Bugs for distance calculation functions

[zbaibg]

Expected behavior

I found two distance calculation functions cannot generate the same results, which results that one bond shorter than the cutoff cannot be found when I use guess_bond()

Actual behavior

Code to reproduce the behavior

Datafile: struc.txt

from MDAnalysis.lib import distances
tmp_lammps_filename="struc.txt"
u = mda.Universe(tmp_lammps_filename, format="DATA")
a,b=distances._nsgrid_capped_self(u.atoms.positions,max_cutoff=3.4,box=u.dimensions)
# Find the row in 'a' where the pair [145,80] appears
row_indices = np.where((a == [145,80]).all(axis=1))[0]
if len(row_indices) > 0:
    print(f"Found pair [145,80] at row {row_indices[0]}")
    print(f"Distance: {b[row_indices[0]]} Å")
else:
    # Also check for [80,145] since order might be reversed
    row_indices = np.where((a == [80,145]).all(axis=1))[0]
    if len(row_indices) > 0:
        print(f"Found pair [80,145] at row {row_indices[0]}")
        print(f"Distance: {b[row_indices[0]]} Å")
    else:
        print("Pair not found")
        
u = mda.Universe(tmp_lammps_filename, format="DATA")
a,b=distances._bruteforce_capped_self(u.atoms.positions,max_cutoff=3.4,box=u.dimensions)
# Find the row in 'a' where the pair [145,80] appears
row_indices = np.where((a == [145,80]).all(axis=1))[0]
if len(row_indices) > 0:
    print(f"Found pair [145,80] at row {row_indices[0]}")
    print(f"Distance: {b[row_indices[0]]} Å")
else:
    # Also check for [80,145] since order might be reversed
    row_indices = np.where((a == [80,145]).all(axis=1))[0]
    if len(row_indices) > 0:
        print(f"Found pair [80,145] at row {row_indices[0]}")
        print(f"Distance: {b[row_indices[0]]} Å")
    else:
        print("Pair not found")

Here _nsgrid_capped_self does not work, which prints:
Pair not found

Here _bruteforce_capped_self works which prints:
Found pair [80,145] at row 829
Distance: 1.3481745221090606 Å
....

## Current version of MDAnalysis ##

- Which version are you using? 2.8.0
- Which version of Python (`python -V`)?: Python 3.12.0
- Which operating system?centos:9

[yuxuanzhuang]

Hi @zbaibg, thanks for reporting this issue!

It appears to be related to how NSGrid calculates images in a triclinic box, similar to #3133. Richard @richardjgowers, would you mind taking a look at this when you get a chance?