majiayu000 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(alsoph.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.outPseudopotentials download URL:
https://pseudopotentials.quantum-espresso.org/upf_files/<FILENAME>.UPFCommon 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.UPFAlternative sources: SSSP or PseudoDojo
- Si:
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/alloywith 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)
- Prepare structure (use pymatgen to read CIF/POSCAR and generate QE input)
- Download pseudopotentials
- Run SCF calculation:
pw.x < scf.in > scf.out - Post-process: bands, DOS, charge density, etc.
MD Simulation (LAMMPS or ASE+MACE)
- Prepare structure and force field
- Set up LAMMPS input or ASE calculator
- Run simulation
- 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:
- Generate INCAR, POSCAR, KPOINTS, POTCAR in the current directory
- Run:
vasp-remote run(submits to cluster or runs locally, waits for results) - Parse
vasprun.xmlwith 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)
- Prepare framework structure (CIF)
- Configure simulation input (guest molecules, temperature, pressure)
- Run RASPA3
- Analyze adsorption isotherm
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
- Identify the relevant skill from the index above
- Read the SKILL.md:
cat ~/.claude/skills/<group>/<sub-skill>/SKILL.md - Choose method: Method A (ASE+MACE, fast) or Method B (QE DFT, accurate) or Method C (VASP)
- Follow the step-by-step code in the SKILL.md — all code is complete and runnable
- Check the "Common Issues" table at the bottom if anything goes wrong