Home

ECS289K Introduction to Quantum Simulations

Instructor: Francois Gygi, Professor, Department of Computer Science, UC Davis

This class provides a hands-on introduction to modern methods of atomic-scale quantum simulations for atoms, molecules, solids and liquids. Quantum simulations of materials rely on fundamental physical principles, including a quantum mechanical description of electronic structure. They have become an important research tool in chemistry, physics and materials science.

Useful links

• ECS 30 Unix Tutorial [PDF]
• Quantum Espresso web site
• Quantum Espresso input data description
• VMD visualization program
• Avogadro molecule building program"
• Qbox first-principles molecular dynamics code
• qbox-1.63.2.tgz
• Qbox Documentation
• SG15 ONCV pseudopotentials for Qbox
• gnuplot-4.4.2.tar.gz
• NIST Computational Chemistry Comparison and Benchmark DataBase (CCCBDB)

Lecture slides

Lecture slides will be posted on Canvas.

Precompiled Qbox for CSIF

Qbox for CSIF-Ubuntu is located in /home/cs289kfg/public/qbox

Use the file /home/cs289kfg/public/install_qbox.sh to in install Qbox in your home directory

In an interactive CSIF session, use " . qbox_setup.sh" to initialize your PATH environment variable

Examples

• Harmonic oscillator harmonic.tgz
• Hydrogen molecule QE h2.tgz
• Silicon cluster Si4 QE si4.tgz
• Silicon band structure QE sibands.tgz
• Silicon 8-atom cell band structure QE si8bands.tgz
• Silicon vacancy in 8-atom cell QE si7bands.tgz
• Silicon energy vs cell size QE sicell.tgz
• Qbox first-principles molecular dynamics (FPMD) of Si₄ fpmd.tgz
• Qbox first-principles molecular dynamics (FPMD) of (H₂O)₃₂ h2o32.tgz
• Qbox first-principles molecular dynamics (FPMD) of liquid silicon (Si₆₄) si64liq.tgz
• Qbox Maximally Localized Wannier Functions (MLWF) in C₆₀ mlwf.tgz
• Qbox vibrational spectrum of CH₄ from diagonalization of the dynamical matrix ch4dynmat.tgz
• Qbox vibrational spectrum of CH₄ from MD simulations ch4vib.tgz

Tools

• A simple command-line reverse polish notation (RPN) calculator calc.C
• A unit conversion program convert.tgz
• Conversion from xyz format to Qbox input xyz_to_sys.py
• Conversion from Qbox output to xyz format qbox_xyz.py
• VMD script for CPK representation of a molecule: cpk.vmd
  Use: vmd -e cpk.vmd -f file.xyz
• VMD script for representation of the charge density: density.vmd (updated 2016-05-06T20:33:03Z)
  Use: vmd -e density.vmd -f file.cube
• VMD script for representation of an orbital: orb.vmd (updated 2016-05-06T20:33:03Z)
  Use: vmd -e orb.vmd -f file.cube
• A program to compute pair correlation functions: gofr.tgz
  

Miscellaneous information

• Visualization of a molecule using VMD on your laptop:
  
  1. Create an xyz file using Qbox with the Qbox plot command (see the plot command description in the Qbox User Guide).
  2. Copy the xyz file to your laptop.
  3. Use VMD on your laptop to visualize the structure, using the cpk.vmd script: (see the Tools section above)
     vmd -e cpk.vmd file.xyz
     
  Visualization of a charge density on your laptop:
  
  1. Create a cube file using Qbox with the Qbox plot -density ... command (see the plot command description in the Qbox User Guide).
  2. Copy the cube file to your laptop.
  3. Use VMD on your laptop to visualize the density, using the density.vmd script: (see the Tools section above)
     vmd -e density.vmd file.xyz
     If needed, adjust the isosurface levels in the Graphics->Representations window.
  Visualization of an orbital on your laptop:
  
  1. Create a cube file using Qbox with the Qbox plot -wf ... command (see the plot command description in the Qbox User Guide).
  2. Copy the cube file to your laptop.
  3. Use VMD on your laptop to visualize the orbital, using the orb.vmd script: (see the Tools section above)
     vmd -e orb.vmd file.xyz
     If needed, adjust the isosurface levels in the Graphics->Representations window.

Topics covered:

• Basic electronic structure theory
• Introduction to Density Functional Theory
• Electronic structure of atoms, molecules and solids
• Pseudopotentials and the plane wave formalism
• First-principles molecular dynamics
• Hands-on exercises using the QuantumEspresso electronic structure code and the Qbox first-principles molecular dynamics code
• Band structure calculations
• Simulation of vibrational spectra
• Computation of formation energies
• Structure optimization
• Visualization of electronic charge density and orbitals