--- MITgcm/doc/tag-index 2003/09/24 06:50:26 1.178 +++ MITgcm/doc/tag-index 2003/12/17 14:22:38 1.230 @@ -1,9 +1,282 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.178 2003/09/24 06:50:26 dimitri Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.230 2003/12/17 14:22:38 adcroft Exp $ Notes on tags used in MITgcmUV ============================== -untagged +o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 + ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure +o added exf_offset_atemp for Celsius to Kelvin conversion of atemp + +checkpoint52d_post +o re-tiled many expts to allow comparison in multi-processor mode + - updated output accordingly + - changed hs94.128x64x5 to use intial T from file rather than use the + random number generator +o add infrastructure in model routines for fizhi and gridalt packages +o change global_ocean.cs32x15 because of Pb with GM on CS-grid. +o changes to permit hi-res, cubed-sphere, configuration + - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F + - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F + - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation + of surface winds for the cube + (A verification experiment, based on global_ocean.cs32x15, but with + pkg/seaice turned on and with on-the-fly interpolation from the NCEP + Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, + complete with example surface forcing files and matlab scripts to look + at the output and compare it with that of global_ocean.cs32x15.) +o packages pickup: $PKG_write_pickup called from packages_write_pickup ; + but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code + to conform to the common rule. +o check-in the first version of the coupler + interfaces for multi-components + set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. + - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). + - atmosphere: use pkg aim_v23 ; no sea-ice for now. + - ocean and atmos. share the same horizontal grid (no interpolation). + - exchanges between component and coupler is done in forward_step +o new verification experiment, cpl_aim+ocn: + coupled ocean - AIM atmosphere on cs32 grid. + +checkpoint52d_pre +o surface flux time-av diagnostic modified for NLFS & RealFreshWater +o add call to AIM pendant S/R in external_forcing & external_fields_load.F + +checkpoint52c_post +o Fixing OPTIONS files for use of exf: + - ALLOW_ECCO not needed + - ECCO_CPPOPTIONS.h should not be included from + EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h + as has been the case in the past + - All cal/exf related options are currently set in + single header file. Should remain so until we + agree on a consistent new policy. +o Removed all CPP options for cal package. + cal has no more CPP options. +o modified STOREs in GAD_ADVECTION +o corrected key comp. for passkey + +checkpoint52b_post +o new version: "thsice" of thermodynamic sea-ice pkg: + - only 1 call from "forward_step"; conserve energy, fresh-water & salt. + - modify fluxes but do not change theta directly; + - light cleaning of bulk_force pkg (still needed with thsice). + - add forcing fields + data files in global_ocean.cs32x15/inp_thsice + + output_thsice.txt to test thsice & bulk_force pkgs. +o put back grid & coriolis monitor output. +checkpoint52b_pre + +o call "do_the_model_io" at the beginning (=> dump initial state) +o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) +o sort out interplay between tamc.h and PTRACERS_OPTIONS.h + (need info on NUMBER_OF_PTRACERS) +o missing PTRACERS headers in some routines +o default tamc.h in pkg/autodiff supposed to crash + to ensure proper customization + +checkpoint52a_post +o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp + - moved surfaceTendencyTice from pkg/seaice to main code + - subroutine FREEZE_SURFACE now limits only surface temperature + and is called in FORWARD_STEP (if allowFreezing=.TRUE.) + => new output.txt for global_ocean.cs32x15 & global_with_exf + - keep the old version of FREEZE for backward compatibility; + global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. + - corresponding modifs for TAF directives +o added surface flux output variables to TIMEAVE_STATVARS +o time-averaged output for pkg/ptracers +o fix problem with ECCO-related divided adjoint + snapshot file was missing some ad-variables, + but no warning issued by TAF + +checkpoint52a_pre +o some bug fixes for #undef REAL4_IS_SLOW + +checkpoint52 = ecco_c52_e35 +o after testing adjoints of checkpoint51u_post + +checkpoint51u_post +o this is the post-merge tag of the ecco-branch + (needs another clean checkout and re-testing) +o various natl_box_adjoint configs and results + but no input fields +o obcs adjoint not yet merged! +o adding ECCO global 1x1 and 2x2 degree configs +o updated/extended some store directives for seaice +o pkg/ecco now containes ecco-specific part of cost function +o top level routines the_main_loop, forward_step + supersede those in model/src/ + previous input data.cost now in data.ecco + (new namelist ecco_cost_nml) +o in ctrl/ cleaned some cross-dependencies and updated CPP options + +checkpoint51t_post +o this is the pre-merge tag of the ecco-branch + +checkpoint51s_post +o cleanup: removed various obsolete #define-s +o pkg/grdchk + - renamed 'ph-grd 3' to 'grad-res' + - merged from ecco-branch + (remaining bug fixes for obcs gradient checks) + - additional high-precision output for testreport + (grep for 'precision_grdchk_result') + +checkpoint51r_post +o cleaned up or removed CPP_OPTIONS.h files +o updated results for some of the tests to reflect the new + optfiles (-ieee: -O0 instead of -O3) + +checkpoint51q_post +o cd_code: + - moved cd_scheme.F -> cd_code_scheme.F + - separate read_checkpoint from cd_code_ini_vars.F + - separated cd_code part from write_checkpoint + - updated AD_SOURCE, generated .flow + - added