PySCF: Example

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

Running PySCF 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 pyscf import scf, gto

mol_h2o = gto.M(atom = "O 0 0 0; H 0 1 0; H 0 0 1", basis = "sto-3g")
rhf_h2o = scf.RHF(mol_h2o)
e_h2o = rhf_h2o.kernel()

The aforementioned input file performs a single-point energy calculation on water molecule at the RHF/STO-3G level of theory.

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/pyscf221-mamba141:latest /bin/bash -c "python test.inp"

then press Enter. Running the aforementioned command should generate the following output in your terminal

converged SCF energy = -74.9611711378677

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/pyscf221-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.

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/pyscf221-mamba141:latest /bin/bash -c "python test.inp >> test.out"

or

apptainer exec docker://molssi/pyscf221-mamba141:latest python test.inp >> test.out