Water molecule using Burai 1.3 and Quantum Espresso

Course: Electronic properties of semiconductors by AB-INITIO

Profesor: Dr. Raciel Jaimes López (Postdoctoral at IER-UNAM)

Simulation of water molecule formation using Burai 1.3 and Quantum Espresso

Viewer by Jmol

Last month I attended the course Electronic properties of semiconductor by AB-Initio at IER-UNAM, on the 1st day we had a quick view about the background of DFT (Density Functional Theory), plane waves and pseudopotentials. During the course, we learn about the open-code Quantum Espresso software which is used for electronic-structure calculation and materials modeling at nano-scale.

Here I share the methodology I follow for the example water-molecule

Install BURAI1.3 on MAC (includes Quantum-Espresso)
- https://burai.readthedocs.io/en/latest/install/download.html
Install MPI for MAC

- https://burai.readthedocs.io/en/latest/install/setting.html

Open BURAI and choose examples/XYZ: Water molecule (H2O.xyz)

4. Move selected atoms and add two more hydrogen atoms (decompose de molecule)

Right-click – Move selected atom

Separate two atoms

Right-click – put an atom

Keep all the parameters.

Save the project with a new name Example: Water-Curse

SCF (), configure PLANE WAVE

SCF command for PlaneWave configuration

Energy cutoff for wave function = 10 Ry and Energy cutoff for charge = 400 Ry (We don’t know the reason about this values, but we will make the first simulation with these parameters – professor recommendation ) This are the initial values for the optimization.

Save the project

Optimize: Open optimize section and don’t change anything and save the project

Optimize configuration

Don’t change any configuration and save the project.

Run the simulation (Let’s see what happen).

Run command: star simulation of 4 Hydrogen and 1 Oxygen atom

Run a Job (# Processors and #Threats) For my computer 1 processor (MPI) and 2 Threats (OpenMP)

HOME TAB: running indication in this tab (red color for calculation)

Begin – 21:30 Hrs , Finish – ?

Same window: Running unlist mode (There is no progress bar, indicator) How can we calculate spent time?

While running, we can open the Water-curse TAB and watch the Results.

There are results for the first iterations (The process is not finished yet).

IN (Blue)

LOG (Blue)

SCF.ene (2 iterations at this time – 21:38 ) Just a couple of minutes.

OPT-ene (14 iterations – 21:40 hrs ) Geometric Optimization

OPT.force (15 iterations – 21:41 hrs) Geometric Optimization ,Optimization is not converged?

Update: When optimization is not converged, it means that calculation has not finished yet.

OPT.movie – Formation of the water molecule (67 Iterations )

We put 4 hydrogen and 1 oxygen atom.
Burai and Quantum-Espresso made the simulation (calculation) to obtain the possible molecule formed at T = 0K, minimum of energy.
Converged at 68 iterations (22:14 ) near 45 minutes of analysis.