This package contains tools for running, analysing, and plotting Chombo simulations.
Chombo input files can be read and written using some utility functions
from chombopy.inputs import read_inputs, write_inputs
inputs = read_inputs('/path/to/inputs')
# inputs is a dictionary, with the key values converted to appropriate python objects:
print(inputs['main.num_cells']) # e.g. [16, 16, 16]
print(inputs['main.verbosity']) # e.g. 3
print(inputs['main.plt_prefix']) # e.g. 'plt'
# You can alter the values
inputs['main.verbosity'] = 0
# And write the file back out
write_inputs('/path/to/new_inputs', inputs)Chombo plot files can be read using the PltFile class:
from chombopy.plotting import PltFile
import matplotlib.pyplot as plt
pf = PltFile('/path/to/file.hdf5')
pf.load_data()
# Get data for the temperature variable on level 2
temperature = pf.get_level_data('Temperature', 2)
# temperature is an xarray.DataSet object, which can be plotted using matplotlib
x = temperature.coords['x']
y = temperature.coords['y']
plt.pcolormesh(x, y, temperature)
# Or you can do some analysis using the xarray/numpy functionality
print(temperature.mean())Further documentation can be found online. To compile the documentation locally, get the code and setup a virtual environment:
$ git clone https://github.com/jrgparkinson/chombopy.git
$ cd chombopy
$ python3 -m venv .venv
$ source .venv/bin/activate
$ python setup.py installThen to build the documentation with Sphinx:
$ cd docs
$ make htmlUnit tests can be run in a similar way to building the documentation. Having got a copy of the code and setup a virtual environment, from the root directory (i.e. /path/to/chombopy), simply run the following from your virtual environment
$ python setup.py install
$ py.testCode coverage will be published to chombopy/docs/test/coverage.html, and test results to chombopy/docs/test/report.html.
