Assignment 0: dense flow over an obstacle#
For this assignment you will run and plot some data from a Veros simulation. Once you have the model running, please answer the questions below, and hand your Notebook in using Brightspace as a PDF.
Run the model#
The model setup file to use is ./hydraulic.py. If you have set up veros on your machine and you have activated the environment (mamba activate eos431) then you should be able to do:
veros run --force-overwrite hydraulic.py
or, if you managed to get mpi to install and your computer has at least 4 cores:
mpirun -np 4 veros run --force-overwrite hydraulic.py -n 4 1
You should see output scroll by like:
Current iteration: 2 (0.00/2.50d | 0.0% | 6.14d/(model year) | 1.0h left)
Current iteration: 3 (0.00/2.50d | 0.0% | 4.49d/(model year) | 44.9m left)
Current iteration: 4 (0.00/2.50d | 0.0% | 3.67d/(model year) | 36.7m left)
Current iteration: 5 (0.00/2.50d | 0.0% | 3.13d/(model year) | 31.3m left)
interspersed with snapshots being written to the netcdf file:
Current iteration: 358 (0.08/2.50d | 3.3% | 1.00d/(model year) | 9.7m left)
Current iteration: 359 (0.08/2.50d | 3.3% | 1.00d/(model year) | 9.7m left)
Writing snapshot at 2.00 hours
Current iteration: 360 (0.08/2.50d | 3.3% | 1.01d/(model year) | 9.7m left)
Current iteration: 361 (0.08/2.50d | 3.3% | 1.01d/(model year) | 9.7m left)
A file hydraulic.snapshot.nc should be increasing in size while you run this.
Note that depending on the speed of your computer this could take a little while to run - after the first 20 iterations, the “time left” indication should be relatively accurate.
Note
Help! my model doesn’t run, or is so painfully slow I can’t wait for it to complete! Please contact the instructor, preferably on Brightspace.
Q1.1#
Make a plot of the evolution of the flow (u) over time, for at least 2 days (no need to show every time step). Ideally, contour temperature as well as color velocity (I usually use pcolormesh). Please take some care to center your colormaps, and label the axes properly (though if the axes limits are repeated, you need not label all the axes). Also use some discretion in choosing the xlimits of your plot.
import xarray as xr
import numpy as np
import matplotlib.pyplot as plt
# use the matplotlib widget
%matplotlib widget
with xr.open_dataset('hydraulic.snapshot.nc') as ds0:
print(ds0)
print(ds0.xt.mean())
ds0 = ds0.isel(Time=0, yt=1, yu=1)
fig, ax = plt.subplots()
ax.pcolormesh(ds0.xu, ds0.zt, ds0.u)
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
File ~/mambaforge/envs/veros/lib/python3.8/site-packages/xarray/backends/file_manager.py:209, in CachingFileManager._acquire_with_cache_info(self, needs_lock)
208 try:
--> 209 file = self._cache[self._key]
210 except KeyError:
File ~/mambaforge/envs/veros/lib/python3.8/site-packages/xarray/backends/lru_cache.py:55, in LRUCache.__getitem__(self, key)
54 with self._lock:
---> 55 value = self._cache[key]
56 self._cache.move_to_end(key)
KeyError: [<class 'netCDF4._netCDF4.Dataset'>, ('/Users/jklymak/Dropbox/Teaching/Eos431Phy441/release/Assign0/hydraulic.snapshot.nc',), 'r', (('clobber', True), ('diskless', False), ('format', 'NETCDF4'), ('persist', False)), 'f5209ca0-551e-4794-b240-f6774fcfcf9c']
During handling of the above exception, another exception occurred:
FileNotFoundError Traceback (most recent call last)
Cell In[2], line 1
----> 1 with xr.open_dataset('hydraulic.snapshot.nc') as ds0:
2 print(ds0)
3 print(ds0.xt.mean())
File ~/mambaforge/envs/veros/lib/python3.8/site-packages/xarray/backends/api.py:541, in open_dataset(filename_or_obj, engine, chunks, cache, decode_cf, mask_and_scale, decode_times, decode_timedelta, use_cftime, concat_characters, decode_coords, drop_variables, inline_array, backend_kwargs, **kwargs)
529 decoders = _resolve_decoders_kwargs(
530 decode_cf,
531 open_backend_dataset_parameters=backend.open_dataset_parameters,
(...)
537 decode_coords=decode_coords,
538 )
540 overwrite_encoded_chunks = kwargs.pop("overwrite_encoded_chunks", None)
--> 541 backend_ds = backend.open_dataset(
542 filename_or_obj,
543 drop_variables=drop_variables,
544 **decoders,
545 **kwargs,
546 )
547 ds = _dataset_from_backend_dataset(
548 backend_ds,
549 filename_or_obj,
(...)
557 **kwargs,
558 )
559 return ds
File ~/mambaforge/envs/veros/lib/python3.8/site-packages/xarray/backends/netCDF4_.py:578, in NetCDF4BackendEntrypoint.open_dataset(self, filename_or_obj, mask_and_scale, decode_times, concat_characters, decode_coords, drop_variables, use_cftime, decode_timedelta, group, mode, format, clobber, diskless, persist, lock, autoclose)
557 def open_dataset(
558 self,
559 filename_or_obj,
(...)
