--- MITgcm/doc/tag-index 2006/01/11 06:04:11 1.598 +++ MITgcm/doc/tag-index 2006/06/23 04:36:25 1.686 @@ -1,9 +1,301 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.598 2006/01/11 06:04:11 edhill Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.686 2006/06/23 04:36:25 jmc Exp $ $Name: $ Notes on tags used in MITgcmUV ============================== +o towards a standard way of dealing with multi-threading in MONITOR + and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. +o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) + to W momentum equation in nonhydrostatic and quasihydrostatic runs. +o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. +o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) +o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL + (problems ? with gradient check in bottom_ctrl_5x5 adjoint test) +o tracer advection: + - clean-up and simplify calc_common_factors.F + - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer + advection subroutine (but still not used within DST advection S/R) +o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) + +checkpoint58j_post +o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields + from file (collects calls previously in FORWARD_STEP) +o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS +o adjoint store dir. adjusted accordingly +o genmake2 + replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. + +checkpoint58i_post +o pkg/seaice: add parameter that allows to scale/turn off effect of seaice + on wind stress (SEAICEstressFactor defaults to 1.) +o Total number of Timers is finite (<=40): comment out 2 non-essential one + in the_main_loop.F to avoid Pb (e.g., when running fizhi test) +o vector_invariant: fix highOrderVorticity(=4.th.Order) advection + on CS-grid: no longer loosing mass. +o exf & curvilinear-grid: no longer modify longitude xC & xG. +o pkg/ggl90: fix sloppy output and fix a bug +o pkg/seaice: added SEAICEuseEVPpickup parameter + - Set to false in order to start EVP solver with + non-EVP pickup files when using SEAICEuseEVP + - fix sign error in diffusion in seaice_calc_rhs + +checkpoint58h_post +* Modifications for bottom topography control + o replace hFacC by _hFacC at various places + o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL + o add non-self-adjoint cg2d_nsa + o update autodiff support routines + o re-initialise hfac after ctrl_depth_ini + o works for 5x5 box, doesnt work for global_ocean.90x40x15 +* Adding verification for 5x5 box (4-layer) bottom topography control + +checkpoint58g_post +o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., + used for mean seasonal cycle, mean diurnal cycle); add an example + in verification/global_ocean.cs32x15/input.thsice/data.diagnostics +o pkg/ggl90: + - add parameter (minimum surface kinetic energy) + - fix bug (avoiding division by zero) +o couple pkg/thsice to pkg/seaice: + - modify advection in seaice to accomodate new scalar fields to be advected + - only muliDimAdection scheme work with seaice/thsice + - mapping of thsice-variables to seaice-variables, back and forth + - does not break the verification experiments, but does not give the + desired results either +o pkg/seaice + - make (default) second order advection a bit less confusing? + +checkpoint58f_post +o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice + to pkg/seaice): + - new routines thsice_map_exf and thsice_get_exf provide the interface + - add an additional formal parameter to thsice_solve4temp +o pkg/exf: + - add new fields wspeed, snowprecip (to be able to couple to thsice) + - correct Stefan-Boltzmann constant + - new parameter for longwave surface emittance + - separate some stuff from exf_bulkformulae into new routines + exf_radiation, exf_wind + - add new parameters and constants: longwave emissivity for ocean, ice + and snow, evaporation parameters over ice + - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute + either wind from stress or stress from wind +o pkg/thSIce: +- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F +- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND + and THSICE_CALC_THICKN +- for now, call to THSICE_GET_BULKF remains inside i,j loops. +- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h + to make debugging easier. +- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output +o pkg/bulk_force: + - clean-up comments and parameters ; + - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; +o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; + generate new output for test-experiment: aim.5l_cs.thSI +o results_ad : rename "output.txt_adm" to "output_adm.txt" and change + testreport accordingly + +checkpoint58e_post +o SEAICE_CGRID adjoint done +o R_STAR adjoint implemented. + * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) + * need to sort out init. of h0facc, etc. +o Make pkg/profile fully independent of ecco,cost, etc. stuff + to be able