Timeline


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matching tags

2019-08-22: Yesterday

11:49 Changeset [11467] by andmirek

Ticket #2197 allocate arrays at the beggining of the run

2019-08-21:

18:32 Scientific Advisory Board/Agenda/2019-01-23 edited by mikebell
added minutes from the meeting (diff)
18:31 Scientific Advisory Board/Agenda/2019-01-23 edited by mikebell
(diff)
18:23 NEMO_DevComm_Minutes_20190123_20190204.2.pdf attached to Scientific Advisory Board/Agenda/2019-01-23 by mikebell
Minutes NEMO Developers' Committee meeting Jan / Feb 2019
18:23 NEMO_DevComm_Minutes_20190123_20190204.pdf attached to Scientific Advisory Board/Agenda/2019-01-23 by mikebell
Minutes NEMO Developers' Committee meeting Jan / Feb 2019
09:18 Changeset [11466] by davestorkey

dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps_rewrite_time_filterswap: Bug fixes for ssh_atf routine in sshwzv.

2019-08-20:

18:03 Changeset [11465] by acc

Branch dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps_rewrite_time_filterswap. Update VORTEX/MY_SRC/domvvl.F90 to be compatible with time swapping changes; now passes SETTE tests

15:39 Changeset [11464] by mattmartin

Commit changes which are in one of Jennie's orca12 branches.

14:14 Changeset [11463] by acc

Branch: dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps_rewrite_time_filterswap. Minor bugfix in step.F90 to enable AGRIF SETTE tests to run. Also merged prettification changes to NST routines from the dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps branch. Neither AGRIF_DEMO nor VORTEX restart perfectly (drifting after 8 and 121 timesteps, respectively).

12:45 Changeset [11462] by kingr

Changes committed back to dev_r5518_obs_oper_update

12:41 Changeset [11461] by kingr

Updated check on min obs depth to use 3D depth array.

11:41 Changeset [11460] by mattmartin

Minor changes.

10:59 Changeset [11459] by cetlod

Revision in chapter TRA : mainly removal obsolete CPP keys and update of namelist parameter

10:32 Changeset [11458] by cguiavarch

Read mmpmask from domain_cfg instead of bottom_level

10:20 Changeset [11457] by cguiavarch

Create a branch to read a mppmask instead of bottom level to remove processor

2019-08-19:

18:27 Changeset [11456] by mattmartin

First wrking version which produces correct seeming results.

17:36 Changeset [11455] by mattmartin

Commit version which compiles and runs. Not fully tested that it is producing the correct answer yet though.

17:28 Changeset [11454] by jcastill

Final changes to make the branch work in uncoupled mode

16:05 Changeset [11453] by clne

Add land mask when outputting wind field, to prevent XIOS errors when running

13:28 Changeset [11452] by jcastill

Changes as in the original branch, plus one bug fix in oce.F90, plus changes to run with the branch but in uncoupled mode - although this is not complete yet

12:51 Changeset [11451] by kingr

Modified sheck on min obs deth to use 3D depth array.

12:38 Changeset [11450] by kingr

Create a branch for fixing reassignment of depth of near-surface obs in obs_prep

10:54 Changeset [11449] by mattmartin

Committed first version of changes to output climatology values at obs locations in the fdbk files.

10:31 Changeset [11448] by jcastill

Clean svn keywords

10:29 Changeset [11447] by jcastill

Update of branch branches/UKMO/dev_r5518_new_runoff_coupling@9566 to r6232 for UKEP runs

10:17 Changeset [11446] by timgraham

Remove OASIS3 legacy code from cpl_oasis.F90. Tested to not change results.

09:18 Changeset [11445] by sciliberti

#2216 revision of LBC chapter: main ones in bdy description and geometry

2019-08-16:

17:58 Changeset [11444] by mattmartin

Delete branch as now merged into dev_r5518_GO6_package_FOAMv14.

13:10 Changeset [11443] by kingr

Revert previous commit.

