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2019-07-19:

19:20 Changeset [11316] by djlea: #2297 Updates to OBS and ASM documentation
19:12 Changeset [11315] by djlea: #2297 Merge in the latest trunk
19:04 Changeset [11314] by djlea: #2297 Updates in response the P Mathiot's review
18:31 Changeset [11313] by emanuelaclementi: Added Surface wave-induced mixing section in ZDF Chapter
18:15 Changeset [11312] by acc: Updated DOM chapter for v4.0 compatibility. Much reduced since many choices and options are now external to NEMO and moved to the DOMAINcfg tool (but they are not documented there). Should consider creating an appendix as a temporary home for some of the material
18:03 Changeset [11311] by djlea: #2297 Fix a few typos
17:29 Changeset [11310] by nicolasmartin: Revert to no background color for inline code
For instance, avoiding bad style when mixing index entries like \np with \forcode
15:53 Changeset [11309] by smasson: dev_r11265_ABL : Gurvan's cosmetic, see #2131
15:04 Changeset [11308] by mathiot: ENHANCE-02_ISF_domcfg: create domisf to isolate isf related work and add new isf geometry computation used by UKESM (ticket #2142)
09:29 Ticket #2307 (better errors handling) created by smasson: in some cases you have an error detection without any message. Something …
09:09 Ticket #2306 (Review of documentation chapter 2 and associated annexes) created by mikebell: ' ==== Context Review of all chapters ==== Proposal Correct derivations …

2019-07-18:

17:53 Changeset [11307] by djlea

#2297 Add author information in the format recommended by C. Levy.

17:46 Changeset [11306] by smasson

dev_r11265_ABL : add ORCA2_ICE_ABL configuration, see #2131

17:22 Changeset [11305] by smasson

dev_r11265_ABL : first implementation of ABL, see #2131

17:17 Changeset [11304] by smasson

dev_r11265_ABL : si3 compatibility, see #2131

17:12 Changeset [11303] by dancopsey

update to be relative to 11081 of NEMO_4.0_mirror

16:50 Changeset [11302] by jcastill

Addition of mixed layer diagnostics, following the changes in zdfmxl.F90 in the branch UKMO/AMM15_v3_6_STABLE_package between revisions 8058 and 10162

16:30 Changeset [11301] by djlea

#2298 Fix comment typo in reference namelist

16:29 Changeset [11300] by davestorkey

Deleting old UKMO branches associated with NEMO 4 beta.

16:27 Changeset [11299] by nicolasmartin

Review of the coding rules chapter: convert it to a shared file for 3 manuals

Move annex_D.tex and NEMO_coding_conv.tex to ./latex/global
Rename NEMO_coding_conv.tex to coding_rules.tex and redesign it as a chapter and not a standalone document
Edit document.tex to include the coding rules by default at the end of the appendix

16:26 Changeset [11298] by davestorkey

Delete old UKMO branches.

16:19 Changeset [11297] by davestorkey

UKMO/NEMO_4.0_GO8_package branch: Merge in changes from
NEMO_4.0_GO8_coupled_iodef.

15:50 Ticket #2305 (FCT monotonicy is lost with adaptive vertical advection) created by jchanut

BE CAREFUL !!! Due to dynamic behaviour of this ticket creation page, it …

15:41 Changeset [11296] by djlea

#2297 Updates to OBS and ASM documentation - first sweep.

15:28 Ticket #2292 (Bugs with adaptive vertical advection: 3) Courant number computation) closed by jchanut

fixed

15:27 Ticket #2291 (Bugs with adaptive vertical advection: 2) Interaction with time splitting) closed by jchanut

fixed

15:26 Ticket #2290 (Bugs with adaptive vertical advection: 1) dynzdf.F90) closed by jchanut

fixed

15:25 Changeset [11295] by mathiot

add sbcclo.F90 + cleaning + comments

15:24 Changeset [11294] by jchanut

#2292, Fixes courant number computation in adaptive vertical advection

15:21 Changeset [11293] by jchanut

#2292, Fixes courant number computation in adaptive vertical advection

15:20 Changeset [11292] by nicolasmartin

Removal of obsolete symbolic links

12:41 Changeset [11291] by laurent

LB: more appropriated use of constant "emiss_w": emissivity of sea water.

12:25 Changeset [11290] by jcastill

Remove svn keywords

12:20 Changeset [11289] by jcastill

Branch to implement mix layer depth diagnostics as in branch UKMO/AMM15_v3_6_STABLE_package@8059

12:01 Changeset [11288] by jchanut

#2291, Adaptive vertical advection: change order of calls with split explicit free surface

11:54 Changeset [11287] by jchanut

#2291, Adaptive vertical advection: change order of calls with split explicit free surface

11:54 Changeset [11286] by dford

Merge in latest version of AMM15_v3_6_STABLE_package_collate.

11:48 Changeset [11285] by dford

Merge in latest revision of dev_r5518_obs_oper_update.

11:35 Changeset [11284] by laurent

LB: gooodbye "coare3p5", hello "coare3p6" + cleaner air humidity handling + support for Relative humidity.

2019-07-17:

17:13 Changeset [11283] by dancopsey: Fix namelist_ref
15:57 Changeset [11282] by jchanut: #2290, fixes bugs with adaptive vertical advection
15:51 Changeset [11281] by jchanut: #2290, fixes bugs with adaptive vertical advection
15:39 Changeset [11280] by kingr: Merged into dev_r5518_obs_oper_update at rvn 11279
15:38 Changeset [11279] by kingr: Minor change to get OBS and AMM15 okg branches merging.
15:30 Changeset [11278] by kingr: Merged into AMM15_v3_6_STABLE_package_collate at rvn 11277.
15:29 Changeset [11277] by kingr: Merged Juan's changes for running AMM15 woth wave coupling.
Corrected minor logic error to allow AMM7-uncoupled to reproduce earlier results.
Few line spacing changes to allow merging with OBS br and trunk rvn 5518.
15:08 Changeset [11276] by mdrudi: revision of CMIP specific diagnostics in chap_DIA.tex in NEMO doc
15:05 Changeset [11275] by smasson: dev_r11265_ABL : add ABL interface, see #2131

2019-07-16:

18:02 Changeset [11274] by dancopsey: Merge in sublimation bug fixes (GMED#449).
11:04 2019WP/ASINTER-01_Guillaume_ABL1D edited by smasson: (diff)
11:03 Changeset [11273] by smasson: dev_r11265_ABL: create branch from HPC-13_IRRMANN_BDY_optimization, see #2131

2019-07-15:

17:31 Changeset [11272] by dancopsey: Add coupled version of the iodef.xml file
17:25 Changeset [11271] by dancopsey: Make branch of GO8 package branch.
17:05 Changeset [11270] by dancopsey: Add input strings to lbc_lnk
16:33 Changeset [11269] by dford: Fix syntax error.
15:47 Scientific Advisory Board/Agenda/2019-09-12 edited by clevy: (diff)
15:33 Scientific Advisory Board/Agenda/2019-09-12 edited by mikebell: (diff)
15:20 Changeset [11268] by smasson: dev_r10984_HPC-13 : introduce a logical to force vertical interpolation if the number of vertical levels in bdy dta == jpk, see #2285
14:41 Scientific Advisory Board/Agenda/2019-09-12 created by clevy
12:58 Changeset [11267] by smasson: dev_r10984_HPC-13 : cleanup the use of freqh as REAL in fldread (done old commit [4144]), see #2285
12:09 Changeset [11266] by laurent: LB: CSWL param now uses NEMO time step (rdt) and previous-t value of t_skin as first guess.

2019-07-12:

17:31 Ticket #2215 (report on communications is not clear when BDY is used) closed by smasson: duplicate: duplicated with #2281
16:02 Changeset [11265] by smasson: dev_r10984_HPC-13 : bugfix for AGRIF, see #2285
15:51 Changeset [11264] by hadjt: Updated the maximum size of the NOOS cross-section size (from 150-275) in DIA/diadct.F90
12:47 Changeset [11263] by smasson: dev_r10984_HPC-13 : merge with trunk@11242, see #2285
11:40 Changeset [11262] by girrmann: dev_r10984_HPC-13 : small modification of lbc_lnk, see #2285
10:28 Changeset [11261] by girrmann: dev_r10984_HPC-13 : bugfix, see #2285
09:38 Changeset [11260] by rrenshaw: further fix for ob below model bathymetry

2019-07-11:

18:29 Changeset [11259] by dford: Check variable names are as expected.
18:21 Changeset [11258] by smasson: dev_r10984_HPC-13 : minor bugfix and cleaning, see #2285
17:57 Changeset [11257] by mathiot: add scaling depending on grid size for eorca1 south of -75N
16:06 Changeset [11256] by rrenshaw: bug fix for obs below model bathymetry
15:51 Changeset [11255] by dford: Check number of variables matches what's expected.
15:46 Changeset [11254] by dford: Add jp_fabm_xeps.
15:45 Changeset [11253] by dford: Add Kd490 obs operator.
15:37 Changeset [11252] by dford: Branch to re-add jp_fabm_xeps variable, to allow Kd490 observation operator.
14:50 Changeset [11251] by dford: Branch to add Kd490 observation operator, and improve name checking when reading feedback files. See Met Office utils ticket 247.
12:43 Changeset [11250] by agn: correctly specify dstokes for nn_osm_wave 0 & 1
11:06 Changeset [11249] by mathiot: branch to adjust ahm (lat←75N) in eorca1, need to avoid blow up in the most south part of Ross and Filschner ice shelves

2019-07-10:

19:01 Changeset [11248] by mathiot: add condition to fill isolated grid point in the bathymetry in zgr_isf to ensure compatibility with ice shelf draft and properly mask bathy,risfdep,mbathy,misfdep after filling subglacial lakes
18:43 Changeset [11247] by mathiot: correction of tmask/wmask used into eiv code to take into account ice shelf cavity
18:26 Changeset [11246] by mathiot: branch to fix masking issue in case of ISF and GM
17:27 Changeset [11245] by girrmann: dev_r10984_HPC-13 : bugfix following [11241], see #2285
14:58 Changeset [11244] by jchanut: #2199, clean old namelist variables
14:19 Changeset [11243] by jchanut: #2222, correct bug in update with key_vertical
12:32 New topic on Skilled created by fborile2: [tides] tide corrections
11:59 Changeset [11242] by jchanut: Remove useless ll_nnogather case if no folding. Prevents from out of bound arrays with small mpp subdomains (<5) and no folding. Should be investigated further.
11:46 Changeset [11241] by girrmann: dev_r10984_HPC-13 : regroup communications in dyn_spg_ts, does not change the result, see #2285
11:37 2019WP/AGRIF-05_jchanut_vert_coord_interp edited by jchanut: (diff)
11:08 Changeset [11240] by girrmann: dev_r10984_HPC-13 : remove a communication in dyn_spg_ts, see #2285
10:54 Changeset [11239] by jcastill: Revert previous change (change variable name) as this was discovered not to be a bug when merging the operational CO7 branch
10:26 Changeset [11238] by jchanut: #2222 AGRIF vertical grid change - Create branch from trunk

2019-07-09:

19:17 Changeset [11237] by djlea: branch of OBS ASM documentation updates (ticket #2297)
19:16 Changeset [11236] by djlea: branch of code bug fixes to OBS and ASM (ticket #2298)
18:11 Changeset [11235] by dford: Revert previous commit, as this wasn't a bug.
18:09 Changeset [11234] by girrmann: dev_r10984_HPC-13 : cleaning of dyn_spg_ts routine, does not change the results, see #2285
17:15 Ticket #2304 (SETTE failed to update some namelist parameter) created by mathiot: ==== Context SETTE failed to update the diaops namelist parameters …
17:09 Changeset [11233] by clem: change a comment in dommsk
17:09 Changeset [11232] by clem: change a comment in dommsk
16:51 Changeset [11231] by clem: remove the imposed closed boundaries when using the nesting tools
16:48 Changeset [11230] by djlea: Change namelist_cfg so that the OBS and ASM tests work. Remove some old debugging output from OBS grid search.
14:22 Changeset [11229] by clem: debug BDY-ice by allowing any number of categories as input. Ticket #2300 may also be solved
14:21 Changeset [11228] by clem: debug BDY-ice by allowing any number of categories as input. Ticket #2300 may also be solved
12:05 Changeset [11227] by davestorkey: branches/UKMO/NEMO_4.0_GO8_package : Add uv, uw, vw diagnostics to diaprod.F90.

2019-07-08:

14:56 Changeset [11226] by jchanut: #2199, remove remaining use of nlcj
14:42 Changeset [11225] by jchanut: #2216, Finalize ZDF chapter - OSMOSIS and Adaptive vertical advection subsections to be updated
11:19 Changeset [11224] by smasson: dev_r10984_HPC-13 : bugfix to work will all configurations, see #2285

2019-07-05:

20:53 Changeset [11223] by smasson: dev_r10984_HPC-13 : cleaning of rewriting of bdydta, see #2285
16:52 Changeset [11222] by cetlod: PISCES_LBC : 1st step of dev
16:44 Changeset [11221] by laurent: LB: "sbcblk_algo_ncar.F90" now uses functions "virt_temp()" and "One_on_L()" defined in "sbcblk_phy.F90".
16:30 Changeset [11220] by cetlod: Create branch for PISCES boundaries conditions moved towards TOP
14:07 Changeset [11219] by jchanut: #2199
1) Define aditionnal arrays to correct the time interpolation of barotropic arrays in corners. Since multiple stages in the time interpolation are necessary, overlapping segments in corners give wrong results otherwise (corrects stage 2 in previous commit)..
2) Added subroutine to correct time extrapolated fluxes at bdy in time splitting routine (updates stage 3 in previous commit).
3) Completly remove non-specified open boundary case. Boundares are now exactly set from parent (no more filtering nor extrapolation for outgoing flows).
At this stage, use of nbondi, nbondj variables has been completly removed.
13:50 2019WP/ASINTER-05_Brodeau_Advanced_Bulk edited by laurent: (diff)
12:21 laurent_team-LB_z.jpg attached to User Manager Plugin Pictures by laurent: laurent's Avatar
12:19 2019WP/ASINTER-05_Brodeau_Advanced_Bulk edited by laurent: (diff)
11:19 Changeset [11218] by mdrudi: revision of chap_DIA.tex in NEMO doc

2019-07-04:

17:31 Changeset [11217] by laurent: LB: more readable "cool-skin/warm-layer" organisation + no "cool-skin/warm-layer" scheme in the presence of sea-ice.
15:33 Changeset [11216] by kingr: Fix logic in sbcflx so that ocean-only AMM7 results are unchanged.
12:34 Changeset [11215] by laurent: LB: inclusion of "cool-skin/warm-layer" support (a la ECMWF) into COARE 3.0 algorithm.
12:30 Changeset [11214] by jchanut: #2216: add AGRIF_DEMO test case in place of Agulhas and remove cpp keys
11:29 Changeset [11213] by jchanut: #2216: Add Romain's update of ZDF chapter

2019-07-03:

21:21 Changeset [11212] by nicolasmartin

Mainly some modifications to enable the compilation of the manual by dedicated LaTeX editors
The compilation options have been gathered within latexmkrc RC file for Latexmk,
this has been tested successfully for 2 cross-platform softwares: Texmaker & Te Xstudio?
Don't be able to test it under TeXShop for MacOS, but it should be portable as
it requires only to modify the configuration of few cmds: LaTeX, PdfLaTeX, Latexmk & PDF viewer
For a comprehensive list of available LaTeX editors, see https://en.wikibooks.org/wiki/LaTeX/Installation#Cross-platform)

Other changes

Rectification of the required list for LaTeX pkgs
Append thanks.tex with the first reviewers of chapters
Configuration of the background color for namelists
Testing of colors for different types of links

18:38 Changeset [11211] by smueller

Quoting of preprocessor key lists in makenemo arguments to avoid incorrect preprocessor key management (ticket #2302)

14:46 Tag change on System Team/Agenda/2019-07-04 by mathiot

Tags VC added

12:08 Changeset [11210] by girrmann

dev_r10984_HPC-13 : remove some communications in bdy treatment in case nn_hls > 1, see #2285

09:09 Changeset [11209] by laurent

LB: making more efficient and more centralized use of physical/thermodynamics functions defined into "OCE/SBC/sbcblk_phy.F90".

2019-07-02:

23:55 Changeset [11208] by smueller: Branching of SETTE for fixing the bug described in ticket #2302
19:32 Changeset [11207] by mathiot: ENHANCE-03_closea: closea correction change to match new closea mask in domain_cfg (ticket #2143)
16:50 Ticket #2220 (adaptive EVP (ice rheology) makes the model crash) closed by clem: invalid: actually reducing the time step (4800s for ORCA2) is sufficient to …
15:31 Ticket #2280 (jperio=0 in parent_domcfg_updated) closed by clem: fixed
15:24 Changeset [11206] by clem: solve ticket #2280 by adding a new namelist parameter in the NESTING namelist to account for jperio of the parent grid
14:25 Changeset [11205] by jchanut: #2199
1) Make sponge independent of sub-domain size. Partially masked open boundary segments are not taken into account anymore. To do so, sponge coefficients should be read in a file for realistic applications (then nesting tools need to be modified accordingly).
2) Replace East-West-North-South barotropic data arrays by a global 2d array. Then apply barotropic open boundary conditions thanks to mi0/mi1, mj0/mj1 indexes.
3) Call AGRIF bdy update one more time in dynspg_ts during extrapolation phase. This removes a dozen lines of code in dynspg_ts routine.
14:09 Ticket #2284 (Bug in NST/agrif_top_update.F90) closed by jchanut: fixed
13:44 Ticket #1982 (Met Office coupling system with "LIM3") closed by clem: fixed: Coupling SI3 with Met Office? environment is now possible (and can be …
13:39 Ticket #2256 (Unphysical values of ice age in SI3.) closed by clem: fixed
13:39 Ticket #2257 (Floating point overflow linked to snow thickness in SI3) closed by clem: fixed
11:25 New topic on Beginner created by duh: [test-case][overflow] Problems regarding test case running in NEMO 4.0
01:50 Tag change on Admin/Ticket Stats by nemo: Tags stats added

