Add lammps_function() - use LAMMPS job in a functional approach

jan-janssen commented 3 months ago

Execute LAMMPS jobs as functions:

import os
from ase.build import bulk
from pyiron_atomistics.lammps.lammps import lammps_function

shell_output, parsed_output, job_crashed = lammps_function(
    working_directory=os.path.abspath("lmp_working_directory"), 
    structure=bulk("Al", cubic=True), 
    potential='2009--Mendelev-M-I--Al-Mg--LAMMPS--ipr1', 
    calc_mode="md", 
    calc_kwargs={"temperature": 500.0, "pressure": 0.0, "n_ionic_steps": 1000, "n_print": 100}, 
    cutoff_radius=None, 
    units="metal", 
    bonds_kwargs={}, 
    enable_h5md=False,
)

coveralls commented 3 months ago

Pull Request Test Coverage Report for Build 9733456196

Details

3 of 24 (12.5%) changed or added relevant lines in 1 file are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.09%) to 70.973%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/lammps.py	3	24	12.5%
<!--	Total:	3	24	12.5%	-->

Totals
Change from base Build 9683374437:	-0.09%
Covered Lines:	10690
Relevant Lines:	15062

Pull Request Test Coverage Report for Build 9733465938

Details

3 of 24 (12.5%) changed or added relevant lines in 1 file are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.09%) to 70.973%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/lammps.py	3	24	12.5%
<!--	Total:	3	24	12.5%	-->

Totals
Change from base Build 9683374437:	-0.09%
Covered Lines:	10690
Relevant Lines:	15062

Pull Request Test Coverage Report for Build 9733933022

Details

4 of 29 (13.79%) changed or added relevant lines in 1 file are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.1%) to 70.956%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/lammps.py	4	29	13.79%
<!--	Total:	4	29	13.79%	-->

Totals
Change from base Build 9683374437:	-0.1%
Covered Lines:	10691
Relevant Lines:	15067

Pull Request Test Coverage Report for Build 9734055299

Details

6 of 36 (16.67%) changed or added relevant lines in 1 file are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.1%) to 70.937%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/lammps.py	6	36	16.67%
<!--	Total:	6	36	16.67%	-->

Totals
Change from base Build 9683374437:	-0.1%
Covered Lines:	10693
Relevant Lines:	15074

Pull Request Test Coverage Report for Build 9734235054

Details

6 of 40 (15.0%) changed or added relevant lines in 1 file are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.1%) to 70.918%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/lammps.py	6	40	15.0%
<!--	Total:	6	40	15.0%	-->

Totals
Change from base Build 9683374437:	-0.1%
Covered Lines:	10693
Relevant Lines:	15078

Pull Request Test Coverage Report for Build 9734319603

Details

6 of 45 (13.33%) changed or added relevant lines in 1 file are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.2%) to 70.894%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/lammps.py	6	45	13.33%
<!--	Total:	6	45	13.33%	-->

Totals
Change from base Build 9683374437:	-0.2%
Covered Lines:	10693
Relevant Lines:	15083

Pull Request Test Coverage Report for Build 9734554281

Details

6 of 45 (13.33%) changed or added relevant lines in 1 file are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.2%) to 70.894%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/lammps.py	6	45	13.33%
<!--	Total:	6	45	13.33%	-->

Totals
Change from base Build 9683374437:	-0.2%
Covered Lines:	10693
Relevant Lines:	15083

Pull Request Test Coverage Report for Build 9779416600

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

6 of 45 (13.33%) changed or added relevant lines in 1 file are covered.
128 unchanged lines in 1 file lost coverage.
Overall coverage decreased (-0.2%) to 70.894%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/lammps.py	6	45	13.33%
<!--	Total:	6	45	13.33%	-->

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/atomistics/structure/atoms.py	128	73.22%
<!--	Total:	128		-->

Totals
Change from base Build 9683374437:	-0.2%
Covered Lines:	10693
Relevant Lines:	15083

💛 - Coveralls

coveralls commented 3 months ago

Pull Request Test Coverage Report for Build 9788532740

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

6 of 45 (13.33%) changed or added relevant lines in 1 file are covered.
128 unchanged lines in 1 file lost coverage.
Overall coverage decreased (-0.2%) to 70.894%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/lammps.py	6	45	13.33%
<!--	Total:	6	45	13.33%	-->

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/atomistics/structure/atoms.py	128	73.22%
<!--	Total:	128		-->

Totals
Change from base Build 9683374437:	-0.2%
Covered Lines:	10693
Relevant Lines:	15083

💛 - Coveralls

coveralls commented 3 months ago

Pull Request Test Coverage Report for Build 9807214073

Details

6 of 45 (13.33%) changed or added relevant lines in 1 file are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.2%) to 70.894%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/lammps.py	6	45	13.33%
<!--	Total:	6	45	13.33%	-->

Totals
Change from base Build 9803890326:	-0.2%
Covered Lines:	10693
Relevant Lines:	15083

pyiron / pyiron_atomistics