Course: Electronic properties of semiconductors by AB-INITIO
Profesor: Dr. Raciel Jaimes López (Postdoctoral at IER-UNAM)
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Simulation of water molecule formation using Burai 1.3 and Quantum Espresso
Viewer by Jmol
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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)
- 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)
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Separate two atoms
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Right-click – put an atom
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Keep all the parameters.
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Save the project with a new name Example: Water-Curse
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- SCF (), configure PLANE WAVE
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SCF command for PlaneWave configuration
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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
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Optimize configuration
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Don’t change any configuration and save the project.
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- Run the simulation (Let’s see what happen).
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Run command: star simulation of 4 Hydrogen and 1 Oxygen atom
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Run a Job (# Processors and #Threats) For my computer 1 processor (MPI) and 2 Threats (OpenMP)
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HOME TAB: running indication in this tab (red color for calculation)
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Begin – 21:30 Hrs , Finish – ?
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Same window: Running unlist mode (There is no progress bar, indicator) How can we calculate spent time?
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While running, we can open the Water-curse TAB and watch the Results.
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There are results for the first iterations (The process is not finished yet).
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IN (Blue)
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LOG (Blue)
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SCF.ene (2 iterations at this time – 21:38 ) Just a couple of minutes.
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OPT-ene (14 iterations – 21:40 hrs ) Geometric Optimization
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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.
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OPT.movie – Formation of the water molecule (67 Iterations )
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- 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.
- Finished simulation (Convergence)
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SCF.ene (Convergence at 5 iterations)
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OPT.ene – Geometric optimization
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OPT.force – Geometric optimization
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- Analysis of optimized formed molecule H2O (water molecule)
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- Use a VIEWER to measure the distance from H to O atom.
- Measure the tetrahedral angle.
Expected:
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| 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
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espresso.log.opt is the file readable by Jmol.
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Measure distance between atoms. 0.097 nm (simulation ) vs 0.09584 nm (theory)
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Angle measurement with JMol: http://biomodel.uah.es/en/DIY/Jmol/help/inicio.en.htm
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Notes
Jesús Capistrán-Martínez
Web: https://www.jesuscapistran.com
e-mail: jecam@ier.unam.mx
Doctorate (2017) Energy Engieenering (UNAM-Mexico)
Web: https://www.jesuscapistran.com
e-mail: jecam@ier.unam.mx
Doctorate (2017) Energy Engieenering (UNAM-Mexico)
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