--- MITgcm/doc/tag-index 2006/12/24 22:30:57 1.760 +++ MITgcm/doc/tag-index 2008/04/24 19:39:28 1.980 @@ -1,15 +1,751 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.760 2006/12/24 22:30:57 jmc Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.980 2008/04/24 19:39:28 jmc Exp $ $Name: $ Notes on tags used in MITgcmUV ============================== +o remove "exp5" (replaced by tutorial_deep_convection). +o pkg/obcs: add code to fix topography gradients normal to open boundaries; + this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; + the code can be turned on by setting OBCSfixTopo = .true. in data.obcs + --> changes results in dome, exp4, internal_wave, seaice_obcs, and + tutorial_plume_on_slope. +o tutorial_deep_convection : + update the set-up and increase resolution and domain size ; start + from pseudo initial conditions = output at t=120mn in order to see + something happening when running testreport. +o pkg/seaice: add os7mp as an advection scheme + add check for advection schemes + add a flag for restoring T and S underneath sea ice +o pkg/my82: add netcdf-support and diagnostics +o thsice pkg: + - Now hsMax limits snow height by turning it into ice following + flooding scheme (and now conserving energy) + - Slight rewriting of the formula in thsice_calc_thick.F + - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos + --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice + +checkpoint59p +o gchem / dic / cfc : + - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); + - add new parameter files: "data.dic" & "data.cfc" ; + - various re-arrangement in initialisation & header file ; + - fix tutorial_global_oce_biogeo for multi-threaded test. +o pkg/dic: test for "pickup_dic" file when restarting ; + if no pickup-file, can restart with a re-initialised pH (same as it did + before) providing pickupStrictlyMatch is set to False. +o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP + + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP +o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2 + and staggerTimeStep is off (needed for stability of Internal-wave dynamics). +o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax, + & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers + (note: not clear to me what lambdaTr1ClimRelax is still used for ...) +o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which + scheme to use for vorticty-term ; + - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F + (with default selectVortScheme, return to original discretisation) + - remove weird combination (e.g.: upwindVorticity & highOrderVorticity) +o pkg/seaice: add a line to the summary to indicate grid type (B/C) +o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the + bottom ; only used with variable horizontal viscosity and non-hydrostatic. + also fix diagnostics VISCAHW & VISCA4W. + +checkpoint59o +o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). +o change the loop ordering in most gad_*_adv_x.F to improve vectorization: + move a few statemens out the main loop into separate loops +o pkg/shelfice: + - sort out freshwater flux; convert freshwater fluxes to mass fluxes + (kg/m^2/s), does not break tests, because in verification/isomip, + rhoConstFresh=rhoConst (by accident) + - rearrange computation of tLoc, sLoc, pLoc to make code more efficient + - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into + new file model/src/seawater.F, so that they are available for all pkgs. + - convert potential temperature into in-situ temperature. This changes the + isomip tests => update tests +o add a flag writePickupAtEnd (default=true) to be able to suppress + writing a pickup at the last timestep +o tools/mpack-1.6 : + - disable automake (not working) and autoconf (not needed). + - update to version 1.6.4 which fix MD5 code on some 64 bits platforms + also cleaner with much less compilation warnings. +o pkg/profiles: + rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg + (for "less than 32 characters name" compiler requirement) +o pkg/obcs and pkg/exf: added capability to specify seaice open boundary + conditions that have a different sampling frequency than S/T/U/V obcs +o pkg/diagnostics (stats-diags): + - fix global Min/Max in case 1 processor get only empty tiles +o genmake2: replace (4 times) + make genmake_tc_1.o >> genmake_warnings 2>&1 + with + COMM="$CC $CFLAGS -c genmake_tc_1.c" + echo $COMM >> genmake_warnings + $COMM >> genmake_warnings 2>&1 + to make genmake2 always see the value of CC as specified in the optfile. +o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid. + - add diagnostics for 1srt & 2nd Order moments and sub-grid variance. + - modify verification advect_cs test to test SOM-advection on CS-grid. +o pkg/ctrl: + - Rewrite of ctrl_map_ini_ecco.F, + introducing a generic routine (ctrl_map_ini_gen.F). + - Modification of ctrl_bound/adctrl_bound handling control vector bounds. + +checkpoint59n +o pkg/diagnostics: for large number of diagnostics, store diagnostic mate + number in dedicate array "hdiag": + - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST + with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST. + - many small changes (integer format) for large number of diagnostics + - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with + a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23. +o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For + usingSphericalGrid, this allows to define the rotated grid coordinates + via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the + geographical coordinates according to the inverse of the rotation defined + by the Euler angles, so that Coriolis parameter and online-interpolation by + exf works with the geographical coordinates on XC/YC/XG/YG. + Naturally, this feature does not work with all packages, so some + combinations are prohibited in config_summary (flt, flt_zonal, ecco, + profiles), because there the coordinates are assumed to be regular + spherical grid coordinates. +o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc: + - introduce isopycnal diffusion coefficient control. +o tools/adjoint_options: + - additional control vector components. +o pkg/mnc: have mnc create marginally meaning full coordinate variables + (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 +o pkg/mypackage: + - add example of read/write pickup for state-var ; + - add entry points to the main code for state-vars diags & write-pickup. +o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year + transitions for useExfYearlyFields + - add new subroutine that determines the file to read from for + use*YearlyFields = .TRUE. and .FALSE. + - add a verification experiment to global_with_exf that tests + useExfYearlyFields with USE_EXF_INTERPOLATION defined +o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in + analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new + subroutines (which could be generated from a template, because they are + almost identical), for now they are included in obcs_prescribe_read.F for + simplicity +o pkg/exf: + - add a little more diagnostic to exf_interp_read (in analogy to + mds_read_field, can be turned off with debugLevel < debugLevA=1) + - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code + ugly but fast by unrolling short inner loops, inserting a unroll=8 + directive in routine lagran, and splitting a loop and making do while the + outermost loop (the latter requires the intoduction of index arrays) +o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice +o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver + http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html +o verification/seaice_obcs: updated for restart test and latest options +o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different + ice rheology (so-called truncated ellipse, that gets rid of tensile stress); + for now this is only available for the C-grid code and also within + #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code + +checkpoint59m +o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) + and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature +o gad_som : fix flux output (& diagnostics) to have same units as other + advection scheme fluxes (was previously multiplied by deltaT). +o added verification/seaice_obcs both to test seaice open boundaries + and to provide an example matlab scrpt for generating them +o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume +o pkg/salt_plume: clean up salt_plume_frac.F to + remove redundancy in PlumeMethod 1 and 4 +o pkg/kpp: added saltplume diagnostics +o pkg/obcs and pkg/seaice: + - do not set uice and vice to zero when OB*icefile are unspecified + - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default + - moved seaice tracer obcs after call to seaice_growth +o pkg/salt_plume: added various options for salt plume depth + criterion and for vertical distribution of the salt + +checkpoint59l +o pkg/ptracers: new version of ptracers pickup: + read meta file and write only fields which are needed to restart. + ( same logic as main pickup file ; also using pickupStrictlyMatch ) +o pkg/seaice: + - add timescale for melting due to warm mixed layer as a means of + setting SEAICE_availHeatFrac more conveniently + - add a CPP-flag/runtime parameter check for flooding algorithm + - reformulated availHeat in seaice_growth.F to be independent of AREA +o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent + unit changes +o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint +o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC + SX vector computer. +o pkg/seaice: + - removed SEAICE_FFIELDS.h and seaice_get_forcing.F + seaice forcing fields can now be read only through pkg/exf + - removed some unused halos +o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP +o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL + or U/VICE from U/VWIND before computing U/VSTRESS + +checkpoint59k +o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between + dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. +o fix un-initialised variable problem (in mom_vecinv & shap_filt): + all experiments pass when compile with un-initialised var. checking option. +o added pkg/salt_plume +o script to test restart (for now, in MITgcm_contrib/jmc_script) +o pkg/seaice: new read/write pickup version. + read meta file and write only fields which are needed to restart. + ( same logic as main pickup file ; also using pickupStrictlyMatch ) +o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) +o lab_sea.hb87: modify the domain & update output.hb87.txt : + lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 + at j=1 & j=Ny+1 : this case is not treated correctly in the restart + process. Fixed here by closing the domain at the Northern