PESMaker Manual

PESMaker builds machine-learning potential datasets from structures you already care about: bulk phases, surfaces, defects, interfaces, and sampled MD frames.

Start Here

Most users should run:

pesmaker validate run.yaml
pesmaker next run.yaml

next is the workflow driver. It runs local PESMaker stages when they are ready, stops before real scheduler submission, and prints exactly what you should do next.

You do not need to remember the full stage chain for normal use.

Read These First

• Quick Start: the shortest practical usage loop.
• Workflow Guide: what next does and why it stops.
• Command Manual: one page per command.
• Minimal YAML Examples: small configs by task type.

Normal Flow

input structures
  -> generated structures
  -> optional GPUMD or LAMMPS-MACE sampling
  -> optional frame selection
  -> VASP SCF setup and submission
  -> extxyz dataset collection
  -> optional NEP training setup

next decides which part of this flow is active by reading the YAML sections and checking files such as generated/manifest.jsonl, sampling trajectories, OUTCAR, train.xyz, and training/submit.sh.

Manual Flow

Manual commands are still available:

pesmaker generate run.yaml
pesmaker sample-setup run.yaml
pesmaker select run.yaml
pesmaker scf-setup run.yaml
pesmaker submit run.yaml
pesmaker collect run.yaml
pesmaker train-setup run.yaml

Use them when you want to debug one stage. Use next when you want the simpler workflow.