LAMMPS: Implement calculate() function

[jan-janssen]

Switch the LAMMPS job to the calculate() function as it is introduced in https://github.com/pyiron/pyiron_base/pull/1477 . The pull request is expected to fail until https://github.com/pyiron/pyiron_base/pull/1477 is merged.

With these new changes it is possible to evaluate LAMMPS jobs as functions. For a classical LAMMPS job you would use:

from pyiron_atomistics import Project

pr = Project("test")
job = pr.create.job.Lammps("lmp")
job.structure = pr.create.structure.ase.bulk("Al", cubic=True)
job.run()

This still works, but in addition you can also use an external executor:

from pyiron_atomistics import Project
from concurrent.futures import ProcessPoolExecutor

pr = Project("test")
job = pr.create.job.Lammps("lmp")
job.structure = pr.create.structure.ase.bulk("Al", cubic=True)

with ProcessPoolExecutor() as exe:
    fs = exe.submit(job.get_calculate_function(), **job.calculate_kwargs)
    shell_output, output_dict, job_crashed = fs.result()

job.save_output(output_dict=output_dict, shell_output=shell_output)

[coveralls]

Pull Request Test Coverage Report for Build 9444291497

Details

• 13 of 13 (100.0%) changed or added relevant lines in 1 file are covered.
• 2 unchanged lines in 1 file lost coverage.
• Overall coverage increased (+0.002%) to 71.187%

---

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/lammps/potential.py	2	62.5%
<!--	Total:	2		-->

Totals
Change from base Build 9438715818:	0.002%
Covered Lines:	10678
Relevant Lines:	15000

---

💛 - Coveralls

[coveralls]

Pull Request Test Coverage Report for Build 9471820921

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

• For more information on this, see Tracking coverage changes with pull request builds.
• To avoid this issue with future PRs, see these Recommended CI Configurations.
• For a quick fix, rebase this PR at GitHub. Your next report should be accurate.

Details

• 17 of 17 (100.0%) changed or added relevant lines in 1 file are covered.
• 217 unchanged lines in 3 files lost coverage.
• Overall coverage decreased (-0.001%) to 71.184%

---

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/lammps/potential.py	2	62.5%
pyiron_atomistics/dft/bader.py	4	92.73%
pyiron_atomistics/vasp/base.py	211	66.1%
<!--	Total:	217		-->

Totals
Change from base Build 9438715818:	-0.001%
Covered Lines:	10679
Relevant Lines:	15002

---

💛 - Coveralls

[coveralls]

Pull Request Test Coverage Report for Build 9476628334

Details

• 17 of 17 (100.0%) changed or added relevant lines in 1 file are covered.
• 2 unchanged lines in 1 file lost coverage.
• Overall coverage increased (+0.002%) to 71.184%

---

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/lammps/potential.py	2	62.5%
<!--	Total:	2		-->

Totals
Change from base Build 9450521916:	0.002%
Covered Lines:	10679
Relevant Lines:	15002

---

💛 - Coveralls

[coveralls]

Pull Request Test Coverage Report for Build 9476697150

Details

• 17 of 17 (100.0%) changed or added relevant lines in 1 file are covered.
• 2 unchanged lines in 1 file lost coverage.
• Overall coverage increased (+0.002%) to 71.184%

---

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/lammps/potential.py	2	62.5%
<!--	Total:	2		-->

Totals
Change from base Build 9450521916:	0.002%
Covered Lines:	10679
Relevant Lines:	15002

---

💛 - Coveralls

[jan-janssen]

This comment is no longer valid.

[jan-janssen]

Waiting for https://github.com/pyiron/pyiron_base/pull/1477

[coveralls]

Pull Request Test Coverage Report for Build 9477283041

Details

• 19 of 19 (100.0%) changed or added relevant lines in 2 files are covered.
• 50 unchanged lines in 3 files lost coverage.
• Overall coverage increased (+0.002%) to 71.201%

---

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/lammps/potential.py	2	62.5%
pyiron_atomistics/lammps/output.py	19	87.18%
pyiron_atomistics/lammps/base.py	29	80.2%
<!--	Total:	50		-->

Totals
Change from base Build 9477094720:	0.002%
Covered Lines:	10693
Relevant Lines:	15018

---

💛 - Coveralls

[coveralls]

Pull Request Test Coverage Report for Build 9609063823

Details

• 73 of 106 (68.87%) changed or added relevant lines in 2 files are covered.
• 4 unchanged lines in 3 files lost coverage.
• Overall coverage decreased (-0.008%) to 71.18%

---

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/output.py	4	5	80.0%
pyiron_atomistics/lammps/base.py	69	101	68.32%
<!--	Total:	73	106	68.87%	-->

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/lammps/base.py	1	79.85%
pyiron_atomistics/lammps/interactive.py	1	45.14%
pyiron_atomistics/lammps/potential.py	2	62.5%
<!--	Total:	4		-->

Totals
Change from base Build 9608395794:	-0.008%
Covered Lines:	10687
Relevant Lines:	15014

---

💛 - Coveralls

[coveralls]

Pull Request Test Coverage Report for Build 9609156113

Details

• 73 of 106 (68.87%) changed or added relevant lines in 2 files are covered.
• 4 unchanged lines in 3 files lost coverage.
• Overall coverage decreased (-0.008%) to 71.18%

---

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/output.py	4	5	80.0%
pyiron_atomistics/lammps/base.py	69	101	68.32%
<!--	Total:	73	106	68.87%	-->

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/lammps/base.py	1	79.85%
pyiron_atomistics/lammps/interactive.py	1	45.14%
pyiron_atomistics/lammps/potential.py	2	62.5%
<!--	Total:	4		-->

Totals
Change from base Build 9608395794:	-0.008%
Covered Lines:	10687
Relevant Lines:	15014

---

💛 - Coveralls

[coveralls]

Pull Request Test Coverage Report for Build 9609216747

Details

• 73 of 106 (68.87%) changed or added relevant lines in 2 files are covered.
• 4 unchanged lines in 3 files lost coverage.
• Overall coverage decreased (-0.008%) to 71.18%

---

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/output.py	4	5	80.0%
pyiron_atomistics/lammps/base.py	69	101	68.32%
<!--	Total:	73	106	68.87%	-->

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/lammps/base.py	1	79.85%
pyiron_atomistics/lammps/interactive.py	1	45.14%
pyiron_atomistics/lammps/potential.py	2	62.5%
<!--	Total:	4		-->

Totals
Change from base Build 9608395794:	-0.008%
Covered Lines:	10687
Relevant Lines:	15014

---

💛 - Coveralls