Timeline
2019-06-17:
- 15:54 Changeset [11128] by
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Create styles folder to gather common files between manuals: NEMO.sty and ametsoc.bst
- 15:41 Changeset [11127] by
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Create branch for surge work
- 15:24 Changeset [11126] by
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Reintroducing ametsoc.bst in latex shared folder
- 15:08 Changeset [11125] by
- 14:49 Changeset [11124] by
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Editing of ametsoc.bst to generate hyperlinks for DOIs or URLs
New version of bibtool resource file:
- Braces as entries delimiter
- All entry types in lowercase (^@...)
- Normalisation of pages field ([0-9]+--[0-9])
- Deletion of url field if doi is here
- Definition of fields order
sort.order = { * = # title # chapter # pages # journal # booktitle # edition # editor # series # volume # number # author # institution # school # year # month # publisher # issn # isbn # doi # url }
- coding the format of citations keys
key.format = { %s(bibkey) # %-2n(author)_ { %+5.1W(journal) # %0s(@book ) { bk } # %0s(@inbook ) { ibk } # %0s(@incollection ) { icol } # %0s(@inproceedings) { iprc } # %0s(@phdthesis ) { phd } # %0s(@techreport ) { rpt } } %2d(year) }
- 14:22 Changeset [11123] by
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Modification of LaTeX subfiles accordingly to new citations keys
- 14:05 Changeset [11122] by
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Upload advanced version of the NEMO bibliography
- Apply global pattern for citation keys: 1stauthor{.2ndauthor{.ea}}_{journal|type}year
- Sorting entry fields wisely
- Removal of redundancies ('doi'='url') by keeping only the DOI field
- Manual editing for disambiguation with lowercase letter starting from the first item: *a, *b
- 12:31 Changeset [11121] by
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Fixes on BibTeX fields
- Restoration of few missing entries from previous cleaning
- Protection of some french names with "von" part
- Use of the proper syntax for doubles quotes: `` ... ''
- Addition of backslash for underscore character in URL
- 12:14 Changeset [11120] by
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Modification of the building process with dedicated build sub-folder
- 11:03 Changeset [11119] by
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minor code fix
- 10:52 Ticket #2299 (Minor bug in PISCES) closed by
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fixed: Done on v4.0 and trunk
- 10:51 Changeset [11118] by
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Bugfix on sea-ice effect on production, see ticket 2299
- 10:50 Changeset [11117] by
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Bugfix on sea-ice effect on production, see ticket 2299
- 10:38 Ticket #2299 (Minor bug in PISCES) created by
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BE CAREFUL !!! Due to dynamic behaviour of this ticket creation page, it …
2019-06-14:
- 20:21 Changeset [11116] by
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Removing of unnecessary entries
- 20:17 Ticket #2298 (Bug fixes to OBS and ASM found when reviewing the documentation) created by
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BE CAREFUL !!! Due to dynamic behaviour of this ticket creation page, it …
- 20:13 Ticket #2297 (Updates to ASM and OBS documentation) created by
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==== Context The documentation for OBS and ASM needs reviewing as it is …
- 19:25 Changeset [11115] by
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Fixed version with unused references
- 16:51 Changeset [11114] by
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trunk:small bug fix in the previous bug correction, ticket #2296
- 16:49 Changeset [11113] by
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small bug fix in the previous bug correction
- 15:57 Changeset [11112] by
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Update the chapter on reference configurations for 4.0 release, see #2216
- 15:55 Changeset [11111] by
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LB: skin temperature now used by ECMWF bulk algorithm, and can be xios-ed ; new module "SBC/sbcblk_skin.F90" ; all physical constants defined in SBC now moved to "DOM/phycst.F90"; all air-properties and other ABL functions gathered in a new module: "SBC/sbcblk_phymbl.F90".
- 15:43 Changeset [11110] by
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UKMO/NEMO_4.0_GO8_package branch: Enable product diagnostics uT, vT, wS etc. (as in GO6 package branch).
