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The Atomistic Cookbook
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The Atomistic Cookbook
  • Recipes grouped by topic
    • Statistical sampling and dynamics
    • Analysis and post-processing
    • Machine learning models
    • Universal ML models
    • Nuclear quantum effects
  • Recipes grouped by software used
    • chemiscope
    • cp2k
    • eon
    • featomic
    • GROMACS
    • i-PI
    • kALDo
    • LAMMPS
    • metatensor
    • PLUMED
    • scikit-matter
    • torch-pme
  • List of all recipes
    • A Guide to PET-MAD-DOS: Model Inference and Fine-Tuning
    • A ML model for the electron density of states
    • Atomistic Water Model for Molecular Dynamics
    • Batch run of CP2K calculations
    • Computing NMR shielding tensors using ShiftML
    • Conservative fine-tuning for a PET model
    • Constant-temperature MD and thermostats
    • Equivariant linear model for polarizability
    • Equivariant model for tensorial properties based on scalar features
    • Finding Reaction Paths with eOn and a Metatomic Potential
    • Fine-tuning the PET-MAD universal potential
    • Generalized Convex Hull construction for the polymorphs of ROY
    • Geometry relaxation with unconstrained MLIPs
    • Hamiltonian Learning for Molecules with Indirect Targets
    • Learning Capabilities with torchpme
    • Local Prediction Rigidity analysis
    • Long-distance Equivariants: a tutorial
    • Long-stride trajectories with a universal FlashMD model
    • MD using direct-force predictions with PET-MAD
    • ML collective variables in PLUMED with metatomic
    • ML/MM Simulations with GROMACS and Metatomic
    • Mendeleev clusters
    • Multiple time stepping and ring-polymer contraction
    • PCA/PCovR Visualization of a training dataset for a potential
    • Path integral metadynamics
    • Path integral molecular dynamics
    • Periodic Hamiltonian learning
    • Phonon dispersions with unconstrained models and uncertainty quantification
    • Quantum heat capacity of water
    • Ring Polymer Instanton Rate Theory: Tunneling Rates
    • Rotating equivariants
    • Sample and Feature Selection with FPS and CUR
    • The PET-MAD universal potential
    • Thermal conductivity from the Boltzmann transport equation
    • Uncertainty Quantification with PET-MAD
    • Water orientation in a pulsed electric field
  • Downloading and running the recipes
  • Contributing a recipe
    • Shared utilities
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All modules for which code is available

  • atomistic_cookbook_utils._command
  • atomistic_cookbook_utils._download
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