--- MITgcm/doc/tag-index 2011/05/29 23:50:06 1.1446 +++ MITgcm/doc/tag-index 2011/10/26 09:30:32 1.1522 @@ -1,9 +1,419 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1446 2011/05/29 23:50:06 jmc Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1522 2011/10/26 09:30:32 mlosch Exp $ $Name: $ Notes on tags used in MITgcmUV ============================== +o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity + (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F) +o pkg/obcs: Stevens BCs (still only for east and west) + - fix Stevens BCs by using intermediate velocities of previous + time step as "baroclinic" contribution rather velocity of one grid cell + inside the boundaries; more consistent but makes the entire treatment + more complicated, requires new pickup files and two new S/Rs: + obcs_copy_uv_n and obcs_save_uv_n + keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY + (undefined by default) + - silently move computation of some grid factors into separate loops to + save some recomputations + - add a hack for non-linear free surface + - add a verification experiment to exp4 that tests this code +o make gluemnc/xplodemnc work with (moron) non-GNU shell tools + +checkpoint63d (2011/10/25) +o pkg/obcs + seaice-dynamics: + - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before + solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB + values (consistent with an implicit method). + - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to + return to older implementation (same results as before); note that none of + the "experimental" OBCS_SEAICE options are implemented in the new version. + - switch test exp. seaice_obcs to use new version (update output). +o pkg/seaice: + - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS) + - add parenthesis in Water-Ice drag calculations (evp & lsr); + - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1; + and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice) + - update output of test exp lab_sea that uses evp or lsr (fwd+ad) + and global_ocean.cs32x15 (icedyn & seaice fwd+ad). +o pkg/layers: + - Include potential density as new coordinate (Thanks to David Munday) +o pkg/dic: + - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add + carbonate computation/output to CALC_PCO2_APPROX +o pkg/generic_advdiff + - make TAF generate code that vectorizes: + gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F +o model/src: + - improve vectorization also for adjoint code of + solve_tridiagonal and solve_pentadiagonal. As this requires up to + 5 new 3D-fields, this code is only turned on for the combination of + ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message + for singular matrix check (only for TARGET_NEC_SX). + - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to + ALLOW_AUTODIFF. This flag now needs to be set outside of + solve_tri/pentadiagonal.F +o pkg/exf: + - fix previous modif in exf_readparms.F (revision 1.66: treatment of + optional namelist EXF_NML_OBCS). + - add many debug-print (to trace down where pkg/cal error msg comes from) +o pkg/mom_vecinv/mom_vi_hdissip.F + - rearrange loops so that vectorization is improved and in particular + the adjoint routine vectorizes. The code is a little longer now, but I + think easier to read. + Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested. +o pkg/seaice: + - allow to specify initial seaice velocity from files (uIceFile,vIceFile) +o pkg/exch2: + - alternative code (without tile x tile matrix) for cumulated (global) sum; + used as default; keep using matrix version in adjustment.cs-32x32x1. +o tools/build_options: + - after merging some MPI and/or multi-threads specific optfiles so that + the modified default optfile support both built (using genmake2 -mpi + for the MPI built, using genmake2 -omp for OpenMP built), + move now obsolete optfiles to tools/build_options/unsupported/ + (add copy of email sent to support list in doc/optfiles_changes.txt) + +checkpoint63c (2011/09/28) +o pkg/ebm: + - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of + test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d) +o pkg/seaice (SItracer pickup) +* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER) + To be done: + - thorough testing of missing fields in S/R seaice_read_pickup + - thorough matching between generic tracers and specific fields used + (e.g. volume-weighted age, area-weighted age, salinity, ...) +o pkg/grdchk: + - all procs calculate and print finite-difference gradient (for testreport) + - change description output used by testreport; + - AD testing: also compare and report Finite-difference gradient; + => update all output_adm*.txt +o test exp. global_ocean_ebm: + - switch back useRealFreshWaterFlux (no problem anymore with run-off); + and turn on exactConserve; update (fwd) output. +o pkg/seaice (LSR): + - print to STDOUT number of solver iterations at SEAICE_monFreq interval. + - modify solver to deal cleanly with u/v switch at face edges (CS-grid): + * identical results with non-CS topology (but save up to half of EXCH calls) + * no much changes in cs-32 verification tests since no ice at face edges + (differences due to convergence criteria, since nb of iterations changed) + * expect some differences on lat-lon-cap grid. + update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice) +o pkg/exch2: + - add new CPP option to disable Cumul-Sum matrix (to save storage when using + many tiles); until alternative coding is added, just add a stop. +o