--- MITgcm/doc/tag-index 2006/07/14 22:34:57 1.704 +++ MITgcm/doc/tag-index 2007/04/19 15:49:24 1.794 @@ -1,14 +1,288 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.704 2006/07/14 22:34:57 gforget Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.794 2007/04/19 15:49:24 mlosch Exp $ $Name: $ Notes on tags used in MITgcmUV ============================== +o pkg/kpp: add code to have mixing in shelf ice caverns + +checkpoint59 +o pkg/exf: + - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND & + ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid + - move exf header files from lower_case.h to UPPER_CASE.h ; + add missing cvs Header & Name + - add adjoint routines and flow dirs for newly used exch_uv_agrid routines + - add namelist param. selectStressGridPosition, exf_monFreq + - retire many _CLIM routines, and remove data.exf_clim + + params moved to data.exf + + climsst, climsss now handled by exf_set_gen, i.e. + climss?period=0 refers to constant field, + climss?period=-12 to monthly forcing + - split up namelists in data.exf +o pkg/seaice: + - remove seaice_exch and seaice_exch_uv + - remove superfluous exchange of theta + - add myThid to seaice_budget_ocean/ice + - add new interface for atmospheric wind forcing (C-grid only) + + new routine + + two new field (taux, tauy for stress over ice) + + removed one global field (DAIRN) for C-grid case only +o pkg/thsise + - 2nd set of modifs for thsice adjoint in conjunction with exf +o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.) + +checkpoint58y_post +o Added capability for latitudinal dependence of Bryan and Lewis, 1979 + vertical diffusivity, similar to that in MOM4; turned on using + #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using + diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file. +o Added capability for 3D specification of background vertical diffusion + coefficient. This is done by (i) #define ALLOW_3D_DIFFKR + in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime + "data" file that contains the 3D vertical diffusivity coefficients. +o ice dynamics (pkg/seaice) with thsice thermodynamics: + - add code within pkg thsice to advect & diffuse sea-ice fields + similar to (and will replace) what has been added in seaice_advdiff.F, + but: - conserving Mass, Heat & Salt. + - better when using non-linear advection scheme (not yet fully tested) + - can also be used in atmospheric set-up (for now, only the diffusion). + +checkpoint58x_post +o IO option for global-file compact format: + - add options when generating topology (utils/exch2/matlab-topology-generator) + - add I/O capability (pkg/mdsio). + - adapt utils/matlab/rdmds.m to read this format. + for now long-line format not yet supported by pkg/mdsio (& exch2). +o shelfice: add a few diagnostics + +checkpoint58w_post +o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: + rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref + (and replace horiVertRatio in NH code). + Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) + and tutorial_plume_on_slope (sensitive to truncation) +o seaice: if ALLOW_ATM_WIND is undefined use wind stress + directly to drive seaice model (C-grid only) +o exf: when input wind-stress (#undef ALLOW_ATM_WIND): + - reintroduce computation of wind from stress, + - compute tau (in exf_bulkformulae.F) from windstress averaged to + mass points to avoid tau = 0 + - fix serious bug: (1/3) in Fortran is not the same as (1./3.) +o rdmnc.m: make it work with "global" files created with gluemnc +o rdmnc.m : some improvements in dealing with singleton dimension + (tested on all testreport mnc output files). +o genmake2: disable pkg/profiles if netcdf test fails. +o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output. +o move call to cal_readparms up to make calendar parameters/variable available + to all packages + +checkpoint58v_post +o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get + useDynP_inEos_Zc tested. +o pkg/exf: changes to properly interpolate/mask/scale initial fields +o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields + and portions thereof. See read_cs.txt for description and examples. +o utils/matlab/cs_grid/bk_line: to compute transport through passages, + add a script (grt_circ_bkl.m) to generate broken-line between 2 points, + following the great-circle arc between those 2 points. +o trap un-initialized variable with pathscale compiler on weddell.mit.edu + (thanks to Constantinos): fix few problems and get (almost) all exp to pass. +o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in + - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) + - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81) + - still needs work (not working with some options ; efficiency to improve) + and serious testing. + - use this scheme for temperature & salinity in 2 advection test exp.: + advect_xy & advect_xz, respectively. + +checkpoint58u_post +o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. +o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. +o testreport: add option "-skipdir" to skip some test. +o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent + momentum calculation. +o gad_advection: fix vertAdvecScheme (if different from advectionScheme) +o some cleaning: usePickupBeforeC35 no longer supported ; remove this option. + remove checkpoint.F and the_correction_step.F (no longer used); + do the k loop inside CYCLE_TRACER (supposed to be more efficient). +o add option (linFSConserveTr) to correct for tracer source/sink due to + Linear Free surface +o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine +o pkg/thsice: fix reading mnc-pickups + +checkpoint58t_post +o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) +o pkg/mdsio: + - clean-up mdsio_readfield.F & mdsio_writefield_new.F and + move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & + mdsio_write_field.F (S/R MDS_WRITE_FIELD); + - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD + - collect old S/R in one file: mdsio_rw_field.F (now just a call to + either MDS_READ_FIELD or MDS_WRITE_FIELD ) + - new S/R (to replace MDSWRITEMETA), which allows to write more + informations (variable names, time ...) to meta files. + - modify rdmds.m to give back the meta file content. +o pkg/diagnostics: change vertical interpolation to be safer, and more + flexible (define p-levels to interpolate to in data.diagnostics); + add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right + diagnostic pointer. +o pkg/seaice: more cleaning up of seaice_growth, added many comments +o pkg/exf: put runoff0 and runoff1 into the appropriate common block +o fix multi-category seaice: + - change cpp flag SEAICE_MULTILEVEL to more meaningful name: + SEAICE_MULTICATEGORY + - fix short wave heat flux +o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics + and allow to use EVP solver. Change forward lab_sea: test both EVP + solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) +o Initial check-in of lab_sea adjoint + (very similar to natl_box_adjoint/code_seaice) + * used C-grid and EVP solver + * used KPP, GM/Redi + * uses inAdExact=.TRUE. + * gradient checks fail for both ADM and TLM + due to sensitive snow melt code in seaice_grwoth (look for "JZ") + f.d. gradients actually seem more problematic than ADM, TLM gradients; + issue is related to forward mismatch between g77 an ifort +o pkg/seaice: overhaul of thermodynamics + - growth.F and groatb.F are replaced by new routine seaice_growth.F + - budget.F is replaced by two new routines seaice_budget_ocean/ice.F + - move a few global fields out of SEAICE.h into seaice_growth.F and + make them 2D (FICE/QNETO/ ...) + - remove FO (it is the same as QNETO) + - introduce a few local fields to avoid modifying external fields such + as atemp, etc. + +checkpoint58s_post +o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F + changed exf_set_gen.F so that + genperiod=0 means input file is one time-constant field and + genperiod=-12 means input file contains 12 monthly means +o CG2D: use pre-computed solver main-diagonal (stored in common block); + this affects truncation error ; generate new output file for exp. which + fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), + global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), + ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), + MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), + tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), + vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) +o start implementation of deep-atmosphere and anelastic formulation +o verification: remove 2nd copy of input files and use script "prepare_run" + to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) +o mom_common/vecinv/fluxform: fix a few initialisation isssues +o profiles: fix for multithreaded case + +o diagnostics: rename few diags: + s/'PRESSURE'/'RCENTER '/g + s/'TICE '/'oceFreez'/g + s/'TAUX '/'oceTAUX '/g + s/'TAUY '/'oceTAUY '/g + s/'SWFLUX '/'oceQsw '/g + s/DIFx/DFxE/g + s/DIFy/DFyE/g + and add few ocean-forcing diagnostics: + atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS +o modifications to pkg/seaice/growth.F and budget.F, which change results of + lab_sea experiment: HSNOW was sometimes treated as effective and sometimes + as actual snow thickness. It now refers everywhere to effective snow + thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. + +checkpoint58r_post +o modifications to pkg/seaice/growth.F, which change results of + lab_sea experiment: fixes pertain to melting snow over open water, to + masking EVAP under sea ice, and to using the correct AREA variable for + computations of