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CHANGES in NEMO/releases/release-4.0.1 – NEMO

source: NEMO/releases/release-4.0.1/CHANGES @ 14503

Last change on this file since 14503 was 14481, checked in by nicolasmartin, 3 years ago

Add CHANGES file which details exhaustively the modifications since release-4.0

  • Find revision numbers between 2 releases
    • Rev 4.0 : svn log --stop-on-copy --limit 1 -r0:HEAD ^/NEMO/releases/release-4.0
    • Rev. 4.0.1: svn log --stop-on-copy --limit 1 -r0:HEAD ^/NEMO/releases/release-4.0.1
  • Generation of CHANGES content (at the root of release-4.0.1)
    • Commits : svn log -r 11697:10606 ^/NEMO/trunk
    • Differences: svn diff --summarize --ignore-properties . ^/NEMO/releases/release-4.0 | sort -k2
File size: 92.2 KB
Line 
1#######
2Commits
3#######
4
5------------------------------------------------------------------------
6r11695 | nicolasmartin | 2019-10-14 15:00:35 +0200 (lun., 14 oct. 2019) | 2 lines
7
8Remove useless files for index styling
9
10------------------------------------------------------------------------
11r11694 | nicolasmartin | 2019-10-14 14:54:50 +0200 (lun., 14 oct. 2019) | 2 lines
12
13Fix to compilte TOP manual
14
15------------------------------------------------------------------------
16r11693 | nicolasmartin | 2019-10-14 14:53:52 +0200 (lun., 14 oct. 2019) | 2 lines
17
18Macros renaming
19
20------------------------------------------------------------------------
21r11690 | nicolasmartin | 2019-10-11 19:05:10 +0200 (ven., 11 oct. 2019) | 2 lines
22
23Update chapters according to previous commit
24
25------------------------------------------------------------------------
26r11688 | nicolasmartin | 2019-10-11 17:59:02 +0200 (ven., 11 oct. 2019) | 2 lines
27
28Load ''grffile'' package to avoid import issue with file extension
29
30------------------------------------------------------------------------
31r11687 | nicolasmartin | 2019-10-11 16:56:47 +0200 (ven., 11 oct. 2019) | 3 lines
32
33Temporary solution to solve LaTeX compilation issue with `\includegraphics` while waiting for TeXLive fix
34For reference, see https://github.com/MiKTeX/miktex-packaging/issues/131
35
36------------------------------------------------------------------------
37r11686 | agn | 2019-10-11 00:37:17 +0200 (ven., 11 oct. 2019) | 1 line
38
39FontAwesome fix for texlive on Mac
40------------------------------------------------------------------------
41r11685 | agn | 2019-10-11 00:16:22 +0200 (ven., 11 oct. 2019) | 1 line
42
43added OSMOSIS documentation to chap_ZDF.tex
44------------------------------------------------------------------------
45r11684 | agn | 2019-10-11 00:16:15 +0200 (ven., 11 oct. 2019) | 1 line
46
47chap_ZDF.tex now compiles
48------------------------------------------------------------------------
49r11683 | agn | 2019-10-11 00:16:09 +0200 (ven., 11 oct. 2019) | 1 line
50
51Monday morning
52------------------------------------------------------------------------
53r11682 | agn | 2019-10-11 00:16:02 +0200 (ven., 11 oct. 2019) | 1 line
54
55Sunday
56------------------------------------------------------------------------
57r11681 | agn | 2019-10-11 00:15:54 +0200 (ven., 11 oct. 2019) | 1 line
58
59Wednsday's changes
60------------------------------------------------------------------------
61r11680 | agn | 2019-10-11 00:15:47 +0200 (ven., 11 oct. 2019) | 1 line
62
63Thursday
64------------------------------------------------------------------------
65r11679 | agn | 2019-10-11 00:15:41 +0200 (ven., 11 oct. 2019) | 1 line
66
67Wednesday's additions
68------------------------------------------------------------------------
69r11678 | agn | 2019-10-11 00:15:35 +0200 (ven., 11 oct. 2019) | 1 line
70
71Tuesday's additions
72------------------------------------------------------------------------
73r11677 | agn | 2019-10-11 00:15:29 +0200 (ven., 11 oct. 2019) | 1 line
74
75added structure figure
76------------------------------------------------------------------------
77r11676 | agn | 2019-10-11 00:15:24 +0200 (ven., 11 oct. 2019) | 1 line
78
79Few more changes tp chap_ZDF.tex
80------------------------------------------------------------------------
81r11675 | agn | 2019-10-11 00:15:18 +0200 (ven., 11 oct. 2019) | 1 line
82
83started on flux-gradient relationship
84------------------------------------------------------------------------
85r11674 | agn | 2019-10-11 00:15:08 +0200 (ven., 11 oct. 2019) | 1 line
86
87start of OSMOSIS docs
88------------------------------------------------------------------------
89r11673 | nicolasmartin | 2019-10-10 17:24:32 +0200 (jeu., 10 oct. 2019) | 2 lines
90
91Fix missing LaTeX pkgs
92
93------------------------------------------------------------------------
94r11653 | davestorkey | 2019-10-04 14:34:02 +0200 (ven., 04 oct. 2019) | 2 lines
95
96Fix for bug in Smagorinsky scheme #2318.
97
98------------------------------------------------------------------------
99r11649 | clem | 2019-10-04 10:57:36 +0200 (ven., 04 oct. 2019) | 1 line
100
101change default parameters for landfast ice (Jef Lemieux pers. communication)
102------------------------------------------------------------------------
103r11640 | clem | 2019-10-02 14:06:19 +0200 (mer., 02 oct. 2019) | 1 line
104
105just correct a print
106------------------------------------------------------------------------
107r11632 | clem | 2019-10-01 20:57:51 +0200 (mar., 01 oct. 2019) | 1 line
108
109limit snow thickness after advection (with Prather) if snow load makes the ice-snow interface to deplet below sea surface (as for UM scheme)
110------------------------------------------------------------------------
111r11630 | nicolasmartin | 2019-10-01 19:37:49 +0200 (mar., 01 oct. 2019) | 2 lines
112
113Review of TRA chapter
114
115------------------------------------------------------------------------
116r11627 | clem | 2019-10-01 15:34:06 +0200 (mar., 01 oct. 2019) | 1 line
117
118change some wrong comments
119------------------------------------------------------------------------
120r11622 | nicolasmartin | 2019-10-01 13:10:55 +0200 (mar., 01 oct. 2019) | 2 lines
121
122Review of "Time Domain" and DOM chapters
123
124------------------------------------------------------------------------
125r11612 | clem | 2019-09-29 10:55:44 +0200 (dim., 29 sept. 2019) | 1 line
126
127make Prather the default advection scheme for ice simulations and drastically reduce the number of communications in Prather routine (by a factor of 10)
128------------------------------------------------------------------------
129r11608 | nicolasmartin | 2019-09-27 12:24:49 +0200 (ven., 27 sept. 2019) | 2 lines
130
131Review of "Model Basics" chapter
132
133------------------------------------------------------------------------
134r11601 | clem | 2019-09-26 16:54:45 +0200 (jeu., 26 sept. 2019) | 1 line
135
136correct the check on conservation for sea ice (does not impact sette tests)
137------------------------------------------------------------------------
138r11599 | nicolasmartin | 2019-09-25 22:19:45 +0200 (mer., 25 sept. 2019) | 2 lines
139
140Cosmetic cleaning
141
142------------------------------------------------------------------------
143r11598 | nicolasmartin | 2019-09-25 22:00:42 +0200 (mer., 25 sept. 2019) | 2 lines
144
145Add template of versioning record at the beginning of chapters
146
147------------------------------------------------------------------------
148r11597 | nicolasmartin | 2019-09-25 20:20:19 +0200 (mer., 25 sept. 2019) | 3 lines
149
150Continuation of coding rules application
151Recovery of some sections deleted by the previous commit
152
153------------------------------------------------------------------------
154r11596 | nicolasmartin | 2019-09-25 19:06:37 +0200 (mer., 25 sept. 2019) | 7 lines
155
156Application of some coding rules
157- Replace comments before sectioning cmds by a single line of 100 characters long to display when
158  every line should break
159- Replace multi blank lines by one single blank line
160- For list environment, put `\item`, label and content on the same line
161- Remove `\newpage` and comments line around ''figure'' envs
162
163------------------------------------------------------------------------
164r11595 | nicolasmartin | 2019-09-25 16:22:05 +0200 (mer., 25 sept. 2019) | 2 lines
165
166Fix the paths for graphics searching
167
168------------------------------------------------------------------------
169r11594 | nicolasmartin | 2019-09-25 16:16:59 +0200 (mer., 25 sept. 2019) | 2 lines
170
171Review svn:ignore and svn:externals properties (3)
172
173------------------------------------------------------------------------
174r11593 | nicolasmartin | 2019-09-25 16:14:06 +0200 (mer., 25 sept. 2019) | 2 lines
175
176Review svn:ignore and svn:externals properties (2)
177
178------------------------------------------------------------------------
179r11592 | nicolasmartin | 2019-09-25 16:11:53 +0200 (mer., 25 sept. 2019) | 2 lines
180
181Review `svn:ignore` and `svn:externals` properties
182
183------------------------------------------------------------------------
184r11591 | nicolasmartin | 2019-09-25 13:52:24 +0200 (mer., 25 sept. 2019) | 1 line
185
186Cleaning, linking and renaming
187------------------------------------------------------------------------
188r11584 | nicolasmartin | 2019-09-20 13:16:06 +0200 (ven., 20 sept. 2019) | 6 lines
189
190Restoration of separate compilation of chapters or appendices
191The command to launch is almost the same as the manual, for instance
192{{{#!console
193$ latexmk -r latex/global/latexmkrc -cd latex/NEMO/subfiles/chap_time_domain
194}}}
195
196------------------------------------------------------------------------
197r11582 | nicolasmartin | 2019-09-20 11:44:31 +0200 (ven., 20 sept. 2019) | 3 lines
198
199New LaTeX commands `\nam` and `\np` to mention namelist content (step 2)
200Finally convert `\forcode{...}` following `\np{}{}` into optional arg of the new command `\np[]{}{}`
201
202------------------------------------------------------------------------
203r11579 | nicolasmartin | 2019-09-19 19:48:19 +0200 (jeu., 19 sept. 2019) | 2 lines
204
205Fix for the sort of the ''blocks'' index
206
207------------------------------------------------------------------------
208r11578 | nicolasmartin | 2019-09-19 19:44:36 +0200 (jeu., 19 sept. 2019) | 3 lines
209
210New LaTeX commands `\nam` and `\np` to mention namelist content (step 2)
211So far so good, the manual compiles successfully 4 times and everything seems in its right place
212
213------------------------------------------------------------------------
214r11577 | nicolasmartin | 2019-09-19 19:01:38 +0200 (jeu., 19 sept. 2019) | 22 lines
215
216New LaTeX commands `\nam` and `\np` to mention namelist content
217(Partial commit to serve as a backup before other large edits)
218In order to benefit of the syntax highlighting and to have a simpler syntax for
219citing namelist block (`\nam`) and parameter (`\np`) with an optional variable assignment (\forcode{...}),
220at this time the only viable solution I found is to require a double marker for
221what it looks like the same item:
2221. Marker with the real name: 'tra_adv' block or 'ln_flx' parameter
2232. Marker with underscore character escaping: 'tra\_adv' block or 'ln\_flx' parameter
224Despite many searches and attempts, I did not find a workaround to edit on-the-fly one or
225the other marker.
226In fact, the problem is on one side that the LaTeX index interprets '_' as a switch for lowering like
227in math mode while on the other hand the backslash is considered for Pygments as a typo in Fortran
228(red box).
