pysrim-docker

Docker executor for PySRIM

Getting Started

To use this package, simply remove calls to run() method of SR and TRIM, and replace them with a call to the executor run dispatch method, e.g.:

from srim.executor import DockerExecutor
from srim import TRIM

executor = DockerExecutor()

trim = TRIM(...)
result = executor.run(trim)

Out of the box, the DockerExecutor uses the costrouc/srim Docker image, and writes the input and output files to a temporary directory.

Example

from srim.executor import DockerExecutor
from srim import Ion, Layer, Target, TRIM

from matplotlib import pyplot as plt

# Construct a 3MeV Nickel ion
ion = Ion('Ni', energy=3.0e6)

# Construct a layer of nick 20um thick with a displacement energy of 30 eV
layer = Layer({
        'Ni': {
            'stoich': 1.0,
            'E_d': 30.0,
            'lattice': 0.0,
            'surface': 3.0
        }}, density=8.9, width=20000.0)

# Construct a target of a single layer of Nickel
target = Target([layer])

# Initialize a TRIM calculation with given target and ion for 25 ions, quick calculation
trim = TRIM(target, ion, number_ions=25, calculation=1)

# Create executor and run TRIM
executor = DockerExecutor()
result = executor.run(trim)

# Pull out ionization
ioniz = result.ioniz

# Plot results
_, ax = plt.subplots()
ax.plot(ioniz.depth, ioniz.ions, label='Ionization from Ions')
ax.plot(ioniz.depth, ioniz.recoils, label='Ionization from Recoils')
plt.show()

Why?

There are a number of different ways that SRIM can be invoked to run simulations. Unix-like OS users have the option of using wine with or without xvfb. Windows users can directly call the binaries. Docker users can choose to defer to a pre-built SRIM container.

By abstracting the executor from the SRIM input file generation, executors can easily be swapped in and out, or extended as necessary.