--- MITgcm/doc/tag-index 2003/02/13 17:51:48 1.53.4.15.2.3 +++ MITgcm/doc/tag-index 2002/11/05 19:15:12 1.96 @@ -1,183 +1,288 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.53.4.15.2.3 2003/02/13 17:51:48 dimitri Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.96 2002/11/05 19:15:12 adcroft Exp $ Notes on tags used in MITgcmUV ============================== -Revision history for branch c24_e25_ice - (branch for adding sea-ice code to ecco-branch) - -02/12/03 cvs tag ecco_ice2 - Added pkg/seaice and modified pkg/exf as per release1_p12_pre - -02/11/03 cvs tag ecco_ice1 - Updated verification/natl_box_forward and natl_box_adjoint - for SGI platform - -12/06/02 - Branched off tag ecco_c44_e25 - -================================================================= - -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 introduced flag for controllin non-hydrostatic metric terms +o removed gravitySign from PARM04 +o switched to g77/ifc from pgf77 in aim experiments + +checkpoint46l_post +o made convective adjustment work with pressure coordinates: + - changed the direction of k-loop in convective_adjustment.F for the + case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) + - adjusted the reference pressure k-index in convective_adjustment.F + - adjusted the convection condition in convect.F (in analogy to + calc_ivdc.F) + - convective_adjustment no longer computes anything on the halos + - removed the warnings about negative salinity from find_rho.F and + find_alpha.F; instead the new routine look_for_neg_salinity, called + at the beginning of find_rho, find_alpha, and find_beta, does a + check of the entire slice, if CPP-option + CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined +checkpoint46l_pre + +checkpoint46k_post +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: JMD95P or MDJWF) + - fixed several errors and redundancies in the data file + - experiment uses looped cells + - added matlab directory with diagnostic scripts for plotting of output + +o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: + - read AIM physics parameters from a file (data.aimphys) + - set defaults values = F.Molteni paper (Clim.Dyn., 2002) + +checkpoint46j_post +o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH +o move wVel computation at the end of the time step, in S/R integr_continuity +o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) +o update timeave pkg for wVel diagnostic. +checkpoint46j_pre + +checkpoint46i_post +o Clean up AIM package (and keep the results unchanged): + include CPP_OPTION and use IMPLICT NONE in all routines ; + declare all the variables _RL ; use _d 0 for all numerical constants. + use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! + +checkpoint46h_post +o cleaned up the use of rhoNil and rhoConst. + - rhoNil should only appear in the LINEAR equation of state, everywhere + else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst + and the dynamical equations are all divided by rhoConst +o introduced new parameter rhoConstFresh, a reference density of fresh + water, to remove the fresh water flux's dependence on rhoNil. The default + value is 999.8 kg/m^3 +o cleanup up external_forcing.F and external_forcing_surf.F + - can now be used by both OCEANIC and OCEANICP +checkpoint46h_pre + + Added code to convert surface volume flux (fresh water) into + a mass flux when using P coordinates in the ocean (OCEANICP). + Note: It assumes you have set rho0=rhoConst=density of fresh water. + +checkpoint46g_post +o Include a new diagnostic variable phiHydLow for the ocean model + - in z-coordinates, it is the bottom pressure anomaly + - in p-coordinates, it is the sea surface elevation + - in both cases, these variable have global drift, reflecting the mass + drift in z-coordinates and the volume drift in p-coordinates + - included time averaging for phiHydLow, be aware of the drift! +o depth-dependent computation of Bo_surf for pressure coordinates + in the ocean (buoyancyRelation='OCEANICP') + - requires a new routine (FIND_RHO_SCALAR) to compute density with only + Theta, Salinity, and Pressure in the parameter list. This routine is + presently contained in find_rho.F. This routine does not give the + correct density for 'POLY3', which would be a z-dependent reference + density. +o cleaned up find_rho + - removed obsolete 'eqn' from the parameter list. +o added two new verification experiments: gop and goz + (4x4 degree global ocean, 15 layers in pressure and height coordinates) +checkpoint46g_pre + +checkpoint46f_post +o Enable tangent linear (forward mode) gradient checks: + - extended active file handling to g_... files + - added TANGENT_SIMULATION to theSimulationMode + - extended grdchk package accordingly +o added tangent linear setup in verification/carbon/code_ftl +o added adjoint setup in verification/front_relax/code_ad + +checkpoint46e_post +o Added new equation of state -> MDJWF + - EOS of McDougall et al., 2002, JAOT, submitted + - caveat: the equation of state is only valid for a smaller (more + realistic?) range of values than JMD95P/Z and UNESCO + - added masks to the calculation of pressure in store_pressure + - added more check values for density in check_eos (ini_eos.F), some of + the old check values are out of the range of the MDJWF-eos, so don't + expect perfect matches for those +checkpoint46e_pre + +checkpoint46d_post +o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and + 'OCEANICP', also initialised field pressure correctly in ini_eos in the + case of pressure coordinates. eosType='JMD95Z' in + combination with buoyancyRelation='OCEANICP' now causes an error. +o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) + in find_alpha/beta. +checkpoint46d_pre + +o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) + so that JMD95Z and JMD95P give approptiate static stability in find_rho. + +checkpoint46c_post +o Changes necessary for ocean in p-coordinates + - Added new buoyancy relation = 'OCEANICP' + - Added new parameters = gravitySign (this used to be contained inside + the factor dRdZ which I added when we first switched to R coordinates). + X GM/Redi is not compatible (yet) + X bottom drag and no-slip need to be debugged. +checkpoint46c_pre + +checkpoint46b_post +o Added new equation of state -> JMD95Z and JMD95P + - EOS of Jackett and McDougall, 1995, JAOT + - moved all EOS parameters into EOS.h + - new routines ini_eos.F, store_pressure.F +o Added UNESCO EOS, but not recommended because it requires + in-situ temperature (see JMD95) +o Modified formatting for knudsen2.f in utils/knudsen2 and added + unesco.f to be used with POLY3 +checkpoint46b_pre + +checkpoint46a_post +o Added (atmospheric) pressure loading + - new field in FFIELDS.h, etc... + - new cpp flag ATMOSPHERIC_LOADING +o Changed hFacC to _hFacC in calc_phi_hyd.F +o Added SHORTWAVE_HEATING to some files for consistency +checkpoint46a_pre + +checkpoint46 +further merges from release1_p5 +o new ctrl package + - adopted from ECCO environment to enable optimization + - added Eliassen Palm fluxes to controls +o added Eliassen Palm flux controls to gradient check package +o cost package + - Compatible with new ctrl package + - added Eliassen Palm cost hooks + - modif's of existing cost functions +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 autodiff package + - flow directives: + + new for S/R do_the_model_io + + enhanced for S/R checkpoint + + new gmredi.flow + - Introduced CPP option ALLOW_AUTODIFF_MONITOR to + disable adcommon.h/g_common.h by default. + - fixed problem for adjoint of global_max +o modified verification/carbon/ +o New setup for adjoint of global_ocean +o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) +o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) +o incorporated hooks for sponge layer code (external_forcing.F) + +checkpoint45d_post +o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) +o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S + (affects plume_on_slope "cg2d" output) +o add new parameter deltaTfreesurf for free-surface time stepping +o exchange gT,gS when using staggerTimeStep & GM & Oly<4 +o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B +o change phiMin in exp1 (to agree with documentation) +o add new flags: + - T,S forcing inside/outside Adams-Bashforth + - turn off temp,salt advection and/or forcing + - for each tracer, define internal flag for multiDimAdvection & A-B +o monitor: change definition of KE to check conservation of Energy + +checkpoint45c_post +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 -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 !!!<<< + +checkpoint45b_post +o cleaned exchange calls in cg2d +o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step +o included CPP option SINGLE_LAYER_MODE in thermodynamics + to configure barotropic setup (Martin Losch) +o moved some initialisations within bi,bj loop in dynamics + (TAF flow dependency) +o in initialise_varia, moved call packages_init_variables + before convective_adjustment_init + (corresponding adjustment of TAF tape initialisation). +o in calc_diffusivity/calc_viscosity extended domain to full overlap. + +checkpoint45a_post +o compute Rho over the whole domain (extend iMin,jMin indices) +o specific exchange for X-slice domain (case Ny=1) +o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code +o solve_for_pressure : set cg2d_x to zero where OBCS are applied + +checkpoint44h_post = checkpoint45 +o Fix to restore differentiability: + place at which packages_init_variables is called in + initialise_varia is crucial for reverse control flow. +o modifications in GMRedi to enable stable adjoint + (corresponding modif's in thermodynamics, dynamics) +o added missing hook for sponge layer code in external_forcing +o modified test cost functions +o storing in gad_advection (plus removal of write(0,*)! +o missing headers TR1.h added in convective_adjustment routines +o errorMessageUnit set non-equal zero in eeboot + (conflict on some platforms, e.g. IBM SP3) +o modified carbon verif. + +checkpoint44h_pre +o vertical grid option: allow to put the Interface at the middle between + 2 cell-centers ; replace delZ in pkg/kpp by drF. +o GM Advective form: Tracers are advected using the residual transport (= + Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. + +checkpoint44g_post +o fix surface correction term in multiDimAdvection (affects plume_on_slope + results) ; ifdef missing in thermodynamics.F + +checkpoint44f_pre,checkpoint44f_post +o added PTRACERS package + This allows an arbitrary number of passive tracers to be integrated + forward simultaneously with the dynamicaly model. + + Implemented so far: + - basic forward algorithm (time-stepping, advection, diffusion, convection) + - I/O and checkpointing + - GM/Redi *but* using the GM/Redi coefficient of Salt + + Not implemented so far: + - KPP + - OBCS + + No specific example supplied (yet) but global_ocean.90x40x15 has the + necessary data.ptracer file. Simply use -enable=ptracers and uncomment + line in data.pkg. + + This package is disabled by default since it increases storage. + + +o testscript: added -cleanup option +o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter + b) enable to filter 2D fields. + +checkpoint44e_pre,post +o re-wrote convective adjustment to use pre-calculated weights + Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F + Adds: model/src/convective_weights.F, convectively_mixtracer.F + Original calls to convect() still in place. + +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 +!!! I forgot to create tag chkpt44d_pre !!! +!!! But chkpt44d_pre = chkpt44c_post !!! + +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: - 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 @@ -185,41 +290,20 @@ - 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 -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 +o check parameters & config (chkpt44a_pre,post) +o OBC and NonLin_FrSurf. 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