Mlip Simulation

MLIP Simulation Skill

Run molecular dynamics and materials calculations using Machine Learning Interatomic Potentials (MLIPs) - achieving near-DFT accuracy at classical MD cost.

Trigger: Use when asked to run simulations with ML potentials, universal potentials, MACE, CHGNet, M3GNet, or when DFT would be too expensive but accuracy matters.

When to Use This vs torch-sim

This skill uses ASE (Atomic Simulation Environment) as the backend. For high-throughput screening (10+ structures), consider using the torch-sim skill instead:

Rule of thumb: For batch operations on many structures, use torch-sim. For single structures or learning, use this ASE-based approach.

See the torch-sim skill for high-throughput patterns.

Available Universal Potentials

MACE-MP-0 (Recommended for General Use)

• Accuracy: Highest among universal potentials
• Parameters: 4.7M (largest model)
• Coverage: 89 elements
• Best for: General property prediction, phonons, surfaces

CHGNet

• Accuracy: Good, includes magnetic moments
• Parameters: ~400K (smallest, fastest)
• Best for: Batteries, Li-ion systems, charged species, oxidation states

M3GNet

• Accuracy: Good generalization
• Parameters: ~200K
• Best for: Fast screening, structure relaxation

SevenNet

• Accuracy: Best for phonons
• Best for: Phonon calculations, vibrational properties

Installation

# MACE (requires PyTorch with CUDA)
pip install mace-torch

# MatGL (M3GNet, CHGNet)
pip install matgl

# ASE (required for all)
pip install ase

# Phonopy (for phonon calculations)
pip install phonopy

# PyMatGen (structure manipulation)
pip install pymatgen

Basic Usage with ASE

Loading Models

from ase import Atoms
from ase.build import bulk

# MACE
from mace.calculators import mace_mp
calc_mace = mace_mp(model="medium", device="cuda")  # or "cpu"

# CHGNet
from chgnet.model import CHGNetCalculator
calc_chgnet = CHGNetCalculator()

# M3GNet
import matgl
from matgl.ext.ase import M3GNetCalculator
pot = matgl.load_model("M3GNet-MP-2021.2.8-PES")
calc_m3gnet = M3GNetCalculator(pot)

Single-Point Calculation

from ase.build import bulk

# Create structure
atoms = bulk('Cu', 'fcc', a=3.6)

# Attach calculator
atoms.calc = calc_mace

# Get energy and forces
energy = atoms.get_potential_energy()
forces = atoms.get_forces()
stress = atoms.get_stress()

print(f"Energy: {energy:.4f} eV")
print(f"Forces shape: {forces.shape}")

Structure Relaxation

from ase.optimize import BFGS

atoms = bulk('Si', 'diamond', a=5.43)
atoms.calc = calc_mace

# Relax structure
opt = BFGS(atoms, trajectory='relax.traj')
opt.run(fmax=0.01)  # eV/Å

print(f"Relaxed energy: {atoms.get_potential_energy():.4f} eV")
print(f"Relaxed cell:\n{atoms.cell}")

Molecular Dynamics

from ase.md.langevin import Langevin
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase import units

# Create supercell
atoms = bulk('Cu', 'fcc', a=3.6) * (4, 4, 4)  # 256 atoms
atoms.calc = calc_mace

# Initialize velocities
MaxwellBoltzmannDistribution(atoms, temperature_K=300)

# Setup MD
dyn = Langevin(
    atoms,
    timestep=1.0 * units.fs,
    temperature_K=300,
    friction=0.01
)

# Run MD
def print_energy(a=atoms):
    print(f"E = {a.get_potential_energy():.4f} eV")

dyn.attach(print_energy, interval=100)
dyn.run(1000)  # 1000 steps = 1 ps

Common Calculations

Lattice Constant Optimization

from ase.build import bulk
from ase.eos import EquationOfState
import numpy as np

atoms = bulk('Cu', 'fcc', a=3.6)
atoms.calc = calc_mace

# Calculate E(V) curve
volumes = []
energies = []
for scale in np.linspace(0.95, 1.05, 7):
    atoms_scaled = atoms.copy()
    atoms_scaled.set_cell(atoms.cell * scale, scale_atoms=True)
    atoms_scaled.calc = calc_mace
    volumes.append(atoms_scaled.get_volume())
    energies.append(atoms_scaled.get_potential_energy())

