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2019-10-12:

16:08 Changeset [11692] by francesca

Update branch to integrate the development starting from the current v4.01 ready trunk

00:07 Changeset [11691] by agn

added OSMOSIS figure

2019-10-11:

19:05 Changeset [11690] by nicolasmartin

Update chapters according to previous commit

19:03 Changeset [11689] by nicolasmartin

Cleaning and renaming for readability
Apply the same rule from the LaTeX labels with the chapter prefix in the name of the figures
Put orphan files in unused subfolder

17:59 Changeset [11688] by nicolasmartin

Load grffile package to avoid import issue with file extension

16:56 Changeset [11687] by nicolasmartin

Temporary solution to solve LaTeX compilation issue with \includegraphics while waiting for TeXLive fix
For reference, see https://github.com/MiKTeX/miktex-packaging/issues/131

00:37 Changeset [11686] by agn

Font Awesome? fix for texlive on Mac

00:16 Changeset [11685] by agn

added OSMOSIS documentation to chap_ZDF.tex

00:16 Changeset [11684] by agn

chap_ZDF.tex now compiles

00:16 Changeset [11683] by agn

Monday morning

00:16 Changeset [11682] by agn

Sunday

00:15 Changeset [11681] by agn

Wednsday's changes

00:15 Changeset [11680] by agn

Thursday

00:15 Changeset [11679] by agn

Wednesday's additions

00:15 Changeset [11678] by agn

Tuesday's additions

00:15 Changeset [11677] by agn

added structure figure

00:15 Changeset [11676] by agn

Few more changes tp chap_ZDF.tex

00:15 Changeset [11675] by agn

started on flux-gradient relationship

00:15 Changeset [11674] by agn

start of OSMOSIS docs

2019-10-10:

17:24 Changeset [11673] by nicolasmartin

Fix missing LaTeX pkgs

12:32 Changeset [11672] by laurent

LB: "sbcblk_skin_coare.F90" now relies on "sbcdcy.F90" (modified) to know dawn/dusk time

2019-10-09:

15:02 Changeset [11671] by acc

Branch 2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles. Final, non-substantive changes to complete this branch. These changes remove all REWIND statements on the old namelist fortran units (now character variables for internal files). These changes have been left until last since they are easily repeated via a script and it may be preferable to use the previous revision for merge purposes and reapply these last changes separately. This branch has been fully SETTE tested.

14:52 Changeset [11670] by acc

Branch 2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles. Final substantive change to enable this branch to work with AGRIF. Most changes have occurred on an AGRIF development branch: /vendors/AGRIF/dev_r11615_ENHANCE-04_namelists_as_internalfiles_agrif which is needed to make this work. Previous commit to this branch has set the svn:externals reference accordingly

14:46 Changeset [11669] by acc

Modify svn externals definition only.

14:01 Changeset [11668] by acc

Branch dev_r11615_ENHANCE-04_namelists_as_internalfiles_agrif. Changes to support 2019/dev_r11615_ENHANCE-04_namelists_as_internalfiles developments.
These changes enable sufficient support for allocatable, zero-dimension character variables defined using the:

CHARACTER(LEN=:), ALLOCATABLE :: cstr

syntax. This is supported by:

  1. Adding : as a valid length identifier at line 1028 in fortran.y (and then rebuilding fortran.c and main.c via make -f Makefile.lex)
  2. Adding a carrayu entry to Agrif_Variable_c type in AGRIF_FILES/modtypes.F90 where carrayu is declared as:
character(:) , allocatable
carrayu
Ensuring correct deallocation of carrayu in AGRIF_FILES/modsauv.F90 and AGRIF_FILES/modutil.F90
  • Substituting carrayu in place of carray0 declarations when character length matches : for zero-dimension variables. This occurs twice in LIB/toamr.c, e.g:
  • if (!strcasecmp(var→v_dimchar ,":") && var→v_nbdim == 0 )
    {
    sprintf (tname_2, "%% carrayu");
    } else {
    sprintf (tname_2, "%% carray%d", var→v_nbdim);
    }

    Any such character variables must be allocated by the user. Typically this is done with lines such as:

