--- MITgcm/doc/tag-index 2006/03/02 02:03:39 1.615 +++ MITgcm/doc/tag-index 2007/05/15 14:34:44 1.817 @@ -1,9 +1,665 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.615 2006/03/02 02:03:39 jmc Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.817 2007/05/15 14:34:44 mlosch Exp $ $Name: $ Notes on tags used in MITgcmUV ============================== +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 laterally only 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 + advection subroutine (but still not used within DST advection S/R) +o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) + +checkpoint58j_post +o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields + from file (collects calls previously in FORWARD_STEP) +o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS +o adjoint store dir. adjusted accordingly +o genmake2 + replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. + +checkpoint58i_post +o pkg/seaice: add parameter that allows to scale/turn off effect of seaice + on wind stress (SEAICEstressFactor defaults to 1.) +o Total number of Timers is finite (<=40): comment out 2 non-essential one + in the_main_loop.F to avoid Pb (e.g., when running fizhi test) +o vector_invariant: fix highOrderVorticity(=4.th.Order) advection + on CS-grid: no longer loosing mass. +o exf & curvilinear-grid: no longer modify longitude xC & xG. +o pkg/ggl90: fix sloppy output and fix a bug +o pkg/seaice: added SEAICEuseEVPpickup parameter + - Set to false in order to start EVP solver with + non-EVP pickup files when using SEAICEuseEVP + - fix sign error in diffusion in seaice_calc_rhs + +checkpoint58h_post +* Modifications for bottom topography control + o replace hFacC by _hFacC at various places + o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL + o add non-self-adjoint cg2d_nsa + o update autodiff support routines + o re-initialise hfac after ctrl_depth_ini + o works for 5x5 box, doesnt work for global_ocean.90x40x15 +* Adding verification for 5x5 box (4-layer) bottom topography control + +checkpoint58g_post +o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., + used for mean seasonal cycle, mean diurnal cycle); add an example + in verification/global_ocean.cs32x15/input.thsice/data.diagnostics +o pkg/ggl90: + - add parameter (minimum surface kinetic energy) + - fix bug (avoiding division by zero) +o couple pkg/thsice to pkg/seaice: + - modify advection in seaice to accomodate new scalar fields to be advected + - only muliDimAdection scheme work with seaice/thsice + - mapping of thsice-variables to seaice-variables, back and forth + - does not break the verification experiments, but does not give the + desired results either +o pkg/seaice + - make (default) second order advection a bit less confusing? + +checkpoint58f_post +o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice + to pkg/seaice): + - new routines thsice_map_exf and thsice_get_exf provide the interface + - add an additional formal parameter to thsice_solve4temp +o pkg/exf: + - add new fields wspeed, snowprecip (to be able to couple to thsice) + - correct Stefan-Boltzmann constant + - new parameter for longwave surface emittance + - separate some stuff from exf_bulkformulae into new routines + exf_radiation, exf_wind + - add new parameters and constants: longwave emissivity for ocean, ice + and snow, evaporation parameters over ice + - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute + either wind from stress or stress from wind +o pkg/thSIce: +- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F +- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND + and THSICE_CALC_THICKN +- for now, call to THSICE_GET_BULKF remains inside i,j loops. +- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h + to make debugging easier. +- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output +o pkg/bulk_force: + - clean-up comments and parameters ; + - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; +o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; + generate new output for test-experiment: aim.5l_cs.thSI +o results_ad : rename "output.txt_adm" to "output_adm.txt" and change + testreport accordingly + +checkpoint58e_post +o SEAICE_CGRID adjoint done +o R_STAR adjoint implemented. + * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) + * need to sort out init. of h0facc, etc. +o Make pkg/profile fully independent of ecco,cost, etc. stuff + to be able to use it in pure forward. + +checkpoint58d_post +o upgrade simple test-experiment to tutorial example: + step.1: duplicate the experiment and (step.2) will remove the old copy. + tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) + tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) + tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) + tutorial_global_oce_biogeo <- copy of dic_example + tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) + tutorial_plume_on_slope <- copy of plume_on_slope + tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) + tutorial_global_oce_optim <- empty for now (David ?) + tutorial_global_oce_in_p <- copy of global_ocean_pressure + some tutorials (R1) were already checked-in under tutorial_examples in release1_branch +o correct a sign problem in cost_scat.F +o obcs and ptracers: fix boundary conditions for advections schemes + with larger stencil +o thsice adjoint: start +o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for + completeness +o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING + and COSINEMETH_III, add comments in default CPP_OPTIONS.h +o ptracers adjoint: + * avoid extensive recomputatations + * fix missing re-init. of gptr (missed by TAF) +o obcs: add a flag (OBCSprintDiags, defaults is true) that allows + me to turn off the excessive output to STDOUT that this package produces +o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common + and add those terms in Vector-Invariant formulation. +o in ctrl pkg, if ALLOW_CAL, use monthly mean controls + if the control period (xx_hfluxperiod etc) is 0 +o in profiles pkg, clean routines and fix details +o in ecco pkg, reading ssh data: + fix problem in case the model does not start at iter0=0 +o fix mnc-pickup/restart for ptracers +o new package prifiles: + code to compute profile-based cost by Gael Forget + (modifs in ecco, ctrl, autodiff) +o Benign bug fix in initialization (spotted by M. Mazloff) of + ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F + +checkpoint58c_post +o adjoint: finish NLFS adjoint and provide reference output in + verification/global_ocean.90x40x15/results_ad_nlfs +o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the + documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in + SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only + with SEAICE_CGRID defined. +o move calendarDumps from "data" to "data.cal" and clean-up the code + with a simple call to pkg/cal S/R: CAL_TIME2WRITE +o add useEXF & useCAL flags (for now, set in hard-coded way) +o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum + (were missing in NH mode, and wrong in quasihydrostatic mode). + waiting for Chris updated version of calc_gw to add those CALLs. +o fix bug in quasihydrostatic S/R ; + add a test for this option: global_ocean.90x40x15.qshyd +o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs. + (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS) +o add on/off flag useOffLine for package OFFLINE +o seaice: + - modify advection so that it works also on the C-grid + - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes + problem in multi-tile runs with C-grid + - add flags for clipping ice velocities and/or masking solver forcing + - fix drag (ocean on ice) formulation and a bug that caused noise in the + C-grid solver + - added a few comments to seaice_diffusion.F + - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V + are now exclusive) + - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which + required re-ordering the code a little: + + make DAIRN global variable (defined in SEAICE) + + move computation of the viscosities eta and zeta into a new separate + routine (because I need to recompute them in seaice_ocean_stress.F) + +checkpoint58b_post +o AIM+thSIce: fix sign of Short-Wave through the Ice ; + update output.txt of exp. aim.5l_cs.thSI +o various mnc cleanups and improvements: + + shrink lookup tables by factor of ~4 + + better error reporting when running out of lookup space + + able to handle longer path/file names (up to 500 chars) +o adjoint: + - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. + - TBD: "hidden" mom_vecinv recomp. in dynamics +o change forcing_In_AB to affects both T,S forcing and Momentum forcing + (allow to differentiate between forcing components using new integer flags: + momForcingOutAB=1/0 & tracForcingOutAB=1/0) + and add new flag to put Dissipation tendency out of Adams-Bashforth. +o ecco + - enable trend removal from SSH anomaly obs. +o adjoint + - a fix for PmEpR when #undef EXACT_CONSERV + - fix of "hidden" recomp. in thermodynamics (no TAF warnings) + - try to fix "hidden" recomp. in forward_step for NLFS + (NLFS seems broken sometimes after I checked it in) +o seaice: + - add c-grid version of the dynamic solver: + + three new routines that are the c-grid substitute lsr, dynsolver + and ostres + + put a few fields that were local to dynsolver into global common + blocks, so that I can move the computation of stresses etc into + seaice_lsr (saves coding but may break the adjoint). + - replace more hardwired parameters by runtime parameters + - add ice masks that mask the rhs of the implicit solvers where there + is no ice (commented out in seaice_dynsolver, because i am not sure + if this works properly), eventually this should replace the clipping + of ice velocities in seaice_dynsolver to +/-40cm/s. +o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly + include it only where its needed +o move balancing of fluxes before the call of external_forcing_surf +o seaice: + - correct units of turning angles (now they are really in degrees) + - move computation of GWATX/Y out of main routine into dynsolver + - initialize GWATX/Y in seaice_init +o Apply mask on Fresh-Water flux (needed for SSH forcing). + update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) +o seaice: add runtime flags for turning angles (default to zero) +o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean + and trend from exf forcing and ctrl control adjustments +o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF + (since checkpoint57x_post) o change the default rotation period to 86164.s = the Earth rotation o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) and based on a reference stratification. Tested within hs94.cs-32x32x5.