MEPD

Minimum Energy Path Discovery tools for efficient reaction path calculations.

This repository contains:

• NEB and related path minimizers
• MLPGI path support
• MSMEP recursive path splitting
• elementary-step analysis utilities

Installation

pip install "git+https://github.com/mtzgroup/mepd.git"

For local development:

uv sync
uv run pytest

Quick Start

from mepd import Chain, ChainInputs, NEB, NEBInputs, StructureNode
from mepd.engines.qcop import QCOPEngine
from mepd.optimizers.cg import ConjugateGradient
import mepd.chainhelpers as ch
from qcio import Structure

start = Structure.from_xyz("start.xyz")
end = Structure.from_xyz("end.xyz")

engine = QCOPEngine(compute_program="chemcloud")

start_node = StructureNode(structure=start)
end_node = StructureNode(structure=end)
start_opt = engine.compute_geometry_optimization(start_node)[-1]
end_opt = engine.compute_geometry_optimization(end_node)[-1]

chain = Chain.model_validate({
    "nodes": [start_opt, end_opt],
    "parameters": ChainInputs(k=0.1, delta_k=0.09),
})
initial_chain = ch.run_geodesic(chain, nimages=15)

neb = NEB(
    initial_chain=initial_chain,
    parameters=NEBInputs(v=True),
    optimizer=ConjugateGradient(timestep=0.5),
    engine=engine,
)
result = neb.optimize_chain()

CLI

The public CLI exposes path minimization and NEB refinement commands:

mepd run --start start.xyz --end end.xyz --inputs inputs.toml
mepd run-refine examples/oxycope.xyz -i expensive.toml -ci cheap.toml --mode neb
mepd refine previous_result.xyz --inputs expensive.toml --mode neb
mepd make-default-inputs --name inputs.toml
mepd-elementarystep path.xyz

Use the Python API for lower-level NEB, MLPGI, MSMEP, and elementary-step workflows.

Maintainers

For questions, contact:

• Jan