--- MITgcm/doc/tag-index 2002/11/15 04:07:00 1.104 +++ MITgcm/doc/tag-index 2004/11/21 22:22:31 1.390 @@ -1,8 +1,1297 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.104 2002/11/15 04:07:00 heimbach Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.390 2004/11/21 22:22:31 jmc Exp $ Notes on tags used in MITgcmUV ============================== +o GMredi: + - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; + - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. + - change the default GMREDI_OPTIONS.h: compile everything except Visbeck +o GCHEM: + - move call to GCHEM_FORCING_SEP, so that it is now called before + the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP + - introduced a useGCHEM runtime flag and applied it everywhere. +o small cleaning of exch2: remove files that are also in eesupp/src + +checkpoint56 +o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 +o mnc: cleanup "full" files--fixes out-of-memory problem +o ECCO-GODAE + * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup + * fully merged and updated from SIO code + windstress sign change affects + - exf_inscal_[u/v]stress + - sign of xx_tau[u/v] adjustments + - signs in cost_scat + * ctrl_get_gen: avoid update of tau[u/v] for first few days + * natl_box_adjoint updated and compressed + * 2-level checkpoint switch added + (tested in EXP. 1 of natl_box_adjoint) + * new switch doInitXX to avoid init. of xx_... in optimcycle=0 +o SVD + * first complete, non-hacked version for SVD calculations + * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... + performed via direct access files admtlm_vector.it???? + (via ctrl_[un]pack) + * optimcycle is used for ARPACK iteration counter + (note: adxx_... is iterated, rather than xx_...; latter is constant!) + * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms + and add linear transforms where necessary + * controls are initial/final SST, SSS (can be extended; need to check + ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F +o mdsio: filename info to both stderr, stdout +o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] + from sign change + +checkpoint55j_post +o isolate dissipation tendency (allow to keep it out off AB) in V.I form. + affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) +o add consistent build directories and .cvsignore files to verification +o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity +o make all subroutines 30 or less characters in length for certain older + compilers to work (a thorough search only turns up two routines in + pkg/ptracers) +o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; + affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) + +checkpoint55i_post +o change arrays for total vertical diffusivity (2.D if explicit, + 3.D if implicit) ; each ptracer uses its own background value. +o added mnc/NetCDF output capability to ocn_compon_interf + - added bits to verification/cpl_aim+ocn so that it can run on + ITRDA and other clusters without the mpirun "-wd" option +o fixed wayward endif in mom_fluxform.F that messed up cyclindrical + configuration +o give MNC the ability to create additional files rather than + exceeding a specified file size limit "MNC_MAX_FILESIZE" + - the default is just less than 2GB which is a practical limit + on many systems +o Compute the non-local term using either KPP vertical diffusivity (=default) + or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) + +checkpoint55h_post +o add verification test "vermix" +o remove all the *_ioinc flags and replace with the single global + outputTypesInclusive flag +o allow to set a vertical profile of vertical diffusivity for T & S +o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS +o useMNC moved from data.mnc to data.pkg + +checkpoint55g_post +o Renaming carbon AD experiments to comply with testreport conventions +o Updating adjoint of Held-Suarez hs94.1x64x5 +o Fixing directives for non-ECCO forward_step, after ECCO directives + have been fixed to avoid recomp. of do_oceanic_phys + Works well for global_ocean.90x40x15, + but recomp. issue remains for carbon +o Updating adjoint output for natl_box_adjoint after + pkg/ecco has been modified (see taga c55d_post) + +checkpoint55f_post +o rename to timeave_init_fixed + +checkpoint55e_post +o some delicate re-shuffle of store directives to avoid one + extra call of do_oceanic_physics + affects ecco_the_main_loop.F, do_oceanic_physics.F + checkpoint_lev1_directives.h +o NB: this may break global_ocean adjoint temporarily, + but it is clear how to fix it. Will do later, need this