to use it in pure forward. + +checkpoint58d_post +o upgrade simple test-experiment to tutorial example: + step.1: duplicate the experiment and (step.2) will remove the old copy. + tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) + tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) + tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) + tutorial_global_oce_biogeo <- copy of dic_example + tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) + tutorial_plume_on_slope <- copy of plume_on_slope + tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) + tutorial_global_oce_optim <- empty for now (David ?) + tutorial_global_oce_in_p <- copy of global_ocean_pressure + some tutorials (R1) were already checked-in under tutorial_examples in release1_branch +o correct a sign problem in cost_scat.F +o obcs and ptracers: fix boundary conditions for advections schemes + with larger stencil +o thsice adjoint: start +o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for + completeness +o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING + and COSINEMETH_III, add comments in default CPP_OPTIONS.h +o ptracers adjoint: + * avoid extensive recomputatations + * fix missing re-init. of gptr (missed by TAF) +o obcs: add a flag (OBCSprintDiags, defaults is true) that allows + me to turn off the excessive output to STDOUT that this package produces +o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common + and add those terms in Vector-Invariant formulation. +o in ctrl pkg, if ALLOW_CAL, use monthly mean controls + if the control period (xx_hfluxperiod etc) is 0 +o in profiles pkg, clean routines and fix details +o in ecco pkg, reading ssh data: + fix problem in case the model does not start at iter0=0 +o fix mnc-pickup/restart for ptracers +o new package prifiles: + code to compute profile-based cost by Gael Forget + (modifs in ecco, ctrl, autodiff) +o Benign bug fix in initialization (spotted by M. Mazloff) of + ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F + +checkpoint58c_post +o adjoint: finish NLFS adjoint and provide reference output in + verification/global_ocean.90x40x15/results_ad_nlfs +o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the + documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in + SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only + with SEAICE_CGRID defined. +o move calendarDumps from "data" to "data.cal" and clean-up the code + with a simple call to pkg/cal S/R: CAL_TIME2WRITE +o add useEXF & useCAL flags (for now, set in hard-coded way) +o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum + (were missing in NH mode, and wrong in quasihydrostatic mode). + waiting for Chris updated version of calc_gw to add those CALLs. +o fix bug in quasihydrostatic S/R ; + add a test for this option: global_ocean.90x40x15.qshyd +o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs. + (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS) +o add on/off flag useOffLine for package OFFLINE +o seaice: + - modify advection so that it works also on the C-grid + - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes + problem in multi-tile runs with C-grid + - add flags for clipping ice velocities and/or masking solver forcing + - fix drag (ocean on ice) formulation and a bug that caused noise in the + C-grid solver + - added a few comments to seaice_diffusion.F + - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V + are now exclusive) + - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which + required re-ordering the code a little: + + make DAIRN global variable (defined in SEAICE) + + move computation of the viscosities eta and zeta into a new separate + routine (because I need to recompute them in seaice_ocean_stress.F) + +checkpoint58b_post +o AIM+thSIce: fix sign of Short-Wave through the Ice ; + update output.txt of exp. aim.5l_cs.thSI +o various mnc cleanups and improvements: + + shrink lookup tables by factor of ~4 + + better error reporting when running out of lookup space + + able to handle longer path/file names (up to 500 chars) +o adjoint: + - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. + - TBD: "hidden" mom_vecinv recomp. in dynamics +o change forcing_In_AB to affects both T,S forcing and Momentum forcing + (allow to differentiate between forcing components using new integer flags: + momForcingOutAB=1/0 & tracForcingOutAB=1/0) + and add new flag to put Dissipation tendency out of Adams-Bashforth. +o ecco + - enable trend removal from SSH anomaly obs. +o adjoint + - a fix for PmEpR when #undef EXACT_CONSERV + - fix of "hidden" recomp. in thermodynamics (no TAF warnings) + - try to fix "hidden" recomp. in forward_step for NLFS + (NLFS seems broken sometimes after I checked it in) +o seaice: + - add c-grid version of the dynamic solver: + + three new routines that are the c-grid substitute lsr, dynsolver + and ostres + + put a few fields that were local to dynsolver into