229
230For instance, `\nam` and `\np` have as of now the aforementioned 2 mandatory arguments in
231the previous order (between braces) + an optional argument for `\np` when the parameter is defined
232(between brackets at the first position):
233- `\nam`: LaTeX code ` in the \nam{tra_adv}{tra\_adv} ` -> PDF ' in the &namtra_adv (namelist X.X) '
234  with syntax highlighting, the hyperlink and the index entry
235- `\np`:  LaTeX code `\np[=.true.]{ln_flx}{ln\_flx}` -> PDF `ln_flux=.true.` with
236  syntax highlighting for the whole string and the entry in the 'parameters' index
237
238------------------------------------------------------------------------
239r11575 | clem | 2019-09-19 12:51:37 +0200 (jeu., 19 sept. 2019) | 1 line
240
241improve one output for sea ice. Does not change anything else in the code
242------------------------------------------------------------------------
243r11572 | nicolasmartin | 2019-09-19 10:47:06 +0200 (jeu., 19 sept. 2019) | 2 lines
244
245Review indexes style
246
247------------------------------------------------------------------------
248r11571 | nicolasmartin | 2019-09-19 10:44:07 +0200 (jeu., 19 sept. 2019) | 2 lines
249
250Cosmetic modifications on section titles
251
252------------------------------------------------------------------------
253r11567 | nicolasmartin | 2019-09-18 17:41:37 +0200 (mer., 18 sept. 2019) | 2 lines
254
255Style improvments
256
257------------------------------------------------------------------------
258r11565 | nicolasmartin | 2019-09-18 16:58:58 +0200 (mer., 18 sept. 2019) | 2 lines
259
260Cleaning of section titles
261
262------------------------------------------------------------------------
263r11563 | nicolasmartin | 2019-09-18 15:36:42 +0200 (mer., 18 sept. 2019) | 2 lines
264
265Miscellaneous changes
266
267------------------------------------------------------------------------
268r11562 | nicolasmartin | 2019-09-18 15:32:36 +0200 (mer., 18 sept. 2019) | 2 lines
269
270New page layout with shorter margins (manual at less than 300 pages)
271
272------------------------------------------------------------------------
273r11561 | nicolasmartin | 2019-09-18 15:24:34 +0200 (mer., 18 sept. 2019) | 2 lines
274
275Apply two thirds ratio on figures width as default
276
277------------------------------------------------------------------------
278r11560 | clem | 2019-09-18 13:31:36 +0200 (mer., 18 sept. 2019) | 1 line
279
280correct the conversion from 1cat to Ncat for ice data at the boundaries when using bdy
281------------------------------------------------------------------------
282r11558 | nicolasmartin | 2019-09-17 17:04:06 +0200 (mar., 17 sept. 2019) | 34 lines
283
284Review all `figure` envs + activation of `listoflistings`
2851. Figure env:
286   - Replace `center` sub-env with only `\centering` cmd
287   - Add alternate caption for `\listoffigures` (shorter one between square brackets, i.e. `\caption[]{}`)
288   - Place `\label` outside of `\caption` and remove useless `\protect`
289
2902. Namelist listings
291   - Put `\nlst` with the namelist inlcusion in a `listing` float env with caption and label
292   - Remove namelist duplicates
293-- This line, and those below, will be ignored--
294M    subfiles/apdx_triads.tex
295M    subfiles/chap_model_basics_zstar.tex
296M    subfiles/chap_SBC.tex
297M    subfiles/apdx_DOMAINcfg.tex
298M    subfiles/apdx_s_coord.tex
299M    subfiles/chap_DOM.tex
300M    subfiles/chap_ASM.tex
301M    subfiles/chap_DIU.tex
302M    subfiles/chap_cfgs.tex
303M    subfiles/chap_ZDF.tex
304M    subfiles/chap_OBS.tex
305M    subfiles/chap_model_basics.tex
306M    subfiles/chap_time_domain.tex
307M    subfiles/apdx_algos.tex
308M    subfiles/chap_TRA.tex
309M    subfiles/chap_DYN.tex
310M    subfiles/chap_misc.tex
311M    subfiles/chap_DIA.tex
312M    subfiles/apdx_invariants.tex
313M    subfiles/chap_LBC.tex
314M    subfiles/apdx_diff_opers.tex
315M    subfiles/chap_STO.tex
316M    subfiles/chap_LDF.tex
317
318------------------------------------------------------------------------
319r11554 | jchanut | 2019-09-17 11:46:30 +0200 (mar., 17 sept. 2019) | 2 lines
320
321#2078: add Franziska's fix to correct input/output paths with AGRIF
322
323------------------------------------------------------------------------
324r11552 | nicolasmartin | 2019-09-16 17:38:22 +0200 (lun., 16 sept. 2019) | 2 lines
325
326add unbreakable space after `\fortran` & `fninety`
327
328------------------------------------------------------------------------
329r11551 | nicolasmartin | 2019-09-16 16:53:24 +0200 (lun., 16 sept. 2019) | 2 lines
330
331Bugfix: no index entries in math env
332
333------------------------------------------------------------------------
334r11548 | clem | 2019-09-13 23:42:32 +0200 (ven., 13 sept. 2019) | 1 line
335
336deactivate the check of conservation in spitz12 because it is too tricky to use
337------------------------------------------------------------------------
338r11544 | nicolasmartin | 2019-09-13 16:37:38 +0200 (ven., 13 sept. 2019) | 2 lines
339
340Missing modifications from previous commit
341
342------------------------------------------------------------------------
343r11543 | nicolasmartin | 2019-09-13 15:57:52 +0200 (ven., 13 sept. 2019) | 7 lines
344
345Implementation of convention for labelling references + files renaming
346Now each reference is supposed to have the information of the chapter in its name
347to identify quickly which file contains the reference (`\label{$prefix:$chap_...`)
348
349Rename the appendices from 'annex_' to 'apdx_' to conform with the prefix used in labels (`apdx:...`)
350Suppress the letter numbering
351
352------------------------------------------------------------------------
353r11537 | clem | 2019-09-12 10:24:48 +0200 (jeu., 12 sept. 2019) | 1 line
354
355make sure SI3 doc can be compiled, plus small edits
356------------------------------------------------------------------------
357r11536 | smasson | 2019-09-11 15:54:18 +0200 (mer., 11 sept. 2019) | 1 line
358
359trunk: merge dev_r10984_HPC-13 into the trunk
360------------------------------------------------------------------------
361r11532 | smasson | 2019-09-11 15:30:16 +0200 (mer., 11 sept. 2019) | 1 line
362
363trunk: merge with v4
364------------------------------------------------------------------------
365r11524 | nicolasmartin | 2019-09-10 16:09:48 +0200 (mar., 10 sept. 2019) | 2 lines
366
367Bugfixes
368
369------------------------------------------------------------------------
370r11522 | nicolasmartin | 2019-09-10 12:21:20 +0200 (mar., 10 sept. 2019) | 5 lines
371
372Review the beginning of the manual
373Move the changelog to the common part shared between 3 manuals
374Add few paragraphs on the development workflow
375Improve the introduction of the manual
376
377------------------------------------------------------------------------
378r11515 | nicolasmartin | 2019-09-09 16:07:20 +0200 (lun., 09 sept. 2019) | 6 lines
379
380Style changes
381* logo for DOI links
382* Tweak cmds to apply manual color to chapter headings
383* Fix headings on bibliography and indexes sections
384* Remove ''minitoc'' pkg and use instead appropriate `\chaptertoc` custom cmd
385
386------------------------------------------------------------------------
387r11459 | cetlod | 2019-08-20 10:59:40 +0200 (mar., 20 août 2019) | 1 line
388
389Revision in chapter TRA : mainly removal obsolete CPP keys and update of namelist parameter
390------------------------------------------------------------------------
391r11445 | sciliberti | 2019-08-19 09:18:20 +0200 (lun., 19 août 2019) | 1 line
392
393#2216 revision of LBC chapter: main ones in bdy description and geometry
394------------------------------------------------------------------------
395r11435 | nicolasmartin | 2019-08-14 14:45:08 +0200 (mer., 14 août 2019) | 18 lines
396
397Various corrections on chapters
398
399Cleaning the indexes by fixing/removing wrong entries (or appending a `?` to unknown items) and
400improve the classification with new index definitions for CPP keys and namelist blocks:
401- from `\key{...}` cmd, ''key_'' prefix no longer precedes the index entry
402- namelist block declaration moves from `\ngn{nam...} `  to `\nam{...}`
403  (i.e. ''\ngn{namtra\_ldf}'' -> ''\nam{tra\_ldf}'')
404  The expected prefix ''nam'' is added to the printed word but not the index entry.
405Now we have indexes with a better sorting instead of all CPP keys under 'K' and namelists blocks under 'N'.
406
407Fix missing space issues with alias commands by adding a trailing backslash (`\NEMO\`, `\ie\`, `\eg\`, ...).
408There is no perfect solution for this, and I prefer not using a particular package to solve it.
409
410Review the initial LaTeX code snippet for the historic changes in chapters
411
412'''Finally, for readability and future diff visualisations, please avoid writing paragraphs with continuous lines'''.
413Break the lines around 80 to 100 characters long
414
415------------------------------------------------------------------------
416r11433 | nicolasmartin | 2019-08-12 21:44:18 +0200 (lun., 12 août 2019) | 39 lines
417
418Pre-implementation of new cover page and new headings style for reference manuals
419
420==== Cover page
421
422The layout of the frontpage has been completely redesigned,
423a coloured banner has been added to emphasize the title and easily identify each manual
424between them.
425The chosen color for each document (blue for NEMO, gray for SI^3^ and green for TOP) will be
426used throughout the manual for the links and in the chapter headings. \\
427The list of authors (writers/editors/reviewers) for the version of the manual is given next to
428the abstract, which is now included in the frontpage.
429A link to an existing ORCID profile for the author precedes its name. \\
430Few 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
431abstract section)
432
433==== Headings
434
435- header: chapter number and title for even pages, same infos for section otherwise
436- footer: name of the manual and page numbering with the total number of pages
437  (reverse order between odd/even pages)
438
439For the chapter heading, a new style 'Bjornstrup' from ''fncychap'' package is now use.
440
441==== Abstract
442
443Split the section in two paragraphs for all manuals
444
4451. Common description with almost the same sentences only customized by the general infos of the model
4462. Specific part for the characteristics of the model
447
448==== Troubleshooting
449
450As announced, I have introduced some icons from ''academicons'' and ''fontawesome'' packages.
451It required to switch from `pdflatex` to `xelatex` for the compilation and it prevents from now
452the building of the whole document.
453Also the PDF generated does not look nice due to the font
454
455Work in progress...
456
457------------------------------------------------------------------------
458r11418 | acc | 2019-08-07 14:25:51 +0200 (mer., 07 août 2019) | 1 line
459
460Minor 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.)
461------------------------------------------------------------------------
462r11416 | jchanut | 2019-08-07 12:11:36 +0200 (mer., 07 août 2019) | 2 lines
463
464#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.
465
466------------------------------------------------------------------------
467r11415 | jchanut | 2019-08-07 11:05:58 +0200 (mer., 07 août 2019) | 2 lines
468
469#2080, correct conditional statement
470
471------------------------------------------------------------------------
472r11414 | jchanut | 2019-08-07 10:58:09 +0200 (mer., 07 août 2019) | 2 lines
473
474#2292, add ztilde diffusive fluxes in Courant number computation
475
476------------------------------------------------------------------------
477r11411 | jchanut | 2019-08-06 17:08:55 +0200 (mar., 06 août 2019) | 2 lines
478
479#2305, a few corrections and comestic changes following Andrew's revision 11407
480
481------------------------------------------------------------------------
482r11410 | gsamson | 2019-08-06 16:50:38 +0200 (mar., 06 août 2019) | 1 line
483
484bugfix for negative Chl values in tra_qsr, see #2312
485------------------------------------------------------------------------
486r11407 | acc | 2019-08-06 15:36:27 +0200 (mar., 06 août 2019) | 1 line
487
488Final 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.
489------------------------------------------------------------------------
490r11388 | acc | 2019-08-01 18:09:07 +0200 (jeu., 01 août 2019) | 1 line
491
492Add 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
493------------------------------------------------------------------------
494r11386 | jchanut | 2019-08-01 17:26:28 +0200 (jeu., 01 août 2019) | 2 lines
495
496#2216, correct description of grid scale dependent mixing coefficient
497
498------------------------------------------------------------------------
499r11351 | davestorkey | 2019-07-25 15:47:05 +0200 (jeu., 25 juil. 2019) | 2 lines
500
501Documentation: correction to slope definitions in Appendix B.
502
503------------------------------------------------------------------------
504r11346 | mdrudi | 2019-07-25 12:11:23 +0200 (jeu., 25 juil. 2019) | 1 line
505
506addition of changes record in chap_DIA.tex
507------------------------------------------------------------------------
508r11344 | clevy | 2019-07-25 10:52:10 +0200 (jeu., 25 juil. 2019) | 1 line
509
510#2216: updates to STO reference manual
511------------------------------------------------------------------------
512r11341 | clevy | 2019-07-25 10:27:15 +0200 (jeu., 25 juil. 2019) | 1 line
513
514bugfix stopar.F90 correct logical check
515------------------------------------------------------------------------
516r11340 | clevy | 2019-07-24 18:35:12 +0200 (mer., 24 juil. 2019) | 1 line
517
518#2216: updates to STO reference manual
519------------------------------------------------------------------------
520r11339 | acc | 2019-07-24 17:10:21 +0200 (mer., 24 juil. 2019) | 1 line
521
522Update of chap_misc.tex for v4.0 compatibility
523------------------------------------------------------------------------
524r11338 | gsamson | 2019-07-24 14:18:39 +0200 (mer., 24 juil. 2019) | 1 line
525
526add a missing CPP key description in SBC chapter
527------------------------------------------------------------------------
528r11337 | mikebell | 2019-07-24 12:31:16 +0200 (mer., 24 juil. 2019) | 1 line
529
530authors of annex A added
531------------------------------------------------------------------------
532r11336 | jchanut | 2019-07-24 12:30:54 +0200 (mer., 24 juil. 2019) | 2 lines
533
534Update LDF chapter, #2216
535
536------------------------------------------------------------------------
537r11335 | mikebell | 2019-07-24 12:16:18 +0200 (mer., 24 juil. 2019) | 1 line
538
539review of chap_model_basics, annex_A and annex_B
540------------------------------------------------------------------------
541r11333 | gsamson | 2019-07-23 17:17:14 +0200 (mar., 23 juil. 2019) | 1 line
542
543#2216: update SBC chapter with corresponding bibliography
544------------------------------------------------------------------------
545r11331 | davestorkey | 2019-07-23 15:02:57 +0200 (mar., 23 juil. 2019) | 2 lines
546
547Documentation: small corrections and tidy up of Appendix B.
548
549------------------------------------------------------------------------
550r11330 | acc | 2019-07-23 13:33:32 +0200 (mar., 23 juil. 2019) | 1 line
551
552Rename annex_F.tex to annex_DOMAINcfg.tex to avoid incorrect order association (it currently appears as appendix E). Alter references accordingly and fix minor latex error in annex_DOMAINcfg.tex
553------------------------------------------------------------------------
554r11326 | acc | 2019-07-23 12:59:20 +0200 (mar., 23 juil. 2019) | 1 line
555
556Delete spurious appendix D inadvertently reinstated in appendices.tex
557------------------------------------------------------------------------
558r11323 | acc | 2019-07-22 17:05:02 +0200 (lun., 22 juil. 2019) | 1 line
559
560Correct a missing reference and add the author table to new appendix
561------------------------------------------------------------------------
562r11321 | acc | 2019-07-22 16:08:52 +0200 (lun., 22 juil. 2019) | 1 line
563
564Introduce new appendix to hold material removed from chap_DOM.tex but which is still relevant to DOMAINcfg.
