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Changeset 7646 for trunk/NEMOGCM/TOOLS/SIREN/src/docsrc – NEMO

Ignore:
Timestamp:
2017-02-06T10:25:03+01:00 (7 years ago)
Author:
timgraham
Message:

Merge of dev_merge_2016 into trunk. UPDATE TO ARCHFILES NEEDED for XIOS2.
LIM_SRC_s/limrhg.F90 to follow in next commit due to change of kind (I'm unable to do it in this commit).
Merged using the following steps:

1) svn merge --reintegrate ​svn+ssh://forge.ipsl.jussieu.fr/ipsl/forge/projets/nemo/svn/trunk .
2) Resolve minor conflicts in sette.sh and namelist_cfg for ORCA2LIM3 (due to a change in trunk after branch was created)
3) svn commit
4) svn switch ​svn+ssh://forge.ipsl.jussieu.fr/ipsl/forge/projets/nemo/svn/trunk
5) svn merge ​svn+ssh://forge.ipsl.jussieu.fr/ipsl/forge/projets/nemo/svn/branches/2016/dev_merge_2016 .
6) At this stage I checked out a clean copy of the branch to compare against what is about to be committed to the trunk.
6) svn commit #Commit code to the trunk

In this commit I have also reverted a change to Fcheck_archfile.sh which was causing problems on the Paris machine.

Location:
trunk/NEMOGCM/TOOLS/SIREN/src/docsrc
Files:
7 edited

Legend:

Unmodified
Added
Removed

  • trunk/NEMOGCM/TOOLS/SIREN/src/docsrc/1_install.md

    r6393 r7646  
    2020  <b> 
    2121  - @ref index 
    22   - @ref md_docsrc_2_quickstart 
    23   - @ref md_docsrc_3_support_bug 
    24   - @ref md_docsrc_4_codingRules 
    25   - @ref md_docsrc_5_changeLog 
     22  - @ref md_src_docsrc_2_quickstart 
     23  - @ref md_src_docsrc_3_support_bug 
     24  - @ref md_src_docsrc_4_codingRules 
     25  - @ref md_src_docsrc_5_changeLog 
    2626  - @ref todo 
    2727  </b> 