global common + blocks, so that I can move the computation of stresses etc into + seaice_lsr (saves coding but may break the adjoint). + - replace more hardwired parameters by runtime parameters + - add ice masks that mask the rhs of the implicit solvers where there + is no ice (commented out in seaice_dynsolver, because i am not sure + if this works properly), eventually this should replace the clipping + of ice velocities in seaice_dynsolver to +/-40cm/s. +o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly + include it only where its needed +o move balancing of fluxes before the call of external_forcing_surf +o seaice: + - correct units of turning angles (now they are really in degrees) + - move computation of GWATX/Y out of main routine into dynsolver + - initialize GWATX/Y in seaice_init +o Apply mask on Fresh-Water flux (needed for SSH forcing). + update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) +o seaice: add runtime flags for turning angles (default to zero) +o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean + and trend from exf forcing and ctrl control adjustments +o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF + (since checkpoint57x_post) +o change the default rotation period to 86164.s = the Earth rotation +o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) + and based on a reference stratification. Tested within hs94.cs-32x32x5. +o seaice advection: add code for choosing between the default (2nd order + central differences) and multiDim advection schemes provided by + pkg/generic_advdiff +o seaice: + - removed all references to SEAICE_GRID.h fields from + dynsolver, advect, diffus, lsr, without changing the results of lab_sea + (cubed-sphere configuration will change a little) + - grid computations in seaice_init are obsolete now. + - cleaned up code a little so that is easier to read (hopefully). + - added new (better?) discretizations of default advection and diffusion + (turn on with SEAICEuseFluxForm) + - replace 1 in 3d global fields by kSurface in growth.F + +checkpoint58a_post +o seaice: + - bug fix in advect.F +o shelfice: + - separate shelfice load anomaly from pload (breaks with time + dependent forcing), => introduce constant field shelficeLoadAnomaly. + Its default is 0., but it may be computed more cleverly from (unknown) + t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be + done offline. A good approximation of the pressure load anomaly is + necessary to avoid large initial adjustment processes underneath + deep-reaching shelfice. + - small fix in ISOMIP shelfice_thermodynamics + - add more sophisticated thermodynamics of Hellmer (1989), this is + now the default + - give a few constants more intuitive names +o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful + if bulk formulae are used in long integration (especially EmPmR). Turn + on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01 + if balancePrintMean, the imbalance that is substracted is printed to + STDOUT. +o fix bug (typo) in obcs_apply_eta.F +o add a new package shelfice which enables us to model the circulation + underneath shelf-ice with draughts of hundreds of meters. + - works + - to do: + include improved thermodynamics + + check whether kSurfC (from model/inc/SURFACE.h) can be used + instead of new field kTopC + + can we use topoFile, Ro_surf and existing code in ini_depth.F + instead of new field R_shelfIce and new code in ini_depth.F + and ini_mask_etc.F? + + adjust vertical mixing schemes? +o seaice pkg: + - add a cpp-flag to include a simple formula for a salinity dependent + freezing point of sea water at the surface + - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and + meridional stresses are now different (and hopefully correct) +o AIM pkg: change threshold on large-scale condensation to conserve Heat. + update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics + and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG) +o pkg/diagnostics: add options and parameters for regional-statistics + diagnostics ; define regions by reading a region-mask from a file + (might add other options later) +o pkg/bulk_force: + - add option and parameters to use AIM surface-flux formulae. + - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ; + others forcing fields (defined in PARM05, parameter file "data") are loaded + from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F). + - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F + - use the right EXCH call for uwind,vwind (to work on CS-grid). + - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h) + and parameters (note: calcWindStress replaces .NOT.readwindstress). + - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). + +checkpoint58 o add "--embed-source" option to genmake2 which, when the supporting tools can be compiled (as determined by genmake2) will turn on the embed_files package which then embeds the entire MITgcm source code