565------------------------------------------------------------------------
566r11318 | jchanut | 2019-07-22 11:24:56 +0200 (lun., 22 juil. 2019) | 2 lines
567
568#2216, wrong namelist name in ZDF chapter
569
570------------------------------------------------------------------------
571r11316 | djlea | 2019-07-19 19:20:02 +0200 (ven., 19 juil. 2019) | 2 lines
572
573#2297 Updates to OBS and ASM documentation
574
575------------------------------------------------------------------------
576r11313 | emanuelaclementi | 2019-07-19 18:31:10 +0200 (ven., 19 juil. 2019) | 1 line
577
578Added Surface wave-induced mixing section in ZDF Chapter
579------------------------------------------------------------------------
580r11312 | acc | 2019-07-19 18:15:22 +0200 (ven., 19 juil. 2019) | 1 line
581
582Updated 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
583------------------------------------------------------------------------
584r11310 | nicolasmartin | 2019-07-19 17:29:48 +0200 (ven., 19 juil. 2019) | 3 lines
585
586Revert to no background color for inline code
587For instance, avoiding bad style when mixing index entries like `\np` with `\forcode`
588
589------------------------------------------------------------------------
590r11299 | nicolasmartin | 2019-07-18 16:27:43 +0200 (jeu., 18 juil. 2019) | 6 lines
591
592Review of the coding rules chapter: convert it to a shared file for 3 manuals
593- Move ''annex_D.tex'' and ''NEMO_coding_conv.tex'' to ''./latex/global''
594- Rename ''NEMO_coding_conv.tex'' to ''coding_rules.tex'' and redesign it as a chapter and not
595  a standalone document
596- Edit ''document.tex'' to include the coding rules by default at the end of the appendix
597
598------------------------------------------------------------------------
599r11293 | jchanut | 2019-07-18 15:21:40 +0200 (jeu., 18 juil. 2019) | 2 lines
600
601#2292, Fixes courant number computation in adaptive vertical advection
602
603------------------------------------------------------------------------
604r11292 | nicolasmartin | 2019-07-18 15:20:29 +0200 (jeu., 18 juil. 2019) | 2 lines
605
606Removal of obsolete symbolic links
607
608------------------------------------------------------------------------
609r11287 | jchanut | 2019-07-18 11:54:49 +0200 (jeu., 18 juil. 2019) | 2 lines
610
611#2291, Adaptive vertical advection: change order of calls with split explicit free surface
612
613------------------------------------------------------------------------
614r11281 | jchanut | 2019-07-17 15:51:21 +0200 (mer., 17 juil. 2019) | 2 lines
615
616#2290, fixes bugs with adaptive vertical advection
617
618------------------------------------------------------------------------
619r11276 | mdrudi | 2019-07-17 15:08:21 +0200 (mer., 17 juil. 2019) | 1 line
620
621revision of CMIP specific diagnostics in chap_DIA.tex in NEMO doc
622------------------------------------------------------------------------
623r11242 | jchanut | 2019-07-10 11:59:14 +0200 (mer., 10 juil. 2019) | 2 lines
624
625Remove 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.
626
627------------------------------------------------------------------------
628r11233 | clem | 2019-07-09 17:09:44 +0200 (mar., 09 juil. 2019) | 1 line
629
630change a comment in dommsk
631------------------------------------------------------------------------
632r11229 | clem | 2019-07-09 14:22:12 +0200 (mar., 09 juil. 2019) | 1 line
633
634debug BDY-ice by allowing any number of categories as input. Ticket #2300 may also be solved
635------------------------------------------------------------------------
636r11225 | jchanut | 2019-07-08 14:42:50 +0200 (lun., 08 juil. 2019) | 2 lines
637
638#2216, Finalize ZDF chapter - OSMOSIS and Adaptive vertical advection subsections to be updated
639
640------------------------------------------------------------------------
641r11218 | mdrudi | 2019-07-05 11:19:53 +0200 (ven., 05 juil. 2019) | 1 line
642
643revision of chap_DIA.tex in NEMO doc
644------------------------------------------------------------------------
645r11214 | jchanut | 2019-07-04 12:30:41 +0200 (jeu., 04 juil. 2019) | 2 lines
646
647#2216: add AGRIF_DEMO test case in place of Agulhas and remove cpp keys
648
649------------------------------------------------------------------------
650r11213 | jchanut | 2019-07-04 11:29:44 +0200 (jeu., 04 juil. 2019) | 2 lines
651
652#2216: Add Romain's update of ZDF chapter
653
654------------------------------------------------------------------------
655r11212 | nicolasmartin | 2019-07-03 21:21:59 +0200 (mer., 03 juil. 2019) | 13 lines
656
657Mainly some modifications to enable the compilation of the manual by dedicated LaTeX editors
658The compilation options have been gathered within ''latexmkrc'' RC file for Latexmk,
659this has been tested successfully for 2 cross-platform softwares: ''Texmaker'' & ''TeXstudio''
660Don't be able to test it under ''TeXShop'' for MacOS, but it should be portable as
661it requires only to modify the configuration of few cmds: LaTeX, PdfLaTeX, Latexmk & PDF viewer
662For a comprehensive list of available LaTeX editors, see https://en.wikibooks.org/wiki/LaTeX/Installation#Cross-platform)
663
664Other changes
665- Rectification of the required list for LaTeX pkgs
666- Append ''thanks.tex'' with the first reviewers of chapters
667- Configuration of the background color for namelists
668- Testing of colors for different types of links
669
670------------------------------------------------------------------------
671r11204 | smueller | 2019-07-01 16:37:33 +0200 (lun., 01 juil. 2019) | 2 lines
672
673Merge of changeset [11175] into the trunk (ticket #2295)
674
675------------------------------------------------------------------------
676r11190 | nicolasmartin | 2019-06-26 18:54:46 +0200 (mer., 26 juin 2019) | 3 lines
677
678Duplicate symbolic links to ''.ist'' index style file (1 in ./main and 1 in ./build)
679For 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''.
680
681------------------------------------------------------------------------
682r11189 | nicolasmartin | 2019-06-26 18:24:07 +0200 (mer., 26 juin 2019) | 2 lines
683
684Enabling index links by moving ''hyperref'' pkg at the end of the LaTeX preamble
685
686------------------------------------------------------------------------
687r11188 | jchanut | 2019-06-26 18:02:11 +0200 (mer., 26 juin 2019) | 2 lines
688
689Add missing link for NEMO doc compilation
690
691------------------------------------------------------------------------
692r11187 | nicolasmartin | 2019-06-26 17:56:45 +0200 (mer., 26 juin 2019) | 9 lines
693
694Modifications and bugfixes
695- Correction of the layout standard Right: `scrreprt` instead of `scrreport`
696- Switch to 2-columns for the bibliography
697- Update `svn:ignore` property for list of figures and tables
698- Update LaTeX dependencies
699- Move `\triad` command declaration to ''./global/latex/new_cmds.tex'' with `\DeclareRobustCommand` specific prefix to prevent issue with \listoffigures
700- LaTeX typos
701- Ignore todonotes.tex for time being
702
703------------------------------------------------------------------------
704r11184 | jchanut | 2019-06-26 16:56:21 +0200 (mer., 26 juin 2019) | 2 lines
705
706Update time domain chapter, #2216
707
708------------------------------------------------------------------------
709r11181 | nicolasmartin | 2019-06-25 19:06:21 +0200 (mar., 25 juin 2019) | 2 lines
710
711Extension of the last changes to SI^3^ and TOP
712
713------------------------------------------------------------------------
714r11179 | nicolasmartin | 2019-06-25 15:46:19 +0200 (mar., 25 juin 2019) | 2 lines
715
716Add alternate section titles to avoid useless index links in ToC
717
718------------------------------------------------------------------------
719r11178 | nicolasmartin | 2019-06-25 13:57:04 +0200 (mar., 25 juin 2019) | 2 lines
720
721Supplement of the last bugfix
722
723------------------------------------------------------------------------
724r11177 | nicolasmartin | 2019-06-25 13:14:45 +0200 (mar., 25 juin 2019) | 2 lines
725
726Bugfix for LaTeX compilation
727
728------------------------------------------------------------------------
729r11176 | nicolasmartin | 2019-06-24 21:55:11 +0200 (lun., 24 juin 2019) | 20 lines
730
731Implementation of multi-indexes instead of an indiscrimate aggregate index
732Creation of 5 sections under ''Indexes'' chapter for the most relevant lists of index entries:
733namelist blocks and parameters, CPP keys, modules and subroutines.
734- ''indexes.tex'' & ''index.ist'': new file in ''global'' directory for index management
735- Add symbolic links under ''main'' to non-existing *.idx before LaTeX compilation to reduce
736  trivial error messages with `makeindex`
737- Create ''latexmkrc'' init file loaded latexmk with '-r' option in order to
738  apply the style rules to the indexes with the sequence of several compilations
739
740Other changes:
741- Define a ''preamble.tex'' with the list of files to load from ''global'' folder
742- Integrate 'Citation' subsubsection in new ''info_page.tex'' for the 2^nd^ page along with 'frontpage.tex' for the cover,
743  in order to have a clear distinction with `\maketitle` in the main LaTeX document
744- Move 'Foreword' chapter from ''subfiles'' to ''main'' as more appropriate
745
746Bugfixes with few attempts of HTML export
747- One single location for defining the paths to search for images with `\graphicspath` in ''packages.tex''
748- Renaming of authors variables (`\1stauthor` -> `\firstauthor` and so one)
749- Update of LaTeX dependencies in terms of new pkgs (''DEPS'')
750
751------------------------------------------------------------------------
752r11174 | nicolasmartin | 2019-06-21 19:19:25 +0200 (ven., 21 juin 2019) | 4 lines
753
754Extension renaming
755As .tex extension seems to be recognized natively by Trac for syntax highlighting, prefer to use it for all files under ''./latex/global''.
756The difference between .tex or .sty is a bit cryptic for what I currently know
757
758------------------------------------------------------------------------
759r11173 | nicolasmartin | 2019-06-21 18:55:47 +0200 (ven., 21 juin 2019) | 2 lines
760
761Removal of bad file
762
763------------------------------------------------------------------------
764r11172 | nicolasmartin | 2019-06-21 14:35:16 +0200 (ven., 21 juin 2019) | 2 lines
765
766Add missing files from previous commits
767
768------------------------------------------------------------------------
769r11171 | nicolasmartin | 2019-06-21 14:33:03 +0200 (ven., 21 juin 2019) | 2 lines
770
771Duplicate the new building process to SI^3^ and TOP
772
773------------------------------------------------------------------------
774r11170 | nicolasmartin | 2019-06-21 12:18:45 +0200 (ven., 21 juin 2019) | 8 lines
775
776Review of the overall building of any reference manual
777Implementation of a compilation process shared between the 3 manuals: now a global ''document.tex'' will be used as the main LaTeX file (a symbolic link will refer to it in each ''./engine/main'' directory).
778At the time of the manual building, a few small LaTeX files will be imported on the fly from the corresponding folder ''./latex/engine/main''.
779- ''definitions.tex'': engine, title, author(s), IPSL publication number and DOI ID
780- ''thanks.tex'': list of collaborators to be thanked for the writing/reviewing
781- ''chapters.tex'': ordered list of chapters (relative path to ''subfiles'')
782- ''appendices.tex'': ordered list of subordinate chapters (relative path to ''subfiles'')
783
784------------------------------------------------------------------------
785r11167 | nicolasmartin | 2019-06-21 11:09:29 +0200 (ven., 21 juin 2019) | 2 lines
786
787Move DOI images into ''badges'' folder
788
789------------------------------------------------------------------------
790r11160 | mathiot | 2019-06-20 18:47:37 +0200 (jeu., 20 juin 2019) | 1 line
791
792merge branch branch_ticket2259 : update nn_fsbc, nn_itend, rn_rdt of ORCA2 and related configuration (ticket #2259), update on sette will be commited soon
793------------------------------------------------------------------------
794r11159 | mathiot | 2019-06-20 17:48:06 +0200 (jeu., 20 juin 2019) | 1 line
795
796fix ticket #2301 (remove iceneg_pres and iceneg_volu from ICE_AGRIF file_def_nemo-ice.xml)
797------------------------------------------------------------------------
798r11154 | nicolasmartin | 2019-06-20 15:43:31 +0200 (jeu., 20 juin 2019) | 2 lines
799
800Bugfixes and changes remaining in the directory
801
802------------------------------------------------------------------------
803r11152 | nicolasmartin | 2019-06-20 15:11:32 +0200 (jeu., 20 juin 2019) | 2 lines
804
805Modifications in NEMO manual disseminated to SI^3^ and TOP
806
807------------------------------------------------------------------------
808r11151 | nicolasmartin | 2019-06-20 14:59:58 +0200 (jeu., 20 juin 2019) | 10 lines
809
810New version of ''NEMO_manual.tex''
811New class `scrreport` for the document (KOMA-script version of default `report`)
812Foreword is now placed before ToC.
813All figures are configured with `1.0\textwidth` as default.
814For compatibilty, `\frontmatter`, `\mainmatter` and `\backmatter` cmds have been removed and old fonts in LaTeX subfiles have been replaced
815- `\bf` -> `\mathbf` or `\bfseries`
816- `\it` -> `\itshape`
817- `\rm` -> `\mathrm` or `\rmfamily`
818- `\tt` -> `\ttfamily`
819
820------------------------------------------------------------------------
821r11150 | nicolasmartin | 2019-06-20 14:13:29 +0200 (jeu., 20 juin 2019) | 4 lines
822
823New version of ''foreword.tex''
824Most of the content have been transfered to the common ''frontpages.tex''.
