4. Quick Start

To use pySED, molecular dynamics (MD) simulations must first be performed using either GPUMD or LAMMPS to generate the required trajectory and velocity data.

Note

After MD simulation, the usage of pySED is the same regardless of the MD engine. We provide two examples below, and strongly recommend repeating one before applying pySED to your own system.

4.1. GPUMD Users

For GPUMD users, we recommend starting with the \(\text{MoS}_2\) example. This case is well-integrated with the latest version of pySED and serves as a comprehensive guide.

• Example folder: MoS2 SED Example

• Jupyter tutorial: MoS2 Tutorial Notebook

Required GPUMD input format:

ensemble       nve
dump_exyz      10     1
run            500000

This produces a dump_exyz file containing atomic coordinates and velocities.

4.2. LAMMPS Users

For LAMMPS users, we recommend starting with the silicon example.

• Example folder: Silicon SED Example

Required LAMMPS input format:

dump            vels  all  custom  ${dt_dump}  vels.dat  id  type  vx  vy  vz
dump_modify     vels  format  line "%d  %d  %0.8g  %0.8g  %0.8g"
dump_modify     vels  sort  id
dump            pos   all  custom  ${dt_dump}  pos.dat   id  type  x  y  z
dump_modify     pos   format  line  "%d  %d  %0.8g  %0.8g  %0.8g"
dump_modify     pos   sort  id

run             2097152

In LAMMPS, the coordinate (pos.dat) and velocity (vels.dat) files are generated separately. These files must be specified in the input_SED.in file when running pySED.

Tip

Always verify that your trajectory files are correctly formatted before running pySED. You can use the pySED -h command to check available options and input requirements.