--- MITgcm/doc/tag-index 2013/02/12 22:26:11 1.1823 +++ MITgcm/doc/tag-index 2013/07/25 01:12:45 1.1901 @@ -1,9 +1,399 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1823 2013/02/12 22:26:11 jmc Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1901 2013/07/25 01:12:45 jmc Exp $ $Name: $ Notes on tags used in MITgcmUV ============================== +o Divided Adjoint (DIVA) with MPI: + - genmake2: do not create local ./mpi_headers dir when no file to copy into. + - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT + and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h. + +checkpoint64k (2013/07/23) +o tools/OAD_support: + - avoid the need for file "oadtempflile" in insertTemplateDir.bash + and remove it from genmake2. +o tools/build_options: + - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out + MPI_HEADER_FILES list (let genmake2 find the missing headers) +o verification/halfpipe_streamice: + - change to driving stress formulation; update both Fwd & AD output. +o tools/genmake2 and Divided Adjoint with MPI: + - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken); + - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set; + - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in + Makefile, which is set by genmake2, and check which mpi-headers are needed. + Note: need to update adjoint_options/adjoint_diva_mpi accordingly. + - update target "CLEAN" (to also remove ./mpi_headers/ dir). +o testreport: + - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, + perform additional runs (number of additional runs is "add_DIVA_runs" taken + from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h"). +o verification/lab_sea (AD test): + - change to test Divided Adjoint Run in this set-up (both standard AD test + and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test. +o pkg atm_ & ocn_compon_interf: + - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old + staggerTimeStep implementation) and disable (retired) corresponding + parameter. +o pkg/offline: + - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01]; + - add S/R OFFLINE_CHECK to print offline parameter summary + and stop if loading a file that is not used; + - enable to calculate GMRedi tensor, KPP mixing and convective index + when the corresponding file(s) is/are not specified (but pkg is used). + - comment out resetting of monitorFreq (to endTime) since it still useful + for monitoring CFL numbers and checking offline fields. +o OpenAD: + - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get + smaller standard output) and generate new (smaller) output (on baudelaire + using gfortran with -ieee) for exp. tutorial_tracer_adjsens +o model/src: + - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F), + (where external_forcing_adjust was called) and change list of arguments; + - merge external_forcing_adjust.F into external_forcing_surf.F + - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F) + which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX, + previously in file "balance_relax.F", now removed); remove corresponding + arrays in FFIELDS.h. + - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement + a hack for getting back surfaceForcingS (loaded from file) when using + ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up. + - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix + (was getting only 11 digits for AD-grad, due to different truncation + error in AD code). + +checkpoint64j (2013/07/04) +o pkg/offline: + - to enable the use of other features with pkg offline (e.g., obcs), + also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come. + - comment out "allowFreezing" (now active) in 2 offline testing exp. +o pkg/exf ALLOW_RUNOFTEMP + - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL + - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice + - changes verification/global_ocean.cs32x15/results/output.seaice.txt +o pkg/atm_phys: + - allows to add some damping on uVel,vVel (strength only function of k). +o verification, ad-tests: + - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, + global_ocean_ebm and offline_exf_seaice.thsice. +o verification/halfpipe_streamice: + - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused + flux input boundary conditions to be ignored; a fix for this bug changed + verification results for forward test. + - add adjoint test. +o pkg/ptracers: + - allow to restart without SOM pickup (resetting SOM to zero). +o pkg/gmredi: + - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added. + - It uses mixing length theory and suppression by steering level effects to + calculate a diffusivity used in the Redi tensor (see Bates et al., submitted + to JPO, for more details). + - It also uses the diffusivity to calculate an eddy induced streamfunction + based on a PV closure (rather than a buoyancy closure as in GM). + - New files added to pkg/gmredi: + gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy + induced overturning streamfunction (called from gmredi_calc_tensor) + gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required + for use in gmredi_k3d + gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate + the eddy diffusivity + +checkpoint64i (2013/06/18) +o