materials-compute

name	materials-compute
description	Materials computation environment reference and skill index. READ THIS FIRST when performing any materials science calculation — contains the master index of all 221 skills across 44 groups.

Materials Computation Environment

This container includes a full materials science computation environment. Use these tools for atomistic simulation tasks.

Available Computation Engines

Quantum ESPRESSO 7.5 (DFT)

• Binary: pw.x (also ph.x, pp.x, bands.x, dos.x, projwfc.x, etc.)

• Location: /opt/qe/bin/

• Use for: electronic structure, band gaps, density of states, phonons, elastic constants

• Run with MPI: mpirun --allow-run-as-root -np N pw.x < input.in > output.out

• Pseudopotentials download URL:

  https://pseudopotentials.quantum-espresso.org/upf_files/<FILENAME>.UPF
  

  Common pseudopotentials (PAW PBE from pslibrary):

  • Si: Si.pbe-n-kjpaw_psl.1.0.0.UPF
  • Cu: Cu.pbe-dn-kjpaw_psl.1.0.0.UPF
  • Al: Al.pbe-n-kjpaw_psl.1.0.0.UPF
  • Ni: Ni.pbe-n-kjpaw_psl.1.0.0.UPF
  • O: O.pbe-n-kjpaw_psl.1.0.0.UPF
  • C: C.pbe-n-kjpaw_psl.1.0.0.UPF
  • H: H.pbe-kjpaw_psl.1.0.0.UPF
  • N: N.pbe-n-kjpaw_psl.1.0.0.UPF
  • Fe: Fe.pbe-spn-kjpaw_psl.1.0.0.UPF
  • Ti: Ti.pbe-spn-kjpaw_psl.1.0.0.UPF
  • Zn: Zn.pbe-dn-kjpaw_psl.1.0.0.UPF
  • Ba: Ba.pbe-spn-kjpaw_psl.1.0.0.UPF
  • Li: Li.pbe-s-kjpaw_psl.1.0.0.UPF
  • Na: Na.pbe-spn-kjpaw_psl.1.0.0.UPF
  • K: K.pbe-spn-kjpaw_psl.1.0.0.UPF

  Example download:

  wget -q https://pseudopotentials.quantum-espresso.org/upf_files/Si.pbe-n-kjpaw_psl.1.0.0.UPF -O Si.UPF
  

  Alternative sources: SSSP or PseudoDojo

LAMMPS (Molecular Dynamics)

• Binary: lmp
• Use for: MD simulations, thermal properties, diffusion, mechanical properties
• Supports OpenKIM potentials (pre-installed)
• Run: lmp -in input.lammps
• EAM potentials: use pair_style eam/alloy with potentials from OpenKIM or download from NIST
• For water: use SPC/E or TIP3P model with pair_style lj/cut/coul/long

RASPA3 (Monte Carlo)

• Binary: raspa3
• Use for: gas adsorption in porous materials (MOFs, zeolites), adsorption isotherms, Henry constants
• Run: cd /path/to/simulation && raspa3
• Input format: JSON files (simulation.json, force_field.json, molecule JSON files)
• Official examples: /usr/share/raspa3/examples/ (basic MC, adsorption, breakthrough, etc.)
• IMPORTANT: Always copy an official example as starting point and modify it:

  cp -r /usr/share/raspa3/examples/basic/1_mc_methane_in_box /tmp/my_sim
  cd /tmp/my_sim && raspa3
  

Python Materials Science Stack

Pre-installed in base conda environment:

• pymatgen: Crystal structure manipulation, phase diagrams, electronic structure analysis
• ASE (Atomic Simulation Environment): Atoms objects, calculators, optimization, MD
• mp-api: Materials Project API access (needs API key)
• MACE-torch: Universal machine learning interatomic potential
• spglib: Space group analysis
• torch: PyTorch (CPU version)
• numpy / scipy / matplotlib: Scientific computing and visualization

Conda/pip available:

The agent can install additional packages as needed:

# Create isolated environment for specific tasks
conda create -n myenv python=3.11 -y
conda activate myenv

# Install additional ML potentials
pip install chgnet sevenn

# Install workflow managers
pip install fireworks jobflow atomate2

Common Workflows

DFT Calculation (QE)

1. Prepare structure (use pymatgen to read CIF/POSCAR and generate QE input)
2. Download pseudopotentials
3. Run SCF calculation: pw.x < scf.in > scf.out
4. Post-process: bands, DOS, charge density, etc.

MD Simulation (LAMMPS or ASE+MACE)

1. Prepare structure and force field
2. Set up LAMMPS input or ASE calculator
3. Run simulation
4. Analyze trajectory: RDF, MSD, thermal conductivity, etc.