825''foreword.tex'' now contains only the 'Abstract' section which is specific for each manual.
826
827------------------------------------------------------------------------
828r11148 | nicolasmartin | 2019-06-20 12:34:10 +0200 (jeu., 20 juin 2019) | 8 lines
829
830Reorganisation of the ''latex'' directory
831Creation of ''frontpages.tex'' to standardise the look of the manuals and few !LaTeX files to facilitate the overall modifications
832- ''minted''       : syntax highlighting
833- ''packages.sty'' : !LaTeX packages to load
834- ''styles.sty''   : gathering of all rules affecting the style
835- ''new_cmds.sty'' : custom LaTeX commands
836- ''todonotes.sty'': insertion of TODO bubbles inline or at the margin
837
838------------------------------------------------------------------------
839r11146 | nicolasmartin | 2019-06-20 12:00:00 +0200 (jeu., 20 juin 2019) | 2 lines
840
841Add DOI badges of the3 reference manuals
842
843------------------------------------------------------------------------
844r11128 | nicolasmartin | 2019-06-17 15:54:04 +0200 (lun., 17 juin 2019) | 2 lines
845
846Create ''styles'' folder to gather common files between manuals: ''NEMO.sty'' and ''ametsoc.bst''
847
848------------------------------------------------------------------------
849r11126 | nicolasmartin | 2019-06-17 15:24:58 +0200 (lun., 17 juin 2019) | 2 lines
850
851Reintroducing ''ametsoc.bst'' in ''latex'' shared folder
852
853------------------------------------------------------------------------
854r11125 | nicolasmartin | 2019-06-17 15:08:12 +0200 (lun., 17 juin 2019) | 4 lines
855
856Move BibTex style file and BibTool cfg to `/utils/dev` global directory for developers
857As these files will be used for the buidling of the 3 manuals (NEMO, SI^3^ and TOP),
858it is relevant to place them in a unique location of the repository and refer to with external definitions
859
860------------------------------------------------------------------------
861r11124 | nicolasmartin | 2019-06-17 14:49:53 +0200 (lun., 17 juin 2019) | 34 lines
862
863
864Editing of ''ametsoc.bst'' to generate hyperlinks for DOIs or URLs
865New version of bibtool resource file:
866- Braces as entries delimiter
867- All entry types in lowercase (`^@...`)
868- Normalisation of ''pages'' field (`[0-9]+--[0-9]`)
869- Deletion of ''url'' field if doi is here
870- Definition of fields order
871  {{{
872  sort.order =
873  { * =
874        # title     # chapter     # pages
875        # journal   # booktitle   # edition # editor # series
876        # volume    # number     
877        # author    # institution # school
878        # year      # month
879        # publisher # issn        # isbn
880        # doi       # url
881  }
882  }}}
883- coding the format of citations keys
884  {{{
885  key.format =
886  { %s(bibkey) # %-2n(author)_
887       {   
888            %+5.1W(journal)
889               # %0s(@book         ) { bk   } # %0s(@inbook       ) { ibk  }
890               # %0s(@incollection ) { icol } # %0s(@inproceedings) { iprc }
891               # %0s(@phdthesis    ) { phd  } # %0s(@techreport   ) { rpt  }
892       }
893    %2d(year)                   
894  }
895}}}
896
897------------------------------------------------------------------------
898r11123 | nicolasmartin | 2019-06-17 14:22:27 +0200 (lun., 17 juin 2019) | 2 lines
899
900Modification of LaTeX subfiles accordingly to new citations keys
901
902------------------------------------------------------------------------
903r11122 | nicolasmartin | 2019-06-17 14:05:58 +0200 (lun., 17 juin 2019) | 6 lines
904
905Upload advanced version of the NEMO bibliography
906- Apply global pattern for citation keys: `1stauthor{.2ndauthor{.ea}}_{journal|type}year`
907- Sorting entry fields wisely
908- Removal of redundancies ('doi'='url') by keeping only the DOI field
909- Manual editing for disambiguation with lowercase letter starting from the first item: `*a`, `*b`
910
911------------------------------------------------------------------------
912r11121 | nicolasmartin | 2019-06-17 12:31:12 +0200 (lun., 17 juin 2019) | 6 lines
913
914Fixes on BibTeX fields
915- Restoration of few missing entries from previous cleaning
916- Protection of some french names with "von" part
917- Use of the proper syntax for doubles quotes: {{{`` ... ''}}}
918- Addition of backslash for underscore character in URL
919
920------------------------------------------------------------------------
921r11120 | nicolasmartin | 2019-06-17 12:14:19 +0200 (lun., 17 juin 2019) | 2 lines
922
923Modification of the building process with dedicated `build` sub-folder
924
925------------------------------------------------------------------------
926r11118 | cetlod | 2019-06-17 10:51:25 +0200 (lun., 17 juin 2019) | 1 line
927
928Bugfix on sea-ice effect on production, see ticket 2299
929------------------------------------------------------------------------
930r11116 | nicolasmartin | 2019-06-14 20:21:45 +0200 (ven., 14 juin 2019) | 2 lines
931
932Removing of unnecessary entries
933
934------------------------------------------------------------------------
935r11115 | nicolasmartin | 2019-06-14 19:25:48 +0200 (ven., 14 juin 2019) | 2 lines
936
937Fixed version with unused references
938
939------------------------------------------------------------------------
940r11114 | cetlod | 2019-06-14 16:51:53 +0200 (ven., 14 juin 2019) | 1 line
941
942trunk:small bug fix in the previous bug correction, ticket #2296
943------------------------------------------------------------------------
944r11112 | mocavero | 2019-06-14 15:57:28 +0200 (ven., 14 juin 2019) | 1 line
945
946Update the chapter on reference configurations for 4.0 release, see #2216
947------------------------------------------------------------------------
948r11109 | cetlod | 2019-06-14 13:57:22 +0200 (ven., 14 juin 2019) | 1 line
949
950trunk:bug fix of the ticket #2296
951------------------------------------------------------------------------
952r11106 | nicolasmartin | 2019-06-13 20:54:01 +0200 (jeu., 13 juin 2019) | 4 lines
953
954Push a second review of NEMO manual from side-by-side edition of 2 previous versions (r11051 & r11052)
955I 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.
956Would have save time by checking the unused entries before...
957
958------------------------------------------------------------------------
959r11078 | jchanut | 2019-06-05 16:17:09 +0200 (mer., 05 juin 2019) | 2 lines
960
961#2284
962
963------------------------------------------------------------------------
964r11077 | jchanut | 2019-06-05 16:13:02 +0200 (mer., 05 juin 2019) | 2 lines
965
966Correct bathymetry at U-points, #2289
967
968------------------------------------------------------------------------
969r11075 | nicolasmartin | 2019-06-04 18:16:20 +0200 (mar., 04 juin 2019) | 4 lines
970
971Submission of an intermediate version of NEMO bibliography
972Manual merge of 2 existing BibTeX entries per each reference in order not to lose a field
973It 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
974
975------------------------------------------------------------------------
976r11072 | girrmann | 2019-06-04 15:14:57 +0200 (mar., 04 juin 2019) | 1 line
977
978trunk : fix bug in flather for bdy, see #2287
979------------------------------------------------------------------------
980r11060 | nicolasmartin | 2019-05-27 15:20:51 +0200 (lun., 27 mai 2019) | 8 lines
981
982Backup a merged bibliography with duplicates commented
983BibTool determines double entries from successive identical citation keys so
984the procedure was in 2 steps
9851. Process r11051 & r11052 versions of NEMO_manual.bib to have the same pattern for citation key
9862. Merge the 2 versions with BibTool configured for duplicate checking: \\
987   `bibtool -d -- preserve.keys=on -- sort=on input_files -o output_file`
988It remains to clean the bibliography by deleting the doubles.
989
990------------------------------------------------------------------------
991r11058 | nicolasmartin | 2019-05-24 21:41:56 +0200 (ven., 24 mai 2019) | 15 lines
992
993Add a configuration file as resource for BibTool to define standard format for our bibliographies
994After the import of several new versions of references, I found some discrepancies that it was easy to address with BibTool
995- Set a common pattern for citation key: `author1[_authors2[_ea]]_journalyear`
996- Suppress a good bunch of trivial fields to reduce the size of the biblio in the different exports
997  `address chapter institution isbn issn issue keywords language note number organisation pages pdf series school type volume`
998  Open to discussion but to me a DOI entry is sufficient if someone wants more information
999- Prevent the use of tab for fields indentation,
1000  better readability for the bib file on Trac browser or in the output of SVN diff
1001- Apply the following order of fields for every entry
1002  `author # title # booktitle # journal # publisher # editor # year # month # doi # url`
1003To apply the rules to a BibTex file, run
1004{{{#!console
1005bibtool -r bibtool.rsc input_file -o output_file
1006}}}
1007
1008------------------------------------------------------------------------
1009r11052 | nicolasmartin | 2019-05-24 12:05:52 +0200 (ven., 24 mai 2019) | 4 lines
1010
1011Upload draft version for new NEMO biblio
1012This is the result of the publications collecting on CrossRef.
1013By mistake, previous commit was supposed to be the one but it was just a small edition.
1014
1015------------------------------------------------------------------------
1016r11051 | nicolasmartin | 2019-05-24 11:50:21 +0200 (ven., 24 mai 2019) | 2 lines
1017
1018Backup intermediate version before further minor modifications
1019
1020------------------------------------------------------------------------
1021r11043 | nicolasmartin | 2019-05-23 15:51:08 +0200 (jeu., 23 mai 2019) | 2 lines
1022
1023Several fixes for the LaTeX compilation of the manuals
1024
1025------------------------------------------------------------------------
1026r11041 | clem | 2019-05-23 14:28:27 +0200 (jeu., 23 mai 2019) | 1 line
1027
1028debug corner points for ice bdy
1029------------------------------------------------------------------------
1030r11037 | nicolasmartin | 2019-05-22 21:03:12 +0200 (mer., 22 mai 2019) | 9 lines
1031
1032Review entries of TOP bibliography
1033Continuation of the work to complete the BibTeX entries with the help of
1034DOI resolver for the retrieval and CrossRef API for the identification.
1035
1036Add `byrd-co2-2008.txt` & `edc-co2.txt` for information which give the original
1037references for using particular CO2 data set from NOAA-NCEI
1038- https://www1.ncdc.noaa.gov/pub/data/paleo/icecore/antarctica/byrd/byrd-co2-2008.txt
1039- https://www1.ncdc.noaa.gov/pub/data/paleo/icecore/antarctica/epica_domec/edc-co2.txt
1040
1041------------------------------------------------------------------------
1042r11034 | nicolasmartin | 2019-05-21 22:42:45 +0200 (mar., 21 mai 2019) | 3 lines
1043
1044Add a simple shell script to build the user guide
1045It checks Python deps, cleans the previous build and exports the guide in HTML format
1046
1047------------------------------------------------------------------------
1048r11033 | nicolasmartin | 2019-05-21 22:36:30 +0200 (mar., 21 mai 2019) | 2 lines
1049
1050Modify the shell code in order to run as expected on different OS (Linux or MacOS)
1051
1052------------------------------------------------------------------------
1053r11032 | nicolasmartin | 2019-05-21 22:34:05 +0200 (mar., 21 mai 2019) | 2 lines
1054
1055Fix few issues in TOP bibliography
1056
1057------------------------------------------------------------------------
1058r11031 | nicolasmartin | 2019-05-21 21:41:02 +0200 (mar., 21 mai 2019) | 2 lines
1059
1060Update the chapters following the new keys for BibTeX entries
1061
1062------------------------------------------------------------------------
1063r11030 | nicolasmartin | 2019-05-21 20:42:31 +0200 (mar., 21 mai 2019) | 8 lines
1064
1065Reconstruction of SI^3^ bibliography in bib format
1066Use of ''biblio'' Emacs package to retrieve BibTeX entries from
1067- existing DOIs in the bbl file
1068- DOIs identified by searching from CrossRef API
1069- classical request on web search engine (few)
10702 references are missing (+ one paper is submitted): TEOS-10 and MaykutThorndike73 and the file was then processed with bibtool for reformatting.
1071I plan to reproduce this procedure for reviewing the other bibliographies (NEMO & TOP) and the references in the user guide.
1072
1073------------------------------------------------------------------------
1074r11026 | nicolasmartin | 2019-05-21 16:54:06 +0200 (mar., 21 mai 2019) | 2 lines
1075
1076Apply previous for SI^3^ specific namelists
1077
1078------------------------------------------------------------------------
1079r11025 | nicolasmartin | 2019-05-21 16:51:24 +0200 (mar., 21 mai 2019) | 2 lines
1080
1081Set mime-type to `text/x-fortran` to all namelists
1082
1083------------------------------------------------------------------------
1084r11023 | nicolasmartin | 2019-05-21 12:21:04 +0200 (mar., 21 mai 2019) | 2 lines
1085
1086Fix typos with comma followed by 'and' in author entries
1087
1088------------------------------------------------------------------------
1089r11022 | nicolasmartin | 2019-05-21 11:49:50 +0200 (mar., 21 mai 2019) | 2 lines
1090
1091Fix the relative path for the bibliography style file to apply it globally
1092
1093------------------------------------------------------------------------
1094r11020 | nicolasmartin | 2019-05-20 22:26:45 +0200 (lun., 20 mai 2019) | 3 lines
1095
1096Apply `svn:ignore` property on TOP subfolders from `./doc/.svnignore` file
1097Cmd to run globally: `svn pset -R svn:ignore -F .svnignore latex`
1098
1099------------------------------------------------------------------------
1100r11019 | nicolasmartin | 2019-05-20 22:21:43 +0200 (lun., 20 mai 2019) | 4 lines
1101
1102Apply more or less same modifications on TOP as for SI^3^ for compliance
1103Despite remaining issues with references, TOP manual can be build like NEMO & SI^3^ with `./build_manual.sh TOP`
1104For the record, the building of the 3 manuals can be launched with `./manual_build.sh all`
1105
1106------------------------------------------------------------------------
1107r11016 | nicolasmartin | 2019-05-20 21:03:20 +0200 (lun., 20 mai 2019) | 2 lines
1108
1109Move figures of TOP manual to global location
1110
1111------------------------------------------------------------------------
1112r11015 | nicolasmartin | 2019-05-20 20:57:09 +0200 (lun., 20 mai 2019) | 12 lines
1113
1114Modification of the content to be in line with the NEMO manual
1115SI^3^ manual can now be build like the NEMO manual with `./manual_build.sh SI3`
1116- Mimick the directory organisation with `main` and `subfiles` folders.