- 13:57 Changeset [11109] by
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trunk:bug fix of the ticket #2296
- 13:41 Ticket #2296 (Bug in the computation of the degradation rate of GOC) closed by
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fixed
- 13:41 Changeset [11108] by
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bug fix of the ticket #2296
- 13:36 Ticket #2296 (Bug in the computation of the degradation rate of GOC) created by
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==== Context In the new version of PISCES available with NEMO4.0, a new …
- 11:50 Changeset [11107] by
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Commit changes from Dan Copsey's sea ice heat coupling
flux fixes in branch:
branches/UKMO/dev_r5518_GO6_fix_zemp_ice_10681
revisions 11028:11088.
2019-06-13:
- 20:54 Changeset [11106] by
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Push a second review of NEMO manual from side-by-side edition of 2 previous versions (r11051 & r11052)
I will made a final review with the first upload of the new version (r11075) and will reduce significantly it as almost the half of the references are not used.
Would have save time by checking the unused entries before…
- 18:20 Changeset [11105] by
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Merged in changes from dev_merge_2017_GC_couple_pkg branch except for zotx1 and zoty1 changes in sbccpl.F90.
- 15:21 Changeset [11104] by
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Make coupling package branch
2019-06-11:
- 20:05 Ticket #1922 (Uninitialized variable in sbcapr.F90) closed by
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duplicate: This ticket has been superseded by ticket #2295.
- 19:44 Ticket #1922 (Uninitialized variable in sbcapr.F90) reopened by
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While the reported bug has been fixed in the release-3.6 version of the …
- 19:28 Ticket #2295 (Subroutine bdy_dta uses an uninitialised namelist parameter unless ...) created by
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==== Context The bug reported in ticket #2235 is also present in the …
- 19:09 Ticket #2294 (Missing rewind on reference namelist for nambdy_tides) created by
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==== Context When we have >1 open boundary, and when using …
- 18:06 Changeset [11103] by
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Added new code to branch
- 16:38 Changeset [11102] by
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dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps_rewrite_time_filterswap : revert change committed by mistake.
- 16:10 Changeset [11101] by
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Merge changes from Met Office GMED ticket 450 to reduce unnecessary
text output from NEMO.
This output, which is typically not switchable, is rarely of interest
in normal (non-debugging) runs and simply redunantley consumes extra
file space.
Further, the presence of this text output has been shown to
significantly degrade performance of models which are run during
Met Office HPC RAID (disk) checks.
The new code introduces switches which are configurable via the
changes made in the associated Met Office MOCI ticket 399.
- 16:07 Changeset [11100] by
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Properly undid premature check into release-4.0
- 15:59 Changeset [11099] by
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dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps_rewrite_time_filterswap : Updates and bug fixes. This version still doesn't pass all SETTE tests.
- 15:17 Changeset [11098] by
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Undid premature check into release-4.0
- 14:59 Changeset [11097] by
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corrected . or. byg in diahth.F90
- 14:59 Changeset [11096] by
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diahth outputs now controlled only by xml
- 14:58 Changeset [11095] by
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use ln_diahth in step_c1d.F90
- 14:58 Changeset [11094] by
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complete merge of diahth.F90
- 14:58 Changeset [11093] by
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original lot of changes to diahth.F90
- 14:58 Changeset [11092] by
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modified namelist_ref to include ln_diahtth key
- 14:58 Changeset [11091] by
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new diahth to work without key_diahth: changes in diahth.F90
- 14:58 Changeset [11090] by
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original lot of changes to diahth.F90
- 14:36 Changeset [11089] by
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Modernized diahth
2019-06-10:
- 17:37 Changeset [11088] by
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Set namelist entry to be false by default.
