How to develop a new atomate2 workflow#

Anatomy of an atomate2 computational workflow (i.e., what do I need to write?)#

Every atomate2 workflow is an instance of jobflow’s Flow class, which is a collection of Job and/or other Flow objects. So your end goal is to produce a Flow .

In the context of computational materials science, Flow objects are most easily created by a Maker, which contains a factory method make() that produces a Flow , given certain inputs. Typically, the input to Maker.make() includes atomic coordinate information in the form of a pymatgen Structure or Molecule object. So the basic signature looks like this:

class ExampleMaker(Maker):
    def make(self, coordinates: Structure) -> Flow:
        # take the input coordinates and return a `Flow `
        return Flow(...)

The Maker class usually contains most of the calculation parameters and other settings that are required to set up the calculation in the correct way. Much of this logic can be written like normal python functions and then turned into a Job via the @job decorator.

One common task encountered in almost any materials science calculation is writing calculation input files to disk so they can be executed by the underlying software (e.g., VASP, Q-Chem, CP2K, etc.). This is preferably done via a pymatgen InputSet class. InputSet is essentially a dict-like container that specifies the files that need to be written, and their contents. Similarly to the way that Maker classes generate Flows, InputSets are most easily created by InputGenerator classes. InputGenerator have a method get_input_set() that typically takes atomic coordinates (e.g., a Structure or Molecule object) and produce an InputSet, e.g.,

class ExampleInputGenerator(InputGenerator):
    def get_input_set(self, coordinates: Structure) -> InputSet:
        # take the input coordinates, determine appropriate
        # input file contents, and return an `InputSet`
        return InputSet(...)

pymatgen already contains InputSet for many common codes, so when developing a workflow Maker it is convenient to use the InputGenerator / InputSet to prepare your files. This is done in atomate2 by making the InputGenerator a class parameter, e.g.,

TODO - the code block below needs refinement. Not exactly sure how write_inputs() fits into aJob

class ExampleMaker(Maker):
    input_set_generator: ExampleInputGenerator = field(

    def make(self, coordinates: Structure) -> Flow:
        # create an`InputSet`
        input_set = self.input_set_generator.get_input_set(coordinates)
        # write the input files
        return Flow(...)

Finally, most atomate2 workflows return structured output in the form of “Task Documents”. Task documents are instances of emmet’s BaseTaskDocument class (similarly to a python @dataclass) that define schemas for storing calculation outputs. emmet already contains calculation schemas for codes utilized by the Materials Project (e.g., VASP, Q-Chem, FEFF) as well as a number of schemas for code-agnostic structural and molecular information (for example, the MaterialsDoc is a schema for solid material calculation data). atomate2 can also interpret output generated by cclib, which is able to parse the output of many additional codes.

TODO - extend code block above to illustrate TaskDoc usage

In summary, a new atomate2 workflow consists of the following components:

  • A Maker that actually generates the workflow

  • One or more Job and/or Flow classes that define the discrete steps in the workflow

  • (optionally) an InputGenerator that produces a pymatgen InputSet for writing calculation input files

  • (optionally) a TaskDocument that defines a schema for storing the output data

Where do I put my code?#

Because of the distributed design of the MP Software Ecosystem, writing a complete new workflow may involve making contributions to more than one GitHub repository. The following guidelines should help you understand where to put your contribution.

  • All workflow code (Job, Flow , Maker) belongs in atomate2

  • InputSet and InputGenerator code belongs in pymatgen. However, if you need to create these classes from scratch (i.e., you are working with a code that is not already supported inpymatgen), then it is recommended to include them in atomate2 at first to facilitate rapid iteration. Once mature, they can be moved to pymatgen or to a pymatgen addon package.

  • TaskDocument schemas should generally be developed in atomate2 alongside the workflow code. We recommend that you first check emmet to see if there is an existing schema that matches what you need. If so, you can import it. If not, check cclib. cclib output can be imported via atomate2.common.schemas.TaskDocument. If neither code has what you need, then new schemas should be developed within atomate2 (or cclib).