--- MITgcm/doc/tag-index 2004/11/21 22:22:31 1.390 +++ MITgcm/doc/tag-index 2004/12/22 07:27:07 1.427 @@ -1,8 +1,147 @@ -$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 1.427 2004/12/22 07:27:07 dimitri Exp $ Notes on tags used in MITgcmUV ============================== +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. + +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 +150,15 @@ - 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