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Changeset 12080 for utils/tools/SIREN/src/docsrc/2_quickstart.md – NEMO

Ignore:
Timestamp:
2019-12-06T10:30:14+01:00 (4 years ago)
Author:
jpaul
Message:

update nemo trunk

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1 edited

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  • utils/tools/SIREN/src/docsrc/2_quickstart.md

    r10212 r12080  
    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 6 Fortran programs : 
     9SIREN is composed of a set of Fortran programs : 
    1010<ul> 
    1111 <li>create_coord.f90 to create regional grid coordinates.</li> 
    … …  
    1717 </li> 
    1818 <li>create_meshmask.f90 to create meshmask or domain_cfg file(s) which contain(s) all the ocean domain informations.</li> 
     19 <li>create_layout.f90 to create/compute the domain layout of your configuration.</li> 
    1920 <li>create_restart.f90 to create initial state file from coarse grid restart 
    2021 or standard outputs. 
    … …  
    3637Here after we briefly describe how to use each programs, 
    3738and so how to create your own regional configuration. 
    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://atlas.mercator-ocean.fr/s/Zgkb65Yrgw3wWQo). 
     39@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). 
    3940 
    4041<!-- ######################################################################  --> 
    … …  
    6162   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
    6263   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
    63 / 
    64  
    65 &namcrs 
     64   cn_dumcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dummy.cfg" 
     65/ 
     66 
     67&namsrc 
    6668   cn_coord0 = "PATH/coordinates_ORCA025.nc" 
    6769   in_perio0 = 4 
    … …  
    8688~~~~~~~~~~~ 
    8789 
     90@note you could define sub domain with coarse grid indices or with coordinates. 
     91 
    8892Let's get describe this namelist.<br/> 
    8993First we have the **namlog** sub-namelist. This sub-namelist set parameters of the log 
    … …  
    9296empty, as done here.<br/> This will create a log file named *create_coord.log* 
    9397 
     98## namcfg 
    9499The **namcfg** sub-namelist defines where found SIREN configuration files.<br/> 
    95100- The variable configuration file defines standard name, default interpolation method, 
    … …  
    97102Obviously, you could add other variables to those already list, in this file. 
    98103- 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*. 
    101  
    102 The **namcrs** sub-namelist set parameters of the wide 
    103 coordinates file, as path to find it, and NEMO periodicity of the wide grid.<br/> 
     104- The dummy configuration file defines useless dimension or variable. these dimension(s) or variable(s) will not be processed. 
     105 
     106@note You could find the generic version of those configuration files in the directory *SIREN/cfg*. 
     107 
     108## namsrc 
     109The **namsrc** sub-namelist set parameters of the coarse/source 
     110coordinates file name, path to find it, and the NEMO periodicity of the grid.<br/> 
    104111 
    105112@note the NEMO periodicity could be choose between 0 to 6: 
    … …  
    121128<dd>global model with a F-point pivot<br/> 
    122129example: ORCA05</dd> 
     130</dd> 
    123131</dl> 
    124132@sa For more information see @ref md_src_docsrc_6_perio 
    125 </dd> 
    126 </dl> 
    127  
     133 
     134## namvar 
    128135The **namvar** sub-namelist lists variables to be used.<br/> 
    129 By default all the variables of the wider coordinates file are used to create 
     136By default all the variables of the coarse/source coordinates file are used to create 
    130137the new coordinates file.<br/>  
    131138The interpolation methods to be used are defined in the configuration variables file (see 
    132 below). So you do not need to fill this sub-namelist too. 
    133  
     139above). So you do not need to fill this sub-namelist too. 
