--- MITgcm/doc/tag-index 1998/06/15 05:13:55 1.5 +++ MITgcm/doc/tag-index 2003/10/02 17:43:57 1.179 @@ -1,8 +1,1242 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.5 1998/06/15 05:13:55 cnh Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.179 2003/10/02 17:43:57 jmc Exp $ Notes on tags used in MITgcmUV ============================== +untagged +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. + +checkpoint51f_pre +o Added on-the-fly spatial interpolation capability + "USE_EXF_INTERPOLATION" to pkg/exf. + - This is a temporary Cartesian-grid hack until + the super-duper ESMF coupler becomes available. + - See verification/global_with_exf/README for usage example. + - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid + flags and modified pkg/seaice accordingly. +o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, + and pkg/kpp/kpp_transport_ptr.F for dealing with tracer + non-local transport term. + +checkpoint51e_post +o pkg/mom_vecinv: + - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) + - add time-ave diagnostic of vorticity advection. +o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. +o atmospheric geopotential: - include water vapor effect; + - use p^kappa in p* scaling. +o land pkg: read initial state from files. +o AIM : add stratospheric drag in the upper level + +checkpoint51d_post +o change function ILNBLNK (=> last non-blank char.) to return zero + (instead of the string length) when the string. char is empty +o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) +o modif's to restore TAMC compatibility + - avoid "_d" constructs in PARAMETER declarations + - avoid interrupting lines by comment lines +o Use cluster local disks for purely local I/O + vs. globally visible disks needed for ctrl stuff + (merged from ecco-branch) + - new active_file_loc... and mdsio_..._loc routines + - affected packages: autodiff, ctrl, grdchk, mdsio + +checkpoint51c_post +o introducing integer flag debugLevel + - debLevZero: suppress all output + - debLevA: standard + - debLevB: equivalent to current debugMode=.TRUE. +o introducing pathname variable mdsioLocalDir for mdsio + that can be specified at runtime + (relevant for cluster I/O to local disk) +` +>>>checkpoint51b_post +adjoint of ptracers +o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM +o extended state in checkpoint_lev?, etc. +o alternative ctrl/cost with tr1 or ptracer +o new comlev1_bibj_ptracers +o new ptracers.flow +o made ptracers_forcing same as external_forcing_s +o added verification for adjoint with ptracers + - adm. grdchk fail so far + - tlm. grdchk OK + - checked tapelev/comlev recomputations: OK +<< affects results of glob_oce_pressure (different truncation error) + update output.txt of ideal_2D_oce & global_ocean_pressure + +checkpoint48d_pre +o in preparation for r*: + new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. + pass the 2 comp. of the grad. as arguments to momentum S/R. + but for the moment, only used if it does not change the results. +o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP + +checkpoint48c_post +Modifications in treatment of initial flux forcing controls +to avoid extra storing of flux fields. + +checkpoint48c_pre +o Added tidal_basin_2d experiment (currently 1D!) +o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) + +checkpoint48b_post +o r* coordinate added in #ifdef NONLIN_FRSURF block. + (modification to pressure gradient not yet implemented) +o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports + (for U & V) that are used for vertical advection of momentum. + +checkpoint48a_post +o In preparation for r*, use temp. array to compute vertical transport + in flux-form momentum pkg. => change results of few test-exp. + Update output of: exp4, exp5, front_relax, global_ocean_pressure, + lab_sea, natl_box & plume_on_slope + +checkpoint48 +o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') + +checkpoint47j_post +o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. +o moved adexch from forward_step to addummy_in_stepping +o added exch in ctrl_map_... +o aveFreq.=0. at end of cost_final to avoid overwrite in + reverse checkpointing loop +o Yet more changes in gmredi: + * adgmredi_calc_tensor + avoiding all recomputation of gmredi_slope_limit + * adgmredi_x/y/rtransport + added flag for excessive storing to avoid recomp. of + u/v/rtans, dTdx/y/z + -> this is not really necessary and very memory-consuming + * adgmredi_slope_psi: + consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff + * gmredi_slope_limit + re-activated full calculation of taperfct for case 'ac02' +o updating verification/ adjoints of carbon, global_ocean.90x40x15 + +checkpoint47i_post +o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. +o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) + default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) +o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) +o