In molecular dynamics simulations, a Frenkel pair consists of a vacancy and an interstitial atom in a material. To calculate the number of Frenkel pairs, you generally follow these steps:

Run the Simulation: Perform a molecular dynamics simulation of the material where you expect to observe the creation of Frenkel pairs. Ensure that the simulation is long enough and under conditions that can create Frenkel pairs.

Identify Vacancies and Interstitials:

Vacancies: Determine the number of vacancies by comparing the number of atoms in your simulation with the number of atoms in the ideal crystal lattice.

Interstitials: Identify interstitial atoms, which are atoms that occupy spaces between the regular lattice sites.

Count Frenkel Pairs:

Direct Counting: Directly count the number of vacancies and interstitials. In an ideal case, the number of Frenkel pairs will be the same as the number of vacancies (assuming each vacancy is associated with a single interstitial).

Pair Analysis: Use spatial or distance-based criteria to match vacancies with interstitials. This might involve checking if interstitials are positioned near vacancies within a certain cutoff distance, reflecting the creation of a Frenkel pair.

Statistical Analysis: Analyze the data to obtain the number of Frenkel pairs per unit cell or per unit volume.

Visualization and Verification: Often, visualizing the simulation with tools can help verify and cross-check the identified Frenkel pairs.

Tools and Software: Depending on the software used (e.g., LAMMPS, GROMACS), there may be built-in functions or scripts available to assist with the identification and counting of Frenkel pairs.

By following these steps, you can calculate the number of Frenkel pairs from your molecular dynamics simulation data.

Maybe this could help - https://docs.mdanalysis.org/1.1.1/documentation_pages/lib/nsgrid.html

Jamal Zrinej thank you so much for the explanation

We are welcome. Good luck

To calculate Frenkel pairs from MD simulations:

All of which can be easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.