  • trunk/NEMOGCM/TOOLS/SIREN/src/docsrc/2_quickstart.md

    r6393 r7646  
    77Actually SIREN creates all the input files you need to run a NEMO regional configuration.<br/> 
    88  
    9 SIREN is composed of a set of 5 Fortran programs : 
     9SIREN is composed of a set of 6 Fortran programs : 
    1010<ul> 
    1111 <li>create_coord.f90 to create regional grid coordinates.</li> 
    … …  
    1616 This break may cause inconsistency between forcing fields  at boundary and regional fields. 
    1717 </li> 
     18 <li>create_meshmask.f90 to create meshmask or domain_cfg file(s) which contain(s) all the ocean domain informations.</li> 
    1819 <li>create_restart.f90 to create initial state file from coarse grid restart 
    1920 or standard outputs. 
    … …  
    3536Here after we briefly describe how to use each programs, 
    3637and so how to create your own regional configuration. 
    37 @note A set of GLORYS files (global reanalysis on *ORCA025* 
    38 grid), as well as examples of namelists are available in dods repository.<br/> 
    39 You could create and forced a first release of your own regional configuration, 
    40 with those files.  
     38@note As demonstrator for a first start a set of GLORYS files (global reanalysis on *ORCA025* grid), as well as examples of namelists are available [here](https://cloud.mercator-ocean.fr/public.php?service=files&t=acf44730538cdda0da548ffc5f99fb55). 
     39 
    4140<!-- ######################################################################  --> 
    4241# Create coordinates file # {#coord} 
    … …  
    6160&namcfg 
    6261   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     62   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
    6363/ 
    6464 
    … …  
    9292empty, as done here.<br/> This will create a log file named *create_coord.log* 
    9393 
    94 The **namcfg** sub-namelist defines where found SIREN configuration file.<br/> 
    95 This configuration file defines standard name, default interpolation method, 
     94The **namcfg** sub-namelist defines where found SIREN configuration files.<br/> 
     95- The variable configuration file defines standard name, default interpolation method, 
    9696axis,... to be used for some known variables.<br/> 
    9797Obviously, you could add other variables to those already list, in this file. 
    98  
    99 @note You could find the generic version of *variable.cfg* in the directory *NEMOGCM/TOOLS/SIREN/cfg*. 
     98- The dimension configuration file defines dimensions allowed. 
     99 
     100@note You could find the generic version of those configuration files in the directory *NEMOGCM/TOOLS/SIREN/cfg*. 
    100101 
    101102The **namcrs** sub-namelist set parameters of the wide 
    102 coordinates file,<br/> as path to find it, and NEMO periodicity of the wide grid.<br/> 
     103coordinates file, as path to find it, and NEMO periodicity of the wide grid.<br/> 
    103104 
    104105@note the NEMO periodicity could be choose between 0 to 6: 
    … …  
    121122example: ORCA05</dd> 
    122123</dl> 
    123 @sa For more information see @ref md_docsrc_6_perio 
     124@sa For more information see @ref md_src_docsrc_6_perio 
    124125</dd> 
    125126</dl> 
    … …  
    150151~~~~~~~~~~~ 
    151152@image html grid_zoom_60.png 
    152 @image latex grid_zoom_40.png 
     153<center>@image latex grid_zoom_40.png 
     154</center> 
    153155<!-- @note ghost cells all around the grid are not shown here. --> 
    154156 
    … …  
    167169~~~~~~~~~~~ 
    168170@image html grid_glob_over_30.png 
    169 @image latex grid_glob_over_20.png 
     171<center>@image latex grid_glob_over_20.png 
     172</center> 
    170173<!-- @note in blue, the east-west overlap band of ORCA grid. --> 
    171174 
    … …  
    184187~~~~~~~~~~~ 
    185188@image html grid_glob_band_30.png 
    186 @image latex grid_glob_band_20.png 
     189<center>@image latex grid_glob_band_20.png 
     190</center> 
    187191 
    188192</ul> 
    … …  
    217221&namcfg 
    218222   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     223   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
    219224/ 
    220225 
    … …  
    251256coordinates file.<br/> 
    252257@note in all SIREN namelist: <br/> 
    253 0 referred to the coarse/wide grid.<br/> 
    254 1 referred to the fine grid. 
     258**0** referred to the coarse/wide grid.<br/> 
     259**1** referred to the fine grid. 
    255260 
    256261In the same way, the **namfin** sub-namelist  set parameters of the fine 
    257262coordinates file.<br/> 
    258263@note in this namelist example, there is no need to set the variable *in_perio1* to define the NEMO 
    259 periodicity of the fine grid.<br/> Indeed, if this variable is not inform, SIREN tries to read it in the attributes of the file.<br/>  
