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Changeset 10115 for NEMO/branches/2018/dev_r5003_MERCATOR6_CRS/NEMOGCM/TOOLS/SIREN/src/docsrc – NEMO

Ignore:
Timestamp:
2018-09-12T15:59:13+02:00 (6 years ago)
Author:
cbricaud
Message:

phase 3.6 coarsening branch with nemo_3.6_rev9192

Location:
NEMO/branches/2018/dev_r5003_MERCATOR6_CRS/NEMOGCM/TOOLS/SIREN/src/docsrc
Files:
3 edited

Legend:

Unmodified
Added
Removed

  • NEMO/branches/2018/dev_r5003_MERCATOR6_CRS/NEMOGCM/TOOLS/SIREN/src/docsrc/2_quickstart.md

    r7261 r10115  
    5959&namcfg 
    6060   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     61   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
    6162/ 
    6263 
    … …  
    8384/ 
    8485~~~~~~~~~~~ 
     86 
     87@note you could define sub domain with coarse grid indices or with coordinates. 
    8588 
    8689Let's get describe this namelist.<br/> 
    … …  
    9093empty, as done here.<br/> This will create a log file named *create_coord.log* 
    9194 
    92 The **namcfg** sub-namelist defines where found SIREN configuration file.<br/> 
    93 This configuration file defines standard name, default interpolation method, 
     95The **namcfg** sub-namelist defines where found SIREN configuration files.<br/> 
     96- The variable configuration file defines standard name, default interpolation method, 
    9497axis,... to be used for some known variables.<br/> 
    9598Obviously, you could add other variables to those already list, in this file. 
    96  
    97 @note You could find the generic version of *variable.cfg* in the directory *NEMOGCM/TOOLS/SIREN/cfg*. 
     99- The dimension configuration file defines dimensions allowed. 
     100 
     101@note You could find the generic version of those configuration files in the directory *NEMOGCM/TOOLS/SIREN/cfg*. 
    98102 
    99103The **namcrs** sub-namelist set parameters of the wide 
    100 coordinates file,<br/> as path to find it, and NEMO periodicity of the wide grid.<br/> 
     104coordinates file, as path to find it, and NEMO periodicity of the wide grid.<br/> 
    101105 
    102106@note the NEMO periodicity could be choose between 0 to 6: 
    … …  
    130134 
    131135The **namnst** sub-namelist defines the subdomain to be used as well as refinment factor.<br/> 
    132 @note Subdomain is defined by indices of the coarse/wide grid.<br/> 
    133136 
    134137<ul> 
    135 <li>you can select area quite every where (excepted too close from the North 
    136 pole), and use the refinment factor you want.</li> 
    137  
    138 ~~~~~~~~~~~ 
    139 &namvar 
     138<li> you could define sub domain with coarse grid indices</li>  
     139 
     140~~~~~~~~~~~ 
     141&namnst 
    140142   in_imin0 = 1070 
    141143   in_imax0 = 1072 
    142144   in_jmin0 = 607 
    143145   in_jmax0 = 609 
     146/ 
     147~~~~~~~~~~~ 
     148 
     149<li>or with coordinates</li> 
     150 
     151~~~~~~~~~~~ 
     152&namnst 
     153   rn_lonmin0 = -97.9  
     154   rn_lonmax0 = -62.3  
     155   rn_latmin0 =   7.7 
     156   rn_latmax0 =  30.8 
     157/ 
     158~~~~~~~~~~~ 
     159 
     160<li>you can select area quite every where (excepted too close from the North 
     161pole), and use the refinment factor you want.</li> 
     162 
     163~~~~~~~~~~~ 
     164&namnst 
     165   in_imin0 = 1070 
     166   in_imax0 = 1072 
     167   in_jmin0 = 607 
     168   in_jmax0 = 609 
    144169 
    145170   in_rhoi = 2 
    … …  
    148173~~~~~~~~~~~ 
    149174@image html grid_zoom_60.png 
    150 @image latex grid_zoom_40.png 
     175<center>@image latex grid_zoom_40.png 
     176</center> 
    151177<!-- @note ghost cells all around the grid are not shown here. --> 
    152178 
     179 
     180 
    153181<li>you can select area crossing the east-west overlap of the global ORCA grid.</li> 
    154182 
    155183~~~~~~~~~~~ 
    156 &namvar           
     184&namnst           