     140 
     141## namnst 
    134142The **namnst** sub-namelist defines the subdomain to be used as well as refinment factor.<br/> 
    135 @note Subdomain is defined by indices of the coarse/wide grid.<br/> 
    136143 
    137144<ul> 
    138 <li>you can select area quite every where (excepted too close from the North 
    139 pole), and use the refinment factor you want.</li> 
    140  
    141 ~~~~~~~~~~~ 
    142 &namvar 
     145<li> you could define sub domain with coarse grid indices</li>  
     146 
     147~~~~~~~~~~~ 
     148&namnst 
    143149   in_imin0 = 1070 
    144150   in_imax0 = 1072 
    145151   in_jmin0 = 607 
    146152   in_jmax0 = 609 
     153/ 
     154~~~~~~~~~~~ 
     155 
     156<li>or with coordinates</li> 
     157 
     158~~~~~~~~~~~ 
     159&namnst 
     160   rn_lonmin0 = -97.9  
     161   rn_lonmax0 = -62.3  
     162   rn_latmin0 =   7.7 
     163   rn_latmax0 =  30.8 
     164/ 
     165~~~~~~~~~~~ 
     166 
     167<li>you can select area quite every where (excepted too close from the North 
     168pole), and use the refinment factor you want.</li> 
     169 
     170~~~~~~~~~~~ 
     171&namnst 
     172   in_imin0 = 1070 
     173   in_imax0 = 1072 
     174   in_jmin0 = 607 
     175   in_jmax0 = 609 
    147176 
    148177   in_rhoi = 2 
    … …  
    158187 
    159188~~~~~~~~~~~ 
    160 &namvar           
     189&namnst           
    161190   in_imin0 = 1402  
    162191   in_imax0 = 62 
    … …  
    176205 
    177206~~~~~~~~~~~ 
    178 &namvar 
     207&namnst 
    179208   in_imin0 = 0 
    180209   in_imax0 = 0 
    … …  
    197226periodicity, as well as source file, indices and refinment used. 
    198227 
    199 @sa For more information about how to create coordinates, see create_coord.f90 
     228@sa For more information and options to create coordinates, see create_coord.f90 
    200229 
    201230<!-- ######################################################################  --> 
    … …  
    224253/ 
    225254 
    226 &namcrs 
     255&namsrc 
    227256   cn_coord0 = "PATH/coordinates_ORCA025.nc" 
    228257   in_perio0 = 4 
    229258/ 
    230259 
    231 &namfin 
     260&namtgt 
    232261   cn_coord1 = "PATH/coord_fine.nc" 
    233262/ 
    … …  
    250279Let's get describe this namelist.<br/> 
    251280 
     281## namlog, namcfg 
    252282First as previously, we have the **namlog** and **namcfg** sub-namelist (see above for more 
    253283explanation).<br/> 
    254284 
    255 Then the **namcrs** sub-namelist set parameters of the wide 
     285## namsrc 
     286Then the **namsrc** sub-namelist set parameters of the source/wide 
    256287coordinates file.<br/> 
    257288@note in all SIREN namelist: <br/> 
    … …  
    259290**1** referred to the fine grid. 
    260291 
    261 In the same way, the **namfin** sub-namelist  set parameters of the fine 
     292## namtgt 
     293In the same way, the **namtgt** sub-namelist  set parameters of the target/fine 
    262294coordinates file.<br/> 
    263295@note in this namelist example, there is no need to set the variable *in_perio1* to define the NEMO 
    … …  
    266298fill it. In other case, you should add it to the namelist. 
    267299 
     300## namvar 
    268301The **namvar** sub-namelist lists variables to be used: 
    269302<dl> 
    … …  
    286319</dl> 
    287320 
     321## namnst 
    288322The **namnst** sub-namelist defines the subdomain refinment factor.<br/> 
    289323Of course those refinment factors have to be convenient with refinment 
    … …  
    292326coordinates. 
    293327 
     328## namout 
    294329Finally, this **namout** sub-namelist defines the output file.<br/> 
    295330 
    … …  
    297332source file, indices, refinment and interpolation method used. 