    260 So if you created the fine coordinates with SIREN, you do not have to 
     264periodicity of the fine grid. Indeed, if this variable is not inform, SIREN tries to read it  
     265in the global attributes of the file. So if you created the fine coordinates with SIREN, you do not have to 
    261266fill it. In other case, you should add it to the namelist. 
    262267 
    … …  
    298303# Merge bathymetry file # {#merge} 
    299304 
    300 The Bathymetry you build differs from the wider one.<br/> 
     305The Bathymetry you build, may differ from the wider one.<br/> 
    301306To avoid issue with boundaries forcing fields, you should merge fine and coarse Bathymetry on boundaries.<br/> 
    302307SIREN allows you to do this.<br/> 
    … …  
    314319&namcfg 
    315320   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     321   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
    316322/ 
    317323 
    … …  
    350356 
    351357The **nambdy** sub-namelist defines the subdomain boundaries.<br/> 
    352 By default SIREN tries to create boundaries for each side. Boundary exist if there is at least one sea point on the second row of each side.<br/> 
    353 So you could let this namelist empty. 
    354  
     358By default SIREN tries to create boundaries for each side. Boundary exist if there is at least one sea point on the second row of each side. So you could let this namelist empty. 
    355359@sa For more information about boundaries, see @ref boundary 
    356360 
    … …  
    359363@sa For more information about how to merge bathymetry, see 
    360364merge_bathy.f90 
     365 
     366<!-- ######################################################################  --> 
     367# Create meshmask (ocean domain informations) # {#meshmask} 
     368 
     369 
     370Depending on the vertical grid you choose to use, NEMO may not see the bathymetry exactly as you defined it just before. To get the ocean domain informations as seen by NEMO, SIREN allows you to create the meshmask file(s) which contain(s) all those informations.<br/> 
     371Morevoer SIREN allows you to create the *domain_cfg* file which is the new input file for NEMO (release 3.7 and upper).<br/> 
     372 
     373To create the meshmask file(s), you have to run : 
     374~~~~~~~~~~~~~~~~~~ 
     375./SIREN/create_meshmask.exe create_meshmask.nam 
     376~~~~~~~~~~~~~~~~~~ 
     377 
     378Here after is an example of namelist for *create_meshmask.exe*.<br/> 
     379In this example, you create one meshmask file named *mesh_mask.nc*.<br/> 
     380It uses coordinates file *coord_fine.nc* to define horizontal grid. 
     381and defines z-coordinate with partial steps. 
     382The minimum depth of the final Bathymetry is 10m.  
     383~~~~~~~~~~~ 
     384&namlog 
     385/ 
     386 
     387&namcfg 
     388   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     389   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
     390/ 
     391 
     392&namin 
     393   cn_bathy = "PATH/bathy_merged.nc" 
     394   cn_coord = "PATH/coord_fine.nc" 
     395   in_perio = 4 
     396/ 
     397 
     398&namhgr 
     399   in_mshhgr = 0 
     400/ 
     401 
     402&namzgr 
     403   ln_zps   = .TRUE. 
     404   in_nlevel= 75 
     405/ 
     406 
     407&namdmin 
     408   dn_hmin=10. 
     409/ 
     410 
     411&namzco 
     412   dn_ppsur   = -3958.951371276829 
     413   dn_ppa0    =   103.953009600000 
     414   dn_ppa1    =     2.415951269000 
     415   dn_ppkth   =    15.351013700000 
     416   dn_ppacr   =     7.000000000000 
     417   dn_ppdzmin = 6. 
     418   dn_pphmax  = 5750. 
     419   ln_dbletanh= .TRUE. 
     420   dn_ppa2    =   100.760928500000 
     421   dn_ppkth2  =    48.029893720000 
     422   dn_ppacr2  =    13.000000000000 
     423/ 
     424 
     425&namzps 
     426   dn_e3zps_min = 25. 
     427   dn_e3zps_rat = 0.2 
     428/ 
     429 
     430&namsco 
     431/ 
     432 
     433&namlbc 
     434/ 
     435 
     436&namwd 
     437/ 
     438 
     439&namgrd 
     440/ 
     441 
     442&namout 
     443   in_msh = 1 
     444/ 
     445~~~~~~~~~~~ 
     446 
     447Let's get describe this namelist more accurately.<br/> 
     448 
     449As previously, we have the **namlog** and **namcfg** describe above.<br/> 
     450 
     451The **namin** sub-namelist defines the Bathymetry to be used. 
     452Mainly SIREN need Bathymetry to create meshmask. 
     453Here we also read coordinates directly on a file.  
     454@note  
     455 1. here again you could add the *in_perio* parameter if need be i.e. if your 
     456Bathymetry was not created by SIREN. 
     457 2. by default SIREN suppress closed sea/lake from the ORCA domain. 
     458 
