--- MITgcm/doc/tag-index 2006/06/19 01:06:57 1.682 +++ MITgcm/doc/tag-index 2007/07/25 21:23:29 1.853 @@ -1,9 +1,562 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.682 2006/06/19 01:06:57 jmc Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.853 2007/07/25 21:23:29 jmc Exp $ $Name: $ Notes on tags used in MITgcmUV ============================== +o exch2: new S/R that only use the cube-tracer (center-position) exchange: + for B-grid vector (not yet tested) and C-grid vector (<- only used + when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). +o starting implementation of Duffy et al. (GRL 1999) salt plume scheme + (#ifdef ALLOW_SALT_PLUME) +o gather_2d/scatter_2d: removed halo regions +o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 + scheme and the corresponding test case (under front_relax dir). For now, + only available with Skew-flux form and not yet tested in realistic set-up. + adjoint: store directives updated, but gradient checks deteriorated, + so maybe GM/Redi adjoint is now broken. +o seaice adjoint + * add AREA, HEFF, HSNOW as control variable + (should not change lab_sea results) + * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 +o pkg/seaice: + * added computation of saltFlux in seaice_growth; + For time being, sea ice salinity is assumed constant + contribution of snow flooding to freshening of sea ice is neglected. + SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it + defaults to 0.0 in order to maintain backward compatibility. + Typical values for SEAICE_salinity are 4 to 10 g/kg. + * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F + * added SEAICE_availHeatFrac, which specifies fraction of surface level + heat content used to melt or grow ice + * commented out cap of HICE: it helps keep ice thinner + * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option + * applied OBCS T/S mask to HEFFM sea ice mask + +checkpoint59d +o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array + for {PKG} state variables, and called from DO_STATEVARS_DIAGS. + (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) +o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" + and change default value of parameter "GM_Small_Number"; + update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, + global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, + tutorial_global_oce_biogeo, tutorial_global_oce_latlon +o pkg/ecco: cost function when applying pkg/smooth to controls +o pkg/ctrl: add forcingPrecond run time parameter +o pkg/seaice: + - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code + - fix bug in metric terms of u-equation in LSR solver (implicit part), + changes verification/lab_sea + - rearrange implicit part of u-equation in LSR solver to make it easier to + read, understand, and debug. This causes changes at the truncation level. + - fix (serious) bug in the boundary conditions (sign error in the implicit + part) of the LSR solver. Changes all LSR results. + - fixed problem with HSNOW initialization to avoid thick snow when AREA + is initilized with small values - does not change lab_sea results. + - added HsnowFile initialization capability +o pkg/smooth: addition to model/src and pkg/ctrl so allow + initialization of pkg/smooth and application to control vector +o pkg/seaice: fix another bug in the LSR no-slip boundary conditons +o dependencies: pkg/profiles requires pkg/cal +o pkg/profiles: + - added option ALLOW_PROFILES_GENERICGRID + -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming + that interpolation information (grid points and coefficients) is provided + within the netcdf input files. + -> sample matlab scripts can be found in MITgcm_contrib/gael + that allow you to prepare netcdf input files. + - also modified: cleaner include statements, cleaner error print statements, + cleaner stops when error, and more tests of the netcdf input files consistency. +o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. +o pkg/seaice: + - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this + requires a new routine: seaice_diagnostics_fill.F + - make sure that seaice does not move if not forced (pressure replacement + method, Hibler and Ip, 1995), changes results + - and new damping criterion for EVP solver according to Hunke, JCP, 2001 + - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). + It is turned off by default (=-1.), because it changes the results. + - make it possible to read AREA from a file, too. + +checkpoint59c +o add S/R and diagnostics for oceanic mixed-layer depth +o move GMRedi call after all vertical mixing schemes (including KPP) +o pkg/thsice: + - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs + (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice +o pkg/obcs: + - bug fix for balance code +o pkg/seaice: + - allow values of SEAICE_elasticParm > 1 + - add new parameter SEAICE_evpTauRelax as an alternative + to SEAICE_elasticParm + - make lsr boundary conditions free slip (by default), changes result + - add code for no slip boundary conditions for lsr + - set minimum of zeta to zero (and not 4e8) (changes results) + - add a cap on AREA after advecting AREA if seaice_growth is not called +o change calculation of Visbeck K: + - no longer depend on tapering scheme; instead, compute slope (limited + by GM_maxSlope). this is equivalent to what was comuted before with + clipping or linear tappering. + - fix vertical averaging (wrong by 1/2 level) + - leave the old version (but will not be maintained) within + #ifdef OLD_VISBECK_CALC / #endif + - update output of exp. ideal_2D_oce +o change error catch in calc_r_star to improve vectorization +o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and + add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). +o adjoint: + Re-organized adjoint checkpointing according to Matt Mazloff + (but with modifs/completions/cleanups) + Storing is now bundled into large arrays to optimized I/O + (and second step in cleanup of the_main_loop) + +checkpoint59b +o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): + - export/import (between ocean & coupler) fields needed for ocean DIC. +o pkg/seaice: + - get rid of three more exchanges seaice_calc_viscosities (required + different loop boundaries in seaice_lsr and seaice_ocean_stress) + - bug fix in seaice_ocean_stress (update of lab_sea required) + - reduce loop boundaries to necessary minimum also in seaice_evp + - go back to the old way of computing deltaC/Z as the adjoint likes that + better +o Refresh of tutorial_global_oce_latlon (includes changing salinity-like + passive tracer to an Age Tracer) + update output.txt +o pkg/exf: + - implement A-grid / C-grid selection for wind-stress input files. + - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) + for now, in exf_bulk_largeyeager04.F only : + - change implementation for case where windspeed + 2. components wind-stress + are read-in. AND use rhoConstFresh to convert evap. +o pkg/seaice: + - use correct EXCH_UV for wind-forcing (on A-grid). + - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding + SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops. +o pkg/exf: + - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC) + EXF_INTERPOLATION: + - merge global_with_exf/code version of exf_interp_read.F + to the main code ; + - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when + reading the file ; Important: This options needs to be defined to recover + previous code. + otherwise, use fixed size array to read in (size=exf_interp_bufferSize). + - no longer loose real*8 precision along the way when using exf_iprec=64. +o pkg/seaice: rearrangement of common blocks (really needs more cleaning up) + - change discretisation of evp-solver in order to avoid another exchange + (changes lab_sea) and clean up a little + - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS) + help the adjoint (this also changes the results slightly) + - add a few "_d 0" where they had been missing in seaice_evp.F + - cleaning up: remove unused seaice_calc_rhs.F +o pkg/exf: some cleaning-up: + - change various "constants" into runtime parameters + - cleaned-up Large&Yeager04 routine which should eventually + replace exf_bulkformulae.F (changed names of S/R and CPP) + and merged various ALLOW_ATM_WIND options + only used with thsice pkg (in thsice_get_exf.F): + - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04) + which are used when useStabilityFct_overIce=TRUE (= the default) + - change default values of ice & snow emissivity and scale downward LW + by ice & snow emissivity. +o pkg/thsice: + fix few little problems, in thsice_calc_thickn.F: + - growth vertically (and not laterally) if iceFrac == iceMaskMax + - melt only laterally if hIce < hThinIce (as the comments say) + and in thsice_extend.F: + - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) + - start to form ice as soon as the minimum ice-volume is reachable. + update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice), + and cpl_aim+ocn +o pkg/kpp + - move computation of surface related input fields to KPP into a new + subroutine kpp_forcing_surf.F + - remove wrong (within bi,bj loops) EXCH calls. + - little cleaning (add argument myThid in last position, cvs header ...) + - for now, fix conservation problem by exchanging KPPviscAz (may not + be the best fix) +o pkg/seaice + - check for inconsistent evp parameter/cpp-flag combination + - remove leftover errIO flat for obsolete name list error handling +o OpenAD + - changed verification/OpenAD to full baroclinic setup (including GM/Redi) + +checkpoint59a +o pkg/seaice: some parameter clarifications and a little bit of clean up +o pkg/thsice: rename run-time parameters: + himin -> hIceMin + himin0 -> hThinIce + hihig -> hThickIce + i0 -> i0swFrac + transCoef -> bMeltCoef + frac_energy -> fracMelting + add new parameters: hNewIceMax, fracFreezing, dhSnowLin + with default values (for now) that do not change the results. + remove old version of thsice vars advection in pkg/seaice. +o in FFIELDS.h: + - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD + - make pLoad & sIceLoad always available (but still only used if + ATMOSPHERIC_LOADING is #define). +o pkg/kpp: replaced _KPP_RL with _RL +o bug fixes for vertical diffusivity computations when both KPP and + 3D diffusivity arrays are used. +o pkg/seaice: fix bug in evp solver, while doing that + - change (improve?) discretization of stress computations for both + cgrid-lsr and evp solver + - add a new routine to compute strain rates + - the above changes lab_sea results + - add no slip conditions for evp solver (off by default), lsr-version + may follow + - fix exchange for shear at Z-points (does not change lab_sea) + - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp + (to force the user to pick a time step since there is not "safe" way + of choosing it) + - add principal stress diagnostics + - rearrange fields for evp a little to avoid having to call a: too many + exchanges and b: exchanges for stress trensor components which we do + not have. + - modify Hibler+Bryan (1987) stress coupling so that it reuses information + of evp, complete rewrite for lsr case (latter is does not yet work + in all cases) +o pkg/kpp: add code to have mixing in shelf ice caverns + - add myThid to all kpp routines (long overdue) + +checkpoint59 +o pkg/exf: + - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND & + ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid + - move exf header files from lower_case.h to UPPER_CASE.h ; + add missing cvs Header & Name + - add adjoint routines and flow dirs for newly used exch_uv_agrid routines + - add namelist param. selectStressGridPosition, exf_monFreq + - retire many _CLIM routines, and remove data.exf_clim + + params moved to data.exf + + climsst, climsss now handled by exf_set_gen, i.e. + climss?period=0 refers to constant field, + climss?period=-12 to monthly forcing + - split up namelists in data.exf +o pkg/seaice: + - remove seaice_exch and seaice_exch_uv + - remove superfluous exchange of theta + - add myThid to seaice_budget_ocean/ice + - add new interface for atmospheric wind forcing (C-grid only) + + new routine + + two new field (taux, tauy for stress over ice) + + removed one global field (DAIRN) for C-grid case only +o pkg/thsise + - 2nd set of modifs for thsice adjoint in conjunction with exf +o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.) + +checkpoint58y_post +o Added capability for latitudinal dependence of Bryan and Lewis, 1979 + vertical diffusivity, similar to that in MOM4; turned on using + #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using + diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file. +o Added capability for 3D specification of background vertical diffusion + coefficient. This is done by (i) #define ALLOW_3D_DIFFKR + in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime + "data" file that contains the 3D vertical diffusivity coefficients. +o ice dynamics (pkg/seaice) with thsice thermodynamics: + - add code within pkg thsice to advect & diffuse sea-ice fields + similar to (and will replace) what has been added in seaice_advdiff.F, + but: - conserving Mass, Heat & Salt. + - better when using non-linear advection scheme (not yet fully tested) + - can also be used in atmospheric set-up (for now, only the diffusion). + +checkpoint58x_post +o IO option for global-file compact format: + - add options when generating topology (utils/exch2/matlab-topology-generator) + - add I/O capability (pkg/mdsio). + - adapt utils/matlab/rdmds.m to read this format. + for now long-line format not yet supported by pkg/mdsio (& exch2). +o shelfice: add a few diagnostics + +checkpoint58w_post +o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: + rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref + (and replace horiVertRatio in NH code). + Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) + and tutorial_plume_on_slope (sensitive to truncation) +o seaice: if ALLOW_ATM_WIND is undefined use wind stress + directly to drive seaice model (C-grid only) +o exf: when input