boundary. +o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. +o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing + a set of consecutive levels in/from a 3-D array. +o pkg/ptracers: + use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). + to-do: fix pkg/diagnostics when large number of diagnostics are defined. + +checkpoint59j +o in pkgs: dic, obcs, offline, rbcs: + standard way to compute coeff. for time interpolation between 2 time reccords + which retains full precision (& make results less dependent on compiler). + update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. +o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those + packages instead of reading ice cover and wind speed separately +o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h + (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad + to allow to compile customized code before the update) +o cleaning-up: + - fix CPP instruction syntax in pkg/obcs + - replace (some) call to MDSIO S/R with call to RW interface S/R ; and + add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio) + - fix some threads issue in IO parts. +o pkg/dic: + - add tons of "_d 0" (--> much better testreports !) + and then update outputs of tutorial_global_oce_biogeo +o pkg/mom_fluxform: + add a special version of momentum advection intended to conserve momentum + next to a bathymetry step or a coastline edge. (default = off = #undef) +o new read/write pickup version: + - for now, only implemented for main (mdsio) pickup file. + - write out only what is needed to restart; merge pickup_nh , pickup_ph + and main pickup together. + - read meta file; read only what is needed to restart; stop if a field + is missing (if pickupStrictlyMatch=T, = the default) or try to restart + if it make sense (even if the restart is not perfect). + - if no meta file, assume that pickup to read corresponds exactly to + a pickup that would currently be written. + - read pickup written in the old format (until checkpoint59i) if it + recognizes an old meta file (no field-list). + - add a meta file in exp. which starts from a pickup: 2 cases: + a) minimal meta file (with just file precision) + pickupStrictlyMatch=F + e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta + b) a meta file describing the content of the associated pickup file + e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta +o pkg/mdsio & pkg/rw: + - new routine to read a meta file ; new set of routine to read + Multiple-fields file (with meta file). +o added open boundary conditions capability for seaice + HSNOW, HSALT, UICE, and VICE + +checkpoint59i +o adjoint: + * fix multiDimAdvection adjoint + (partial recomputation problem by TAF for fVerT(:,:,kDown) + and comlev1 size definition (maxpass vs. max. number of tracers) + * verification/global_ocean.90x45x15 adjoint now tests + NLFS and multiDimAdvection using DST3 (=30) + * verification/lab_sea now tests multiDimAdvection using DST3 (=30) +o pkg/kpp: add "_d 0" to real constant (if missing); + update output of exp: natl_box (10.digits); vermix (std, 7.digits) + and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). +o prepare for "clever pickup" implementation: add new header file "RESTART.h" + for internal parameters related to restart process (formerly from PARAMS.h) + and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. +o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed + as argument. (only atm2d & obcs write_pickup have not yet been updated) +o pkg/monitor: + - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM + - fix mon_stats_rs (statistics over the full domain, even where field is zero) + - account for deep Atmosphere factor and density factor (anelastic) +o added open boundary conditions capability for seaice HEFF and AREA +o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) + thermodynamics + - requires a little reorganization, which affects the testreport results + of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, + so that now the conservative form is tested + - add a few comments +o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* +o add a little bit of code to gad_os7mp_adv_?.F to help vectorization +o add new diagnostics to seaice: advective, diffusive fluxes (only for + multidim-advection, for scheme 2 they are not filled) and transports, + thermodynamic growth rates +o change units of EmPmR (inside the code, + within coupling interface) + from m/s to kg/m2/s (mass flux) but leave input file unchanged. + Affects results @ truncation level (cg2d match) and update output of + experiments: lab_sea(6), global_ocean.90x40x15(10), + global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) + + adjoint results: global_ocean_ebm(11) and lab_sea (12). + Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). + Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). + +checkpoint59h +o pkg/exf: + - improve vectorization by moving if-statement out of loops in + exf_mapfields, exf_radiation + - exf_bulkformulae.F: introduce 2D fields and vectorize code +o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package +o testreport: + - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE + monitor & update offline_exf_seaice exp. output. + - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) +o pkg/seaice: + - bug fix in the evp solver: boundary conditions were affected be + masking of zMax/zMin (changes