llnl / llnl/MemSurfer

Computing surface yields unexpected error

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Dominant language
C++
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Description

Hello,

I'm trying to compute a surface for a CG pure POPC membrane.
In pseudocode, the procedure I'm following looks like:

```
import MDAnalysis
from memsurfer import Membrane

u = MDAnalysis.Universe(pdb_file, xtc_file)

frame = u.trajectory[-1]

atoms = u.select_atoms('name PO4')
bbox = np.zeros((2,3))
bbox[1,:] = frame.dimensions[:3]

membrane = Membrane.compute(atoms.positions, atoms.resnames, bbox = bbox, periodic = True)
```

Which yields the following error
```
terminate called after throwing an instance of 'std::length_error'
what(): cannot create std::vector larger than max_size()
```

It looks like it has something to do with the box dimensions (maybe?) but I have no Idea how to fix it.

I also tried computing a surface from a random distribution of points within the same bounds as my membrane, and get the same error.

Thank you very much in advance for your help!

Contributor guide

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Research direction

Start by reproducing the supplied Membrane.compute call with the POPC coordinates, periodic bounding box, and random points, then inspect the box-dimension and periodic-processing path that produces std::length_error. Done means the same inputs no longer terminate with the exception and surface computation completes or reports a clear input error.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp, python
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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