--- MITgcm/doc/tag-index 2004/10/08 17:03:43 1.364 +++ MITgcm/doc/tag-index 2005/10/14 12:45:43 1.573 @@ -1,8 +1,640 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.364 2004/10/08 17:03:43 edhill Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.573 2005/10/14 12:45:43 mlosch Exp $ +$Name: $ Notes on tags used in MITgcmUV ============================== +o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef + and sRef for convenience, handy, when you want to initialize + ptracers in a large domain with a constant non-zero value. Also, + untangle ptracers_init.F a little. + +checkpoint57v_post +o change dome exp. to use variable viscosity in side-drag terms. +o remove all the files from the cfc_offline test since they are now + incorporated into tutorial_cfc_offline which has been producing + identical results for a few days of testing +o add new parameter: sideDragFactor to enable half-slip-side BC + and change side-drag S/R to use viscosity from mom_calc_visc + (can switch back by setting sideDragFactor=0.); affects results at + truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), + global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). +o vorticity & strain are now computed without masking, to account for + no-slip-side BC in variable viscosity calculation ; mask is applied + anyway later on, before computing advection/coriolis terms. +o modify exp4 to test new obcs support for reading from external files + and for passive tracers +o fix behavior of ptracers_monitor when monitor output is written to a + netcdf-file; still not independent of monitor.F (writes in the same + file). +o change default value of tRef (put a uniform, meaningful value for ocean + & atmos) and initialize sRef (was missing, as Martin mentioned). +o Redefine viscC?Leith*. Change the coefficients of Leith viscosity + to be proportional to enstrophy dissipation length. Thus, + viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) + This is now consistent with Smagorinsky and with the manual. + +checkpoint57u_post +o OBCS and PTRACERS: add open boundary support for passive tracers + - either use homogenous (pseudo) v.Neumann conditions or prescribe + OB-values from file; this is not different from the way theta and salinity + are treated + - however, Orlanski-radiation conditions are not supported, and the model + will stop if you use pTracers and Orlanski at the same time. + - beefed up the rountine obcs_external_fields_load: now only those open + boundary values are overwritten with values from files for which there + are really files, otherwise the OB-fields remain untouched. This makes + it possible to use different OBs at different ends of the domain (as + with EXF) +o reduce number of exch calls in shap_filt (s2). +o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ + truncation level) 4/5 MLAdjust test results (11&12 digits match). + +checkpoint57t_post +o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 +o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get + same truncation, independent of the face number: affects affects several + test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). +o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); + note that biharmonic viscosity + no-slip was not tested in any experiment. +o fix bug in non-linear free-surf side-drag ; generate new output for + global_ocean.cs32x15(+.thsice) & global_ocean_pressure. +o make mnc honor the writeBinaryPrec flag for most kinds of output +o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum +o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation + error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). +o add brackets in multi-terms sum to get same truncation, independent of + the face number (manage to get exactly same value of gU,gV at the cs-edge) + affects several test. exp. Update global_ocean.cs32x15 (+.thsice). +o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax + and viscA4Remax, which allow one to limit the minimum viscosity by specifying + a maximum grid-scale Reynolds number. Also, changes all length calculations + in the case of grid anisotropy to geometric mean of dx**2 and dy**2. + Suggested values of viscosity parameters found in mom_calc_visc. + Many new viscosity diagnostics available. + +checkpoint57s_post +o Add clearing-house for viscosity calculations, mom_calc_visc and + correct numerous bugs in LeithD and Smagorinsky discretizations. + mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be + used simultaneously, and to be used in mom_vecinv and mom_fluxform. + Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) + and with Strain-Tension viscous term calculation (mom_hdissip.F). + The Strain-Tension form is now called with useStrainTensonVisc=.true. + ViscAhStrain and viscAhTension are now retired. +o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". +o In response to JMC's bug report, genmake2 now ignores any soft-links + that it finds in the *current* directory when searching for files. + Soft-links found in any other source directories will still work as + they did before. +o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls + a C routine to unlimit the stack size +o mnc-ify pkg/aim snapshot vars +o mnc-ify pkg/land