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
  1. Install  BURAI1.3 on MAC (includes Quantum-Espresso)
  2. Install MPI for MAC
  1. 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
  1. 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

  1. Optimize: Open optimize section and don’t change anything and save the project
Optimize configuration
Don’t change any configuration and save the project.

  1. 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.

  1. Finished simulation (Convergence)
SCF.ene (Convergence at 5 iterations)
OPT.ene  – Geometric optimization
OPT.force  – Geometric optimization

  1. 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/Why-isnt-the-water-molecule-linear
9.1 Files created on the water-curse 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)

Notes

Jesús Capistrán-Martínez
Web: https://www.jesuscapistran.com
e-mail: jecam@ier.unam.mx
Doctorate (2017) Energy Engieenering (UNAM-Mexico)

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