APE

Automatic process exploration (APE) logo

Automatic process exploration (APE) discovers elementary processes and the states they connect on a potential-energy surface. The exploration is guided by the diversity of local atomic environments.

The APE method is described in the original work cited below. These tutorials cover running APE using SODA’s parallel execution and data-collection infrastructure.

Start with installation and SODA basics if you need a build or an introduction to the runtime.

Examples

Follow an example using EAM or MACE to learn how to prepare and run an APE calculation.

Example

What you will do

Requirements

First exploration with EAM

Prepare Pd surface inputs, run a short exploration, and inspect states, processes, and local environments.

APE-enabled build, CPU cores, and the bundled Pd EAM potential.

Exploration with MACE

Set up MACE forces and descriptors, select a GPU build, and reuse the analysis steps.

Native MACE-enabled APE build, a compatible GPU/APU, and external model files.

Inputs live in the repository’s examples/ape/ directories. Each walkthrough points to the files to copy into a separate run directory; edit those copies for your calculation.

Tip

Before starting APE, optimize your input structures with the same potential or model you will use for exploration. Use the optimized structures as pos.con or pos.xyz (or the numbered pos0, pos1, … inputs), preserving the intended cell, periodic boundaries, and fixed atoms. Re-optimize when changing the potential.

More tutorials on choosing descriptors, tuning exploration, and interpreting kinetic networks are coming soon.

Settings and analysis

  • APE settings: short explanations of relevant config.ini entries and SODA command-line options.

  • Analyzing APE output: read states and processes, export structures, and query the local environments used by the DECAF classifier.

References

Lai, K. C., et al. “Automatic Process Exploration through Machine Learning Assisted Transition State Searches.” Physical Review Letters 134, 096201 (2025). doi:10.1103/PhysRevLett.134.096201.

Cite the APE work for the exploration method and SODA for the supporting infrastructure used in the calculation. See Citing SODA for the framework reference and references for the potential or model used.