abinit
FreeGenerate and manage ABINIT DFT calculations. Use when the user requests ABINIT, or needs DFPT phonons, GW calculations, or BSE optical spectra.
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Use when the user asks to create a moire pattern, twisted bilayer structure, magic angle graphene, or any twisted 2D heterostructure.
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A moire superlattice forms when two identical 2D layers are stacked with a relative twist angle. The resulting interference pattern creates a periodic supercell with properties that depend strongly on the twist angle.
Common applications:
{"tool": "catgo_moire_search", "arguments": {
"structure": "<current viewer structure>",
"max_angle": 30,
"tolerance": 0.01
}}
Searches for twist angles that produce commensurate superlattices (exact periodic boundary conditions). Returns a list of angles with supercell sizes, atom counts, and lattice mismatch.
| Parameter | Description | Default |
|---|---|---|
structure | 2D monolayer structure (auto-fetched from viewer) | (required) |
max_angle | Maximum twist angle to search (degrees) | 30 |
tolerance | Commensurability tolerance | 0.01 |
{"tool": "catgo_moire_build", "arguments": {
"structure": "<current viewer structure>",
"angle": 21.79,
"interlayer_distance": 3.35
}}
| Parameter | Description | Default |
|---|---|---|
structure | 2D monolayer structure | (required) |
angle | Twist angle in degrees (from search results) | (required) |
interlayer_distance | Distance between layers in Angstroms | 3.35 |
/moire/search (POST), /moire/build (POST){"tool": "catgo_fetch", "arguments": {
"action": "crystal", "formula": "C", "source": "mc3d"
}}
Or load a graphene structure from file.
{"tool": "catgo_moire_search", "arguments": {
"max_angle": 10,
"tolerance": 0.01
}}
The result lists angles sorted by supercell size. Small angles produce very large supercells (thousands of atoms).
Pick an angle from the search results:
{"tool": "catgo_moire_build", "arguments": {
"angle": 5.09,
"interlayer_distance": 3.35
}}
{"tool": "catgo_view", "arguments": {"action": "get_state"}}
Check: two layers visible, correct interlayer spacing, moire pattern in the xy plane.
Magic-angle TBG (~1.1 deg) has ~11,000+ atoms. Use an MLP for relaxation:
{"tool": "catgo_workflow_engine", "arguments": {
"action": "create", "params": {"name": "TBG moire relaxation"}
}}
{"tool": "catgo_workflow_engine", "arguments": {
"action": "add_task", "params": {
"workflow_id": "<wf_id>",
"task_type": "geo_opt",
"params": {"software": "mlp", "mlp_model": "mace",
"system_name": "TBG-5.09deg"}
}
}}
| Angle (deg) | Approx. Atoms (graphene) | Notes |
|---|---|---|
| 21.79 | ~28 | Smallest commensurate, good for testing |
| 13.17 | ~76 | Small, DFT-feasible |
| 9.43 | ~148 | Moderate |
| 5.09 | ~508 | Large, MLP recommended |
| 3.89 | ~868 | Very large |
| 1.08 | ~11,164 | Magic angle, MLP or tight-binding only |
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Generate and manage ABINIT DFT calculations. Use when the user requests ABINIT, or needs DFPT phonons, GW calculations, or BSE optical spectra.
The English summary is being prepared. Showing the original description.
Use when the user asks to place an adsorbate molecule on a surface, find adsorption sites, or set up a surface+adsorbate model for DFT.
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Use when the user asks for adsorption energy, binding energy, or wants to compare how strongly a molecule binds to a surface.
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Use when the user asks to analyze computational results: Gibbs free energy, OER/HER/CO2RR overpotentials, adsorption energy, convergence tests, DOS/d-band analysis, or Bader charge analysis.
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Use AmberTools antechamber for molecular force field parameterization. Generates GAFF/GAFF2 parameters and AM1-BCC or RESP charges for use in AMBER or LAMMPS classical MD simulations.
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One-shot recipes for adding, deleting, moving, and replacing individual atoms in the active CatGo viewer structure. Use whenever the user asks to "add an atom", "delete atoms", "remove this atom", "move atom N", "replace H with Li", or any single-atom edit — including "add a hydrogen on top of atom 12" / "delete atoms 5–9" / "swap the oxygen at site 3 for fluorine". Skips the discovery loop (no need to list structure tools or check adsorption sites first); goes straight to the matching `catgo_structure` action. Triggers in Chinese on 加原子, 删原子, 减原子, 移动原子, 替换原子, 增加氢, 删除氧, 把 ... 换成 ....
The English summary is being prepared. Showing the original description.