MPAS-Limited-Area

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MPAS-Limited-Area

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Python tool to create a regional subset of a global MPAS Mesh

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# MPAS Limited-Area - v2.2

MPAS Limited-Area is a python tool that takes an MPAS global grid and produces
a regional area grid given a region specifications. Regions can be specified in
a number of different ways, making limited-area extensible and flexible.

# Download and Installing<a name="Installing"/>

To download this command line script, clone this repository into the location
of your choosing. To install it, add the base directory to your path
environment variable:

```
$ git clone git@github.com:MiCurry/MPAS-Limited-Area.git
$ setenv PATH ${PATH}:/path/to/MPAS-Limited-Area
```

Then, run the `create_region` command-line script:
```Bash
$ # Running the script with no arguments will produce a usage output
Usage: create_region [-h] [-v VERBOSE] points grid create_region
create_region: error: the following arguments are required: points, grid
```

**Note**: It may be necessary to install the dependencies for this program if
they have not been currently installed by you, or your administrator.  You can
install all the dependencies for this repository by running  `pip install -r
requirements.txt`. This will install all the necessary dependencies needed to
run this program.

It may also be necessary to update the Python 'shebang' (`#!/usr/bin/env
python`) at the top of the `create_region` script, depending on your python
environment. For instance, if you have multiple installations of python, you
may need to specify which python to use within the shebang i.e.:

```
#!/user/bin/env python3
```
or
```
#!/user/bin/env python2
```

# Running<a name="Running"/>

`create_region` can create regional subsets from global MPAS grid files or MPAS
static files.

At any point in time, you can pass the `-h` or `--help` flag to `create_region`
to generate a help message, usage statement and a list of options. The command
line usage is:

``` bash
$ create_region [options] points grid
```

Where `points` is a points specification file, and where `grid` is a global
MPAS NetCDF grid file. You'll find example points file in the points-example
directory within the docs directory of this repository and below in the *Points
Syntax* section.

## Notes on creating regions from .grid.nc files<a name="concave">

When creating region subsets from `grid.nc` files, it is important to take a
few things into account. Because of the way the init_atmosphere model 
interpolates some static data, it is possible to create incorrect static
feilds on a concave mesh, during the static interpolation of the 
init_atmosphere model.

Creating a mesh that is either **concave** in overall shape, or spans
significant longitudes near the poles will cause init_atmosphere model
to incorrectly interpolate some static fields.

Thus, when subsetting a region of a `grid.nc` file, it is import to ensure
the subsetted region's shape is **convex** in shape.

If you would like to have a convex region or region that spans many longitudes
you can avoid this problem to by simply using this program on meshes that contain
statc fields (i.e. `static.nc` files).

## Notes on Creating Large Regions (nCells >= 2,000,000)<a name="large-Regions">

If the region you create is significantly large ( >= 2,000,000 grid cells) you
will need to change the NetCDF file version of the regional grid file. To do
this, you can change the `format` keyword argument of the `LimitedArea`
initialization call within the `create_region` script to `NETCDF3_64BIT_DATA`:

``` Python
regional_area = LimitedArea(args.grid,
                            args.points,
                            format='NETCDF3_64BIT_DATA',
                            **kwargs)
```

# Points (pts) Syntax<a name="Points">

A number of pts syntax files are available in `docs/points-examples`.

The points syntax is a simple file format that can be used to specify a region.
There are a number of different methods for defining or generating a region.
Currently these include: `Polygon/Custom`, `Ellipse`, `Circle`, and `Channel`.

Each method will differ slightly in the syntax used to describe a region, but a
number of keywords will be required by each method.

Each pts file will need to specify the following keywords followed by an
appropriate value:

1. `Name:` - The desired name of your region. The specified keyword will be
              appended to the outputed region.
 2. `Type:` - The method for generating the region [custom/circle]
 3. `Point: `- A latitude, longitude coordinate separated by a comma of a point
               that is inside the desired region. **Note**: For the circle
               method and ellipse method, this point will be used as the center
               of the circle and ellipse. `Point` is not used with the channel
               method.

The value after `Name:` will be the name of the new regional mesh.

If the `Name` within the pts file was set to be the following:
```
Name: region_name
```

Then the resulting regional MPAS grid will be named the following:
`region_name.grid.nc` if the region was created from the
`x1.10242.grid.nc`.

## Polygon<a name="polygon">

A polygon points file would look like the following:
```
Name: Desired_name_of_region 
Type: custom
Point: lat, lon     # Point that inside the region
lat1, lon1          # List of points specifying the region
lat2, lon2
lat3, lon3
...
latN, LonN
```

For the polygon method, the value of `Type:` must be specified as `custom`.
The value of `Point:` must be a latitude, longitude point that lies within the
desired region in degrees.

After the `Point` specification, any number of coordinate points (in degrees)
that define the desired boundary can be listed. Points should be listed in
counter-clockwise order.

An example polygon method for defining CONUS region (`conus.custom.pts`):
```
Name: conus
Type: custom
Point: 40.0, -100.0
50.0, -129.0
50.0, -65.0
20.0, -65.0
20.0, -129.0
```

**NOTE:** When creating regional meshes with the polygon method it is
necessary to **not create concave** regions. Doing so will result in MPAS
init_atmosphere producing erroneous results while interpolating static fields.
Please see the section on [concave regions](#concave).

## Circle<a name="circle">

The circle method produces a regional circle subset of a global grid given a
center point (`Point`) and a radius from that point (`Radius`).

An example circle points specification would look like the following:
```
Name: my_circle
Type: circle
Point: 53.5, -4.5
Radius: 655000.0 # Meters
```

Here `Point` is used to specify the center of the circle and `Radius` is used
to specify the radius of the circle (in meters). **NOTE**: The radius must
be larger then at least the smallest grid cell, else unexpected behavior will
occur.

An example circle method for defining a circle around Colorado, USA is:
```
Name: colorado
Type: circle
Point: 40.0, -105.0
radius: 400000.0
```

## Ellipse<a name='ellipse'>

The ellipse method produces an ellipse shape region and is specified by a
semi-major and semi-minor axis length, as well as an orientation:

```
Name: my_ellipse
Type: ellipse
Point: 55.0, 93.0        # Latitude, Longitude (degrees)
Semi-major-axis: 6500000 # Meters
Semi-minor-axis: 3000000 # Meters
Orientation-angle: 15.0     # Clockwise rotation from due north (degrees)
```

## Equatorial Channel

The equatorial channel method can be used to specify a channel parallel to the
equator, across longitudes and between two latitude points.

For instance, one can specify a region between the tropics as:

```
Name: tropics
Type: channel
Upper-lat: 23.43676
lower-lat: -23.43676
```

### **Caution on creating channels of `grid.nc` files**

Depending on the location of a specified channel, erroneous results can be
caused during some interpolation static fields by the init_atmosphere core.
This will cause erroneous results within result `static.nc` files and will
cause resulting files to be unusable.

Thus, it is **highly** recommended to only use the channel method upon
`static.nc` files. Doing so will avoid this problem and will also save time
interpolating the static fields on different regions.

# Reporting Bugs<a name="bugs">

If you encounter a bug and wish to report it, please do so on this Github
repository's Issues page! Thank you!

# Release Notes <a name="release">

## 2.2
* Update usage of 'numpy' for compatibility with NumPy 2.x

## 2.1
* Regions created from init.nc files are named as name.init.nc

## 2.0

* Added ability to subset fields dimensioned by time

## 1.1

* Change units for specifying the radius in the circle points method from
  kilometers to meters.

## 1.0

* Initial public release
* Subsets mpas grid.nc and static.nc files

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