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ROMS Ocean Model Example¶
The Regional Ocean Modeling System (ROMS) is an open source hydrodynamic model that is used for simulating currents and water properties in coastal and estuarine regions. ROMS is one of a few standard ocean models, and it has an active user community.
ROMS uses a regular C-Grid in the horizontal, similar to other structured grid ocean and atmospheric models, and a stretched vertical coordinate (see the ROMS documentation for more details). Both of these require special treatment when using xarray
to analyze ROMS ocean model output. This example notebook shows how to create a lazily evaluated vertical coordinate, and make some basic plots. The xgcm
package is required to do
analysis that is aware of the horizontal C-Grid.
[1]:
import numpy as np
import cartopy.crs as ccrs
import cartopy.feature as cfeature
import matplotlib.pyplot as plt
%matplotlib inline
import xarray as xr
Load a sample ROMS file. This is a subset of a full model available at
http://barataria.tamu.edu/thredds/catalog.html?dataset=txla_hindcast_agg
The subsetting was done using the following command on one of the output files:
#open dataset
ds = xr.open_dataset('/d2/shared/TXLA_ROMS/output_20yr_obc/2001/ocean_his_0015.nc')
# Turn on chunking to activate dask and parallelize read/write.
ds = ds.chunk({'ocean_time': 1})
# Pick out some of the variables that will be included as coordinates
ds = ds.set_coords(['Cs_r', 'Cs_w', 'hc', 'h', 'Vtransform'])
# Select a a subset of variables. Salt will be visualized, zeta is used to
# calculate the vertical coordinate
variables = ['salt', 'zeta']
ds[variables].isel(ocean_time=slice(47, None, 7*24),
xi_rho=slice(300, None)).to_netcdf('ROMS_example.nc', mode='w')
So, the ROMS_example.nc
file contains a subset of the grid, one 3D variable, and two time steps.
Load in ROMS dataset as an xarray object¶
[2]:
# load in the file
ds = xr.tutorial.open_dataset("ROMS_example.nc", chunks={"ocean_time": 1})
# This is a way to turn on chunking and lazy evaluation. Opening with mfdataset, or
# setting the chunking in the open_dataset would also achieve this.
ds
---------------------------------------------------------------------------
PermissionError Traceback (most recent call last)
File /usr/lib/python3/dist-packages/pooch/utils.py:262, in make_local_storage(path, env)
258 if action == "create":
259 # When running in parallel, it's possible that multiple jobs will
260 # try to create the path at the same time. Use exist_ok to avoid
261 # raising an error.
--> 262 os.makedirs(path, exist_ok=True)
263 else:
File /usr/lib/python3.13/os.py:217, in makedirs(name, mode, exist_ok)
216 try:
--> 217 makedirs(head, exist_ok=exist_ok)
218 except FileExistsError:
219 # Defeats race condition when another thread created the path
File /usr/lib/python3.13/os.py:217, in makedirs(name, mode, exist_ok)
216 try:
--> 217 makedirs(head, exist_ok=exist_ok)
218 except FileExistsError:
219 # Defeats race condition when another thread created the path
File /usr/lib/python3.13/os.py:227, in makedirs(name, mode, exist_ok)
226 try:
--> 227 mkdir(name, mode)
228 except OSError:
229 # Cannot rely on checking for EEXIST, since the operating system
230 # could give priority to other errors like EACCES or EROFS
PermissionError: [Errno 13] Permission denied: '/sbuild-nonexistent'
The above exception was the direct cause of the following exception:
PermissionError Traceback (most recent call last)
Cell In[2], line 2
1 # load in the file
----> 2 ds = xr.tutorial.open_dataset("ROMS_example.nc", chunks={"ocean_time": 1})
4 # This is a way to turn on chunking and lazy evaluation. Opening with mfdataset, or
5 # setting the chunking in the open_dataset would also achieve this.
6 ds
File /usr/lib/python3/dist-packages/xarray/tutorial.py:165, in open_dataset(name, cache, cache_dir, engine, **kws)
162 downloader = pooch.HTTPDownloader(headers=headers)
164 # retrieve the file
--> 165 filepath = pooch.retrieve(
166 url=url, known_hash=None, path=cache_dir, downloader=downloader
167 )
168 ds = _open_dataset(filepath, engine=engine, **kws)
169 if not cache:
File /usr/lib/python3/dist-packages/pooch/core.py:227, in retrieve(url, known_hash, fname, path, processor, downloader, progressbar)
222 action, verb = download_action(full_path, known_hash)
224 if action in ("download", "update"):
225 # We need to write data, so create the local data directory if it
226 # doesn't already exist.