as requested by Daniel +o various changes to mnc including: + - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format + - output can now be grouped so that all files within a group + change the ITER portion of their names in lock-step together + - can now read ("global") PER-FACE (in addition to PER-TILE) files + and works with both EXCH1 and EXCH2 (but needs more testing) + - writing works for all verification test cases w/ g77 on Linux + +checkpoint57r_post +o make MNC variable initialization happen earlier +o add diagnostics for (almost) each term of the momentum Eq. +o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. +o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) +o remove MINIMAL_TAVE_OUTPUT option ; + add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). +o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src + allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) +o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) +o add time-dependent SST, SSS control +o cost terms in ecco/ modularized (new cost_generic.F) +o cost_averages routines are modularized (new cost_averagesgeneric.F) +o new infrastructure for seaice model vs. obs misfits in seaice/ + * driver from the_main_loop.F is seaice_cost_driver.F + * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) + * gradient check in Exp. 6a of natl_box_adjoint/ +o natl_box_adjoint input_seaice for Lab. Sea now available online via wget + (see README file) + +checkpoint57q_post +o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) +o fix annoying months-old bug in mnc/mdsio output for seaice pkg + - bug was reported by Jean-Michel and Ian Fenty +o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) + update exp. cpl_aim+ocn output. +o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT + Needed for high-res. runs with large global files + to be able to limit tapelev size +o Changed some tests for adjoint: + * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT + * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT + * global_ocean.90x40x15/ back to default 3-level checkpointing +o Modifications to enable scripted COMMON to MODULE conversion + * verification/OpenAD/code/ has necessary scripts and description; + * converts, compiles and runs successfully; + +checkpoint57p_post +o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F +o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED + (already the case for some pkgs, including recent MNC_init, e.g. thsice) +o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) +o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F + (was already the case for dissipation with mom_vecinv, + and also the case for grad.PhiHyd when staggered-timeStep) + This will allow to put dissipation out-off the AB time-stepping. + Unfortunately, affects truncation error. Update output of exp. that "fails" + (cg2d matching number) and leave the others for later: front_relax(10), + global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), + matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). + +checkpoint57o_post +o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and + (2) its ready to be documented during the 20050801 DocFest +o MNC-ify the gmredi package -- tested and works w/ and w/o mnc + for ideal_2D_oce and lab_sea on linux_ia32_g77 +o set to #undef CTRL_SET_OLD_MAXCVARS_30 + in global1x1_tot/code_seaice_adj to access indices 32, 33 + (worth another tag) + +checkpoint57n_post +o adding precip control xx_precip 32 +o adding swflux control xx_swflux 33 +o Replacing 10 forcing penalty cost routines by 1 generic. +o Implementing partitioning in time-mean and variable adjustment + for atmos. state. +o Time-mean constant error is now read in data.ecco (instead of hard-coded) +o in natl_box_adjoint: + * updated exp 1 to 10 + (but does not have time-mean vs. variable split results yet) +o updated global1x1/*_seaice_adj/ + to incorporate latest changes +o enable useSingleCpuIO for mdsio vector routines + (applies in particular to tapelev I/O) +o removed inefficient K-loop in all active_file*control*.F + +checkpoint57m_post +o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) + and advect_cs (use EXCH-2 and standard cs-32 grid files). +o pkg/exch2: filling of face-corner halo regions is optional + (ifdef W2_FILL_NULL_REGIONS) and is turned off by default. + +checkpoint57l_post + tag before updating tutorials (pre-release-2) +o add cos & sin of grid-direction orientation angle (curvilinear grid only, + for output and interpolation of input fields onto model grid) +o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). + Affects results of exp. rotating_tank ; update output.txt. +o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor + and taking the square quantity and/or using a fraction-weight field. +o fix aim_diagnostics_init.F mate numbers. +o add mnc output capability to diagnostics/diagstat and update + our cvsignore files for the ACSII output generated + +checkpoint57k_post +o lab_sea now uses diagnostics package and provides a suite of + new EXF diagnostics output. + +checkpoint57j_post +o exf + * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): + Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); + terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. + * extended