Heterostructure Assembly

Overview

A heterostructure is a layered stack of two different materials joined at an interface. The Zur-McGill (ZSL) algorithm finds superlattice matches that minimize lattice mismatch between substrate and film.

Common applications:

• Catalysis: oxide support + metal film (TiO2/Pt, Al2O3/Pd)
• Electronics: semiconductor junctions (GaAs/AlAs, Si/Ge)
• 2D vdW stacks: graphene/hBN, MoS2/WSe2
• Energy: electrode/electrolyte interfaces for batteries
• Photocatalysis: type-II heterojunctions for charge separation

MCP Tools

catgo_hetero_search -- Find lattice-matched superlattices

{"tool": "catgo_hetero_search", "arguments": {
  "substrate": {"<pymatgen structure dict>": "..."},
  "film": {"<pymatgen structure dict>": "..."},
  "params": {
    "substrate_miller": [0, 0, 1],
    "film_miller": [0, 0, 1],
    "max_area": 400,
    "max_area_ratio_tol": 0.09,
    "max_length_tol": 0.09,
    "max_angle_tol": 0.09,
    "max_results": 20,
    "mode": "bulk"
  }
}}

Returns matches sorted by area, with available terminations for each match.

Parameter	Description	Default
substrate	Substrate structure dict	(required)
film	Film structure dict	(required)
substrate_miller	Substrate surface orientation	[0,0,1]
film_miller	Film surface orientation	[0,0,1]
max_area	Maximum supercell area (A^2)	400
max_area_ratio_tol	Area ratio tolerance	0.09
max_length_tol	Length mismatch tolerance	0.09
max_angle_tol	Angle mismatch tolerance	0.09
max_results	Max number of matches to return	20
mode	"bulk" or "slab" input mode	"bulk"

catgo_hetero_build -- Build the interface

{"tool": "catgo_hetero_build", "arguments": {
  "substrate": {"<pymatgen structure dict>": "..."},
  "film": {"<pymatgen structure dict>": "..."},
  "match": {"match_id": 0},
  "termination_index": 0,
  "params": {
    "gap": 2.0,
    "vacuum": 20.0,
    "substrate_thickness": 10.0,
    "film_thickness": 10.0,
    "twist_angle": 0.0
  }
}}

Parameter	Description	Default
match	Match from search results (match_id)	(required)
termination_index	Which termination to use	0
gap	Interface gap in Angstroms	2.0
vacuum	Vacuum above the slab in Angstroms	20.0
substrate_thickness	Substrate slab thickness	10.0
film_thickness	Film slab thickness	10.0
twist_angle	In-plane rotation of the film	0.0

catgo_hetero_build_intermat -- One-step build (JARVIS pipeline)

An alternative builder that does search + build in one step using the intermat/JARVIS method. Useful when you want a quick result without separately inspecting matches.

{"tool": "catgo_hetero_build_intermat", "arguments": {
  "substrate": {"<pymatgen structure dict>": "..."},
  "film": {"<pymatgen structure dict>": "..."},
  "params": {
    "substrate_miller": [0, 0, 1],
    "film_miller": [0, 0, 1],
    "separation": 3.0,
    "vacuum": 25.0
  }
}}

Router: /heterostructure/search (POST), /heterostructure/build (POST), /heterostructure/build-intermat (POST), and more

Additional endpoints: /batch-build, /build-manual, /search-lateral, /build-lateral, /grid-scan.

Complete Workflow: TiO2/Pt Interface

Step 1: Fetch both materials

{"tool": "catgo_fetch", "arguments": {
  "action": "crystal", "formula": "TiO2", "source": "mp"
}}

Save this structure, then fetch the second:

{"tool": "catgo_fetch", "arguments": {
  "action": "crystal", "formula": "Pt", "source": "mp"
}}

Step 2: Search for lattice matches

{"tool": "catgo_hetero_search", "arguments": {
  "substrate": "<TiO2 structure>",
  "film": "<Pt structure>",
  "params": {
    "substrate_miller": [1, 1, 0],
    "film_miller": [1, 1, 1],
    "max_area": 200
  }
}}

Review the returned matches. Each lists:

• Superlattice area
• Strain (length and angle mismatch)
• Available terminations (e.g., O-terminated vs Ti-terminated)

Step 3: Build the interface

Select the best match (smallest area with acceptable strain):

{"tool": "catgo_hetero_build", "arguments": {
  "substrate": "<TiO2 structure>",
  "film": "<Pt structure>",
  "match": {"match_id": 0},
  "termination_index": 0,
  "params": {
    "gap": 2.5,
    "vacuum": 20.0,
    "substrate_thickness": 12.0,
    "film_thickness": 10.0
  }
}}

Step 4: Verify

{"tool": "catgo_view", "arguments": {"action": "get_state"}}

Check: correct interface geometry, appropriate vacuum, no overlapping atoms at the interface.

Step 5: Relax the interface

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "create", "params": {"name": "TiO2-Pt interface relax"}
}}

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "add_task", "params": {
    "workflow_id": "<wf_id>",
    "task_type": "geo_opt",
    "params": {"software": "vasp", "ENCUT": 520,
               "system_name": "TiO2-Pt interface"}
  }
}}

Tolerance Guidelines

Mismatch Level	Tolerance Values	Use Case
Tight	0.03	Epitaxial growth, accurate interfaces
Standard	0.09	General screening, most applications
Loose	0.15	Exploratory, when few matches found

Tighter tolerances produce fewer but higher-quality matches. Loosen tolerances if no matches are found, or increase max_area.

Common Pitfalls

1. Both substrate and film must be bulk crystals (not slabs). The builder cuts slabs internally based on the Miller indices you specify.
2. Large max_area values (> 500 A^2) can produce structures with thousands of atoms. Start small and increase if needed.
3. The gap parameter controls the initial interface distance before relaxation. Too small (< 1.5 A) causes atomic overlap; too large (> 4 A) may not capture interface bonding.
4. Always relax the interface with DFT. The as-built structure has ideal geometry that does not reflect real interface reconstruction.
5. For oxide/metal interfaces, use DFT+U on the oxide side. The metal does not need U corrections.
6. Van der Waals corrections (DFT-D3) are important for weakly bonded interfaces (2D/2D stacks, vdW heterostructures).
7. Strain from lattice mismatch is applied to the film by default. For large mismatches (> 5%), the film may be significantly distorted. Consider if this is physically reasonable.