12:32 Changeset [11442] by mattmartin

Introduction of stochastic physics in NEMO, based on Andrea Storto's code.
For details, see ticket https://code.metoffice.gov.uk/trac/utils/ticket/251.

2019-08-15:

18:19 Changeset [11441] by dancopsey

Make test greater than zero.

16:43 Changeset [11440] by mattmartin

Update after Dan's review.

13:03 Changeset [11439] by kingr

Removed section which changed obs depths where depth shallower than some limit - if the depths are too shallow, the obs should be QCed out rather than assumed valid at a different depth.

11:35 Changeset [11438] by dancopsey

Allow the user to turn off the creation of abort files.
Merge in changes from dev_r5518_GO6_package_abort_switch revison 10675.

10:44 Changeset [11437] by mattmartin

Create a branch for including climatology in the fdbk files

2019-08-14:

16:16 Changeset [11436] by timgraham

Get rid of modification to sbc_cpl_init and sbc_cpl_alloc so that number of models is no longer hard coded in the latter. This must be leftover from CICE

14:45 Changeset [11435] by nicolasmartin

Various corrections on chapters

Cleaning the indexes by fixing/removing wrong entries (or appending a ? to unknown items) and
improve the classification with new index definitions for CPP keys and namelist blocks:

  • from \key{...} cmd, key_ prefix no longer precedes the index entry
  • namelist block declaration moves from \ngn{nam...} to \nam{...} (i.e. \ngn{namtra\_ldf}\nam{tra\_ldf}) The expected prefix nam is added to the printed word but not the index entry.

Now we have indexes with a better sorting instead of all CPP keys under 'K' and namelists blocks under 'N'.

Fix missing space issues with alias commands by adding a trailing backslash (\NEMO\, \ie\, \eg\, …).
There is no perfect solution for this, and I prefer not using a particular package to solve it.

Review the initial LaTeX code snippet for the historic changes in chapters

Finally, for readability and future diff visualisations, please avoid writing paragraphs with continuous lines.
Break the lines around 80 to 100 characters long

2019-08-13:

09:18 Changeset [11434] by davestorkey

dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps_rewrite_time_filterswap :
Bug fix for trctrp.F90 and rewrite of trcrad.F90.
This version passes all SETTE tests involving PISCES, but fails the following idealised tests at this stage:
ISOMIP, OVERFLOW, LOCK_EXCHANGE.

2019-08-12:

21:44 Changeset [11433] by nicolasmartin

Pre-implementation of new cover page and new headings style for reference manuals

Cover page

The layout of the frontpage has been completely redesigned,
a coloured banner has been added to emphasize the title and easily identify each manual
between them.
The chosen color for each document (blue for NEMO, gray for SI3 and green for TOP) will be
used throughout the manual for the links and in the chapter headings.
The list of authors (writers/editors/reviewers) for the version of the manual is given next to
the abstract, which is now included in the frontpage.
A link to an existing ORCID profile for the author precedes its name.
Few settings have been added to each definitions.tex in order to adjust the rendering of the cover page (vertical spaces above and below the title, a subtitle, the width for authors list and
abstract section)

Headings

  • header: chapter number and title for even pages, same infos for section otherwise
  • footer: name of the manual and page numbering with the total number of pages (reverse order between odd/even pages)

For the chapter heading, a new style 'Bjornstrup' from fncychap package is now use.

