pyiron/pyiron_atomistics

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pyiron_atomistics - an integrated development environment (IDE) for atomistic simulation in computational materials science.

Stars: 55
Forks: 18
Open beginner issues: 0
Indexed issues: 143
Avg merge: 3h 32m
Merged PRs (30d): 13

Dominant language: Python
License: BSD-3-Clause
Last GitHub push: Sep 15, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: help wanted good first issue

Beginner friendly Everything

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143 open issues indexed

Recursion error with `h5io` Open

bug

pyiron/pyiron_atomistics#1788 · 6 comments · 1 assignee · Opened Aug 12, 2025
Why does it have to be `p`? Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

pyiron/pyiron_atomistics#1774 · 1 comment · Opened Jul 22, 2025
job.restart for aborted jobs Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

pyiron/pyiron_atomistics#1736 · Opened May 27, 2025
[Documentation] Collect usage Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

pyiron/pyiron_atomistics#1734 · Opened May 22, 2025
How to assign the number of nodes and the number of cores when submitting pyiron jobs without automattically setting the number of nodes as ncores/40 on cmti and ncores/256 on cmmg Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

pyiron/pyiron_atomistics#1730 · 4 comments · Opened May 19, 2025
VASP metadata for reloaded jobs Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

pyiron/pyiron_atomistics#1677 · Opened Feb 24, 2025
Wrong Voronoi volume for hcp atoms Open

bug

pyiron/pyiron_atomistics#1630 · 2 assignees · Opened Dec 17, 2024
Calphy crash in collect with n_print_steps!=0 Open

bug

pyiron/pyiron_atomistics#1616 · 1 reaction · 1 assignee · Opened Dec 2, 2024
create.structure.ase.read fails for trajectories Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 48/100

pyiron/pyiron_atomistics#1604 · Opened Nov 18, 2024
How to load jobs which finished in old kernel (pyiron/old latest Python3.10) in new kernel (pyiron/old latest Python3.11) Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 30/100

pyiron/pyiron_atomistics#1585 · 2 comments · Opened Oct 14, 2024
`get_resolved_dos()` Inconsistent Behavior with `atom_indices` Type Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

pyiron/pyiron_atomistics#1584 · Opened Oct 11, 2024
Can't use off-diagonal pressures with non-triclinic boxes. Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

pyiron/pyiron_atomistics#1580 · 2 comments · Opened Oct 6, 2024
hdf5 files are opened too often in DataContainer when loading SPHInX jobs Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

pyiron/pyiron_atomistics#1574 · 7 comments · Opened Aug 29, 2024
CI conda setup allows defaults Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

pyiron/pyiron_atomistics#1544 · Opened Aug 26, 2024
Cell (along with other properties) cannot be accessed from `project_hdf5` in Sphinx Open

bug major

Difficulty 5/5 Over a week Newbie friendliness 25/100

pyiron/pyiron_atomistics#1508 · 2 comments · Opened Jul 26, 2024
Pyiron read_cube_file() does not work for certain formats of cube files. Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

pyiron/pyiron_atomistics#1425 · Opened May 24, 2024
job crashes early in hdfio Open

bug

pyiron/pyiron_atomistics#1422 · 10 comments · 1 assignee · Opened May 21, 2024
job.restart copies OUTPUT of parent job?? Open

pyiron/pyiron_atomistics#1575 · 9 comments · 3 assignees · Opened May 16, 2024
Phonopy and magmom Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 38/100

pyiron/pyiron_atomistics#1392 · 1 comment · Opened Apr 17, 2024
get_structure() for sphinx jobs gives error Open

bug

pyiron/pyiron_atomistics#1378 · 6 comments · 2 assignees · Opened Apr 12, 2024
[Lammps] Include concept of `group` in pyiron Open

enhancement

pyiron/pyiron_atomistics#1371 · 1 reaction · 1 assignee · Opened Apr 5, 2024
Indexing Atoms broken on __getitem__ Open

bug

pyiron/pyiron_atomistics#1343 · 3 comments · 1 assignee · Opened Feb 26, 2024
Lammps input impossible to subclass nicely Open

bug

Difficulty 5/5 Over a week Newbie friendliness 25/100

pyiron/pyiron_atomistics#1336 · 1 comment · Opened Feb 22, 2024
Separate animation module Open

enhancement

pyiron/pyiron_atomistics#1288 · 1 comment · 1 assignee · Opened Jan 11, 2024
How to make SPHInX input writer independent of pyiron while using `DataContainer` Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

pyiron/pyiron_atomistics#1274 · 6 comments · Opened Dec 30, 2023
LAMMPS interactive indicies bug Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 25/100

pyiron/pyiron_atomistics#1260 · Opened Dec 13, 2023
would be nice if pyiron can parse a failed lammps job Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

pyiron/pyiron_atomistics#1247 · 5 comments · Opened Dec 4, 2023
[Pre-bug/Awareness] Vasp changed POSCAR, added "/" after species specification Open

bug

Difficulty 5/5 Over a week Newbie friendliness 10/100

pyiron/pyiron_atomistics#1232 · 1 comment · Opened Nov 30, 2023
Vasprun parser doesn't parse everything that is intended Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 48/100

pyiron/pyiron_atomistics#1226 · Opened Nov 29, 2023
sphinx eigenvalue parser problem fix (again) Open

bug

pyiron/pyiron_atomistics#1208 · 2 comments · 2 assignees · Opened Nov 14, 2023
No JTH potential for Si Open

bug

pyiron/pyiron_atomistics#1202 · 27 comments · 1 assignee · Opened Nov 9, 2023
Inconsistent Free Energy Calculation with D3 Correction in pyiron HDF5 Files Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

pyiron/pyiron_atomistics#1193 · 2 comments · Opened Oct 23, 2023
Interactive LAMMPS has the wrong working directory Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

pyiron/pyiron_atomistics#1165 · Opened Sep 15, 2023
How to turn off an automatically generated "fix" when using .calc_vcsgc() command Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

pyiron/pyiron_atomistics#1150 · 6 comments · Opened Sep 5, 2023
get_structure test currently disabled due to legacy data set Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

pyiron/pyiron_atomistics#1142 · Opened Aug 23, 2023
new get_primitive_cell() is not working anymore in some cases Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

pyiron/pyiron_atomistics#1161 · 7 comments · Opened Aug 23, 2023
LAMMPS job scripts require a date attached to them Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

pyiron/pyiron_atomistics#1101 · 4 comments · Opened Jul 3, 2023
Vasp stresses are confusing and unit is a mystery Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 20/100

pyiron/pyiron_atomistics#1071 · 2 comments · Opened May 30, 2023
get_structure raises AttributeError for QuasiNewton job Open

bug

pyiron/pyiron_atomistics#1067 · 1 assignee · Opened May 29, 2023
copy_template for Sphinx raises error Open

pyiron/pyiron_atomistics#1069 · 2 comments · 1 assignee · Opened May 29, 2023
ElasticTensor jobs issues Open

bug

pyiron/pyiron_atomistics#1059 · 9 comments · 1 assignee · Opened May 24, 2023
Sorry. But, the problem was not solved. Should I reinstall pyiron in the "cmti001.bc.rzg.mpg.de"? Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

pyiron/pyiron_atomistics#1048 · 16 comments · Opened May 21, 2023
readthedocs is broken again Open

documentation

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

pyiron/pyiron_atomistics#1038 · 2 comments · Opened May 11, 2023
pyiron cannot catch job status after job is submitted Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

pyiron/pyiron_atomistics#1034 · 1 comment · Opened May 8, 2023
Extend Murnaghan warning message Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

pyiron/pyiron_atomistics#1015 · Opened Apr 21, 2023
Potentials with no Config and no Filename - should they be supported Open

bug

pyiron/pyiron_atomistics#1013 · 3 comments · 1 assignee · Opened Apr 19, 2023
Spin constraints should be supported in pyiron syntax for vasp Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

pyiron/pyiron_atomistics#1002 · 5 comments · Opened Apr 13, 2023
VASP POTCAR POSCAR sorting is inconsistent Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 42/100

pyiron/pyiron_atomistics#988 · 8 comments · Opened Mar 15, 2023
Wrongly stored settings and missing warning when continuing job on remote cluster Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 42/100

pyiron/pyiron_atomistics#962 · 1 comment · Opened Feb 20, 2023
SPHInX rerun fails Open

bug

pyiron/pyiron_atomistics#959 · 1 assignee · Opened Feb 17, 2023

pyiron/pyiron_atomistics

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