Course: Electronic properties of semiconductors by ABINITIO
Profesor: Dr. Raciel Jaimes López (Postdoctoral at IERUNAM)
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 ABInitio at IERUNAM, 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 opencode Quantum Espresso software which is used for electronicstructure calculation and materials modeling at nanoscale.
Here I share the methodology I follow for the example watermolecule
 Install BURAI1.3 on MAC (includes QuantumEspresso)
 Install MPI for MAC
 Open BURAI and choose examples/XYZ: Water molecule (H2O.xyz)
4. Move selected atoms and add two more hydrogen atoms (decompose de molecule)

Separate two atoms

Rightclick – put an atom

Keep all the parameters.

Save the project with a new name Example: WaterCurse

 SCF (), configure PLANE WAVE
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 Watercurse 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.

OPTene (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 QuantumEspresso 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.
 Finished simulation (Convergence)
SCF.ene (Convergence at 5 iterations)

OPT.ene – Geometric optimization

OPT.force – Geometric optimization

 Analysis of optimized formed molecule H2O (water molecule)

 Use a VIEWER to measure the distance from H to O atom.
 Measure the tetrahedral angle.
Expected:
URL: https://www.quora.com/Whyisntthewatermoleculelinear 
9.1 Files created on the watercurse project: Which is the water structure file?
9.2 Use Jmol (View) to open analysis
espresso.log.opt is the file readable by Jmol.

Measure distance between atoms. 0.097 nm (simulation ) vs 0.09584 nm (theory)

Angle measurement with JMol: http://biomodel.uah.es/en/DIY/Jmol/help/inicio.en.htm

Notes
Jesús CapistránMartínez
Web: https://www.jesuscapistran.com
email: jecam@ier.unam.mx
Doctorate (2017) Energy Engieenering (UNAMMexico)
Web: https://www.jesuscapistran.com
email: jecam@ier.unam.mx
Doctorate (2017) Energy Engieenering (UNAMMexico)