Abstract

Split the section in two paragraphs for all manuals

  1. Common description with almost the same sentences only customized by the general infos of the model
  2. Specific part for the characteristics of the model

Troubleshooting

As announced, I have introduced some icons from academicons and fontawesome packages.
It required to switch from pdflatex to xelatex for the compilation and it prevents from now
the building of the whole document.
Also the PDF generated does not look nice due to the font

Work in progress…

2019-08-09:

18:26 Changeset [11432] by csanchez

Added changes from Bijoy to set cpl_mslp in a namelist

18:08 Changeset [11431] by csanchez

Branch created for the coupling of MSLP from coupled system rathern than external source

17:17 Changeset [11430] by csanchez

Branch deleted, copied from the wrong branch

16:36 Changeset [11429] by csanchez

Branch created to add code to read coupled mslp from OASIS coupling files

15:52 Changeset [11428] by acc

Branch 2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps. Prettification of NST routines to reduce long lines and incease code readability. No functional changes. SETTE tested

15:44 Changeset [11427] by davestorkey

dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps_rewrite_time_filterswap :
Restore independent time level indices for TOP in order to enable the option for
TOP to have a different timestep to OCE (nn_dttrc > 1). But note that this version of
the code only works for nn_dttrc=1. Also sort out the time-level swapping for OFF.
This commit passes the GYRE_PISCES and ORCA2_OFF_PISCES tests but fails restartability
and bit-comparison with the control for ORCA2_ICE_PISCES.

12:49 Changeset [11426] by davestorkey

branches/2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps_rewrite_time_filterswap : Merge in changes from main IMMERSE branch.

2019-08-08:

19:15 Changeset [11425] by mathiot

ENHANCE-02_ISF_nemo : bug correction when oasis provide the ice shelf melt (ticket #2142)

18:08 Changeset [11424] by mattmartin

Remove the MAX statementsin zdftke which were added as part of the STOPACK changes in order to reproduce the results from the standard GO6 branch.

16:02 Changeset [11423] by mathiot

ENHANCE-02_ISF_nemo : add UKESM ice sheet coupling method (ticket #2142)

15:40 Changeset [11422] by jchanut

#1791, merge with trunk

14:09 Changeset [11421] by acc

Branch 2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps. Minor changes to restore AGRIF restartability. All SETTE tests now passing except WAGRIF_DEMO_ST reproducibility which drifts after 11 timesteps (but always has on the NOC cluster)

13:40 Changeset [11420] by mattmartin

Specify working precision for some new variables.

10:33 Changeset [11419] by mattmartin

Reduce differences with the trunk by changing trabbl.F90 code.

2019-08-07:

16:20 Ticket #1636 ("Now" bottom tracer gradients in later diffusion with zps ?) closed by jchanut
fixed
14:25 Changeset [11418] by acc

Minor correction to make sure full vertical velocity is used in diagnostic output from diawri.F90 when using adaptive-implicit vertical advection (ln_zad_Aimp=.true.)

13:04 Changeset [11417] by mattmartin

Fixed bug in zdftke code for stopack.

12:11 Changeset [11416] by jchanut

#1636: remove overwriting of before tracer gradients over partial cells by now values. Should make tracer diffusion more robust. Now density gradients are now computed in hpg_zps only.

11:08 Ticket #2305 (FCT monotonicy is lost with adaptive vertical advection) closed by jchanut
fixed
11:06 Ticket #2080 (bug in z tilde?) closed by jchanut
fixed
11:05 Changeset [11415] by jchanut

#2080, correct conditional statement

10:58 Changeset [11414] by jchanut

#2292, add ztilde diffusive fluxes in Courant number computation

2019-08-06:

17:59 Changeset [11413] by gsamson

dev_r11265_ABL : see #2131

  • merge src and cfgs from HPC-13_IRRMANN_BDY_optimization branch @ r11402 with dev_r11265_ABL branch @ r11363
  • change ORCA2 results due to ice rheology "cleaning" (see commit r11377)
17:57 Changeset [11412] by acc

Branch dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps: commit changes to VORTEX/MY_SRC/domvvl.F90 that were omitted from previous commits. This still fails restartability (in common with all AGRIF tests on this branch) but will compile and run.

