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atomistic-workflows

Sets up and reports atomistic calculations so they are reproducible and converged, covering ASE Atoms, calculators, optimizers and MD drivers, pymatgen structures, symmetry analysis and the Materials Project API, LAMMPS and GROMACS input basics for molecular dynamics, convergence tests for k-points, plane-wave cutoffs and timesteps, the unit system each code uses, energy-minimization stopping criteria, and archiving of exact input files. Use for DFT, classical or machine-learned potential simulations of molecules, crystals, surfaces and liquids; use molecular-dynamics for biomolecular trajectory analysis and pymatgen for detailed library usage.

backend/cli/skills/chemistry/atomistic-workflows/SKILL.md

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# Atomistic workflows

An atomistic number is defined only together with its code, units, convergence parameters
and stopping criteria; a "DFT energy" without k-mesh and cutoff cannot be reproduced.

## ASE

1. `Atoms(symbols, positions, cell, pbc)`; `ase.io.read` and `write` convert between
   formats (`read("traj.xyz", index=":")` for all frames). Internal units are eV and
   angstrom; `ase.units` supplies `fs`, `kB`, `Hartree` and `Bohr` for conversion (the
   native time unit is about 10.18 fs, so always multiply by `units.fs`). Attach a
   calculator with `atoms.calc = ...` (`EMT`, `ase.calculators.vasp.Vasp`,
   `espresso.Espresso`, `lammpslib.LAMMPSlib`, a machine-learned potential), then
   `get_potential_energy()`, `get_forces()`, `get_stress()` (eV per cubic angstrom).