--- MITgcm/doc/tag-index 2008/03/02 23:38:43 1.965 +++ MITgcm/doc/tag-index 2008/06/20 21:43:18 1.1005 @@ -1,9 +1,137 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.965 2008/03/02 23:38:43 jmc Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1005 2008/06/20 21:43:18 heimbach Exp $ $Name: $ Notes on tags used in MITgcmUV ============================== +o autodiff + Change default for TAF usage by removing argument '-nonew_arg' + This changes TAF subroutine argument list (ordering of active var.) + Omission of this flag leads to incompatibility w.r.t. TAMC + To restore TAMC-compatibility, need following modifs: + * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility + * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY + Tested TAF version is 1.9.22 + N.B.: exch2 hand-written adjoint code currently not TAMC compatible + +checkpoint60 +--->>> This is the last checkpoint for which generating the adjoint +--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" +--->>> by default. +--->>> Future checkpoints will ommit this flag by default. +o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. +o pkg/grdchk: Add gradient check to etan0 perturbations. +o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). +o pkg/autodiff: more flexibility in zeroadj. + model/src: modifying do_oceanic_phys.F accordingly. +o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. +o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option + special setup of gmredi for which the adjoint is stable + enough for parameter optimization. +o bridging the gap between eddy stress and GM. + -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) + along with a change in CPP option (now ALLOW_EDDYPSI). + -> when using GM w/ GM_AdvForm: + The total eddy streamfunction (Psi = eddyPsi + K x Slope) + is applied either in the tracer Eq. or in momentum Eq. + depending on data.gmredi (intro. GM_InMomAsStress). + -> ALLOW_EDDYPSI_CONTROL for estimation purpose. + The key modifications are in model/src/taueddy_external_forcing.F + pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F + +checkpoint59r +o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array + from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); + fix option to read coriolis(@ cell-corner) from files with CS-grid. +o pkg/mnc: add some attributes to standard 1D-coordinate variables +o pkg/diagnostics: enforce missing_value attribute for scalar variables at + mass points, when using mnc for output + - add runtime parameter (missing_value, missing_value_int) to override + default (which is the value of getcon('UNDEF')) +o pkg/mnc: prepare mnc for the actual use of missing values with the + diagnostics package: small fix in mnc_cw_readwrite.template and more + initialisation of never used fields + - replace mnc_common.h and mnc_id_header.h with corresponding upper case + versions +o pkg/thsice/thsice_ini_vars.F added default initial values so that + thermodynamics sea ice solver does not blow up when some initial fields + are missing. +o move from external_forcing_surf.F to ini_forcing.F + the p-coord. hack consisting in using pLoad to set phi0surf ; + update output of tutorial_global_oce_in_p (affected @ truncation level). +o Freshen up a bit hs94.1x64x5, notably: + remove rotationPeriod and tRef=5*0. (adjoint only), and add + exactConserv=.TRUE. +o pkg/generic_advdiff: + change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only + applies to files where Temperature & Salinity 2nd Order moments are used. +o pkg/ptracers: add second-order moment advection schemes (80 and 81); + this uses a dynamically allocated internal state data structure + (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) + and requires a fortran 90 compiler + +checkpoint59q +o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) + (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) +o Refresh tutorial_global_oce_biogeo, notably: + - change bathymetry (put back seamounts in ACC, use hFacs) + - change EOS (POLY3 --> JMD95Z) + - use Bryan-Lewis vertical diffusivity + - use multidimensional advection + - remove old virtual virtual in dic pkg, now done through ptracer pkg + - change a couple of parameters in dic pkg +o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F +o pkg/obcs: change default to OBCSfixTopo = .true., + - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result + - replace "debugMode" with "debugLevel .GE. debLevB" +o implementation of TAF directives for gchem,cfc,dic +o remove "exp5" (replaced by tutorial_deep_convection). +o pkg/obcs: add code to fix topography gradients normal to open boundaries; + this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; + the code can be turned on by setting OBCSfixTopo = .true. in data.obcs + --> changes results in exp4, seaice_obcs +o tutorial_deep_convection : + update the set-up and increase resolution and domain size ; start + from pseudo initial conditions = output at t=120mn in order to see + something happening when running testreport. +o pkg/seaice: add os7mp as an advection scheme + add check for advection schemes + add a flag for restoring T and S underneath sea ice +o pkg/my82: add netcdf-support and diagnostics +o thsice pkg: + - Now hsMax limits snow height by turning it into ice following + flooding scheme (and now conserving energy) + - Slight rewriting of the formula in thsice_calc_thick.F + - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos + --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice + +checkpoint59p +o gchem / dic / cfc : + - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); + - add new parameter files: "data.dic" & "data.cfc" ; + - various re-arrangement in initialisation & header file ; + - fix tutorial_global_oce_biogeo for multi-threaded test. +o pkg/dic: test for "pickup_dic" file when restarting ; + if no pickup-file, can restart with a re-initialised pH (same as it did + before) providing pickupStrictlyMatch is set to False. +o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP + + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP +o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2 + and staggerTimeStep is off (needed for stability of Internal-wave dynamics). +o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax, + & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers + (note: not clear to me what lambdaTr1ClimRelax is still used for ...) +o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which + scheme to use for vorticty-term ; + - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F + (with default selectVortScheme, return to original discretisation) + - remove weird combination (e.g.: upwindVorticity & highOrderVorticity) +o pkg/seaice: add a line to the summary to indicate grid type (B/C) +o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the + bottom ; only used with variable horizontal viscosity and non-hydrostatic. + also fix diagnostics VISCAHW & VISCA4W. + +checkpoint59o o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). o change the loop ordering in most gad_*_adv_x.F to improve vectorization: move a few statemens out the main loop into separate loops @@ -18,6 +146,10 @@ isomip tests => update tests o add a flag writePickupAtEnd (default=true) to be able to suppress writing a pickup at the last timestep +o tools/mpack-1.6 : + - disable automake (not working) and autoconf (not needed). + - update to version 1.6.4 which fix MD5 code on some 64 bits platforms + also cleaner with much less compilation warnings. o pkg/profiles: rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg (for "less than 32 characters name" compiler requirement)