     459 
     460The **namhgr** sub-namelist defines the horizontal grid. 
     461the type of horizontal mesh is choose between :<ul> 
     462<li> in_mshhgr=0 : curvilinear coordinate on the sphere read in coordinate.nc</li> 
     463<li> in_mshhgr=1 : geographical mesh on the sphere with regular grid-spacing</li> 
     464<li> in_mshhgr=2 : f-plane with regular grid-spacing</li> 
     465<li> in_mshhgr=3 : beta-plane with regular grid-spacing</li> 
     466<li> in_mshhgr=4 : Mercator grid with T/U point at the equator</li> 
     467<li> in_mshhgr=5 : beta-plane with regular grid-spacing and rotated domain (GYRE configuration)</li> 
     468</ul> 
     469 
     470The **namzgr** sub-namelist allows to choose the type of vertical grid (z-coordinate full steps, partial steps, sigma or hybrid coordinates) and the number of level. 
     471 
     472The **namdmin** sub-namelist defines the minimum ocean depth. It could be defines in meter (>0) or in number of level (<0). 
     473 
     474The **namzco** sub-namelist defines parameters to compute z-coordinate vertical grid (**needed for all type of vertical grid**) 
     475<!-- By default, those parameters are defined the same way than in GLORYS (i.e. 75 vertical levels).<br/> --> 
     476 
     477The **namzps** sub-namelist defines extra parameters needed to define z-coordinates partial steps. 
     478 
     479The **namsco** sub-namelist defines extra parameters needed to define sigma or hybrid coordinates (not needed here). 
     480 
     481<!--The **namcla** sub-namelist defines cross land advection for exchanges through some straits only used for ORCA2 (see namgrd).--> 
     482 
     483The **namlbc** sub-namelist defines lateral boundary conditions at the coast. It is needed to modify the fmask. 
     484 
     485The **namwd** sub-namelist defines the wetting and drying parameters if activated (see namzgr sub-namelist) 
     486 
     487The **namgrd** sub-namelist allows to use configuration 1D or to choose vertical scale factors (e3.=dk or old definition). 
     488 
     489Finally, this **namout** sub-namelist defines the number output file(s).<br/> 
     490@note To create the domain_cfg file, you should put **in_msh=0**. 
     491 
     492@sa For more information about how to create meshmask, see create_meshmask.f90 
    361493 
    362494<!-- ######################################################################  --> 
    … …  
    367499time step). Or you could start from "partial" information about ocean state (Temperature and Salinity for example). 
    368500 
    369 Siren allows you to create both of those initial state.<br/> 
     501SIREN allows you to create both of those initial state.<br/> 
    370502To create the initial state, you have to run:<br/> 
    371503~~~~~~~~~~~~~~~~~~ 
    … …  
    374506 
    375507Here after is an example of namelist for *create_restart.exe*.<br/> 
    376 In this example, you create an initial state split on 81 "processors", and named restar_out.nc.<br/> 
     508In this example, you create an initial state split on 81 "processors", and named restart_out.nc.<br/> 
    377509The initial state is composed of temperature and salinity refined from an extraction of GLORYS fields. 
    378510~~~~~~~~~~~~~~~~~~ 
    … …  
    382514&namcfg 
    383515   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     516   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
    384517/ 
    385518 
    … …  
    442575Finally, this **namout** sub-namelist defines the output files.<br/> 
    443576Here we ask for output on 81 processors, with *restart_out.nc* as file "basename".<br/> 
    444 So SIREN computes the optimal layout for 81 porcessors 
     577So SIREN computes the optimal layout for 81 processors 
    445578available,<br/> 
    446 and split restart on output files named *restart_out_num.nc*, where *num* is the porc number. 
     579and split restart on output files named *restart_out_num.nc*, where *num* is the proc number. 
    447580 
    448581@note SIREN could also create the other fields you may need for 
    … …  
    481614&namcfg 
    482615   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     616   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
    483617/ 
    484618 
    … …  
    592726   <b> 
    593727   - @ref index 
    594    - @ref md_docsrc_1_install 
    595    - @ref md_docsrc_2_quickstart 
    596    - @ref md_docsrc_3_support_bug 
    597    - @ref md_docsrc_4_codingRules 
    598    - @ref md_docsrc_5_changeLog 
     728   - @ref md_src_docsrc_1_install 
     729   - @ref md_src_docsrc_2_quickstart 
     730   - @ref md_src_docsrc_3_support_bug 
     731   - @ref md_src_docsrc_4_codingRules 
     732   - @ref md_src_docsrc_5_changeLog 
    599733   - @ref todo 
    600734   </b> 

