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
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:
- Create an xyz file using Qbox with the Qbox plot command (see the plot command description in the Qbox User Guide).
- Copy the xyz file to your laptop.
- 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
- Create a cube file using Qbox with the Qbox plot -density ... command (see the plot command description in the Qbox User Guide).
- Copy the cube file to your laptop.
- 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.
- Create a cube file using Qbox with the Qbox plot -wf ... command (see the plot command description in the Qbox User Guide).
- Copy the cube file to your laptop.
- 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