    157185   in_imin0 = 1402  
    158186   in_imax0 = 62 
    … …  
    165193~~~~~~~~~~~ 
    166194@image html grid_glob_over_30.png 
    167 @image latex grid_glob_over_20.png 
     195<center>@image latex grid_glob_over_20.png 
     196</center> 
    168197<!-- @note in blue, the east-west overlap band of ORCA grid. --> 
    169198 
    … …  
    171200 
    172201~~~~~~~~~~~ 
    173 &namvar 
     202&namnst 
    174203   in_imin0 = 0 
    175204   in_imax0 = 0 
    … …  
    182211~~~~~~~~~~~ 
    183212@image html grid_glob_band_30.png 
    184 @image latex grid_glob_band_20.png 
     213<center>@image latex grid_glob_band_20.png 
     214</center> 
    185215 
    186216</ul> 
    … …  
    215245&namcfg 
    216246   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     247   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
    217248/ 
    218249 
    … …  
    249280coordinates file.<br/> 
    250281@note in all SIREN namelist: <br/> 
    251 0 referred to the coarse/wide grid.<br/> 
    252 1 referred to the fine grid. 
     282**0** referred to the coarse/wide grid.<br/> 
     283**1** referred to the fine grid. 
    253284 
    254285In the same way, the **namfin** sub-namelist  set parameters of the fine 
    255286coordinates file.<br/> 
    256287@note in this namelist example, there is no need to set the variable *in_perio1* to define the NEMO 
    257 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/>  
    258 So if you created the fine coordinates with SIREN, you do not have to 
     288periodicity of the fine grid. Indeed, if this variable is not inform, SIREN tries to read it  
     289in the global attributes of the file. So if you created the fine coordinates with SIREN, you do not have to 
    259290fill it. In other case, you should add it to the namelist. 
    260291 
    … …  
    296327# Merge bathymetry file # {#merge} 
    297328 
    298 The Bathymetry you build differs from the wider one.<br/> 
     329The Bathymetry you build, may differ from the wider one.<br/> 
    299330To avoid issue with boundaries forcing fields, you should merge fine and coarse Bathymetry on boundaries.<br/> 
    300331SIREN allows you to do this.<br/> 
    … …  
    312343&namcfg 
    313344   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     345   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
    314346/ 
    315347 
    … …  
    348380 
    349381The **nambdy** sub-namelist defines the subdomain boundaries.<br/> 
    350 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/> 
    351 So you could let this namelist empty. 
    352  
     382By 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. 
    353383@sa For more information about boundaries, see @ref boundary 
    354384 
    … …  
    365395time step). Or you could start from "partial" information about ocean state (Temperature and Salinity for example). 
    366396 
    367 Siren allows you to create both of those initial state.<br/> 
     397SIREN allows you to create both of those initial state.<br/> 
    368398To create the initial state, you have to run:<br/> 
    369399~~~~~~~~~~~~~~~~~~ 
    … …  
    372402 
    373403Here after is an example of namelist for *create_restart.exe*.<br/> 
    374 In this example, you create an initial state split on 81 "processors", and named restar_out.nc.<br/> 
     404In this example, you create an initial state split on 81 "processors", and named restart_out.nc.<br/> 
    375405The initial state is composed of temperature and salinity refined from an extraction of GLORYS fields. 
    376406~~~~~~~~~~~~~~~~~~ 
    … …  
    380410&namcfg 
    381411   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     412   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
    382413/ 
    383414 
    … …  
    479510&namcfg 
    480511   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     512   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
    481513/ 
    482514 