17:08 Changeset [11411] by jchanut

#2305, a few corrections and comestic changes following Andrew's revision 11407

16:52 Ticket #2312 (potential negative surface Chl values with OTF interpolation in traqsr.F90) closed by gsamson
fixed
16:50 Changeset [11410] by gsamson

bugfix for negative Chl values in tra_qsr, see #2312

16:44 Ticket #2312 (potential negative surface Chl values with OTF interpolation in traqsr.F90) created by gsamson
==== Context OTF interpolation can create surface Chl negative values …
16:41 Changeset [11409] by dancopsey

Fix compile errors.

16:20 Changeset [11408] by dancopsey

Apply option to scale by sea ice fractions from the last coupling time.

15:36 Changeset [11407] by acc

Final documentation tweaks to the adaptive-implicit vertical advection section of chap_ZDF.tex and associated code changes. The code changes are mostly cosmetic or to align with the documentation but this does include a modified version of traadv_fct.F90 (thanks to Jerome) which correctly accounts for any implicit component of the vertical velocity when computing anti-diffusive fluxes for flux correction. The changes have null effect when ln_zad_Aimp is .false. and have been SETTE tested with ORCA2_ICE_PISCES with ln_zad_Aimp = .true.

15:26 Changeset [11406] by acc

Additional figures for the adaptive-implicit vertical advection section of the ZDF chapter (latex to follow shortly)

15:16 Changeset [11405] by andmirek

ticket #2195: read weights for blk using XIOS

14:12 New reply on Beginner created by puotila
Compilation of AGRIF_DEMO fails with gcc
11:15 Changeset [11404] by mattmartin

Included control of the STOPACK options so that it can be switched on/off with the main ln_stopack logical.

10:37 Ticket #2311 (minor bug in code to do Euler timestep in dyn_nxt) created by davestorkey
BE CAREFUL !!! Due to dynamic behaviour of this ticket creation page, it …
10:14 Ticket #2310 (bug in timestepping in OFF?) created by davestorkey
BE CAREFUL !!! Due to dynamic behaviour of this ticket creation page, it …

2019-08-05:

19:14 Changeset [11403] by mathiot

ENHANCE-02_ISF_nemo : add comments, renaming file (AGRIF), add isfload module (ticket #2142)

17:26 Changeset [11402] by clem

debug previous commit

16:00 New reply on Beginner created by nicolasmartin
Compilation of AGRIF_DEMO fails with gcc
14:36 Changeset [11401] by clem

add new functionality for initialization. Now you can use a simplified restart for starting a simulation (as for the initialization)

10:54 Changeset [11400] by mattmartin

Getting it to compile.

10:50 Changeset [11399] by mattmartin

Remove this branch as it is replaced by another.

2019-08-02:

18:43 Changeset [11398] by smasson

dev_r10984_HPC-13 : add nammpp parameter ln_listonly, see #2285

18:31 Changeset [11397] by clem

rewrite iceistate.F90, add new variables (optional) for input fields, and prepare the code for a simplified ice restart

16:28 Changeset [11396] by andmirek

branch for ticket #2195

16:19 Changeset [11395] by mathiot

ENHANCE-02_ISF_nemo : Initial commit isf simplification (add ISF directory, moved isf routine in and split isf cavity and isf parametrisation, …) (ticket #2142)

15:14 Changeset [11394] by mattmartin

First implementation of STOPACK in the GO6 package branch.

14:32 Changeset [11393] by mattmartin

Create a branch for including stochastic model perturbations

14:24 New topic on Beginner created by puotila
Compilation of AGRIF_DEMO fails with gcc
11:07 Changeset [11392] by girrmann

dev_r10984_HPC-13 : merge DYN with BDY@11391, see #2308

11:03 Changeset [11391] by smasson

dev_r10984_HPC-13 : flowri compiling without key_iomput, see #2285

10:43 Changeset [11390] by girrmann

dev_r10984_HPC-13 : merge DYN with BDY @11389, see #2308

09:51 Changeset [11389] by smasson

dev_r10984_HPC-13 : add timing of each time step, see #2285

2019-08-01:

18:09 Changeset [11388] by acc

Add adaptive-implicit vertical advection section to ZDF chapter. May still need a few tweaks next week and refers to an updated traadv_fct.F90 which is not yet submitted. Finals tests are in progress