gmredi: fix few bugs. + +checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) +This will be a good checkpoint to plug into the ecco-branch. +o few modif.'s to get latest version adjointed + (mainly kick out code in ini_linear_phisurf) +o modif's to run adjoint with exactConserv +o case GM_BOLUS_ADVEC should be cleaned + S/R gmredi_slope_psi should be cleaned +o verification/carbon now has exactConserv=.TRUE. + +checkpoint47g_post +o time-average AIM output: becomes independent from statvars time-average + (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) +o After TAF bug fix: + Tested adjoint of gmredi package. + Tests were done with checkpoint47 rather than with latest + checkpoint47f_post since the latter is broken for the adjoint + verification/carbon/ contains both ADM and TLM gradient checks. +Here they are, before they get changed/lost/stolen. +Mostly modif.'s to fix numerical sensitivities. +Gradient checks OK for +- GM_taper_scheme: + * clipping + * ac02 + * linear + * glw91 + * dm95 + * ldd97 +- GMREDI_OPTIONS: + * GM_VISBECK_VARIABLE_K + * GM_NON_UNITY_DIAGONAL + * GM_EXTRA_DIAGONAL + * GM_BOLUS_ADVEC +in conjunction with data.gmredi parameters to be checked in +in a few minutes under verification/carbon/code/ + +checkpoint47f_post +Merging from 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 + +checkpoint47e_post +o created a tag prior to creating a branch + +checkpoint47d_post +o fixed bug in the oceanic pressure coordinates code: vertical viscosity + at the bottom boundary had an erroneous half slip boundary condition +o added bottom drag and no slip boundary condition capabilities to + oceanic pressure coordinates code +o added new verification experiment global_ocean_pressure, this experiment is + also described in the tutorial section of the manual +checkpoint47d_pre + +checkpoint47c_post +o Added a verification experiment for a global cubed-sphere ocean run + - verification/global_ocean.cubed32x32x30 + - uses pkg/therm_seaice and pkg/bulk_forcing + +o allow to run AIM physics with SPEEDY input files (from Franco Molteni) +o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) + when using P-coordinate; only implemented for atmospheric config. +o OCEANICP & realFreshWater: include P-E direct effect on wVel ; + NOTES: requires option NONLIN_FRSURF to be "#define". +o update advect_xz/results/output.txt (left from checkpoint44g_post) + +checkpoint47b_post +Merging from 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 + +checkpoint47a_post +o new pkg: aim_v23 + = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. + for now, keep the same surface forcing as before. + - Part-Cell implemented into AIM; check that Heat & Water are conserved + - aim.5l_cs: use new aim pkg (run 10yr & get better results than before) + - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg +o add diagnostic of surface correction term in monitor output + +o bulk_force and therm_seaice +- Two packages: bulk_force (Bulk forcing) + and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 +- Earlier integration from Stephaine Dutkiewicz + and Patrick Heimbach. +- Two ifdef statements for compile time, + ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE + +checkpoint47 +differentiable version of checkpoint46n_post +o bug fix in quasihydrostaticterms +o * "clean" adjoint code (in terms of extensive recomputations) + can now be obtained for all GMREDI options (i.e. for + - GM_VISBECK_VARIABLE_K + - GM_NON_UNITY_DIAGONAL + - GM_EXTRA_DIAGONAL + - GM_BOLUS_ADVEC ) + * However, wrong gradient check problem remains unsolved. + * New CPP options have been introduced for different + tapering schemes +o external_fields_load now part of differentiation list +o pressure needs multiple storing; + would be nice to have store_pressure at beginning or + end of forward_step, e.g. by having phiHyd global (5-dim.) + (NB: pressure is needed for certain cases in find_rho, + which is also invoked through convective_adjustment). +o recomputations in find_rho for cases + 'JMD95'/'UNESCO' or 'MDJWF' are OK. +o #define ATMOSPHERIC_LOADING should be differentiable +o ini_forcing shifted to begining of initialise_varia +o Incorporating QNVS line search routines into MITgcm + (this is separate code, and therefore not under pkg) + lsopt/, optim/ +o Updated verification/carbon/ + - #define GM_VISBECK_VARIABLE_K + - GM_taper_scheme = 'ldd97' + +checkpoint46n_post +Merging from 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 +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). + +checkpoint46m_post +o modified testscript to return -- when there are no lines of "%MON" output +o added new flag "quasiHydrostatic" for QH mode + and new routine quasihydrostaticterms() +o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) + New routine: mom_u_coriolis_nh() +o fixed sign of non-hydrostatic metric terms in u and v equations. + Depend on correct sign of gravitySign. +o added work.pc* to .cvsignore in aim directories using ifc +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 + +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 + 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 + 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. + +checkpoint44 +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 + +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 +o re-arranged Adams-Bashforth scheme for tracers to allow easier + implementation of forward-in-time forcing terms +o more mods for non-linear free-surface including new variable +o modified multi-dim method to work on cube +o bug fix in KPP (from DM) + +checkpoint40pre9 +o added DST advection schemes +o fix MPI bug on SGI's +o modifications for non-linear free-surface +o fixed conditionals for fixed flow/passive tracer only mode +o added tension/strain form of stress tensor +o changes to commenting of arguments for TAF/TAMC +o added/updated many matlab scripts +o added multi-dimensional advection method for tracers + +checkpoint40pre8 +o new package rw/ + Added method for dumping intermediate local arrays: + mdsio_writetile - same as mdsio_writefield except works from inside + bi,bj loop + mdsio_writelocal - same as mdsio_writetile except works for local + arrays + write_local_r? - higher-level wrapper for mdsio_writelocal + Controlled by diagFreq. Defaults to zero (ie. no dumps) + Example given at end of mom_vecinv.F that dumps some local arrays. +o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to + control flux-form versus vector invariant code. + Switch is runtime flag vectorInvariantMomentum (defaults to false) + or genmake -DISABLE ... +o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F + (additional storing is now needed for case vecinv; + currently nothing implemented to switch this storing off + in case fluxform is used since no CPP flag available). + +checkpoint40pre7 +o bug fix in dynamics.F + calc_viscosity called before k=1,Nr loop. +o added some #ifdef's ALLOW_PASSIVE_TRACER +o cleaned initialisations in ctrl_map_ini + related to TAF + +checkpoint40pre6 +o split dynamics into thermodynamics & dynamics +o corresponding split of calc_diffusivity into + calc_diffusivity, calc_viscosity + (kpp_calc_diff, kpp_calc_visc). +o Added diffkr, kapgm to control variables +o bug fix in gmredi_slope_limit for ldd97 + +checkpoint40pre5 +o proper initialization of Adams-Bashforth time stepping + + uses forward step for very first step of model (iter=0) +o re-generated *all* output since almost all output is modified by this + change (sorry but we've been putting this one off for about 2 years) + + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were + *not* regenerated since they are already out of date and I don't + want to create the impression that they are suddenly working. +o removed KAP stuff for DEC's +o modified/added many .cvsignore files in */code and */input +o added new expt "solid-body.cs-32x32x1" + + this uses an alternative form of ini_curvilinear_grid.F which + is not necessarily any better than the current one... + +checkpoint40pre4 +o added re-initialisations of utrans,vtrans,rtrans in + calc_common_factors which are crucial for TAF. +o extended iMin,jMin range for calc_common_factors, + calc_diffusivity +o added option ALLOW_PASSIVE_TRACER +o a few minor updates and fixes + +checkpoint40pre3 +o created calc_gtr1.F for gad package +o split the_main_loop and re-introduced forward_step +o some recomputations of nIter0 for TAMC + +checkpoint40pre2 +o Updated to latest branch of AJA, JMC +o Added gradient check package +o Added routines for passive tracer handling +o Added carbon sequestration sensitivity experiment + +checkpoint39 + o Modifications and fixes to support TAMC + (mainly missing or wrong directives) + o Corrected common blocks when fooling TAMC to produce adjoint I/O + in addummy_in_stepping + o Updated verification/vero/ (bug fixes in code/, correct pickups in input/) + o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs. + o Included following packages: + cal: calendar + exf: external forcing + ecco: essential routines to control use of cal, exf + (NB: this is not the full ECCO environment) + o disabled some packages by default in genmake + +checkpoint38 + o see notes_c37_adj.txt + o corrected wrong layer index in external_forcing_t + o replaced the_main_loop/forward_step by the_main_loop + o removed forceoutput from write_state + (replaced criteria for initial/final state) + o added runtime flag for pre-C35 pickups: usePickupBeforeC35 + +checkpoint37 + o mdsio.F routine split and packaged in pkg/mdsio + (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not + used unless genmake -disable=mdsio) + o allow a more precise