Creating a custom job about pyiron HOT 6 CLOSED

from pyiron_base import PythonTemplateJob
from pyiron_atomistics import Project, Atoms
# Our Atoms inherit from ASE.Atoms, so you can use it directly
from ase.calculators.emt import EMT

class EMTJob(PythonTemplateJob):
    def __init__(self, project, job_name):
        super(EMTJob, self).__init__(project, job_name)
        # The template job comes with `input` and `output` attributes that will  
        # handle all the (de)serialization for you
        self.input.atoms = pr.atomistics.structure.bulk('Cu')  # Or whatever default
        # self.output.energy = None  # Let's just populate the field for now
        
    @property
    def structure(self):
        """
        'structure' is the canonical name for an `Atoms` object in pyiron.
        The Murnhaghan job is expecting(?) a `structure` attribute on its input jobs.
        """
        return self.input.atoms
    
    @structure.setter
    def structure(self, structure: Atoms):
        if isinstance(structure, Atoms):
            self.input.atoms = structure
        else:
            raise TypeError(f"Expected an Atoms object but got {type(structure)}")
        
    def run_static(self):
        """
        `run` is actually already a method higher up the job inheritence tree,
        it does things like let the project know the job exists -- this is why you 
        weren't seeing the job in `job_table`.
        What we actually want to define is `run_static`.
        ...This definitely needs to be better documented!!! (Actually, the whole 
        run paradigm needs some work to make it simpler and clearer, but documentation
        would be a good enough start!)
        """
        print("RUNNING")
        self.structure.set_calculator(EMT())
        self.output.energy = self.structure.get_potential_energy()
        # With the output attribute, all we need to do is tell the job to
        # write itself:
        self.to_hdf()
        
        # Buuuuut, the Murnhaghan job doesn't know about this functionality,
        # so we still need to use the old-school way of writing directly to a
        # particular place in the HDF. Note that Murnhaghan looks at "energy_pot"
        # not just "energy". It also expects that value to be a list of energies.
        # Murn is also expecting a (list of) volume(s) stored in a particular place,
        # so we'll write that too
        with self.project_hdf5.open("output/generic") as h5out: 
            h5out["energy_pot"] = [self.output.energy]
            h5out["volume"] = [self.structure.get_volume()]
            
        
        # Ok, now we're really done
        self.status.finished = True
        
pr = Project('emt')
pr.remove_jobs(silently=True, recursive=True)

job = pr.create_job(job_type=EMTJob, job_name="Al_1")
job.structure = pr.atomistics.structure.bulk("Al")
job.run()
print(job.output.energy)

loaded = pr.load("Al_1")
print(loaded.output.energy)
# The job shows up in the job table, and can be loaded later

pr.remove_jobs(silently=True, recursive=True)

job = pr.create_job(job_type=EMTJob, job_name="Cu_1")
job.structure = pr.atomistics.structure.bulk("Cu")

murn = pr.atomistics.job.Murnaghan("murn")
murn.ref_job = job
murn.input["num_points"] = 5  # I just want it faster
murn.run()
murn.plot()  # Looks right for me!

# Lastly I'll wipe everything from storage because this is just
# an example
pr.remove_jobs(silently=True, recursive=True)
pr.remove(enable=True)