Chemistry Workflows

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A chemistry workflow

The add workflow was super basic, so now let's try a more advanced workflow involving a crystal structure.

Here, we will make a workflow that (i) converts a structure to a primitive unitcell and (ii) writes it to a CIF file:

from simmate.engine import workflow

@workflow
def write_primitive(structure, directory, **kwargs):
    new_structure = structure.get_primitive_structure()
    new_structure.to(directory / "primitive.cif", fmt="cif")

status = write_primitive.run(structure="POSCAR")
result = status.result()

Note

Make sure you run this in the same folder that contains the POSCAR file from earlier tutorials.

There are several advanced things going in this workflow.

1. We provided POSCAR filename (as a python string) -- However, our function is using structure as if it was a toolkit object (because it calls get_primitive_structure). Behind the scenes, Simmate took our POSCAR input, decided it was a structure file, and converted it to a toolkit.Structure object for us!
2. We didn't provide a directory but Simmate built one for us. This is why we can have the code directory / "primitive.cif" actually write the file to our new folder.

These advanced feature work let's us run our workflow in new ways. For example, we could run the workflow like so:

status = write_primitive.run(
    structure={
        "database_table": "MatprojStructure",
        "database_id": "mp-123",
    },
    directory="MyNewFolder",
    compress_output=True,
)
result = status.result()

This time, we pulled our structure from the database, specified the name of the folder we wanted to make, and that we wanted the final folder converted to a zip file once it's done.

So we have lots of new functionality, and all we had to do was add @workflow

Tip

There are plenty of trick that empower how you run workflows, so be sure to read through our Parameters and Full Guides section.

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