17:54 Changeset [11387] by acc

Additional figures for the adaptive-implicit vertcal advection section of the ZDF chapter (to be submitted)

17:26 Changeset [11386] by jchanut

#2216, correct description of grid scale dependent mixing coefficient

17:25 Ticket #2309 (print statements in iceberg model) created by andmirek
==== Context ORCA2_ICE_PISCES sette test prints information about time …
14:05 Changeset [11385] by clem

remove key_floats from the code and replace it by a logical ln_floats

09:14 New topic on Jobs created by mikebell
[permanent] NEMO System Team Scientist at Met Office | Closing 18 Aug. 2019

2019-07-31:

18:05 Changeset [11384] by mattmartin

Included Andrea Storto's STOPACK code into NEMO3.6 branch.

17:59 Changeset [11383] by clem

do not compile diadct with key_agrif (it fails)

17:08 Changeset [11382] by clem

cleaning diags

16:44 Changeset [11381] by girrmann

dev_r10984_HPC-13 : repair faulty commit [11380], see #2308

15:56 Changeset [11380] by girrmann

dev_r10984_HPC-13 : adding extra halos in dyn_spg_ts is now possible, only works with a single halo when used with tide or bdy, see #2308

15:49 Changeset [11379] by mattmartin

Create a branch for including stochastic model perturbations

15:39 Ticket #2308 (Optimization of the communications in DYN) created by girrmann
==== Summary ||=Action || HPC-13_IRRMANN_DYN_optimization
14:54 Changeset [11378] by girrmann

creating new branch from dev_r10984_HPC-13_IRRMANN_BDY_optimization

14:26 Changeset [11377] by clem

clean rheology, add a couple of outputs and remove landfast_home option

11:50 Changeset [11376] by clem

add variables in context_nemo.xml for all config

11:49 Changeset [11375] by clem

add variables in context_nemo.xml for all config

09:30 Changeset [11374] by clem

remove inopportune stop related to harmonic diags

2019-07-30:

17:33 Changeset [11373] by smasson

dev_r10984_HPC-13 : timing working with more than 9999 cores, see #2285

16:38 Changeset [11372] by deazer

Small bug fix, local variable calculated after it is used
just change order to make sure it is calculated in time

16:16 Changeset [11371] by clem

continue cleaning the ice outputs

10:56 Changeset [11370] by dancopsey

Correction. oce only fluxes shoudl be just for open ocean. Setting sea ice fluxes to zero.

2019-07-29:

18:32 Changeset [11369] by dancopsey

Initialise some missing ice fluxes.

18:14 Changeset [11368] by dancopsey

Make branch.

18:10 Changeset [11367] by dancopsey

More print statements including fix

17:42 Changeset [11366] by clem

complete previous commit with doc update

17:33 Changeset [11365] by clem

Remove key_diaharm and key_diadct. Replace namdct by nam_diadct

16:54 Changeset [11364] by smasson

dev_r10984_HPC-13 : update BENCH to be more robust, see #2285

16:47 Changeset [11363] by gsamson

dev_r11265_ABL : see #2131

  • fix xml files to get xios working with ABL
  • introduce rdt_abl = rdt * nn_fsbc to get ABL working with nn_fsbc > 1
  • does not change results compared to rev11360 with nn_fsbc = 1
13:54 Changeset [11362] by clem

debug the ice output by adding a missing value to the outputed fields. Unfortunately this method imposes a value of 1.e20 where there is no ice, which is annoying when using ncview for example, but this is the only way (from what I know) to output averages

11:26 Changeset [11361] by jcastill

First version of the new observation branch - it compiles, but has not been tested

2019-07-26:

20:07 Changeset [11360] by gsamson

dev_r11265_ABL : see #2131

  • use the same tm_su everywhere (Lupkes 2015 bulk and abl)
  • cosmetic changes in sbcblk.F90
  • change the results when using L15 because of tm_su calculation differences
  • identical results when using constant sea-ice drag coefficient
18:29 Changeset [11359] by smasson

dev_r10984_HPC-13 : add new machine and update BENCH scripts, see #2285

16:10 Changeset [11358] by smasson

dev_r10984_HPC-13 : supress output files with nn_stock and nn_write = -1, see #2285

15:05 Changeset [11357] by gsamson

dev_r11265_ABL : ABL compatibility with SAS (no diff with blk when using ABL src or not in ORCA2_SAS_ICE cfg), see #2131

14:33 Changeset [11356] by deazer

Update bdyini.F90 to use strict lt or gt checks on bdy indexes to indicate if inside domain or not
Also remove bdyini.F90 from WAD MY_SRC test case

11:32 Changeset [11355] by dancopsey

Add lots of print statements printing out values of files throughout the ocean_ice timestep.. New output will be in files crash_stats_419.out and crash_stats_68.out.

09:30 Changeset [11354] by smasson

dev_r10984_HPC-13 : add missing lwm in all usrdef_nam.F90

2019-07-25:

16:55 Changeset [11353] by smasson

dev_r10984_HPC-13 : merge with trunk@11352, see #2285

16:42 Changeset [11352] by smasson

dev_r10984_HPC-13 : small bugfixes

15:47 Changeset [11351] by davestorkey

Documentation: correction to slope definitions in Appendix B.

14:58 Changeset [11350] by jcastill

Clear svn keywords

14:54 Changeset [11349] by jcastill

Copy of branches/UKMO/r6232_obs_oper_update for NEMO 4.0

14:02 Changeset [11348] by gsamson

dev_r11265_ABL :

  • merge HPC-13_IRRMANN_BDY_optimization branch @ rev11332 with dev_r11265_ABL branch @ rev11334
  • allow ln_dm2dc option with ABL
  • cosmetic change in sbcabl.F90

identical results with rev11334 for bulk and abl orca2

13:07 Changeset [11347] by jcastill

Remove outdated comment

12:11 Changeset [11346] by mdrudi

addition of changes record in chap_DIA.tex

10:55 Changeset [11345] by jcastill

Some fixes to the pressure correction, when the pressure is received by coupling

10:52 Changeset [11344] by clevy

#2216: updates to STO reference manual

10:46 Changeset [11343] by jcastill

Some fixes to the pressure correction, when the pressure is received by coupling

10:33 Changeset [11342] by clevy

bugfix stopar.F90 correct logical check

10:27 Changeset [11341] by clevy

bugfix stopar.F90 correct logical check

2019-07-24:

18:35 Changeset [11340] by clevy

#2216: updates to STO reference manual

17:10 Changeset [11339] by acc

Update of chap_misc.tex for v4.0 compatibility

14:18 Changeset [11338] by gsamson

add a missing CPP key description in SBC chapter

12:31 Changeset [11337] by mikebell

authors of annex A added

12:30 Changeset [11336] by jchanut

Update LDF chapter, #2216

12:16 Changeset [11335] by mikebell

review of chap_model_basics, annex_A and annex_B

11:20 Changeset [11334] by flemarie

Follow-on to the ABL implementation (see ticket #2131)

  • Modification of diawri.F90 to output ABL variables with IOIPSL (i.e. without key_iomput)
  • Modification of ice_var_agg in icevar.F90 to allow the use of tm_su in ABL and bulk
  • Error handling in case ln_abl = .true. and ABL sources were not compiled
  • ABL now works with SI3 considering an average over ice categories
  • Update reference namelist to avoid runtime warnings due to nam_tide
  • Sanity checks with ORCA2 for the following configurations :

1 - ABL src + ln_blk = .true.
2 - ABL src + ln_abl = .true.
3 - no ABL src + ln_blk = .true.

All configurations are MPP reproducible and configurations 1 and 3 results are identical

Note: See TracTimeline for information about the timeline view.