  • trunk/NEMOGCM/TOOLS/SIREN/src/docsrc/3_support_bug.md

    r6393 r7646  
    2020   <b> 
    2121   - @ref index 
    22    - @ref md_docsrc_1_install 
    23    - @ref md_docsrc_2_quickstart 
    24    - @ref md_docsrc_3_support_bug 
    25    - @ref md_docsrc_4_codingRules 
    26    - @ref md_docsrc_5_changeLog 
     22   - @ref md_src_docsrc_1_install 
     23   - @ref md_src_docsrc_2_quickstart 
     24   - @ref md_src_docsrc_3_support_bug 
     25   - @ref md_src_docsrc_4_codingRules 
     26   - @ref md_src_docsrc_5_changeLog 
    2727   - @ref todo 
    2828   </b> 

  • trunk/NEMOGCM/TOOLS/SIREN/src/docsrc/4_codingRules.md

    r6393 r7646  
    1515_GET_COMMAND_ARGUMENT_.<br/> 
    1616There exist no equivalent for those Fortran 03 intrinsec functions in Fortran 
    17 95.<br/> At least none convenient for compilers tested (see @ref md_docsrc_1_install).  
     1795.<br/> At least none convenient for compilers tested (see @ref md_src_docsrc_1_install).  
    1818 
    1919#  Free Form Source {#free} 
    … …  
    9393   <b> 
    9494   - @ref index 
    95    - @ref md_docsrc_1_install 
    96    - @ref md_docsrc_2_quickstart 
    97    - @ref md_docsrc_3_support_bug 
    98    - @ref md_docsrc_5_changeLog 
     95   - @ref md_src_docsrc_1_install 
     96   - @ref md_src_docsrc_2_quickstart 
     97   - @ref md_src_docsrc_3_support_bug 
     98   - @ref md_src_docsrc_5_changeLog 
    9999   - @ref todo 
    100100   </b> 

  • trunk/NEMOGCM/TOOLS/SIREN/src/docsrc/5_changeLog.md

    r6393 r7646  
    33@tableofcontents 
    44 
    5 # Release $Revision$ 
    6 Initial release (2016-03-17) 
     5# Release $Date:: 2016-11-16 #$ ($Revision: 7235 $) 
    76 
     7## New Features 
     8- create_meshmask.f90 program to create meshmask from coordinates and bathymetry files. 
     9- create_meshmask.f90 allows to write domain_cfg file. 
     10- merge_bathy.f90: allow to choose the number of boundary point with coarse grid value. 
     11- dimension.f90: dimension allowed read in configuration file. 
     12- variable.f90: allow to add scalar value. 
     13- create_meshmask.f90: choose vertical scale factors (e3.=dk[depth] or old definition). 
    814## Changes 
    9 ## New Features 
     15- create_coord.f90: allow to define sub domain with coarse grid indices or coordinates. 
     16- grid.f90:grid__get_closest_str: add function to get closest grid point using coarse grid coordinates strucutre. 
     17- iom_cdf.f90:iom_cdf__get_info: define cdf4 as cdf. 
     18- variable.f90: add subroutine to clean global array of extra information, and define logical for variable to be used. 
     19- create_coord.f90: dimension to be used select from configuration file. 
     20- create_bathy.f90: dimension to be used select from configuration file. 
     21- merge_bathy.f90: dimension to be used select from configuration file. 
     22- create_boundary.f90: dimension to be used select from configuration file. 
     23- create_restart.f90: dimension to be used select from configuration file. 
    1024## Bug fixes 
     25- boundary.f90:boundary_check: take into account that boundaries are compute on T point, but expressed on U,V point. 
     26- grid.f90:grid__get_closest_str: use max of zero and east-west overlap instead of east-west overlap. 
     27- mpp.f90: compare index to td_lay number of proc instead of td_mpp (bug fix) . 
     28 
     29# Initial Release 2016-03-17 
    1130 
    1231 <HR> 
    1332   <b> 
    1433   - @ref index 
    15    - @ref md_docsrc_1_install 
    16    - @ref md_docsrc_2_quickstart 
    17    - @ref md_docsrc_3_support_bug 
    18    - @ref md_docsrc_4_codingRules 
     34   - @ref md_src_docsrc_1_install 
     35   - @ref md_src_docsrc_2_quickstart 
     36   - @ref md_src_docsrc_3_support_bug 
     37   - @ref md_src_docsrc_4_codingRules 
    1938   - @ref todo 
    2039   </b> 