# Fit equation of state
eos = EquationOfState(volumes, energies)
v0, e0, B = eos.fit()
a_opt = (4 * v0) ** (1/3)  # For FCC
print(f"Optimal lattice constant: {a_opt:.4f} Å")
print(f"Bulk modulus: {B / units.GPa:.1f} GPa")

Elastic Constants

from ase.build import bulk

atoms = bulk('Cu', 'fcc', a=3.6)
atoms.calc = calc_mace

# Use stress-strain method
from ase.constraints import StrainFilter
from ase.optimize import BFGS

# First relax
sf = StrainFilter(atoms)
opt = BFGS(sf)
opt.run(fmax=0.001)

# Then calculate elastic constants
# (See ASE documentation for full elastic tensor calculation)

Formation Energy

def formation_energy(compound_atoms, element_energies):
    """
    Calculate formation energy.

    compound_atoms: ASE Atoms object for compound
    element_energies: dict like {'Li': -1.9, 'O': -4.9}
    """
    compound_atoms.calc = calc_mace
    E_compound = compound_atoms.get_potential_energy()

    # Count atoms
    symbols = compound_atoms.get_chemical_symbols()
    from collections import Counter
    counts = Counter(symbols)

    # Reference energy
    E_ref = sum(element_energies[el] * n for el, n in counts.items())

    # Formation energy per atom
    E_form = (E_compound - E_ref) / len(compound_atoms)
    return E_form

Diffusion Coefficient from MD

import numpy as np
from ase.md.langevin import Langevin
from ase import units

def calculate_diffusion(atoms, calc, T, n_steps=10000, dt=1.0):
    """Calculate diffusion coefficient from MSD."""
    atoms = atoms.copy()
    atoms.calc = calc

    # Initialize
    MaxwellBoltzmannDistribution(atoms, temperature_K=T)

    # Setup MD
    dyn = Langevin(atoms, timestep=dt*units.fs, temperature_K=T, friction=0.01)

    # Track positions
    positions = [atoms.get_positions().copy()]

    for i in range(n_steps):
        dyn.run(1)
        if i % 10 == 0:
            positions.append(atoms.get_positions().copy())

    positions = np.array(positions)

    # Calculate MSD
    r0 = positions[0]
    msd = np.mean(np.sum((positions - r0)**2, axis=2), axis=1)

    # Time array
    times = np.arange(len(msd)) * 10 * dt  # fs

    # Fit linear region (skip initial ballistic)
    from scipy.stats import linregress
    start = len(msd) // 4
    slope, _, _, _, _ = linregress(times[start:], msd[start:])

    # D = MSD / (6 * t) for 3D
    D = slope / 6  # Ų/fs
    D_cm2s = D * 1e-4  # Convert to cm²/s

    return D_cm2s

Phonon Calculations

With Phonopy

from phonopy import Phonopy
from phonopy.structure.atoms import PhonopyAtoms
from ase.build import bulk
import numpy as np

# Create structure
atoms = bulk('Si', 'diamond', a=5.43)

# Convert to phonopy format
phonopy_atoms = PhonopyAtoms(
    symbols=atoms.get_chemical_symbols(),
    cell=atoms.cell,
    scaled_positions=atoms.get_scaled_positions()
)

# Create phonopy object with supercell
phonon = Phonopy(phonopy_atoms, supercell_matrix=[[2,0,0],[0,2,0],[0,0,2]])

# Generate displacements
phonon.generate_displacements(distance=0.01)
supercells = phonon.get_supercells_with_displacements()

# Calculate forces for each displacement
forces = []
for sc in supercells:
    # Convert to ASE
    atoms_sc = Atoms(
        symbols=sc.symbols,
        positions=sc.positions,
        cell=sc.cell,
        pbc=True
    )
    atoms_sc.calc = calc_mace
    f = atoms_sc.get_forces()
    forces.append(f)

