create_coord.f90 to create regional grid coordinates.
create_bathy.f90 to create regional grid bathymetry.
merge_bathy.f90 to merge regional grid bathymetry with wider grid bathymetry at boundaries.
Note
the goal of this step is to avoid break in Bathymetry. This break may cause inconsistency between forcing fields at boundary and regional fields.
create_restart.f90 to create initial state file from coarse grid restart or standard outputs.
Note
this program could also be used to refined other input fields from a wider configuations (as runoff, chlorophyll etc...)
create_boundary.F90 to create boundaries conditions from wider configurations output fields.

Warning

SIREN can not:

create global configuration.
create configuarion around or close to North pole.
change number of vertical level.

Here after we briefly describe how to use each programs, and so how to create your own regional configuration.

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.

Create coordinates file

To create your own configuration, you first have to create a coordinates file on your domain of study.
SIREN allows you to create this coordinates file from a wider coordinates file.
The coordinates file created could simply be an extraction, or a refinment of the wide grid.

To create this new cooridnates file, you have to run :

./SIREN/create_coord.exe create_coord.nam

Here after is an example of namelist for create_coord.exe.
In this example, you create a coordinates file named coord_fine.nc.
This new coordinates file is refined from an extraction of coordinates_ORCA025.nc.

&namlog
/
&namcfg
   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg"
   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg"
/
&namcrs
   cn_coord0 = "PATH/coordinates_ORCA025.nc"
   in_perio0 = 4
/
&namvar
/
&namnst
   in_imin0 = 1070
   in_imax0 = 1072
   in_jmin0 = 607
   in_jmax0 = 609
   in_rhoi = 2
   in_rhoj = 3
/
&namout
   cn_fileout = "PATH/coord_fine.nc"
/

Note: you could define sub domain with coarse grid indices or with coordinates.

Let's get describe this namelist.
First we have the namlog sub-namelist. This sub-namelist set parameters of the log file.
All the parameters of this sub-namelist have default value, so you could let it empty, as done here.
This will create a log file named create_coord.log

The namcfg sub-namelist defines where found SIREN configuration files.

The variable configuration file defines standard name, default interpolation method, axis,... to be used for some known variables.
Obviously, you could add other variables to those already list, in this file.
The dimension configuration file defines dimensions allowed.

Note: You could find the generic version of those configuration files in the directory NEMOGCM/TOOLS/SIREN/cfg.

The namcrs sub-namelist set parameters of the wide coordinates file, as path to find it, and NEMO periodicity of the wide grid.

Note

the NEMO periodicity could be choose between 0 to 6:

in_perio=0: standard regional model
in_perio=1: east-west cyclic model
in_perio=2: model with symmetric boundary condition across the equator
in_perio=3: regional model with North fold boundary and T-point pivot
in_perio=4: global model with a T-point pivot.
example: ORCA2, ORCA025, ORCA12
in_perio=5: regional model with North fold boundary and F-point pivot
in_perio=6: global model with a F-point pivot
example: ORCA05

See Also: For more information see NEMO periodicity

The namvar sub-namelist lists variables to be used.
By default all the variables of the wider coordinates file are used to create the new coordinates file.
The interpolation methods to be used are defined in the configuration variables file (see below). So you do not need to fill this sub-namelist too.

The namnst sub-namelist defines the subdomain to be used as well as refinment factor.

you could define sub domain with coarse grid indices

&namnst

in_imin0 = 1070

in_imax0 = 1072

in_jmin0 = 607

in_jmax0 = 609

/
or with coordinates

&namnst

rn_lonmin0 = -97.9

rn_lonmax0 = -62.3

rn_latmin0 = 7.7

rn_latmax0 = 30.8

/
you can select area quite every where (excepted too close from the North pole), and use the refinment factor you want.

&namnst

in_imin0 = 1070

in_imax0 = 1072

in_jmin0 = 607

in_jmax0 = 609

in_rhoi = 2

in_rhoj = 3

/
you can select area crossing the east-west overlap of the global ORCA grid.

