ASE: Example

Here, we demonstrate the non-interactive usage of the ASE image recipe.

Running ASE Non-interactively

First, let’s create a temporary folder, temp in your home directory and cd to it

mkdir ~/temp && cd ~/temp

Use your favorite text editor to create a new input file. Let’s call it test.inp and copy-paste the following code block into it and then, save it.

from ase import Atoms
from ase.calculators.emt import EMT

atom = Atoms('N')
atom.calc = EMT()
e_atom = atom.get_potential_energy()

d = 1.1
molecule = Atoms('2N', [(0., 0., 0.), (0., 0., d)])
molecule.calc = EMT()
e_molecule = molecule.get_potential_energy()

e_atomization = e_molecule - 2 * e_atom

print('Nitrogen atom energy: %5.2f eV' % e_atom)
print('Nitrogen molecule energy: %5.2f eV' % e_molecule)
print('Atomization energy: %5.2f eV' % -e_atomization)

This input file calculates the atomization energy of nitrogen molecule from the total energies of isolated nitrogen molecule and nitrogen atom.

At this stage, the content of your directory should look like the following

temp
└── test.inp

It’s time to copy the docker run command from the catalog, paste it into your terminal and edit it to look like the following command line

docker run --rm -w /home -v $PWD:/home molssi/ase322-mamba141:latest /bin/bash -c "python test.inp"

then press Enter.

Note

The same Docker image recipe can also be used with Apptainer (Singularity) to obtain the same result via the following command

apptainer exec docker://molssi/ase322-mamba141:latest python test.inp

Note that Apptainer binds /home/$USER, /tmp and current working directory ($PWD) from the host system to the running container by default. For further details see the Apptainer documentation.

If nothing goes wrong, you should see the following lines in your terminal

Nitrogen atom energy:  5.10 eV
Nitrogen molecule energy:  0.44 eV
Atomization energy:  9.76 eV

Note

You can store the generated output in a separate output file by changing the command as follows

docker run --rm -w /home -v $PWD:/home molssi/ase322-mamba141:latest /bin/bash -c "python test.inp >> test.out"

or

apptainer exec docker://molssi/ase322-mamba141:latest python test.inp >> test.out