    IF ( .NOT. ALLOCATED(cdnambuff) ) ALLOCATE( CHARACTER(LEN=kleng)
    cdnambuff )

    making AGRIF accept the CHARACTER(LEN=kleng) :: construct within the ALLOCATE statement was beyond my skills. Fortunately, for the current purpose, this
    isn't necessary since such allocations only occur within utility routines in which the appropriate tabvar has been passed down. So:

    !$AGRIF_DO_NOT_TREAT

    IF ( .NOT. ALLOCATED(cdnambuff) ) ALLOCATE( CHARACTER(LEN=kleng)
    cdnambuff )
    !$AGRIF_END_DO_NOT_TREAT

    avoids the issue.

    12:40 Changeset [11667] by acc

    New AGRIF development branch for AGRIF changes associated with 2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles developments. Primarily this introduces some support for allocatable, zero-dimension character arrays using the CHARACTER(LEN=:) , ALLOCATABLE :: cstr syntax. Changes are minimal but LEX additions necessitate rebuilding fortran.c and main.c which end up looking very different

    12:17 Changeset [11666] by laurent

    LB: improved syntax

    11:48 Changeset [11665] by laurent

    LB: syntax improvement.

    2019-10-08:

    19:32 Changeset [11664] by smueller

    Inclusion of selected long-periodic tidal constituents in the computation of the tidal potential (ticket #2194)

    18:36 Changeset [11663] by smueller

    Addition of a namelist parameter to enable the selectability of alternative tidal parameter sets and tide-potential computations

    17:24 Changeset [11662] by nicolasmartin

    Idem as before

    17:24 Changeset [11661] by nicolasmartin

    Move custom bash Emacs fontification in a more appropriate place

    12:09 Changeset [11660] by laurent

    LB: xios output of evaporation in sbcblk.F90

    2019-10-07:

    20:23 Changeset [11659] by mathiot

    ENHANCE-03_domcfg: update README.rst (ticket #2143)

    19:55 Changeset [11658] by mathiot

    ENHANCE-03_domcfg: forced local domain to read the overlap region + re-arange the ocean output print (ticket #2143)

    11:50 Changeset [11657] by dancopsey

    Couple the correct sea ice meltpond variables

    2019-10-04:

    21:03 Changeset [11656] by mathiot

    ENHANCE-03_closea: add heat/fw fluxes output from closed seas + rm useless USE statements + add USE ONLY when reasonable + ensure heat conservation during the redistribution process (ticket #2143)

    17:24 Changeset [11655] by smueller

    Addition of explicit job-name specification in the batch-script template for the NOC HPC system

    15:15 Changeset [11654] by mathiot

    ENHANCE-03_domcfg: forced the tools to write data over the EW overlap region. Issue in some eORCA1 decomposition without (ticket #2143)

    14:34 Changeset [11653] by davestorkey

    Fix for bug in Smagorinsky scheme #2318.

    13:40 Changeset [11652] by andmirek

    Ticket #2314. Fix previous commit. Gives the same solution as Eric local copy for ORCA1.

    12:07 Changeset [11651] by davestorkey

    UKMO/NEMO_4.0_GO8_package : Apply Smagorinsky bug fix (#2318) in GO8 package branch as temporary measure before we pick it up from trunk.

    10:59 Changeset [11650] by clem

    change arch file for jean-zay machine. Necessary to get restartability/reproducibility

    10:57 Changeset [11649] by clem

    change default parameters for landfast ice (Jef Lemieux pers. communication)

    2019-10-03:

    17:57 Changeset [11648] by acc

    Branch 2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles. Introduce broadcast of namelist character buffer from single reader to all others. This completes the second stage but there is still an issue with AGRIF that may scupper this whole concept

    15:56 Changeset [11647] by laurent

    LB

    14:13 Changeset [11646] by andmirek

    Ticket #2314 changes for GO8 for tests

    12:00 Changeset [11645] by clem

    make sette work for jean-zay machine

    10:06 Changeset [11644] by cetlod

    Create branch to include CMIP6 diagnostics, see ticket #2315

    2019-10-02:

    16:29 Changeset [11643] by marc

    Adding in Dr Hook to our OMIP branch.

