Hello everyone!
I am trying to generate a nanorod structure of nitinol using a cif file.
Here is the relevant part of my code:
Read the LAMMPS data file converted from the CIF file
read_data nitinol.data
Replicate the unit cell to create a larger structure
replicate 20 20 50 # Adjust replication factors for the desired nanorod length
Define a cylindrical region to create the nanorod
region nanorod cylinder z 29.8806613 29.8806613 10.0 INF INF # Cylinder with radius of 10 units along z-axis
Delete atoms outside the cylindrical region to form the nanorod
delete_atoms region nanorod
But the delete_atoms command here removes the atoms inside the nanorod and creates a cylindrical hole inside the simulation box.
How can I remove the atoms that are outside the region nanorod?