now. + +checkpoint55d_post +o ECCO specific cost function terms (up-to-date with 1x1 runs) +o ecco_cost_weights is modified to 1x1 runs +o modifs to allow observations to be read in as + single file or yearly files +o enable to read exf forcing fields as either + single file or yearly files (flag useExfYearlyFields) +checkpoint55d_pre + +o switch between 2-level and 3-level checkpointing +o add ability of MNC to write local and "partial" (eg. 2D slices where + the full 3D field is never actually stored) arrays to NetCDF files + with the correct (that is, the complete multi-dimensional) set of + array indicies + - used in mom_vecinv() to write the diagFreq output + - tested (demonstrated) in verification/aim.5l_cs +o further mnc-ification + - add verification/lab_sea to the list with mnc setups + - fix undefined mnc v-names in cd_code + - add kpp to mnc output (both snapshot and timeave) +o non-hydrostatic code + - added horizontal viscosity parameter viscAhW for w, that replaces viscAh + in calc_gw.F + - defaults to viscAh + - this is useful, when I want to use viscAh=0 (e.g., only biharmonic + friction or Leith) in non-hydrostatic mode, as long as there is + no biharmonic friction and/or Leigth or equivalent for vertical velocity. +o pkg/cost + extend simple cost functions to treat time mean quantities + (T,U,V) via cost_accumulate_state from cost_tile +o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to + be 2 times larger than the minimum size the advection scheme requires. + now get a perfect conservation of salt in advect_cs test-exp (updated) +o GGL90 (Gaspar's TKE mixed layer) + - add horizontal diffusion of TKE, requires exchanges in + do_fields_blocking_exchanges, horizontal diffusivity is zero by + default. In OPA there is no horizontal diffusion of TKE but the + mixing coefficients are computed from a horizontal average of TKE of + 6 points or so. I think that diffusion has a little more physical + justification. + - clean up ggl90_calc in the hope of reducing memory usage (this hope + was in vain) + - mask tke-variable in ggl90_init +o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) +o fix biharmonic diffusion on CS-grid. +o more obcs stuff + - added obcs_external_fields_load as an alternative to the EXF-pkg option + for reading boundary values. This routine is called from + obcs_prescribe_read + - updated obcs_check + - changed sponge layer relaxation parameter units for days to seconds + - turned off sponge layer by default + - changed argument list of OBCS_CALC to myTime+deltaTclock + - fixed about 35 bugs in obcs_external_fields_load + +checkpoint55c_post +o obcs stuff + - new runtime flags useOBCSprescribe, useOBCSbalance + - re-arranged obcs_calc + - moved exf_getobcs to obcs_prescibe_read + obcs_prescibe_read is called after ORLANSKI stuff + and independent of it (executable can contain all). + - updated obcs_check + - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. + These may be necessary only if tangential velocities are + prescribed at OB, not sure, needs testing. +o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments + which simplifies the calls and passes the ifc check-bounds test + +checkpoint55b_post +o add a 2D scalar, Z location, exchange_2 routine. +o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows + to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] + affects advect_cs results (for the wrong reason): update output.txt +o use a more standard discretization for biharmonic viscosity ; + (original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) + affects results of dome set-up: update output.txt +o fix gad_advection.F (CubedSphere part), back to version 1.23 +o fix bug in mom_vi_del2uv.F (CubedSphere part). + +checkpoint55a_post +o merged code to + * prescribe/read time-dependent open boundaries + (works in conjunction with exf, cal) + * sponge layer code for open boundaries + * each boundary N/S/E/W now has its own CPP option + (healthy for the adjoint) + +checkpoint55 +o up-to-date adjoint of previous breaks + - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix + - global_ocean_ebm: adjoint still needs fix (TLM ok) + - global_ocean.90x40x15: extended GMREDI_OPTIONS.h + - carbon: * remove tr1-related adjoint verification + * add ptracer as control variable +o remove all tr1-related code (ALLOW_PASSIVE_TRACER) + (adjoint stuff still has some tr1 'names', but all use ptracer arrays) + +checkpoint54f_post +o in verification/carbin/ remove experiment related to + ALLOW_PASSIVE_TRACER (array tr1 etc) + code_ad/ input_ad/ results_ad + +o add two new packages + - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) + + subject to optimization (memory) + - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) + + subject to reordering (many GOTOs in the original code) + + so far opps is called for every (i,j) point, and then operates in + the vertical; one may want to reorder the scheme in order operate in + horizontal slabs at the cost of (a lot of) memory, at least ten new 3D + fields) +o overhaul of IO so that we now have flags for MDSIO and/or MNC + - all verification tests compile and run with linux_ia32_g77 + - defaults are compatible with current input files--nothing + should change if you were not previously using MNC + - MNC output has been added in numerous places (eg. timeave) + but there are still a few writes not yet do-able with MNC + (this is in progress) + - flags now allow for either/or/both use of MDSIO and MNC and + documentation will soon follow + - numerous small formatting cleanups for ProTeX +o add version info (via BUILD_INFO.h) to MNC and stdout + +checkpoint54e_post +o add two new packages + - pp81 (Packanowski and Philander, 1981), Richardson number and + stratification dependent mixing + - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme + - these scheme operate in a similar manner as KPP (without ghat, of + course), however there is only one diffusivity that is used for both + temperature and salinity (and passive tracers)ç +o add offline package +o add "verification/dic_example" which contains a dic-gchem-ptracer setup + provided by Stephanie Dutkiewicz +o genmake2: add ability to search for C compilers and cleanup test output + - fixes recent SX-6 problems and should help with others (eg. HP-UX) + +checkpoint54d_post +o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed +o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, + leading to additional shift by 5 days each year of integration + (i.e. leading to considerable offset over the years) +o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep +o start with no AB and no initial filtering (staggerTimeStep): + change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 +o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F + (external loading & cpl import/export stay in forward_step.F) +o update coupling interface to work with new staggerTimeStep +o change MDSIO ptracers_pickup. +o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); +o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") +o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) + +checkpoint54c_post +o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr + this affects (truncation error) output.txt of test-exp: + global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box +o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) +o change Qnet to always be the net heat flux, (+upward). + affects (truncation error) output of natl_box exp.: updated +o define the max number of passive tracers in PTRACERS_SIZE.h +o start to test mnc routinely in exp0 +o add sea-ice loading (sIceLoad) as a new forcing field. + +checkpoint54b_post +o add testreport "-j JOBS" option for parallel builds (tested and pretty + impressive on Altix and Opteron systems) +o diagnostics can now write NetCDF files through the mnc package +o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output +o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added +o staggerTimeStep & NLFS: rescale T & S surface tendencies. + affects (truncation error) output of lab_sea & natl_box exp.: updated +o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) + +checkpoint54a_post +o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). +o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) +o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) +o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) + + internal_wave (shift in writing cg2d_ini_res) +checkpoint54a_pre + +o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice + - modified verification/lab_sea and natl_box_adjoint accordingly + +checkpoint54 +checkpoint53g_post +o prepare splitting of thermodynamics: store convect.counter in common block +o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) + output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave +o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection +o new parameter "nShapS": allow to treat differently S from T (nShapT) +o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) +o restore adjointability + +checkpoint53f_post +o modifications that affect AIM experiment results (update output.txt): + - no