    16:28 Changeset [11642] by acc

    Branch 2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles. Bugfixes on previous commit; fix substring starting point so that it advances correctly when reading namelist block with the loop.

    15:12 Changeset [11641] by acc

    Branch 2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles. Further substantive changes to the BDY routines that read multiple copies of some namelists from namelist_cfg. Special treatment is required to replicate the original behaviour with internal files. These changes emulate previous behaviour but removal of the reliance on multiple, same-named namelist blocks would be preferable.

    14:06 Changeset [11640] by clem

    just correct a print

    13:13 Changeset [11639] by rrenshaw

    regional mean and transport diagnostics added for reanalysis

    12:53 Changeset [11638] by laurent

    LB: preliminary inclusion of "STATION_ASF" test-case!

    12:48 Changeset [11637] by laurent

    LB: preliminary inclusion of "STATION_ASF" test-case!

    12:41 Changeset [11636] by mathiot

    revert yesterday changes and update mpp_loc_generic.h90 with the trunk version instead (ticket #2143)

    12:25 Changeset [11635] by rrenshaw

    updated branch for amm7 reanalysis

    10:50 Changeset [11634] by rrenshaw

    Add Rob's change ticket 246 to use surface data at coorect depth

    2019-10-01:

    21:06 Changeset [11633] by mathiot

    modification for in case a domain is a land domain (MINLOC return 0 as indices for the min) (ticket #2143)

    20:57 Changeset [11632] by clem

    limit snow thickness after advection (with Prather) if snow load makes the ice-snow interface to deplet below sea surface (as for UM scheme)

    20:22 Changeset [11631] by laurent

    LB: syntax improved…

    19:37 Changeset [11630] by nicolasmartin

    Review of TRA chapter

    18:17 Changeset [11629] by mathiot

    ENHANCE-03_closea: cosmetic changes (ticket #2143)

    18:12 Changeset [11628] by mathiot

    ENHANCE-03_domcfg: add cpp_ENHANCE-03_domcfg.fcm and remove make_closea_masks.py (as now managed in the F90 code and remove compilation file (ticket #2143)

    15:34 Changeset [11627] by clem

    change some wrong comments

    15:25 Changeset [11626] by laurent

    LB: syntax improved…

    15:18 Changeset [11625] by jchanut

    #2222, add initialization to 0 of tracer open boundary data with vertical interpolation + various neutral optimizations

    15:07 Changeset [11624] by acc

    Branch 2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles. Substantive changes required to replace all namelists with internal files. These are the key changes only; to compile and run tests all REWIND and CLOSE operations on the (no longer) units have to be removed. These changes affect many more files but can be scripted so are not included here in order to make a later merge easier. The scripts used to prepare code for testing are included on: wiki:2019WP/ENHANCE-04_AndrewC-reporting/Internal_Namelists. With these additional changes this code passes most SETTE tests but the AGRIF preprocessor does not currently accept the new allocatable character strings. To be investigated.

    14:59 Changeset [11623] by laurent

    LB: syntax improved…

    13:10 Changeset [11622] by nicolasmartin

    Review of "Time Domain" and DOM chapters

    2019-09-30:

    18:26 Changeset [11621] by clem

    modify path for jeanzay arch files

    16:37 Changeset [11620] by davestorkey

    UKMO/NEMO_4.0_momentum_trends : remove option to thickness-weight time mean of utrd_tau fields.
    (Tiny error and utrd_tau fields not required for budgets).

    15:57 Changeset [11619] by laurent

    LB: new cool-skin and warm-layer parameterizations for ECMWF and COARE3.6, COARE3.0 uses same CSWL param as for COARE3.6.

    15:49 Changeset [11618] by laurent

    LB: new cool-skin and warm-layer parameterizations for ECMWF and COARE3.6, COARE3.0 uses same CSWL param as for COARE3.6.

    15:33 Changeset [11617] by laurent

    LB: new cool-skin and warm-layer parameterizations for ECMWF and COARE3.6, COARE3.0 uses same CSWL param as for COARE3.6.