    298333 
    299 @sa For more information about how to create bathymetry, see 
     334@sa For more information and options to create bathymetry, see 
    300335create_bathy.f90 
    301336 
    … …  
    322357/ 
    323358 
    324 &namcrs 
     359&namsrc 
    325360   cn_bathy0 = "PATH/bathy_meter_ORCA025.nc" 
    326361   in_perio0 = 4 
    327362/ 
    328363 
    329 &namfin 
     364&namtgt 
    330365   cn_bathy1 = "PATH/bathy_fine.nc" 
    331366/ 
    … …  
    343378/ 
    344379~~~~~~~~~~~~~~~~~~ 
     380 
     381## namlog, namcfg 
    345382In this namelist, you find again the **namlog**, **namcfg** describe above. 
    346383 
    347 Then the **namcrs** sub-namelist sets parameters of the wider grid. 
    348 However this time, this is the coarse/wide grid Bathymetry wich have to be informed. 
    349  
    350 The **namfin** sub-namelist defines parameters of the fine grid Bathymetry. 
     384## namsrc 
     385Then the **namsrc** sub-namelist sets parameters of the source/wide grid. 
     386However this time, this is the source/wide grid Bathymetry wich have to be informed. 
     387 
     388## namtgt 
     389The **namtgt** sub-namelist defines parameters of the target/fine grid Bathymetry. 
    351390@note here again you could add the *in_perio1* parameter if need be i.e. if your 
    352391fine grid Bathymetry was not created by SIREN. 
    353392 
     393## namnst 
    354394The **namnst** sub-namelist defines the subdomain refinment factor. 
    355395 
    356  
     396## nambdy 
    357397The **nambdy** sub-namelist defines the subdomain boundaries.<br/> 
    358398By 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. 
    359399@sa For more information about boundaries, see @ref boundary 
    360400 
     401## namout 
    361402Finally, this **namout** sub-namelist defines the output file.<br/> 
    362403 
    363 @sa For more information about how to merge bathymetry, see 
     404@sa For more information and options to merge bathymetry, see 
    364405merge_bathy.f90 
    365406 
    … …  
    390431/ 
    391432 
    392 &namin 
     433&namsrc 
    393434   cn_bathy = "PATH/bathy_merged.nc" 
    394435   cn_coord = "PATH/coord_fine.nc" 
    … …  
    447488Let's get describe this namelist more accurately.<br/> 
    448489 
     490## namlog, namcfg 
    449491As previously, we have the **namlog** and **namcfg** describe above.<br/> 
    450492 
    451 The **namin** sub-namelist defines the Bathymetry to be used. 
     493## namsrc 
     494The **namsrc** sub-namelist defines the Bathymetry to be used. 
    452495Mainly SIREN need Bathymetry to create meshmask. 
    453496Here we also read coordinates directly on a file.  
    … …  
    457500 2. by default SIREN suppress closed sea/lake from the ORCA domain. 
    458501 
    459  
     502## namhgr 
    460503The **namhgr** sub-namelist defines the horizontal grid. 
    461504the type of horizontal mesh is choose between :<ul> 
    … …  
    468511</ul> 
    469512 
     513## namzgr 
    470514The **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. 
    471515 
     516## namdmin 
    472517The **namdmin** sub-namelist defines the minimum ocean depth. It could be defines in meter (>0) or in number of level (<0). 
    473518 
     519## namzco 
    474520The **namzco** sub-namelist defines parameters to compute z-coordinate vertical grid (**needed for all type of vertical grid**) 
    475521<!-- By default, those parameters are defined the same way than in GLORYS (i.e. 75 vertical levels).<br/> --> 
    476522 
     523## namzps 
    477524The **namzps** sub-namelist defines extra parameters needed to define z-coordinates partial steps. 
    478525 
     526## namsco 
    479527The **namsco** sub-namelist defines extra parameters needed to define sigma or hybrid coordinates (not needed here). 
    480528 
    481529<!--The **namcla** sub-namelist defines cross land advection for exchanges through some straits only used for ORCA2 (see namgrd).--> 
    482530 
     531## namlbc 
    483532The **namlbc** sub-namelist defines lateral boundary conditions at the coast. It is needed to modify the fmask. 
