Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

'nojump' raises an exception when used with triclinic systems #105

Closed
p-j-smith opened this issue Mar 11, 2023 · 1 comment
Closed

'nojump' raises an exception when used with triclinic systems #105

p-j-smith opened this issue Mar 11, 2023 · 1 comment
Assignees
Labels
bug Something isn't working wontfix This will not be worked on

Comments

@p-j-smith
Copy link
Owner

Describe the bug
lipyphilic.transformations.nojump can't be used with triclinic systems - it always raises a ValueError because the system is triclinic, even if the lipyphilic.transformations.triclinic_to_orthorhombic is used first.

To Reproduce

from lipyphilic._simple_systems.simple_systems import TRICLINIC
from lipyphilic.transformations import nojump, triclinic_to_orthorhombic

universe = MDAnalysis.Universe(TRICLINIC)
atoms = universe.atoms
universe.trajectory.add_transformations(
    triclinic_to_orthorhombic(ag=atoms),
    nojump(ag=atoms, nojump_x=True, nojump_y=True, nojump_z=True),
)

Expected behaviour
No error is raised.

Actual behaviour
The following error is raised:

Traceback (most recent call last):
  File "<string>", line 3, in <module>
  File "/Users/paul/git/lipyphilic/src/lipyphilic/transformations.py", line 197, in __init__
    raise ValueError("nojump requires an orthorhombic box. Please use the on-the-fly "
ValueError: nojump requires an orthorhombic box. Please use the on-the-fly transformation :class:`lipyphilic.transformations.triclinic_to_orthorhombic` before calling nojump

Additional context

  • Which version of lipyphilic are you using?
    0.10
  • Which version of Python are you using?
    3.10
@p-j-smith p-j-smith added the bug Something isn't working label Mar 11, 2023
@p-j-smith p-j-smith self-assigned this Mar 11, 2023
@p-j-smith p-j-smith moved this to 📋 Backlog in lipyphilic 1.0 Mar 11, 2023
@p-j-smith
Copy link
Owner Author

There are a few issues with this transformation (see also #113), and now that there is an implementation in MDAnalysis I will remove the one in lipyphilic and recommend people to use MDAnalysis.transformations.NoJump instead.

@github-project-automation github-project-automation bot moved this from 📋 Backlog to ✅ Done in lipyphilic 1.0 Aug 20, 2023
@p-j-smith p-j-smith added the wontfix This will not be worked on label Aug 20, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working wontfix This will not be worked on
Projects
Status: Done
Development

No branches or pull requests

1 participant