--- MITgcm/doc/tag-index 2007/06/19 12:39:54 1.839 +++ MITgcm/doc/tag-index 2007/10/15 00:30:04 1.892 @@ -1,9 +1,182 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.839 2007/06/19 12:39:54 mlosch Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.892 2007/10/15 00:30:04 jmc Exp $ $Name: $ Notes on tags used in MITgcmUV ============================== +o pkg/monitor: + - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM + - fix mon_stats_rs (statistics over the full domain, even where field is zero) + - account for deep Atmosphere factor and density factor (anelastic) +o added open boundary conditions capability for seaice HEFF and AREA +o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) + thermodynamics + - requires a little reorganization, which affects the testreport results + of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, + so that now the conservative form is tested + - add a few comments +o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* +o add a little bit of code to gad_os7mp_adv_?.F to help vectorization +o add new diagnostics to seaice: advective, diffusive fluxes (only for + multidim-advection, for scheme 2 they are not filled) and transports, + thermodynamic growth rates +o change units of EmPmR (inside the code) from m/s to kg/m2/s (mass flux) but + leave input file unchanged. Affects results @ truncation level (cg2d match) + and update output of experiments: lab_sea(6), global_ocean.90x40x15(10), + global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) + + adjoint results: global_ocean_ebm(11) and lab_sea (12). + Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). + +checkpoint59h +o pkg/exf: + - improve vectorization by moving if-statement out of loops in + exf_mapfields, exf_radiation + - exf_bulkformulae.F: introduce 2D fields and vectorize code +o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package +o testreport: + - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE + monitor & update offline_exf_seaice exp. output. + - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) +o pkg/seaice: + - bug fix in the evp solver: boundary conditions were affected be + masking of zMax/zMin (changes results) + - minor bug fix in boundary conditions in seaice_calc_strainrates + (changes results for no_slip) + - seaice_lsr.F: make interpolation of eta dependent on boundaries + - replace hardcoded lower limit for zeta (zMin) by runtime parameter + - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean + stress formulation and no-slip boundary conditions +o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP + in gad_calc_rhs.F ; add few safety stops in initialisation phase. +o pkg/seaice: a first HSALT time stepping equation has been checked in +o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV + in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem + without requiring DO-IF statements +o pkg/thsice: + use continuous power-law function for partition of energy between lateral + melting/freezing and thinning/thickening ; old code using step function + still available with #undef THSICE_FRACEN_POWERLAW + update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice +o testreport: change AD testing : check against results/output_adm.txt + using same scripts as for forward test. + +checkpoint59g +o adjoint testing: in preparation for changing testreport: + - output format: cost and grad written on separated lines + - ad output results in directory "results" (instead of "results_ad") +o pkg/seaice: adding ice salinity HSALT as a prognostic variable +o pkg/seaice: changes for using pkg/seaice with pkg/obcs +o pkg/ecco: allow user defined cost function contributions +o testreport: + Allow to choose (per experiment) the list of tested output variables + and the main variable (used to issue a pass/FAIL ) ; + - for now, done by adding the specific list in file: [exp]/input/tr_checklist + - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; + Also modify printing of summary: + a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) + b) echo the list of tested variables in the individual summary.txt of + each experiment. +o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of + threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) + (but still depend on the tile decompostion of the domain). +o pkg/seaice: change a discretization detail to make the B-grid code + "more symmetric". This change is likely to remove all "ridges/leads" that + where quasi-aligned with the grid in B-grid solutions. It may also be + the solution to the stress coupling issues with the B-grid. +o each tested exp: add a "run" directory with a standard ".cvsignore" file ; + remove .cvsignore from input dir. (since testreport no longer run here). +o pkg/thsice: + - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" + - fix reshaping of sea-ice just after advection: + melt all the ice only if ice-volume is too small. + - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): + prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; + and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). +o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water + tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. +o define mass2rUnit & rUnit2mass as units conversion factor, used for surface + forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit + (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; + and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error + of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 + -> update output.txt +o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): + this affects truncation error: -> update output.txt of exp: + global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, + ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. + +checkpoint59f +o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) +o pkg/ctrl: ctrl_bound forces parameter corrections to stay in + a bounded range (in forward mode) +o pkg/ecco, ctrl, autodiff and mom_common: + internal parameter controls, completements of implementations +o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. +o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; + (not seem any difference in testing results). +o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains + at face corners. +o pkg/generic_advdiff: + - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) + loop range indices for computing vertical advection tendency + and do the calculation in the interior only (no overlap) ; + for now, only implemented for SOM advection (to save CPU time). + - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) +o exch2 adjoint + First set of changes: + - add exch2 hand-written adjoint templates + - exch2 hand-written no longer use TAF-flag 'nownew_arg' + This will require cleanup in pkg/autodiff/*.F + (changed routines currently kept separate in verif. code/) + - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC + that used to hide exch2 or cubed-sphere specific code + (commented via 'cph-exch2') +o pkg/seaice + - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. +o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update + output of global_ocean.cs32x15.thsice . + +checkpoint59e +o exch2: new S/R that only use the cube-tracer (center-position) exchange: + for B-grid vector (not yet tested) and C-grid vector (<- only used + when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). +o starting implementation of Duffy et al. (GRL 1999) salt plume scheme + (#ifdef ALLOW_SALT_PLUME) +o gather_2d/scatter_2d: removed halo regions +o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 + scheme and the corresponding test case (under front_relax dir). For now, + only available with Skew-flux form and not yet tested in realistic set-up. + adjoint: store directives updated, but gradient checks deteriorated, + so maybe GM/Redi adjoint is now broken. +o seaice adjoint + * add AREA, HEFF, HSNOW as control variable + (should not change lab_sea results) + * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 +o pkg/seaice: + * added computation of saltFlux in seaice_growth; + For time being, sea ice salinity is assumed constant + contribution of snow flooding to freshening of sea ice is neglected. + SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it + defaults to 0.0 in order to maintain backward compatibility. + Typical values for SEAICE_salinity are 4 to 10 g/kg. + * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F + * added SEAICE_availHeatFrac, which specifies fraction of surface level + heat content used to melt or grow ice + * commented out cap of HICE: it helps keep ice thinner + * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option + * applied OBCS T/S mask to HEFFM sea ice mask + +checkpoint59d +o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array + for {PKG} state variables, and called from DO_STATEVARS_DIAGS. + (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) +o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" + and change default value of parameter "GM_Small_Number"; + update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, + global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, + tutorial_global_oce_biogeo, tutorial_global_oce_latlon +o pkg/ecco: cost function when applying pkg/smooth to controls +o pkg/ctrl: add forcingPrecond run time parameter o pkg/seaice: - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code - fix bug in metric terms of u-equation in LSR solver (implicit part), @@ -12,6 +185,9 @@ read, understand, and debug. This causes changes at the truncation level. - fix (serious) bug in the boundary conditions (sign error in the implicit part) of the LSR solver. Changes all LSR results. + - fixed problem with HSNOW initialization to avoid thick snow when AREA + is initilized with small values - does not change lab_sea results. + - added HsnowFile initialization capability o pkg/smooth: addition to model/src and pkg/ctrl so allow initialization of pkg/smooth and application to control vector o pkg/seaice: fix another bug in the LSR no-slip boundary conditons @@ -25,7 +201,6 @@ that allow you to prepare netcdf input files. - also modified: cleaner include statements, cleaner error print statements, cleaner stops when error, and more tests of the netcdf input files consistency. - o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. o pkg/seaice: - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this @@ -159,7 +334,9 @@ ATMOSPHERIC_LOADING is #define). o pkg/kpp: replaced _KPP_RL with _RL o bug fixes for vertical diffusivity computations when both KPP and - 3D diffusivity arrays are used. + 3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F + are no longer updating the vertical diffusivity array + (passed as argument) but are (re-) setting those arrays. o pkg/seaice: fix bug in evp solver, while doing that - change (improve?) discretization of stress computations for both cgrid-lsr and evp solver