--- MITgcm/doc/tag-index 2001/09/27 14:24:19 1.50 +++ MITgcm/doc/tag-index 2003/03/07 22:24:06 1.53.4.32.2.1 @@ -1,8 +1,331 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.50 2001/09/27 14:24:19 adcroft Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.53.4.32.2.1 2003/03/07 22:24:06 dimitri Exp $ Notes on tags used in MITgcmUV ============================== +Branch icebear + + + +7 mar 03 + Branched off ecco_c44_e27 + Bug fix in pkg/ctrl/ctrl_init.F + + +==================================================================== + +ecco_c44_e27 +o exf: + - Enable initialisation of forcing fields to constant + (runtime) values. + - in exf_getffields.F + Reduce i-/j-loop to interior domain, discarding overlaps. + That also fixes wrong TAF-key computations for key_1, key_2 + with bulf formulae. + - exf_init.F modify #ifdef for exf_init_evap + - exf_getffieldrec.F, ctrl_getrec.F + The following INT-usages are not safe: + fldsecs = int(fldsecs/fldperiod)*fldperiod + fldcount = int(fldsecs/fldperiod) + 1 + and were modified. + - added repeatPeriod (from MAIN branch) +o grdchk: updated and merged + - has both ADM and TLM checks + - works for single- and multi-proc. + - output cleaned + - worked successfully for parallel DIVA + Needed one update in EEPARAMS.h and updates in ctrl package + More modif's may be necessary for ECCO code to support TLM. +o autodiff: checkpoint_lev... + - updated storing for bulk formulae (some arrays were missing) + - added state for seaice package + - synchronized with main branch +o DIVA: + Modif.s in + - cost_init.F + - cost_averagesfields.F + - ecco_the_main_loop.F + - ecco_the_model_main.F + and added cost_final_restore.F cost_final_store.F + o With these changes, it is possible to fully separate + the first forward run to compute the cost function (mdthe_main_loop) + and adjoint runs over individual DIVA intervals (adthe_main_loop) + into separate model executions. + This enables better tuning of DIVA to given queue sizes. + o Loss of cost function value in consecutive DIVA runs is + fixed by storing to 'costfinal' file. + o Appropriate call of ctrl_unpack/_pack,grdchk_main at + beginning/end of adjoint integration is accounted for. + The current changes apply to TAF-1.4.26. + TAF has one remaining bug, requiring one manual change + (see MITgcm manual). +o bug fix plus modif for ubar, vbar in cost_averagesfields +o cal: synchronized between MAIN and ecco-branch + +icebear4 +o Added cost_ice for sea-ice volume sensitivity experiment. +o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT +o Reduced derivative singularities in pkg/seaice. +o Updated verification/natl_box_adjoint + +icebear3 +o Removed spurious iikey and idkey +o pkg/exf + - bug fix in treatment of downward radiation +o pkg/seaice + - added initial sea-ice thickness parameter SEAICE_initialHEFF +o updated verification/natl_box_adjoint + +icebear2 +o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, + kpp_transport_t.F,and ecco_the_main_loop.F +o adjoint-friendly modifications to pkg/seaice +o added verification/lab_sea as per release1_p12_pre + +ecco_c44_e26 +o Merging pkg/exf and pkg/seaice from cvs tag ecco_ice2 +o exf: Modifications to correctly handle evap field for adjoint +o grdchk: + Added code to perform gradient checks for bulk formulae/atmos. state + (atemp, aqh, uwind, vwind). + NOTE: + This package is out of synch with c48 package. + The latter also has the tangent linear gradient checks. + Need to be merged. +o verification/natl_box_adjoint: + * added new setup: code_bulk/, input_bulk, results_bulk + (Experiment 2, described in README) + uses bulk formulae and atmos. state as control instead of + air-sea fluxes. + Performs gradient checks for first 4 elements of atemp control. + * changed standard verification to perform + gradient checks on first 4 elements on hflux control. + * gmredi switched off (will come after merge with c48). + +ecco_c44_e25 +o Merging some GM changes from main trunk (c47) to ecco-branch. +o Updating verif. natl_box_adjoint with GMRedi. +o Adding setup with explicit differentiaton of pressure solver. +o Bug fix: missing OBCS_OPTIONS.h for sponge layer code. +o (Re-?) Commiting old bug fixes in kpp to ecco-branch + (kpp_calc.F, kpp_routines.F) +o exf: + updated external forcing package + - cleaned old exfa stuff + - bug fixes + (missing OBCS_OPTIONS.h in two routines) + - enable easy to use "no forcing". + - added exf I/O for atmospheric loading + - added exf I/O for runoff data + - transfered scaling between exf <-> MITgcm to exf namelist + +ecco_c44_e24 +o modifications to gradient check package (Martin Losch) + - enable centered differences + - modified format of standard output +o bug fix for nwettile contents + so far assumed global sum in first entry (1,1,k), + needed for global control vector + -> introduced new variable nwet[c/w/s]global(nr) +o shifts of calls to cal/exf package to be accessible + in MITgcm stand-alone +o shifted packages_init_variables before convective_adjustment_ini + (corresponding update of TAF tape initialisation). +o removed auxiliary field in impldiff + (caused numerical differences for GMRedi cases) +o updated obcs control part (G. Gebbie) +o removed some f90 comments ("!") +o Bug fixes and updates in cost package + * cost_final: correct multiplier mult_tauv, mult_sflux + * cost_hyd: added call cost_ssh + * cost_init_barfiles.F: replaced arrays by tmpfld's + * cost_readtopexmean.F: ersmask -> tpmeanmask + * cost_weights.F: corrected wtheta[2], wsalt[2] +o cleaned exchanges in cg2d.F + +ecco_c44_e23 +merged patches between release1_p1 and release1_p2: +o fixed array boundary problem for adjoint + (related to partial recomputation within subroutine + related to dynamics -> calc_viscosity -> mom_... +o fixed recomputation in thermodynamics +o prepare (but not complete) recomputation problem in impldiff +o fixed problem for adjoint of global_max +o switched off sponge layer code in external_forcing +Bug fix in ctrl_mask_set_yz (spotted by G. Gebbie) + +ecco_c44_e22 +o Finally, the merges with the Scripps cost function terms: + Various additions, modifications, quality checks. +o Plus: Included switch ALLOW_AUTODIFF_MONITOR to handle + monitoring of adjoint state. +o Plus: removed comm_stats, ini_communication_patterns from diff. list + (no more need to "keep" MPI headers for adjoint generation) +o Plus: exf changes: + o added run-off routine + o additional storing needed for ustress,vstess + because of state-dependent quality check + o added missing initialisations +o Plus: genmake with MAKEDEPEND variable was still missing in ecco-branch +NB: - verification/natl_box_adjoint/ 240 steps run + * looks ok under Linux (twain.lcs.mit.edu) + * looks ok on MIT SUN's (fjord.mit.edu) + * NaN in reverse mode on Scripps SUN's at iter=214 + * NaN in reverse mode on IBM SP3 (BlueHorizon) at iter=204 + - 1 year forward int. global 2x2 deg. produces similar cost functions + * all cost terms of new code are slightly smaller (0.5 to 3%). + +ecco_c44_e21 +o reversed order of ctrl/cost initialisation +o gmredi_slope_psi.F: Inconsistent types in MIN/MAX expressions +o modified to enable ctrl field swapping +o bug fix for global sum of ncvarlength in ctrl_init +o no more call to ctrl_unpack from ctrl_init +o no more write of ctrl vector in ctrl_pack + however, init. of control vector from ctrl_unpack +o various bug fixes & consistent nobcs handling in + ctrl_pack/unpack routines (by G. Gebbie) +o optim package: Added obcs control part for lsopt I/O + (by G. Gebbie) +o missing call to obcs_diags +o moved calls in packages_init_fixed to packages_readparms + because some quantities are needed earlier. + +ecco_c44_e20 +o before major merges from the Scripps setup + here are two small updates: + - field swapping for surface flux controls enabled + (remains t.b.d. for atmos. state plus obcs) + - bug fix in active_file.F for xz-/yz- routines + - added missing xz-/yz- routines to active_file_ad.F + +ecco_c44_e19 +o merged necessary patches: + - AD-related changes for GMRedi + - fixes i KPP (delZ -> drF) + - hook to OBCS songe layer code in external_forcing + - errorMessageUnit non-zero in eeboot.F + - included GMREDI, EXACT_CONSERV to natl_box_adjoint verif. + +ecco_c44_e18 +o sponge layer code for obcs was missing + - added hook in external_forcing.F + - added storing for TAF +o new routine cost_init_barfiles to initialise + adjoint fields adtbar, adsbar, adpsbar + (needed in conjunction with corrected ladinit for active I/O) +o cleaned up and corrected order in packages_readparms, ecco_readparms +o corrected and simplified weights for obcs controls + - weight fields simplified + - bug fix in ctrl_pack + - no more write of control vector in ctrl_pack +o i/j index bug fixes in cost_ssh_mean + +ecco_c44_e17 +o bug fixes in cost package + * wrong identifier for active I/O of monthly mean psbar + (cost_averagesfields, cost_ssh) xx_psbar_dummy + * cleaned all identifier for active I/O of monthly fields + * wrong ladinit in various cost routines +o merge with interval (chkpt44c_post - chkpt44d_post) + * added missing EXCLUDE_MONITOR flags + * changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi + (incompatible typ in MIN/MAX expressions caused problems + on IBM SP3) + * in genmake added variable MAKEDEPEND + plus resetting for case SunOS + added timer_stats.c routine for IBM SP3 + * removed variables in dynamics + +ecco_c44_e16 +o new ECCO checkpoint, the first since ecco_c43_e15 + which is branched from MITgcm. + All changes were merged in between (see ecco-branch-mod? tags). +o last changes: + * assuming path for TAF and TAMC are known (e.g. in $path) + * genmake: + - added tools/xmakedepend to circumvene shortcoming of + SUN's makedepend (size too small) + - invoking ../tools/xmakedepend instead of makedepend + - changed compiler flags for case SunOS + +ecco-branch-mod5 +o mod's to reproduce open boundary run +o enable field swapping for OB's and climatology +o update store directives for OB control +o added option ALLOW_OBCS_PRESCRIBE +o call of getobcs now out of obcs_calc (param. list modified) + +ecco-branch-mod4 +o this is the second part of changes necessary to reconcile + the natl_box_adjoint verification (with and without grdchk). + >>>!!! CHANGES BETWEEN THE TAGS ecco-branch-mod3 !!!<<< + >>>!!! AND ecco-branch-mod4 !!!<<< + >>>!!! SHOULD BE MERGED INTO THE MAIN TRUNK !!!<<< + - genmake: removed $S64 overwrite for case SunOS + - pkg/exf: update and corrections for field swapping and obcs + - pkg/ecco: parameter lists for the_model_main, the_main_loop + harmonized between ECCO and MITgcm + - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice + updated checkpointing_lev... lists for obcs + - model/src: minor changes in forward_step, plot_field + - pkg/mdsio: added mdsio_gl_slice + +ecco-branch-mod3 +o this is the first part of changes necessary to reconcile + natl_box_adjoint verification (with and without grdchk). + This set of changes is relevant for ECCO only. + The next set/tag of changes (ecco-branch-mod4) + should be merged into the main trunk. + - update some options + - parameter lists of ecco_the_model_main and ecco_the_main_loop + differed from those of the MITgcm counterparts. + +ecco-branch-mod2 +o update ecco-branch-mod1 to checkpoint44 +o exclude from updates: + - verification/ + - adjoint/ + - pkg/cost + - pkg/ctrl + - pkg/ecco + - pkg/obcs + - model/src/the_model_main.F + - model/src/the_main_loop.F + +checkpoint44 +o apply Shapiro filter on T&S before calc_PhiHyd (stagger time stepping) +o fix bug in mom_vi_del2uv +o added some stuff for AD + +ecco-branch-mod1 +o based on c43 +o replaced packages cost, ctrl, ecco, obcs +o removed MITgcm verif.'s, added ECCO verif.'s +o added lsopt, optim for line search optimization. + +checkpoint43 +o added two new advection tests +o added global 4x4 degree ocean test +o added test of H&S94 with free surface on cube +o some final mods for gradient check, adjoint,... + +checkpoint42 + Fixed AD-related problems: +o Store directives up-to-date with re-arranged Adams-Bashforth + (mainly thermodynamics.F) +o New store directives for multi-dim. advection schemes + * new CPP flag ALLOW_MULTI_DIM_ADVECTION + * new common block and key passkey + (mainly gad_advection.F) +o Modified store directives for split of dynamics/thermodynamics + for the case ALLOW_KPP +o Cleaned argument list for timestep_tracer.F + +checkpoint41 +o re-formatted/added comments in prologues of key subroutines + to work with protex + checkpoint40 o moved calc_gs, calc_gt and calc_tr1 back to model/src o added FLT (floats) package from Arne along with demo. experiment