&namnst

in_imin0 = 1402

in_imax0 = 62

in_jmin0 = 490

in_jmax0 = 570

in_rhoi = 5

in_rhoj = 5

/
you can select east-west cyclic area.

&namnst

in_imin0 = 0

in_imax0 = 0

in_jmin0 = 390

in_jmax0 = 450

in_rhoi = 1

in_rhoj = 1

/

Finally the namout sub-namelist defines the output file.

Note: All the output files created by SIREN include information about NEMO periodicity, as well as source file, indices and refinment used.

See Also: For more information about how to create coordinates, see create_coord.f90

Create bathymetry file

Then you need a Bathymetry file.
SIREN allows you to create a Bathymetry extracted or refined from a wider Bathymetry grid.

To create this new bathymetry, you have to run :

./SIREN/create_bathy.exe create_bathy.nam

Here after is an example of namelist for create_bathy.exe.
In this example, you create a bathymetry file named bathy_fine.nc.
This new bathymetry file is refined from an extraction of bathy_meter_ORCA025.nc.
Moreover a minimum value of 5m is imposed to the output Bathymetry.

&namlog
/
&namcfg
   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg"
   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg"
/
&namcrs
   cn_coord0 = "PATH/coordinates_ORCA025.nc"
   in_perio0 = 4
/
&namfin
   cn_coord1 = "PATH/coord_fine.nc"
/
&namvar
   cn_varfile = "Bathymetry:PATH/bathy_meter_ORCA025.nc"
   cn_varinfo = "Bathymetry: min=5"
/
&namnst
   in_rhoi = 2
   in_rhoj = 3
/
&namout
   cn_fileout = "PATH/bathy_fine.nc"      
/

Let's get describe this namelist.

First as previously, we have the namlog and namcfg sub-namelist (see above for more explanation).

Then the namcrs sub-namelist set parameters of the wide coordinates file.

Note: in all SIREN namelist:
0 referred to the coarse/wide grid.
1 referred to the fine grid.

In the same way, the namfin sub-namelist set parameters of the fine coordinates file.

Note: in this namelist example, there is no need to set the variable in_perio1 to define the NEMO periodicity of the fine grid. Indeed, if this variable is not inform, SIREN tries to read it in the global attributes of the file. So if you created the fine coordinates with SIREN, you do not have to fill it. In other case, you should add it to the namelist.

The namvar sub-namelist lists variables to be used:

cn_varfile

defines the variable name ("Bathymetry" here) and the input file associated with.

Warning: The domain of the input Bathymetry have to be larger than the output domain.

Note

if the input file is at coarse grid resolution (same than cn_coord0), the ouptut Bathymetry will be refined on fine grid.
if the input file is a wider bathymetry (already at fine grid resolution), the output Bathymetry will be extracted from this one.

cn_varinfo

defines user's requests for a variable.

Note

Default interpolation method for the Bathymetry, is cubic interpolation.
So you may want to specify a minimum value to avoid negative value, or to change interpolation method.
example:

cn_varinfo="Bathymetry: min=1"'
cn_varinfo="Bathymetry: int=linear"

The namnst sub-namelist defines the subdomain refinment factor.
Of course those refinment factors have to be convenient with refinment from coarse grid cn_coord0 to fine grid cn_coord1.

Note: subdomain indices are automatically deduced from fine and coarse grid coordinates.

Finally, this namout sub-namelist defines the output file.

Note: All the output files create by SIREN include information about source file, indices, refinment and interpolation method used.

See Also: For more information about how to create bathymetry, see create_bathy.f90

Merge bathymetry file

The Bathymetry you build, may differ from the wider one.
To avoid issue with boundaries forcing fields, you should merge fine and coarse Bathymetry on boundaries.
SIREN allows you to do this.

To create this merged bathymetry, you have to run :

./SIREN/merge_bathy.exe merge_bathy.nam

Here after is an example of namelist for merge_bathy.exe.