surface-geopotential gradient for the atmosphere + taking into account the change in space of Alpha (=1/rho) at the surface. + o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit] + (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa]) + o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and + Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential + [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere). + o Time-Average diagnostics defined as a pseudo package "timeave". + o pickup files : old pickup (before c35) did not work with new code (c35 + and after) unless activating 2 commented lines in initialise-varia. + o Non-Hydrostatic pickup file Pb fixed. + o bug with Rigid-lid version (since c35) fixed. + +checkpoint36 + o implement Crank-Nickelson barotropic time-stepping + o recover Time-Average diagnostics + o fix Pb in checkpoint (PR#19) + o AIM become a standard package ; clean unused CPP_kees + +checkpoint35 + o subtantial rewrite of dynamics.f + o allows staggered time-stepping + o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt + o added bottom drag (linear + quadratic) + +checkpoint34 + o Modified exchange routines for correct reverse simulation. + o Added verification output to comply with bug fix in impldiff.F + as of c33 (exp2, natl_box). + o Corrected store directives in dynamics.F + o Corrected array boundaries in impldiff.F + o Corrected array dimensions in gmredi. + Added temporary scalars to avoid storage by TAMC (gmredi, kpp). + o Added routine GLOBAL_SUM_INT to global_sum.F + o Added mdsio_gl.F for ECCO purposes. + +checkpoint33 + o Fixed bug in lower BC in impldiff.F + o Fixed confusion about units of forcing arrays in FFIELDS.h + namely Fu,Fv,Qnet,Qsw,EmPmR: + - Removed verification/natl_box/code/external_fields_scale.F + (did not differ from that in model/src) + - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units + (see FFIELDS.h for description) + - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F, + kpp_calc.F and kpp_transport_t.F + - Removed model/src/external_fields_scale.F and calls to it + - verification/natl_box uses flux data with "atmospheric" sign so + a special version of external_fields_load.F is used to + change the data as it's read in. This way, the arrays + have the right units and signs at all times tha a user could + possibly use them. + o Corrected genmake to delete a temporary file during configuration + +checkpoint32 + o Scaling of forcing fields moved from external_forcing.F to + external_fields_scale.F, called directly after loading fields. + o Surface relaxation terms added to surface tendency fields in + extra subroutine. + o impldiff.F changed to avoid storing by TAMC of huge intermediate + fields. + o Changes in GMRedi to comply with packaging structure. + o Modifications and bug fixes in KPP package. + o Verification experiment for KPP added (verification/nat_box/) + +checkpoint31 + o Packages interface brought in line with defined standard + -> new routines packages_...F + -> changes in initialise_fixed.F, initialise_varia.F + -> enables initialisation interface for ECCO package + o Rescaling of external forcing fields immediately after read + (removed from external_forcing.F) + -> new: surface_fields_scale.F + -> affects ini_foorcing.F, external_fields_load.F + o Computation of surface tendencies before tendency updates. + -> new: external_forcing_surf.F + o Change of variable names useGMRedi, useKPP, useECCO + o Further changes in dynamics.F, impldiff.F for TAMC + o Tested for experiments 0, 2, 4. + - not yet tested for GMRedi. + - not yet tested for KPP. + +checkpoint30 + o Updates for OBCs + o New experiment for test OBCs (internal_wave) + o New output.txt in verification/exp4/results/ + o Updates for KPP: calculation of viscosity corrected, new variables + kpp_dumpFreq and kpp_taveFreq + o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) + and entry for T90 in genmake + +checkpoint29 + o packaged KPP and GM/Redi + +checkpoint28 + o Corrected initialization of hFacMin for difference vertical coordinates + o Modified calculation of partial cell thickness to more robust algorithm + o config_summary.F: replaced write_1D_... by write_0D_... + read_write.F: added subroutines write_0D_... + o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho: + included some initialisations required for TAMC. + o routine calc_isoslopes: modified sqrt computation to make it + differentiable for zero argument. + o routines dynamics, impldiff: + included store directives and tape key computations required for TAMC. + o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC + +checkpoint27 + o fixed calc_isoslopes() to so that cancellation of terms in tensor + formulation works properly with variable resolution. + o restructured the calling tree between the_model_main() and dynamics() + o split initialise() into