Tutorials

• First steps through pyiron
  • Perform a LAMMPS MD simulation
  • Analyze the calculation
  • Perform a series of jobs
  • Create a series of projects
• Energy volume curve
  • Theory
  • Initialisation
  • Atomistic structure
  • Measure energies by looping over different volumes
    • Launch calculations
    • Analyse results
  • Murnaghan Job
  • Analysis
  • Energy cut-off dependence
• Creating structures in pyiron
  • Bulk crystals
    • Using create_structure()
    • Using create_ase_bulk()
  • Creating surfaces (using ASE)
  • Creating structures without importing the project class
    • Using the ASE spacegroup class
  • Accessing the properties of the structure object
  • Point defects
    • Creating a single vacancy
    • Creating multiple vacancies
    • Random substitutial alloys
  • Explicit definition of the structure
  • Importing from cif/other file formats
• Data mining using pyiron tables
  • Creating a dummy job to get list of potentials
  • Creating a Murnaghan job for each potential in their respective subprojects
  • Analysis using PyironTables
    • Defining filter functions
    • Defining functions that act on jobs
    • Creating a pyiron table
• Phonopy in pyiron
  • Helper functions
  • Thermal Expansion
    • Relax the unit cell
    • Relax the bulk supercell
    • Calculate phonons
    • Calculate thermal expansivity
  • Vacancies and diffusion
    • Stable vacancy structures
    • DOS
    • Attempt frequency
• Workfunction of hcp (0001) surfaces
  • Calculating the Workfunction of Mg(0001)
    • Structure creation
    • Using selective dynamics
    • Setup and execution
    • Submitting to the queue (optional)
    • Choosing an appropriate executable
    • Execution
    • Post processing
  • Looping over a series of hcp(0001) surfaces
    • Loading and analyzing
    • Compiling data in a table using pandas
• Molecular dynamics simulations of bulk water
  • Creating the initial structure
  • Equilibrate water structure
  • Full equilibration
  • Structure analysis
    • Distribution of the O-H bond length
    • Distribution of the O-O bond lengths
• Importing finished VASP calculations