  • trunk/NEMOGCM/TOOLS/SIREN/src/docsrc/6_perio.md

    r6393 r7646  
    66<dd>ghost cells (solid walls) are imposed at all model boundaries.</dd>  
    77@image html perio0_20.png  
    8 @image latex perio0_20.png 
     8<center>@image latex perio0_20.png  
     9</center> 
    910<dt>cyclic east-west boundary (in_perio=1)</dt> 
    1011<dd>first and last rows are closed, whilst the first column is set to the value of the last-but-one column and the last column to the value of the second one.</dd>   
    1112@image html perio1_20.png  
    12 @image latex perio1_20.png 
     13<center>@image latex perio1_20.png  
     14</center> 
    1315<dt>symmetric boundary condition across the equator. (in_perio=2)</dt> 
    1416<dd>last row, and first and last columns are closed. </dd>  
    1517@image html perio2_20.png  
    16 @image latex perio2_20.png 
     18<center>@image latex perio2_20.png  
     19</center> 
    1720<dt>North fold boundary with a T -point pivot (in_perio=3)</dt> 
    1821<dd>first row, and first and last columns are closed. </dd>  
    1922@image html perio3_20.png  
    20 @image latex perio3_20.png 
     23<center>@image latex perio3_20.png  
     24</center> 
    2125<dt>North fold boundary with a T -point pivot and cyclic east-west boundary (in_perio=4)</dt> 
    2226<dd>first row is closed. The first column is set to the value of the last-but-one column and the last column to the value of the second one. </dd>  
    2327@image html perio4_20.png  
    24 @image latex perio4_20.png 
     28<center>@image latex perio4_20.png  
     29</center> 
    2530<dt>North fold boundary with a F -point pivot (in_perio=5)</dt> 
    2631<dd>first row, and first and last columns are closed. </dd>  
    2732@image html perio5_20.png  
    28 @image latex perio5_20.png 
     33<center>@image latex perio5_20.png  
     34</center> 
    2935<dt>North fold boundary with a F -point pivot and cyclic east-west boundary (in_perio=6)</dt> 
    3036<dd>first row is closed. The first column is set to the value of the last-but-one column and the last column to the value of the second one.</dd>  
    3137@image html perio6_20.png  
    32 @image latex perio6_20.png 
     38<center>@image latex perio6_20.png  
     39</center> 
    3340</dl> 
    3441@sa For more information about NEMO periodicity, see _Model Boundary Condition_ chapter in [NEMO documentation](http://www.nemo-ocean.eu/About-NEMO/Reference-manuals)) 

  • trunk/NEMOGCM/TOOLS/SIREN/src/docsrc/main.dox

    r6393 r7646  
    22 @mainpage About  
    33 
    4  SIREN is a software to create regional configuration with [NEMO](http://www.nemo-ocean.eu).<br/>  
    5  Actually SIREN create input files needed for a basic NEMO configuration.<br/> 
     4 SIREN is a software to set up regional configuration with [NEMO](http://www.nemo-ocean.eu).<br/>  
     5 Actually SIREN creates the input files you need to run a NEMO regional configuration.<br/> 
     6  
     7 SIREN allows you to create your own regional configuration embedded in a wider one.<br/> 
    68 
    7  SIREN allows you to create your own regional configuration embedded in a wider one.<br/> 
    8  In order to help you, a set of GLORYS files (global reanalysis on ORCA025 grid), as well as examples 
    9  of namelists are available in dods repository. 
     9 To know how to install SIREN see @ref md_src_docsrc_1_install. 
    1010 
    11  @note This software was created, and is maintain by the Configuration Manager Working Group, composed 
    12  of NEMO system team members. 
    13   
    14  To know how to install SIREN see @ref md_docsrc_1_install. 
    15  
    16  You could find a tutorial for a quick start with SIREN in @ref md_docsrc_2_quickstart.<br/> 
     11 You could find a tutorial for a quick start with SIREN in @ref md_src_docsrc_2_quickstart.<br/> 
    1712 For more information about how to use each component of SIREN 
    1813 - see create_coord.f90 to create fine grid coordinate file 
    1914 - see create_bathy.f90 to create fine grid bathymetry 
    2015 - see merge_bathy.f90 to merge fine grid bathymetry 
     16 - see create_meshmask.f90 to create mesh mask or domain_cfg file. 
    2117 - see create_restart.f90 to create initial state file, or other fields. 
    2218 - see create_boundary.F90 to create boundary condition 
    … …  
    2420<HR> 
    2521   <b> 
    26    - @ref md_docsrc_1_install 
    27    - @ref md_docsrc_2_quickstart 
    28    - @ref md_docsrc_3_support_bug 
    29    - @ref md_docsrc_4_codingRules 
    30    - @ref md_docsrc_5_changeLog 
     22   - @ref md_src_docsrc_1_install 
     23   - @ref md_src_docsrc_2_quickstart 
     24   - @ref md_src_docsrc_3_support_bug 
     25   - @ref md_src_docsrc_4_codingRules 
     26   - @ref md_src_docsrc_5_changeLog 
    3127   - @ref todo 
    3228   </b> 
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