&namlog
/
&namcfg
   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg"
   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg"
/
&namcrs
   cn_bathy0 = "PATH/bathy_meter_ORCA025.nc"
   in_perio0 = 4
/
&namfin
   cn_bathy1 = "PATH/bathy_fine.nc"
/
&namnst
   in_rhoi = 3
   in_rhoj = 3
/
&nambdy
/
&namout
   cn_fileout = "PATH/bathy_merged.nc"      
/

In this namelist, you find again the namlog, namcfg describe above.

Then the namcrs sub-namelist sets parameters of the wider grid. However this time, this is the coarse/wide grid Bathymetry wich have to be informed.

The namfin sub-namelist defines parameters of the fine grid Bathymetry.

Note: here again you could add the in_perio1 parameter if need be i.e. if your fine grid Bathymetry was not created by SIREN.

The namnst sub-namelist defines the subdomain refinment factor.

The nambdy sub-namelist defines the subdomain boundaries.
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. So you could let this namelist empty.

See Also: For more information about boundaries, see Create boundaries conditions

Finally, this namout sub-namelist defines the output file.

See Also: For more information about how to merge bathymetry, see merge_bathy.f90

Create initial state

To run your configuration you need an inital state of the ocean.
You could start from a restart file (with all NEMO variables fields at one time step). Or you could start from "partial" information about ocean state (Temperature and Salinity for example).

SIREN allows you to create both of those initial state.
To create the initial state, you have to run:

./SIREN/create_restart.exe create_restart.nam

Here after is an example of namelist for create_restart.exe.
In this example, you create an initial state split on 81 "processors", and named restart_out.nc.
The initial state is composed of temperature and salinity refined from an extraction of GLORYS fields.

&namlog
/
&namcfg
   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg"
   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg"
/
&namcrs
   cn_coord0 = "PATH/coordinates_ORCA025.nc"
   in_perio0 = 4
/
&namfin
   cn_coord1 = "PATH/coord_fine.nc"
   cn_bathy1 = "PATH/bathy_merged.nc"
/
&namzgr
/
&namzps
/
&namvar
   cn_varfile = "votemper:GLORYS_gridT.nc",
                "vosaline:GLORYS_gridS.nc"
/
&namnst
   in_rhoi = 3
   in_rhoj = 3
/
&namout
   cn_fileout = "PATH/restart_out.nc"      
   in_nproc = 81
/

Let's get describe this namelist more accurately.

As previously, we have the namlog and namcfg sub-namelists, as well as the namcrs sub-namelist to set parameters of the wide coordinates file (see above for more explanation).

Then the namfin sub-namelist set parameters of the fine grid coordinates and bathymetry.

The namzgr and namzps sub-namelists define respectively parameters for vertical grid and partial step.
By default, those parameters are defined the same way than in GLORYS (i.e. 75 vertical levels).
So you could let it empty.

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).

the namvar sub-namelist lists variables to be used.
Here we use votemper (temperature) get from GLORYS_gridT.nc file, and vosaline (salinity) get from GLORYS_gridS.nc file.

Note: To get all variables of a restart file. You have to use:
cn_varfile = "all:PATH/restart.dimg"

The namnst sub-namelist defines the subdomain refinment factor, as seen previously.

Finally, this namout sub-namelist defines the output files.
Here we ask for output on 81 processors, with restart_out.nc as file "basename".
So SIREN computes the optimal layout for 81 processors available,
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 your configuration.
To do so, you just have to run create_restart.exe with other variable(s) from other input file(s).
For example, to get runoff fields, you could use:
cn_varfile = "sorunoff:PATH/runoff_GLORYS.nc"

...

cn_fileout = "PATH/runoff_out.nc"

See Also: For more information about how to create initial state or other fields, see create_restart.f90

Create boundaries conditions

Finally to force your configuration, you may need boundaries conditions.
NEMO read physical boundaries conditions from temperature, salinity, currents, and sea surface height.