pkg/kpp: + - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F + to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list). +o optfiles: + - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles + into corresponding standard one, which now support different build: + (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built) + - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael) +o pkg/obcs (seaice): + - add missing EXCH for uIce,vIce after applying OBCS; + - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding + argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R + EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F; + - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared) + - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi + and eedata.mth for MPI and mutlti-threaded testing. +o pkg/flt: + - make FLT EXCH working with multi-threads (and MPI + multi-threads); + - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h; + - fix pickup and trajectories + profiles output with multi-threads; + - add parameter to select group of fields to write along trajectory and + profile (default unchanged); + - only call PORT_RAND* function when flt_noise <> 0; + - add multi-threaded test for verification exp. flt_example. +o eesupp/src: + - fix S/R ALL_PROC_DIE for MPI+multi-threads. + - USE_OMP_THREADING: check that number of threads (from eedata) matches + actual number (from env.var. setting). +o pkg/ebm: + - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file. + - add multi-threaded test for verification exp. global_ocean_ebm + +checkpoint63b (2011/08/29) +o pkg/ebm: + - fix sign of runoff; + - update directly forcing fields (Qnet,EmPmR) to use standard + external_forcing_surf.F (remove ebm_forcing_surf.F); + - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F); + - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm) + and apply relaxation towards corresponding SST field (2-D map or ZonAver). + - update global_ocean_ebm parameters file data and update output (fwd+ad). +o verification/matrix_example: + - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for + MPI and mutlti-threaded testing. +o pkg/matrix: + - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ; + - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter); + - fix for multi-threaded (remove DATA statement); + - use standard DIFFERENT_MULTIPLE function; + - add MATRIX_OPTIONS.h +o verification/matrix_example: + To allow to split the domain in several tiles, change the domain size + from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on + Western side) of land points. +o (*_)write_pickup: + - fix few bugs in mypackage_read/write_pickup.F + - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into + array of length 1 (was caught by compiler syntax-check). +o pkg/diagnostics (velocity potential solver): + - fix initialisation of main diagonal matrix (for overlap values) +o tools/build_options: + - towards single optfile for MPI and non-MPI built: merge few +mpi optfile + into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11) + - linux_amd64_gfortran: merge +mpi_generic version into standard optfile: + * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ; + * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list; + and use "-devel" testreport option for standard testing on baudelaire. +o pkg/grdchk: + - Assume that all gradient-check position are within the same tile + corresponding to global indices (iGloTile,jGloTile) and that + positions (i,j indices or nbeg) are local to this tile; + - set tile local-indices and proc. number according to tile global-indices; + - remove grdchkwhichproc from namelist (retired param); + - send adjoint gradient to all procs so that all procs print it to STDOUT; + - switch on MPI test for global_ocean.90x40x15 AD test experiment. +o adding package bbl (Bottom Boundary Layer) + description in MITgcm/pkg/bbl/bbl_description.tex + example/test experiment in MITgcm_contrib/bbl +o adjoint verifications + - changed 5 experiments to multi-tiles + * global_ocean.90x40x15 + * obcs_ctrl + * offline_exf_seaice + * tutorial_dic_adjoffline + * tutorial_tracer_adjsens + changed reference output for those that crossed tile boundaries + (changed choices of gradient check positions) + - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi) + - temporary bug fix in grdchk_loc.F for obcs +o genmake2 & testreport + - add target "obj" (just for OBJFILES files) to Makefile; + - add option to specify FEXTRAFLAGS on command line. +o pkg/mypackage: + - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS + +checkpoint63a (2011/08/02) +o pkg/diagnostics (velocity potential): + - fix velocity-potential calculation when using OBCS: balance net inflow + at each level (new S/R OBCS_DIAG_BALANCE). + - fix some of the problems with OBCS in stream-function calculation. +o pkg/exf/exf_readparms.F + - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF, + EXF_NML_OBCS) more consistent, so that you need not have these lists + in data.exf when they are not used. +o optim/optim_readdata.F: + - add some output about obcs variables that might help debugging + - add a check about nvarlength +o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec +o pkg/diagnostics (velocity potential): + - fix mask for OBCS (still problems in stream-function with OBCS); + - add specific parameter (default = main code CG2D params) for solver; + - in case of poor convergence, use solution corresponding to lowest