1117- Regarding the particular case of namelists
1118  - Remove the duplicates already contained in the global `namelists` folder at 1st level of `./doc`
1119  - Keep the `namelists` sub-folder only for `namdyn_adv` & `namsbc` which already exist in ocean namelists
1120- Rewriting of `SI3_manual.tex` with `NEMO_manual.tex` as template to easily highlight differences
1121- Updating of several paths for figures/namelists inclusion or LaTeX files referencing
1122- LaTeX source:
1123  - Replacement of `\forfile` command for namelists with pre-configured `\nlst` alias
1124  -      "      "" `\bm` with `\mathbf` (save installation of an extra package)
1125
1126------------------------------------------------------------------------
1127r11013 | nicolasmartin | 2019-05-20 18:32:57 +0200 (lun., 20 mai 2019) | 2 lines
1128
1129Add explicit option for latexmk to ensure PDF export
1130
1131------------------------------------------------------------------------
1132r11010 | nicolasmartin | 2019-05-20 17:30:58 +0200 (lun., 20 mai 2019) | 2 lines
1133
1134Move figures of SI3 manual to global location
1135
1136------------------------------------------------------------------------
1137r11008 | nicolasmartin | 2019-05-20 17:07:21 +0200 (lun., 20 mai 2019) | 2 lines
1138
1139Fix execution rights on new scripts
1140
1141------------------------------------------------------------------------
1142r11007 | nicolasmartin | 2019-05-20 16:58:48 +0200 (lun., 20 mai 2019) | 2 lines
1143
1144Edit NEMO_manual LaTeX files to comply with previous path modification
1145
1146------------------------------------------------------------------------
1147r11005 | nicolasmartin | 2019-05-20 16:53:03 +0200 (lun., 20 mai 2019) | 2 lines
1148
1149Updating of the namelists
1150
1151------------------------------------------------------------------------
1152r11004 | nicolasmartin | 2019-05-20 16:51:02 +0200 (lun., 20 mai 2019) | 7 lines
1153
1154Review of main building script
1155- 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)
1156- Renaming to explicit `manual_build.sh`
1157- Addition of basic checking for LaTeX installation (latexmk binary)
1158- Implementation of loop and argument reading in order to use the same script for the 3 manuals
1159- Improvment of code commentary
1160
1161------------------------------------------------------------------------
1162r10996 | girrmann | 2019-05-17 18:02:04 +0200 (ven., 17 mai 2019) | 1 line
1163
1164trunk : fixed reproductibility issue in dynkeg.F90 with bdy, see #2283
1165------------------------------------------------------------------------
1166r10994 | clem | 2019-05-17 15:08:34 +0200 (ven., 17 mai 2019) | 1 line
1167
1168couple of commits to 1) deal with ice concentration reaching 1 (so, no more limitations in the max ice concentration imposed in the namelist), 2) deal with very small negative values that can occur due to roundoff errors
1169------------------------------------------------------------------------
1170r10991 | nicolasmartin | 2019-05-16 22:54:07 +0200 (jeu., 16 mai 2019) | 2 lines
1171
1172First part of content synchronisation between trunk & 4.0
1173
1174------------------------------------------------------------------------
1175r10990 | nicolasmartin | 2019-05-16 21:07:17 +0200 (jeu., 16 mai 2019) | 20 lines
1176
1177Global review of the building and editing operations on NEMO guide
1178- Addition of README.rst for users and editors
1179- Waiver of the use of `requirements_*` files for the installation of Python dependencies,
1180  instead run the following commands
1181  - `pip install sphinx sphinxcontrib.bibtex sphinx_rtd_theme`
1182    for building and offline editing   (`make html    `)
1183  - `pip install sphinx-autobuild`
1184    for online editing on local server (`make htmllive`)
1185- Put offline and online editing builds in distinct folders to prevent confusion and
1186  provide a backup for comparison
1187  - `make html    ` -> ''./build/html    ''
1188  - `make htmllive` -> ''./build/htmllive''
1189- Fix a coding issue in `conf.py` to display a clean revision number
1190
1191Due to the state of the forge server (deprecated Python 3 library),
1192the guide builded internally does not have the expected rendering and
1193thus can not be made available to users in this version.
1194As a consequence, the online version of the guide will be updated upon request and
1195imported from a external build.
1196
1197------------------------------------------------------------------------
1198r10983 | girrmann | 2019-05-15 14:50:08 +0200 (mer., 15 mai 2019) | 1 line
1199
1200trunk: Remove Potential MPI deadlock if rimwidth>1, see #2282
1201------------------------------------------------------------------------
1202r10982 | girrmann | 2019-05-15 14:37:26 +0200 (mer., 15 mai 2019) | 1 line
1203
1204trunk:Regroup communication report, See #2281
1205------------------------------------------------------------------------
1206r10973 | cetlod | 2019-05-13 17:08:48 +0200 (lun., 13 mai 2019) | 1 line
1207
1208trunk : bugfix in Lability of big particles, see ticket #2278
1209------------------------------------------------------------------------
1210r10951 | jamesharle | 2019-05-09 12:27:16 +0200 (jeu., 09 mai 2019) | 3 lines
1211
1212namelist_cfg REWIND moved inside loop for nambdy_dta reading as, by
1213default, there is only a single nambdy_dta block (See ticket #2274)
1214
1215------------------------------------------------------------------------
1216r10945 | clem | 2019-05-07 19:29:25 +0200 (mar., 07 mai 2019) | 1 line
1217
1218finish repairing the code when only ice dynamics is activated
1219------------------------------------------------------------------------
1220r10934 | jamesharle | 2019-05-07 11:29:45 +0200 (mar., 07 mai 2019) | 3 lines
1221
1222Update code to accommodate multiple instances of nb_jpk_bdy (See ticket
1223#2274)
1224
1225------------------------------------------------------------------------
1226r10932 | clem | 2019-05-05 21:45:27 +0200 (dim., 05 mai 2019) | 1 line
1227
1228make sure a simulation can run when some parts of ice thermodynamics are deactivated (only for very specific use)
1229------------------------------------------------------------------------
1230r10930 | clem | 2019-05-05 21:37:21 +0200 (dim., 05 mai 2019) | 1 line
1231
1232solve a problem of conservation when ice advection is called twice (because of a cfl that is too large)
1233------------------------------------------------------------------------
1234r10926 | clem | 2019-05-03 14:32:10 +0200 (ven., 03 mai 2019) | 1 line
1235
1236complete previous commit
1237------------------------------------------------------------------------
1238r10924 | clem | 2019-05-03 12:00:23 +0200 (ven., 03 mai 2019) | 1 line
1239
1240solve a problem of restartability and reproducibility if ln_cndflx is activated in the ice model (used for coupling at the Met-Office)
1241------------------------------------------------------------------------
1242r10911 | clem | 2019-04-29 18:11:12 +0200 (lun., 29 avril 2019) | 1 line
1243
1244Major change: the advection scheme UMx has been revisited to clean all the unphysical values which occured. Minor change: the ref config SPITZ12 has been slightly modified to test more parameterizations that are available in the code (melt ponds and landfast)
1245------------------------------------------------------------------------
1246r10909 | clem | 2019-04-29 17:58:14 +0200 (lun., 29 avril 2019) | 1 line
1247
1248correct a problem with indices for ice BDY at the eastern and northern boundaries
1249------------------------------------------------------------------------
1250r10907 | clem | 2019-04-29 17:54:07 +0200 (lun., 29 avril 2019) | 1 line
1251
1252solve ticket #2275
1253------------------------------------------------------------------------
1254r10896 | cetlod | 2019-04-26 10:41:49 +0200 (ven., 26 avril 2019) | 1 line
1255
1256Adding a first Draft of TOP documentation
1257------------------------------------------------------------------------
1258r10891 | clem | 2019-04-24 14:36:13 +0200 (mer., 24 avril 2019) | 1 line
1259
12601) correct ice velocity at the ice edge => it changes (slightly) the ice properties at the edge. 2) apply bdy_ice_dyn at each subtime step of rheology => it changes ice velocties at the boundaries quite drastically.
1261------------------------------------------------------------------------
1262r10882 | clem | 2019-04-17 17:40:17 +0200 (mer., 17 avril 2019) | 1 line
1263
1264correct the comments on the units of salt fluxes that were confusing
1265------------------------------------------------------------------------
1266r10873 | cetlod | 2019-04-15 14:34:21 +0200 (lun., 15 avril 2019) | 1 line
1267
1268trunk : Initialisation of some local arrays, see ticket:2272
1269------------------------------------------------------------------------
1270r10869 | cetlod | 2019-04-15 12:34:03 +0200 (lun., 15 avril 2019) | 1 line
1271
1272trunk:Change units of Nitrogen deposition data in PISCES, see ticket:2271
1273------------------------------------------------------------------------
1274r10835 | smueller | 2019-04-03 17:04:18 +0200 (mer., 03 avril 2019) | 2 lines
1275
1276Merge of changesets [10832] and [10833] into the trunk, see ticket #2267
1277
1278------------------------------------------------------------------------
1279r10824 | clem | 2019-04-02 15:32:49 +0200 (mar., 02 avril 2019) | 1 line
1280
1281output cfl diagnostics (courant numbers) in netcdf => add cfl_cu, cfl_cv, cfl_cw
1282------------------------------------------------------------------------
1283r10817 | smasson | 2019-03-29 18:23:45 +0100 (ven., 29 mars 2019) | 1 line
1284
1285trunk: report [10815] and [10816] from v4
1286------------------------------------------------------------------------
1287r10814 | nicolasmartin | 2019-03-29 17:50:37 +0100 (ven., 29 mars 2019) | 3 lines
1288
1289Add DRAFT watermark as default for the PDF export of the manual
1290Do not check how it looks with the HTML version
1291
1292------------------------------------------------------------------------
1293r10808 | smasson | 2019-03-27 21:36:05 +0100 (mer., 27 mars 2019) | 1 line
1294
1295trunk: update namelist_ref, according to changes done in v4 in [10779] and [10807]
1296------------------------------------------------------------------------
1297r10794 | cetlod | 2019-03-22 10:25:28 +0100 (ven., 22 mars 2019) | 1 line
1298
1299trunk : minor bugfix in PISCES
1300------------------------------------------------------------------------
1301r10790 | nicolasmartin | 2019-03-21 17:47:24 +0100 (jeu., 21 mars 2019) | 2 lines
1302
1303Add revision number to the guide homepage and limite verbosity of LaTeX compilation
1304
1305------------------------------------------------------------------------
1306r10788 | cetlod | 2019-03-21 12:15:14 +0100 (jeu., 21 mars 2019) | 1 line
1307
1308trunk: Some bugfixes at ice/biogeochmeical interfaces, see ticket #2262
1309------------------------------------------------------------------------
1310r10786 | clem | 2019-03-20 19:59:24 +0100 (mer., 20 mars 2019) | 1 line
1311
1312fix tickets #2256 and #2257
1313------------------------------------------------------------------------
1314r10784 | clem | 2019-03-20 19:36:44 +0100 (mer., 20 mars 2019) | 1 line
1315
1316solve ticket #2261
1317------------------------------------------------------------------------
1318r10781 | clem | 2019-03-20 19:19:05 +0100 (mer., 20 mars 2019) | 1 line
1319
1320increase the number max of communications (only necessary when bdy + ice + barotropic window = 2)
1321------------------------------------------------------------------------
1322r10742 | jchanut | 2019-03-12 12:00:06 +0100 (mar., 12 mars 2019) | 2 lines
1323
1324Bug with ENT scheme #2254
1325
1326------------------------------------------------------------------------
1327r10721 | cetlod | 2019-02-25 11:46:32 +0100 (lun., 25 févr. 2019) | 1 line
1328
1329trunk : Minor bugfixes on Offline configurations, see ticket 2251
1330------------------------------------------------------------------------
1331r10720 | cetlod | 2019-02-25 11:46:18 +0100 (lun., 25 févr. 2019) | 1 line
1332
1333trunk : Minor bugfixes on Offline configurations, see ticket 2251
1334------------------------------------------------------------------------
1335r10716 | mathiot | 2019-02-22 16:26:39 +0100 (ven., 22 févr. 2019) | 1 line
1336
1337missing #undef ERRVAL in r10665 (ticket #2228)
1338------------------------------------------------------------------------
1339r10714 | mathiot | 2019-02-22 16:13:22 +0100 (ven., 22 févr. 2019) | 1 line
1340
1341fix ticket #1595 included into the trunk
1342------------------------------------------------------------------------
1343r10702 | mathiot | 2019-02-20 10:44:07 +0100 (mer., 20 févr. 2019) | 1 line
1344
1345merge branch fix_ticket2238_solution1 into the trunk (ticket #2238)
1346------------------------------------------------------------------------
1347r10694 | cetlod | 2019-02-18 16:20:20 +0100 (lun., 18 févr. 2019) | 1 line
1348
1349Minor correction of offline block-namelist
1350------------------------------------------------------------------------
1351r10691 | mathiot | 2019-02-15 17:41:15 +0100 (ven., 15 févr. 2019) | 1 line
1352
1353merge fix_ticket2229 into the trunk (ticket #2229)
1354------------------------------------------------------------------------
1355r10665 | mathiot | 2019-02-13 11:40:04 +0100 (mer., 13 févr. 2019) | 1 line
1356
1357include fix for ticket #2228
1358------------------------------------------------------------------------
1359r10647 | smueller | 2019-02-07 15:38:10 +0100 (jeu., 07 févr. 2019) | 2 lines
1360
1361Merge of changeset [10646] into the trunk; see ticket #2236
1362
1363------------------------------------------------------------------------
1364r10645 | jamesharle | 2019-02-07 10:30:03 +0100 (jeu., 07 févr. 2019) | 2 lines
1365
1366Update variable name for ticket #2233
1367
1368------------------------------------------------------------------------
1369r10641 | jamesharle | 2019-02-06 13:48:11 +0100 (mer., 06 févr. 2019) | 3 lines
1370
1371Correction for un-initialised variable wn_25h in 25hour meaning
1372diagnostics (see ticket #2233).
