--- MITgcm/doc/tag-index 2002/12/10 04:28:01 1.109 +++ MITgcm/doc/tag-index 2003/05/23 20:19:15 1.160 @@ -1,8 +1,334 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.109 2002/12/10 04:28:01 jmc Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.160 2003/05/23 20:19:15 dimitri Exp $ Notes on tags used in MITgcmUV ============================== +checkpoint50g_post +o merged with release1_p17 (pkg/seaice and verification/lab_sea) + - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics + - LSR sea-ice dynamic solver moved to SouthWest B-grid location and + made the default because of faster convergence than ADI + +checkpoint50f_post +o exf totally restructured + - replaced all exf_set_ routines by one generic exf_set_gen.F + and made sure it's still differentiable + - split exf_getffields.F into new exf_bulkformulae.F + - exf_inscal_/exf_outscal_ suffixes consistent with field names + - updated adjoint/makefile and relevant verif. accordingly + +checkpoint50f_pre + o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; + + change Evap over land. (update aim.5l_cs output) + o added missing .cvsignores and made uniform across expts + o changed configuration of tidal_basin_2d expt + o added pkg/debug functions for tracing code in fatal crashes + o tidied pkg/monitor to use MONITOR_OPTIONS.h + o new fn in pkg/monitor to stop model if solution grows too big + o removed lots of single quotes from comments + +checkpoint50e_post +o make KPP work with PTRACERS + - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is + nearly a copy of kpp_transport_s + - there is no analogue to SurfaceTendencyS, so I have to use + gPtr(of the surface layer) instead +o add a new platform SunFire+mpi (SunFire 15000) to genmake +checkpoint50e_pre + +checkpoint50d_post +o change kpp output from multiple-record state files to single-record state + files analogous to write_state.F +o reduce the output frequency of cg3d-related stuff to the monitor frequency, + analogous to the cg2d-related output. +o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, + so that writing to internal file fn (with length 512) fails. +checkpoint50d_pre + +checkpoint50c_post +o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) +o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. +o add time-average diagnostic of U*V and vertical diffusive flux for theta. +o bug fixed in convective adjustment diagnostic (multi-tile set-up). +o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. + +checkpoint50c_pre +Merging from release1_p13: +o bug fix for pkg/seaice dynamic solver +o Added SEAICE_initialHEFF to pkg/seaice + +checkpoint50b_post +o store u*,v* in gU,V instead of in guNm1,gvNm1 +o in order to put the momForcing out of the Adams-Bashforth: + move forcing & CD-scheme calls from mom_fluxform & mom_vecinv + to timestep.F +o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays +o re-generate output for highly sensitive test-exp: + global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box + +checkpoint50b_pre +o restore the use of momAdvection & useCoriolis flags (mom_vecinv) +o corrected CPP option mismatch in exf_Bulk... functions for case + #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP + +checkpoint50a_post +o Bug fix for merging between c50 and KPP. + ikey was passed from thermodynamics to kpp_calc via + common block rather than being recomputed in kpp_calc, + in contradiction with new key itdkey. + New key ikppkey created, and tamc.h headers updated. + +checkpoint50 +- 2nd step of merge with ecco-branch: + merge changes in ecco-branch back into main trunk +- bug fix in find_alpha +- more storing in gmredi_calc_tensor.F, kpp_routines.F +- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC +- merged some sliced AD support routines + +checkpoint49 +merged from ecco-branch: +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. +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 + - the_main_loop.F + - 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 cal: synchronized between MAIN and ecco-branch + +checkpoint48i_post +o Changes to restore differentiability of code w.r.t. previous tag + (mostly adding new routines to make list and replacing + pressure by totPhiHyd). +o Updated and merged grdchk package + - has both ADM and TLM checks + - works for single- and multi-proc. + - output cleaned + - worked successfully for parallel DIVA +o genmake: + - Adding -platform=SP4 + - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). +o Modif. for DIVA: + ctrl_unpack should not be called in intermediate DIVA interval. + (similar thing would apply for active files such as + tbar, sbar, psbar, which should not be reinitialised; + only relevant for ecco-branch) + +checkpoint48h_post +o improve "ini_p_ground" when using finite difference form for calc_phi_hyd +o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F +o Added SEAICE_initialHEFF to pkg/seaice +o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT + +checkpoint48g_post +--- EOS: +o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF + store total Potential in totPhyHyd for diagnostics & EOS. +o fix restart and overlap Pb when using Z-coord and EOS funct. of P +--- Pressure/geopotential gradient: +o use Ro_surf & R_low instead of hFac in cal_phi_hyd: +o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind + ( changes results of global_ocean_pressure ) +o NLFS + z-coord.: add eta*Rho' contribution. +o accurate phiHyd when using interface-W at the middle between 2 centers + ( changes results of ideal_2D_oce ) +o includes r* 2nd term in potential gradient. + +checkpoint48f_post +Merging from release1_p12: +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). +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 +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 + +checkpoint48e_post +o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) +o dynamics: change definition of computational domain & adapt mom_fluxform + accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. +o following exp works with Olx=Oly=2 (and pass through checkbounds option): + adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 + exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 + global_ocean.90x40x15 global_with_exf global_ocean_pressure + inverted_barometer solid-body.cs-32x32x1 + (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) + +checkpoint48d_post +o in preparation for r*: + a) use pre-computed gradient of hydrostatic potential: + changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce + b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: + => 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.