    15:23 Changeset [11616] by laurent

    LB: new cool-skin and warm-layer parameterizations for ECMWF and COARE3.6, COARE3.0 uses same CSWL param as for COARE3.6.

    15:18 Changeset [11615] by laurent

    LB: new cool-skin and warm-layer parameterizations for ECMWF and COARE3.6, COARE3.0 uses same CSWL param as for COARE3.6.

    14:34 Changeset [11614] by acc

    New development branch: 2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles to try out improvements to namelist handling. See wiki:2019WP/ENHANCE-04_AndrewC-reporting/Internal_Namelists for the initial ideas. This work forms part of #2167

    11:07 Changeset [11613] by davestorkey

    UKMO/NEMO_4.0_momentum_trends branch : first set of code changes.

    2019-09-29:

    10:55 Changeset [11612] by clem

    make Prather the default advection scheme for ice simulations and drastically reduce the number of communications in Prather routine (by a factor of 10)

    2019-09-27:

    17:41 Changeset [11611] by davestorkey

    Branch to implement revised momentum trends diagnostics to correspond more closely to terms in the primitive equations.

    14:08 Changeset [11610] by jchanut

    #2222, fixes to enable compiling AGRIF with TOP

    13:38 Changeset [11609] by cetlod

    dev_PISCES_LBC : minor improvments

    12:24 Changeset [11608] by nicolasmartin

    Review of "Model Basics" chapter

    11:59 Changeset [11607] by jchanut

    #2222, remove slight unconsistencies in update with or without key_vertical defined

    10:10 Changeset [11606] by cetlod

    Add batch template for CNRS new computer JEAN-ZAY

    2019-09-26:

    21:23 Changeset [11605] by jamesharle

    #2222, tidy _wp for some variables. There are small difference in
    simulations of the AGRIF_DEMO config with Pacific only nest (same
    vertical grid) with and without key_vertical.

    18:48 Changeset [11604] by mathiot

    ENHANCE-03_domcfg: remove useless variable in domclo and domutil + cosmetics changes (ticket #2143)

    17:27 Changeset [11603] by jchanut

    #2222, 1) correct time interpolation of barotropic velocities in corners. 2) Clean remapping module and enable remapping several variables at the same time. At this stage, vertical remapping doesn't change VORTEX results with an identical vertical grid ONLY in one way mode and a linearized free surface (within truncature errors).

    17:16 Changeset [11602] by mathiot

    ENHANCE-03_domcfg: remove gde3w_0 as outputed in domcfg.nc (ticket #2143)

    16:54 Changeset [11601] by clem

    correct the check on conservation for sea ice (does not impact sette tests)

    13:58 Changeset [11600] by cetlod

    Typo correction in namelists

    2019-09-25:

    22:19 Changeset [11599] by nicolasmartin

    Cosmetic cleaning

    22:00 Changeset [11598] by nicolasmartin

    Add template of versioning record at the beginning of chapters

    20:20 Changeset [11597] by nicolasmartin

    Continuation of coding rules application
    Recovery of some sections deleted by the previous commit

    19:06 Changeset [11596] by nicolasmartin

    Application of some coding rules

    • Replace comments before sectioning cmds by a single line of 100 characters long to display when every line should break
    • Replace multi blank lines by one single blank line
    • For list environment, put \item, label and content on the same line
    • Remove \newpage and comments line around figure envs
    16:22 Changeset [11595] by nicolasmartin

    Fix the paths for graphics searching

    16:16 Changeset [11594] by nicolasmartin

    Review svn:ignore and svn:externals properties (3)

    16:14 Changeset [11593] by nicolasmartin

    Review svn:ignore and svn:externals properties (2)

    16:11 Changeset [11592] by nicolasmartin

    Review svn:ignore and svn:externals properties

    13:52 Changeset [11591] by nicolasmartin

    Cleaning, linking and renaming

    2019-09-23:

    18:25 Changeset [11590] by jchanut

    #2222: 1) create remapping module (vremap) and integration of D. Engwirda piecewise polynomial recontruction package (PPR_LIB cpp key). 2) Various bug corrections with key_vertical activated.