wind-stress (#undef ALLOW_ATM_WIND): + - reintroduce computation of wind from stress, + - compute tau (in exf_bulkformulae.F) from windstress averaged to + mass points to avoid tau = 0 + - fix serious bug: (1/3) in Fortran is not the same as (1./3.) +o rdmnc.m: make it work with "global" files created with gluemnc +o rdmnc.m : some improvements in dealing with singleton dimension + (tested on all testreport mnc output files). +o genmake2: disable pkg/profiles if netcdf test fails. +o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output. +o move call to cal_readparms up to make calendar parameters/variable available + to all packages + +checkpoint58v_post +o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get + useDynP_inEos_Zc tested. +o pkg/exf: changes to properly interpolate/mask/scale initial fields +o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields + and portions thereof. See read_cs.txt for description and examples. +o utils/matlab/cs_grid/bk_line: to compute transport through passages, + add a script (grt_circ_bkl.m) to generate broken-line between 2 points, + following the great-circle arc between those 2 points. +o trap un-initialized variable with pathscale compiler on weddell.mit.edu + (thanks to Constantinos): fix few problems and get (almost) all exp to pass. +o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in + - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) + - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81) + - still needs work (not working with some options ; efficiency to improve) + and serious testing. + - use this scheme for temperature & salinity in 2 advection test exp.: + advect_xy & advect_xz, respectively. + +checkpoint58u_post +o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. +o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. +o testreport: add option "-skipdir" to skip some test. +o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent + momentum calculation. +o gad_advection: fix vertAdvecScheme (if different from advectionScheme) +o some cleaning: usePickupBeforeC35 no longer supported ; remove this option. + remove checkpoint.F and the_correction_step.F (no longer used); + do the k loop inside CYCLE_TRACER (supposed to be more efficient). +o add option (linFSConserveTr) to correct for tracer source/sink due to + Linear Free surface +o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine +o pkg/thsice: fix reading mnc-pickups + +checkpoint58t_post +o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) +o pkg/mdsio: + - clean-up mdsio_readfield.F & mdsio_writefield_new.F and + move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & + mdsio_write_field.F (S/R MDS_WRITE_FIELD); + - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD + - collect old S/R in one file: mdsio_rw_field.F (now just a call to + either MDS_READ_FIELD or MDS_WRITE_FIELD ) + - new S/R (to replace MDSWRITEMETA), which allows to write more + informations (variable names, time ...) to meta files. + - modify rdmds.m to give back the meta file content. +o pkg/diagnostics: change vertical interpolation to be safer, and more + flexible (define p-levels to interpolate to in data.diagnostics); + add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right + diagnostic pointer. +o pkg/seaice: more cleaning up of seaice_growth, added many comments +o pkg/exf: put runoff0 and runoff1 into the appropriate common block +o fix multi-category seaice: + - change cpp flag SEAICE_MULTILEVEL to more meaningful name: + SEAICE_MULTICATEGORY + - fix short wave heat flux +o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics + and allow to use EVP solver. Change forward lab_sea: test both EVP + solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) +o Initial check-in of lab_sea adjoint + (very similar to natl_box_adjoint/code_seaice) + * used C-grid and EVP solver + * used KPP, GM/Redi + * uses inAdExact=.TRUE. + * gradient checks fail for both ADM and TLM + due to sensitive snow melt code in seaice_grwoth (look for "JZ") + f.d. gradients actually seem more problematic than ADM, TLM gradients; + issue is related to forward mismatch between g77 an ifort +o pkg/seaice: overhaul of thermodynamics + - growth.F and groatb.F are replaced by new routine seaice_growth.F + - budget.F is replaced by two new routines seaice_budget_ocean/ice.F + - move a few global fields out of SEAICE.h into seaice_growth.F and + make them 2D (FICE/QNETO/ ...) + - remove FO (it is the same as QNETO) + - introduce a few local fields to avoid modifying external fields such + as atemp, etc. + +checkpoint58s_post +o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F + changed exf_set_gen.F so that + genperiod=0 