error message for wrong absorber site

[deyulu]

Lightshow throws out a confusing error message (see below) about missing POSCAR file, when the absorber element user specified was not part of the system. The error message could be more accurate.

---

FileNotFoundError Traceback (most recent call last)
/var/folders/ff/xfhfm9fn6svg3lt1y0jm5n9w0000gq/T/ipykernel_17669/995942095.py in
----> 1 database.write("test1", options=[ocean_params], absorbing_atoms=["Cu"])

~/opt/miniconda3/envs/xas_ben/lib/python3.9/site-packages/lightshow/database.py in write(self, root, absorbing_atoms, options, pbar, copy_script, write_unit_cells)
511
512 if write_unit_cells:
--> 513 self._write_unit_cells(root, pbar=pbar)
514
515 self._write_origin_paths(root, pbar=pbar)

~/opt/miniconda3/envs/xas_ben/lib/python3.9/site-packages/lightshow/database.py in _write_unit_cells(self, root, pbar)
334 for key, structure in tqdm(self._structures.items(), disable=not pbar):
335 fname = Path(root) / key / "POSCAR"
--> 336 structure.to(fmt="POSCAR", filename=str(fname))
337
338 def _write_origin_paths(self, root, pbar=False):

~/opt/miniconda3/envs/xas_ben/lib/python3.9/site-packages/pymatgen/core/structure.py in to(self, filename, fmt, **kwargs)
2809
2810 if filename:
-> 2811 writer.write_file(filename)
2812 return str(writer)
2813

~/opt/miniconda3/envs/xas_ben/lib/python3.9/site-packages/pymatgen/io/vasp/inputs.py in write_file(self, filename, **kwargs)
599 the Poscar.get_str method and are passed through directly.
600 """
--> 601 with zopen(filename, mode="wt") as file:
602 file.write(self.get_str(**kwargs))
603

~/opt/miniconda3/envs/xas_ben/lib/python3.9/site-packages/monty/io.py in zopen(filename, *args, **kwargs)
43 if ext in (".XZ", ".LZMA"):
44 return lzma.open(filename, *args, **kwargs)
---> 45 return open(filename, *args, **kwargs) # pylint: disable=R1732
46
47

FileNotFoundError: [Errno 2] No such file or directory: '/Users/deyulu/work/Cu-L_edge/test1/mp-2657/POSCAR'

[matthewcarbone]

@deyulu I'm not sure if I know what's going on here, but it doesn't appear that this is a Lightshow issue. Can you confirm if you're still having this problem? We might have actually resolved this over Zoom, I just don't remember.

[deyulu]

@matthewcarbone Now I remember. The issue was that if the absorber element is not in the POSCAR, lightshow gives an error message of missing POSCAR file instead of missing atom type. If nothing changed since, I believe that this issue still remains.

[matthewcarbone]

@deyulu I'm not sure the error you posted is enough for me to help with this. Can you post a reproducible code you used that generated this error? Once I figure out exactly what is going on I can try to clarify the error message. Best if you can reproduce this with data I have or can get from the Materials Project. Thanks!

[deyulu]

@matthewcarbone I'll send you a notebook in email.