MLIP Calculation (ASE + MACE)

from ase.io import read
from mace.calculators import mace_mp
calc = mace_mp(model="medium", device="cpu")
atoms = read("structure.cif")
atoms.calc = calc
energy = atoms.get_potential_energy()
forces = atoms.get_forces()

VASP (via vasp-remote)

If the user has configured VASP access (run /add-vasp), use vasp-remote to execute VASP calculations:

1. Generate INCAR, POSCAR, KPOINTS, POTCAR in the current directory
2. Run: vasp-remote run (submits to cluster or runs locally, waits for results)
3. Parse vasprun.xml with pymatgen

Check if VASP is available: vasp-remote config 2>/dev/null. If not configured, fall back to Method A (MACE) or Method B (QE).

Monte Carlo (RASPA3)

1. Prepare framework structure (CIF)
2. Configure simulation input (guest molecules, temperature, pressure)
3. Run RASPA3
4. Analyze adsorption isotherm

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Skill Reference Index

IMPORTANT: Before performing any materials science computation, check the relevant skill guide below. Each skill provides complete, runnable code for three approaches: ASE+MACE (fast screening), QE DFT (accurate), and VASP (future external). Read the SKILL.md in the skill directory for step-by-step instructions.

Skills are located at ~/.claude/skills/<group>/<sub-skill>/SKILL.md.

Structure & Symmetry

Skill Group	Sub-skills	Use For
structure-tools	input-generation, structure-editing, symmetry-analysis, format-conversion, structure-matching, xrd-pattern, pdf-analysis, advanced-optimization	VASP/QE input files, editing structures, symmetry finding, format conversion, advanced structure optimization
structure-models	supercell-builder, surface-builder, alloy-builder, defect-builder, heterostructure, nanowire-nanotube, quantum-dot, moire-superlattice	Build supercells, surfaces, alloys, defects, heterostructures, nanowires, quantum dots, moire patterns
kpath-utilities	bulk-kpath, 2d-kpath, 1d-kpath, phonopy-kpath, cp2k-kpath	K-point paths for band structure in any code

Electronic Structure

Skill Group	Sub-skills	Use For
electronic-structure	scf-relax, band-structure, density-of-states, projected-dos, spatially-resolved-dos, vasp-bands, convergence-testing, inverse-participation-ratio	SCF, relaxation, band structure, DOS, PDOS, IPR, convergence tests
band-advanced	3d-band-structure, hybrid-dft-bands, band-unfolding	3D bands, HSE/PBE0 bands, supercell band unfolding
fermi-surface	3d-fermi-surface, 2d-fermi-surface, projected-fermi-surface	Fermi surface visualization (bulk and 2D)
advanced-electronic	hubbard-u, spin-orbit-coupling, gw-approximation, van-der-waals, topological-invariants	DFT+U, SOC, GW, vdW-DF, Z2 invariants

Mechanical & Thermal Properties

Skill Group	Sub-skills	Use For
mechanical-properties	elastic-constants, stress-strain-method, energy-strain-method, equation-of-state, angular-mechanics	Elastic tensor, bulk/shear modulus, EOS, angular-dependent mechanics
thermal-properties	phonon, phonon-from-outcar, molecular-dynamics, msd-diffusion, rdf-analysis, vacf-vdos, md-trajectory-tools, bond-distribution, gruneisen-qha, thermal-conductivity, anharmonicity, free-energy-calculation, quasi-harmonic-debye	Phonons, MD analysis, MSD, RDF, VDOS, bond distributions, QHA, thermal conductivity, free energy, Debye model
thermoconductivity	lattice-thermal-conductivity	Lattice thermal conductivity (BTE)

Bonding & Charge Analysis

Skill Group	Sub-skills	Use For
bonding-analysis	charge-density, charge-density-difference, planar-charge, bader-charge, bader2pqr, elf-analysis, lobster-cohp, orbital-projection, stm-simulation, charge-format-conversion	Charge density, CDD, Bader, ELF, COHP, orbital projections, STM simulation
potential-analysis	work-function, planar-average, macroscopic-average	Work function, planar/macroscopic averaged potential
wavefunction-analysis	real-space-wavefunction, wavefunction-parity	Real-space wavefunction visualization, parity analysis

Optical, Magnetic & Transport

Skill Group	Sub-skills	Use For
optical-properties	dielectric-function, absorption-spectrum, optical-conductivity, joint-dos, transition-dipole, slme	Dielectric function, absorption, optical conductivity, JDOS, SLME
magnetic-properties	magnetic-anisotropy, magnetic-ordering, spin-polarized	MAE, magnetic ground state, spin-polarized calculations
spin-texture	2d-spin-texture, 3d-spin-texture	Spin texture for 2D/3D materials with SOC
transport-properties	boltzmann-transport, kpoints-transport	Boltzmann transport (BoltzTraP), transport k-meshes
electron-phonon	elph-coupling, superconductivity, deformation-potential, electronic-transport	Electron-phonon coupling, Tc, deformation potentials

