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Using the Structure Builder

Generate supercells, surface slabs, nanoparticles, and substitution structures step by step.

Apr 10, 20266 min read
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Using the Structure Builder

MatCraft's structure builder tools let you create derivative structures from any material in the database. This tutorial walks through each tool with a practical example.

Prerequisites

  • A MatCraft account (builder tools require authentication)
  • A target material in mind (we will use silicon, mp-149, as our example)

Building a Supercell

Supercells are needed for defect calculations, molecular dynamics, and studying finite-size effects.

Step 1: Navigate to the material detail page for Si (mp-149)

Step 2: Click the Builder tab, then select Supercell

Step 3: Set the expansion factors:

  • a: 2, b: 2, c: 2 (creates 8 copies of the unit cell)

Step 4: Click Build. The viewer updates to show the 2x2x2 supercell with 16 Si atoms.

Step 5: Download the supercell as POSCAR for use in VASP calculations.

Creating a Surface Slab

Surface slabs are essential for studying catalysis, adsorption, and thin film properties.

Step 1: On the same material page, select Surface in the Builder tab

Step 2: Enter Miller indices: h=1, k=1, l=0

Step 3: Set the slab parameters:

  • Layers: 6 (enough for converged surface energy)
  • Vacuum: 15 Angstroms (prevents interaction between periodic images)

Step 4: Click Build. The viewer shows the slab with a visible vacuum gap.

Step 5: Download as POSCAR. The c-axis will be much longer than a and b due to the vacuum.

Carving a Nanoparticle

Nanoparticles are useful for studying size-dependent properties and catalytic clusters.

Step 1: Select Nanoparticle in the Builder tab

Step 2: Set the radius to 8.0 Angstroms

Step 3: Click Build. The viewer shows a spherical cluster of Si atoms.

Step 4: Note the atom count displayed (approximately 100 atoms for this radius). For larger nanoparticles, increase the radius gradually.

Step 5: Download as XYZ format (nanoparticles are non-periodic).

Making a Substitution

Substitutions enable rapid screening of dopants and alloy compositions.

Step 1: Select Substitution in the Builder tab

Step 2: Choose the source element (Si) and target element (Ge)

Step 3: Click Build. All Si atoms are replaced with Ge, creating a hypothetical Ge structure with Si's lattice parameters.

Step 4: Download the substituted structure. Remember that the lattice is NOT relaxed — you should run a geometry optimization with your DFT code.

Combining Tools

For advanced workflows, chain the tools:

  1. Build a 3x3x3 supercell of your material
  2. Export it, manually replace one atom in the POSCAR file to create a dilute dopant
  3. Use the resulting structure for a defect formation energy calculation

API Workflow

For automated screening, use the API:

python
from matcraft import MatCraftClient

client = MatCraftClient(token="YOUR_TOKEN")

# Build supercell and export
result = client.build_supercell("mp-149", nx=2, ny=2, nz=2)
result.export("poscar", path="Si_supercell.vasp")

# Build surface
surface = client.build_surface("mp-149", h=1, k=1, l=0, layers=5)
surface.export("poscar", path="Si_110_surface.vasp")