Dear Jaffri,

In Materials Studio, removing a specific list of atoms by index isn't straightforward through the GUI, but you can do it using Python scripting @MaterialsScript API. Here's how you can remove a list of atoms;

Python Script for Materials Studio

from MaterialsScript import *

# Open the document (Assume your file is 'xyz.xsd'

doc = Documents.Open('your_file.xsd')

# Define the list of atom indexes to remove (1-based index)

atom_indices = [1, 4, 8, 12, 56, 45]

# Convert to 0-based index for scripting

atom_indices = [i-1 for i in atom_indices]

# Sort in descending order to avoid index shifts' issues

atom_indices.sort(reverse=True)

# Remove the atoms

for index in atom_indices:

doc.DeleteAtom(doc.Atoms[index])

# Save it

doc.SaveAs('modified_structure.xsd')

To Run the Script:

>Open Materials Studio.

>>Go2 Scripting > Python Script Editor.

>>>Paste the script above.

>>>>Replace 'xyz.xsd' with your actual structure filename.

>>>>> Run the script, and it will remove the specified atoms.

I use LAMMPS

In LAMMPS atoms cannot be deleted by index directly, but you can achieve this by using the delete_atoms command in combination with groups. The process involves creating a data file where the unwanted atoms are marked and then removed.

Assume you have a LAMMPS data file (cell.data) structured as:

Atoms

1 1 0 0 0

2 1 1 0 0

3 1 0 1 0

4 1 1 1 0

etc...

Each line represents an atom with an ID, atom type and coordinates.

Define a group of atoms to remove in LAMMPS input

Create a LAMMPS input script with the following commands:

units metal

dimension 3

boundary p p p

atom_style atomic

read_data supercell.data # Load the geometric structure

# Define a group with specific atom IDs

group to_remove id 1 4 8 12 56 45

# Delete the specified atoms

delete_atoms group to_remove

# Write the modified structure to a new data file

write_data modfd_cell.data

# Run minimization or simulation as needed...