residual. +o pkg/seaice/seaice_growth.F: small changes that permit vectorizable + adjoint code. In general statements like tmpscal=fld(i,j) are problematic + and should be avoided where possible. +o model/src (rStar): + - include r* effect on reference-state (PhiRef) in totPhiHyd + (so that it's really the potential anomaly at the cell center); + affect solution only if z* with full pressure in EOS. + - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and + update output (because of z* in totPhiHyd and viscA4 changes); + - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly + @ constant r) until interpolation at constant r is implemented. +o pkg/diagnostics + - fix RCENTER diagnostics in case cell center is not at interface middle +o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use + this eos with eosType = 'TEOS10', in data (PARM01). This eos implies + that THETA and SALT are "conservative temperature" and "absolute + salinity" +o pkg/ctrl + - fix computation of endrec in s/r ctrl_init_rec + - ctrl_pack/unpack_*: remove unused variables and some obsolete code +o pkg/seaice/seaice_growth.F + - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code, + remove then obsolete STORE directives + - fix STORE directives for tice and tices, so that only the + appropriate part of the fields are stored (and not the entire + field); update global_ocean.cs32x15.seaice AD output. + - cosmetic changes: adjust CPP flags and indentation for better + legibilty +o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by + Chris Wilson) +o pkg/gmredi: + Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF), + and test it in verification exp. "front_relax.bvp" (update output.bvp.txt) + +checkpoint63 (2011/07/11) +o pkg/exch2: + - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h + - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the + (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y + increments, calculates Cumul-Sum @ tile origin and sends results to each tile. +o pkg/diagnostics: + - deal with pairs of post-processed diags which are computed together; in + particular, re-order list of diags within 1 file to save 2nd computation. + - add S/R to compute velocity stream-function (called after velocity-potential + calculation) from divergence free transport -> new diagnostics "PsiVEL". + - add parameter to select grid-point location where PsiVEL == 0. +o eesupp/src: + new S/R to calculate cumulated sum on tiled array, corner grid-cell location + (specific S/R needed with exch2 topology - for now, just print an error msg) +o pkg/shelfice + - Implement friction velocity-dependent transfer coefficients following + Holland and Jenkins, JPO, 1999 + Original code by M. Losch with small modifs. + Enable with CPP option SHI_ALLOW_GAMMAFRICT + and runtime flag SHELFICEuseGammaFrict +o verification lab_sea & global_ocean.cs32x15: + - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local): + does not miss some dependencies (but is slower) and also works with many files + (default makedepend limitation for AD built). + - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested). +o pkg/diagnostics: + - add run-time parameter "useMissingValue" (def=False) to fill land-point + (i.e., where mask=0) with MissingValue ; used only in MNC output file. + This replaces CPP-option DIAGNOSTICS_MISSING_VALUE. + - Extend the use of "missing_value" setting from data.diagnostics for the case + of counter-diagnostics (where fraction-weight is zero). This applies both to + MNC and MDS output files. +o pkg/seaice/seaice_growth.F: + - add 'a priori' cap of latent heat flux based on actual mass considerations + when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the + non-legacy seaice_solve4temp. + - add diagnostic of the residual sublimation freshwater flux (the freshwater + flux taken from the ocean if the total actual latent heat fluxes exceed + the maximum) + - remove the CPP switch around the *_FWbySublim unit change and move diagnostic + fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F. + - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef + SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim). + - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET. + - bug fix : missing part to Martin's r_FWbySublim pathological case fix. +o verification 1D_ocean_ice_column: + made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet + update results +o pkg/diagnostics: + - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P') + which are not filled-up but computed from other diags ; In this case, the mate + diag points to the primary (filled-up) diag to used for post processing. + - Update Velocity-potential computation using post-processed diag framework. + ==> Change the ordering of fields and time-periods in MDS output file + when using periodic averaging: now writes one time record with the full set + of fields for this time period, then the next time reccord (it used to be + one field with the full set of time records then the next field). + Note: this is now similar to NetCDF (MNC) output file. <== + +checkpoint62z (2011/06/21) +o adjoint monitor: + - Add adjoint monitor output for packages exf, seaice + and update relevant testreport output +o pkg/seaice: + - re-order diags inits so that they appear in order in available_diagnostics.log + - added diags: hsnow thermo. rates of change, area preceeding ridiging process, + area/heff/hsnow preceeding thermodynamic growth/melt. + - modified diag: SIdA; output