Changeset 7025 for branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/docsrc/2_quickstart.md

Timestamp:

2016-10-13T11:08:38+02:00 (8 years ago)

Author:

jpaul

Message:

see ticket #1781

File:

• branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/docsrc/2_quickstart.md (modified) (10 diffs)

branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/docsrc/2_quickstart.md

@@ -7 +7 @@
 Actually SIREN creates all the input files you need to run a NEMO regional configuration.<br/>
  
-SIREN is composed of a set of 5 Fortran programs :
+SIREN is composed of a set of 6 Fortran programs :
 <ul>
  <li>create_coord.f90 to create regional grid coordinates.</li>
@@ -16 +16 @@
  This break may cause inconsistency between forcing fields  at boundary and regional fields.
  </li>
+ <li>create_meshmask.f90 to create meshmask file(s) which contain(s) all the ocean domain informations.</li>
  <li>create_restart.f90 to create initial state file from coarse grid restart
  or standard outputs.
@@ -35 +36 @@
 Here after we briefly describe how to use each programs,
 and so how to create your own regional configuration.
-@note A set of GLORYS files (global reanalysis on *ORCA025*
-grid), as well as examples of namelists are available in dods repository.<br/>
-You could create and forced a first release of your own regional configuration,
-with those files. 
+@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=877fb1b6e4f589340fc0df1ea6a53228).
+
 <!-- ######################################################################  -->
 # Create coordinates file # {#coord}
@@ -121 +120 @@
 example: ORCA05</dd>
 </dl>
-@sa For more information see @ref md_docsrc_6_perio
+@sa For more information see @ref md_src_docsrc_6_perio
 </dd>
 </dl>
@@ -150 +149 @@
 ~~~~~~~~~~~
 @image html grid_zoom_60.png
-@image latex grid_zoom_40.png
+<center>@image latex grid_zoom_40.png
+</center>
 <!-- @note ghost cells all around the grid are not shown here. -->
 
@@ -167 +167 @@
 ~~~~~~~~~~~
 @image html grid_glob_over_30.png
-@image latex grid_glob_over_20.png
+<center>@image latex grid_glob_over_20.png
+</center>
 <!-- @note in blue, the east-west overlap band of ORCA grid. -->
 