# Set forces and calculate phonons
phonon.forces = forces
phonon.produce_force_constants()

# Calculate dispersion
path = [[[0,0,0], [0.5,0,0.5], [0.5,0.25,0.75], [0,0,0], [0.5,0.5,0.5]]]
labels = ['$\\Gamma$', 'X', 'K', '$\\Gamma$', 'L']
phonon.run_band_structure(path, labels=labels)

# Plot
phonon.plot_band_structure().savefig('phonon_dispersion.png')

Known Limitations

Systematic Errors

When MLIPs Fail

1. Chemistry far from training data: Exotic elements, unusual oxidation states
2. Surfaces and interfaces: Higher errors than bulk
3. Alloy thermodynamics: Binary mixing energies often wrong
4. Reaction barriers: May not capture transition states
5. Long-range interactions: Charge transfer, van der Waals

Validation Strategy

Always validate MLIP results against:

1. DFT (at least for a few key structures)
2. Experimental data
3. Materials Project database

# Example: Compare to Materials Project
from mp_api.client import MPRester

with MPRester() as mpr:
    docs = mpr.summary.search(formula="Cu")
    mp_data = docs[0]

print(f"MP formation energy: {mp_data.formation_energy_per_atom:.4f} eV/atom")
print(f"MLIP formation energy: {my_mlip_result:.4f} eV/atom")
print(f"Difference: {abs(mp_data.formation_energy_per_atom - my_mlip_result):.4f} eV/atom")

GPU Acceleration

MACE with CUDA

# Explicitly use GPU
calc = mace_mp(model="medium", device="cuda")

# Check GPU memory
import torch
print(f"GPU memory: {torch.cuda.memory_allocated()/1e9:.2f} GB")

Performance Tips

1. Batch calculations: Process multiple structures together
2. Use appropriate model size: "small" for screening, "large" for accuracy
3. GPU memory: Large systems may need memory management
4. Parallel MD: Consider LAMMPS for large-scale GPU MD
5. High-throughput: For 10+ structures, use torch-sim skill (100x faster)

Integration with LAMMPS

For large-scale MD, MACE can be used with LAMMPS:

# Convert MACE model for LAMMPS
mace_create_lammps_model --model MACE-MP-0 --output mace.lammps

# LAMMPS input with MACE
units metal
atom_style atomic

read_data structure.data

pair_style mace
pair_coeff * * mace.lammps Cu

# Run MD
velocity all create 300 12345
fix 1 all nvt temp 300 300 0.1
run 10000

Workflow Examples

High-Throughput Screening

def screen_structures(structures, calc, property_func):
    """Screen many structures for a property."""
    results = []
    for name, atoms in structures.items():
        atoms.calc = calc
        try:
            prop = property_func(atoms)
            results.append({'name': name, 'property': prop, 'status': 'success'})
        except Exception as e:
            results.append({'name': name, 'property': None, 'status': str(e)})
    return results

# Example: Screen for stability
def stability_metric(atoms):
    return atoms.get_potential_energy() / len(atoms)

results = screen_structures(my_structures, calc_mace, stability_metric)

Fine-Tuning (Advanced)

# Fine-tuning requires MACE training code
# See: https://github.com/ACEsuit/mace

# Basic workflow:
# 1. Prepare training data (ASE database or xyz files)
# 2. Load pretrained model
# 3. Fine-tune with small learning rate
# 4. Validate on held-out set

# Example command (simplified):
# mace_run_train \
#   --model="MACE" \
#   --foundation_model="MACE-MP-0" \
#   --train_file="my_data.xyz" \
#   --valid_fraction=0.1 \
#   --lr=0.0001 \
#   --max_num_epochs=100

Quick Reference

Model Selection Guide

Typical Workflow

1. Structure preparation: Build or fetch from Materials Project
2. Model selection: Choose based on chemistry and property
3. Validation: Compare small test to DFT/experiment
4. Production: Run full calculation
5. Analysis: Extract properties, compare to literature
6. Documentation: Report model used, limitations

Resources

• MACE: https://github.com/ACEsuit/mace
• MatGL: https://github.com/materialsvirtuallab/matgl
• Matbench Discovery: https://matbench-discovery.materialsproject.org/
• ASE: https://wiki.fysik.dtu.dk/ase/
• Phonopy: https://phonopy.github.io/phonopy/