CD_CODE_VARS.h to the_main_loop + - Moving cd_code specific store dir.s to pkg/cd_code +o ctrl package totally restructured + - pack/unpack now optional and decoupled from + xx_/adxx_ I/O + - ctrl_pack/unpack cleaned + (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) + - confined inclusion of AD_CONFIG.h to where necessary. +o genmake2: changed AD dependencies from SRCFILES to AD_FILES + +checkpoint51p_post +o create initial cd_code package + - WARNING: the initialization of fields within packages + is broken because INI_FIELDS (where READ_CHECKPOINT is + called) is called *before* PACKAGES_INIT_VARIABLES. + This seems to be backwards since + 1) its important to initially zero the entire field including + the "halo" region + 2) zeroing needs to be done *before* reading pickup info + and the pickup call might or might not happen in any + particular run + - this needs an overhaul for R2 +o cleanup verification/*/code/GMREDI_OPTIONS.h +o cleanup testreport + +checkpoint51o_post +o bringing AD-related verif's up to date with genmake2 + - carbon/ + - global_ocean.90x40x15/ + - hs.94.1x64x5/ + - (front_relax/ ) +o (more) consistent directory structure for AD-related verif.'s +o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK +o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF +o bug fix in find_alpha.F for MDJWF: + - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for + change rho -> rho-rhoConst + - replace call find_rho to find_rhonum +o initialisation of rFlx extended to full array (required by TAF) + and shifted to thermodynamics +o removed PTRACERS.h in ptracers routine +o added surfacetendencyPtr to S/R parameter list pracers_forcing +o Correcting initialisations for fVerU, fVerV. +o helping TAF to recognize dependency on kUp for + fVerU, fVerV +o Replacing delZ by delR in pkg/ctrl/ +checkpoint51o_pre + +o undid all of cp51 pending some cleanups and discussion +o added the [#include "AD_CONFIG.h"] statement to all files that need + it for adjoint/tl #defines + o re-worked the build logic in genmake2 to support AD_CONFIG.h + o removed tools/genmake since it no longer works + +checkpoint51n_post +o modifications to make FREEZE flux visible to pkg/kpp + - moved surfaceTendencyTice from pkg/seaice to main code + - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP + - subroutine FREEZE now limits only surface temperature + (this means new output.txt for global_ocean.90x40x15, + global_ocean.cs32x15, and global_with_exf) +o added surface flux output variables to TIMEAVE_STATVARS + +checkpoint51n_pre +o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F +o added [#include "AD_CONFIG.h"] to all files that use the following + defines: + - ALLOW_ADJOINT_RUN + - ALLOW_TANGENTLINEAR_RUN + - ALLOW_ECCO_OPTIMIZATION + +checkpoint51m_post +o incorporating changes to get TAMC/TAF working in genmake2 + - added new TAMC/TAF targets to the Makefile + - various cleanups related to package handling + - these changes should have no impact on the forward model + +checkpoint51l_post +o changes to pkg/cal and pkg/exf that allow and speed-up long integrations + - faster algorithm for cal_addtime.F + - higher precision arithmetic, where needed + - pkg/exf *startdate variables changed from calendar date to + model integration time + +checkpoint51l_pre +o add salt flux to forcing fields (used when salty sea-ice forms or melts) +o enable to apply restoring on S & T only in a latitude band. +o update output (external_forcing_surf modif. change truncation errors) + global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box + +checkpoint51k_post +o change default to: useNHMTerms=.FALSE. + - new output.txt for atmos. exp (NHMTerms were wrong but now turned off): + adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 + - new output.txt for idealized oceanic exp (NHMTerms are now turned off): + exp1, ideal_2D_oce + - change data file of oceanic exp (leave the results unchanged for now) + exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box +o set gravitySign automatically according to the vertical coordinate used + (and change sign: back to "logical" value: +1 when R increases downward) +o added an include barrier to the default CPP_OPTIONS.h and + removed the #include "PACKAGES_CONFIG.h" from it +o fix a bug in mom_fluxform (from chk51j_post) + +checkpoint51j_post +o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ +o adjusted some flow directives (dynamics, thermodynamics) +o added cubed-sphere case to test cost function +o heckpoint_lev?_directives.h now include + pkg-specific directives, whenever those are enabled. +o Moving pkg-specific flow directives to corresponding pkg + Moving pkg-specific differentiation list to corresponding pkg + Moving pkg-specific checkpoint-lev storing to corresponding pkg + ---> conventions are + - pkg_ad.flow + - pkg_ad_diff.list + - pkg_ad_check_lev?_dir.h + +checkpoint51i_post +o merge of the branch-genmake2 + - knowingly breaks the older genmake + - automatic generation of all ALLOW_${PKG_NAME} defines + - new testreport supersedes older testscript +o large number of package inclusion and header cleanups +checkpoint51i_pre + +o new output for adjoin of global ocean vector invariant +o fix for checkpoint of thermodynamic seaice and bulk_force +o Steph gchem various cleanups + +checkpoint 51h_pre +o fixed some single quotes +o modify gchem pkg to be more versatile +o modifications to clean up dic pkg +o add pkg/cfc + +checkpoint51g_post +o provide links for ARPACK and ADM*TLM +o start removing verification/vero/ +o update AD-related stuff + (in particular some IF-statements in model/src/ routines) +o adding to verification/global_ocean.90x40x15/ adjoint of + vector invariant setup + +checkpoint51f_post +o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation of tracer Green's fucntions for ocean inversion project.