574 autoclose=False,
575 ):
577 filename_or_obj = _normalize_path(filename_or_obj)
--> 578 store = NetCDF4DataStore.open(
579 filename_or_obj,
580 mode=mode,
581 format=format,
582 group=group,
583 clobber=clobber,
584 diskless=diskless,
585 persist=persist,
586 lock=lock,
587 autoclose=autoclose,
588 )
590 store_entrypoint = StoreBackendEntrypoint()
591 with close_on_error(store):
File ~/mambaforge/envs/veros/lib/python3.8/site-packages/xarray/backends/netCDF4_.py:382, in NetCDF4DataStore.open(cls, filename, mode, format, group, clobber, diskless, persist, lock, lock_maker, autoclose)
376 kwargs = dict(
377 clobber=clobber, diskless=diskless, persist=persist, format=format
378 )
379 manager = CachingFileManager(
380 netCDF4.Dataset, filename, mode=mode, kwargs=kwargs
381 )
--> 382 return cls(manager, group=group, mode=mode, lock=lock, autoclose=autoclose)
File ~/mambaforge/envs/veros/lib/python3.8/site-packages/xarray/backends/netCDF4_.py:329, in NetCDF4DataStore.__init__(self, manager, group, mode, lock, autoclose)
327 self._group = group
328 self._mode = mode
--> 329 self.format = self.ds.data_model
330 self._filename = self.ds.filepath()
331 self.is_remote = is_remote_uri(self._filename)
File ~/mambaforge/envs/veros/lib/python3.8/site-packages/xarray/backends/netCDF4_.py:391, in NetCDF4DataStore.ds(self)
389 @property
390 def ds(self):
--> 391 return self._acquire()
File ~/mambaforge/envs/veros/lib/python3.8/site-packages/xarray/backends/netCDF4_.py:385, in NetCDF4DataStore._acquire(self, needs_lock)
384 def _acquire(self, needs_lock=True):
--> 385 with self._manager.acquire_context(needs_lock) as root:
386 ds = _nc4_require_group(root, self._group, self._mode)
387 return ds
File ~/mambaforge/envs/veros/lib/python3.8/contextlib.py:113, in _GeneratorContextManager.__enter__(self)
111 del self.args, self.kwds, self.func
112 try:
--> 113 return next(self.gen)
114 except StopIteration:
115 raise RuntimeError("generator didn't yield") from None
File ~/mambaforge/envs/veros/lib/python3.8/site-packages/xarray/backends/file_manager.py:197, in CachingFileManager.acquire_context(self, needs_lock)
194 @contextlib.contextmanager
195 def acquire_context(self, needs_lock=True):
196 """Context manager for acquiring a file."""
--> 197 file, cached = self._acquire_with_cache_info(needs_lock)
198 try:
199 yield file
File ~/mambaforge/envs/veros/lib/python3.8/site-packages/xarray/backends/file_manager.py:215, in CachingFileManager._acquire_with_cache_info(self, needs_lock)
213 kwargs = kwargs.copy()
214 kwargs["mode"] = self._mode
--> 215 file = self._opener(*self._args, **kwargs)
216 if self._mode == "w":
217 # ensure file doesn't get overridden when opened again
218 self._mode = "a"
File src/netCDF4/_netCDF4.pyx:2464, in netCDF4._netCDF4.Dataset.__init__()
File src/netCDF4/_netCDF4.pyx:2027, in netCDF4._netCDF4._ensure_nc_success()
FileNotFoundError: [Errno 2] No such file or directory: '/Users/jklymak/Dropbox/Teaching/Eos431Phy441/release/Assign0/hydraulic.snapshot.nc'
# YOUR CODE HERE
raise NotImplementedError()
---------------------------------------------------------------------------
NotImplementedError Traceback (most recent call last)
Cell In[3], line 2
1 # YOUR CODE HERE
----> 2 raise NotImplementedError()
NotImplementedError:
Q1.2 Describe:#
Describe the flow that is shown in your plot.
the water is moving. Why?
why do you think the shallow layer of water is moving in the negative x direction?
we often discuss flows being in “steady state”. Does this flow acheive steady state? If so, where?
the water flowing in the bottom layer clearly accelerates. Do you think it transports more water?
YOUR ANSWER HERE
Q1.3 Hovmoller diagram:#
If you did the above properly, you selected a given Time for each frame. For ths problem, choose a certain depth, and plot the velocity as function of xu on the x axis and Time on the y axis. This is called a Hovmoller diagram and is a very useful way to see signals propagating. Do a couple of interesting depths.
Note
Time in Veros is stored as np.timedelta64 which is time since the model run started in nanoseconds. Nanoseconds are pretty useless time unit, so convert to something more convenient (I used hours): ds0['Time'] = ds0.Time / np.timedelta64(1, 'h')
# YOUR CODE HERE
raise NotImplementedError()
---------------------------------------------------------------------------
NotImplementedError Traceback (most recent call last)
Cell In[4], line 2
1 # YOUR CODE HERE
----> 2 raise NotImplementedError()
NotImplementedError:
Q1.4 Describe#
Describe the signals seen in the Hovmoller diagram - refer to the time slice plots to help orient yourself.
YOUR ANSWER HERE