You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
The input from an FHI-AIMS geometry.in file is not read correctly if the atomic coordinates are specified as fractional coordinates (using the atom_frac keyword); see e.g. the attached geometry.in.txt file here:
geometry.in.txt](https://github.com/user-attachments/files/16351689/geometry.in.txt)
The attached file contains a single layer of FeCl2, the elementary surface unit cell being repeated 5x5. So the structure should appear as a homogeneous hexagonal layer in AFM images (simulated using the Lennard-Jones potentials), but it does not.
I already know what the problem is and how to solve it (essentially a wrong order of matrix multiplication inside the loadGeometryIN function in ppafm/io.py), so I will assign myself and create the PR to resolve the issue.
The text was updated successfully, but these errors were encountered:
The input from an FHI-AIMS geometry.in file is not read correctly if the atomic coordinates are specified as fractional coordinates (using the
atom_frac
keyword); see e.g. the attachedgeometry.in.txt
file here:geometry.in.txt](https://github.com/user-attachments/files/16351689/geometry.in.txt)
The attached file contains a single layer of FeCl2, the elementary surface unit cell being repeated 5x5. So the structure should appear as a homogeneous hexagonal layer in AFM images (simulated using the Lennard-Jones potentials), but it does not.
I already know what the problem is and how to solve it (essentially a wrong order of matrix multiplication inside the
loadGeometryIN
function inppafm/io.py
), so I will assign myself and create the PR to resolve the issue.The text was updated successfully, but these errors were encountered: