Ase

Claude Plugin for CompChem , Drug Discovery & Organic Chemistry reasoning

Install

npx -y skills add Kdevos12/ALKYL --skill ase

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Use when working with ASE (Atomic Simulation Environment) for atomistic simulations. Covers structure building, geometry optimization, molecular dynamics, NEB/transition states, vibrational analysis, and calculator interfaces (ORCA, xTB, GPAW, LAMMPS).

SKILL.md

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ASE — Atomic Simulation Environment

ASE 3.24.0 (December 2024). Central object: Atoms. Calculators are decoupled — swap between EMT, xTB, ORCA, GPAW without changing workflow.

When to Use This Skill

Building and manipulating atomic structures (molecules, surfaces, bulk, slabs)
Geometry optimization (DFT, semi-empirical, force fields)
Molecular dynamics: NVE, NVT (Langevin, Berendsen), NPT
Transition state search: NEB, climbing image, AutoNEB
Vibrational analysis, IR spectra, zero-point energy, thermochemistry
Interfacing with ORCA, GPAW, xTB, VASP, LAMMPS, Quantum ESPRESSO
Reading/writing structure files: CIF, XYZ, TRAJ, SDF, PDB, VASP POSCAR

Quick Start

from ase import Atoms
from ase.build import molecule
from ase.calculators.emt import EMT
from ase.optimize import BFGS

# Build water molecule
atoms = molecule('H2O')
atoms.calc = EMT()  # fast toy calculator

# Geometry optimization
opt = BFGS(atoms, trajectory='h2o.traj', logfile='opt.log')
opt.run(fmax=0.05)  # eV/Å convergence criterion

print(atoms.get_potential_energy())  # eV
print(atoms.get_forces())            # eV/Å

Router — What to Read

Task	Reference
Atoms object, cell, PBC, building molecules/surfaces/bulk	`references/atoms-structures.md`
Calculators: EMT, ORCA, xTB, GPAW, LAMMPS, config	`references/calculators.md`
Geometry optimization, constraints, filters, unit cells	`references/optimization.md`
Molecular dynamics: NVE/NVT/NPT, thermostats, trajectories	`references/molecular-dynamics.md`
NEB, climbing image, IDPP, AutoNEB, barrier extraction	`references/neb-transitions.md`
Vibrations, phonons, IR, ZPE, thermochemistry	`references/vibrations-analysis.md`

Key Modules

Module	Import	Role
`Atoms`	`from ase import Atoms`	Core structure object
`units`	`from ase import units`	Unit conversions (eV, Å, fs…)
`io`	`from ase import io`	Read/write all formats
`build`	`from ase.build import …`	molecule, bulk, surface, slab
`optimize`	`from ase.optimize import BFGS, FIRE, LBFGS`	Geometry optimizers
`md`	`from ase.md.verlet import VelocityVerlet`	Molecular dynamics
`mep`	`from ase.mep import NEB, DyNEB`	Minimum energy paths
`vibrations`	`from ase.vibrations import Vibrations`	Normal modes
`phonons`	`from ase.phonons import Phonons`	Phonon dispersion
`constraints`	`from ase.constraints import FixAtoms, FixBondLength`	Constraints
`filters`	`from ase.filters import ExpCellFilter, FrechetCellFilter`	Cell optimization
`db`	`from ase.db import connect`	ASE database

Installation

pip install ase          # latest (3.24.0+)
conda install -c conda-forge ase

# Verify
python -c "import ase; print(ase.__version__)"

Unit Conversions

from ase import units

units.eV           # 1.0 (internal unit)
units.Hartree      # 27.2114 eV
units.kcal / units.mol  # 0.04336 eV
units.fs           # femtosecond in ASE time units
units.bar          # pressure
units.Bohr         # 0.529177 Å

Related Skills

ase + scientific-skills:rowan — cloud QM (DFT, pKa) for heavy calculations
ase + scientific-skills:pymatgen — materials/crystallography workflows
scripts: chem_qm.py — ORCA/Gaussian input gen + output parsing
scientific-skills:biopython — PDB structure loading for biomolecular systems