cp2k / cp2k-output-tools Goto Github PK
View Code? Open in Web Editor NEWPython tools to handle CP2K output files
License: MIT License
Python tools to handle CP2K output files
License: MIT License
As the title. Besides energies, we usually need the forces information for cutoff test. it seems that this tools can't parse the force section.
thanks!
Dependabot can't resolve your Python dependency files.
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The error Dependabot encountered was:
Creating virtualenv cp2k-output-tools-l6k8E8Wb-py3.8 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
[PackageNotFound]
Package pytest-console-scripts (0.2.0) not found.
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i just run the template at readme.md, and regex.search is not work.
Version:
python 3.11
regex 2023.8.8
click 8.1.3
numpy 1.24.3
TypeError Traceback (most recent call last)
Cell In[8], line 2
1 with open('out.out', 'r') as f:
----> 2 for match in parse_iter(str(f.read())):
3 print(match.values)
4 #print(f.read())
File C:\Program Files\Python311\Lib\site-packages\cp2k_output_tools\parser.py:33, in parse_iter(content, matchers, key_mangling)
31 def parse_iter(content: str, matchers: List[Callable] = builtin_matchers, key_mangling: bool = False) -> Iterator[Dict[str, Any]]:
32 """Yields the structured data found in the block matches"""
---> 33 for block in parse_iter_blocks(content, matchers, key_mangling):
34 yield block.data
File C:\Program Files\Python311\Lib\site-packages\cp2k_output_tools\parser.py:22, in parse_iter_blocks(content, matchers, key_mangling)
20 """Yield BlockMatch objects containing both structured data and metadata for each found match"""
21 for matcher in matchers:
---> 22 match = matcher(content)
24 if match:
25 if key_mangling:
File C:\Program Files\Python311\Lib\site-packages\cp2k_output_tools\blocks\program_info.py:75, in match_program_info(content, start, end, as_tree_obj)
71 def match_program_info(
72 content: str, start: int = 0, end: int = sys.maxsize, as_tree_obj: bool = False
73 ) -> Optional[Union[BlockMatch, ProgramInfo]]:
74 spans = []
---> 75 match = PROGRAM_INFO_START_RE.search(content, start, end)
77 if not match:
78 return None
TypeError: string indices must be integers
Dependabot couldn't authenticate with https://pypi.python.org/simple/.
You can provide authentication details in your Dependabot dashboard by clicking into the account menu (in the top right) and selecting 'Config variables'.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv cp2k-output-tools-yXix9tuM-py3.8 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
[PackageNotFound]
Package pytest-console-scripts (0.2.0) not found.
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
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