  • NEMO/branches/2018/dev_r5003_MERCATOR6_CRS/NEMOGCM/TOOLS/SIREN/src/docsrc/5_changeLog.md

    r7261 r10115  
    33@tableofcontents 
    44 
    5 # Release 
    6 Initial release (2016-04-11) 
     5# Release $Date:: 2016-11-16 #$ ($Revision: 7235 $) 
     6 
     7## New Features 
     8- merge_bathy.f90: allow to choose the number of boundary point with coarse grid value. 
     9- dimension.f90: dimension allowed read in configuration file. 
     10- variable.f90: allow to add scalar value. 
     11## Changes 
     12- create_coord.f90: allow to define sub domain with coarse grid indices or coordinates. 
     13- grid.f90:grid__get_closest_str: add function to get closest grid point using coarse grid coordinates strucutre. 
     14- iom_cdf.f90:iom_cdf__get_info: define cdf4 as cdf. 
     15- variable.f90: add subroutine to clean global array of extra information, and define logical for variable to be used. 
     16- create_coord.f90: dimension to be used select from configuration file. 
     17- create_bathy.f90: dimension to be used select from configuration file. 
     18- merge_bathy.f90: dimension to be used select from configuration file. 
     19- create_boundary.f90: dimension to be used select from configuration file. 
     20- create_restart.f90: dimension to be used select from configuration file. 
     21## Bug fixes 
     22- boundary.f90:boundary_check: take into account that boundaries are compute on T point, but expressed on U,V point. 
     23- grid.f90:grid__get_closest_str: use max of zero and east-west overlap instead of east-west overlap. 
     24- mpp.f90: compare index to td_lay number of proc instead of td_mpp (bug fix) . 
     25- iom_cdf.f90 : check if attribute cl_value is not bug (in read file) 
     26 
     27# Release 2016-07-01 
    728 
    829## Changes 
    930## New Features 
    1031## Bug fixes 
     32 - correct check of boundary indices 
     33 
     34# Initial Release 2016-04-11 
    1135 
    1236 <HR> 

  • NEMO/branches/2018/dev_r5003_MERCATOR6_CRS/NEMOGCM/TOOLS/SIREN/src/docsrc/6_perio.md

    r7261 r10115  
    66<dd>ghost cells (solid walls) are imposed at all model boundaries.</dd>  
    77@image html perio0_20.png  
    8 @latexonly 
    9 \begin{center} 
    10 \includegraphics{perio0_20.png} 
    11 \end{center} 
    12 @endlatexonly 
     8<center>@image latex perio0_20.png  
     9</center> 
    1310<dt>cyclic east-west boundary (in_perio=1)</dt> 
    1411<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>   
    1512@image html perio1_20.png  
    16 @latexonly 
    17 \begin{center} 
    18 \includegraphics{perio1_20.png} 
    19 \end{center} 
    20 @endlatexonly 
     13<center>@image latex perio1_20.png  
     14</center> 
    2115<dt>symmetric boundary condition across the equator. (in_perio=2)</dt> 
    2216<dd>last row, and first and last columns are closed. </dd>  
    2317@image html perio2_20.png  
    24 @latexonly 
    25 \begin{center} 
    26 \includegraphics{perio2_20.png} 
    27 \end{center} 
    28 @endlatexonly 
     18<center>@image latex perio2_20.png  
     19</center> 
    2920<dt>North fold boundary with a T -point pivot (in_perio=3)</dt> 
    3021<dd>first row, and first and last columns are closed. </dd>  
    3122@image html perio3_20.png  
    32 @latexonly 
    33 \begin{center} 
    34 \includegraphics{perio3_20.png} 
    35 \end{center} 
    36 @endlatexonly 
     23<center>@image latex perio3_20.png  
     24</center> 
    3725<dt>North fold boundary with a T -point pivot and cyclic east-west boundary (in_perio=4)</dt> 
    3826<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>  
    3927@image html perio4_20.png  
    40 @latexonly 
    41 \begin{center} 
    42 \includegraphics{perio4_20.png} 
    43 \end{center} 
    44 @endlatexonly 
     28<center>@image latex perio4_20.png  
     29</center> 
    4530<dt>North fold boundary with a F -point pivot (in_perio=5)</dt> 
    4631<dd>first row, and first and last columns are closed. </dd>  
    4732@image html perio5_20.png  
    48 @latexonly 
    49 \begin{center} 
    50 \includegraphics{perio5_20.png} 
    51 \end{center} 
    52 @endlatexonly 
     33<center>@image latex perio5_20.png  
     34</center> 
    5335<dt>North fold boundary with a F -point pivot and cyclic east-west boundary (in_perio=6)</dt> 
    5436<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>  
    5537@image html perio6_20.png  
    56 @image html perio5_20.png  
    57 @latexonly 
    58 \begin{center} 
    59 \includegraphics{perio6_20.png} 
    60 \end{center} 
    61 @endlatexonly 
     38<center>@image latex perio6_20.png  
     39</center> 
    6240</dl> 
    6341@sa For more information about NEMO periodicity, see _Model Boundary Condition_ chapter in [NEMO documentation](http://www.nemo-ocean.eu/About-NEMO/Reference-manuals)) 
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