    17:12 Changeset [11589] by gsamson

    dev_r11265_ABL : see #2131

    • ABL_TOOLS first working version (README empty and arch files ignored for now)
    16:53 Changeset [11588] by dancopsey

    Move test for nn_iceini_file to after it is loaded from namelist.

    2019-09-20:

    18:50 Changeset [11587] by gsamson

    dev_r11265_ABL : see #2131

    • merge trunk @ r11584 with dev_r11265_ABL branch @ r11586 (except doc directory)
    • change ORCA2 results compared to dev_r11265_ABL branch @ r11586 (TBI)
    17:28 Changeset [11586] by gsamson

    dev_r11265_ABL : see #2131

    • merge HPC-13_IRRMANN_BDY_optimization branch @ r11535 (last commit) with dev_r11265_ABL branch @ r11414 (except doc directory)
    • change ORCA2 results due to changes in HPC-13_IRRMANN_BDY_optimization branch
    14:54 Changeset [11585] by dancopsey

    Make nn_iceini_file public

    13:16 Changeset [11584] by nicolasmartin

    Restoration of separate compilation of chapters or appendices
    The command to launch is almost the same as the manual, for instance

    $ latexmk -r latex/global/latexmkrc -cd latex/NEMO/subfiles/chap_time_domain
    
    11:49 Changeset [11583] by dancopsey

    Change nn_iceini_file in the reference namelist

    11:44 Changeset [11582] by nicolasmartin

    New LaTeX commands \nam and \np to mention namelist content (step 2)
    Finally convert \forcode{...} following \np{}{} into optional arg of the new command \np[]{}{}

    11:40 Changeset [11581] by dancopsey

    Create nn_iceini_file=2 option that loads sea ice restart file.

    10:10 Changeset [11580] by jchanut

    #2199, remove useless boundary data interpolation at domain edges (used previously with 1 ghost cell and near boundary filtering)

    2019-09-19:

    19:48 Changeset [11579] by nicolasmartin

    Fix for the sort of the blocks index

    19:44 Changeset [11578] by nicolasmartin

    New LaTeX commands \nam and \np to mention namelist content (step 2)
    So far so good, the manual compiles successfully 4 times and everything seems in its right place

    19:01 Changeset [11577] by nicolasmartin

    New LaTeX commands \nam and \np to mention namelist content
    (Partial commit to serve as a backup before other large edits)
    In order to benefit of the syntax highlighting and to have a simpler syntax for
    citing namelist block (\nam) and parameter (\np) with an optional variable assignment (\forcode{…}),
    at this time the only viable solution I found is to require a double marker for
    what it looks like the same item:

    1. Marker with the real name: 'tra_adv' block or 'ln_flx' parameter
    2. Marker with underscore character escaping: 'tra\_adv' block or 'ln\_flx' parameter

    Despite many searches and attempts, I did not find a workaround to edit on-the-fly one or
    the other marker.
    In fact, the problem is on one side that the LaTeX index interprets '_' as a switch for lowering like
    in math mode while on the other hand the backslash is considered for Pygments as a typo in Fortran
    (red box).

    For instance, \nam and \np have as of now the aforementioned 2 mandatory arguments in
    the previous order (between braces) + an optional argument for \np when the parameter is defined
    (between brackets at the first position):

    • \nam: LaTeX code in the \nam{tra_adv}{tra\_adv} → PDF ' in the &namtra_adv (namelist X.X) ' with syntax highlighting, the hyperlink and the index entry
    • \np: LaTeX code \np[=.true.]{ln_flx}{ln\_flx} → PDF ln_flux=.true. with syntax highlighting for the whole string and the entry in the 'parameters' index
    17:33 Changeset [11576] by dancopsey

    Make branch to initialise sea ice from a restart file

    12:51 Changeset [11575] by clem

    improve one output for sea ice. Does not change anything else in the code

    12:08 Changeset [11574] by jchanut

    #2222, import changes from dev_r10973_AGRIF-01_jchanut_small_jpi_jpj (i.e. #2199)