- 17:36 Changeset [11087] by
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Allow false value for namelist entry to be the default
- 16:55 Ticket #2293 (agn) created by
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==== Context The dia_hth routine in diahth.F90 still only works with a …
2019-06-09:
- 13:41 Changeset [11086] by
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LB: initial commit from trunk at r11085
2019-06-07:
- 12:59 Ticket #2292 (Bugs with adaptive vertical advection: 3) Courant number computation) created by
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==== Context Adaptive (based on courant number) vertical advection, …
2019-06-06:
- 17:39 Changeset [11085] by
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code fixes
- 17:22 New reply on Skilled created by
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[AGRIF] Intel build (with key_agrif) based on ORCA2_LIM seg faults
- 16:30 Changeset [11084] by
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UKMO/NEMO_4.0_old_tidal_mixing : Update to be relative to rev 11081 of NEMO_4.0_mirror.
- 16:29 Changeset [11083] by
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UKMO/NEMO_4.0_GO6_mixing : Update to be relative to rev 11081 of NEMO_4.0_mirror.
- 16:21 Changeset [11082] by
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UKMO/NEMO_4.0_GO8_package : update to be relative to 11081 of NEMO_4.0_mirror.
- 16:11 Changeset [11081] by
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UKMO/NEMO_4.0_mirror : update to be a copy of rev 11079 of release-4.0.
- 15:32 Changeset [11080] by
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Latest changes from Jason
2019-06-05:
- 17:16 Ticket #2291 (Bugs with adaptive vertical advection: 2) Interaction with time splitting) created by
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==== Context Adaptive (based on courant number) vertical advection, …
- 16:48 Ticket #2290 (Bugs with adaptive vertical advection: 1) dynzdf.F90) created by
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==== Context Adaptive (based on courant number) vertical advection, …
- 16:18 Changeset [11079] by
- 16:17 Changeset [11078] by
- 16:14 Ticket #2289 (Edge bathymetry values are wrong in the OVERFLOW test case (at U-points)) closed by
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fixed
- 16:13 Changeset [11077] by
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Correct bathymetry at U-points, #2289
- 16:11 Changeset [11076] by
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Correct bathymetry at U-points, #2289
- 16:07 Ticket #2289 (Edge bathymetry values are wrong in the OVERFLOW test case (at U-points)) created by
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==== Context Trivial bug in OVERFLOW test case: bathymetry computation at …
- 09:40 Ticket #2288 (BDY is not compatible with high order schemes) created by
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==== Context BDY is not compatible with high order schemes (bilaplacien, …
2019-06-04:
- 18:16 Changeset [11075] by
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Submission of an intermediate version of NEMO bibliography
Manual merge of 2 existing BibTeX entries per each reference in order not to lose a field
It remains to make a check from the diff view under Trac or a diff tool and a final cleaning for indentation and new citations keys
- 17:47 Ticket #2287 (Bug in bdy with flather) closed by
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fixed
- 17:46 Changeset [11074] by
- 17:09 Developers/Good Practices/Usual Commands edited by
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(diff)
- 16:58 Developers/SVN Quick Reference created by
- 16:48 Developers/Good Practices edited by
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(diff)
- 16:46 Developers/Good Practices edited by
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(diff)
- 15:16 Changeset [11073] by
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v4 : fix bug in flather for bdy, see #2287
- 15:14 Changeset [11072] by
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trunk : fix bug in flather for bdy, see #2287
- 15:07 Ticket #2287 (Bug in bdy with flather) created by
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==== Context For eastern and northern boundaries (flagu = -1 and flagv = …
- 14:58 Changeset [11071] by
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dev_r10984_HPC-13 : step 2, remove unneeded communications, see #2285
2019-06-03:
- 15:04 Changeset [11070] by
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code fixes
- 12:23 Changeset [11069] by
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ticket #2197 glob sum for parallel architecture
- 11:36 2019WP/HPC-12_Mocavero_mpi3 edited by
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(diff)
- 11:35 2019WP/HPC-12_Mocavero_mpi3 edited by
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(diff)
2019-05-29:
- 15:20 Changeset [11068] by
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Branch for changes required for inclusion of spectral optics model (coupled via FABM).
- 11:34 Changeset [11067] by
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dev_r10984_HPC-13 : new implementation of lbc_bdy_lnk in prevision of step 2, regroup communications, see #2285
2019-05-28:
- 18:00 Changeset [11066] by
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changes to add regional means output and correction for section transports
- 16:54 Changeset [11065] by
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new branch for changes to branch for AMM7/AMM15 3.6 suite
- 13:10 Changeset [11064] by
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Deleting branch as changes merged back.