pkg/cheapaml: + - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code + that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics) + with pkg/cheapaml. +o utils/python: add subpackage for cubed sphere function, first example is + simple cs.pcol to plot 2D fields on a map +o pkg/streamice: + - This is a new package in MITgcm, which solves dynamic equations for ice + sheets and ice streams + - At the moment it is independent of atmosphere/ocean dynamics, or any + other physical packages in MITgcm, even ShelfIce (although it is anticipat- + ed that this will change) + - There is a new verification exercise that tests it, halfpipe_streamice, + evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a + rectangular embayment + - halfpipe_streamice is forward-only for now, will have TAF test soon + - for questions, email dgoldber@mit.edu +o pkg/thsice: + - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing + of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40); + - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new + call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect ); + - allow precip from pkg/cheapaml to make snow over seaice. +o pkg/cfc: + - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC + - remove atmos CFC 2-D arrays from common bloc (now local variables) + - change some hard-coded constant to run time parameter for reading and + and interpolating atmospheric CFC ; keep same default as previously. + - more flexible reading of Atmos CFC (number of records no longer hard-coded) + - put arguments in standard order: myTime, myIter, myThid + - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of + atmospheric CFC ; fix for the case myIter < PTRACERS_iter0. + - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf + - new routine to print summary of CFC params and check for consistency. +o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff, + similar to thsice_advdiff. + Note that for the B-grid case the routine parameters uc/vc are overwritten. +o pkg/cfc: + - change time interpolation for atmospheric CFC-11 (now same as for CFC-12); + update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline. + - fix interpolation of atmphspheric CFC between Sorthern and Northern + hemisphere value. +o pkg/seaice: + - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml) +o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics; + so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE. + - requires an additional time level that is stored in the pickup + - you can start with AB2 from a pickup without this time level with + pickupStrictlyMatch = .false. + +checkpoint64h (2013/05/26) +o pkg/cheapaml: + - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux); + affect machine truncation (but exp cheapAML_box still pass with 13 digits). + - consistent treatment of uWind,vWind location: assume everywhere in + pkg/cheapaml that they are on C-grid (@ uVel,vVel location) + (Note: was already the case for Tair,Qair advection); + add option (INCONSISTENT_WIND_LOCATION) to recover old results. + - compute diabatic forcing only in the interior (excluding overlap regions) + - fill in array "Qsw" (for short-wave heating); + - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars + before any update (consistent with MITgcm state var diagnostics); + - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if + non periodic ; + adjusted for uWind,vWind (C-grid). +o pkg/seaice: + - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and + add explicitly pkg/exf in experiments that currently use pkg/seaice. + - allows to compile pkg/seaice without pkg/exf. +o tools/OAD_support: + - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds + of array "ourStepOf" in function rvNextAction (revolve.F90). +o pkg/aim_compon_interf renamed to pkg/atm_compon_interf + - change pkg name (to be used with other atmospheric physics pkg) + but by-pass CVS when making the new pkg so that we keep the CVS history. +o pkg/offline: + - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F + (previously called from pkg/dic_surfforcing_init.F) +o model/src: + - re-order sequence of calls within packages_init_variables.F, using + standard order, except for: + DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top), + CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom) +o new pkg: atm_phys + - add entry point and source code (previously in contrib + verification_other/atm_gray/code_gray/) for new pkg "atm_phys" + (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008). + - re-order sequence of calls within packages_readparms.F, + packages_init_fixed.F and packages_write_pickup.F + (but skip packages_init_variables.F because of TAF issues). + - update contrib/*/atm_gray/ experiment. +o pkg/seaice (ITD code): + - simplify and fix the writing of pickup-files for ITD case +o pkg/seaice (ITD code): + - introduce floe size dependent lateral melt for ITD case; + - cleaning (avoid division by zero, change to f77 syntax, remove tabs) + - update seaice_itd experiment main output. +o pkg/thsice: + - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and + declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F; + changed accordingly