advection of S at top interface Nr (pkg/generic_advdiff) + - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) +o AIM pkg: + - include stability function into surf.Flux derivative relative to Tsurf + - calculate clear-sky radiation & surface temp. change (for diagnostics) + +checkpoint53e_post +o merged cylindrical coord configuration +o added rotating_tank experiment +checkpoint53e_pre + +checkpoint53d_post +o faulks upgraded: re-generate output.txt that have changed: + global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box +o Added Bryan and Lewis, 1979, vertical diffusivity profile +o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. +o added Sadourny discretization of Coriolis + - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h + - re-enabled use of omega3 (useAbsVorticity) +o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for + vector-invariant equations + - note: does *NOT* yet use same variable visc. for no-slip BC's. +o recoded the lateral boundary conditions for non-hydrostatic w, this time + hopefully without new bugs + - still to do: biharmonic friction for non-hydrostatic w +o bug fix for mom_*_sidedrag: rA -> rAs,rAw +o regenerated output for global_ocean_ebm (using -ieee) +o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation + of mom_common/ + - simple re-arrangement of instructions within computing loop +checkpoint53d_pre + +checkpoint53c_post +o new version of coupler for AIM+thSIce and Ocean models + - new fields (SSS,h_MixLayer ...) are exchanged through the coupler + - land: change Evaporation of snow + - aim with thSIce: fix bug in snow-precip. +o changes to calc_gw.F + - bug fix for w^2 term near the bottom boundary + - (hopefully) improve the lateral slip boundary condtions for use with + partial/looped cells + - because the bug fix changes two verification experiments anyway (exp5 + and plume on slope), change the lateral boundary condition from half slip + to the value of no_slip_sides +o ebm package wasnt quite up to the parallel task. Fixed that. +o Adjoint of EBM package + verification + * TLM OK + * ADM not sufficient accuracy yet (needs further testing) + +checkpoint53b_post +o Commiting new energy balance model to repository + * package is pkg/ebm + * verif. is verification/global_ocean_ebm + * references are in ebm_driver.F +C * X. Wang, P. Stone and J. Marotzke, 1999: +C Global thermohaline circulation. Part I: +C Sensitivity to atmospheric moisture transport. +C J. Climate 12(1), 71-82 +C * X. Wang, P. Stone and J. Marotzke, 1999: +C Global thermohaline circulation. Part II: +C Sensitivity with interactive transport. +C J. Climate 12(1), 83-91 +C * M. Nakamura, P. Stone and J. Marotzke, 1994: +C Destabilization of the thermohaline circulation +C by atmospheric eddy transports. +C J. Climate 7(12), 1870-1882 +o Will need long integration testing. +checkpoint53b_pre + +o created pkg/mom_common in preparation for variable viscosity code +o renamed and split ini_mnc_io +o pkg/land: only liquid water can diffuse or run-off +o AIM using land: soil wetness availability account for snow +o added printMapIncludesZeros to EEPARMS namelist + +checkpoint53a_post +o restore TAMC compatiility for exf_constants.h + (no usage of _d in .h) +o Additional storing in KPP in an attempt to fix + TAMC problem with adjoint of KPP code. + (no success...) + Identical code works fine with TAF. +o Fixed verification/natl_box_adjoint experiments. + Initial conditions for Experiments 4 and 5 are now + set to "SEAICE_initialHEFF=0", which is more reasonable, + and hence gives results closer to that of Experiment 2. + Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. + +checkpoint53 +o stable checkpoint with up to date adjoint + TLM tests only run for 1st grdchk at the moment. Its unclear if + this is a code problem or a problem with resetting code for g_ + variables that is being autogenerated wrong. + Otherwise: + o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. + o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) + are both still in chaos following their security messes. + +checkpoint52n_post +o various build (mostly genmake2) changes including: + - ability to build/run more easily within Cygwin and MacOS X + - more complicated Makefiles with a stronger dependence on Gnu Make +o pkg/seaice modifications + - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost + of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer + and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm + - changed proxy for geostrophic velocity and updated + verification/lab_sea/results/* accordingly + - removed ADI dynamic solver from pkg/seaice + - replaced all occurrences of 1/CSTICE or 1/CSUICE + they caused a segmentation fault under certain circumstances + - removed unused field WATR +o bug fix in exf-package: + - u/vwind are defined at tracer/pressure points. The values of u/vwindmask + now reflect that. +o small fixes in the cal-package: + - set reference date to first of January for the 'model'-calendar + - failing of cal_CheckDate in cal_FullDate now actually results in a + warning +o small modifications in exf-package to increase flexibility: + - change climtempfreeze from a constant to a runtime parameter that + is specified in data.exf_clim (default = -1.9) + - introduce runtime parameter windstressmax (default = 2.0) that is + specified in data.exf +o fix in pkg/thsice: + - update Evap (Tsf changes) to be consistent with Latent heat flux + - maintain snow precipitation unchanged (even if Tsf >=0). + both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice + +checkpoint52m_post +o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; + this does not change any of the results, because myIter=0 in swfrac always + lead to jwtype=2 (the default anyway), but the call makes little sense + as a default +o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated +o re-work pkg/thsice interface with ocean & bulk_force pkg to allow + atmospheric model (AIM) to use it ; add a "slab ocean" component. +o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) +o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice +o extending useSingleCpuIO option to work with new exch2 I/O format + - old-style, missing-tile I/O is still accessible by defining CPP + option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h +o monitor package can write to NetCDF files and/or STDOUT +o fix re-definition bug in MNC_GRID_INIT_ALL() +o doc/api_reference added + - a framework for building an API Reference Manual using all + the "protex" comments embedded in the code + - see pkg/generic_advdiff, pkg/mnc for examples +o MNC: + - make myThid the last argument for all subroutines + - new default for the grid files: NO halos + - add useMNC and other run-time flags + - separate per-file-group handling of the unlimited dimension + - early initialization of MNC w/ flags read at the eeboot stage + and lookup tables set in initialize_fixed + - write all MNC output to a freshly-created directory +o thermodynamics sea-ice (thsice) is now tested with testreport. +o test exp. advect_cs: use the standard cs32 grid ; update output. +o Added functionality to grdchk: + pick global i,j,k position (or nearest wet) where to perform check. + +checkpoint52l_post +o new land formulation: + a) use ground enthalpy as prognostic variable to ensure exact + energy conservation. + b) account for water temperature and for latent heat of freezing + in all processes (rain, run-off, ground storage) + c) compute surface and ground temperature implicitly. +o aim_v23 modification for new land model: + a) Treat separately land / ocean / sea-ice surface fluxes + to allow implicit computation of land & sea-ice surface temp. + b) add snow precipitation. +checkpoint52l_pre + +o fix problem (when 1 tile is empty) in min/max monitor. +o fix bug in timeAve (u,vZetatave in common block) +o no restoring terms under ice for pkg/seaice +o moved SEAICE_DO_DIAGS to S/R do_the_model_io +o bug fix for pkg/seaice pickups +o change MNC call locations and add coordinate attributes +o mask vorticity at the corner ; affects global_ocean.cs output +o fix ini_curvilinear_grid ; test CS experiments with mpi +o aim.5l_cs: modify sea-ice fraction input file ; update output +o exf: Adding simple range check routine for exf fields after read + +checkpoint52k_post +o removed top-level directory "diags" + - we migrated these functions to pkg/timeave a long time ago +o fixed bug introduced in pkg/monitor +o accuracy ctrlprec = 32 insuffient for gradient checks using + averaged fields (I/O via cost_averages) + -> use ctrl.h in active_file*.F to control I/O precision. +o paramter list of CALL ADTHE_MAIN_LOOP +o added initial do_the_model_io to ecco +o set all ...Freq to zero after cost_final + taveFreq, dumpFreq, pChkptFreq +o MAIN and ECCO differentiability restored + +checkpoint52j_post +o fix nchklev in tamc.h for global_ocean... +o Bringing flow and store directives up-to-date +o Really weird thing! + call do_the_model_io from the_main_loop with parameters + starttime, niter0, instead of mytime, myiter, screws up the adjoint: + TAF places a faulty re-call of initialise_varia + after cost_final call which should not be there! +checkpoint52j_pre + +o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and + error messages +o fix errorMessageUnit problem. remove old version of mdsio from eesup/src +o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating + debug output +o modfied mdsio_writefield.F to handle non-global files under exch2 +o update AIM Cubed-Sphere exp (aim.5l_cs): + use land, p*, and Franco.M forcing fields with fractional land-sea mask. +o update AIM Equatorial Channel exp: + use standard aim_v23 pkg and change the SST fields to be more realistic. +o globalFile now works with exch2 +o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and + mon_vort3.F to make exch2 friendly with >1 tile per cube face +o limit timeave output for hi-res integrations + +checkpoint52i_post +o removed CPP_EEOPTIONS.h from verification/*/code +o updated the tiling for global_ocean_pressure +checkpoint52i_pre + +o update aim.5l_LatLon using the standard aim_v23 pkg (instead of + the old pkg/aim). + +checkpoint52h_pre +o shortened offending lines in exch2_send_rx?.template +o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator +o genmake2: add build & execute test for NetCDF code +o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed + old grid files, moved CPP_EEMACROS.h to pkg/exch2 +o added useSingleCPUIO flag to monitor.F and mon_out.F +o added temporary hack for sea-ice dynamics on the cube: + metric terms are ignored and it is assumed that + there is no sea-ice on cube faces 1, 2, 4, and 5. + +checkpoint52f_post +o added exch2 cube routines to pkg/exch2 +o modified hs94.cs-32x32x5 to use it +o added new grid files to hs94.cs-32x32x5 +checkpoint52f_pre + +checkpoint52e_post +o first attempt to solve vertical advection (momemtum & T,S) Implicitly + for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) +o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) + to work with implicit vertical advection and AB ; +o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. +o update output (gad_calc_rhs.F changes affect truncation error) of exp: + front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box +checkpoint52e_pre + +o fix bug in impldiff when Nr=1 or Nr=2. +o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt +o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. +o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 + ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure +o added exf_offset_atemp for Celsius to Kelvin conversion of atemp +o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 +o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations + +checkpoint52d_post +o re-tiled many expts to allow comparison in multi-processor mode + - updated output accordingly + - changed hs94.128x64x5 to use intial T from file rather than use the + random number generator +o add infrastructure in model routines for fizhi and gridalt packages +o change global_ocean.cs32x15 because of Pb with GM on CS-grid. +o changes to permit hi-res, cubed-sphere, configuration + - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F + - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F + - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation + of surface winds for the cube + (A verification experiment, based on global_ocean.cs32x15, but with + pkg/seaice turned on and with on-the-fly interpolation from the NCEP + Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, + complete with example surface forcing files and matlab scripts to look + at the output and compare it with that of global_ocean.cs32x15.) +o packages pickup: $PKG_write_pickup called from packages_write_pickup ; + but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code + to conform to the common rule. +o check-in the first version of the coupler + interfaces for multi-components + set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. + - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). + - atmosphere: use pkg aim_v23 ; no sea-ice for now. + - ocean and atmos. share the same horizontal grid (no interpolation). + - exchanges between component and coupler is done in forward_step +o new verification experiment, cpl_aim+ocn: + coupled ocean - AIM atmosphere on cs32 grid. + +checkpoint52d_pre +o surface flux time-av diagnostic modified for NLFS & RealFreshWater +o add call to AIM pendant S/R in external_forcing & external_fields_load.F + +checkpoint52c_post +o Fixing OPTIONS files for use of exf: + - ALLOW_ECCO not needed + - ECCO_CPPOPTIONS.h should not be included from + EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h + as has been the case in the past + - All cal/exf related options are currently set in + single header file. Should remain so until we + agree on a consistent new policy. +o Removed all CPP options for cal package. + cal has no more CPP options. +o modified STOREs in GAD_ADVECTION +o corrected key comp. for passkey + +checkpoint52b_post +o new version: "thsice" of thermodynamic sea-ice pkg: + - only 1 call from "forward_step"; conserve energy, fresh-water & salt. + - modify fluxes but do not change theta directly; + - light cleaning of bulk_force pkg (still needed with thsice). + - add forcing fields + data files in global_ocean.cs32x15/inp_thsice + + output_thsice.txt to test thsice & bulk_force pkgs. +o put back grid & coriolis monitor output. +checkpoint52b_pre + +o call "do_the_model_io" at the beginning (=> dump initial state) +o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) +o sort out interplay between tamc.h and PTRACERS_OPTIONS.h + (need info on NUMBER_OF_PTRACERS) +o missing PTRACERS headers in some routines +o default tamc.h in pkg/autodiff supposed to crash + to ensure proper customization + +checkpoint52a_post +o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp + - moved surfaceTendencyTice from pkg/seaice to main code + - subroutine FREEZE_SURFACE now limits only surface temperature + and is called in FORWARD_STEP (if allowFreezing=.TRUE.) + => new output.txt for global_ocean.cs32x15 & global_with_exf + - keep the old version of FREEZE for backward compatibility; + global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. + - corresponding modifs for TAF directives +o added surface flux output variables to TIMEAVE_STATVARS +o time-averaged output for pkg/ptracers +o fix problem with ECCO-related divided adjoint + snapshot file was missing some ad-variables, + but no warning issued by TAF + +checkpoint52a_pre +o some bug fixes for #undef REAL4_IS_SLOW + +checkpoint52 = ecco_c52_e35 +o after testing adjoints of checkpoint51u_post + +checkpoint51u_post +o this is the post-merge tag of the ecco-branch + (needs another clean checkout and re-testing) +o various natl_box_adjoint configs and results + but no input fields +o obcs adjoint not yet merged! +o adding ECCO global 1x1 and 2x2 degree configs +o updated/extended some store directives for seaice +o pkg/ecco now containes ecco-specific part of cost function +o top level routines the_main_loop, forward_step + supersede those in model/src/ + previous input data.cost now in data.ecco + (new namelist ecco_cost_nml) +o in ctrl/ cleaned some cross-dependencies and updated CPP options + +checkpoint51t_post +o this is the pre-merge tag of the ecco-branch + +checkpoint51s_post +o cleanup: removed various obsolete #define-s +o pkg/grdchk + - renamed 'ph-grd 3' to 'grad-res' + - merged from ecco-branch + (remaining bug fixes for obcs gradient checks) + - additional high-precision output for testreport + (grep for 'precision_grdchk_result') + +checkpoint51r_post +o cleaned up or removed CPP_OPTIONS.h files +o updated results for some of the tests to reflect the new + optfiles (-ieee: -O0 instead of -O3) + +checkpoint51q_post +o cd_code: + - moved cd_scheme.F -> cd_code_scheme.F + - separate read_checkpoint from cd_code_ini_vars.F + - separated cd_code part from write_checkpoint + - updated AD_SOURCE, generated .flow + - added CD_CODE_VARS.h to the_main_loop + - Moving cd_code specific store dir.s to pkg/cd_code +o ctrl package totally restructured + - pack/unpack now optional and decoupled from + xx_/adxx_ I/O + - ctrl_pack/unpack cleaned + (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) + - confined inclusion of AD_CONFIG.h to where necessary. +o genmake2: changed AD dependencies from SRCFILES to AD_FILES + +checkpoint51p_post +o create initial cd_code package + - WARNING: the initialization of fields within packages + is broken because INI_FIELDS (where READ_CHECKPOINT is + called) is called *before* PACKAGES_INIT_VARIABLES. + This seems to be backwards since + 1) its important to initially zero the entire field including + the "halo" region + 2) zeroing needs to be done *before* reading pickup info + and the pickup call might or might not happen in any + particular run + - this needs an overhaul for R2 +o cleanup verification/*/code/GMREDI_OPTIONS.h +o cleanup testreport + +checkpoint51o_post +o bringing AD-related verif's up to date with genmake2 + - carbon/ + - global_ocean.90x40x15/ + - hs.94.1x64x5/ + - (front_relax/ ) +o (more) consistent directory structure for AD-related verif.'s +o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK +o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF +o bug fix in find_alpha.F for MDJWF: + - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for + change rho -> rho-rhoConst + - replace call find_rho to find_rhonum +o initialisation of rFlx extended to full array (required by TAF) + and shifted to thermodynamics +o removed PTRACERS.h in ptracers routine +o added surfacetendencyPtr to S/R parameter list pracers_forcing +o Correcting initialisations for fVerU, fVerV. +o helping TAF to recognize dependency on kUp for + fVerU, fVerV +o Replacing delZ by delR in pkg/ctrl/ +checkpoint51o_pre + +o undid all of cp51 pending some cleanups and discussion +o added the [#include "AD_CONFIG.h"] statement to all files that need + it for adjoint/tl #defines + o re-worked the build logic in genmake2 to support AD_CONFIG.h + o removed tools/genmake since it no longer works + +checkpoint51n_post +o modifications to make FREEZE flux visible to pkg/kpp + - moved surfaceTendencyTice from pkg/seaice to main code + - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP + - subroutine FREEZE now limits only surface temperature + (this means new output.txt for global_ocean.90x40x15, + global_ocean.cs32x15, and global_with_exf) +o added surface flux output variables to TIMEAVE_STATVARS + +checkpoint51n_pre +o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F +o added [#include "AD_CONFIG.h"] to all files that use the following + defines: + - ALLOW_ADJOINT_RUN + - ALLOW_TANGENTLINEAR_RUN + - ALLOW_ECCO_OPTIMIZATION + +checkpoint51m_post +o incorporating changes to get TAMC/TAF working in genmake2 + - added new TAMC/TAF targets to the Makefile + - various cleanups related to package handling + - these changes should have no impact on the forward model + +checkpoint51l_post +o changes to pkg/cal and pkg/exf that allow and speed-up long integrations + - faster algorithm for cal_addtime.F + - higher precision arithmetic, where needed + - pkg/exf *startdate variables changed from calendar date to + model integration time + +checkpoint51l_pre +o add salt flux to forcing fields (used when salty sea-ice forms or melts) +o enable to apply restoring on S & T only in a latitude band. +o update output (external_forcing_surf modif. change truncation errors) + global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box + +checkpoint51k_post +o change default to: useNHMTerms=.FALSE. + - new output.txt for atmos. exp (NHMTerms were wrong but now turned off): + adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 + - new output.txt for idealized oceanic exp (NHMTerms are now turned off): + exp1, ideal_2D_oce + - change data file of oceanic exp (leave the results unchanged for now) + exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box +o set gravitySign automatically according to the vertical coordinate used + (and change sign: back to "logical" value: +1 when R increases downward) +o added an include barrier to the default CPP_OPTIONS.h and + removed the #include "PACKAGES_CONFIG.h" from it +o fix a bug in mom_fluxform (from chk51j_post) + +checkpoint51j_post +o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ +o adjusted some flow directives (dynamics, thermodynamics) +o added cubed-sphere case to test cost function +o heckpoint_lev?_directives.h now include + pkg-specific directives, whenever those are enabled. +o Moving pkg-specific flow directives to corresponding pkg + Moving pkg-specific differentiation list to corresponding pkg + Moving pkg-specific checkpoint-lev storing to corresponding pkg + ---> conventions are + - pkg_ad.flow + - pkg_ad_diff.list + - pkg_ad_check_lev?_dir.h + +checkpoint51i_post +o merge of the branch-genmake2 + - knowingly breaks the older genmake + - automatic generation of all ALLOW_${PKG_NAME} defines + - new testreport supersedes older testscript +o large number of package inclusion and header cleanups +checkpoint51i_pre + +o new output for adjoin of global ocean vector invariant +o fix for checkpoint of thermodynamic seaice and bulk_force +o Steph gchem various cleanups + +checkpoint 51h_pre +o fixed some single quotes +o modify gchem pkg to be more versatile +o modifications to clean up dic pkg +o add pkg/cfc + +checkpoint51g_post +o provide links for ARPACK and ADM*TLM +o start removing verification/vero/ +o update AD-related stuff + (in particular some IF-statements in model/src/ routines) +o adding to verification/global_ocean.90x40x15/ adjoint of + vector invariant setup + +checkpoint51f_post +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