--- MITgcm/doc/tag-index 2013/05/10 20:19:37 1.1867 +++ MITgcm/doc/tag-index 2013/07/25 01:12:45 1.1901 @@ -1,9 +1,179 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1867 2013/05/10 20:19:37 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)