1373
1374------------------------------------------------------------------------
1375r10638 | nicolasmartin | 2019-02-05 20:33:19 +0100 (mar., 05 févr. 2019) | 2 lines
1376
1377Use explicit `@HEAD` for external definitons + HTTPS URLs for Zenodo badges
1378
1379------------------------------------------------------------------------
1380r10629 | smasson | 2019-02-04 17:07:39 +0100 (lun., 04 févr. 2019) | 1 line
1381
1382trunk: bugfix in mpp for bdy, back to v3.6, see #2213, #2224, #2225
1383------------------------------------------------------------------------
1384r10627 | nicolasmartin | 2019-02-01 20:23:41 +0100 (ven., 01 févr. 2019) | 2 lines
1385
1386Right mime-type `text/x-bibtex` and not `text/x-tex`
1387
1388------------------------------------------------------------------------
1389r10626 | nicolasmartin | 2019-02-01 20:19:22 +0100 (ven., 01 févr. 2019) | 2 lines
1390
1391Fix typo in previous commit
1392
1393------------------------------------------------------------------------
1394r10625 | nicolasmartin | 2019-02-01 20:12:59 +0100 (ven., 01 févr. 2019) | 2 lines
1395
1396Set mime-type for online rendering
1397
1398------------------------------------------------------------------------
1399r10617 | smasson | 2019-02-01 11:07:11 +0100 (ven., 01 févr. 2019) | 1 line
1400
1401trunk: missing bugfix on sbccpl and add TOYATM in tools
1402------------------------------------------------------------------------
1403r10615 | smasson | 2019-01-31 18:15:42 +0100 (jeu., 31 janv. 2019) | 1 line
1404
1405trunk: improve information/error messages in mppini
1406------------------------------------------------------------------------
1407r10614 | smueller | 2019-01-31 18:10:55 +0100 (jeu., 31 janv. 2019) | 2 lines
1408
1409Merge of changeset [10613] into the trunk
1410
1411------------------------------------------------------------------------
1412r10611 | clem | 2019-01-31 15:48:06 +0100 (jeu., 31 janv. 2019) | 1 line
1413
1414go back to regular EVP instead of adaptive EVP because of model crash
1415------------------------------------------------------------------------
1416r10610 | nicolasmartin | 2019-01-30 16:51:15 +0100 (mer., 30 janv. 2019) | 2 lines
1417
1418Add LaTeX requirements file + downloading of `figures` directory if not present when compiling
1419
1420------------------------------------------------------------------------
1421r10609 | nicolasmartin | 2019-01-30 16:22:57 +0100 (mer., 30 janv. 2019) | 2 lines
1422
1423Add another Python requirements file for online edition of NEMO guide with sphinx-autobuild (`make htmllive`)
1424
1425------------------------------------------------------------------------
1426r10608 | nicolasmartin | 2019-01-30 14:38:36 +0100 (mer., 30 janv. 2019) | 2 lines
1427
1428Rectify Python3 requirements for guide compilation (tested in virtualenv)
1429
1430------------------------------------------------------------------------
1431
1432#######
1433Changes
1434#######
1435
1436M       cfgs/AGRIF_DEMO/EXPREF/1_namelist_cfg
1437M       cfgs/AGRIF_DEMO/EXPREF/2_namelist_cfg
1438M       cfgs/AGRIF_DEMO/EXPREF/3_namelist_cfg
1439M       cfgs/AGRIF_DEMO/EXPREF/namelist_cfg
1440M       cfgs/AGRIF_DEMO/zooms.bib
1441M       cfgs/AMM12/EXPREF/context_nemo.xml
1442M       cfgs/AMM12/EXPREF/file_def_nemo-oce.xml
1443M       cfgs/AMM12/EXPREF/namelist_cfg
1444M       cfgs/C1D_PAPA/EXPREF/namelist_cfg
1445M       cfgs/C1D_PAPA/MY_SRC/usrdef_nam.F90
1446M       cfgs/GYRE_BFM/EXPREF/context_nemo.xml
1447M       cfgs/GYRE_BFM/EXPREF/namelist_cfg
1448M       cfgs/GYRE_PISCES/EXPREF/context_nemo.xml
1449M       cfgs/GYRE_PISCES/EXPREF/namelist_cfg
1450M       cfgs/ORCA2_ICE_PISCES/EXPREF/context_nemo.xml
1451M       cfgs/ORCA2_ICE_PISCES/EXPREF/file_def_nemo-ice.xml
1452M       cfgs/ORCA2_ICE_PISCES/EXPREF/file_def_nemo-oce.xml
1453M       cfgs/ORCA2_ICE_PISCES/EXPREF/file_def_nemo-pisces.xml
1454M       cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_cfg
1455M       cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_ice_cfg
1456M       cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_top_cfg
1457M       cfgs/ORCA2_OFF_PISCES/EXPREF/context_nemo.xml
1458M       cfgs/ORCA2_OFF_PISCES/EXPREF/file_def_nemo.xml
1459M       cfgs/ORCA2_OFF_PISCES/EXPREF/namelist_cfg
1460M       cfgs/ORCA2_OFF_PISCES/EXPREF/namelist_top_cfg
1461M       cfgs/ORCA2_OFF_TRC/EXPREF/context_nemo.xml
1462M       cfgs/ORCA2_OFF_TRC/EXPREF/namelist_cfg
1463M       cfgs/ORCA2_SAS_ICE/EXPREF/namelist_cfg
1464M       cfgs/README.rst
1465M       cfgs/SHARED/domain_def_nemo.xml
1466M       cfgs/SHARED/field_def_nemo-ice.xml
1467M       cfgs/SHARED/field_def_nemo-oce.xml
1468M       cfgs/SHARED/field_def_nemo-pisces.xml
1469M       cfgs/SHARED/grid_def_nemo.xml
1470M       cfgs/SHARED/namelist_ice_ref
1471M       cfgs/SHARED/namelist_pisces_ref
1472M       cfgs/SHARED/namelist_ref
1473M       cfgs/SHARED/namelist_top_ref
1474M       cfgs/SPITZ12/EXPREF/file_def_nemo-ice.xml
1475M       cfgs/SPITZ12/EXPREF/file_def_nemo-oce.xml
1476M       cfgs/SPITZ12/EXPREF/namelist_cfg
1477M       cfgs/SPITZ12/EXPREF/namelist_ice_cfg
1478A       doc/bin
1479A       doc/bin/manuals_checking.sh
1480A       doc/bin/nlsts_releases.sh
1481A       doc/bin/nlsts_update.sh
1482D       doc/guide_build.sh
1483D       doc/latex/DEPS
1484D       doc/latex/global
1485D       doc/latex/global/ametsoc.bst
1486D       doc/latex/global/annex_D.tex
1487D       doc/latex/global/coding_rules.tex
1488D       doc/latex/global/document.tex
1489D       doc/latex/global/epilogue.tex
1490D       doc/latex/global/frontpage.tex
1491D       doc/latex/global/highlighting.tex
1492D       doc/latex/global/index.ist
1493D       doc/latex/global/index.tex
1494D       doc/latex/global/info_page.tex
1495D       doc/latex/global/latexmk.pl
1496D       doc/latex/global/new_cmds.tex
1497D       doc/latex/global/packages.tex
1498D       doc/latex/global/prologue.tex
1499D       doc/latex/global/styles.tex
1500D       doc/latex/global/todonotes.tex
1501M       doc/latex/HTML_latex2html.sh
1502D       doc/latex/NEMO/build
1503D       doc/latex/NEMO/main/abstract.tex
1504A       doc/latex/NEMO/main/ametsoc.bst
1505D       doc/latex/NEMO/main/appendices.tex
1506D       doc/latex/NEMO/main/authors.tex
1507D       doc/latex/NEMO/main/bibliography.bib
1508D       doc/latex/NEMO/main/blocks.idx
1509D       doc/latex/NEMO/main/chapters.tex
1510D       doc/latex/NEMO/main/introduction.tex
1511D       doc/latex/NEMO/main/keys.idx
1512D       doc/latex/NEMO/main/modules.idx
1513A       doc/latex/NEMO/main/NEMO_coding_conv.tex
1514A       doc/latex/NEMO/main/NEMO_manual.bib
1515A       doc/latex/NEMO/main/NEMO_manual.ist
1516A       doc/latex/NEMO/main/NEMO_manual.sty
1517M       doc/latex/NEMO/main/NEMO_manual.tex
1518D       doc/latex/NEMO/main/parameters.idx
1519D       doc/latex/NEMO/main/settings.tex
1520D       doc/latex/NEMO/main/subroutines.idx
1521A       doc/latex/NEMO/subfiles/annex_A.tex
1522A       doc/latex/NEMO/subfiles/annex_B.tex
1523A       doc/latex/NEMO/subfiles/annex_C.tex
1524A       doc/latex/NEMO/subfiles/annex_D.tex
1525A       doc/latex/NEMO/subfiles/annex_E.tex
1526A       doc/latex/NEMO/subfiles/annex_iso.tex
1527D       doc/latex/NEMO/subfiles/apdx_algos.tex
1528D       doc/latex/NEMO/subfiles/apdx_diff_opers.tex
1529D       doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex
1530D       doc/latex/NEMO/subfiles/apdx_invariants.tex
1531D       doc/latex/NEMO/subfiles/apdx_s_coord.tex
1532D       doc/latex/NEMO/subfiles/apdx_triads.tex
1533D       doc/latex/NEMO/subfiles/blocks.idx
1534M       doc/latex/NEMO/subfiles/chap_ASM.tex
1535D       doc/latex/NEMO/subfiles/chap_cfgs.tex
1536A       doc/latex/NEMO/subfiles/chap_CONFIG.tex
1537M       doc/latex/NEMO/subfiles/chap_conservation.tex
1538M       doc/latex/NEMO/subfiles/chap_DIA.tex
1539M       doc/latex/NEMO/subfiles/chap_DIU.tex
1540M       doc/latex/NEMO/subfiles/chap_DOM.tex
1541M       doc/latex/NEMO/subfiles/chap_DYN.tex
1542M       doc/latex/NEMO/subfiles/chap_LBC.tex
1543M       doc/latex/NEMO/subfiles/chap_LDF.tex
1544M       doc/latex/NEMO/subfiles/chap_misc.tex
1545M       doc/latex/NEMO/subfiles/chap_model_basics.tex
1546M       doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex
1547M       doc/latex/NEMO/subfiles/chap_OBS.tex
1548M       doc/latex/NEMO/subfiles/chap_SBC.tex
1549M       doc/latex/NEMO/subfiles/chap_STO.tex
1550M       doc/latex/NEMO/subfiles/chap_time_domain.tex
1551M       doc/latex/NEMO/subfiles/chap_TRA.tex
1552M       doc/latex/NEMO/subfiles/chap_ZDF.tex
1553A       doc/latex/NEMO/subfiles/foreword.tex
1554A       doc/latex/NEMO/subfiles/introduction.tex
1555D       doc/latex/NEMO/subfiles/keys.idx
1556D       doc/latex/NEMO/subfiles/modules.idx
1557D       doc/latex/NEMO/subfiles/parameters.idx
1558D       doc/latex/NEMO/subfiles/subroutines.idx
1559D       doc/latex/SI3/build
1560A       doc/latex/SI3/Figures
1561A       doc/latex/SI3/Figures/albedo_cloud_correction.png
1562A       doc/latex/SI3/Figures/albedo_dependencies.png
1563A       doc/latex/SI3/Figures/drafts
1564A       doc/latex/SI3/Figures/drafts/ice_cats.ai
1565A       doc/latex/SI3/Figures/drafts/Ice_scheme.pptx
1566A       doc/latex/SI3/Figures/drafts/radiation_atm_ice_oce.pptx
1567A       doc/latex/SI3/Figures/drafts/radiative_transfer.ppt
1568A       doc/latex/SI3/Figures/drafts/thermogrid.ppt
1569A       doc/latex/SI3/Figures/drafts/time_stepping.pptx
1570A       doc/latex/SI3/Figures/g_h.png
1571A       doc/latex/SI3/Figures/ice_cats.eps
1572A       doc/latex/SI3/Figures/ice_cats_new.eps
1573A       doc/latex/SI3/Figures/ice_scheme.png
1574A       doc/latex/SI3/Figures/Openwater_eb.png
1575A       doc/latex/SI3/Figures/radiation_atm_ice_oce.png
1576A       doc/latex/SI3/Figures/radiative_transfer.png
1577A       doc/latex/SI3/Figures/scripts
