--- MITgcm/doc/tag-index 2003/02/27 22:29:13 1.53.2.32 +++ MITgcm/doc/tag-index 2002/04/04 11:22:52 1.53.4.12 @@ -1,224 +1,116 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.53.2.32 2003/02/27 22:29:13 dimitri Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.53.4.12 2002/04/04 11:22:52 heimbach Exp $ Notes on tags used in MITgcmUV ============================== -untagged -o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F -o Added SEAICE_initialHEFF to pkg/seaice -o SEAICE_WRITE_PICKUP needs to be called before WRITE_CHECKPOINT - -release1_p12 -o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, - kpp_transport_t.F, forward_step.F, and the_main_loop.F -o pkg/seaice: - - adjoint-friendly modifications - - added a SEAICE_WRITE_PICKUP at end of the_model_main.F - -release1_p12_pre -o Updated useSingleCpuIO option in mdsio_writefield.F to - work with multi-field files, e.g., for single-file pickup. -o pkg/seaice: - - bug fix in growth.F: QNET for no shortwave case - - added HeffFile for specifying initial sea-ice thickness - - changed SEAICE_EXTERNAL_FLUXES wind stress implementation - -release1_p11 -o Modifications for using pkg/exf with pkg/seaice - - improved description of the various forcing configurations - - added basic radiation bulk formulae to pkg/exf - - units/sign fix for evap computation in exf_getffields.F - - updated verification/global_with_exf/results/output.txt -o Added pkg/sbo for computing IERS Special Bureau for the Oceans - (SBO) core products, including oceanic mass, center-of-mass, - angular, and bottom pressure (see pkg/sbo/README.sbo). -o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F - to avoid negative values in shallow regions. - - updated verification/natl_box/results/output.txt - - updated verification/lab_sea/results/output.txt -o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F -o Added useSingleCpuIO option (see PARAMS.h). - -release1_p10 -o modifications for using pkg/exf with pkg/seaice - - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING - and SEAICE_EXTERNAL_FLUXES - - pkg/exf CPP options EXF_READ_EVAP and - EXF_NO_BULK_COMPUTATIONS - - usage examples are Experiments 8 and 9 in - verification/lab_sea/README - - verification/lab_sea default experiment now uses - pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf - -release1_p9 -o pkg/seaice - - removed GOTO's and added taf directives - - double precision constants to reduce the g77 (Linux) - to F77 (SGI) differences reported in release1_p8 -o tools/genmake - - added SGI options -o verification/testscript - - updated to that of checkpoint47a_post -o verification/global_ocean.90x40x15/input/eedata - - modified for SGI f77 compatibility -o verification/lab_sea - - added description of sea-ice model - - added missing matlab routines - - added test of thermodynamics parallelization - -release1_p8 -o verification/natl_box: - updating new external_fields_load routine -o New package: pkg/seaice - Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). - The sea-ice code is based on Hibler (1979-1980). - Two sea-ice dynamic solvers, ADI and LSR, are included. - In addition to computing prognostic sea-ice variables and diagnosing - the forcing/external data fields that drive the ocean model, - SEAICE_MODEL also sets theta to the freezing point under sea-ice. - The implied surface heat flux is then stored in variable - surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and - kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the - non-local transport term. Because this call precedes model - thermodynamics, temperature under sea-ice may not be "exactly" at - the freezing point by the time theta is dumped or time-averaged. - N.B.: fairly large differences in accuracy occur across - different platforms/compilers; comparison between - g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) - generated output gives: - T S U V - C D M c m s m s m s m s - n p a R g m m e . m m e . m m e . m m e . - f n k u 2 i a a d i a a d i a a d i a a d - g d e n d n x n . n x n . n x n . n x n . - - Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea - -release1_p7 -o GAD: - - generated new common blocks to account for call of - same gad routines with differing traceridentities - (needed to modify tracerIdentity indices in GAD.h) - - generated separate common blocks for case useCubedSphereExchange - (Department of Futurology) - - parameter lists to gmredi_?transport: added tracerIdentity - - added new key indices to tamc.h -o external_fields_load: - - added this routine to TAF list - - needed to make some common blocks global and additional storing - along the same lines as exf package (checkpoint_lev?