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.
This container includes a full materials science computation environment. Use these tools for atomistic simulation tasks.
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.pbe-n-kjpaw_psl.1.0.0.UPFCu.pbe-dn-kjpaw_psl.1.0.0.UPFAl.pbe-n-kjpaw_psl.1.0.0.UPFNi.pbe-n-kjpaw_psl.1.0.0.UPFO.pbe-n-kjpaw_psl.1.0.0.UPFC.pbe-n-kjpaw_psl.1.0.0.UPFH.pbe-kjpaw_psl.1.0.0.UPFN.pbe-n-kjpaw_psl.1.0.0.UPFFe.pbe-spn-kjpaw_psl.1.0.0.UPFTi.pbe-spn-kjpaw_psl.1.0.0.UPFZn.pbe-dn-kjpaw_psl.1.0.0.UPFBa.pbe-spn-kjpaw_psl.1.0.0.UPFLi.pbe-s-kjpaw_psl.1.0.0.UPFNa.pbe-spn-kjpaw_psl.1.0.0.UPFK.pbe-spn-kjpaw_psl.1.0.0.UPFExample 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
lmplmp -in input.lammpspair_style eam/alloy with potentials from OpenKIM or download from NISTpair_style lj/cut/coul/longraspa3cd /path/to/simulation && raspa3simulation.json, force_field.json, molecule JSON files)/usr/share/raspa3/examples/ (basic MC, adsorption, breakthrough, etc.)cp -r /usr/share/raspa3/examples/basic/1_mc_methane_in_box /tmp/my_sim
cd /tmp/my_sim && raspa3
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
pw.x < scf.in > scf.outfrom 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()
If the user has configured VASP access (run /add-vasp), use vasp-remote to execute VASP calculations:
vasp-remote run (submits to cluster or runs locally, waits for results)vasprun.xml with pymatgenCheck if VASP is available: vasp-remote config 2>/dev/null. If not configured, fall back to Method A (MACE) or Method B (QE).
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.
| 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 |
| 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 |
| 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) |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
cat ~/.claude/skills/<group>/<sub-skill>/SKILL.md