1578A       doc/latex/SI3/Figures/scripts/albedo_cloud_correction.m
1579A       doc/latex/SI3/Figures/scripts/albedo_hi.m
1580A       doc/latex/SI3/Figures/scripts/ice_cats.pro
1581A       doc/latex/SI3/Figures/scripts/Thermal_properties.pro
1582A       doc/latex/SI3/Figures/Thermal_properties.png
1583A       doc/latex/SI3/Figures/thermogrid.eps
1584A       doc/latex/SI3/Figures/time_stepping.png
1585A       doc/latex/SI3/Figures/yield_curve.png
1586D       doc/latex/SI3/main
1587D       doc/latex/SI3/main/abstract.tex
1588D       doc/latex/SI3/main/appendices.tex
1589D       doc/latex/SI3/main/authors.tex
1590D       doc/latex/SI3/main/bibliography.bib
1591D       doc/latex/SI3/main/blocks.idx
1592D       doc/latex/SI3/main/chapters.tex
1593D       doc/latex/SI3/main/introduction.tex
1594D       doc/latex/SI3/main/keys.idx
1595D       doc/latex/SI3/main/modules.idx
1596D       doc/latex/SI3/main/parameters.idx
1597D       doc/latex/SI3/main/settings.tex
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1599D       doc/latex/SI3/main/subroutines.idx
1600A       doc/latex/SI3/namelists/namalb
1601A       doc/latex/SI3/namelists/namdia
1602A       doc/latex/SI3/namelists/namdyn
1603M       doc/latex/SI3/namelists/namdyn_adv
1604A       doc/latex/SI3/namelists/namdyn_rdgrft
1605A       doc/latex/SI3/namelists/namdyn_rhg
1606A       doc/latex/SI3/namelists/namforcing
1607A       doc/latex/SI3/namelists/namini
1608A       doc/latex/SI3/namelists/namitd
1609A       doc/latex/SI3/namelists/nampar
1610D       doc/latex/SI3/namelists/namsbc
1611A       doc/latex/SI3/namelists/namthd
1612A       doc/latex/SI3/namelists/namthd_da
1613A       doc/latex/SI3/namelists/namthd_do
1614A       doc/latex/SI3/namelists/namthd_pnd
1615A       doc/latex/SI3/namelists/namthd_sal
1616A       doc/latex/SI3/namelists/namthd_zdf
1617D       doc/latex/SI3/subfiles
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1619D       doc/latex/SI3/subfiles/blocks.idx
1620D       doc/latex/SI3/subfiles/chap_bdy_agrif.tex
1621D       doc/latex/SI3/subfiles/chap_domain.tex
1622D       doc/latex/SI3/subfiles/chap_dynamics.tex
1623D       doc/latex/SI3/subfiles/chap_interfaces.tex
1624D       doc/latex/SI3/subfiles/chap_miscellaneous.tex
1625D       doc/latex/SI3/subfiles/chap_model_basics.tex
1626D       doc/latex/SI3/subfiles/chap_output_diagnostics.tex
1627D       doc/latex/SI3/subfiles/chap_radiative_transfer.tex
1628D       doc/latex/SI3/subfiles/chap_ridging_rafting.tex
1629D       doc/latex/SI3/subfiles/chap_single_category_use.tex
1630D       doc/latex/SI3/subfiles/chap_thermo.tex
1631D       doc/latex/SI3/subfiles/chap_transport.tex
1632D       doc/latex/SI3/subfiles/keys.idx
1633D       doc/latex/SI3/subfiles/modules.idx
1634D       doc/latex/SI3/subfiles/parameters.idx
1635D       doc/latex/SI3/subfiles/subroutines.idx
1636D       doc/latex/SI3/subfiles/todolist.tex
1637A       doc/latex/SI3/tex_main
1638A       doc/latex/SI3/tex_main/SI3_manual.bbl
1639A       doc/latex/SI3/tex_main/SI3_manual.tex
1640A       doc/latex/SI3/tex_sub
1641A       doc/latex/SI3/tex_sub/abstract_foreword.tex
1642A       doc/latex/SI3/tex_sub/ametsoc.bst
1643A       doc/latex/SI3/tex_sub/chap_bdy_agrif.tex
1644A       doc/latex/SI3/tex_sub/chap_domain.tex
1645A       doc/latex/SI3/tex_sub/chap_dynamics.tex
1646A       doc/latex/SI3/tex_sub/chap_interfaces.tex
1647A       doc/latex/SI3/tex_sub/chap_miscellaneous.tex
1648A       doc/latex/SI3/tex_sub/chap_model_basics.tex
1649A       doc/latex/SI3/tex_sub/chap_output_diagnostics.tex
1650A       doc/latex/SI3/tex_sub/chap_radiative_transfer.tex
1651A       doc/latex/SI3/tex_sub/chap_ridging_rafting.tex
1652A       doc/latex/SI3/tex_sub/chap_single_category_use.tex
1653A       doc/latex/SI3/tex_sub/chap_thermo.tex
1654A       doc/latex/SI3/tex_sub/chap_transport.tex
1655A       doc/latex/SI3/tex_sub/introduction.tex
1656A       doc/latex/SI3/tex_sub/todolist.tex
1657D       doc/latex/.svnignore
1658D       doc/latex/TOP/build
1659D       doc/latex/TOP/main
1660D       doc/latex/TOP/main/abstract.tex
1661D       doc/latex/TOP/main/appendices.tex
1662D       doc/latex/TOP/main/authors.tex
1663D       doc/latex/TOP/main/bibliography.bib
1664D       doc/latex/TOP/main/blocks.idx
1665D       doc/latex/TOP/main/chapters.tex
1666D       doc/latex/TOP/main/introduction.tex
1667D       doc/latex/TOP/main/keys.idx
1668D       doc/latex/TOP/main/modules.idx
1669D       doc/latex/TOP/main/parameters.idx
1670D       doc/latex/TOP/main/settings.tex
1671D       doc/latex/TOP/main/subroutines.idx
1672D       doc/latex/TOP/main/TOP_manual.tex
1673D       doc/latex/TOP/subfiles
1674D       doc/latex/TOP/subfiles/blocks.idx
1675D       doc/latex/TOP/subfiles/byrd-co2-2008.txt
1676D       doc/latex/TOP/subfiles/edc-co2.txt
1677D       doc/latex/TOP/subfiles/keys.idx
1678D       doc/latex/TOP/subfiles/miscellaneous.tex
1679D       doc/latex/TOP/subfiles/model_description.tex
1680D       doc/latex/TOP/subfiles/model_setup.tex
1681D       doc/latex/TOP/subfiles/modules.idx
1682D       doc/latex/TOP/subfiles/parameters.idx
1683D       doc/latex/TOP/subfiles/subroutines.idx
1684D       doc/manual_build.sh
1685M       doc/namelists/namage
1686M       doc/namelists/namalb
1687M       doc/namelists/nambdy
1688M       doc/namelists/nambdy_dta
1689M       doc/namelists/namberg
1690M       doc/namelists/namc14_fcg
1691M       doc/namelists/namc14_sbc
1692M       doc/namelists/namc14_typ
1693M       doc/namelists/namc1d_uvd
1694M       doc/namelists/namcfc
1695A       doc/namelists/namdct
1696M       doc/namelists/namdia
1697D       doc/namelists/nam_diadct
1698M       doc/namelists/nam_diaharm
1699M       doc/namelists/namdom
1700D       doc/namelists/namdom_domcfg
1701M       doc/namelists/namdta_dyn
1702M       doc/namelists/namdyn
1703M       doc/namelists/namdyn_adv
1704M       doc/namelists/namdyn_rdgrft
1705M       doc/namelists/namdyn_rhg
1706M       doc/namelists/namdyn_vor
1707M       doc/namelists/namflo
1708A       doc/namelists/namforcing
1709M       doc/namelists/namhsb
1710M       doc/namelists/namini
1711M       doc/namelists/namitd
1712M       doc/namelists/namlobdet
1713M       doc/namelists/namlobdom
1714M       doc/namelists/namlobnut
1715M       doc/namelists/namlobopt
1716M       doc/namelists/namlobphy
1717M       doc/namelists/namlobrat
1718M       doc/namelists/namlobsed
1719M       doc/namelists/namlobzoo
1720M       doc/namelists/nammpp
1721M       doc/namelists/namobs
1722M       doc/namelists/namp4zlim
1723M       doc/namelists/namp4zmes
1724M       doc/namelists/namp4zmort
1725M       doc/namelists/namp4zprod
1726M       doc/namelists/namp4zzoo
1727M       doc/namelists/namp5zlim
1728M       doc/namelists/namp5zmes
1729M       doc/namelists/namp5zmort
1730M       doc/namelists/namp5zprod
1731M       doc/namelists/namp5zquota
1732M       doc/namelists/namp5zzoo
1733M       doc/namelists/nampar
1734M       doc/namelists/nampisatm
1735M       doc/namelists/nampisbio
1736M       doc/namelists/nampiscal
1737M       doc/namelists/nampisdmp
1738M       doc/namelists/nampisext
1739M       doc/namelists/nampisfer
1740M       doc/namelists/nampisice
1741M       doc/namelists/nampislig
1742M       doc/namelists/nampismass
1743M       doc/namelists/nampismod
1744M       doc/namelists/nampisopt
1745M       doc/namelists/nampispoc
1746M       doc/namelists/nampisrem
1747M       doc/namelists/nampissbc
1748M       doc/namelists/namrun
1749M       doc/namelists/namsbc
1750M       doc/namelists/namsbc_apr
1751M       doc/namelists/namsbc_blk
1752M       doc/namelists/namsbc_flx
1753M       doc/namelists/namsbc_iif
1754M       doc/namelists/namsbc_isf
1755M       doc/namelists/namsbc_rnf
1756M       doc/namelists/namsbc_sas
1757M       doc/namelists/namsbc_ssr
1758M       doc/namelists/namsbc_wave
1759M       doc/namelists/namthd
1760M       doc/namelists/namthd_da
1761M       doc/namelists/namthd_do
1762M       doc/namelists/namthd_pnd
1763M       doc/namelists/namthd_sal
1764M       doc/namelists/namthd_zdf
1765M       doc/namelists/namtra_eiv
1766M       doc/namelists/namtra_mle
1767M       doc/namelists/namtra_qsr
1768M       doc/namelists/namtrc
1769M       doc/namelists/namtrc_adv
1770M       doc/namelists/namtrc_bc
1771M       doc/namelists/namtrc_bdy
1772M       doc/namelists/namtrc_dmp
1773M       doc/namelists/namtrc_dta
1774M       doc/namelists/namtrc_ice
1775M       doc/namelists/namtrc_ldf
1776M       doc/namelists/namtrc_rad
1777M       doc/namelists/namtrc_run
1778M       doc/namelists/namtrc_snk
1779M       doc/namelists/namtrc_trd
1780M       doc/namelists/namtsd
1781M       doc/namelists/namwad
1782D       doc/namelists/namzgr_domcfg
1783D       doc/namelists/namzgr_sco_domcfg
1784A       doc/PDF_creation.sh
1785D       doc/README.rst
1786M       doc/rst/Makefile
1787M       doc/rst/README.rst
1788M       doc/rst/requirements.txt
1789M       doc/rst/source/configurations.bib
1790M       doc/rst/source/conf.py
1791M       doc/rst/source/definitions.rst
1792M       doc/rst/source/global.rst
1793M       doc/rst/source/_templates/layout.html
1794A       doc/.svnignore
1795D       doc/tools
1796D       doc/tools/check_pkg.py
1797D       doc/tools/manuals_checking.sh
1798D       doc/tools/nlsts_releases.sh
1799D       doc/tools/nlsts_update.sh
1800D       doc/tools/shr_func.sh
1801M       INSTALL.rst
1802M       README.rst
1803M       REFERENCES.bib
1804M       src/ICE/ice1d.F90
1805M       src/ICE/icealb.F90
1806M       src/ICE/icecor.F90
1807M       src/ICE/icectl.F90
1808M       src/ICE/icedia.F90
1809M       src/ICE/icedyn_adv.F90
1810M       src/ICE/icedyn_adv_pra.F90
1811M       src/ICE/icedyn_adv_umx.F90
1812M       src/ICE/icedyn.F90
1813M       src/ICE/icedyn_rdgrft.F90
1814M       src/ICE/icedyn_rhg_evp.F90
1815M       src/ICE/icedyn_rhg.F90
1816M       src/ICE/ice.F90