- 13:08 Changeset [11063] by
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Add missing lbc_lnk and option to relax chlorophyll to climatology. See Met Office utils ticket 216.
- 13:06 Changeset [11062] by
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Fix compile issues for when I am running GO6+MEDUSA.
- 12:52 Changeset [11061] by
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Fix compile issues for when I am running GO6+MEDUSA.
2019-05-27:
- 15:20 Changeset [11060] by
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Backup a merged bibliography with duplicates commented
Bib Tool? determines double entries from successive identical citation keys so
the procedure was in 2 steps
- Process r11051 & r11052 versions of NEMO_manual.bib to have the same pattern for citation key
- Merge the 2 versions with Bib Tool? configured for duplicate checking:
bibtool -d -- preserve.keys=on -- sort=on input_files -o output_file
It remains to clean the bibliography by deleting the doubles.
- 13:34 Ticket #2286 (Passive tracer vertical diffusivity in trazdf.F90 (PISCES offline)) created by
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==== Context When running PISCES offline simulations in 1D, I noticed …
- 13:05 Changeset [11059] by
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dev_r10984_HPC-13 : simplify bdyini.F90 following extension of bdy detection, see #2285
2019-05-24:
- 21:41 Changeset [11058] by
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Add a configuration file as resource for Bib Tool? to define standard format for our bibliographies
After the import of several new versions of references, I found some discrepancies that it was easy to address with Bib Tool?
- Set a common pattern for citation key: author1[_authors2[_ea]]_journalyear
- Suppress a good bunch of trivial fields to reduce the size of the biblio in the different exports address chapter institution isbn issn issue keywords language note number organisation pages pdf series school type volume Open to discussion but to me a DOI entry is sufficient if someone wants more information
- Prevent the use of tab for fields indentation, better readability for the bib file on Trac browser or in the output of SVN diff
- Apply the following order of fields for every entry author # title # booktitle # journal # publisher # editor # year # month # doi # url
To apply the rules to a Bib Tex? file, run
bibtool -r bibtool.rsc input_file -o output_file
- 17:36 Changeset [11057] by
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2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps_rewrite_time_filterswap : Rewrite time filtering of tracers and SSH. This version now bit compares with the base code for ORCA1 starting from a restart.
To do:
- Check that it bit compares with an Euler timestep.
- Full SETTE tests.
- Check that it compiles with C1D.
- Check that TOP works (see 1).
- 15:52 Changeset [11056] by
- 14:57 Changeset [11055] by
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Put the switch back in again.
- 14:54 Changeset [11054] by
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Put the switch back in again.
- 12:53 Changeset [11053] by
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2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps_rewrite_time_filterswap : Merge in latest changes from main branch and finish conversion of "h" variables. NB. This version still doesn't work!
- 12:05 Changeset [11052] by
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Upload draft version for new NEMO biblio
This is the result of the publications collecting on Cross Ref?.
By mistake, previous commit was supposed to be the one but it was just a small edition.
- 11:50 Changeset [11051] by
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Backup intermediate version before further minor modifications
- 10:27 Changeset [11050] by
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2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps_rewrite_time_filterswap : Rewrite dynnxt.F90 and rename dynatf.F90 with time level swapping in stp. This doesn't work yet but committing for the record before I merge in Andrew's changes to the main branch.
- 10:22 Changeset [11049] by
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dev_r10984_HPC-13 : CYCLE instruction is not systematic anymore, computation is done on the halo whenever possible and overwritten by lbc_bdy instruction, see #2285
2019-05-23:
- 18:36 Changeset [11048] by
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dev_r10984_HPC-13 : Step 1, boundary is now detected all over the local domain, this does not change the result. Improve bdy treatment for bdy_rnf in bdytra.F90, this changes the result when keyword runoff is specified in namelist
- 18:26 Changeset [11047] by
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2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps : Add missing initialisation of time-level indices for the AGRIF zooms. This enables AGRF SETTE tests to be reactivated but initial tests suggest minor reproducibility and restartability issues. These tests have always been sensitive to optimisation levels on the NOC cluster though so need an independent test on another system
- 18:02 Changeset [11046] by
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Take the switch back out again. It was decided not that this is a bug so should be automatically picked up.
- 17:58 Changeset [11045] by
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Take the switch back out again. It was decided not that this is a bug so should be automatically picked up.
- 17:13 Changeset [11044] by
- 15:51 Changeset [11043] by
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Several fixes for the LaTeX compilation of the manuals
- 15:46 Changeset [11042] by
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dev_r10984_HPC-13 : update with trunk at revision 11041
- 14:28 Changeset [11041] by
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debug corner points for ice bdy
- 14:27 Changeset [11040] by
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debug corner points for ice bdy
- 09:38 Changeset [11039] by
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code fix
2019-05-22:
- 22:44 Changeset [11038] by
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code fixes
- 21:03 Changeset [11037] by
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Review entries of TOP bibliography
Continuation of the work to complete the BibTeX entries with the help of
DOI resolver for the retrieval and Cross Ref? API for the identification.
Add byrd-co2-2008.txt & edc-co2.txt for information which give the original
references for using particular CO2 data set from NOAA-NCEI
- 15:44 Changeset [11036] by
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2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps : Remove now redundant TARGET qualifiers from oce and dom_oce arrays
- 15:10 Changeset [11035] by
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Apply changes from UKMO GMED ticket 453 to fix OOB bugs in
the calculation of diagnostic tnpeo and to apply the correct calculation
as per the current NEMO vn4.0 and 3.6_STABLE code bases, in place of the
existing incorrect formula. Thus, tnpeo diagnostic values will change
following this update.
Model prognostics and eveolution are unaffected.
2019-05-21:
- 22:42 Changeset [11034] by
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Add a simple shell script to build the user guide
It checks Python deps, cleans the previous build and exports the guide in HTML format
- 22:36 Changeset [11033] by
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Modify the shell code in order to run as expected on different OS (Linux or MacOS)
- 22:34 Changeset [11032] by
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Fix few issues in TOP bibliography
- 21:41 Changeset [11031] by
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Update the chapters following the new keys for BibTeX entries
- 20:42 Changeset [11030] by
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Reconstruction of SI3 bibliography in bib format
Use of biblio Emacs package to retrieve BibTeX entries from
- existing DOIs in the bbl file
- DOIs identified by searching from Cross Ref? API
- classical request on web search engine (few)
2 references are missing (+ one paper is submitted): TEOS-10 and MaykutThorndike73 and the file was then processed with bibtool for reformatting.
I plan to reproduce this procedure for reviewing the other bibliographies (NEMO & TOP) and the references in the user guide.
- 18:03 Changeset [11029] by
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Upgraded previous version of this branch.
- 17:55 Changeset [11028] by
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Branch off the teh GO6 package branch at revision 10681
- 17:33 Changeset [11027] by
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2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps : Final renaming conversions and removal of temporary pointers. All non-AGRIF SETTE tests are passing (including test cases). AGRIF tests compile and link but segment on first call to Agrif_Regrid. NST changes are therefore a work in progress but nothing is broken that was not broken before
- 16:54 Changeset [11026] by
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Apply previous for SI3 specific namelists
- 16:51 Changeset [11025] by
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Set mime-type to text/x-fortran to all namelists
- 16:07 Changeset [11024] by
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dev_r10984_HPC-13 : imrpove bdy treatment ssh and neumann, see #2285
- 12:21 Changeset [11023] by
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Fix typos with comma followed by 'and' in author entries
- 11:49 Changeset [11022] by
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Fix the relative path for the bibliography style file to apply it globally
- 09:54 Changeset [11021] by
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Branch of a branch to rewrite time filtering and swapping as part of KERNEL-02 action. Branch of a branch so as not to break bit comparison tests in main branch. Will merge back when happy.
2019-05-20:
- 22:26 Changeset [11020] by
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Apply svn:ignore property on TOP subfolders from ./doc/.svnignore file
Cmd to run globally: svn pset -R svn:ignore -F .svnignore latex
- 22:21 Changeset [11019] by
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Apply more or less same modifications on TOP as for SI3 for compliance
Despite remaining issues with references, TOP manual can be build like NEMO & SI3 with ./build_manual.sh TOP
For the record, the building of the 3 manuals can be launched with ./manual_build.sh all
- 21:25 Changeset [11018] by
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Update pdf version, conversion seems to be better from png
- 21:24 Changeset [11017] by
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Remove useless upper path level + Add eps & pdf format to fix inclusion issues
- 21:03 Changeset [11016] by
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Move figures of TOP manual to global location
- 20:57 Changeset [11015] by
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Modification of the content to be in line with the NEMO manual
SI3 manual can now be build like the NEMO manual with ./manual_build.sh SI3
- Mimick the directory organisation with main and subfiles folders.
- Regarding the particular case of namelists
- Remove the duplicates already contained in the global namelists folder at 1st level of ./doc
- Keep the namelists sub-folder only for namdyn_adv & namsbc which already exist in ocean namelists
- Rewriting of SI3_manual.tex with NEMO_manual.tex as template to easily highlight differences
- Updating of several paths for figures/namelists inclusion or LaTeX files referencing
- LaTeX source:
- Replacement of \forfile command for namelists with pre-configured \nlst alias
- " "" \bm with \mathbf (save installation of an extra package)
- 19:05 Changeset [11014] by
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Add eps & pdf format for figures to fix inclusion issues
- 18:32 Changeset [11013] by
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Add explicit option for latexmk to ensure PDF export
- 18:18 Changeset [11012] by
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#1791, report domvvl change in VORTEX test case. Modification of domvvl there should be removed.
- 17:39 Changeset [11011] by
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Remove useless upper path level
- 17:30 Changeset [11010] by
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Move figures of SI3 manual to global location
- 17:07 Changeset [11009] by
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Updates following review.
- 17:07 Changeset [11008] by
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Fix execution rights on new scripts
- 16:58 Changeset [11007] by
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Edit NEMO_manual LaTeX files to comply with previous path modification
- 16:56 Changeset [11006] by
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Reorganisation of the directory for upcoming addition of SI3/TOP figures
- 16:53 Changeset [11005] by
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Updating of the namelists
- 16:51 Changeset [11004] by
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Review of main building script
- Exportig Python package checking to external script check_pkg.py for sharing it with the verification of deps for the user guide (sphinx, extension and theme)
- Renaming to explicit manual_build.sh
- Addition of basic checking for LaTeX installation (latexmk binary)
- Implementation of loop and argument reading in order to use the same script for the 3 manuals
- Improvment of code commentary
- 15:47 Changeset [11003] by
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dev_r10984_HPC-13 : create developpement branch
- 15:43 Ticket #2285 (Optimization of the communications in BDY) created by
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==== Summary ||=Action || HPC-13_IRRMANN_BDY_optimization …
- 14:53 Changeset [11002] by
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vvl interp, #1791: 1) Add resting depth at F-points. 2) Rewrite dom_vvl_interpol with 2 aditionnal methods for horizontal interpolation at U-V-F points (nmet=0,1,2 in subroutine header). Set nmet=1, i.e. interpolate interfaces instead of scale factors anomaly. 3) Changes in the rest of the code: consider input array in dom_vvl_interpol at T point for F scale factors interpolation.
- 14:19 Changeset [11001] by
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2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps : C1D and step.F90. Passes SETTE. Compiles with key_c1d.
- 13:20 Changeset [11000] by
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Relabel name of the switch that turns on the fix.
- 12:24 Changeset [10999] by
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Fix for ticket #1791
- 10:27 Changeset [10998] by
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2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps : ICE changes. Passess non-AGRIF sette tests apart from ORCA2_SAS_ICE which doesn't seem to work for me at the moment.