EVAP, PRECIP, HSNOW, and GHEFF +o add ability to read bathy, salt, and theta using MNC (off by def) +o add flooding algorithm and advection of HSNOW for pkg/seaice; + both are turned off by default and do no change any results +o seaice advection with pkg/thsice: a step toward the use of non-linear + advection scheme, but #ifdef or commented out for now (requires more EXCH). +o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens + (identical results) and the standard version of EXTERNAL_FIELDS_LOAD + in natl_box (affects results @ truncation level: update output.txt) +o multi-threading and IO: + - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. + - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls + (needed to work with SingleCpuIO): tested in all verif. exp. +o GAD: use simpler DST3 formulation as default (old version left within #ifdef) + affects the results (but none of the verification test uses this scheme). +o Adding some pkg/diagnostics capability to pkg/seaice + (will certainly be subject to changes) +o ctrl: adding new control variables: + lwflux, lwdown, evap, snowprecip, apressure, runoff + +checkpoint58q_post +o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up + 1/6-deg Southern Ocean configuration by 8% on IBM Datastar and + high_res_cube configuration by 4% on Columbia. +o clean-up multi-threaded problems (reported by debugger tcheck on ACES); + add (in global_with_exf/code) a version of EXF_INTERP_READ without + dynamical allocation (seems to work in multi-threaded). +o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using + single CPU io) so that TAF does not have to see EESUPPORT.h +o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) + +checkpoint58p_post +o obcs: stop if obcs is used with useCDscheme = .true. +o shelfice: + - fix a sign error so that no slip at shelfice interface works + - remove stop for combination non-hydrostatic code and shelfice. That does + not mean, that the results are correct, but at least they are numerically + stable +o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) +o added adjoint exch routined for all exch*3d* routines + and updated flow directives + +checkpoint58o_post +o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; + remove old subroutines (_XY_ & _XYZ_); update the adjoint version. +o change controling S/R for writing pickup file (new S/R do_write_pickup) + and clean-up reading/writing of pickup files. +o fix local version of read/write pickup (NH part) in rotating_tank/code +o simplify EXCH interface: + - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) + - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version +o added the regrid package +o shelfice: + - add a simple boundary layer scheme to reduce noise + - fix the indexing in shelfice_u/v_drag so that there will be actually drag + +checkpoint58n_post +o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to + local variable (not in common block). +o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. + - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); + - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls + to work with SingleCpuIO. +o add "_d 0" to real constant of pkg/cfc subroutines ; + update exp. cfc_exemple & tutorial_cfc_offline output files. +o multi-threading and IO: + - all threads call READ_FLD S/R (needed if using SingleCpuIO): + (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. + - barrier before and after reading. + - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) + - avoid using MDS_WRITELOCAL for LAND pkg output. + - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics + common-block variables ; Allows multi-threading with master-thread IO. +o change default MAX_NO_THREADS from 32 to 4 ; + and stop cleanly when MAX_NO_THREADS is too small. +o add S/R BAR_CHECK to check multi-threaded barrier synchronization + +checkpoint58m_post +o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. + and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 +o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. + keep global_ocean.90x40x15 (for AD testing) with former secondary test + (".qshyd") as the main test (mv output.qshyd.txt to output.txt) +o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; + add MITgcm_tutorials (= code + all the tutorials) +o ecco, option to compute cost for total ssh (mean+anom) o consistent with addition of ptracer and ssh in pkg/profiles o profiles: adding ptracer and ssh o testreport: change multi-test output-file name (from output.txt.{name} to output.{name}.txt) -o profiles: now ok for mutli-threaded case +o profiles: now ok for mutli-tiles case o seaice: add 4 parameters for different advection schemes for area, (effective) seaice thickness, enthalphy, and snow height. Their default is the standard parameter SEAICEadvScheme