2019-07-01:

16:52 Ticket #2295 (Subroutine bdy_dta uses an uninitialised namelist parameter unless ...) closed by smueller: fixed: source:/NEMO/trunk@11204 passes the AMM12 tests of the SETTE test suite.
16:37 Changeset [11204] by smueller: Merge of changeset [11175] into the trunk (ticket #2295)
14:37 Changeset [11203] by jcastill: Remove the svn keywords that were introduced in the last modification
12:44 Changeset [11202] by jcastill: Copy of branch branches/UKMO/dev_r5518_obs_oper_update@11130 without namelist_ref changes to allow merging with coupling and biogeochemistry branches
12:10 Changeset [11201] by mathiot: ENHANCE-03_domcfg : add management of closed seas in domain cfg by flood filling and lat/lon seed instead of i/j box definition (ticket #2143)
10:51 Changeset [11200] by emmafiedler: Avoid multiple lines of write statement and change of variable name following CICE review

2019-06-28:

17:43 Changeset [11199] by mathiot: update branch to head of version 4.0 (ticket #2298)
16:36 Changeset [11198] by girrmann: dev_r10984_HPC-13 : delete mpp_bdy_generic.h90 now unused following [11195], see # 2285
14:21 Changeset [11197] by mathiot: ENHANCE-03_domcfg: daymod.f90 not used (ticket #2143)
14:20 Changeset [11196] by mathiot: ENHANCE-03_domcfg: USE dianam useless in iom.F90 (ticket #2143)
12:59 Changeset [11195] by girrmann: dev_r10984_HPC-13 : update of trc_bdy following [11191], merge of lbc_lnk and lbc_bdy_lnk in a single lbc_lnk routine, see #2285

2019-06-27:

16:51 Changeset [11194] by smasson: dev_r10984_HPC-13 : reorganization of lbclnk, part 1: bugfix following [11192], see #2285
12:47 Changeset [11193] by smasson: dev_r10984_HPC-13 : reorganization of lbclnk, part 1: missing delete of lbc_lnk_generic.h90 in [11192], see #2285
12:40 Changeset [11192] by smasson: dev_r10984_HPC-13 : reorganization of lbclnk, part 1: simpler mpp_lnk_generic.h90 supress lbc_lnk_generic.h90, see #2285
10:14 Changeset [11191] by girrmann: dev_r10984_HPC-13 : bdy treatment can now handel a rim 0 and a rim 1, results are unchanged when only rim 1 is provided, see #2288 and #2285

2019-06-26:

18:54 Changeset [11190] by nicolasmartin

Duplicate symbolic links to .ist index style file (1 in ./main and 1 in ./build)
For unknown reason, the LaTeX compilation process seems to differ between Mac and Linux: Mac wants to have the index style file in ./build whereas Linux requires it in ./main.

18:24 Changeset [11189] by nicolasmartin

Enabling index links by moving hyperref pkg at the end of the LaTeX preamble

18:02 Changeset [11188] by jchanut

Add missing link for NEMO doc compilation

17:56 Changeset [11187] by nicolasmartin

Modifications and bugfixes

Correction of the layout standard Right: scrreprt instead of scrreport
Switch to 2-columns for the bibliography
Update svn:ignore property for list of figures and tables
Update LaTeX dependencies
Move \triad command declaration to ./global/latex/new_cmds.tex with \DeclareRobustCommand specific prefix to prevent issue with \listoffigures
LaTeX typos
Ignore todonotes.tex for time being

17:02 Changeset [11186] by kingr

Merging changes from AMM15_v3_6_STABLE_package_collate r10728:11063

16:58 Changeset [11185] by jchanut

Add new flowchart figure, #2216

16:56 Changeset [11184] by jchanut

Update time domain chapter, #2216

16:09 Changeset [11183] by girrmann

dev_r10984_HPC-13 : improvement of neumann boundary condition, changes the results, see #2285

12:08 Changeset [11182] by laurent

LB: adding possibility to use dew-point temperature rather than specific humidity as "air humidity" ⇒ ln_humi_dpt@namsbc_blk

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