_directives.h) -o exf: - updated external forcing package - - bug fixes carried over from ecco-branch - (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 -o Adding new verification experiment global_with_exf. - This verification experiment is almost identical to the - global_ocean.90x40x15 experiment, except that it uses - the exf (and cal) package instead of the - external_fields_load routine (cf README file). - -release1_p6 -o fixed the verification/global_ocean.90x40x15 experiment: - - new bathymetry (the world according to A., JMC, and M.) - - new initial fields and forcing fields (*.bin files) - - new POLY3.COEFFS (for the next release one should switch to a full - equation of state) - - fixed several errors and redundancies in the data file - - experiment uses looped cells - - added matlab directory with diagnostic scripts for plotting of output - -release1_p5 -o import recent fix from MAIN branch: - - use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S - - change phiMin in exp1 (to agree with documentation) - from checkpoint45 to checkpoint45a_post: - - specific exchange for X-slice domain (case Ny=1) - - argument futureIter of S/R obcs_calc missing in - exp4 & internal_wave /code - - solve_for_pressure : set cg2d_x to zero where OBCS are applied - from checkpoint44f_post to checkpoint44g_post: - - fix surface correction term in multiDimAdvection - (affects plume_on_slope results -o bug fix in packages_readparms (missing ALLOW_CALENDAR) -o bug fix in CG2D.h (correct array size for LETS_MAKE_JAM -o Adjoint-related bug fixes in kpp: - - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix - - kpp_routines: store of Rib avoids partial recomputation bug of TAF. -o added Eliassen-Palm flux hooks (dynamics,ini_fields) -o removed unused TAF keys iikey, idkey (dynamics,thermodynamics) -o flow directives: - - new for S/R do_the_model_io - - enhanced for S/R checkpoint -o added Eliassen Palm flux controls to gradient check package -o new ctrl package - - adopted from ECCO environment to enable optimization - - added Eliassen Palm fluxes to controls - - adjusted global_ocean.90x40x15/ and carbon/ accordingly - -release1_p4 -o Removed f90 comments ("!") -o Modified initialisations to enable exf package for MITgcm - (without invoking ECCO_PACKAGE). -o modifications to gradient check package (Martin Losch) - - enable centered differences - - modified format of standard output - -release1_p3 -o added tangent linear setup to verification/carbon/ -o added adjoint sensitivity setup to verification/global_ocean... -o moved packages_init_variables before convective_adjustment -o output of verif. which use GMRedi brought up-to-date with - MAIN trunk (those were re-created after changes in GMRedi) -o included CPP option SINGLE_LAYER_MODE - to configure barotropic setup (Martin Losch). -o Removed auxiliary variable in impldiff - (caused numerical differences with MAIN trunk routine). -o Introduced CPP option ALLOW_AUTODIFF_MONITOR to - disable adcommon.h/g_common.h by default. -o Cleaned exchange calls in cg2d. - -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 +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 -release1_p1 +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 - - modified test cost function and carbon verif. + - included GMREDI, EXACT_CONSERV to natl_box_adjoint verif. -release1_chkpt44d_post = chkpt44d_post - -chkpt44d_pre,post -o added missing EXCLUDE_MONITOR flags -o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi - (incompatible typ in MIN/MAX expressions caused problems - on IBM SP3) -o in genmake added variable MAKEDEPEND - plus resetting for case SunOS -o added timer_stats.c routine for IBM SP3 -o removed variables in dynamics - -o real fresh water flux implemented with non-linear free-surface. - -chkpt44c_pre,post -o few fix (mask in shap_s2, EmPmR in external_field_load, - USE_NATURAL_BCS in solve_for_P); -o add arguments myIter & myTime to S/R obcs_calc & solve_for_P - -checkpoint44b_pre/_post -o merge of relevant stuff from the ecco-branch: +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 @@ -226,20 +118,41 @@ - 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 - added directive for divided adjoint in the_main_loop - pkg/mdsio: added mdsio_gl_slice -o check parameters & config (chkpt44a_pre,post) -o OBC and NonLin_FrSurf. +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 select when filters are applied ; add options to zonal_filter (data.zonfilt) -o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) -o update AIM experiments (NCEP input files) -o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) 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