means input file is one time-constant field and + genperiod=-12 means input file contains 12 monthly means +o CG2D: use pre-computed solver main-diagonal (stored in common block); + this affects truncation error ; generate new output file for exp. which + fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), + global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), + ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), + MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), + tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), + vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) +o start implementation of deep-atmosphere and anelastic formulation +o verification: remove 2nd copy of input files and use script "prepare_run" + to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) +o mom_common/vecinv/fluxform: fix a few initialisation isssues +o profiles: fix for multithreaded case + +o diagnostics: rename few diags: + s/'PRESSURE'/'RCENTER '/g + s/'TICE '/'oceFreez'/g + s/'TAUX '/'oceTAUX '/g + s/'TAUY '/'oceTAUY '/g + s/'SWFLUX '/'oceQsw '/g + s/DIFx/DFxE/g + s/DIFy/DFyE/g + and add few ocean-forcing diagnostics: + atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS +o modifications to pkg/seaice/growth.F and budget.F, which change results of + lab_sea experiment: HSNOW was sometimes treated as effective and sometimes + as actual snow thickness. It now refers everywhere to effective snow + thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. + +checkpoint58r_post +o modifications to pkg/seaice/growth.F, which change results of + lab_sea experiment: fixes pertain to melting snow over open water, to + masking EVAP under sea ice, and to using the correct AREA variable for + computations of EVAP, PRECIP, HSNOW, and GHEFF +o add ability to read bathy, salt, and theta using MNC (off by def) +o add flooding algorithm and advection of HSNOW for pkg/seaice; + both are turned off by default and do no change any results +o seaice advection with pkg/thsice: a step toward the use of non-linear + advection scheme, but #ifdef or commented out for now (requires more EXCH). +o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens + (identical results) and the standard version of EXTERNAL_FIELDS_LOAD + in natl_box (affects results @ truncation level: update output.txt) +o multi-threading and IO: + - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. + - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls + (needed to work with SingleCpuIO): tested in all verif. exp. +o GAD: use simpler DST3 formulation as default (old version left within #ifdef) + affects the results (but none of the verification test uses this scheme). +o Adding some pkg/diagnostics capability to pkg/seaice + (will certainly be subject to changes) +o ctrl: adding new control variables: + lwflux, lwdown, evap, snowprecip, apressure, runoff + +checkpoint58q_post +o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up + 1/6-deg Southern Ocean configuration by 8% on IBM Datastar and + high_res_cube configuration by 4% on Columbia. +o clean-up multi-threaded problems (reported by debugger tcheck on ACES); + add (in global_with_exf/code) a version of EXF_INTERP_READ without + dynamical allocation (seems to work in multi-threaded). +o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using + single CPU io) so that TAF does not have to see EESUPPORT.h +o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) + +checkpoint58p_post +o obcs: stop if obcs is used with useCDscheme = .true. +o shelfice: + - fix a sign error so that no slip at shelfice interface works + - remove stop for combination non-hydrostatic code and shelfice. That does + not mean, that the results are correct, but at least they are numerically + stable +o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) +o added adjoint exch routined for all exch*3d* routines + and updated flow directives + +checkpoint58o_post +o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; + remove old subroutines (_XY_ & _XYZ_); update the adjoint version. +o change controling S/R for writing pickup file (new S/R do_write_pickup) + and clean-up reading/writing of pickup files. +o fix local version of read/write pickup (NH part) in rotating_tank/code +o simplify EXCH interface: + - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) + - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version +o added the regrid package +o shelfice: + - add a simple boundary layer scheme to reduce noise + - fix the indexing in shelfice_u/v_drag so that there will be actually drag + +checkpoint58n_post +o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to + local variable (not in common