diagnostics output + - now includes all EXF variables + - hs, hl moved to common block + - separate S/R for diagnostics, called after ctrl vector is added + - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet + - EXFqnet contains true Qnet (i.e. includes qsw) + * updated verif. lab_sea, global_with_exf + * Rearranging hflux (exf_mapfields -> exf_getforcing) + to ensure that diagnostics sees a true EXFqnet +o add matlab scripts for CS-grid vectors (in utils/cs_grid) +o diagnostics pkg: change pointers so that 1 diagnostic can be used + several times with different frequencies. +o mnc-ify the thsice package as requested by Daniel Enderton + - the monitor--MNC output needs work + - many attributes need to be added (most are currently blank) +o mnc-ify theaim_v23 package as requested by Daniel Enderton + - many attributes need to be added (most are currently blank) +o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) +o add Sadourny like discretization to the 4th.O vorticity advection scheme +o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. + update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, + fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). +o fix few little things to avoid floating error with -ftrapuv (ifort v9) + (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) + +checkpoint57i_post +o Diagnostics package was changed: diagnostic allocation is now deactivated + by setting an empty file name in the namelist (used to be by setting 0 frequency) +o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; + add 1rst Order upwind vertical Shear. +o add a quick fix for A/B checkpointing in OFFLINE mode +o add IGNORE_TIME define and -ignore_time option to genmake2 as an + end-run around the C/Fortran linking horror in eesup/src/timers.F +o added pkg/runclock: allows user to terminate run based on wall clock +o added non-hydrostatic scaling parameter: nh_am2 +o pkg/my82: futile attempt to make results compiler-independent by adding + some "_d 0", etc. no effect. +o for mnc output, fill the 'T' coordinate var with myTime and create a + separate 'iter' variable for iteration count +o pkg/diagnostics: + add new capability: output of Global/Regional & per-level statistics ; + tested against monitor output (including land & thSIce) on various exp. +o make seaice-pkg I/O type flags (MNC/MDS) more standard. + +checkpoint57h_done + tag after changing user customized files (DIAGNOSTICS_SIZE.h, + data.diagnostics, data.gchem, data.ptracers) is done. + +o pkg/diagnostics: prepare for Global/Regional statistics. + add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h +o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE + and rename it: DIFFERENT_MULTIPLE + +checkpoint57h_post +o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers +o pkg/diagnostics: change output frequency, now in seconds (instead + of Nb of iterations). This requires to change data.diagnostics. +checkpoint57h_pre + +o in mnc, let the user create the output dir if both mnc_outdir_date + and mnc_outdir_num are false +o add fflags() to pkg/diagnostics which allows one to specify, on a + per-file basis, the file precision [default behavior is unchanged] +o added diagnostics to pkg/kpp, including computation of mixed layer + depth based on a temperature/density criterion +o updated verification/natl_box to test the new pkg/kpp diagnostics +o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) +o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) +o fix mnc flags in pkg/seaice so that they are "owned" by seaice, + not mnc -- this mistake was found by JMC and is now corrected + +checkpoint57g_post +o add Adams-Bashforth 3rd Order time stepping: + - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) + - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... +checkpoint57g_pre + +o make lambda[Theta,Salt]ClimRelax spatially varying + (default remains spatially uniform constant based on tau) +o added new control variables + * init. uVel, vVel, etanN + * lambda[Theta,Salt]ClimRelax +o separate masks used for ctrl_pack/unpack 'from write_grid' output + (suggested by G. Forget) + +checkpoint57f_post +o add parameter "baseTime" = model base time = time at iteration zero + new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to + account for baseTime shift +o move Coriolis arrays from PARAMS.h to GRID.h +checkpoint57f_pre + +o mnc-ifying the seaice package +o introduced an alternative length scale calculation for use in the limiting + maximum viscosity (off by default, see mom_vi_hdissip.F for details) +o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S +o added modified Leith scheme with viscosity proportional to grad(Hdiv) + as well as grad(vort3). Made it compatible with both approximate form + for the cubed sphere and full form of these gradients. Added flag + useFullLeith to select between approximate and full form. +o add "d0" in getcon.F to reduce differences between compilers/platforms + update output.txt of exp. fizhi-gridalt-hs +o change port_rand funtion to allow to set the seed. +o fix obscure MNC bug involving conversion between reals and integers + - it caused no problems with certain (eg. gcc, ifc) compilers