    484533 
     534## namwd 
    485535The **namwd** sub-namelist defines the wetting and drying parameters if activated (see namzgr sub-namelist) 
    486536 
     537## namgrd 
    487538The **namgrd** sub-namelist allows to use configuration 1D or to choose vertical scale factors (e3.=dk or old definition). 
    488539 
     540## namout 
    489541Finally, this **namout** sub-namelist defines the number output file(s).<br/> 
    490542@note To create the domain_cfg file, you should put **in_msh=0**. 
    491543 
    492544@sa For more information about how to create meshmask, see create_meshmask.f90 
     545 
     546<!-- ######################################################################  --> 
     547# Create layout (domain layout) # {#layout} 
     548 
     549To run faster your configuration you may need to run it on multiprocessor. To do so you first need to know on which domain layout and so on how many processor you could do it. 
     550.<br/> 
     551 
     552To create/compute the domain layout, you have to run : 
     553~~~~~~~~~~~~~~~~~~ 
     554./SIREN/create_layout.exe create_layout.nam 
     555~~~~~~~~~~~~~~~~~~ 
     556 
     557Here after is an example of namelist for *create_layout.exe*.<br/> 
     558In this example, you compute the domain layout on 40 processors.<br/> 
     559~~~~~~~~~~~ 
     560&namlog 
     561/ 
     562 
     563&namcfg 
     564   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     565   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
     566/ 
     567 
     568&namvar 
     569   cn_varfile = "Bathymetry:PATH/bathy_merged.nc" 
     570/ 
     571 
     572&namout 
     573   in_nproc = 40 
     574/ 
     575~~~~~~~~~~~ 
     576 
     577Let's get describe this namelist more accurately.<br/> 
     578 
     579## namlog, namcfg 
     580As previously, we have the **namlog** and **namcfg** describe above.<br/> 
     581 
     582## namvar 
     583The **namvar** sub-namelist lists variables to be used. 
     584Mainly SIREN need Bathymetry to compute the domain layout, or at least the mask of your domain. 
     585 
     586## namout 
     587The **namout** sub-namelist defines the number of processor you want to work on. 
     588 
     589@sa For more information and options to create layout, see create_layout.f90 
    493590 
    494591<!-- ######################################################################  --> 
    … …  
    517614/ 
    518615 
    519 &namcrs 
     616&namsrc 
    520617   cn_coord0 = "PATH/coordinates_ORCA025.nc" 
    521618   in_perio0 = 4 
    522619/ 
    523620 
    524 &namfin 
     621&namtgt 
    525622   cn_coord1 = "PATH/coord_fine.nc" 
    526623   cn_bathy1 = "PATH/bathy_merged.nc" 
    … …  
    550647Let's get describe this namelist more accurately.<br/> 
    551648 
     649## namlog, namcfg 
    552650As previously, we have the **namlog** and **namcfg** sub-namelists, as well as  
    553 the **namcrs** sub-namelist to set parameters of the wide coordinates file (see above for more 
     651 
     652## namsrc 
     653the **namsrc** sub-namelist to set parameters of the source/wide coordinates file (see above for more 
    554654explanation).<br/> 
    555655 
    556 Then the **namfin** sub-namelist set parameters of the fine 
     656## namtgt 
     657Then the **namtgt** sub-namelist set parameters of the target/fine 
    557658grid coordinates and bathymetry.<br/> 
    558659 
     660## namzgr, namzps 
    559661The **namzgr** and **namzps** sub-namelists define respectively parameters for vertical grid 
    560662and partial step.<br> 
    … …  
    563665@note If you use forcing fields other than GLORYS, you have to be sure it uses the same vertical grid. In other case, you need to get information about the parametrisation use, and to put it in those sub-namelist (see create_restart.f90). 