block). +o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. + - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); + - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls + to work with SingleCpuIO. +o add "_d 0" to real constant of pkg/cfc subroutines ; + update exp. cfc_exemple & tutorial_cfc_offline output files. +o multi-threading and IO: + - all threads call READ_FLD S/R (needed if using SingleCpuIO): + (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. + - barrier before and after reading. + - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) + - avoid using MDS_WRITELOCAL for LAND pkg output. + - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics + common-block variables ; Allows multi-threading with master-thread IO. +o change default MAX_NO_THREADS from 32 to 4 ; + and stop cleanly when MAX_NO_THREADS is too small. +o add S/R BAR_CHECK to check multi-threaded barrier synchronization + +checkpoint58m_post +o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. + and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 +o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. + keep global_ocean.90x40x15 (for AD testing) with former secondary test + (".qshyd") as the main test (mv output.qshyd.txt to output.txt) +o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; + add MITgcm_tutorials (= code + all the tutorials) +o ecco, option to compute cost for total ssh (mean+anom) +o consistent with addition of ptracer and ssh in pkg/profiles +o profiles: adding ptracer and ssh +o testreport: change multi-test output-file name + (from output.txt.{name} to output.{name}.txt) +o profiles: now ok for mutli-tiles case +o seaice: add 4 parameters for different advection schemes for area, + (effective) seaice thickness, enthalphy, and snow height. Their default + is the standard parameter SEAICEadvScheme +o calc_gw: + - add cosFacU in zonal viscous flux (harmonic.visc.). + - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. + of tutorial_plume_on_slope. +o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). +o calc_gw: true flux-form, account for horizontal grid spacing. + update rotating_tank results, but not plume_on_slope (affected at + truncation level, 11 digits). + +checkpoint58l_post +o calc_gw: + - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V + - remove side-drag for now (need to fix it); update plume_on_slope results. + - fix for partial-cell & non-uniform dz; update plume_on_slope results. +o commit code to make SST/SSS weights spatially variable + (based on either variable in-situ or variable initial T/S weights) +o pkg/ecco: + * commit code to relax deviations of xx_theta, xx_salt to 5*sigma, + now based on horizontally varying weights wthetaLev, wsaltLev + * cost_averagesflags now returns year indices in addition to day, month + * sflux balance is performed on annual basis + (sflxumm, sfluxmm2, bal_sfluxmm) + * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, + including separate counting and multipliers +o pkg/rbcs + * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing + +checkpoint58k_post +o testreport: + - always build in dir. "build" (if not there, mkdir build instead of building + & running in input) + - run in dir run (if it exists), in build otherwise. + - call prepare_run (if input/prepare_run exists) + - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. +o pkg/exf modifications to interpolation and rotation routines for more + reasonable treatment of North Pole singularity: for tracers North Pole + value is set to northernmost zonal-mean value, for zonal velocity it is + set to zero, and for meridional velocity it is set to northernmost value. +o pkg/exf/exf_check_range.F + - add tile index to diagnostics and move stop statement to the very + end of the routine. +o pkg/diagnostics: (diagnostics_main_init.F) + define title of isomorphic variables according to the current config. +o pkg/thsice with pkg/seaice dynamics: +- fix domain of computation (interior only, required for exf) and do exchanges +- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient +o towards a standard way of dealing with multi-threading in MONITOR + and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. +o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) + to W momentum equation in nonhydrostatic and quasihydrostatic runs. +o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. +o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) +o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL + (problems ? with gradient check in bottom_ctrl_5x5 adjoint test) o tracer advection: - clean-up and simplify calc_common_factors.F - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer