Sam Dareska

```python from pyiron_atomistics import Project pr = Project('SPX') spx = pr.create.job.Sphinx('spx') spx.structure = pr.create.structure.bulk('Al', cubic=True) spx.run() spx = pr.load('spx') spx.run(delete_existing_job=True) ``` This fails probably because the lazy input is not...

`calc_minimize(pressure=[0, 0, 0])` does not work for undefined structure

3

```python lmp = pr.create.job.Lammps('lmp') lmp.calc_minimize(pressure=[0, 0, 0]) ``` This code raises the error: ```python-traceback --------------------------------------------------------------------------- TypeError Traceback (most recent call last) /tmp/ipykernel_37410/1534360834.py in () 1 lmp = pr.create.job.Lammps('lmp_test') ----> 2...

Why is there distinction between `hdf` and `self._hdf`?

5

https://github.com/pyiron/pyiron_atomistics/blob/212ecf7665bbb0b80f92ebbbe196df5602e3edbd/pyiron_atomistics/lammps/base.py#L976-L988 While `to_hdf` requires the HDF variable, atomistics jobs use the private variable `self._hdf` within `to_hdf`. Is there a particular reason that the function argument `hdf` should not be used?

How to make generic DFT input

3

While solving [this issue](https://github.com/pyiron/pyiron_atomistics/issues/314), I realized there's no generic DFT interface. In this particular case, I would like to have the plane wave k points, which in VASP and SPHInX...

https://github.com/pyiron/pyiron_atomistics/blob/b096732c16dd19d4522ca57ea1ac10979736b765/pyiron_atomistics/lammps/control.py#L302

What's the difference between `spins` and `initial_magmoms`?

1

I see `initial_magmoms` in `structure.arrays` and `spin` in tags. In HDF, the one is stored in `structure/spins` and the other one in `structure/tags/spin`. And in structure attributes, the one is...

`non_modal` changes the logging level

2

```python lmp = pr.create.job.Lammps('lmp') lmp.structure = pr.create.structure.bulk('Al', cubic=True) lmp.server.run_mode.non_modal = True murn = lmp.create_job('Murnaghan', 'murn') murn.server.run_mode.non_modal = True murn.run() ``` For some reason this changes the logging level.

`TrainingContainer` cannot be pickled

1

```python container = pr.create.job.TrainingContainer('container') for job in pr.iter_jobs(): container.include_job(job) df = container.to_pandas() df.to_pickle('name_of_the_file.pkl') ``` This fails, because the `Atoms`-object contains a mysterious `None` towards the beginning (i.e. `df.drop(columns=['atoms'].to_pickle('blablabla.pkl')` works).

Translate structure into a unique key

17

It's been some time since I started wondering whether there is a simple way to translate a structure to a unique key, in order to use it in the job...

Why is `SparseList` in `atomistics`?

1

Shouldn't [`SparseList`](https://github.com/pyiron/pyiron_atomistics/blob/master/pyiron_atomistics/atomistics/structure/sparse_list.py) be rather in pyiron_base?