Advanced topics

In this section you can find scripts that illustrate the use of icet for advanced applications. The scripts and database that are used in the following sections can be downloaded as a single zip archive. To this end, run the following command from the command line:

curl -O https://icet.materialsmodeling.org/advanced_topics.zip
unzip advanced_topics.zip

Structure generation

• Structure enumeration
  • Import modules
  • Generate binary structures
  • Generate binary structures in the dilute limit
  • Generate structures with vacancies
  • Generate surface slabs with adsorbates
  • Source code
• Generating training structures
  • Import modules
  • Set up the cluster space
  • Generate a pool of random structures
  • Running the structure annealing
  • Source code
• Mapping structures
  • Import modules
  • Prepare dummy structures
  • Map relaxed structure onto ideal structure
  • Structures with vacancies
  • Source code
• Special quasirandom structures
  • Import modules
  • Generate binary SQS cells
  • Generate SQS cells by enumeration
  • Generate SQS cells for a system with sublattices
  • Generate a structure matching an arbitrary cluster vector
  • Source code
• Cluster vectors
  • Import modules
  • Generate prototype structure
  • Initialize cluster space
  • Cluster vector for monoelemental supercell
  • Cluster vector for alloy supercell
  • Source code

CE construction

• Training of cluster expansions
  • Selecting cutoffs
    • Setup
    • Scan pair cutoff
    • Plot results of pair cutoff scan
    • Third-order cutoff
    • Fourth-order cutoff
  • Hyper-parameter scans
    • Preparations
    • ARDR: Hyperparameter scan
    • RFE: Hyperparameter scan
    • LASSO: Hyperparameter scan
    • Adaptive-LASSO: Hyperparameter scan
    • Plot results
  • EnsembleOptimizer
    • Uncertainty predictions for structures
• Training with constraints and weights
  • Exact constraints
  • Weighted constraints
• Bayesian cluster expansions
  • Setting up a cluster space
  • Setting up the inverse covariance matrix
  • Training a cluster expansion
• Customizing cluster spaces
  • A motivating example
  • Inspecting orbits
  • Merging orbits
• Constituent strain calculations
  • Define \(\Delta E_\text{CS} (\hat{\mathbf{k}}, c)\)
  • Fit a cluster expansion with strain
  • Run Monte Carlo with strain cluster expansions
  • Source code

Sampling CEs

• Data container
  • Accessing a data container
  • Extracting data
  • Updating data container
  • Data analysis
• Hybrid ensembles
  • Controlling the species and sites involved
• Wang-Landau simulations
  • Background
  • 2D Ising model
  • Running a WL simulation
  • Analyzing a WL simulation
  • Representative configurations
  • Size-dependence of transition temperature
  • Parallelizing Wang-Landau simulations
  • Further tips
  • Source code
• Thermodynamic integration and temperature-integration simulations
  • Background
  • 2D Ising model
  • Running a TI simulation
  • Running a TEI simulation
  • Comparing with the analytical solution
  • Source code
• Parallel Monte Carlo simulations
  • Source code