70 lines
4.7 KiB
Plaintext
70 lines
4.7 KiB
Plaintext
Traceback (most recent call last):
|
||
File "/opt/msspec/msspec_venv/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 154, in wrapped
|
||
asyncio.get_running_loop()
|
||
RuntimeError: no running event loop
|
||
|
||
During handling of the above exception, another exception occurred:
|
||
|
||
Traceback (most recent call last):
|
||
File "/opt/msspec/msspec_venv/lib/python3.11/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
|
||
executenb(
|
||
File "/opt/msspec/msspec_venv/lib/python3.11/site-packages/nbclient/client.py", line 1319, in execute
|
||
return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
|
||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||
File "/opt/msspec/msspec_venv/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 158, in wrapped
|
||
return loop.run_until_complete(inner)
|
||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||
File "/opt/pyenv/versions/3.11.3/lib/python3.11/asyncio/base_events.py", line 653, in run_until_complete
|
||
return future.result()
|
||
^^^^^^^^^^^^^^^
|
||
File "/opt/msspec/msspec_venv/lib/python3.11/site-packages/nbclient/client.py", line 709, in async_execute
|
||
await self.async_execute_cell(
|
||
File "/opt/msspec/msspec_venv/lib/python3.11/site-packages/nbclient/client.py", line 1062, in async_execute_cell
|
||
await self._check_raise_for_error(cell, cell_index, exec_reply)
|
||
File "/opt/msspec/msspec_venv/lib/python3.11/site-packages/nbclient/client.py", line 918, in _check_raise_for_error
|
||
raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
|
||
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
|
||
------------------
|
||
from ase.io import read
|
||
from ase.visualize import view
|
||
from msspec.calculator import MSSPEC
|
||
|
||
|
||
cluster = read('copper.cif')
|
||
# view the cluster
|
||
view(cluster, viewer='x3d')
|
||
------------------
|
||
|
||
|
||
[31m---------------------------------------------------------------------------[39m
|
||
[31mFileNotFoundError[39m Traceback (most recent call last)
|
||
[36mCell[39m[36m [39m[32mIn[3][39m[32m, line 6[39m
|
||
[32m 2[39m [38;5;28;01mfrom[39;00m[38;5;250m [39m[34;01mase[39;00m[34;01m.[39;00m[34;01mvisualize[39;00m[38;5;250m [39m[38;5;28;01mimport[39;00m view
|
||
[32m 3[39m [38;5;28;01mfrom[39;00m[38;5;250m [39m[34;01mmsspec[39;00m[34;01m.[39;00m[34;01mcalculator[39;00m[38;5;250m [39m[38;5;28;01mimport[39;00m MSSPEC
|
||
[32m----> [39m[32m6[39m cluster = [43mread[49m[43m([49m[33;43m'[39;49m[33;43mcopper.cif[39;49m[33;43m'[39;49m[43m)[49m
|
||
[32m 7[39m [38;5;66;03m# view the cluster[39;00m
|
||
[32m 8[39m view(cluster, viewer=[33m'[39m[33mx3d[39m[33m'[39m)
|
||
|
||
[36mFile [39m[32m/opt/msspec/msspec_venv/lib/python3.11/site-packages/ase/io/formats.py:808[39m, in [36mread[39m[34m(filename, index, format, parallel, do_not_split_by_at_sign, **kwargs)[39m
|
||
[32m 806[39m [38;5;28;01mif[39;00m index [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m:
|
||
[32m 807[39m index = -[32m1[39m
|
||
[32m--> [39m[32m808[39m [38;5;28mformat[39m = [38;5;28mformat[39m [38;5;129;01mor[39;00m [43mfiletype[49m[43m([49m[43mfilename[49m[43m,[49m[43m [49m[43mread[49m[43m=[49m[38;5;28;43misinstance[39;49m[43m([49m[43mfilename[49m[43m,[49m[43m [49m[38;5;28;43mstr[39;49m[43m)[49m[43m)[49m
|
||
[32m 810[39m io = get_ioformat([38;5;28mformat[39m)
|
||
[32m 811[39m [38;5;28;01mif[39;00m [38;5;28misinstance[39m(index, ([38;5;28mslice[39m, [38;5;28mstr[39m)):
|
||
|
||
[36mFile [39m[32m/opt/msspec/msspec_venv/lib/python3.11/site-packages/ase/io/formats.py:983[39m, in [36mfiletype[39m[34m(filename, read, guess)[39m
|
||
[32m 980[39m [38;5;28;01mreturn[39;00m ext
|
||
[32m 982[39m [38;5;28;01mif[39;00m orig_filename == filename:
|
||
[32m--> [39m[32m983[39m fd = [43mopen_with_compression[49m[43m([49m[43mfilename[49m[43m,[49m[43m [49m[33;43m'[39;49m[33;43mrb[39;49m[33;43m'[39;49m[43m)[49m
|
||
[32m 984[39m [38;5;28;01melse[39;00m:
|
||
[32m 985[39m fd = orig_filename [38;5;66;03m# type: ignore[assignment][39;00m
|
||
|
||
[36mFile [39m[32m/opt/msspec/msspec_venv/lib/python3.11/site-packages/ase/io/formats.py:612[39m, in [36mopen_with_compression[39m[34m(filename, mode)[39m
|
||
[32m 609[39m [38;5;28;01mreturn[39;00m lzma.open(filename, mode)
|
||
[32m 610[39m [38;5;28;01melse[39;00m:
|
||
[32m 611[39m [38;5;66;03m# Either None or unknown string[39;00m
|
||
[32m--> [39m[32m612[39m [38;5;28;01mreturn[39;00m [38;5;28;43mopen[39;49m[43m([49m[43mfilename[49m[43m,[49m[43m [49m[43mmode[49m[43m)[49m
|
||
|
||
[31mFileNotFoundError[39m: [Errno 2] No such file or directory: 'copper.cif'
|
||
|