pkg/atm2d. + +checkpoint64g (2013/05/01) +o pkg/exf ALLOW_RUNOFTEMP + - if defined, river and glacier runoff temperature can be read-in from + runoftempfile; runoftempfile needs to have same format as runofffile +o pkg/thsice (& pkg/bulk_force): + - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account + for energy content of Precip + RunOff & Evap (like with pkg/exf). + - change computation domain to always be the interior (without overlap). + - fix bug (wrong overlap) when using EXF and stressReduction > 0. +o verification/tutorial_global_oce_biogeo: + - add preliminary OpenAD setup (still has problems) +o pkg/seaice: + - turn some parameters for choosing the convergence criterion of + the inexact Newton method (JFNK) into runtime parameters for convenience + - clean up seaice_calc_viscosities.F: remove/retire two options for + SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes + the results of lab_sea/input because a division has been replaced by + a multiplication with the reciprocal (sumNorm) + - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve + convergence of solver (changes results, of course), and to test some + new features +o model/src: + - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call. + - remove unused forcing field "dQdT" and associated parameter "dQdTFile". + - move forcing adjustment (balancing surface forcing) in specific S/R + where might also be applied exchanges (if needed) to forcing arrays. +o pkg/shelfice: + - allow to specify the Ice-Shelf mass per unit area (instead of + shelficeLoadAnomaly) and do the conversion from one to the other + - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA + to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and + (b) will be loaded in time (before calling INI_PRESSURE) in case it is + needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc + - update isomip experiment forward output (get machine truncation error + from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly) +o verification/offline_exf_seaice: + revise data.seaice in input.thermo and input_ad and update results accordingly + HO = 0.2, SEAICE_areaLossFormula = 2, + SEAICE_growMeltByConv = .TRUE., + SEAICE_doOpenWaterMelt = .TRUE., + Improve consistency with input.thsice and fix the spurious 500m ice corners +o verification/global_ocean.cs32x15: + - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0., + in icedyn (thsice+seaice-dyn) test and update output. +o verification/offline_exf_seaice: + - adjust list of tested variables (with testreport) and update + standard test output with better slection of monitored fields. +o pkg/cd_code: + - swtich off Adams-Bashforth on the 1rst iteration. Update output of + experiment lab_sea.hb87 +o tools/genmake2: + - change default makedepend from the system default to tools/xmakedepend: + When no makedepend is specified, select tools/xmakedepend it the test pass, + otherwise select the system default (if exist and pass the test) or + try to build cyrus-makedepend ; stop if none of the 3 works. +o pkg/exf & pkg/thsice: + - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account + for energy content of Precip + RunOff & Evap. Assumes: + 1) Rain has same temp as Air. + 2) Snow has no heat capacity (consistent with seaice & thsice pkgs) + 3) Run-Off comes at the temp of surface water (with same Cp) + 4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be + put directly into Latent Heat flux & should use water-vapor heat capacity. + 5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent + with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL). +o pkg/seaice: simplify the use of CPP flags in JFNK-related files + (compile when SEAICE_ALLOW_JFNK is defined) +o pkg/thsice: + - fix oceanic flux diagnostics & timeave (left from new sequence of calls + implementation): move THSICE_AVE call after the advection (called directly + from thsice_do_advect.F). +o verification/global_ocean.90x40x15 and OpenAD: + New experiment for OpenAD is identical to the one in input_ad except that + multiDimAdvection=.FALSE., + There is still an issue with this. +o pkg/thsice: + - account for ice velocity (ocean relative velocity) in turbulent heat flux + at the base of the ice; update output of global_ocean.cs32x15 (icedyn) + and offline_exf_seaice (main test). + +checkpoint64f (2013/03/31) +o verification/OpenAD: + - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran. +o verification/isomip, pkg/shelfice and OpenAD: + - add OpenAD setup to this exp and make shelfice package work with OpenAD +o verification/tutorial_global_oce_biogeo: + - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h) +o verification/offline_exf_seaice: + - replace adjoint experiment (now similar to fwd input.thermo/ setup). +o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD: + - add OpenAD setup to this exp and make ptracers package work with OpenAD +o pkg/seaice/seaice_evp.F: + mask the asymmetric contribution of the ice-ocean stress (when + the turningAngle is non-zero) over open water to avoid stripes + in the EVP-solutions after many EVP-substeps. This does not change + the verification experiment (because turningAngle=0 in that experiment), + but will affect other EVP solutions with