initialise_fixed() and initialise_varia() + o introduced initialization file pSurfInitFile for free surface (cg2d_x) + in new routine ini_psurf() + +checkpoint26 + o moved some #ifdef in optional routines to encompass everything + except the argument declarations. This was using up some memory. + o fixed macros like _ADT to work with both versions of Linux cpp + o cleaned up some unused and uninitialized variables + (helps when debugging with strict compile options) + o split up CPP_EEOPTIONS.h into options and macros + (macros are now in eesupp/inc/CPP_EEMACROS.h) + o patch for 2 processor JAM mode + +checkpoint25 + o updates for OBCs and NH + o dramatically reduced memory usage + o added "JAM" routines for use on Artic network + o parameterization of convection by implicit vertical diffusion + o added a diagnostic of convective index + o moved call to calc_divg_hat() from dynamics() to solve_for_pressure() + (this is was partly for OBCs and NH but also in anticipation of + an explicit free-surface option) + o initial state input files for U and V + +checkpoint24 + o Removed some spurious "REAL"s + o Updated KPP to latest version from JPL + o Added a COS(latitude) in horizontal viscosity + +checkpoint23 + o Added del^4 diffusion for salt and temperature + o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) + +checkpoint22 + o Made many small changes: implicit none, format(i5), etc... + o Introduced KPP mixing scheme (compiles and runs but *not* tested) + +checkpoint21 + o Introduced new I/O package that supports direct-access records (mdsio.F) + o Split-up mid-level I/O routines + o Updated input data for experiments 0,1,2,4 and 5 + o Finally removed the genmake.* scripts (everyone seems happy with genmake) + +checkpoint20 + o Tidied up open-boundaries some more + o Added non-hydrostatic code + o Fixed some input data + o Modified MPI start-up to work in "coupled" context. + +checkpoint19 + o Tidied up directory structure for verification experiments. + o Added new code for open boundaries. + o Corrected advective terms near boundaries. + o Added CPP flag for "old UV" geometry and corrected spherical geometry. + o Implemented free-slip/no-slip BCs and del^4 dissipation. + o Split default parameters out of ini_parms.F into set_defaults.F. + +checkpoint18 + o Further changes for optional code generation with + CPP - ugh! + +checkpoint17 + o Beginning to incorporating modularity + for supporting atmos. and ocean configs. + o Small changes for TAMC complinace + o New ultra simple test case. Barotropic box + configuration "exp0". + +checkpoint16 + o Minor changes to exchange routines to support + accumulation in reverse mode. Adjoint of an + assignment is an addition. + o Changes to support compilation by TAMC (LR(1) + syntax) and by g77 under Linux ( 72 character + limit ). + +checkpoint15 + Rewrote exchange routines to allow + o General tile <-> tile connectivity. + o TAMC reverse mode flag ( is this really needed? ) + o Variable width overlap and exchange region widths. + o Hooks for sharing data via DMA, Arctic, Memory Channel, + shmput/shmget, VIA, SYSV shmem and every other cool + communication method. + +checkpoint14 + Consistent isomorphism chages made. These allow dynamical core + to support both pressure and meters as a vertical coordinate. + +checkpoint13 + Release which corrects global_max problem and a couple + of KGM time-averaging diagnostic errors. Also contains + a double-gyre experiment setup as well as the baseline + 4 degree global template. The double gyre template is + organised to allow it to be applied automatically to + the baseline configuration. + +branch-point-rdot + A few tidy-ups have been made bt the real point of this + check-point (excuse the pun) is to allow a branch to be + made for the purposes of adding the rDot alterations. + I don't want to commit the rDot to the main-trunk until + we've actually tested it... + +checkpoint12 + Tidy up and added generic genmake script (formerly + configure script). + Released to testers. + +checkpoint11 + Re-arranged initialise() and introduced ini_vertical_grid() + and ini_masks_etc(). + +checkpoint10 + Introduced the configure script. + Separated out the diags package. + Added template for writing time-averages of tile/intermediate quantities. + Updated SIZE.h in exp2 and made the data big-endian. + +checkpoint9 + MPI fix. Filename changes (meta/data). salbin*y stuff. + General tidy-up. + SST.bin SSS.bin added to verification/exp2 + +checkpoint8 + Inludes time-dependant forcing and time-averaging. + Works at 4x4 and 2.8125x2.8125 global + +checkpoint7-4degree-ref + Branch from checkpoint7. Released for application to + global modeling and general modeling - process studies, regional + model etc.. + Configured for verification/exp2 - 4 degree global, two process. + checkpoint7 Created by cnh Simple 4 degree global simulation