actual effect, as the description states. + - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. + - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. + (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; + and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) + - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. + - added diagnostics for seaice generic tracers (SItr*). + - added SItrUnit and SItrNameLong run time param (for SItr* diags). + - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. + I. Fenty: 18-Jun-2011: + Minor changes to seaice package: + 1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and + added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) + - Differentiated "regularization variables" from "floor variables" + * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor + * hiceMin became SEAICE_hice_reg (old hiceMin) + (with _reg meaning regularization variable) + - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion + so as to ensure energy conservation when going between phases + - A22 was not used anywhere + 2) Changed regularization procedure for heffActual and hsnowActual to ensure + well-boundedness and smooth adjoint in seaice_growth.F + 3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells + because the old regularization always set heffActual >= 0.05 cm + 4) Changed the model so that the default behavior is to put a small (10^-5) "floor" + on AREA when HEFF > 0. + - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to + requiring that DISABLE_AREA_FLOOR *not* be defined + Affected verifications: + - 1D_ocean_ice_column (output.txt output_adm.txt) + - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) +o pkg/diagnostics: + - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). + - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument + (was _RL, now integer) with option = 0 to retrieve all levels. + - add pieces of code to compute velocity potential at each level (new diagnostics + PhiVEL, works only when UVELMASS & VVELMASS are also turned on); + for now, using same params as CG2D (target-resisual, max Nb of iter ...). + - fix few issues with counter diagnostics in diagnostics_setdiag.F & + diagstats_setdiag.F (if diagnostic counter is itself a counter diag) + and in diagnostics_fract_fill.F (do not need a valid pointer for the + diagnostics counter-mate); check that definition of counter-diagnostic + includes a valid counter-mate (in diagnostics_set_levels.F). +o model/src (rStar): + - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); + affect solution only if z* with full pressure in EOS; + update output of test-exp global_ocean.90x40x15. +o pkg/seaice: + - introduce siEps=1e-5 parameter + - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5). + - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code. + - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer. + For now it covers, and was tested for, ice salinity and age (attached to HEFF), + as well as ice cover age and ridging index (attached to AREA). + For now the run time parameters (in data.seaice/SEAICE_PARM03) are + SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA'). + Up to SItrMaxNum=3 tracers can be used simultaneously. +o pkg/salt_plume: + -introduce SPsalFRAC run time parameter that sets the fraction of the + salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically) + that gets vertically redistributed (fluxed down) by pkg/salt_plume. +o model debug options: + - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored + in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h). + - Refine debug-msg printing selection (3 new levels): + debugMode : controls printing of debug messages (sequence of S/R calls). + debugLevel : controls printing of algorithm-relevant auxiliary/debug messages + debLevZero = 0 ; /* level of disabled aux. msg printing */ + debLevA = 1 ; /* level of minimum aux. msg printing */ + debLevB = 2 ; /* level of low aux. print (report read-file opening)*/ + debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */ + debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */ + debLevE = 5 ; /* level of extensive debug printing */ + New debugLevel default: with default debugMode value (=F), + = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.; + and if debugMode=T, default debugLevel = 4 (debLevD). + Relation with previous settings: + debLevB (=2) corresponds to former debLevA (=1) + debLevD (=4) corresponds to former debLevB (=2) + Note: + a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before); + b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs); + to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5) + - Add new parameter (printResidualFreq, read from PARM02 namelist) to print + detailed CG solvers convergence; off (=0) by default, except if debugLevel=5. +o pkg/obcs: + - change OBCSfixTopo default from True to False (should not change the results); + keep OBCSfixTopo=T in verification-exp. seaice_obcs. +o pkg/thsice: + - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in + 2nd layer seaice sublimation (unlikely to happen) + - use Interior mask for OBCS in thsice_advection.F (similar to what is + done in gad_advection & seaice_advection). +o adjoint: + bug fix spotted by Gael Forget: + seaice_advection and thsice_advection still had + legacy CPP options to avoid CS corner updates for adjoint o pkg/seaice: => Change some of the defaults (2011/05/29): - change SEAICEuseFluxForm default (from False to True)