but the + new version is now more standards-compliant +o adjoint-related modifications + * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint + * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 + * mom_vi_hdissip: to be able to use Leith scheme in adjoint + +checkpoint57e_post +o Adding eddy stress controls a la Ferreira et al. +checkpoint57e_pre (actually was tagged: eckpoint57e_pre) + +o fizhi pkg: fix AtoC and CtoA when called with same input & output array + update output.txt of exp. fizhi-gridalt-hs +o add more "Z" dimensions and associated coordinate vars to MNC +o pkg/exf: added twoDigitYear capability for option useExfYearlyFields +o parameter calendarDumps: when set, approximate months (30-31 days) and years + (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, + KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar + months and years. Requires pkg/cal. +o diagnostics: add pickup functionality + - off by default for backwards compatibility + - current version only uses MDSIO -- MNC will be added +o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. +o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) + +checkpoint57d_post +o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing +o modify verification/ideal_2D_oce so that it tests the creation of mnc + output from the diagnostics package +o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up +o make genmake2 more portable by using ".$FS" instead of ".f" for more + of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) +o add coordinate variables to the MNC output from the diagnostics package +o change MNC-flags default value: true when useMNC=TRUE +o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F + the ability (off by default) to read the grid information using MNC +o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt +o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging +o do snap-shot diagnostics at the middle of the time-interval (instead of + at the end). +o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add + new test for AIM with thSIce + slab-ocean +o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) +o move state variable diagnostics to the beginning of the time step ; + (note: still needs some work specially for snap-shot diagnostics) + duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z + +checkpoint57c_post +o Change testing option (-ieee) to get closer agreement between g77 & ifort +o generate new output.txt files on faulks with g77 & the new -ieee option +checkpoint57c_pre + +o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); + update output.txt of exp. global_ocean.90x40x15 +o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer + results; update global_ocean_pressure & global_ocean.cs32x15 output.txt +o add saltFlux(+File) forcing capability with periodicExternalForcing +o allow to use pkg diagnostics for GM-Redi & ThSIce output +o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. +o improvements for the MNC output from DIAGNOSTICS: + - correct handling of the unlimitied dimension + - all dims now have associated coordinate variables + - variables located at U, V, and Corner ("Z") points are now written + with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that + *all* data points are output +o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice +o added pkg/seaice/seaice_monitor.F +o mdsio_readfield.F can now read files visible only to master MPI process. +o pkg/seaice: some test code for ice-modified ocean stress +o exf_getffields interpolation defaults to bilinear for all scalar forcing + fields (remains bicubic for wind velocity and stress). This avoids, e.g., + spurious negative numbers for precipitation and humidity. Will cause + some small numerical differences for integrations using pkg/exf/exf_interp.F. +o pkg/ctrl/ + * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O + May be enabled via doPackDiag + * introduce z-scaling of + + gradient (doZscalePack) and + + control (doZscaleUnpack) +o pkg/mdsio/ + * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F + * N.B.: leave tiled I/O for tapelev (i.e. mds...vector) + +checkpoint57b_post +o simplify options in diagnostics_fill arguments (remove weird combinations) +o fix MNC coordinate variables so that they now contain per-face index + values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in + general, EXCH2 grids are only aligned to a "local" coordinate system +o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) +o Implement instantaneous output within pkg diagnostics: + setting a negative frequency in data.diagnostics produces + "snap-shot" output (as opposed to time-average if freq > 0) +o move out off EQUIVALENCE all diagnostics that fizhi does not use ; + NOTE: change ptracer diagnostics name: use 2 characters to work with + more than 9 tracers. Add also diagnostics of advect & diffus flux. +o more CF compliance: convert all MNC 'iter' variables to 'T' so that it + becomes the coordinate variable for the 'T' dimension +o add CF-style coordinate variables to MNC + - just a first cut: numbers are meaningless on the cubesphere and + missing along the T axis but otherwise it works! +o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX +o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. +o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) + this is based directly on what the model compute, so that the content of + each diagnostics might be affected by switching options (e.g., implicitDiffusion) +o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) +o clean up build options files for SunOS, in particular + - remove -traditional from xmakedepend + - change -xarch=v9 to -xarch=native for f77 + - restore use of make (not gmake) + - add CC=gcc if using g77 +o changes per discussion of AM, JMC, & EH3 today: + - move redundant "grid" variables out of "state" -- in preparation of + creating proper CF-style coordinate variables and in recognition + that any/all grid variables can be easily copied (eg. w/NCO) from + the grid files into any of the other NetCDF files + - *always* output grid variables with MDSIO (this will eventually be + changed) + - output MNC grid file if useMNC is true +o every instance of _END_MASTER() has been found and replaced with + _END_MASTER( myThid ) in order to satisfy certain picky Sun + preprocessors +o re-arrange diagnostics pkg initialisation: + - allow each package to extend the available diagnostics list + - add some checking and fix small problems (multi-threaded, ...) + - new S/R diagnostics_fill (replace fill_diagnostics): + look through the short list of active diag. (instead of the long list) + create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active + +checkpoint57a_post +o this set of changes restores TAMC compatibility + tested for global_ocean.90x40x15 adjoint on trough + (what a pain) + +checkpoint57a_pre +o some modifs in tools/build_options for sunos +o call ctrl_pack for ctrl at end for optimcycle=0 + +checkpoint57 +o add horizontal bi-harmonic viscosity for vertical velocity + - new parameter viscA4W (defaults to viscA4) + - affects only non-hydrostatic code + - to be done: no-slip lateral boundary conditions +o switch back to "sflux = sflux - runoff" in exf_getforcing.F +o implement Implicit Vertical advection for pTracers +o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) + (implemented also for implicit vertical diffusion & advection) +o OBCS: extend application of tracer open boundary conditions + to a strip beyond the boundary of width Olx/Oly +o add call monitor to TAF set of required calls (flow directives) + and include in natl_box_adjoint +o untangle a few ifdefs related to cost, ctrl, autodiff + untangel a few ALLOW_ECCO_OPTIMIZATION +o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) + (theta2, salt2 in ecco_cost_weights) + +checkpoint56c_post +o OBCS as control variables + - update ctrl_ad_diff.list, obcs_ad_diff.list + - remove balance of obcs controls from default + - fix index bug nobcs in ctrl_init + - fix dummy fields filen in ctrl_pack + - add dummy weights for obcs +o lsopt: comment out fort.94 output +o optim: + - remove unnecessary header files + - adjusted namelists + - add xerbla.F to Makefile +o exf: + - multiple modifications of exf_check_range + - unit change in exf_init_runoff from [m/year] to [m/s] +o mdsio: + - i/o-vector change debugLevel from debLevA to debLevB + +checkpoint56b_post +o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that + is called from DO_THE_MODEL_IO + - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE + - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) + - clean up PTRACERS_WRITE_TIMEAVE a little +o add another verification experiment that tests both the cfc-pkg and + the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with + reactive tendencies treated inline with regular timestepping +o testreport previously did a lousy job of comparing small numbers, so + we (Ed and Martin) changed the way the cut-off of 1.e-12 is + implemented in the little c-progam tmp_cmpnum.c which is embedded in + testreport. +o ptracers_monitor: bug fix for MPI + +checkpoint56a_post +o GCHEM: finish reorganizating the package + - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency + (introduces another 3D-array for each passive tracer, but only if + GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING + gchemTendency is not needed because the timestep is done separately) + - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY + - GCHEM is now---more or less cleanly---separate from PTRACERS + - to bo done: handling of surfaceForcingPtr that is needed for KPP not + so clear to me how that should be done in a general way. +o CFC: improve formatting of output in CFC_ATMOS +o PTRACERS: + - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so + that ALL experiments with ptracers enable can be checked. This makes + GCHEM_MONITOR obsolete. + - include a runtime parameter PTRACERS_monitorFreq that defaults to + monitorFreq + - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true +o add PTRACERS (PTR0[1-5]) to testreport output +o exf_check_range: + * default changed to .TRUE. + * will check values for niter0 if debLevA, every timestep if debLevB + * STOP in exf_check_range if 'out of range' + * range chosen generous to allow for potential extema + TBD: a version with stricter range + permitted range would be runtime parameters +o GMredi: + - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; + - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. + - change the default GMREDI_OPTIONS.h: compile everything except Visbeck +o GCHEM: + - move call to GCHEM_FORCING_SEP, so that it is now called before + the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP + - introduced a useGCHEM runtime flag and applied it everywhere. + - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; + this flag is now only visible within GCHEM-pkg routines. + - moved gchem_forcing_int temporarily into ptracers_forcing, this will + be replaced by a 3D array that is computed before thermodynamics; for + this, the tracer ID iTracer had to be included into the parameter list + of ptracers_forcing + - set up forward_step to call gchem_forcing, that will replace + gchem_forcing_int in ptracers_forcing + - cleaning up +o small cleaning of exch2: remove files that are also in eesupp/src + +checkpoint56 +o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 +o mnc: cleanup "full" files--fixes out-of-memory problem +o ECCO-GODAE + * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup + * fully merged and updated from SIO code + windstress sign change affects + - exf_inscal_[u/v]stress + - sign of xx_tau[u/v] adjustments + - signs in cost_scat + * ctrl_get_gen: avoid update of tau[u/v] for first few days + * natl_box_adjoint updated and compressed + * 2-level checkpoint switch added + (tested in EXP. 1 of natl_box_adjoint) + * new switch doInitXX to avoid init. of xx_... in optimcycle=0 +o SVD + * first complete, non-hacked version for SVD calculations + * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... + performed via direct access files admtlm_vector.it???? + (via ctrl_[un]pack) + * optimcycle is used for ARPACK iteration counter + (note: adxx_... is iterated, rather than xx_...; latter is constant!) + * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms + and add linear transforms where necessary + * controls are initial/final SST, SSS (can be extended; need to check + ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F +o mdsio: filename info to both stderr, stdout +o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] + from sign change + +checkpoint55j_post +o isolate dissipation tendency (allow to keep it out off AB) in V.I form. + affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) +o add consistent build directories and .cvsignore files to verification +o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity +o make all subroutines 30 or less characters in length for certain older + compilers to work (a thorough search only turns up two routines in + pkg/ptracers) +o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; + affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) + +checkpoint55i_post +o change arrays for total vertical diffusivity (2.D if explicit, + 3.D if implicit) ; each ptracer uses its own background value. +o added mnc/NetCDF output capability to ocn_compon_interf + - added bits to verification/cpl_aim+ocn so that it can run on + ITRDA and other clusters without the mpirun "-wd" option +o fixed wayward endif in mom_fluxform.F that messed up cyclindrical + configuration +o give MNC the ability to create additional files rather than + exceeding a specified file size limit "MNC_MAX_FILESIZE" + - the default is just less than 2GB which is a practical limit + on many systems +o Compute the non-local term using either KPP vertical diffusivity (=default) + or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) + +checkpoint55h_post +o add verification test "vermix" +o remove all the *_ioinc flags and replace with the single global + outputTypesInclusive flag +o allow to set a vertical profile of vertical diffusivity for T & S +o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS +o useMNC moved from data.mnc to data.pkg + +checkpoint55g_post +o Renaming carbon AD experiments to comply with testreport conventions +o Updating adjoint of Held-Suarez hs94.1x64x5 +o Fixing directives for non-ECCO forward_step, after ECCO directives + have been fixed to avoid recomp. of do_oceanic_phys + Works well for global_ocean.90x40x15, + but recomp. issue remains for carbon +o Updating adjoint output for natl_box_adjoint after + pkg/ecco has been modified (see taga c55d_post) + +checkpoint55f_post +o rename to timeave_init_fixed + +checkpoint55e_post +o some delicate re-shuffle of store directives to avoid one + extra call of do_oceanic_physics + affects ecco_the_main_loop.F, do_oceanic_physics.F + checkpoint_lev1_directives.h +o NB: this may break global_ocean adjoint temporarily, + but it is clear how to fix it. Will do later, need this now. + +checkpoint55d_post +o ECCO specific cost function terms (up-to-date with 1x1 runs) +o ecco_cost_weights is modified to 1x1 runs +o modifs to allow observations to be read in as + single file or yearly files +o enable to read exf forcing fields as either + single file or yearly files (flag useExfYearlyFields) +checkpoint55d_pre + +o switch between 2-level and 3-level checkpointing o add ability of MNC to write local and "partial" (eg. 2D slices where the full 3D field is never actually stored) arrays to NetCDF files with the correct (that is, the complete multi-dimensional) set of