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In this class, we will use the Quantum ESPRESSO calculator as implemented in the Atomic Simulation Envrionment (ASE) for density functional theory (DFT) calculations. ASE provides Python modules for manipulating atoms, performing calculations, and analyzing and visualizing the results. ASE scripts are simply regular Python scripts that incorporate the ASE modules. For detailed documentation, refer to the official ASE website. We will be demonstrating all the features you will need to use on the project website, but you may want to explore additional functionality on your own.
Here is an example of a few commonly used modules for a calculation and how you would use them in your Python scripts:
from ase import Atoms
from ase import optimize
from espresso import espresso
import numpy as np
The modules provide functions that can be used for setting up the system and performing calculations. The ase.optimize
module is needed for performing geometry optimizations, the espresso
module is needed to use the Quantum ESPRESSO calculator, and the numpy
module is needed for using certain mathematical functions.
Typically, the script will first read a trajectory file (.traj
) that contains the structure, then set up the Quantum ESPRESSO calculator, and then perform the calculation (often a structural optimization). You can use the ASE graphical user interface ase-gui
to view trajectory files or to setup or modify structures. To visualize a trajectory file, simply type:
ase-gui <trajectory_file>.traj
ASE supports a variety of file formats. More information about ASE can be found in the official documentation.
ase-gui
)As mentioned above, you can use the graphical user interface to view atomic structures. It is also convenient for adding or manipulating atoms inside your system. Read all the details here.
Log on to Stampede, download an example and take a look (the other files will all be used in the remainder of these examples):
wget https://cbe544.github.io/ASE/archive.tar.gz
tar -zxvf archive.tar.gz
cd Archive
ase-gui Ti2C.traj
You should see the following window:
To add an atom, select an existing atom and go to Edit > Add atoms
or press Ctrl+A
. After selecting OK, the atom will be placed on top of the atom you selected. If you did not select an atom, the new atom will be centered in the unit cell. If you want to move the atom, you can use Tools > Move atoms
or Ctrl+M
. The atom should have a green outline and you can use your arrow keys to move its position. You can simply hold down Ctrl
to select multiple atoms.
For the extended surfaces (e.g., 111) you can repeat the slab. This is convenient for identifying symmetric sites, which might not be obvious at first glance from the unit cell. To do this:
Next: move on to Getting Started with DFT Calculations when you’re ready to start doing some DFT!