Electronic Charge Density Mesh Calculation¶
This tutorial explains how to calculate and visualize the electronic charge density mesh of crystalline silicon in its standard equilibrium cubic-diamond crystal structure, based on Density Functional Theory (DFT). Quantum ESPRESSO is used as the simulation engine.
Quantum ESPRESSO version
This tutorial applies to Quantum ESPRESSO versions 5.2.1, 5.4.0, 6.0.0, 6.3, and later.
1. Create a job¶
Silicon in its cubic-diamond crystal structure is the default material loaded on new job creation, unless the default was changed after account creation. If silicon is still the default, it is automatically loaded when the Job Designer is opened.
2. Select the workflow¶
Workflows for calculating the electronic density mesh through Quantum ESPRESSO can be imported from the Workflows Bank into the account-owned collection. The workflow can then be selected and added to the job being created.
3. Set sampling in reciprocal space¶
A high k-point density is critical for computing the electronic density with sufficient accuracy and for properly visualizing the resulting charge density iso-surfaces.
For Quantum ESPRESSO, the "Electronic Density Mesh" workflow contains a single unit that produces an output file called density.xsf.
The k-point grid is set to 18 × 18 × 18. The validity of this grid size for yielding meV-level accuracy can be verified by performing a convergence study.
4. Submit the job¶
Before submitting the job, the Compute tab of Job Designer should be reviewed to verify the compute parameters. Silicon is a small structure, so 4 CPUs and 1 minute of calculation runtime are sufficient.
5. Examine the results¶
Once the computation completes, the Files tab of Job Viewer shows the files and directories associated with the job. The file of interest is "density.xsf", which contains the electronic charge density.
6. Open the Remote Desktop¶
In order to visualize the electron density mesh graphically, a Remote Desktop Connection should be opened so that graphical visualization tools can be run. Instructions for opening the Remote Desktop Interface are available here.
If the default project was used, the "density.xsf" file is located at:
/home/<username>/data/<username>/<job name>/. The full path is also shown in the Files tab of Job Viewer.
7. Visualize charge density with XCrySDen¶
Open the XCrySDen application. Navigate to File → Open, and browse to the directory where "density.xsf" was saved. The charge density is then displayed. Adjust the iso-surface value and toggle the iso-surface buttons to explore the data.
8. Visualize charge density with VESTA¶
Alternatively, open the VESTA application. Navigate to File → Open and browse to the directory containing "density.xsf". The electron density is displayed in the VESTA interface.
9. Video walkthrough¶
The animation below demonstrates the steps involved in creating, executing, and visualizing an electronic charge density mesh computation on silicon using Quantum ESPRESSO and VESTA.
In the final part of the animation, the iso-surface value is adjusted to make the electronic density visible as yellow iso-surfaces, showing how the electron density is concentrated around the second atom in the two-atom basis of crystalline silicon. The electron densities around other atoms are truncated by the sides of the unit cell (appearing as blue planes on the edges).