--- MITgcm/doc/tag-index 2002/02/10 20:07:14 1.60 +++ MITgcm/doc/tag-index 2005/02/09 23:45:41 1.449 @@ -1,8 +1,1855 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.60 2002/02/10 20:07:14 jmc Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.449 2005/02/09 23:45:41 jmc Exp $ Notes on tags used in MITgcmUV ============================== +o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up +o make genmake2 more portable by using ".$FS" instead of ".f" for more + of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) +o add coordinate variables to the MNC output from the diagnostics package +o change MNC-flags default value: true when useMNC=TRUE +o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F + the ability (off by default) to read the grid information using MNC +o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt +o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging +o do snap-shot diagnostics at the middle of the time-interval (instead of + at the end). +o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add + new test for AIM with thSIce + slab-ocean +o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) +o move state variable diagnostics to the beginning of the time step ; + (note: still needs some work specially for snap-shot diagnostics) + duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z + +checkpoint57c_post +o Change testing option (-ieee) to get closer agreement between g77 & ifort +o generate new output.txt files on faulks with g77 & the new -ieee option +checkpoint57c_pre + +o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); + update output.txt of exp. global_ocean.90x40x15 +o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer + results; update global_ocean_pressure & global_ocean.cs32x15 output.txt +o add saltFlux(+File) forcing capability with periodicExternalForcing +o allow to use pkg diagnostics for GM-Redi & ThSIce output +o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. +o improvements for the MNC output from DIAGNOSTICS: + - correct handling of the unlimitied dimension + - all dims now have associated coordinate variables + - variables located at U, V, and Corner ("Z") points are now written + with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that + *all* data points are output +o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice +o added pkg/seaice/seaice_monitor.F +o mdsio_readfield.F can now read files visible only to master MPI process. +o pkg/seaice: some test code for ice-modified ocean stress +o exf_getffields interpolation defaults to bilinear for all scalar forcing + fields (remains bicubic for wind velocity and stress). This avoids, e.g., + spurious negative numbers for precipitation and humidity. Will cause + some small numerical differences for integrations using pkg/exf/exf_interp.F. +o pkg/ctrl/ + * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O + May be enabled via doPackDiag + * introduce z-scaling of + + gradient (doZscalePack) and + + control (doZscaleUnpack) +o pkg/mdsio/ + * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F + * N.B.: leave tiled I/O for tapelev (i.e. mds...vector) + +checkpoint57b_post +o simplify options in diagnostics_fill arguments (remove weird combinations) +o fix MNC coordinate variables so that they now contain per-face index + values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in + general, EXCH2 grids are only aligned to a "local" coordinate system +o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) +o Implement instantaneous output within pkg diagnostics: + setting a negative frequency in data.diagnostics produces + "snap-shot" output (as opposed to time-average if freq > 0) +o move out off EQUIVALENCE all diagnostics that fizhi does not use ; + NOTE: change ptracer diagnostics name: use 2 characters to work with + more than 9 tracers. Add also diagnostics of advect & diffus flux. +o more CF compliance: convert all MNC 'iter' variables to 'T' so that it + becomes the coordinate variable for the 'T' dimension +o add CF-style coordinate variables to MNC + - just a first cut: numbers are meaningless on the cubesphere and + missing along the T axis but otherwise it works! +o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX +o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. +o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) + this is based directly on what the model compute, so that the content of + each diagnostics might be affected by switching options (e.g., implicitDiffusion) +o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) +o clean up build options files for SunOS, in particular + - remove -traditional from xmakedepend + - change -xarch=v9 to -xarch=native for f77 + - restore use of make (not gmake) + - add CC=gcc if using g77 +o changes per discussion of AM, JMC, & EH3 today: + - move redundant "grid" variables out of "state" -- in preparation of + creating proper CF-style coordinate variables and in recognition + that any/all grid variables can be easily copied (eg. w/NCO) from + the grid files into any of the other NetCDF files + - *always* output grid variables with MDSIO (this will eventually be + changed) + - output MNC grid file if useMNC is true +o every instance of _END_MASTER() has been found and replaced with + _END_MASTER( myThid ) in order to satisfy certain picky Sun + preprocessors +o re-arrange diagnostics pkg initialisation: + - allow each package to extend the available diagnostics list + - add some checking and fix small problems (multi-threaded, ...) + - new S/R diagnostics_fill (replace fill_diagnostics): + look through the short list of active diag. (instead of the long list) + create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active + +checkpoint57a_post +o this set of changes restores TAMC compatibility + tested for global_ocean.90x40x15 adjoint on trough + (what a pain) + +checkpoint57a_pre +o some modifs in tools/build_options for sunos +o call ctrl_pack for ctrl at end for optimcycle=0 + +checkpoint57 +o add horizontal bi-harmonic viscosity for vertical velocity + - new parameter viscA4W (defaults to viscA4) + - affects only non-hydrostatic code + - to be done: no-slip lateral boundary conditions +o switch back to "sflux = sflux - runoff" in exf_getforcing.F +o implement Implicit Vertical advection for pTracers +o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) + (implemented also for implicit vertical diffusion & advection) +o OBCS: extend application of tracer open boundary conditions + to a strip beyond the boundary of width Olx/Oly +o add call monitor to TAF set of required calls (flow directives) + and include in natl_box_adjoint +o untangle a few ifdefs related to cost, ctrl, autodiff + untangel a few ALLOW_ECCO_OPTIMIZATION +o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) + (theta2, salt2 in ecco_cost_weights) + +checkpoint56c_post +o OBCS as control variables + - update ctrl_ad_diff.list, obcs_ad_diff.list + - remove balance of obcs controls from default + - fix index bug nobcs in ctrl_init + - fix dummy fields filen in ctrl_pack + - add dummy weights for obcs +o lsopt: comment out fort.94 output +o optim: + - remove unnecessary header files + - adjusted namelists + - add xerbla.F to Makefile +o exf: + - multiple modifications of exf_check_range + - unit change in exf_init_runoff from [m/year] to [m/s] +o mdsio: + - i/o-vector change debugLevel from debLevA to debLevB + +checkpoint56b_post +o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that + is called from DO_THE_MODEL_IO + - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE + - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) + - clean up PTRACERS_WRITE_TIMEAVE a little +o add another verification experiment that tests both the cfc-pkg and + the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with + reactive tendencies treated inline with regular timestepping +o testreport previously did a lousy job of comparing small numbers, so + we (Ed and Martin) changed the way the cut-off of 1.e-12 is + implemented in the little c-progam tmp_cmpnum.c which is embedded in + testreport. +o ptracers_monitor: bug fix for MPI + +checkpoint56a_post +o GCHEM: finish reorganizating the package + - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency + (introduces another 3D-array for each passive tracer, but only if + GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING + gchemTendency is not needed because the timestep is done separately) + - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY + - GCHEM is now---more or less cleanly---separate from PTRACERS + - to bo done: handling of surfaceForcingPtr that is needed for KPP not + so clear to me how that should be done in a general way. +o CFC: improve formatting of output in CFC_ATMOS +o PTRACERS: + - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so + that ALL experiments with ptracers enable can be checked. This makes + GCHEM_MONITOR obsolete. + - include a runtime parameter PTRACERS_monitorFreq that defaults to + monitorFreq + - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true +o add PTRACERS (PTR0[1-5]) to testreport output +o exf_check_range: + * default changed to .TRUE. + * will check values for niter0 if debLevA, every timestep if debLevB + * STOP in exf_check_range if 'out of range' + * range chosen generous to allow for potential extema + TBD: a version with stricter range + permitted range would be runtime parameters +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. + - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; + this flag is now only visible within GCHEM-pkg routines. + - moved gchem_forcing_int temporarily into ptracers_forcing, this will + be replaced by a 3D array that is computed before thermodynamics; for + this, the tracer ID iTracer had to be included into the parameter list + of ptracers_forcing + - set up forward_step to call gchem_forcing, that will replace + gchem_forcing_int in ptracers_forcing + - cleaning up +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 +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