To create the boundaries condition with SIREN, you have to run:

./SIREN/create_boundary.exe create_boundary.nam

Here after is an example of namelist for create_boundary.exe.
In this example, you create boundaries conditions named boundary_out.nc on each side of the domain.
The boundaries contain information about temperature, salinity, currents and sea surface height refined from an extraction of GLORYS fields.

&namlog
/
&namcfg
   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg"
   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg"
/
&namcrs
   cn_coord0 = "PATH/coordinates_ORCA025.nc"
   in_perio0 = 4
/
&namfin
   cn_coord1 = "PATH/coord_fine.nc"
   cn_bathy1 = "PATH/bathy_fine.nc"
/
&namzgr
/
&namzps
/
&namvar
   cn_varfile="votemper:GLORYS_gridT.nc",
              "vosaline:GLORYS_gridS.nc",
              "vozocrtx:GLORYS_gridU.nc",
              "vomecrty:GLORYS_gridV.nc",
              "sossheig:GLORYS_grid2D.nc"
/
&namnst
   in_rhoi = 3
   in_rhoj = 3
/
&nambdy
/
&namout
   cn_fileout = "PATH/boundary_out.nc"      
/

Let's get describe this namelist more accurately.

As previously, we have the namlog and namcfg sub-namelists, as well as the namcrs sub-namelist to set parameters of the wide coordinates file (see above for more explanation).

Then the namfin sub-namelist set parameters of the fine grid coordinates and bathymetry.

The namzgr and namzps sub-namelists define respectively parameters for vertical grid and partial step.
By default, those parameters are defined the same way than in GLORYS (i.e. 75 vertical levels).
So you could let it empty.

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).

the namvar sub-namelist lists variables to be used.
Here we get votemper (temperature) from GLORYS_gridT.nc file, vosaline (salinity) from GLORYS_gridS.nc file, vozocrtx (zonal velocity) from GLORYS_gridU.nc, vomecrty (meridional velocity) from GLORYS_gridV.nc, and sossheig (sea surface height) from GLORYS_grid2D.nc.

The namnst sub-namelist defines the subdomain refinment factor.

The nambdy sub-namelist defines the subdomain boundaries.
By default SIREN tries to create boundaries for each side (Boundary is created if sea point exist on the second row of each side).
So you could let this namelist empty.

Note: SIREN allows you to place boundaries away from the side of the domain. To do so you have to define your boundary.
That means you have to give on fine grid the index of the boundary (how far from the border your boundary is), the width of your boundary, and finally first and last point of your boundary (the length of your boundary).
So to define a north boundary, you have to add in the sub-namelist nambdy, the parameter:
cn_north="index,first:last(width)"

Finally, this namout sub-namelist defines the output files.
Here we ask for output with boundary_out.nc as file "basename".
So SIREN creates output files named boundary_out_west.nc, boundary_out_east.nc, boundary_out_north.nc, and boundary_out_south.nc depending if boundary exist or not.

See Also: For more information about how to create boundaries condition, see create_boundary.F90

Create and run NEMO configuration

So now you created all the input files you need for your physical configuration, you have to create the "NEMO configuration".
To do so, go to the directory NEMOGCM/CONFIG/, and run:

./makenemo -n MY_CONFIG -d "OPA_SRC"

This creates your configuration "MY_CONFIG" in the directory NEMOGCM/CONFIG.
you could check the cpp_keys used in file cpp_MY_CONFIG.fcm, and re-run makenemo if need be.

Once makenemo has run successfully, the opa executable is available in directory NEMOGCM/CONFIG/MY_CONFIG/EXP00.
Then you just have to put all your input files in this directory, fill the namelist namelist_cfg, and run:

mpirun ./opa

Note: no surface forcing here. weighted function needed to do interpolation on the fly, could be created by WEIGHT tools already inside NEMO.

See Also: For more information about how to create NEMO configuration see NEMO Quick Start Guide.

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Table of Contents

Create coordinates file

Create bathymetry file

Merge bathymetry file

Create initial state

Create boundaries conditions

Create and run NEMO configuration