@@ -184 +185 @@
 ~~~~~~~~~~~
 @image html grid_glob_band_30.png
-@image latex grid_glob_band_20.png
+<center>@image latex grid_glob_band_20.png
+</center>
 
 </ul>
@@ -361 +363 @@
 
 <!-- ######################################################################  -->
+# Create meshmask (ocean domain informations) # {#meshmask}
+
+
+Depending on the vertical grid you choose to use, NEMO may not see the bathymetry 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.
+
+To create this new meshmask file(s), you have to run :
+~~~~~~~~~~~~~~~~~~
+./SIREN/create_meshmask.exe create_meshmask.nam
+~~~~~~~~~~~~~~~~~~
+
+Here after is an example of namelist for *create_meshmask.exe*.<br/>
+In this example, you create one meshmask file named *mesh_mask.nc*.<br/>
+It uses coordinates file *coord_fine.nc* to define horizontal grid.
+and defines z-coordinate with partial steps.
+The minimum depth of the final Bathymetry is 10m. 
+~~~~~~~~~~~
+&namlog
+/
+
+&namcfg
+   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg"
+/
+
+&namin
+   cn_bathy = "PATH/bathy_merged.nc"
+   cn_coord = "PATH/coord_fine.nc"
+   in_perio = 4
+/
+
+&namhgr
+   in_mshhgr = 0
+/
+
+&namzgr
+   ln_zps   = .TRUE.
+   in_nlevel= 75
+/
+
+&namdmin
+   dn_hmin=10.
+/
+
+&namzco
+   dn_ppsur   = -3958.951371276829
+   dn_ppa0    =   103.953009600000
+   dn_ppa1    =     2.415951269000
+   dn_ppkth   =    15.351013700000
+   dn_ppacr   =     7.000000000000
+   dn_ppdzmin = 6.
+   dn_pphmax  = 5750.
+   ln_dbletanh= .TRUE.
+   dn_ppa2    =   100.760928500000
+   dn_ppkth2  =    48.029893720000
+   dn_ppacr2  =    13.000000000000
+/
+
+&namzps
+   dn_e3zps_min = 25.
+   dn_e3zps_rat = 0.2
+/
+
+&namsco
+/
+
+&namcla
+/
+
+&namlbc
+/
+
+&namwd
+/
+
+&namgrd
+/
+
+&namzoom
+/
+
+&namout
+   in_msh = 1
+/
+~~~~~~~~~~~
+
+Let's get describe this namelist more accurately.<br/>
+
+As previously, we have the **namlog** and **namcfg** describe above.<br/>
+
+The **namin** sub-namelist defines the Bathymetry to be used.
+Mainly SIREN need Bathymetry to create meshmask.
+Here we also read coordinates directly on a file. 
+@note here again you could add the *in_perio* parameter if need be i.e. if your
+Bathymetry was not created by SIREN.<br/>
+@note By default SIREN suppress closed sea/lake from the ORCA domain.
+
+The **namhgr** sub-namelist defines the horizontal grid.
+the type of horizontal mesh is choose between :<ul>
+<li> in_mshhgr=0 : curvilinear coordinate on the sphere read in coordinate.nc</li>
+<li> in_mshhgr=1 : geographical mesh on the sphere with regular grid-spacing</li>
+<li> in_mshhgr=2 : f-plane with regular grid-spacing</li>
+<li> in_mshhgr=3 : beta-plane with regular grid-spacing</li>
+<li> in_mshhgr=4 : Mercator grid with T/U point at the equator</li>
+<li> in_mshhgr=5 : beta-plane with regular grid-spacing and rotated domain (GYRE configuration)</li>
+</ul>
+
+The **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.
+
+The **namdmin** sub-namelist dfines the minimum ocean depth. It could be defines in meter (>0) or in number of level (<0).
+
+The **namzco** sub-namelist defines respectively parameters to compute z-coordinate vertical grid (**needed for all type of vertical grid**)
+<!-- By default, those parameters are defined the same way than in GLORYS (i.e. 75 vertical levels).<br/> -->
+
+The **namzps** sub-namelist defines extra parameters needed to define z-coordinates partial steps.
+
+The **namsco** sub-namelist defines extra parameters needed to define sigma or hybrid coordinates (not needed here).
+
+The **namcla** sub-namelist defines cross land advection for exchanges through some straits only used for ORCA2 (see namgrd).
+
+The **namlbc** sub-namelist defines lateral boundary conditions at the coast. It is needed to modify the fmask.
+
+The **namwd** sub-namelist defines the wetting and drying parameters if activated (see namzgr sub-namelist)
+
+The **namgrd** and **namzoom** sub-namelists define grid configuration. Those namelist only activated local correction.
+
+Finally, this **namout** sub-namelist defines the number output file(s).<br/>
+
+@sa For more information about how to create meshmask, see create_meshmask.f90
+
+<!-- ######################################################################  -->
 # Create initial state # {#restart}
 
@@ -442 +573 @@
 Finally, this **namout** sub-namelist defines the output files.<br/>
 Here we ask for output on 81 processors, with *restart_out.nc* as file "basename".<br/>
-So SIREN computes the optimal layout for 81 porcessors
+So SIREN computes the optimal layout for 81 processors
 available,<br/>
-and split restart on output files named *restart_out_num.nc*, where *num* is the porc number.
+and split restart on output files named *restart_out_num.nc*, where *num* is the proc number.
 
 @note SIREN could also create the other fields you may need for
@@ -592 +723 @@
    <b>
    - @ref index
-   - @ref md_docsrc_1_install
-   - @ref md_docsrc_2_quickstart
-   - @ref md_docsrc_3_support_bug
-   - @ref md_docsrc_4_codingRules
-   - @ref md_docsrc_5_changeLog
+   - @ref md_src_docsrc_1_install
+   - @ref md_src_docsrc_2_quickstart
+   - @ref md_src_docsrc_3_support_bug
+   - @ref md_src_docsrc_4_codingRules
+   - @ref md_src_docsrc_5_changeLog
    - @ref todo
    </b>