1817M       src/ICE/iceistate.F90
1818M       src/ICE/iceitd.F90
1819M       src/ICE/icerst.F90
1820M       src/ICE/icesbc.F90
1821M       src/ICE/icestp.F90
1822M       src/ICE/icethd_da.F90
1823M       src/ICE/icethd_dh.F90
1824M       src/ICE/icethd_do.F90
1825M       src/ICE/icethd.F90
1826M       src/ICE/icethd_pnd.F90
1827M       src/ICE/icethd_sal.F90
1828M       src/ICE/icethd_zdf_bl99.F90
1829M       src/ICE/icethd_zdf.F90
1830M       src/ICE/iceupdate.F90
1831M       src/ICE/icevar.F90
1832M       src/ICE/icewri.F90
1833M       src/NST/agrif_top_update.F90
1834M       src/NST/agrif_user.F90
1835M       src/OCE/ASM/asminc.F90
1836M       src/OCE/BDY/bdydta.F90
1837M       src/OCE/BDY/bdydyn2d.F90
1838M       src/OCE/BDY/bdydyn3d.F90
1839M       src/OCE/BDY/bdyice.F90
1840M       src/OCE/BDY/bdyini.F90
1841M       src/OCE/BDY/bdylib.F90
1842M       src/OCE/BDY/bdy_oce.F90
1843M       src/OCE/BDY/bdytides.F90
1844M       src/OCE/BDY/bdytra.F90
1845M       src/OCE/BDY/bdyvol.F90
1846M       src/OCE/C1D/c1d.F90
1847M       src/OCE/C1D/dtauvd.F90
1848M       src/OCE/C1D/dyndmp.F90
1849M       src/OCE/C1D/step_c1d.F90
1850M       src/OCE/CRS/crsdom.F90
1851M       src/OCE/CRS/crsini.F90
1852M       src/OCE/CRS/crslbclnk.F90
1853M       src/OCE/DIA/dia25h.F90
1854M       src/OCE/DIA/diacfl.F90
1855M       src/OCE/DIA/diadct.F90
1856M       src/OCE/DIA/diaharm.F90
1857M       src/OCE/DIA/diahsb.F90
1858M       src/OCE/DIA/diahth.F90
1859M       src/OCE/DIA/diaptr.F90
1860M       src/OCE/DIA/diatmb.F90
1861M       src/OCE/DIA/diawri.F90
1862M       src/OCE/DIU/diurnal_bulk.F90
1863M       src/OCE/DOM/domain.F90
1864M       src/OCE/DOM/dommsk.F90
1865M       src/OCE/DOM/domvvl.F90
1866M       src/OCE/DOM/domwri.F90
1867M       src/OCE/DOM/dtatsd.F90
1868M       src/OCE/DOM/iscplhsb.F90
1869M       src/OCE/DOM/iscplini.F90
1870M       src/OCE/DYN/dynadv.F90
1871M       src/OCE/DYN/dynhpg.F90
1872M       src/OCE/DYN/dynkeg.F90
1873M       src/OCE/DYN/dynspg.F90
1874M       src/OCE/DYN/dynspg_ts.F90
1875M       src/OCE/DYN/dynvor.F90
1876M       src/OCE/DYN/dynzdf.F90
1877M       src/OCE/DYN/sshwzv.F90
1878M       src/OCE/DYN/wet_dry.F90
1879M       src/OCE/FLO/flo4rk.F90
1880M       src/OCE/FLO/floats.F90
1881M       src/OCE/FLO/floblk.F90
1882M       src/OCE/FLO/flodom.F90
1883M       src/OCE/FLO/flo_oce.F90
1884M       src/OCE/FLO/florst.F90
1885M       src/OCE/FLO/flowri.F90
1886M       src/OCE/ICB/icbclv.F90
1887M       src/OCE/ICB/icbini.F90
1888M       src/OCE/ICB/icblbc.F90
1889M       src/OCE/ICB/icb_oce.F90
1890M       src/OCE/ICB/icbrst.F90
1891M       src/OCE/ICB/icbstp.F90
1892M       src/OCE/ICB/icbutl.F90
1893M       src/OCE/IOM/in_out_manager.F90
1894M       src/OCE/IOM/iom.F90
1895M       src/OCE/IOM/iom_nf90.F90
1896M       src/OCE/IOM/restart.F90
1897M       src/OCE/LBC/lbclnk.F90
1898A       src/OCE/LBC/lbc_lnk_generic.h90
1899M       src/OCE/LBC/lbc_lnk_multi_generic.h90
1900M       src/OCE/LBC/lbcnfd.F90
1901M       src/OCE/LBC/lbc_nfd_nogather_generic.h90
1902M       src/OCE/LBC/lib_mpp.F90
1903A       src/OCE/LBC/mpp_bdy_generic.h90
1904M       src/OCE/LBC/mppini.F90
1905M       src/OCE/LBC/mpp_lnk_generic.h90
1906M       src/OCE/LBC/mpp_loc_generic.h90
1907M       src/OCE/LBC/mpp_nfd_generic.h90
1908M       src/OCE/LDF/ldfdyn.F90
1909M       src/OCE/LDF/ldftra.F90
1910M       src/OCE/module_example
1911M       src/OCE/nemogcm.F90
1912M       src/OCE/OBS/diaobs.F90
1913M       src/OCE/SBC/fldread.F90
1914M       src/OCE/SBC/sbcapr.F90
1915M       src/OCE/SBC/sbcblk.F90
1916M       src/OCE/SBC/sbccpl.F90
1917M       src/OCE/SBC/sbcflx.F90
1918M       src/OCE/SBC/sbcice_cice.F90
1919M       src/OCE/SBC/sbcice_if.F90
1920M       src/OCE/SBC/sbcisf.F90
1921M       src/OCE/SBC/sbcmod.F90
1922M       src/OCE/SBC/sbc_oce.F90
1923M       src/OCE/SBC/sbcrnf.F90
1924M       src/OCE/SBC/sbcssr.F90
1925M       src/OCE/SBC/sbcwave.F90
1926M       src/OCE/SBC/tideini.F90
1927M       src/OCE/SBC/updtide.F90
1928M       src/OCE/step.F90
1929M       src/OCE/STO/stopar.F90
1930M       src/OCE/stpctl.F90
1931M       src/OCE/timing.F90
1932M       src/OCE/TRA/eosbn2.F90
1933M       src/OCE/TRA/traadv.F90
1934M       src/OCE/TRA/traadv_fct.F90
1935M       src/OCE/TRA/trabbc.F90
1936M       src/OCE/TRA/trabbl.F90
1937M       src/OCE/TRA/tradmp.F90
1938M       src/OCE/TRA/traldf_iso.F90
1939M       src/OCE/TRA/tramle.F90
1940M       src/OCE/TRA/traqsr.F90
1941M       src/OCE/TRD/trdini.F90
1942M       src/OCE/TRD/trdmxl.F90
1943M       src/OCE/TRD/trdmxl_rst.F90
1944M       src/OCE/TRD/trdvor.F90
1945M       src/OCE/USR/usrdef_nam.F90
1946M       src/OCE/ZDF/zdfdrg.F90
1947M       src/OCE/ZDF/zdfgls.F90
1948M       src/OCE/ZDF/zdfiwm.F90
1949M       src/OCE/ZDF/zdfosm.F90
1950M       src/OCE/ZDF/zdfphy.F90
1951M       src/OCE/ZDF/zdfric.F90
1952M       src/OCE/ZDF/zdftke.F90
1953M       src/OFF/dtadyn.F90
1954M       src/OFF/nemogcm.F90
1955M       src/SAO/nemogcm.F90
1956M       src/SAO/sao_data.F90
1957M       src/SAS/diawri.F90
1958M       src/SAS/nemogcm.F90
1959M       src/SAS/sbcssm.F90
1960M       src/SAS/step.F90
1961M       src/TOP/AGE/trcnam_age.F90
1962M       src/TOP/C14/trcnam_c14.F90
1963M       src/TOP/CFC/trcnam_cfc.F90
1964M       src/TOP/PISCES/P2Z/p2zbio.F90
1965M       src/TOP/PISCES/P2Z/p2zopt.F90
1966M       src/TOP/PISCES/P2Z/p2zsed.F90
1967M       src/TOP/PISCES/P4Z/p4zfechem.F90
1968M       src/TOP/PISCES/P4Z/p4zflx.F90
1969M       src/TOP/PISCES/P4Z/p4zligand.F90
1970M       src/TOP/PISCES/P4Z/p4zlim.F90
1971M       src/TOP/PISCES/P4Z/p4zlys.F90
1972M       src/TOP/PISCES/P4Z/p4zmeso.F90
1973M       src/TOP/PISCES/P4Z/p4zmicro.F90
1974M       src/TOP/PISCES/P4Z/p4zmort.F90
1975M       src/TOP/PISCES/P4Z/p4zopt.F90
1976M       src/TOP/PISCES/P4Z/p4zpoc.F90
1977M       src/TOP/PISCES/P4Z/p4zprod.F90
1978M       src/TOP/PISCES/P4Z/p4zrem.F90
1979M       src/TOP/PISCES/P4Z/p4zsbc.F90
1980M       src/TOP/PISCES/P4Z/p4zsed.F90
1981M       src/TOP/PISCES/P4Z/p4zsms.F90
1982M       src/TOP/PISCES/P4Z/p5zlim.F90
1983M       src/TOP/PISCES/P4Z/p5zmeso.F90
1984M       src/TOP/PISCES/P4Z/p5zmicro.F90
1985M       src/TOP/PISCES/P4Z/p5zmort.F90
1986M       src/TOP/PISCES/P4Z/p5zprod.F90
1987M       src/TOP/PISCES/SED/sedini.F90
1988M       src/TOP/PISCES/SED/sedrst.F90
1989M       src/TOP/PISCES/sms_pisces.F90
1990M       src/TOP/PISCES/trcice_pisces.F90
1991M       src/TOP/PISCES/trcini_pisces.F90
1992M       src/TOP/PISCES/trcnam_pisces.F90
1993M       src/TOP/README.rst
1994M       src/TOP/trcbc.F90
1995M       src/TOP/trcbdy.F90
1996M       src/TOP/trcdta.F90
1997M       src/TOP/trcice.F90
1998M       src/TOP/trcini.F90
1999M       src/TOP/trcnam.F90
2000M       src/TOP/trcrst.F90
2001M       src/TOP/TRP/trcadv.F90
2002M       src/TOP/TRP/trcdmp.F90
2003M       src/TOP/TRP/trcldf.F90
2004M       src/TOP/TRP/trcrad.F90
2005M       src/TOP/TRP/trcsbc.F90
2006M       src/TOP/TRP/trcsink.F90
2007M       src/TOP/TRP/trdmxl_trc.F90
2008M       tests/BENCH/EXPREF/best_jpni_jpnj_eorca025
2009M       tests/BENCH/EXPREF/best_jpni_jpnj_eorca12
2010M       tests/BENCH/EXPREF/namelist_cfg_orca025_like
2011M       tests/BENCH/EXPREF/namelist_cfg_orca12_like
2012M       tests/BENCH/EXPREF/namelist_cfg_orca1_like
2013M       tests/BENCH/EXPREF/namelist_ice_cfg
2014M       tests/BENCH/EXPREF/namelist_top_cfg
2015M       tests/BENCH/EXPREF/sh_bench
2016M       tests/BENCH/EXPREF/submit_bench
2017A       tests/BENCH/MY_SRC/diawri.F90
2018M       tests/BENCH/MY_SRC/usrdef_istate.F90
2019M       tests/BENCH/MY_SRC/usrdef_nam.F90
2020M       tests/BENCH/MY_SRC/usrdef_zgr.F90
2021M       tests/BENCH/MY_SRC/zdfiwm.F90
2022M       tests/CANAL/EXPREF/context_nemo.xml
2023M       tests/CANAL/EXPREF/namelist_cfg
2024M       tests/CANAL/MY_SRC/diawri.F90
2025M       tests/CANAL/MY_SRC/domvvl.F90
2026M       tests/CANAL/MY_SRC/usrdef_nam.F90
2027M       tests/ICE_ADV1D/EXPREF/namelist_cfg
2028M       tests/ICE_ADV1D/EXPREF/namelist_cfg_120pts
2029M       tests/ICE_ADV1D/EXPREF/namelist_cfg_240pts
2030M       tests/ICE_ADV1D/EXPREF/namelist_cfg_60pts
2031M       tests/ICE_ADV1D/MY_SRC/usrdef_nam.F90
2032M       tests/ICE_ADV2D/EXPREF/namelist_cfg
2033M       tests/ICE_ADV2D/MY_SRC/usrdef_nam.F90
2034M       tests/ICE_AGRIF/EXPREF/1_namelist_cfg
2035M       tests/ICE_AGRIF/EXPREF/file_def_nemo-ice.xml
2036M       tests/ICE_AGRIF/EXPREF/namelist_cfg
2037M       tests/ICE_AGRIF/MY_SRC/usrdef_nam.F90
2038M       tests/ISOMIP/EXPREF/context_nemo.xml
2039M       tests/ISOMIP/EXPREF/namelist_cfg
2040M       tests/ISOMIP/MY_SRC/usrdef_nam.F90
2041M       tests/LOCK_EXCHANGE/EXPREF/context_nemo.xml
2042M       tests/LOCK_EXCHANGE/EXPREF/namelist_FCT2_flux_ubs_cfg
2043M       tests/LOCK_EXCHANGE/MY_SRC/usrdef_nam.F90
2044M       tests/OVERFLOW/EXPREF/context_nemo.xml
2045M       tests/OVERFLOW/EXPREF/namelist_sco_FCT2_flux_cen-ahm1000_cfg
2046M       tests/OVERFLOW/EXPREF/namelist_sco_FCT2_flux_ubs_cfg
2047M       tests/OVERFLOW/EXPREF/namelist_sco_FCT4_flux_ubs_cfg
2048M       tests/OVERFLOW/EXPREF/namelist_zps_FCT2_flux_ubs_cfg
2049M       tests/OVERFLOW/EXPREF/namelist_zps_FCT4_flux_ubs_cfg
2050M       tests/OVERFLOW/EXPREF/namelist_zps_FCT4_vect_een_cfg
2051M       tests/OVERFLOW/MY_SRC/usrdef_nam.F90
2052M       tests/OVERFLOW/MY_SRC/usrdef_zgr.F90
2053M       tests/README.rst
2054M       tests/test_cases.bib
2055M       tests/VORTEX/EXPREF/1_namelist_cfg
2056M       tests/VORTEX/EXPREF/context_nemo.xml
2057M       tests/VORTEX/EXPREF/namelist_cfg
2058M       tests/VORTEX/MY_SRC/domvvl.F90
2059M       tests/VORTEX/MY_SRC/usrdef_nam.F90
2060M       tests/WAD/EXPREF/context_nemo.xml
2061M       tests/WAD/EXPREF/namelist_cfg
2062M       tests/WAD/MY_DOCS/references.bib
2063A       tests/WAD/MY_SRC/bdyini.F90
2064M       tests/WAD/MY_SRC/usrdef_nam.F90
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