & ThSIce output +o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. +o improvements for the MNC output from DIAGNOSTICS: + - correct handling of the unlimitied dimension + - all dims now have associated coordinate variables + - variables located at U, V, and Corner ("Z") points are now written + with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that + *all* data points are output +o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice +o added pkg/seaice/seaice_monitor.F +o mdsio_readfield.F can now read files visible only to master MPI process. +o pkg/seaice: some test code for ice-modified ocean stress +o exf_getffields interpolation defaults to bilinear for all scalar forcing + fields (remains bicubic for wind velocity and stress). This avoids, e.g., + spurious negative numbers for precipitation and humidity. Will cause + some small numerical differences for integrations using pkg/exf/exf_interp.F. +o pkg/ctrl/ + * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O + May be enabled via doPackDiag + * introduce z-scaling of + + gradient (doZscalePack) and + + control (doZscaleUnpack) +o pkg/mdsio/ + * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F + * N.B.: leave tiled I/O for tapelev (i.e. mds...vector) + +checkpoint57b_post +o simplify options in diagnostics_fill arguments (remove weird combinations) +o fix MNC coordinate variables so that they now contain per-face index + values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in + general, EXCH2 grids are only aligned to a "local" coordinate system +o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) +o Implement instantaneous output within pkg diagnostics: + setting a negative frequency in data.diagnostics produces + "snap-shot" output (as opposed to time-average if freq > 0) +o move out off EQUIVALENCE all diagnostics that fizhi does not use ; + NOTE: change ptracer diagnostics name: use 2 characters to work with + more than 9 tracers. Add also diagnostics of advect & diffus flux. +o more CF compliance: convert all MNC 'iter' variables to 'T' so that it + becomes the coordinate variable for the 'T' dimension +o add CF-style coordinate variables to MNC + - just a first cut: numbers are meaningless on the cubesphere and + missing along the T axis but otherwise it works! +o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX +o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. +o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) + this is based directly on what the model compute, so that the content of + each diagnostics might be affected by switching options (e.g., implicitDiffusion) +o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) +o clean up build options files for SunOS, in particular + - remove -traditional from xmakedepend + - change -xarch=v9 to -xarch=native for f77 + - restore use of make (not gmake) + - add CC=gcc if using g77 +o changes per discussion of AM, JMC, & EH3 today: + - move redundant "grid" variables out of "state" -- in preparation of + creating proper CF-style coordinate variables and in recognition + that any/all grid variables can be easily copied (eg. w/NCO) from + the grid files into any of the other NetCDF files + - *always* output grid variables with MDSIO (this will eventually be + changed) + - output MNC grid file if useMNC is true +o every instance of _END_MASTER() has been found and replaced with + _END_MASTER( myThid ) in order to satisfy certain picky Sun + preprocessors +o re-arrange diagnostics pkg initialisation: + - allow each package to extend the available diagnostics list + - add some checking and fix small problems (multi-threaded, ...) + - new S/R diagnostics_fill (replace fill_diagnostics): + look through the short list of active diag. (instead of the long list) + create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active + +checkpoint57a_post +o this set of changes restores TAMC compatibility + tested for global_ocean.90x40x15 adjoint on trough + (what a pain) + +checkpoint57a_pre +o some modifs in tools/build_options for sunos +o call ctrl_pack for ctrl at end for optimcycle=0 + +checkpoint57 +o add horizontal bi-harmonic viscosity for vertical velocity + - new parameter viscA4W (defaults to viscA4) + - affects only non-hydrostatic code + - to be done: no-slip lateral boundary conditions +o switch back to "sflux = sflux - runoff" in exf_getforcing.F +o implement Implicit Vertical advection for pTracers +o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) + (implemented also for implicit vertical diffusion & advection) +o OBCS: extend application of tracer open boundary conditions + to a strip beyond the boundary of width Olx/Oly +o add call monitor to TAF set of required calls (flow directives) + and include in natl_box_adjoint +o untangle a few ifdefs related to cost, ctrl, autodiff + untangel a few ALLOW_ECCO_OPTIMIZATION +o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) + (theta2, salt2 in ecco_cost_weights) + +checkpoint56c_post +o OBCS as control variables + - update ctrl_ad_diff.list, obcs_ad_diff.list + - remove balance of obcs controls from default + - fix index bug nobcs in ctrl_init + - fix dummy fields filen in ctrl_pack + - add dummy weights for obcs +o lsopt: comment out fort.94 output +o optim: + - remove unnecessary header files + - adjusted namelists + - add xerbla.F to Makefile +o exf: + - multiple modifications of exf_check_range + - unit change in exf_init_runoff from [m/year] to [m/s] +o mdsio: + - i/o-vector change debugLevel from debLevA to debLevB + +checkpoint56b_post +o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that + is called from DO_THE_MODEL_IO + - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE + - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) + - clean up PTRACERS_WRITE_TIMEAVE a little +o add another verification experiment that tests both the cfc-pkg and + the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with + reactive tendencies treated inline with regular timestepping +o testreport previously did a lousy job of comparing small numbers, so + we (Ed and Martin) changed the way the cut-off of 1.e-12 is + implemented in the little c-progam tmp_cmpnum.c which is embedded in + testreport. +o ptracers_monitor: bug fix for MPI + +checkpoint56a_post +o GCHEM: finish reorganizating the package + - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency + (introduces another 3D-array for each passive tracer, but only if + GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING + gchemTendency is not needed because the timestep is done separately) + - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY + - GCHEM is now---more or less cleanly---separate from PTRACERS + - to bo done: handling of surfaceForcingPtr that is needed for KPP not + so clear to me how that should be done in a general way. +o CFC: improve formatting of output in CFC_ATMOS +o PTRACERS: + - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so + that ALL experiments with ptracers enable can be checked. This makes + GCHEM_MONITOR obsolete. + - include a runtime parameter PTRACERS_monitorFreq that defaults to + monitorFreq + - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true +o add PTRACERS (PTR0[1-5]) to testreport output +o exf_check_range: + * default changed to .TRUE. + * will check values for niter0 if debLevA, every timestep if debLevB + * STOP in exf_check_range if 'out of range' + * range chosen generous to allow for potential extema + TBD: a version with stricter range + permitted range would be runtime parameters o GMredi: - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. @@ -11,6 +287,15 @@ - move call to GCHEM_FORCING_SEP, so that it is now called before the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP - introduced a useGCHEM runtime flag and applied it everywhere. + - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; + this flag is now only visible within GCHEM-pkg routines. + - moved gchem_forcing_int temporarily into ptracers_forcing, this will + be replaced by a 3D array that is computed before thermodynamics; for + this, the tracer ID iTracer had to be included into the parameter list + of ptracers_forcing + - set up forward_step to call gchem_forcing, that will replace + gchem_forcing_int in ptracers_forcing + - cleaning up o small cleaning of exch2: remove files that are also in eesupp/src checkpoint56