turningAngle.ne.0 +o verification, AD & TLM output: + - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple + additions and multiplications which affect results at machine truncation + level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5, + lab_sea.noseaicedyn & offline_exf_seaice) and TLM output + (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12 + digits of matching. +o pkg/seaice: + modify lsr-algorithm so that it vectorizes AND converges by using a + "zebra" method: split vector loop into two with step size 2; this + solves a general convergence problem for the JFNK solver on a vector + computer. It has the potential to even improve convergence for + non-vector machines, but it does change the results so it is turned + off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and + SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h + +checkpoint64e (2013/03/05) +o pkg/ecco and several verification experiments: + Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F + from ecco package, and revert to unified routine in model/src/ + Adjust verification experiments accordingly, especially gloal_oce_llc90 + Should conclude long-standing work by Gael to reconsile the_main_loop with + ECCO and will enable OpenAD's revolve loop in ECCO setup. +o pkg/generic_advdiff: + - implement compressible flow method for multi-dim advection (similar to + gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since + TAF generates many recomputations) to use it; no yet coded with implicit + vertical advection. + - change experiment advect_cs (new output) and advect_xy (same output) + to test compressible flow multi-dim advection. +o pkg/generic_advdiff: + - fix SOM advection for unusual cases (linear Free-Surf in r*, other + cases where linear Free-Surf is not @ k=1, e.g., useShelfIce) +o pkg/seaice: + - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this + bug affects two verification experiments (lab_sea and lab_sea.hb87), + recover old (wrong) results by setting noSlipFac = 2. in + seaice_calc_strainrates.F; + - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0 + - add runtime parameter SEAICE_JFNKepsilon for that finite difference + gradient in the Jacobian times vector operation (s/r seaice_jacvec) + - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update) +o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code: + - new subroutines seaice_lsr_tridiagu/v + - introduce loop bounds i/jmin/max to be able to use a restricted + additive Schwarz method, but not used for now. + - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS + - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner +o OpenAD support + Reorganize S/R call for overall time-stepping loop to facilitate + OpenAD revolve loop replacement + (new S/R main_do_loop.F) +o model/src: + - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3; + - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R + ADAMS_BASHFORTH2. +o pkg/cheapaml: + - add new parameter (default=F, same as before) to disable full domain + (including land) periodicity in X & Y dir. + - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of + prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer + into single S/R CHEAPAML_TIMESTEP. + +checkpoint64d (2013/02/17) +o pkg/monitor (angular momentum): + - do not add Eta contribution to the total AM if using rigid-lid; + - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta). + - horizontal discretisation: compute Zonal wind contribution separately for + each component (instead of from cell centered averaged) and use the 4 + grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part. + - Check that AM is conserved with linear dynamics (momAdvection=F and linear + FreeSurf) if using vectorInvariant momentum. +o model/src (horizontal grid): + - move initialisation of all horizontal grid arrays to null value + from specific horizontal grid S/R to main S/R INI_GRID; + - add 2 new arrays to project model C-grid velocity on to zonal direction + (similar to AngleCosC & -AngleSinC but at U and V point location) and + compute them in S/R CALC_GRID_ANGLES. +o pkg/seaice: replace a hard coded parameter by a runtime parameter + SEAICE_JFNK_tolIter +o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in + preconditioner for JFNK (run LSR into the overlaps as far as possible, + i.e OLx/y-2, but overwrite the solution in the overlaps) + - extend loop range in seaice_calc_viscosity + - add new parameters SEAICE_OLx/y (default = OLx/y-2) + - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs + - slightly modify loops in tridiagonal solver lsr-preconditioner + - by default remove the extra exchange in seaice_preconditioner with a + replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE + - modify offline_exf_seaice so that old results without RAS are reproduced + for output.dyn_jfnk.txt + in seaice_fgmres.F (unrelated to RAS) + - add a cpp-flag option for a re-ordered mapping (potentially more + efficient), but because this changes the results, turn it off by + default + - replace the save statement by local common blocks o utils/matlab: - fix tile-offset in rdmnc.m when output was produced using EXCH2. - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)