    11:18 Changeset [11573] by jchanut

    #2222, merged with trunk

    10:47 Changeset [11572] by nicolasmartin

    Review indexes style

    10:44 Changeset [11571] by nicolasmartin

    Cosmetic modifications on section titles

    2019-09-18:

    19:51 Changeset [11570] by jchanut

    #2222, delete som external properties

    19:30 Changeset [11569] by jchanut

    #2222, useless branch

    17:52 Changeset [11568] by mathiot

    ENHANCE-02_ISF: fix compatibility issue between rn_hmin and ice shelf (ticket #2142)

    17:41 Changeset [11567] by nicolasmartin

    Style improvments

    17:16 Changeset [11566] by jchanut

    #2222, Start new developing branch for AGRIF vertical interpolation

    16:58 Changeset [11565] by nicolasmartin

    Cleaning of section titles

    16:11 Changeset [11564] by jchanut

    #2199, merged with trunk

    15:36 Changeset [11563] by nicolasmartin

    Miscellaneous changes

    15:32 Changeset [11562] by nicolasmartin

    New page layout with shorter margins (manual at less than 300 pages)

    15:24 Changeset [11561] by nicolasmartin

    Apply two thirds ratio on figures width as default

    13:31 Changeset [11560] by clem

    correct the conversion from 1cat to Ncat for ice data at the boundaries when using bdy

    10:53 Changeset [11559] by mattmartin

    Added code to include variable slip condition which is used by orca12 into the main GO6 FOAM branch so that the branch list doesn't need to be different for orca12 and orca025.

    2019-09-17:

    17:04 Changeset [11558] by nicolasmartin

    Review all figure envs + activation of listoflistings

    1. Figure env:
      • Replace center sub-env with only \centering cmd
      • Add alternate caption for \listoffigures (shorter one between square brackets, i.e. \caption[]{})
      • Place \label outside of \caption and remove useless \protect
    1. Namelist listings
      • Put \nlst with the namelist inlcusion in a listing float env with caption and label
      • Remove namelist duplicates

    — This line, and those below, will be ignored—
    M subfiles/apdx_triads.tex
    M subfiles/chap_model_basics_zstar.tex
    M subfiles/chap_SBC.tex
    M subfiles/apdx_DOMAINcfg.tex
    M subfiles/apdx_s_coord.tex
    M subfiles/chap_DOM.tex
    M subfiles/chap_ASM.tex
    M subfiles/chap_DIU.tex
    M subfiles/chap_cfgs.tex
    M subfiles/chap_ZDF.tex
    M subfiles/chap_OBS.tex
    M subfiles/chap_model_basics.tex
    M subfiles/chap_time_domain.tex
    M subfiles/apdx_algos.tex
    M subfiles/chap_TRA.tex
    M subfiles/chap_DYN.tex
    M subfiles/chap_misc.tex
    M subfiles/chap_DIA.tex
    M subfiles/apdx_invariants.tex
    M subfiles/chap_LBC.tex
    M subfiles/apdx_diff_opers.tex
    M subfiles/chap_STO.tex
    M subfiles/chap_LDF.tex

    14:57 Changeset [11557] by mattmartin

    Remove updated pressure correction branch as it has been merged into the main GO6 FOAM branch.

    14:55 Changeset [11556] by mattmartin

    Commit changes to bias pressure correction from ticket https://code.metoffice.gov.uk/trac/utils/ticket/262.

    14:20 Changeset [11555] by mattmartin

    Code changes after Dan's review (comments and alignment changes only).

    11:46 Changeset [11554] by jchanut

    #2078: add Franziska's fix to correct input/output paths with AGRIF

    2019-09-16:

    18:54 Changeset [11553] by mathiot

    ENHANCE-02_ISF: fix coupling issue (ticket #2142)

    17:38 Changeset [11552] by nicolasmartin

    add unbreakable space after \fortran & fninety

    16:53 Changeset [11551] by nicolasmartin

    Bugfix: no index entries in math env

    16:24 Changeset [11550] by rrenshaw

    implement Sarah's boundary changes, changeset 11328

    14:48 Changeset [11549] by jchanut

    #2199: Take into account masked open boundaries in sponge definition. Output sponge values.

    Note: See TracTimeline for information about the timeline view.