Ferroelectric & Piezoelectric

Skill Group	Sub-skills	Use For
ferroelectric	polarization, born-effective-charge, dielectric-tensor, piezoelectric, ferroelectric-switching	Berry phase polarization, Born charges, dielectric tensor, piezoelectric tensor
piezoelectric	piezoelectric-tensor	Piezoelectric constants from DFPT

Catalysis & Defects

Skill Group	Sub-skills	Use For
catalysis-electrochem	thermal-corrections, neb-analysis, band-center, reaction-kinetics, imaginary-freq-correction, implicit-solvation	Adsorbate thermodynamics, NEB, d-band center, Arrhenius kinetics, imaginary freq fix, solvation effects
catalyst-screening	d-band-center, scaling-relations, overpotential	D-band theory, adsorption scaling, OER/HER overpotential
defects-reactions	vacancy-formation, substitution-defect, interstitial-defect, point-defect, defect-thermodynamics, migration-barrier, neb-transition-state, reaction-pathway, adsorption-energy, surface-adsorption, surface-energy, configuration-coordinate, activation-relaxation-technique	Point defects, formation energies, NEB barriers, adsorption, surface energy, CC diagrams, ART saddle point search
surface-energy	surface-energy-calc, wulff-construction	Surface energy convergence, Wulff shape

2D Materials & Semiconductors

Skill Group	Sub-skills	Use For
2d-materials	vacuum-resize, layer-manipulation, band-edges, stacking-energy	Vacuum control, layer centering, band alignment, stacking PES (gamma surface)
semiconductor-kit	band-gap, effective-mass, angular-effective-mass, fermi-velocity	Band gap, effective mass (isotropic & angular), Fermi velocity

Monte Carlo & Phase Diagrams

Skill Group	Sub-skills	Use For
monte-carlo	gcmc-simulation, adsorption-isotherm, gas-adsorption, gas-separation, pore-analysis	GCMC with RASPA3, isotherms, selectivity, pore size distribution
phase-diagram	convex-hull, pourbaix-diagram	Thermodynamic convex hull, Pourbaix diagrams
phase-transition	phase-diagram, mpmorph-melting, order-parameter, amorphous-structure, melting-point-coexistence, metadynamics	Phase boundaries, melting point, order parameters, amorphous structures, coexistence method, metadynamics FES
alloy-disorder	cluster-expansion, sqs-generation	Cluster expansion, special quasirandom structures

Code Interfaces & MLIP

Skill Group	Sub-skills	Use For
code-interfaces	vasp-qe-converter, boltztrap-interface, phonopy-interface, wannier90-interface, ifc-analysis	VASP↔QE conversion, BoltzTraP, phonopy, Wannier90, IFC tensors
wannier-functions	wannier90-workflow	Wannier90 tight-binding from DFT
mlip-guide	universal-mlip, mace-advanced, mlip-validation, torchsim-batch	MACE-MP-0 usage, fine-tuning, validation against DFT, batch screening

Other

Skill Group	Sub-skills	Use For
battery-electrode	intercalation-voltage, ion-diffusion	Battery voltage profiles, ion migration barriers
topological	z2-invariant, berry-curvature	Z2 topological invariant, Berry curvature
spectroscopy	raman-ir, xas-xanes	Raman/IR spectra, XAS/XANES simulation
dft-corrections	hubbard-u, spin-orbit-coupling, vdw-correction	When and how to apply DFT corrections
high-throughput	screening-workflow, batch-calculations, batch-screening, materials-filtering, phase-stability, property-prediction, matpes-dual-static, convergence-automation	High-throughput screening, batch computation, automated convergence testing
materials-databases	materials-project, 2d-semiconductors	Query Materials Project, 2D materials databases
interface	heterostructure, grain-boundary	Heterostructure and grain boundary construction
biomolecular-md	openmm-simulation	Biomolecular MD with OpenMM
molecular-qchem	gaussian-qchem-workflow	Molecular quantum chemistry workflows

How to Use a Skill

1. Identify the relevant skill from the index above
2. Read the SKILL.md: cat ~/.claude/skills/<group>/<sub-skill>/SKILL.md
3. Choose method: Method A (ASE+MACE, fast) or Method B (QE DFT, accurate) or Method C (VASP)
4. Follow the step-by-step code in the SKILL.md — all code is complete and runnable
5. Check the "Common Issues" table at the bottom if anything goes wrong