    564666 
     667## namvar 
    565668the **namvar** sub-namelist lists variables to be used.<br/> 
    566669Here we use *votemper* (temperature) get from *GLORYS_gridT.nc* file, and *vosaline* 
    … …  
    571674~~~~~~~~~~~~~~~~~~ 
    572675 
     676## namnst 
    573677The **namnst** sub-namelist defines the subdomain refinment factor, as seen previously.<br/> 
    574678 
     679## namout 
    575680Finally, this **namout** sub-namelist defines the output files.<br/> 
    576681Here we ask for output on 81 processors, with *restart_out.nc* as file "basename".<br/> 
    … …  
    589694~~~~~~~~~~~~~~~~~~ 
    590695 
    591 @sa For more information about how to create initial state or other fields, see 
     696@sa For more information and options to create initial state or other fields, see 
    592697create_restart.f90 
    593698 
    … …  
    617722/ 
    618723 
    619 &namcrs 
     724&namsrc 
    620725   cn_coord0 = "PATH/coordinates_ORCA025.nc" 
    621726   in_perio0 = 4 
    622727/ 
    623728 
    624 &namfin 
     729&namtgt 
    625730   cn_coord1 = "PATH/coord_fine.nc" 
    626731   cn_bathy1 = "PATH/bathy_fine.nc" 
    … …  
    656761Let's get describe this namelist more accurately.<br/> 
    657762 
     763## namlog, namcfg 
    658764As previously, we have the **namlog** and **namcfg** sub-namelists, as well as  
    659 the **namcrs** sub-namelist to set parameters of the wide coordinates file (see above for more 
     765 
     766## namsrc 
     767the **namcrs** sub-namelist to set parameters of the source/wide coordinates file (see above for more 
    660768explanation).<br/> 
    661769 
    662 Then the **namfin** sub-namelist set parameters of the fine 
     770## namtgt 
     771Then the **namtgt** sub-namelist set parameters of the target/fine 
    663772grid coordinates and bathymetry.<br/> 
    664773 
     774## namzgr, namzps 
    665775The **namzgr** and **namzps** sub-namelists define respectively parameters for vertical grid 
    666776and partial step.<br> 
    … …  
    669779@note If you use forcing fields other than GLORYS, you have to be sure it uses the same vertical grid. In other case, you need to get information about the parametrisation use, and to put it in those sub-namelist (see create_boundary.F90). 
    670780 
     781## namvar 
    671782the **namvar** sub-namelist lists variables to be used.<br/> 
    672783Here we get *votemper* (temperature) from *GLORYS_gridT.nc* file, *vosaline* 
    … …  
    675786height) from *GLORYS_grid2D.nc*. 
    676787 
     788## namnst 
    677789The **namnst** sub-namelist defines the subdomain refinment factor.<br/> 
    678790 
     791## nambdy 
    679792The **nambdy** sub-namelist defines the subdomain boundaries.<br/> 
    680793By default SIREN tries to create boundaries for each side (Boundary is created if sea point exist on the second row of each side).<br/> 
    … …  
    691804~~~~~~~~~~~~~~~~~~ 
    692805 
     806## namout 
    693807Finally, this **namout** sub-namelist defines the output files.<br/> 
    694808Here we ask for output with *boundary_out.nc* as file "basename".<br/> 
    … …  
    697811depending if boundary exist or not. 
    698812 
    699 @sa For more information about how to create boundaries condition, see 
     813@sa For more information and options to create boundaries condition, see 
    700814create_boundary.F90 
    701815 
    … …  
    705819To do so, go to the directory *NEMOGCM/CONFIG/*, and run: 
    706820~~~~~~~~~~~~~~~~~~ 
    707 ./makenemo -n MY_CONFIG -d "OCE_SRC" 
     821./makenemo -n MY_CONFIG -d "OPA_SRC" 
    708822~~~~~~~~~~~~~~~~~~ 
    709823This creates your configuration "MY_CONFIG" in the directory *NEMOGCM/CONFIG*.<br/> 
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