--- MITgcm/doc/tag-index 2004/12/22 07:27:07 1.427 +++ MITgcm/doc/tag-index 2005/08/10 03:41:44 1.530 @@ -1,14 +1,269 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.427 2004/12/22 07:27:07 dimitri Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.530 2005/08/10 03:41:44 heimbach Exp $ +$Name: $ Notes on tags used in MITgcmUV ============================== +o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT + Needed for high-res. runs with large global files + to be able to limit tapelev size +o Changed some tests for adjoint: + * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT + * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT + * global_ocean.90x40x15/ back to default 3-level checkpointing + +checkpoint57p_post +o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F +o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED + (already the case for some pkgs, including recent MNC_init, e.g. thsice) +o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) +o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F + (was already the case for dissipation with mom_vecinv, + and also the case for grad.PhiHyd when staggered-timeStep) + This will allow to put dissipation out-off the AB time-stepping. + Unfortunately, affects truncation error. Update output of exp. that "fails" + (cg2d matching number) and leave the others for later: front_relax(10), + global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), + matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). + +checkpoint57o_post +o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and + (2) its ready to be documented during the 20050801 DocFest +o MNC-ify the gmredi package -- tested and works w/ and w/o mnc + for ideal_2D_oce and lab_sea on linux_ia32_g77 +o set to #undef CTRL_SET_OLD_MAXCVARS_30 + in global1x1_tot/code_seaice_adj to access indices 32, 33 + (worth another tag) + +checkpoint57n_post +o adding precip control xx_precip 32 +o adding swflux control xx_swflux 33 +o Replacing 10 forcing penalty cost routines by 1 generic. +o Implementing partitioning in time-mean and variable adjustment + for atmos. state. +o Time-mean constant error is now read in data.ecco (instead of hard-coded) +o in natl_box_adjoint: + * updated exp 1 to 10 + (but does not have time-mean vs. variable split results yet) +o updated global1x1/*_seaice_adj/ + to incorporate latest changes +o enable useSingleCpuIO for mdsio vector routines + (applies in particular to tapelev I/O) +o removed inefficient K-loop in all active_file*control*.F + +checkpoint57m_post +o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) + and advect_cs (use EXCH-2 and standard cs-32 grid files). +o pkg/exch2: filling of face-corner halo regions is optional + (ifdef W2_FILL_NULL_REGIONS) and is turned off by default. + +checkpoint57l_post + tag before updating tutorials (pre-release-2) +o add cos & sin of grid-direction orientation angle (curvilinear grid only, + for output and interpolation of input fields onto model grid) +o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). + Affects results of exp. rotating_tank ; update output.txt. +o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor + and taking the square quantity and/or using a fraction-weight field. +o fix aim_diagnostics_init.F mate numbers. +o add mnc output capability to diagnostics/diagstat and update + our cvsignore files for the ACSII output generated + +checkpoint57k_post +o lab_sea now uses diagnostics package and provides a suite of + new EXF diagnostics output. + +checkpoint57j_post +o exf + * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): + Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); + terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. + * extended diagnostics output + - now includes all EXF variables + - hs, hl moved to common block + - separate S/R for diagnostics, called after ctrl vector is added + - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet + - EXFqnet contains true Qnet (i.e. includes qsw) + * updated verif. lab_sea, global_with_exf + * Rearranging hflux (exf_mapfields -> exf_getforcing) + to ensure that diagnostics sees a true EXFqnet +o add matlab scripts for CS-grid vectors (in utils/cs_grid) +o diagnostics pkg: change pointers so that 1 diagnostic can be used + several times with different frequencies. +o mnc-ify the thsice package as requested by Daniel Enderton + - the monitor--MNC output needs work + - many attributes need to be added (most are currently blank) +o mnc-ify theaim_v23 package as requested by Daniel Enderton + - many attributes need to be added (most are currently blank) +o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) +o add Sadourny like discretization to the 4th.O vorticity advection scheme +o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. + update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, + fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). +o fix few little things to avoid floating error with -ftrapuv (ifort v9) + (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) + +checkpoint57i_post +o Diagnostics package was changed: diagnostic allocation is now deactivated + by setting an empty file name in the namelist (used to be by setting 0 frequency) +o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; + add 1rst Order upwind vertical Shear. +o add a quick fix for A/B checkpointing in OFFLINE mode +o add IGNORE_TIME define and -ignore_time option to genmake2 as an + end-run around the C/Fortran linking horror in eesup/src/timers.F +o added pkg/runclock: allows user to terminate run based on wall clock +o added non-hydrostatic scaling parameter: nh_am2 +o pkg/my82: futile attempt to make results compiler-independent by adding + some "_d 0", etc. no effect. +o for mnc output, fill the 'T' coordinate var with myTime and create a + separate 'iter' variable for iteration count +o pkg/diagnostics: + add new capability: output of Global/Regional & per-level statistics ; + tested against monitor output (including land & thSIce) on various exp. +o make seaice-pkg I/O type flags (MNC/MDS) more standard. + +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)