results) + - minor bug fix in boundary conditions in seaice_calc_strainrates + (changes results for no_slip) + - seaice_lsr.F: make interpolation of eta dependent on boundaries + - replace hardcoded lower limit for zeta (zMin) by runtime parameter + - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean + stress formulation and no-slip boundary conditions +o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP + in gad_calc_rhs.F ; add few safety stops in initialisation phase. +o pkg/seaice: a first HSALT time stepping equation has been checked in +o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV + in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem + without requiring DO-IF statements +o pkg/thsice: + use continuous power-law function for partition of energy between lateral + melting/freezing and thinning/thickening ; old code using step function + still available with #undef THSICE_FRACEN_POWERLAW + update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice +o testreport: change AD testing : check against results/output_adm.txt + using same scripts as for forward test. + +checkpoint59g +o adjoint testing: in preparation for changing testreport: + - output format: cost and grad written on separated lines + - ad output results in directory "results" (instead of "results_ad") +o pkg/seaice: adding ice salinity HSALT as a prognostic variable +o pkg/seaice: changes for using pkg/seaice with pkg/obcs +o pkg/ecco: allow user defined cost function contributions +o testreport: + Allow to choose (per experiment) the list of tested output variables + and the main variable (used to issue a pass/FAIL ) ; + - for now, done by adding the specific list in file: [exp]/input/tr_checklist + - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; + Also modify printing of summary: + a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) + b) echo the list of tested variables in the individual summary.txt of + each experiment. +o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of + threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) + (but still depend on the tile decompostion of the domain). +o pkg/seaice: change a discretization detail to make the B-grid code + "more symmetric". This change is likely to remove all "ridges/leads" that + where quasi-aligned with the grid in B-grid solutions. It may also be + the solution to the stress coupling issues with the B-grid. +o each tested exp: add a "run" directory with a standard ".cvsignore" file ; + remove .cvsignore from input dir. (since testreport no longer run here). +o pkg/thsice: + - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" + - fix reshaping of sea-ice just after advection: + melt all the ice only if ice-volume is too small. + - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): + prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; + and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). +o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water + tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. +o define mass2rUnit & rUnit2mass as units conversion factor, used for surface + forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit + (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; + and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error + of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 + -> update output.txt +o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): + this affects truncation error: -> update output.txt of exp: + global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, + ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. + +checkpoint59f +o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) +o pkg/ctrl: ctrl_bound forces parameter corrections to stay in + a bounded range (in forward mode) +o pkg/ecco, ctrl, autodiff and mom_common: + internal parameter controls, completements of implementations +o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. +o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; + (not seem any difference in testing results). +o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains + at face corners. +o pkg/generic_advdiff: + - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) + loop range indices for computing vertical advection tendency + and do the calculation in the interior only (no overlap) ; + for now, only implemented for SOM advection (to save CPU time). + - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) +o exch2 adjoint + First set of changes: + - add exch2 hand-written adjoint templates + - exch2 hand-written no longer use TAF-flag 'nownew_arg' + This will require cleanup in pkg/autodiff/*.F + (changed routines currently kept separate in verif. code/) + - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC + that used to hide exch2 or cubed-sphere specific code + (commented via 'cph-exch2') +o pkg/seaice + - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. +o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update + output of global_ocean.cs32x15.thsice . + +checkpoint59e +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; pkg/kpp/kpp_calc_diff_s & _t.F + are no longer updating the vertical diffusivity array + (passed as argument) but are (re-) setting those arrays. +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 runoff into the appropriate common block +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