--> 227 make_local_storage(path)
229 get_logger().info(
230 "%s data from '%s' to file '%s'.",
231 verb,
232 url,
233 str(full_path),
234 )
236 if downloader is None:
File /usr/lib/python3/dist-packages/pooch/utils.py:276, in make_local_storage(path, env)
272 if env is not None:
273 message.append(
274 f"Use environment variable '{env}' to specify a different location."
275 )
--> 276 raise PermissionError(" ".join(message)) from error
PermissionError: [Errno 13] Permission denied: '/sbuild-nonexistent' | Pooch could not create data cache folder '/sbuild-nonexistent/.cache/xarray_tutorial_data'. Will not be able to download data files.
Add a lazilly calculated vertical coordinates¶
Write equations to calculate the vertical coordinate. These will be only evaluated when data is requested. Information about the ROMS vertical coordinate can be found (here)[https://www.myroms.org/wiki/Vertical_S-coordinate]
In short, for Vtransform==2
as used in this example,
\(Z_0 = (h_c \, S + h \,C) / (h_c + h)\)
\(z = Z_0 (\zeta + h) + \zeta\)
where the variables are defined as in the link above.
[3]:
if ds.Vtransform == 1:
Zo_rho = ds.hc * (ds.s_rho - ds.Cs_r) + ds.Cs_r * ds.h
z_rho = Zo_rho + ds.zeta * (1 + Zo_rho / ds.h)
elif ds.Vtransform == 2:
Zo_rho = (ds.hc * ds.s_rho + ds.Cs_r * ds.h) / (ds.hc + ds.h)
z_rho = ds.zeta + (ds.zeta + ds.h) * Zo_rho
ds.coords["z_rho"] = z_rho.transpose() # needing transpose seems to be an xarray bug
ds.salt
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[3], line 1
----> 1 if ds.Vtransform == 1:
2 Zo_rho = ds.hc * (ds.s_rho - ds.Cs_r) + ds.Cs_r * ds.h
3 z_rho = Zo_rho + ds.zeta * (1 + Zo_rho / ds.h)
NameError: name 'ds' is not defined
A naive vertical slice¶
Creating a slice using the s-coordinate as the vertical dimension is typically not very informative.
[4]:
ds.salt.isel(xi_rho=50, ocean_time=0).plot()
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[4], line 1
----> 1 ds.salt.isel(xi_rho=50, ocean_time=0).plot()
NameError: name 'ds' is not defined
We can feed coordinate information to the plot method to give a more informative cross-section that uses the depths. Note that we did not need to slice the depth or longitude information separately, this was done automatically as the variable was sliced.
[5]:
section = ds.salt.isel(xi_rho=50, eta_rho=slice(0, 167), ocean_time=0)
section.plot(x="lon_rho", y="z_rho", figsize=(15, 6), clim=(25, 35))
plt.ylim([-100, 1]);
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[5], line 1
----> 1 section = ds.salt.isel(xi_rho=50, eta_rho=slice(0, 167), ocean_time=0)
2 section.plot(x="lon_rho", y="z_rho", figsize=(15, 6), clim=(25, 35))
3 plt.ylim([-100, 1]);
NameError: name 'ds' is not defined
A plan view¶
Now make a naive plan view, without any projection information, just using lon/lat as x/y. This looks OK, but will appear compressed because lon and lat do not have an aspect constrained by the projection.
[6]:
ds.salt.isel(s_rho=-1, ocean_time=0).plot(x="lon_rho", y="lat_rho")
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[6], line 1
----> 1 ds.salt.isel(s_rho=-1, ocean_time=0).plot(x="lon_rho", y="lat_rho")
NameError: name 'ds' is not defined
And let’s use a projection to make it nicer, and add a coast.
[7]:
proj = ccrs.LambertConformal(central_longitude=-92, central_latitude=29)
fig = plt.figure(figsize=(15, 5))
ax = plt.axes(projection=proj)
ds.salt.isel(s_rho=-1, ocean_time=0).plot(
x="lon_rho", y="lat_rho", transform=ccrs.PlateCarree()
)
coast_10m = cfeature.NaturalEarthFeature(
"physical", "land", "10m", edgecolor="k", facecolor="0.8"
)
ax.add_feature(coast_10m)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[7], line 4
2 fig = plt.figure(figsize=(15, 5))
3 ax = plt.axes(projection=proj)
----> 4 ds.salt.isel(s_rho=-1, ocean_time=0).plot(
5 x="lon_rho", y="lat_rho", transform=ccrs.PlateCarree()
6 )
8 coast_10m = cfeature.NaturalEarthFeature(
9 "physical", "land", "10m", edgecolor="k", facecolor="0.8"
10 )
11 ax.add_feature(coast_10m)
NameError: name 'ds' is not defined

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