Add ElasticMatrixJob

[jan-janssen]

from pyiron_atomistics import Project

pr = Project("elastic")
job_lmp = pr.create.job.Lammps("lmp")
job_lmp.structure = pr.create.structure.ase.bulk("Al", cubic=True)
job_elastic = pr.create.job.ElasticMatrixJob("elastic")
job_elastic.ref_job = job_lmp
job_elastic.run()

[jan-janssen]

We now have both the ElasticTensor and the ElasticMatrixJob, having both can be confusing for new users. To my understanding the ElasticMatrixJob is more stable at least for DFT calculation. So I am wondering if it makes sense to move the ElasticTensor to pyiron_contrib.

[coveralls]

Pull Request Test Coverage Report for Build 8616626851

Details

• 1 of 1 (100.0%) changed or added relevant line in 1 file are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage remained the same at 93.195%

---

Totals
Change from base Build 8572185654:	0.0%
Covered Lines:	14244
Relevant Lines:	15284

---

💛 - Coveralls

[samwaseda]

I'm fine with moving ElasticTensor to pyiron_contrib, but does ElasticMatrixJob work for any structure, like if there's a vacancy for example?

[jan-janssen]

I'm fine with moving ElasticTensor to pyiron_contrib, but does ElasticMatrixJob work for any structure, like if there's a vacancy for example?

@HaithamGaafer Is this something you can test? You can install the current version of pyiron_gpl using:

conda install -c conda-forge pyiron-gpl=0.0.5 

Once it is installed you should be able to execute the example code above by adding the import statement for pyiron_gpl on top of the example:

import pyiron_gpl
from pyiron_atomistics import Project

pr = Project("elastic")
job_lmp = pr.create.job.Lammps("lmp")
structure =  pr.create.structure.ase.bulk("Al", cubic=True)
job_lmp.structure = structure
job_elastic = pr.create.job.ElasticMatrixJob("elastic")
job_elastic.ref_job = job_lmp
job_elastic.run()

This should work on your laptop without any issue. Once this is working you can delete an atom from the structure using:

structure =  pr.create.structure.ase.bulk("Al", cubic=True)
structure.set_repeat([3,3,3])
del structure[0]
job_lmp.structure = structure