Quickstart

PyAR helps you search chemically meaningful structures:

  • low-energy aggregates and clusters from fragments or formulas

  • AFIR-style reaction candidates from two reactants

  • microsolvation shells around a solute

  • bond scans between two fragments

If you want to see published chemistry problems that used these tasks, see Selected Publications.

See also

Selected Publications for a short list of papers that used PyAR in aggregation, reaction discovery, solvation-style growth, catalyst formation, and chemical-space exploration.

Install

python -m pip install .

For development:

python -m pip install -e .

Check the CLI

pyar-cli --help

Choose a chemistry task

Aggregate two one-atom fragments when you want to find low-energy dimer or cluster geometries:

pyar-cli aggregate C H -as 1 4 -N 8
pyar-cli -a C H -as 1 4 -N 8

Generate a starting aggregate directly from a formula when you already know the composition:

pyar-cli --aggregate --formula C5H4 -N 8

Run a reaction search when you want to explore bond formation or close-contact reaction pathways between two reactants:

pyar-cli react A.xyz B.xyz -N 8 -gmin 100 -gmax 1000 --software xtb
pyar-cli -r A.xyz B.xyz -N 8 -gmin 100 -gmax 1000 --software xtb

Scan a bond when you want a simple reaction-coordinate probe:

pyar-cli scan-bond 1 2 A.xyz B.xyz -N 8
pyar-cli --scan-bond 1 2 A.xyz B.xyz -N 8

Run a solvation search when you want to add units around a central core. Microsolvation is the classic case, but the same task is also useful for building coordination complexes, such as adding ligands to a transition metal center:

pyar-cli solvate solute.xyz solvent.xyz --software xtb -ss 10 -N 16
pyar-cli -s solute.xyz solvent.xyz --software xtb -ss 10 -N 16

Notes

  • In aggregate mode, bare element symbols such as C and H are accepted.

  • If --software is omitted for aggregate mode, PyAR generates trial geometries only and skips quantum-chemistry optimization.

  • --formula is only valid together with --aggregate.

  • Reaction runs with registered energy-gradient providers such as xtb and aimnet_2 use geomeTRIC/TRIC for AFIR-biased optimization, then use gamma=0.0 for product relaxation.